U.S. patent application number 10/407484 was filed with the patent office on 2004-07-22 for nucleic acid and corresponding protein entitled 98p4b6 useful in treatment and detection of cancer.
Invention is credited to Challita-Eid, Pia M., Faris, Mary, Ge, Wangmao, Jakobovits, Aya, Raitano, Arthur B..
Application Number | 20040141975 10/407484 |
Document ID | / |
Family ID | 46299133 |
Filed Date | 2004-07-22 |
United States Patent
Application |
20040141975 |
Kind Code |
A1 |
Raitano, Arthur B. ; et
al. |
July 22, 2004 |
Nucleic acid and corresponding protein entitled 98P4B6 useful in
treatment and detection of cancer
Abstract
A novel gene 098P4B6 (also designated STEAP-2) and its encoded
protein, and variants thereof, are described wherein 98P4B6
exhibits tissue specific expression in normal adult tissue, and is
aberrantly expressed in the cancers listed in Table I.
Consequently, 98P4B6 provides a diagnostic, prognostic,
prophylactic and/or therapeutic target for cancer. The 98P4B6 gene
or fragment thereof, or its encoded protein, or variants thereof,
or a fragment thereof, can be used to elicit a humoral or cellular
immune response; antibodies or T cells reactive with 98P4B6 can be
used in active or passive immunization.
Inventors: |
Raitano, Arthur B.; (Los
Angeles, CA) ; Ge, Wangmao; (Culver City, CA)
; Jakobovits, Aya; (Beverly Hills, CA) ;
Challita-Eid, Pia M.; (Encino, CA) ; Faris, Mary;
(Los Angeles, CA) |
Correspondence
Address: |
Kate H. Murashige
Morrison & Foerster LLP
Suite 500
3811 Valley Centre Drive
San Diego
CA
92130
US
|
Family ID: |
46299133 |
Appl. No.: |
10/407484 |
Filed: |
April 4, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10407484 |
Apr 4, 2003 |
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09455486 |
Dec 6, 1999 |
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09455486 |
Dec 6, 1999 |
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09323873 |
Jun 1, 1999 |
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6329503 |
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60091183 |
Jun 30, 1998 |
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60087520 |
Jun 1, 1998 |
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Current U.S.
Class: |
424/155.1 ;
514/19.3; 514/21.6; 530/387.1 |
Current CPC
Class: |
A61K 39/00 20130101;
A61K 2039/505 20130101; C07K 16/3069 20130101; A61K 38/00 20130101;
C12Q 2600/16 20130101; C12Q 2600/106 20130101; C12Q 2600/136
20130101; C07K 16/30 20130101; C07K 2319/30 20130101; C07K 14/705
20130101; C12Q 1/6886 20130101; C12Q 2600/154 20130101; G01N 33/574
20130101; C07K 2319/00 20130101; A61K 51/1045 20130101; C07K
14/4748 20130101 |
Class at
Publication: |
424/155.1 ;
530/387.1; 514/015 |
International
Class: |
A61K 038/08; A61K
039/395 |
Claims
1. A composition that comprises, consists essentially of, or
consists of: a) a peptide of eight, nine, ten, or eleven contiguous
amino acids of a protein of FIG. 2; b) a peptide of Tables
VIII-XXI; c) a peptide of Tables XXII to XLV; or, d) a peptide of
Tables XLVI to XLIX.
2. A composition of claim 1 that comprises a protein related to a
protein of FIG. 2.
3. A protein of claim 2 that is at least 90, 91, 92, 93, 94, 95,
96, 97, 98, or 99% homologous to an entire amino acid sequence
shown in FIG. 2.
4. A composition of claim 1 wherein the substance comprises a CTL
polypeptide or an analog thereof, from the amino acid sequence of a
protein of FIG. 2.
5. A composition of claim 4 further limited by a proviso that the
epitope is not an entire amino acid sequence of FIG. 2.
6. A composition of claim 1 further limited by a proviso that the
polypeptide is not an entire amino acid sequence of a protein of
FIG. 2.
7. A composition of claim 1 that comprises an antibody polypeptide
epitope from an amino acid sequence of FIG. 2.
8. A composition of claim 7 further limited by a proviso that the
epitope is not an entire amino acid sequence of FIG. 2.
9. A composition of claim 7 wherein the antibody epitope comprises
a peptide region of at least 5 amino acids of FIG. 2 in any whole
number increment up to the end of said peptide, wherein the epitope
comprises an amino acid position selected from: a) an amino acid
position having a value greater than 0.5 in the Hydrophilicity
profile of FIG. 5, b) an amino acid position having a value less
than 0.5 in the Hydropathicity profile of FIG. 6; c) an amino acid
position having a value greater than 0.5 in the Percent Accessible
Residues profile of FIG. 7; d) an amino acid position having a
value greater than 0.5 in the Average Flexibility profile of FIG.
8; e) an amino acid position having a value greater than 0.5 in the
Beta-turn profile of FIG. 9; f) a combination of at least two of a)
through e); g) a combination of at least three of a) through e); h)
a combination of at least four of a) through e); or i) a
combination of five of a) through e).
10. A polynucleotide that encodes a protein of claim 1.
11. A polynucleotide of claim 10 that comprises a nucleic acid
molecule set forth in FIG. 2.
12. A polynucleotide of claim 10 further limited by a proviso that
the encoded protein is not an entire amino acid sequence of FIG.
2.
13. A composition of claim 11 wherein the substance comprises a
polynucleotide that comprises a coding sequence of a nucleic acid
sequence of FIG. 2.
14. A polynucleotide of claim 22 that further comprises an
additional nucleotide sequence that encodes an additional peptide
of claim 1.
15. A composition comprising a polynucleotide that is fully
complementary to a polynucleotide of claim 10.
16. A method of generating a mammalian immune response directed to
a protein of FIG. 2, the method comprising: exposing cells of the
mammal's immune system to a portion of a) a 98B4B6-related protein
and/or b) a nucleotide sequence that encodes said protein, whereby
an immune response is generated to said protein.
17. A method of generating an immune response of claim 16, said
method comprising: providing a 98B4B6-related protein that
comprises at least one T cell or at least one B cell epitope; and,
contacting the epitope with a mammalian immune system T cell or B
cell respectively, whereby the T cell or B cell is activated.
18. A method of claim 17 wherein the immune system cell is a B
cell, whereby the induced B cell generates antibodies that
specifically bind to the 98B4B6-related protein.
19. A method of claim 17 wherein the immune system cell is a T cell
that is a cytotoxic T cell (CTL), whereby the activated CTL kills
an autologous cell that expresses the 98B4B6-related protein.
20. A method of claim 17 wherein the immune system cell is a T cell
that is a helper T cell (HTL), whereby the activated HTL secretes
cytokines that facilitate the cytotoxic activity of a cytotoxic T
cell (CTL) or the antibody-producing activity of a B cell.
21. A method for detecting, in a sample, the presence of a
98B4B6-related protein or a 98B4B6-related polynucleotide,
comprising steps of: contacting the sample with a substance that
specifically binds to the 98B4B6-related protein or to the
98B4B6-related polynucleofide, respectively; and, determining that
there is a complex of the substance with the 98B4B6-related protein
or the substance with the 98B4B6-related polynucleofide,
respectively.
22. A method of claim 21 for detecting the presence of a
98B4B6-related protein in a sample comprising steps of: contacting
the sample with an antibody or fragment thereof either of which
specifically bind to the 98B4B6-related protein; and, determining
that there is a complex of the antibody or fragment thereof and the
98B4B6-related protein.
23. A method of claim 21 further comprising a step of: taking the
sample from a patient who has or who is suspected of having
cancer.
24. A method of claim 21 for detecting the presence of a protein of
FIG. 2 mRNA in a sample comprising: producing cDNA from the sample
by reverse transcription using at least one primer; amplifying the
cDNA so produced using 98B4B6 polynucleotides as sense and
antisense primers, wherein the 98B4B6 polynucleotides used as the
sense and antisense primers serve to amplify a 98B4B6 cDNA; and,
detecting the presence of the amplified 98B4B6 cDNA.
25. A method of claim 21 for monitoring one or more 98B4B6 gene
products in a biological sample from a patient who has or who is
suspected of having cancer, the method comprising: determining the
status of one or more 98B4B6 gene products expressed by cells in a
tissue sample from an individual; comparing the status so
determined to the status of one or more 98B4B6 gene products in a
corresponding normal sample; and, identifying the presence of one
or more aberrant gene products of 98B4B6 in the sample relative to
the normal sample.
26. The method of claim 25 further comprising a step of determining
if there are one or more elevated gene products of a 98B4B6 mRNA or
a 98B4B6 protein, whereby the presence of one or more elevated gene
products in the test sample relative to the normal tissue sample
indicates the presence or status of a cancer.
27. A method of claim 26 wherein the cancer occurs in a tissue set
forth in Table 1.
28. A composition comprising: a substance that a) modulates the
status of a protein of FIG. 2, or b) a molecule that is modulated
by a protein of FIG. 2, whereby the status of a cell that expresses
a protein of FIG. 2 is modulated.
29. A composition of claim 28, further comprising a physiologically
acceptable carrier.
30. A pharmaceutical composition that comprises the composition of
claim 28 in a human unit dose form.
31. A composition of claim 28 wherein the substance comprises an
antibody or fragment thereof that specifically binds to a protein
of FIG. 2.
32. An antibody or fragment thereof of claim 31, which is
monoclonal.
33. An antibody of claim 31, which is a human antibody, a humanized
antibody or a chimeric antibody.
34. A non-human transgenic animal that produces an antibody of
claim 31.
35. A hybridoma that produces an antibody of claim 32.
36. A method of delivering a cytotoxic agent or a diagnostic agent
to a cell that expresses a protein of FIG. 2, said method
comprising: providing the cytotoxic agent or the diagnostic agent
conjugated to an antibody or fragment thereof of claim 4; and,
exposing the cell to the antibody-agent or fragment-agent
conjugate.
37. A composition of claim 28 wherein the substance comprises a
polynucleotide that encodes an antibody or fragment thereof, either
of which immunospecifically bind to a protein of FIG. 2.
38. A composition of claim 28 wherein the substance comprises a) a
ribozyme that cleaves a polynucleotide having a 98B4B6 coding
sequence, or b) a nucleic acid molecule that encodes the ribozyme;
and, a physiologically acceptable carrier.
39. A composition of claim 28 wherein the substance comprises human
T cells, wherein said T cells specifically recognize a 98B4B6
peptide subsequence in the context of a particular HLA
molecule.
40. A method of inhibiting growth of cancer cells that express a
protein of FIG. 2, the method comprising: administering to the
cells the composition of claim 28.
41. A method of claim 40 of inhibiting growth of cancer cells that
express a protein of FIG. 2, the method comprising steps of:
administering to said cells an antibody or fragment thereof, either
of which specifically bind to a 98B4B6-related protein.
42. A method of claim 40 of inhibiting growth of cancer cells that
express a protein of FIG. 2, the method comprising steps of:
administering to said cells a 98B4B6-related protein.
43. A method of claim 40 of inhibiting growth of cancer cells that
express a protein of FIG. 2, the method comprising steps of:
administering to said cells a polynucleotide comprising a coding
sequence for a 98B4B6-related protein or comprising a
polynucleotide complementary to a coding sequence for a
98B4B6-related protein.
44. A method of claim 40 of inhibiting growth of cancer cells that
express a protein of FIG. 2, the method comprising steps of:
administering to said cells a ribozyme that cleaves a
polynucleotide that encodes a protein of FIG. 2.
45. A method of claim 40 of inhibiting growth of cancer cells that
express a protein of FIG. 2 and a particular HLA molecule, the
method comprising steps of: administering human T cells to said
cancer cells, wherein said T cells specifically recognize a peptide
subsequence of a protein of FIG. 2 while the subsequence is in the
context of the particular HLA molecule.
46. A method of claim 40, the method comprising steps of:
administering a vector that delivers a nucleotide that encodes a
single chain monoclonal antibody, whereby the encoded single chain
antibody is expressed intracellularly within cancer cells that
express a protein of FIG. 2.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation-in-part of pending U.S.
patent application Ser. No. 09/455,486, filed 6 Dec. 1999, and
claims priority from U.S. patent application Ser. No. 09/323,873,
now U.S. Pat. No. 6,329, 503 filed 1 Jun. 1999, and this
application claims priority from U.S. provisional application U.S.
Ser. No. not yet assigned, filed 20 Dec. 2002 and U.S. provisional
patent application No. 60/317,840, filed Sep. 6, 2001 and U.S.
provisional patent application No. 60/370,387 filed Apr. 5, 2002.
This application relates to U.S. provisional patent application No.
60/087,520, filed Jun. 1, 1998 and U.S. provisional patent
application No. 60/091,183, filed Jun. 30, 1998 and U.S. patent
application Ser. No. 10/01 1,095, filed Dec. 6, 2001 and U.S.
patent application Ser. No. 10/010,667, filed Dec. 6, 2001 and U.S.
provisional patent application No. 60/296,656, filed Jun. 6, 2001,
and U.S. patent application Ser. No. 10/165,044, filed Jun. 6,
2002. The contents of the applications listed in this paragraph are
fully incorporated by reference herein.
STATEMENT OF RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED
RESEARCH
[0002] Not applicable.
FIELD OF THE INVENTION
[0003] The invention described herein relates to genes and their
encoded proteins, termed 98P4B6 or STEAP-2, expressed in certain
cancers, and to diagnostic and therapeutic methods and compositions
useful in the management of cancers that express 98P4B6.
BACKGROUND OF THE INVENTION
[0004] Cancer is the second leading cause of human death next to
coronary disease. Worldwide, millions of people die from cancer
every year. In the United States alone, as reported by the American
Cancer Society, cancer causes the death of well over a half-million
people annually, with over 1.2 million new cases diagnosed per
year. While deaths from heart disease have been declining
significantly, those resulting from cancer generally are on the
rise. In the early part of the next century, cancer is predicted to
become the leading cause of death.
[0005] Worldwide, several cancers stand out as the leading killers.
In particular, carcinomas of the lung, prostate, breast, colon,
pancreas, and ovary represent the primary causes of cancer death.
These and virtually all other carcinomas share a common lethal
feature. With very few exceptions, metastatic disease from a
carcinoma is fatal. Moreover, even for those cancer patients who
initially survive their primary cancers, common experience has
shown that their lives are dramatically altered. Many cancer
patients experience strong anxieties driven by the awareness of the
potential for recurrence or treatment failure. Many cancer patients
experience physical debilitations following treatment. Furthermore,
many cancer patients experience a recurrence.
[0006] Worldwide, prostate cancer is the fourth most prevalent
cancer in men. In North America and Northern Europe, it is by far
the most common cancer in males and is the second leading cause of
cancer death in men. In the United States alone, well over 30,000
men die annually of this disease--second only to lung cancer.
Despite the magnitude of these figures, there is still no effective
treatment for metastatic prostate cancer. Surgical prostatectomy,
radiation therapy, hormone ablation therapy, surgical castration
and chemotherapy continue to be the main treatment modalities.
Unfortunately, these treatments are ineffective for many and are
often associated with undesirable consequences.
[0007] On the diagnostic front, the lack of a prostate tumor marker
that can accurately detect early-stage, localized tumors remains a
significant limitation in the diagnosis and management of this
disease. Although the serum prostate specific antigen (PSA) assay
has been a very useful tool, however its specificity and general
utility is widely regarded as lacking in several important
respects.
[0008] Progress in identifying additional specific markers for
prostate cancer has been improved by the generation of prostate
cancer xenografts that can recapitulate different stages of the
disease in mice. The LAPC (Los Angeles Prostate Cancer) xenografts
are prostate cancer xenografts that have survived passage in severe
combined immune deficient (SCID) mice and have exhibited the
capacity to mimic the transition from androgen dependence to
androgen independence (Klein et al, 1997, Nat. Med. 3:402). More
recently identified prostate cancer markers include PCTA-1 (Su et
al., 1996, Proc. Natl. Acad. Sci. USA 93: 7252), prostate-specific
membrane (PSM) antigen (Pinto et al., Clin Cancer Res 1996 Sep. 2
(9): 1445-51), STEAP (Hubert, et al., Proc Natl Acad Sci U S A.
1999 Dec. 7; 96(25): 14523-8) and prostate stem cell antigen (PSCA)
(Reiter et al., 1998, Proc. Natl. Acad. Sci. USA 95: 1735).
[0009] While previously identified markers such as PSA, PSM, PCTA
and PSCA have facilitated efforts to diagnose and treat prostate
cancer, there is need for the identification of additional markers
and therapeutic targets for prostate and related cancers in order
to further improve diagnosis and therapy.
[0010] Renal cell carcinoma (RCC) accounts for approximately 3
percent of adult malignancies. Once adenomas reach a diameter of 2
to 3 cm, malignant potential exists. In the adult, the two
principal malignant renal tumors are renal cell adenocarcinoma and
transitional cell carcinoma of the renal pelvis or ureter. The
incidence of renal cell adenocarcinoma is estimated at more than
29,000 cases in the United States, and more than 11,600 patients
died of this disease in 1998. Transitional cell carcinoma is less
frequent, with an incidence of approximately 500 cases per year in
the United States.
[0011] Surgery has been the primary therapy for renal cell
adenocarcinoma for many decades. Until recently, metastatic disease
has been refractory to any systemic therapy. With recent
developments in systemic therapies, particularly immunotherapies,
metastatic renal cell carcinoma may be approached aggressively in
appropriate patients with a possibility of durable responses.
Nevertheless, there is a remaining need for effective therapies for
these patients.
[0012] Of all new cases of cancer in the United States, bladder
cancer represents approximately 5 percent in men (fifth most common
neoplasm) and 3 percent in women (eighth most common neoplasm). The
incidence is increasing slowly, concurrent with an increasing older
population. In 1998, there was an estimated 54,500 cases, including
39,500 in men and 15,000 in women. The age-adjusted incidence in
the United States is 32 per 100,000 for men and eight per 100,000
in women. The historic male/female ratio of 3:1 may be decreasing
related to smoking patterns in women. There were an estimated
11,000 deaths from bladder cancer in 1998 (7,800 in men and 3,900
in women). Bladder cancer incidence and mortality strongly increase
with age and will be an increasing problem as the population
becomes more elderly.
[0013] Most bladder cancers recur in the bladder. Bladder cancer is
managed with a combination of transurethral resection of the
bladder (TUR) and intravesical chemotherapy or immunotherapy. The
multifocal and recurrent nature of bladder cancer points out the
limitations of TUR. Most muscle-invasive cancers are not cured by
TUR alone. Radical cystectomy and urinary diversion is the most
effective means to eliminate the cancer but carry an undeniable
impact on urinary and sexual function. There continues to be a
significant need for treatment modalities that are beneficial for
bladder cancer patients.
[0014] An estimated 130,200 cases of colorectal cancer occurred in
2000 in the United States, including 93,800 cases of colon cancer
and 36,400 of rectal cancer. Colorectal cancers are the third most
common cancers in men and women. Incidence rates declined
significantly during 1992-1996 (-2.1% per year). Research suggests
that these declines have been due to increased screening and polyp
removal, preventing progression of polyps to invasive cancers.
There were an estimated 56,300 deaths (47,700 from colon cancer,
8,600 from rectal cancer) in 2000, accounting for about 11% of all
U.S. cancer deaths.
[0015] At present, surgery is the most common form of therapy for
colorectal cancer, and for cancers that have not spread, it is
frequently curative. Chemotherapy, or chemotherapy plus radiation,
is given before or after surgery to most patients whose cancer has
deeply perforated the bowel wall or has spread to the lymph nodes.
A permanent colostomy (creation of an abdominal opening for
elimination of body wastes) is occasionally needed for colon cancer
and is infrequently required for rectal cancer. There continues to
be a need for effective diagnostic and treatment modalities for
colorectal cancer.
[0016] There were an estimated 164,100 new cases of lung and
bronchial cancer in 2000, accounting for 14% of all U.S. cancer
diagnoses. The incidence rate of lung and bronchial cancer is
declining significantly in men, from a high of 86.5 per 100,000 in
1984 to 70.0 in 1996. In the 1990s, the rate of increase among
women began to slow. In 1996, the incidence rate in women was 42.3
per 100,000.
[0017] Lung and bronchial cancer caused an estimated 156,900 deaths
in 2000, accounting for 28% of all cancer deaths. During 1992-1996,
mortality from lung cancer declined significantly among men (-1.7%
per year) while rates for women were still significantly increasing
(0.9% per year). Since 1987, more women have died each year of lung
cancer than breast cancer, which, for over 40 years, was the major
cause of cancer death in women. Decreasing lung cancer incidence
and mortality rates most likely resulted from decreased smoking
rates over the previous 30 years; however, decreasing smoking
patterns among women lag behind those of men. Of concern, although
the declines in adult tobacco use have slowed, tobacco use in youth
is increasing again.
[0018] Treatment options for lung and bronchial cancer are
determined by the type and stage of the cancer and include surgery,
radiation therapy, and chemotherapy. For many localized cancers,
surgery is usually the treatment of choice. Because the disease has
usually spread by the time it is discovered, radiation therapy and
chemotherapy are often needed in combination with surgery.
Chemotherapy alone or combined with radiation is the treatment of
choice for small cell lung cancer; on this regimen, a large
percentage of patients experience remission, which in some cases is
long lasting. There is however, an ongoing need for effective
treatment and diagnostic approaches for lung and bronchial
cancers.
[0019] An estimated 182,800 new invasive cases of breast cancer
were expected to occur among women in the United States during
2000. Additionally, about 1,400 new cases of breast cancer were
expected to be diagnosed in men in 2000. After increasing about 4%
per year in the 1980s, breast cancer incidence rates in women have
leveled off in the 1990s to about 110.6 cases per 100,000.
[0020] In the U.S. alone, there were an estimated 41,200 deaths
(40,800 women, 400 men) in 2000 due to breast cancer. Breast cancer
ranks second among cancer deaths in women. According to the most
recent data, mortality rates declined significantly during
1992-1996 with the largest decreases in younger women, both white
and black. These decreases were probably the result of earlier
detection and improved treatment.
[0021] Taking into account the medical circumstances and the
patient's preferences, treatment of breast cancer may involve
lumpectomy (local removal of the tumor) and removal of the lymph
nodes under the arm; mastectomy (surgical removal of the breast)
and removal of the lymph nodes under the arm; radiation therapy;
chemotherapy; or hormone therapy. Often, two or more methods are
used in combination. Numerous studies have shown that, for early
stage disease, long-term survival rates after lumpectomy plus
radiotherapy are similar to survival rates after modified radical
mastectomy. Significant advances in reconstruction techniques
provide several options for breast reconstruction after mastectomy.
Recently, such reconstruction has been done at the same time as the
mastectomy.
[0022] Local excision of ductal carcinoma in situ (DCIS) with
adequate amounts of surrounding normal breast tissue may prevent
the local recurrence of the DCIS. Radiation to the breast and/or
tamoxifen may reduce the chance of DCIS occurring in the remaining
breast tissue. This is important because DCIS, if left untreated,
may develop into invasive breast cancer. Nevertheless, there are
serious side effects or sequelae to these treatments. There is,
therefore, a need for efficacious breast cancer treatments.
[0023] There were an estimated 23,100 new cases of ovarian cancer
in the United States in 2000. It accounts for 4% of all cancers
among women and ranks second among gynecologic cancers. During
1992-1996, ovarian cancer incidence rates were significantly
declining. Consequent to ovarian cancer, there were an estimated
14,000 deaths in 2000. Ovarian cancer causes more deaths than any
other cancer of the female reproductive system.
[0024] Surgery, radiation therapy, and chemotherapy are treatment
options for ovarian cancer. Surgery usually includes the removal of
one or both ovaries, the fallopian tubes (salpingo-oophorectomy),
and the uterus (hysterectomy). In some very early tumors, only the
involved ovary will be removed, especially in young women who wish
to have children. In advanced disease, an attempt is made to remove
all intra-abdominal disease to enhance the effect of chemotherapy.
There continues to be an important need for effective treatment
options for ovarian cancer.
[0025] There were an estimated 28,300 new cases of pancreatic
cancer in the United States in 2000. Over the past 20 years, rates
of pancreatic cancer have declined in men. Rates among women have
remained approximately constant but may be beginning to decline.
Pancreatic cancer caused an estimated 28,200 deaths in 2000 in the
United States. Over the past 20 years, there has been a slight but
significant decrease in mortality rates among men (about -0.9% per
year) while rates have increased slightly among women.
[0026] Surgery, radiation therapy, and chemotherapy are treatment
options for pancreatic cancer. These treatment options can extend
survival and/or relieve symptoms in many patients but are not
likely to produce a cure for most. There is a significant need for
additional therapeutic and diagnostic options for pancreatic
cancer.
SUMMARY OF THE INVENTION
[0027] The present invention relates to a gene, designated 98P4B6,
that has now been found to be over-expressed in the cancer(s)
listed in Table I. Northern blot expression analysis of 98P4B6 gene
expression in normal tissues shows a restricted expression pattern
in adult tissues. The nucleotide (FIG. 2) and amino acid (FIG. 2,
and FIG. 3) sequences of 98P4B6 are provided. The tissue-related
profile of 98P4B6 in normal adult tissues, combined with the
over-expression observed in the tissues listed in Table I, shows
that 98P4B6 is aberrantly over-expressed in at least some cancers,
and thus serves as a useful diagnostic, prophylactic, prognostic,
and/or therapeutic target for cancers of the tissue(s) such as
those listed in Table I.
[0028] The invention provides polynucleotides corresponding or
complementary to all or part of the 98P4B6 genes, mRNAs, and/or
coding sequences, preferably in isolated form, including
polynucleotides encoding 98P4B6-related proteins and fragments of
4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,
22, 23, 24, 25, or more than 25 contiguous amino acids; at least
30, 35, 40, 45, 50, 55, 60, 65, 70, 80, 85, 90, 95, 100 or more
than 100 contiguous amino acids of a 98P4B6-related protein, as
well as the peptides/proteins themselves; DNA, RNA, DNA/RNA
hybrids, and related molecules, polynucleotides or oligonucleotides
complementary or having at least a 90% homology to the 98P4B6 genes
or mRNA sequences or parts thereof, and polynucleotides or
oligonucleotides that hybridize to the 98P4B6 genes, mRNAs, or to
98P4B6-encoding polynucleotides. Also provided are means for
isolating cDNAs and the genes encoding 98P4B6. Recombinant DNA
molecules containing 98P4B6 polynucleotides, cells transformed or
transduced with such molecules, and host-vector systems for the
expression of 98P4B6 gene products are also provided. The invention
further provides antibodies that bind to 98P4B6 proteins and
polypeptide fragments thereof, including polyclonal and monoclonal
antibodies, murine and other mammalian antibodies, chimeric
antibodies, humanized and fully human antibodies, and antibodies
labeled with a detectable marker or therapeutic agent. In certain
embodiments, there is a proviso that the entire nucleic acid
sequence of FIG. 2 is not encoded and/or the entire amino acid
sequence of FIG. 2 is not prepared. In certain embodiments, the
entire nucleic acid sequence of FIG. 2 is encoded and/or the entire
amino acid sequence of FIG. 2 is prepared, either of which are in
respective human unit dose forms.
[0029] The invention further provides methods for detecting the
presence and status of 98P4B6 polynucleotides and proteins in
various biological samples, as well as methods for identifying
cells that express 98P4B6. A typical embodiment of this invention
provides methods for monitoring 98P4B6 gene products in a tissue or
hematology sample having or suspected of having some form of growth
dysregulation such as cancer.
[0030] The invention further provides various immunogenic or
therapeutic compositions and strategies for treating cancers that
express 98P4B6 such as cancers of tissues listed in Table I,
including therapies aimed at inhibiting the transcription,
translation, processing or function of 98P4B6 as well as cancer
vaccines. In one aspect, the invention provides compositions, and
methods comprising them, for treating a cancer that expresses
98P4B6 in a human subject wherein the composition comprises a
carrier suitable for human use and a human unit dose of one or more
than one agent that inhibits the production or function of 98P4B6.
Preferably, the carrier is a uniquely human carrier. In another
aspect of the invention, the agent is a moiety that is
immunoreactive with 98P4B6 protein. Non-limiting examples of such
moieties include, but are not limited to, antibodies (such as
single chain, monoclonal, polyclonal, humanized, chimeric, or human
antibodies), functional equivalents thereof (whether naturally
occurring or synthetic), and combinations thereof. The antibodies
can be conjugated to a diagnostic or therapeutic moiety. In another
aspect, the agent is a small molecule as defined herein.
[0031] In another aspect, the agent comprises one or more than one
peptide which comprises a cytotoxic T lymphocyte (CTL) epitope that
binds an HLA class I molecule in a human to elicit a CTL response
to 98P4B6 and/or one or more than one peptide which comprises a
helper T lymphocyte (HTL) epitope which binds an HLA class II
molecule in a human to elicit an HTL response. The peptides of the
invention may be on the same or on one or more separate polypeptide
molecules. In a further aspect of the invention, the agent
comprises one or more than one nucleic acid molecule that expresses
one or more than one of the CTL or HTL response stimulating
peptides as described above. In yet another aspect of the
invention, the one or more than one nucleic acid molecule may
express a moiety that is immunologically reactive with 98P4B6 as
described above. The one or more than one nucleic acid molecule may
also be, or encodes, a molecule that inhibits production of 98P4B6.
Non-limiting examples of such molecules include, but are not
limited to, those complementary to a nucleotide sequence essential
for production of 98P4B6 (e.g. antisense sequences or molecules
that form a triple helix with a nucleotide double helix essential
for 98P4B6 production) or a ribozyme effective to lyse 98P4B6
mRNA.
[0032] Note that to determine the starting position of any peptide
set forth in Tables VIII-XXI and XXII to XLIX (collectively HLA
Peptide Tables) respective to its parental protein, e.g., variant
1, variant 2, etc., reference is made to three factors: the
particular variant, the length of the peptide in an HLA Peptide
Table, and the Search Peptides in Table VII. Generally, a unique
Search Peptide is used to obtain HLA peptides of a particular for a
particular variant. The position of each Search Peptide relative to
its respective parent molecule is listed in Table VII. Accordingly,
if a Search Peptide begins at position "X", one must add the value
"X-1" to each position in Tables VIII-XXI and XXII to XLIX to
obtain the actual position of the HLA peptides in their parental
molecule. For example, if a particular Search Peptide begins at
position 150 of its parental molecule, one must add 150-1, i.e.,
149 to each HLA peptide amino acid position to calculate the
position of that amino acid in the parent molecule.
[0033] One embodiment of the invention comprises an HLA peptide,
that occurs at least twice in Tables VIII-XXI and XXII to XLIX
collectively, or an oligonucleotide that encodes the HLA peptide.
Another embodiment of the invention comprises an HLA peptide that
occurs at least once in Tables VIII-XXI and at least once in tables
XXII to XLIX, or an oligonucleotide that encodes the HLA
peptide.
[0034] Another embodiment of the invention is antibody epitopes,
which comprise a peptide regions, or an oligonucleotide encoding
the peptide region, that has one two, three, four, or five of the
following characteristics:
[0035] i) a peptide region of at least 5 amino acids of a
particular peptide of FIG. 3, in any whole number increment up to
the full length of that protein in FIG. 3, that includes an amino
acid position having a value equal to or greater than 0.5, 0.6,
0.7, 0.8, 0.9, or having a value equal to 1.0, in the
Hydrophilicity profile of FIG. 5;
[0036] ii) a peptide region of at least 5 amino acids of a
particular peptide of FIG. 3, in any whole number increment up to
the full length of that protein in FIG. 3, that includes an amino
acid position having a value equal to or less than 0.5, 0.4, 0.3,
0.2, 0.1, or having a value equal to 0.0, in the Hydropathicity
profile of FIG. 6;
[0037] iii) a peptide region of at least 5 amino acids of a
particular peptide of FIG. 3, in any whole number increment up to
the full length of that protein in FIG. 3, that includes an amino
acid position having a value equal to or greater than 0.5, 0.6,
0.7, 0.8, 0.9, or having a value equal to 1.0, in the Percent
Accessible Residues profile of FIG. 7;
[0038] iv) a peptide region of at least 5 amino acids of a
particular peptide of FIG. 3, in any whole number increment up to
the full length of that protein in FIG. 3, that includes an amino
acid position having a value equal to or greater than 0.5, 0.6,
0.7, 0.8, 0.9, or having a value equal to 1.0, in the Average
Flexibility profile of FIG. 8; or
[0039] v) a peptide region of at least 5 amino acids of a
particular peptide of FIG. 3, in any whole number increment up to
the full length of that protein in FIG. 3, that includes an amino
acid position having a value equal to or greater than 0.5, 0.6,
0.7, 0.8, 0.9, or having a value equal to 1.0, in the Beta-turn
profile of FIG. 9.
BRIEF DESCRIPTION OF THE FIGURES
[0040] FIG. 1. The 98P4B6 SSH sequence of 183 nucleotides.
[0041] FIG. 2. A) The cDNA and amino acid sequence of 98P4B6
variant 1 (also called "98P4B6 v.1" or "98P4B6 variant 1") is shown
in FIG. 2A. The start methionine is underlined. The open reading
frame extends from nucleic acid 355-1719 including the stop
codon.
[0042] B) The cDNA and amino acid sequence of 98P4B6 variant 2
(also called "98P4B6 v.2") is shown in FIG. 2B. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 4-138 including the stop codon.
[0043] C) The cDNA and amino acid sequence of 98P4B6 variant 3
(also called "98P4B6 v.3") is shown in FIG. 2C. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 188-1552 including the stop codon.
[0044] D) The cDNA and amino acid sequence of 98P4B6 variant 4
(also called "98P4B6 v.4") is shown in FIG. 2D. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 318-1682 including the stop codon.
[0045] E) The cDNA and amino acid sequence of 98P4B6 variant 5
(also called "98P4B6 v.5") is shown in FIG. 2E. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 318-1577 including the stop codon.
[0046] F) The cDNA and amino acid sequence of 98P4B6 variant 6
(also called "98P4B6 v.6") is shown in FIG. 2F. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 318-1790 including the stop codon.
[0047] G) The cDNA and amino acid sequence of 98P4B6 variant 7
(also called "98P4B6 v.7") is shown in FIG. 2G. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 295-2025 including the stop codon.
[0048] H) The cDNA and amino acid sequence of 98P4B6 variant 8
(also called "98P4B6 v.8") is shown in FIG. 2H. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0049] I) The cDNA and amino acid sequence of 98P4B6 variant 9
(also called "98P4B6 v.9") is shown in FIG. 21. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0050] J) The cDNA and amino acid sequence of 98P4B6 variant 10
(also called "98P4B6v.10")is shown in FIG. 2J. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0051] K) The cDNA and amino acid sequence of 98P4B6 variant 11
(also called "98P4B6 v.11") is shown in FIG. 2K. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0052] L) The cDNA and amino acid sequence of 98P4B6 variant 12
(also called "98P4B6 v.12") is shown in FIG. 2L. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0053] M) The cDNA and amino acid sequence of 98P4B6 variant 13
(also called "98P4B6 v.13") is shown in FIG. 2M. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0054] N) The cDNA and amino acid sequence of 98P4B6 variant 14
(also called "98P4B6 v.14") is shown in FIG. 2N. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0055] O) The cDNA and amino acid sequence of 98P4B6 variant 15
(also called "98P4B6 v.15") is shown in FIG. 20. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0056] P) The cDNA and amino acid sequence of 98P4B6 variant 16
(also called "98P4B6 v.16") is shown in FIG. 2P. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0057] Q) The cDNA and amino acid sequence of 98P4B6 variant 17
(also called "98P4B6 v.17") is shown in FIG. 2Q. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0058] R) The cDNA and amino acid sequence of 98P4B6 variant 18
(also called "98P4B6 v.18") is shown in FIG. 2R. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0059] S) The cDNA and amino acid sequence of 98P4B6 variant 19
(also called "98P4B6 v.19") is shown in FIG. 2S. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 355-1719 including the stop codon.
[0060] T) The cDNA and amino acid sequence of 98P4B6 variant 20
(also called "98P4B6 v.20") is shown in FIG. 2T. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 295-2025 including the stop codon.
[0061] U) The cDNA and amino acid sequence of 98P4B6 variant 21
(also called "98P4B6 v.21") is shown in FIG. 2U. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 295-2025 including the stop codon.
[0062] V) The cDNA and amino acid sequence of 98P4B6 variant 22
(also called "98P4B6 v.22") is shown in FIG. 2V. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 295-2025 including the stop codon.
[0063] W) The cDNA and amino acid sequence of 98P4B6 variant 23
(also called "98P4B6 v.23") is shown in FIG. 2W. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 295-2025 including the stop codon.
[0064] X) The cDNA and amino acid sequence of 98P4B6 variant 24
(also called "98P4B6 v.24") is shown in FIG. 2X. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 295-2025 including the stop codon.
[0065] Y) The cDNA and amino acid sequence of 98P4B6 variant 25
(also called "98P4B6 v.25") is shown in FIG. 2Y. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0066] Z) The cDNA and amino acid sequence of 98P4B6 variant 26
(also called "98P4B6 v.26") is shown in FIG. 2. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0067] AA) The cDNA and amino acid sequence of 98P4B6 variant 27
(also called "98P4B6 v.27") is shown in FIG. 2AA. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0068] AB) The cDNA and amino acid sequence of 98P4B6 variant 28
(also called "98P4B6 v.28") is shown in FIG. 2AB. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0069] AC) The cDNA and amino acid sequence of 98P4B6 variant 29
(also called "98P4B6 v.29") is shown in FIG. 2AC. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0070] AD) The cDNA and amino acid sequence of 98P4B6 variant 30
(also called "98P4B6 v.30") is shown in FIG. 2AD. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0071] AE) The cDNA and amino acid sequence of 98P4B6 variant 31
(also called "98P4B6 v.31") is shown in FIG. 2AE. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0072] AF) The cDNA and amino acid sequence of 98P4B6 variant 32
(also called "98P4B6 v.32") is shown in FIG. 2AF. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0073] AG) The cDNA and amino acid sequence of 98P4B6 variant 33
(also called "98P4B6 v.33") is shown in FIG. 2AG. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0074] AH) The cDNA and amino acid sequence of 98P4B6 variant 34
(also called "98P4B6 v.34") is shown in FIG. 2AH. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0075] AI) The cDNA and amino acid sequence of 98P4B6 variant 35
(also called "98P4B6 v.35") is shown in FIG. 2AI. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0076] AJ) The cDNA and amino acid sequence of 98P4B6 variant 36
(also called "98P4B6 v.36") is shown in FIG. 2AJ. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0077] AK) The cDNA and amino acid sequence of 98P4B6 variant 37
(also called "98P4B6 v.37") is shown in FIG. 2AK. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0078] AL) The cDNA and amino acid sequence of 98P4B6 variant 38
(also called "98P4B6 v.38") is shown in FIG. 2AL. The codon for the
start methionine is underlined. The open reading frame extends from
nucleic acid 394-1866 including the stop codon.
[0079] FIG. 3.
[0080] A) The amino acid sequence of 98P4B6 v.1 is shown in FIG.
3A; it has 454 amino acids.
[0081] B) The amino acid sequence of 98P4B6 v.2 is shown in FIG.
3B; it has 45 amino acids.
[0082] C) The amino acid sequence of 98P4B6 v.5 is shown in FIG.
3C; it has 419 amino acids.
[0083] D) The amino acid sequence of 98P4B6 v.6 is shown in FIG.
3D; it has 490 amino acids.
[0084] E) The amino acid sequence of 98P4B6 v.7 is shown in FIG.
3E; it has 576 amino acids.
[0085] F) The amino acid sequence of 98P4B6 v.8 is shown in FIG.
3F; it has 490 amino acids.
[0086] G) The amino acid sequence of 98P4B6 v.13 is shown in FIG.
3G; it has 454 amino acids.
[0087] H) The amino acid sequence of 98P4B6 v.14 is shown in FIG.
3H; it has 454 amino acids.
[0088] I) The amino acid sequence of 98P4B6 v.21 is shown in FIG.
31; it has 576 amino acids.
[0089] J) The amino acid sequence of 98P4B6 v.25 is shown in FIG.
3J; it has 490 amino acids.
[0090] As used herein, a reference to 98P4B6 includes all variants
thereof, including those shown in FIGS. 2, 3, 10, and 11, unless
the context clearly indicates otherwise.
[0091] FIG. 4. Comparison of 98P4B6 with known genes: Human STAMP1,
human six transmembrane epithelial antigen of prostate 2 and mouse
six transmembrane epithelial antigen of prostate 2. FIG. 4(A)
Alignment of 98P4B6 variant 1 to human STAMP1 (gi 15418732). FIG.
4(B) Alignment of 98P4B6 variant 1 with human STEAP2 (gi:23308593).
FIG. 4(C) Alignment of 98P4B6 variant 1 with mouse STEAP2 (gi
28501136). FIG. 4(D): Clustal Alignment of the three 98P4B6
variants, depicting that 98P4B6 V1B contains an additional 62 aa at
its N-terminus relative to V1, and that 98P4B6 V2 carries a I to T
point mutation at aa 225 relative to V1.
[0092] FIG. 5. Hydrophilicity amino acid profile of 98P4B6v.1, v.2,
v.5, v.6, and v.7 determined by computer algorithm sequence
analysis using the method of Hopp and Woods (Hopp T. P., Woods K.
R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828) accessed on
the Protscale website located on the World Wide Web at
(expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular
biology server.
[0093] FIG. 6. Hydropathicity amino acid profile of 98P4B6v.1, v.2,
v.5, v.6, and v.7 determined by computer algorithm sequence
analysis using the method of Kyte and Doolittle (Kyte J., Doolittle
R. F., 1982. J. Mol. Biol. 157:105-132) accessed on the ProtScale
website located on the World Wide Web at
(.expasy.ch/cgi-bin/protscale.pl) through the ExPasy molecular
biology server.
[0094] FIG. 7. Percent accessible residues amino acid profile of
98P4B6v.1, v.2, v.5, v.6, and v.7 determined by computer algorithm
sequence analysis using the method of Janin (Janin J., 1979 Nature
277:491-492) accessed on the ProtScale website located on the World
Wide Web at (.expasy.ch/cgi-bin/protscale.pl) through the ExPasy
molecular biology server.
[0095] FIG. 8. Average flexibility amino acid profile of 98P4B6v.1,
v.2, v.5, v.6, and v.7 determined by computer algorithm sequence
analysis using the method of Bhaskaran and Ponnuswamy (Bhaskaran
R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res.
32:242-255) accessed on the ProtScale website located on the World
Wide Web at (.expasy.ch/cgi-bin/protscale.pl) through the ExPasy
molecular biology server.
[0096] FIG. 9. Beta-turn amino acid profile of 98P4B6v.1, v.2, v.5,
v.6, and v.7 determined by computer algorithm sequence analysis
using the method of Deleage and Roux (Deleage, G., Roux B. 1987
Protein Engineering 1:289-294) accessed on the ProtScale website
located on the World Wide Web at (.expasy.ch/cgi-bin/protscale.pl)
through the ExPasy molecular biology server.
[0097] FIG. 10. FIG. 10(a): Schematic alignment of SNP variants of
98P4B6 v.1. Variants 98P4B6 v.9 through v.19 were variants with
single nucleotide difference from v.1. Though these SNP variants
were shown separately, they could also occur in any combinations
and in any transcript variants, as shown in FIG. 12, that contains
the bases. SNP in regions of other transcript variants, such as
v.2, v.6 and v.8, not common with v.1 were not shown here. Numbers
correspond to those of 98P4B6 v.1. Black box shows the same
sequence as 98P4B6 v.1. SNPs are indicated above the box. FIG.
10(b): Schematic alignment of SNP variants of 98P4B6 v.7. Variants
98P4B6 v.20 through v.24 were variants with single nucleotide
difference from v.7. Though these SNP variants were shown
separately, they could also occur in any combinations and in any
transcript variants, as shown in FIG. 12, that contains the bases.
Those SNP in regions common with v.1 were not shown here. Numbers
correspond to those of 98P4B6 v.7. Black box shows the same
sequence as 98P4B6 v.7. SNPs are indicated above the box. FIG.
10(c): Schematic alignment of SNP variants of 98P4B6 v.8. Variants
98P4B6 v.25 through v.38 were variants with single nucleotide
difference from v.8. Though these SNP variants were shown
separately, they could also occur in any combinations and in any
transcript variants, as shown in FIG. 12, that contains the bases.
Those SNP in regions of common with v.1 were not shown here.
Numbers correspond to those of 98P4B6 v.8. Black box shows the same
sequence as 98P4B6 v.8. SNPs are indicated above the box.
[0098] FIG. 11. Schematic alignment of protein variants of 98P4B6.
Protein variants corresponded to nucleotide variants. Nucleotide
variants 98P4B6 v.3, v.4, v.9 through v.12, and v.15 through v.19
coded for the same protein as v.1. Nucleotide variants 98P4B6 v.6
and v.8 coded the same protein except for single amino acid at 475,
which is an "M" in v.8. Variants v.25 was translated from v.25, a
SNP variant of v.8, with one amino acid difference at 565.
Similarly, v.21 differed from v.7 by one amino acid at 565. Single
amino acid differences were indicated above the boxes. Black boxes
represent the same sequence as 98P4B6 v.1. Numbers underneath the
box correspond to 98P4B6 v.1.
[0099] FIG. 12. Structure of transcript variants of 98P4B6. Variant
98P4B6 v.2 through v.8 were transcript variants of v.1. Variant v.2
was a single exon transcript whose 3' portion was the same as the
last exon of v.1. The first two exons of v.3 were in intron 1 of v.
1. Variants v.4, v.5 and v.6 spliced out 224-334 in the first exon
of v.1. In addition, v.5 spliced out exon 5 while v.6 spliced out
exon 6 but extended exon 5 of v.1. Variant v.7 used alternative
transcription start and different 3' exons. Variant v.8 extended 5'
end and kept the whole intron 5 of v.1. The first 35 bases of v.1
were not in the nearby 5' region of v.1 on the current assembly of
the human genome. Ends of exons in the transcripts are marked above
the boxes. Potential exons of this gene are shown in order as on
the human genome. Poly A tails and single nucleotide differences
are not shown in the figure. Numbers in "()" underneath the boxes
correspond to those of 98P4B6 v.1. Lengths of introns and exons are
not proportional.
[0100] FIG. 13. Secondary structure and transmembrane domains
prediction for 98P4B6 protein variants. 13(A), 13(B), 13(C), 13(D),
13(E): The secondary structure of 98P4B6 protein variant 1 (SEQ ID
NO: 193), Variant 2 (SEQ ID NO: 194), Variant 5 (SEQ ID NO: 195),
Variant 6 (SEQ ID NO: 196), and Variant 7 (SEQ ID NO: 197) were
predicted using the HNN--Hierarchical Neural Network method
(Guermeur, 1997, located on the World Wide Web at
.pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html- , accessed
from the ExPasy molecular biology server located on the World Wide
Web at .expasy.ch/tools. This method predicts the presence and
location of alpha helices, extended strands, and random coils from
the primary protein sequence. The percent of the protein in a given
secondary structure is also listed.
[0101] 13(F), 13(H), 13(J), 13(L), and 13(N): Schematic
representations of the probability of existence of transmembrane
regions and orientation of 98P4B6 variants 1, 2, 5-7, respectively,
based on the TMpred algorithm of Hofmann and Stoffel which utilizes
TMBASE (K. Hofmann, W. Stoffel. TMBASE--A database of membrane
spanning protein segments Biol. Chem. Hoppe-Seyler 374:166,1993).
13(G), 13(I), 13(K), 13(M), and 13(O): Schematic representations of
the probability of the existence of transmembrane regions and the
extracellular and intracellular orientation of 98P4B6 variants 1,
2, 5-7, respectively, based on the TMHMM algorithm of Sonnhammer,
von Heijne, and Krogh (Erik L. L. Sonnhammer, Gunnar von Heijne,
and Anders Krogh: A hidden Markov model for predicting
transmembrane helices in protein sequences. In Proc. of Sixth Int.
Conf. on Intelligent Systems for Molecular Biology, p 175-182 Ed J.
Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C.
Sensen Menlo Park, Calif.: AAAI Press, 1998). The TMpred and TMHMM
algorithms are accessed from the ExPasy molecular biology server
located on the World Wide Web at .expasy.ch/tools/.
[0102] FIG. 14. 98P4B6 Expression in Human Normal and Patient
Cancer Tissues. First strand cDNA was generated from normal
stomach, normal brain, normal heart, normal liver, normal skeletal
muscle, normal testis, normal prostate, normal bladder, normal
kidney, normal colon, normal lung, normal pancreas, and a pool of
cancer specimens from prostate cancer patients, bladder cancer
patients, kidney cancer patients, colon cancer patients, lung
cancer patients, pancreas cancer patients, and a pool of 2 patient
prostate metastasis to lymph node. Normalization was performed by
PCR using primers to actin. Semi-quantitative PCR, using primers
directed to 98P4B6 v.1, v.13, and v.14 (A), or directed
specifically to the splice variants 98P4B6 v.6 and v.8 (B), was
performed at 26 and 30 cycles of amplification. Samples were run on
an agarose gel, and PCR products were quantitated using the
Alphalmager software. Results show strong expression of 98P4B6 v.1,
v.13, and v.14 and its splice variants v.6 and v.8 in normal
prostate and in prostate cancer. Expression was also detected in
bladder cancer, kidney cancer, colon cancer, lung cancer, pancreas
cancer, breast cancer, cancer metastasis as well as in the prostate
cancer metastasis to lymph node specimens, compared to all normal
tissues tested.
[0103] FIG. 15. 98P4B6 Expression in lung, ovary, prostate,
bladder, cervix, uterus and pancreas patient cancer specimens.
First strand cDNA was prepared from a panel of patient cancer
specimens. Normalization was performed by PCR using primers to
actin. Semi-quantitative PCR, using primers to 98P4B6 v.1, v.13,
and v.14, was performed at 26 and 30 cycles of amplification.
Samples were run on an agarose gel, and PCR products were
quantitated using the Alphalmager software. Expression was recorded
as absent, low, medium or strong. Results show expression of 98P4B6
in the majority of all patient cancer specimens tested.
[0104] FIG. 16. Expression of 98P4B6 in stomach cancer patient
specimens. (A) RNA was extracted from normal stomach (N) and from
10 different stomach cancer patient specimens (T). Northern blot
with 10 .mu.g of total RNA/lane was probed with 98P4B6 sequence.
Results show strong expression of 98P4B6 in the stomach tumor
tissues and lower expression in normal stomach. The lower panel
represents ethidium bromide staining of the blot showing quality of
the RNA samples. (B) Expression of 98P4B6 was assayed in a panel of
human stomach cancers (T) and their respective matched normal
tissues (N) on RNA dot blots. 98P4B6 was detected in 7 out of 8
stomach tumors but not in the matched normal tissue.
[0105] FIG. 17. Detection of 98P4B6 expression with polyclonal
antibody. 293T cells were transfected with
98P4B6.GFP.pcDNA3.1/mychis construct clone A12 or clone B12.
STEAP1.GFP vector was used as a positive control. And as a negative
control an empty vector was used. Forty hours later, cell Iysates
were collected. Samples were run on an SDS-PAGE acrylamide gel,
blotted and stained with either anti-GFP antibody (A), anti-98P4B6
antibody generated against amino acids 198-389 (B), or anti-98P4B6
antibody generated against amino acids 153-165. The blot was
developed using the ECL chemiluminescence kit and visualized by
autoradiography. Results show expression of the expected 98P4B6.GFP
fusion protein as detected by the anti-GFP antibody. Also, we were
able to raise 2 different polyclonal antibodies that recognized the
98P4B6.GFP fusion proteins as shown in B and C.
[0106] FIG. 18. Detection of 98P4B6 expression with polyclonal
antibody. 293T cells were transfected with
98P4B6.GFP.pcDNA3.1/mychis construct clone A12 or clone B12.
Expression of the 98P4B6.GFP fusion protein was detected by flow
cytometry (A) and by flurorescent microscopy (B). Results show
strong green fluorescence in the majority of the cells. The fusion
protein localized to the perinuclear area and to the cell
membrane.
[0107] FIG. 19. STEAP-2 Characteristics. The expression of STEAP-2
in normal tissues is predominantly restricted to the prostate.
STEAP-2 is expressed in several cancerous tissues. In
patient-derived prostate, colon, and lung cancer specimens; and
Multiple cancer cell lines, including prostate, colon, Ewing's
sarcoma, lung, kidney, pancreas and testis. By ISH, STEAP-2
expression appears to be primarily limited to ductal epithelial
cells.
[0108] FIG. 20. STEAP-2 Induces Tyrosine Phosphorylation in PC3
Cells. STEAP-2 induces the tyrosine phosphorylation of proteins at
140-150, 120, 75-80, 62 and 40 kDa.
[0109] FIG. 21. STEAP-2 Enhances Tyrosine Phosphorylation in NIH
3T3 Cells. STEAP-2 enhances the phosphorylation of p135-140, p78-75
by STEAP-2 in NIH 3T3 cells. STEAP-2 C-Flag enhances the
phosphorylation of p180, and induces the de-phosphorylation of
p132, p82 and p75.
[0110] FIG. 22. STEAP-2 Induces ERK Phosphorylation. STEAP-2
Induces ERK phosphorylation in PC3 and 3T3 cells in 0.5 and 10%
FBS. Lack or ERK phosphorylation in 3T3-STEAP-2-cflag cells.
Potential role as dominant negative.
[0111] FIG. 23. STEAP Enhances Calcium Flux in PC3 cells.
PC-STEAP-1 and PC3-STEAP-2 exhibit enhanced calcium flux in
response to LPA. PC3-STEAP-1 demonstrates susceptibility to the L
type calcium channel inhibitor, conotoxin. PC3-STEAP-2 shown
susceptibility to the PQ type calcium channel inhibitor, agatoxin.
NDGA and TEA had no effect on the proliferation of PC3-STEAP-2
cells.
[0112] FIG. 24. STEAP-2 Alters the Effect of Paclitaxel on PC3
Cells. Other Chemotherapeutics Tested without yielding a
differential response between STEAP-expressing and control cells
were Flutamide, Genistein, Rapamycin. STEAP-2 confers partial
resistance to Paclitaxel in PC3 cells. Over 8 fold increase in
percent survival of PC3-STEAP-2 relative to PC3-Neo cells.
[0113] FIG. 25. Inhibition of Apoptosis by STEAP-2. PC3 cells were
treated with paclitaxel for 60 hours and analyzed for apoptosis by
annexinV-PI staining. Expression of STEAP-2 partially inhibits
apoptosis by paclitaxel.
[0114] FIG. 26. STEAP-2 Attenuates Paclitaxel Mediated Apoptosis.
PC3 cells were treated with paclitaxel for 68 hours and analyzed
for apoptosis. Expression of STEAP-2, but not STEAP-2CFlag,
partially inhibits apoptosis by paclitaxel.
DETAILED DESCRIPTION OF THE INVENTION
[0115] Outline of Sections
[0116] I.) Definitions
[0117] II.) 98P4B6 Polynucleotides
[0118] II.A.) Uses of 98P4B6 Polynucleotides
[0119] II.A.1.) Monitoring of Genetic Abnormalities
[0120] II.A.2.) Antisense Embodiments
[0121] II.A.3.) Primers and Primer Pairs
[0122] II.A.4.) Isolation of 98P4B6-Encoding Nucleic Acid
Molecules
[0123] II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector
Systems
[0124] III) 98P4B6-related Proteins
[0125] III.A.) Motif-bearing Protein Embodiments
[0126] III.B.) Expression of 98P4B6-related Proteins
[0127] III.C.) Modifications of 98P4B6-related Proteins
[0128] III.D.) Uses of 98P4B6-related Proteins
[0129] IV.) 98P4B6 Antibodies
[0130] V.) 98P4B6 Cellular Immune Responses
[0131] VI.) 98P4B6 Transgenic Animals
[0132] VII.) Methods for the Detection of 98P4B6
[0133] VIII.) Methods for Monitoring the Status of 98P4B6-related
Genes and Their Products
[0134] IX.) Identification of Molecules That Interact With
98P4B6
[0135] X.) Therapeutic Methods and Compositions
[0136] X.A.) Anti-Cancer Vaccines
[0137] X.B.) 98P4B6 as a Target for Antibody-Based Therapy
[0138] X.C.) 98P4B6 as a Target for Cellular Immune Responses
[0139] X.C.1. Minigene Vaccines
[0140] X.C.2. Combinations of CTL Peptides with Helper Peptides
[0141] X.C.3. Combinations of CTL Peptides with T Cell Priming
Agents
[0142] X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL
and/or HTL Peptides
[0143] X.D.) Adoptive Immunotherapy
[0144] X.E.) Administration of Vaccines for Therapeutic or
Prophylactic Purposes
[0145] XI.) Diagnostic and Prognostic Embodiments of 98P4B6.
[0146] XII.) Inhibition of 98P4B6 Protein Function
[0147] XII.A.) Inhibition of 98P4B6 With Intracellular
Antibodies
[0148] XII.B.) Inhibition of 98P4B6 with Recombinant Proteins
[0149] XII.C.) Inhibition of 98P4B6 Transcription or
Translation
[0150] XII.D.) General Considerations for Therapeutic
Strategies
[0151] XIII.) Identification, Characterization and Use of
Modulators of 98P4B6
[0152] XIV.) KITS/Articles of Manufacture
[0153] I.) Definitions:
[0154] Unless otherwise defined, all terms of art, notations and
other scientific terms or terminology used herein are intended to
have the meanings commonly understood by those of skill in the art
to which this invention pertains. In some cases, terms with
commonly understood meanings are defined herein for clarity and/or
for ready reference, and the inclusion of such definitions herein
should not necessarily be construed to represent a substantial
difference over what is generally understood in the art. Many of
the techniques and procedures described or referenced herein are
well understood and commonly employed using conventional
methodology by those skilled in the art, such as, for example, the
widely utilized molecular cloning methodologies described in
Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd.
edition (1989) Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y. As appropriate, procedures involving the use of
commercially available kits and reagents are generally carried out
in accordance with manufacturer defined protocols and/or parameters
unless otherwise noted.
[0155] The terms "advanced prostate cancer", "locally advanced
prostate cancer", "advanced disease" and "locally advanced disease"
mean prostate cancers that have extended through the prostate
capsule, and are meant to include stage C disease under the
American Urological Association (AUA) system, stage C1-C2 disease
under the Whitmore-Jewett system, and stage T3-T4 and N+ disease
under the TNM (tumor, node, metastasis) system. In general, surgery
is not recommended for patients with locally advanced disease, and
these patients have substantially less favorable outcomes compared
to patients having clinically localized (organ-confined) prostate
cancer. Locally advanced disease is clinically identified by,
palpable evidence of induration beyond the lateral border of the
prostate, or asymmetry or induration above the prostate base.
Locally advanced prostate cancer is presently diagnosed
pathologically following radical prostatectomy if the tumor invades
or penetrates the prostatic capsule, extends into the surgical
margin, or invades the seminal vesicles.
[0156] "Altering the native glycosylation pattern" is intended for
purposes herein to mean deleting one or more carbohydrate moieties
found in native sequence 98P4B6 (either by removing the underlying
glycosylation site or by deleting the glycosylation by chemical
and/or enzymatic means), and/or adding one or more glycosylation
sites that are not present in the native sequence 98P4B6. In
addition, the phrase includes qualitative changes in the
glycosylation of the native proteins, involving a change in the
nature and proportions of the various carbohydrate moieties
present.
[0157] The term "analog" refers to a molecule which is structurally
similar or shares similar or corresponding attributes with another
molecule (e.g. a 98P4B6-related protein). For example, an analog of
a 98P4B6 protein can be specifically bound by an antibody or T cell
that specifically binds to 98P4B6.
[0158] The term "antibody" is used in the broadest sense.
Therefore, an "antibody" can be naturally occurring or man-made
such as monoclonal antibodies produced by conventional hybridoma
technology. Anti-98P4B6 antibodies comprise monoclonal and
polyclonal antibodies as well as fragments containing the
antigen-binding domain and/or one or more complementarity
determining regions of these antibodies.
[0159] An "antibody fragment" is defined as at least a portion of
the variable region of the immunoglobulin molecule that binds to
its target, i.e., the antigen-binding region. In one embodiment it
specifically covers single anti-98P4B6 antibodies and clones
thereof (including agonist, antagonist and neutralizing antibodies)
and anti-98P4B6 antibody compositions with polyepitopic
specificity.
[0160] The term "codon optimized sequences" refers to nucleotide
sequences that have been optimized for a particular host species by
replacing any codons having a usage frequency of less than about
20%. Nucleotide sequences that have been optimized for expression
in a given host species by elimination of spurious polyadenylation
sequences, elimination of exon/intron splicing signals, elimination
of transposon-like repeats and/or optimization of GC content in
addition to codon optimization are referred to herein as an
"expression enhanced sequences."
[0161] A "combinatorial library" is a collection of diverse
chemical compounds generated by either chemical synthesis or
biological synthesis by combining a number of chemical "building
blocks" such as reagents. For example, a linear combinatorial
chemical library, such as a polypeptide (e.g., mutein) library, is
formed by combining a set of chemical building blocks called amino
acids in every possible way for a given compound length (i.e., the
number of amino acids in a polypeptide compound). Numerous chemical
compounds are synthesized through such combinatorial mixing of
chemical building blocks (Gallop et al., J. Med. Chem. 37(9):
1233-1251 (1994)).
[0162] Preparation and screening of combinatorial libraries is well
known to those of skill in the art. Such combinatorial chemical
libraries include, but are not limited to, peptide libraries (see,
e.g., U.S. Pat. No. 5,010,175, Furka, Pept. Prot. Res. 37:487-493
(1991), Houghton et al., Nature, 354:84-88 (1991)), peptoids (PCT
Publication No WO 91/19735), encoded peptides (PCT Publication WO
93/20242), random bio-oligomers (PCT Publication WO 92/00091),
benzodiazepines (U.S. Pat. No. 5,288,514), diversomers such as
hydantoins, benzodiazepines and dipeptides (Hobbs et al., Proc.
Nat. Acad. Sci. USA 90:6909-6913 (1993)), vinylogous polypeptides
(Hagihara et al., J. Amer. Chem. Soc. 114:6568 (1992)), nonpeptidal
peptidomimetics with a Beta-D-Glucose scaffolding (Hirschmann et
al., J. Amer. Chem. Soc. 114:9217-9218 (1992)), analogous organic
syntheses of small compound libraries (Chen et al., J. Amer. Chem.
Soc. 116:2661 (1994)), oligocarbamates (Cho, et al., Science
261:1303 (1993)), and/or peptidyl phosphonates (Campbell et al., J.
Org. Chem. 59:658 (1994)). See, generally, Gordon et al., J. Med.
Chem. 37:1385 (1994), nucleic acid libraries (see, e.g.,
Stratagene, Corp.), peptide nucleic acid libraries (see, e.g., U.S.
Pat. No. 5,539,083), antibody libraries (see, e.g., Vaughn et al.,
Nature Biotechnology 14(3): 309-314 (1996), and PCT/US96/10287),
carbohydrate libraries (see, e.g., Liang et al., Science
274:1520-1522 (1996), and U.S. Pat. No. 5,593,853), and small
organic molecule libraries (see, e.g., benzodiazepines, Baum,
C&EN, January 18, page 33 (1993); isoprenoids, U.S. Pat. No.
5,569,588; thiazolidinones and metathiazanones, U.S. Pat. No.
5,549,974; pyrrolidines, U.S. Pat. Nos. 5,525,735 and 5,519,134;
morpholino compounds, U.S. Pat. No. 5,506, 337; benzodiazepines,
U.S. Pat. No. 5,288,514; and the like).
[0163] Devices for the preparation of combinatorial libraries are
commercially available (see, e.g., 357 NIPS, 390 NIPS, Advanced
Chem Tech, Louisville Ky.; Symphony, Rainin, Woburn, Mass.; 433A,
Applied Biosystems, Foster City, Calif.; 9050, Plus, Millipore,
Bedford, NIA). A number of well-known robotic systems have also
been developed for solution phase chemistries. These systems
include automated workstations such as the automated synthesis
apparatus developed by Takeda Chemical Industries, LTD. (Osaka,
Japan) and many robotic systems utilizing robotic arms (Zymate H,
Zymark Corporation, Hopkinton, Mass.; Orca, Hewlett-Packard, Palo
Alto, Calif.), which mimic the manual synthetic operations
performed by a chemist. Any of the above devices are suitable for
use with the present invention. The nature and implementation of
modifications to these devices (if any) so that they can operate as
discussed herein will be apparent to persons skilled in the
relevant art. In addition, numerous combinatorial libraries are
themselves commercially available (see, e.g., ComGenex, Princeton,
N.J.; Asinex, Moscow, RU; Tripos, Inc., St. Louis, Mo.; ChemStar,
Ltd, Moscow, RU; 3D Pharmaceuticals, Exton, Pa.; Martek
Biosciences, Columbia, Md.; etc.).
[0164] The term "cytotoxic agent" refers to a substance that
inhibits or prevents the expression activity of cells, function of
cells and/or causes destruction of cells. The term is intended to
include radioactive isotopes chemotherapeutic agents, and toxins
such as small molecule toxins or enzymatically active toxins of
bacterial, fungal, plant or animal origin, including fragments
and/or variants thereof. Examples of cytotoxic agents include, but
are not limited to auristatins, auromycins, maytansinoids, yttrium,
bismuth, ricin, ricin A-chain, combrestatin, duocarmycins,
dolostatins, doxorubicin, daunorubicin, taxol, cisplatin, cc1065,
ethidium bromide, mitomycin, etoposide, tenoposide, vincristine,
vinblastine, colchicine, dihydroxy anthracin dione, actinomycin,
diphtheria toxin, Pseudomonas exotoxin (PE) A, PE40, abrin, abrin A
chain, modeccin A chain, alpha-sarcin, gelonin, mitogellin,
retstrictocin, phenomycin, enomycin, curicin, crotin,
calicheamicin, Sapaonaria officinalis inhibitor, and glucocorticoid
and other chemotherapeutic agents, as well as radioisotopes such as
At.sup.211, I.sup.131, I.sup.125, Y.sup.90, Re.sup.186, Re.sup.188,
Sm.sup.153, Bi.sup.212or213, P.sup.32 and radioactive isotopes of
Lu including Lu.sup.177. Antibodies may also be conjugated to an
anti-cancer pro-drug activating enzyme capable of converting the
pro-drug to its active form.
[0165] The "gene product" is sometimes referred to herein as a
protein or mRNA. For example, a "gene product of the invention" is
sometimes referred to herein as a "cancer amino acid sequence",
"cancer protein", "protein of a cancer listed in Table I", a
"cancer mRNA", "mRNA of a cancer listed in Table I", etc. In one
embodiment, the cancer protein is encoded by a nucleic acid of FIG.
2. The cancer protein can be a fragment, or alternatively, be the
full-length protein to the fragment encoded by the nucleic acids of
FIG. 2. In one embodiment, a cancer amino acid sequence is used to
determine sequence identity or similarity. In another embodiment,
the sequences are naturally occurring allelic variants of a protein
encoded by a nucleic acid of FIG. 2. In another embodiment, the
sequences are sequence variants as further described herein.
[0166] "High throughput screening" assays for the presence,
absence, quantification, or other properties of particular nucleic
acids or protein products are well known to those of skill in the
art. Similarly, binding assays and reporter gene assays are
similarly well known. Thus, e.g., U.S. Pat. No. 5,559,410 discloses
high throughput screening methods for proteins; U.S. Pat. No.
5,585,639 discloses high throughput screening methods for nucleic
acid binding (i.e., in arrays); while U.S. Pat. Nos. 5,576,220 and
5,541,061 disclose high throughput methods of screening for
ligand/antibody binding.
[0167] In addition, high throughput screening systems are
commercially available (see, e.g., Amersham Biosciences,
Piscataway, N.J.; Zymark Corp., Hopkinton, Mass.; Air Technical
Industries, Mentor, Ohio; Beckman Instruments, Inc. Fullerton,
Calif.; Precision Systems, Inc., Natick, Mass.; etc.). These
systems typically automate entire procedures, including all sample
and reagent pipetting, liquid dispensing, timed incubations, and
final readings of the microplate in detector(s) appropriate for the
assay. These configurable systems provide high throughput and rapid
start up as well as a high degree of flexibility and customization.
The manufacturers of such systems provide detailed protocols for
various high throughput systems. Thus, e.g., Zymark Corp. provides
technical bulletins describing screening systems for detecting the
modulation of gene transcription, ligand binding, and the like.
[0168] The term "homolog" refers to a molecule which exhibits
homology to another molecule, by for example, having sequences of
chemical residues that are the same or similar at corresponding
positions.
[0169] "Human Leukocyte Antigen" or "HLA" is a human class I or
class II Major Histocompatibility Complex (MHC) protein (see, e.g.,
Stites, et al., IMMUNOLOGY, 8.sup.TH ED., Lange Publishing, Los
Altos, Calif. (1994).
[0170] The terms "hybridize", "hybridizing", "hybridizes" and the
like, used in the context of polynucleotides, are meant to refer to
conventional hybridization conditions, preferably such as
hybridization in 50% formamide/6.times.SSC/0.1% SDS/100 .mu.g/ml
ssDNA, in which temperatures for hybridization are above 37 degrees
C. and temperatures for washing in 0.1.times.SSC/0.1% SDS are above
55 degrees C.
[0171] The phrases "isolated" or "biologically pure" refer to
material which is substantially or essentially free from components
which normally accompany the material as it is found in its native
state. Thus, isolated peptides in accordance with the invention
preferably do not contain materials normally associated with the
peptides in their in situ environment. For example, a
polynucleotide is said to be "isolated" when it is substantially
separated from contaminant polynudeotides that correspond or are
complementary to genes other than the 98P4B6 genes or that encode
polypeptides other than 98P4B6 gene product or fragments thereof. A
skilled artisan can readily employ nucleic acid isolation
procedures to obtain an isolated 98P4B6 polynucleotide. A protein
is said to be "isolated," for example, when physical, mechanical or
chemical methods are employed to remove the 98P4B6 proteins from
cellular constituents that are normally associated with the
protein. A skilled artisan can readily employ standard purification
methods to obtain an isolated 98P4B6 protein. Alternatively, an
isolated protein can be prepared by chemical means.
[0172] The term "mammal" refers to any organism classified as a
mammal, including mice, rats, rabbits, dogs, cats, cows, horses and
humans. In one embodiment of the invention, the mammal is a mouse.
In another embodiment of the invention, the mammal is a human.
[0173] The terms "metastatic prostate cancer" and "metastatic
disease" mean prostate cancers that have spread to regional lymph
nodes or to distant sites, and are meant to include stage D disease
under the AUA system and stage T.times.N.times.M+ under the TNM
system. As is the case with locally advanced prostate cancer,
surgery is generally not indicated for patients with metastatic
disease, and hormonal (androgen ablation) therapy is a preferred
treatment modality. Patients with metastatic prostate cancer
eventually develop an androgen-refractory state within 12 to 18
months of treatment initiation. Approximately half of these
androgen-refractory patients die within 6 months after developing
that status. The most common site for prostate cancer metastasis is
bone. Prostate cancer bone metastases are often osteoblastic rather
than osteolytic (i.e., resulting in net bone formation). Bone
metastases are found most frequently in the spine, followed by the
femur, pelvis, rib cage, skull and humerus. Other common sites for
metastasis include lymph nodes, lung, liver and brain. Metastatic
prostate cancer is typically diagnosed by open or laparoscopic
pelvic lymphadenectomy, whole body radionuclide scans, skeletal
radiography, and/or bone lesion biopsy.
[0174] The term "modulator" or "test compound" or "drug candidate"
or grammatical equivalents as used herein describe any molecule,
e.g., protein, oligopeptide, small organic molecule,
polysaccharide, polynucleotide, etc., to be tested for the capacity
to directly or indirectly alter the cancer phenotype or the
expression of a cancer sequence, e.g., a nucleic acid or protein
sequences, or effects of cancer sequences (e.g., signaling, gene
expression, protein interaction, etc.) In one aspect, a modulator
will neutralize the effect of a cancer protein of the invention. By
"neutralize" is meant that an activity of a protein is inhibited or
blocked, along with the consequent effect on the cell. In another
aspect, a modulator will neutralize the effect of a gene, and its
corresponding protein, of the invention by normalizing levels of
said protein. In preferred embodiments, modulators alter expression
profiles, or expression profile nucleic acids or proteins provided
herein, or downstream effector pathways. In one embodiment, the
modulator suppresses a cancer phenotype, e.g. to a normal tissue
fingerprint. In another embodiment, a modulator induced a cancer
phenotype. Generally, a plurality of assay mixtures is run in
parallel with different agent concentrations to obtain a
differential response to the various concentrations. Typically, one
of these concentrations serves as a negative control, i.e., at zero
concentration or below the level of detection.
[0175] Modulators, drug candidates or test compounds encompass
numerous chemical classes, though typically they are organic
molecules, preferably small organic compounds having a molecular
weight of more than 100 and less than about 2,500 Daltons.
Preferred small molecules are less than 2000, or less than 1500 or
less than 1000 or less than 500 D. Candidate agents comprise
functional groups necessary for structural interaction with
proteins, particularly hydrogen bonding, and typically include at
least an amine, tarbonyl, hydroxyl or carboxyl group, preferably at
least two of the functional chemical groups. The candidate agents
often comprise cyclical carbon or heterocyclic structures and/or
aromatic or polyaromatic structures substituted with one or more of
the above functional groups. Modulators also comprise biomolecules
such as peptides, saccharides, fatty acids, steroids, purines,
pyrimidines, derivatives, structural analogs or combinations
thereof. Particularly preferred are peptides. One class of
modulators are peptides, for example of from about five to about 35
amino acids, with from about five to about 20 amino acids being
preferred, and from about 7 to about 15 being particularly
preferred. Preferably, the cancer modulatory protein is soluble,
includes a non-transmembrane region, and/or, has an N-terminal Cys
to aid in solubility. In one embodiment, the C-terminus of the
fragment is kept as a free acid and the N-terminus is a free amine
to aid in coupling, i.e., to cysteine. In one embodiment, a cancer
protein of the invention is conjugated to an immunogenic agent as
discussed herein. In one embodiment, the cancer protein is
conjugated to BSA. The peptides of the invention, e.g., of
preferred lengths, can be linked to each other or to other amino
acids to create a longer peptide/protein. The modulatory peptides
can be digests of naturally occurring proteins as is outlined
above, random peptides, or "biased" random peptides. In a preferred
embodiment, peptide/protein-based modulators are antibodies, and
fragments thereof, as defined herein.
[0176] Modulators of cancer can also be nucleic acids. Nucleic acid
modulating agents can be naturally occurring nucleic acids, random
nucleic acids, or "biased" random nucleic acids. For example,
digests of prokaryotic or eukaryotic genomes can be used in an
approach analogous to that outlined above for proteins.
[0177] The term "monoclonal antibody" refers to an antibody
obtained from a population of substantially homogeneous antibodies,
i.e., the antibodies comprising the population are identical except
for possible naturally occurring mutations that are present in
minor amounts.
[0178] A "motif", as in biological motif of a 98P4B6-related
protein, refers to any pattern of amino acids forming part of the
primary sequence of a protein, that is associated with a particular
function (e.g. protein-protein interaction, protein-DNA
interaction, etc) or modification (e.g. that is phosphorylated,
glycosylated or amidated), or localization (e.g. secretory
sequence, nuclear localization sequence, etc.) or a sequence that
is correlated with being immunogenic, either humorally or
cellularly. A motif can be either contiguous or capable of being
aligned to certain positions that are generally correlated with a
certain function or property. In the context of HLA motifs, "motif"
refers to the pattern of residues in a peptide of defined length,
usually a peptide of from about 8 to about 13 amino acids for a
class I HLA motif and from about 6 to about 25 amino acids for a
class II HLA motif, which is recognized by a particular HLA
molecule. Peptide motifs for HLA binding are typically different
for each protein encoded by each human HLA allele and differ in the
pattern of the primary and secondary anchor residues.
[0179] A "pharmaceutical excipient" comprises a material such as an
adjuvant, a carrier, pH-adjusting and buffering agents, tonicity
adjusting agents, wetting agents, preservative, and the like.
[0180] "Pharmaceutically acceptable" refers to a non-toxic, inert,
and/or composition that is physiologically compatible with humans
or other mammals.
[0181] The term "polynucleotide" means a polymeric form of
nucleotides of at least 10 bases or base pairs in length, either
ribonucleotides or deoxynucleotides or a modified form of either
type of nucleotide, and is meant to include single and double
stranded forms of DNA and/or RNA. In the art, this term if often
used interchangeably with "oligonucleotide". A polynucleotide can
comprise a nucleotide sequence disclosed herein wherein thymidine
(T), as shown for example in FIG. 2, can also be uracil (U); this
definition pertains to the differences between the chemical
structures of DNA and RNA, in particular the observation that one
of the four major bases in RNA is uracil (U) instead of thymidine
(T).
[0182] The term "polypeptide" means a polymer of at least about 4,
5, 6, 7, or 8 amino acids. Throughout the specification, standard
three letter or single letter designations for amino acids are
used. In the art, this term is often used interchangeably with
"peptide" or "protein".
[0183] An HLA "primary anchor residue" is an amino acid at a
specific position along a peptide sequence which is understood to
provide a contact point between the immunogenic peptide and the HLA
molecule. One to three, usually two, primary anchor residues within
a peptide of defined length generally defines a "motif" for an
immunogenic peptide. These residues are understood to fit in close
contact with peptide binding groove of an HLA molecule, with their
side chains buried in specific pockets of the binding groove. In
one embodiment, for example, the primary anchor residues for an HLA
class I molecule are located at position 2 (from the amino terminal
position) and at the carboxyl terminal position of a 8, 9, 10, 11,
or 12 residue peptide epitope in accordance with the invention.
Alternatively, in another embodiment, the primary anchor residues
of a peptide binds an HLA class II molecule are spaced relative to
each other, rather than to the termini of a peptide, where the
peptide is generally of at least 9 amino acids in length. The
primary anchor positions for each motif and supermotif are set
forth in Table IV. For example, analog peptides can be created by
altering the presence or absence of particular residues in the
primary and/or secondary anchor positions shown in Table IV. Such
analogs are used to modulate the binding affinity and/or population
coverage of a peptide comprising a particular HLA motif or
supermotif.
[0184] "Radioisotopes" include, but are not limited to the
following (non-limiting exemplary uses are also set forth):
[0185] Examples of Medical Isotopes:
[0186] Isotope
[0187] Description of use
[0188] Actinium-225
[0189] (AC-225)
[0190] See Thorium-229 (Th-229)
[0191] Actinium-227
[0192] (AC-227)
[0193] Parent of Radium-223 (Ra-223) which is an alpha emitter used
to treat metastases in the skeleton resulting from cancer (i.e.,
breast and prostate cancers), and cancer radioimmunotherapy
[0194] Bismuth-212
[0195] (Bi-212)
[0196] See Thorium-228 (Th-228)
[0197] Bismuth-213
[0198] (Bi-213)
[0199] See Thorium-229 (Th-229)
[0200] Cadmium-109
[0201] (Cd-109)
[0202] Cancer detection
[0203] Cobalt-60
[0204] (Co-60)
[0205] Radiation source for radiotherapy of cancer, for food
irradiators, and for sterilization of medical supplies
[0206] Copper-64
[0207] (Cu-64)
[0208] A positron emitter used for cancer therapy and SPECT
imaging
[0209] Copper-67
[0210] (Cu-67)
[0211] Beta/gamma emitter used in cancer radioimmunotherapy and
diagnostic studies (i.e., breast and colon cancers, and
lymphoma)
[0212] Dysprosium-166
[0213] (Dy-166)
[0214] Cancer radioimmunotherapy
[0215] Erbium-169
[0216] (Er-169)
[0217] Rheumatoid arthritis treatment, particularly for the small
joints associated with fingers and toes
[0218] Europium-152
[0219] (Eu-152)
[0220] Radiation source for food irradiation and for sterilization
of medical supplies
[0221] Europium-154
[0222] (Eu-154)
[0223] Radiation source for food irradiation and for sterilization
of medical supplies
[0224] Gadolinium-153
[0225] (Gd-153)
[0226] Osteoporosis detection and nuclear medical quality assurance
devices
[0227] Gold-198
[0228] (Au-198)
[0229] Implant and intracavity therapy of ovarian, prostate, and
brain cancers
[0230] Holmium-166
[0231] (Ho-166)
[0232] Multiple myeloma treatment in targeted skeletal therapy,
cancer radioimmunotherapy, bone marrow ablation, and rheumatoid
arthritis treatment
[0233] Iodine-125
[0234] (I-125)
[0235] Osteoporosis detection, diagnostic imaging, tracer drugs,
brain cancer treatment, radiolabeling, tumor imaging, mapping of
receptors in the brain, interstitial radiation therapy,
brachytherapy for treatment of prostate cancer, determination of
glomerular filtration rate (GFR), determination of plasma volume,
detection of deep vein thrombosis of the legs
[0236] Iodine-131
[0237] (1-131)
[0238] Thyroid function evaluation, thyroid disease detection,
treatment of thyroid cancer as well as other non-malignant thyroid
diseases (i.e., Graves disease, goiters, and hyperthyroidism),
treatment of leukemia, lymphoma, and other forms of cancer (e.g.,
breast cancer) using radioimmunotherapy
[0239] Iridium-192
[0240] (Ir-192)
[0241] Brachytherapy, brain and spinal cord tumor treatment,
treatment of blocked arteries (i.e., arteriosclerosis and
restenosis), and implants for breast and prostate tumors
[0242] Lutetium-177
[0243] (Lu-177)
[0244] Cancer radioimmunotherapy and treatment of blocked arteries
(i.e., arteriosclerosis and restenosis)
[0245] Molybdenum-99
[0246] (Mo-99)
[0247] Parent of Technetium-99 m (Tc-99 m) which is used for
imaging the brain, liver, lungs, heart, and other organs.
Currently, Tc-99 m is the most widely used radioisotope used for
diagnostic imaging of various cancers and diseases involving the
brain, heart, liver, lungs; also used in detection of deep vein
thrombosis of the legs
[0248] Osmium-194
[0249] (Os-194)
[0250] Cancer radioimmunotherapy
[0251] Palladium-103
[0252] (Pd-103)
[0253] Prostate cancer treatment
[0254] Platinum-195 m
[0255] (Pt-195 m)
[0256] Studies on biodistribution and metabolism of cisplatin, a
chemotherapeutic drug
[0257] Phosphorus-32
[0258] (P-32)
[0259] Polycythemia rubra vera (blood cell disease) and leukemia
treatment, bone cancer diagnosis/treatment; colon, pancreatic, and
liver cancer treatment; radiolabeling nucleic acids for in vitro
research, diagnosis of superficial tumors, treatment of blocked
arteries (i.e., arteriosclerosis and restenosis), and intracavity
therapy
[0260] Phosphorus-33
[0261] (P-33)
[0262] Leukemia treatment, bone disease diagnosis/treatment,
radiolabeling, and treatment of blocked arteries (i.e.,
arteriosclerosis and restenosis)
[0263] Radium-223
[0264] (Ra-223)
[0265] See Actinium-227 (Ac-227)
[0266] Rhenium-186
[0267] (Re-186)
[0268] Bone cancer pain relief, rheumatoid arthritis treatment, and
diagnosis and treatment of lymphoma and bone, breast, colon, and
liver cancers using radioimmunotherapy
[0269] Rhenium-188
[0270] (Re-188)
[0271] Cancer diagnosis and treatment using radioimmunotherapy,
bone cancer pain relief, treatment of rheumatoid arthritis, and
treatment of prostate cancer
[0272] Rhodium-105
[0273] (Rh-105)
[0274] Cancer radioimmunotherapy
[0275] Samarium-145
[0276] (Sm-145)
[0277] Ocular cancer treatment
[0278] Samarium-153
[0279] (Sm-153)
[0280] Cancer radioimmunotherapy and bone cancer pain relief
[0281] Scandium-47
[0282] (Sc-47)
[0283] Cancer radioimmunotherapy and bone cancer pain relief
[0284] Selenium-75
[0285] (Se-75)
[0286] Radiotracer used in brain studies, imaging of adrenal cortex
by gamma-scintigraphy, lateral locations of steroid secreting
tumors, pancreatic scanning, detection of hyperactive parathyroid
glands, measure rate of bile acid loss from the endogenous pool
[0287] Strontium-85
[0288] (Sr-85)
[0289] Bone cancer detection and brain scans
[0290] Strontium-89
[0291] (Sr-89)
[0292] Bone cancer pain relief, multiple myeloma treatment, and
osteoblastic therapy
[0293] Technetium-99m
[0294] (Tc-99m)
[0295] See Molybdenum-99 (Mo-99)
[0296] Thorium-228
[0297] (Th-228)
[0298] Parent of Bismuth-212 (Bi-212) which is an alpha emitter
used in cancer radioimmunotherapy
[0299] Thorium-229
[0300] (Th-229)
[0301] Parent of Actinium-225 (Ac-225) and grandparent of
Bismuth-213 (Bi-213) which are alpha emitters used in cancer
radioimmunotherapy
[0302] Thulium-170
[0303] (Tm-170)
[0304] Gamma source for blood irradiators, energy source for
implanted medical devices
[0305] Tin-117 m
[0306] (Sn-117 m)
[0307] Cancer immunotherapy and bone cancer pain relief
[0308] Tungsten-188
[0309] (W-188)
[0310] Parent for Rhenium-188 (Re-188) which is used for cancer
diagnostics/treatment, bone cancer pain relief, rheumatoid
arthritis treatment, and treatment of blocked arteries (i.e.,
arteriosclerosis and restenosis)
[0311] Xenon-127
[0312] (Xe-127)
[0313] Neuroimaging of brain disorders, high resolution SPECT
studies, pulmonary function tests, and cerebral blood flow
studies
[0314] Ytterbium-175
[0315] (Yb-175)
[0316] Cancer radioimmunotherapy
[0317] Yttrium-90
[0318] (Y-90)
[0319] Microseeds obtained from irradiating Yttrum-89 (Y-89) for
liver cancer treatment
[0320] Yttrium-91
[0321] (Y-91)
[0322] A gamma-emitting label for Yttrium-90 (Y-90) which is used
for cancer radioimmunotherapy (i.e., lymphoma, breast, colon,
kidney, lung, ovarian, prostate, pancreatic, and inoperable liver
cancers)
[0323] By "randomized" or grammatical equivalents as herein applied
to nucleic acids and proteins is meant that each nucleic acid and
peptide consists of essentially random nucleotides and amino acids,
respectively. These random peptides (or nucleic acids, discussed
herein) can incorporate any nucleotide or amino acid at any
position. The synthetic process can be designed to generate
randomized proteins or nucleic acids, to allow the formation of all
or most of the possible combinations over the length of the
sequence, thus forming a library of randomized candidate bioactive
proteinaceous agents.
[0324] In one embodiment, a library is "fully randomized," with no
sequence preferences or constants at any position. In another
embodiment, the library is a "biased random" library. That is, some
positions within the sequence either are held constant, or are
selected from a limited number of possibilities. For example, the
nucleotides or amino acid residues are randomized within a defined
class, e.g., of hydrophobic amino acids, hydrophilic residues,
sterically biased (either small or large) residues, towards the
creation of nucleic acid binding domains, the creation of
cysteines, for cross-linking, prolines for SH-3 domains, serines,
threonines, tyrosines or histidines for phosphorylation sites,
etc., or to purines, etc.
[0325] A "recombinant" DNA or RNA molecule is a DNA or RNA molecule
that has been subjected to molecular manipulation in vitro.
[0326] Non-limiting examples of small molecules include compounds
that bind or interact with 98P4B6, ligands including hormones,
neuropeptides, chemokines, odorants, phospholipids, and functional
equivalents thereof that bind and preferably inhibit 98P4B6 protein
function. Such non-limiting small molecules preferably have a
molecular weight of less than about 10 kDa, more preferably below
about 9, about 8, about 7, about 6, about 5 or about 4 kDa. In
certain embodiments, small molecules physically associate with, or
bind, 98P4B6 protein; are not found in naturally occurring
metabolic pathways; and/or are more soluble in aqueous than
non-aqueous solutions
[0327] "Stringency" of hybridization reactions is readily
determinable by one of ordinary skill in the art, and generally is
an empirical calculation dependent upon probe length, washing
temperature, and salt concentration. In general, longer probes
require higher temperatures for proper annealing, while shorter
probes need lower temperatures. Hybridization generally depends on
the ability of denatured nucleic acid sequences to reanneal when
complementary strands are present in an environment below their
melting temperature. The higher the degree of desired homology
between the probe and hybridizable sequence, the higher the
relative temperature that can be used. As a result, it follows that
higher relative temperatures would tend to make the reaction
conditions more stringent, while lower temperatures less so. For
additional details and explanation of stringency of hybridization
reactions, see Ausubel et al., Current Protocols in Molecular
Biology, Wiley Interscience Publishers, (1995).
[0328] "Stringent conditions" or "high stringency conditions", as
defined herein, are identified by, but not limited to, those that:
(1) employ low ionic strength and high temperature for washing, for
example 0.015 M sodium chloride/0.0015 M sodium citrate/0.1% sodium
dodecyl sulfate at 50.degree. C.; (2) employ during hybridization a
denaturing agent, such as formamide, for example, 50% (v/v)
formamide with 0.1% bovine serum albumin/0.1% Ficoll/0.1%
polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5 with
750 mM sodium chloride, 75 mM sodium citrate at 42.degree. C.; or
(3) employ 50% formamide, 5.times.SSC (0.75 M NaCl, 0.075 M sodium
citrate), 50 mM sodium phosphate (pH 6.8), 0.1% sodium
pyrophosphate, 5.times.Denhardt's solution, sonicated salmon sperm
DNA (50 .mu.g/ml), 0.1% SDS, and 10% dextran sulfate at 42.degree.
C., with washes at 42.degree. C. in 0.2.times.SSC (sodium
chloride/sodium. citrate) and 50% formamide at 55.degree. C.,
followed by a high-stringency wash consisting of 0.1.times.SSC
containing EDTA at 55.degree. C. "Moderately stringent conditions"
are described by, but not limited to, those in Sambrook et al.,
Molecular Cloning: A Laboratory Manual, New York: Cold Spring
Harbor Press, 1989, and include the use of washing solution and
hybridization conditions (e.g., temperature, ionic strength and %
SDS) less stringent than those described above. An example of
moderately stringent conditions is overnight incubation at
37.degree. C. in a solution comprising: 20% formamide, 5.times.SSC
(150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH
7.6), 5.times.Denhardt's solution, 10% dextran sulfate, and 20
mg/mL denatured sheared salmon sperm DNA, followed by washing the
filters in 1.times.SSC at about 37-50.degree. C. The skilled
artisan will recognize how to adjust the temperature, ionic
strength, etc. as necessary to accommodate factors such as probe
length and the like.
[0329] An HLA "supermotif" is a peptide binding specificity shared
by HLA molecules encoded by two or more HLA alleles. Overall
phenotypic frequencies of HLA-supertypes in different ethnic
populations are set forth in Table IV (F). The non-limiting
constituents of various supetypes are as follows:
[0330] A2: A*0201, A*0202, A*0203, A*0204, A* 0205, A*0206, A*6802,
A*6901, A*0207
[0331] A3: A3, A11, A31, A*3301, A*6801, A*0301, A*1101, A*3101
[0332] B7: B7, B*3501-03, B*51, B*5301, B*5401, B*5501, B*5502,
B*5601, B*6701, B*7801, B*0702, B*5101, B*5602
[0333] B44: B*3701, B*4402, B*4403, B*60 (B*4001), B61 (B*4006)
[0334] A1: A*0102, A*2604, A*3601, A*4301, A*8001
[0335] A24: A*24, A*30, A*2403, A*2404, A*3002, A*3003
[0336] B27: B*1401-02, B*1503, B*1509, B*1510, B*1518, B*3801-02,
B*3901, B*3902, B*3903-04, B*4801-02, B*7301, B*2701-08
[0337] B58: B*1516, B*1517, B*5701, B*5702, B58
[0338] B62: B*4601, B52, B*1501 (B62), B*1502 (B75), B*1513
(B77)
[0339] Calculated population coverage afforded by different
HLA-supertype combinations are set forth in Table IV (G).
[0340] As used herein "to treat" or "therapeutic" and grammatically
related terms, refer to any improvement of any consequence of
disease, such as prolonged survival, less morbidity, and/or a
lessening of side effects which are the byproducts of an
alternative therapeutic modality; full eradication of disease is
not required.
[0341] A "transgenic animal" (e.g., a mouse or rat) is an animal
having cells that contain a transgene, which transgene was
introduced into the animal or an ancestor of the animal at a
prenatal, e.g., an embryonic stage. A "transgene" is a DNA that is
integrated into the genome of a cell from which a transgenic animal
develops.
[0342] As used herein, an HLA or cellular immune response "vaccine"
is a composition that contains or encodes one or more peptides of
the invention. There are numerous embodiments of such vaccines,
such as a cocktail of one or more individual peptides; one or more
peptides of the invention comprised by a polyepitopic peptide; or
nucleic acids that encode such individual peptides or polypeptides,
e.g., a minigene that encodes a polyepitopic peptide. The "one or
more peptides" can include any whole unit integer from 1-150 or
more, e.g., at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23,24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35, 36, 37, 38, 39, 40,41, 42,43,44, 45,46,47,48, 49,
50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120,
125, 130, 135, 140, 145, or 150 or more peptides of the invention.
The peptides or polypeptides can optionally be modified, such as by
lipidation, addition of targeting or other sequences. HLA class I
peptides of the invention can be admixed with, or linked to, HLA
class II peptides, to facilitate activation of both cytotoxic T
lymphocytes and helper T lymphocytes. HLA vaccines can also
comprise peptide-pulsed antigen presenting cells, e.g., dendritic
cells.
[0343] The term "variant" refers to a molecule that exhibits a
variation from a described type or norm, such as a protein that has
one or more different amino acid residues in the corresponding
position(s) of a specifically described protein (e.g. the 98P4B6
protein shown in FIG. 2 or FIG. 3. An analog is an example of a
variant protein. Splice isoforms and single nudeotides
polymorphisms (SNPs) are further examples of variants.
[0344] The "98P4B6-related proteins" of the invention include those
specifically identified herein, as well as allelic variants,
conservative substitution variants, analogs and homologs that can
be isolated/generated and characterized without undue
experimentation following the methods outlined herein or readily
available in the art. Fusion proteins that combine parts of
different 98P4B6 proteins or fragments thereof, as well as fusion
proteins of a 98P4B6 protein and a heterologous polypeptide are
also included. Such 98P4B6 proteins are collectively referred to as
the 98P4B6-related proteins, the proteins of the invention, or
98P4B6. The term "98P4B6-related protein" refers to a polypeptide
fragment or a 98P4B6 protein sequence of 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, or more
than 25amino acids; or, at least 30, 35, 40, 45, 50, 55, 60, 65,
70, 80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140,
145, 150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225,
250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550,
575, or 576 or more amino acids.
[0345] II.) 98P4B6 Polynucleotides
[0346] One aspect of the invention provides polynucleotides
corresponding or complementary to all or part of a 98P486 gene,
mRNA, and/or coding sequence, preferably in isolated form,
including polynucleotides encoding a 98P4B6-related protein and
fragments thereof, DNA, RNA, DNA/RNA hybrid, and related molecules,
polynucleotides or oligonucleotides complementary to a 98P4B6 gene
or mRNA sequence or a part thereof, and polynucleotides or
oligonucleotides that hybridize to a 98P4B6 gene, mRNA, or to a
98P4B6 encoding polynucleotide (collectively, "98P4B6
polynucleotides"). In all instances when referred to in this
section, T can also be U in FIG. 2.
[0347] Embodiments of a 98P4B6 polynucleotide include: a 98P4B6
polynucleotide having the sequence shown in FIG. 2, the nucleotide
sequence of 98P4B6 as shown in FIG. 2 wherein T is U; at least 10
contiguous nucleotides of a polynucleotide having the sequence as
shown in FIG. 2; or, at least 10 contiguous nucleotides of a
polynucleotide having the sequence as shown in FIG. 2 where T is U.
For example, embodiments of 98P4B6 nucleotides comprise, without
limitation:
[0348] (I) a polynucleotide comprising, consisting essentially of,
or consisting of a sequence as shown in FIG. 2, wherein T can also
be U;
[0349] (II) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2A, from nucleotide
residue number 355 through nucleotide residue number 1719,
including the stop codon, wherein T can also be U;
[0350] (III) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2B, from
nucleotide residue number 4 through nucleotide residue number 138,
including the stop codon, wherein T can also be U;
[0351] (IV) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2C, from nucleotide
residue number 188 through nucleotide residue number 1552,
including the a stop codon, wherein T can also be U;
[0352] (V) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2D, from nucleotide
residue number 318 through nucleotide residue number 1682,
including the stop codon, wherein T can also be U;
[0353] (VI) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2E, from nucleotide
residue number 318 through nucleotide residue number 1577,
including the stop codon, wherein T can also be U;
[0354] (VII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2F, from
nudeotide residue number 318 through nucleotide residue number
1790, including the stop codon, wherein T can also be U;
[0355] (VII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2G, from
nucleotide residue number 295 through nucleotide residue number
2025, including the stop codon, wherein T can also be U;
[0356] (IX) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2H, from nucleotide
residue number 394 through nucleotide residue number 1866,
including the stop codon, wherein T can also be U;
[0357] (X) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2I, from nucleotide
residue number 355 through nucleotide residue number 1719,
including the stop codon, wherein T can also be U;
[0358] (XI) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2J, from nucleotide
residue number 355 through nucleotide residue number 1719,
including the stop codon, wherein T can also be U;
[0359] (XII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2K, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0360] (XIII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2L, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0361] (XIV) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2M, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0362] (XV) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2N, from nucleotide
residue number 355 through nucleotide residue number 1719,
including the stop codon, wherein T can also be U;
[0363] (XVI) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 20, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0364] (XVII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2P, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0365] (XVIII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2Q, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0366] (XIX) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2R, from
nucleotide residue number 355 through nucleotide residue number
1719, including the stop codon, wherein T can also be U;
[0367] (XX) a polynucleotide comprising, consisting essentially of,
or consisting of the sequence as shown in FIG. 2S, from nucleotide
residue number 355 through nucleotide residue number 1719,
including the stop codon, wherein T can also be U;
[0368] (XXI) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2T, from
nucleotide residue number 295 through nucleotide residue number
2025, including the stop codon, wherein T can also be U;
[0369] (XXII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2U, from
nucleotide residue number 295 through nucleotide residue number
2025, including the stop codon, wherein T can also be U;
[0370] (XXIII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2V, from
nucleotide residue number 295 through nucleotide residue number
2025, including the stop codon, wherein T can also be U;
[0371] (XXIV) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2W, from
nucleotide residue number 295 through nucleotide residue number
2025, including the stop codon, wherein T can also be U;
[0372] (XXV) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2X, from
nucleotide residue number 295 through nucleotide residue number
2025, including the stop codon, wherein T can also be U;
[0373] (XXVI) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2Y, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0374] (XXVII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2Z, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0375] (XXVIII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2A, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0376] (XXIX) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AB, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0377] (XXX) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AC, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0378] (XXXI) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AD, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0379] (XXXII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AE, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0380] (XXXIII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AF, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0381] (XXIV) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2G, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0382] (XXXV) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AH, from
nucleotide residue number 394 through nudeotide residue number
1866, including the stop codon, wherein T can also be U;
[0383] (XXXVI) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AI, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0384] (XXXVII) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AJ, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0385] (XXXVIII) a polynucleotide comprising, consisting
essentially of, or consisting of the sequence as shown in FIG. 2AK,
from nudeotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0386] (XXXIX) a polynucleotide comprising, consisting essentially
of, or consisting of the sequence as shown in FIG. 2AL, from
nucleotide residue number 394 through nucleotide residue number
1866, including the stop codon, wherein T can also be U;
[0387] (XL) a polynucleotide that encodes a 98P4B6-related protein
that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100%
homologous to an entire amino acid sequence shown in FIG.
2A-AL;
[0388] (XLI) a polynucleotide that encodes a 98P4B6-related protein
that is at least 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100%
identical to an entire amino acid sequence shown in FIG. 2A-AL;
[0389] (XLII) a polynucleotide that encodes at least one peptide
set forth in Tables VIII-XXI and XXII-XLIX;
[0390] (XLIII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3A, 3G, and 3H in any whole number
increment up to 454 that includes at least 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s)
having a value greater than 0.5 in the Hydrophilicity profile of
FIG. 5;
[0391] (XLIV) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3A, 3G, and 3H in any whole number
increment up to 454 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value
less than 0.5 in the Hydropathicity profile of FIG. 6;
[0392] (XLV) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3A, 3G, and 3H in any whole number
increment up to 454 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Percent Accessible Residues profile
of FIG. 7;
[0393] (XLVI) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3A, 3G, and 3H in any whole number
increment up to 454 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Average Flexibility profile of FIG.
8;
[0394] (XLVII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3A, 3G, and 3H in any whole number
increment up to 454 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Beta-turn profile of FIG. 9;
[0395] (XLVIII) a polynucleotide that encodes a peptide region of
at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3B in any whole number increment up to
45 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35 amino acid position(s) having a value greater than 0.5
in the Hydrophilicity profile of FIG. 5;
[0396] (XLIX) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3B in any whole number increment up to
45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35 amino acid position(s) having a value less than 0.5 in
the Hydropathicity profile of FIG. 6;
[0397] (L) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3B in any whole number increment up to
45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35 amino acid position(s) having a value greater than 0.5
in the Percent Accessible Residues profile of FIG. 7;
[0398] (LI) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3B in any whole number increment up to
45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35 amino acid position(s) having a value greater than 0.5
in the Average Flexibility profile of FIG. 8;
[0399] (LII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3B in any whole number increment up to
45 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35 amino acid position(s) having a value greater than 0.5
in the Beta-turn profile of FIG. 9
[0400] (LII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3C in any whole number increment up to
419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35 amino acid position(s) having a value greater than
0.5 in the Hydrophilicity profile of FIG. 5;
[0401] (LIV) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3C in any whole number increment up to
419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35 amino acid position(s) having a value less than 0.5
in the Hydropathicity profile of FIG. 6;
[0402] (LV) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3C in any whole number increment up to
419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35 amino acid position(s) having a value greater than 0.5
in the Percent Accessible Residues profile of FIG. 7;
[0403] (LVI) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3C in any whole number increment up to
419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35 amino acid positon(s) having a value greater than
0.5 in the Average Flexibility profile of FIG. 8;
[0404] (LVII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIG. 3C in any whole number increment up to
419 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
32, 33, 34, 35 amino acid position(s) having a value greater than
0.5 in the Beta-turn profile of FIG. 9
[0405] (LVIII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3D, 3F, and 3J in any whole number
increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Hydrophilicity profile of FIG. 5;
[0406] (LIX) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3D, 3F, and 3J in any whole number
increment up to 490 that includes 1, 2, 3,4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a value
less than 0.5 in the Hydropathicity profile of FIG. 6;
[0407] (LX) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3D, 3F, and 3J in any whole number
increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Percent Accessible Residues profile
of FIG. 7;
[0408] (LXI) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3D, 3F, and 3J in any whole number
increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Average Flexibility profile of FIG.
8;
[0409] (LXII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3D, 3F, and 3J in any whole number
increment up to 490 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Beta-turn profile of FIG. 9
[0410] (LXIII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3E and 3I in any whole number increment
up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35 amino acid position(s) having a value greater
than 0.5 in the Hydrophilicity profile of FIG. 5;
[0411] (LXIV) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3E and 3I in any-whole number increment
up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35 amino acid position(s) having a value less than
0.5 in the Hydropathicity profile of FIG. 6;
[0412] (LXV) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3E and 3I in any whole number increment
up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35 amino acid position(s) having a value greater
than 0.5 in the Percent Accessible Residues profile of FIG. 7;
[0413] (LXVI) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3E and 3I in any whole number increment
up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35 amino acid position(s) having a value greater
than 0.5 in the Average Flexibility profile of FIG. 8;
[0414] (LXVII) a polynucleotide that encodes a peptide region of at
least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino
acids of a peptide of FIGS. 3E and 3I in any whole number increment
up to 576 that includes 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35 amino acid position(s) having a value greater
than 0.5 in the Beta-turn profile of FIG. 9
[0415] (LXVIII) a polynucleotide that is fully complementary to a
polynucleotide of any one of (I)-(LXVII).
[0416] (LXIX) a peptide that is encoded by any of (I) to (LXVIII);
and
[0417] (LXX) a composition comprising a polynucleotide of any of
(I)-(LXVIII) or peptide of (LXIX) together with a pharmaceutical
excipient and/or in a human unit dose form.
[0418] (LXXI) a method of using a polynucleotide of any
(I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a
method to modulate a cell expressing 98P4B6,
[0419] (LXXII) a method of using a polynucleotide of any
(I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a
method to diagnose, prophylax, prognose, or treat an individual who
bears a cell expressing 98P4B6
[0420] (LXXIII) a method of using a polynucleotide of any
(I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a
method to diagnose, prophylax, prognose, or treat an individual who
bears a cell expressing 98P4B6, said cell from a cancer of a tissue
listed in Table I;
[0421] (LXXIV) a method of using a polynucleotide of any
(I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a
method to diagnose, prophylax, prognose, or treat a a cancer;
[0422] (LXXV) a method of using a polynucleotide of any
(I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a
method to diagnose, prophylax, prognose, or treat a a cancer of a
tissue listed in Table I; and,
[0423] (LXXVI) a method of using a polynucleotide of any
(I)-(LXVIII) or peptide of (LXIX) or a composition of (LXX) in a
method to identify or characterize a modulator of a cell;
expressing 98P4B6.
[0424] As used herein, a range is understood to disclose
specifically all whole unit positions thereof.
[0425] Typical embodiments of the invention disclosed herein
include 98P4B6 polynucleotides that encode specific portions of
98P4B6 mRNA sequences (and those which are complementary to such
sequences) such as those that encode the proteins and/or fragments
thereof, for example:
[0426] (a) 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,
80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145,
150, 155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250,
275, 300, 325, 350, 375, 400, 410, 420, 430, 440, 450 or 454 or
more contiguous amino acids of 98P4B6 variant 1; the maximal
lengths relevant for other variants are: variant 2, 44 amino acids;
variant 5, 419 amino acids, variant 6, 490 amino acids, variant 7,
576 amino acids, variant 8, 490 amino acids, variant 13, 454 amino
acids, variant 14, 454 amino acids, variant 21, 576 amino acids,
and variant 25, 490 amino acids.
[0427] For example, representative embodiments of the invention
disclosed herein include: polynucleotides and their encoded
peptides themselves encoding about amino acid 1 to about amino acid
10 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides
encoding about amino acid 10 to about amino acid 20 of the 98P4B6
protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about
amino acid 20 to about amino acid 30 of the 98P4B6 protein shown in
FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 30 to
about amino acid 40 of the 98P4B6 protein shown in FIG. 2 or FIG.
3, polynucleotides encoding about amino acid 40 to about amino acid
50 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides
encoding about amino acid 50 to about amino acid 60 of the 98P4B6
protein shown in FIG. 2 or FIG. 3, polynucleotides encoding about
amino acid 60 to about amino acid 70 of the 98P4B6 protein shown in
FIG. 2 or FIG. 3, polynucleotides encoding about amino acid 70 to
about amino acid 80 of the 98P4B6 protein shown in FIG. 2 or FIG.
3, polynucleotides encoding about amino acid 80 to about amino acid
90 of the 98P4B6 protein shown in FIG. 2 or FIG. 3, polynucleotides
encoding about amino acid 90 to about amino acid 100 of the 98P4B6
protein shown in FIG. 2 or FIG. 3, in increments of about 10 amino
acids, ending at the carboxyl terminal amino acid set forth in FIG.
2 or FIG. 3. Accordingly, polynucleotides encoding portions of the
amino acid sequence (of about 10 amino acids), of amino acids, 100
through the carboxyl terminal amino acid of the 98P4B6 protein are
embodiments of the invention. Wherein it is understood that each
particular amino acid position discloses that position plus or
minus five amino acid residues.
[0428] Polynucleotides encoding relatively long portions of a
98P4B6 protein are also within the scope of the invention. For
example, polynucleotides encoding from about amino acid 1 (or 20 or
30 or 40 etc.) to about amino acid 20, (or 30, or 40 or 50 etc.) of
the 98P4B6 protein "or variant" shown in FIG. 2 or FIG. 3 can be
generated by a variety of techniques well known in the art. These
polynucleotide fragments can include any portion of the 98P4B6
sequence as shown in FIG. 2.
[0429] Additional illustrative embodiments of the invention
disclosed herein include 98P4B6 polynucleotide fragments encoding
one or more of the biological motifs contained within a 98P4B6
protein "or variant" sequence, including one or more of the
motif-bearing subsequences of a 98P4B6 protein "or variants" set
forth in Tables VIII-XXI and XXII-XLIX. In another embodiment,
typical polynucleotide fragments of the invention encode one or
more of the regions of 98P4B6 protein or variant that exhibit
homology to a known molecule. In another embodiment of the
invention, typical polynucleotide fragments can encode one or more
of the 98P4B6 protein or variant N-glycosylation sites, cAMP and
cGMP-dependent protein kinase phosphorylation sites, casein kinase
II phosphorylation sites or N-myristoylation site and amidation
sites.
[0430] Note that to determine the starting position of any peptide
set forth in Tables VIII-XXI and Tables XXII to XLIX (collectively
HLA Peptide Tables) respective to its parental protein, e.g.,
variant 1, variant 2, etc., reference is made to three factors: the
particular variant, the length of the peptide in an HLA Peptide
Table, and the Search Peptides listed in Table VII. Generally, a
unique Search Peptide is used to obtain HLA peptides for a
particular variant. The position of each Search Peptide relative to
its respective parent molecule is listed in Table VII. Accordingly,
if a Search Peptide begins at position "X", one must add the value
"X minus 1" to each position in Tables VIII-XXI and Tables XXII-IL
to obtain the actual position of the HLA peptides in their parental
molecule. For example if a particular Search Peptide begins at
position 150 of its parental molecule, one must add 150-1, i.e.,
149 to each HLA peptide amino acid position to calculate the
position of that amino acid in the parent molecule.
[0431] II.A.) Uses of 98P4B6 Polynucleotides
[0432] II.A.1.) Monitoring of Genetic Abnormalities
[0433] The polynucleotides of the preceding paragraphs have a
number of different specific uses. The human 98P4B6 gene maps to
the chromosomal location set forth in the Example entitled
"Chromosomal Mapping of 98P4B6." For example, because the 98P4B6
gene maps to this chromosome, polynucleotides that encode different
regions of the 98P4B6 proteins are used to characterize cytogenetic
abnormalities of this chromosomal locale, such as abnormalities
that are identified as being associated with various cancers. In
certain genes, a variety of chromosomal abnormalities including
rearrangements have been identified as frequent cytogenetic
abnormalities in a number of different cancers (see e.g. Krajinovic
et al., Mutat. Res. 382(3-4): 81-83(1998); Johansson et al., Blood
86(10): 3905-3914(1995) and Finger et al., P.N.A.S. 85(23):
9158-9162 (1988)). Thus, polynucleotides encoding specific regions
of the 98P4B6 proteins provide new tools that can be used to
delineate, with greater precision than previously possible,
cytogenetic abnormalities in the chromosomal region that encodes
98P4B6 that may contribute to the malignant phenotype. In this
context, these polynucleotides satisfy a need in the art for
expanding the sensitivity of chromosomal screening in order to
identify more subtle and less common chromosomal abnormalities (see
e.g. Evans et al., Am. J. Obstet. Gynecol 171(4): 1055-1057
(1994)).
[0434] Furthermore, as 98P4B6 was shown to be highly expressed in
prostate and other cancers, 98P4B6 polynucleotides are used in
methods assessing the status of 98P4B6 gene products in normal
versus cancerous tissues. Typically, polynucleotides that encode
specific regions of the 98P4B6 proteins are used to assess the
presence of perturbations (such as deletions, insertions, point
mutations, or alterations resulting in a loss of an antigen etc.)
in specific regions of the 98P4B6 gene, such as regions containing
one or more motifs. Exemplary assays include both RT-PCR assays as
well as single-strand conformation polymorphism (SSCP) analysis
(see, e.g., Marrogi et al., J. Cutan. Pathol. 26(8): 369-378
(1999), both of which utilize polynucleotides encoding specific
regions of a protein to examine these regions within the
protein.
[0435] II.A.2.) Antisense Embodiments
[0436] Other specifically contemplated nucleic acid related
embodiments of the invention disclosed herein are genomic DNA,
cDNAs, ribozymes, and antisense molecules, as well as nucleic acid
molecules based on an alternative backbone, or including
alternative bases, whether derived from natural sources or
synthesized, and include molecules capable of inhibiting the RNA or
protein expression of 98P4B6. For example, antisense molecules can
be RNAs or other molecules, including peptide nucleic acids (PNAs)
or non-nucleic acid molecules such as phosphorothioate derivatives
that specifically bind DNA or RNA in a base pair-dependent manner.
A skilled artisan can readily obtain these classes of nucleic acid
molecules using the 98P4B6 polynucleotides and polynucleotide
sequences disclosed herein.
[0437] Antisense technology entails the administration of exogenous
oligonucleotides that bind to a target polynucleotide located
within the cells. The term "antisense" refers to the fact that such
oligonucleotides are complementary to their intracellular targets,
e.g., 98P4B6. See for example, Jack Cohen, Oligodeoxynucleotides,
Antisense Inhibitors of Gene Expression, CRC Press, 1989; and
Synthesis 1:1-5 (1988). The 98P4B6 antisense oligonucleotides of
the present invention include derivatives such as
S-oligonucleotides (phosphorothioate derivatives or S-oligos, see,
Jack Cohen, supra), which exhibit enhanced cancer cell growth
inhibitory action. S-oligos (nucleoside phosphorothioates) are
isoelectronic analogs of an oligonucleotide (O-oligo) in which a
nonbridging oxygen atom of the phosphate group is replaced by a
sulfur atom. The S-oligos of the present invention can be prepared
by treatment of the corresponding O-oligos with
3H-1,2-benzodithiol-3-one-1,1-dioxide, which is a sulfur transfer
reagent. See, e.g., lyer, R. P. et al., J. Org. Chem. 55:4693-4698
(1990); and lyer, R. P. et al., J. Am. Chem. Soc. 112:1253-1254
(1990). Additional 98P4B6 antisense oligonucleotides of the present
invention include morpholino antisense oligonucleotides known in
the art (see, e.g., Partridge et al., 1996, Antisense & Nucleic
Acid Drug Development 6: 169-175).
[0438] The 98P4B6 antisense oligonucleotides of the present
invention typically can be RNA or DNA that is complementary to and
stably hybridizes with the first 100 5' codons or last 100 3'
codons of a 98P4B6 genomic sequence or the corresponding mRNA.
Absolute complementarity is not required, although high degrees of
complementarity are preferred. Use of an oligonucleotide
complementary to this region allows for the selective hybridization
to 98P4B6 mRNA and not to mRNA specifying other regulatory subunits
of protein kinase. In one embodiment, 98P4B6 antisense
oligonucleotides of the present invention are 15 to 30-mer
fragments of the antisense DNA molecule that have a sequence that
hybridizes to 98P4B6 mRNA. Optionally, 98P4B6 antisense
oligonucleotide is a 30-mer oligonucleotide that is complementary
to a region in the first 10 5' codons or last 10 3' codons of
98P4B6. Alternatively, the antisense molecules are modified to
employ ribozymes in the inhibition of 98P4B6 expression, see, e.g.,
L. A. Couture & D. T. Stinchcomb; Trends Genet 12: 510-515
(1996).
[0439] II.A.3.) Primers and Primer Pairs
[0440] Further specific embodiments of these nucleotides of the
invention include primers and primer pairs, which allow the
specific amplification of polynucleotides of the invention or of
any specific parts thereof, and probes that selectively or
specifically hybridize to nucleic acid molecules of the invention
or to any part thereof. Probes can be labeled with a detectable
marker, such as, for example, a radioisotope, fluorescent compound,
bioluminescent compound, a chemiluminescent compound, metal
chelator or enzyme. Such probes and primers are used to detect the
presence of a 98P4B6 polynucleotide in a sample and as a means for
detecting a cell expressing a 98P4B6 protein.
[0441] Examples of such probes include polypeptides comprising all
or part of the human 98P4B6 cDNA sequence shown in FIG. 2. Examples
of primer pairs capable of specifically amplifying 98P4B6 mRNAs are
also described in the Examples. As will be understood by the
skilled artisan, a great many different primers and probes can be
prepared based on the sequences provided herein and used
effectively to amplify and/or detect a 98P4B6 mRNA.
[0442] The 98P4B6 polynucleotides of the invention are useful for a
variety of purposes, including but not limited to their use as
probes and primers for the amplification and/or detection of the
98P4B6 gene(s), mRNA(s), or fragments thereof; as reagents for the
diagnosis and/or prognosis of prostate cancer and other cancers; as
coding sequences capable of directing the expression of 98P4B6
polypeptides; as tools for modulating or inhibiting the expression
of the 98P4B6 gene(s) and/or translation of the 98P4B6
transcript(s); and as therapeutic agents.
[0443] The present invention includes the use of any probe as
described herein to identify and isolate a 98P4B6 or 98P4B6 related
nucleic acid sequence from a naturally occurring source, such as
humans or other mammals, as well as the isolated nucleic acid
sequence per se, which would comprise all or most of the sequences
found in the probe used.
[0444] II.A.4.) Isolation of 98P4B6-Encoding Nucleic Acid
Molecules
[0445] The 98P4B6 cDNA sequences described herein enable the
isolation of other polynucleotides encoding 98P4B6 gene product(s),
as well as the isolation of polynucleotides encoding 98P4B6 gene
product homologs, alternatively spliced isoforms, allelic variants,
and mutant forms of a 98P4B6 gene product as well as
polynucleotides that encode analogs of 98P4B6-related proteins.
Various molecular cloning methods that can be employed to isolate
full length cDNAs encoding a 98P4B6 gene are well known (see, for
example, Sambrook, J. et al., Molecular Cloning: A Laboratory
Manual, 2d edition, Cold Spring Harbor Press, New York, 1989;
Current Protocols in Molecular Biology. Ausubel et al., Eds., Wiley
and Sons, 1995). For example, lambda phage cloning methodologies
can be conveniently employed, using commercially available cloning
systems (e.g., Lambda ZAP Express, Stratagene). Phage clones
containing 98P4B6 gene cDNAs can be identified by probing with a
labeled 98P4B6 cDNA or a fragment thereof. For example, in one
embodiment, a 98P4B6 cDNA (e.g., FIG. 2) or a portion thereof can
be synthesized and used as a probe to retrieve overlapping and
full-length cDNAs corresponding to a 98P4B6 gene. A 98P4B6 gene
itself can be isolated by screening genomic DNA libraries,
bacterial artificial chromosome libraries (BACs), yeast artificial
chromosome libraries (YACs), and the like, with 98P4B6 DNA probes
or primers.
[0446] II.A.5.) Recombinant Nucleic Acid Molecules and Host-Vector
Systems
[0447] The invention also provides recombinant DNA or RNA molecules
containing a 98P4B6 polynucleotide, a fragment, analog or homologue
thereof, including but not limited to phages, plasmids, phagemids,
cosmids, YACs, BACs, as well as various viral and non-viral vectors
well known in the art, and cells transformed or transfected with
such recombinant DNA or RNA molecules. Methods for generating such
molecules are well known (see, for example, Sambrook et al., 1989,
supra).
[0448] The invention further provides a host-vector system
comprising a recombinant DNA molecule containing a 98P4B6
polynucleotide, fragment, analog or homologue thereof within a
suitable prokaryotic or eukaryotic host cell. Examples of suitable
eukaryotic host cells include a yeast cell, a plant cell, or an
animal cell, such as a mammalian cell or an insect cell (e.g., a
baculovirus-infectible cell such as an Sf9 or HighFive cell).
Examples of suitable mammalian cells include various prostate
cancer cell lines such as DU145 and TsuPr1, other transfectable or
transducible prostate cancer cell lines, primary cells (PrEC), as
well as a number of mammalian cells routinely used for the
expression of recombinant proteins (e.g., COS, CHO, 293, 293T
cells). More particularly, a polynucleotide comprising the coding
sequence of 98P4B6 or a fragment, analog or homolog thereof can be
used to generate 98P4B6 proteins or fragments thereof using any
number of host-vector systems routinely used and widely known in
the art.
[0449] A wide range of host-vector systems suitable for the
expression of 98P4B6 proteins or fragments thereof are available,
see for example, Sambrook et al.,1989, supra; Current Protocols in
Molecular Biology, 1995, supra). Preferred vectors for mammalian
expression include but are not limited to pcDNA 3.1 myc-His-tag
(Invitrogen) and the retroviral vector pSR.alpha.tkneo (Muller et
al., 1991, MCB 11:1785). Using these expression vectors, 98P4B6 can
be expressed in several prostate cancer and non-prostate cell
lines, including for example 293, 293T, rat-1, NIH 3T3 and TsuPr1.
The host-vector systems of the invention are useful for the
production of a 98P4B6 protein or fragment thereof. Such
host-vector systems can be employed to study the functional
properties of 98P4B6 and 98P4B6 mutations or analogs.
[0450] Recombinant human 98P4B6 protein or an analog or homolog or
fragment thereof can be produced by mammalian cells transfected
with a construct encoding a 98P4B6-related nucleotide. For example,
293T cells can be transfected with an expression plasmid encoding
98P4B6 or fragment, analog or homolog thereof, a 98P4B6-related
protein is expressed in the 293T cells, and the recombinant 98P4B6
protein is isolated using standard purification methods (e.g.,
affinity purification using anti-98P4B6 antibodies). In another
embodiment, a 98P4B6 coding sequence is subcloned into the
retroviral vector pSR.alpha.MSVtkneo and used to infect various
mammalian cell lines, such as NIH 3T3, TsuPr1, 293 and rat-1 in
order to establish 98P4B6 expressing cell lines. Various other
expression systems well known in the art can also be employed.
Expression constructs encoding a leader peptide joined in frame to
a 98P4B6 coding sequence can be used for the generation of a
secreted form of recombinant 98P4B6 protein.
[0451] As discussed herein, redundancy in the genetic code permits
variation in 98P4B6 gene sequences. In particular, it is known in
the art that specific host species often have specific codon
preferences, and thus one can adapt the disclosed sequence as
preferred for a desired host. For example, preferred analog codon
sequences typically have rare codons (i.e., codons having a usage
frequency of less than about 20% in known sequences of the desired
host) replaced with higher frequency codons. Codon preferences for
a specific species are calculated, for example, by utilizing codon
usage tables available on the INTERNET such as at URL
dna.affrc.go.jp/.about.nakamura/codon.html.
[0452] Additional sequence modifications are known to enhance
protein expression in a cellular host. These include elimination of
sequences encoding spurious polyadenylation signals, exon/intron
splice site signals, transposon-like repeats, and/or other such
well-characterized sequences that are deleterious to gene
expression. The GC content of the sequence is adjusted to levels
average for a given cellular host, as calculated by reference to
known genes expressed in the host cell. Where possible, the
sequence is modified to avoid predicted hairpin secondary mRNA
structures. Other useful modifications include the addition of a
translational initiation consensus sequence at the start of the
open reading frame, as described in Kozak, Mol. Cell Biol.,
9:5073-5080 (1989). Skilled artisans understand that the general
rule that eukaryotic ribosomes initiate translation exclusively at
the 5' proximal AUG codon is abrogated only under rare conditions
(see, e.g., Kozak PNAS 92(7): 2662-2666, (1995) and Kozak NAR
15(20): 8125-8148 (1987)).
[0453] III.) 98P4B6-Related Proteins
[0454] Another aspect of the present invention provides
98P4B6-related proteins. Specific embodiments of 98P4B6 proteins
comprise a polypeptide having all or part of the amino acid
sequence of human 98P4B6 as shown in FIG. 2 or FIG. 3.
Alternatively, embodiments of 98P4B6 proteins comprise variant,
homolog or analog polypeptides that have alterations in the amino
acid sequence of 98P4B6 shown in FIG. 2 or FIG. 3.
[0455] Embodiments of a 98P4B6 polypeptide include: a 98P4B6
polypeptide having a sequence shown in FIG. 2, a peptide sequence
of a 98P4B6 as shown in FIG. 2 wherein T is U; at least 10
contiguous nucleotides of a polypeptide having the sequence as
shown in FIG. 2; or, at least 10 contiguous peptides of a
polypeptide having the sequence as shown in FIG. 2 where T is U.
For example, embodiments of 98P4B6 peptides comprise, without
limitation:
[0456] (I) a protein comprising, consisting essentially of, or
consisting of an amino acid sequence as shown in FIG. 2A-AL or FIG.
3A-J;
[0457] (II) a 98P4B6-related protein that is at least 90, 91, 92,
93, 94, 95, 96, 97, 98, 99 or 100% homologous to an entire amino
acid sequence shown in FIG. 2A-AL;
[0458] (III) a 98P4B6-related protein that is at least 90, 91, 92,
93, 94, 95, 96, 97, 98, 99 or 100% identical to an entire amino
acid sequence shown in FIG. 2A-AL or 3A-J;
[0459] (IV) a protein that comprises at least one peptide set forth
in Tables VIII to XLIX, optionally with a proviso that it is not an
entire protein of FIG. 2;
[0460] (V) a protein that comprises at least one peptide set forth
in Tables VIII-XXI, collectively, which peptide is also set forth
in Tables XXII to XLIX, collectively, optionally with a proviso
that it is not an entire protein of FIG. 2;
[0461] (VI) a protein that comprises at least two peptides selected
from the peptides set forth in Tables VIII-XLIX, optionally with a
proviso that it is not an entire protein of FIG. 2;
[0462] (VII) a protein that comprises at least two peptides
selected from the peptides set forth in Tables VIII to XLIX
collectively, with a proviso that the protein is not a contiguous
sequence from an amino acid sequence of FIG. 2;
[0463] (VIII) a protein that comprises at least one peptide
selected from the peptides set forth in Tables VIII-XXI; and at
least one peptide selected from the peptides set forth in Tables
XXII to XLIX, with a proviso that the protein is not a contiguous
sequence from an amino acid sequence of FIG. 2;
[0464] (IX) a polypeptide comprising at least 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS.
3A, 3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number
increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490
respectively that includes at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s) having a
value greater than 0.5 in the Hydrophilicity profile of FIG. 5;
[0465] (X) a polypeptide comprising at least 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,
29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS. 3A,
3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment
up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490
respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s)
having a value less than 0.5 in the Hydropathicity profile of FIG.
6;
[0466] (XI) a polypeptide comprising at least 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS.
3A, 3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number
increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490
respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s)
having a value greater than 0.5 in the Percent Accessible Residues
profile of FIG. 7;
[0467] (XII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, 35 amino acids of a protein of FIGS.
3A, 3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number
increment up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490
respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s)
having a value greater than 0.5 in the Average Flexibility profile
of FIG. 8;
[0468] (XIII) a polypeptide comprising at least 5, 6, 7, 8, 9, 10,
11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,
28, 29, 30, 31, 32, 33, 34, amino acids of a protein of FIGS. 3A,
3B, 3C, 3D, 3E, 3F, 3G, 3H, 3I or 3J in any whole number increment
up to 454, 45, 419, 490, 576, 490, 454, 454, 576, or 490
respectively that includes at least at least 1, 2, 3, 4, 5, 6, 7,
8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 amino acid position(s)
having a value greater than 0.5 in the Beta-turn profile of FIG.
9;
[0469] (XIV) a peptide that occurs at least twice in Tables
VIII-XXI and XXII to XLIX, collectively;
[0470] (XV) a peptide that occurs at least three times in Tables
VIII-XXI and XXII to XLIX, collectively;
[0471] (XVI) a peptide that occurs at least four times in Tables
VIII-XXI and XXII to XLIX, collectively;
[0472] (XVII) a peptide that occurs at least five times in Tables
VIII-XXI and XXII to XLIX, collectively;
[0473] (XVIII) a peptide that occurs at least once in Tables
VIII-XXI, and at least once in tables XXII to XLIX;
[0474] (XIX) a peptide that occurs at least once in Tables
VIII-XXI, and at least twice in tables XXII to XLIX;
[0475] (XX) a peptide that occurs at least twice in Tables
VIII-XXI, and at least once in tables XXII to XLIX;
[0476] (XXI) a peptide that occurs at least twice in Tables
VIII-XXI, and at least twice in tables XXII to XLIX;
[0477] (XXII) a peptide which comprises one two, three, four, or
five of the following characteristics, or an oligonucleotide
encoding such peptide:
[0478] i) a region of at least 5 amino acids of a particular
peptide of FIG. 3, in any whole number increment up to the full
length of that protein in FIG. 3, that includes an amino acid
position having a value equal to or greater than 0.5, 0.6, 0.7,
0.8, 0.9, or having a value equal to 1.0, in the Hydrophilicity
profile of FIG. 5;
[0479] ii) a region of at least 5 amino acids of a particular
peptide of FIG. 3, in any whole number increment up to the full
length of that protein in FIG. 3, that includes an amino acid
position having a value equal to or less than 0.5, 0.4, 0.3, 0.2,
0.1, or having a value equal to 0.0, in the Hydropathicity profile
of FIG. 6;
[0480] iii) a region of at least 5 amino acids of a particular
peptide of FIG. 3, in any whole number increment up to the full
length of that protein in FIG. 3, that includes an amino acid
position having a value equal to or greater than 0.5, 0.6, 0.7,
0.8, 0.9, or having a value equal to 1.0, in the Percent Accessible
Residues profile of FIG. 7;
[0481] iv) a region of at least 5 amino acids of a particular
peptide of FIG. 3, in any whole number increment up to the full
length of that protein in FIG. 3, that includes an amino acid
position having a value equal to or greater than 0.5, 0.6, 0.7,
0.8, 0.9, or having a value equal to 1.0, in the Average
Flexibility profile of FIG. 8; or,
[0482] v) a region of at least 5 amino acids of a particular
peptide of FIG. 3, in any whole number increment up to the full
length of that protein in FIG. 3, that includes an amino acid
position having a value equal to or greater than 0.5, 0.6, 0.7,
0.8, 0.9, or having a value equal to 1.0, in the Beta-turn profile
of FIG. 9;
[0483] (XXIII) a composition comprising a peptide of (I)-(XXII) or
an antibody or binding region thereof together with a
pharmaceutical excipient and/or in a human unit dose form.
[0484] (XXIV) a method of using a peptide of (I)-(XXII), or an
antibody or binding region thereof or a composition of (XXIII) in a
method to modulate a cell expressing 98P4B6,
[0485] (XXV) a method of using a peptide of (I)-(XXII) or an
antibody or binding region thereof or a composition of (XXIII) in a
method to diagnose, prophylax, prognose, or treat an individual who
bears a cell expressing 98P4B6
[0486] (XXVI) a method of using a peptide of (I)-(XXII) or an
antibody or binding region thereof or a composition (XXIII) in a
method to diagnose, prophylax, prognose, or treat an individual who
bears a cell expressing 98P4B6, said cell from a cancer of a tissue
listed in Table I;
[0487] (XXVII) a method of using a peptide of (I)-(XXII) or an
antibody or binding region thereof or a composition of (XXIII) in a
method to diagnose, prophylax, prognose, or treat a a cancer;
[0488] (XXVIII) a method of using a peptide of (I)-(XXII) or an
antibody or binding region thereof or a composition of (XXIII) in a
method to diagnose, prophylax, prognose, or treat a a cancer of a
tissue listed in Table I; and,
[0489] (XXIX) a method of using a a peptide of (I)-(XXII) or an
antibody or binding region thereof or a composition (XXIII) in a
method to identify or characterize a modulator of a cell expressing
98P4B6.
[0490] As used herein, a range is understood to specifically
disclose all whole unit positions thereof.
[0491] Typical embodiments of the invention disclosed herein
include 98P4B6 polynucleotides that encode specific portions of
98P4B6 mRNA sequences (and those which are complementary to such
sequences) such as those that encode the proteins and/or fragments
thereof, for example:
[0492] (a)4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,
20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80,
85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150,
155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 225, 250, 275,
300, 325, 350, 375, 400, 410, 420, 430, 440, 450, or 454 more
contiguous amino acids of 98P4B6 variant 1; the maximal lengths
relevant for other variants are: variant 52, 45 amino acids;
variant 5, 419 amino acids, variant 6, 490, variant 7, 576 amino
acids, variant 8, 490 amino acids, variant 13, 454, variant 14, 454
amino acids, variant 21, 576 amino acids, and variant 25, 490 amino
acids.
[0493] In general, naturally occurring allelic variants of human
98P4B6 share a high degree of structural identity and homology
(e.g., 90% or more homology). Typically, allelic variants of a
98P4B6 protein contain conservative amino acid substitutions within
the 98P4B6 sequences described herein or contain a substitution of
an amino acid from a corresponding position in a homologue of
98P4B6. One class of 98P4B6 allelic variants are proteins that
share a high degree of homology with at least a small region of a
particular 98P4B6 amino acid sequence, but further contain a
radical departure from the sequence, such as a non-conservative
substitution, truncation, insertion or frame shift. In comparisons
of protein sequences, the terms, similarity, identity, and homology
each have a distinct meaning as appreciated in the field of
genetics. Moreover, orthology and paralogy can be important
concepts describing the relationship of members of a given protein
family in one organism to the members of the same family in other
organisms.
[0494] Amino acid abbreviations are provided in Table II.
Conservative amino acid substitutions can frequently be made in a
protein without altering either the conformation or the function of
the protein. Proteins of the invention can comprise 1, 2, 3, 4, 5,
6, 7, 8, 9, 10, 11, 12, 13, 14, 15 conservative substitutions. Such
changes include substituting any of isoleucine (I), valine (V), and
leucine (L) for any other of these hydrophobic amino acids;
aspartic acid (D) for glutamic acid (E) and vice versa; glutamine
(Q) for asparagine (N) and vice versa; and serine (S) for threonine
(T) and vice versa. Other substitutions can also be considered
conservative, depending on the environment of the particular amino
acid and its role in the three-dimensional structure of the
protein. For example, glycine (G) and alanine (A) can frequently be
interchangeable, as can alanine (A) and valine (V). Methionine (M),
which is relatively hydrophobic, can frequently be interchanged
with leucine and isoleucine, and sometimes with valine. Lysine (K)
and arginine (R) are frequently interchangeable in locations in
which the significant feature of the amino acid residue is its
charge and the differing pK's of these two amino acid residues are
not significant. Still other changes can be considered
"conservative" in particular environments (see, e.g. Table III
herein; pages 13-15 "Biochemistry" 2.sup.nd ED. Lubert Stryer ed
(Stanford University); Henikoff et al., PNAS 1992 Vol 89
10915-10919; Lei et al., J Biol Chem 1995 May 19;
270(20):11882-6).
[0495] Embodiments of the invention disclosed herein include a wide
variety of art-accepted variants or analogs of 98P4B6 proteins such
as polypeptides having amino acid insertions, deletions and
substitutions. 98P4B6 variants can be made using methods known in
the art such as site-directed mutagenesis, alanine scanning, and
PCR mutagenesis. Site-directed mutagenesis (Carter et al., Nucl.
Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res.,
10:6487 (1987)), cassette mutagenesis (Wells et al., Gene, 34:315
(1985)), restriction selection mutagenesis (Wells et al., Philos.
Trans. R. Soc. London SerA, 317:415 (1986)) or other known
techniques can be performed on the cloned DNA to produce the 98P4B6
variant DNA.
[0496] Scanning amino acid analysis can also be employed to
identify one or more amino acids along a contiguous sequence that
is involved in a specific biological activity such as a
protein-protein interaction. Among the preferred scanning amino
acids are relatively small, neutral amino acids. Such amino acids
include alanine, glycine, serine, and cysteine. Alanine is
typically a preferred scanning amino acid among this group because
it eliminates the side-chain beyond the beta-carbon and is less
likely to alter the main-chain conformation of the variant. Alanine
is also typically preferred because it is the most common amino
acid. Further, it is frequently found in both buried and exposed
positions (Creighton, The Proteins, (W.H. Freeman & Co., N.Y.);
Chothia, J. Mol. Biol., 150:1 (1976)). If alanine substitution does
not yield adequate amounts of variant, an isosteric amino acid can
be used.
[0497] As defined herein, 98P4B6 variants, analogs or homologs,
have the distinguishing attribute of having at least one epitope
that is "cross reactive" with a 98P4B6 protein having an amino acid
sequence of FIG. 3. As used in this sentence, "cross reactive"
means that an antibody or T cell that specifically binds to a
98P4B6 variant also specifically binds to a 98P4B6 protein having
an amino acid sequence set forth in FIG. 3. A polypeptide ceases to
be a variant of a protein shown in FIG. 3, when it no longer
contains any epitope capable of being recognized by an antibody or
T cell that specifically binds to the starting 98P4B6 protein.
Those skilled in the art understand that antibodies that recognize
proteins bind to epitopes of varying size, and a grouping of the
order of about four or five amino acids, contiguous or not, is
regarded as a typical number of amino acids in a minimal epitope.
See, e.g., Nair et al., J. Immunol 2000 165(12): 6949-6955; Hebbes
et al., Mol Immunol (1989) 26(9):865-73; Schwartz et al., J Immunol
(1985) 135(4):2598-608.
[0498] Other classes of 98P4B6-related protein variants share 70%,
75%, 80%, 85% or 90% or more similarity with an amino acid sequence
of FIG. 3, or a fragment thereof. Another specific class of 98P4B6
protein variants or analogs comprises one or more of the 98P4B6
biological motifs described herein or presently known in the art.
Thus, encompassed by the present invention are analogs of 98P4B6
fragments (nucleic or amino acid) that have altered functional
(e.g. immunogenic) properties relative to the starting fragment. It
is to be appreciated that motifs now or which become part of the
art are to be applied to the nucleic or amino acid-sequences of
FIG. 2 or FIG. 3.
[0499] As discussed herein, embodiments of the claimed invention
include polypeptides containing less than the full amino acid
sequence of a 98P4B6 protein shown in FIG. 2 or FIG. 3. For
example, representative embodiments of the invention comprise
peptides/proteins having any 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,
15 or more contiguous amino acids of a 98P4B6 protein shown in FIG.
2 or FIG. 3.
[0500] Moreover, representative embodiments of the invention
disclosed herein include polypeptides consisting of about amino
acid 1 to about amino acid 10 of a 98P4B6 protein shown in FIG. 2
or FIG. 3, polypeptides consisting of about amino acid 10 to about
amino acid 20 of a 98P4B6 protein shown in FIG. 2 or FIG. 3,
polypeptides consisting of about amino acid 20 to about amino acid
30 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides
consisting of about amino acid 30 to about amino acid 40 of a
98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting
of about amino acid 40 to about amino acid 50 of a 98P4B6 protein
shown in FIG. 2 or FIG. 3, polypeptides consisting of about amino
acid 50 to about amino acid 60 of a 98P4B6 protein shown in FIG. 2
or FIG. 3, polypeptides consisting of about amino acid 60 to about
amino acid 70 of a 98P4B6 protein shown in FIG. 2 or FIG. 3,
polypeptides consisting of about amino acid 70 to about amino acid
80 of a 98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides
consisting of about amino acid 80 to about amino acid 90 of a
98P4B6 protein shown in FIG. 2 or FIG. 3, polypeptides consisting
of about amino acid 90 to about amino acid 100 of a 98P4B6 protein
shown in FIG. 2 or FIG. 3, etc. throughout the entirety of a 98P4B6
amino acid sequence. Moreover, polypeptides consisting of about
amino acid 1 (or 20 or 30 or 40 etc.) to about amino acid 20, (or
130, or 140 or 150 etc.) of a 98P4B6 protein shown in FIG. 2 or
FIG. 3 are embodiments of the invention. It is to be appreciated
that the starting and stopping positions in this paragraph refer to
the specified position as well as that position plus or minus 5
residues.
[0501] 98P4B6-related proteins are generated using standard peptide
synthesis technology or using chemical cleavage methods well known
in the art. Alternatively, recombinant methods can be used to
generate nucleic acid molecules that encode a 98P4B6-related
protein. In one embodiment, nucleic acid molecules provide a means
to generate defined fragments of a 98P4B6 protein (or variants,
homologs or analogs thereof).
[0502] III.A.) Motif-Bearing Protein Embodiments
[0503] Additional illustrative embodiments of the invention
disclosed herein include 98P4B6 polypeptides comprising the amino
acid residues of one or more of the biological motifs contained
within a 98P4B6 polypeptide sequence set forth in FIG. 2 or FIG. 3.
Various motifs are known in the art, and a protein can be evaluated
for the presence of such motifs by a number of publicly available
Internet sites (see, e.g., URL addresses: pfam.wustl.edu/;
searchlauncher.bcm.tmc.edu/seq-search/struc-p- redict.html;
psort.ims.u-tokyo.ac.jp/; cbs.dtu.dk/;
ebi.ac.uk/interpro/scan.html; expasy.ch/tools/scnpsit1.html;
Epimatrix.TM. and Epimer.TM., Brown University,
brown.edu/Research/TB-HIV- _Lab/epimatrix/epimatrix.html; and
BIMAS, bimas.dcrt.nih.gov/.).
[0504] Motif bearing subsequences of all 98P4B6 variant proteins
are set forth and identified in Tables VIII-XXI and XXII-XLIX.
[0505] Table V sets forth several frequently occurring motifs based
on pfam searches (see URL address pfam.wustl.edu/). The columns of
Table V list (1) motif name abbreviation, (2) percent identity
found amongst the different member of the motif family, (3) motif
name or description and (4) most common function; location
information is included if the motif is relevant for location.
[0506] Polypeptides comprising one or more of the 98P4B6 motifs
discussed above are useful in elucidating the specific
characteristics of a malignant phenotype in view of the observation
that the 98P4B6 motifs discussed above are associated with growth
dysregulation and because 98P4B6 is overexpressed in certain
cancers (See, e.g., Table I). Casein kinase II, cAMP and
camp-dependent protein kinase, and Protein Kinase C, for example,
are enzymes known to be associated with the development of the
malignant phenotype (see e.g. Chen et al., Lab Invest., 78(2):
165-174 (1998); Gaiddon et al., Endocrinology 136(10): 4331-4338
(1995); Hall et al., Nucleic Acids Research 24(6): 1119-1126
(1996); Peterziel et al., Oncogene 18(46): 6322-6329 (1999) and
O'Brian, Oncol. Rep. 5(2): 305-309 (1998)). Moreover, both
glycosylation and myristoylation are protein modifications also
associated with cancer and cancer progression (see e.g. Dennis et
al., Biochem. Biophys. Acta 1473(1):21-34 (1999); Raju et al., Exp.
Cell Res. 235(1): 145-154 (1997)). Amidation is another protein
modification also associated with cancer and cancer progression
(see e.g. Treston et al., J. Natl. Cancer Inst. Monogr. (13):
169-175 (1992)).
[0507] In another embodiment, proteins of the invention comprise
one or more of the immunoreactive epitopes identified in accordance
with art-accepted methods, such as the peptides set forth in Tables
VIII-XXI and XXII-XLIX. CTL epitopes can be determined using
specific algorithms to identify peptides within a 98P4B6 protein
that are capable of optimally binding to specified HLA alleles
(e.g., Table IV; Epimatrix.TM. and Epimer.TM., Brown University,
URL brown.edu/Research/TB-HIV_Lab/epima- trix/epimatrix.html; and
BIMAS, URL bimas.dcrt.nih.gov/.) Moreover, processes for
identifying peptides that have sufficient binding affinity for HLA
molecules and which are correlated with being immunogenic epitopes,
are well known in the art, and are carried out without undue
experimentation. In addition, processes for identifying peptides
that are immunogenic epitopes, are well known in the art, and are
carried out without undue experimentation either in vitro or in
vivo.
[0508] Also known in the art are principles for creating analogs of
such epitopes in order to modulate immunogenicity. For example, one
begins with an epitope that bears a CTL or HTL motif (see, e.g.,
the HLA Class I and HLA Class II motifs/supermotifs of Table IV).
The epitope is analoged by substituting out an amino acid at one of
the specified positions, and replacing it with another amino acid
specified for that position. For example, on the basis of residues
defined in Table IV, one can substitute out a deleterious residue
in favor of any other residue, such as a preferred residue;
substitute a less-preferred residue with a preferred residue; or
substitute an originally-occurring preferred residue with another
preferred residue. Substitutions can occur at primary anchor
positions or at other positions in a peptide; see, e.g., Table
IV.
[0509] A variety of references reflect the art regarding the
identification and generation of epitopes in a protein of interest
as well as analogs thereof. See, for example, WO 97/33602 to
Chesnut et al.; Sette, Immunogenetics 1999 50(3-4): 201-212; Sette
et al., J. Immunol. 2001 166(2): 1389-1397; Sidney et al., Hum.
Immunol. 1997 58(1): 12-20; Kondo et al., Immunogenetics 1997
45(4): 249-258; Sidney et al., J. Immunol. 1996 157(8): 3480-90;
and Falk et al., Nature 351: 290-6 (1991); Hunt et a., Science
255:1261-3 (1992); Parker et al., J. Immunol. 149:3580-7 (1992);
Parker et al., J. Immunol. 152:163-75 (1994)); Kast et al., 1994
152(8): 3904-12; Borras-Cuesta et al., Hum. Immunol. 2000 61(3):
266-278; Alexander et al., J. Immunol. 2000 164(3); 164(3):
1625-1633; Alexander et al., PMID: 7895164, UI: 95202582;
O'Sullivan et al., J. Immunol. 1991 147(8): 2663-2669; Alexander et
al., Immunity 1994 1(9): 751-761 and Alexander et al., Immunol.
Res. 1998 18(2): 79-92.
[0510] Related embodiments of the invention include polypeptides
comprising combinations of the different motifs set forth in Table
VI, and/or, one or more of the predicted CTL epitopes of Tables
VIII-XXI and XXII-XLIX, and/or, one or more of the predicted HTL
epitopes of Tables XLVI-XLIX, and/or, one or more of the T cell
binding motifs known in the art. Preferred embodiments contain no
insertions, deletions or substitutions either within the motifs or
within the intervening sequences of the polypeptides, In addition,
embodiments which include a number of either N-terminal and/or
C-terminal amino acid residues on either side of these motifs may
be desirable (to, for example, include a greater portion of the
polypeptide architecture in which the motif is located). Typically,
the number of N-terminal and/or C-terminal amino acid residues on
either side of a motif is between about 1 to about 100 amino acid
residues, preferably 5 to about 50 amino acid residues.
[0511] 98P4B6-related proteins are embodied in many forms,
preferably in isolated form. A purified 98P4B6 protein molecule
will be substantially free of other proteins or molecules that
impair the binding of 98P4B6 to antibody, T cell or other ligand.
The nature and degree of isolation and purification will depend on
the intended use. Embodiments of a 98P4B6-related proteins include
purified 98P4B6-related proteins and functional, soluble
98P4B6-related proteins. In one embodiment, a functional, soluble
98P4B6 protein or fragment thereof retains the ability to be bound
by antibody, T cell or other ligand.
[0512] The invention also provides 98P4B6 proteins comprising
biologically active fragments of a 98P4B6 amino acid sequence shown
in FIG. 2 or FIG. 3. Such proteins exhibit properties of the
starting 98P4B6 protein, such as the ability to elicit the
generation of antibodies that specifically bind an epitope
associated with the starting 98P4B6 protein; to be bound by such
antibodies; to elicit the activation of HTL or CTL; and/or, to be
recognized by HTL or CTL that also specifically bind to the
starting protein.
[0513] 98P4B6-related polypeptides that contain particularly
interesting structures can be predicted and/or identified using
various analytical techniques well known in the art, including, for
example, the methods of Chou-Fasman, Garnier-Robson,
Kyte-Doolittle, Eisenberg, Karplus-Schultz or Jameson-Wolf
analysis, or based on immunogenicity. Fragments that contain such
structures are particularly useful in generating subunit-specific
anti-98P4B6 antibodies or T cells or in identifying cellular
factors that bind to 98P4B6. For example, hydrophilicity profiles
can be generated, and immunogenic peptide fragments identified,
using the method of Hopp, T. P. and Woods, K. R., 1981, Proc. Natl.
Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity profiles can be
generated, and immunogenic peptide fragments identified, using the
method of Kyte, J. and Doolitte, R. F., 1982, J. Mol. Biol.
157:105-132. Percent (%) Accessible Residues profiles can be
generated, and immunogenic peptide fragments identified, using the
method of Janin J., 1979, Nature 277:491-492. Average Flexibility
profiles can be generated, and immunogenic peptide fragments
identified, using the method of Bhaskaran R., Ponnuswamy P. K.,
1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles can
be generated, and immunogenic peptide fragments identified, using
the method of Deleage, G., Roux B., 1987, Protein Engineering
1:289-294.
[0514] CTL epitopes can be determined using specific algorithms to
identify peptides within a 98P4B6 protein that are capable of
optimally binding to specified HLA alleles (e.g., by using the
SYFPEITHI site at World Wide Web URL syfpeithi.bmi-heidelberg.com/;
the listings in Table IV(A)-(E); Epimatrix.TM. and Epimer.TM.,
Brown University, URL
(brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and
BIMAS, URL bimas.dcrt.nih.gov/). Illustrating this, peptide
epitopes from 98P4B6 that are presented in the context of human MHC
Class I molecules, e.g., HLA-A1, A2, A3, A11, A24, B7 and B35 were
predicted (see, e.g., Tables VIII-XXI, XXII-XLIX). Specifically,
the complete amino acid sequence of the 98P4B6 protein and relevant
portions of other variants, i.e., for HLA Class I predictions 9
flanking residues on either side of a point mutation or exon
juction, and for HLA Class II predictions 14 flanking residues on
either side of a point mutation or exon junction corresponding to
that variant, were entered into the HLA Peptide Motif Search
algorithm found in the Bioinformatics and Molecular Analysis
Section (BIMAS) web site listed above; in addition to the site
SYFPEITHI, at URL syfpeithi.bmi-heidelberg.com/.
[0515] The HLA peptide motif search algorithm was developed by Dr.
Ken Parker based on binding of specific peptide sequences in the
groove of HLA Class I molecules, in particular HLA-A2 (see, e.g.,
Falk et al., Nature 351: 290-6 (1991); Hunt et al., Science
255:1261-3(1992); Parker et al., J. Immunol. 149:3580-7(1992);
Parker et al., J. Immunol. 152:163-75 (1994)). This algorithm
allows location and ranking of 8-mer, 9-mer, and 10-mer peptides
from a complete protein sequence for predicted binding to HLA-A2 as
well as numerous other HLA Class I molecules. Many HLA class I
binding peptides are 8-, 9-, 10 or 11-mers. For example, for Class
I HLA-A2, the epitopes preferably contain a leucine (L) or
methionine (M) at position 2 and a valine (V) or leucine (L) at the
C-terminus (see, e.g., Parker et al., J. Immunol. 149:3580-7
(1992)). Selected results of 98P4B6 predicted binding peptides are
shown in Tables VIII-XXI and XXII-XLIX herein. In Tables VIII-XXI
and XXII-XLVII, selected candidates, 9-mers and 10-mers, for each
family member are shown along with their location, the amino acid
sequence of each specific peptide, and an estimated binding score.
In Tables XLVI-XLIX, selected candidates, 15-mers, for each family
member are shown along with their location, the amino acid sequence
of each specific peptide, and an estimated binding score. The
binding score corresponds to the estimated half time of
dissociation of complexes containing the peptide at 37.degree. C.
at pH 6.5. Peptides with the highest binding score are predicted to
be the most tightly bound to HLA Class I on the cell surface for
the greatest period of time and thus represent the best immunogenic
targets for T-cell recognition.
[0516] Actual binding of peptides to an HLA allele can be evaluated
by stabilization of HLA expression on the antigen-processing
defective cell line T2 (see, e.g., Xue et al., Prostate 30:73-8
(1997) and Peshwa et al., Prostate 36:129-38 (1998)).
Immunogenicity of specific peptides can be evaluated in vitro by
stimulation of CD8+ cytotoxic T lymphocytes (CTL) in the presence
of antigen presenting cells such as dendritic cells.
[0517] It is to be appreciated that every epitope predicted by the
BIMAS site, Epimer.TM. and Epimatrix.TM. sites, or specified by the
HLA class I or class II motifs available in the art or which become
part of the art such as set forth in Table IV (or determined using
World Wide Web site URL syfpeithi.bmi-heidelberg.com/, or BIMAS,
bimas.dcrt.nih.gov/) are to be "applied" to a 98P4B6 protein in
accordance with the invention. As used in this context "applied"
means that a 98P4B6 protein is evaluated, e.g., visually or by
computer-based patterns finding methods, as appreciated by those of
skill in the relevant art. Every subsequence of a 98P4B6 protein of
8, 9, 10, or 11 amino acid residues that bears an HLA Class I
motif, or a subsequence of 9 or more amino acid residues that bear
an HLA Class II motif are within the scope of the invention.
[0518] III.B.) Expression of 98P4B6-Related Proteins
[0519] In an embodiment described in the examples that follow,
98P4B6 can be conveniently expressed in cells (such as 293T cells)
transfected with a commercially available expression vector such as
a CMV-driven expression vector encoding 98P4B6 with a C-terminal
6.times.His and MYC tag (pcDNA3.1/mycHIS, Invitrogen or Tag5,
GenHunter Corporation, Nashville Tenn.). The Tag5 vector provides
an IgGK secretion signal that can be used to facilitate the
production of a secreted 98P4B6 protein in transfected cells. The
secreted HIS-tagged 98P4B6 in the culture media can be purified,
e.g., using a nickel column using standard techniques.
[0520] III.C.) Modifications of 98P4B6-Related Proteins
[0521] Modifications of 98P4B6-related proteins such as covalent
modifications are included within the scope of this invention. One
type of covalent modification includes reacting targeted amino acid
residues of a 98P4B6 polypeptide with an organic derivatizing agent
that is capable of reacting with selected side chains or the N- or
C-terminal residues of a 98P4B6 protein. Another type of covalent
modification of a 98P4B6 polypeptide included within the scope of
this invention comprises altering the native glycosylation pattern
of a protein of the invention. Another type of covalent
modification of 98P4B6 comprises linking a 98P4B6 polypeptide to
one of a variety of nonproteinaceous polymers, e.g., polyethylene
glycol (PEG), polypropylene glycol, or polyoxyalkylenes, in the
manner set forth in U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144;
4,670,417; 4,791,192 or 4,179,337.
[0522] The 98P4B6-related proteins of the present invention can
also be modified to form a chimeric molecule comprising 98P4B6
fused to another, heterologous polypeptide or amino acid sequence.
Such a chimeric molecule can be synthesized chemically or
recombinantly. A chimeric molecule can have a protein of the
invention fused to another tumor-associated antigen or fragment
thereof. Alternatively, a protein in accordance with the invention
can comprise a fusion of fragments of a 98P4B6 sequence (amino or
nucleic acid) such that a molecule is created that is not, through
its length, directly homologous to the amino or nucleic acid
sequences shown in FIG. 2 or FIG. 3. Such a chimeric molecule can
comprise multiples of the same subsequence of 98P4B6. A chimeric
molecule can comprise a fusion of a 98P4B6-related protein with a
polyhistidine epitope tag, which provides an epitope to which
immobilized nickel can selectively bind, with cytokines or with
growth factors. The epitope tag is generally placed at the amino-
or carboxyl-terminus of a 98P4B6 protein. In an alternative
embodiment, the chimeric molecule can comprise a fusion of a
98P4B6-related protein with an immunoglobulin or a particular
region of an immunoglobulin. For a bivalent form of the chimeric
molecule (also referred to as an "immunoadhesin"), such a fusion
could be to the Fc region of an IgG molecule. The Ig fusions
preferably include the substitution of a soluble (transmembrane
domain deleted or inactivated) form of a 98P4B6 polypeptide in
place of at least one variable region within an Ig molecule. In a
preferred embodiment, the immunoglobulin fusion includes the hinge,
CH2 and CH3, or the hinge, CH1, CH2 and CH3 regions of an IgGI
molecule. For the production of immunoglobulin fusions see, e.g.,
U.S. Pat. No. 5,428,130 issued Jun. 27, 1995.
[0523] III.D.) Uses of 98P4B6-Related Proteins
[0524] The proteins of the invention have a number of different
specific uses. As 98P4B6 is highly expressed in prostate and other
cancers, 98P4B6-related proteins are used in methods that assess
the status of 98P4B6 gene products in normal versus cancerous
tissues, thereby elucidating the malignant phenotype. Typically,
polypeptides from specific regions of a 98P4B6 protein are used to
assess the presence of perturbations (such as deletions,
insertions, point mutations etc.) in those regions (such as regions
containing one or more motifs). Exemplary assays utilize antibodies
or T cells targeting 98P4B6-related proteins comprising the amino
acid residues of one or more of the biological motifs contained
within a 98P4B6 polypeptide sequence in order to evaluate the
characteristics of this region in normal versus cancerous tissues
or to elicit an immune response to the epitope. Alternatively,
98P4B6-related proteins that contain the amino acid residues of one
or more of the biological motifs in a 98P4B6 protein are used to
screen for factors that interact with that region of 98P4B6.
[0525] 98P4B6 protein fragments/subsequences are particularly
useful in generating and characterizing domain-specific antibodies
(e.g., antibodies recognizing an extracellular or intracellular
epitope of a 98P4B6 protein), for identifying agents or cellular
factors that bind to 98P4B6 or a particular structural domain
thereof, and in various therapeutic and diagnostic contexts,
including but not limited to diagnostic assays, cancer vaccines and
methods of preparing such vaccines.
[0526] Proteins encoded by the 98P4B6 genes, or by analogs,
homologs or fragments thereof, have a variety of uses, including
but not limited to generating antibodies and in methods for
identifying ligands and other agents and cellular constituents that
bind to a 98P4B6 gene product Antibodies raised against a 98P4B6
protein or fragment thereof are useful in diagnostic and prognostic
assays, and imaging methodologies in the management of human
cancers characterized by expression of 98P4B6 protein, such as
those listed in Table I. Such antibodies can be expressed
intracellularly and used in methods of treating patients with such
cancers. 98P4B6-related nucleic acids or proteins are also used in
generating HTL or CTL responses.
[0527] Various immunological assays useful for the detection of
98P4B6 proteins are used, including but not limited to various
types of radioimmunoassays, enzyme-linked immunosorbent assays
(ELISA), enzyme-linked immunofluorescent assays (ELIFA),
immunocytochemical methods, and the like. Antibodies can be labeled
and used as immunological imaging reagents capable of detecting
98P4B6-expressing cells (e.g., in radioscintigraphic imaging
methods). 98P4B6 proteins are also particularly useful in
generating cancer vaccines, as further described herein.
[0528] IV.) 98P4B6 Antibodies
[0529] Another aspect of the invention provides antibodies that
bind to 98P4B6-related proteins. Preferred antibodies specifically
bind to a 98P4B6-related protein and do not bind (or bind weakly)
to peptides or proteins that are not 98P4B6-related proteins under
physiological conditions. In this context, examples of
physiological conditions include: 1) phosphate buffered saline; 2)
Tris-buffered saline containing 25 mM Tris and 150 mM NaCl; or
normal saline (0.9% NaCl); 4) animal serum such as human serum; or,
5) a combination of any of 1) through 4); these reactions
preferably taking place at pH 7.5, alternatively in a range of pH
7.0 to 8.0, or alternatively in a range of pH 6.5 to 8.5; also,
these reactions taking place at a temperature between 4.degree. C.
to 37.degree. C. For example, antibodies that bind 98P4B6 can bind
98P4B6-related proteins such as the homologs or analogs
thereof.
[0530] 98P4B6 antibodies of the invention are particularly useful
in cancer (see, e.g., Table I) diagnostic and prognostic assays,
and imaging methodologies. Similarly, such antibodies are useful in
the treatment, diagnosis, and/or prognosis of other cancers, to the
extent 98P4B6 is also expressed or overexpressed in these other
cancers. Moreover, intracellularly expressed antibodies (e.g.,
single chain antibodies) are therapeutically useful in treating
cancers in which the expression of 98P4B6 is involved, such as
advanced or metastatic prostate cancers.
[0531] The invention also provides various immunological assays
useful for the detection and quantification of 98P4B6 and mutant
98P4B6-related proteins. Such assays can comprise one or more
98P4B6 antibodies capable of recognizing and binding a
98P4B6-related protein, as appropriate. These assays are performed
within various immunological assay formats well known in the art,
including but not limited to various types of radioimmunoassays,
enzyme-linked immunosorbent assays (ELISA), enzyme-linked
immunofluorescent assays (ELIFA), and the like.
[0532] Immunological non-antibody assays of the invention also
comprise T cell immunogenicity assays (inhibitory or stimulatory)
as well as major histocompatibility complex (MHC) binding
assays.
[0533] In addition, immunological imaging methods capable of
detecting prostate cancer and other cancers expressing 98P4B6 are
also provided by the invention, including but not limited to
radioscintigraphic imaging methods using labeled 98P4B6 antibodies.
Such assays are clinically useful in the detection, monitoring, and
prognosis of 98P4B6 expressing cancers such as prostate cancer.
[0534] 98P4B6 antibodies are also used in methods for purifying a
98P4B6-related protein and for isolating 98P4B6 homologues and
related molecules. For example, a method of purifying a
98P4B6-related protein comprises incubating a 98P4B6 antibody,
which has been coupled to a solid matrix, with a lysate or other
solution containing a 98P4B6-related protein under conditions that
permit the 98P4B6 antibody to bind to the 98P4B6-related protein;
washing the solid matrix to eliminate impurities; and eluting the
98P4B6-related protein from the coupled antibody. Other uses of
98P4B6 antibodies in accordance with the invention include
generating anti-idiotypic antibodies that mimic a 98P4B6
protein.
[0535] Various methods for the preparation of antibodies are well
known in the art. For example, antibodies can be prepared by
immunizing a suitable mammalian host using a 98P4B6-related
protein, peptide, or fragment, in isolated or immunoconjugated form
(Antibodies: A Laboratory Manual, CSH Press, Eds., Harlow, and Lane
(1988); Harlow, Antibodies, Cold Spring Harbor Press, NY (1989)).
In addition, fusion proteins of 98P4B6 can also be used, such as a
98P4B6 GST-fusion protein. In a particular embodiment, a GST fusion
protein comprising all or most of the amino acid sequence of FIG. 2
or FIG. 3 is produced, then used as an immunogen to generate
appropriate antibodies. In another embodiment, a 98P4B6-related
protein is synthesized and used as an immunogen.
[0536] In addition, naked DNA immunization techniques known in the
art are used (with or without purified 98P4B6-related protein or
98P4B6 expressing cells) to generate an immune response to the
encoded immunogen (for review, see Donnelly et al., 1997, Ann. Rev.
Immunol. 15: 617-648).
[0537] The amino acid sequence of a 98P4B6 protein as shown in FIG.
2 or FIG. 3 can be analyzed to select specific regions of the
98P4B6 protein for generating antibodies. For example,
hydrophobicity and hydrophilicity analyses of a 98P4B6 amino acid
sequence are used to identify hydrophilic regions in the 98P4B6
structure. Regions of a 98P4B6 protein that show immunogenic
structure, as well as other regions and domains, can readily be
identified using various other methods known in the art, such as
Chou-Fasman, Garnier-Robson, Kyte-Doolittle, Eisenberg,
Karplus-Schultz or Jameson-Wolf analysis. Hydrophilicity profiles
can be generated using the method of Hopp, T. P. and Woods, K. R.,
1981, Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828. Hydropathicity
profiles can be generated using the method of Kyte, J. and
Doolittle, R. F., 1982, J. Mol. Biol. 157:105-132. Percent (%)
Accessible Residues profiles can be generated using the method of
Janin J., 1979, Nature 277:491-492. Average Flexibility profiles
can be generated using the method of Bhaskaran R., Ponnuswamy P.
K., 1988, Int. J. Pept. Protein Res. 32:242-255. Beta-turn profiles
can be generated using the method of Deleage, G., Roux B., 1987,
Protein Engineering 1:289-294. Thus, each region identified by any
of these programs or methods is within the scope of the present
invention. Methods for the generation of 98P4B6 antibodies are
further illustrated by way of the examples provided herein. Methods
for preparing a protein or polypeptide for use as an immunogen are
well known in the art. Also well known in the art are methods for
preparing immunogenic conjugates of a protein with a carrier, such
as BSA, KLH or other carrier protein. In some circumstances, direct
conjugation using, for example, carbodiimide reagents are used; in
other instances linking reagents such as those supplied by Pierce
Chemical Co., Rockford, Ill., are effective. Administration of a
98P4B6 immunogen is often conducted by injection over a suitable
time period and with use of a suitable adjuvant, as is understood
in the art. During the immunization schedule, titers of antibodies
can be taken to determine adequacy of antibody formation.
[0538] 98P4B6 monoclonal antibodies can be produced by various
means well known in the art. For example, immortalized cell lines
that secrete a desired monoclonal antibody are prepared using the
standard hybridoma technology of Kohler and Milstein or
modifications that immortalize antibody-producing B cells, as is
generally known. Immortalized cell lines that secrete the desired
antibodies are screened by immunoassay in which the antigen is a
98P4B6-related protein. When the appropriate immortalized cell
culture is identified, the cells can be expanded and antibodies
produced either from in vitro cultures or from ascites fluid.
[0539] The antibodies or fragments of the invention can also be
produced, by recombinant means. Regions that bind specifically to
the desired regions of a 98P4B6 protein can also be produced in the
context of chimeric or complementarity-determining region (CDR)
grafted antibodies of multiple species origin. Humanized or human
98P4B6 antibodies can also be produced, and are preferred for use
in therapeutic contexts. Methods for humanizing murine and other
non-human antibodies, by substituting one or more of the non-human
antibody CDRs for corresponding human antibody sequences, are well
known (see for example, Jones et al., 1986, Nature 321: 522-525;
Riechmann et al., 1988, Nature 332: 323-327; Verhoeyen et al.,
1988, Science 239: 1534-1536). See also, Carter et al., 1993, Proc.
Natl. Acad. Sci. USA 89:4285 and Sims et al., 1993, J. Immunol.
151: 2296.
[0540] Methods for producing fully human monoclonal antibodies
include phage display and transgenic methods (for review, see
Vaughan et al., 1998, Nature Biotechnology 16: 535-539). Fully
human 98P4B6 monoclonal antibodies can be generated using cloning
technologies employing large human Ig gene combinatorial libraries
(i.e., phage display) (Griffiths and Hoogenboom, Building an in
vitro immune system: human antibodies from phage display libraries.
In: Protein Engineering of Antibody Molecules for Prophylactic and
Therapeutic Applications in Man, Clark, M. (Ed.), Nottingham
Academic, pp 45-64 (1993); Burton and Barbas, Human Antibodies from
combinatorial libraries. Id., pp 65-82). Fully human 98P4B6
monoclonal antibodies can also be produced using transgenic mice
engineered to contain human immunoglobulin gene loci as described
in PCT Patent Application WO98/24893, Kucherlapati and Jakobovits
et al., published Dec. 3, 1997 (see also, Jakobovits, 1998, Exp.
Opin. Invest. Drugs 7(4): 607-614; U.S. Pat. No. 6,162,963 issued
19 Dec. 2000; U.S. Pat. No. 6,150,584 issued 12 Nov. 2000; and,
U.S. Pat. No. 6,114,598 issued 5 Sep. 2000). This method avoids the
in vitro manipulation required with phage display technology and
efficiently produces high affinity authentic human antibodies.
[0541] Reactivity of 98P4B6 antibodies with a 98P4B6-related
protein can be established by a number of well known means,
including Western blot, immunoprecipitation, ELISA, and FACS
analyses using, as appropriate, 98P4B6-related proteins,
98P4B6-expressing cells or extracts thereof. A 98P4B6 antibody or
fragment thereof can be labeled with a detectable marker or
conjugated to a second molecule. Suitable detectable markers
include, but are not limited to, a radioisotope, a fluorescent
compound, a bioluminescent compound, chemiluminescent compound, a
metal chelator or an enzyme. Further, bi-specific antibodies
specific for two or more 98P4B6 epitopes are generated using
methods generally known in the art. Homodimeric antibodies can also
be generated by cross-linking techniques known in the art (e.g.,
Wolff et al., Cancer Res. 53: 2560-2565).
[0542] V.) 98P4B6 Cellular Immune Responses
[0543] The mechanism by which T cells recognize antigens has been
delineated. Efficacious peptide epitope vaccine compositions of the
invention induce a therapeutic or prophylactic immune responses in
very broad segments of the world-wide population. For an
understanding of the value and efficacy of compositions of the
invention that induce cellular immune responses, a brief review of
immunology-related technology is provided.
[0544] A complex of an HLA molecule and a peptidic antigen acts as
the ligand recognized by HLA-restricted T cells (Buus, S. et al.,
Cell 47:1071, 1986; Babbitt, B. P. et al., Nature 317:359, 1985;
Townsend, A. and Bodmer, H., Annu. Rev. Immunol. 7:601, 1989;
Germain, R. N., Annu. Rev. Immunol. 11:403, 1993). Through the
study of single amino acid substituted antigen analogs and the
sequencing of endogenously bound, naturally processed peptides,
critical residues that correspond to motifs required for specific
binding to HLA antigen molecules have been identified and are set
forth in Table IV (see also, e.g., Southwood, et al., J. Immunol.
160:3363, 1998; Rammensee, et al., Immunogenetics 41:178, 1995;
Rammensee et al., SYFPEITHI, access via World Wide Web at URL
(134.2.96.221/scripts.hlaserver.dll/home.htm); Sette, A. and
Sidney, J. Curr. Opin. Immunol. 10:478,1998; Engelhard, V. H.,
Curr. Opin. Immunol. 6:13,1994; Sette, A. and Grey, H. M., Curr.
Opin. Immunol. 4:79, 1992; Sinigaglia, F. and Hammer, J. Curr.
Biol. 6:52, 1994; Ruppert et al., Cell 74:929-937, 1993; Kondo et
al., J. Immunol. 155:4307-4312, 1995; Sidney et al., J. Immunol.
157:3480-3490, 1996; Sidney et al., Human Immunol. 45:79-93, 1996;
Sette, A. and Sidney, J. Immunogenetics 1999 November;
50(3-4):201-12, Review).
[0545] Furthermore, x-ray crystallographic analyses of HLA-peptide
complexes have revealed pockets within the peptide binding
cleft/groove of HLA molecules which accommodate, in an
allele-specific mode, residues borne by peptide ligands; these
residues in turn determine the HLA binding capacity of the peptides
in which they are present. (See, e.g., Madden, D. R. Annu. Rev.
Immunol. 13:587, 1995; Smith, et al., Immunity 4:203, 1996; Fremont
et al., Immunity 8:305, 1998; Stern et al., Structure 2:245, 1994;
Jones, E. Y. Curr. Opin. Immunol. 9:75, 1997; Brown, J. H. et al.,
Nature 364:33, 1993; Guo, H. C. et al., Proc. Natl. Acad. Sci. USA
90:8053, 1993; Guo, H. C. et al., Nature 360:364, 1992; Silver, M.
L. et al., Nature 360:367, 1992; Matsumura, M. et al., Science
257:927, 1992; Madden et al., Cell 70:1035, 1992; Fremont, D. H. et
al., Science 257:919, 1992; Saper, M. A. , Bjorkman, P. J. and
Wiley, D. C., J. Mol. Biol. 219:277, 1991.)
[0546] Accordingly, the definition of class I and class II
allele-specific HLA binding motifs, or class I or class II
supermotifs allows identification of regions within a protein that
are correlated with binding to particular HLA antigen(s).
[0547] Thus, by a process of HLA motif identification, candidates
for epitope-based vaccines have been identified; such candidates
can be further evaluated by HLA-peptide binding assays to determine
binding affinity and/or the time period of association of the
epitope and its corresponding HLA molecule. Additional confirmatory
work can be performed to select, amongst these vaccine candidates,
epitopes with preferred characteristics in terms of population
coverage, and/or immunogenicity.
[0548] Various strategies can be utilized to evaluate cellular
immunogenicity, including:
[0549] 1) Evaluation of primary T cell cultures from normal
individuals (see, e.g., Wentworth, P. A. et al., Mol. Immunol.
32:603, 1995; Celis, E. et al., Proc. Natl. Acad. Sci. USA 91:2105,
1994; Tsai, V. et al., J. Immunol. 158:1796, 1997; Kawashima, I. et
al., Human Immunol 59:1, 1998). This procedure involves the
stimulation of peripheral blood lymphocytes (PBL) from normal
subjects with a test peptide in the presence of antigen presenting
cells in vitro over a period of several weeks. T cells specific for
the peptide become activated during this time and are detected
using, e.g., a lymphokine- or .sup.51Cr-release assay involving
peptide sensitized target cells.
[0550] 2) Immunization of HLA transgenic mice (see, e.g.,
Wentworth, P. A. et al., J. Immunol 26:97, 1996; Wentworth, P. A.
et al., Int. Immunol 8:651, 1996; Alexander, J. et al., J. Immunol.
159:4753, 1997). For example, in such methods peptides in
incomplete Freund's adjuvant are administered subcutaneously to HLA
transgenic mice. Several weeks following immunization, splenocytes
are removed and cultured in vitro in the presence of test peptide
for approximately one week. Peptide-specific T cells are detected
using, e.g., a .sup.51Cr-release assay involving peptide sensitized
target cells and target cells expressing endogenously generated
antigen.
[0551] 3) Demonstration of recall T cell responses from immune
individuals who have been either effectively vaccinated and/or from
chronically ill patients (see, e.g., Rehermann, B. et al., J. Exp.
Med. 181:1047, 1995; Doolan, D. L. et al., Immunity 7:97, 1997;
Bertoni, R. et al., J. Clin. Invest. 100:503, 1997; Threlkeld, S.
C. et al., J. Immunol. 159:1648, 1997; Diepolder, H. M. et al., J.
Virol. 71:6011, 1997). Accordingly, recall responses are detected
by culturing PBL from subjects that have been exposed to the
antigen due to disease and thus have generated an immune response
"naturally", or from patients who were vaccinated against the
antigen. PBL from subjects are cultured in vitro for 1-2 weeks in
the presence of test peptide plus antigen presenting cells (APC) to
allow activation of "memory" T cells, as compared to "naive" T
cells. At the end of the culture period, T cell activity is
detected using assays including .sup.51Cr release involving
peptide-sensitized targets, T cell proliferation, or lymphokine
release.
[0552] VI.) 98P4B6 Transgenic Animals
[0553] Nucleic acids that encode a 98P4B6-related protein can also
be used to generate either transgenic animals or "knock out"
animals that, in turn, are useful in the development and screening
of therapeutically useful reagents. In accordance with established
techniques, cDNA encoding 98P4B6 can be used to clone genomic DNA
that encodes 98P4B6. The cloned genomic sequences can then be used
to generate transgenic animals containing cells that express DNA
that encode 98P4B6. Methods for generating transgenic animals,
particularly animals such as mice or rats, have become conventional
in the art and are described, for example, in U.S. Pat. No.
4,736,866 issued 12 Apr. 1988, and U.S. Pat. No. 4,870,009 issued
26 Sep. 1989. Typically, particular cells would be targeted for
98P4B6 transgene incorporation with tissue-specific enhancers.
[0554] Transgenic animals that include a copy of a transgene
encoding 98P4B6 can be used to examine the effect of increased
expression of DNA that encodes 98P4B6. Such animals can be used as
tester animals for reagents thought to confer protection from, for
example, pathological conditions associated with its
overexpression. In accordance with this aspect of the invention, an
animal is treated with a reagent and a reduced incidence of a
pathological condition, compared to untreated animals that bear the
transgene, would indicate a potential therapeutic intervention for
the pathological condition.
[0555] Alternatively, non-human homologues of 98P4B6 can be used to
construct a 98P4B6 "knock out" animal that has a defective or
altered gene encoding 98P4B6 as a result of homologous
recombination between the endogenous gene encoding 98P4B6 and
altered genomic DNA encoding 98P4B6 introduced into an embryonic
cell of the animal. For example, cDNA that encodes 98P4B6 can be
used to clone genomic DNA encoding 98P4B6 in accordance with
established techniques. A portion of the genomic DNA encoding
98P4B6 can be deleted or replaced with another gene, such as a gene
encoding a selectable marker that can be used to monitor
integration. Typically, several kilobases of unaltered flanking DNA
(both at the 5' and 3' ends) are included in the vector (see, e.g.,
Thomas and Capecchi, Cell, 51:503 (1987) for a description of
homologous recombination vectors). The vector is introduced into an
embryonic stem cell line (e.g., by electroporation) and cells in
which the introduced DNA has homologously recombined with the
endogenous DNA are selected (see, e.g., Li et at., Cell, 69:915
(1992)). The selected cells are then injected into a blastocyst of
an animal (e.g., a mouse or rat) to form aggregation chimeras (see,
e.g., Bradley, in Teratocarcinomas and Embryonic Stem Cells: A
Practical Approach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp.
113-152). A chimeric embryo can then be implanted into a suitable
pseudopregnant female foster animal, and the embryo brought to term
to create a "knock out" animal. Progeny harboring the homologously
recombined DNA in their germ cells can be identified by standard
techniques and used to breed animals in which all cells of the
animal contain the homologously recombined DNA. Knock out animals
can be characterized, for example, for their ability to defend
against certain pathological conditions or for their development of
pathological conditions due to absence of a 98P4B6 polypeptide.
[0556] VII.) Methods for the Detection of 98P4B6
[0557] Another aspect of the present invention relates to methods
for detecting 98P4B6 polynucleotides and 98P4B6-related proteins,
as well as methods for identifying a cell that expresses 98P4B6.
The expression profile of 98P4B6 makes it a diagnostic marker for
metastasized disease. Accordingly, the status of 98P4B6 gene
products provides information useful for predicting a variety of
factors including susceptibility to advanced stage disease, rate of
progression, and/or tumor aggressiveness. As discussed in detail
herein, the status of 98P4B6 gene products in patient samples can
be analyzed by a variety protocols that are well known in the art
including immunohistochemical analysis, the variety of Northern
blotting techniques including in situ hybridization, RT-PCR
analysis (for example on laser capture micro-dissected samples),
Western blot analysis and issue array analysis.
[0558] More particularly, the invention provides assays for the
detection of 98P4B6 polynucleotides in a biological sample, such as
serum, bone, prostate, and other tissues, urine, semen, cell
preparations, and the like. Detectable 98P4B6 polynucleotides
include, for example, a 98P4B6 gene or fragment thereof, 98P4B6
mRNA, alternative splice variant 98P4B6 mRNAs, and recombinant DNA
or RNA molecules that contain a 98P4B6 polynucleotide. A number of
methods for amplifying and/or detecting the presence of 98P4B6
polynucleotides are well known in the art and can be employed in
the practice of this aspect of the invention.
[0559] In one embodiment, a method for detecting a 98P4B6 mRNA in a
biological sample comprises producing cDNA from the sample by
reverse transcription using at least one primer; amplifying the
cDNA so produced using a 98P4B6 polynucleotides as sense and
antisense primers to amplify 98P4B6 cDNAs therein; and detecting
the presence of the amplified 98P4B6 cDNA. Optionally, the sequence
of the amplified 98P4B6 cDNA can be determined.
[0560] In another embodiment, a method of detecting a 98P4B6 gene
in a biological sample comprises first isolating genomic DNA from
the sample; amplifying the isolated genomic DNA using 98P4B6
polynucleotides as sense and antisense primers; and detecting the
presence of the amplified 98P4B6 gene. Any number of appropriate
sense and antisense probe combinations can be designed from a
98P4B6 nucleotide sequence (see, e.g., FIG. 2) and used for this
purpose.
[0561] The invention also provides assays for detecting the
presence of a 98P4B6 protein in a tissue or other biological sample
such as serum, semen, bone, prostate, urine, cell preparations, and
the like. Methods for detecting a 98P4B6-related protein are also
well known and include, for example, immunoprecipitation,
immunohistochemical analysis, Western blot analysis, molecular
binding assays, ELISA, ELIFA and the like. For example, a method of
detecting the presence of a 98P4B6-related protein in a biological
sample comprises first contacting the sample with a 98P4B6
antibody, a 98P4B6-reactive fragment thereof, or a recombinant
protein containing an antigen-binding region of a 98P4B6 antibody;
and then detecting the binding of 98P4B6-related protein in the
sample.
[0562] Methods for identifying a cell that expresses 98P4B6 are
also within the scope of the invention. In one embodiment, an assay
for identifying a cell that expresses a 98P4B6 gene comprises
detecting the presence of 98P4B6 mRNA in the cell. Methods for the
detection of particular mRNAs in cells are well known and include,
for example, hybridization assays using complementary DNA probes
(such as in situ hybridization using labeled 98P4B6 riboprobes,
Northern blot and related techniques) and various nucleic acid
amplification assays (such as RT-PCR using complementary primers
specific for 98P4B6, and other amplification type detection
methods, such as, for example, branched DNA, SISBA, TMA and the
like). Alternatively, an assay for identifying a cell that
expresses a 98P4B6 gene comprises detecting the presence of
98P4B6-related protein in the cell or secreted by the cell. Various
methods for the detection of proteins are well known in the art and
are employed for the detection of 98P4B6-related proteins and cells
that express 98P4B6-related proteins.
[0563] 98P4B6 expression analysis is also useful as a tool for
identifying and evaluating agents that modulate 98P4B6 gene
expression. For example, 98P4B6 expression is significantly
upregulated in prostate cancer, and is expressed in cancers of the
tissues listed in Table I. Identification of a molecule or
biological agent that inhibits 98P4B6 expression or over-expression
in cancer cells is of therapeutic value. For example, such an agent
can be identified by using a screen that quantifies 98P4B6
expression by RT-PCR, nucleic acid hybridization or antibody
binding.
[0564] VIII.) Methods for Monitoring the Status of 98P4B6-Related
Genes and Their Products
[0565] Oncogenesis is known to be a multistep process where
cellular growth becomes progressively dysregulated and cells
progress from a normal physiological state to precancerous and then
cancerous states (see, e.g., Alers et al., Lab Invest. 77(5):
437-438 (1997) and Isaacs et al., Cancer Surv. 23: 19-32 (1995)).
In this context, examining a biological sample for evidence of
dysregulated cell growth (such as aberrant 98P4B6 expression in
cancers) allows for early detection of such aberrant physiology,
before a pathologic state such as cancer has progressed to a stage
that therapeutic options are more limited and or the prognosis is
worse. In such examinations, the status of 98P4B6 in a biological
sample of interest can be compared, for example, to the status of
98P4B6 in a corresponding normal sample (e.g. a sample from that
individual or alternatively another individual that is not affected
by a pathology). An alteration in the status of 98P4B6 in the
biological sample (as compared to the normal sample) provides
evidence of dysregulated cellular growth. In addition to using a
biological sample that is not affected by a pathology as a normal
sample, one can also use a predetermined normative value such as a
predetermined normal level of mRNA expression (see, e.g., Grever et
al., J. Comp. Neurol. 1996 Dec. 9; 376(2): 306-14 and U.S. Pat. No.
5,837,501) to compare 98P4B6 status in a sample.
[0566] The term "status" in this context is used according to its
art accepted meaning and refers to the condition or state of a gene
and its products. Typically, skilled artisans use a number of
parameters to evaluate the condition or state of a gene and its
products. These include, but are not limited to the location of
expressed gene products (including the location of 98P4B6
expressing cells) as well as the level, and biological activity of
expressed gene products (such as 98P4B6 mRNA, polynucleotides and
polypeptides). Typically, an alteration in the status of 98P4B6
comprises a change in the location of 98P4B6 and/or 98P4B6
expressing cells and/or an increase in 98P4B6 mRNA and/or protein
expression.
[0567] 98P4B6 status in a sample can be analyzed by a number of
means well known in the art, including without limitation,
immunohistochemical analysis, in situ hybridization, RT-PCR
analysis on laser capture micro-dissected samples, Western blot
analysis, and tissue array analysis. Typical protocols for
evaluating the status of a 98P4B6 gene and gene products are found,
for example in Ausubel et al. eds., 1995, Current Protocols In
Molecular Biology, Units 2 (Northern Blotting), 4 (Southern
Blotting), 15 (Immunoblotting) and 18 (PCR Analysis). Thus, the
status of 98P4B6 in a biological sample is evaluated by various
methods utilized by skilled artisans including, but not limited to
genomic Southern analysis (to examine, for example perturbations in
a 98P4B6 gene), Northern analysis and/or PCR analysis of 98P4B6
mRNA (to examine, for example alterations in the polynucleotide
sequences or expression levels of 98P4B6 mRNAs), and, Western
and/or immunohistochemical analysis (to examine, for example
alterations in polypeptide sequences, alterations in polypeptide
localization within a sample, alterations in expression levels of
98P4B6 proteins and/or associations of 98P4B6 proteins with
polypeptide binding partners). Detectable 98P4B6 polynucleotides
include, for example, a 98P4B6 gene or fragment thereof, 98P4B6
mRNA, alternative splice variants, 98P4B6 mRNAs, and recombinant
DNA or RNA molecules containing a 98P4B6 polynucleotide.
[0568] The expression profile of 98P4B6 makes it a diagnostic
marker for local and/or metastasized disease, and provides
information on the growth or oncogenic potential of a biological
sample. In particular, the status of 98P4B6 provides information
useful for predicting susceptibility to particular disease stages,
progression, and/or tumor aggressiveness. The invention provides
methods and assays for determining 98P4B6 status and diagnosing
cancers that express 98P4B6, such as cancers of the tissues listed
in Table I. For example, because 98P4B6 mRNA is so highly expressed
in prostate and other cancers relative to normal prostate tissue,
assays that evaluate the levels of 98P4B6 mRNA transcripts or
proteins in a biological sample can be used to diagnose a disease
associated with 98P4B6 dysregulation, and can provide prognostic
information useful in defining appropriate therapeutic options.
[0569] The expression status of 98P4B6 provides information
including the presence, stage and location of dysplastic,
precancerous and cancerous cells, predicting susceptibility to
various stages of disease, and/or for gauging tumor aggressiveness.
Moreover, the expression profile makes it useful as an imaging
reagent for metastasized disease. Consequently, an aspect of the
invention is directed to the various molecular prognostic and
diagnostic methods for examining the status of 98P4B6 in biological
samples such as those from individuals suffering from, or suspected
of suffering from a pathology characterized by dysregulated
cellular growth, such as cancer.
[0570] As described above, the status of 98P4B6 in a biological
sample can be examined by a number of well-known procedures in the
art. For example, the status of 98P4B6 in a biological sample taken
from a specific location in the body can be examined by evaluating
the sample for the presence or absence of 98P4B6 expressing cells
(e.g. those that express 98P4B6 mRNAs or proteins). This
examination can provide evidence of dysregulated cellular growth,
for example, when 98P4B6-expressing cells are found in a biological
sample that does not normally contain such cells (such as a lymph
node), because such alterations in the status of 98P4B6 in a
biological sample are often associated with dysregulated cellular
growth. Specifically, one indicator of dysregulated cellular growth
is the metastases of cancer cells from an organ of origin (such as
the prostate) to a different area of the body (such as a lymph
node). In this context, evidence of dysregulated cellular growth is
important for example because occult lymph node metastases can be
detected in a substantial proportion of patients with prostate
cancer, and such metastases are associated with known predictors of
disease progression (see, e.g., Murphy et al., Prostate 42(4):
315-317 (2000);Su et al., Semin. Surg. Oncol. 18(1): 17-28 (2000)
and Freeman et al., J Urol 1995 August 154(2 Pt 1):474-8).
[0571] In one aspect, the invention provides methods for monitoring
98P4B6 gene products by determining the status of 98P4B6 gene
products expressed by cells from an individual suspected of having
a disease associated with dysregulated cell growth (such as
hyperplasia or cancer) and then comparing the status so determined
to the status of 98P4B6 gene products in a corresponding normal
sample. The presence of aberrant 98P4B6 gene products in the test
sample relative to the normal sample provides an indication of the
presence of dysregulated cell growth within the cells of the
individual.
[0572] In another aspect, the invention provides assays useful in
determining the presence of cancer in an individual, comprising
detecting a significant increase in 98P4B6 mRNA or protein
expression in a test cell or tissue sample relative to expression
levels in the corresponding normal cell or tissue. The presence of
98P4B6 mRNA can, for example, be evaluated in tissues including but
not limited to those listed in Table I. The presence of significant
98P4B6 expression in any of these tissues is useful to indicate the
emergence, presence and/or severity of a cancer, since the
corresponding normal tissues do not express 98P4B6 mRNA or express
it at lower levels.
[0573] In a related embodiment, 98P4B6 status is determined at the
protein level rather than at the nucleic acid level. For example,
such a method comprises determining the level of 98P4B6 protein
expressed by cells in a test tissue sample and comparing the level
so determined to the level of 98P4B6 expressed in a corresponding
normal sample. In one embodiment, the presence of 98P4B6 protein is
evaluated, for example, using immunohistochemical methods. 98P4B6
antibodies or binding partners capable of detecting 98P4B6 protein
expression are used in a variety of assay formats well known in the
art for this purpose.
[0574] In a further embodiment, one can evaluate the status of
98P4B6 nucleotide and amino acid sequences in a biological sample
in order to identify perturbations in the structure of these
molecules. These perturbations can include insertions, deletions,
substitutions and the like. Such evaluations are useful because
perturbations in the nucleotide and amino acid sequences are
observed in a large number of proteins associated with a growth
dysregulated phenotype (see, e.g., Marrogi et al., 1999, J. Cutan.
Pathol. 26(8):369-378). For example, a mutation in the sequence of
98P4B6 may be indicative of the presence or promotion of a tumor.
Such assays therefore have diagnostic and predictive value where a
mutation in 98P4B6 indicates a potential loss of function or
increase in tumor growth.
[0575] A wide variety of assays for observing perturbations in
nucleotide and amino acid sequences are well known in the art. For
example, the size and structure of nucleic acid or amino acid
sequences of 98P4B6 gene products are observed by the Northern,
Southern, Western, PCR and DNA sequencing protocols discussed
herein. In addition, other methods for observing perturbations in
nucleotide and amino acid sequences such as single strand
conformation polymorphism analysis are well known in the art (see,
e.g., U.S. Pat. No. 5,382,510 issued 7 Sep. 1999, and U.S. Pat. No.
5,952,170 issued 17 Jan. 1995).
[0576] Additionally, one can examine the methylation status of a
98P4B6 gene in a biological sample. Aberrant demethylation and/or
hypermethylation of CpG islands in gene 5' regulatory regions
frequently occurs in immortalized and transformed cells, and can
result in altered expression of various genes. For example,
promoter hypermethylation of the pi-class glutathione S-transferase
(a protein expressed in normal prostate but not expressed in
>90% of prostate carcinomas) appears to permanently silence
transcription of this gene and is the most frequently detected
genomic alteration in prostate carcinomas (De Marzo et al., Am. J.
Pathol. 155(6): 1985-1992 (1999)). In addition, this alteration is
present in at least 70% of cases of high-grade prostatic
intraepithelial neoplasia (PIN) (Brooks et al., Cancer Epidemiol.
Biomarkers Prev., 1998, 7:531-536). In another example, expression
of the LAGE-I tumor specific gene (which is not expressed in normal
prostate but is expressed in 25-50% of prostate cancers) is induced
by deoxy-azacytidine in lymphoblastoid cells, suggesting that
tumoral expression is due to demethylation (Lethe et al., Int. J.
Cancer 76(6): 903-908 (1998)). A variety of assays for examining
methylation status of a gene are well known in the art. For
example, one can utilize, in Southern hybridization approaches,
methylation-sensitive restriction enzymes that cannot cleave
sequences that contain methylated CpG sites to assess the
methylation status of CpG islands. In addition, MSP (methylation
specific PCR) can rapidly profile the methylation status of all the
CpG sites present in a CpG island of a given gene. This procedure
involves initial modification of DNA by sodium bisulfite (which
will convert all unmethylated cytosines to uracil) followed by
amplification using primers specific for methylated versus
unmethylated DNA. Protocols involving methylation interference can
also be found for example in Current Protocols In Molecular
Biology, Unit 12, Frederick M. Ausubel et al. eds., 1995.
[0577] Gene amplification is an additional method for assessing the
status of 98P4B6. Gene amplification is measured in a sample
directly, for example, by conventional Southern blotting or
Northern blotting to quantitate the transcription of mRNA (Thomas,
1980, Proc. Natl. Acad. Sci. USA, 77:5201-5205), dot blotting (DNA
analysis), or in situ hybridization, using an appropriately labeled
probe, based on the sequences provided herein. Alternatively,
antibodies are employed that recognize specific duplexes, including
DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or
DNA-protein duplexes. The antibodies in turn are labeled and the
assay carried out where the duplex is bound to a surface, so that
upon the formation of duplex on the surface, the presence of
antibody bound to the duplex can be detected.
[0578] Biopsied tissue or peripheral blood can be conveniently
assayed for the presence of cancer cells using for example,
Northern, dot blot or RT-PCR analysis to detect 98P4B6 expression.
The presence of RT-PCR amplifiable 98P4B6 mRNA provides an
indication of the presence of cancer. RT-PCR assays are well known
in the art RT-PCR detection assays for tumor cells in peripheral
blood are currently being evaluated for use in the diagnosis and
management of a number of human solid tumors. In the prostate
cancer field, these include RT-PCR assays for the detection of
cells expressing PSA and PSM (Verkaik et al., 1997, Urol. Res.
25:373-384; Ghossein et al., 1995, J. Clin. Oncol. 13:1195-2000;
Heston et al., 1995, Clin. Chem. 41:1687-1688).
[0579] A further aspect of the invention is an assessment of the
susceptibility that an individual has for developing cancer. In one
embodiment, a method for predicting susceptibility to cancer
comprises detecting 98P4B6 mRNA or 98P4B6 protein in a tissue
sample, its presence indicating susceptibility to cancer, wherein
the degree of 98P4B6 mRNA expression correlates to the degree of
susceptibility. In a specific embodiment, the presence of 98P4B6 in
prostate or other tissue is examined, with the presence of 98P4B6
in the sample providing an indication of prostate cancer
susceptibility (or the emergence or existence of a prostate tumor).
Similarly, one can evaluate the integrity 98P4B6 nucleotide and
amino acid sequences in a biological sample, in order to identify
perturbations in the structure of these molecules such as
insertions, deletions, substitutions and the like. The presence of
one or more perturbations in 98P4B6 gene products in the sample is
an indication of cancer susceptibility (or the emergence or
existence of a tumor).
[0580] The invention also comprises methods for gauging tumor
aggressiveness. In one embodiment, a method for gauging
aggressiveness of a tumor comprises determining the level of 98P4B6
mRNA or 98P4B6 protein expressed by tumor cells, comparing the
level so determined to the level of 98P4B6 mRNA or 98P4B6 protein
expressed in a corresponding normal tissue taken from the same
individual or a normal tissue reference sample, wherein the degree
of 98P4B6 mRNA or 98P4B6 protein expression in the tumor sample
relative to the normal sample indicates the degree of
aggressiveness. In a specific embodiment, aggressiveness of a tumor
is evaluated by determining the extent to which 98P4B6 is expressed
in the tumor cells, with higher expression levels indicating more
aggressive tumors. Another embodiment is the evaluation of the
integrity of 98P4B6 nucleotide and amino acid sequences in a
biological sample, in order to identify perturbations in the
structure of these molecules such as insertions, deletions,
substitutions and the like. The presence of one or more
perturbations indicates more aggressive tumors.
[0581] Another embodiment of the invention is directed to methods
for observing the progression of a malignancy in an individual over
time. In one embodiment, methods for observing the progression of a
malignancy in an individual over time comprise determining the
level of 98P4B6 mRNA or 98P4B6 protein expressed by cells in a
sample of the tumor, comparing the level so determined to the level
of 98P4B6 mRNA or 98P4B6 protein expressed in an equivalent tissue
sample taken from the same individual at a different time, wherein
the degree of 98P4B6 mRNA or 98P4B6 protein expression in the tumor
sample over time provides information on the progression of the
cancer. In a specific embodiment, the progression of a cancer is
evaluated by determining 98P4B6 expression in the tumor cells over
time, where increased expression over time indicates a progression
of the cancer. Also, one can evaluate the integrity 98P4B6
nucleotide and amino acid sequences in a biological sample in order
to identify perturbations in the structure of these molecules such
as insertions, deletions, substitutions and the like, where the
presence of one or more perturbations indicates a progression of
the cancer.
[0582] The above diagnostic approaches can be combined with any one
of a wide variety of prognostic and diagnostic protocols known in
the art. For example, another embodiment of the invention is
directed to methods for observing a coincidence between the
expression of 98P4B6 gene and 98P4B6 gene products (or
perturbations in 98P4B6 gene and 98P4B6 gene products) and a factor
that is associated with malignancy, as a means for diagnosing and
prognosticating the status of a tissue sample. A wide variety of
factors associated with malignancy can be utilized, such as the
expression of genes associated with malignancy (e.g. PSA, PSCA and
PSM expression for prostate cancer etc.) as well as gross
cytological observations (see, e.g., Bocking et al., 1984, Anal.
Quant. Cytol. 6(2):74-88; Epstein, 1995, Hum. Pathol. 26(2):223-9;
Thorson et al., 1998, Mod. Pathol. 11(6):543-51; Baisden et al.,
1999, Am. J. Surg. Pathol. 23(8):918-24). Methods for observing a
coincidence between the expression of 98P4B6 gene and 98P4B6 gene
products (or perturbations in 98P4B6 gene and 98P4B6 gene products)
and another factor that is associated with malignancy are useful,
for example, because the presence of a set of specific factors that
coincide with disease provides information crucial for diagnosing
and prognosticating the status of a tissue sample.
[0583] In one embodiment, methods for observing a coincidence
between the expression of 98P4B6 gene and 98P4B6 gene products (or
perturbations in 98P4B6 gene and 98P4B6 gene products) and another
factor associated with malignancy entails detecting the
overexpression of 98P4B6 mRNA or protein in a tissue sample,
detecting the overexpression of PSA mRNA or protein in a tissue
sample (or PSCA or PSM expression), and observing a coincidence of
98P4B6 mRNA or protein and PSA mRNA or protein overexpression (or
PSCA or PSM expression). In a specific embodiment, the expression
of 98P4B6 and PSA mRNA in prostate tissue is examined, where the
coincidence of 98P4B6 and PSA mRNA overexpression in the sample
indicates the existence of prostate cancer, prostate cancer
susceptibility or the emergence or status of a prostate tumor.
[0584] Methods for detecting and quantifying the expression of
98P4B6 mRNA or protein are described herein, and standard nucleic
acid and protein detection and quantification technologies are well
known in the art. Standard methods for the detection and
quantification of 98P4B6 mRNA include in situ hybridization using
labeled 98P4B6 riboprobes, Northern blot and related techniques
using 98P4B6 polynucleotide probes, RT-PCR analysis using primers
specific for 98P4B6, and other amplification type detection
methods, such as, for example, branched DNA, SISBA, TMA and the
like. In a specific embodiment, semi-quantitative RT-PCR is used to
detect and quantify 98P4B6 mRNA expression. Any number of primers
capable of amplifying 98P4B6 can be used for this purpose,
including but not limited to the various primer sets specifically
described herein. In a specific embodiment, polyclonal or
monoclonal antibodies specifically reactive with the wild-type
98P4B6 protein can be used in an immunohistochemical assay of
biopsied tissue.
[0585] IX.) Identification of Molecules that Interact with
98P4B6
[0586] The 98P4B6 protein and nucleic acid sequences disclosed
herein allow a skilled artisan to identify proteins, small
molecules and other agents that interact with 98P4B6, as well as
pathways activated by 98P4B6 via any one of a variety of art
accepted protocols. For example, one can utilize one of the
so-called interaction trap systems (also referred to as the
"two-hybrid assay"). In such systems, molecules interact and
reconstitute a transcription factor which directs expression of a
reporter gene, whereupon the expression of the reporter gene is
assayed. Other systems identify protein-protein interactions in
vivo through reconstitution of a eukaryotic transcriptional
activator, see, e.g., U.S. Pat. No. 5,955,280 issued 21 Sep. 1999,
U.S. Pat. No. 5,925,523 issued 20 Jul. 1999, U.S. Pat. No.
5,846,722 issued 8 Dec. 1998 and U.S. Pat. No. 6,004,746 issued 21
Dec. 1999. Algorithms are also available in the art for
genome-based predictions of protein function (see, e.g., Marcotte,
et al., Nature 402: 4 Nov. 1999, 83-86).
[0587] Alternatively one can screen peptide libraries to identify
molecules that interact with 98P4B6 protein sequences. In such
methods, peptides that bind to 98P4B6 are identified by screening
libraries that encode a random or controlled collection of amino
acids. Peptides encoded by the libraries are expressed as fusion
proteins of bacteriophage coat proteins, the bacteriophage
particles are then screened against the 98P4B6 protein(s).
[0588] Accordingly, peptides having a wide variety of uses, such as
therapeutic, prognostic or diagnostic reagents, are thus identified
without any prior information on the structure of the expected
ligand or receptor molecule. Typical peptide libraries and
screening methods that can be used to identify molecules that
interact with 98P4B6 protein sequences are disclosed for example in
U.S. Pat. No. 5,723,286 issued 3 Mar. 1998 and U.S. Pat. No.
5,733,731 issued 31 Mar. 1998.
[0589] Alternatively, cell lines that express 98P4B6 are used to
identify protein-protein interactions mediated by 98P4B6. Such
interactions can be examined using immunoprecipitation techniques
(see, e.g., Hamilton B. J., et al. Biochem. Biophys. Res. Commun.
1999, 261:646-51). 98P4B6 protein can be immunoprecipitated from
98P4B6-expressing cell lines using anti-98P4B6 antibodies.
Alternatively, antibodies against His-tag can be used in a cell
line engineered to express fusions of 98P4B6 and a His-tag (vectors
mentioned above). The immunoprecipitated complex can be examined
for protein association by procedures such as Western blotting,
.sup.35S-methionine labeling of proteins, protein microsequencing,
silver staining and two-dimensional gel electrophoresis.
[0590] Small molecules and ligands that interact with 98P4B6 can be
identified through related embodiments of such screening assays.
For example, small molecules can be identified that interfere with
protein function, including molecules that interfere with 98P4B6's
ability to mediate phosphorylation and de-phosphorylation,
interaction with DNA or RNA molecules as an indication of
regulation of cell cycles, second messenger signaling or
tumorigenesis. Similarly, small molecules that modulate
98P4B6-related ion channel, protein pump, or cell communication
functions are identified and used to treat patients that have a
cancer that expresses 98P4B6 (see, e.g., Hille, B., Ionic Channels
of Excitable Membranes 2.sup.nd Ed., Sinauer Assoc., Sunderland,
Mass., 1992). Moreover, ligands that regulate 98P4B6 function can
be identified based on their ability to bind 98P4B6 and activate a
reporter construct. Typical methods are discussed for example in
U.S. Pat. No. 5,928,868 issued 27 Jul. 1999, and include methods
for forming hybrid ligands in which at least one ligand is a small
molecule. In an illustrative embodiment, cells engineered to
express a fusion protein of 98P4B6 and a DNA-binding protein are
used to co-express a fusion protein of a hybrid ligand/small
molecule and a cDNA library transcriptional activator protein. The
cells further contain a reporter gene, the expression of which is
conditioned on the proximity of the first and second fusion
proteins to each other, an event that occurs only if the hybrid
ligand binds to target sites on both hybrid proteins. Those cells
that express the reporter gene are selected and the unknown small
molecule or the unknown ligand is identified. This method provides
a means of identifying modulators, which activate or inhibit
98P4B6.
[0591] An embodiment of this invention comprises a method of
screening for a molecule that interacts with a 98P4B6 amino acid
sequence shown in FIG. 2 or FIG. 3, comprising the steps of
contacting a population of molecules with a 98P4B6 amino acid
sequence, allowing the population of molecules and the 98P4B6 amino
acid sequence to interact under conditions that facilitate an
interaction, determining the presence of a molecule that interacts
with the 98P4B6 amino acid sequence, and then separating molecules
that do not interact with the 98P4B6 amino acid sequence from
molecules that do. In a specific embodiment, the method further
comprises purifying, characterizing and identifying a molecule that
interacts with the 98P4B6 amino acid sequence. The identified
molecule can be used to modulate a function performed by 98P4B6. In
a preferred embodiment, the 98P4B6 amino acid sequence is contacted
with a library of peptides.
[0592] X.) Therapeutic Methods and Compositions
[0593] The identification of 98P4B6 as a protein that is normally
expressed in a restricted set of tissues, but which is also
expressed in prostate and other cancers, opens a number of
therapeutic approaches to the treatment of such cancers. As
contemplated herein, 98P4B6 functions as a transcription factor
involved in activating tumor-promoting genes or repressing genes
that block tumorigenesis.
[0594] Accordingly, therapeutic approaches that inhibit the
activity of a 98P4B6 protein are useful for patients suffering from
a cancer that expresses 98P4B6. These therapeutic approaches
generally fall into two classes. One class comprises various
methods for inhibiting the binding or association of a 98P4B6
protein with its binding partner or with other proteins. Another
class comprises a variety of methods for inhibiting the
transcription of a 98P4B6 gene or translation of 98P4B6 mRNA.
[0595] X.A.) Anti-Cancer Vaccines
[0596] The invention provides cancer vaccines comprising a
98P4B6-related protein or 98P4B6-related nucleic acid. In view of
the expression of 98P4B6, cancer vaccines prevent and/or treat
98P4B6-expressing cancers with minimal or no effects on non-target
tissues. The use of a tumor antigen in a vaccine that generates
humoral and/or cell-mediated immune responses as anti-cancer
therapy is well known in the art and has been employed in prostate
cancer using human PSMA and rodent PAP immunogens (Hodge et al.,
1995, Int. J. Cancer 63:231-237; Fong et al., 1997, J. Immunol.
159:3113-3117).
[0597] Such methods can be readily practiced by employing a
98P4B6-related protein, or a 98P4B6-encoding nucleic acid molecule
and recombinant vectors capable of expressing and presenting the
98P4B6 immunogen (which typically comprises a number of antibody or
T cell epitopes). Skilled artisans understand that a wide variety
of vaccine systems for delivery of immunoreactive epitopes are
known in the art (see, e.g., Heryln et al., Ann Med 1999 Feb.
31(1):66-78; Maruyama et al., Cancer Immunol Immunother 2000 June
49(3):123-32) Briefly, such methods of generating an immune
response (e.g. humoral and/or cell-mediated) in a mammal, comprise
the steps of: exposing the mammal's immune system to an
immunoreactive epitope (e.g. an epitope present in a 98P4B6 protein
shown in FIG. 3 or analog or homolog thereof) so that the mammal
generates an immune response that is specific for that epitope
(e.g. generates antibodies that specifically recognize that
epitope). In a preferred method, a 98P4B6 immunogen contains a
biological motif, see e.g., Tables VIII-XXI and XXII-XLIX, or a
peptide of a size range from 98P4B6 indicated in FIG. 5, FIG. 6,
FIG. 7, FIG. 8, and FIG. 9.
[0598] The entire 98P4B6 protein, immunogenic regions or epitopes
thereof can be combined and delivered by various means. Such
vaccine compositions can include, for example, lipopeptides
(e.g.,Vitiello, A. et al., J. Clin. Invest. 95:341, 1995), peptide
compositions encapsulated in poly(DL-lactide-co-glycolide) ("PLG")
microspheres (see, e.g., Eldridge, et al., Molec. Immunol.
28:287-294, 1991: Alonso et al., Vaccine 12:299-306, 1994; Jones et
al., Vaccine 13:675-681, 1995), peptide compositions contained in
immune stimulating complexes (ISCOMS) (see, e.g., Takahashi et al.,
Nature 344:873-875, 1990; Hu et al., Clin Exp Immunol. 113:235-243,
1998), multiple antigen peptide systems (MAPs) (see e.g., Tam, J.
P., Proc. Natl. Acad. Sci. U.S.A. 85:5409-5413,1988; Tam, J. P., J.
Immunol Methods 196:17-32,1996), peptides formulated as multivalent
peptides; peptides for use in ballistic delivery systems, typically
crystallized peptides, viral delivery vectors (Perkus, M. E. et
al., In: Concepts in vaccine development, Kaufmann, S. H. E., ed.,
p. 379, 1996; Chakrabarti, S. et al., Nature 320:535, 1986; Hu, S.
L. et al., Nature 320:537, 1986; Kieny, M.-P. et al., AIDS
Bio/Technology 4:790, 1986; Top, F. H. et al., J. Infect. Dis.
124:148, 1971; Chanda, P. K. et al., Virology 175:535, 1990),
particles of viral or synthetic origin (e.g., Kofler, N. et al., J.
Immunol. Methods. 192:25, 1996; Eldridge, J. H. et al., Sem.
Hematol. 30:16, 1993; Falo, L. D., Jr. et al., Nature Med. 7:649,
1995), adjuvants (Warren, H. S., Vogel, F. R., and Chedid, L. A.
Annu. Rev. Immunol. 4:369, 1986; Gupta, R. K. et al., Vaccine
11:293, 1993), liposomes (Reddy, R. et al., J. Immunol. 148:1585,
1992; Rock, K. L., Immunol. Today 17:131, 1996), or, naked or
particle absorbed cDNA (Ulmer, J. B. et al., Science 259:1745,
1993; Robinson, H. L., Hunt, L. A., and Webster, R. G., Vaccine
11:957, 1993; Shiver, J. W. et al., In: Concepts in vaccine
development, Kaufmann, S. H. E., ed., p. 423, 1996; Cease, K. B.,
and Berzofsky, J. A., Annu. Rev. Immunol 12:923, 1994 and Eldridge,
J. H. et al., Sem. Hematol. 30:16, 1993). Toxin-targeted delivery
technologies, also known as receptor mediated targeting, such as
those of Avant Immunotherapeutics, Inc. (Needham, Mass.) may also
be used.
[0599] In patients with 98P4B6-associated cancer, the vaccine
compositions of the invention can also be used in conjunction with
other treatments used for cancer, e.g., surgery, chemotherapy, drug
therapies, radiation therapies, etc. including use in combination
with immune adjuvants such as IL-2, IL-12, GM-CSF, and the
like.
[0600] Cellular Vaccines:
[0601] CTL epitopes can be determined using specific algorithms to
identify peptides within 98P4B6 protein that bind corresponding HLA
alleles (see e.g., Table IV; Epimer.TM. and Epimatrix.TM., Brown
University (URL
brown.edu/Research/TB-HIV_Lab/epimatrix/epimatrix.html); and,
BIMAS, (URL bimas.dcrt.nih.gov/; SYFPEITHI at URL
syfpeithi.bmi-heidelberg.com/). In a preferred embodiment, a 98P4B6
immunogen contains one or more amino acid sequences identified
using techniques well known in the art, such as the sequences shown
in Tables VIII-XXI and XXII-XLIX or a peptide of 8, 9, 10 or 11
amino acids specified by an HLA Class I motif/supermotif (e.g.,
Table IV (A), Table IV (D), or Table IV (E)) and/or a peptide of at
least 9 amino acids that comprises an HLA Class II motif/supermotif
(e.g., Table IV (B) or Table IV (C)). As is appreciated in the art,
the HLA Class I binding groove is essentially closed ended so that
peptides of only a particular size range can fit into the groove
and be bound, generally HLA Class I epitopes are 8, 9, 10, or 11
amino acids long. In contrast, the HLA Class II binding groove is
essentially open ended; therefore a peptide of about 9 or more
amino acids can be bound by an HLA Class II molecule. Due to the
binding groove differences between HLA Class I and II, HLA Class I
motifs are length specific, i.e., position two of a Class I motif
is the second amino acid in an amino to carboxyl direction of the
peptide. The amino acid positions in a Class II motif are relative
only to each other, not the overall peptide, i.e., additional amino
acids can be attached to the amino and/or carboxyl termini of a
motif-bearing sequence. HLA Class II epitopes are often 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 amino
acids long, or longer than 25 amino acids.
[0602] Antibody-Based Vaccines
[0603] A wide variety of methods for generating an immune response
in a mammal are known in the art (for example as the first step in
the generation of hybridomas). Methods of generating an immune
response in a mammal comprise exposing the mammal's immune system
to an immunogenic epitope on a protein (e.g. a 98P4B6 protein) so
that an immune response is generated. A typical embodiment consists
of a method for generating an immune response to 98P4B6 in a host,
by contacting the host with a sufficient amount of at least one
98P4B6 B cell or cytotoxic T-cell epitope or analog thereof; and at
least one periodic interval thereafter re-contacting the host with
the 98P4B6 B cell or cytotoxic T-cell epitope or analog thereof. A
specific embodiment consists of a method of generating an immune
response against a 98P4B6-related protein or a man-made
multiepitopic peptide comprising: administering 98P4B6 immunogen
(e.g. a 98P4B6 protein or a peptide fragment thereof, a 98P4B6
fusion protein or analog etc.) in a vaccine preparation to a human
or another mammal. Typically, such vaccine preparations further
contain a suitable adjuvant (see, e.g., U.S. Pat. No. 6,146,635) or
a universal helper epitope such as a PADRE.TM. peptide (Epimmune
Inc., San Diego, Calif.; see, e.g., Alexander et al., J. Immunol.
2000 164(3); 164(3): 1625-1633; Alexander et al., Immunity 1994
1(9): 751-761 and Alexander et al., Immunol. Res. 1998 18(2):
79-92). An alternative method comprises generating an immune
response in an individual against a 98P4B6 immunogen by:
administering in vivo to muscle or skin of the individual's body a
DNA molecule that comprises a DNA sequence that encodes a 98P4B6
immunogen, the DNA sequence operatively linked to regulatory
sequences which control the expression of the DNA sequence; wherein
the DNA molecule is taken up by cells, the DNA sequence is
expressed in the cells and an immune response is generated against
the immunogen (see, e.g., U.S. Pat. No. 5,962,428). Optionally a
genetic vaccine facilitator such as anionic lipids; saponins;
lectins; estrogenic compounds; hydroxylated lower alkyls; dimethyl
sulfoxide; and urea is also administered. In addition, an
antiidiotypic antibody can be administered that mimics 98P4B6, in
order to generate a response to the target antigen.
[0604] Nucleic Acid Vaccines:
[0605] Vaccine compositions of the invention include nucleic
acid-mediated modalities. DNA or RNA that encode protein(s) of the
invention can be administered to a patient. Genetic immunization
methods can be employed to generate prophylactic or therapeutic
humoral and cellular immune responses directed against cancer cells
expressing 98P4B6. Constructs comprising DNA encoding a
98P4B6-related protein/immunogen and appropriate regulatory
sequences can be injected directly into muscle or skin of an
individual, such that the cells of the muscle or skin take-up the
construct and express the encoded 98P4B6 protein/immunogen.
Alternatively, a vaccine comprises a 98P4B6-related protein.
Expression of the 98P4B6-related protein immunogen results in the
generation of prophylactic or therapeutic humoral and cellular
immunity against cells that bear a 98P4B6 protein. Various
prophylactic and therapeutic genetic immunization techniques known
in the art can be used (for review, see information and references
published at Internet address genweb.com). Nucleic acid-based
delivery is described, for instance, in Wolff et. al, Science
247:1465 (1990) as well as U.S. Pat. Nos. 5,580,859; 5,589,466;
5,804,566; 5,739,118; 5,736,524; 5,679,647; WO 98/04720. Examples
of DNA-based delivery technologies include "naked DNA", facilitated
(bupivicaine, polymers, peptide-mediated) delivery, cationic lipid
complexes, and particle-mediated ("gene gun") or pressure-mediated
delivery (see, e.g., U.S. Pat. No. 5,922,687).
[0606] For therapeutic or prophylactic immunization purposes,
proteins of the invention can be expressed via viral or bacterial
vectors. Various viral gene delivery systems that can be used in
the practice of the invention include, but are not limited to,
vaccinia, fowlpox, canarypox, adenovirus, influenza, poliovirus,
adeno-associated virus, lentivirus, and sindbis virus (see, e.g.,
Restifo, 1996, Curr. Opin. Immunol. 8:658-663; Tsang et al. J. Nat.
Cancer Inst. 87:982-990 (1995)). Non-viral delivery systems can
also be employed by introducing naked DNA encoding a 98P4B6-related
protein into the patient (e.g., intramuscularly or intradermally)
to induce an anti-tumor response.
[0607] Vaccinia virus is used, for example, as a vector to express
nucleotide sequences that encode the peptides of the invention.
Upon introduction into a host, the recombinant vaccinia virus
expresses the protein immunogenic peptide, and thereby elicits a
host immune response. Vaccinia vectors and methods useful in
immunization protocols are described in, e.g., U.S. Pat. No.
4,722,848. Another vector is BCG (Bacille Calmette Guerin). BCG
vectors are described in Stover et al., Nature 351:456-460 (1991).
A wide variety of other vectors useful for therapeutic
administration or immunization of the peptides of the invention,
e.g. adeno and adeno-associated virus vectors, retroviral vectors,
Salmonella typhi vectors, detoxified anthrax toxin vectors, and the
like, will be apparent to those skilled in the art from the
description herein.
[0608] Thus, gene delivery systems are used to deliver a
98P4B6-related nucleic acid molecule. In one embodiment, the
full-length human 98P4B6 cDNA is employed. In another embodiment,
98P4B6 nucleic acid molecules encoding specific cytotoxic T
lymphocyte (CTL) and/or antibody epitopes are employed.
[0609] Ex Vivo Vaccines
[0610] Various ex vivo strategies can also be employed to generate
an immune response. One approach involves the use of antigen
presenting cells (APCs) such as dendritic cells (DC) to present
98P4B6 antigen to a patient's immune system. Dendritic cells
express MHC class I and II molecules, B7 co-stimulator, and IL-12,
and are thus highly specialized antigen presenting cells. In
prostate cancer, autologous dendritic cells pulsed with peptides of
the prostate-specific membrane antigen (PSMA) are being used in a
Phase I clinical trial to stimulate prostate cancer patients'
immune systems (Tjoa et al., 1996, Prostate 28:65-69; Murphy et
al., 1996, Prostate 29:371-380). Thus, dendritic cells can be used
to present 98P4B6 peptides to T cells in the context of MHC class I
or II molecules. In one embodiment, autologous dendritic cells are
pulsed with 98P4B6 peptides capable of binding to MHC class I
and/or class II molecules. In another embodiment, dendritic cells
are pulsed with the complete 98P4B6 protein. Yet another embodiment
involves engineering the overexpression of a 98P4B6 gene in
dendritic cells using various implementing vectors known in the
art, such as adenovirus (Arthur et al., 1997, Cancer Gene Ther.
4:17-25), retrovirus (Henderson et al., 1996, Cancer Res.
56:3763-3770), lentivirus, adeno-associated virus, DNA transfection
(Ribas et al., 1997, Cancer Res. 57:2865-2869), or tumor-derived
RNA transfection (Ashley et al., 1997, J. Exp. Med. 186:1177-1182).
Cells that express 98P4B6 can also be engineered to express immune
modulators, such as GM-CSF, and used as immunizing agents.
[0611] X.B.) 98P4B6 as a Target for Antibody-Based Therapy
[0612] 98P4B6 is an attractive target for antibody-based
therapeutic strategies. A number of antibody strategies are known
in the art for targeting both extracellular and intracellular
molecules (see, e.g., complement and ADCC mediated killing as well
as the use of intrabodies). Because 98P4B6 is expressed by cancer
cells of various lineages relative to corresponding normal cells,
systemic administration of 98P4B6-immunoreactive compositions are
prepared that exhibit excellent sensitivity without toxic,
non-specific and/or non-target effects caused by binding of the
immunoreactive composition to non-target organs and tissues.
Antibodies specifically reactive with domains of 98P4B6 are useful
to treat 98P4B6-expressing cancers systemically, either as
conjugates with a toxin or therapeutic agent, or as naked
antibodies capable of inhibiting cell proliferation or
function.
[0613] 98P4B6 antibodies can be introduced into a patient such that
the antibody binds to 98P4B6 and modulates a function, such as an
interaction with a binding partner, and consequently mediates
destruction of the tumor cells and/or inhibits the growth of the
tumor cells. Mechanisms by which such antibodies exert a
therapeutic effect can include complement-mediated cytolysis,
antibody-dependent cellular cytotoxicity, modulation of the
physiological function of 98P4B6, inhibition of ligand binding or
signal transduction pathways, modulation of tumor cell
differentiation, alteration of tumor angiogenesis factor profiles,
and/or apoptosis.
[0614] Those skilled in the art understand that antibodies can be
used to specifically target and bind immunogenic molecules such as
an immunogenic region of a 98P4B6 sequence shown in FIG. 2 or FIG.
3. In addition, skilled artisans understand that it is routine to
conjugate antibodies to cytotoxic agents (see, e.g., Slevers et al.
Blood 93:11 3678-3684 (Jun. 1, 1999)). When cytotoxic and/or
therapeutic agents are delivered directly to cells, such as by
conjugating them to antibodies specific for a molecule expressed by
that cell (e.g. 98P4B6), the cytotoxic agent will exert its known
biological effect (i.e. cytotoxicity) on those cells.
[0615] A wide variety of compositions and methods for using
antibody-cytotoxic agent conjugates to kill cells are known in the
art. In the context of cancers, typical methods entail
administering to an animal having a tumor a biologically effective
amount of a conjugate comprising a selected cytotoxic and/or
therapeutic agent linked to a targeting agent (e.g. an anti-98P4B6
antibody) that binds to a marker (e.g. 98P4B6) expressed,
accessible to binding or localized on the cell surfaces. A typical
embodiment is a method of delivering a cytotoxic and/or therapeutic
agent to a cell expressing 98P4B6, comprising conjugating the
cytotoxic agent to an antibody that immunospecifically binds to a
98P4B6 epitope, and, exposing the cell to the antibody-agent
conjugate. Another illustrative embodiment is a method of treating
an individual suspected of suffering from metastasized cancer,
comprising a step of administering parenterally to said individual
a pharmaceutical composition comprising a therapeutically effective
amount of an antibody conjugated to a cytotoxic and/or therapeutic
agent.
[0616] Cancer immunotherapy using anti-98P4B6 antibodies can be
done in accordance with various approaches that have been
successfully employed in the treatment of other types of cancer,
including but not limited to colon cancer (Arlen et al., 1998,
Crit. Rev. Immunol. 18:133-138), multiple myeloma (Ozaki et al.,
1997, Blood 90:3179-3186, Tsunenari et al., 1997, Blood
90:2437-2444), gastric cancer (Kasprzyk et al., 1992, Cancer Res.
52:2771-2776), B-cell lymphoma (Funakoshi et al., 1996, J.
Immunother. Emphasis Tumor Immunol. 19:93-101), leukemia (Zhong et
al., 1996, Leuk. Res. 20:581-589), colorectal cancer (Moun et al.,
1994, Cancer Res. 54:6160-6166; Velders et al., 1995, Cancer Res.
55:4398-4403), and breast cancer (Shepard et al., 1991, J. Clin.
Immunol. 11:117-127). Some therapeutic approaches involve
conjugation of naked antibody to a toxin or radioisotope, such as
the conjugation of Y.sup.91 or I.sup.131 to anti-CD20 antibodies
(e.g., Zevalin.TM., IDEC Pharmaceuticals Corp. or Bexxar.TM.,
Coulter Pharmaceuticals), while others involve co-administration of
antibodies and other therapeutic agents, such as Herceptin.TM.
(trastuzumab) with paclitaxel (Genentech, Inc.). The antibodies can
be conjugated to a therapeutic agent. To treat prostate cancer, for
example, 98P4B6 antibodies can be administered in conjunction with
radiation, chemotherapy or hormone ablation. Also, antibodies can
be conjugated to a toxin such as calicheamicin (e.g., Mylotarg.TM.,
Wyeth-Ayerst, Madison, N.J., a recombinant humanized IgG.sub.4
kappa antibody conjugated to antitumor antibiotic calicheamicin) or
a maytansinoid (e.g., taxane-based Tumor-Activated Prodrug, TAP,
platform, ImmunoGen, Cambridge, Mass., also see e.g., U.S. Pat. No.
5,416,064).
[0617] Although 98P4B6 antibody therapy is useful for all stages of
cancer, antibody therapy can be particularly appropriate in
advanced or metastatic cancers. Treatment with the antibody therapy
of the invention is indicated for patients who have received one or
more rounds of chemotherapy. Alternatively, antibody therapy of the
invention is combined with a chemotherapeutic or radiation regimen
for patients who have not received chemotherapeutic treatment.
Additionally, antibody therapy can enable the use of reduced
dosages of concomitant chemotherapy, particularly for patients who
do not tolerate the toxicity of the chemotherapeutic agent very
well. Fan et al. (Cancer Res. 53:4637-4642, 1993), Prewett et al.
(International J. of Onco. 9:217-224, 1996), and Hancock et al.
(Cancer Res. 51:4575-4580, 1991) describe the use of various
antibodies together with chemotherapeutic agents.
[0618] Although 98P4B6 antibody therapy is useful for all stages of
cancer, antibody therapy can be particularly appropriate in
advanced or metastatic cancers. Treatment with the antibody therapy
of the invention is indicated for patients who have received one or
more rounds of chemotherapy. Alternatively, antibody therapy of the
invention is combined with a chemotherapeutic or radiation regimen
for patients who have not received chemotherapeutic treatment.
Additionally, antibody therapy can enable the use of reduced
dosages of concomitant chemotherapy, particularly for patients who
do not tolerate the toxicity of the chemotherapeutic agent very
well.
[0619] Cancer patients can be evaluated for the presence and level
of 98P4B6 expression, preferably using immunohistochemical
assessments of tumor tissue, quantitative 98P4B6 imaging, or other
techniques that reliably indicate the presence and degree of 98P4B6
expression. Immunohistochemical analysis of tumor biopsies or
surgical specimens is preferred for this purpose. Methods for
immunohistochemical analysis of tumor tissues are well known in the
art.
[0620] Anti-98P4B6 monoclonal antibodies that treat prostate and
other cancers include those that initiate a potent immune response
against the tumor or those that are directly cytotoxic. In this
regard, anti-98P4B6 monoclonal antibodies (mAbs) can elicit tumor
cell lysis by either complement-mediated or antibody-dependent cell
cytotoxicity (ADCC) mechanisms, both of which require an intact Fc
portion of the immunoglobulin molecule for interaction with
effector cell Fc receptor sites on complement proteins. In
addition, anti-98P4B6 mAbs that exert a direct biological effect on
tumor growth are useful to treat cancers that express 98P4B6.
Mechanisms by which directly cytotoxic mAbs act include: inhibition
of cell growth, modulation of cellular differentiation, modulation
of tumor angiogenesis factor profiles, and the induction of
apoptosis. The mechanism(s) by which a particular anti-98P4B6 mAb
exerts an anti-tumor effect is evaluated using any number of in
vitro assays that evaluate cell death such as ADCC, ADMMC,
complement-mediated cell lysis, and so forth, as is generally known
in the art.
[0621] In some patients, the use of murine or other non-human
monoclonal antibodies, or human/mouse chimeric mAbs can induce
moderate to strong immune responses against the non-human antibody.
This can result in clearance of the antibody from circulation and
reduced efficacy. In the most severe cases, such an immune response
can lead to the extensive formation of immune complexes which,
potentially, can cause renal failure. Accordingly, preferred
monoclonal antibodies used in the therapeutic methods of the
invention are those that are either fully human or humanized and
that bind specifically to the target 98P4B6 antigen with high
affinity but exhibit low or no antigenicity in the patient.
[0622] Therapeutic methods of the invention contemplate the
administration of single anti-98P4B6 mAbs as well as combinations,
or cocktails, of different mAbs. Such mAb cocktails can have
certain advantages inasmuch as they contain mAbs that target
different epitopes, exploit different effector mechanisms or
combine directly cytotoxic mAbs with mAbs that rely on immune
effector functionality. Such mAbs in combination can exhibit
synergistic therapeutic effects. In addition, anti-98P4B6 mAbs can
be administered concomitantly with other therapeutic modalities,
including but not limited to various chemotherapeutic agents,
androgen-blockers, immune modulators (e.g., IL-2, GM-CSF), surgery
or radiation. The anti-98P4B6 mAbs are administered in their
"naked" or unconjugated form, or can have a therapeutic agent(s)
conjugated to them.
[0623] Anti-98P4B6 antibody formulations are administered via any
route capable of delivering the antibodies to a tumor cell. Routes
of administration include, but are not limited to, intravenous,
intraperitoneal, intramuscular, intratumor, intradermal, and the
like. Treatment generally involves repeated administration of the
anti-98P4B6 antibody preparation, via an acceptable route of
administration such as intravenous injection (IV), typically at a
dose in the range of about 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8,
0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or 25 mg/kg body
weight. In general, doses in the range of 10-1000 mg mAb per week
are effective and well tolerated.
[0624] Based on clinical experience with the Herceptin.TM. mAb in
the treatment of metastatic breast cancer, an initial loading dose
of approximately 4 mg/kg patient body weight IV, followed by weekly
doses of about 2 mg/kg IV of the anti-98P4B6 mAb preparation
represents an acceptable dosing regimen. Preferably, the initial
loading dose is administered as a 90-minute or longer infusion. The
periodic maintenance dose is administered as a 30 minute or longer
infusion, provided the initial dose was well tolerated. As
appreciated by those of skill in the art, various factors can
influence the ideal dose regimen in a particular case. Such factors
include, for example, the binding affinity and half life of the Ab
or mAbs used, the degree of 98P4B6 expression in the patient, the
extent of circulating shed 98P4B6 antigen, the desired steady-state
antibody concentration level, frequency of treatment, and the
influence of chemotherapeutic or other agents used in combination
with the treatment method of the invention, as well as the health
status of a particular patient.
[0625] Optionally, patients should be evaluated for the levels of
98P4B6 in a given sample (e.g. the levels of circulating 98P4B6
antigen and/or 98P4B6 expressing cells) in order to assist in the
determination of the most effective dosing regimen, etc. Such
evaluations are also used for monitoring purposes throughout
therapy, and are useful to gauge therapeutic success in combination
with the evaluation of other parameters (for example, urine
cytology and/or ImmunoCyt levels in bladder cancer therapy, or by
analogy, serum PSA levels in prostate cancer therapy).
[0626] Anti-idiotypic anti-98P4B6 antibodies can also be used in
anti-cancer therapy as a vaccine for inducing an immune response to
cells expressing a 98P4B6-related protein. In particular, the
generation of anti-idiotypic antibodies is well known in the art;
this methodology can readily be adapted to generate anti-idiotypic
anti-98P4B6 antibodies that mimic an epitope on a 98P4B6-related
protein (see, for example, Wagner et al., 1997, Hybridoma 16:
33-40; Foon et al., 1995, J. Clin. Invest. 96:334-342; Herlyn et
al., 1996, Cancer Immunol. Immunother. 43:65-76). Such an
anti-idiotypic antibody can be used in cancer vaccine
strategies.
[0627] X.C.) 98P4B6 as a Target for Cellular Immune Responses
[0628] Vaccines and methods of preparing vaccines that contain an
immunogenically effective amount of one or more HLA-binding
peptides as described herein are further embodiments of the
invention. Furthermore, vaccines in accordance with the invention
encompass compositions of one or more of the claimed peptides. A
peptide can be present in a vaccine individually. Alternatively,
the peptide can exist as a homopolymer comprising multiple copies
of the same peptide, or as a heteropolymer of various peptides.
Polymers have the advantage of increased immunological reaction
and, where different peptide epitopes are used to make up the
polymer, the additional ability to induce antibodies and/or CTLs
that react with different antigenic determinants of the pathogenic
organism or tumor-related peptide targeted for an immune response.
The composition can be a naturally occurring region of an antigen
or can be prepared, e.g., recombinantly or by chemical
synthesis.
[0629] Carriers that can be used with vaccines of the invention are
well known in the art, and include, e.g., thyroglobulin, albumins
such as human serum albumin, tetanus toxoid, polyamino acids such
as poly L-lysine, poly L-glutamic acid, influenza, hepatitis B
virus core protein, and the like. The vaccines can contain a
physiologically tolerable (i.e., acceptable) diluent such as water,
or saline, preferably phosphate buffered saline. The vaccines also
typically include an adjuvant. Adjuvants such as incomplete
Freund's adjuvant, aluminum phosphate, aluminum hydroxide, or alum
are examples of materials well known in the art. Additionally, as
disclosed herein, CTL responses can be primed by conjugating
peptides of the invention to lipids, such as
tripalmitoyl-S-glycerylcysteinlyseryl-serine (P.sub.3CSS).
Moreover, an adjuvant such as a synthetic
cytosine-phosphorothiolated-guanine-containi- ng (CpG)
oligonucleotides has been found to increase CTL responses 10- to
100-fold. (see, e.g. Davila and Celis, J. Immunol. 165:539-547
(2000)) Upon immunization with a peptide composition in accordance
with the invention, via injection, aerosol, oral, transdermal,
transmucosal, intrapleural, intrathecal, or other suitable routes,
the immune system of the, host responds to the vaccine by producing
large amounts of CTLs and/or HTLs specific for the desired antigen.
Consequently, the host becomes at least partially immune to later
development of cells that express or overexpress 98P4B6 antigen, or
derives at least some therapeutic benefit when the antigen was
tumor-associated.
[0630] In some embodiments, it may be desirable to combine the
class I peptide components with components that induce or
facilitate neutralizing antibody and or helper T cell responses
directed to the target antigen. A preferred embodiment of such a
composition comprises class I and class II epitopes in accordance
with the invention. An alternative embodiment of such a composition
comprises a class I and/or class II epitope in accordance with the
invention, along with a cross reactive HTL epitope such as
PADRE.TM. (Epimmune, San Diego, Calif.) molecule (described e.g.,
in U.S. Pat. No. 5,736,142).
[0631] A vaccine of the invention can also include
antigen-presenting cells (APC), such as dendritic cells (DC), as a
vehicle to present peptides of the invention. Vaccine compositions
can be created in vitro, following dendritic cell mobilization and
harvesting, whereby loading of dendritic cells occurs in vitro. For
example, dendritic cells are transfected, e.g., with a minigene in
accordance with the invention, or are pulsed with peptides. The
dendritic cell can then be administered to a patient to elicit
immune responses in vivo. Vaccine compositions, either DNA- or
peptide-based, can also be administered in vivo in combination with
dendritic cell mobilization whereby loading of dendritic cells
occurs in vivo.
[0632] Preferably, the following principles are utilized when
selecting an array of epitopes for inclusion in a polyepitopic
composition for use in a vaccine, or for selecting discrete
epitopes to be included in a vaccine and/or to be encoded by
nucleic acids such as a minigene. It is preferred that each of the
following principles be balanced in order to make the selection.
The multiple epitopes to be incorporated in a given vaccine
composition may be, but need not be, contiguous in sequence in the
native antigen from which the epitopes are derived.
[0633] 1.) Epitopes are selected which, upon administration, mimic
immune responses that have been observed to be correlated with
tumor clearance. For HLA Class I this includes 3-4 epitopes that
come from at least one tumor associated antigen (TAA). For HLA
Class II a similar rationale is employed; again 3-4 epitopes are
selected from at least one TAA (see, e.g., Rosenberg et al.,
Science 278:1447-1450). Epitopes from one TAA may be used in
combination with epitopes from one or more additional TAAs to
produce a vaccine that targets tumors with varying expression
patterns of frequently-expressed TAAs.
[0634] 2.) Epitopes are selected that have the requisite binding
affinity established to be correlated with immunogenicity: for HLA
Class I an IC.sub.50 of 500 nM or less, often 200 nM or less; and
for Class II an IC.sub.50 of 1000 nM or less.
[0635] 3.) Sufficient supermotif bearing-peptides, or a sufficient
array of allele-specific motif-bearing peptides, are selected to
give broad population coverage. For example, it is preferable to
have at least 80% population coverage. A Monte Carlo analysis, a
statistical evaluation known in the art, can be employed to assess
the breadth, or redundancy of, population coverage.
[0636] 4.) When selecting epitopes from cancer-related antigens it
is often useful to select analogs because the patient may have
developed tolerance to the native epitope.
[0637] 5.) Of particular relevance are epitopes referred to as
"nested epitopes". Nested epitopes occur where at least two
epitopes overlap in a given peptide sequence. A nested peptide
sequence can comprise B cell, HLA class I and/or HLA class II
epitopes. When providing nested epitopes, a general objective is to
provide the greatest number of epitopes per sequence. Thus, an
aspect is to avoid providing a peptide that is any longer than the
amino terminus of the amino terminal epitope and the carboxyl
terminus of the carboxyl terminal epitope in the peptide. When
providing a multi-epitopic sequence, such as a sequence comprising
nested epitopes, it is generally important to screen the sequence
in order to insure that it does not have pathological or other
deleterious biological properties.
[0638] 6.) If a polyepitopic protein is created, or when creating a
minigene, an objective is to generate the smallest peptide that
encompasses the epitopes of interest. This principle is similar, if
not the same as that employed when selecting a peptide comprising
nested epitopes. However, with an artificial polyepitopic peptide,
the size minimization objective is balanced against the need to
integrate any spacer sequences between epitopes in the polyepitopic
protein. Spacer amino acid residues can, for example, be introduced
to avoid junctional epitopes (an epitope recognized by the immune
system, not present in the target antigen, and only created by the
man-made juxtaposition of epitopes), or to facilitate cleavage
between epitopes and thereby enhance epitope presentation.
Junctional epitopes are generally to be avoided because the
recipient may generate an immune response to that non-native
epitope. Of particular concern is a junctional epitope that is a
"dominant epitope." A dominant epitope may lead to such a zealous
response that immune responses to other epitopes are diminished or
suppressed.
[0639] 7.) Where the sequences of multiple variants of the same
target protein are present, potential peptide epitopes can also be
selected on the basis of their conservancy. For example, a
criterion for conservancy may define that the entire sequence of an
HLA class I binding peptide or the entire 9-mer core of a class II
binding peptide be conserved in a designated percentage of the
sequences evaluated for a specific protein antigen.
[0640] X.C.1. Minigene Vaccines
[0641] A number of different approaches are available which allow
simultaneous delivery of multiple epitopes. Nucleic acids encoding
the peptides of the invention are a particularly useful embodiment
of the invention. Epitopes for inclusion in a minigene are
preferably selected according to the guidelines set forth in the
previous section. A preferred means of administering nucleic acids
encoding the peptides of the invention uses minigene constructs
encoding a peptide comprising one or multiple epitopes of the
invention.
[0642] The use of multi-epitope minigenes is described below and
in, Ishioka et al., J. Immunol. 162:3915-3925, 1999; An, L. and
Whitton, J. L., J. Virol. 71:2292, 1997; Thomson, S. A. et al., J.
Immunol. 157:822, 1996; Whitton, J. L. et al., J. Virol. 67:348,
1993; Hanke, R. et al., Vaccine 16:426, 1998. For example, a
multi-epitope DNA plasmid encoding supermotif- and/or motif-bearing
epitopes derived 98P4B6, the PADRE.RTM. universal helper T cell
epitope or multiple HTL epitopes from 98P4B6 (see e.g., Tables
VIII-XXI and XXII to XLIX), and an endoplasmic
reticulum-translocating signal sequence can be engineered. A
vaccine may also comprise epitopes that are derived from other
TAAs.
[0643] The immunogenicity of a multi-epitopic minigene can be
confirmed in transgenic mice to evaluate the magnitude of CTL
induction responses against the epitopes tested. Further, the
immunogenicity of DNA-encoded epitopes in vivo can be correlated
with the in vitro responses of specific CTL lines against target
cells transfected with the DNA plasmid. Thus, these experiments can
show that the minigene serves to both: 1.) generate a CTL response
and 2.) that the induced CTLs recognized cells expressing the
encoded epitopes.
[0644] For example, to create a DNA sequence encoding the selected
epitopes (minigene) for expression in human cells, the amino acid
sequences of the epitopes may be reverse translated. A human codon
usage table can be used to guide the codon choice for each amino
acid. These epitope-encoding DNA sequences may be directly
adjoined, so that when translated, a continuous polypeptide
sequence is created. To optimize expression and/or immunogenicity,
additional elements can be incorporated into the minigene design.
Examples of amino acid sequences that can be reverse translated and
included in the minigene sequence include: HLA class I epitopes,
HLA class II epitopes, antibody epitopes, a ubiquitination signal
sequence, and/or an endoplasmic reticulum targeting signal. In
addition, HLA presentation of CTL and HTL epitopes may be improved
by including synthetic (e.g. poly-alanine) or naturally-occurring
flanking sequences adjacent to the CTL or HTL epitopes; these
larger peptides comprising the epitope(s) are within the scope of
the invention.
[0645] The minigene sequence may be converted to DNA by assembling
oligonucleotides that encode the plus and minus strands of the
minigene. Overlapping oligonucleotides (30-100 bases long) may be
synthesized, phosphorylated, purified and annealed under
appropriate conditions using well known techniques. The ends of the
oligonucleotides can be joined, for example, using T4 DNA ligase.
This synthetic minigene, encoding the epitope polypeptide, can then
be cloned into a desired expression vector.
[0646] Standard regulatory sequences well known to those of skill
in the art are preferably included in the vector to ensure
expression in the target cells. Several vector elements are
desirable: a promoter with a down-stream cloning site for minigene
insertion; a polyadenylation signal for efficient transcription
termination; an E. coli origin of replication; and an E. coli
selectable marker (e.g. ampicillin or kanamycin resistance).
Numerous promoters can be used for this purpose, e.g., the human
cytomegalovirus (hCMV) promoter. See, e.g., U.S. Pat. Nos.
5,580,859 and 5,589,466 for other suitable promoter sequences.
[0647] Additional vector modifications may be desired to optimize
minigene expression and immunogenicity. In some cases, introns are
required for efficient gene expression, and one or more synthetic
or naturally-occurring introns could be incorporated into the
transcribed region of the minigene. The inclusion of mRNA
stabilization sequences and sequences for replication in mammalian
cells may also be considered for increasing minigene
expression.
[0648] Once an expression vector is selected, the minigene is
cloned into the polylinker region downstream of the promoter. This
plasmid is transformed into an appropriate E. coli strain, and DNA
is prepared using standard techniques. The orientation and DNA
sequence of the minigene, as well as all other elements included in
the vector, are confirmed using restriction mapping and DNA
sequence analysis. Bacterial cells harboring the correct plasmid
can be stored as a master cell bank and a working cell bank.
[0649] In addition, immunostimulatory sequences (ISSs or CpGs)
appear to play a role in the immunogenicity of DNA vaccines. These
sequences may be included in the vector, outside the minigene
coding sequence, if desired to enhance immunogenicity.
[0650] In some embodiments, a bi-cistronic expression vector which
allows production of both the minigene-encoded epitopes and a
second protein (included to enhance or decrease immunogenicity) can
be used. Examples of proteins or polypeptides that could
beneficially enhance the immune response if co-expressed include
cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules
(e.g., LeIF), costimulatory molecules, or for HTL responses, pan-DR
binding proteins (PADRE.TM., Epimmune, San Diego, Calif.). Helper
(HTL) epitopes can be joined to intracellular targeting signals and
expressed separately from expressed CTL epitopes; this allows
direction of the HTL epitopes to a cell compartment different than
that of the CTL epitopes. If required, this could facilitate more
efficient entry of HTL epitopes into the HLA class II pathway,
thereby improving HTL induction. In contrast to HTL or CTL
induction, specifically decreasing the immune response by
co-expression of immunosuppressive molecules (e.g. TGF-.beta.) may
be beneficial in certain diseases.
[0651] Therapeutic quantities of plasmid DNA can be produced for
example, by fermentation in E. coli, followed by purification.
Aliquots from the working cell bank are used to inoculate growth
medium, and grown to saturation in shaker flasks or a bioreactor
according to well-known techniques. Plasmid DNA can be purified
using standard bioseparation technologies such as solid phase
anion-exchange resins supplied by QIAGEN, Inc. (Valencia, Calif. If
required, supercoiled DNA can be isolated from the open circular
and linear forms using gel electrophoresis or other methods.
[0652] Purified plasmid DNA can be prepared for injection using a
variety of formulations. The simplest of these is reconstitution of
lyophilized DNA in sterile phosphate-buffer saline (PBS). This
approach, known as "naked DNA," is currently being used for
intramuscular (IM) administration in clinical trials. To maximize
the immunotherapeutic effects of minigene DNA vaccines, an
alternative method for formulating purified plasmid DNA may be
desirable. A variety of methods have been described, and new
techniques may become available. Cationic lipids, glycolipids, and
fusogenic liposomes can also be used in the formulation (see, e.g.,
as described by WO 93/24640; Mannino & Gould-Fogerite, Bio
Techniques 6(7): 682 (1988); U.S. Pat. No. 5,279,833; WO 91/06309;
and Felgner, et al., Proc. Nat'l Acad. Sci. USA 84:7413 (1987). In
addition, peptides and compounds referred to collectively as
protective, interactive, non-condensing compounds (PINC) could also
be complexed to purified plasmid DNA to influence variables such as
stability, intramuscular dispersion, or trafficking to specific
organs or cell types.
[0653] Target cell sensitization can be used as a functional assay
for expression and HLA class I presentation of minigene-encoded CTL
epitopes. For example, the plasmid DNA is introduced into a
mammalian cell line that is suitable as a target for standard CTL
chromium release assays. The transfection method used will be
dependent on the final formulation. Electroporation can be used for
"naked" DNA, whereas cationic lipids allow direct in vitro
transfection. A plasmid expressing green fluorescent protein (GFP)
can be co-transfected to allow enrichment of transfected cells
using fluorescence activated cell sorting (FACS). These cells are
then chromium-51 (.sup.5Cr) labeled and used as target cells for
epitope-specific CTL lines; cytolysis, detected by .sup.51Cr
release, indicates both production of, and HLA presentation of,
minigene-encoded CTL epitopes. Expression of HTL epitopes may be
evaluated in an analogous manner using assays to assess HTL
activity.
[0654] In vivo immunogenicity is a second approach for functional
testing of minigene DNA formulations. Transgenic mice expressing
appropriate human HLA proteins are immunized with the DNA product.
The dose and route of administration are formulation dependent
(e.g., IM for DNA in PBS, intraperitoneal (i.p.) for
lipid-complexed DNA). Twenty-one days after immunization,
splenocytes are harvested and restimulated for one week in the
presence of peptides encoding each epitope being tested.
Thereafter, for CTL effector cells, assays are conducted for
cytolysis of peptide-loaded, .sup.51Cr-labeled target cells using
standard techniques. Lysis of target cells that were sensitized by
HLA loaded with peptide epitopes, corresponding to minigene-encoded
epitopes, demonstrates DNA vaccine function for in vivo induction
of CTLs. Immunogenicity of HTL epitopes is confirmed in transgenic
mice in an analogous manner.
[0655] Alternatively, the nucleic acids can be administered using
ballistic delivery as described, for instance, in U.S. Pat. No.
5,204,253. Using this technique, particles comprised solely of DNA
are administered. In a further alternative embodiment, DNA can be
adhered to particles, such as gold particles.
[0656] Minigenes can also be delivered using other bacterial or
viral delivery systems well known in the art, e.g., an expression
construct encoding epitopes of the invention can be incorporated
into a viral vector such as vaccinia.
[0657] X.C.2. Combinations of CTL Peptides with Helper Peptides
[0658] Vaccine compositions comprising CTL peptides of the
invention can be modified, e.g., analoged, to provide desired
attributes, such as improved serum half life, broadened population
coverage or enhanced immunogenicity.
[0659] For instance, the ability of a peptide to induce CTL
activity can be enhanced by linking the peptide to a sequence which
contains at least one epitope that is capable of inducing a T
helper cell response. Although a CTL peptide can be directly linked
to a T helper peptide, often CTL epitope/HTL epitope conjugates are
linked by a spacer molecule. The spacer is typically comprised of
relatively small, neutral molecules, such as amino acids or amino
acid mimetics, which are substantially uncharged under
physiological conditions. The spacers are typically selected from,
e.g., Ala, Gly, or other neutral spacers of nonpolar amino acids or
neutral polar amino acids. It will be understood that the
optionally present spacer need not be comprised of the same
residues and thus may be a hetero- or homo-oligomer. When present,
the spacer will usually be at least one or two residues, more
usually three to six residues and sometimes 10 or more residues.
The CTL peptide epitope can be linked to the T helper peptide
epitope either directly or via a spacer either at the amino or
carboxy terminus of the CTL peptide. The amino terminus of either
the immunogenic peptide or the T helper peptide may be
acylated.
[0660] In certain embodiments, the T helper peptide is one that is
recognized by T helper cells present in a majority of a genetically
diverse population. This can be accomplished by selecting peptides
that bind to many, most, or all of the HLA class II molecules.
Examples of such amino acid bind many HLA Class II molecules
include sequences from antigens such as tetanus toxoid at positions
830-843 (QYIKANSKFIGITE; SEQ ID NO: 97), Plasmodium falciparum
circumsporozoite (CS) protein at positions 378-398
(DIEKKIAKMEKASSVFNWNS; SEQ ID NO: 98), and Streptococcus 18 kD
protein at positions 116-131 (GAVDSILGGVATYGAA; SEQ ID NO: 99).
Other examples include peptides bearing a DR 1-4-7 supermotif, or
either of the DR3 motifs.
[0661] Alternatively, it is possible to prepare synthetic peptides
capable of stimulating T helper lymphocytes, in a loosely
HLA-restricted fashion, using amino acid sequences not found in
nature (see, e.g., PCT publication WO 95/07707). These synthetic
compounds called Pan-DR-binding epitopes (e.g., PADRE.TM.,
Epimmune, Inc., San Diego, Calif.) are designed, most preferably,
to bind most HLA-DR (human HLA class II) molecules. For instance, a
pan-DR-binding epitope peptide having the formula: XKXVAAWTLKAAX
(SEQ ID NO: 100), where "X" is either cyclohexylalanine,
phenylalanine, or tyrosine, and a is either D-alanine or L-alanine,
has been found to bind to most HLA-DR alleles, and to stimulate the
response of T helper lymphocytes from most individuals, regardless
of their HLA type. An alternative of a pan-DR binding epitope
comprises all "L" natural amino acids and can be provided in the
form of nucleic acids that encode the epitope.
[0662] HTL peptide epitopes can also be modified to alter their
biological properties. For example, they can be modified to include
D-amino acids to increase their resistance to proteases and thus
extend their serum half life, or they can be conjugated to other
molecules such as lipids, proteins, carbohydrates, and the like to
increase their biological activity. For example, a T helper peptide
can be conjugated to one or more palmitic acid chains at either the
amino or carboxyl termini.
[0663] X.C.3. Combinations of CTL Peptides with T Cell Priming
Agents
[0664] In some embodiments it may be desirable to include in the
pharmaceutical compositions of the invention at least one component
which primes B lymphocytes or T lymphocytes. Lipids have been
identified as agents capable of priming CTL in vivo. For example,
palmitic acid residues can be attached to the .epsilon.- and
.alpha.-amino groups of a lysine residue and then linked, e.g., via
one or more linking residues such as Gly, Gly-Gly-, Ser, Ser-Ser,
or the like, to an immunogenic peptide. The lipidated peptide can
then be administered either directly in a micelle or particle,
incorporated into a liposome, or emulsified in an adjuvant, e.g.,
incomplete Freund's adjuvant. In a preferred embodiment, a
particularly effective immunogenic composition comprises palmitic
acid attached to .epsilon.- and .alpha.-amino groups of Lys, which
is attached via linkage, e.g., Ser-Ser, to the amino terminus of
the immunogenic peptide.
[0665] As another example of lipid priming of CTL responses, E.
coli lipoproteins, such as
tripalmitoyl-S-glycerylcysteinlyseryl-serine (P.sub.3CSS) can be
used to prime virus specific CTL when covalently attached to an
appropriate peptide (see, e.g., Deres, et al., Nature 342:561,
1989). Peptides of the invention can be coupled to P.sub.3CSS, for
example, and the lipopeptide administered to an individual to prime
specifically an immune response to the target antigen. Moreover,
because the induction of neutralizing antibodies can also be primed
with P.sub.3CSS-conjugated epitopes, two such compositions can be
combined to more effectively elicit both humoral and cell-mediated
responses.
[0666] X.C.4. Vaccine Compositions Comprising DC Pulsed with CTL
andlor HTL Peptides
[0667] An embodiment of a vaccine composition in accordance with
the invention comprises ex vivo administration of a cocktail of
epitope-bearing peptides to PBMC, or isolated DC therefrom, from
the patient's blood. A pharmaceutical to facilitate harvesting of
DC can be used, such as Progenipoietin.TM. (Pharmacia-Monsanto, St.
Louis, Mo.) or GM-CSF/IL-4. After pulsing the DC with peptides and
prior to reinfusion into patients, the DC are washed to remove
unbound peptides. In this embodiment, a vaccine comprises
peptide-pulsed DCs which present the pulsed peptide epitopes
complexed with HLA molecules on their surfaces.
[0668] The DC can be pulsed ex vivo with a cocktail of peptides,
some of which stimulate CTL responses to 98P4B6. Optionally, a
helper T cell (HTL) peptide, such as a natural or artificial
loosely restricted HLA Class II peptide, can be included to
facilitate the CTL response. Thus, a vaccine in accordance with the
invention is used to treat a cancer which expresses or
overexpresses 98P4B6.
[0669] X.D. Adoptive Immunotherapy
[0670] Antigenic 98P4B6-related peptides are used to elicit a CTL
and/or HTL response ex vivo, as well. The resulting CTL or HTL
cells, can be used to treat tumors in patients that do not respond
to other conventional forms of therapy, or will not respond to a
therapeutic vaccine peptide or nucleic acid in accordance with the
invention. Ex vivo CTL or HTL responses to a particular antigen are
induced by incubating in tissue culture the patient's, or
genetically compatible, CTL or HTL precursor cells together with a
source of antigen-presenting cells (APC), such as dendritic cells,
and the appropriate immunogenic peptide. After an appropriate
incubation time (typically about 7-28 days), in which the precursor
cells are activated and expanded into effector cells, the cells are
infused back into the patient, where they will destroy (CTL) or
facilitate destruction (HTL) of their specific target cell (e.g., a
tumor cell). Transfected dendritic cells may also be used as
antigen presenting cells.
[0671] X.E. Administration of Vaccines for Therapeutic or
Prophylactic Purposes
[0672] Pharmaceutical and vaccine compositions of the invention are
typically used to treat and/or prevent a cancer that expresses or
overexpresses 98P4B6. In therapeutic applications, peptide and/or
nucleic acid compositions are administered to a patient in an
amount sufficient to elicit an effective B cell, CTL and/or HTL
response to the antigen and to cure or at least partially arrest or
slow symptoms and/or complications. An amount adequate to
accomplish this is defined as "therapeutically effective dose."
Amounts effective for this use will depend on, e.g., the particular
composition administered, the manner of administration, the stage
and severity of the disease being treated, the weight and general
state of health of the patient, and the judgment of the prescribing
physician.
[0673] For pharmaceutical compositions, the immunogenic peptides of
the invention, or DNA encoding them, are generally administered to
an individual already bearing a tumor that expresses 98P4B6. The
peptides or DNA encoding them can be administered individually or
as fusions of one or more peptide sequences. Patients can be
treated with the immunogenic peptides separately or in conjunction
with other treatments, such as surgery, as appropriate.
[0674] For therapeutic use, administration should generally begin
at the first diagnosis of 98P4B6-associated cancer. This is
followed by boosting doses until at least symptoms are
substantially abated and for a period thereafter. The embodiment of
the vaccine composition (i.e., including, but not limited to
embodiments such as peptide cocktails, polyepitopic polypeptides,
minigenes, or TAA-specific CTLs or pulsed dendritic cells)
delivered to the patient may vary according to the stage of the
disease or the patient's health status. For example, in a patient
with a tumor that expresses 98P4B6, a vaccine comprising
98P4B6-specific CTL may be more efficacious in killing tumor cells
in patient with advanced disease than alternative embodiments.
[0675] It is generally important to provide an amount of the
peptide epitope delivered by a mode of administration sufficient to
stimulate effectively a cytotoxic T cell response; compositions
which stimulate helper T cell responses can also be given in
accordance with this embodiment of the invention.
[0676] The dosage for an initial therapeutic immunization generally
occurs in a unit dosage range where the lower value is about 1, 5,
50, 500, or 1,000 .mu.g and the higher value is about 10,000;
20,000; 30,000; or 50,000 .mu.g. Dosage values for a human
typically range from about 500 .mu.g to about 50,000 .mu.g per 70
kilogram patient. Boosting dosages of between about 1.0 .mu.g to
about 50,000 .mu.g of peptide pursuant to a boosting regimen over
weeks to months may be administered depending upon the patient's
response and condition as determined by measuring the specific
activity of CTL and HTL obtained from the patient's blood.
Administration should continue until at least clinical symptoms or
laboratory tests indicate that the neoplasia, has been eliminated
or reduced and for a period thereafter. The dosages, routes of
administration, and dose schedules are adjusted in accordance with
methodologies known in the art.
[0677] In certain embodiments, the peptides and compositions of the
present invention are employed in serious disease states, that is,
life-threatening or potentially life threatening situations. In
such cases, as a result of the minimal amounts of extraneous
substances and the relative nontoxic nature of the peptides in
preferred compositions of the invention, it is possible and may be
felt desirable by the treating physician to administer substantial
excesses of these peptide compositions relative to these stated
dosage amounts.
[0678] The vaccine compositions of the invention can also be used
purely as prophylactic agents. Generally the dosage for an initial
prophylactic immunization generally occurs in a unit dosage range
where the lower value is about 1, 5, 50, 500, or 1000 .mu.g and the
higher value is about 10,000; 20,000; 30,000; or 50,000 .mu.g.
Dosage values for a human typically range from about 500 .mu.g to
about 50,000 .mu.g per 70 kilogram patient. This is followed by
boosting dosages of between about 1.0 .mu.g to about 50,000 .mu.g
of peptide administered at defined intervals from about four weeks
to six months after the initial administration of vaccine. The
immunogenicity of the vaccine can be assessed by measuring the
specific activity of CTL and HTL obtained from a sample of the
patient's blood.
[0679] The pharmaceutical compositions for therapeutic treatment
are intended for parenteral, topical, oral, nasal, intrathecal, or
local (e.g. as a cream or topical ointment) administration.
Preferably, the pharmaceutical compositions are administered
parentally, e.g., intravenously, subcutaneously, intradermally, or
intramuscularly. Thus, the invention provides compositions for
parenteral administration which comprise a solution of the
immunogenic peptides dissolved or suspended in an acceptable
carrier, preferably an aqueous carrier.
[0680] A variety of aqueous carriers may be used, e.g., water,
buffered water, 0.8% saline, 0.3% glycine, hyaluronic acid and the
like. These compositions may be sterilized by conventional,
well-known sterilization techniques, or may be sterile filtered.
The resulting aqueous solutions may be packaged for use as is, or
lyophilized, the lyophilized preparation being combined with a
sterile solution prior to administration.
[0681] The compositions may contain pharmaceutically acceptable
auxiliary substances as required to approximate physiological
conditions, such as pH-adjusting and buffering agents, tonicity
adjusting agents, welting agents, preservatives, and the like, for
example, sodium acetate, sodium lactate, sodium chloride, potassium
chloride, calcium chloride, sorbitan monolaurate, triethanolamine
oleate, etc.
[0682] The concentration of peptides of the invention in the
pharmaceutical formulations can vary widely, i.e., from less than
about 0.1%, usually at or at least about 2% to as much as 20% to
50% or more by weight, and will be selected primarily by fluid
volumes, viscosities, etc., in accordance with the particular mode
of administration selected.
[0683] A human unit dose form of a composition is typically
included in a pharmaceutical composition that comprises a human
unit dose of an acceptable carrier, in one embodiment an aqueous
carrier, and is administered in a volume/quantity that is known by
those of skill in the art to be used for administration of such
compositions to humans (see, e.g., Remington's Pharmaceutical
Sciences, 17.sup.th Edition, A. Gennaro, Editor, Mack Publishing
Co., Easton, Pa., 1985). For example a peptide dose for initial
immunization can be from about 1 to about 50,000 .mu.g, generally
100-5,000 .mu.g, for a 70 kg patient. For example, for nucleic
acids an initial immunization may be performed using an expression
vector in the form of naked nucleic acid administered IM (or SC or
ID) in the amounts of 0.5-5 mg at multiple sites. The nucleic acid
(0.1 to 1000 .mu.g) can also be administered using a gene gun.
Following an incubation period of 3-4 weeks, a booster dose is then
administered. The booster can be recombinant fowlpox virus
administered at a dose of 5-10.sup.7 to 5.times.10.sup.9 pfu.
[0684] For antibodies, a treatment generally involves repeated
administration of the anti-98P4B6 antibody preparation, via an
acceptable route of administration such as intravenous injection
(IV), typically at a dose in the range of about 0.1 to about 10
mg/kg body weight. In general, doses in the range of 10-500 mg mAb
per week are effective and well tolerated. Moreover, an initial
loading dose of approximately 4 mg/kg patient body weight IV,
followed by weekly doses of about 2 mg/kg IV of the anti-98P4B6 mAb
preparation represents an acceptable dosing regimen. As appreciated
by those of skill in the art, various factors can influence the
ideal dose in a particular case. Such factors include, for example,
half life of a composition, the binding affinity of an Ab, the
immunogenicity of a substance, the degree of 98P4B6 expression in
the patient, the extent of circulating shed 98P4B6 antigen, the
desired steady-state concentration level, frequency of treatment,
and the influence of chemotherapeutic or other agents used in
combination with the treatment method of the invention, as well as
the health status of a particular patient. Non-limiting preferred
human unit doses are, for example, 500 .mu.g-1 mg, 1 mg-50 mg, 50
mg-100 mg, 100 mg-200 mg, 200 mg-300 mg, 400 mg-500 mg, 500 mg-600
mg, 600 mg-700 mg, 700 mg-800 mg, 800 mg-900 mg, 900 mg-1 g, or 1
mg-700 mg. In certain embodiments, the dose is in a range of 2-5
mg/kg body weight, e.g., with follow on weekly doses of 1-3 mg/kg;
0.5 mg, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mg/kg body weight followed,
e.g., in two, three or four weeks by weekly doses; 0.5-10 mg/kg
body weight, e.g., followed in two, three or four weeks by weekly
doses; 225, 250, 275, 300, 325, 350, 375, 400 mg m.sup.2 of body
area weekly; 1-600 mg m.sup.2 of body area weekly; 225-400 mg
m.sup.2 of body area weekly; these does can be followed by weekly
doses for 2, 3, 4, 5, 6, 7, 8, 9, 19, 11, 12 or more weeks.
[0685] In one embodiment, human unit dose forms of polynucleotides
comprise a suitable dosage range or effective amount that provides
any therapeutic effect. As appreciated by one of ordinary skill in
the art a therapeutic effect depends on a number of factors,
including the sequence of the polynucleotide, molecular weight of
the polynucleotide and route of administration. Dosages are
generally selected by the physician or other health care
professional in accordance with a variety of parameters known in
the art, such as severity of symptoms, history of the patient and
the like. Generally, for a polynucleotide of about 20 bases, a
dosage range may be selected from, for example, an independently
selected lower limit such as about 0.1, 0.25, 0.5, 1, 2, 5, 10, 20,
30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400 or 500 mg/kg up to
an independently selected upper limit, greater than the lower
limit, of about 60, 80, 100, 200, 300, 400, 500, 750, 1000, 1500,
2000, 3000, 4000, 5000, 6000, 7000, 8000, 9000 or 10,000 mg/kg. For
example, a dose may be about any of the following: 0.1 to 100
mg/kg, 0.1 to 50 mg/kg, 0.1 to 25 mg/kg, 0.1 to 10 mg/kg, 1 to 500
mg/kg, 100 to 400 mg/kg, 200 to 300 mg/kg, 1 to 100 mg/kg, 100 to
200 mg/kg, 300 to 400 mg/kg, 400 to 500 mg/kg, 500 to 1000 mg/kg,
500 to 5000 mg/kg, or 500 to 10,000 mg/kg. Generally, parenteral
routes of administration may require higher doses of polynucleotide
compared to more direct application to the nucleotide to diseased
tissue, as do polynucleotides of increasing length.
[0686] In one embodiment, human unit dose forms of T-cells comprise
a suitable dosage range or effective amount that provides any
therapeutic effect. As appreciated by one of ordinary skill in the
art, a therapeutic effect depends on a number of factors. Dosages
are generally selected by the physician or other health care
professional in accordance with a variety of parameters known in
the art, such as severity of symptoms, history of the patient and
the like. A dose may be about 10.sup.4 cells to about 10.sup.6
cells, about 10.sup.6 cells to about 10.sup.8 cells, about 10.sup.8
to about 10.sup.11 cells, or about 10.sup.8 to about
5.times.10.sup.10 cells. A dose may also about 10.sup.6
cells/m.sup.2 to about 10.sup.10 cells/m.sup.2, or about 10.sup.6
cells/m.sup.2 to about 10.sup.8 cells/m.sup.2.
[0687] Proteins(s) of the invention, and/or nucleic acids encoding
the protein(s), can also be administered via liposomes, which may
also serve to: 1) target the proteins(s) to a particular tissue,
such as lymphoid tissue; 2) to target selectively to diseases
cells; or, 3) to increase the half-life of the peptide composition.
Liposomes include emulsions, foams, micelles, insoluble monolayers,
liquid crystals, phospholipid dispersions, lamellar layers and the
like. In these preparations, the peptide to be delivered is
incorporated as part of a liposome, alone or in conjunction with a
molecule which binds to a receptor prevalent among lymphoid cells,
such as monoclonal antibodies which bind to the CD45 antigen, or
with other therapeutic or immunogenic compositions. Thus, liposomes
either filled or decorated with a desired peptide of the invention
can be directed to the site of lymphoid cells, where the liposomes
then deliver the peptide compositions. Liposomes for use in
accordance with the invention are formed from standard
vesicle-forming lipids, which generally include neutral and
negatively charged phospholipids and a sterol, such as cholesterol.
The selection of lipids is generally guided by consideration of,
e.g., liposome size, acid lability and stability of the liposomes
in the blood stream. A variety of methods are available for
preparing liposomes, as described in, e.g., Szoka, et al., Ann.
Rev. Biophys. Bioeng. 9:467 (1980), and U.S. Pat. Nos. 4,235,871,
4,501,728, 4,837,028, and 5,019,369.
[0688] For targeting cells of the immune system, a ligand to be
incorporated into the liposome can include, e.g., antibodies or
fragments thereof specific for cell surface determinants of the
desired immune system cells. A liposome suspension containing a
peptide may be administered intravenously, locally, topically, etc.
in a dose which varies according to, inter alia, the manner of
administration, the peptide being delivered, and the stage of the
disease being treated.
[0689] For solid compositions, conventional nontoxic solid carriers
may be used which include, for example, pharmaceutical grades of
mannitol, lactose, starch, magnesium stearate, sodium saccharin,
talcum, cellulose, glucose, sucrose, magnesium carbonate, and the
like. For oral administration, a pharmaceutically acceptable
nontoxic composition is formed by incorporating any of the normally
employed excipients, such as those carriers previously listed, and
generally 10-95% of active ingredient, that is, one or more
peptides of the invention, and more preferably at a concentration
of 25%-75%.
[0690] For aerosol administration, immunogenic peptides are
preferably supplied in finely divided form along with a surfactant
and propellant. Typical percentages of peptides are about 0.01%-20%
by weight, preferably about 1%-10%. The surfactant must, of course,
be nontoxic, and preferably soluble in the propellant.
Representative of such agents are the esters or partial esters of
fatty acids containing from about 6 to 22 carbon atoms, such as
caproic, octanoic, lauric, palmitic, stearic, linoleic, linolenic,
olesteric and oleic acids with an aliphatic polyhydric alcohol or
its cyclic anhydride. Mixed esters, such as mixed or natural
glycerides may be employed. The surfactant may constitute about
0.1%-20% by weight of the composition, preferably about 0.25-5%.
The balance of the composition is ordinarily propellant. A carrier
can also be included, as desired, as with, e.g., lecithin for
intranasal delivery.
[0691] XI.) Diagnostic and Prognostic Embodiments of 98P4B6.
[0692] As disclosed herein, 98P4B6 polynucleotides, polypeptides,
reactive cytotoxic T cells (CTL), reactive helper T cells (HTL) and
anti-polypeptide antibodies are used in well known diagnostic,
prognostic and therapeutic assays that examine conditions
associated with dysregulated cell growth such as cancer, in
particular the cancers listed in Table I (see, e.g., both its
specific pattern of tissue expression as well as its overexpression
in certain cancers as described for example in the Example entitled
"Expression analysis of 98P4B6 in normal tissues, and patient
specimens").
[0693] 98P4B6 can be analogized to a prostate associated antigen
PSA, the archetypal marker that has been used by medical
practitioners for years to identify and monitor the presence of
prostate cancer (see, e.g., Merrill et al., J. Urol.
163(2):503-5120 (2000); Polascik et al., J. Urol. August;
162(2):293-306(1999) and Fortier et al., J. Nat. Cancer Inst.
91(19): 1635-1640(1999)). A variety of other diagnostic markers are
also used in similar contexts including p53 and K-ras (see, e.g.,
Tulchinsky et al., Int J Mol Med 1999 July 4(1):99-102 and Minimoto
et al., Cancer Detect Prev 2000;24(1):1-12). Therefore, this
disclosure of 98P4B6 polynucleotides and polypeptides (as well as
98P4B6 polynucleotide probes and anti-98P4B6 antibodies used to
identify the presence of these molecules) and their properties
allows skilled artisans to utilize these molecules in methods that
are analogous to those used, for example, in a variety of
diagnostic assays directed to examining conditions associated with
cancer.
[0694] Typical embodiments of diagnostic methods which utilize the
98P4B6 polynucleotides, polypeptides, reactive T cells and
antibodies are analogous to those methods from well-established
diagnostic assays, which employ, e.g., PSA polynucleotides,
polypeptides, reactive T cells and antibodies. For example, just as
PSA polynucleotides are used as probes (for example in Northern
analysis, see, e.g., Sharief et al., Biochem. Mol. Biol. Int.
33(3):567-74(1994)) and primers (for example in PCR analysis, see,
e.g., Okegawa et al., J. Urol. 163(4): 1189-1190 (2000)) to observe
the presence and/or the level of PSA mRNAs in methods of monitoring
PSA overexpression or the metastasis of prostate cancers, the
98P4B6 polynucleotides described herein can be utilized in the same
way to detect 98P4B6 overexpression or the metastasis of prostate
and other cancers expressing this gene. Alternatively, just as PSA
polypeptides are used to generate antibodies specific for PSA which
can then be used to observe the presence and/or the level of PSA
proteins in methods to monitor PSA protein overexpression (see,
e.g., Stephan et al., Urology 55(4):560-3 (2000)) or the metastasis
of prostate cells (see, e.g., Alanen et al., Pathol. Res. Pract.
192(3):233-7 (1996)), the 98P4B6 polypeptides described herein can
be utilized to generate antibodies for use in detecting 98P4B6
overexpression or the metastasis of prostate cells and cells of
other cancers expressing this gene.
[0695] Specifically, because metastases involves the movement of
cancer cells from an organ of origin (such as the lung or prostate
gland etc.) to a different area of the body (such as a lymph node),
assays which examine a biological sample for the presence of cells
expressing 98P4B6 polynucleotides and/or polypeptides can be used
to provide evidence of metastasis. For example, when a biological
sample from tissue that does not normally contain 98P4B6-expressing
cells (lymph node) is found to contain 98P4B6-expressing cells such
as the 98P4B6 expression seen in LAPC4 and LAPC9, xenografts
isolated from lymph node and bone metastasis, respectively, this
finding is indicative of metastasis.
[0696] Alternatively 98P4B6 polynucleotides and/or polypeptides can
be used to provide evidence of cancer, for example, when cells in a
biological sample that do not normally express 98P4B6 or express
98P4B6 at a different level are found to express 98P4B6 or have an
increased expression of 98P4B6 (see, e.g., the 98P4B6 expression in
the cancers listed in Table I and in patient samples etc. shown in
the accompanying Figures). In such assays, artisans may further
wish to generate supplementary evidence of metastasis by testing
the biological sample for the presence of a second tissue
restricted marker (in addition to 98P4B6) such as PSA, PSCA etc.
(see, e.g., Alanen et al., Pathol. Res. Pract. 192(3): 233-237
(1996)).
[0697] Just as PSA polynucleotide fragments and polynucleotide
variants are employed by skilled artisans for use in methods of
monitoring PSA, 98P4B6 polynucleotide fragments and polynucleotide
variants are used in an analogous manner. In particular, typical
PSA polynucleotides used in methods of monitoring PSA are probes or
primers which consist of fragments of the PSA cDNA sequence.
Illustrating this, primers used to PCR amplify a PSA polynucleotide
must include less than the whole PSA sequence to function in the
polymerase chain reaction. In the context of such PCR reactions,
skilled artisans generally create a variety of different
polynucleotide fragments that can be used as primers in order to
amplify different portions of a polynucleotide of interest or to
optimize amplification reactions (see, e.g., Caetano-Anolles, G.
Biotechniques 25(3): 472-476, 478-480 (1998); Robertson et al.,
Methods Mol. Biol. 98:121-154 (1998)). An additional illustration
of the use of such fragments is provided in the Example entitled
"Expression analysis of 98P4B6 in normal tissues, and patient
specimens," where a 98P4B6 polynucleotide fragment is used as a
probe to show the expression of 98P4B6 RNAs in cancer cells. In
addition, variant polynucleotide sequences are typically used as
primers and probes for the corresponding mRNAs in PCR and Northern
analyses (see, e.g., Sawai et al., Fetal Diagn. Ther. 1996
November-December 11(6):407-13 and Current Protocols In Molecular
Biology, Volume 2, Unit 2, Frederick M. Ausubel et al. eds.,
1995)). Polynucleotide fragments and variants are useful in this
context where they are capable of binding to a target
polynucleotide sequence (e.g., a 98P4B6 polynucleotide shown in
FIG. 2 or variant thereof) under conditions of high stringency.
[0698] Furthermore, PSA polypeptides which contain an epitope that
can be recognized by an antibody or T cell that specifically binds
to that epitope are used in methods of monitoring PSA. 98P4B6
polypeptide fragments and polypeptide analogs or variants can also
be used in an analogous manner. This practice of using polypeptide
fragments or polypeptide variants to generate antibodies (such as
anti-PSA antibodies or T cells) is typical in the art with a wide
variety of systems such as fusion proteins being used by
practitioners (see, e.g., Current Protocols In Molecular Biology,
Volume 2, Unit 16, Frederick M. Ausubel et al. eds., 1995). In this
context, each epitope(s) functions to provide the architecture with
which an antibody or T cell is reactive. Typically, skilled
artisans create a variety of different polypeptide fragments that
can be used in order to generate immune responses specific for
different portions of a polypeptide of interest (see, e.g., U.S.
Pat. No. 5,840,501 and U.S. Pat. No. 5,939,533). For example it may
be preferable to utilize a polypeptide comprising one of the 98P4B6
biological motifs discussed herein or a motif-bearing subsequence
which is readily identified by one of skill in the art based on
motifs available in the art. Polypeptide fragments, variants or
analogs are typically useful in this context as long as they
comprise an epitope capable of generating an antibody or T cell
specific for a target polypeptide sequence (e.g. a 98P4B6
polypeptide shown in FIG. 3).
[0699] As shown herein, the 98P4B6 polynucleotides and polypeptides
(as well as the 98P4B6 polynucleotide probes and anti-98P4B6
antibodies or T cells used to identify the presence of these
molecules) exhibit specific properties that make them useful in
diagnosing cancers such as those listed in Table I. Diagnostic
assays that measure the presence of 98P4B6 gene products, in order
to evaluate the presence or onset of a disease condition described
herein, such as prostate cancer, are used to identify patients for
preventive measures or further monitoring, as has been done so
successfully with PSA. Moreover, these materials satisfy a need in
the art for molecules having similar or complementary
characteristics to PSA in situations where, for example, a definite
diagnosis of metastasis of prostatic origin cannot be made on the
basis of a test for PSA alone (see, e.g., Alanen et al., Pathol.
Res. Pract. 192(3):233-237 (1996)), and consequently, materials
such as 98P4B6 polynucleotides and polypeptides (as well as the
98P4B6 polynucleotide probes and anti-98P4B6 antibodies used to
identify the presence of these molecules) need to be employed to
confirm a metastases of prostatic origin.
[0700] Finally, in addition to their use in diagnostic assays, the
98P4B6 polynucleotides disclosed herein have a number of other
utilities such as their use in the identification of oncogenetic
associated chromosomal abnormalities in the chromosomal region to
which the 98P4B6 gene maps (see the Example entitled "Chromosomal
Mapping of 98P4B6" below). Moreover, in addition to their use in
diagnostic assays, the 98P4B6-related proteins and polynucleotides
disclosed herein have other utilities such as their use in the
forensic analysis of tissues of unknown origin (see, e.g., Takahama
K Forensic Sci Int 1996 June 28;80(1-2): 63-9).
[0701] Additionally, 98P4B6-related proteins or polynucleotides of
the invention can be used to treat a pathologic condition
characterized by the over-expression of 98P4B6. For example, the
amino acid or nucleic acid sequence of FIG. 2 or FIG. 3, or
fragments of either, can be used to generate an immune response to
a 98P4B6 antigen. Antibodies or other molecules that react with
98P4B6 can be used to modulate the function of this molecule, and
thereby provide a therapeutic benefit.
[0702] XII.) Inhibition of 98P4B6 Protein Function
[0703] The invention includes various methods and compositions for
inhibiting the binding of 98P4B6 to its binding partner or its
association with other protein(s) as well as methods for inhibiting
98P4B6 function.
[0704] XII.A.) Inhibition of 98P4B6 with Intracellular
Antibodies
[0705] In one approach, a recombinant vector that encodes single
chain antibodies that specifically bind to 98P4B6 are introduced
into 98P4B6 expressing cells via gene transfer technologies.
Accordingly, the encoded single chain anti-98P4B6 antibody is
expressed intracellularly, binds to 98P4B6 protein, and thereby
inhibits its function. Methods for engineering such intracellular
single chain antibodies are well known. Such intracellular
antibodies, also known as "intrabodies", are specifically targeted
to a particular compartment within the cell, providing control over
where the inhibitory activity of the treatment is focused. This
technology has been successfully applied in the art (for review,
see Richardson and Marasco, 1995, TIBTECH vol. 13). Intrabodies
have been shown to virtually eliminate the expression of otherwise
abundant cell surface receptors (see, e.g., Richardson et al.,
1995, Proc. Natl. Acad. Sci. USA 92: 3137-3141; Beerli et al.,
1994, J. Biol. Chem. 289: 23931-23936; Deshane et al., 1994, Gene
Ther. 1: 332-337).
[0706] Single chain antibodies comprise the variable domains of the
heavy and light chain joined by a flexible linker polypeptide, and
are expressed as a single polypeptide. Optionally, single chain
antibodies are expressed as a single chain variable region fragment
joined to the light chain constant region. Well-known intracellular
trafficking signals are engineered into recombinant polynucleotide
vectors encoding such single chain antibodies in order to target
precisely the intrabody to the desired intracellular compartment.
For example, intrabodies targeted to the endoplasmic reticulum (ER)
are engineered to incorporate a leader peptide and, optionally, a
C-terminal ER retention signal, such as the KDEL amino acid motif.
Intrabodies intended to exert activity in the nucleus are
engineered to include a nuclear localization signal. Lipid moieties
are joined to intrabodies in order to tether the intrabody to the
cytosolic side of the plasma membrane. Intrabodies can also be
targeted to exert function in the cytosol. For example, cytosolic
intrabodies are used to sequester factors within the cytosol,
thereby preventing them from being transported to their natural
cellular destination.
[0707] In one embodiment, intrabodies are used to capture 98P4B6 in
the nucleus, thereby preventing its activity within the nucleus.
Nuclear targeting signals are engineered into such 98P4B6
intrabodies in order to achieve the desired targeting. Such 98P4B6
intrabodies are designed to bind specifically to a particular
98P4B6 domain. In another embodiment, cytosolic intrabodies that
specifically bind to a 98P4B6 protein are used to prevent 98P4B6
from gaining access to the nucleus, thereby preventing it from
exerting any biological activity within the nucleus (e.g.,
preventing 98P4B6 from forming transcription complexes with other
factors).
[0708] In order to specifically direct the expression of such
intrabodies to particular cells, the transcription of the intrabody
is placed under the regulatory control of an appropriate
tumor-specific promoter and/or enhancer. In order to target
intrabody expression specifically to prostate, for example, the PSA
promoter and/or promoter/enhancer can be utilized (See, for
example, U.S. Pat. No. 5,919,652 issued 6 Jul. 1999).
[0709] XII.B.) Inhibition of 98P4B6 with Recombinant Proteins
[0710] In another approach, recombinant molecules bind to 98P4B6
and thereby inhibit 98P4B6 function. For example, these recombinant
molecules prevent or inhibit 98P4B6 from accessing/binding to its
binding partner(s) or associating with other protein(s). Such
recombinant molecules can, for example, contain the reactive
part(s) of a 98P4B6 specific antibody molecule. In a particular
embodiment, the 98P4B6 binding domain of a 98P4B6 binding partner
is engineered into a dimeric fusion protein, whereby the fusion
protein comprises two 98P4B6 ligand binding domains linked to the
Fc portion of a human IgG, such as human IgG1. Such IgG portion can
contain, for example, the C.sub.H2 and C.sub.H3 domains and the
hinge region, but not the C.sub.H1 domain. Such dimeric fusion
proteins are administered in soluble form to patients suffering
from a cancer associated with the expression of 98P4B6, whereby the
dimeric fusion protein specifically binds to 98P4B6 and blocks
98P4B6 interaction with a binding partner. Such dimeric fusion
proteins are further combined into multimeric proteins using known
antibody linking technologies.
[0711] XII.C.) Inhibition of 98P4B6 Transcription or
Translation
[0712] The present invention also comprises various methods and
compositions for inhibiting the transcription of the 98P4B6 gene.
Similarly, the invention also provides methods and compositions for
inhibiting the translation of 98P4B6 mRNA into protein.
[0713] In one approach, a method of inhibiting the transcription of
the 98P4B6 gene comprises contacting the 98P4B6 gene with a 98P4B6
antisense polynucleotide. In another approach, a method of
inhibiting 98P4B6 mRNA translation comprises contacting a 98P4B6
mRNA with an antisense polynucleotide. In another approach, a
98P4B6 specific ribozyme is used to cleave a 98P4B6 message,
thereby inhibiting translation. Such antisense and ribozyme based
methods can also be directed to the regulatory regions of the
98P4B6 gene, such as 98P4B6 promoter and/or enhancer elements.
Similarly, proteins capable of inhibiting a 98P4B6 gene
transcription factor are used to inhibit 98P4B6 mRNA transcription.
The various polynucleotides and compositions useful in the
aforementioned methods have been described above. The use of
antisense and ribozyme molecules to inhibit transcription and
translation is well known in the art.
[0714] Other factors that inhibit the transcription of 98P4B6 by
interfering with 98P4B6 transcriptional activation are also useful
to treat cancers expressing 98P4B6. Similarly, factors that
interfere with 98P4B6 processing are useful to treat cancers that
express 98P4B6. Cancer treatment methods utilizing such factors are
also within the scope of the invention.
[0715] XII.D.) General Considerations for Therapeutic
Strategies
[0716] Gene transfer and gene therapy technologies can be used to
deliver therapeutic polynudeotide molecules to tumor cells
synthesizing 98P4B6 (i.e., antisense, ribozyme, polynudeotdes
encoding intrabodies and other 98P4B6 inhibitory molecules). A
number of gene therapy approaches are known in the art. Recombinant
vectors encoding 98P4B6 antisense polynudeotides, ribozymes,
factors capable of interfering with 98P4B6 transcription, and so
forth, can be delivered to target tumor cells using such gene
therapy approaches.
[0717] The above therapeutic approaches can be combined with any
one of a wide variety of surgical, chemotherapy or radiation
therapy regimens. The therapeutic approaches of the invention can
enable the use of reduced dosages of chemotherapy (or other
therapies) and/or less frequent administration, an advantage for
all patients and particularly for those that do not tolerate the
toxicity of the chemotherapeutic agent well.
[0718] The anti-tumor activity of a particular composition (e.g.,
antisense, ribozyme, intrabody), or a combination of such
compositions, can be evaluated using various in vitro and in vivo
assay systems. In vitro assays that evaluate therapeutic activity
include cell growth assays, soft agar assays and other assays
indicative of tumor promoting activity, binding assays capable of
determining the extent to which a therapeutic composition will
inhibit the binding of 98P4B6 to a binding partner, etc.
[0719] In vivo, the effect of a 98P4B6 therapeutic composition can
be evaluated in a suitable animal model. For example, xenogenic
prostate cancer models can be used, wherein human prostate cancer
explants or passaged xenograft tissues are introduced into immune
compromised animals, such as nude or SCID mice (Klein et al., 1997,
Nature Medicine 3: 402-408). For example, PCT Patent Applicaton
WO98/16628 and U.S. Pat. No. 6,107,540 describe various xenograft
models of human prostate cancer capable of recapitulating the
development of primary tumors, micrometastasis, and the formation
of osteoblastic metastases characteristic of late stage disease.
Efficacy can be predicted using assays that measure inhibition of
tumor formation, tumor regression or metastasis, and the like.
[0720] In vivo assays that evaluate the promotion of apoptosis are
useful in evaluating therapeutic compositions. In one embodiment,
xenografts from tumor bearing mice treated with the therapeutic
composition can be examined for the presence of apoptotic foci and
compared to untreated control xenograft-bearing mice. The extent to
which apoptotic foci are found in the tumors of the treated mice
provides an indication of the therapeutic efficacy of the
composition.
[0721] The therapeutic compositions used in the practice of the
foregoing methods can be formulated into pharmaceutical
compositions comprising a carrier suitable for the desired delivery
method. Suitable carriers include any material that when combined
with the therapeutic composition retains the anti-tumor function of
the therapeutic composition and is generally non-reactive with the
patient's immune system. Examples include, but are not limited to,
any of a number of standard pharmaceutical carriers such as sterile
phosphate buffered saline solutions, bacteriostatic water, and the
like (see, generally, Remington's Pharmaceutical Sciences 16.sup.th
Edition, A. Osal., Ed., 1980).
[0722] Therapeutic formulations can be solubilized and administered
via any route capable of delivering the therapeutic composition to
the tumor site. Potentially effective routes of administration
include, but are not limited to, intravenous, parenteral,
intraperitoneal, intramuscular, intratumor, intradermal,
intraorgan, orthotopic, and the like. A preferred formulation for
intravenous injection comprises the therapeutic composition in a
solution of preserved bacteriostatic water, sterile unpreserved
water, and/or diluted in polyvinylchloride or polyethylene bags
containing 0.9% sterile Sodium Chloride for Injection, USP.
Therapeutic protein preparations can be lyophilized and stored as
sterile powders, preferably under vacuum, and then reconstituted in
bacteriostatic water (containing for example, benzyl alcohol
preservative) or in sterile water prior to injection.
[0723] Dosages and administration protocols for the treatment of
cancers using the foregoing methods will vary with the method and
the target cancer, and will generally depend on a number of other
factors appreciated in the art.
[0724] XIII.) Identification, Characterization and Use of
Modulators of 98P4B6
[0725] Methods to Identify and Use Modulators
[0726] In one embodiment, screening is performed to identify
modulators that induce or suppress a particular expression profile,
suppress or induce specific pathways, preferably generating the
associated phenotype thereby. In another embodiment, having
identified differentially expressed genes important in a particular
state; screens are performed to identify modulators that alter
expression of individual genes, either increase or decrease. In
another embodiment, screening is performed to identify modulators
that alter a biological function of the expression product of a
differentially expressed gene. Again, having identified the
importance of a gene in a particular state, screens are performed
to identify agents that bind and/or modulate the biological
activity of the gene product.
[0727] In addition, screens are done for genes that are induced in
response to a candidate agent. After identifying a modulator (one
that suppresses a cancer expression pattern leading to a normal
expression pattern, or a modulator of a cancer gene that leads to
expression of the gene as in normal tissue) a screen is performed
to identify genes that are specifically modulated in response to
the agent. Comparing expression profiles between normal tissue and
agent-treated cancer tissue reveals genes that are not expressed in
normal tissue or cancer tissue, but are expressed in agent treated
tissue, and vice versa. These agent-specific sequences are
identified and used by methods described herein for cancer genes or
proteins. In particular these sequences and the proteins they
encode are used in marking or identifying agent-treated cells. In
addition, antibodies are raised against the agent-induced proteins
and used to target novel therapeutics to the treated cancer tissue
sample.
[0728] Modulator-Related Identification and Screening Assays:
[0729] Gene Expression-Related Assays
[0730] Proteins, nucleic acids, and antibodies of the invention are
used in screening assays. The cancer-associated proteins,
antibodies, nucleic acids, modified proteins and cells containing
these sequences are used in screening assays, such as evaluating
the effect of drug candidates on a "gene expression profile,"
expression profile of polypeptides or alteration of biological
function. In one embodiment, the expression profiles are used,
preferably in conjunction with high throughput screening techniques
to allow monitoring for expression profile genes after treatment
with a candidate agent (e.g., Davis, G F, et al., J Biol Screen
7:69 (2002); Zlokarnik, et al., Science 279:84-8 (1998); Heid,
Genome Res 6:986-94, 1996).
[0731] The cancer proteins, antibodies, nucleic acids, modified
proteins and cells containing the native or modified cancer
proteins or genes are used in screening assays. That is, the
present invention comprises methods for screening for compositions
which modulate the cancer phenotype or a physiological function of
a cancer protein of the invention. This is done on a gene itself or
by evaluating the effect of drug candidates on a "gene expression
profile" or biological function. In one embodiment, expression
profiles are used, preferably in conjunction with high throughput
screening techniques to allow monitoring after treatment with a
candidate agent, see Zlokamik, supra.
[0732] A variety of assays are executed directed to the genes and
proteins of the invention. Assays are run on an individual nucleic
acid or protein level. That is, having identified a particular gene
as up regulated in cancer, test compounds are screened for the
ability to modulate gene expression or for binding to the cancer
protein of the invention. "Modulation" in this context includes an
increase or a decrease in gene expression. The preferred amount of
modulation will depend on the original change of the gene
expression in normal versus tissue undergoing cancer, with changes
of at least 10%, preferably 50%, more preferably 100-300%, and in
some embodiments 300-1000% or greater. Thus, if a gene exhibits a
4-fold increase in cancer tissue compared to normal tissue, a
decrease of about four-fold is often desired; similarly, a 10-fold
decrease in cancer tissue compared to normal tissue a target value
of a 10-fold increase in expression by the test compound is often
desired. Modulators that exacerbate the type of gene expression
seen in cancer are also useful, e.g., as an upregulated target in
further analyses.
[0733] The amount of gene expression is monitored using nucleic
acid probes and the quantification of gene expression levels, or,
alternatively, a gene product itself is monitored, e.g., through
the use of antibodies to the cancer protein and standard
immunoassays. Proteomics and separation techniques also allow for
quantification of expression.
[0734] Expression Monitoring to Identify Compounds that Modify Gene
Expression
[0735] In one embodiment, gene expression monitoring, i.e., an
expression profile, is monitored simultaneously for a number of
entities. Such profiles will typically involve one or more of the
genes of FIG. 2. In this embodiment, e.g., cancer nucleic acid
probes are attached to biochips to detect and quantify cancer
sequences in a particular cell. Alternatively, PCR can be used.
Thus, a series, e.g., wells of a microtiter plate, can be used with
dispensed primers in desired wells. A PCR reaction can then be
performed and analyzed for each well.
[0736] Expression monitoring is performed to identify compounds
that modify the expression of one or more cancer-associated
sequences, e.g., a polynucleotide sequence set out in FIG. 2.
Generally, a test modulator is added to the cells prior to
analysis. Moreover, screens are also provided to identify agents
that modulate cancer, modulate cancer proteins of the invention,
bind to a cancer protein of the invention, or interfere with the
binding of a cancer protein of the invention and an antibody or
other binding partner.
[0737] In one embodiment, high throughput screening methods involve
providing a library containing a large number of potential
therapeutic compounds (candidate compounds). Such "combinatorial
chemical libraries" are then screened in one or more assays to
identify those library members (particular chemical species or
subclasses) that display a desired characteristic activity. The
compounds thus identified can serve as conventional "lead
compounds," as compounds for screening, or as therapeutics.
[0738] In certain embodiments, combinatorial libraries of potential
modulators are screened for an ability to bind to a cancer
polypeptide or to modulate activity. Conventionally, new chemical
entities with useful properties are generated by identifying a
chemical compound (called a "lead compound") with some desirable
property or activity, e.g., inhibiting activity, creating variants
of the lead compound, and evaluating the property and activity of
those variant compounds. Often, high throughput screening (HTS)
methods are employed for such an analysis.
[0739] As noted above, gene expression monitoring is conveniently
used to test candidate modulators (e.g., protein, nucleic acid or
small molecule). After the candidate agent has been added and the
cells allowed to incubate for a period, the sample containing a
target sequence to be analyzed is, e.g., added to a biochip.
[0740] If required, the target sequence is prepared using known
techniques. For example, a sample is treated to lyse the cells,
using known lysis buffers, electroporation, etc., with purification
and/or amplification such as PCR performed as appropriate. For
example, an in vitro transcription with labels covalently attached
to the nucleotides is performed. Generally, the nucleic acids are
labeled with biotin-FITC or PE, or with cy3 or cy5.
[0741] The target sequence can be labeled with, e.g., a
fluorescent, a chemiluminescent, a chemical, or a radioactive
signal, to provide a means of detecting the target sequence's
specific binding to a probe. The label also can be an enzyme, such
as alkaline phosphatase or horseradish peroxidase, which when
provided with an appropriate substrate produces a product that is
detected. Alternatively, the label is a labeled compound or small
molecule, such as an enzyme inhibitor, that binds but is not
catalyzed or altered by the enzyme. The label also can be a moiety
or compound, such as, an epitope tag or biotin which specifically
binds to streptavidin. For the example of biotin, the streptavidin
is labeled as described above, thereby, providing a detectable
signal for the bound target sequence. Unbound labeled streptavidin
is typically removed prior to analysis.
[0742] As will be appreciated by those in the art, these assays can
be direct hybridization assays or can comprise "sandwich assays",
which include the use of multiple probes, as is generally outlined
in U.S. Pat. Nos. 5,681,702; 5,597,909; 5,545,730; 5,594,117;
5,591,584; 5,571,670; 5,580,731; 5,571,670; 5,591,584; 5,624,802;
5,635,352; 5,594,118; 5,359,100; 5,124,246; and 5,681,697. In this
embodiment, in general, the target nucleic acid is prepared as
outlined above, and then added to the biochip comprising a
plurality of nucleic acid probes, under conditions that allow the
formation of a hybridization complex.
[0743] A variety of hybridization conditions are used in the
present invention, including high, moderate and low stringency
conditions as outlined above. The assays are generally run under
stringency conditions which allow formation of the label probe
hybridization complex only in the presence of target. Stringency
can be controlled by altering a step parameter that is a
thermodynamic variable, including, but not limited to, temperature,
formamide concentration, salt concentration, chaotropic salt
concentration pH, organic solvent concentration, etc. These
parameters may also be used to control non-specific binding, as is
generally outlined in U.S. Pat. No. 5,681,697. Thus, it can be
desirable to perform certain steps at higher stringency conditions
to reduce non-specific binding.
[0744] The reactions outlined herein can be accomplished in a
variety of ways. Components of the reaction can be added
simultaneously, or sequentially, in different orders, with
preferred embodiments outlined below. In addition, the reaction may
include a variety of other reagents. These include salts, buffers,
neutral proteins, e.g. albumin, detergents, etc. which can be used
to facilitate optimal hybridization and detection, and/or reduce
nonspecific or background interactions. Reagents that otherwise
improve the efficiency of the assay, such as protease inhibitors,
nuclease inhibitors, anti-microbial agents, etc., may also be used
as appropriate, depending on the sample preparation methods and
purity of the target. The assay data are analyzed to determine the
expression levels of individual genes, and changes in expression
levels as between states, forming a gene expression profile.
[0745] Biological Activity-Related Assays
[0746] The invention provides methods identify or screen for a
compound that modulates the activity of a cancer-related gene or
protein of the invention. The methods comprise adding a test
compound, as defined above, to a cell comprising a cancer protein
of the invention. The cells contain a recombinant nucleic acid that
encodes a cancer protein of the invention. In another embodiment, a
library of candidate agents is tested on a plurality of cells.
[0747] In one aspect, the assays are evaluated in the presence or
absence or previous or subsequent exposure of physiological
signals, e.g. hormones, antibodies, peptides, antigens, cytokines,
growth factors, action potentials, pharmacological agents including
chemotherapeutics, radiation, carcinogenics, or other cells (i.e.,
cell-cell contacts). In another example, the determinations are
made at different stages of the cell cycle process. In this way,
compounds that modulate genes or proteins of the invention are
identified. Compounds with pharmacological activity are able to
enhance or interfere with the activity of the cancer protein of the
invention. Once identified, similar structures are evaluated to
identify critical structural features of the compound.
[0748] In one embodiment, a method of modulating (e.g., inhibiting)
cancer cell division is provided; the method comprises
administration of a cancer modulator. In another embodiment, a
method of modulating (e.g., inhibiting) cancer is provided; the
method comprises administration of a cancer modulator. In a further
embodiment, methods of treating cells or individuals with cancer
are provided; the method comprises administration of a cancer
modulator.
[0749] In one embodiment, a method for modulating the status of a
cell that expresses a gene of the invention is provided. As used
herein status comprises such art-accepted parameters such as
growth, proliferation, survival, function, apoptosis, senescence,
location, enzymatic activity, signal transduction, etc. of a cell.
In one embodiment, a cancer inhibitor is an antibody as discussed
above. In another embodiment, the cancer inhibitor is an antisense
molecule. A variety of cell growth, proliferation, and metastasis
assays are known to those of skill in the art, as described
herein.
[0750] High Throughput Screening to Identify Modulators
[0751] The assays to identify suitable modulators are amenable to
high throughput screening. Preferred assays thus detect enhancement
or inhibition of cancer gene transcription, inhibition or
enhancement of polypeptide expression, and inhibition or
enhancement of polypeptide activity.
[0752] In one embodiment, modulators evaluated in high throughput
screening methods are proteins, often naturally occurring proteins
or fragments of naturally occurring proteins. Thus, e.g., cellular
extracts containing proteins, or random or directed digests of
proteinaceous cellular extracts, are used. In this way, libraries
of proteins are made for screening in the methods of the invention.
Particularly preferred in this embodiment are libraries of
bacterial, fungal, viral, and mammalian proteins, with the latter
being preferred, and human proteins being especially preferred.
Particularly useful test compound will be directed to the class of
proteins to which the target belongs, e.g., substrates for enzymes,
or ligands and receptors.
[0753] Use of Soft Agar Growth and Colony Formation to Identify and
Characterize Modulators
[0754] Normal cells require a solid substrate to attach and grow.
When cells are transformed, they lose this phenotype and grow
detached from the substrate. For example, transformed cells can
grow in stirred suspension culture or suspended in semi-solid
media, such as semi-solid or soft agar. The transformed cells, when
transfected with tumor suppressor genes, can regenerate normal
phenotype and once again require a solid substrate to attach to and
grow. Soft agar growth or colony formation in assays are used to
identify modulators of cancer sequences, which when expressed in
host cells, inhibit abnormal cellular proliferation and
transformation. A modulator reduces or eliminates the host cells'
ability to grow suspended in solid or semisolid media, such as
agar.
[0755] Techniques for soft agar growth or colony formation in
suspension assays are described in Freshney, Culture of Animal
Cells a Manual of Basic Technique (3rd ed., 1994). See also, the
methods section of Garkavtsev et al. (1996), supra.
[0756] Evaluation of Contact Inhibition and Growth Density
Limitation to Identify and Characterize Modulators
[0757] Normal cells typically grow in a flat and organized pattern
in cell culture until they touch other cells. When the cells touch
one another, they are contact inhibited and stop growing.
Transformed cells, however, are not contact inhibited and continue
to grow to high densities in disorganized foci. Thus, transformed
cells grow to a higher saturation density than corresponding normal
cells. This is detected morphologically by the formation of a
disoriented monolayer of cells or cells in foci. Alternatively,
labeling index with (.sup.3H)-thymidine at saturation density is
used to measure density limitation of growth, similarly an MTT or
Alamar blue assay will reveal proliferation capacity of cells and
the the ability of modulators to affect same. See Freshney (1994),
supra. Transformed cells, when transfected with tumor suppressor
genes, can regenerate a normal phenotype and become contact
inhibited and would grow to a lower density.
[0758] In this assay, labeling index with .sup.3H)-thymidine at
saturation density is a preferred method of measuring density
limitation of growth. Transformed host cells are transfected with a
cancer-associated sequence and are grown for 24 hours at saturation
density in non-limiting medium conditions. The percentage of cells
labeling with (.sup.3H)-thymidine is determined by incorporated
cpm.
[0759] Contact independent growth is used to identify modulators of
cancer sequences, which had led to abnormal cellular proliferation
and transformation. A modulator reduces or eliminates contact
independent growth, and returns the cells to a normal
phenotype.
[0760] Evaluation of Growth Factor or Serum Dependence to Identify
and Characterize Modulators
[0761] Transformed cells have lower serum dependence than their
normal counterparts (see, e.g., Temin, J. Natl. Cancer Inst.
37:167-175 (1966); Eagle et al., J. Exp. Med 131:836-879 (1970));
Freshney, supra. This is in part due to release of various growth
factors by the transformed cells. The degree of growth factor or
serum dependence of transformed host cells can be compared with
that of control. For example, growth factor or serum dependence of
a cell is monitored in methods to, identify and characterize
compounds that modulate cancer-associated sequences of the
invention.
[0762] Use of Tumor-Specific Marker Levels to Identify and
Characterize Modulators
[0763] Tumor cells release an increased amount of certain factors
(hereinafter "tumor specific markers") than their normal
counterparts. For example, plasminogen activator (PA) is released
from human glioma at a higher level than from normal brain cells
(see, e.g., Gullino, Angiogenesis, Tumor Vascularization, and
Potential Interference with Tumor Growth, in Biological Responses
in Cancer, pp. 178-184 (Mihich (ed.) 1985)). Similarly, Tumor
Angiogenesis Factor (TAF) is released at a higher level in tumor
cells than their normal counterparts. See, e.g., Folkman,
Angiogenesis and Cancer, Sem Cancer Biol. (1992)), while bFGF is
released from endothelial tumors (Ensoli, B et al).
[0764] Various techniques which measure the release of these
factors are described in Freshney (1994), supra. Also, see, Unkless
et al., J. Biol. Chem. 249:4295-4305 (1974); Strickland &
Beers, J. Biol. Chem. 251:5694-5702 (1976); Whur et al., Br. J.
Cancer 42:305 312 (1980); Gullino, Angiogenesis, Tumor
Vascularization, and Potential Interference with Tumor Growth, in
Biological Responses in Cancer, pp. 178-184 (Mihich (ed.) 1985);
Freshney, Anticancer Res. 5:111-130 (1985). For example, tumor
specific marker levels are monitored in methods to identify and
characterize compounds that modulate cancer-associated sequences of
the invention.
[0765] Invasiveness into Matrigel to Identify and Characterize
Modulators
[0766] The degree of invasiveness into Matrigel or an extracellular
matrix constituent can be used as an assay to identify and
characterize compounds that modulate cancer associated sequences.
Tumor cells exhibit a positive correlation between malignancy and
invasiveness of cells into Matrigel or some other extracellular
matrix constituent. In this assay, tumorigenic cells are typically
used as host cells. Expression of a tumor suppressor gene in these
host cells would decrease invasiveness of the host cells.
Techniques described in Cancer Res. 1999; 59:6010; Freshney (1994),
supra, can be used. Briefly, the level of invasion of host cells is
measured by using filters coated with Matrigel or some other
extracellular matrix constituent. Penetration into the gel, or
through to the distal side of the filter, is rated as invasiveness,
and rated histologically by number of cells and distance moved, or
by prelabeling the cells with .sup.1251 and counting the
radioactivity on the distal side of the filter or bottom of the
dish. See, e.g., Freshney (1984), supra.
[0767] Evaluation of Tumor Growth in Vivo to Identify and
Characterize Modulators
[0768] Effects of cancer-associated sequences on cell growth are
tested in transgenic or immune-suppressed organisms. Transgenic
organisms are prepared in a variety of art-accepted ways. For
example, knock-out transgenic organisms, e.g., mammals such as
mice, are made, in which a cancer gene is disrupted or in which a
cancer gene is inserted. Knock-out transgenic mice are made by
insertion of a marker gene or other heterologous gene into the
endogenous cancer gene site in the mouse genome via homologous
recombination. Such mice can also be made by substituting the
endogenous cancer gene with a mutated version of the cancer gene,
or by mutating the endogenous cancer gene, e.g., by exposure to
carcinogens.
[0769] To prepare transgenic chimeric animals, e.g., mice, a DNA
construct is introduced into the nuclei of embryonic stem cells.
Cells containing the newly engineered genetic lesion are injected
into a host mouse embryo, which is re-implanted into a recipient
female. Some of these embryos develop into chimeric mice that
possess germ cells some of which are derived from the mutant cell
line. Therefore, by breeding the chimeric mice it is possible to
obtain a new line of mice containing the introduced genetic lesion
(see, e.g., Capecchi et al., Science 244:1288 (1989)). Chimeric
mice can be derived according to U.S. Pat. No. 6,365,797, issued 2
Apr. 2002; U.S. Pat. No. 6,107,540 issued 22 Aug. 2000; Hogan et
al., Manipulating the Mouse Embryo: A laboratory Manual, Cold
Spring Harbor Laboratory (1988) and Teratocarcinomas and Embryonic
Stem Cells: A Practical Approach, Robertson, ed., IRL Press,
Washington, D.C., (1987).
[0770] Alternatively, various immune-suppressed or immune-deficient
host animals can be used. For example, a genetically athymic "nude"
mouse (see, e.g., Giovanella et al., J. Natl. Cancer Inst. 52:921
(1974)), a SCID mouse, a thymectornized mouse, or an irradiated
mouse (see, e.g., Bradley et al., Br. J. Cancer 38:263 (1978);
Selby et al., Br. J. Cancer 41:52 (1980)) can be used as a host.
Transplantable tumor cells (typically about 10.sup.6 cells)
injected into isogenic hosts produce invasive tumors in a high
proportion of cases, while normal cells of similar origin will not.
In hosts which developed invasive tumors, cells expressing
cancer-assodated sequences are injected subcutaneously or
orthotopically. Mice are then separated into groups, including
control groups and treated experimental groups) e.g. treated with a
modulator). After a suitable length of time, preferably 4-8 weeks,
tumor growth is measured (e.g., by volume or by its two largest
dimensions, or weight) and compared to the control. Tumors that
have statistically significant reduction (using, e.g., Student's T
test) are said to have inhibited growth.
[0771] In Vitro Assays to Identify and Characterize Modulators
[0772] Assays to identify compounds with modulating activity can be
performed in vitro. For example, a cancer polypeptide is first
contacted with a potential modulator and incubated for a suitable
amount of time, e.g., from 0.5 to 48 hours. In one embodiment, the
cancer polypeptide levels are determined in vitro by measuring the
level of protein or mRNA. The level of protein is measured using
immunoassays such as Western blotting, ELISA and the like with an
antibody that selectively binds to the cancer polypeptide or a
fragment thereof. For measurement of mRNA, amplification, e.g.,
using PCR, LCR, or hybridization assays, e. g., Northern
hybridization, RNAse protection, dot blotting, are preferred. The
level of protein or mRNA is detected using directly or indirectly
labeled detection agents, e.g., fluorescently or radioactively
labeled nucleic acids, radioactively or enzymatically labeled
antibodies, and the like, as described herein.
[0773] Alternatively, a reporter gene system can be devised using a
cancer protein promoter operably linked to a reporter gene such as
luciferase, green fluorescent protein, CAT, or P-gal. The reporter
construct is typically transfected into a cell. After treatment
with a potential modulator, the amount of reporter gene
transcription, translation, or activity is measured according to
standard techniques known to those of skill in the art (Davis G F,
supra; Gonzalez, J. & Negulescu, P. Curr. Opin. Biotechnol.
1998: 9:624).
[0774] As outlined above, in vitro screens are done on individual
genes and gene products. That is, having identified a particular
differentially expressed gene as important in a particular state,
screening of modulators of the expression of the gene or the gene
product itself is performed.
[0775] In one embodiment, screening for modulators of expression of
specific gene(s) is performed. Typically, the expression of only
one or a few genes is evaluated. In another embodiment, screens are
designed to first find compounds that bind to differentially
expressed proteins. These compounds are then evaluated for the
ability to modulate differentially expressed activity. Moreover,
once initial candidate compounds are identified, variants can be
further screened to better evaluate structure activity
relationships.
[0776] Binding Assays to Identify and Characterize Modulators
[0777] In binding assays in accordance with the invention, a
purified or isolated gene product of the invention is generally
used. For example, antibodies are generated to a protein of the
invention, and immunoassays are run to determine the amount and/or
location of protein. Alternatively, cells comprising the cancer
proteins are used in the assays.
[0778] Thus, the methods comprise combining a cancer protein of the
invention and a candidate compound such as a ligand, and
determining the binding of the compound to the cancer protein of
the invention. Preferred embodiments utilize the human cancer
protein; animal models of human disease of can also be developed
and used. Also, other analogous mammalian proteins also can be used
as appreciated by those of skill in the art. Moreover, in some
embodiments variant or derivative cancer proteins are used.
[0779] Generally, the cancer protein of the invention, or the
ligand, is non-diffusibly bound to an insoluble support. The
support can, e.g., be one having isolated sample receiving areas (a
microtiter plate, an array, etc.). The insoluble supports can be
made of any composition to which the compositions can be bound, is
readily separated from soluble material, and is otherwise
compatible with the overall method of screening. The surface of
such supports can be solid or porous and of any convenient
shape.
[0780] Examples of suitable insoluble supports include microtiter
plates, arrays, membranes and beads. These are typically made of
glass, plastic (e.g., polystyrene), polysaccharide, nylon,
nitrocellulose, or Teflon.TM., etc. Microtiter plates and arrays
are especially convenient because a large number of assays can be
carried out simultaneously, using small amounts of reagents and
samples. The particular manner of binding of the composition to the
support is not crucial so long as it is compatible with the
reagents and overall methods of the invention, maintains the
activity of the composition and is nondiffusable. Preferred methods
of binding include the use of antibodies which do not sterically
block either the ligand binding site or activation sequence when
attaching the protein to the support, direct binding to "sticky" or
ionic supports, chemical crosslinking, the synthesis of the protein
or agent on the surface, etc. Following binding of the protein or
ligand/binding agent to the support, excess unbound material is
removed by washing. The sample receiving areas may then be blocked
through incubation with bovine serum albumin (BSA), casein or other
innocuous protein or other moiety.
[0781] Once a cancer protein of the invention is bound to the
support, and a test compound is added to the assay. Alternatively,
the candidate binding agent is bound to the support and the cancer
protein of the invention is then added. Binding agents include
specific antibodies, non-natural binding agents identified in
screens of chemical libraries, peptide analogs, etc.
[0782] Of particular interest are assays to identify agents that
have a low toxicity for human cells. A wide variety of assays can
be used for this purpose, including proliferation assays, cAMP
assays, labeled in vitro protein-protein binding assays,
electrophoretic mobility shift assays, immunoassays for protein
binding, functional assays (phosphorylation assays, etc.) and the
like.
[0783] A determination of binding of the test compound (ligand,
binding agent, modulator, etc.) to a cancer protein of the
invention can be done in a number of ways. The test compound can be
labeled, and binding determined directly, e.g., by attaching all or
a portion of the cancer protein of the invention to a solid
support, adding a labeled candidate compound (e.g., a fluorescent
label), washing off excess reagent, and determining whether the
label is present on the solid support. Various blocking and washing
steps can be utilized as appropriate.
[0784] In certain embodiments, only one of the components is
labeled, e.g., a protein of the invention or ligands labeled.
Alternatively, more than one component is labeled with different
labels, e.g., I.sup.125, for the proteins and a fluorophor for the
compound. Proximity reagents, e.g., quenching or energy transfer
reagents are also useful.
[0785] Competitive Binding to Identify and Characterize
Modulators
[0786] In one embodiment, the binding of the "test compound" is
determined by competitive binding assay with a "competitor." The
competitor is a binding moiety that binds to the target molecule
(e.g., a cancer protein of the invention). Competitors include
compounds such as antibodies, peptides, binding partners, ligands,
etc. Under certain circumstances, the competitive binding between
the test compound and the competitor displaces the test compound.
In one embodiment, the test compound is labeled. Either the test
compound, the competitor, or both, is added to the protein for a
time sufficient to allow binding. Incubations are performed at a
temperature that facilitates optimal activity, typically between
four and 40.degree. C. Incubation periods are typically optimized,
e.g., to facilitate rapid high throughput screening; typically
between zero and one hour will be sufficient. Excess reagent is
generally removed or washed away. The second component is then
added, and the presence or absence of the labeled component is
followed, to indicate binding.
[0787] In one embodiment, the competitor is added first, followed
by the test compound. Displacement of the competitor is an
indication that the test compound is binding to the cancer protein
and thus is capable of binding to, and potentially modulating, the
activity of the cancer protein. In this embodiment, either
component can be labeled. Thus, e.g., if the competitor is labeled,
the presence of label in the post-test compound wash solution
indicates displacement by the test compound. Alternatively, if the
test compound is labeled, the presence of the label on the support
indicates displacement.
[0788] In an alternative embodiment, the test compound is added
first, with incubation and washing, followed by the competitor. The
absence of binding by the competitor indicates that the test
compound binds to the cancer protein with higher affinity than the
competitor. Thus, if the test compound is labeled, the presence of
the label on the support, coupled with a lack of competitor
binding, indicates that the test compound binds to and thus
potentially modulates the cancer protein of the invention.
[0789] Accordingly, the competitive binding methods comprise
differential screening to identity agents that are capable of
modulating the activity of the cancer proteins of the invention. In
this embodiment, the methods comprise combining a cancer protein
and a competitor in a first sample. A second sample comprises a
test compound, the cancer protein, and a competitor. The binding of
the competitor is determined for both samples, and a change, or
difference in binding between the two samples indicates the
presence of an agent capable of binding to the cancer protein and
potentially modulating its activity. That is, if the binding of the
competitor is different in the second sample relative to the first
sample, the agent is capable of binding to the cancer protein.
[0790] Alternatively, differential screening is used to identify
drug candidates that bind to the native cancer protein, but cannot
bind to modified cancer proteins. For example the structure of the
cancer protein is modeled and used in rational drug design to
synthesize agents that interact with that site, agents which
generally do not bind to site-modified proteins. Moreover, such
drug candidates that affect the activity of a native cancer protein
are also identified by screening drugs for the ability to either
enhance or reduce the activity of such proteins.
[0791] Positive controls and negative controls can be used in the
assays. Preferably control and test samples are performed in at
least triplicate to obtain statistically significant results.
Incubation of all samples occurs for a time sufficient to allow for
the binding of the agent to the protein. Following incubation,
samples are washed free of non-specifically bound material and the
amount of bound, generally labeled agent determined. For example,
where a radiolabel is employed, the samples can be counted in a
scintillation counter to determine the amount of bound
compound.
[0792] A variety of other reagents can be included in the screening
assays. These include reagents like salts, neutral proteins, e.g.
albumin, detergents, etc. which are used to facilitate optimal
protein-protein binding and/or reduce non-specific or background
interactions. Also reagents that otherwise improve the efficiency
of the assay, such as protease inhibitors, nuclease inhibitors,
anti-microbial agents, etc., can be used. The mixture of components
is added in an order that provides for the requisite binding.
[0793] Use of Polynucleotides to Down-Regulate or Inhibit a Protein
of the Invention.
[0794] Polynucleotide modulators of cancer can be introduced into a
cell containing the target nucleotide sequence by formation of a
conjugate with a ligand-binding molecule, as described in WO
91/04753. Suitable ligand-binding molecules include, but are not
limited to, cell surface receptors, growth factors, other
cytokines, or other ligands that bind to cell surface receptors.
Preferably, conjugation of the ligand binding molecule does not
substantially interfere with the ability of the ligand binding
molecule to bind to its corresponding molecule or receptor, or
block entry of the sense or antisense oligonucleotide or its
conjugated version into the cell. Alternatively, a polynucleotide
modulator of cancer can be introduced into a cell containing the
target nucleic acid sequence, e.g., by formation of a
polynucleotide-lipid complex, as described in WO 90/10448. It is
understood that the use of antisense molecules or knock out and
knock in models may also be used in screening assays as discussed
above, in addition to methods of treatment.
[0795] Inhibitory and Antisense Nucleotides
[0796] In certain embodiments, the activity of a cancer-associated
protein is down-regulated, or entirely inhibited, by the use of
antisense polynucleotide or inhibitory small nuclear RNA (snRNA),
i.e., a nucleic acid complementary to, and which can preferably
hybridize specifically to, a coding mRNA nucleic acid sequence,
e.g., a cancer protein of the invention, mRNA, or a subsequence
thereof. Binding of the antisense polynucleotide to the mRNA
reduces the translation and/or stability of the mRNA.
[0797] In the context of this invention, antisense polynucleotides
can comprise naturally occurring nucleotides, or synthetic species
formed from naturally occurring subunits or their close homologs.
Antisense polynucleotides may also have altered sugar moieties or
inter-sugar linkages. Exemplary among these are the
phosphorothioate and other sulfur containing species which are
known for use in the art. Analogs are comprised by this invention
so long as they function effectively to hybridize with nucleotides
of the invention. See, e.g., Isis Pharmaceuticals, Carlsbad,
Calif.; Sequitor, Inc., Natick, Mass.
[0798] Such antisense polynucleotides can readily be synthesized
using recombinant means, or can be synthesized in vitro. Equipment
for such synthesis is sold by several vendors, including Applied
Biosystems. The preparation of other oligonucleotides such as
phosphorothioates and alkylated derivatives is also well known to
those of skill in the art.
[0799] Antisense molecules as used herein include antisense or
sense oligonucleotides. Sense oligonucleotides can, e.g., be
employed to block transcription by binding to the anti-sense
strand. The antisense and sense oligonucleotide comprise a single
stranded nucleic acid sequence (either RNA or DNA) capable of
binding to target mRNA (sense) or DNA (antisense) sequences for
cancer molecules. Antisense or sense oligonucleotides, according to
the present invention, comprise a fragment generally at least about
12 nucleotides, preferably from about 12 to 30 nucleotides. The
ability to derive an antisense or a sense oligonucleotide, based
upon a cDNA sequence encoding a given protein is described in,
e.g., Stein & Cohen (Cancer Res. 48:2659 (1988 and van der Krol
et al. (BioTechniques 6:958 (1988)).
[0800] Ribozymes
[0801] In addition to antisense polynucleotides, ribozymes can be
used to target and inhibit transcription of cancer-associated
nucleotide sequences. A ribozyme is an RNA molecule that
catalytically cleaves other RNA molecules. Different kinds of
ribozymes have been described, including group I ribozymes,
hammerhead ribozymes, hairpin ribozymes, RNase P, and axhead
ribozymes (see, e.g., Castanotto et al., Adv. in Pharmacology 25:
289-317 (1994) for a general review of the properties of different
ribozymes).
[0802] The general features of hairpin ribozymes are described,
e.g., in Hampel et al., Nucl. Acids Res. 18:299-304 (1990);
European Patent Publication No. 0360257; U.S. Pat. No. 5,254,678.
Methods of preparing are well known to those of skill in the art
(see, e.g., WO 94/26877; Ojwang et al., Proc. Natl. Acad. Sci. USA
90:6340-6344 (1993); Yamada et al., Human Gene Therapy 1:39-45
(1994); Leavitt et al., Proc. Natl. Acad Sci. USA 92:699-703
(1995); Leavitt et al., Human Gene Therapy 5: 1151-120 (1994); and
Yamada et al., Virology 205: 121-126 (1994)).
[0803] Use of Modulators in Phenotypic Screening
[0804] In one embodiment, a test compound is administered to a
population of cancer cells, which have an associated cancer
expression profile. By "administration" or "contacting" herein is
meant that the modulator is added to the cells in such a manner as
to allow the modulator to act upon the cell, whether by uptake and
intracellular action, or by action at the cell surface. In some
embodiments, a nucleic acid encoding a proteinaceous agent (i.e., a
peptide) is put into a viral construct such as an adenoviral or
retroviral construct, and added to the cell, such that expression
of the peptide agent is accomplished, e.g., PCT US97/01019.
Regulatable gene therapy systems can also be used. Once the
modulator has been administered to the cells, the cells are washed
if desired and are allowed to incubate under preferably
physiological conditions for some period. The cells are then
harvested and a new gene expression profile is generated. Thus,
e.g., cancer tissue is screened for agents that modulate, e.g.,
induce or suppress, the cancer phenotype. A change in at least one
gene, preferably many, of the expression profile indicates that the
agent has an effect on cancer activity. Similarly, altering a
biological function or a signaling pathway is indicative of
modulator activity. By defining such a signature for the cancer
phenotype, screens for new drugs that alter the phenotype are
devised. With this approach, the drug target need not be known and
need not be represented in the original gene/protein expression
screening platform, nor does the level of transcript for the target
protein need to change. The modulator inhibiting function will
serve as a surrogate marker
[0805] As outlined above, screens are done to assess genes or gene
products. That is, having identified a particular differentially
expressed gene as important in a particular state, screening of
modulators of either the expression of the gene or the gene product
itself is performed.
[0806] Use of Modulators to Affect Peptides of the Invention
[0807] Measurements of cancer polypeptide activity, or of the
cancer phenotype are performed using a variety of assays. For
example, the effects of modulators upon the function of a cancer
polypeptide(s) are measured by examining parameters described
above. A physiological change that affects activity is used to
assess the influence of a test compound on the polypeptides of this
invention. When the functional outcomes are determined using intact
cells or animals, a variety of effects can be assesses such as, in
the case of a cancer associated with solid tumors, tumor growth,
tumor metastasis, neovascularization, hormone release,
transcriptional changes to both known and uncharacterized genetic
markers (e.g., by Northern blots), changes in cell metabolism such
as cell growth or pH changes, and changes in intracellular second
messengers such as cGNIP.
[0808] Methods of Identifyinq Characterizing Cancer-Associated
Sequences
[0809] Expression of various gene sequences is correlated with
cancer. Accordingly, disorders based on mutant or variant cancer
genes are determined. In one embodiment, the invention provides
methods for identifying cells containing variant cancer genes,
e.g., determining the presence of, all or part, the sequence of at
least one endogenous cancer gene in a cell. This is accomplished
using any number of sequencing techniques. The invention comprises
methods of identifying the cancer genotype of an individual, e.g.,
determining all or part of the sequence of at least one gene of the
invention in the individual. This is generally done in at least one
tissue of the individual, e.g., a tissue set forth in Table I, and
may include the evaluation of a number of tissues or different
samples of the same tissue. The method may include comparing the
sequence of the sequenced gene to a known cancer gene, i.e., a
wild-type gene to determine the presence of family members,
homologies, mutations or variants. The sequence of all or part of
the gene can then be compared to the sequence of a known cancer
gene to determine if any differences exist. This is done using any
number of known homology programs, such as BLAST, Bestfit, etc. The
presence of a difference in the sequence between the cancer gene of
the patient and the known cancer gene correlates with a disease
state or a propensity for a disease state, as outlined herein.
[0810] In a preferred embodiment, the cancer genes are used as
probes to determine the number of copies of the cancer gene in the
genome. The cancer genes are used as probes to determine the
chromosomal localization of the cancer genes. Information such as
chromosomal localization finds use in providing a diagnosis or
prognosis in particular when chromosomal abnormalities such as
translocations, and the like are identified in the cancer gene
locus.
[0811] XIV.) Kits/Articles of Manufacture
[0812] For use in the diagnostic and therapeutic applications
described herein, kits are also within the scope of the invention.
Such kits can comprise a carrier, package or container that is
compartmentalized to receive one or more containers such as vials,
tubes, and the like, each of the container(s) comprising one of the
separate elements to be used in the method. For example, the
container(s) can comprise a probe that is or can be detectably
labeled. Such probe can be an antibody or polynucleotide specific
for a FIG. 2-related protein or a FIG. 2 gene or message,
respectively. Where the method utilizes nucleic acid hybridization
to detect the target nucleic acid, the kit can also have containers
containing nucleotide(s) for amplification of the target nucleic
acid sequence and/or a container comprising a reporter-means, such
as a biotin-binding protein, such as avidin or streptavidin, bound
to a reporter molecule, such as an enzymatic, florescent, or
radioisotope label. The kit can include all or part of the amino
acid sequences in FIG. 2 or FIG. 3 or analogs thereof, or a nucleic
acid molecules that encodes such amino acid sequences.
[0813] The kit of the invention will typically comprise the
container described above and one or more other containers
comprising materials desirable from a commercial and user
standpoint, including buffers, diluents, filters, needles,
syringes; carrier, package, container, vial and/or tube labels
listing contents and/or instructions for use, and package inserts
with instructions for use.
[0814] A label can be present on the container to indicate that the
composition is used for a specific therapy or non-therapeutic
application, such as a diagnostic or laboratory application, and
can also indicate directions for either in vivo or in vitro use,
such as those described herein. Directions and or other information
can also be included on an insert(s) or label(s) which is included
with or on the kit.
[0815] The terms "kit" and "article of manufacture" can be used as
synonyms.
[0816] In another embodiment of the invention, an article(s) of
manufacture containing compositions, such as amino acid
sequence(s), small molecule(s), nucleic acid sequence(s), and/or
antibody(s), e.g., materials useful for the diagnosis, prognosis,
prophylaxis and/or treatment of neoplasias of tissues such as those
set forth in Table I is provided. The article of manufacture
typically comprises at least one container and at least one label.
Suitable containers include, for example, bottles, vials, syringes,
and test tubes. The containers can be formed from a variety of
materials such as glass or plastic. The container can hold amino
acid sequence(s), small molecule(s), nucleic acid sequence(s),
and/or antibody(s), in one embodiment the container holds a
polynucleotide for use in examining the mRNA expression profile of
a cell, together with reagents used for this purpose.
[0817] The container can alternatively hold a composition which is
effective for treating, diagnosis, prognosing or prophylaxing a
condition and can have a sterile access port (for example the
container can be an intravenous solution bag or a vial having a
stopper pierceable by a hypodermic injection needle). The active
agents in the composition can be an antibody capable of
specifically binding 98P4B6 and modulating the function of
98P4B6.
[0818] The label can be on or associated with the container. A
label a can be on a container when letters, numbers or other
characters forming the label are molded or etched into the
container itself; a label can be associated with a container when
it is present within a receptacle or carrier that also holds the
container, e.g., as a package insert. The label can indicate that
the composition is used for diagnosing, treating, prophylaxing or
prognosing a condition, such as a neoplasia of a tissue set forth
in Table I. The article of manufacture can further comprise a
second container comprising a pharmaceutically-acceptable buffer,
such as phosphate-buffered saline, Ringer's solution and/ordextrose
solution. It can further include other materials desirable from a
commercial and user standpoint, including other buffers, diluents,
filters, stirrers, needles, syringes, and/or package inserts with
indications and/or instructions for use.
EXAMPLES
[0819] Various aspects of the invention are further described and
illustrated by way of the several examples that follow, none of
which are intended to limit the scope of the invention.
Example 1
SSH-Generated Isolation of cDNA Fragment of the 98P4B6 Gene
[0820] To isolate genes that are over-expressed in prostate cancer
we used the Suppression Subtractive Hybridization (SSH) procedure
using cDNA derived from prostate tissues. The 98P4B6 SSH cDNA
sequence was derived from normal prostate minus LAPC-4AD prostate
xenograft cDNAs. The 98P4B6 cDNA was identified as highly expressed
in prostate cancer.
[0821] Materials and Methods
[0822] Human Tissues:
[0823] The patient cancer and normal tissues were purchased from
different sources such as the NDRI (Philadelphia, Pa.). mRNA for
some normal tissues were purchased from Clontech, Palo Alto,
Calif.
[0824] RNA Isolation:
[0825] Tissues were homogenized in Trizol reagent (Life
Technologies, Gibco BRL) using 10 ml/g tissue isolate total RNA.
Poly A RNA was purified from total RNA using Qiagen's Oligotex mRNA
Mini and Midi kits. Total and mRNA were quantified by
spectrophotometric analysis (O.D. 260/280 nm) and analyzed by gel
electrophoresis.
[0826] Oligonucleotides:
[0827] The following HPLC purified oligonucleotides were used.
[0828] DPNCDN (cDNA Synthesis Primer):
[0829] 5'TTTTGATCAAGCTT.sub.303' (SEQ ID NO: 101)
[0830] Adaptor 1:
1 5'CTAATACGACTCACTATAGGGCTCGAGCGGC (SEQ ID NO: 102) CGCCCGGGCAG3'
3'GGCCCGTCCTAG5' (SEQ ID NO: 103)
[0831] Adaptor 2:
2 5'GTAATACGACTCACTATAGGGCAGCGTGGTC (SEQ ID NO: 104) GCGGCCGAG3'
3'CGGCTCCTAG5' (SEQ ID NO: 105)
[0832] PCR Primer 1:
[0833] 5'CTAATACGACTCACTATAGGGC3' (SEQ ID NO: 106)
[0834] Nested Primer (NP)1:
[0835] 5'TCGAGCGGCCGCCCGGGCAGGA3' (SEQ ID NO: 107)
[0836] Nested Primer (NP)2:
[0837] 5'AGCGTGGTCGCGGCCGAGGA3' (SEQ ID NO: 108)
[0838] Suppression Subtractive Hybridization:
[0839] Suppression Subtractive Hybridization (SSH) was used to
identify cDNAs corresponding to genes that may be differentially
expressed in prostate cancer. The SSH reaction utilized cDNA from
prostate cancer xenograft and normal tissues.
[0840] The gene 98P4B6 sequence was derived from normal prostate
tissue minus prostate cancer xenograft LAPC-4AD cDNA subtraction.
The SSH DNA sequence (FIG. 1) was identified.
[0841] The cDNA derived from LAPC-4AD was used as the source of the
"driver" cDNA, while the cDNA from normal prostate was used as the
source of the "tester" cDNA. Double stranded cDNAs corresponding to
tester and driver cDNAs were synthesized from 2 .mu.g of
poly(A).sup.+ RNA isolated from the relevant tissue, as described
above, using CLONTECH's PCR-Select cDNA Subtraction Kit and 1 ng of
oligonucleotide DPNCDN as primer. First- and second-strand
synthesis were carried out as described in the Kit's user manual
protocol (CLONTECH Protocol No. PT 1117-1, Catalog No. K1804-1).
The resulting cDNA was digested with Dpn II for 3 hrs at
370.degree. C. Digested cDNA was extracted with phenol/chloroform
(1:1) and ethanol precipitated.
[0842] Driver cDNA was generated by combining in a 1:1 ratio Dpn II
digested cDNA from the relevant tissue source (see above) with
digested cDNAs derived from normal tissue.
[0843] Tester cDNA was generated by diluting 1 .mu.l of Dpn II
digested cDNA from the relevant tissue source (see above) (400 ng)
in 5 .mu.l of water. The diluted cDNA (2 .mu.l, 160 ng) was then
ligated to 2 .mu.l of Adaptor 1 and Adaptor 2 (10 .mu.M), in
separate ligation reactions, in a total volume of 10 .mu.l at
16.degree. C. overnight, using 400 u of T4 DNA ligase (CLONTECH).
Ligation was terminated with 1 .mu.l of 0.2 M EDTA and heating at
72.degree. C. for 5 min.
[0844] The first hybridization was performed by adding 1.5 .mu.l
(600 ng) of driver cDNA to each of two tubes containing 1.5 .mu.l
(20 ng) Adaptor 1- and Adaptor 2-ligated tester cDNA. In a final
volume of 4 .mu.l, the samples were overlaid with mineral oil,
denatured in an MJ Research thermal cycler at 98.degree. C. for 1.5
minutes, and then were allowed to hybridize for 8 hrs at 68.degree.
C. The two hybridizations were then mixed together with an
additional 1 .mu.l of fresh denatured driver cDNA and were allowed
to hybridize overnight at 68.degree. C. The second hybridization
was then diluted in 200 .mu.l of 20 mM Hepes, pH 8.3, 50 mM NaCl,
0.2 mM EDTA, heated at 70.degree. C. for 7 min. and stored at
-20.degree. C.
[0845] PCR Amplification, Cloning and Sequencing of Gene Fragments
Generated from SSH:
[0846] To amplify gene fragments resulting from SSH reactions, two
PCR amplifications were performed. In the primary PCR reaction 1
.mu.l of the diluted final hybridization mix was added to 1 .mu. of
PCR primer 1 (10 .mu.M), 0.5 .mu.l dNTP mix (10 .mu.M), 2.5 .mu.l
10.times.reaction buffer (CLONTECH) and 0.5 .mu.l
50.times.Advantage cDNA polymerase Mix (CLONTECH) in a final volume
of 25 .mu.l. PCR 1 was conducted using the following conditions:
75.degree. C. for 5 min., 94.degree. C. for 25 sec., then 27 cycles
of 94.degree. C. for 10 sec, 66.degree. C. for 30 sec, 72.degree.
C. for 1.5 min. Five separate primary PCR reactions were performed
for each experiment. The products were pooled and diluted 1:10 with
water. For the secondary PCR reaction, 1 .mu.l from the pooled and
diluted primary PCR reaction was added to the same reaction mix as
used for PCR 1, except that primers NP1 and NP2 (10 .mu.M) were
used instead of PCR primer 1. PCR 2 was performed using 10-12
cycles of 94.degree. C. for 10 sec, 68.degree. C. for 30 sec, and
72.degree. C. for 1.5 minutes. The PCR products were analyzed using
2% agarose gel electrophoresis.
[0847] The PCR products were inserted into pCR2.1 using the T/A
vector cloning kit (Invitrogen). Transformed E. coli were subjected
to blue/white and ampicillin selection. White colonies were picked
and arrayed into 96 well plates and were grown in liquid culture
overnight. To identify inserts, PCR amplification was performed on
1 ul of bacterial culture using the conditions of PCR1 and NP1 and
NP2 as primers. PCR products were analyzed using 2% agarose gel
electrophoresis.
[0848] Bacterial clones were stored in 20% glycerol in a 96 well
format. Plasmid DNA was prepared, sequenced, and subjected to
nucleic acid homology searches of the GenBank, dBest, and NCI-CGAP
databases.
[0849] RT-PCR Expression Analysis:
[0850] First strand cDNAs can be generated from 1 .mu.g of mRNA
with oligo (dT)12-18 priming using the Gibco-BRL Superscript
Preamplification system. The manufacturer's protocol was used which
included an incubation for 50 min at 42.degree. C. with reverse
transcriptase followed by RNAse H treatment at 37.degree. C. for 20
min. After completing the reaction, the volume can be increased to
200 .mu.l with water prior to normalization. First strand cDNAs
from 16 different normal human tissues can be obtained from
Clontech.
[0851] Normalization of the first strand cDNAs from multiple
tissues was performed by using the primers
5'atatcgccgcgctcgtcgtcgacaa3' (SEQ ID NO: 109) and
5'agccacacgcagctcattgtagaagg 3' (SEQ ID NO: 110) to amplify
.beta.-actin. First strand cDNA (5 .mu.l) were amplified in a total
volume of 50 .mu.l containing 0.4 .mu.M primers, 0.2 .mu.M each
dNTPs, 1.times.PCR buffer (Clontech, 10 mM Tris-HCL, 1.5 mM
MgCl.sub.2, 50 mM KCl, pH8.3) and 1.times.Klentaq DNA polymerase
(Clontech). Five .mu.l of the PCR reaction can be removed at 18,
20, and 22 cycles and used for agarose gel electrophoresis. PCR was
performed using an MJ Research thermal cycler under the following
conditions: Initial denaturation can be at 94.degree. C. for 15
sec, followed by a 18, 20, and 22 cycles of 94.degree. C. for 15,
65.degree. C. for 2 min, 72.degree. C. for 5 sec. A final extension
at 72.degree. C. was carried out for 2 min. After agarose gel
electrophoresis, the band intensities of the 283 bp .beta.-actin
bands from multiple tissues were compared by visual inspection.
Dilution factors for the first strand cDNAs were calculated to
result in equal .beta.-actin band intensities in all tissues after
22 cycles of PCR. Three rounds of normalization can be required to
achieve equal band intensities in all tissues after 22 cycles of
PCR.
[0852] To determine expression levels of the 98P4B6 gene, 5 .mu.l
of normalized first strand cDNA were analyzed by PCR using 26, and
30 cycles of amplification. Semi-quantitative expression analysis
can be achieved by comparing the PCR products at cycle numbers that
give light band intensities. The primers used for RT-PCR were
designed using the 98P4B6 SSH sequence and are listed below:
[0853] 98P4B6.1
[0854] 5'-GACTGAGCTGGAACTGGAATTTGT-3' (SEQ ID NO: 111)
[0855] 98P4B6.2
[0856] 5'-TTTGAGGAGACTTCATCTCACTGG-3' (SEQ ID NO: 112)
Example 2
Isolation of Full Length 98P4B6 Encoding cDNA
[0857] The 98P4B6 SSH cDNA sequence was derived from a substraction
consisting of normal prostate minus prostate cancer xenograft. The
SSH cDNA sequence (FIG. 1) was designated 98P4B6.
[0858] The 98P4B6 SSH DNA sequence of 183 bp is shown in FIG. 1.
Full-length 98P4B6 v.1 (clone GTD3) of 2453 bp was cloned from
prostate cDNA library, revealing an ORF of 454 amino acids (FIG. 2
and FIG. 3). 98P4B6 v.6 was also cloned from normal prostate
library. Other variants of 98P4B6 were also identified and these
are listed in FIGS. 2 and 3.
[0859] 98P4B6 v.2, v.3, v.4, v.5, v.6, v.7 and v.8 are splice
variants of 98P4B6 v.1. 98P4B6 v.9 through v.19 are SNP variants
and differ from v.1 by one amino acid. 98P4B6 v.20 through v.24 are
SNP variants of v.7. 98P4B6 v.25 through v.38 are SNP variants of
v.8. Though these SNP variants were shown separately, they could
also occur in any combinations and in any transcript variants.
Example 3
Chromosomal Mapping of 98P4B6
[0860] Chromosomal localization can implicate genes in disease
pathogenesis. Several chromosome mapping approaches are available
including fluorescent in situ hybridization (FISH), human/hamster
radiation hybrid (RH) panels (Walter et al., 1994; Nature Genetics
7:22; Research Genetics, Huntsville Ala.), human-rodent somatic
cell hybrid panels such as is available from the Cornell Institute
(Camden, N.J.), and genomic viewers utilizing BLAST homologies to
sequenced and mapped genomic clones (NCBI, Bethesda, Md.).
[0861] 98P4B6 maps to chromosome 7q21 using 98P4B6 sequence and the
NCBI BLAST tool: located on the World Wide Web at
.ncbi.nlm.nih.gov/genome/seq-
/page.cgi?F=HsBlast.html&&ORG=Hs).
Example 4
Expression Analysis of 98P4B6
[0862] Expression analysis by RT-PCR demonstrated that 98P4B6 is
strongly expressed in prostate cancer patient specimens (FIG. 14).
First strand cDNA was generated from normal stomach, normal brain,
normal heart, normal liver, normal skeletal muscle, normal testis,
normal prostate, normal bladder, normal kidney, normal colon,
normal lung, normal pancreas, and a pool of cancer specimens from
prostate cancer patients, bladder cancer patients, kidney cancer
patients, colon cancer patients, lung cancer patients, pancreas
cancer patients, and a pool of 2 patient prostate metastasis to
lymph node. Normalization was performed by PCR using primers to
actin. Semi-quantitative PCR, using primers directed to 98P4B6 v.1,
v.13, or/and v.14 (A), or directed specifically to the splice
variants 98P4B6 v.6 and v.8 (B), was performed at 26 and 30 cycles
of amplification. Samples were run on an agarose gel, and PCR
products were quantitated using the Alphalmager software. Results
show strong expression of 98P4B6 and its splice variants v.6 and
v.8 in normal prostate and in prostate cancer. Expression was also
detected in bladder cancer, kidney cancer, colon cancer, lung
cancer, pancreas cancer, breast cancer, cancer metastasis as well
as in the prostate cancer metastasis to lymph node specimens,
compared to all normal tissues tested. As noted below, e.g., in
Example 6, as 98P4B6 v.1 is in expressed in cancer tissues such as
those listed in Table 1, the other protein-encoding 98P4B6 variants
are expressed in these tissues as well; this principle is
corroborated by data in (FIG. 14) for the proteins herein
designated 98P4B6 v.6 or v.8 is found, e.g., in prostate, lung,
ovary, bladder, breast, colon, kidney and pancreas, cancers, as
well as in the literature (Porkka et al., Lab Invest, 2002 and
Korkmaz et al., JBC, 2002) where the protein 98P4B6 v.8 is
identified in normal prostate and prostate cancer.
[0863] When the genomic region to which a gene maps is modulated in
a particular cancer, the alternative transcripts or splice variants
of the gene are modulated as well. Disclosed herein is that 98P4B6
has a particular expression profile related to cancer. Alternative
transcripts and splice variants of 98P4B6 are also involved in
cancers in the same or additional tissues, thus serving as
tumor-associated markers/antigens.
[0864] Expression of 98P4B6 v.1, v.13, and/or v.14 was detected in
prostate, lung, ovary, bladder, cervix, uterus and pancreas cancer
patient specimens (FIG. 15). First strand cDNA was prepared from a
panel of patient cancer specimens. Normalization was performed by
PCR using primers to actin. Semi-quantitative PCR, using primers to
98P4B6, was performed at 26 and 30 cycles of amplification. Samples
were run on an agarose gel, and PCR products were quantitated using
the Alphalmager software. Expression was recorded as absent, low,
medium or strong. Results show expression of 98P4B6 in the majority
of all patient cancer specimens tested.
[0865] FIG. 16 shows that 98P4B6 is expressed in stomach cancer
patient specimens. (A) RNA was extracted from normal stomach (N)
and from 10 different stomach cancer patient specimens (T).
Northern blot with 10 .mu.g of total RNA/lane was probed with
98P4B6 sequence. Results show strong expression of 98P4B6 in the
stomach tumor tissues and lower expression in normal stomach. The
lower panel represents ethidium bromide staining of the blot
showing quality of the RNA samples. (B) Expression of 98P4B6 was
assayed in a panel of human stomach cancers (T) and their
respective matched normal tissues (N) on RNA dot blots. 98P4B6 was
detected in 7 out of 8 stomach tumors but not in the matched normal
tissues.
Example 5
Transcript Variants of 98P4B6
[0866] Transcript variants are variants of mature mRNA from the
same gene which arise by alternative transcription or alternative
splicing. Alternative transcripts are transcripts from the same
gene but start transcription at different points. Splice variants
are mRNA variants spliced differently from the same transcript. In
eukaryotes, when a multi-exon gene is transcribed from genomic DNA,
the initial RNA is spliced to produce functional mRNA, which has
only exons and is used for translation into an amino acid sequence.
Accordingly, a given gene can have zero to many alternative
transcripts and each transcript can have zero to many splice
variants. Each transcript variant has a unique exon makeup, and can
have different coding and/or non-coding (5' or 3' end) portions,
from the original transcript. Transcript variants can code for
similar or different proteins with the same or a similar function
or can encode proteins with different functions, and can be
expressed in the same tissue at the same time or in different
tissues at the same time or in the same tissue at different times
or in different tissues at different times. Proteins encoded by
transcript variants can have similar or different cellular or
extracellular localizations, e.g., secreted versus
intracellular.
[0867] Transcript variants are identified by a variety of
art-accepted methods. For example, alternative transcripts and
splice variants are identified by full-length cloning experiment,
or by use of full-length transcript and EST sequences. First, all
human ESTs were grouped into clusters which show direct or indirect
identity with each other. Second, ESTs in the same duster were
further grouped into sub-clusters and assembled into a consensus
sequence. The original gene sequence is compared to the consensus
sequence(s) or other full-length sequences. Each consensus sequence
is a potential splice variant for that gene. Even when a variant is
identified that is not a full-length clone, that portion of the
variant is very useful for antigen generation and for further
cloning of the full-length splice variant, using techniques known
in the art.
[0868] Moreover, computer programs are available in the art that
identify transcript variants based on genomic sequences.
Genomic-based transcript variant identification programs include
FgenesH (A. Salamov and V. Solovyev, "Ab initio gene finding in
Drosophila genomic DNA," Genome Research. 2000 April;10(4):516-22);
Grail (URL compbio.ornl.gov/Grail-bin- /EmptyGrailForm) and GenScan
(URL genes.mit.edu/GENSCAN.html). For a general discussion of
splice variant identification protocols see., e.g., Southan, C., A
genomic perspective on human proteases, FEBS Lett. 2001 Jun. 8;
498(2-3):214-8; de Souza, S. J., et al., Identification of human
chromosome 22 transcribed sequences with ORF expressed sequence
tags, Proc. Natl Acad Sci U S A. 2000 Nov. 7; 97(23):12690-3.
[0869] To further confirm the parameters of a transcript variant, a
variety of techniques are available in the art, such as full-length
cloning, proteomic validation, PCR-based validation, and 5' RACE
validation, etc. (see e.g., Proteomic Validation: Brennan, S. O.,
et al., Albumin banks peninsula: a new termination variant
characterized by electrospray mass spectrometry, Biochem Biophys
Acta. 1999 Aug. 17;1433(1-2):321-6; Ferranti P, et al.,
Differential splicing of pre-messenger RNA produces multiple forms
of mature caprine alpha(s1)-casein, Eur J Biochem. 1997 Oct.
1;249(1):1-7. For PCR-based Validation: Wellmann S, et al.,
Specific reverse transcription-PCR quantification of vascular
endothelial growth factor (VEGF) splice variants by LightCycler
technology, Clin Chem. 2001 April ;47(4):654-60; Jia, H. P., et
al., Discovery of new human beta-defensins using a genomics-based
approach, Gene. 2001 Jan. 24; 263(1-2):211-8. For PCR-based and 5'
RACE Valdation: Brigle, K. E., et al., Organization of the murine
reduced folate carrier gene and identification of variant splice
forms, Biochem Biophys Acta. 1997 Aug. 7; 1353(2): 191-8).
[0870] It is known in the art that genomic regions are modulated in
cancers. Recently, Porkka et al. (2002) reported that transcript
variants of STEAP2 were expressed and were found in both normal and
malignant prostate tissue (Porkka, K. P., et al. Cloning and
characterization of a novel six-transmembrane protein STEAP2,
expressed in normal and malignant prostate. Laboratory
Investigation 2002 November; 82(11):1573-1582). Another group of
scientists also reported that transcript variants of STEAP2 (98P4B6
v.6 herein) also were expressed significantly higher in prostate
cancer than normal prostate (Korkmaz, K. S., et al. Molecular
cloning and characterization of STAMP1, a highly prostate-specific
six transmembrane protein that is overexpressed in prostate cancer.
The Journal of Biological Chemistry. 2002 September
277(39):36689-36696.). When the genomic region to which a gene maps
is modulated in a particular cancer, the alternative transcripts or
splice variants of the gene are modulated as well. Disclosed herein
is that 98P4B6 has a particular expression profile related to
cancer. Alternative transcripts and splice variants of 98P4B6 are
also involved in cancers in the same or additional tissues, thus
serving as tumor-associated markers/antigens.
[0871] Using the full-length gene and EST sequences, seven
transcript variants were identified, designated as 98P4B6 v.2, v.3,
v.4, v.5, v.6, v.7 and v.8, as shown in FIG. 12. The boundaries of
exons in the original transcript, 98P4B6 v.1 were shown in Table
LI. The first 22 bases of v.1 were not in the nearby 5' region of
v.1 on the current assembly of the human genome. Compared with
98P4B6 v.1, variant v.2 was a single exon transcript whose 3'
portion was the same as the last exon of v.1. The first two exons
of v.3 were in intron 1 of v. 1. Variants v.4, v.5, and v.6 spliced
out 224-334 in the first exon of v.1. In addition, v.5 spliced out
exon 5 while v.6 spliced out exon 6 but extended exon 5 of v.1.
Variant v.7 used alternative transcription start and different 3'
exons. Variant v.8 extended 5' end and kept the whole intron 5 of
v.1. Theoretically, each different combination of exons in spatial
order, e.g. exons 2 and 3, is a potential splice variant.
[0872] Tables LII through LV are set forth on a variant-by-variant
basis. Tables LII(a)-(g) show the nucleotide sequence of the
transcript variant. Tables LII (a)-(g) show the alignment of the
transcript variant with the nucleic acid sequence of 98P4B6 v.1.
Tables LIV(a)-(g) lay out the amino acid translation of the
transcript variant for the identified reading frame orientation.
Tables LV(a)-(g) display alignments of the amino acid sequence
encoded by the splice variant with that of 98P4B6 v.1.
Additionally, single nucleotide polymorphisms (SNP) are noted in
the alignment.
Example 6
Single Nucleotide Polymorphisms of 98P4B6
[0873] A Single Nucleotide Polymorphism (SNP) is a single base pair
variation in a nucleotide sequence at a specific location. At any
given point of the genome, there are four possible nucleotide base
pairs: A/T, C/G, G/C and T/A. Genotype refers to the specific base
pair sequence of one or more locations in the genome of an
individual. Haplotype refers to the base pair sequence of more than
one location on the same DNA molecule (or the same chromosome in
higher organisms), often in the context of one gene or in the
context of several tightly linked genes. SNP that occurs on a cDNA
is called cSNP. This cSNP may change amino acids of the protein
encoded by the gene and thus change the functions of the protein.
Some SNP cause inherited diseases; others contribute to
quantitative variations in phenotype and reactions to environmental
factors including diet and drugs among individuals. Therefore, SNP
and/or combinations of alleles (called haplotypes) have many
applications, including diagnosis of inherited diseases,
determination of drug reactions and dosage, identification of genes
responsible for diseases, andlanalysis of the genetic relationship
between individuals (P. Nowotny, J. M. Kwon and A. M. Goate, "SNP
analysis to dissect human traits," Curr. Opin. Neurobiol. 2001
October; 11 (5):637-641; M. Pirmohamed and B. K. Park, "Genetic
susceptibility to adverse drug reactions," Trends Pharmacol. Sci.
2001 June; 22(6):298-305; J. H. Riley, C. J. Allan, E. Lai and A.
Roses, "The use of single nucleotide polymorphisms in the isolation
of common disease genes," Pharmacogenomics. 2000 February ;
1(1):39-47; R. Judson, J. C. Stephens and A. Windemuth, "The
predictive power of haplotypes in clinical response,"
Pharmacogenomics. 2000 February; 1(1):15-26).
[0874] SNP are identified by a variety of art-accepted methods (P.
Bean, "The promising voyage of SNP target discovery," Am. Clin.
Lab. 2001 October-November; 20(9):18-20; K. M. Weiss, "In search of
human variation," Genome Res. 1998 July; 8(7):691-697; M. M. She,
"Enabling large-scale pharmacogenetic studies by high-throughput
mutation detection and genotyping technologies," Clin. Chem. 2001
February; 47(2):164-172). For example, SNP can be identified by
sequencing DNA fragments that show polymorphism by gel-based
methods such as restriction fragment length polymorphism (RFLP) and
denaturing gradient gel electrophoresis (DGGE). They can also be
discovered by direct sequencing of DNA samples pooled from
different individuals or by comparing sequences from different DNA
samples. With the rapid accumulation of sequence data in public and
private databases, one can discover SNP by comparing sequences
using computer programs (Z. Gu, L. Hillier and P. Y. Kwok, "Single
nucleotide polymorphism hunting in cyberspace," Hum. Mutat. 1998;
12(4):221-225). SNP can be verified and genotype or haplotype of an
individual can be determined by a variety of methods including
direct sequencing and high throughput microarrays (P. Y. Kwok,
"Methods for genotyping single nucleotide polymorphisms," Annu.
Rev. Genomics Hum. Genet. 2001; 2:235-258; M. Kokoris, K. Dix, K.
Moynihan, J. Mathis, B. Erwin, P. Grass, B. Hines and A.
Duesterhoeft, "High-throughput SNP genotyping with the Masscode
system," Mol. Diagn. 2000 December; 5(4):329-340).
[0875] Using the methods described above, eleven SNP were
identified in the original transcript, 98P4B6 v.1, at positions 46
(A/G), 179 (C/T), 180 (A/G), 269 (A/G), 404 (G/T), 985 (C/T), 1170
(T/C), 1497 (A/G), 1746 (T/G), 2046 (T/G) and 2103 (T/C). The
transcripts or proteins with alternative allele were designated as
variant 98P4B6 v.9 through v.19, as shown in FIG. 10a. FIG. 11
shows the schematic alignment of protein variants, corresponding to
nucleotide variants. Nucleotide variants that code for the same
amino acid sequence as v.1 are not shown in FIG. 11. These alleles
of the SNP, though shown separately here, can occur in different
combinations (haplotypes) and in any one of the transcript variants
(such as 98P4B6 v.5) that contains the site of the SNP. In
addition, there were SNP in other transcript variants in regions
not shared with v.1. For example, there were fourteen SNP in the
fifth intron of v.1, which was part of transcript variants v.2, v.6
and v.8. These SNP are shown in FIG. 10c and listed as following
(numbers relative v.8): 1760 (G/A), 1818 (G/T), 1870 (C/T), 2612
(T/C), 2926 (T/A), 4241 (TIA), 4337 (A/G), 4338 (A/C), 4501 (A/G),
4506 (C/T), 5434 (C/A), 5434 (C/G), 5434 (C/T) and 5589 (C/A). FIG.
10b shows the SNP in the unique regions of transcript variant v.7:
1956 (A/C), 1987 (T/A), 2010 (G/C), 2010 (G/T) and 2059 (G/A)
(numbers correspond to nucleotide sequence of v.7).
Example 7
Production of Recombinant 98P4B6 in Prokaryotic Systems
[0876] To express recombinant 98P4B6 and 98P4B6 variants in
prokaryotic cells, the full or partial length 98P4B6 and 98P4B6
variant cDNA sequences are cloned into any one of a variety of
expression vectors known in the art. One or more of the following
regions of 98P4B6 variants are expressed: the full length sequence
presented in FIGS. 2 and 3, or any 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more
contiguous amino acids from 98P4B6, variants, or analogs
thereof.
[0877] A. In Vitro Transcription and Translation Constructs:
[0878] pCRII:
[0879] To generate 98P4B6 sense and anti-sense RNA probes for RNA
in situ investigations, pCRII constructs (Invitrogen, Carlsbad
Calif.) are generated encoding either all or fragments of the
98P4B6 cDNA. The pCRII vector has Sp6 and T7 promoters flanking the
insert to drive the transcription of 98P4B6 RNA for use as probes
in RNA in situ hybridization experiments. These probes are used to
analyze the cell and tissue expression of 98P4B6 at the RNA level.
Transcribed 98P4B6 RNA representing the cDNA amino acid coding
region of the 98P4B6 gene is used in in vitro translation systems
such as the TnT.TM. Coupled Reticulolysate System (Promega, Corp.,
Madison, Wis.) to synthesize 98P4B6 protein.
[0880] B. Bacterial Constructs:
[0881] pGEX Constructs:
[0882] To generate recombinant 98P4B6 proteins in bacteria that are
fused to the Glutathione S-transferase (GST) protein, all or parts
of the 98P4B6 cDNA protein coding sequence are cloned into the pGEX
family of GST-fusion vectors (Amersham Pharmacia Biotech,
Piscataway, N.J.). These constructs allow controlled expression of
recombinant 98P4B6 protein sequences with GST fused at the
amino-terminus and a six histidine epitope (6.times.His) at the
carboxyl-terminus. The GST and 6.times.His tags permit purification
of the recombinant fusion protein from induced bacteria with the
appropriate affinity matrix and allow recognition of the fusion
protein with anti-GST and anti-His antibodies. The 6.times.His tag
is generated by adding 6 histidine codons to the cloning primer at
the 3' end, e.g., of the open reading frame (ORF). A proteolytic
cleavage site, such as the PreScission.TM. recognition site in
pGEX-6P-1, may be employed such that it permits cleavage of the GST
tag from 98P4B6-related protein. The ampicillin resistance gene and
pBR322 origin permits selection and maintenance of the pGEX
plasmids in E. coli. A glutathione-S-transferase (GST) fusion
protein encompassing amino acids 2-204 of the STEAP-2 protein
sequence was generated in the pGEX vector. The recombinant
GST-STEAP-2 fusion protein was purified from induced bacteria by
glutathione-sepaharose affinity chromatography and used as
immunogen for generation of a polyclonal antibody.
[0883] pMAL Constructs:
[0884] To generate, in bacteria, recombinant 98P4B6 proteins that
are fused to maltose-binding protein (MBP), all or parts of the
98P4B6 cDNA protein coding sequence are fused to the MBP gene by
cloning into the pMAL-c2X and pMAL-p2X vectors (New England
Biolabs, Beverly, Mass.). These constructs allow controlled
expression of recombinant 98P4B6 protein sequences with MBP fused
at the amino-terminus and a 6.times.His epitope tag at the
carboxyl-terminus. The MBP and 6.times.His tags permit purification
of the recombinant protein from induced bacteria with the
appropriate affinity matrix and allow recognition of the fusion
protein with anti-MBP and anti-His antibodies. The 6.times.His
epitope tag is generated by adding 6 histidine codons to the 3'
cloning primer. A Factor Xa recognition site permits cleavage of
the pMAL tag from 98P4B6. The pMAL-c2X and pMAL-p2X vectors are
optimized to express the recombinant protein in the cytoplasm or
periplasm respectively. Periplasm expression enhances folding of
proteins with disulfide bonds.
[0885] pET Constructs:
[0886] To express 98P4B6 in bacterial cells, all or parts of the
98P4B6 cDNA protein coding sequence are cloned into the pET family
of vectors (Novagen, Madison, Wis.). These vectors allow tightly
controlled expression of recombinant 98P4B6 protein in bacteria
with and without fusion to proteins that enhance solubility, such
as NusA and thioredoxin (Trx), and epitope tags, such as
6.times.His and S-Tag.TM. that aid purification and detection of
the recombinant protein. For example, constructs are made utilizing
pET NusA fusion system 43.1 such that regions of the 98P4B6 protein
are expressed as amino-terminal fusions to NusA.
[0887] C. Yeast Constructs:
[0888] pESC Constructs:
[0889] To express 98P4B6 in the yeast species Saccharomyces
cerevisiae for generation of recombinant protein and functional
studies, all or parts of the 98P4B6 cDNA protein coding sequence
are cloned into the pESC family of vectors each of which contain 1
of 4 selectable markers, HIS3, TRP1, LEU2, and URA3 (Stratagene, La
Jolla, Calif.). These vectors allow controlled expression from the
same plasmid of up to 2 different genes or cloned sequences
containing either Flag.TM. or Myc epitope tags in the same yeast
cell. This system is useful to confirm protein-protein interactions
of 98P4B6. In addition, expression in yeast yields similar
post-translational modifications, such as glycosylations and
phosphorylations, that are found when expressed in eukaryotic
cells.
[0890] pESP Constructs:
[0891] To express 98P4B6 in the yeast species Saccharomyces pombe,
all or parts of the 98P4B6 cDNA protein coding sequence are cloned
into the pESP family of vectors. These vectors allow controlled
high level of expression of a 98P4B6 protein sequence that is fused
at either the amino terminus or at the carboxyl terminus to GST
which aids purification of the recombinant protein. A Flag.TM.
epitope tag allows detection of the recombinant protein with
anti-Flag.TM. antibody.
Example 8
Production of Recombinant 98P4B6 in Higher Eukaryotic Systems
[0892] A. Mammalian Constructs:
[0893] To express recombinant 98P4B6 in eukaryotic cells, the full
or partial length 98P4B6 cDNA sequences can be cloned into any one
of a variety of expression vectors known in the art. One or more of
the following regions of 98P4B6 are expressed in these constructs,
amino acids 1 to 255, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more
contiguous amino acids from 98P4B6 v.1 through v.11; amino acids 1
to 1266, or any 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30 or more contiguous amino
acids from 98P4B6 v.12 and v.13, variants, or analogs thereof.
[0894] The constructs can be transfected into any one of a wide
variety of mammalian cells such as 293T cells. Transfected 293T
cell lysates can be probed with the anti-98P4B6 polyclonal serum,
described herein.
[0895] pcDNA4/HisMax Constructs:
[0896] To express 98P4B6 in mammalian cells, a 98P4B6 ORF, or
portions thereof, of 98P4B6 are cloned into pcDNA4/HisMax Version A
(Invitrogen, Carlsbad, Calif.). Protein expression is driven from
the cytomegalovirus (CMV) promoter and the SP16 translational
enhancer. The recombinant protein has Xpress.TM. and six histidine
(6.times.His) epitopes fused to the amino-terminus. The
pcDNA4/HisMax vector also contains the bovine growth hormone (BGH)
polyadenylation signal and transcription termination sequence to
enhance mRNA stability along with the SV40 origin for episomal
replication and simple vector rescue in cell lines expressing the
large T antigen. The Zeocin resistance gene allows for selection of
mammalian cells expressing the protein and the ampicillin
resistance gene and ColEl origin permits selection and maintenance
of the plasmid in E. coli.
[0897] pcDNA3.11MycHis Constructs:
[0898] To express 98P4B6 in mammalian cells, a 98P4B6 ORF, or
portions thereof, of 98P4B6 with a consensus Kozak translation
initiation site was cloned into pcDNA3.1/MycHis Version A
(Invitrogen, Carlsbad, Calif.). Protein expression is driven from
the cytomegalovirus (CMV) promoter. The recombinant proteins have
the myc epitope and 6.times.His epitope fused to the
carboxyl-terminus. The pcDNA3.1/MycHis vector also contains the
bovine growth hormone (BGH) polyadenylation signal and
transcription termination sequence to enhance mRNA stability, along
with the SV40 origin for episomal replication and simple vector
rescue in cell lines expressing the large T antigen. The Neomycin
resistance gene can be used, as it allows for selection of
mammalian cells expressing the protein and the ampicillin
resistance gene and ColE1 origin permits selection and maintenance
of the plasmid in E. coli.
[0899] pcDNA3.1IGFP Construct:
[0900] To express 98P4B6 in mammalian cells and to allow detection
of the recombinant proteins using fluorescence, the 98P4B6 ORF
sequence was codon optimized according to Mirzabekov et al. (1999),
and was cloned into pcDNA3.1/GFP vector to generate
98P4B6.GFP.pcDNA3.1 construct. Protein expression was driven from
the cytomegalovirus (CMV) promoter. The recombinant protein had the
Green Fluorescent Protein (GFP) fused to the carboxyl-terminus
facilitating non-invasive, in vivo detection and cell biology
studies. The pcDNA3.1/GFP vector also contains the bovine growth
hormone (BGH) polyadenylation signal and transcription termination
sequence to enhance mRNA stability along with the SV40 origin for
episomal replication and simple vector rescue in cell lines
expressing the large T antigen. The Neomycin resistance gene allows
for selection of mammalian cells that express the protein, and the
ampicillin resistance gene and ColE1 origin permits selection and
maintenance of the plasmid in E coli.
[0901] Transfection of 98P4B6.GFP.pcDNA3.1 into 293T cells was
performed as shown in FIGS. 17 and 18. Results show strong
expression of the fusion protein by western blot analysis (FIG.
17), flow cytometry (FIG. 18A) and fluorescent microscopy (FIG.
18B).
[0902] Additional constructs with an amino-terminal GFP fusion are
made in pcDNA3.1/NT-GFP-TOPO spanning the entire length of a 98P4B6
protein.
[0903] PAPtag:
[0904] A 98P4B6 ORF, or portions thereof, is cloned into pAPtag-5
(GenHunter Corp. Nashville, Tenn.). This construct generates an
alkaline phosphatase fusion at the carboxyl-terminus of a 98P4B6
protein while fusing the IgG.sub.K signal sequence to the
amino-terminus. Constructs are also generated in which alkaline
phosphatase with an amino-terminal IgG.sub.K signal sequence is
fused to the amino-terminus of a 98P4B6 protein. The resulting
recombinant 98P4B6 proteins are optimized for secretion into the
media of transfected mammalian cells and can be used to identify
proteins such as ligands or receptors that interact with 98P4B6
proteins. Protein expression is driven from the CMV promoter and
the recombinant proteins also contain myc and 6.times.His epitopes
fused at the carboxyl-terminus that facilitates detection and
purification. The Zeocin resistance gene present in the vector
allows for selection of mammalian cells expressing the recombinant
protein and the ampicillin resistance gene permits selection of the
plasmid in E. coli.
[0905] pTag5:
[0906] A 98P4B6 ORF, or portions thereof, is cloned into pTag-5.
This vector is similar to pAPtag but without the alkaline
phosphatase fusion. This construct generates 98P4B6 protein with an
amino-terminal IgG.sub.K signal sequence and myc and 6.times.His
epitope tags at the carboxyl-terminus that facilitate detection and
affinity purification. The resulting recombinant 98P4B6 protein is
optimized for secretion into the media of transfected mammalian
cells, and is used as immunogen or ligand to identify proteins such
as ligands or receptors that interact with the 98P4B6 proteins.
Protein expression is driven from the CMV promoter. The Zeocin
resistance gene present in the vector allows for selection of
mammalian cells expressing the protein, and the ampicillin
resistance gene permits selection of the plasmid in E. coli.
[0907] PsecFc:
[0908] A 98P4B6 ORF, or portions thereof, is also cloned into
psecFc. The psecFc vector was assembled by cloning the human
immunoglobulin G1 (IgG) Fc (hinge, CH2, CH3 regions) into pSecTag2
(Invitrogen, California). This construct generates an IgG1 Fc
fusion at the carboxyl-terminus of the 98P4B6 proteins, while
fusing the IgGK signal sequence to N-terminus. 98P4B6 fusions
utilizing the murine IgG1 Fc region are also used. The resulting
recombinant 98P4B6 proteins are optimized for secretion into the
media of transfected mammalian cells, and can be used as immunogens
or to identify proteins such as ligands or receptors that interact
with 98P4B6 protein. Protein expression is driven from the CMV
promoter. The hygromycin resistance gene present in the vector
allows for selection of mammalian cells that express the
recombinant protein, and the ampicillin resistance gene permits
selection of the plasmid in E coli.
[0909] pSR.alpha. Constructs:
[0910] To generate mammalian cell lines that express 98P4B6
constitutively, 98P4B6 ORF, or portions thereof, of 98P4B6 were
cloned into pSR.alpha. constructs. Amphotropic and ecotropic
retroviruses were generated by transfection of pSR.alpha.
constructs into the 293T-10A1 packaging line or co-transfection of
pSR.alpha. and a helper plasmid (containing deleted packaging
sequences) into the 293 cells, respectively. The retrovirus is used
to infect a variety of mammalian cell lines, resulting in the
integration of the cloned gene, 98P4B6, into the host cell-lines.
Protein expression is driven from a long terminal repeat (LTR). The
Neomycin resistance gene present in the vector allows for selection
of mammalian cells that express the protein, and the ampicillin
resistance gene and ColE1 origin permit selection and maintenance
of the plasmid in E. coli. The retroviral vectors can thereafter be
used for infection and generation of various cell lines using, for
example, PC3, NIH 3T3, TsuPr1, 293 or rat-1 cells.
[0911] Additional pSR.alpha. constructs are made that fuse an
epitope tag such as the FLAG.TM. tag to the carboxyl-terminus of
98P4B6 sequences to allow detection using anti-Flag antibodies. For
example, the FLAG.TM. sequence 5' gat tac aag gat gac gac gat aag
3' (SEQ ID NO: 113) is added to cloning primer at the 3' end of the
ORF. Additional pSR.alpha. constructs are made to produce both
amino-terminal and carboxyl-terminal GFP and myc/6.times.His fusion
proteins of the full-length 98P4B6 proteins.
[0912] Additional Viral Vectors:
[0913] Additional constructs are made for viral-mediated delivery
and expression of 98P4B6. High virus titer leading to high level
expression of 98P4B6 is achieved in viral delivery systems such as
adenoviral vectors and herpes amplicon vectors. A 98P4B6 coding
sequences or fragments thereof are amplified by PCR and subcloned
into the AdEasy shuttle vector (Stratagene). Recombination and
virus packaging are performed according to the manufacturer's
instructions to generate adenoviral vectors. Alternatively, 98P4B6
coding sequences or fragments thereof are cloned into the HSV-1
vector (Imgenex) to generate herpes viral vectors. The viral
vectors are thereafter used for infection of various cell lines
such as PC3, NIH 3T3, 293 or rat-1 cells.
[0914] Regulated Expression Systems:
[0915] To control expression of 98P4B6 in mammalian cells, coding
sequences of 98P4B6, or portions thereof, are cloned into regulated
mammalian expression systems such as the T-Rex System (Invitrogen),
the GeneSwitch System (Invitrogen) and the tightly-regulated
Ecdysone System (Sratagene). These systems allow the study of the
temporal and concentration dependent effects of recombinant 98P4B6.
These vectors are thereafter used to control expression of 98P4B6
in various cell lines such as PC3, NIH 3T3, 293 or rat-1 cells.
[0916] B. Baculovirus Expression Systems
[0917] To generate recombinant 98P4B6 proteins in a baculovirus
expression system, 98P4B6 ORF, or portions thereof, are cloned into
the baculovirus transfer vector pBlueBac 4.5 (Invitrogen), which
provides a His-tag at the N-terminus. Specifically, pBlueBac-98P4B6
is co-transfected with helper plasmid pBac-N-Blue (Invitrogen) into
SF9 (Spodoptera frugiperda) insect cells to generate recombinant
baculovirus (see Invitrogen instruction manual for details).
Baculovirus is then collected from cell supernatant and purified by
plaque assay.
[0918] Recombinant 98P4B6 protein is then generated by infection of
HighFive insect cells (Invitrogen) with purified baculovirus.
Recombinant 98P4B6 protein can be detected using anti-98P4B6 or
anti-His-tag antibody. 98P4B6 protein can be purified and used in
various cell-based assays or as immunogen to generate polyclonal
and monoclonal antibodies specific for 98P4B6.
Example 9
Antigenicity Profiles and Secondary Structure
[0919] FIGS. 5(A-E), FIGS. 6(A-E), FIGS. 7(A-E), FIGS. 8(A-E), and
FIGS. 9(A-E) depict graphically five amino acid profiles of 98P4B6
variants 1, 2, 5-7, each assessment available by accessing the
ProtScale website located on the World Wide Web at
.expasy.ch/cgi-bin/protscale.pl) on the ExPasy molecular biology
server.
[0920] These profiles: FIG. 5, Hydrophilicity, (Hopp T. P., Woods
K. R., 1981. Proc. Natl. Acad. Sci. U.S.A. 78:3824-3828); FIG. 6,
Hydropathicity, (Kyte J., Doolittle R. F., 1982. J. Mol. Biol.
157:105-132); FIG. 7, Percentage Accessible Residues (Janin J.,
1979 Nature 277:491-492); FIG. 8, Average Flexibility, (Bhaskaran
R., and Ponnuswamy P. K., 1988. Int. J. Pept. Protein Res.
32:242-255); FIG. 9, Beta-turn (Deleage, G., Roux B. 1987 Protein
Engineering 1:289-294); and optionally others available in the art,
such as on the ProtScale website, were used to identify antigenic
regions of each of the 98P4B6 variant proteins. Each of the above
amino acid profiles of 98P4B6 variants were generated using the
following ProtScale parameters for analysis: 1) A window size of 9;
2) 100% weight of the window edges compared to the window center;
and, 3) amino acid profile values normalized to lie between 0 and
1.
[0921] Hydrophilicity (FIG. 5), Hydropathicity (FIG. 6) and
Percentage Accessible Residues (FIG. 7) profiles were used to
determine stretches of hydrophilic amino acids (i.e., values
greater than 0.5 on the Hydrophilicity and Percentage Accessible
Residues profile, and values less than 0.5 on the Hydropathicity
profile). Such regions are likely to be exposed to the aqueous
environment, be present on the surface of the protein, and thus
available for immune recognition, such as by antibodies.
[0922] Average Flexibility (FIG. 8) and Beta-turn (FIG. 9) profiles
determine stretches of amino acids (i.e., values greater than 0.5
on the Beta-turn profile and the Average Flexibility profile) that
are not constrained in secondary structures such as beta sheets and
alpha helices. Such regions are also more likely to be exposed on
the protein and thus accessible to immune recognition, such as by
antibodies.
[0923] Antigenic sequences of the 98P4B6 variant proteins
indicated, e.g., by the profiles set forth in FIGS. 5(A-E), FIGS.
6(A-E), FIGS. 7(A-E), FIGS. 8(A-E), and/or FIGS. 9(A-E) are used to
prepare immunogens, either peptides or nucleic acids that encode
them, to generate therapeutic and diagnostic anti-98P4B6
antibodies. The immunogen can be any 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 35, 40, 45, 50
or more than 50 contiguous amino acids, or the corresponding
nucleic acids that encode them, from the 98P4B6 protein variants 1,
2, 5-7 listed in FIGS. 2 and 3. In particular, peptide immunogens
of the invention can comprise, a peptide region of at least 5 amino
acids of FIGS. 2 and 3 in any whole number increment that includes
an amino acid position having a value greater than 0.5 in the
Hydrophilicity profiles of FIG. 5; a peptide region of at least 5
amino acids of FIGS. 2 and 3 in any whole number increment that
includes an amino acid position having a value less than 0.5 in the
Hydropathicity profile of FIGS. 6; a peptide region of at least 5
amino acids of FIGS. 2 and 3 in any whole number increment that
includes an amino acid position having a value greater than 0.5 in
the Percent Accessible Residues profiles of FIG. 7; a peptide
region of at least 5 amino acids of FIGS. 2 and 3 in any whole
number increment that includes an amino acid position having a
value greater than 0.5 in the Average Flexibility profiles on FIG.
8; and, a peptide region of at least 5 amino acids of FIGS. 2 and 3
in any whole number increment that includes an amino acid position
having a value greater than 0.5 in the Beta-turn profile of FIGS. 9
. Peptide immunogens of the invention can also comprise nucleic
acids that encode any of the forgoing.
[0924] All immunogens of the invention, peptide or nucleic acid,
can be embodied in human unit dose form, or comprised by a
composition that includes a pharmaceutical excipient compatible
with human physiology.
[0925] The secondary structure of 98P4B6 protein variants 1, 2,
5-7, namely the predicted presence and location of alpha helices,
extended strands, and random coils, is predicted from the primary
amino acid sequence using the HNN--Hierarchical Neural Network
method (Guermeur, 1997,
htp://pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html),
accessed from the ExPasy molecular biology server (located on the
World Wide Web at .expasy.ch/tools/). The analysis indicates that
98P4B6 variant 1 is composed of 54.41% alpha helix, 12.33% extended
strand, and 33.26% random coil (FIG. 13A). Variant 2 is composed of
17.78% alpha helix, 6.67% extended strand, and 75.56% random coil
(FIG. 13B). Variant 5 is composed of 51.55% alpha helix, 13.13%
extended strand, and 35.32% random coil (FIG. 13C). Variant 6 is
composed of 54.49% alpha helix, 11.84% extended strand, and 33.67%
random coil (FIG. 13D). Variant 7 is composed of 48.26% alpha
helix, 15.28% extended strand, and 36.46% random coil (FIG.
13E).
[0926] Analysis for the potential presence of transmembrane domains
in the 98P4B6 variant proteins was carried out using a variety of
transmembrane prediction algorithms accessed from the ExPasy
molecular biology server (located on the World Wide Web at
.expasy.ch/tools/). Shown graphically in FIGS. 13F and 13G are the
results of analysis of variant 1 depicting the presence and
location of 6 transmembrane domains using the TMpred program (FIG.
13F) and 5 transmembrane domains using the TMHMM program (FIG.
13G). Shown graphically in FIGS. 13H and 13I are the results of
analysis of variant 2 depicting the presence and location of 1
transmembrane domains using the TMpred program (FIG. 13H) and no
transmembrane domains using the TMHMM program (FIG. 13I). Shown
graphically in FIGS. 13J and 13K are the results of analysis of
variant 5 depicting the presence and location of 6 transmembrane
domains using the TMpred program (FIG. 13J) and 4 transmembrane
domains using the TMHMM program (FIG. 13K). Shown graphically in
FIGS. 13L and 13M are the results of analysis of variant 6
depicting the presence and location of 6 transmembrane domains
using the TMpred program (FIG. 13L) and 6 transmembrane domains
using the TMHMM program (FIG. 13M). Shown graphically in FIGS. 13N
and 13O are the results of analysis of variant 7 depicting the
presence and location of 6 transmembrane domains using the TMpred
program (FIG. 13N) and 4 transmembrane domains using the TMHMM
program (FIG. 13O). The results of each program, namely the amino
acids encoding the transmembrane domains are summarized in Table
VI.
Example 10
Generation of 98P4B6 Polyclonal Antibodies
[0927] Polyclonal antibodies can be raised in a mammal, for
example, by one or more injections of an immunizing agent and, if
desired, an adjuvant. Typically, the immunizing agent and/or
adjuvant will be injected in the mammal by multiple subcutaneous or
intraperitoneal injections. In addition to immunizing with a full
length 98P4B6 protein variant, computer algorithms are employed in
design of immunogens that, based on amino acid sequence analysis
contain characteristics of being antigenic and available for
recognition by the immune system of the immunized host (see Example
9 entitled "Antigenicity Profiles and Secondary Structure"). Such
regions would be predicted to be hydrophilic, flexible, in
beta-turn conformations, and be exposed on the surface of the
protein (see, e.g., FIGS. 5(A-E), FIGS. 6(A & B), FIGS. 7(A-E),
FIGS. 8(A -E), or FIGS. 9(A-E) for amino acid profiles that
indicate such regions of 98P4B6 protein variants).
[0928] For example, recombinant bacterial fusion proteins or
peptides containing hydrophilic, flexible, beta-turn regions of
98P4B6 protein variants are used as antigens to generate polyclonal
antibodies in New Zealand White rabbits or monoclonal antibodies as
described in Example 11. For example, in 98P4B6 variant 1, such
regions include, but are not limited to, amino acids 153-165, amino
acids 240-260, and amino acids 345-358. In sequence specific for
variant 2, such regions include, but are not limited to, amino
acids 26-38. In sequence specific for variant 5, such regions
include, but are not limited to, amino acids 400-410. In sequence
specific for variant 6, such regions include, but are not limited
to, amino acids 455-490. In sequence specific for variant 7, such
regions include, but are not limited to, amino acids 451-465 and
amino acids 472-498. It is useful to conjugate the immunizing agent
to a protein known to be immunogenic in the mammal being immunized.
Examples of such immunogenic proteins include, but are not limited
to, keyhole limpet hemocyanin (KLH), serum albumin, bovine
thyroglobulin, and soybean trypsin inhibitor. In one embodiment, a
peptide encoding amino acids 153-165 of 98P4B6 variant 1 was
conjugated to KLH and used to immunize a rabbit. Alternatively the
immunizing agent may include all or portions of the 98P4B6 variant
proteins, analogs or fusion proteins thereof. For example, the
98P4B6 variant 1 amino acid sequence can be fused using recombinant
DNA techniques to any one of a variety of fusion protein partners
that are well known in the art, such as glutathione-S-transferas- e
(GST) and HIS tagged fusion proteins. In another embodiment, amino
acids 2-204 of 98P4B6 variant 1 was fused to GST using recombinant
techniques and the pGEX expression vector, expressed, purified and
used to immunize a rabbit. Such fusion proteins are purified from
induced bacteria using the appropriate affinity matrix.
[0929] Other recombinant bacterial fusion proteins that may be
employed include maltose binding protein, LacZ, thioredoxin, NusA,
or an immunoglobulin constant region (see the section entitled
"Production of 98P4B6 in Prokaryotic Systems" and Current Protocols
In Molecular Biology, Volume 2, Unit 16, Frederick M. Ausubul et
al. eds., 1995; Linsley, P. S., Brady, W., Urnes, M., Grosmaire,
L., Damle, N., and Ledbetter, L.(1991) J. Exp. Med. 174,
561-566).
[0930] In addition to bacterial derived fusion proteins, mammalian
expressed protein antigens are also used. These antigens are
expressed from mammalian expression vectors such as the Tag5 and
Fc-fusion vectors (see the section entitled "Production of
Recombinant 98P4B6 in Eukaryotic Systems"), and retain
post-translational modifications such as glycosylations found in
native protein. In one embodiment, amino acids 324-359 of variant
1, encoding an extracellular loop between transmembrane domains, is
cloned into the Tag5 mammalian secretion vector. The recombinant
protein is purified by metal chelate chromatography from tissue
culture supernatants of 293T cells stably expressing the
recombinant vector. The purified Tag5 98P4B6 protein is then used
as immunogen.
[0931] During the immunization protocol, it is useful to mix or
emulsify the antigen in adjuvants that enhance the immune response
of the host animal. Examples of adjuvants include, but are not
limited to, complete Freund's adjuvant (CFA) and MPL-TDM adjuvant
(monophosphoryl Lipid A, synthetic trehalose dicorynomycolate).
[0932] In a typical protocol, rabbits are initially immunized
subcutaneously with up to 200 .mu.g, typically 100-200 .mu.g, of
fusion protein or peptide conjugated to KLH mixed in complete
Freund's adjuvant (CFA). Rabbits are then injected subcutaneously
every two weeks with up to 200 .mu.g, typically 100-200 .mu.g, of
the immunogen in incomplete Freund's adjuvant (IFA). Test bleeds
are taken approximately 7-10 days following each immunization and
used to monitor the titer of the antiserum by ELISA.
[0933] To test reactivity and specificity of immune serum, such as
the rabbit serum derived from immunization with the Tag5-98P4B6
variant 1 protein, the full-length 98P4B6 variant 1 cDNA is cloned
into pCDNA 3.1 myc-his expression vector (Invitrogen, see the
Example entitled "Production of Recombinant 98P4B6 in Eukaryotic
Systems"). After transfection of the constructs into 293T cells,
cell lysates are probed with the anti-98P4B6 serum and with
anti-His antibody (Santa Cruz Biotechnologies, Santa Cruz, Calif.)
to determine specific reactivity to denatured 98P4B6 protein using
the Western blot technique. Detection of 98P4B6 variant 1 protein
expressed in 293T with polyclonal antibodies raised to a GST-fusion
protein and peptide is shown in FIGS. 17B and 17C, respectively. In
addition, the immune serum is tested by fluorescence microscopy,
flow cytometry and immunoprecipitation against 293T and other
recombinant 98P4B6-expressing cells to determine specific
recognition of native protein. Western blot, immunoprecipitation,
fluorescent microscopy, and flow cytometric techniques using cells
that endogenously express 98P4B6 are also carried out to test
reactivity and specificity.
[0934] Anti-serum from rabbits immunized with 98P4B6 variant fusion
proteins, such as GST and MBP fusion proteins, are purified by
depletion of antibodies reactive to the fusion partner sequence by
passage over an affinity column containing the fusion partner
either alone or in the context of an irrelevant fusion protein. For
example, antiserum derived from a GST-98P4B6 variant 1 fusion
protein was first purified by passage over a column of GST protein
covalently coupled to AffiGel matrix (BioRad, Hercules, Calif.).
The antiserum is then affinity purified by passage over a column
composed of a MBP-98P4B6 fusion protein covalently coupled to
Affigel matrix. The serum is then further purified by protein G
affinity chromatography to isolate the IgG fraction. Sera from
other His-tagged antigens and peptide immunized rabbits as well as
fusion partner depleted sera are affinity purified by passage over
a column matrix composed of the original protein immunogen or free
peptide, such as the anti-peptide polyclonal antibody used in FIG.
17C.
Example 11
Generation of 98P4B6 Monoclonal Antibodies (mAbs)
[0935] In one embodiment, therapeutic mAbs to 98P4B6 variants
comprise those that react with epitopes specific for each variant
protein or specific to sequences in common between the variants
that would disrupt or modulate the biological function of the
98P4B6 variants, for example those that would disrupt the
interaction with ligands and binding partners. Immunogens for
generation of such mAbs include those designed to encode or contain
the entire 98P4B6 protein variant sequence, regions of the 98P4B6
protein variants predicted to be antigenic from computer analysis
of the amino acid sequence (see, e.g., FIGS. 5(A-E), FIGS. 6(A-E),
FIGS. 7(A-E), FIGS. 8(A-E), or FIGS. 9(A-E), and Example 9 entitled
"Antigenicity Profiles and Secondary Structure"). Immunogens
include peptides, recombinant bacterial proteins, and mammalian
expressed Tag 5 proteins and human and murine IgG FC fusion
proteins. In addition, cells engineered to express high levels of a
respective 98P4B6 variant, such as 293T-98P4B6 variant 1 or
300.19-98P4B6 variant 1 murine Pre-B cells, are used to immunize
mice.
[0936] To generate mAbs to a 98P4B6 variant, mice are first
immunized intraperitoneally (IP) with, typically, 10-50 .mu.g of
protein immunogen or 10.sup.7 98P4B6-expressing cells mixed in
complete Freund's adjuvant. Mice are then subsequently immunized IP
every 2-4 weeks with, typically, 10-50 .mu.g of protein immunogen
or 10.sup.7 cells mixed in incomplete Freund's adjuvant.
Alternatively, MPL-TDM adjuvant is used in immunizations. In
addition to the above protein and cell-based immunization
strategies, a DNA-based immunization protocol is employed in which
a mammalian expression vector encoding a 98P4B6 variant sequence is
used to immunize mice by direct injection of the plasmid DNA. For
example, amino acids 324-359 is cloned into the Tag5 mammalian
secretion vector and the recombinant vector is used as immunogen.
In another example the same amino acids are cloned into an
Fc-fusion secretion vector in which the 98P4B6 variant 1 sequence
is fused at the amino-terminus to an IgK leader sequence and at the
carboxyl-terminus to the coding sequence of the human or murine IgG
Fc region. This recombinant vector is then used as immunogen. The
plasmid immunization protocols are used in combination with
purified proteins expressed from the same vector and with cells
expressing the respective 98P4B6 variant.
[0937] During the immunization protocol, test bleeds are taken 7-10
days following an injection to monitor titer and specificity of the
immune response. Once appropriate reactivity and specificity is
obtained as determined by ELISA, Western blotting,
immunoprecipitation, fluorescence microscopy, and flow cytometric
analyses, fusion and hybridoma generation is then carried out with
established procedures well known in the art (see, e.g., Harlow and
Lane, 1988).
[0938] In one embodiment for generating 98P4B6 monoclonal
antibodies, a Tag5-98P4B6 variant 1 antigen encoding amino acids
324-359, is expressed and purified from stably transfected 293T
cells. Balb C mice are initially immunized intraperitoneally with
25 .mu.g of the Tag5-98P4B6 variant 1 protein mixed in complete
Freund's adjuvant. Mice are subsequently immunized every two weeks
with 25 .mu.g of the antigen mixed in incomplete Freund's adjuvant
for a total of three immunizations. ELISA using the Tag5 antigen
determines the titer of serum from immunized mice. Reactivity and
specificity of serum to full length 98P4B6 variant 1 protein is
monitored by Western blotting, immunoprecipitation and flow
cytometry using 293T cells transfected with an expression vector
encoding the 98P4B6 variant 1 cDNA (see e.g., the Example entitled
"Production of Recombinant 98P4B6 in Eukaryotic Systems" and FIG.
20). Other recombinant 98P4B6 variant 1-expressing cells or cells
endogenously expressing 98P4B6 variant 1 are also used. Mice
showing the strongest reactivity are rested and given a final
injection of Tag5 antigen in PBS and then sacrificed four days
later. The spleens of the sacrificed mice are harvested and fused
to SPO/2 myeloma cells using standard procedures (Harlow and Lane,
1988). Supernatants from HAT selected growth wells are screened by
ELISA, Western blot, immunoprecipitation, fluorescent microscopy,
and flow cytometry to identify 98P4B6 specific antibody-producing
clones.
[0939] To generate monoclonal antibodies that are specific for each
98P4B6 variant protein, immunogens are designed to encode sequences
unique for each variant. In one embodiment, a Tag5 antigen encoding
the full sequence of 98P4B6 variant 2 (AA1-45) is produced,
purified and used as immunogen to derive monoclonal antibodies
specific to 98P4B6 variant 2. In another embodiment, an antigenic
peptide composed of amino acids 400-410 of 98P4B6 variant 5 is
coupled to KLH and used as immunogen. In another embodiment, a GST
fusion protein encoding amino acids 455-490 of 98P4B6 of variant 6
is used as immunogen to derive variant 6 specific monoclonal
antibodies. In another embodiment, a peptide composed of amino
acids 472-498 of variant 7 is coupled to KLH and used as immunogen
to generate variant 7 specific monoclonal antibodies. Hybridoma
supernatants are then screened on the respective antigen and then
further screened on cells expressing the specific variant and
cross-screened on cells expressing the other variants to derive
variant-specific monoclonal antibodies.
[0940] The binding affinity of a 98P4B6 variant monoclonal antibody
is determined using standard technologies. Affinity measurements
quantify the strength of antibody to epitope binding and are used
to help define which 98P4B6 variant monoclonal antibodies preferred
for diagnostic or therapeutic use, as appreciated by one of skill
in the art. The BlAcore system (Uppsala, Sweden) is a preferred
method for determining binding affinity. The BlAcore system uses
surface plasmon resonance (SPR, Welford K. 1991, Opt. Quant. Elect.
23:1; Morton and Myszka, 1998, Methods in Enzymology 295: 268) to
monitor biomolecular interactions in real time. BlAcore analysis
conveniently generates association rate constants, dissociation
rate constants, equilibrium dissociation constants, and affinity
constants.
Example 12
HLA Class I and Class II Binding Assays
[0941] HLA class I and class II binding assays using purified HLA
molecules are performed in accordance with disclosed protocols
(e.g., PCT publications WO 94/20127 and WO 94/03205; Sidney et al.,
Current Protocols in Immunology 18.3.1 (1998); Sidney, et al., J.
Immunol. 154:247 (1995); Sette, et al., Mol. Immunol. 31:813
(1994)). Briefly, purified MHC molecules (5 to 500 nM) are
incubated with various unlabeled peptide inhibitors and 1-10 nM
.sup.125I-radiolabeled probe peptides as described. Following
incubation, MHC-peptide complexes are separated from free peptide
by gel filtration and the fraction of peptide bound is determined.
Typically, in preliminary experiments, each MHC preparation is
titered in the presence of fixed amounts of radiolabeled peptides
to determine the concentration of HLA molecules necessary to bind
10-20% of the total radioactivity. All subsequent inhibition and
direct binding assays are performed using these HLA
concentrations.
[0942] Since under these conditions [label]<[HLA] and
IC.sub.50.gtoreq.[HLA], the measured IC.sub.50 values are
reasonable approximations of the true K.sub.D values. Peptide
inhibitors are typically tested at concentrations ranging from 120
.mu.g/ml to 1.2 ng/ml, and are tested in two to four completely
independent experiments. To allow comparison of the data obtained
in different experiments, a relative binding figure is calculated
for each peptide by dividing the IC.sub.50 of a positive control
for inhibition by the IC.sub.50 for each tested peptide (typically
unlabeled versions of the radiolabeled probe peptide). For database
purposes, and inter-experiment comparisons, relative binding values
are compiled. These values can subsequently be converted back into
IC.sub.50 nM values by dividing the IC.sub.50 nM of the positive
controls for inhibition by the relative binding of the peptide of
interest. This method of data compilation is accurate and
consistent for comparing peptides that have been tested on
different days, or with different lots of purified MHC.
[0943] Binding assays as outlined above may be used to analyze HLA
supermotif and/or HLA motif-bearing peptides (see Table IV).
Example 13
Identification of HLA Supermotif- and Motif-Bearing CTL Candidate
Epitopes
[0944] HLA vaccine compositions of the invention can include
multiple epitopes. The multiple epitopes can comprise multiple HLA
supermotifs or motifs to achieve broad population coverage. This
example illustrates the identification and confirmation of
supermotif- and motif-bearing epitopes for the inclusion in such a
vaccine composition. Calculation of population coverage is
performed using the strategy described below.
[0945] Computer Searches and Algorithms for Identification of
Supermotif and/or Motif-Bearing Epitopes
[0946] The searches performed to identify the motif-bearing peptide
sequences in the Example entitled "Antigenicity Profiles" and
Tables VIII-XXI and XXII-XLIX employ the protein sequence data from
the gene product of 98P4B6 set forth in FIGS. 2 and 3, the specific
search peptides used to generate the tables are listed in Table
VII.
[0947] Computer searches for epitopes bearing HLA Class I or Class
II supermotifs or motifs are performed as follows. All translated
98P4B6 protein sequences are analyzed using a text string search
software program to identify potential peptide sequences containing
appropriate HLA binding motifs; such programs are readily produced
in accordance with information in the art in view of known
motif/supermotif disclosures. Furthermore, such calculations can be
made mentally.
[0948] Identified A2-, A3-, and DR-supermotif sequences are scored
using polynomial algorithms to predict their capacity to bind to
specific HLA-Class I or Class II molecules. These polynomial
algorithms account for the impact of different amino acids at
different positions, and are essentially based on the premise that
the overall affinity (or .DELTA.G) of peptide-HLA molecule
interactions can be approximated as a linear polynomial function of
the type:
".DELTA.G"=a.sub.1i.times.a.sub.2i.times.a.sub.3i . . .
.times.a.sub.ni
[0949] where a.sub.ji is a coefficient which represents the effect
of the presence of a given amino acid (j) at a given position (i)
along the sequence of a peptide of n amino acids. The crucial
assumption of this method is that the effects at each position are
essentially independent of each other (i.e., independent binding of
individual side-chains). When residue j occurs at position i in the
peptide, it is assumed to contribute a constant amount ji to the
free energy of binding of the peptide irrespective of the sequence
of the rest of the peptide.
[0950] The method of derivation of specific algorithm coefficients
has been described in Gulukota et al., J. Mol. Biol. 267:1258-126,
1997; (see also Sidney et al., Human Immunol. 45:79-93, 1996; and
Southwood et al., J. Immunol 160:3363-3373, 1998). Briefly, for all
i positions, anchor and non-anchor alike, the geometric mean of the
average relative binding (ARB) of all peptides carrying j is
calculated relative to the remainder of the group, and used as the
estimate of j.sub.i. For Class II peptides, if multiple alignments
are possible, only the highest scoring alignment is utilized,
following an iterative procedure. To calculate an algorithm score
of a given peptide in a test set, the ARB values corresponding to
the sequence of the peptide are multiplied. If this product exceeds
a chosen threshold, the peptide is predicted to bind. Appropriate
thresholds are chosen as a function of the degree of stringency of
prediction desired.
[0951] Selection of HLA-A2 Supertype Cross-Reactive Peptides
[0952] Protein sequences from 98P4B6 are scanned utilizing motif
identification software, to identify 8-, 9- 10- and 11-mer
sequences containing the HLA-A2-supermotif main anchor specificity.
Typically, these sequences are then scored using the protocol
described above and the peptides corresponding to the
positive-scoring sequences are synthesized and tested for their
capacity to bind purified HLA-A*0201 molecules in vitro (HLA-A*0201
is considered a prototype A2 supertype molecule).
[0953] These peptides are then tested for the capacity to bind to
additional A2-supertype molecules (A*0202, A*0203, A*0206, and
A*6802). Peptides that bind to at least three of the five
A2-supertype alleles tested are typically deemed A2-supertype
cross-reactive binders. Preferred peptides bind at an affinity
equal to or less than 500 nM to three or more HLA-A2 supertype
molecules.
[0954] Selection of HLA-A3 Supermotif-Bearing Epitopes
[0955] The 98P4B6 protein sequence(s) scanned above is also
examined for the presence of peptides with the HLA-A3-supermotif
primary anchors. Peptides corresponding to the HLA A3
supermotif-bearing sequences are then synthesized and tested for
binding to HLA-A*0301 and HLA-A*1101 molecules, the molecules
encoded by the two most prevalent A3-supertype alleles. The
peptides that bind at least one of the two alleles with binding
affinities of .ltoreq.500 nM, often .ltoreq.200 nM, are then tested
for binding cross-reactivity to the other common A3-supertype
alleles (e.g., A*3101, A*3301, and A*6801) to identify those that
can bind at least three of the five HLA-A3-supertype molecules
tested.
[0956] Selection of HLA-B7 Supermotif Bearing Epitopes
[0957] The 98P4B6 protein(s) scanned above is also analyzed for the
presence of 8-, 9- 10-, or 11-mer peptides with the
HLA-B7-supermotif. Corresponding peptides are synthesized and
tested for binding to HLA-B*0702, the molecule encoded by the most
common B7-supertype allele (i.e., the prototype B7 supertype
allele). Peptides binding B*0702 with IC.sub.50 of .ltoreq.500 nM
are identified using standard methods. These peptides are then
tested for binding to other common B7-supertype molecules (e.g.,
B*3501, B*5101, B*5301, and B*5401). Peptides capable of binding to
three or more of the five B7-supertype alleles tested are thereby
identified.
[0958] Selection of A1 and A24 Motif-Bearing Epitopes
[0959] To further increase population coverage, HLA-A1 and -A24
epitopes can also be incorporated into vaccine compositions. An
analysis of the 98P4B6 protein can also be performed to identify
HLA-A1- and A24-motif-containing sequences.
[0960] High affinity and/or cross-reactive binding epitopes that
bear other motif and/or supermotifs are identified using analogous
methodology.
Example 14
Confirmation of Immunogenicity
[0961] Cross-reactive candidate CTL A2-supermotif-bearing peptides
that are identified as described herein are selected to confirm in
vitro immunogenicity. Confirmation is performed using the following
methodology:
[0962] Target Cell Lines for Cellular Screening:
[0963] The .221A2.1 cell line, produced by transferring the
HLA-A2.1 gene into the HLA-A, -B, -C null mutant human
B-lymphoblastoid cell line 721.221, is used as the peptide-loaded
target to measure activity of HLA-A2.1-restricted CTL. This cell
line is grown in RPMI-1640 medium supplemented with antibiotics,
sodium pyruvate, nonessential amino acids and 10% (v/v) heat
inactivated FCS. Cells that express an antigen of interest, or
transfectants comprising the gene encoding the antigen of interest,
can be used as target cells to confirm the ability of
peptide-specific CTLs to recognize endogenous antigen.
[0964] Primary CTL Induction Cultures:
[0965] Generation of Dendritic Cells (DC):
[0966] PBMCs are thawed in RPMI with 30 .mu.g/ml DNAse, washed
twice and resuspended in complete medium (RPMI-1640 plus 5% AB
human serum, non-essential amino acids, sodium pyruvate,
L-glutamine and penicillin/streptomycin). The monocytes are
purified by plating 10.times.10.sup.6 PBMC/well in a 6-well plate.
After 2 hours at 37.degree. C., the non-adherent cells are removed
by gently shaking the plates and aspirating the supernatants. The
wells are washed a total of three times with 3 ml RPMI to remove
most of the non-adherent and loosely adherent cells. Three ml of
complete medium containing 50 ng/ml of GM-CSF and 1,000 U/ml of
IL-4 are then added to each well. TNF.alpha. is added to the DCs on
day 6 at 75 ng/ml and the cells are used for CTL induction cultures
on day 7.
[0967] Induction of CTL with DC and Peptide:
[0968] CD8+ T-cells are isolated by positive selection with Dynal
immunomagnetic beads (Dynabeads.RTM. M450) and the
detacha-bead.RTM. reagent. Typically about 200-250.times.10.sup.6
PBMC are processed to obtain 24.times.10.sup.6 CD8.sup.+ T-cells
(enough for a 48-well plate culture). Briefly, the PBMCs are thawed
in RPMI with 30 .mu.g/ml DNAse, washed once with PBS containing 1%
human AB serum and resuspended in PBS/1% AB serum at a
concentration of 20.times.10.sup.6 cells/ml. The magnetic beads are
washed 3 times with PBS/AB serum, added to the cells (140 .mu.l
beads/20.times.10.sup.6 cells) and incubated for 1 hour at
4.degree. C. with continuous mixing. The beads and cells are washed
4.times. with PBS/AB serum to remove the nonadherent cells and
resuspended at 100.times.10.sup.6 cells/ml (based on the original
cell number) in PBS/AB serum containing 100 .mu.l/ml
detacha-bead.RTM. reagent and 30 .mu.g/ml DNAse. The mixture is
incubated for 1 hour at room temperature with continuous mixing.
The beads are washed again with PBS/AB/DNAse to collect the CD8+
T-cells. The DC are collected and centrifuged at 1300 rpm for 5-7
minutes, washed once with PBS with 1% BSA, counted and pulsed with
40 .mu.g/ml of peptide at a cell concentration of
1-2.times.10.sup.6/ml in the presence of 3 .mu.g/ml
.beta..sub.2-microglobulin for 4 hours at 20.degree. C. The DC are
then irradiated (4,200 rads), washed 1 time with medium and counted
again.
[0969] Setting Up Induction Cultures:
[0970] 0.25 ml cytokine-generated DC (at 1.times.10.sup.5 cells/ml)
are co-cultured with 0.25 ml of CD8+ T-cells (at 2.times.10.sup.6
cell/ml) in each well of a 48-well plate in the presence of 10
ng/ml of IL-7. Recombinant human IL-10 is added the next day at a
final concentration of 10 ng/ml and rhuman IL-2 is added 48 hours
later at 10 IU/ml.
[0971] Restimulation of the Induction Cultures with Peptide-Pulsed
Adherent Cells:
[0972] Seven and fourteen days after the primary induction, the
cells are restimulated with peptide-pulsed adherent cells. The
PBMCs are thawed and washed twice with RPMI and DNAse. The cells
are resuspended at 5.times.10.sup.6 cells/ml and irradiated at
.about.4200 rads. The PBMCs are plated at 2.times.10.sup.6 in 0.5
ml complete medium per well and incubated for 2 hours at 37.degree.
C. The plates are washed twice with RPMI by tapping the plate
gently to remove the nonadherent cells and the adherent cells
pulsed with 10 .mu.g/ml of peptide in the presence of 3 .mu.g/ml
.beta..sub.2 microglobulin in 0.25 ml RPMI/5%AB per well for 2
hours at 37.degree. C. Peptide solution from each well is aspirated
and the wells are washed once with RPMI. Most of the media is
aspirated from the induction cultures (CD8+ cells) and brought to
0.5 ml with fresh media. The cells are then transferred to the
wells containing the peptide-pulsed adherent cells. Twenty four
hours later recombinant human IL-10 is added at a final
concentration of 10 ng/ml and recombinant human IL2 is added the
next day and again 2-3 days later at 50 IU/ml (Tsai et al.,
Critical Reviews in Immunology 18(1-2):65-75, 1998). Seven days
later, the cultures are assayed for CTL activity in a .sup.51Cr
release assay. In some experiments the cultures are assayed for
peptide-specific recognition in the in situ IFN.gamma. ELISA at the
time of the second restimulation followed by assay of endogenous
recognition 7 days later. After expansion, activity is measured in
both assays for a side-by-side comparison.
[0973] Measurement of CTL Lytic Activity by .sup.51Cr Release.
[0974] Seven days after the second restimulation, cytotoxicity is
determined in a standard (5 hr) .sup.51Cr release assay by assaying
individual wells at a single E:T. Peptide-pulsed targets are
prepared by incubating the cells with 10 .mu.g/ml peptide overnight
at 37.degree. C.
[0975] Adherent target cells are removed from culture flasks with
trypsin-EDTA. Target cells are labeled with 200 .mu.Ci of .sup.51Cr
sodium chromate (Dupont, Wilmington, Del.) for 1 hour at 37.degree.
C. Labeled target cells are resuspended at 10.sup.6 per ml and
diluted 1:10 with K562 cells at a concentration of
3.3.times.10.sup.6/ml (an NK-sensitive erythroblastoma cell line
used to reduce non-specific lysis). Target cells (100 .mu.l) and
effectors (100 .mu.l) are plated in 96 well round-bottom plates and
incubated for 5 hours at 37.degree. C. At that time, 100 .mu.l of
supernatant are collected from each well and percent lysis is
determined according to the formula:
[(cpm of the test sample-cpm of the spontaneous .sup.51Cr release
sample)/(cpm of the maximal .sup.51Cr release sample-cpm of the
spontaneous .sup.51Cr release sample)].times.100.
[0976] Maximum and spontaneous release are determined by incubating
the labeled targets with 1% Triton X-100 and media alone,
respectively. A positive culture is defined as one in which the
specific lysis (sample-background) is 10% or higher in the case of
individual wells and is 15% or more at the two highest E:T ratios
when expanded cultures are assayed.
[0977] In situ Measurement of Human IFN.gamma. Production as an
Indicator of Peptide-specific and Endogenous Recognition
[0978] Immulon 2 plates are coated with mouse anti-human IFN.gamma.
monoclonal antibody (4 .mu.g/ml 0.1M NaHCO.sub.3, pH8.2) overnight
at 4.degree. C. The plates are washed with Ca.sup.2+,
Mg.sup.2+-free PBS/0.05% Tween 20 and blocked with PBS/10% FCS for
two hours, after which the CTLs (100 .mu.l/well) and targets (100
.mu.l/well) are added to each well, leaving empty wells for the
standards and blanks (which received media only). The target cells,
either peptide-pulsed or endogenous targets, are used at a
concentration of 1.times.10.sup.6 cells/ml. The plates are
incubated for 48 hours at 37.degree. C. with 5% CO.sub.2.
[0979] Recombinant human IFN-gamma is added to the standard wells
starting at 400 pg or 1200 pg/100 microliter/well and the plate
incubated for two hours at 37.degree. C. The plates are washed and
100 .mu.l of biotinylated mouse anti-human IFN-gamma monoclonal
antibody (2 microgram/ml in PBS/3%FCS/0.05% Tween 20) are added and
incubated for 2 hours at room temperature. After washing again, 100
microliter HRP-streptavidin (1:4000) are added and the plates
incubated for one hour at room temperature. The plates are then
washed 6.times. with wash buffer, 100 microliter/well developing
solution (TMB 1:1) are added, and the plates allowed to develop for
5-15 minutes. The reaction is stopped with 50 microliter/well 1 M
H.sub.3PO.sub.4 and read at OD450. A culture is considered positive
if it measured at least 50 pg of IFN-gamma/well above background
and is twice the background level of expression.
[0980] CTL Expansion.
[0981] Those cultures that demonstrate specific lytic activity
against peptide-pulsed targets and/or tumor targets are expanded
over a two week period with anti-CD3. Briefly, 5.times.10.sup.4
CD8+ cells are added to a T25 flask containing the following:
1.times.10.sup.6 irradiated (4,200 rad) PBMC (autologous or
allogeneic) per ml, 2.times.10.sup.5 irradiated (8,000 rad)
EBV-transformed cells per ml, and OKT3 (anti-CD3) at 30 ng per ml
in RPMI-1640 containing 10% (v/v) human AB serum, non-essential
amino acids, sodium pyruvate, 25 .mu.M 2-mercaptoethanol,
L-glutamine and penicillin/streptomycin. Recombinant human IL2 is
added 24 hours later at a final concentration of 200 IU/ml and
every three days thereafter with fresh media at 50 IU/ml. The cells
are split if the cell concentration exceeds 1.times.10.sup.6/ml and
the cultures are assayed between days 13 and 15 at E:T ratios of
30, 10, 3 and 1:1 in the .sup.51Cr release assay or at
1.times.10.sup.6/ml in the in situ IFN.gamma. assay using the same
targets as before the expansion.
[0982] Cultures are expanded in the absence of anti-CD3+ as
follows. Those cultures that demonstrate specific lytic activity
against peptide and endogenous targets are selected and
5.times.10.sup.4 CD8.sup.+ cells are added to a T25 flask
containing the following: 1.times.10.sup.6 autologous PBMC per ml
which have been peptide-pulsed with 10 .mu.g/ml peptide for two
hours at 37.degree. C. and irradiated (4,200 rad); 2.times.10.sup.5
irradiated (8,000 rad) EBV-transformed cells per ml RPMI-1640
containing 10%(v/v) human AB serum, non-essential M, sodium
pyruvate, 25 mM 2-ME, L-glutamine and gentamicin.
[0983] Immunogenicity of A2 Supermotif-Bearing Peptides
[0984] A2-supermotif cross-reactive binding peptides are tested in
the cellular assay for the ability to induce peptide-specific CTL
in normal individuals. In this analysis, a peptide is typically
considered to be an epitope if it induces peptide-specific CTLs in
at least individuals, and preferably, also recognizes the
endogenously expressed peptide.
[0985] Immunogenicity can also be confirmed using PBMCs isolated
from patients bearing a tumor that expresses 98P4B6. Briefly, PBMCs
are isolated from patients, re-stimulated with peptide-pulsed
monocytes and assayed for the ability to recognize peptide-pulsed
target cells as well as transfected cells endogenously expressing
the antigen.
[0986] Evaluation of A*03/A11 Immunogenicity
[0987] HLA-A3 supermotif-bearing cross-reactive binding peptides
are also evaluated for immunogenicity using methodology analogous
for that used to evaluate the immunogenicity of the HLA-A2
supermotif peptides.
[0988] Evaluation of B7 Immunogenicity
[0989] Immunogenicity screening of the B7-supertype cross-reactive
binding peptides identified as set forth herein are confirmed in a
manner analogous to the confirmation of A2- and
A3-supermotif-bearing peptides.
[0990] Peptides bearing other supermotifs/motifs, e.g., HLA-A1,
HLA-A24 etc. are also confirmed using similar methodology
Example 15
Implementation of the Extended Supermotif to Improve the Binding
Capacity of Native Epitopes by Creating Analogs
[0991] HLA motifs and supermotifs (comprising primary and/or
secondary residues) are useful in the identification and
preparation of highly cross-reactive native peptides, as
demonstrated herein. Moreover, the definition of HLA motifs and
supermotifs also allows one to engineer highly cross-reactive
epitopes by identifying residues within a native peptide sequence
which can be analoged to confer upon the peptide certain
characteristics, e.g. greater cross-reactivity within the group of
HLA molecules that comprise a supertype, and/or greater binding
affinity for some or all of those HLA molecules. Examples of
analoging peptides to exhibit modulated binding affinity are set
forth in this example.
[0992] Analoging at Primary Anchor Residues
[0993] Peptide engineering strategies are implemented to further
increase the cross-reactivity of the epitopes. For example, the
main anchors of A2-supermotif-bearing peptides are altered, for
example, to introduce a preferred L, I, V, or M at position 2, and
I or V at the C-terminus.
[0994] To analyze the cross-reactivity of the analog peptides, each
engineered analog is initially tested for binding to the prototype
A2 supertype allele A*0201, then, if A*0201 binding capacity is
maintained, for A2-supertype cross-reactivity.
[0995] Alternatively, a peptide is confirmed as binding one or all
supertype members and then analoged to modulate binding affinity to
any one (or more) of the supertype members to add population
coverage.
[0996] The selection of analogs for immunogenicity in a cellular
screening analysis is typically further restricted by the capacity
of the parent wild type (WT) peptide to bind at least weakly, i.e.,
bind at an IC.sub.50 of 5000 nM or less, to three of more A2
supertype alleles. The rationale for this requirement is that the
WT peptides must be present endogenously in sufficient quantity to
be biologically relevant. Analoged peptides have been shown to have
increased immunogenicity and cross-reactivity by T cells specific
for the parent epitope (see, e.g., Parkhurst et al., J. Immunol.
157:2539, 1996; and Pogue et al., Proc. Natl. Acad. Sci. USA
92:8166,1995).
[0997] In the cellular screening of these peptide analogs, it is
important to confirm that analog-specific CTLs are also able to
recognize the wild-type peptide and, when possible, target cells
that endogenously express the epitope.
[0998] Analoging of HLA-A3 and B7-Supermotif-Bearing Peptides
[0999] Analogs of HLA-A3 supermotif-bearing epitopes are generated
using strategies similar to those employed in analoging HLA-A2
supermotif-bearing peptides. For example, peptides binding to 3/5
of the A3-supertype molecules are engineered at primary anchor
residues to possess a preferred residue (V, S, M, or A) at position
2.
[1000] The analog peptides are then tested for the ability to bind
A*03 and A*11 (prototype A3 supertype alleles). Those peptides that
demonstrate .ltoreq.500 nM binding capacity are then confirmed as
having A3-supertype cross-reactivity.
[1001] Similarly to the A2- and A3-motif bearing peptides, peptides
binding 3 or more B7-supertype alleles can be improved, where
possible, to achieve increased cross-reactive binding or greater
binding affinity or binding half life. B7 supermotif-bearing
peptides are, for example, engineered to possess a preferred
residue (V, I, L, or F) at the C-terminal primary anchor position,
as demonstrated by Sidney et al. (J. Immunol. 157:3480-3490,
1996).
[1002] Analoging at primary anchor residues of other motif and/or
supermotif-bearing epitopes is performed in a like manner.
[1003] The analog peptides are then be confirmed for
immunogenicity, typically in a cellular screening assay. Again, it
is generally important to demonstrate that analog-specific CTLs are
also able to recognize the wild-type peptide and, when possible,
targets that endogenously express the epitope.
[1004] Analoging at Secondary Anchor Residues
[1005] Moreover, HLA supermotifs are of value in engineering highly
cross-reactive peptides and/or peptides that bind HLA molecules
with increased affinity by identifying particular residues at
secondary anchor positions that are associated with such
properties. For example, the binding capacity of a B7
supermotif-bearing peptide with an F residue at position 1 is
analyzed. The peptide is then analoged to, for example, substitute
L for F at position 1. The analoged peptide is evaluated for
increased binding affinity, binding half life and/or increased
cross-reactivity. Such a procedure identifies analoged peptides
with enhanced properties.
[1006] Engineered analogs with sufficiently improved binding
capacity or cross-reactivity can also be tested for immunogenicity
in HLA-B7-transgenic mice, following for example, IFA immunization
or lipopeptide immunization. Analoged peptides are additionally
tested for the ability to stimulate a recall response using PBMC
from patients with 98P4B6-expressing tumors.
[1007] Other Analoging Strategies
[1008] Another form of peptide analoging, unrelated to anchor
positions, involves the substitution of a cysteine with
.alpha.-amino butyric acid. Due to its chemical nature, cysteine
has the propensity to form disulfide bridges and sufficiently alter
the peptide structurally so as to reduce binding capacity.
Substitution of .alpha.-amino butyric acid for cysteine not only
alleviates this problem, but has been shown to improve binding and
crossbinding capabilities in some instances (see, e.g., the review
by Sette et al., In: Persistent Viral Infections, Eds. R. Ahmed and
I. Chen, John Wiley & Sons, England, 1999).
[1009] Thus, by the use of single amino acid substitutions, the
binding properties and/or cross-reactivity of peptide ligands for
HLA supertype molecules can be modulated.
Example 16
Identification and Confirmation of 98P4B6-Derived Sequences with
HLA-DR Binding Motifs
[1010] Peptide epitopes bearing an HLA class II supermotif or motif
are identified and confirmed as outlined below using methodology
similar to that described for HLA Class I peptides.
[1011] Selection of HLA-DR-Supermotif-Bearing Epitopes.
[1012] To identify 98P4B6-derived, HLA class II HTL epitopes, a
98P4B6 antigen is analyzed for the presence of sequences bearing an
HLA-DR-motif or supermotif. Specifically, 15-mer sequences are
selected comprising a DR-supermotif, comprising a 9-mer core, and
three-residue N- and C-terminal flanking regions (15 amino acids
total).
[1013] Protocols for predicting peptide binding to DR molecules
have been developed (Southwood et al., J. Immunol. 160:3363-3373,
1998). These protocols, specific for individual DR molecules, allow
the scoring, and ranking, of 9-mer core regions. Each protocol not
only scores peptide sequences for the presence of DR-supermotif
primary anchors (i.e., at position 1 and position 6) within a 9-mer
core, but additionally evaluates sequences for the presence of
secondary anchors. Using allele-specific selection tables (see,
e.g., Southwood et al., ibid.), it has been found that these
protocols efficiently select peptide sequences with a high
probability of binding a particular DR molecule. Additionally, it
has been found that performing these protocols in tandem,
specifically those for DR1, DR4w4, and DR7, can efficiently select
DR cross-reactive peptides.
[1014] The 98P4B6-derived peptides identified above are tested for
their binding capacity for various common HLA-DR molecules. All
peptides are initially tested for binding to the DR molecules in
the primary panel: DR1, DR4w4, and DR7. Peptides binding at least
two of these three DR molecules are then tested for binding to
DR2w2 .beta.1, DR2w2 .beta.2, DR6w19, and DR9 molecules in
secondary assays. Finally, peptides binding at least two of the
four secondary panel DR molecules, and thus cumulatively at least
four of seven different DR molecules, are screened for binding to
DR4w15, DR5w11, and DR8w2 molecules in tertiary assays. Peptides
binding at least seven of the ten DR molecules comprising the
primary, secondary, and tertiary screening assays are considered
cross-reactive DR binders. 98P4B6-derived peptides found to bind
common HLA-DR alleles are of particular interest.
[1015] Selection of DR3 Motif Peptides
[1016] Because HLA-DR3 is an allele that is prevalent in Caucasian,
Black, and Hispanic populations, DR3 binding capacity is a relevant
criterion in the selection of HTL epitopes. Thus, peptides shown to
be candidates may also be assayed for their DR3 binding capacity.
However, in view of the binding specificity of the DR3 motif,
peptides binding only to DR3 can also be considered as candidates
for inclusion in a vaccine formulation.
[1017] To efficiently identify peptides that bind DR3, target
98P4B6 antigens are analyzed for sequences carrying one of the two
DR3-specific binding motifs reported by Geluk et al. (J. Immunol.
152:5742-5748, 1994). The corresponding peptides are then
synthesized and confirmed as having the ability to bind DR3 with an
affinity of 1 .mu.M or better, i.e., less than 1 .mu.M. Peptides
are found that meet this binding criterion and qualify as HLA class
II high affinity binders.
[1018] DR3 binding epitopes identified in this manner are included
in vaccine compositions with DR supermotif-bearing peptide
epitopes.
[1019] Similarly to the case of HLA class I motif-bearing peptides,
the class II motif-bearing peptides are analoged to improve
affinity or cross-reactivity. For example, aspartic acid at
position 4 of the 9-mer core sequence is an optimal residue for DR3
binding, and substitution for that residue often improves DR 3
binding.
Example 17
Immunogenicity of 98P4B6-Derived HTL Epitopes
[1020] This example determines immunogenic DR supermotif- and DR3
motif-bearing epitopes among those identified using the methodology
set forth herein.
[1021] Immunogenicity of HTL epitopes are confirmed in a manner
analogous to the determination of immunogenicity of CTL epitopes,
by assessing the ability to stimulate HTL responses and/or by using
appropriate transgenic mouse models. Immunogenicity is determined
by screening for: 1.) in vitro primary induction using normal PBMC
or 2.) recall responses from patients who have 98P4B6-expressing
tumors.
Example 18
Calculation of Phenotypic Frequencies of HLA-Supertypes in Various
Ethnic Backgrounds to Determine Breadth of Population Coverage
[1022] This example illustrates the assessment of the breadth of
population coverage of a vaccine composition comprised of multiple
epitopes comprising multiple supermotifs and/or motifs.
[1023] In order to analyze population coverage, gene frequencies of
HLA alleles are determined. Gene frequencies for each HLA allele
are calculated from antigen or allele frequencies utilizing the
binomial distribution formulae gf=1-(SQRT(1-af)) (see, e.g., Sidney
et al., Human Immunol 45:79-93, 1996). To obtain overall phenotypic
frequencies, cumulative gene frequencies are calculated, and the
cumulative antigen frequencies derived by the use of the inverse
formula [af=1-(1-Cgf).sup.2].
[1024] Where frequency data is not available at the level of DNA
typing, correspondence to the serologically defined antigen
frequencies is assumed. To obtain total potential supertype
population coverage no linkage disequilibrium is assumed, and only
alleles confirmed to belong to each of the supertypes are included
(minimal estimates). Estimates of total potential coverage achieved
by inter-loci combinations are made by adding to the A coverage the
proportion of the non-A covered population that could be expected
to be covered by the B alleles considered (e.g., total=A+B*(1-A)).
Confirmed members of the A3-like supertype are A3, A11, A31,
A*3301, and A*6801. Although the A3-like supertype may also include
A34, A66, and A*7401, these alleles were not included in overall
frequency calculations. Likewise, confirmed members of the A2-like
supertype family are A*0201, A*0202, A*0203, A*0204, A*0205,
A*0206, A*0207, A*6802, and A*6901. Finally, the B7-like
supertype-confirmed alleles are: B7, B*3501-03, B51, B*5301,
B*5401, B*5501-2, B*5601, B*6701, and B*7801 (potentially also
B*1401, B*3504-06, B*4201, and B*5602).
[1025] Population coverage achieved by combining the A2-, A3- and
B7-supertypes is approximately 86% in five major ethnic groups.
Coverage may be extended by including peptides bearing the A1 and
A24 motifs. On average, A1 is present in 12% and A24 in 29% of the
population across five different major ethnic groups (Caucasian,
North American Black, Chinese, Japanese, and Hispanic). Together,
these alleles are represented with an average frequency of 39% in
these same ethnic populations. The total coverage across the major
ethnicities when A1 and A24 are combined with the coverage of the
A2-, A3- and B7-supertype alleles is >95%, see, e.g., Table IV
(G). An analogous approach can be used to estimate population
coverage achieved with combinations of class II motif-bearing
epitopes.
[1026] Immunogenicity studies in humans (e.g., Bertoni et al., J.
Clin. Invest. 100:503, 1997; Doolan et al., Immunity 7:97, 1997;
and Threlkeld et al., J. Immunol. 159:1648, 1997) have shown that
highly cross-reactive binding peptides are almost always recognized
as epitopes. The use of highly cross-reactive binding peptides is
an important selection criterion in identifying candidate epitopes
for inclusion in a vaccine that is immunogenic in a diverse
population.
[1027] With a sufficient number of epitopes (as disclosed herein
and from the art), an average population coverage is predicted to
be greater than 95% in each of five major ethnic populations. The
game theory Monte Carlo simulation analysis, which is known in the
art (see e.g., Osborne, M. J. and Rubinstein, A. "A course in game
theory" MIT Press, 1994), can be used to estimate what percentage
of the individuals in a population comprised of the Caucasian,
North American Black, Japanese, Chinese, and Hispanic ethnic groups
would recognize the vaccine epitopes described herein. A preferred
.percentage is 90%. A more preferred percentage is 95%.
Example 19
CTL Recognition of Endogenously Processed Antigens after
Priming
[1028] This example confirms that CTL induced by native or analoged
peptide epitopes identified and selected as described herein
recognize endogenously synthesized, i.e., native antigens.
[1029] Effector cells isolated from transgenic mice that are
immunized with peptide epitopes, for example HLA-A2
supermotif-bearing epitopes, are re-stimulated in vitro using
peptide-coated stimulator cells. Six days later, effector cells are
assayed for cytotoxicity and the cell lines that contain
peptide-specific cytotoxic activity are further re-stimulated. An
additional six days later, these cell lines are tested for
cytotoxic activity on .sup.51Cr labeled Jurkat-A2.1/K.sup.b target
cells in the absence or presence of peptide, and also tested on
.sup.51Cr labeled target cells bearing the endogenously synthesized
antigen, i.e. cells that are stably transfected with 98P4B6
expression vectors.
[1030] The results demonstrate that CTL lines obtained from animals
primed with peptide epitope recognize endogenously synthesized
98P4B6 antigen. The choice of transgenic mouse model to be used for
such an analysis depends upon the epitope(s) that are being
evaluated. In addition to HLA-A*0201/K.sup.b transgenic mice,
several other transgenic mouse models including mice with human
A11, which may also be used to evaluate A3 epitopes, and B7 alleles
have been characterized and others (e.g., transgenic mice for
HLA-A1 and A24) are being developed. HLA-DR1 and HLA-DR3 mouse
models have also been developed, which may be used to evaluate HTL
epitopes.
Example 20
Activity of CTL-HTL Conjugated Epitopes in Transgenic Mice
[1031] This example illustrates the induction of CTLs and HTLs in
transgenic mice, by use of a 98P4B6-derived CTL and HTL peptide
vaccine compositions. The vaccine composition used herein comprise
peptides to be administered to a patient with a 98P4B6-expressing
tumor. The peptide composition can comprise multiple CTL and/or HTL
epitopes. The epitopes are identified using methodology as
described herein. This example also illustrates that enhanced
immunogenicity can be achieved by inclusion of one or more HTL
epitopes in a CTL vaccine composition; such a peptide composition
can comprise an HTL epitope conjugated to a CTL epitope. The CTL
epitope can be one that binds to multiple HLA family members at an
affinity of 500 nM or less, or analogs of that epitope. The
peptides may be lipidated, if desired.
[1032] Immunization Procedures:
[1033] Immunization of transgenic mice is performed as described
(Alexander et al., J. Immunol. 159:4753-4761, 1997). For example,
A2/K.sup.b mice, which are transgenic for the human HLA A2.1 allele
and are used to confirm the immunogenicity of HLA-A*0201 motif- or
HLA-A2 supermotif-bearing epitopes, and are primed subcutaneously
(base of the tail) with a 0.1 ml of peptide in Incomplete Freund's
Adjuvant, or if the peptide composition is a lipidated CTL/HTL
conjugate, in DMSO/saline, or if the peptide composition is a
polypeptide, in PBS or Incomplete Freund's Adjuvant. Seven days
after priming, splenocytes obtained from these animals are
restimulated with syngenic irradiated LPS-activated lymphoblasts
coated with peptide.
[1034] Cell Lines:
[1035] Target cells for peptide-specific cytotoxicity assays are
Jurkat cells transfected with the HLA-A2.1/K.sup.b chimeric gene
(e.g., Vitiello et al., J. Exp. Med. 173:1007, 1991)
[1036] In Vitro CTL Activation:
[1037] One week after priming, spleen cells (30.times.10.sup.6
cells/flask) are co-cultured at 37.degree. C. with syngeneic,
irradiated (3000 rads), peptide coated lymphoblasts
(10.times.10.sup.6 cells/flask) in 10 ml of culture medium/T25
flask. After six days, effector cells are harvested and assayed for
cytotoxic activity.
[1038] Assay for cytotoxic activity: Target cells (1.0 to
1.5.times.10.sup.6) are incubated at 37.degree. C. in the presence
of 200 .mu.l of .sup.51Cr. After 60 minutes, cells are washed three
times and resuspended in R10 medium. Peptide is added where
required at a concentration of 1 .mu.g/mi. For the assay, 10.sup.4
51Cr-labeled target cells are added to different concentrations of
effector cells (final volume of 200 .mu.l) in U-bottom 96-well
plates. After a six hour incubation period at 37.degree. C., a 0.1
ml aliquot of supernatant is removed from each well and
radioactivity is determined in a Micromedic automatic gamma
counter. The percent specific lysis is determined by the formula:
percent specific release=100.times.(experimental
release-spontaneous release)/(maximum release-spontaneous release).
To facilitate comparison between separate CTL assays run under the
same conditions, % .sup.51Cr release data is expressed as lytic
units/10.sup.6 cells. One lytic unit is arbitrarily defined as the
number of effector cells required to achieve 30% lysis of 10,000
target cells in a six hour .sup.51Cr release assay. To obtain
specific lytic units/10.sup.6, the lytic units/10.sup.6 obtained in
the absence of peptide is subtracted from the lytic units/10.sup.6
obtained in the presence of peptide. For example, if 30% .sup.51Cr
release is obtained at the effector (E): target (T) ratio of 50:1
(i.e., 5.times.10.sup.5 effector cells for 10,000 targets) in the
absence of peptide and 5:1 (i.e., 5.times.10.sup.4 effector cells
for 10,000 targets) in the presence of peptide, the specific lytic
units would be: [(1150,000)-(1/500,000)].times.10.sup.6=18 LU.
[1039] The results are analyzed to assess the magnitude of the CTL
responses of animals injected with the immunogenic CTL/HTL
conjugate vaccine preparation and are compared to the magnitude of
the CTL response achieved using, for example, CTL epitopes as
outlined above in the Example entitled "Confirmation of
Immunogenicity." Analyses similar to this may be performed to
confirm the immunogenicity of peptide conjugates containing
multiple CTL epitopes and/or multiple HTL epitopes. In accordance
with these procedures, it is found that a CTL response is induced,
and concomitantly that an HTL response is induced upon
administration of such compositions.
Example 21
Selection of CTL and HTL Epitopes for Inclusion in a
98P4B6-Specific Vaccine
[1040] This example illustrates a procedure for selecting peptide
epitopes for vaccine compositions of the invention. The peptides in
the composition can be in the form of a nucleic acid sequence,
either single or one or more sequences (ie., minigene) that encodes
peptide(s), or can be single and/or polyepitopic peptides.
[1041] The following principles are utilized when selecting a
plurality of epitopes for inclusion in a vaccine composition. Each
of the following principles is balanced in order to make the
selection.
[1042] Epitopes are selected which, upon administration, mimic
immune responses that are correlated with 98P4B6 clearance. The
number of epitopes used depends on observations of patients who
spontaneously clear 98P4B6. For example, if it has been observed
that patients who spontaneously clear 98P4B6-expressing cells
generate an immune response to at least three (3) epitopes from
98P4B6 antigen, then at least three epitopes should be included for
HLA class I. A similar rationale is used to determine HLA class II
epitopes.
[1043] Epitopes are often selected that have a binding affinity of
an IC.sub.50 of 500 nM or less for an HLA class I molecule, or for
class II, an IC.sub.50 of 1000 nM or less; or HLA Class I peptides
with high binding scores from the BIMAS web site, at URL
bimas.dcrt.nih.gov/.
[1044] In order to achieve broad coverage of the vaccine through
out a diverse population, sufficient supermotif bearing peptides,
or a sufficient array of allele-specific motif bearing peptides,
are selected to give broad population coverage. In one embodiment,
epitopes are selected to provide at least 80% population coverage.
A Monte Carlo analysis, a statistical evaluation known in the art,
can be employed to assess breadth, or redundancy, of population
coverage.
[1045] When creating polyepitopic compositions, or a minigene that
encodes same, it is typically desirable to generate the smallest
peptide possible that encompasses the epitopes of interest. The
principles employed are similar, if not the same, as those employed
when selecting a peptide comprising nested epitopes. For example, a
protein sequence for the vaccine composition is selected because it
has maximal number of epitopes contained within the sequence, i.e.,
it has a high concentration of epitopes. Epitopes may be nested or
overlapping (i.e., frame shifted relative to one another). For
example, with overlapping epitopes, two 9-mer epitopes and one
10-mer epitope can be present in a 10 amino acid peptide. Each
epitope can be exposed and bound by an HLA molecule upon
administration of such a peptide. A multi-epitopic, peptide can be
generated synthetically, recombinantiy, or via cleavage from the
native source. Alternatively, an analog can be made of this native
sequence, whereby one or more of the epitopes comprise
substitutions that alter the cross-reactivity and/or binding
affinity properties of the polyepitopic peptide. Such a vaccine
composition is administered for therapeutic or prophylactic
purposes. This embodiment provides for the possibility that an as
yet undiscovered aspect of immune system processing will apply to
the native nested sequence and thereby facilitate the production of
therapeutic or prophylactic immune response-inducing vaccine
compositions. Additionally such an embodiment provides for the
possibility of motif-bearing epitopes for an HLA makeup that is
presently unknown. Furthermore, this embodiment (absent the
creating of any analogs) directs the immune response to multiple
peptide sequences that are actually present in 98P4B6, thus
avoiding the need to evaluate any junctional epitopes. Lastly, the
embodiment provides an economy of scale when producing nucleic acid
vaccine compositions. Related to this embodiment, computer programs
can be derived in accordance with principles in the art, which
identify in a target sequence, the greatest number of epitopes per
sequence length.
[1046] A vaccine composition comprised of selected peptides, when
administered, is safe, efficacious, and elicits an immune response
similar in magnitude to an immune response that controls or clears
cells that bear or overexpress 98P4B6.
Example 22
Construction of "Minigene" Multi-Epitope DNA Plasmids
[1047] This example discusses the construction of a minigene
expression plasmid. Minigene plasmids may, of course, contain
various configurations of B cell, CTL and/or HTL epitopes or
epitope analogs as described herein.
[1048] A minigene expression plasmid typically includes multiple
CTL and HTL peptide epitopes. In the present example, HLA-A2, -A3,
-B7 supermotif-bearing peptide epitopes and HLA-A1 and -A24
motif-bearing peptide epitopes are used in conjunction with DR
supermotif-bearing epitopes and/or DR3 epitopes. HLA class I
supermotif or motif-bearing peptide epitopes derived 98P4B6, are
selected such that multiple supermotifs/motifs are represented to
ensure broad population coverage. Similarly, HLA class II epitopes
are selected from 98P4B6 to provide broad population coverage, i.e.
both HLA DR-1-4-7 supermotif-bearing epitopes and HLA DR-3
motif-bearing epitopes are selected for inclusion in the minigene
construct. The selected CTL and HTL epitopes are then incorporated
into a minigene for expression in an expression vector.
[1049] Such a construct may additionally include sequences that
direct the HTL epitopes to the endoplasmic reticulum. For example,
the Ii protein may be fused to one or more HTL epitopes as
described in the art, wherein the CLIP sequence of the li protein
is removed and replaced with an HLA class II epitope sequence so
that HLA class II epitope is directed to the endoplasmic reticulum,
where the epitope binds to an HLA class II molecules.
[1050] This example illustrates the methods to be used for
construction of a minigene-bearing expression plasmid. Other
expression vectors that may be used for minigene compositions are
available and known to those of skill in the art.
[1051] The minigene DNA plasmid of this example contains a
consensus Kozak sequence and a consensus murine kappa Ig-light
chain signal sequence followed by CTL and/or HTL epitopes selected
in accordance with principles disclosed herein. The sequence
encodes an open reading frame fused to the Myc and His antibody
epitope tag coded for by the pcDNA 3.1 Myc-His vector.
[1052] Overlapping oligonucleotides that can, for example, average
about 70 nucleotides in length with 15 nucleotide overlaps, are
synthesized and HPLC-purified. The oligonucleotides encode the
selected peptide epitopes as well as appropriate linker
nucleotides, Kozak sequence, and signal sequence. The final
multiepitope minigene is assembled by extending the overlapping
oligonucleotides in three sets of reactions using PCR. A
Perkin/Elmer 9600 PCR machine is used and a total of 30 cycles are
performed using the following conditions: 95.degree. C. for 15 sec,
annealing temperature (5.degree. below the lowest calculated Tm of
each primer pair) for 30 sec, and 72.degree. C. for 1 min.
[1053] For example, a minigene is prepared as follows. For a first
PCR reaction, 5 .mu.g of each of two oligonucleotides are annealed
and extended: In an example using eight oligonucleotides, i.e.,
four pairs of primers, oligonucleotides 1+2, 3+4, 5+6, and 7+8 are
combined in 100 .mu.l reactions containing Pfu polymerase buffer
(1.times.=10 mM KCL, 10 mM (NH4).sub.2SO.sub.4, 20 mM
Tris-chloride, pH 8.75, 2 mM MgSO.sub.4, 0.1% Triton X-100, 100
.mu.g/ml BSA), 0.25 mM each dNTP, and 2.5 U of Pfu polymerase. The
full-length dimer products are gel-purified, and two reactions
containing the product of 1+2 and 3+4, and the product of 5+6 and
7+8 are mixed, annealed, and extended for 10 cycles. Half of the
two reactions are then mixed, and 5 cycles of annealing and
extension carried out before flanking primers are added to amplify
the full length product. The full-length product is gel-purified
and cloned into pCR-blunt (Invitrogen) and individual clones are
screened by sequencing.
Example 23
The Plasmid Construct and the Degree to Which it Induces
Immunogenicity
[1054] The degree to which a plasmid construct, for example a
plasmid constructed in accordance with the previous Example, is
able to induce immunogenicity is confirmed in vitro by determining
epitope presentation by APC following transduction or transfection
of the APC with an epitope-expressing nucleic acid construct. Such
a study determines "antigenicity" and allows the use of human APC.
The assay determines the ability of the epitope to be presented by
the APC in a context that is recognized by a T cell by quantifying
the density of epitope-HLA class I complexes on the cell surface.
Quantitation can be performed by directly measuring the amount of
peptide eluted from the APC (see, e.g., Sijts et al., J. Immunol.
156:683-692, 1996; Demotz et al., Nature 342:682-684, 1989); or the
number of peptide-HLA class I complexes can be estimated by
measuring the amount of lysis or lymphokine release induced by
diseased or transfected target cells, and then determining the
concentration of peptide necessary to obtain equivalent levels of
lysis or lymphokine release (see, e.g., Kageyama et al., J.
Immunol. 154:567-576, 1995).
[1055] Alternatively, immunogenicity is confirmed through in vivo
injections into mice and subsequent in vitro assessment of CTL and
HTL activity, which are analyzed using cytotoxicity and
proliferation assays, respectively, as detailed e.g., in Alexander
et al., Immunity 1:751-761, 1994.
[1056] For example, to confirm the capacity of a DNA minigene
construct containing at least one HLA-A2 supermotif peptide to
induce CTLs in vivo, HLA-A2.1/K.sup.b transgenic mice, for example,
are immunized intramuscularly with 100 .mu.g of naked cDNA. As a
means of comparing the level of CTLs induced by cDNA immunization,
a control group of animals is also immunized with an actual peptide
composition that comprises multiple epitopes synthesized as a
single polypeptide as they would be encoded by the minigene.
[1057] Splenocytes from immunized animals are stimulated twice with
each of the respective compositions (peptide epitopes encoded in
the minigene or the polyepitopic peptide), then assayed for
peptide-specific cytotoxic activity in a .sup.51Cr release assay.
The results indicate the magnitude of the CTL response directed
against the A2-restricted epitope, thus indicating the in vivo
immunogenicity of the minigene vaccine and polyepitopic
vaccine.
[1058] It is, therefore, found that the minigene elicits immune
responses directed toward the HLA-A2 supermotif peptide epitopes as
does the polyepitopic peptide vaccine. A similar analysis is also
performed using other HLA-A3 and HLA-B7 transgenic mouse models to
assess CTL induction by HLA-A3 and HLA-B7 motif or supermotif
epitopes, whereby it is also found that the minigene elicits
appropriate immune responses directed toward the provided
epitopes.
[1059] To confirm the capacity of a class II epitope-encoding
minigene to induce HTLs in vivo, DR transgenic mice, or for those
epitopes that cross react with the appropriate mouse MHC molecule,
I-A.sup.b-restricted mice, for example, are immunized
intramuscularly with 100 .mu.g of plasmid DNA. As a means of
comparing the level of HTLs induced by DNA immunization, a group of
control animals is also immunized with an actual peptide
composition emulsified in complete Freund's adjuvant. CD4+ T cells,
i.e. HTLs, are purified from splenocytes of immunized animals and
stimulated with each of the respective compositions (peptides
encoded in the minigene). The HTL response is measured using a
.sup.3H-thymidine incorporation proliferation assay, (see, e.g.,
Alexander et al. Immunity 1:751-761, 1994). The results indicate
the magnitude of the HTL response, thus demonstrating the in vivo
immunogenicity of the minigene.
[1060] DNA minigenes, constructed as described in the previous
Example, can also be confirmed as a vaccine in combination with a
boosting agent using a prime boost protocol. The boosting agent can
consist of recombinant protein (e.g., Barnett et al., Aids Res. and
Human Retroviruses 14, Supplement 3:S299-S309, 1998) or recombinant
vaccinia, for example, expressing a minigene or DNA encoding the
complete protein of interest (see, e.g., Hanke et al., Vaccine
16:439-445, 1998; Sedegah et al., Proc. Natl. Acad. Sci USA
95:7648-53, 1998; Hanke and McMichael, Immunol. Letters 66:177-181,
1999; and Robinson et al., Nature Med. 5:526-34, 1999).
[1061] For example, the efficacy of the DNA minigene used in a
prime boost protocol is initially evaluated in transgenic mice. In
this example, A2.1/K.sup.b transgenic mice are immunized IM with
100 .mu.g of a DNA minigene encoding the immunogenic peptides
including at least one HLA-A2 supermotif-bearing peptide. After an
incubation period (ranging from 3-9 weeks), the mice are boosted IP
with 10.sup.7 pfu/mouse of a recombinant vaccinia virus expressing
the same sequence encoded by the DNA minigene. Control mice are
immunized with 100 .mu.g of DNA or recombinant vaccinia without the
minigene sequence, or with DNA encoding the minigene, but without
the vaccinia boost. After an additional incubation period of two
weeks, splenocytes from the mice are immediately assayed for
peptide-specific activity in an ELISPOT assay. Additionally,
splenocytes are stimulated in vitro with the A2-restricted peptide
epitopes encoded in the minigene and recombinant vaccinia, then
assayed for peptide-specific activity in an alpha, beta and/or
gamma IFN ELISA.
[1062] It is found that the minigene utilized in a prime-boost
protocol elicits greater immune responses toward the HLA-A2
supermotif peptides than with DNA alone. Such an analysis can also
be performed using HLA-A11 or HLA-B7 transgenic mouse models to
assess CTL induction by HLA-A3 or HLA-B7 motif or supermotif
epitopes. The use of prime boost protocols in humans is described
below in the Example entitled "Induction of CTL Responses Using a
Prime Boost Protocol."
Example 24
Peptide Compositions for Prophylactic Uses
[1063] Vaccine compositions of the present invention can be used to
prevent 98P4B6 expression in persons who are at risk for tumors
that bear this antigen. For example, a polyepitopic peptide epitope
composition (or a nucleic acid comprising the same) containing
multiple CTL and HTL epitopes such as those selected in the above
Examples, which are also selected to target greater than 80% of the
population, is administered to individuals at risk for a
98P4B6-associated tumor.
[1064] For example, a peptide-based composition is provided as a
single polypeptide that encompasses multiple epitopes. The vaccine
is typically administered in a physiological solution that
comprises an adjuvant, such as Incomplete Freunds Adjuvant. The
dose of peptide for the initial immunization is from about 1 to
about 50,000 .mu.g, generally 100-5,000 .mu.g, for a 70 kg patient.
The initial administration of vaccine is followed by booster
dosages at 4 weeks followed by evaluation of the magnitude of the
immune response in the patient, by techniques that determine the
presence of epitope-specific CTL populations in a PBMC sample.
Additional booster doses are administered as required. The
composition is found to be both safe and efficacious as a
prophylaxis against 98P4B6-associated disease.
[1065] Alternatively, a composition typically comprising
transfecting agents is used for the administration of a nucleic
acid-based vaccine in accordance with methodologies known in the
art and disclosed herein.
Example 25
Polyepitopic Vaccine Compositions Derived from Native 98P4B6
Sequences
[1066] A native 98P4B6 polyprotein sequence is analyzed, preferably
using computer algorithms defined for each class I and/or class II
supermotif or motif, to identify "relatively short" regions of the
polyprotein that comprise multiple epitopes. The "relatively short"
regions are preferably less in length than an entire native
antigen. This relatively short sequence that contains multiple
distinct or overlapping, "nested" epitopes can be used to generate
a minigene construct. The construct is engineered to express the
peptide, which corresponds to the native protein sequence. The
"relatively short" peptide is generally less than 250 amino acids
in length, often less than 100 amino acids in length, preferably
less than 75 amino acids in length, and more preferably less than
50 amino acids in length. The protein sequence of the vaccine
composition is selected because it has maximal number of epitopes
contained within the sequence, i.e., it has a high concentration of
epitopes. As noted herein, epitope motifs may be nested or
overlapping (i.e., frame shifted relative to one another). For
example, with overlapping epitopes, two 9-mer epitopes and one
10-mer epitope can be present in a 10 amino acid peptide. Such a
vaccine composition is administered for therapeutic or prophylactic
purposes.
[1067] The vaccine composition will include, for example, multiple
CTL epitopes from 98P4B6 antigen and at least one HTL epitope. This
polyepitopic native sequence is administered either as a peptide or
as a nucleic acid sequence which encodes the peptide.
Alternatively, an analog can be made of this native sequence,
whereby one or more of the epitopes comprise substitutions that
alter the cross-reactivity and/or binding affinity properties of
the polyepitopic peptide.
[1068] The embodiment of this example provides for the possibility
that an as yet undiscovered aspect of immune system processing will
apply to the native nested sequence and thereby facilitate the
production of therapeutic or prophylactic immune response-inducing
vaccine compositions. Additionally, such an embodiment provides for
the possibility of motif-bearing epitopes for an HLA makeup(s) that
is presently unknown. Furthermore, this embodiment (excluding an
analoged embodiment) directs the immune response to multiple
peptide sequences that are actually present in native 98P4B6, thus
avoiding the need to evaluate any junctional epitopes. Lastly, the
embodiment provides an economy of scale when producing peptide or
nucleic acid vaccine compositions.
[1069] Related to this embodiment, computer programs are available
in the art which can be used to identify in a target sequence, the
greatest number of epitopes per sequence length.
Example 26
Polyepitopic Vaccine Compositions from Multiple Antigens
[1070] The 98P4B6 peptide epitopes of the present invention are
used in conjunction with epitopes from other target
tumor-associated antigens, to create a vaccine composition that is
useful for the prevention or treatment of cancer that expresses
98P4B6 and such other antigens. For example, a vaccine composition
can be provided as a single polypeptide that incorporates multiple
epitopes from 98P4B6 as well as tumor-associated antigens that are
often expressed with a target cancer associated with 98P4B6
expression, or can be administered as a composition comprising a
cocktail of one or more discrete epitopes. Alternatively, the
vaccine can be administered as a minigene construct or as dendritic
cells which have been loaded with the peptide epitopes in
vitro.
Example 27
Use of Peptides to Evaluate an Immune Response
[1071] Peptides of the invention may be used to analyze an immune
response for the presence of specific antibodies, CTL or HTL
directed to 98P4B6. Such an analysis can be performed in a manner
described by Ogg et al., Science 279:2103-2106, 1998. In this
Example, peptides in accordance with the invention are used as a
reagent for diagnostic or prognostic purposes, not as an
immunogen.
[1072] In this example highly sensitive human leukocyte antigen
tetrameric complexes ("tetramers") are used for a cross-sectional
analysis of, for example, 98P4B6 HLA-A*0201-specific CTL
frequencies from HLA A*0201-positive individuals at different
stages of disease or following immunization comprising a 98P4B6
peptide containing an A*0201 motif. Tetrameric complexes are
synthesized as described (Musey et al., N. Engl. J. Med. 337:1267,
1997). Briefly, purified HLA heavy chain (A*0201 in this example)
and .beta.2-microglobulin are synthesized by means of a prokaryotic
expression system. The heavy chain is modified by deletion of the
transmembrane-cytosolic tail and COOH-terminal addition of a
sequence containing a BirA enzymatic biotinylation site. The heavy
chain, .beta.2-microglobulin, and peptide are refolded by dilution.
The 45-kD refolded product is isolated by fast protein liquid
chromatography and then biotinylated by BirA in the presence of
biotin (Sigma, St. Louis, Mo.), adenosine 5' triphosphate and
magnesium. Streptavidin-phycoerythrin conjugate is added in a 1:4
molar ratio, and the tetrameric product is concentrated to 1 mg/ml.
The resulting product is referred to as tetramer-phycoerythrin.
[1073] For the analysis of patient blood samples, approximately one
million PBMCs are centrifuged at 300 g for 5 minutes and
resuspended in 50 .mu.l of cold phosphate-buffered saline.
Tri-color analysis is performed with the tetramer-phycoerythrin,
along with anti-CD8-Tricolor, and anti-CD38. The PBMCs are
incubated with tetramer and antibodies on ice for 30 to 60 min and
then washed twice before formaldehyde fixation. Gates are applied
to contain >99.98% of control samples. Controls for the
tetramers include both A*0201-negative individuals and
A*0201-positive non-diseased donors. The percentage of cells
stained with the tetramer is then determined by flow cytometry. The
results indicate the number of cells in the PBMC sample that
contain epitope-restricted CTLs, thereby readily indicating the
extent of immune response to the 98P4B6 epitope, and thus the
status of exposure to 98P4B6, or exposure to a vaccine that elicits
a protective or therapeutic response.
Example 28
Use of Peptide Epitopes to Evaluate Recall Responses
[1074] The peptide epitopes of the invention are used as reagents
to evaluate T cell responses, such as acute or recall responses, in
patients. Such an analysis may be performed on patients who have
recovered from 98P4B6-associated disease or who have been
vaccinated with a 98P4B6 vaccine.
[1075] For example, the class I restricted CTL response of persons
who have been vaccinated may be analyzed. The vaccine may be any
98P4B6 vaccine. PBMC are collected from vaccinated individuals and
HLA typed. Appropriate peptide epitopes of the invention that,
optimally, bear supermotifs to provide cross-reactivity with
multiple HLA supertype family members, are then used for analysis
of samples derived from individuals who bear that HLA type.
[1076] PBMC from vaccinated individuals are separated on
Ficoll-Histopaque density gradients (Sigma Chemical Co., St. Louis,
Mo.), washed three times in HBSS (GIBCO Laboratories), resuspended
in RPMI-1640 (GIBCO Laboratories) supplemented with L-glutamine (2
mM), penicillin (50 U/ml), streptomycin (50 .mu.g/ml), and Hepes
(10 mM) containing 10% heat-inactivated human AB serum (complete
RPMI) and plated using microculture formats. A synthetic peptide
comprising an epitope of the invention is added at 10 .mu.g/ml to
each well and HBV core 128-140 epitope is added at 1 .mu.g/ml to
each well as a source of T cell help during the first week of
stimulation.
[1077] In the microculture format, 4.times.10.sup.5 PBMC are
stimulated with peptide in 8 replicate cultures in 96-well round
bottom plate in 100 .mu.l/well of complete RPMI. On days 3 and 10,
100 .mu.l of complete RPMI and 20 U/ml final concentration of rIL-2
are added to each well. On day 7 the cultures are transferred into
a 96-well flat-bottom plate and restimulated with peptide, rIL-2
and 10.sup.5 irradiated (3,000 rad) autologous feeder cells. The
cultures are tested for cytotoxic activity on day 14. A positive
CTL response requires two or more of the eight replicate cultures
to display greater than 10% specific .sup.51Cr release, based on
comparison with non-diseased control subjects as previously
described (Rehermann, et al., Nature Med. 2:1104,1108, 1996;
Rehermann et al., J. Clin. Invest. 97:1655-1665, 1996; and
Rehermann et al. J. Clin. Invest. 98:1432-1440, 1996).
[1078] Target cell lines are autologous and allogeneic
EBV-transformed B-LCL that are either purchased from the American
Society for Histocompatibility and Immunogenetics (ASHI, Boston,
Mass.) or established from the pool of patients as described
(Guilhot, et al. J. Virol. 66:2670-2678, 1992).
[1079] Cytotoxicity assays are performed in the following manner.
Target cells consist of either allogeneic HLA-matched or autologous
EBV-transformed B lymphoblastoid cell line that are incubated
overnight with the synthetic peptide epitope of the invention at 10
.mu.M, and labeled with 100 .mu.Ci of .sup.51Cr (Amersham Corp.,
Arlington Heights, Ill.) for 1 hour after which they are washed
four times with HBSS.
[1080] Cytolytic activity is determined in a standard 4-h, split
well .sup.51Cr release assay using U-bottomed 96 well plates
containing 3,000 targets/well. Stimulated PBMC are tested at
effector/target (EIT) ratios of 20-50:1 on day 14. Percent
cytotoxicity is determined from the formula:
100.times.[(experimental release-spontaneous release)/maximum
release-spontaneous release)]. Maximum release is determined by
lysis of targets by detergent (2% Triton X-100; Sigma Chemical Co.,
St. Louis, Mo.). Spontaneous release is <25% of maximum release
for all experiments.
[1081] The results of such an analysis indicate the extent to which
HLA-restricted CTL populations have been stimulated by previous
exposure to 98P4B6 or a 98P4B6 vaccine.
[1082] Similarly, Class II restricted HTL responses may also be
analyzed. Purified PBMC are cultured in a 96-well flat bottom plate
at a density of 1.5.times.10.sup.5 cells/well and are stimulated
with 10 .mu.g/ml synthetic peptide of the invention, whole 98P4B6
antigen, or PHA. Cells are routinely plated in replicates of 4-6
wells for each condition. After seven days of culture, the medium
is removed and replaced with fresh medium containing 10 U/ml IL-2.
Two days later, 1 .mu.Ci .sup.3H-thymidine is added to each well
and incubation is continued for an additional 18 hours. Cellular
DNA is then harvested on glass fiber mats and analyzed for
.sup.3H-thymidine incorporation. Antigen-specific T cell
proliferation is calculated as the ratio of 3H-thymidine
incorporation in the presence of antigen divided by the
.sup.3H-thymidine incorporation in the absence of antigen.
Example 29
Induction of Specific CTL Response in Humans
[1083] A human clinical trial for an immunogenic composition
comprising CTL and HTL epitopes of the invention is set up as an
IND Phase I, dose escalation study and carried out as a randomized,
double-blind, placebo-controlled trial. Such a trial is designed,
for example, as follows:
[1084] A total of about 27 individuals are enrolled and divided
into 3 groups:
[1085] Group I: 3 subjects are injected with placebo and 6 subjects
are injected with 5 .mu.g of peptide composition;
[1086] Group II: 3 subjects are injected with placebo and 6
subjects are injected with 50 .mu.g peptide composition;
[1087] Group III: 3 subjects are injected with placebo and 6
subjects are injected with 500 .mu.g of peptide composition.
[1088] After 4 weeks following the first injection, all subjects
receive a booster inoculation at the same dosage.
[1089] The endpoints measured in this study relate to the safety
and tolerability of the peptide composition as well as its
immunogenicity. Cellular immune responses to the peptide
composition are an index of the intrinsic activity of this the
peptide composition, and can therefore be viewed as a measure of
biological efficacy. The following summarize the clinical and
laboratory data that relate to safety and efficacy endpoints.
[1090] Safety: The incidence of adverse events is monitored in the
placebo and drug treatment group and assessed in terms of degree
and reversibility.
[1091] Evaluation of Vaccine Efficacy: For evaluation of vaccine
efficacy, subjects are bled before and after injection. Peripheral
blood mononuclear cells are isolated from fresh heparinized blood
by Ficoll-Hypaque density gradient centrifugation, aliquoted in
freezing media and stored frozen. Samples are assayed for CTL and
HTL activity.
[1092] The vaccine is found to be both safe and efficacious.
Example 30
Phase II Trials in Patients Expressing 98P4B6
[1093] Phase II trials are performed to study the effect of
administering the CTL-HTL peptide compositions to patients having
cancer that expresses 98P4B6. The main objectives of the trial are
to determine an effective dose and regimen for inducing CTLs in
cancer patients that express 98P4B6, to establish the safety of
inducing a CTL and HTL response in these patients, and to see to
what extent activation of CTLs improves the clinical picture of
these patients, as manifested, e.g., by the reduction and/or
shrinking of lesions. Such a study is designed, for example, as
follows:
[1094] The studies are performed in multiple centers. The trial
design is an open-label, uncontrolled, dose escalation protocol
wherein the peptide composition is administered as a single dose
followed six weeks later by a single booster shot of the same dose.
The dosages are 50, 500 and 5,000 micrograms per injection.
Drug-associated adverse effects (severity and reversibility) are
recorded.
[1095] There are three patient groupings. The first group is
injected with 50 micrograms of the peptide composition and the
second and third groups with 500 and 5,000 micrograms of peptide
composition, respectively. The patients within each group range in
age from 21-65 and represent diverse ethnic backgrounds. All of
them have a tumor that expresses 98P4B6.
[1096] Clinical manifestations or antigen-specific T-cell responses
are monitored to assess the effects of administering the peptide
compositions. The vaccine composition is found to be both safe and
efficacious in the treatment of 98P4B6-associated disease.
Example 31
Induction of CTL Responses Using a Prime Boost Protocol
[1097] A prime boost protocol similar in its underlying principle
to that used to confirm the efficacy of a DNA vaccine in transgenic
mice, such as described above in the Example entitled "The Plasmid
Construct and the Degree to Which It Induces Immunogenicity," can
also be used for the administration of the vaccine to humans. Such
a vaccine regimen can include an initial administration of, for
example, naked DNA followed by a boost using recombinant virus
encoding the vaccine, or recombinant protein/polypeptide or a
peptide mixture administered in an adjuvant.
[1098] For example, the initial immunization may be performed using
an expression vector, such as that constructed in the Example
entitled "Construction of "Minigene" Multi-Epitope DNA Plasmids" in
the form of naked nucleic acid administered IM (or SC or ID) in the
amounts of 0.5-5 mg at multiple sites. The nucleic acid (0.1 to
1000 .mu.g) can also be administered using a gene gun. Following an
incubation period of 3-4 weeks, a booster dose is then
administered. The booster can be recombinant fowlpox virus
administered at a dose of 5-10.sup.7 to 5.times.10.sup.9 pfu. An
alternative recombinant virus, such as an MVA, canarypox,
adenovirus, or adeno-associated virus, can also be used for the
booster, or the polyepitopic protein or a mixture of the peptides
can be administered. For evaluation of vaccine efficacy, patient
blood samples are obtained before immunization as well as at
intervals following administration of the initial vaccine and
booster doses of the vaccine. Peripheral blood mononuclear cells
are isolated from fresh heparinized blood by Ficoll-Hypaque density
gradient centrifugation, aliquoted in freezing media and stored
frozen. Samples are assayed for CTL and HTL activity.
[1099] Analysis of the results indicates that a magnitude of
response sufficient to achieve a therapeutic or protective immunity
against 98P4B6 is generated.
Example 32
Administration of Vaccine Compositions Using Dendritic Cells
(DC)
[1100] Vaccines comprising peptide epitopes of the invention can be
administered using APCs, or "professional" APCs such as DC. In this
example, peptide-pulsed DC are administered to a patient to
stimulate a CTL response in vivo. In this method, dendritic cells
are isolated, expanded, and pulsed with a vaccine comprising
peptide CTL and HTL epitopes of the invention. The dendritic cells
are infused back into the patient to elicit CTL and HTL responses
in vivo. The induced CTL and HTL then destroy or facilitate
destruction, respectively, of the target cells that bear the 98P4B6
protein from which the epitopes in the vaccine are derived.
[1101] For example, a cocktail of epitope-comprising peptides is
administered ex vivo to PBMC, or isolated DC therefrom. A
pharmaceutical to facilitate harvesting of DC can be used, such as
Progenipoietin.TM. (Monsanto, St. Louis, Mo.) or GM-CSF/IL-4. After
pulsing the DC with peptides, and prior to reinfusion into
patients, the DC are washed to remove unbound peptides.
[1102] As appreciated clinically, and readily determined by one of
skill based on clinical outcomes, the number of DC reinfused into
the patient can vary (see, e.g., Nature Med. 4:328, 1998; Nature
Med. 2:52, 1996 and Prostate 32:272, 1997). Although
2-50.times.10.sup.6 DC per patient are typically administered,
larger number of DC, such as 10.sup.7 or 10.sup.8 can also be
provided. Such cell populations typically contain between 50-90%
DC.
[1103] In some embodiments, peptide-loaded PBMC are injected into
patients without purification of the DC. For example, PBMC
generated after treatment with an agent such as Progenipoietin.TM.
are injected into patients without purification of the DC. The
total number of PBMC that are administered often ranges from
10.sup.8 to 10.sup.10. Generally, the cell doses injected into
patients is based on the percentage of DC in the blood of each
patient, as determined, for example, by immunofluorescence analysis
with specific anti-DC antibodies. Thus, for example, if
Progenipoietin.TM. mobilizes 2% DC in the peripheral blood of a
given patient, and that patient is to receive 5.times.10.sup.6 DC,
then the patient will be injected with a total of
2.5.times.10.sup.8 peptide-loaded PBMC. The percent DC mobilized by
an agent such as Progenipoietin.TM. is typically estimated to be
between 2-10%, but can vary as appreciated by one of skill in the
art.
[1104] Ex Vivo Activation of CTL/HTL responses
[1105] Alternatively, ex vivo CTL or HTL responses to 98P4B6
antigens can be induced by incubating, in tissue culture, the
patient's, or genetically compatible, CTL or HTL precursor cells
together with a source of APC, such as DC, and immunogenic
peptides. After an appropriate incubation time (typically about
7-28 days), in which the precursor cells are activated and expanded
into effector cells, the cells are infused into the patient, where
they will destroy (CTL) or facilitate destruction (HTL) of their
specific target cells, i.e., tumor cells.
Example 33
An Alternative Method of Identifying and Confirming Motif-Bearing
Peptides
[1106] Another method of identifying and confirming motif-bearing
peptides is to elute them from cells bearing defined MHC molecules.
For example, EBV transformed B cell lines used for tissue typing
have been extensively characterized to determine which HLA
molecules they express. In certain cases these cells express only a
single type of HLA molecule. These cells can be transfected with
nucleic acids that express the antigen of interest, e.g. 98P4B6.
Peptides produced by endogenous antigen processing of peptides
produced as a result of transfection will then bind to HLA
molecules within the cell and be transported and displayed on the
cell's surface. Peptides are then eluted from the HLA molecules by
exposure to mild acid conditions and their amino acid sequence
determined, e.g., by mass spectral analysis (e.g., Kubo et al., J.
Immunol. 152:3913, 1994). Because the majority of peptides that
bind a particular HLA molecule are motif-bearing, this is an
alternative modality for obtaining the motif-bearing peptides
correlated with the particular HLA molecule expressed on the
cell.
[1107] Alternatively, cell lines that do not express endogenous HLA
molecules can be transfected with an expression construct encoding
a single HLA allele. These cells can then be used as described,
i.e., they can then be transfected with nucleic acids that encode
98P4B6 to isolate peptides corresponding to 98P4B6 that have been
presented on the cell surface. Peptides obtained from such an
analysis will bear motif(s) that correspond to binding to the
single HLA allele that is expressed in the cell.
[1108] As appreciated by one in the art, one can perform a similar
analysis on a cell bearing more than one HLA allele and
subsequently determine peptides specific for each HLA allele
expressed. Moreover, one of skill would also recognize that means
other than transfection, such as loading with a protein antigen,
can be used to provide a source of antigen to the cell.
Example 34
Complementary Polynucleotides
[1109] Sequences complementary to the 98P4B6-encoding sequences, or
any parts thereof, are used to detect, decrease, or inhibit
expression of naturally occurring 98P4B6. Although use of
oligonucleotides comprising from about 15 to 30 base pairs is
described, essentially the same procedure is used with smaller or
with larger sequence fragments. Appropriate oligonucleotides are
designed using, e.g., OLIGO 4.06 software (National Biosciences)
and the coding sequence of 98P4B6. To inhibit transcription, a
complementary oligonucleotide is designed from the most unique 5'
sequence and used to prevent promoter binding to the coding
sequence. To inhibit translation, a complementary oligonucleotide
is designed to prevent ribosomal binding to a 98P4B6-encoding
transcript.
Example 35
Purification of Naturally-Occurring or Recombinant 98P4B6 Using
98P4B6-Specific Antibodies
[1110] Naturally occurring or recombinant 98P4B6 is substantially
purified by immunoaffinity chromatography using antibodies specific
for 98P4B6. An immunoaffinity column is constructed by covalently
coupling anti-98P4B6 antibody to an activated chromatographic
resin, such as CNBr-activated SEPHAROSE (Amersham Pharmacia
Biotech). After the coupling, the resin is blocked and washed
according to the manufacturers instructions.
[1111] Media containing 98P4B6 are passed over the immunoaffinity
column, and the column is washed under conditions that allow the
preferential absorbance of 98P4B6 (e.g., high ionic strength
buffers in the presence of detergent). The column is eluted under
conditions that disrupt antibody/98P4B6 binding (e.g., a buffer of
pH 2 to pH 3, or a high concentration of a chaotrope, such as urea
or thiocyanate ion), and GCR.P is collected.
Example 36
Identification of Molecules which Interact with 98P4B6
[1112] 98P4B6, or biologically active fragments thereof, are
labeled with 121 1 Bolton-Hunter reagent. (See, e.g., Bolton et al.
(1973) Biochem. J. 133:529.) Candidate molecules previously arrayed
in the wells of a multi-well plate are incubated with the labeled
98P4B6, washed, and any wells with labeled 98P4B6 complex are
assayed. Data obtained using different concentrations of 98P4B6 are
used to calculate values for the number, affinity, and association
of 98P4B6 with the candidate molecules.
Example 37
In Vivo Assay for 98P4B6 Tumor Growth Promotion
[1113] The effect of the 98P4B6 protein on tumor cell growth is
evaluated in vivo by gene overexpression in tumor-bearing mice. For
example, prostate (PC3), lung (A427), stomach, ovarian (PA1) and
uterus cell lines are engineered to express 98P4B6. SCID mice are
injected subcutaneously on each flank with 1.times.10.sup.6 of PC3,
A427, PA1, or NIH-3T3 cells containing tkNeo empty vector or
98P4B6. At least two strategies may be used: (1) Constitutive
98P4B6 expression under regulation of a promoter such as a
constitutive promoter obtained from the genomes of viruses such as
polyoma virus, fowlpox virus (UK 2,211,504 published 5 Jul. 1989),
adenovirus (such as Adenovirus 2), bovine papilloma virus, avian
sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus,
and Simian Virus 40 (SV40), or from heterologous mammalian
promoters, e.g., the actin promoter or an immunoglobulin promoter,
provided such promoters are compatible with the host cell systems,
and (2) Regulated expression under control of an inducible vector
system, such as ecdysone, tet, etc., provided such promoters are
compatible with the host cell systems. Tumor volume is then
monitored at the appearance of palpable tumors and followed over
time to determine if 98P4B6-expressing cells grow at a faster rate
and whether tumors produced by 98P4B6-expressing cells demonstrate
characteristics of altered aggressiveness (e.g. enhanced
metastasis, vascularization, reduced responsiveness to
chemotherapeutic drugs).
[1114] Additionally, mice can be implanted with 1.times.10.sup.5 of
the same cells orthotopically to determine if 98P4B6 has an effect
on local growth in the prostate or on the ability of the cells to
metastasize, specifically to lungs, lymph nodes, and bone
marrow.
[1115] The assay is also useful to determine the 98P4B6 inhibitory
effect of candidate therapeutic compositions, such as for example,
98P4B6 intrabodies, 98P4B6 antisense molecules and ribozymes.
Example 38
98P4B6 Monoclonal Antibody-Mediated Inhibition of Tumors in
Vivo
[1116] The significant expression of 98P4B6 in prostate, lung,
stomach, ovary, and uterus cancer tissues, its restrictive
expression in normal tissues, together with its expected cell
surface expression makes 98P4B6 an excellent target for antibody
therapy. Similarly, 98P4B6 is a target for T-cell based
immunotherapy. Thus, the therapeutic efficacy of anti-98P4B6 mAbs
in human prostate cancer xenograft mouse models is evaluated by
using androgen-independent LAPC-4 and LAPC-9 xenografts (Craft, N.,
et al., Cancer Res, 1999. 59(19): p. 5030-6) and the androgen
independent recombinant cell line PC3-98P4B6 (see, e.g., Kaighn, M.
E., et al., Invest Urol, 1979. 17(1): p. 16-23). Similar approaches
using patient derived xenografts or xenograft cell lines are used
for cancers listed in Table I.
[1117] Antibody efficacy on tumor growth and metastasis formation
is studied, e.g., in a mouse orthotopic prostate cancer xenograft
models and mouse lung, uterus, or stomach xenograft models. The
antibodies can be unconjugated, as discussed in this Example, or
can be conjugated to a therapeutic modality, as appreciated in the
art. Anti-98P4B6 mAbs inhibit formation of both the
androgen-dependent LAPC-9 and androgen-independent PC3-98P4B6 tumor
xenografts. Anti-98P4B6 mAbs also retard the growth of established
orthotopic tumors and prolonged survival of tumor-bearing mice.
These results indicate the utility of anti-98P4B6 mAbs in the
treatment of local and advanced stages of cancer. (See, e.g.,
(Saffran, D., et al., PNAS 10:1073-1078 or URL located on the World
Wide Web at .pnas.org/cgi/doi/10.1073/pnas.051624698).
[1118] Administration of the anti-98P4B6 mAbs can lead to
retardation of established orthotopic tumor growth and inhibition
of metastasis to distant sites, resulting in a significant
prolongation in the survival of tumor-bearing mice. These studies
indicate that 98P4B6 is an attractive target for immunotherapy and
demonstrate the therapeutic potential of anti-98P4B6 mAbs for the
treatment of local and metastatic cancer. This example demonstrates
that unconjugated 98P4B6 monoclonal antibodies are effective to
inhibit the growth of human prostate tumor xenografts, as well as
lung, uterus, or stomach xenograft grown in SCID mice; accordingly
a combination of such efficacious monoclonal antibodies is also
effective.
[1119] Tumor Inhibition Using Multiple Unconjugated 98P4B6 mAbs
[1120] Materials and Methods
[1121] 98P4B6 Monoclonal Antibodies:
[1122] Monoclonal antibodies are raised against 98P4B6 as described
in Example 11 entitled "Generation of 98P4B6 Monoclonal Antibodies
(mAbs)." The antibodies are characterized by ELISA, Western blot,
FACS, and immunoprecipitation for their capacity to bind 98P4B6.
Epitope mapping data for the anti-98P4B6 mAbs, as determined by
ELISA and Western analysis, recognize epitopes on the 98P4B6
protein. Immunohistochemical analysis of cancer tissues and cells
with these antibodies is performed.
[1123] The monoclonal antibodies are purified from ascites or
hybridoma tissue culture supernatants by Protein-G Sepharose
chromatography, dialyzed against PBS, filter sterilized, and stored
at -20.degree. C. Protein determinations are performed by a
Bradford assay (Bio-Rad, Hercules, Calif.). A therapeutic
monoclonal antibody or a cocktail comprising a mixture of
individual monoclonal antibodies is prepared and used for the
treatment of mice receiving subcutaneous or orthotopic injections
of LAPC-9 tumor xenografts.
[1124] Cancer Xenografts and Cell Lines
[1125] The LAPC-9 xenograft, which expresses a wild-type androgen
receptor and produces prostate-specific antigen (PSA), is passaged
in 6- to 8-week-old male ICR-severe combined immunodeficient (SCID)
mice (Taconic Farms) by s.c. trocar implant (Craft, N., et at.,
supra). The prostate (PC3), lung (A427), ovarian (PA1) carcinoma
cell lines (American Type Culture Collection) are maintained in
RPMI or DMEM supplemented with L-glutamine and 10% FBS.
[1126] PC3-98P4B6, A427-98P4B6, PA1-98P4B6 and 3T3-98P4B6 cell
populations are generated by retroviral gene transfer as described
in Hubert, R. S., et al., STEAP: a prostate-specific cell-surface
antigen highly expressed in human prostate tumors. Proc Natl Acad
Sci U S A, 1999. 96(25): p. 14523-8. Anti-98P4B6 staining is
detected by using an FITC-conjugated goat anti-mouse antibody
(Southern Biotechnology Associates) followed by analysis on a
Coulter Epics-XL f low cytometer.
[1127] Xenograft Mouse Models.
[1128] Subcutaneous (s.c.) tumors are generated by injection of
1.times.10.sup.6 LAPC-9, PC3, PC3-98P4B6, A427, A427-98P4B6, PA1,
PA1-98P4B6, 3T3 or 3T3-98P4B6 cells mixed at a 1:1 dilution with
Matrigel (Collaborative Research) in the right flank of male SCID
mice. To test antibody efficacy on tumor formation, i.p. antibody
injections are started on the same day as tumor-cell injections. As
a control, mice are injected with either purified mouse IgG (ICN)
or PBS; or a purified monoclonal antibody that recognizes an
irrelevant antigen not expressed in human cells. In preliminary
studies, no difference is found between mouse IgG or PBS on tumor
growth. Tumor sizes are determined by vernier caliper measurements,
and the tumor volume is calculated as
length.times.width.times.height. Mice with s.c. tumors greater than
1.5 cm in diameter are sacrificed. PSA levels are determined by
using a PSA ELISA kit (Anogen, Mississauga, Ontario). Circulating
levels of anti-98P4B6 mAbs are determined by a capture ELISA kit
(Bethyl Laboratories, Montgomery, Tex.). (See, e.g., (Saffran, D.,
et al., PNAS 10:1073-1078 or URL located on the World Wide Web at
.pnas.org/cgi/doi/10.1073/pnas.051624698)
[1129] Orthotopic injections are performed under anesthesia by
using ketamine/xylazine. For prostate orthotopic studies, an
incision is made through the abdominal muscles to expose the
bladder and seminal vesicles, which then are delivered through the
incision to expose the dorsal prostate. LAPC-9 or PC3 cells
(5.times.10.sup.5) mixed with Matrigel are injected into each
dorsal lobe in a 10-.mu.l volume. To monitor tumor growth, mice are
bled on a weekly basis for determination of PSA levels. The mice
are segregated into groups for the appropriate treatments, with
anti-98P4B6 or control mAbs being injected i.p.
[1130] Anti-98P4B6 mAbs Inhibit Growth of 98P4B6-Expressing
Xenograft-Cancer Tumors
[1131] The effect of anti-98P4B6 mAbs on tumor formation is tested
by using LAPC-9 and PC3-98P4B6 orthotopic models. As compared with
the s.c. tumor model, the orthotopic model, which requires
injection of tumor cells directly in the mouse prostate, lung, or
ovary, respectively, results in a local tumor growth, development
of metastasis in distal sites, deterioration of mouse health, and
subsequent death (Saffran, D., et al., PNAS supra; Fu, X., et al.,
Int J Cancer, 1992. 52(6): p. 987-90; Kubota, T., J Cell Biochem,
1994. 56(1): p. 4-8). The features make the orthotopic model more
representative of human disease progression and allowed us to
follow the therapeutic effect of mAbs on clinically relevant end
points.
[1132] Accordingly, tumor cells are injected into the mouse
prostate, lung, or ovary, and 2 days later, the mice are segregated
into two groups and treated with either: a) 200-500 .mu.g, of
anti-98P4B6 Ab, or b) PBS three times per week for two to five
weeks.
[1133] A major advantage of the orthotopic cancer model is the
ability to study the development of metastases. Formation of
metastasis in mice bearing established orthotopic tumors is studies
by IHC analysis on lung sections using an antibody against a
prostate-specific cell-surface protein STEAP expressed at high
levels in LAPC-9 xenografts (Hubert, R. S., et al., Proc Natl Acad
Sci U S A, 1999. 96(25): p. 14523-8).
[1134] Mice bearing established orthotopic LAPC-9 or PC3-98P4B6
tumors are administered 1000 .mu.g injections of either anti-98P4B6
mAb or PBS over a 4-week period. Mice in both groups are allowed to
establish a high tumor burden (PSA levels greater than 300 ng/ml
for IAPC-9), to ensure a high frequency of metastasis formation in
mouse lungs. Mice then are killed and their prostate and lungs are
analyzed for the presence of tumor cells by IHC analysis.
[1135] These studies demonstrate a broad anti-tumor efficacy of
anti-98P4B6 antibodies on initiation and progression of prostate
cancer in xenograft mouse models. Anti-98P4B6 antibodies inhibit
tumor formation of both androgen-dependent and androgen-independent
tumors as well as retarding the growth of already established
tumors and prolong the survival of treated mice. Moreover,
anti-98P4B6 mAbs demonstrate a dramatic inhibitory effect on the
spread of local prostate tumor to distal sites, even in the
presence of a large tumor burden. Thus, anti-98P4B6 mAbs are
efficacious on major clinically relevant end points (tumor growth),
prolongation of survival, and health.
Example 39
Therapeutic and Diagnostic Use of Anti-98P4B6 Antibodies in
Humans
[1136] Anti-98P4B6 monoclonal antibodies are safely and effectively
used for diagnostic, prophylactic, prognostic and/or therapeutic
purposes in humans. Western blot and immunohistochemical analysis
of cancer tissues and cancer xenografts with anti-98P4B6 mAb show
strong extensive staining in carcinoma but significantly lower or
undetectable levels in normal tissues. Detection of 98P4B6 in
carcinoma and in metastatic disease demonstrates the usefulness of
the mAb as a diagnostic and/or prognostic indicator. Anti-98P4B6
antibodies are therefore used in diagnostic applications such as
immunohistochemistry of kidney biopsy specimens to detect cancer
from suspect patients.
[1137] As determined by flow cytometry, anti-98P4B6 mAb
specifically binds to carcinoma cells. Thus, anti-98P4B6 antibodies
are used in diagnostic whole body imaging applications, such as
radioimmunoscintigraphy and radioimmunotherapy, (see, e.g.,
Potamianos S., et. al. Anticancer Res 20(2A):925-948 (2000)) for
the detection of localized and metastatic cancers that exhibit
expression of 98P4B6. Shedding or release of an extracellular
domain of 98P4B6 into the extracellular milieu, such as that seen
for alkaline phosphodiesterase B10 (Meerson, N. R., Hepatology
27:563-568 (1998)), allows diagnostic detection of 98P4B6 by
anti-98P4B6 antibodies in serum and/or urine samples from suspect
patients.
[1138] Anti-98P4B6 antibodies that specifically bind 98P4B6 are
used in therapeutic applications for the treatment of cancers that
express 98P4B6. Anti-98P4B6 antibodies are used as an unconjugated
modality and as conjugated form in which the antibodies are
attached to one of various therapeutic or imaging modalities well
known in the art, such as a prodrugs, enzymes or radioisotopes. In
preclinical studies, unconjugated and conjugated anti-98P4B6
antibodies are tested for efficacy of tumor prevention and growth
inhibition in the SCID mouse cancer xenograft models, e.g., kidney
cancer models AGS-K3 and AGS-K6, (see, e.g., the Example entitled
"98P4B6 Monoclonal Antibody-mediated Inhibition of Bladder and Lung
Tumors In Vivo"). Either conjugated and unconjugated anti-98P4B6
antibodies are used as a therapeutic modality in human clinical
trials either alone or in combination with other treatments as
described in following Examples.
Example 40
Human Clinical Trials for the Treatment and Diagnosis of Human
Carcinomas Through use of Human Anti-98P4B6 Antibodies In Vivo
[1139] Antibodies are used in accordance with the present invention
which recognize an epitope on 98P4B6, and are used in the treatment
of certain tumors such as those listed in Table I. Based upon a
number of factors, including 98P4B6 expression levels, tumors such
as those listed in Table I are presently preferred indications. In
connection with each of these indications, three clinical
approaches are successfully pursued.
[1140] I.) Adjunctive Therapy:
[1141] In adjunctive therapy, patients are treated with anti-98P4B6
antibodies in combination with a chemotherapeutic or antineoplastic
agent and/or radiation therapy. Primary cancer targets, such as
those listed in Table I, are treated under standard protocols by
the addition anti-98P4B6 antibodies to standard first and second
line therapy. Protocol designs address effectiveness as assessed by
reduction in tumor mass as well as the ability to reduce usual
doses of standard chemotherapy. These dosage reductions allow
additional and/or prolonged therapy by reducing dose-related
toxicity of the chemotherapeutic agent. Anti-98P4B6 antibodies are
utilized in several adjunctive clinical trials in combination with
the chemotherapeutic or antineoplastic agents adriamycin (advanced
prostrate carcinoma), cisplatin (advanced head and neck and lung
carcinomas), taxol (breast cancer), and doxorubicin
(preclinical).
[1142] II.) Monotherapy:
[1143] In connection with the use of the anti-98P4B6 antibodies in
monotherapy of tumors, the antibodies are administered to patients
without a chemotherapeutic or antineoplastic agent. In one
embodiment, monotherapy is conducted clinically in end stage cancer
patients with extensive metastatic disease. Patients show some
disease stabilization. Trials demonstrate an effect in refractory
patients with cancerous tumors.
[1144] III.) Imaging Agent:
[1145] Through binding a radionuclide (e.g., iodine or yttrium
(I.sup.131, Y.sup.90) to anti-98P4B6 antibodies, the radiolabeled
antibodies are utilized as a diagnostic and/or imaging agent. In
such a role, the labeled antibodies localize to both solid tumors,
as well as, metastatic lesions of cells expressing 98P4B6. In
connection with the use of the anti-98P4B6 antibodies as imaging
agents, the antibodies are used as an adjunct to surgical treatment
of solid tumors, as both a pre-surgical screen as well as a
post-operative follow-up to determine what tumor remains and/or
returns. In one embodiment, a (.sup.111In)-98P4B6 antibody is used
as an imaging agent in a Phase I human clinical trial in patients
having a carcinoma that expresses 98P4B6 (by analogy see, e.g.,
Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991)). Patients are
followed with standard anterior and posterior gamma camera. The
results indicate that primary lesions and metastatic lesions are
identified
[1146] Dose and Route of Administration
[1147] As appreciated by those of ordinary skill in the art, dosing
considerations can be determined through comparison with the
analogous products that are in the clinic. Thus, anti-98P4B6
antibodies can be administered with doses in the range of 5 to 400
Mg/m.sup.2, with the lower doses used, e.g., in connection with
safety studies. The affinity of anti-98P4B6 antibodies relative to
the affinity of a known antibody for its target is one parameter
used by those of skill in the art for determining analogous dose
regimens. Further, anti-98P4B6 antibodies that are fully human
antibodies, as compared to the chimeric antibody, have slower
clearance; accordingly, dosing in patients with such fully human
anti-98P4B6 antibodies can be lower, perhaps in the range of 50 to
300 mg/m.sup.2, and still remain efficacious. Dosing in mg/m.sup.2,
as opposed to the conventional measurement of dose in mg/kg, is a
measurement based on surface area and is a convenient dosing
measurement that is designed to include patients of all sizes from
infants to adults.
[1148] Three distinct delivery approaches are useful for delivery
of anti-98P4B6 antibodies. Conventional intravenous delivery is one
standard delivery technique for many tumors. However, in connection
with tumors in the peritoneal cavity, such as tumors of the
ovaries, biliary duct, other ducts, and the like, intraperitoneal
administration may prove favorable for obtaining high dose of
antibody at the tumor and to also minimize antibody clearance. In a
similar manner, certain solid tumors possess vasculature that is
appropriate for regional perfusion. Regional perfusion allows for a
high dose of antibody at the site of a tumor and minimizes short
term clearance of the antibody.
[1149] Clinical Development Plan (CDP)
[1150] Overview:
[1151] The CDP follows and develops treatments of anti-98P4B6
antibodies in connection with adjunctive therapy, monotherapy, and
as an imaging agent. Trials initially demonstrate safety and
thereafter confirm efficacy in repeat doses. Trails are open label
comparing standard chemotherapy with standard therapy plus
anti-98P4B6 antibodies. As will be appreciated, one criteria that
can be utilized in connection with enrollment of patients is 98P4B6
expression levels in their tumors as determined by biopsy.
[1152] As with any protein or antibody infusion-based therapeutic,
safety concerns are related primarily to (i) cytokine release
syndrome, i.e., hypotension, fever, shaking, chills; (ii) the
development of an immunogenic response to the material (i.e.,
development of human antibodies by the patient to the antibody
therapeutic, or HAHA response); and, (iii) toxicity to normal cells
that express 98P4B6. Standard tests and follow-up are utilized to
monitor each of these safety concerns. Anti-98P4B6 antibodies are
found to be safe upon human administration.
Example 41
Human Clinical Trial Adjunctive Therapy with Human Anti-98P4B6
Antibody and Chemotherapeutic Agent
[1153] A phase I human clinical trial is initiated to assess the
safety of six intravenous doses of a human anti-98P4B6 antibody in
connection with the treatment of a solid tumor, e.g., a cancer of a
tissue listed in Table I. In the study, the safety of single doses
of anti-98P4B6 antibodies when utilized as an adjunctive therapy to
an antineoplastic or chemotherapeutic agent as defined herein, such
as, without limitation: cisplafin, topotecan, doxorubicin,
adriamycin, taxol, or the like, is assessed. The trial design
includes delivery of six single doses of an anti-98P4B6 antibody
with dosage of antibody escalating from approximately about 25
mg/m.sup.2 to about 275 mg/m.sup.2 over the course of the treatment
in accordance with the following schedule:
3 Day 0 Day 7 Day 14 Day 21 Day 28 Day 35 mAb Dose 25 75 125 175
225 275 mg/m.sup.2 mg/m.sup.2 mg/m.sup.2 mg/m.sup.2 mg/m.sup.2
mg/m.sup.2 Chemotherapy + + + + + + (standard dose)
[1154] Patients are closely followed for one-week following each
administration of antibody and chemotherapy. In particular,
patients are assessed for the safety concerns mentioned above: (i)
cytokine release syndrome, i.e., hypotension, fever, shaking,
chills; (ii) the development of an immunogenic response to the
material (i.e., development of human antibodies by the patient to
the human antibody therapeutic, or HAHA response); and, (iii)
toxicity to normal cells that express 98P4B6. Standard tests and
follow-up are utilized to monitor each of these safety concerns.
Patients are also assessed for clinical outcome, and particularly
reduction in tumor mass as evidenced by MRI or other imaging.
[1155] The anti-98P4B6 antibodies are demonstrated to be safe and
efficacious, Phase II trials confirm the efficacy and refine
optimum dosing.
Example 42
Human Clinical Trial: Monotherapy with Human Anti-98P4B6
Antibody
[1156] Anti-98P4B6 antibodies are safe in connection with the
above-discussed adjunctive trial, a Phase II human clinical trial
confirms the efficacy and optimum dosing for monotherapy. Such
trial is accomplished, and entails the same safety and outcome
analyses, to the above-described adjunctive trial with the
exception being that patients do not receive chemotherapy
concurrently with the receipt of doses of anti-98P4B6
antibodies.
Example 43
Human Clinical Trial: Diagnostic Imaging with Anti-98P4B6
Antibody
[1157] Once again, as the adjunctive therapy discussed above is
safe within the safety criteria discussed above, a human clinical
trial is conducted concerning the use of anti-98P4B6 antibodies as
a diagnostic imaging agent. The protocol is designed in a
substantially similar manner to those described in the art, such as
in Divgi et al. J. Natl. Cancer Inst. 83:97-104 (1991). The
antibodies are found to be both safe and efficacious when used as a
diagnostic modality.
Example 44
Homology Comparison of 98P4B6 to Known Sequences
[1158] The 98P4B6 gene is homologous to a cloned and sequenced
gene, namely human STAMP1 (gi 15418732) (Korkmaz, K. S et al., J.
Biol. Chem. 2002, 277: 36689), showing 99% identity and 99%
homology to that gene (FIG. 4). The 98P4B6 protein also shows 99%
identity and 99% homology to another human six transmembrane
epithelial antigen of prostate 2 (gi 23308593) (Walker, M. G et
al., Genome Res. 1999, 9: 1198; Porkka, K. P., Helenius, M. A. and
Visakorpi, T, Lab. Invest. 2002, 82: 1573). The closest mouse
homolog to 98P4B6is six transmembrane epithelial antigen of
prostate 2 (gi 28501136), with 97% identity and 99% homology. We
have identified several variants of the 98P4B6 protein, including 4
splice variants and 3 SNPs (FIG. 11). The 98P4B6 v.1 protein
consists of 454 amino acids, with calculated molecular weight of 52
kDa, and pl of 8.7. It is a 6 transmembrane protein that can
localize to the cell surface or possibly to the endoplasmic
reticulum (Table VI). Several 98P4B6 variants, including v.1,
v.5-8, v.13, v.14, v.21, v.25 share similar features, such protein
motifs with functional significance, as well as structural
commonalities such as multiple transmembrane domains. The 98P4B6
v.2 is a short protein with no known motifs.
[1159] Motif analysis revealed the presence of several known
motifs, including oxido-reductase, homocysteine hydrolase and
dudulin motifs. Variant v.7 and SNPs of this variant also carry an
Ets motif, often associated with transcriptional activity.
[1160] Several oxidoreductases have been identified in mammalian
cells, including the NADH/quinone oxidoreductase. This protein
associate with the cell membrane and function as a proton/Na+ pump,
which regulates the protein degradation of the tumor suppressor
p53, and protects mammalian cells from oxidative stress,
cytotoxicity, and mutages (Asher G, et al., Proc Natl Acad Sci U S
A. 2002, 99:13125; Jaiswal A K, Arch Biochem Biophys 2000, 375:62
Yano T, Mol Aspects Med 2002, 23:345). Homocysteine hydrolase is an
enzyme known to catalyze the breakdown of S-adenosylhomocysteine to
homocysteine and adenosine, ultimately regulating
trans-methylation, therby regulating protein expression, cell cycle
and proliferation (Turner MAet al. Cell Biochem Biophys
2000;33:101;Zhang et al., J Biol Chem. 2001; 276:35867)
[1161] This information indicates that 98P4B6 plays a role in the
cell growth of mammalian cells, regulate gene transcription and
transport of electrons and small molecules. Accordingly, when
98P4B6 functions as a regulator of cell growth, tumor formation, or
as a modulator of transcription involved in activating genes
associated with inflammation, tumorigenesis, or proliferation,
98P4B6 is used for therapeutic, diagnostic, prognostic and/or
preventative purposes. In addition, when a molecule, such as a
variant or polymorphism of 98P4B6 is expressed in cancerous
tissues, it is used for therapeutic, diagnostic, prognostic and/or
preventative purposes.
Example 45
Phenotypic Effects of STEAP-2 Expression
[1162] Experiments regarding the expression of STEAP-2 protein
having the amino acid sequence shown in FIG. 2 and encoded by a
cDNA insert in a plasmid deposited with the American Type Culture
Collection on 2 Jul. 1999 and assigned as ATCC Accession No.
PTA-311. As deduced from the coding sequence, the open reading
frame encodes 454 amino acids with 6 transmembrane domains. A
summary of the characteristics associated with STEAP-2 protein is
shown on FIG. 19.
[1163] The data set forth in the present patent application provide
an expression profile of the STEAP-2 protein that is predominantly
specific for the prostate among normal tissues, for certain types
of prostate tumors as well as other tumors. This evidence is based
on detecting messenger RNA using Northern blotting. In keeping with
standard practice in this industry, Northern blots are routinely
used to assess gene expression, as it does not require the time
consuming process of synthesizing the relevant protein, raising
antibodies, assuring the specificity of the antibodies, required
for Western blotting of proteins and the histological examination
of tissues. Northern blotting offers a credible and efficient
method of assessing RNA expression and expression levels.
[1164] This Example demonstrates that STEAP-2 protein is, indeed,
produced. In summary, the experiments show that PC-3 cells and 3T3
cells which were modified to contain an expression system for
STEAP-2 showed enhanced levels of tyrosine phosphorylation in
general, and of phosphorylation of ERK protein in particular. The
data also show that PC-3 cells that contain an expression system
for STEAP-2 showed modified calcium flux, a modified response to
paclitaxel, and a general inhibition of drug-induced apoptosis.
These are effects exhibited at the protein level, thus these data
alone are probative that the STEAP-2 protein exists.
[1165] Furthermore, although such phenotypic effects are
protein-mediated, further evidence indicates that the STEAP-2
protein itself is the mediator of the effects. This evidence is
obtained by utilizing a modified STEAP-2 protein. An expression
system is stably introduced into PC3 and 3T3 cells which allows the
expression of a modified form of STEAP-2, designated STEAP-2CFl,
where "Fl" stands for flag. STEAP-2CFl is a STEAP-2 protein having
a peptide extension, i.e., a Flag epitope that alters the physical
conformation of this protein. The Flag epitope is a string 8 amino
acids, often introduced at either the amino or carboxy termini of
protein as a means of identifying and following a recombinant
protein in engineered cells (Slootstra J W et al., Mol Divers 1997,
2:156). In most cases, the introduction of the Flag epitope at
either termini of a protein has little effect on the natural
function and location of that protein (Molloy S S et al., EMBO J
1994, 13:18). However, this is dependent on the characteristics of
the protein being Flag tagged. Recent studies have shown that a
Flag tag affects the function and conformation of select proteins
such as the CLN3 protein (see, e.g., Haskell R E, et al. Mol Genet
Metab 1999, 66:253). As with CLN3, introducing a Flag epitope tag
to the C-terminus of STEAP-2 alters the physical conformation and
properties of this protein. Altering the STEAP-2 protein with the
C-Flag epitope resulted in a significant decrease in the effects
otherwise observed, including phosphorylation of ERK and resistance
to drug-induced cell death. The data indicate that it is the
STEAP-2 protein that mediated these phenotypic effects. Finally, in
vitro translation studies using rabbit reticulocyte lysate, showed
that the STEAP-2 protein is translated and exhibits the expected
molecular weight.
[1166] FIGS. 20 and 21 show the results obtained when PC-3 and 3T3
cells, respectively, were modified to contain the retroviral
expression system pSR encoding the indicated proteins, including
STEAP-1, STEAP-2 and STEAP-2CFl, respectively. Gene-specific
protein expression was driven from a long terminal repeat (LTR),
and the Neomycin resistance gene was used for selection of
mammalian cells that stably express the protein. PC-3 and 3T3 cells
were transduced with the retrovirus, selected in the presence of
G418 and cultured under conditions which permit expression of the
STEAP-2 coding sequence. The cells were grown overnight in low
concentrations of FBS (0.5-1% FBS) and were then stimulated with
10% FBS. The cells were lysed in RIPA buffer and quantitated for
protein concentration. Whole cell lysates were separated by
SDS-PAGE and analyzed by Western blotting using anti-phospho-ERK
(Cell Signaling Inc.) or anti-phosphotyrosine (UBI) antibodies
(FIGS. 20, 21, and 22). As shown on FIG. 20, as compared to
untransformed PC-3 cells, cells modified to contain STEAP-2 contain
enhanced amounts of phosphorylated tyrosine. Similar results from
an analogous experiment on 3T3 cells are shown on page 3. In this
latter experiment, the STEAP-2CFl expression system was also
transfected into 3T3 cells, which cells were used as a control. As
shown on FIG. 21, the enhanced phosphorylation found in the
presence of native STEAP-2 was significantly reduced when the
conformation of the protein was altered. These results thus show
conclusively that the STEAP-2 protein was produced and mediated the
above-described phenotypic effects.
[1167] FIG. 22 shows similar results, both in PC-3 and 3T3 cells
where phosphorylation of ERK, specifically, is detected. The
protocol is similar to that set forth in paragraph 5 above, except
that rather than probing the gels with antibodies specific for
phosphotyrosine the gels were probed both the anti-ERK and
anti-phospho-ERK antibodies. As shown on FIG. 22, in the presence
of 10% FBS, both PC-3 cells and 3T3 cells modified to express
STEAP-2 showed phosphorylation of ERK which was not detectable in
cells transformed to contain STEAP-2CFl. In contrast to control
PC-3 cells which exhibit no background ERK phosphorylation, control
3T3-neo cells show low levels of endogenous ERK phosphorylation.
Treatment with 10% FBS enhanced phosphorylation of ERK protein in
cells expressing STEAP-2 relative to 3T3-neo cells, while no
increase in ERK phosphorylation was observed in 3T3 cells
expressing modified STEAP-2, i.e. STEAP-2 CFl.
[1168] Other effects on cellular metabolism in cells modified to
contain a STEAP-2 expression system were also shown in our data.
FIG. 23 shows that when cells with and without expression systems
for STEAP-2 were measured for calcium flux in the presence of LPA,
calcium flux was enhanced in the STEAP-2 containing cells. Using
FACS analysis and commercially available indicators (Molecular
Probes), parental cells and cells expressing STEAP-2 were compared
for their ability to transport calcium. PC3-neo and PC3-STEAP-2
cells were loaded with calcium responsive indicators Fluo4 and Fura
red, incubated in the presence or absence of calcium and LPA, and
analyzed by flow cytometry. PC3 cells expressing a known calcium
transporter, PC3-83P3H3 pCaT were used as positive control (Biochem
Biophys Res Commun. 2001, 282:729). The table on FIG. 23 shows that
STEAP-2 mediates calcium flux in response to LPA, and that the
magnitude of calcium flux is comparable to that produced by a known
calcium channel.
[1169] In addition, STEAP-2 expressing PC3 cells demonstrated
increased sensitivity to agatoxin, a calcium channel blocker as
compared to PC3-neo cells. These results indicate that STEAP-2
expression renders PC3 cells sensitive to treatment with the Ca++
channel inhibitors. Information derived from the above experiments
provides a mechanism by which cancer cells are regulated. This is
particularly relevant in the case of calcium, as calcium channel
inhibitors have been reported to induce the death of certain cancer
cells, including prostate cancer cell lines (see, e.g., Batra S,
Popper L D, Hartley-Asp B. Prostate. 1991, 19:299).
[1170] FIG. 24 shows that cells transfected with a STEAP-2
expression system have enhanced ability to survive exposure to
paclitaxel. In order to determine the effect of STEAP-2 on
survival, PC3 cells lacking or expressing STEAP-2 were treated with
chemotherapeutic agents currently used in the clinic. Effect of
treatment was evaluated by measuring cell proliferation using the
Alamare blue assay (FIG. 23). While only 5.2% of PC3-neo cells were
able to metabolize Alamare Blue and proliferate in the presence of
5 .mu.M paclitaxel, 44.8% of PC3-STEAP-2 cells survived under the
same conditions. These results indicate that expression of STEAP-2
imparts resistance to paclitaxel. These findings have significant
in vivo implications, as they indicate that STEAP-2 provides a
growth advantage for prostate tumor cells in patients treated with
common therapeutic agents.
[1171] A more detailed form of these results is shown on FIGS. 25
and 26. Results in these two pages demonstrate the mode of action
by which STEAP-2 supports the survival of PC3 cells. In these
studies, PC3 cells expressing or lacking STEAP-2 were treated with
paclitaxel for 60 hours, and assayed for apoptosis using annexin V
conjugated to FITC and propidium iodide staining. In apoptotic
cells, the membrane phospholipid phosphatidylserine (PS) is
translocated from the inner to the outer leaflet of the membrane,
thereby exposing PS to the external cellular environment. PS is
recognized by and binds to annexin V, providing scientists with a
reliable means of identifying cells undergoing programmed cell
death. Staining with propidium iodide identifies dead cells. FIG.
25 show that expression of STEAP-2 inhibits paclitaxel-mediated
apoptosis by 45% relative to paclitaxel-treated PC3-neo cells. The
protective effect of STEAP-2 is inhibited when STEAP-2 is modified
by the presence of Flag at its C-terminus FIG. 26.
[1172] The publicly available literature contains several examples
of prostate and other cancers that exhibit similar phenotypic
characteristics as those observed in PC3 cells that express
STEAP-2. In particular, clinical studies have reported transient
tumor regression and/or only partial responses in patients treated
with paclitaxel. For instance, only around 50% of prostate cancer
patients entered in a single agent clinical trial of paclitaxel
showed reduced PSA levels when treated with doses of paclitaxel
that induced grade 3 and grade 4 toxicity; a much higher level of
response would have been expected based on this dose level, thus
this data indicates the development of paclitaxel resistance in
prostate cancer patients (Beer T M et al., Ann Oncol 2001,
12:1273). A similar phenomenon of reduced responsiveness and
progressive tumor recurrence was observed in other studies (see,
e.g., Obasaju C, and Hudes G R. Hematol Oncol Clin North Am
2001,15:525). In addition, inhibition of calcium flux in cells that
endogenously express STEAP-2, such as LNCaP cells, induces their
cell death (Skryma R et al., J Physiol. 2000, 527:71).
[1173] Thus, STEAP-2 protein is produced not only in the cells
tested, but also in unmodified tumor cells or unmodified prostate
cells where the presence of mRNA has been shown. The Northern blot
data in the specification clearly show that the messenger RNA
encoding STEAP-2 is produced in certain prostate and tumor cells.
The 3T3 and PC-3 cells, which are themselves tumor cell lines, are
clearly able to translate the messenger RNA into protein. Because
it has been shown that there is no barrier to translation of the
message in cells similar to those tumor and prostate cells in which
the mRNA has been shown to be produced, it can properly be
concluded that the protein itself can be detected in the unmodified
tumor or prostate cells, given the fact that it is shown that mRNA
is produced. This conclusion is also supported by the patterns of
phenotypic changes seen in cells specifically modified to express
STEAP-2, these changes comport with changes seen in cancer cells.
Based on the above data, it is scientifically concluded that cells
and tissues which produce mRNA encoding STEAP-2 also produce the
protein itself.
Example 46
Identification and Confirmation of Potential Signal Transduction
Pathways
[1174] Many mammalian proteins have been reported to interact with
signaling molecules and to participate in regulating signaling
pathways (J Neurochem. 2001; 76:217-223. Using immunoprecipitation
and Western blotting techniques, proteins are identified that
associate with 98P4B6 and mediate signaling events. Several
pathways known to play a role in cancer biology can be regulated by
98P4B6, including phospholipid pathways such as P13K, AKT, etc,
adhesion and migration pathways, including FAK, Rho, Rac-1, etc, as
well as mitogenic/survival cascades such as ERK, p38, etc (Cell
Growth Differ. 2000,11:279; J Biol Chem. 1999, 274:801; Oncogene.
2000,19:3003, J. Cell Biol. 1997, 138:913.).
[1175] To confirm that 98P4B6 directly or indirectly activates
known signal transduction pathways in cells, luciferase (luc) based
transcriptional reporter assays are carried out in cells expressing
individual genes. These transcriptional reporters contain
consensus-binding sites for known transcription factors that lie
downstream of well-characterized signal transduction pathways. The
reporters and examples of these associated transcription factors,
signal transduction pathways, and activation stimuli are listed
below.
[1176] 1. NFkB-luc, NFkB/Rel; Ik-kinase/SAPK;
growth/apoptosis/stress
[1177] 2. SRE-luc, SRF/TCF/ELK1; MAPK/SAPK;
growth/differentiation
[1178] 3. AP-1-luc, FOS/JUN; MAPK/SAPK/PKC;
growth/apoptosis/stress
[1179] 4. ARE-luc, androgen receptor; steroids/MAPK;
growth/differentiation/apoptosis
[1180] 5. p53-luc, p53; SAPK; growth/differentiation/apoptosis
[1181] 6. CRE-luc, CREB/ATF2; PKA/p38; growth/apoptosis/stress
[1182] Gene-mediated effects can be assayed in cells showing mRNA
expression. Luciferase reporter plasmids can be introduced by
lipid-mediated transfection (TFX-50, Promega). Luciferase activity,
an indicator of relative transcriptional activity, is measured by
incubation of cell extracts with luciferin substrate and
luminescence of the reaction is monitored in a luminometer.
[1183] Signaling pathways activated by 98P4B6 are mapped and used
for the identification and validation of therapeutic targets. When
98P4B6 is involved in cell signaling, it is used as target for
diagnostic, prognostic, preventative and/or therapeutic
purposes.
Example 47
98P4B6 Functions as a Proton or Small Molecule Transporter
[1184] Sequence and homology analysis of 98P4B6 indicate that the
98P4B6 may function as a transporter. To confirm that STEAP-1
functions as an ion channel, FACS analysis and fluorescent
microscopy techniques are used (Gergely L, et al., Clin Diagn Lab
Immunol. 1997; 4:70; Skryma R, et al., J Physiol. 2000, 527: 71).
Using FACS analysis and commercially available indicators
(Molecular Probes), parental cells and cells expressing 98P4B6 are
compared for their ability to transport electrons, sodium, calcium;
as well as other small molecules in cancer and normal cell lines.
For example, PC3 and PC3-98P4B6 cells were loaded with calcium
responsive indicators Fluo4 and Fura red, incubated in the presence
or absence of calcium and lipophosphatidic acid (LPA), and analyzed
by flow cytometry. Ion flux represents an important mechanism by
which cancer cells are regulated. This is particularly true in the
case of calcium, as calcium channel inhibitors have been reported
to induce the death of certain cancer cells, including prostate
cancer cell lines (Batra S, Popper L D, Hartley-Asp B. Prostate.
1991, 19: 299). Similar studies are conducted using sodium,
potassium, pH, etc indicators.
[1185] Due to its homology to an oxidoreductase, 98P4B6 can
participate in imparting drug resistance by mobilizing and
transporting small molecules. The effect of 98P4B6 on small
molecule transport is investigated using a modified MDR assay.
Control and 98P4B6 expressing cells are loaded with a fluorescent
small molecule such as calcein AM. Extrusion of calcein from the
cell is measured by examining the supernatants for fluorescent
compound. MDR-like activity is confirmed using MDR inhibitors.
[1186] When 98P4B6 functions as a transporter, it is used as target
for diagnostic, prognostic, preventative and/or therapeutic
purposes.
Example 48
Involvement in Tumor Progression
[1187] The 98P4B6 gene can contribute to the growth of cancer
cells. The role of 98P4B6 in tumor growth is confirmed in a variety
of primary and transfected cell lines including prostate as well as
NIH 3T3 cells engineered to stably express 98P4B6. Parental cells
lacking 98P4B6 and cells expressing 98P4B6 are evaluated for cell
growth using a well-documented proliferation assay (Fraser S P,
Grimes J A, Djamgoz M B. Prostate. 2000;44:61, Johnson D E, Ochieng
J, Evans S L. Anticancer Drugs. 1996, 7:288).
[1188] To confirm the role of 98P4B6 in the transformation process,
its effect in colony forming assays is investigated. Parental
NIH-3T3 cells lacking 98P4B6 are compared to NIH-3T3 cells
expressing 98P4B6, using a soft agar assay under stringent and more
permissive conditions (Song Z. et al. Cancer Res.
2000;60:6730).
[1189] To confirm the role of 98P4B6 in invasion and metastasis of
cancer cells, a well-established assay is used, e.g., a Transwell
Insert System assay (Becton Dickinson) (Cancer Res. 1999; 59:6010).
Control cells, including prostate and fibroblast cell lines lacking
98P4B6 are compared to cells expressing 98P4B6. Cells are loaded
with the fluorescent dye, calcein, and plated in the top well of
the Transwell insert coated with a basement membrane analog.
Invasion is determined by fluorescence of cells in the lower
chamber relative to the fluorescence of the entire cell
population.
[1190] 98P4B6 can also play a role in cell cycle and apoptosis.
Parental cells and cells expressing 98P4B6 are compared for
differences in cell cycle regulation using a well-established BrdU
assay (Abdel-Malek Z A. J Cell Physiol. 1988, 136:247). In short,
cells are grown under both optimal (full serum) and limiting (low
serum) conditions are labeled with BrdU and stained with anti-BrdU
Ab and propidium iodide. Cells are analyzed for entry into the G1,
S, and G2M phases of the cell cycle. Alternatively, the effect of
stress on apoptosis is evaluated in control parental cells and
cells expressing 98P4B6, including normal and tumor prostate cells.
Engineered and parental cells are treated with various
chemotherapeutic agents, such as etoposide, flutamide, etc, and
protein synthesis inhibitors, such as cycloheximide. Cells are
stained with annexin V-FITC and cell death is measured by FACS
analysis. The modulation of cell death by 98P4B6 can play a
critical role in regulating tumor progression and tumor load.
[1191] When 98P4B6 plays a role in cell growth, transformation,
invasion or apoptosis, it is used as a target for diagnostic,
prognostic, preventative and/or therapeutic purposes.
Example 49
Involvement in Angiogenesis
[1192] Angiogenesis or new capillary blood vessel formation is
necessary for tumor growth (Hanahan D, Folkman J. Cell. 1996,
86:353; Folkman J. Endocrinology. 1998 139:441). Based on the
effect of phsophodieseterase inhibitors on endothelial cells,
98P4B6 plays a role in angiogenesis (DeFouw L et al., Microvasc Res
2001, 62:263). Several assays have been developed to measure
angiogenesis in vitro and in vivo, such as the tissue culture
assays endothelial cell tube formation and endothelial cell
proliferation. Using these assays as well as in vitro
neo-vascularization, the role of 98P4B6 in angiogenesis,
enhancement or inhibition, is confirmed.
[1193] For example, endothelial cells engineered to express 98P4B6
are evaluated using tube formation and proliferation assays. The
effect of 98P4B6 is also confirmed in animal models in vivo. For
example, cells either expressing or lacking 98P4B6 are implanted
subcutaneously in immunocompromised mice. Endothelial cell
migration and angiogenesis are evaluated 5-15 days later using
immunohistochemistry techniques. 98P4B6 affects angiogenesis, and
it is used as a target for diagnostic, prognostic, preventative
and/or therapeutic purposes.
Example 50
Regulation of Transcription
[1194] The localization of 98P4B6 and its similarity to hydrolases
as well as its Ets motif (v.7) indicate that 98P4B6 is effectively
used as a modulator of the transcriptional regulation of eukaryotic
genes. Regulation of gene expression is confirmed, e.g., by
studying gene expression in cells expressing or lacking 98P4B6. For
this purpose, two types of experiments are performed.
[1195] In the first set of experiments, RNA from parental and
98P4B6-expressing cells are extracted and hybridized to
commercially available gene arrays (Clontech) (Smid-Koopman E et
al. Br J Cancer. 2000. 83:246). Resting cells as well as cells
treated with FBS or androgen are compared. Differentially expressed
genes are identified in accordance with procedures known in the
art. The differentially expressed genes are then mapped to
biological pathways (Chen K et al. Thyroid. 2001. 11:41.).
[1196] In the second set of experiments, specific transcriptional
pathway activation is evaluated using commercially available
(Stratagene) luciferase reporter constructs including: NFkB-luc,
SRE-luc, ELK1-luc, ARE-luc, p53-luc, and CRE-luc. These
transcriptional reporters contain consensus binding sites for known
transcription factors that lie downstream of well-characterized
signal transduction pathways, and represent a good tool to
ascertain pathway activation and screen for positive and negative
modulators of pathway activation.
[1197] Thus, 98P4B6 plays a role in gene regulation. When 98P4B6 is
involved in gene regulation it is used as a target for diagnostic,
prognostic, preventative and/or therapeutic purposes.
Example 51
Protein-Protein Association
[1198] Several 6TM proteins have been shown to interact with other
proteins, thereby regulating signal transduction, gene
transcription, transformation, and cell adhesion. Using
immunoprecipitation techniques as well as two yeast hybrid systems,
proteins are identified that associate with 98P4B6.
Immunoprecipitates from cells expressing 98P4B6 and cells lacking
98P4B6 are compared for specific protein-protein associations.
[1199] Studies are performed to confirm the extent of association
of 98P4B6 with effector molecules, such as nuclear proteins,
transcription factors, kinases, phsophates etc. Studies comparing
98P4B6 positive and 98P4B6 negative cells as well as studies
comparing unstimulated/resting cells and cells treated with
epithelial cell activators, such as cytokines, growth factors,
androgen and anti-integrin Ab reveal unique interactions.
[1200] In addition, protein-protein interactions are confirmed
using two yeast hybrid methodology (Curr Opin Chem Biol. 1999,
3:64). A vector carrying a library of proteins fused to the
activation domain of a transcription factor is introduced into
yeast expressing a 98P4B6-DNA-binding domain fusion protein and a
reporter construct. Protein-protein interaction is detected by
colorimetric reporter activity. Specific association with effector
molecules and transcription factors directs one of skill to the
mode of action of 98P4B6, and thus identifies therapeutic,
prognostic, preventative and/or diagnostic targets for cancer. This
and similar assays are also used to identify and screen for small
molecules that interact with 98P4B6.
[1201] Thus it is found that 98P4B6 associates with proteins and
small molecules. Accordingly, 98P4B6and these proteins and small
molecules are used for diagnostic, prognostic, preventative and/or
therapeutic purposes.
[1202] Throughout this application, various website data content,
publications, patent applications and patents are referenced.
(Websites are referenced by their Uniform Resource Locator, or URL,
addresses on the World Wide Web.) The disclosures of each of these
references are hereby incorporated by reference herein in their
entireties.
[1203] The present invention is not to be limited in scope by the
embodiments disclosed herein, which are intended as single
illustrations of individual aspects of the invention, and any that
are functionally equivalent are within the scope of the invention.
Various modifications to the models and methods of the invention,
in addition to those described herein, will become apparent to
those skilled in the art from the foregoing description and
teachings, and are similarly intended to fall within the scope of
the invention. Such modifications or other embodiments can be
practiced without departing from the true scope and spirit of the
invention.
4TABLE I Tissues that Express 98P4B6: a. Malignant Tissues a
Bladder b. Breast c. Cervix d. Colon e. Kidney f. Lung g. Ovary h.
Pancreas i. Prostate j. Stomach k. Uterus
[1204]
5TABLE II Amino Acid Abbreviations SINGLE LETTER THREE LETTER FULL
NAME F Phe phenylalanine L Leu leucine S Ser serine Y Tyr tyrosine
C Cys cysteine W Trp tryptophan P Pro proline H His histidine Q Gln
glutamine R Arg arginine I Ile isoleucine M Met methionine T Thr
threonine N Asn asparagine K Lys lysine V Val valine A Ala alanine
D Asp aspartic acid E Glu glutamic acid G Gly glycine
[1205]
6TABLE III Amino Acid Substitution Matrix Adapted from the GCG
Software 9.0 BLOSUM62 amino acid substitution matrix (block
substitution matrix). The higher the value, the more likely a
substitution is found in related, natural proteins. (See world wide
web URL ikp.unibe.ch/manual/blosum62.html) A C D E F G H I K L M N
P Q R S T V W Y . 4 0 -2 -1 -2 0 -2 -1 -1 -1 -1 -2 -1 -1 -1 1 0 0
-3 -2 A 9 -3 -4 -2 -3 -3 -1 -3 -1 -1 -3 -3 -3 -3 -1 -1 -1 -2 -2 C 6
2 -3 -1 -1 -3 -1 -4 -3 1 -1 0 -2 0 -1 -3 -4 -3 D 5 -3 -2 0 -3 1 -3
-2 0 -1 2 0 0 -1 -2 -3 -2 E 6 -3 -1 0 -3 0 0 -3 -4 -3 -3 -2 -2 -1 1
3 F 6 -2 -4 -2 -4 -3 0 -2 -2 -2 0 -2 -3 -2 -3 G 8 -3 -1 -3 -2 1 -2
0 0 -1 -2 -3 -2 2 H 4 -3 2 1 -3 -3 -3 -3 -2 -1 3 -3 -1 I 5 -2 -1 0
-1 1 2 0 -1 -2 -3 -2 K 4 2 -3 -3 -2 -2 -2 -1 1 -2 -1 L 5 -2 -2 0 -1
-1 -1 1 -1 -1 M 6 -2 0 0 1 0 -3 -4 -2 N 7 -1 -2 -1 -1 -2 -4 -3 P 5
1 0 -1 -2 -2 -1 Q 5 -1 -1 -3 -3 -2 R 4 1 -2 -3 -2 S 5 0 -2 -2 T 4
-3 -1 V 11 2 W 7 Y
[1206]
7TABLE IV HLA Class I/II Motifs/Supermotifs
[1207]
8TABLE IV (A) HLA Class I Supermotifs/Motifs POSITION POSITION
POSITION 3 (Primary C Terminus 2 (Primary Anchor) Anchor) (Primary
Anchor) SUPERMOTIF A1 TILVMS FWY A2 LIVMATQ IVMATL A3 VSMATLI RK
A24 YFWIVLMT FIYWLM B7 P VILFMWYA B27 RHK FYLWMIVA B44 ED FWYLIMVA
B58 ATS FWYLIVMA B62 QLIVMP FWYMIVLA MOTIFS A1 TSM Y A1 DEAS Y A2.1
LMVQIAT VLIMAT A3 LMVISATFCGD KYRHFA A11 VTMLISAGNCDF KRYH A24 YFWM
FLIW A*3101 MVTALIS RK A*3301 MVALFIST RK A*6801 AVTMSLI RK B*0702
P LMFWYAIV B*3501 P LMFWYIVA B51 P LIVFWYAM B*5301 P IMFWYALV
B*5401 P ATIVLMFWY Bolded residues are preferred, italicized
residues are less preferred: A peptide is considered motif-bearing
if it has primary anchors at each primary anchor position for a
motif or supermotif as specified in the above table.
[1208]
9TABLE IV (B) HLA Class II Supermotif 1 6 9 W, F, Y, V, I, L A, V,
I, L, P, C, S, T A, V, I, L, C, S, T, M, Y
[1209]
10TABLE IV (C) HLA Class II Motifs MOTIFS 1.degree. anchor 1 2 3 4
5 1.degree. anchor 6 7 8 9 DR4 preferred FMYLIVW M T I VSTCPALIM MH
MH deleterious W R WDE DR1 preferred MFLIVWY PAMQ VMATSPLIC M AVM
deleterious C CH FD CWD GDE D DR7 preferred MFLIVWY M W A IVMSACTPL
M IV deleterious C G GRD N G DR3 MOTIFS 1.degree. anchor 1 2 3
1.degree. anchor 4 5 1.degree. anchor 6 Motif a preferred LIVMFY D
Motif b preferred LIVMFAY DNQEST KRH DR Supermotif MFLIVWY
VMSTACPLI Italicized residues indicate less preferred or
"tolerated" residues
[1210]
11TABLE IV (D) HLA Class I Supermotifs SUPER- POSITION: MOTIFS 1 2
3 4 5 6 7 8 C-terminus A1 1.degree. Anchor 1.degree. Anchor TILVMS
FWY A2 1.degree. Anchor 1.degree. Anchor {overscore (LIVMATQ)}
LIVMAT A3 Preferred 1.degree. Anchor YFW YFW YFW P 1.degree. Anchor
VSMATLI (4/5) (3/5) (4/5) (4/5) RK deleterious DE(3/5); DE P(5/5)
(4/5) A24 1.degree. Anchor 1.degree. Anchor {overscore (YFWIVLMT)}
FIYWLM B7 Preferred FWY(5/5) 1.degree. Anchor FWY FWY 1.degree.
Anchor LIVM(3/5) P (4/5) (3/5) {overscore (VILFMWYA)} deleterious
DE(3/5); DE G QN DE P(5/5); (3/5) (4/5) (4/5) (4/5) G(4/5); A(3/5);
QN(3/5) B27 1.degree. Anchor 1.degree. Anchor RHK {overscore
(FYLWMIVA)} B44 1.degree. Anchor 1.degree. Anchor ED {overscore
(FWYLIMVA)} B58 1.degree. Anchor 1.degree. Anchor ATS {overscore
(FWYLIVMA)} B62 1.degree. Anchor 1.degree. Anchor QLIVMP {overscore
(FWYMIVLA)} Italicized residues indicate less preferred or
"tolerated" residues
[1211]
12TABLE IV (E) HLA Class I Motifs POSITION 9 or C- C- 1 2 3 4 5 6 7
8 terminus terminus A1 preferred GFYW 1.degree. Anchor DEA YFW P
DEQN YFW 1.degree. Anchor 9-mer STM Y deleterious DE RHKLIVMP A G A
A1 preferred GRHK ASTCLIVM 1.degree. Anchor GSTC ASTC LIVM DE
1.degree. Anchor 9-mer DEAS Y deleterious A RHKDEPYFW DE PQN RHK PG
GP A1 preferred YFW 1.degree. Anchor DEAQN A YFWQN PASTC GDE P
1.degree. Anchor 10-mer STM Y deleterious GP RHKGLIVM DE RHK QNA
RHKYFW RHK A A1 preferred YFW STCLIVM 1.degree. Anchor A YFW PG G
YFW 1.degree. Anchor 10-mer DEAS Y deleterious RHK RHKDEPYFW P G
PRHK QN A2.1 preferred YFW 1.degree. Anchor YFW STC YFW A P
1.degree. Anchor 9-mer LMIVQAT VLIMAT deleterious DEP DERKH RKH
DERKH POSITION: C- 1 2 3 4 5 6 7 8 9 terminus A2.1 pre- AYFW
1.degree. Anchor LVIM G G FYWLVIM 1.degree. Anchor 10-mer ferred
LMIVQAT VLIMAT dele- DEP DE RKHA P RKH DERKH RKH te- rious A3 pre-
RHK 1.degree. Anchor YFW PRHKYFW A YFW P 1.degree. Anchor ferred
{overscore (LMVISATFCGD)} KYRHFA dele- DEP DE te- rious A11 pre- A
1.degree. Anchor YFW YFW A YFW YFW P 1.degree. Anchor ferred
{overscore (VTLMISAGNCDF)} KRYH dele- DEP A G te- rious A24 pre-
YFWRHK 1.degree. Anchor STC YFW YFW 1.degree. Anchor 9-mer ferred
YFWM FLIW dele- DEG DE G QNP DERHK G AQN te- rious A24 Pre-
1.degree. Anchor P YFWP P 1.degree. Anchor 10-mer ferred YFWM FLIW
Dele- GDE QN RHK DE A QN DEA te- rious A3101 Pre- RHK 1.degree.
Anchor YFW P YFW YFW AP 1.degree. Anchor ferred MVTALIS RK Dele-
DEP DE ADE DE DE DE te- rious A3301 Pre- 1.degree. Anchor YFW AYFW
1.degree. Anchor ferred {overscore (MVALFIST)} RK Dele- GP DE te-
rious A6801 Pre- YFWSTC 1.degree. Anchor YFW YFW P 1.degree. Anchor
ferred AVTMSLI LIVM RK Dele- GP DEG RHK A te- rious B0702 Pre-
RHKFWY 1.degree. Anchor RHK RHK RHK RHK PA 1.degree. Anchor ferred
P {overscore (LMFWY)} AIV Dele- DEQNP DEP DE DE GDE QN DE te- rious
B3501 Pre- FWYLIVM 1.degree. Anchor FWY FWY 1.degree. Anchor ferred
P {overscore (LMFWYIVA)} dele- AGP G G te- rious POSITION: 9 or C-
C- 1 2 3 4 5 6 7 8 terminus terminus A1 pre- GFYW 1.degree. Anchor
DEA YFW P DEQN YFW 1.degree. Anchor 9-mer ferred STM Y dele- DE
RHKLIVMP A G A te- rious A1 pre- GRHK ASTCLIVM 1.degree. Anchor
GSTC A LIVM DE 1.degree. Anchor 9-mer ferred DEAS STC Y dele- A
RHKDEP DE PQN RHK PG GP te- YFW rious dele- AGP G G te- rious B51
Pre- LIVMFWY 1.degree. Anchor FWY STC FWY G FWY 1.degree. Anchor
ferred P {overscore (LIVFWYAM)} dele- AGPDERHKSTC DE G DEQN GDE te-
rious B5301 pre- LIVMFWY 1.degree. Anchor FWY STC FWY LIVM FWY
1.degree. Anchor ferred P FWY {overscore (IMFWYALV)} dele- AGPQN G
RHKQN DE te- rious B5401 pre- FWY 1.degree. Anchor FWYLIVM LIVM
ALIVM FWYAP 1.degree. Anchor ferred P {overscore (ATIVLMFWY)} dele-
GPQNDE GDESTC RHKDE DE QNDGE DE te- rious
[1212]
13TABLE IV (F) Summary of HLA-supertypes Overall phenotypic
frequencies of HLA-supertypes in different ethnic populations
Specificity Phenotypic frequency Supertype Position 2 C-Terminus
Caucasian N.A. Black Japanese Chinese Hispanic Average B7 P
AILMVFWY 43.2 55.1 57.1 43.0 49.3 49.5 A3 AILMVST RK 37.5 42.1 45.8
52.7 43.1 44.2 A2 AILMVT AILMVT 45.8 39.0 42.4 45.9 43.0 42.2 A24
YF (WIVLMT) FI (YWLM) 23.9 38.9 58.6 40.1 38.3 40.0 B44 E (D)
FWYLIMVA 43.0 21.2 42.9 39.1 39.0 37.0 A1 TI (LVMS) FWY 47.1 16.1
21.8 14.7 26.3 25.2 B27 RHK FYL (WMI) 28.4 26.1 13.3 13.9 35.3 23.4
B62 QL (IVMP) FWY (MIV) 12.6 4.8 36.5 25.4 11.1 18.1 B58 ATS FWY
(LIV) 10.0 25.1 1.6 9.0 5.9 10.3
[1213]
14TABLE IV (G) Calculated population coverage afforded by different
HLA-supertype combinations Phenotypic frequency HLA-supertypes
Caucasian N.A Blacks Japanese Chinese Hispanic Average A2, A3 and
B7 83.0 86.1 87.5 88.4 86.3 86.2 A2, A3, B7, A24, B44 99.5 98.1
100.0 99.5 99.4 99.3 and A1 99.9 99.6 100.0 99.8 99.9 99.8 A2, A3,
B7, A24 B44, A1, B27, B62, and B58 Motifs indicate the residues
defining supertype specificites. The motifs incorporate residues
determined on the basis of published data to be recognized by
multiple alleles within the supertype. Residues within brackets are
additional residues also predicted to be tolerated by multiple
alleles within the supertype.
[1214]
15TABLE V Frequently Occurring Motifs avrg. % Name identity
Description Potential Function zf-C2H2 34% Zinc finger, C2H2 type
Nucleic acid-binding protein functions as transcription factor,
nuclear location probable cytochrome_b_N 68% Cytochrome b(N-
membrane bound oxidase, generate terminal)/b6/petB superoxide lg
19% Immunoglobulin domain domains are one hundred amino acids long
and include a conserved intradomain disulfide bond. WD40 18% WD
domain, G-beta repeat tandem repeats of about 40 residues, each
containing a Trp-Asp motif. Function in signal transduction and
protein interaction PDZ 23% PDZ domain may function in targeting
signaling molecules to sub-membranous sites LRR 28% Leucine Rich
Repeat short sequence motifs involved in protein-protein
interactions Pkinase 23% Protein kinase domain conserved catalytic
core common to both serine/threonine and tyrosine protein kinases
containing an ATP binding site and a catalytic site PH 16% PH
domain pleckstrin homology involved in intracellular signaling or
as constituents of the cytoskeleton EGF 34% EGF-like domain 30-40
amino-acid long found in the extracellular domain of membrane-
bound proteins or in secreted proteins Rvt 49% Reverse
transcriptase (RNA-dependent DNA polymerase) Ank 25% Ank repeat
Cytoplasmic protein, associates integral membrane proteins to the
cytoskeleton Oxidored_q1 32% NADH- membrane associated. Involved in
Ubiquinone/plastoquinone proton translocation across the (complex
I), various chains membrane Efhand 24% EF hand calcium-binding
domain, consists of a12 residue loop flanked on both sides by a 12
residue alpha-helical domain Rvp 79% Retroviral aspartyl Aspartyl
or acid proteases, centered on protease a catalytic aspartyl
residue Collagen 42% Collagen triple helix repeat extracellular
structural proteins involved (20 copies) in formation of connective
tissue. The sequence consists of the G-X-Y and the polypeptide
chains forms a triple helix. Fn3 20% Fibronectin type III domain
Located in the extracellular ligand- binding region of receptors
and is about 200 amino acid residues long with two pairs of
cysteines involved in disulfide bonds 7tm_1 19% 7 transmembrane
receptor seven hydrophobic transmembrane (rhodopsin family)
regions, with the N-terminus located extracellularly while the
C-terminus is cytoplasmic. Signal through G proteins
[1215]
16TABLE VI Motifs and Post-translational Modifications of 98P4B6
cAMP- and cGMP-dependent protein kinase phosphorylation site.
176-179 RKET (SEQ ID NO: 114) Protein kinase C phosphorylation
site. 235-237 SVK Casein kinase II phosphorylation site. 9-12 SATD
(SEQ ID NO: 115) 50-53 TVME (SEQ ID NO: 116) 130-133 SCTD (SEQ ID
NO: 117) 172-175 SPEE (SEQ ID NO: 118) N-myristoylation site. 14-19
GLSIST (SEQ ID NO: 119) G-protein coupled receptors family 1
signature. 52-68 MESSVLLAMAFDRFVAV (SEQ ID NO: 120)
[1216]
17TABLE VII Search Peptides v.1 aa1-454 (SEQ ID NO: 121) 9-mers,
10-mers and 15-mers MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD
FAKSLTIRLI RCGYHVVIGS RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS
LWDLRHLLVG KILIDVSNNM RINQYPESNA EYLASLFPDS LIVKGFNVVS AWALQLGPKD
ASRQVYICSN NIQARQQVIE LARQLNFIPI DLGSLSSARE IENLPLRLFT LWRGPVVVAI
SLATFFFLYS FVRDVIHPYA RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY
QLYYGTKYRR FPPWLETWLQ CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ
VHANIENSWN EEEVWRIEMY ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY
VALLISTFHV LIYGWKRAFE EEYYRFYTPP NFVLALVLPS IVILDLLQLC RYPD v.2
aa1-45 (SEQ ID NO: 122) 9-mers, 10-mers, 15-mers SGSPGLQALSL
SLSSGFTPFS CLSLPSSWDY RCPPPCPADF FLYF v.5, (one aa diff at 211 and
different c-terminal) Part A 9-mers: aa203-219 NLPLRLFTFWRGPVVVA
(SEQ ID NO: 123) 10-mers: aa202-220 ENLPLRLFTFWRGPVVVAI (SEQ ID NO:
124) 15-mers: aa197-225 SAREIENLPLRLFTFWRGPVVVAISLATF (SEQ ID NO:
125) Part B 9-mers: aa388-419 WREFSFIQIFCSFADTQTELELEFVFL- LTLLL
(SEQ ID NO: 126) 10-mers: aa387-419
NWREFSFIQIFCSFADTQTELELEFVFLLTLLL (SEQ ID NO: 127) 15-mers:
aa382-419 VSNALNWREFSFIQIFCSFADTQTELELEFVFLLTLLL (SEQ ID NO: 128)
v.6, (different from our original in 445-490) 9-mers; aa447-490
(SEQ ID NO: 129) VLPSIVILGKIILFLPCISRKLKRIK-
KGWEKSQFLEEGIGGTIPHVSPERVTVM 10-mers: aa446-490 (SEQ ID NO: 130)
LVLPSIVILGKIILFLPCISRKLKRIKKGWEKSQFLEEGIGGTIPHVSPERVTVM 15-mers:
aa441-490 (SEQ ID NO: 131)
NFVLALVLPSIVILGKIILFLPCISRKLKRIKKGWEKSQFLEEGIGGTIPHVSPERVTVM v.7,
(deleting our original 340-394, 392-576 is different) Part A
9-mers: aa334-350 FLNMAYQQSTLGYVALL (SEQ ID NO: 132) 10-mers:
aa333-351 LFLNMAYQQSTLGYVALLI (SEQ ID NO: 133) 15-mers: aa328-355
RSERYLFLNMAYQQSTLGYVALLIST- FHV (SEQ ID NO: 134) Part B 9-mers:
aa384-576 (SEQ ID NO: 135)
PSIVILDLSVEVLASPAAAWKCLGANILRGGLSEIVLPIEWQQDRKIPPLSTP- PPPAMWTEEAGA
TAEAQESGIRNKSSSSSQIPVVGVVTEDDEAQDSIDPPESPDRAL- KAANSWRNPVLPHTNGVGPL
WEFLLRLLKSQAASGTLSLAFTSWSLGEFLGSGTWMK- LETIILSKLT QEQKSKHCMF SLISGS
10-mers: aa383-576 (SEQ ID NO: 136)
LPSIVILDLSVEVLASPAAAWKCLGANILRGGLSEIVLPIEWQQDRKIPPLSTPPPP- AMWTEEAG
ATAEAQESGIRNKSSSSSQIPVVGVVTEDDEAQDSIDPPESPDRALKAA- NSWRNPVLPHTNGVGP
LWEFLLRLLKSQAASGTLSLAFTSWSLG EFLGSGTWMK LETIILSKLT QEQKSKHCMF
SLISGS 15-mers: aa378-576 (SEQ ID NO: 137)
VLALVLPSIVILDLSVEVLASPAAAWKCLGANILRGGLS- EIVLPIEWQQDRKIPPLSTPPPPAMW
TEEAGATAEAQESGIRNKSSSSSQIPVVGVV- TEDDEAQDSIDPPESPDRALKAANSWRNPVLPHT
NGVGPLWEFLLRLLKSQAASGTL- SLAFTSWSLG EFLGSGTWMK LETIILSKLT
QEQKSKHCMF SLISGS v.8, SNP variant of v.6, one aa different at 475
9-mers: aa466-482 KSQFLEEGMGGTIPHVS (SEQ ID NO: 138) 10-mers:
aa465-483 EKSQFLEEGMGGTIPHVSP (SEQ ID NO: 139) 15-mers: aa460-489
IKKGWEKSQFLEEGMGGTIPHVSPERVTV (SEQ ID NO: 140) V13 9-mers: aa9-25
SPKSLSETFLPNGINGI (SEQ ID NO: 141) 10-mers: aa8-26
GSPKSLSETFLPNGINGIK (SEQ ID NO: 142) 15-mers: aa3-31
SISMMGSPKSLSETFLPNGINGIKDARKV (SEQ ID NO: 143) v.14 9-mers:
aa203-219 NLPLRLFTFWRGPVVVA (SEQ ID NO: 144) 10-mers: aa202-220
ENLPLRLFTFWRGPVVVAI (SEQ ID NO: 145) 15-mers: aa197-225
SAREIENLPLRLFTFWRGPVVVAISLATF (SEQ ID NO: 146) V.21 9-mers 557-572
SKLTQEQKTKHCMFSLI (SEQ ID NO: 147) 10-mers 556-573
LSKLTQEQKTKHCMFSLIS (SEQ ID NO: 148) 15-mers 551-576
LETIILSKLTQEQKTKHCMFSLISGS (SEQ ID NO: 149) V.25 9-mers aa 447-463
ILFLPCISQKLKRIKKG (SEQ ID NO: 150) 10-mers aa 446-464
IILFLPCISQKLKRIKKGW (SEQ ID NO: 151) 15-mers aa440-468
VILGKIILFLPCISQKLKRIKKGWEKSQF (SEQ ID NO: 152)
[1217]
18TABLE VIII Start Subsequence Score V1-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 443
ILDLLQLCR 25.000 129 NAEYLASLF 9.000 294 WLETWLQCR 9.000 113
LIDVSNNMR 5.000 200 EIENLPLRL 4.500 244 QSDFYKIPI 3.750 405
ISTFHVLIY 3.750 13 LSETCLPNG 2.700 221 SLATFFFLY 2.500 263
AITLLSLVY 2.500 276 LAAAYQLYY 2.500 419 FEEEYYRFY 2.250 155
QLGPKDASR 2.000 66 ASEFFPHVV 1.350 272 LAGLLAAAY 1.000 35 VIGSGDFAK
1.000 178 VIELARQLN 0.900 356 RIEMYISFG 0.900 418 AFEEEYYRF 0.900
319 YSLCLPMRR 0.750 43 KSLTIRLIR 0.750 327 RSERYLFLN 0.675 427
YTPPNFVLA 0.500 304 QLGLLSFFF 0.500 257 KTLPIVAIT 0.500 135
SLFPDSLIV 0.500 223 ATFFFLYSF 0.500 275 LLAAAYQLY 0.500 385
ALNWREFSF 0.500 219 AISLATFFF 0.500 16 TCLPNGING 0.500 90 FVAIHREHY
0.500 87 NIIFVAIHR 0.500 249 KIPIEIVNK 0.400 137 FPDSLIVKG 0.250
189 PIDLGSLSS 0.250 241 RNQQSDFYK 0.250 351 EEEVWRIEM 0.225 349
WNEEEVWRI 0.225 125 YPESNAEYL 0.225 420 EEEYYRFYT 0.225 388
WREFSFIQS 0.225 198 AREIENLPL 0.225 57 VIGSRNPKF 0.200 56 VVIGSRNPK
0.200 217 VVAISLATF 0.200 3 SISMMGSPK 0.200 417 RAFEEEYYR 0.200 436
LVLPSIVIL 0.200 377 TSIPSVSNA 1.150 158 PKDASRQVY 0.125 101
LWDLRHLLV 0.125 117 SNNMRINQY 0.125 392 SFIQSTLGY 0.125 202
ENLPLRLFT 0.125 330 RYLFLNMAY 0.125 38 SGDFAKSLT 0.125 98 YTSLWDLRH
0.125 406 STFHVLIYG 0.125 218 VAISLATFF 0.100 167 ICSNNIQAR 0.100
400 YVALLISTF 0.100 235 VIHPYARNQ 0.100 381 SVSNALNWR 0.100 22
INGIKDARK 0.100 21 GINGIKDAR 0.100 281 QLYYGTKYR 0.100 322
CLPMRRSER 0.100 411 LIYGWKRAF 0.100 191 DLGSLSSAR 0.100 409
HVLIYGWKR 0.100 344 NIENSWNEE 0.090 251 PIEIVNKTL 0.090 308
LSFFFAMVH 0.075 195 LSSAREIEN 0.075 116 VSNNMRINQ 0.075 280
YQLYYGTKY 0.075 220 ISLATFFFL 0.075 175 RQQVIELAR 0.075 127
ESNAEYLAS 0.075 432 FVLALVLPS 0.050 12 SLSETCLPN 0.050 106
HLLVGKILI 0.050 311 FFAMVHVAY 0.050 269 LVYLAGLLA 0.050 216
VVVAISLAT 0.050 124 QYPESNAEY 0.050 166 YICSNNIQA 0.050 258
TLPIVAITL 0.050 18 LPNGINGIK 0.050 435 ALVLPSIVI 0.050 25 IKDARKVTV
0.050 73 VVDVTHHED 0.050 222 LATFFFLYS 0.050 184 QLNFIPIDL 0.050
367 SLGLLSLLA 0.050 46 TIRLIRCGY 0.050 306 GLLSFFFAM 0.050 261
IVAITLLSL 0.050 203 NLPLRLFTL 0.050 V2-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 5; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 23
LSLPSSWDY 7.500 33 CPPPCPADF 0.500 36 PCPADFFLY 0.250 9 LSLSLSSGF
0.150 37 CPADFFLYF 0.125 17 FTPFSCLSL 0.125 24 SLPSSWDYR 0.100 12
SLSSGFTPF 0.100 14 SSFGTPGSC 0.075 5 GLQALSLSL 0.050 7 QALSLSLSS
0.050 13 LSSGFTPFS 0.030 2 GSPGLQALS 0.030 20 FSCLSLPSS 0.030 1
SGSPGLQAL 0.025 32 RCPPPCPAD 0.020 35 PPCPADFFL 0.013 3 SPGLQALSL
0.013 21 SCLSLPSSW 0.010 8 ALSLSLSSG 0.010 10 SLSLSSGFT 0.010 11
LSLSSGFTP 0.007 25 LPSSWDYRC 0.005 16 GFTPFSCLS 0.005 28 SWDYRCPPP
0.005 31 YRCPPPCPA 0.005 15 SGFTPFSCL 0.003 34 PPPCPADFF 0.003 6
LQALSLSLS 0.002 22 CLSLPSSWD 0.001 19 PFSCLSLPS 0.000 18 TPFSCLSLP
0.000 4 PGLQALSLS 0.000 27 SSWDYRCPP 0.000 26 PSSWDYRCP 0.000 29
WDYRCPPPC 0.000 30 DYRCPPPCP 0.000 V5A-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
NLPLRLFTF 0.500 7 FTFWRGPVV 0.050 3 PLRLFTFWR 0.005 5 RLFTFWRGP
0.001 6 LFTFWRGPV 0.001 4 LRLFTFWRG 0.001 2 LPLRLFTFW 0.000 9
FWRGPVVVA 0.000 8 TFWRGPVVV 0.000 V5B-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 5; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 21
ELEFVFLLT 4.500 17 QTELELEFV 2.250 19 ELELEFVFL 1.800 1 WREFSFIQI
0.225 16 TQTELELEF 0.075 4 FSFIQIFCS 0.075 24 FVFLLTLLL 0.050 13
FADTQTELE 0.050 18 TELELEFVF 0.025 8 QIFCSFADT 0.020 10 FCSFADTQT
0.010 6 FIQIFCSFA 0.010 2 REFSFIQIF 0.005 5 SFIQIFCSF 0.005 15
DTQTELELE 0.003 20 LELEFVFLL 0.003 22 LEFVFLLTL 0.003 14 ADTQTELEL
0.003 3 EFSFIQIFC 0.003 11 CSFADTQTE 0.002 7 IQIFCSFAD 0.001 23
EFVFLLTLL 0.001 12 SFADTQTEL 0.001 9 IFCSFADTQ 0.001
V6-HLA-A1-9MERS-98P4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 34 FLEEGIGGT 0.900 12 ILFLPCISR 0.500 6 VILGKIILF 0.500
2 LPSIVILGK 0.250 42 TIPHVSPER 0.200 45 HVSPERVTV 0.200 13
LFLPCISRK 0.100 16 PCISRKLKR 0.050 1 VLPSIVILG 0.050 15 LPCISRKLK
0.050 5 IVILGKIIL 0.050 35 LEEGIGGTI 0.045 41 GTIPHVSPE 0.025 38
GIGGTIPHV 0.020 10 KILLFLPCI 0.020 31 KSQFLEEGI 0.015 46 VSPERVTVM
0.015 37 EGIGGTIPH 0.013 4 SIVILGKII 0.010 14 FLPCISRKL 0.010 11
IILFLPCIS 0.010 19 SRKLKRIKK 0.005 7 ILGKIILFL 0.005 26 KKGWEKSQF
0.005 18 ISRKLKRIK 0.003 33 QFLEEGIGG 0.003 43 IPHVSPERV 0.003 9
GKIILFLPC 0.003 39 IGGTIPHVS 0.003 28 GWEKSQFLE 0.002 3 PSIVILGKI
0.002 32 SQFLEEGIG 0.002 23 KRIKKGWEK 0.001 17 CISRKLKRI 0.001 40
GGTIPHVSP 0.001 30 EKSQFLEEG 0.001 27 KGWEKSQFL 0.000 8 LGKIILFLP
0.000 24 RIKKGWEKS 0.000 21 KLKRIKKGW 0.000 36 EEGIGGTIP 0.000 44
PHVSPERVT 0.000 20 RKLKRIKKG 0.000 25 IKKGWEKSQ 0.000 29 WEKSQFLEE
0.000 22 LKRIKKGWE 0.000 V7A-HLA-A1-9mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position os specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. 5 LSETFLPNG 2.700 4
SLSETFLPN 0.050 7 ETFLPNGIN 0.025 8 TFLPNGING 0.025 9 FLPNGINGI
0.010 3 KSLSETFLP 0.007 1 SPKSLSETF 0.003 6 SETFLPNGI 0.001 2
PKSLSETFL 0.000 V7B-HLA-A1-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 15; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 5 AYQQSTLGY 0.125 9 STLGYVALL 0.050
8 QSTLGYVAL 0.030 1 FLNMAYQQS 0.010 4 MAYQQSTLG 0.010 3 NMAYQQSTL
0.005 7 QQSTLGYVA 0.003 2 LNMAYQQST 0.003 6 YQQSTLGYV 0.002
V7C-HLA-A1-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 15;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 167 KLETIILSK 90.00 59 WTEEAGATA 4.500 13 LASPAAAWK
4.000 69 AQESGIRNK 2.700 38 PIEWQQDRK 1.800 66 TAEAQESGI 0.900 9
SVEVLASPA 0.900 143 ASGTLSLAF 0.750 99 SIDPPESPD 0.500 51 STPPPPAMW
0.500 5 ILDLSVEVL 0.500 21 KCLGANILR 0.500 90 VTEDDEAQD 0.450 50
LSTPPPPAM 0.300 32 LSEIVLPIE 0.270 151 FTSWSLGEF 0.250 156
LGEFLGSGT 0.225 175 KLTQEQKSK 0.200 159 FLGSGTWMK 0.200 177
TQEQKSKHC 0.135 128 GPLWEFLLR 0.125 145 GTLSLAFTS 0.125 52
TPPPPAMWT 0.125 126 GVGPLWELF 0.100 35 IVLPIEWQQ 0.100 100
IDPPESPDR 0.100 104 ESPDRALKA 0.075 78 SSSSSQIPV 0.075 154
WSLGEFLGS 0.075 131 WEFLLRLLK 0.050 22 CLGANILRG 0.050 68 EAQESGIRN
0.050 184 HCMFSLISG 0.050 7 DLSVEVLAS 0.050 170 TIILSKLTQ 0.050 2
SIVILDLSV 0.050 17 AAAWKCLGA 0.050 141 QAASGTLSL 0.050 123
HTNGVGPLW 0.050 31 GLSEIVLPI 0.050 130 LWEFLLRLL 0.045 173
LSKLTQEQK 0.030 80 SSSQIPVVG 0.030 81 SSQIPVVGV 0.030
V7C-HLA-A1-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 15;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 79 SSSSQIPVV 0.030 125 NGVGPLWEF 0.025 65 ATAEAQESG
0.025 37 LPIEWQQDR 0.025 92 EDDEAQDSI 0.025 169 ETIILSKLT 0.025 176
LTQEQKSKH 0.025 91 TEDDEAQDS 0.025 102 PPESPDRAL 0.022 103
PESPDRALK 0.020 11 EVLASPAAA 0.020 83 QIPVVGVVT 0.020 4 VILDLSVEV
0.020 12 VLASPAAAW 0.020 42 QQDRKIPPL 0.015 71 ESGIRNKSS 0.015 96
AQDSIDPPE 0.015 14 ASPAAAWKC 0.015 82 SQIPVVGVV 0.015 139 KSQAASGTL
0.015 147 LSLAFTSWS 0.015 29 RGGLSEIVL 0.013 105 SPDRALKAA 0.013
162 SGTWMKLET 0.013 160 LGSGTWMKL 0.013 127 VGPLWEFLL 0.013 146
TLSLAFTSW 0.010 88 GVVTEDDEA 0.010 142 AASGTLSLA 0.010 64 GATAEAQES
0.010 119 PVLPHTNGV 0.010 46 KIPPLSTPP 0.010 62 EAGATAEAQ 0.010 109
ALKAANSWR 0.010 148 SLAFTSWSL 0.010 112 AANSWRNPV 0.010 149
LAFTSWSLG 0.010 34 EIVLPIEWQ 0.010 116 WRNPVLPHT 0.010 24 GANILRGGL
0.010 89 VVTEDDEAQ 0.010 155 SLGEFLGSG 0.010 120 VLPHTNGVG 0.010
181 KSKHCMFSL 0.008 113 ANSWRNPVL 0.005 67 AEAQESGIR 0.005 185
CMGSLISGS 0.005 144 SGTLSLAFT 0.005 93 DDEAQDSID 0.005 60 TEEAGATAE
0.005 8 LSVEVLASP 0.003 183 KHCMFSLIS 0.003 25 ANILRGGLS 0.003 165
WMKLETIIL 0.003 101 DPPESPDRA 0.003 15 SPAAAWKCL 0.003
[1218]
19TABLE IX Start Subsequence Score V1-HLA-A1-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 178
VIELARQLNF 45.000 443 ILDLLQLCRY 25.000 294 WLETWLQCRK 18.000 135
SLFPDSLIVK 10.000 200 EIENLPLRLF 9.000 356 RIEMYISFGI 4.500 220
ISLATFFFLY 3.750 391 FSFIQSTLGY 3.750 76 VTHHEDALTK 2.500 404
LISTFHVLIY 2.500 262 VAITLLSLVY 2.500 275 LLAAAYQLYY 2.500 113
LIDVSNNMRI 2.500 351 EEEVWRIEMY 2.250 418 AFEEEYYRFY 2.250 123
NQYPESNAEY 1.500 13 LSETCLPNGI 1.350 137 FPDSLIVKGF 1.250 427
YTPPNFVLAL 1.250 257 KTLPIVAITL 1.250 271 YLAGLLAAAY 1.000 34
GVIGSGDFAK 1.000 321 LCLPMRRSER 1.000 198 AREIENLPLR 0.900 116
VSNNMRINQY 0.750 327 RSERYLFLNM 0.675 38 SGDFAKSLTI 0.625 384
NALNWREFSF 0.500 218 VAISLATFFF 0.500 274 GLLAAAYQLY 0.500 81
DALTKTNIIF 0.500 322 CLPMRRSERY 0.500 73 VVDVTHHEDA 0.500 232
VRDVIHPYAR 0.500 442 VILDLLQLCR 0.500 125 YPESNAEYLA 0.450 129
NAEYLASLFP 0.450 21 GINGIKDARK 0.400 2 ESISMMGSPK 0.300 66
ASEFFPHVVD 0.270 419 FEEEYYRFYT 0.225 350 NEEEVWRIEM 0.225 222
LATFFFLYSF 0.200 56 VVIGSRNPKF 0.200 281 QLYYGTKYRR 0.200 55
HVVIGSRNPK 0.200 278 AAYQLYYGTK 0.200 417 RAFEEEYYRF 0.200 216
VVVAISLATF 0.200 248 YKIPIEIVNK 0.200 317 VAYSLCLPMR 0.200 17
CLPNGINGIK 0.200 244 QSDFYKIPIE 0.150 377 TSIPSVSNAL 0.150 382
VSNALNWREF 0.150 202 ENLPLRLFTL 0.125 101 LWDLRHLLVG 0.125 329
ERYLFLNMAY 0.125 15 ETCLPNGING 0.125 396 STLGYVALLI 0.125 45
LTIRLIRCGY 0.125 86 TNIIFVAIHR 0.125 32 TVGVIGSGDF 0.100 235
VIHPYARNQQ 0.100 410 VLIYGWKRAF 0.100 112 ILIDVSNNMR 0.100 166
YICSNNIQAR 0.100 16 TCLPNGINGI 0.100 217 VVAISLATFF 0.100 155
QLGPKDASRQ 0.100 344 NIENSWNEEE 0.090 139 DSLIVKGFNV 0.075 405
ISTFHVLIYG 0.075 366 MSLGLLSLLA 0.075 11 KSLSETCLPN 0.075 134
ASLFPDSLIV 0.075 43 KSLTIRLIRC 0.075 303 KQLGLLSFFF 0.075 361
ISFGIMSLGL 0.075 304 QLGLLSFFFA 0.050 107 LLVGKILIDV 0.050 60
SRNPKFASEF 0.050 269 LVYLAGLLAA 0.050 434 LALVLPSIVI 0.050 397
TLFYVALLIS 0.050 364 GIMSLGLLSL 0.050 401 VALLISTFHV 0.050 147
NVVSAWALQL 0.050 189 PIDLGSLSSA 0.050 264 ITLLSLVYLA 0.050 307
LLSFFFAMVH 0.050 310 FFFAMVHVAY 0.050 209 FTLWRGPVVV 0.050 194
SLSSAREIEN 0.050 240 ARNQQSDFYK 0.050 298 WLQCRKQLG 0.050 440
SIVILDLLQL 0.050 221 SLATFFFLYS 0.050 436 LVLPSIVILD 0.050 406
STFHVLIYGW 0.050 V2-HLA-A1-10mers-98PB6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 32 RCPPPCPADF 2.000 23 LSLPSSWDYR
1.500 35 PPCPADFFLY 0.625 22 CLSLPSSWDY 0.500 33 CPPPCPADFF 0.250
11 LSLSSGFTPF 0.150 8 ALSLSLSSGF 0.100 13 LSSGFTPFSC 0.075 2
GSPGLQALSL 0.075 28 SWDYRCPPPC 0.050 1 SGSPGLQALS 0.050 36
PCPADFFLYF 0.050 16 GFTPFSCLSL 0.025 12 SLSSGFTPFS 0.020 24
SLPSSWDYRC 0.020 20 FSCLSLPSSW 0.015 14 SSGFTPFSCL 0.015 9
LSLSLSSGFT 0.015 18 TPFSCLSLPS 0.013 7 QALSLSLSSG 0.010 5
GLQALSLSLS 0.010 6 LQALSLSLSS 0.007 10 SLSLSSGFTP 0.005 15
SGFTPFSCLS 0.003 3 SPGLQALSLS 0.003 17 FTPFSCLSLP 0.003 34
PPPCPADFFL 0.001 4 PGLQALSLSL 0.001 31 YRCPPPCPAD 0.001 21
SCLSLPSSWD 0.001 27 SSWDYRCPPP 0.000 25 LPSSWDYRCP 0.000 26
PSSWDYRCPP 0.000 19 PFSCLSLPSS 0.000 30 DYRCPPPCPA 0.000 29
WDYRCPPPCP 0.000 V5A-HLA-A1-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 11; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 1 ENLPLRLFTF 1.250 8 FTFWRGPVVV 0.050
3 LPLRLFTFWR 0.013 2 NLPLRLFTFW 0.010 6 RLFTFWRGPV 0.010 7
LFTFWRGPVV 0.001 4 PLRLFTFWRG 0.000 10 FWRGPVVVAI 0.000 5
LRLFTFWRGP 0.000 9 TFWRGPVVVA 0.000 V5B-HLA-A1-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 18
QTELELEFVF 112.500 20 ELELEFVFLL 4.500 22 ELEFVFLLTL 4.500 14
FADTQTELEL 2.500 16 DTQTELELEF 1.250 2 WREFSFIQIF 0.450 5
FSFIQIFCSF 0.150 12 CSFADTQTEL 0.015 9 QIFCSFADTQ 0.010 7
FIQIFCSFAD 0.005 8 IQIFCSFADT 0.003 21 LELEFVFLLT 0.003 4
EFSFIQIFCS 0.003 24 EFVFLLTLLL 0.003 3 REFSFIQIFC 0.003 17
TQTELELEFV 0.002 11 FCSFADTQTE 0.001 19 TELELEFVFL 0.001 6
SFIQIFCSFA 0.001 10 IFCSFADTQT 0.001 23 LEFVFLLTLL 0.001 1
NWREFSFIQI 0.000 15 ADTQTELELE 0.000 13 SFADTQTELE 0.000
V6-HLA-A1-10mers-98B4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus nine. 42 GTIPHVSPER 5.000 2 VLPSIVILGK 1.000 35 FLEEGIGGTI
0.900 1 LVLPSIVLG 0.500 12 IILFLPCISR 0.500 6 IVILGKIILF 0.500 13
ILFLPCISRK 0.200 15 FLPCISRKLK 0.200 16 LPCISRKLKR 0.125 46
KVSPERVTVM 0.100 7 VILGKIILFL 0.050 5 SIVILGKIIL 0.050 18
CISRKLKRIK 0.020 19 ISRKLKRIKK 0.015 32 KSQFLEEGIG 0.015 39
GIGGTIPHVS 0.010 43 TIPHVSPERV 0.010 11 KIILFLPCIS 0.010 33
SQFLEEGIGG 0.007 38 EGIGGTIPHV 0.005 14 LFLPCISRKL 0.005 36
LEEGIGGTIP 0.005 37 EEGIGGTIPH 0.003 3 LPSIVILGKI 0.003 44
IPHVSPERVT 0.003 29 GWEKSQFLEE 0.002 4 PSIVILGKII 0.002 9
LGKIILFLPC 0.001 23 LKRIKKGWEK 0.001 17 PCISRKLKRI 0.001 10
GKIILFLPCI 0.001 26 IKKGWEKSQF 0.001 34 QFLEEGIGGT 0.001 31
EKSQFLEEGI 0.001 27 KKGWEKSQFL 0.001 8 ILGKIILFLP 0.001 40
IGGTIPHVSP 0.001 41 GGTIPHVSPE 0.000 28 KGWEKSQFLE 0.000 25
RIKKGWEKSQ 0.000 45 PHVSPERVTV 0.000 21 RKLKRIKKGW 0.000 20
SRKLKRIKKG 0.000 30 WEKSQFLEEG 0.000 24 KRIKKGWEKS 0.000 22
KLKRIKKGWE 0.000 V7A-HLA-A1-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 15; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 6 LSETFLPNGI 1.350 10 FLPNGINGIK
0.200 8 KEFLPNGING 0.125 4 KSLSETFLPN 0.075 5 SLSETFLPNG 0.020 1
GSPKSLSETF 0.015 9 TFLPNGINGI 0.005 7 SETFLPNGIN 0.001 2 SPKSLSETFL
0.000 3 PKSLSETFLP 0.000 V7B-HLA-A1-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 5 MAYQQSTLGY 2.500 10
STLGYVALLI 0.125 9 QSTLGYVALL 0.030 2 FLNMAYQQST 0.010 4 NMAYQQSTLG
0.005 7 YQQSTLGYVA 0.003 8 QQSTLGYVAL 0.003 3 LNMAYQQSTL 0.003 6
AYQQSTLGYV 0.001 1 LFLNMAYQQS 0.001 V7C-HLA-A1-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 100
SIDPPESPDR 100.000 67 TAEAQESGIR 9.000 33 LSEIVLPIEW 6.750 131
LWEFLLRLLK 4.500 91 VTEDDEAQDS 2.250 10 SVEVLASPAA 1.800 52
STPPPPAMWT 1.250 6 ILDLSVEVLA 1.000 168 KLETIILSKL 0.900 103
PPESPDRALK 0.900 127 GVGPLWEFLL 0.500 143 AASGTLSLAF 0.500 13
VLASPAAAWK 0.400 51 LSTPPPPAMW 0.300 60 WTEEAGATAE 0.225 157
LGEFLGSGTW 0.225 69 EAQESGIRNK 0.200 97 AQDSIDPPES 0.150 70
AQESGIRNKS 0.135 178 TQEQKSKHCM 0.135 170 ETIILSKLTQ 0.125 128
VGPLWEFLLR 0.125 37 VLPIEWQQDR 0.100 14 LASPAAAWKC 0.100 61
TEEAGATAEA 0.090 39 PIEWQQDRKI 0.090 162 GSGTWMKLET 0.075 78
KSSSSSQIPV 0.075 160 FLGSGTWMKL 0.050 22 KCLGANILRG 0.050 167
MKLETIILSK 0.050 38 LPIEWQQDRK 0.050 80 SSSSQIPVVG 0.030 79
SSSSSQIPVV 0.030 83 SQIPVVGVVT 0.030 144 ASGTLSLAFT 0.030 81
SSSQIPVVGV 0.030 146 GTLSLAFTSW 0.025 66 ATAEAQESGI 0.025 152
FTSWSLGEFL 0.025 125 TNGVGPLWEF 0.025 92 TEDDEAQDSI 0.025 177
LTQEQKSKHC 0.025 21 WKCLGANILR 0.025 106 SPDRALKAAN 0.025 94
DDEAQDSIDP 0.022 12 EVLASPAAAW 0.020 4 IVILDLSVEV 0.020 173
ILSKLTQEQK 0.020 47 KIPPLSTPPP 0.020 113 AANSWRNPVL 0.020 72
ESGIRNKSSS 0.015 43 QQDRKIPPLS 0.015 15 ASPAAAWKCL 0.015 140
KSQAASGTLS 0.015 9 LSVEVLASPA 0.015 82 SSQIPVVGVV 0.015 155
WSLGEFLGSG 0.015 105 ESPDRALKAA 0.015 148 LSLAFTSWSL 0.015 124
HTNGVGPLWE 0.013 129 GPLWEFLLRL 0.013 31 GGLSEIVLPI 0.013 145
SGTLSLAFTS 0.013 185 HCMFSLISGS 0.010 149 SLAFTSWSLG 0.010 65
GATAEAQESG 0.010 112 KAANSWRNPV 0.010 142 QAASGTLSLA 0.010 25
GANILRGGLS 0.010 159 EFLGSGTWMK 0.010 23 CLGANILRGG 0.010 109
RALKAANSWR 0.010 176 KLTQEQKSKH 0.010 35 EIVLPIEWQQ 0.010 175
SKLTQEQKSK 0.010 18 AAAWKCLGAN 0.010 36 IVLPIEWQQD 0.010 5
VILDLSVEVL 0.010 172 IILSKLTQEQ 0.010 156 SLGEFLGSGT 0.010 120
PVLPHTNGVG 0.010 147 TLSLAFTSWS 0.010 89 GVVTEDDEAQ 0.010 153
TSWSLGEFLG 0.008 2 PSIVILDLSV 0.008 141 SQAASGTLSL 0.007 150
LAFTSWSLGE 0.005 17 PAAAWKCLGA 0.005 101 IDPPESPDRA 0.005 151
AFTSWSLGEF 0.005 117 WRNPVLPHTN 0.005 42 WQQDRKIPPL 0.003 104
PESPDRALKA 0.003 24 LGANILRGGL 0.003 119 NPVLPHTNGV 0.003 118
RNPVLPHTNG 0.003 102 DPPESPDRAL 0.003 53 TPPPPAMWTE 0.003 1
LPSIVILDLS 0.003
[1219]
20TABLE X Start Subsequence Score V1-HLA-A0201-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 227
FLYSFVRDV 1789.612 402 ALLISTFHV 1492.586 307 LLSFFFAMV 853.681 306
GLLSFFFAM 769.748 100 SLWDLRHLL 726.962 333 FLNMAYQQV 479.909 140
SLIVKGFNV 403.402 203 NLPLRLFTL 284.974 210 TLWRGPVVV 236.685 65
FASEFFPHV 131.539 135 SLFPDSLIV 105.510 274 GLLAAAYQL 79.041 393
FIQSTLGYV 72.344 48 RLIRCGYHV 69.552 365 IMSLGLLSL 60.325 5
SMMGSPKSL 57.085 220 ISLATFFFL 53.163 271 YLAGLLAAA 52.561 265
TLLSLVYLA 42.278 433 VLALVLPSI 40.792 442 VILDLLQLC 40.518 112
ILIDVSNNM 34.627 360 YISFGIMSL 31.077 403 LLISTFHVL 28.290 369
GLLSLLAVT 26.001 17 CLPNGINGI 23.995 108 LVGKILIDV 23.795 264
ITLLSLVYL 23.608 258 TLPIVAITL 21.362 184 QLNFIPIDL 21.362 313
AMVHVAYSL 15.428 410 VLIYGWKRA 14.358 141 LIVKGFNVV 12.665 305
LGLLSFFFA 12.364 44 SLTIRLIRC 11.426 436 LVLPSIVIL 11.087 397
TLGYVALLI 10.433 386 LNWREFSFI 10.042 180 ELARQLNFI 9.989 254
IVNKTLPIV 9.756 404 LISTFHVLI 9.267 357 IEMYISFGI 7.401 441
IVILDLLQL 7.309 261 IVAITLLSL 7.309 209 FTLWRGPVV 6.741 368
LGLLSLLAV 6.568 367 SLGLLSLLA 4.968 153 ALQLGPKDA 4.968 146
FNVVSAWAL 4.811 389 REFSFIQST 4.686 435 ALVLPSIVI 4.277 187
FIPIDLGSL 4.040 374 LAVTSIPSV 3.777 262 VAITLLSLV 3.777 299
LQCRKQLGL 3.682 335 NMAYQQVHA 3.588 291 FPPWLETWL 3.528 331
YLFLNMAYQ 3.209 148 VVSAWALQL 3.178 166 YICSNNIQA 3.142 353
EVWRIEMYI 3.125 221 SLATFFFLY 3.121 378 SIPSVSNAL 2.937 164
QVYICSNNI 2.921 268 SLVYLAGLL 2.777 396 STLGYVALL 2.525 434
LALVLPSIV 2.491 304 QLGLLSFFF 2.377 269 LVYLAGLLA 2.365 37
GSGDFAKSL 2.173 366 MSLGLLSLL 2.017 267 LSLVYLAGL 2.017 242
NQQSDFYKI 2.010 177 QVIELARQL 1.533 224 TFFFLYSFV 1.474 349
WNEEEVWRI 1.418 128 SNAEYLASL 1.315 106 HLLVGKILI 1.312 257
KTLPIVAIT 1.264 303 KQLGLLSFF 1.238 428 TPPNFVLAL 1.219 34
GVIGSGDFA 1.172 216 VVVAISLAT 1.108 314 MVHVAYSLC 1.108 371
LSLLAVTSI 0.985 91 VAIHREHYT 0.968 85 KTNIIFVAI 0.964 133 LASLFPDSL
0.939 425 RFYTPPNFV 0.850 250 IPIEIVNKT 0.780 49 LIRCGYHVV 0.760 83
LTKTNIIFV 0.727 132 YLASLFPDS 0.651 427 YTPPNFVLA 0.603 171
NIQARQQVI 0.588 259 LPIVAITLL 0.545 438 LPSIVILDL 0.545 278
AAYQLYYGT 0.497 170 NNIQARQQV 0.454 385 ALNWREFSF 0.432
V2-HLA-A0201-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
5; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 5 GLQALSLSL 21.362 10 SLSLSSGFT 5.328 17
FTPFSCLSL 1.365 15 SGFTPFSCL 0.980 1 SGSPGLQAL 0.321 14 SSGFTPFSC
0.188 8 ALSLSLSSG 0.171 12 SLSSGFTPF 0.142 3 SPGLQALSL 0.139 29
WDYRCPPPC 0.102 35 PPCPADFFL 0.098 22 CLSLPSSWD 0.082 37 CPADFFLYF
0.079 24 SLPSSWDYR 0.068 25 LPSSWDYRC 0.055 6 LQALSLSLS 0.030 23
LSLPSSWDY 0.023 13 LSSGFTPFS 0.017 20 FSCLSLPSS 0.005 7 QALSLSLSS
0.004 11 LSLSSGFTP 0.004 27 SSWDYRCPP 0.003 31 YRCPPPCPA 0.003 9
LSLSLSSGF 0.003 21 SCLSLPSSW 0.002 18 TPFSCLSLP 0.001 2 GSPGLQALS
0.000 33 CPPPCPADF 0.000 16 GFTPFSCLS 0.000 36 PCPADFFLY 0.000 32
RCPPPCPAD 0.000 4 PGLQALSLS 0.000 34 PPPCPADFF 0.000 19 PFSCLSLPS
0.000 28 SWDYRCPPP 0.000 26 PSSWDYRCP 0.000 30 DYRCPPPCP 0.000
V5A-HLA-A0201-9mers-98PB6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 7 FTFWRGPVV 6.741 1 NLPLRLFTF 0.994 8
TFWRGPVVV 0.164 5 RLFTFWRGP 0.071 2 LPLRLFTFW 0.032 6 LFTFWRGPV
0.011 3 PLRLFTFWR 0.003 4 LRLFTFWRG 0.001 9 FWRGPVVVA 0.000
V5B-HLA-A0201-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 20 LELEFVFLL 543.025 6 FIQIFCSFA 65.673 24
FVFLLTLLL 31.814 22 LEFVFLLTL 22.835 8 QIFCSFADT 7.203 19 ELELEFVFL
1.072 17 QTELELEFV 0.383 10 FCSFADTQT 0.224 4 FSFIQIFCS 0.110 21
ELEFVFLLT 0.068 12 SFADTQTEL 0.061 18 TELELEFVF 0.052 16 TQTELELEF
0.031 14 ADTQTELEL 0.030 2 REFSFIQIF 0.019 7 IQIFCSFAD 0.015 23
EFVFLLTLL 0.003 3 EFSFIQIFC 0.001 1 WREFSFIQI 0.001 11 CSFADTQTE
0.000 13 FADTQTELE 0.000 5 SFIQIFCSF 0.000 9 IFCSFADTQ 0.000 15
DTQTELELE 0.000 V6-HLA-A0201-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 13; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 7 ILGKIILFL 459.398 27 KGWEKSQFL
91.350 10 KIILFLPCI 43.882 38 GIGGTIPHV 21.996 14 FLPCISRKL 19.653
17 CISRKLKRI 3.299 34 FLEEGIGGT 2.689 5 IVILGKIIL 1.303 4 SIVILGKII
0.588 43 IPHVSPERV 0.378 1 VLPSIVILG 0.291 46 VSPERVTVM 0.213 45
HVSPERVTV 0.207 6 VILGKIILF 0.148 31 KSQFLEEGL 0.117 12 ILFLPCISR
0.094 11 IILFLPCIS 0.026 9 GKIILFLPC 0.013 21 KLKRIKKGW 0.009 35
LEEGIGGTI 0.003 42 TIPHVSPER 0.002 32 SQFLEEGIG 0.001 20 RKLKRIKKG
0.001 33 QFLEEGIGG 0.001 41 GTIPHVSPE 0.000 3 PSIVILGKI 0.000 2
LPSIVILGK 0.000 26 KKGWEKSQF 0.000 39 IGGTIPHVS 0.000 24 RIKKGWEKS
0.000 15 LPCISRKLK 0.000 13 LFLPCISRK 0.000 40 GGTIPHVSP 0.000 29
WEKSQFLEE 0.000 8 LGKIILFLP 0.000 23 KRIKKGWEK 0.000 37 EGIGGTIPH
0.000 30 EKSQFLEEG 0.000 44 PHVSPERVT 0.000 36 EEGIGGTIP 0.000 16
PCISRKLKR 0.000 22 LKRIKKGWE 0.000 25 IKKGWEKSQ 0.000 18 ISRKLKRIK
0.000 28 GWEKSQFLE 0.000 19 SRKLKRIKK 0.000
V7A-HLA-A0201-9mers-98PB6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 9 FLPNGINGI 110.379 4 SLSETFLPN 0.581 6
SETFLPNGI 0.203 3 KSLSETFLP 0.007 2 PKSLSETFL 0.004 5 LSETFLPNG
0.000 8 TFLPNGING 0.000 7 ETFLPNGIN 0.000 1 SPKSLSETF 0.000
V7B-HLA-A0201-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 6 YQQSTLGYV 53.345 3 NMAYQQSTL 15.428 9
STLGYVALL 2.525 1 FLNMAYQQS 0.514 2 LNMAYQQST 0.306 8 QSTLGYVAL
0.209 7 QQSTLGYVA 0.207 4 MAYQQSTLG 0.006 5 AYQQSTLGY 0.000
V7C-A0201-9mers-98PB6 Each peptide is a portion of SEQ ID NO: 15;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 4 VILDLSVEV 246.631 148 SLAFTSWSL 160.218 129 PLWEFLLRL
139.780 31 GLSEIVLPI 98.381 57 AMWTEEAGA 29.780 2 SIVILDLSV 9.563
126 GVGPLWEFL 8.564 5 ILDLSVEVL 6.712 152 TSWSLGEFL 3.119 27
ILRGGLSEI 3.100 42 QQDRKIPPL 1.993 168 LETIILSKL 1.624 127
VGPLWEFLL 1.375 163 GTWMKLETI 1.355 81 SSQIPVVGV 1.044 165
WMKLETIIL 1.018 112 AANSWRNPV 0.966 82 SQIPVVGVV 0.864 134
LLRLLKSQA 0.642 144 SGTLSLAFT 0.615 133 FLLRLLKSQ 0.583 39
IEWQQDRKI 0.572 159 FLGSGTWMK 0.514 119 PVLPHTNGV 0.495 185
CMFSLISGS 0.458 78 SSSSSQIPV 0.454 79 SSSSQIPVV 0.428 83 QIPVVGVVT
0.420 160 LGSGTWMKL 0.403 155 SLGEFLGSG 0.347 141 QAASGTLSL 0.297
136 RLLKSQAAS 0.276 52 TPPPPAMWT 0.268 14 ASPAAAWKC 0.243 15
SPAAAWKCL 0.237 181 KSKHCMFSL 0.228 88 GVVTEDDEA 0.213 22 CLGANILRG
0.171 10 VEVLASPAA 0.164 142 AASGTLSLA 0.159 146 TLSLAFTSW 0.142 12
VLASPAAAW 0.127 11 EVLASPAAA 0.121 49 PLSTPPPPA 0.109 178 QEQKSKHCM
0.097 59 WTEEAGATA 0.083 17 AAAWKCLGA 0.069 147 LSLAFTSWS 0.064 139
KSQAASGTL 0.063 35 IVLPIEWQQ 0.062 29 RGGLSEIVL 0.057 113 ANSWRNPVL
0.057 20 SKCLGANIL 0.056 50 LSTPPPPAM 0.055 175 KLTQEQKSK 0.052 162
SGTWMKLET 0.049 6 LDLSVEVLA 0.043 36 VLPIEWQQD 0.043 24 GANILRGGL
0.039 177 TQEQKSKHC 0.032 105 SPDRALKAA 0.030 171 IILSKLTQE 0.030
41 WQQDRKIPP 0.028 9 SVEVLASPA 0.028 182 SKHCMFSLI 0.028 172
ILSKLTQEQ 0.025 145 GTLSLAFTS 0.022 138 LKSQAASGT 0.018 154
WSLGEFLGS 0.016 76 NKSSSSSQI 0.014 7 DLSVEVLAS 0.013 149 LAFTSWSLG
0.011 116 WRNPVLPHT 0.011 104 ESPDRALKA 0.010 66 TAEAQESGI 0.009
125 NVGVPLWEF 0.008 169 ETIILSKLT 0.008 167 KLETIILSK 0.008 26
NILRGGLSE 0.008 140 SQAASGTLS 0.008 61 EEAGATAEA 0.007 176
LTQEQKSKH 0.007 46 KIPPLSTPP 0.007 120 VLPHTNGVG 0.007 166
MKLETIILS 0.006 156 LGEFLGSGT 0.005 158 EFLGSGTWM 0.005 131
WEFLLRLLK 0.005 101 DPPESPDRA 0.005 89 VVTEDDEAQ 0.004 137
LLKSQAASG 0.004 135 LRLLKSQAA 0.004 108 RALKAANSW 0.004 28
LRGGLSEIV 0.003 109 ALKAANSWR 0.003 18 AAWKCLGAN 0.003 91 TEDDEAQDS
0.002 164 TWMKLETII 0.002 3 IVILDLSVE 0.002 65 ATAEAQESG 0.002
[1220]
21TABLE XI Start Subsequence Score V1-HLA-A0201-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 100
SLWDLRHLLV 2366.855 306 GLLSFFFAMV 1585.012 82 ALTKTNIIFV 879.833
304 QLGLLSFFFA 301.110 373 LLAVTSIPSV 271.948 107 LLVGKILIDV
271.948 132 YLASLFPDSL 182.973 219 AISLATFFFL 178.032 367
SLGLLSLLAV 159.970 385 ALNWREFSFI 109.023 298 WLQCRKQLGL 98.267 437
VLPSIVILDL 83.527 266 LLSLVYLAGL 83.527 403 LLISTFHVLI 67.396 402
ALLISTFHVL 61.573 365 IMSLGLLSLL 60.325 140 SLIVKGFNVV 54.181 258
TLPIVAITLL 49.134 433 VLALVLPSIV 48.478 48 RLIRCGYHVV 42.774 370
LLSLLAVTSI 40.792 210 TLWRGPVVVA 38.884 263 AITLLSLVYL 37.157 432
FVLALVLPSI 35.735 401 VALLISTFHV 35.242 207 RLFTLWRGPV 33.455 227
FLYSFVRDVI 30.852 223 ATFFFLYSFV 29.487 65 FASEFFPHVV 28.385 364
GIMSLGLLSL 24.997 261 IVAITLLSLV 23.795 435 ALVLPSIVIL 20.145 90
FVAIHREHYT 16.497 179 IELARQLNFI 16.141 427 YTPPNFVLAL 11.929 67
SEFFPHVVDV 11.509 111 KILIDVSNNM 8.846 305 LGLLSFFFAM 8.542 172
IQARQQVIEL 8.469 249 KIPIEIVNKT 8.248 183 RQLNFIPIDL 8.014 95
REHYTSLWDL 7.165 440 SIVILDLLQL 6.756 209 FTLWRGPVVV 6.741 308
LSFFFAMVHV 6.568 57 VIGSRNPKFA 6.387 419 FEEEYYRFYT 5.579 394
IQSTLGYVAL 5.523 269 LVYLAGLLAA 5.439 313 AMVHVAYSLC 5.382 312
FAMVHVAYSL 5.050 268 SLVYLAGLLA 4.968 92 AIHREHYTSL 4.406 243
QQSDFYKIPI 4.337 257 KTLPIVAITL 3.842 231 FVRDVIHPYA 3.427 314
MVHVAYSLCL 3.178 303 KQLGLLSFFF 3.121 221 SLATFFFLYS 2.959 144
KGFNVVSAWA 2.310 286 TKYRRFPPWL 1.984 147 NVVSAWALQL 1.869 199
REIENLPLRL 1.703 441 IVILDLLQLC 1.700 389 REFSFIQSTL 1.537 226
FFLYSFVRDV 1.437 24 GIKDARKVTV 1.372 201 IENLPLRLFT 1.355 393
FIQSTLGYVA 1.288 64 KFASEFFPHV 1.221 152 WALQLGPKDA 1.174 345
IENSWNEEEV 1.127 299 LQCRKQLGLL 1.101 163 RQVYICSNNI 1.058 428
TPPNFVLALV 1.044 264 ITLLSLVYLA 0.998 113 LIDVSNNMRI 0.975 250
IPIEIVNKTL 0.972 43 KSLTIRLIRC 0.966 323 LPMRRSERYL 0.965 424
YRFYTPPNFV 0.904 36 IGSGDFAKSL 0.901 361 ISFGIMSLGL 0.877 4
ISMMGSPKSL 0.877 336 MAYQQVHANI 0.788 139 DSLIVKGFNV 0.731 12
SLSETCLPNG 0.703 275 LLAAAYQLYY 0.697 134 ASLFPDSLIV 0.689 121
RINQYPESNA 0.683 253 EIVNKTLPIV 0.676 98 YTSLWDLRHL 0.628 398
LGYVALLIST 0.609 16 TCLPNGINGI 0.580 396 STLGYVALLI 0.536 356
RIEMYISFGI 0.532 202 ENLPLRLFTL 0.516 99 TSLWDLRHLL 0.516 273
AGLLAAAYQL 0.516 332 LFLNMAYQQV 0.456 V2-HLA-A0201-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 5; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 24
SLPSSWDYRC 4.968 12 SLSSGFTPFS 1.557 22 CLSLPSSWDY 0.559 13
LSSGFTPFSC 0.320 14 SSGFTPFSCL 0.265 9 LSLSLSSGFT 0.219 5
GLQALSLSLS 0.171 2 GSPGLQALSL 0.139 34 PPPCPADFFL 0.098 10
SLSLSSGFTP 0.086 8 ALSLSLSSGF 0.075 16 GFTPFSCLSL 0.015 6
LQALSLSLSS 0.013 4 PGLQALSLSL 0.011 7 QALSLSLSSG 0.009 15
SGFTPFSCLS 0.007 11 LSLSSGFTPF 0.006 27 SSWDYRCPPP 0.003 23
LSLPSSWDYR 0.003 20 FSCLSLPSSW 0.002 17 FTPFSCLSLP 0.002 21
SCLSLPSSWD 0.002 18 TPFSCLSLPS 0.002 33 CPPPCPADFF 0.001 3
SPGLQALSLS 0.001 32 RCPPPCPADF 0.000 1 SGSPGLQALS 0.000 36
PCPADFFLYF 0.000 29 WDYRCPPPCP 0.000 28 SWDYRCPPPC 0.000 35
PPCPADFFLY 0.000 25 LPSSWDYRCP 0.000 31 YRCPPPCPAD 0.000 30
DYRCPPPCPA 0.000 19 PFSCLSLPSS 0.000 26 PSSWDYRCPP 0.000
V5A-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 RLFTFWRGPV 33.455 8 FTFWRGPVVV 6.741 2
NLPLRLFTFW 0.779 3 LPLRLFTFWR 0.074 7 LFTFWRGPVV 0.034 9 TFWRGPVVVA
0.027 1 ENLPLRLFTF 0.002 4 PLRLFTFWRG 0.002 10 FWRGPVVVAI 0.001 5
LRLFTFWRGP 0.000 V5B-HLA-A0201-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 11; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 17 TQTELELEFV 179.213 19
TELELEFVFL 65.849 21 LELEFVFLLT 7.100 23 LEEVFLLTLL 6.009 20
ELELEFVFLL 5.198 8 IQIFCSFADT 2.440 3 REFSFIQIFC 1.966 22
ELEFVFLLTL 0.896 14 FADTQTELEL 0.546 12 CSFADTQTEL 0.516 6
SFIQIFCSFA 0.072 7 FIQIFCSFAD 0.055 5 FSFIQIFCSF 0.016 9 QIFCSFADTQ
0.014 10 IFCSFADTQT 0.009 24 EFVFLLTLLL 0.001 1 NWREFSFIQI 0.001 11
FCSFADTQTE 0.000 18 QTELELEFVF 0.000 16 DTWTELELEF 0.000 4
EFSFIQIFCS 0.000 15 ADTQTELELE 0.000 13 SFADTQTELE 0.000 2
WREFSFIQIF 0.000 V6-HLA-A0201-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 13; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 7 VILGKIILFL 233.719 43
TIPHVSPERV 4.686 35 FLEEGIGGTI 1.637 5 SIVILGKIIL 1.204 27
KKGWEKSQFL 0.571 8 ILGKIILFLP 0.338 13 ILFLPCISRK 0.216 10
GKIILFLPCI 0.127 1 LVLPSIVILG 0.094 38 EGIGGTIPHV 0.078 15
FLPCISRKLK 0.069 28 KGWEKSQFLE 0.067 2 VLPSIVILGK 0.058 3
LPSIVILGKI 0.035 33 SQFLEEGIGG 0.028 6 IVILGKIILF 0.025 34
QFLEEGIGGT 0.023 14 LFLPCISRKL 0.019 11 KIILFLPCIS 0.015 46
HVSPERVTVM 0.014 12 IILFLPCISR 0.013 44 IPHVSPERVT 0.007 39
GIGGTIPHVS 0.004 9 LGKIILFLPC 0.004 17 PCISRKLKRI 0.003 22
KLKRIKKGWE 0.001 45 PHVSPERVTV 0.001 30 WEKSQFLEEG 0.001 4
PSIVILGKII 0.001 31 EKSQFLEEGI 0.001 21 RKLKRIKKGW 0.000 41
GGTIPHVSPE 0.000 42 GTIPHVSPER 0.000 18 CISRKLKRIK 0.000 40
IGGTIPHVSP 0.000 16 LPCISRKLKR 0.000 37 EEGIGGTIPH 0.000 32
KSQFLEEGIG 0.000 25 RIKKGWEKSQ 0.000 24 KRIKKGWEKS 0.000 23
LKRIKKGWEK 0.000 36 LEEGIGGTIP 0.000 19 ISRKLKRIKK 0.000 26
IKKGWEKSQF 0.000 20 SRKLKRIKKG 0.000 29 GWEKSQFLEE 0.000
V7A-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 5 SLSETFLPNG 2.670 9 TFLPNGINGI 0.062 2
SPKSLSETFL 0.027 4 KSLSETFLPN 0.012 6 LSETFLPNGI 0.007 10
FLPNGINGIK 0.004 8 ETFLPNGING 0.000 1 GSPKSLSETF 0.000 7 SETFLPNGIN
0.000 3 PKSLSETFLP 0.000 V7B-HLA-A0201-10mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 15; each start position is specified,
the length of peptide is 10 amino acids, and the end position for
each peptide is the start position plus nine. 2 FLNMAYQQST 34.279 8
QQSTLGYVAL 3.249 7 YQQSTLGYVA 0.950 3 LNMAYQQSTL 0.877 10
STLGYVALLI 0.536 9 QSTLGYVALL 0.321 4 NMAYQQSTLG 0.054 6 AYQQSTLGYV
0.016 5 MAYQQSTLGY 0.006 1 LFLNMAYQQS 0.000
V7C-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 160 FLGSGTWMKL 167.054 42 WQQDRKIPPL 93.953 134
FLLRLLKSQA 84.555 5 VILDLSVEVL 35.002 156 SLGEFLGSGT 30.553 27
NILRGGLSEI 12.208 168 KLETIILSKL 11.006 127 GVGPLWEFLL 10.841 4
IVILDLSVEV 10.346 130 PLWEFLLRLL 7.357 148 LSLAFTSWSL 6.579 58
AMWTEEAGAT 5.807 129 GPLWEFLLRL 4.510 152 FTSWSLGEFL 3.678 112
KAANSWRNPV 3.381 6 ILDLSVEVLA 3.378 141 SQAASGTLSL 2.166 158
GEFLGSGTWM 1.966 28 ILRGGLSEIV 1.805 78 KSSSSSQIPV 1.589 147
TLSLAFTSWS 1.557 19 AAWKCLGANI 1.203 81 SSSQIPVVGV 1.044 14
LASPAAAWKC 0.880 135 LLRLLKSQAA 0.642 126 NGVGPLWEFL 0.639 144
ASGTLSLAFT 0.615 66 ATAEAQESGI 0.594 31 GGLSEIVLPI 0.580 52
STPPPPAMWT 0.569 164 GTWMKLETII 0.493 177 LTQEQKSKHC 0.481 119
NPVLPHTNGV 0.454 138 LLKSQAASGT 0.443 79 SSSSSQIPVV 0.428 181
QKSKHCMFSL 0.396 83 SQIPVVGVVT 0.310 137 RLLKSQAASG 0.276 176
KLTQEQKSKH 0.261 169 LETIILSKLT 0.246 15 ASPAAAWKCL 0.237 9
LSVEVLASPA 0.226 11 VEVLASPAAA 0.164 92 TEDDEAQDSI 0.163 142
QAASGTLSLA 0.159 13 VLASPAAAWK 0.139 149 SLAFTSWSLG 0.127 113
AANSWRNPVL 0.122 50 PLSTPPPPAM 0.109 163 SGTWMKLETI 0.077 122
LPHTNGVGPL 0.071 32 GLSEIVLPIE 0.058 132 WEFLLRLLKS 0.057 82
SSQIPVVGVV 0.056 162 GSGTWMKLET 0.049 23 CLGANILRGG 0.034 178
TQEQKSKHCM 0.032 24 LGANILRGGL 0.031 10 SVEVLASPAA 0.028 88
VGVVTEDDEA 0.027 37 VLPIEWQQDR 0.025 121 VLPHTNGVGP 0.025 153
TSWSLGEFLG 0.023 105 ESPDRALKAA 0.023 166 WMKLETILLS 0.020 110
ALKAANSWRN 0.020 182 KSKHCMFSLI 0.016 22 KCLGANILRG 0.014 36
IVLPEIWQQD 0.014 172 IILSKLTQEQ 0.013 173 ILSKLTQEQK 0.012 2
PSIVILDLSV 0.010 155 WSLGEFLGSG 0.009 115 NSWRNPVLPH 0.009 90
VVTEDDEAQD 0.009 102 DPPESPDRAL 0.009 125 TNGVGPLWEF 0.008 146
GTLSLAFTSW 0.007 47 KIPPLSTPPP 0.007 139 LKSQAASGTL 0.007 61
TEEAGATAEA 0.006 101 IDPPESPDRA 0.006 57 PAMWTEEAGA 0.006 59
MWTEEAGATA 0.005 171 TIILSKLTQE 0.005 84 QIPVVGVVTE 0.005 165
TWMKLETIIL 0.005 109 RALKAANSWR 0.004 97 AQDSIDPPES 0.003 43
QQDRKIPPLS 0.003 145 SGTLSLAFTS 0.003 49 PPLSTPPPPA 0.003 8
DLSVEVLASP 0.003 76 RNKSSSSSQI 0.002 104 PESPDRALKA 0.002 29
LRGGLSEIVL 0.002 3 SIVILDLSVE 0.002 12 EVLASPAAAW 0.002 34
SEIVLPIEWQ 0.002 140 KSQAASGTLS 0.002
[1221]
22TABLE XII Start Subsequence Score V1-HLA-A3-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 221
SLATFFFLY 108.000 306 GLLSFFFAM 24.300 294 WLETWLQCR 18.000 281
QLYYGTKYR 10.000 249 KIPIEIVNK 9.000 103 DLRHLLVGK 9.000 274
GLLAAAYQL 8.100 443 ILDLLQLCR 8.000 223 ATFFFLYSF 6.750 304
QLGLLSFFF 6.000 155 QLGPKDASR 6.000 385 ALNWREFSF 6.000 35
VIGSGDFAK 6.000 409 HVLIYGWKR 5.400 56 VVIGSRNPK 4.500 313
AMVHVAYSL 4.050 82 ALTKTNIIF 4.000 322 CLPMRRSER 4.000 275
LLAAAYQLY 4.000 135 SLFPDSLIV 3.000 100 SLWDLRHLL 3.000 21
GINGIKDAR 2.700 403 LLISTFHVL 2.700 265 TLLSLVYLA 2.700 435
ALVLPSIVI 2.700 203 NLPLRLFTL 2.700 205 PLRLFTLWR 2.400 3 SISMMGSPK
2.000 258 TLPIVAITL 1.800 184 QLNFIPIDL 1.800 397 TLGYVALLI 1.800
365 IMSLGLLSL 1.800 307 LLSFFFAMV 1.800 87 NIIFVAIHR 1.800 106
HLLVGKILI 1.800 433 VLALVLPSI 1.350 191 DLGSLSSAR 1.200 210
TLWRGPVVV 1.000 140 SLIVKGFNV 0.900 17 CLPNGINGI 0.900 231
FVRDVIHPY 0.900 48 RLIRCGYHV 0.900 402 ALLISTFHV 0.900 227
FLYSFVRDV 0.900 417 RAFEEEYYR 0.900 263 AITLLSLVY 0.800 5 SMMGSPKSL
0.675 369 GLLSLLAVT 0.675 396 STLGYVALL 0.608 303 KQLGLLSFF 0.608
44 SLTIRLIRC 0.600 381 SVSNALNWR 0.600 46 TIRLIRCGY 0.600 219
AISLATFFF 0.600 280 YQLYYGTKY 0.540 411 LIYGWKRAF 0.450 271
YLAGLLAAA 0.450 112 ILIDVSNNM 0.450 85 KTNIIFVAI 0.405 90 FVAIHREHY
0.400 367 SLGLLSLLA 0.400 113 LIDVSNNMR 0.400 148 VVSAWALQL 0.360
175 RQQVIELAR 0.360 217 VVAISLATF 0.300 164 QVYICSNNI 0.300 400
YVALLISTF 0.300 43 KSLTIRLIR 0.270 441 IVILDLLQL 0.270 268
SLVYLAGLL 0.270 180 ELARQLNFI 0.270 353 EVWRIEMYI 0.270 358
EMYISFGIM 0.270 276 LAAAYQLYY 0.240 436 LVLPSIVIL 0.203 335
NMAYQQVHA 0.200 57 VIGSRNPKF 0.200 269 LVYLAGLLA 0.200 333
FLNMAYQQV 0.200 261 IVAITLLSL 0.180 225 FFFLYSFVR 0.180 360
YISFGIMSL 0.180 437 VLPSIVILD 0.180 404 LISTFHVLI 0.180 242
NQQSDFYKI 0.162 257 KTLPIVAIT 0.152 331 YLFLNMAYQ 0.150 410
VLIYGWKRA 0.150 34 GVIGSGDFA 0.135 18 LPNGINGIK 0.135 107 LLVGKILID
0.135 241 RNQQSDFYK 0.120 405 ISTFHVLIY 0.120 132 YLASLFPDS 0.120
428 TPPNFVLAL 0.108 153 ALQLGPKDA 0.100 108 LVGKILIDV 0.090 378
SIPSVSNAL 0.090 141 LIVKGFNVV 0.090 282 LYYGTKYRR 0.090
V2-HLA-A3-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 5;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 12 SLSSGFTPF 6.000 24 SLPSSWDYR 4.000 5 GLQALSLSL 3.600
37 CPADFFLYF 0.360 23 LSLPSSWDY 0.135 17 FTPFSCLSL 0.060 36
PCPADFFLY 0.036 8 ALSLSLSSG 0.030 22 CLSLPSSWD 0.030 10 SLSLSSGFT
0.030 33 CPPPCPADF 0.030 25 LPSSWDYRC 0.018 9 LSLSLSSGF 0.015 15
SGFTPFSCL 0.013 3 SPGLQALSL 0.012 34 PPPCPADFF 0.003 14 SSGFTPFSC
0.003 21 SCLSLPSSW 0.003 35 PPCPADFFL 0.003 6 LQALSLSLS 0.002 18
TPFSCLSLP 0.002 27 SSWDYRCPP 0.002 1 SGSPGLQAL 0.001 7 QALSLSLSS
0.001 29 WDYRCPPPC 0.001 13 LSSGFTPFS 0.001 2 GSPGLQALS 0.001 16
GFTPFSCLS 0.001 31 YRCPPPCPA 0.000 11 LSLSSGFTP 0.000 32 RCPPPCPAD
0.000 20 FSCLSLPSS 0.000 28 SWDYRCPPP 0.000 4 PGLQALSLS 0.000 30
DYRCPPPCP 0.000 19 PFSCLSLPS 0.000 26 PSSWDYRCP 0.000
V5A-HLA-A3-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 11;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 1 NLPLRLFTF 9.000 3 PLRLFTFWR 3.600 7 FTFWRGPVV 0.050 5
RLFTFWRGP 0.030 2 LPLRLFTFW 0.009 9 FWRGPVVVA 0.001 8 TFWRGPVVV
0.001 4 LRLFTFWRG 0.000 6 LFTFWRGPV 0.000 V5B-HLA-A3-9mers-98P4B6
Each peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 24
FVFLLTLLL 0.600 19 ELELEFVFL 0.540 21 ELEFVFLLT 0.270 16 TQTELELEF
0.180 8 QIFCSFADT 0.150 2 REFSFIQIF 0.135 20 LELEFVFLL 0.109 22
LEFVFLLTL 0.081 6 FIQIFCSFA 0.060 18 TELELEFVF 0.041 17 QTELELEFV
0.015 5 SFIQIFCSF 0.013 4 FSFIQIFCS 0.005 1 WREFSFIQI 0.004 7
IQIFCSFAD 0.003 14 ADTQTELEL 0.001 10 FCSFADTQT 0.001 12 SFADTQTEL
0.001 11 CSFADTQTE 0.001 15 DTQTELELE 0.000 23 EFVFLLTLL 0.000 13
FADTQTELE 0.000 3 EFSFIQIFC 0.000 9 IFCSFADTQ 0.000
V6-HLA-A3-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 12 ILFLPCISR 60.000 7 ILGKIILFL 2.700 6 VILGKIILF 1.350
10 KILLFLPCI 1.215 2 LPSIVILGK 0.900 42 TIPHVSPER 0.600 21
KLKRIKKGW 0.450 23 KRIKKGWEK 0.270 5 IVILGKIIL 0.180 1 VLPSIVILG
0.180 38 GIGGTIPHV 0.135 15 LPCISRKLK 0.100 14 FLPCISRKL 0.090 13
LFLPCISRK 0.068 34 FLEEGIGGT 0.068 17 CISRKLKRI 0.045 4 SIVILGKII
0.045 19 SRKLKRIKK 0.040 45 HVSPERVTV 0.030 41 GTIPHVSPE 0.020 27
KGWEKSQFL 0.014 16 PCISRKLKR 0.012 18 ISRKLKRIK 0.010 31 KSQFLEEGI
0.009 26 KKGWEKSQF 0.006 11 IILFLPCIS 0.006 9 GKIILFLPC 0.005 46
VSPERVTVM 0.005 24 RIKKGWEKS 0.004 43 IPHVSPERV 0.002 35 LEEGIGGTI
0.001 32 SQFLEEGIG 0.001 29 WEKSQFLEE 0.000 3 PSIVILGKI 0.000 37
EFIFFTIPH 0.000 28 GWEKSQFLE 0.000 8 LGKIILFLP 0.000 33 QFLEEGIGG
0.000 40 GGTIPHVSP 0.000 39 IGGTIPHVS 0.000 25 IKKGWEKSQ 0.000 30
EKSQFLEEG 0.000 20 RKLKRIKKG 0.000 36 EEGIGGTIP 0.000 22 LKRIKKGWE
0.000 44 PHVSPERVT 0.000 V7A-HLA-A3-9mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. 9 FLPNGINGI 0.900 4
SLSETFLPN 0.180 1 SPKSLSETF 0.020 6 SETFLPNGI 0.002 3 KSLSETFLP
0.001 7 ETFLPNGIN 0.001 5 LSETFLPNG 0.000 8 TFLPNGING 0.000 2
PKSLSETFL 0.000 V7B-HLA-A3-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 15; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 9 STLGYVALL 0.608 3 NMAYQQSTL 0.600
1 FLNMAYQQS 0.040 7 QQSTLGYVA 0.018 5 AYQQSTLGY 0.008 8 QSTLGYVAL
0.003 6 YQQSTLGYV 0.003 4 MAYQQSTLG 0.001 2 LNMAYQQST 0.001
V7C-HLA-A3-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 15;
each start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. 167 KLETIILSK 270.000 159 FLGSGTWMK 60.000 175
KLTQEQKSK 30.000 31 GLSEIVLPI 24.300 129 GLSEIVLPI 24.300 109
ALKAANSWR 4.000 148 SLAFTWESL 1.800 5 ILDLSVEVL 1.800 27 ILRGGLSEI
1.350 165 WMKLETIIL 1.200 128 GPLWEFLLR 1.080 57 AMWTEEAGA 1.000
163 GTWMKLETI 0.675 146 TLSLAFTSW 0.600 131 WEFLLRLLK 0.600 21
KCLGANILR 0.540 12 VLASPAAAW 0.300 185 CMFSLISGS 0.300 13 LASPAAAWK
0.300 37 LPIEWQQDR 0.270 126 GVGPLWEFL 0.270 38 PIEWQQDRK 0.200 134
LLRLLKSDA 0.200 173 LSKLTQEQK 0.100 88 GVVTEDDEA 0.090 69 AQESGIRNK
0.090 7 DLSVEVLAS 0.072 2 SIVILDLSV 0.060 136 RLLKSQAAS 0.060 22
CLGANILRG 0.060 151 FTWESLGEF 0.045 155 SLGEFLGSG 0.041 181
KSKHCMFSL 0.041 125 NGVGPLWEF 0.030 49 PLSTPPPPA 0.030 4 VILDLSVEV
0.030 145 GTLSLAFTS 0.027 42 QQDRKIPPL 0.027 123 HTNGVGPLW 0.022 51
STPPPPAMW 0.022 133 FLLRLLKSQ 0.022 35 IVLPIEWQQ 0.020 36 VLPIEWQQD
0.020 172 ILSKLTQEQ 0.020 143 ASFTLSLAF 0.020 9 SVEVLASPA 0.020 137
LLKSQAASG 0.020 82 SQIPVVGVV 0.018 179 EQKSKHCMF 0.018 59 WTEEAGATA
0.015 83 QIPVVGVVT 0.015 152 TSWSLGEFL 0.015 176 LTQEQKSKH 0.015 73
GIRNKSSSS 0.012 141 QAASGTLSL 0.012 46 KIPPLSTPP 0.009 11 EVLASPAAA
0.009 103 PESPDRALK 0.009 100 IDPPESPDR 0.006 112 AANSWRNPV 0.006
170 TIILSKLTQ 0.006 120 VLPHTNGVG 0.006 66 TAEAQESGI 0.006 26
NILRGGLSE 0.006 127 VGPLWEFLL 0.005 24 GANILRGGL 0.005 142
AASGTLSLA 0.005 81 SSQIPVVGV 0.005 52 TPPPPAMWT 0.005 3 IVILDLSVE
0.005 171 IILSKLTQE 0.005 119 PVLPHTNGV 0.005 99 SIDPPESPD 0.005
168 LETIILSKL 0.004 17 AAAWKCLGA 0.004 67 AEAQESGIR 0.004 108
RALKAANSW 0.003 15 SPAAAWKCL 0.003 86 VVGVVTEDD 0.003 177 TQEQKSKHC
0.003 14 ASPAAAWKC 0.003 89 VVTEDDEAQ 0.003 154 WSLGEFLGS 0.003 139
KSQAASGTL 0.003 157 GEFLGSGTW 0.003 50 LSTPPPPAM 0.002 34 EIVLPIEWQ
0.002 85 PVVGVVTED 0.002 78 SSSSSQIPV 0.002 182 SKHCMFSLI 0.002 160
LGSGTWMKL 0.002 115 SWRNPVLPH 0.002 33 SEIVLPIEW 0.002 79 SSSSQIPVV
0.002 105 SPDRALKAA 0.002 65 ATAEAQESG 0.002 64 GATAEAQES 0.001 29
RGGLSEIVL 0.001 113 ANSWRNPVL 0.001 140 SQAASGTLS 0.001
[1222]
23TABLE XIII Start Subsequence Score V1-HLA-A3-10-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 100
SLWDLRHLLV 2.000 76 VTHHEDALTK 2.000 370 LLSLLAVTSI 1.800 132
YLASLFPDSL 1.800 304 QLGLLSFFFA 1.800 385 ALNWREFSFI 1.800 435
ALVLPSIVIL 1.350 303 KQLGLLSFFF 1.215 307 LLSFFFAMVH 1.200 442
VILDLLQLCR 1.200 298 WLQCRKQLGL 1.200 365 IMSLGLLSLL 0.900 410
VLIYGWKRAF 0.900 140 SLIVKGFNVV 0.900 207 RLFTLWRGPV 0.900 258
TLPIVAITLL 0.900 123 NQYPESNAEY 0.900 278 AAYQLYYGTK 0.900 364
GIMSLGLLSL 0.810 427 YTPPNFVLAL 0.810 220 ISLATFFFLY 0.810 221
SLATFFFLYS 0.720 257 KTLPIVAITL 0.608 333 FLNMAYQQVH 0.600 268
SLVYLAGLLA 0.600 324 PMRRSERYLF 0.600 82 ALTKTNIIFV 0.600 367
SLGLLSLLAV 0.600 203 NLPLRLFTLW 0.600 166 YICSNNIQAR 0.600 219
AISLATFFFL 0.540 147 NVVSAWALQL 0.540 150 SAWALQLGPK 0.450 56
VVIGSRNPKF 0.450 417 RAFEEEYYRF 0.450 45 LTIRLIRCGY 0.450 216
VVVAISLATF 0.450 178 VIELARQLNF 0.400 204 LPLRLFTLWR 0.360 358
EMYISFGIMS 0.360 314 MVHVAYSLCL 0.360 48 RLIRCGYHVV 0.300 317
VAYSLCLPMR 0.300 331 YLFLNMAYQQ 0.300 313 AMVHVAYSLC 0.300 373
LLAVTSIPSV 0.300 269 LVYLAGLLAA 0.300 440 SIVILDLLQL 0.270 222
LATFFFLYSF 0.270 154 LQLGP KDASR 0.270 85 KTNIIFVAIH 0.270 356
RIEMYISFGI 0.270 406 STFHVLIYGW 0.225 396 STLGYVALLI 0.203 432
FVLALVLPSI 0.203 217 VVAISLATFF 0.200 433 VLALVLPSIV 0.200 391
FSFIQSTLGY 0.200 369 GLLSLLAVTS 0.180 224 TFFFLYSFVR 0.180 49
LIRCGYHVVI 0.180 103 DLRHLLVGKI 0.162 111 KILIDVSNNM 0.135 249
KIPIEIVNKT 0.135 264 ITLLSLVYLA 0.135 5 SMMGSPKSLS 0.135 113
LIDVSNNMRI 0.120 262 VAITLLSLVY 0.120 372 SLLAVTSIPS 0.120 397
TLGYVALLIS 0.120 157 GPKDASRQVY 0.120 172 IQARQQVIEL 0.108 243
QQSDFYKIPI 0.108 347 NSWNEEEVWR 0.100 39 GDFAKSLTIR 0.090 218
VAISLATFFF 0.090 384 NALNWREFSF 0.090 285 GTKYRRFPPW 0.090
V2-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO: 5;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus nine. 22 CLSLPSSWDY 12.000 8 ALSLSLSSGF 2.000 24 SLPSSWDYRC
1.800 5 GLQALSLSLS 0.180 12 SLSSGFTPFS 0.120 10 SLSLSSGFTP 0.060 35
PPCPADFFLY 0.054 11 LSLSSGFTPF 0.045 23 LSLPSSWDYR 0.045 33
CPPPCPADFF 0.045 36 PCPADFFLYF 0.036 32 RCPPPCPADF 0.030 2
GSPGLQALSL 0.027 14 SSGFTPFSCL 0.013 16 GFTPFSCLSL 0.005 13
LSSGFTPFSC 0.005 18 TPFSCLSLPS 0.004 6 LQALSLSLSS 0.002 34
PPPCPADFFL 0.002 17 FTPFSCLSLP 0.002 20 FSCLSLPSSW 0.001 3
SPGLQALSLS 0.001 15 SGFTPFSCLS 0.001 27 SSWDYRCPPP 0.001 21
SCLSLPSSWD 0.000 7 QALSLSLSSG 0.000 9 LSLSLSSGFT 0.000 28
SWDYRCPPPC 0.000 4 PGLQALSLSL 0.000 29 WDYRCPPPCP 0.000 30
DYRCPPPCPA 0.000 1 SGSPGLQALS 0.000 31 YRCPPPCPAD 0.000 26
PSSWDYRCPP 0.000 25 LPSSWDYRCP 0.000 19 PFSCLSLPSS 0.000
V5A-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 RLFTFWRGPV 0.900 2 NLPLRLFTFW 0.600 3
LPLRLFTFWR 0.540 8 FTFWRGPVVV 0.050 4 PLRLFTFWRG 0.018 1 ENLPLRLFTF
0.012 9 TFWRGPVVVA 0.005 10 FWRGPVVVAI 0.004 7 LFTFWRGPVV 0.000 5
LRLFTFWRGP 0.000 V5B-HLA-A3-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 11; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 20 ELELEFVFLL 4.860 22 ELEFVFLLTL
1.620 18 QTELELEFVF 0.300 5 FSFIQIFCSF 0.225 16 DTQTELELEF 0.060 9
QIFCSFADTQ 0.030 12 CSFADTQTEL 0.015 8 IQIFCSFADT 0.013 23
LEFVFLLTLL 0.013 17 TQTELELEFV 0.013 19 TELELEFVFL 0.012 14
FADTQTELEL 0.012 2 WREFSFIQIF 0.009 3 REFSFIQIFC 0.009 21
LELEFVFLLT 0.006 7 FIQIFCSFAD 0.006 1 NWREFSFIQI 0.005 6 SFIQIFCSFA
0.001 24 EFVFLLTLLL 0.001 11 FCSFADTQTE 0.000 10 IFCSFADTQT 0.000 4
EFSFIQIFCS 0.000 15 ADTQTELELE 0.000 13 SFADTQTELE 0.000
V6-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus nine. 13 ILFLPCISRK 150.000 2 VLPSIVILGK 90.000 15 FLPCISRKLK
10.000 42 GTIPHVSPER 2.025 12 IILFLPCISR 1.800 6 IVILGKIILF 0.900 7
VILGKIILFL 0.608 35 FLEEGIGGTI 0.405 19 ISRKLKRIKK 0.200 18
CISRKLKRIK 0.200 5 SIVILGKIIL 0.180 8 ILGKIILFLP 0.135 46
HVSPERVTVM 0.090 16 LPCISRKLKR 0.080 23 LKRIKKGWEK 0.060 1
LVLPSIVILG 0.041 39 GIGGTIPHVS 0.027 43 TIPHVSPERV 0.020 22
KLKRIKKGWE 0.018 11 KIILFLPCIS 0.018 10 GKIILFLPCI 0.012 33
SQFLEEGIGG 0.006 3 LPSIVILGKI 0.004 26 IKKGWEKSQF 0.003 25
RIKKGWEKSQ 0.003 27 KKGWEKSQFL 0.002 28 KGWEKSQFLE 0.001 9
LGKIILFLPC 0.001 17 PCISRKLKRI 0.001 29 KWEKSQFLEE 0.000 37
EEGIGGTIPH 0.000 30 WEKSQFLEEG 0.000 21 RKLKRIKKGW 0.000 4
PSIVILGKII 0.000 38 EGIGGTIPHV 0.000 14 LFLPCISRKL 0.000 41
GGTIPHVSPE 0.000 24 KRIKKGWEKS 0.000 31 EKSQFLEEGI 0.000 44
IPHVSPERVT 0.000 34 QFLEEGIGGT 0.000 32 KSQFLEEGIG 0.000 36
LEEGIGGTIP 0.000 45 PHVSPERVTV 0.000 40 IGGTIPHVSP 0.000 20
SRKLKRIKKG 0.000 V7A-HLA-A3-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 15; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 10 FLPNGINGIK 9.000 5 SLSETFLPNG
0.135 1 GPSKSLSETF 0.030 2 SPKSLSETFL 0.006 6 LSETFLPNGI 0.003 8
ETFLPNGING 0.003 4 KSLSETFLPN 0.003 9 TFLPNGINGI 0.002 7 SETFLPNGIN
0.000 3 PKSLSETFLP 0.000 V7B-HLA-A3-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 5 MAYQQSTLGY 0.400 2
FLNMAYQQST 0.300 10 STLGYVALLI 0.203 9 QSTLGYVALL 0.027 4
NMAYQQSTLG 0.020 7 YQQSTLGYVA 0.018 8 QQSTLGYVAL 0.018 3 LNMAYQQSTL
0.002 6 AYQQSTLGYV 0.000 1 LFLNMAYQQS 0.000
V7C-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 13 VLASPAAAWK 20.000 173 ILSKLTQEQK 20.000 37
VLPIEWQQDR 12.000 168 KLETIILSKL 4.050 127 GVGPLWEFLL 2.430 160
FLGSGTWMKL 1.200 100 SIDPPESPDR 0.600 176 KLTQEQKSKH 0.600 38
LPIEWQQDRK 0.450 164 GTWMKLETII 0.450 134 FLLRLLKSQA 0.300 6
ILDLSVEVLA 0.300 28 ILRGGLSEIV 0.300 5 VILDLSVEVL 0.270 129
GPLWEFLLRL 0.243 167 MKLETIILSK 0.203 32 GLSEIVLPIE 0.203 135
LLRLLKSQAA 0.200 156 SLGEFLGSGT 0.150 58 AMWTEEAGAT 0.150 146
GTLSLAFTSW 0.135 27 NILRGGLSEI 0.135 166 WMKLETIILS 0.120 147
TLSLAFTSWS 0.120 138 LLKSQAASGT 0.100 130 PLWEFLLRLL 0.068 143
AASGTLSLAF 0.060 110 ALKAANSWRN 0.060 109 RALKAANSWR 0.060 66
ATAEAQESGI 0.045 115 NSWRNPVLPH 0.045 159 EFLGSGTWMK 0.041 131
LWEFLLRLLK 0.040 141 SQAASGTLSL 0.036 152 FTSWSLGEFL 0.030 50
PLSTPPPPAM 0.030 137 RLLKSQAASG 0.030 4 IVILKLSVEV 0.030 19
AAWKCLGANI 0.030 125 TNGVGPLWEF 0.027 42 WQQDRKIPPL 0.027 182
KSKHCMFSLI 0.027 31 GGLSEIVLPI 0.024 128 VGPLWEFLLR 0.024 52
STPPPPAMWT 0.022 103 PPESPDRALK 0.020 10 SVEVLASPAA 0.020 149
SLAFTSWSLG 0.020 121 VLPHTNGVGP 0.020 112 KAANSWRNPV 0.018 175
SKLTQEQKSK 0.015 148 LSLAFTSWSL 0.013 12 EVLASPAAAW 0.013 8
DLSVEVLASP 0.013 69 EAQESGIRNK 0.013 74 GIRNKSSSSS 0.012 67
TAEAQESGIR 0.012 83 SQIPVVGVVT 0.010 89 GVVTEDDEAQ 0.009 47
KIPPLSTPPP 0.009 14 LASPAAAWKC 0.009 158 GEFLGSGTWM 0.009 21
WKCLGANILR 0.008 177 LTQEQKSKHC 0.007 179 QEQKSKHCMF 0.006 113
AANSWRNPVL 0.006 84 QIPVVGVVTE 0.006 178 TQEQKSKHCM 0.006 150
LAFTSWSLGE 0.006 78 KSSSSSQIPV 0.006 122 LPHTNGVGPL 0.005 3
SIVILDLSVE 0.005 36 IVLPIEWQQD 0.005 23 CLGANILRGG 0.005 171
TIILSKLTQE 0.005 81 SSSQIPVVGV 0.005 22 KCLGANILRG 0.004 35
EIVLPIEWQQ 0.004 119 NPVLPHTNGV 0.003 162 GSGTWMKLET 0.003 142
QAASGTLSLA 0.003 124 HTNGVGPLWE 0.003 90 VVTEDDEAQD 0.003 172
IILSKLTQEQ 0.003 181 QKSKHCMFSL 0.003 9 LSVEVLASPA 0.002 51
LSTPPPPAMW 0.002 87 VVGVVTEDDE 0.002 33 LSEIVLPIEW 0.002 91
VTEDDEAQDS 0.002 165 TWMKLETIIL 0.002 29 LRGGLSEIVL 0.002 70
AWESGIRNKS 0.002 132 WEFLLRLLKS 0.002 43 QQDRKIPPLS 0.002 92
TEDDEAQDSI 0.002 79 SSSSSQIPVV 0.002 60 WTEEAGATAE 0.002 153
TSWSLGEFLG 0.002 15 ASPAAAWKCL 0.002
[1223]
24TABLE XIV Start Subsequence Score V1-HLA-A1101-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 56
VVIGSRNPK 3.000 409 HVLIYGWKR 1.200 249 KIPIEIVNK 1.200 35
VIGSGDFAK 1.200 175 RQQVIELAR 0.720 417 RAFEEEYYR 0.480 3 SISMMGSPK
0.400 279 AYQLYYGTK 0.400 136 LFPDSLIVK 0.400 381 SVSNALNWR 0.400
241 RNQQSDFYK 0.360 282 LYYGTKYRR 0.320 225 FFFLYSFVR 0.240 21
GINGIKDAR 0.240 53 GYHVVIGSR 0.240 87 NIIFVAIHR 0.240 18 LPNGINGIK
0.200 443 ILDLLQLCR 0.160 103 DLRHLLVGK 0.120 34 GVIGSGDFA 0.090
322 CLPMRRSER 0.080 113 LIDVSNNMR 0.080 155 QLGPKDASR 0.080 318
AYSLCLPMR 0.080 269 LVYLAGLLA 0.080 281 QLYYGTKYR 0.080 294
WLETWLQCR 0.080 97 HYTSLWDLR 0.080 295 LETWLQCRK 0.060 441
IVILDLLQL 0.060 306 GLLSFFFAM 0.054 199 REIENLPLR 0.054 22
INGIKDARK 0.040 148 VVSAWALQL 0.040 77 THHEDALTK 0.040 108
LVGKILIDV 0.040 223 ATFFFLYSF 0.040 261 IVAITLLSL 0.040 167
ICSNNIQAR 0.040 164 QVYICSNNI 0.040 43 KSLTIRLIR 0.036 233
RDVIHPYAR 0.036 48 RLIRCGYHV 0.036 274 GLLAAAYQL 0.036 330
RYLFLNMAY 0.036 408 FHVLIYGWK 0.030 85 KTNIIFVAI 0.030 436
LVLPSIVIL 0.030 303 KQLGLLSFF 0.027 353 EVWRIEMYI 0.024 191
DLGSLSSAR 0.024 254 IVNKTLPIV 0.020 90 FVAIHREHY 0.020 151
AWALQLGPK 0.020 83 LTKTNIIFV 0.020 98 YTSLWDLRH 0.020 231 FVRDVIHPY
0.020 400 YVALLISTF 0.020 217 VVAISLATF 0.020 402 ALLISTFHV 0.018
64 KFASEFFPH 0.018 140 SLIVKGFNV 0.018 214 GPVVVAISL 0.018 135
SLFPDSLIV 0.016 205 PLRLFTLWR 0.016 209 FRLWRGPVV 0.015 264
ITLLSLVYL 0.015 396 STLGYVALL 0.015 319 YSLCLPMRR 0.012 394
IQSTLGYVA 0.012 30 KVTVGVIGS 0.012 270 VYLAGLLAA 0.012 203
NLPLRLFTL 0.012 425 RFYTPPNFV 0.012 242 NQQSDFYKI 0.012 287
KYRRFPPWL 0.012 435 ALVLPSIVI 0.012 265 TLLSLVYLA 0.012 299
LQCRKQLGL 0.012 313 AMVHVAYSL 0.012 40 DFAKSLTIR 0.012 106
HLLVGKILI 0.012 426 FYTPPNFVL 0.012 385 ALNWREFSF 0.012 219
AISLATFFF 0.012 304 QLGLLSFFF 0.012 221 SLATFFFLY 0.012 427
YTPPNFVLA 0.010 285 GTKYRRFPP 0.009 280 YQLYYGTKY 0.009 397
TLGYVALLI 0.008 367 SLGLLSLLA 0.008 166 YICSNNIQA 0.008 258
TLPIVAITL 0.008 317 VAYSLCLPM 0.008 100 SLWDLRHLL 0.008 210
TLWRGPVVV 0.008 365 IMSLGLLSL 0.008 263 AITLLSLVY 0.008 360
YISFGIMSL 0.008 V2-HLA-A1101-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 24 SLPSSWDYR 0.080 5 GLQALSLSL 0.024
17 FTPFSCLSL 0.020 3 SPGLQALSL 0.004 12 SLSSGFTPF 0.004 37
CPADFFLYF 0.004 21 SCLSLPSSW 0.003 33 CPPPCPADF 0.002 23 LSLPSSWDY
0.001 6 LQALSLSLS 0.001 16 GFTPFSCLS 0.001 32 RCPPPCPAD 0.001 36
PCPADFFLY 0.001 35 PPCPADFFL 0.001 7 QALSLSLSS 0.001 10 SLSLSSGFT
0.000 15 SGFTPFSCL 0.000 22 CLSLPSSWD 0.000 8 ALSLSLSSG 0.000 18
TPFSCLSLP 0.000 25 LPSSWDYRC 0.000 9 LSLSLSSGF 0.000 1 SGSPGLQAL
0.000 31 YRCPPPCPA 0.000 34 PPPCPADFF 0.000 30 DYRCPPPCP 0.000 11
LSLSSGFTP 0.000 14 SSGFTPFSC 0.000 2 GSPGLQALS 0.000 19 PFSCLSLPS
0.000 29 WDYRCPPPC 0.000 27 SSWDYRCPP 0.000 13 LSSGFTPFS 0.000 20
FSCLSLPSS 0.000 28 SWDYRCPPP 0.000 4 PGLQALSLS 0.000 26 PSSWDYRCP
0.000 V5A-HLA-A1101-9mers-98P4B6 Each peptide is a portion of SEQ
ID NO: 11; each start position is specified, the length of peptide
is 9 amino acids, and the end position for each peptide is the
start position plus eight. 3 PLRLFTFWR 0.024 7 FTFWRGPVV 0.020 1
NLPLRLFTF 0.012 8 TFWRGPVVV 0.004 2 LPLRLFTFW 0.003 6 LFTFWRGPV
0.002 5 RLFTFWRGP 0.000 9 FWRGPVVVA 0.000 4 LRLFTFWRG 0.000
V5B-HLA-A11-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 24 FVFLLTLLL 0.080 16 TQTELELEF 0.012 17
QTELELEFV 0.010 6 FIQIFCSFA 0.004 2 REFSFIQIF 0.004 5 SFIQIFCSF
0.003 7 IQIFCSFAD 0.003 18 TELELEFVF 0.003 20 LELEFVFLL 0.003 22
LEFVFLLTL 0.002 12 SFADTQTEL 0.002 19 ELELEFVFL 0.001 23 EFVFLLTLL
0.001 8 QIFCSFADT 0.001 14 ADTQTELEL 0.000 1 WREFSFIQI 0.000 15
DTQTELELE 0.000 21 ELEFVFLLT 0.000 9 IFCSFADTQ 0.000 13 FADTQTELE
0.000 10 FCSFADTQT 0.000 4 FSFIQIFCS 0.000 3 EFSFIQIFC 0.000 11
CSFADTQTE 0.000 V6-HLA-A1101-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 13; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 2 LPSIVILGK 0.400 12 ILFLPCISR 0.320
13 LFLPCISRK 0.300 23 KRIKKGWEK 0.180 15 LPCISRKLK 0.100 42
TIPHVSPER 0.080 5 IVILGKIIL 0.060 19 SRKLKRIKK 0.040 45 HVSPERVTV
0.020 10 KILLFLPCI 0.018 16 PCISRKLKR 0.012 6 VILGKIILF 0.012 38
GIGGTIPHV 0.012 7 ILGKIILFL 0.008 21 KLKRIKKGW 0.006 41 GTIPHVSPE
0.005 4 SIVILGKII 0.003 18 ISRKLKRIK 0.002 17 CISRKLKRI 0.002 43
IPHVSPERV 0.002 32 SQFLEEGIG 0.001 24 RIKKGWEKS 0.001 27 KGWEKSQFL
0.001 1 VLPSIVILG 0.001 26 KKGWEKSQF 0.001 11 IILFLPCIS 0.001 33
QFLEEGIGG 0.001 31 KSQFLEEGI 0.001 35 LEEGIGGTI 0.001 14 FLPCISRKL
0.000 34 FLEEGIGGT 0.000 46 VSPERVTVM 0.000 9 GKIILFLPC 0.000 28
GWEKSQFLE 0.000 37 EGIGGTIPH 0.000 29 WEKSQFLEE 0.000 8 LGKIILFLP
0.000 40 GGTIPHVSP 0.000 20 RKLKRIKKG 0.000 3 PSIVILGKI 0.000 22
LKRIKKGWE 0.000 39 IGGTIPHVS 0.000 36 EEGIGGTIP 0.000 25 IKKGWEKSQ
0.000 30 EKSQFLEEG 0.000 44 PHVSPERVT 0.000
V7A-HLA-A1101-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 9 FLPNGINGI 0.004 1 SPKSLSETF 0.002 4
SLSETFLPN 0.001 7 ETFLPNGIN 0.001 8 TFLPNGING 0.001 6 SETFLPNGI
0.001 3 KSLSETFLP 0.000 2 PKSLSETFL 0.000 5 LSETFLPNG 0.000
V7B-HLA-A1101-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 9 STLGYVALL 0.015 7 QQSTLGYVA 0.012 5
AYQQSTLGY 0.008 6 YQQSTLGYV 0.006 3 NMAYQQSTL 0.004 4 MAYQQSTLG
0.000 1 FLNMAYQQS 0.000 8 QSTLGYVAL 0.000 2 LNMAYQQST 0.000
V7C-HLA-A1101-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 167 KLETIILSK 2.400 159 FLGSGTWMK 0.800 175
KLTQEQKSK 0.600 21 KCLGANILR 0.360 128 GPLWEFLLR 0.360 131
WEFLLRLLK 0.240 13 LASPAAAWK 0.200 88 GVVTEDDEA 0.090 109 ALKAANSWR
0.080 69 AQESGIRNK 0.060 163 GTWMKLETI 0.060 37 LPIEWQQDR 0.060 126
GVGPLWEFL 0.060 38 PIEWQQDRK 0.040 31 GLSEIVLPI 0.024 173 LSKLTQEQK
0.020 9 SVEVLASPA 0.020 145 GTLSLAFTS 0.013 2 SIVILDLSV 0.012 67
AEAQESGIR 0.012 151 FTSWSLGEF 0.010 176 LTQEQKSKH 0.010 51
STPPPPAMW 0.010 59 WTEEAGATA 0.010 123 HTNGVGPLW 0.010 11 EVLASPAAA
0.009 82 SQIPVVGVV 0.009 108 RALKAANSW 0.009 57 AMWTEEAGA 0.008 165
WMKLETIIL 0.008 148 SLAFTSWSL 0.008 4 VILDLSVEV 0.006 103 PESPDRALK
0.006 42 QQDRKIPPL 0.006 24 GANILRGGL 0.006 35 IVLPIEWQQ 0.006 5
ILDLSVEVL 0.004 134 LLRLLKSQA 0.004 100 IDPPESPDR 0.004 141
QAASGTLSL 0.004 27 ILRGGLSEI 0.004 146 TLSLAFTSW 0.004 12 VLASPAAAW
0.004 17 AAAWKCLGA 0.004 157 GEFLGSGTW 0.004 3 IVILDLSVE 0.003 119
PVLPHTNGV 0.003 89 VVTEDDEAQ 0.002 66 TAEAQESGI 0.002 86 VVGVVTEDD
0.002 142 AASGTLSLA 0.002 112 AANSWRNPV 0.002 181 KSKHCMFSL 0.002
136 RLLKSQAAS 0.002 179 EQKSKHCMF 0.002 33 SEIVLPIEW 0.002 129
PLWEFLLRL 0.002 170 TIILSKLTQ 0.001 73 GIRNKSSSS 0.001 29 RGGLSEIVL
0.001 46 KIPPLSTPP 0.001 41 WQQDRKIPP 0.001 26 NILRGGLSE 0.001 105
SPDRALKAA 0.001 65 ATAEAQESG 0.001 15 SPAAAWKCL 0.001 90 VTEDDEAQD
0.001 158 EFLGSGTWM 0.001 10 VEVLASPAA 0.001 22 CLGANILRG 0.001 185
CMFSLISGS 0.001 184 HCMFSLISG 0.001 127 VGPLWEFLL 0.001 139
KSQAASGTL 0.001 125 NGVGPLWEF 0.001 64 GATAEAQES 0.001 140
SQAASGTLS 0.001 171 IILSKLTQE 0.001 96 AQDSIDPPE 0.001 168
LETIILSKL 0.001 178 QEQKSKHCM 0.001 101 DPPESPDRA 0.001 164
TWMKLETII 0.000 49 PLSTPPPPA 0.000 18 AAWKCLGAN 0.000 143 ASGTLSLAF
0.000 150 AFTSWSLGE 0.000 36 VLPIEWQQD 0.000 83 QIPVVGVVT 0.000 160
LGSGTWMKL 0.000 52 TPPPPAMWT 0.000 172 ILSKLTQEQ 0.000 115
SWRNPVLPH 0.000 99 SIDPPESPD 0.000 149 LAFTSWSLG 0.000 113
ANSWRNPVL 0.000 155 SLGEFLGSG 0.000 137 LLKSQAASG 0.000 120
VLPHTNGVG 0.000 78 SSSSSQIPV 0.000
[1224]
25TABLE XV Start Subsequence Score V1-HLA-A1101-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 34
GVIGSGDFAK 27.000 55 HVVIGSRNPK 3.000 76 VTHHEDALTK 2.000 135
SLFPDSLIVK 1.600 21 GINGIKDARK 1.200 294 WLETWLQCRK 0.400 278
AAYQLYYGTK 0.400 150 SAWALQLGPK 0.400 17 CLPNGINGIK 0.400 281
QLYYGTKYRR 0.320 442 VILDLLQLCR 0.240 224 TFFFLYSFVR 0.240 407
TFHVLIYGWK 0.200 154 LQLGPKDASR 0.180 318 AYSLCLPMRR 0.160 204
LPLRLFTLWR 0.120 112 ILIDVSNNMR 0.120 280 YQLYYGTKYR 0.090 257
KTLPIVAITL 0.090 303 KQLGLLSFFF 0.081 166 YICSNNIQAR 0.080 269
LVYLAGLLAA 0.080 317 VAYSLCLPMR 0.080 240 ARNQQSDFYK 0.060 321
LCLPMRRSER 0.060 147 NVVSAWALQL 0.060 183 RQLNFIPIDL 0.054 364
GIMSLGLLSL 0.048 406 STFHVLIYGW 0.040 254 IVNKTLPIVA 0.040 314
MVHVAYSLCL 0.040 316 HVAYSLCLPM 0.040 356 RIEMYISFGI 0.036 425
RFYTPPNFVL 0.036 102 WDRLRHLLVGK 0.030 248 YKIPIEIVNK 0.030 56
VVIGSRNPKF 0.030 285 GTKYRRFPPW 0.030 216 VVVAISLATF 0.030 83
LTKTNIIFVA 0.030 85 KTNIIFVAIH 0.030 396 STLGYVALLI 0.030 432
FVLALVLPSI 0.030 264 ITLLSLVYLA 0.030 163 RQVYICSNNI 0.027 416
KRAFEEEYYR 0.024 86 RNIIFVAIHR 0.024 39 GDFAKSLTIR 0.024 417
RAFEEEYYRF 0.024 207 RLFTLWRGPV 0.024 217 VVAISLATFF 0.020 223
ATFFFLYSFV 0.020 400 YVALLISTFH 0.020 261 IVAITLLSLV 0.020 32
TVGVIGSGDF 0.020 142 IVKGFNVVSA 0.020 231 FVRDVIHPYA 0.020 73
VVDVTHHEDA 0.020 340 QVHANIENSW 0.020 427 YTPPNFVLAL 0.020 399
GYVALLISTF 0.018 111 KILIDVSNNM 0.018 274 GLLAAAYQLY 0.018 48
RLIRCGYHVV 0.018 306 GLLSFFFAMV 0.018 100 SLWDLRHLLV 0.016 45
LTIRLIRCGY 0.015 209 FTLWRGPVVV 0.015 409 HVLIYGWKRA 0.015 408
FHVLIYGWKR 0.012 243 QQSDFYKIPI 0.012 440 SIVILDLLQL 0.012 24
GIKDARKVTV 0.012 304 QLGLLSFFFA 0.012 145 GFNVVSAWAL 0.012 359
MYISFGIMSL 0.012 172 IQARQQVIEL 0.012 121 RINGYPESNA 0.012 123
NQYPESNAEY 0.012 165 VYICSNNIQA 0.012 107 LLVGKILIDV 0.012 219
AISLATFFFL 0.012 268 SLVYLAGLLA 0.012 376 VTSIPSVSNA 0.010 2
ESISMMGSPK 0.009 401 VALLISTFHV 0.009 214 VPVVVAISLA 0.009 218
VAISLATFFF 0.009 384 VALNWREFSF 0.009 367 SLGLLSLLAV 0.008 307
LLSFFFAMVH 0.008 437 VLPSIVILDL 0.008 227 FLYSFVRDVI 0.008 42
AKSLTIRLIR 0.008 113 LIDVSNNMRI 0.008 210 TLWRGPVVVA 0.008 178
VIELARQLNF 0.008 298 WLQCRKQLGL 0.008 404 LISTFHVLIY 0.008 82
ALTKTNIIFV 0.008 V2-HLA-A1101-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 16 GFTPFSCLSL 0.012 22
CLSLPSSWDY 0.008 23 LSLPSSWDYR 0.006 32 RCPPPCPADF 0.006 8
ALSLSLSSGF 0.004 33 CPPPCPADFF 0.002 6 LQALSLSLSS 0.001 2
GSPGLQALSL 0.001 5 GLQALSLSLS 0.001 10 SLSLSSGFTP 0.001 30
DYRCPPPCPA 0.001 17 FTPFSCLSLP 0.001 18 TPFSCLSLPS 0.001 24
SLPSSWDYRC 0.001 35 PPCPADFFLY 0.001 34 PPPCPADFFL 0.001 36
PCPADFFLYF 0.000 12 SLSSGFTPFS 0.000 11 LSLSSGFTPF 0.000 21
SCLSLPSSWD 0.000 7 QALSLSLSSG 0.000 3 SPGLQALSLS 0.000 20
FSCLSLPSSW 0.000 14 SSGFTPFSCL 0.000 4 PGLQALSLSL 0.000 13
LSSGFTPFSC 0.000 29 WDYRCPPPCP 0.000 27 SSWDYRCPPP 0.000 15
SGFTPFSCLS 0.000 9 LSLSLSSGFT 0.000 31 YRCPPPCPAD 0.000 19
PFSCLSLPSS 0.000 25 LPSSWDYRCP 0.000 28 SWDYRCPPPC 0.000 1
SGSPGLQALS 0.000 26 PSSWDYRCPP 0.000 V5A-HLA-A1101-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 3
LPLRLFTFWR 0.180 6 RLFTFWRGPV 0.024 8 FTFWRGPVVV 0.020 9 TFWRGPVVVA
0.004 2 NLPLRLFTFW 0.004 7 LFTFWRGPVV 0.002 1 ENLPLRLFTF 0.001 10
FWRGPVVVAI 0.000 4 PLRLFTFWRG 0.000 5 LRLFTFWRGP 0.000
V5B-HLA-A1101-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 18 QTELELEFVF 0.030 16 DTWTELELEF 0.006 17
TQTELELEFV 0.006 14 FADTQTELEL 0.004 20 ELELEFVFLL 0.004 6
SFIQIFCSFA 0.003 22 ELEFVFLLTL 0.002 24 EFVFLLTLLL 0.002 7
FIQIFCSFAD 0.001 23 LEFVFLLTLL 0.001 8 IQIFCSFADT 0.001 19
TELELEFVFL 0.001 9 QIFCSFADTQ 0.001 3 REFSFIQIFC 0.001 1 NWREFSFIQI
0.000 12 CSFADTQTEL 0.000 5 FSFIQIFCSF 0.000 13 SFADTQTELE 0.000 2
WREFSFIQIF 0.000 11 FCSFADTQTE 0.000 10 IFCSFADTQT 0.000 4
EFSFIQIFCS 0.000 21 LELEFVFLLT 0.000 15 ADTQTELELE 0.000
V6-HLA-A1101-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
13; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 42 GTIPHVSPER 0.900 2 VLPSIVILGK 0.800 13
ILFLPCISRK 0.800 12 IILFLPCISR 0.240 15 FLPCISRKLK 0.200 16
LPCISRKLKR 0.080 6 IVILGKIILF 0.060 19 ISRKLKRIKK 0.040 18
CISRKLKRIK 0.040 23 LKRIKKGWEK 0.040 46 HVSPERVTVM 0.020 5
SIVILGKIIL 0.012 7 VILGKIILFL 0.012 1 LVLPSIVILG 0.006 35
FLEEGIGGTI 0.004 43 TIPHVSPERV 0.004 33 SQFLEEGIGG 0.002 3
LPSIVILGKI 0.002 11 KILLFLPCIS 0.002 39 GIGGTIPHVS 0.001 8
ILGKIILFLP 0.001 22 KLKRIKKGWE 0.001 10 GKIILFLPCI 0.001 25
RIKKGWEKSQ 0.001 27 KKGWEKSQFL 0.001 21 RKLKRIKKGW 0.000 28
KGWEKSQFLE 0.000 37 EEGIGGTIPH 0.000 14 LFLPCISRKL 0.000 34
QFLEEGIGGT 0.000 26 IKKGWEKSQF 0.000 17 PCISRKLKRI 0.000 29
GWEKSQFLEE 0.000 24 KRIKKGWEKS 0.000 38 EGIGGTIPHV 0.000 41
GGTIPHVSPE 0.000 32 KSQFLEEGIG 0.000 36 LEEGIGGTIP 0.000 31
EKSQFLEEGI 0.000 30 WEKSQFLEEG 0.000 9 LGKIILFLPC 0.000 45
PHVSPERVTV 0.000 44 IPHVSPERVT 0.000 40 IGGTIPHVSP 0.000 4
PSIVILGKII 0.000 20 SKRLKRIKKG 0.000 V7A-HLA-A1101-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 10
FLPNGINGIK 0.400 9 TFLPNGINGI 0.003 2 SPKSLSETFL 0.002 8 ETFLPNGING
0.001 1 GSPKSLSETF 0.001 5 SLSETFLPNG 0.000 6 LSETFLPNGI 0.000 4
KSLSETFLPN 0.000 7 SETFLPNGIN 0.000 3 PKSLSETFLP 0.000
V7B-HLA-A1101-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 10 STLGYVALLI 0.030 7 YQQSTLGYVA 0.012 5
MAYQQSTLGY 0.008 8 QQSTLGYVAL 0.006 6 AYQQSTLGYV 0.004 3 LNMAYQQSTL
0.001 2 FLNMAYQQST 0.000 4 NMAYQQSTLG 0.000 1 LFLNMAYQQS 0.000 9
QSTLGYVALL 0.000 V7C-HLA-A1101-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 173 ILSKLTQEQK 0.400 13
VLASPAAAWK 0.400 38 LPIEWQQDRK 0.300 109 RALKAANSWR 0.180 127
GVGPLWEFLL 0.180 159 EFLGSGTWMK 0.180 100 SIDPPESPDR 0.080 37
VLPIEWQQDR 0.080 167 MKLETIILSK 0.060 164 GTWMKLETII 0.060 146
GTLSLAFTSW 0.045 131 LWEFLLRLLK 0.040 67 TAEAQESGIR 0.040 4
IVILDLSVEV 0.030 103 PPESPDRALK 0.020 10 SVEVLASPAA 0.020 129
GPLWEFLLRL 0.018 175 SKLTQEQKSK 0.015 176 KLTQEQKSKH 0.012 141
SQAASGTLSL 0.012 168 KLETIILSKL 0.012 66 ATAEAQESGI 0.010 152
FTSWSLGEFL 0.010 12 EVLASPAAAW 0.009 89 GVVTEDDEAQ 0.009 160
FLGSGTWMKL 0.008 21 WKCLGANILR 0.008 128 VGPLWEFLLR 0.008 5
VILDLSVEVL 0.006 112 KAANSWRNPV 0.006 134 FLLRLLKSQA 0.006 69
EAQESGIRNK 0.006 27 NILRGGLSEI 0.006 178 TQEQKSKHCM 0.006 42
WQQDRKIPPL 0.006 6 ILDLSVEVLA 0.004 135 LLRLLKSQAA 0.004 143
AASGTLSLAF 0.004 19 AAWKCLGANI 0.004 28 ILRGGLSEIV 0.004 158
GEFLGSGTWM 0.004 36 IVLPIEWQQD 0.003 119 NPVLPHTNGV 0.003 124
HTNGVGPLWE 0.002 113 AANSWRNPVL 0.002 122 LPHTNGVGPL 0.002 52
STPPPPAMWT 0.002 90 VVTEDDEAQD 0.002 142 QAASGTLSLA 0.002 87
VVGVVTEDDE 0.002 151 AFTSWSLGEF 0.002 31 GGLSEIVLPI 0.002 137
RLLKSQAASG 0.002 22 KCLGANILRG 0.002 74 GIRNKSSSSS 0.001 47
SIPPLSTPPP 0.001 32 GLSEIVLPIE 0.001 76 RNKSSSSSQI 0.001 78
KSSSSSQIPV 0.001 60 WTEEAGATAE 0.001 91 VTEDDEAQDS 0.001 83
SQIPVVGVVT 0.001 170 ETIILSKLTQ 0.001 11 VEVLASPAAA 0.001 165
TWMKLETIIL 0.001 125 TNGVGPLWEF 0.001 110 ALKAANSWRN 0.001 166
WMKLETIILS 0.001 115 NSWRNPVLPH 0.001 150 LAFTSWSLGE 0.001 58
AMWTEEAGAT 0.001 3 SIVILDLSVE 0.001 182 KSKHCMFSLI 0.001 171
TIILSKLTQE 0.001 70 AQESGIRNKS 0.001 181 QKSKHCMFSL 0.001 172
IILSKLTQEQ 0.001 148 LSLAFTSWSL 0.001 65 GATAEAQESG 0.001 25
GANILRGGLS 0.001 97 AQDSIDPPES 0.001 43 QQDRKIPPLS 0.001 92
TEDDEAQDSI 0.001 61 TEEAGATAEA 0.001 179 QEQKSKHCMF 0.001 177
LTQEQKSKHC 0.001 147 TLSLAFTSWS 0.000 121 VLPHTNGVGP 0.000 17
PAAAWKCLGA 0.000 138 LLKSQAASGT 0.000 29 LRGGLSEIVL 0.000 53
TPPPPAMWTE 0.000 14 LASPAAAWKC 0.000 84 QIPVVGVVTE 0.000 50
PLSTPPPPAM 0.000 185 HCMFSLISGS 0.000 57 PAMWTEEAGA 0.000 149
SLAFTSWSLG 0.000 33 LSEIVLPIEW 0.000 156 SLGEFLGSGT 0.000
[1225]
26TABLE XVI Start Subsequence Score V1-HLA-A24-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 287
KYRRFPPWL 400.000 426 FYTPPNFVL 240.000 337 AYQQVHANI 105.000 283
YYGTKYRRF 100.000 228 LYSFVRDVI 70.000 390 EFSFIQSTL 28.000 362
SFGIMSLGL 20.000 418 AFEEEYYRF 18.000 330 RYLFLNMAY 18.000 378
SIPSVSNAL 10.080 124 QYPESNAEY 9.900 399 GYVALLIST 9.000 177
QVIELARQL 8.640 184 QLNFIPIDL 8.400 258 TLPIVAITL 8.400 313
AMVHVAYSL 8.400 214 GPVVVAISL 8.400 246 DFYKIPIEI 7.700 270
VYLAGLLAA 7.500 359 MYISFGIMS 7.500 268 SLVYLAGLL 7.200 291
FPPSLETWL 7.200 366 MSLGLLSLL 7.200 220 ISLATFFFL 7.200 403
LLISTFHVL 7.200 303 KQLGLLSFF 7.200 436 LVLPSIVIL 7.200 200
EIENLPLRL 7.200 61 RNPKFASEF 6.600 428 TPPNFVLAL 6.000 274
GLLAAAYQL 6.000 125 YPESNAEYL 6.000 363 FGIMSLGLL 6.000 264
ITLLSLVYL 6.000 396 STLGYVALL 6.000 297 TWLQCRKQL 6.000 259
LPIVAITLL 6.000 5 SMMGSPKSL 6.000 203 NLPLRLFTL 6.000 441 IVILDLLQL
6.000 187 FIPIDLGSL 6.000 146 FNVVSAWAL 6.000 267 LSLVYLAGL 6.000
99 TSLWDLRHL 6.000 100 SLWDLRHLL 5.760 438 LPSIVILDL 5.600 85
KTNIIFVAI 5.040 247 FYKIPIEIV 5.000 423 YYRFYTPPN 5.000 128
SNAEYLASL 4.800 41 FAKSLTIRL 4.800 37 GSGDFAKSL 4.800 173 QARQQVIEL
4.400 300 QCRKQLGLL 4.000 75 DVTHHEDAL 4.000 395 QSTLGYVAL 4.000
299 LQCRKQLGL 4.000 133 LASLFPDSL 4.000 365 IMSLGLLSL 4.000 148
VVSAWALQL 4.000 360 YISFGIMSL 4.000 261 IVAITLLSL 4.000 196
SSAREIENL 4.000 129 NAEYLASLF 3.600 218 VAISLATFF 3.600 385
ALNWREFSF 3.000 33 VGVIGSGDF 3.000 400 YVALLISTF 2.400 304
QLGLLSFFF 2.400 383 SNALNWREF 2.200 57 VIGSRNPKF 2.200 223
ATFFFLYSF 2.000 411 LIYGWKRAF 2.000 219 AISLATFFF 2.000 62
NPKFASEFF 2.000 82 ALTKTNIIF 2.000 239 YARNQQSDF 2.000 217
VVAISLATF 2.000 242 NQQSDFYKI 1.980 81 DALTKTNII 1.800 17 CLPNGINGI
1.800 349 WNEEEVWRI 1.800 171 NIQARQQVI 1.800 290 RFPPWLETW 1.800
105 RHLLVGKIL 1.680 193 GSLSSAREI 1.650 112 ILIDVSNNM 1.512 435
ALVLPSIVI 1.500 106 HLLVGKILI 1.500 134 ASLFPDSLI 1.500 253
EIVNKTLPI 1.500 371 LSLLAVTSI 1.500 353 EVWRIEMYI 1.400 397
TLGYVALLI 1.400 433 VLALVLPSI 1.400 186 NFIPIDLGS 1.260 164
QVYICSNII 1.200 180 ELARQLNFI 1.200 425 RFYTPPNFV 1.200 386
LNWREFSFI 1.200 V2-HLA-A24-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 5 GLQALSLSL 7.200 17 FTPFSCLSL 6.000
1 SGSPGLQAL 5.760 15 SGFTPFSCL 4.800 3 SPGLQALSL 4.000 33 CPPPCPADF
3.600 9 LSLSLSSGF 3.600 37 CPADFFLYF 2.880 12 SLSSGFTPF 2.400 16
GFTPFSCLS 0.600 30 DYRCPPPCP 0.500 35 PPCPADFFL 0.480 34 PPPCPADFF
0.300 23 LSLPSSWDY 0.180 2 GSPGLQALS 0.180 21 SCLSLPSSW 0.180 7
QALSLSLSS 0.180 14 SSGFTPFSC 0.100 10 SLSLSSGFT 0.100 6 LQALSLSLS
0.100 25 LPSSWDYRC 0.100 13 LSSGFTPFS 0.100 20 FSCLSLPSS 0.100 19
PFSCLSLPS 0.060 32 RCPPPCPAD 0.036 36 PCPADFFLY 0.018 24 SLPSSWDYR
0.015 4 PGLQALSLS 0.015 11 LSLSSGFTP 0.015 27 SSWDYRCPP 0.012 31
YRCPPPCPA 0.012 18 TPFSCLSLP 0.010 29 WDYRCPPPC 0.010 8 ALSLSLSSG
0.010 28 SWDYRCPPP 0.010 22 CLSLPSSWD 0.010 26 PSSWDYRCP 0.001
V5A-HLA-A24-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 1 NLPLRLFTF 3.000 8 TFWRGPVVV 0.500 6
LFTFWRGPV 0.500 2 LPLRLFTFW 0.216 7 FTFWRGPVV 0.100 9 FWRGPVVVA
0.100 5 RLFTFWRGP 0.020 4 LRLFTFWRG 0.002 3 PLRLFTFWR 0.001
V5B-HLA-A24-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 23 EFVFLLTLL 36.000 12 SFADTQTEL 26.400 5
SFIQIFCSF 25.200 19 ELELEFVFL 7.200 24 FVFLLTLLL 4.800 16 TQTELELEF
3.168 20 LELEFVFLL 0.720 3 EFSFIQIFC 0.700 2 REFSFIQIF 0.480 14
ADTQTELEL 0.440 18 TELELEFVF 0.432 22 LEFVFLLTL 0.400 21 ELEFVFLLT
0.252 1 WREFSFIQI 0.180 6 FIQIFCSFA 0.150 17 QTELELEFV 0.150 8
QIFCSFADT 0.120 10 FCSFADTQT 0.100 4 FSFIQIFCS 0.100 9 IFCSFADTQ
0.050 7 IQIFCSFAD 0.015 15 DTQTELELE 0.015 11 CSFADTQTE 0.012 13
FADTQTELE 0.010 V6-HLA-A24-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 13; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 27 KGWEKSQFL 11.520 14 FLPCISRKL
9.240 5 IVILGKIIL 6.000 7 ILGKIILFL 5.600 31 KSQFLEEGI 3.600 10
KIILFLPCI 3.000 6 VILGKIILF 3.000 4 SIVILGKII 1.800 17 CISRKLKRI
1.000 46 VSPERVTVM 0.900 26 KKGWEKSQF 0.400 21 KLKRIKKGW 0.280 3
PSIVILGKI 0.231 24 RIKKGWEKS 0.220 35 LEEGIGGTI 0.210 34 FLEEGIGGT
0.180 11 IILFLPCIS 0.180 39 IGGTIPHVS 0.140 45 HVSPERVTV 0.120 38
GIGGTIPHV 0.100 43 IPHVSPERV 0.100 33 QFLEEGIGG 0.090 13 LFLPCISRK
0.090 42 TIPHVSPER 0.023 9 GKILLFLPC 0.022 1 VLPSIVILG 0.021 41
GTIPHVSPE 0.018 28 GWEKSQFLE 0.015 37 EGIGGTIPH 0.015 2 LPSIVILGK
0.014 8 LKGIILFLP 0.014 18 ISRKLKRIK 0.012 32 SQFLEEGIG 0.010 40
GGTIPHVSP 0.010 15 LPCISRKLK 0.010 12 ILFLPCISR 0.010 23 KRIKKGWEK
0.003 20 RKLKRIKKG 0.003 16 PCISRKLKR 0.002 44 PHVSPERVT 0.002 29
WEKSQFLEE 0.001 19 SRKLKRIKK 0.001 30 EKSQFLEEG 0.001 22 LKRIKKGWE
0.001 25 IKKGWEKSQ 0.001 36 EEGIGGTIP 0.001
V7A-HLA-A24-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 1 SPKSLSETF 2.400 9 FLPNGINGI 1.800 4
SLSETFLPN 0.144 6 SETFLPNGI 0.144 7 ETFLPNGIN 0.100 8 TFLPNGING
0.090 2 PKSLSETFL 0.040 3 KSLSETFLP 0.030 5 LSETFLPNG 0.015
V7B-HLA-A24-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 5 AYQQSTLGY 7.500 9 STLGYVALL 6.000 8
QSTLGYVAL 4.000 3 NMAYQQSTL 4.000 1 FLNMAYQQS 0.180 2 LNMAYQQST
0.180 6 YQQSTLGYV 0.150 7 QQSTLGYVA 0.120 4 MAYQQSTLG 0.010
V7C-HLA-A24-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 139 KSQAASGTL 12.000 29 RGGLSEIVL 8.000 181
KSKHCMFSL 8.000 130 LWEFLLRLL 7.200 24 GANILRGGL 7.200 127
VGPLWEFLL 6.000 126 GVGPLWEFL 5.760 152 TSWSLGEFL 4.800 160
LGSGTWMKL 4.400 148 SLAFTSWSL 4.000 42 QQDRKIPPL 4.000 15 SPAAAWKCL
4.000 141 QAASGTLSL 4.000 5 ILDLSVEVL 4.000 165 WMKLETIIL 4.000 113
ANSWRNPVL 4.000 158 EFLGSGTWM 3.750 125 NGVGPLWEF 3.300 143
ASGTLSLAF 2.400 151 FTSWSLGEF 2.200 179 EQKSKHCMF 2.000 164
TWMKLETII 1.800 31 GLSEIVLPI 1.680 66 TAEAQESGI 1.500 19 AWKCLGANI
1.200 27 ILRGGLSEI 1.100 163 GTWMKLETI 1.000 132 EFLLRLLKS 0.825
168 LETIILSKL 0.616 102 PPESPDRAL 0.600 50 LSTPPPPAM 0.600 129
PLWEFLLRL 0.480 20 WKCLGANIL 0.480 108 RALKAANSW 0.360 117
RNPVLPHTN 0.360 136 RLLKSQAAS 0.300 82 SQIPVVGVV 0.252 4 VILDLSVEV
0.238 123 HTNGVGPLW 0.210 83 QIPVVGVVT 0.210 104 ESPDRALKA 0.198 51
STPPPPAMW 0.180 145 GTLSLAFTS 0.180 154 WSLGEFLGS 0.180 68
EAQESGIRN 0.180 9 SVEVLASPA 0.180 59 WTEEAGATA 0.180 156 LGEFLGSGT
0.180 52 TPPPPAMWT 0.180 112 AANSWRNPV 0.180 101 DPPESPDRA 0.180 2
SIVILDLSV 0.180 169 ETIILSKLT 0.180 88 GVVTEDDEA 0.165 14 ASPAAAWKC
0.165 25 ANILRGGLS 0.150 72 SGIRNKSSS 0.150 11 EVLASPAAA 0.150 81
SSQIPVVGV 0.150 177 TQEQKSKHC 0.150 147 LSLAFTSWS 0.150 64
GATAEAQES 0.132 134 LLRLLKSQA 0.120 146 TLSLAFTSW 0.120 185
CMFSLISGS 0.120 182 SKHCMFSLI 0.120 58 MWTEEAGAT 0.120 92 EDDEAQDSI
0.120 39 IEWQQDRKI 0.110 162 SGTWMKLET 0.110 17 AAAWKCLGA 0.100 79
SSSSQIPVV 0.100 140 SQAASGTLS 0.100 76 NKSSSSSQI 0.100 142
AASGTLSLA 0.100 105 SPDRALKAA 0.100 57 AMWTEEAGA 0.100 144
SGTLSLAFT 0.100 18 AAWKCLGAN 0.100 7 DLSVEVLAS 0.100 78 SSSSSQIPV
0.100 12 VLASPAAAW 0.100 73 GIRNKSSSS 0.100 71 ESGIRNKSS 0.100 178
QEQKSKHCM 0.075 150 AFTWESLGE 0.050 46 KIPPLSTPP 0.043 167
KLETIILSK 0.042 122 PHTNGVGPL 0.040 21 KCLGANILR 0.030 116
WRNPVLPHT 0.025 35 IVLPIEWQQ 0.025 8 LSVEVLASP 0.025 77 KSSSSSQIP
0.024 119 PVLPHTNGV 0.022 37 LPIEWQQDR 0.022 1 PSIVILDLS 0.021 6
LDLSVEVLA 0.021 32 LSEIVLPIE 0.021 183 KHCMFSLIS 0.020
[1226]
27TABLE XVII Start Subsequence Score V1-HLA-A24-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 124
QYPESNAEYL 360.000 359 MYISFGIMSL 300.000 399 GYVALLISTF 180.000
282 LYYGTKYRRF 100.000 423 YYRFYTPPNF 100.000 290 RFPPWLETWL 86.400
425 RFYTPPNFVL 40.000 186 NFIPIDLGSL 36.000 145 GFNVVSAWAL 30.000
40 DFAKSLTIRL 24.000 257 KTLPIVAITL 20.160 362 SFGIMSLGLL 20.000
213 RGPVVVAISL 16.800 377 TSIPSVSNAL 12.096 131 EYLASLFPDS 10.800
250 IPIEIVNKTL 10.080 238 PYARNQQSDF 10.000 270 VYLAGLLAAA 8.000
437 VLPSIVILDL 84.00 312 FAMVHVAYSL 8.400 279 AYQLYYGTKY 8.250 165
VYICSNNIQA 7.500 176 QQVIELARQL 7.200 202 ENLPLRLFTL 7.200 99
TLSWDLRHLL 7.200 427 YTPPNFVLAL 7.200 303 KQLGLLSFFF 7.200 267
LSLVYLAGLL 7.200 426 FYTPPNFVLA 7.200 402 ALLISTFHVL 7.200 53
GYHVVIGSRN 7.000 247 FYKIPIEIVN 7.000 364 GIMSLGLLSL 6.000 127
ESNAEYLASL 6.000 61 RNPKFASEFF 6.000 298 WLQCRKQLGL 6.000 4
ISMMGSPKSL 6.000 273 AGLLAAAYQL 6.000 323 LPMRRSERYL 6.000 147
NVVSAWALQL 6.000 435 ALVLPSIVIL 6.000 440 SIVILDLLQL 6.000 258
TLPIVAITLL 6.000 438 LPSIVILDLL 5.600 422 EYYRFYTPPN 5.000 219
AISLATFFFL 4.800 417 RAFEEEYYRF 4.800 365 IMSLGLLSLL 4.800 197
SAREIENLPL 4.800 172 IQARQQVIEL 4.400 356 RIEMYISFGI 4.200 36
IGSGDFAKSL 4.000 98 YTSLWDLRHL 4.000 132 YLASLFPDSL 4.000 296
ETWLQCRKQL 4.000 266 LLSLVYLAGL 4.000 195 LSSAREIENL 4.000 314
MVHVAYSLCL 4.000 263 AITLLSLVYL 4.000 299 LQCRKQLGLL 4.000 92
AIHREHYTSL 4.000 361 ISFGIMSLGL 4.000 9 SPKSLSETCL 4.000 395
QSTLGYVALL 4.000 394 IQSTLGYVAL 4.000 241 RNQQSDFYKI 3.960 163
RQVYICSNNI 3.600 382 VSNALNWREF 3.300 56 VVIGSRNPKF 3.300 384
NALNWREFSF 3.000 410 VLIYGWKRAF 3.000 216 VVVAISLATF 3.000 178
VIELARQLNF 3.000 218 VAISLATFFF 3.000 200 EIENLPLRLF 3.000 81
DALTKTNIIF 3.000 128 SNAEYLASLF 2.880 137 FPDSLIVKGF 2.800 111
KILIDVSNNM 2.520 217 VVAISLATFF 2.400 16 TCLPNGINGI 2.160 327
RSERYLFLNM 2.160 13 LSETCLPNGI 2.160 396 STLGYVALLI 2.100 432
FVLALVLPSI 2.100 354 VWRIEMYISF 2.000 222 LATFFFLYSF 2.000 32
TVGVIGSGDF 2.000 385 ALNWREFSFI 1.800 170 NNIQARQQVI 1.800 348
SWNEEEVWRI 1.800 199 REIENLPLRL 1.728 403 LLISTFHVLI 1.500 330
RYLFLNMAYQ 1.500 434 LALVLPSIVI 1.500 211 LWRGPVVVAI 1.400 336
MAYQQVHANI 1.400 227 FLYSFVRDVI 1.400 103 DLRHLLVGKI 1.320
V2-HLA-A24-10mers-98P4B6 Each peptide is a portion of SEQ ID NO: 5;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus nine. 16 GFTPFSCLSL 24.000 32 RCPPPCPADF 7.200 2 GSPGLQALSL
6.000 30 DYRCPPPCPA 5.000 14 SSGFTPFSCL 4.800 11 LSLSSGFTPF 3.600
33 CPPPCPADFF 3.600 8 ALSLSLSSGF 2.500 4 PGLQALSLSL 0.720 34
PPPCPADFFL 0.600 36 PCPADFFLYF 0.360 9 LSLSLSSGFT 0.150 5
GLQALSLSLS 0.150 24 SLPSSWDYRC 0.150 1 SGSPGLQALS 0.144 6
LQALSLSLSS 0.120 20 FSCLSLPSSW 0.120 18 TPFSCLSLPS 0.120 15
SGFTPFSCLS 0.100 12 SLSSGFTPFS 0.100 28 SWDYRCPPPC 0.100 13
LSSGFTPFSC 0.100 3 SPGLQALSLS 0.100 22 CLSLPSSWDY 0.100 19
PFSCLSLPSS 0.050 23 LSLPSSWDYR 0.018 7 QALSLSLSSG 0.015 17
FTPFSCLSLP 0.015 21 SCLSLPSSWD 0.015 35 PPCPADFFLY 0.014 27
SSWDYRCPPP 0.012 25 LPSSWDYRCP 0.010 10 SLSLSSGFTP 0.010 31
YRCPPPCPAD 0.001 29 WDYRCPPCP 0.001 26 PSSWDYRCPP 0.001
V5A-HLA-A24-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 1 ENLPLRLFTF 3.600 10 FWRGPVVVAI 1.400 7
LFTFWRGPVV 0.500 9 TFWRGPVVVA 0.500 2 NLPLRLFTFW 0.216 6 RLFTFWRGPV
0.200 8 FTFWRGPVVV 0.100 3 LPLRLFTFWR 0.015 5 LRLFTFWRGP 0.002 4
PLRLFTFWRG 0.001 V5B-HLA-A24-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 11; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 24 EFVFLLTLLL 36.000 22
ELEFVFLLTL 6.000 20 ELELEFVFLL 6.000 12 CSFADTQTEL 4.400 14
FADTQTELEL 4.400 16 DTQTELELEF 3.960 18 QTELELEFVF 3.600 5
FSFIQIFCSF 3.360 1 NWREFSFIQI 1.440 19 TELELEFVFL 0.864 6
SFIQIFCSFA 0.750 4 EFSFIQIFCS 0.500 10 IFCSFADTQT 0.500 23
LEFVFLLTLL 0.480 2 WREFSFIQIF 0.360 8 IQIFCSFADT 0.180 17
TQTELELEFV 0.120 13 SFADTQTELE 0.060 21 LELEFVFLLT 0.030 3
REFSFIQIFC 0.028 7 FIQIFCSFAD 0.015 11 FCSFADTQTE 0.012 9
QIFCSFADTQ 0.010 15 ADTWTELELE 0.001 V6-HLA-A24-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 13; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 14
LFLPCISRKL 55.440 7 VILGKIILFL 8.400 5 SIVILGKIIL 6.000 6
IVILGKIILF 3.000 35 FLEEGIGGTI 2.520 3 LPSIVILGKI 1.540 27
KKGWEKSQFL 0.960 34 QFLEEGIGGT 0.900 46 HVSPERVTVM 0.600 11
KIILFLPCIS 0.360 26 IKKGWEKSQF 0.200 4 PSIVILGKII 0.180 38
EGIGGTIPHV 0.150 17 PCISRKLKRI 0.150 43 TIPHVSPERV 0.150 10
GKIILFLPCI 0.150 9 LGKIILFLPC 0.144 39 GIGGTIPHVS 0.140 31
EKSQFLEEGI 0.120 44 IPHVSPERVT 0.100 21 RKLKRIKKGW 0.042 24
KRIKKGWEKS 0.033 32 KSQFLEEGIS 0.030 42 GTIPHVSPER 0.028 1
LVLPSIVILG 0.025 28 KGWEKSQFLE 0.024 2 VLPSIVILGK 0.021 25
RIKKGWEKSQ 0.020 22 KLKRIKKGWE 0.020 29 GWEKSQFLEE 0.020 12
IILFLPCISR 0.015 15 FLPCISRKLK 0.015 8 ILGKIILFLP 0.014 18
CISRKLKRIK 0.012 16 LPCISRKLKR 0.011 19 ISRKLKRIKK 0.011 33
SQFLEEGIGG 0.010 41 GGTIPHVSPE 0.010 40 IGGTIPHVSP 0.010 13
ILFLPCISRK 0.010 36 LEEGIGGTIP 0.002 45 PHVSPERVTV 0.002 20
SRKLKRIKKG 0.001 30 WEKSQFLEEG 0.001 23 LKRIKKGWEK 0.001 37
EEGIGGTIPH 0.001 V7A-HLA-A24-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 9 TFLPNGINGI 10.800 2
SPKSLSETFL 4.000 1 GSPKSLSETF 3.600 6 LSETFLPNGI 2.160 4 KSLSETFLPN
0.360 10 FLPNGINGIK 0.021 5 SLSETFLPNG 0.012 7 SETFLPNGIN 0.010 8
ETFLPNGING 0.010 3 PKSLSETFLP 0.000 VtB-HLA-A24-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 6
AYQQSTLGYV 7.500 3 LNMAYQQSTL 6.000 8 QQSTLGYVAL 4.000 9 QSTLGYVALL
4.000 10 STLGYVALLI 2.100 1 LFLNMAYQQS 0.900 7 YQQSTLGYVA 0.180 2
FLNMAYQQST 0.180 5 MAYQQSTLGY 0.100 4 NMAYQQSTLG 0.010
V7C-HLA-A24-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 168 KLETIILSKL 18.480 151 AFTSWSLGEF 11.000 5
VILDLSVEVL 7.200 42 WQQDRKIPPL 7.200 126 NGVGPLWEFL 7.200 102
DPPESPDRAL 7.200 113 AANSWRNPVL 6.000 129 GPLWEFLLRL 6.000 148
LSLAFTSWSL 6.000 15 ASPAAAWKCL 6.000 165 TWMKLETIIL 6.000 24
LGANILRGGL 4.800 20 AWKCLGANIL 4.800 127 GVGPLWEFLL 4.800 152
FTSWSLGEFL 4.800 160 FLGSGTWMKL 4.400 122 LPHTNGVGPL 4.000 141
SQAASGTLSL 4.000 182 KSKHCMFSLI 2.400 143 AASGTLSLAF 2.400 125
TNGVGPLWEF 2.200 31 GGLSEIVLPI 2.100 76 RNKSSSSSQI 2.000 27
NILRGGLSEI 1.650 164 GTWMKLETII 1.200 19 AAWKCLGANI 1.200 66
ATAEAQESGI 1.200 163 SGTWMKLETI 1.000 178 TQEQKSKHCM 0.750 130
PLWEFLLRLL 0.576 29 LRGGLSEIVL 0.400 181 QKSKHCMFSL 0.400 139
LKSQAASGTL 0.400 179 QEQKSKHCMF 0.300 140 KSQAASGTLS 0.300 70
AQESGIRNKS 0.277 83 SQIPVVGVVT 0.252 112 KAANSWRNPV 0.240 91
VTEDDEAQDS 0.216 9 LSVEVLASPA 0.216 82 SSQIPVVGVV 0.210 78
KSSSSSQIPV 0.200 4 IVILDLSVEV 0.198 33 LSEIVLPIEW 0.198 119
NPVLPHTNGV 0.180 105 ESPDRALKAA 0.180 52 STPPPPAMWT 0.180 177
LTQEQKSKHC 0.180 134 FLLRLLKSQ 0.180 185 HCMFSLISGS 0.180 146
GTLSLAFTSW 0.180 39 PIEWQQDRKI 0.165 88 VGVVTEDDEA 0.165 10
SVEVLASPAA 0.150 73 SGIRNKSSSS 0.150 25 GANILRGGLS 0.150 157
LGEFLGSGTW 0.150 12 EVLASPAAAW 0.150 156 SLGEFLGSGT 0.144 1
LPSIVILDLS 0.140 6 ILDLSVEVLA 0.140 116 SWRNPVLPHT 0.140 43
QQDRKIPPLS 0.140 64 AGATAEAQES 0.132 14 LASPAAAWKC 0.132 174
LSKLTQEQKS 0.132 51 LSTPPPPAMW 0.120 92 TEDDEAQDSI 0.120 135
LLRLLKSQAA 0.120 106 SPDRALKAAN 0.120 59 MWTEEAGATA 0.120 28
ILRGGLSEIV 0.120 154 SWSLGEFLGS 0.120 145 STGLSLAFTS 0.120 162
GSGTWMKLET 0.110 97 AQDSIDPPES 0.110 147 TLSLAFTSWS 0.100 180
EQKSKHCMFS 0.100 79 SSSSSQIPVV 0.100 152 QAASGTLSLA 0.100 18
AAAWKCLGAN 0.100 138 LLKSQAASGT 0.100 110 ALKAANSWRN 0.100 144
ASGTLSLAFT 0.100 74 GIRNKSSSSS 0.100 81 SSSQIPVVGV 0.100 166
WMKLETIILS 0.100 72 ESGIRNKSSS 0.100 58 AMWTEEAGAT 0.100 133
EFLLRLLKSQ 0.090 159 EFLGSGTWMK 0.075 158 GEFLGSGTWM 0.050 50
PLSTPPPPAM 0.050 47 KIPPLSTPPP 0.036 22 KCLGANILRG 0.030 118
RNPVLPHTNG 0.030 109 RALKAANSWR 0.030 137 RLLKSQAASG 0.030 96
EAQDSIDPPE 0.025 172 IILSKLTQEQ 0.024
[1227]
28TABLE XVIII Start Subsequence Score V1-HLA-B7-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 173
QARQQVIEL 120.000 214 GPVVVAISL 80.000 259 LPIVAITLL 80.000 428
TPPNFVLAL 80.000 438 LPSIVILDL 80.000 291 FPPWLETWL 80.000 300
QCRKQLGLL 40.000 125 YPESNAEYL 24.000 177 QVIELARQL 20.000 148
VVSAWALQL 20.000 251 IVAITLLSL 20.000 75 DVTHHEDAL 20.000 441
IVILDLLQL 20.000 436 LVLPSIVIL 20.000 41 FAKSLTIRL 12.000 313
AMVHVAYSL 12.000 133 LASLFPDSL 12.000 5 SMMGSPKSL 12.000 27
DARKVTVGV 6.000 100 SLWDLRHLL 6.000 146 FNVVSAWAL 4.000 220
ISLATFFFL 4.000 187 FIPIDLGSL 4.000 128 SNAEYLASL 4.000 363
FGIMSLGLL 4.000 274 GLLAAAYQL 4.000 365 IMSLGLLSL 4.000 366
MSLGLLSLL 4.000 184 QLNFIPIDL 4.000 93 IHREHYTSL 4.000 324
PMRRSERYL 4.000 395 QSTLGYVAL 4.000 267 LSLVYLAGL 4.000 268
SLVYLAGLL 4.000 360 YISFGIMSL 4.000 196 SSAREIENL 4.000 378
SIPSVSNAL 4.000 258 TLPIVAITL 4.000 299 LQCRKQLGL 4.000 99
TSLWDLRHL 4.000 403 LLISTFHVL 4.000 37 GSGDFAKSL 4.000 203
NLPLRLFTL 4.000 264 ITLLSLVYL 4.000 396 STLGYVALL 4.000 287
KYRRFPPWL 4.000 157 GPKDASRQV 4.000 317 VAYSLCLPM 3.000 9 SPKSLSETC
2.000 250 IPIEIVNKT 2.000 353 EVWRIEMYI 2.000 49 LIRCGYHVV 2.000
164 QVYICSNNI 2.000 134 ASLFPDSLI 1.800 435 ALVLPSIVI 1.800 200
EIENLPLRL 1.200 81 DALTKTNII 1.200 323 LPMRRSERY 1.200 108
LVGKILIDV 1.000 358 EMYISFGIM 1.000 112 ILIDVSNNM 1.000 254
IVNKTLPIV 1.000 231 FVRDVIHPY 1.000 328 SERYLFLNM 1.000 306
GLLSFFFAM 1.000 278 AAYQLYYGT 0.800 402 ALLISTFHV 0.600 297
TWLQCRKQL 0.600 262 VAITLLSLV 0.600 239 YARNQQSDF 0.600 434
LALVLPSIV 0.600 65 FASEFFPHV 0.600 161 ASRQVYICS 0.600 426
FYTPPNFVL 0.600 374 LAVTSIPSV 0.600 314 MVHVAYSLC 0.500 34
GVIGSGDFA 0.500 216 VVVAISLAT 0.500 269 LVYLAGLLA 0.500 237
HPYARNQQS 0.400 371 LSLLAVTSI 0.400 85 KTNIIFVAI 0.400 390
EFSFIQSTL 0.400 439 PSIVILDLL 0.400 397 TLGYVALLI 0.400 430
PNFVLALVL 0.400 362 SFGIMSLGL 0.400 171 NIQARQQVI 0.400 180
ELARQLNFI 0.400 193 GSLSSAREI 0.400 386 LNWREFSFI 0.400 204
LPLRLFTLW 0.400 429 PPNFVLALV 0.400 188 IPIDLGSLS 0.400 279
IPSVSNALN 0.400 62 NPKFASEFF 0.400 326 RRSERYLFL 0.400 433
VLALVLPSI 0.400 253 EIVNKTLPI 0.400 106 HLLVGKILI 0.400
V2-HLA-B7-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 5;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus eight. 3 SPGLQALSL 80.000 35 PPCPADFFL 8.000 15 SGFTPFSCL
6.000 1 SGSPGLQAL 4.000 17 FTPFSCLSL 4.000 5 GLQALSLSL 4.000 25
LPSSWDYRC 2.000 37 CPADFFLYF 0.400 33 CPPPCPADF 0.400 18 TPFSCLSLP
0.200 10 SLSLSSGFT 0.100 14 SSGFTPFSC 0.100 7 QALSLSLSS 0.060 34
PPPCPADFF 0.060 8 ALSLSLSSG 0.030 23 LSLPSSWDY 0.020 12 SLSSGFTPF
0.020 21 SCLSLPSSW 0.020 6 LQALSLSLS 0.020 13 LSSGFTPFS 0.020 2
GSPGLQALS 0.020 9 LSLSLSSGF 0.020 20 FSCLSLPSS 0.020 32 RCPPPCPAD
0.015 22 CLSLPSSWD 0.015 31 YRCPPPCPA 0.015 30 DYRCPPPCP 0.015 27
SSWDYRCPP 0.015 29 WDYRCPPPC 0.010 24 SLPSSWDYR 0.010 11 LSLSSGFTP
0.010 36 PCPADFFLY 0.002 16 GFTPFSCLS 0.002 4 PGLQALSLS 0.002 26
PSSWDYRCP 0.001 28 SWDYRCPPP 0.000 19 PFSCLSLPS 0.000
V5A-HLA-B7-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 11;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus eight. 2 LPLRLFTFW 0.400 7 FTFWRGPVV 0.200 9 FWRGPVVVA 0.150 6
LFTFWRGPV 0.030 8 TFWRGPVVV 0.020 1 NLPLRLFTF 0.020 3 PLRLFTFWR
0.010 5 RLFTFWRGP 0.010 4 LRLFTFWRG 0.001 V5B-HLA-B7-9mers-98P4B6
Each peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus eight. 24
FVFLLTLLL 20.000 14 ADTQTELEL 1.200 19 ELELEFVFL 1.200 12 SFADTQTEL
0.400 23 EFVGLLTLL 0.400 22 LEFVFLLTL 0.400 20 LELEFVFLL 0.400 10
FCSFADTQT 0.100 8 QIFCSFADT 0.100 6 FIQIFCSFA 0.100 17 QTELELEFV
0.060 21 ELEFVFLLT 0.030 4 FSFIQIFCS 0.020 16 TQTELELEF 0.020 1
WREFSFIQI 0.012 11 CSFADTQTE 0.010 3 EFSFIQIFC 0.010 7 IQIFCSFAD
0.010 15 DTQTELELE 0.010 13 FADTQTELE 0.009 5 SFIQIFCSF 0.002 2
REFSFIQIF 0.002 18 TELELFVF 0.002 9 IFCSFADTQ 0.001
V6-HLA-B7-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus eight. 5 IVILGKIIL 20.000 14 FLPCISRKL 4.000 43 IPHVSPERV
4.000 7 ILGKIILFL 4.000 27 KGWEKSQFL 4.000 45 HVSPERVTV 1.500 46
VSPERVTVM 1.000 31 KSQFLEEGI 0.400 4 SIVILGKII 0.400 17 CISRKLKRI
0.400 10 KIILFLPCI 0.400 15 LPCISRKLK 0.300 38 GIGGTIPHV 0.200 2
LPSIVILGK 0.200 18 ISRKLKRIK 0.100 3 PSIVILGKI 0.040 34 FLEEGIGGT
0.030 11 IILFLPCIS 0.020 39 IGGTIPHVS 0.020 6 VILGKIILF 0.020 24
RIKKGWEKS 0.020 21 KLKRIKKGW 0.020 40 GGTIPHVSP 0.015 12 ILFLPCISR
0.015 35 LEEGIGGTI 0.012 37 EGIGGTIPH 0.010 22 LKRIKKGWE 0.010 8
LGKIILFLP 0.010 32 SQFLEEGIG 0.010 41 GTIPHVSPE 0.010 1 VLPSIVILG
0.010 9 GKIILFLPC 0.010 42 TIPHVSPER 0.010 26 KKGWEKSQF 0.002 19
SRKLKRIKK 0.002 44 PHVSPERVT 0.002 36 EEGIGGTIP 0.001 20 RKLKRIKKG
0.001 29 WEKSQFLEE 0.001 13 LFLPCISRK 0.001 25 IKKGWEKSQ 0.001 30
EKSQFLEEG 0.001 33 QFLEEGIGG 0.001 23 KRIKKGWEK 0.001 16 PCISRKLKR
0.001 28 GWEKSQFLE 0.000 V7A-HLA-B7-9mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus eight. 9 FLPNGINGI 0.400 1
SPKSLSETF 0.400 5 SETFLPNGI 0.040 2 PKSLSETFL 0.040 7 ETFLPNGIN
0.030 4 SLSETFLPN 0.020 3 KSLSETFLP 0.010 5 LSETFLPNG 0.003 8
TFLPNGING 0.001 V7B-HLA-B7-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus eight. 9 STLGYVALL 4.000 8 QSTLGYVAL 4.000
3 NMAYQQSTL 4.000 2 LNMAYQQST 3.000 6 YQQSTLGYV 0.200 7 QQSTLGYVA
0.100 4 MAYQQSTLG 0.030 1 FLNMAYQQS 0.020 5 AYQQSTLGY 0.006
V7C-HLA-B7-9mers-98P4B6 Each peptide is a portion of SEQ ID NO: 15;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus eight. 15 SPAAAWKCL 80.000 126 GVGPLWEFL 20.000 24 GANILRGGL
18.000 113 ANSWRNPVL 12.000 141 QAASGTLSL 12.000 127 VGPLWEFLL
4.000 148 SLAFTSWSL 4.000 181 KSKHCMFSL 4.000 29 RGGLSEIVL 4.000
139 KSQAASGTL 4.000 27 ILRGGLSEI 4.000 165 WMKLETIIL 4.000 152
TSWSLGEFL 4.000 160 LGSGTWMKL 4.000 102 PPESPDRAL 3.600 52
TPPPPAMWT 3.000 112 AANSWRNPV 2.700 101 DPPESPDRA 2.000 50
LSTPPPPAM 1.500 5 ILDLSVEVL 1.200 42 QQDRKIPPL 1.200 134 LLRLLKSQA
1.000 142 AASGTLSLA 0.900 17 AAAWKCLGA 0.900 105 SPDRALKAA 0.600 11
EVLASPAAA 0.500 88 GVVTEDDEA 0.500 31 GLSEIVLPI 0.400 20 WKCLGANIL
0.400 168 LETIILSKL 0.400 163 GTWMKLETI 0.400 129 PLWEFLLRL 0.400
66 TAEAQESGI 0.360 81 SSQIPVVGV 0.300 57 AMWTEEAGA 0.300 14
ASPAAAWKC 0.300 118 NPVLPHTNG 0.300 84 IPVVGVVTE 0.200 79 SSSSQIPVV
0.200 55 PPAMWTEEA 0.200 82 SQIPVVGVV 0.200 37 LPIEWQQDR 0.200 78
SSSSSQIPV 0.200 73 GIRNKSSSS 0.200 4 VILDLSVEV 0.200 2 SIVILDLSV
0.200 47 IPPLSTPPP 0.200 128 GPLWEFLLR 0.200 121 LPHTNGVGP 0.200 18
AAWKCLGAN 0.180 9 SVEVLASPA 0.150 164 TWMKLETII 0.120 19 AWKCLGANI
0.120 130 LWEFLLRLL 0.120 104 ESPDRALKA 0.100 158 EFLGSGTWM 0.100
162 SGTWMKLET 0.100 169 ETIILSKLT 0.100 83 QIPVVGVVT 0.100 178
QEQKSKHCM 0.100 144 SGTLSLAFT 0.100 119 PVLPHTNGV 0.100 143
ASGTLSLAF 0.060 64 GATAEAQES 0.060 68 EAQESGIRN 0.060 25 ANILRGGLS
0.060 108 RALKAANSW 0.060 35 IVLPIEWQQ 0.050 86 VVGVVTEDD 0.050 3
IVILDLSVE 0.050 89 VVTEDDEAQ 0.050 122 PHTNGVGPL 0.040 76 NKSSSSSQI
0.040 182 SKHCMFSLI 0.040 39 IEWQQDRKI 0.040 12 VLASPAAAW 0.030 62
EAGATAEAQ 0.030 125 NGVGPLWEF 0.030 13 LASPAAAWK 0.030 109
ALKAANSWR 0.030 63 AGATAEAQE 0.030 95 EAQDSIDPP 0.030 65 ATAEAQESG
0.030 149 LAFTSWSLG 0.030 111 KAANSWRNP 0.030 51 STPPPPAMW 0.030
184 HCMFSLISG 0.030 59 WTEEAGATA 0.030 156 LGEFLGSGT 0.030 177
TQEQKSKHC 0.030 140 SQAASGTLS 0.020 48 PPLSTPPPP 0.020 71 ESGIRNKSS
0.020 123 HTNGVGPLW 0.020 72 SGIRNKSSS 0.020 179 EQKSKHCMF 0.020
185 CMFSLISGS 0.020 54 PPPAMWTEE 0.020 147 LSLAFTSWS 0.020 28
LRGGLSEIV 0.020
[1228]
29TABLE XIX Start Subsequence Score V1-HLA-B7-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 323
LPMRRSERYL 240.000 197 SAREIENLPL 120.000 328 LPSIVILDLL 80.000 9
SPKSLSETCL 80.000 250 IPIEIVNKTL 80.000 312 RAMVH VAYSL 36.000 147
NVVSAWALQL 20.000 314 MVHV AYSLCL 20.000 364 GIMSLGLLSL 12.000 263
AITLLSLVYL 12.000 219 AISLATFFFL 12.000 402 ALLISTFHVL 12.000 435
ALVLPSIVIL 12.000 273 AGLLAAAYQL 12.000 4 ISMMGSPKSL 12.000 92
AIHREHYTSL 12.000 27 DARKVTVGVI 12.000 181 LARQLNFIPI 12.000 429
PPNFVLALVL 8.000 296 ETWLQCRKQL 6.000 99 TSLWDLRHLL 6.000 316 HVA
YSLCLPM 5.000 231 FVRDVIHPYA 5.000 195 LSSAREIENL 4.000 257
KTLPIVAITL 4.000 377 TSIPSVSNAL 4.000 266 LLSLVYLAGL 4.000 202
ENLPLRLFTL 4.000 132 YLASLFPDSL 4.000 299 LQCRKQLGLL 4.000 176
QQVIELARQL 4.000 427 YTPPNFVLAL 4.000 394 IQSTLGYVAL 4.000 213
RGPVVVAISL 4.000 365 IMSLGLLSLL 4.000 49 LIRCGYHVVI 4.000 428
TPPNFVLALV 4.000 103 DLRHLLVGKI 4.000 36 IGSGDFAKSL 4.000 98
YTSLWDLRHL 4.000 298 WLQCRKQLGL 4.000 325 MRRS ERYLFL 4.000 361
ISFGIMSLGL 4.000 258 TLPIVAITLL 4.000 172 IQARQQVIEL 4.000 127
ESNAEYLASL 4.000 440 SIVILDLLQL 4.000 183 RQLNFIPIDL 4.000 267
LSLVYLAGLL 4.000 437 VLPSIVILDL 4.000 395 QSTLGYVALL 4.000 173
QARQQVIELA 3.000 432 FVLALVLPSI 2.000 214 GPVVVAISLA 2.000 434
LALVLPSIVI 1.800 133 LASLFPDSLI 1.800 385 ALNWREFSFI 1.200 336
MAYQQVHANI 1.200 41 FAKSLTIRLI 1.200 111 KILIDVSNNM 1.000 261
IVAITLLSLV 1.000 305 LGLLSFFFAM 1.000 277 AA AYQLYYGT 0.900 161
ASRQVYICSN 0.600 239 YARNQQSDFY 0.600 255 VNKTLPIVAI 0.600 401
VALLISTFHV 0.600 125 YPESNAEYLA 0.600 157 GPKDASRQVY 0.600 227
FLYSFVRDVI 0.600 82 ALTKTNIIFV 0.600 425 RFYTPPNFVL 0.600 65
FASEFFPHVV 0.600 134 ASLFPDSLIV 0.600 223 ATFFFLYSFV 0.600 269
LVYLAGLLAA 0.500 142 IVKGFNVVSA 0.500 75 DVTHHEDALT 0.500 441
IVILDLLQLC 0.500 409 HVLIYGWKRA 0.500 254 IVNKTLPIVA 0.500 90
FVAIHREHYT 0.500 375 AVTSIPSVSN 0.450 199 REIENLPLRL 0.400 95
REHYTSLWDL 0.400 379 IPSVSNALNW 0.400 259 LPIVAITLLS 0.400 211
LWRGPVVVAI 0.400 163 RQVYICSNNI 0.400 145 GFNVVSAWAL 0.400 186
NFIPIDLGSL 0.400 188 IPIDLGSLSS 0.400 370 LLSLLAVTSI 0.400 359
MYISFGIMSL 0.400 16 TCLPNGINGI 0.400 124 CYP ESNAEYL 0.400 170
NNIQARQQVI 0.400 243 QQSDFYKIPI 0.400 241 RNQQSDFYKI 0.400 74
VDVTHHEDAL 0.400 V2-HLA-B7-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 34 PPPCPADFFL 8.000 14 SSGFTPFSCL
6.000 2 GSPGLQALSL 4.000 33 CPPPCPADFF 0.600 18 TPFSCLSLPS 0.400 16
GFTPFSCLSL 0.400 3 SPGLQALSLS 0.400 4 PGLQALSLSL 0.400 25
LPSSWDYRCP 0.200 30 DYRCPPPCPA 0.150 24 SLPSSWDYRC 0.100 13
LSSGFTPFSC 0.100 9 LSLSLSSGFT 0.100 8 ALSLSLSSGF 0.060 35
PPCPADFFLY 0.040 7 QALSLSLSSG 0.030 15 SGFTPFSCLS 0.020 22
CLSLPSSWDY 0.020 11 LSLSSGFTPF 0.020 6 LQALSLSLSS 0.020 32
RCPPPCPADF 0.020 1 SGSPGLQALS 0.020 20 FSCLSLPSSW 0.020 12
SLSSGFTPFS 0.020 5 GLQALSLSLS 0.020 21 SCLSLPSSWD 0.015 10
SLSLSSGFTP 0.010 17 FTPFSCLSLP 0.010 27 SSWDYRCPPP 0.010 23
LSLPSSWDYR 0.010 28 SWDYRCPPPC 0.003 36 PCPADFFLYF 0.002 26
PSSWDYRCPP 0.002 31 YRCPPPCPAD 0.002 29 WDYRCPPPCP 0.002 19
PFSCLSLPSS 0.000 8 FTFWRGPVVV 0.200 3 LPLRLFTFWR 0.200 2 NLPLRLFTFW
0.020 7 LFTFWRGPVV 0.020 1 ENLPLRLFTF 0.020 9 TFWRGPVVVA 0.015 4
PLRLFTFWRG 0.010 5 LRLFTFWRGP 0.001 V5B-HLA-B7-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 12
CSFADTQTEL 4.000 14 FADTQTELEL 3.600 20 ELELEFVFLL 1.200 22
ELEFVFLLTL 1.200 23 LEFVFLLTLL 0.400 1 NWREFSFIQI 0.400 19
TELELEFVFL 0.400 24 EFVFLLTLLL 0.400 17 TQTELELEFV 0.200 8
IQIFCSFADT 0.100 5 FSFIQIFCSF 0.020 16 DTQTELELEF 0.020 10
IFCSFADTQT 0.010 21 LELEFVFLLT 0.010 6 SFIQIFCSFA 0.010 3
REFSFIQIFC 0.010 9 QIFCSFADTQ 0.010 7 FIQIFCSFAD 0.010 11
FCSFADTQTE 0.010 18 QTELELEFVF 0.006 15 ADTQTELELE 0.003 4
EFSFIQIFCS 0.002 13 SFADTQTELE 0.001 2 WREFSFIQIF 0.001
V6-HLA-B7-10mers-98P4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptide is 10 amino
acids, and the end position for each peptide is the start position
plus nine. 3 LPSIVILGKI 8.000 46 HVSPERVTVM 4.000 5 SIVILGKIIL
4.000 7 VILGKIILFL 4.000 44 IPHVSPERVT 3.000 14 LFLPCISRKL 0.400 27
KKGWEKSQFL 0.400 16 LPCISRKLKR 0.200 43 TIPHVSPERV 0.200 38
EGIGGTIPHV 0.200 19 ISRKLKRIKK 0.140 35 FLEEGIGGTI 0.120 9
LGKIILFLPC 0.100 6 IVILGKIILF 0.100 1 LVLPSIVILG 0.050 10
GKIILFLPCI 0.040 4 PSIVILGKII 0.040 31 EKSQFLEEGI 0.040 17
PCISRKLKRI 0.040 11 KIILFLPCIS 0.020 39 GIGGTIPHVS 0.020 15
FLPCISRKLK 0.015 40 IGGTIPHVSP 0.015 12 ILLFLPCISR 0.015 34
QFLEEGIGGT 0.010 2 VLPSIVILGK 0.010 33 SQFLEEGIGG 0.010 25
RIKKGWEKSQ 0.010 32 KSQFLEEGIG 0.010 13 ILFLPCISRK 0.010 22
KLKRIKKGWE 0.010 8 ILGKIILFLP 0.010 41 GGTIPHVSPE 0.010 18
CISRKLKRIK 0.010 28 KGWEKSQFLE 0.10 42 GTIPHVSPER 0.010 23
LKRIKKGWEK 0.010 45 PHVSPERVTV 0.003 24 KRIKKGWEKS 0.002 26
IKKGWEKSQF 0.002 21 RKLKRIKKGW 0.002 20 SRKLKRIKKG 0.001 37
EEGIGGTIPH 0.001 30 WEKSQFLEEG 0.001 29 GWEKSQFLEE 0.000 36
LEEGIGGTIP 0.000 V7A-HLA-B7-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 3; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 2 SPKSLSETFL 80.000 6 LSETFLPNGI
0.120 9 TFLPNGINGI 0.040 1 GSPKSLSETF 0.020 4 KSLSETFLPN 0.020 10
FLPNGINGIK 0.010 5 SLSETFLPNG 0.010 8 ETFLPNGING 0.010 7 SETFLPNGIN
0.003 3 PKSLSETFLP 0.000 V7B-HLA-B7-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 3 LNMAYQQSTL 12.000 8
QQSTLGYVAL 4.000 9 QSTLGYVALL 4.000 10 STLGYVALLI 0.400 7
YQQSTLGYVA 0.100 2 FLNMAYQQST 0.100 6 AYQQSTLGYV 0.060 5 MAYQQSTLGY
0.060 4 NMAYQQSTLG 0.010 1 LFLNMAYQQS 0.002
V7C-HLA-B7-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 102 DPPESPDRAL 120.000 122 LPHTNGVGPL 80.000
129 GPLWEFLLRL 80.000 113 AANSWRNPVL 36.000 127 GVGPLWEFLL 20.000
15 ASPAAAWKCL 12.000 24 LGANILRGGL 5.000 152 FTSWSLGEFL 4.000 42
WQQDRKIPPL 4.000 160 FLGSGTWMKL 4.000 5 VILDLSVEVL 4.000 126
NGVGPLWEFL 4.000 141 SQAASGTLSL 4.000 119 NPVLPHTNGV 4.000 148
LSLAFTSWSL 4.000 19 AAWKCLGANI 3.600 28 ILRGGLSEIV 2.000 168
KLETIILSKL 1.200 20 AWKCLGANIL 1.200 165 TWMKLETIIL 1.200 66
ATAEAQESGI 1.200 4 IVILDLSVEV 1.000 135 LLRLLKSQAA 1.000 112
KAANSWRNPV 0.900 164 GTWMKLETII 0.400 139 LKSQAASGTL 0.400 181
QKSKHCMFSL 0.400 76 RNKSSSSSQI 0.400 29 LRGGLSEIVL 0.400 1
LPSIVILDLS 0.400 130 PLWEFLLRLL 0.400 27 NILRGGLSEI 0.400 31
GGLSEIVLPI 0.400 163 SGTWMKLETI 0.400 182 KSKHCMFSLI 0.400 144
ASGTLSLAFT 0.300 49 PPLSTPPPPA 0.300 81 SSSQIPVVGV 0.300 142
QAASGTLSLA 0.300 14 LASPAAAWKC 0.300 58 AMWTEEAGAT 0.300 178
TQEQKSKHCM 0.300 16 SPAAAWKCLG 0.200 85 IPVVGVVTED 0.200 82
SSQIPVVGVV 0.200 48 IPPLSTPPPP 0.200 55 PPPAMWTEEA 0.200 78
KSSSSSQIPV 0.200 79 SSSSSQIPVV 0.200 74 GIRNKSSSSS 0.200 53
TPPPPAMWTE 0.200 38 LPIEWQQDRK 0.200 18 AAAWKCLGAN 0.180 143
AASGTLSLAF 0.180 50 PLSTPPPPAM 0.150 10 SVEVLASPAA 0.150 52
STPPPPAMWT 0.150 44 QDRKIPPLST 0.150 12 EVLASPAAAW 0.150 106
SPDRALKAAN 0.120 158 GEFLGSGTWN 0.100 156 SLGEFLGSGT 0.100 162
GSGTWMKLET 0.100 88 VGVVTEDDEA 0.100 134 FLLRLLKSQA 0.100 138
LLKSQAASGT 0.100 177 LTQEQKSKHC 0.100 83 AQIPVVGVVT 0.100 105
ESPDRALKAA 0.100 116 SWRNPVLPHT 0.100 9 LSVEVLASPA 0.100 57
PAMWTEEAGA 0.090 185 HCMFSLISGS 0.060 110 ALKAANSWRN 0.060 25
GANILRGGLS 0.060 64 AGATAEAQES 0.060 36 IVLPIEWQQD 0.050 87
VVGVVTEDDE 0.050 90 VVTEDDEAQD 0.050 89 BVVTEDDEAQ 0.050 90
VVTEDDEAQD 0.050 89 GVVTEDDEAQ 0.050 150 LAFTSWSLGE 0.030 125
TNGVGPLWEF 0.030 109 RALKAANSWR 0.030 96 EAQDSIDPPE 0.030 63
EAGATAEAQE 0.030 26 ANILRGGLSE 0.030 51 LSTPPPPAMW 0.030 69
EAQESGIRNK 0.030 17 PAAAWKCLGA 0.030 65 GATAEAQESG 0.030 114
ANSWRNPVLP 0.030 6 ILDLSVEVLA 0.030 70 AQESGIRNKS 0.027 147
TLSLAAFTSWS 0.020 146 GTLSLAFTSW 0.020 140 KSQAASGTLS 0.020 180
EQKSKHCMFS 0.020 56 PPAMWTEEAG 0.020 145 SGTLSLAFTS 0.020 72
ESBIFNKSSS 0.020
[1229]
30TABLE XX Start Subsequence Score V1-HLA-B3501-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 62
NPKFASEFF 60.000 323 LPMRRSERY 40.000 157 GPKDASRQV 24.000 259
LPIVAITLL 20.000 428 TPPNFVLAL 20.000 291 FPPWLETWL 20.000 438
LPSIVILDL 20.000 214 GPVVAISL 20.000 231 FVRDVIHPY 12.000 37
GSGDFAKSL 10.000 405 ISTFHVLIY 10.000 204 LPLRLFTLW 10.000 239
YARNQQSDF 9,000 41 FAKSLTIRL 9.000 173 QARQQVIEL 9.000 99 TSLWDLRHL
7.500 196 SSAREIENL 7.500 9 SPKSLSETC 6.000 317 VAYSLCLPM 6.000 276
LAAAYQLYY 6.000 272 LAGLLAAAY 6.000 125 YPESNAEYL 6.000 46
TIRLIRCGY 6.000 267 LSLVYLAGL 5.000 395 QSTLGYVAL 5.000 366
MSLGLLSLL 5.000 220 ISLATFFFL 5.000 250 IPIEIVNKT 4.000 112
ILIDVSNNM 4.000 188 IPIDLGSLS 4.000 347 NSWNEEEVW 3.750 133
LASLFPDSL 3.000 300 QCRKQLGLL 3.000 218 VAISLATFF 3.000 177
QVIELARQL 2.000 303 KQLGLLSFF 2.000 371 LSLLAVTSI 2.000 128
SNAEYLASL 2.000 275 LLAAAYQLY 2.000 61 RNPKFASEF 2.000 100
SLWDLRHLL 2.000 237 HPYARNQQS 2.000 379 IPSVSNALN 2.000 117
SNNMRINQY 2.000 306 GLLSFFFAM 2.000 134 ASLFPDSLI 2.000 221
SLATFFFLY 2.000 193 GSLSSAREI 2.000 263 AITLLSLVY 2.000 90
FVAIHREHY 2.000 280 YQLYYGTKY 2.000 358 EMYISFGIM 2.000 27
DARKVTVGV 1.800 441 IVILDLLQL 1.500 161 ASRQVYICS 1.500 59
GSRNPKFAS 1.500 187 FIPIDLGSL 1.500 81 DALTKTNII 1.200 65 FASEFFPHV
1.200 365 IMSLGLLSL 1.000 184 QLNFIPIDL 1.000 385 ALNWREFSF 1.000
148 VVSAWALQL 1.000 274 GLLAAAYQL 1.000 144 KGFNVVSAW 1.000 146
FNVVSAWAL 1.000 383 SNALNWREF 1.000 304 QLGLLSFFF 1.000 363
FGIMSLGLL 1.000 217 VVAISLATF 1.000 57 VIGSRNPKF 1.000 313
AMVHVAYSL 1.000 411 LIYGWKRAF 1.000 378 SIPSVSNAL 1.000 264
ITLLSLVYL 1.000 75 DVTHHEDAL 1.000 436 LVLPSIVIL 1.000 82 ALTKTNIIF
1.000 403 LLISTFHVL 1.000 299 LQCRKQLGL 1.000 400 YVALLISTF 1.000
258 TLPIVAITL 1.000 268 SLVYLAGLL 1.000 5 SMMGSPKSL 1.000 223
ATFFFLYSF 1.000 33 VGVIGSGDF 1.000 396 STLGYVALL 1.000 261
IVAITLLSL 1.000 360 YISFGIMSL 1.000 219 AISLATFFF 1.000 203
NLPLRLFTL 1.000 129 NAEYLASLF 0.900 85 KTNIIFVAI 0.800 127
ESNAEYLAS 0.750 386 LNWREFSFI 0.600 434 LALVLPSIV 0.600 416
KRAFEEEYY 0.600 328 SERYLFLNM 0.600 287 KYRRFPPWL 0.600 24
GIKDARKVT 0.600 V2-HLA-B3501-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 37 CPADFFLYF 40.000 33 CPPPCPADF
20.000 3 SPGLQALSL 20.000 23 LSLPSSWDY 10.000 9 LSLSLSSGF 5.000 35
PPCPADFFL 2.000 34 PPPCPADFF 2.000 25 LPSSWDYRC 2.000 15 SGFTPFSCL
1.000 1 SGSPGLQAL 1.000 12 SLSSGFTPF 1.000 5 GLQALSLSL 1.000 17
FTPFSCLSL 1.000 20 FSCLSLPSS 0.500 2 GSPGLQALS 0.500 13 LSSGFTPFS
0.500 14 SSGFTPFSC 0.500 21 SCLSLPSSW 0.500 7 QALSLSLSS 0.300 35
PCPADFFLY 0.300 18 TPFSCLSLP 0.200 6 LQALSLSLS 0.100 10 SLSLSSGFT
0.100 27 SSWDYRCPP 0.100 11 LSLSSGFTP 0.050 32 RCPPPCPAD 0.020 8
ALSLSLSSG 0.010 22 CLSLPSSWD 0.010 29 WDYRCPPPC 0.010 24 SLPSSWDYR
0.010 31 YRCPPPCPA 0.010 4 PGLQALSLS 0.010 16 GFTPFSCLS 0.010 26
PSSWDYRCP 0.008 30 DYRCPPPCP 0.003 19 PFSCLSLPS 0.001 28 SWDYRCPPP
0.000 V5A-HLA-B3501-9mers-98P4B6 Each peptide is a portion of SEQ
ID NO: 11; each start position is specified, the length of peptide
is 9 amino acids, and the end position for each peptide is the
start position plus eight. 2 LRLRLFTFW 10.000 1 NLPLRLFTF 1.000 7
FTFWRGPVV 0.200 9 FWRGPVVVA 0.030 6 LFTFWRGPV 0.020 5 RLFTFWRGP
0.020 8 TFWRGPVVV 0.020 3 PLRLFTFWR 0.003 4 LRLFTFWRG 0.001
V5B-HLA-B3501-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 16 TQTELELEF 2.000 24 FVFLLTLLL 1.000 4
FSFIQIFCS 0.500 19 ELELEFVFL 0.450 12 SFADTQTEL 0.200 18 TELELEFVF
0.200 20 LELEFVFLL 0.200 2 REFSFIQIF 0.200 22 LEFVFLLTL 0.100 10
FCSFADTQT 0.100 8 QIFCSFADT 0.100 23 EFVFLLTLL 0.100 6 FIQIFCSFA
0.100 14 ADTQTELEL 0.100 5 SFIQIFCSF 0.100 17 QTELELEFV 0.090 11
CSFADTQTE 0.075 21 ELEFVFLLT 0.030 15 DTQTELELE 0.015 1 WREFSFIQI
0.012 7 IQIFCSFAD 0.010 3 EFSFIQIFC 0.010 13 FADTQTELE 0.009 9
IFCSFADTQ 0.001 V6-HLA-B3501-9mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 13; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. 46 VSPERVTVM 20.000 27 KGWEKSQFL
4.000 43 IPHVSPERV 4.000 31 KSQFLEEGI 4.000 21 KLKRIKKGW 3.000 14
FLPCISRKL 1.000 6 VILGKIILF 1.000 5 IVILGKIIL 1.000 7 ILGKIILFL
1.000 10 KIILFLPCI 0.800 24 RIKKGWEKS 0.600 17 CISRKLKRI 0.400 4
SIVILGKII 0.400 45 HVSPERVTV 0.300 26 KKGWEKSQF 0.300 2 LPSIVILGK
0.200 15 LPCISRKLK 0.200 38 GIGGTIPHV 0.200 3 PSIVILGKI 0.200 18
ISRKLKRIK 0.150 39 IGGTIPHVS 0.100 11 IILFLPCIS 0.100 34 FLEEGIGGT
0.060 8 LGKIILFLP 0.030 32 SQFLEEGIG 0.015 35 LEEGIGGTI 0.012 37
EGIGGTIPH 0.010 41 GTIPHVSPE 0.010 40 GGTIPHVSP 0.010 1 VLPSIVILIG
0.010 9 GKIILFLPC 0.010 12 ILFLPCISR 0.010 42 TIPHVSPER 0.010 33
QFLEEGIGG 0.003 29 WEKSQFLEE 0.003 25 IKKGWEKSQ 0.003 22 LKRIKKGWE
0.003 19 SRKLKRIKK 0.003 20 RKLKRIKKG 0.002 23 KRIKKGWEK 0.002 44
PHVSPERVT 0.001 13 LFLPCISRK 0.001 30 EKSQFLEEG 0.001 16 PCISRKLKR
0.001 36 EEGIGGTIP 0.001 28 GWEKSQFLE 0.000
V7A-HLA-B3501-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 1 SPKSLSETF 60.000 9 FLPNGINGI 0.400 4
SLSETFLPN 0.200 3 KSLSETFLP 0.150 7 ETFLPNGIN 0.100 6 SETFLPNGI
0.040 5 LSETFLPNG 0.015 2 PKSLSETFL 0.010 8 TFLPNGING 0.001
V7B-HLA-B3501-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 8 QSTLGYVAL 5.000 9 STLGYVALL 1.000 3
NMAYQQSTL 1.000 6 YQQSTLGYV 0.200 5 AYQQSTLGY 0.200 7 QQSTLGYVA
0.100 1 FLNMAYQQS 0.100 2 LNMAYQQST 0.100 4 MAYQQSTLG 0.030
V7C-HLA-B3501-9mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. 181 KSKHCMFSL 30.000 15 SPAAAWKCL 20.000 139
KSQAASGTL 10.000 50 LSTPPPPAM 10.000 152 TSWSLGEFL 5.000 143
ASGTLSLAF 5.000 165 WMKLETIIL 4.500 101 DPPESPDRA 4.000 179
EQKSKHCMF 3.000 24 GANILRGGL 3.000 141 QAASGTLSL 3.000 108
RALKAANSW 3.000 29 RGGLSEIVL 2.000 52 TPPPPAMWT 2.000 27 ILRGGLSEI
1.200 78 SSSSSQIPV 1.000 126 GVGPLWEFL 1.000 113 ANSWRNPVL 1.000
104 ESPDRALKA 1.000 160 LGSGTWMKL 1.000 127 VGPLWEFLL 1.000 79
SSSSQIPVV 1.000 148 SLAFTSWSL 1.000 151 FTSWSLGEF 1.000 125
NGVGPLWEF 1.000 81 SSQIPVVGV 1.000 31 GLSEIVLPI 0.800 154 WSLGEFLGS
0.750 102 PPESPDRAL 0.600 112 AANSWRNPV 0.600 105 SPDRALKAA 0.600
68 EAQESGIRN 0.600 51 STPPPPAMW 0.500 147 LSLAFTSWS 0.500 146
TLSLAFTSW 0.500 12 VLAPSPAAAW 0.500 71 ESGIRNKSS 0.500 123
HTNGVGPLW 0.500 14 ASPAAAWKC 0.500 64 GATAEAQES 0.450 163 GTWMKLETI
0.400 37 LPIEWQQDR 0.400 4 VILDLSVEV 0.400 66 TAEAQESGI 0.360 134
LLRLLKSQA 0.300 42 QQDRKIPPL 0.300 73 GIRNKSSSS 0.300 17 AAAWKCLGA
0.300 142 AASGTLSLA 0.300 128 GPLWEFLLR 0.300 18 AAWKCLGAN 0.300 5
ILDLSVEVL 0.300 136 RLLKSQAAS 0.200 82 SQIPVVGVV 0.200 47 IPPLSTPPP
0.200 55 PPAMWTEEA 0.200 121 LPHTNGVGP 0.200 129 PLWEFLLRL 0.200
178 QEQKSKHCM 0.200 117 RNPVLPHTN 0.200 2 SIVILDLSV 0.200 158
EFLGSGTWM 0.200 84 IPVVGVVTE 0.200 118 NPVLPHTNG 0.200 57 AMWTEEAGA
0.150 173 LSKLTQEQK 0.150 7 DLSVEVLAS 0.150 88 GVVTEDDEA 0.150 19
AWKCLGANI 0.120 98 DSIDPPESP 0.100 145 GTLSLAFTS 0.100 83 QIPVVGVVT
0.100 8 LSVEVLASP 0.100 168 LETIILSKL 0.100 169 ETIILSKLT 0.100 162
SGTWMKLET 0.100 11 EVLASPAAA 0.100 25 ANILRGGLS 0.100 72 SGIRNKSSS
0.100 144 SGTLSLAFT 0.100 140 SQAASGTLS 0.100 77 KSSSSSQIP 0.100
185 CMFSLISGS 0.100 20 WKCLGANIL 0.100 95 EAQDSIDPP 0.060 111
KAANSWRNP 0.060 75 RNKSSSSSQ 0.060 59 WTEEAGATA 0.060 1 PSIVILDLS
0.050 80 SSSQIPVVG 0.050 157 GEFLGSGTW 0.050 33 SEIVLPIEW 0.050 161
GSGTWMKLE 0.050 114 NSWRNPVLP 0.050 76 NKSSSSSQI 0.040 164
TWMKLETII 0.040 182 SKHCMFSLI 0.040 39 IEWQQDRKI 0.040 58 MWTEEAGAT
0.030 89 VVTEDDEAQ 0.030
[1230]
31TABLE XXI Start Subsequence Score V1-HLA-B3501-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 157
GPKDASRQVY 240.000 9 SPKSLSETCL 60.000 250 IPIEIVNKTL 40.000 197
SAREIENLPL 27.000 323 LPMRRSERYL 20.000 438 LPSIVILDLL 20.000 239
YARNQQSDFY 18.000 417 RAFEEEYYRF 18.000 379 IPSVSNALNW 10.000 116
VSNNMRINQY 10.000 391 FSFIQSTLGY 10.000 220 ISLATFFFLY 10.000 195
LSSAREIENL 7.500 137 FPDSLIVKGF 6.000 327 RSERYLFLNM 6.000 262
VAITLLSLVY 6.000 361 ISFGIMSLGL 5.000 395 QSTLGYVALL 5.000 267
LSLVYLAGLL 5.000 99 TSLWDLRHLL 5.000 127 ESNAEYLASL 5.000 4
ISMMGSPKSL 5.000 382 VSNALNWREF 5.000 377 TSIPSVSNAL 5.000 428
TPPNFVLALV 4.000 188 IPIDLGSLSS 4.000 111 KILIDVSNNM 4.000 181
LARQLNFIPI 3.600 27 DARKVTVGVI 3.600 41 FAKSLTIRLI 3.600 384
NALNWREFSF 3.000 312 FAMVHVAYSL 3.000 222 LATFFFLYSF 3.000 81
DALTKTNIIF 3.000 218 VAISLATFFF 3.000 322 CLPMRRSERY 2.000 429
PPNFVLALVL 2.000 316 HVAYSLCLPM 2.000 61 RNPKFASEFF 2.000 257
KTLPIVAITL 2.000 259 LPIVAITLLS 2.000 45 LTIRLIRCGY 2.000 275
LLAAAYQLYY 2.000 274 GLLAAAYQLY 2.000 303 KQLGLLSFFF 2.000 128
SNAEYLASLF 2.000 123 NQYPESNAEY 2.000 305 LGLLSFFFAM 2.000 404
LISTFHVLIY 2.000 213 RGPVVVAISL 2.000 271 YLAGLLAAAY 2.000 183
RQLNFIPIDL 2.000 214 GPVVVAISLA 2.000 134 ASLFPDSLIV 1.500 440
SIVILDLLQL 1.500 98 YTSLWDLRHL 1.500 161 ASRQVYICSN 1.500 285
GTKYRRFPPW 1.500 103 DLRHLLVGKI 1.200 336 MAYQQVHANI 1.200 255
VNKTLPIVAI 1.200 65 FASEFFPHVV 1.200 49 LIRCGYHVVI 1.200 434
LALVLPSIVI 1.200 133 LASLFPDSLI 1.200 24 GIKDARKVTV 1.200 241
RNQQSDFYKI 1.200 32 TVGVIGSGDF 1.000 435 ALVLPSIVIL 1.000 273
AGLLAAAYQL 1.000 36 IGSGDFAKSL 1.000 308 LSFFFAMVHV 1.000 56
VVIGSRNPKF 1.000 176 QQVIELARQL 1.000 296 ETWLQCRKQL 1.000 43
KSLTIRLIRC 1.000 202 ENLPLRLFTL 1.000 147 NVVSAWALQL 1.000 217
VVAISLATFF 1.000 216 VVVAISLATF 1.000 132 YLASLFPDSL 1.000 364
GIMSLGLLSL 1.000 365 IMSLGLLSLL 1.000 92 AIHRHYTSL 1.000 314
MVHVAYSLCL 1.000 410 VLIYGWKRAF 1.000 299 LQCRKQLGLL 1.000 394
IQSTLGYVAL 1.000 11 KSLSETCLPN 1.000 263 AITLLSLVYL 1.000 172
IQARQQVIEL 1.000 219 AISLATFFFL 1.000 298 WLQCRKQLGL 1.000 37
GSGDFAKSLT 1.000 402 ALLISTFHVL 1.000 258 TLPIVAITLL 1.000 427
YTPPNFVLAL 1.000 139 DSLIVKGFNV 1.000 437 VLPSIVILDL 1.000 266
LLSLVYLAGL 1.000 V2-HLA-B3501-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 33 CPPPCPADFF 20.000 35
PPCPADFFLY 6.000 14 SSGFTPFSCL 5.000 11 LSLSSGFTPF 5.000 2
GSPGLQALSL 5.000 20 FSCLSLPSSW 2.500 34 PPPCPADFFL 2.000 3
SPGLQALSLS 2.000 22 CLSLPSSWDY 2.000 32 RCPPPCPADF 2.000 18
TPFSCLSLPS 2.000 8 ALSLSLSSGF 1.000 9 LSLSLSSGFT 0.500 13
LSSGFTPFSC 0.500 25 LPSSWDYRCP 0.300 4 PGLQALSLSL 0.100 15
SGFTPFSCLS 0.100 27 SSWDYRCPPP 0.100 16 GFTPFSCLSL 0.100 6
LQALSLSLSS 0.100 1 SGSPGLQALS 0.100 24 SLPSSWDYRC 0.100 36
PCPADFFLYF 0.100 5 GLQALSLSLS 0.100 12 SLSSGFTPFS 0.100 23
LSLPSSWDYR 0.050 7 QALSLSLSSG 0.030 30 DYRCPPPCPA 0.030 17
FTPFSCLSLP 0.010 10 SLSLSSGFTP 0.010 21 SCLSLPSSWD 0.010 26
PSSWDYRCPP 0.005 28 SWDYRCPPPC 0.003 29 WSYRCPPPCP 0.001 19
PFSCLSLPSS 0.001 31 YRCPPPCPAD 0.001 V5A-HLA-B3501-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 1
ENLPLRLFTF 1.000 2 NLPLRLFTFW 0.500 6 RLFTFWRGPV 0.500 8 FTFWRGPVVV
0.200 3 LPLRLFTFWR 0.200 10 FWRGPVVVAI 0.120 7 LFTFWRGPVV 0.020 9
TFWRGPVVVA 0.010 4 PLRLFTFWRG 0.003 5 LRLFTFWRGP 0.001
V5B-HLA-B3501-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 12 CSFADTQTEL 5.000 5 FSFIQIFCSF 5.000 16
DTQTELELEF 1.000 14 FADTQTELEL 0.900 17 TQTELELEFV 0.600 22
ELEFVFLLTL 0.300 18 QTELELEFVF 0.300 20 ELELEFVFLL 0.300 19
TELELEFVFL 0.300 1 NWREFSFIQI 0.240 8 IQIFCSFADT 0.100 23
LEFVFLLTLL 0.100 24 EFVFLLTLLL 0.100 2 WREFSFIQIF 0.030 3
REFSFIQIFC 0.020 21 LELEFVFLLT 0.020 11 FCSFADTQTE 0.015 10
IFCSFADTQT 0.010 7 FIQIFCSFAD 0.010 4 EFSFIQIFCS 0.010 9 QIFCSFADTQ
0.010 6 SFIQIFCSFA 0.010 13 SFADTQTELE 0.002 15 ADTQTELELE 0.002
V6-HLA-B3501-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
13; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 3 LPSIVILGKI 8.000 44 IPHVSPERVT 2.000 46
HVSPERVTVM 2.000 6 IVILGKIILF 1.000 7 VILGKIILFL 1.000 5 SIVILGKIIL
1.000 26 IKKGWEKSQF 0.450 9 LGKIILFLPC 0.300 35 FLEEGIGGTI 0.240 43
TIPHVSPERV 0.200 11 KIILFLPCIS 0.200 27 KKGWEKSQFL 0.200 38
EGIGGTIPHV 0.200 16 LPCISRKLKR 0.200 4 PSIVILGKII 0.200 32
KSQFLEEGIG 0.150 19 ISRKLKRIKK 0.150 39 GIGGTIPHVS 0.100 14
LFLPCISRKL 0.100 21 RKLKRIKKGW 0.100 25 RIKKGWEKSQ 0.060 22
KLKRIKKGWE 0.060 10 GKIILFLPCI 0.040 28 KGWEKSQFLE 0.040 17
PCISRKLKRI 0.040 31 EKSQFLEEGI 0.040 24 KRIKKGWEKS 0.020 34
QFLEEGIGGT 0.020 33 SQFLEEGIGG 0.015 13 ILFLPCISRK 0.010 18
CISRKLKRIK 0.010 8 ILGKIILFLP 0.010 2 VLPSIVILGK 0.010 40
IGGTIPHVSP 0.010 15 FLPCISRKLK 0.010 41 GGTIPHVSPE 0.010 1
LVLPSIVILG 0.010 42 GTIPHVSPER 0.010 12 IILFLPCISR 0.010 45
PHVSPERVTV 0.003 20 SRKLKRIKKG 0.003 30 WEKSQFLEEG 0.003 23
LKRIKKGWEK 0.003 37 EEGIGGTIPH 0.001 36 LEEGIGGTIP 0.000 29
GWEKSQFLEE 0.000 V7A-HLA-3501-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 2 SPKSLSETFL 60.000 1
GSPKSLSETF 5.000 4 KSLSETFLPN 1.000 6 LSETFLPNGI 0.600 9 TFLPNGINGI
0.040 5 SLSETFLPNG 0.020 10 FLPNGINGIK 0.010 7 SETFLPNGIN 0.010 8
ETFLPNGING 0.010 3 PKSLSETFLP 0.000 V7B-HLA-B3501-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
MAYQQSTLGY 6.000 9 QSTLGYVALL 0.500 3 LNMAYQQSTL 1.000 8 QQSTLGYVAL
1.000 10 STLGYVALLI 0.400 7 YQQSTLGYVA 0.100 2 FLNMAYQQST 0.100 6
AYQQSTLGYV 0.020 4 NMAYQQSTLG 0.010 1 LFLNMAYQQS 0.010
V7C-HLA-B3501-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 100 SIDPPESPDR 100.000 67 TAEQESGIR 9.000 33
LSEIVLPIEW 6.750 131 LWEFLLRLLK 4.500 91 VTEDDEAQDS 2.250 10
SVEVLASPAA 1.800 52 STPPPPAMWT 1.250 6 ILDLSVEVLA 1.000 168
KLETIILSKL 0.900 103 PPESPDRALK 0.900 127 GVGPLWEFLL 0.500 143
AASGTLSLAF 0.500 13 VLASPAAAWK 0.400 51 LSTPPPPAMW 0.300 60
WTEEAGATAE 0.225 157 LGEFLGSGTW 0.225 69 EAQESGIRNK 0.200 97
AQDSIDPPES 0.150 70 AQESGIRNKS 0.135 178 TQEQKSKHCM 0.135 170
ETIILSKLTQ 0.125 128 VGPLWEFLLR 0.125 37 VLPIEWQQDR 0.100 14
LASPAAAWKC 0.100 61 TEEAGATAEA 0.090 39 PEIWQQDRKI 0.090 162
GSGTWMKLET 0.075 78 KSSSSSQIPV 0.075 160 FLGSGTWMKL 0.050 22
KCLGANILRG 0.050 167 MKLETIILSK 0.050 38 LPIEWQQDRK 0.050 80
SSSSQIPVVG 0.030 79 SSSSSQIPVV 0.030 83 SQIPVVGVVT 0.030 144
ASGTLSLAFT 0.030 81 SSSQIPVVGV 0.030 146 GTLSLAFTSW 0.025 66
ATAEAQESGI 0.025 152 FTSWSLGEFL 0.025 125 TNGVGPLWEF 0.025 92
TEDDEAQDSI 0.025 177 LTQEQKSKHC 0.025 21 WKCLGANILR 0.025 106
SPDRALKAAN 0.025 94 DDEAQDSIDP 0.022 12 EVLASPAAAW 0.020 4
IVILDLSVEV 0.020 173 ILSKLTQEQK 0.020 47 KIPPLSTPPP 0.020 113
AANSWRNPVL 0.020 72 ESGIRNKSSS 0.015 43 QQDRKIPPLS 0.015 15
ASPAAAWKCL 0.015 140 KSQAASGTLS 0.015 9 LSVEVLASPA 0.015 82
SSQIPVVGVV 0.015 155 WSLGEFLGSG 0.015 105 ESPDRALKAA 0.015 148
LSLAFTSWSL 0.015 124 HTNGVGPLWE 0.013 129 GPLWEFLLRL 0.013 31
GGLSEIVLPI 0.013 145 SGTLSLAFTS 0.013 185 HCMFSLISGS 0.010 149
SLAFTSWSLG 0.010 65 GATAEAQESG 0.010 112 KAANSWRNPV 0.010 142
QAASGTLSLA 0.010 25 GANILRGGLS 0.010 159 EFLGSGTWMK 0.010 23
CLGANILRGG 0.010 109 RALKAANSWR 0.010 176 KLTQEQKSKH 0.010 35
EIVLPIEWQQ 0.010 175 SKLTQEQKSK 0.010 18 AAAWKCLGAN 0.010 36
IVLPIEWQQD 0.010 5 VILDLSVEVL 0.010 172 IILSKLTQEQ 0.010 156
SLGEFLGSGT 0.010 120 PVLPHTNGVG 0.010 147 TLSLAFTSWS 0.010 89
GVVTEDDEAQ 0.010 153 TSWSLGEFLG 0.008 2 PSIVILDLSV 0.008 141
SQAASGTLSL 0.007 150 LAFTSWSLGE 0.005 17 PAAAWKCLGA 0.005 101
IDPPESPDRA 0.005 151 AFTSWSLGEF 0.005 117 WRNPVLPHTN 0.005 42
WQQDRKIPPL 0.003 104 PESPDRALKA 0.003 24 LGAINILRGGL 0.003 119
NPVLPHTNGV 0.003 118 RNPVLPHTNG 0.003 102 DPPESPDRAL 0.003 53
TPPPPAMWTE 0.003 1 LPSIVILDLS 0.003
[1231]
32TABLE VIII Start Subsequence Score V8-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 4
FLEEGMGGT 0.900 5 LEEGMGGTI 0.045 1 KSQFLEEGM 0.015 7 EGMGGTIPH
0.013 8 GMGGTIPHV 0.010 9 MGGTIPHVS 0.003 3 QFLEEGMGG 0.003 2
SQFLEEGMG 0.002 6 EEGMGGTIP 0.001 V13-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 5
LSETFLPNG 2.700 4 SLSETFLPN 0.050 7 ETFLPNGIN 0.025 8 TFLPNGING
0.025 9 FLPNGINGI 0.010 3 KSLSETFLP 0.007 1 SPKSLSETF 0.003 6
SETFLPNGI 0.001 2 PKSLSETFL 0.000 V14-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
NLPLRLFTF 0.500 7 FTFWRGPVV 0.050 3 PLRLFTFWR 0.005 5 RLFTFWRGP
0.001 6 LFTFWRGPV 0.001 4 LRLFTFWRG 0.001 2 LPLRLFTFW 0.000 9
FWRGPVVVA 0.000 8 TFWRGPVVV 0.000 V21-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 2
KLTQEQKTK 0.200 4 TQEQKTKHC 0.135 3 LTQEQKTKH 0.025 8 KTKHCMFSL
0.013 6 EQKTKHCMF 0.002 9 TKHCMFSLI 0.001 1 SKLTQEQKT 0.001 7
QKTKHCMFS 0.000 5 QEQKTKHCM 0.000 V25-HLA-A1-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 2
LFLPCISQK 0.100 1 ILFLPCISQ 0.050 5 PCISQKLKR 0.050 4 LPCISQKLK
0.050 7 ISQKLKRIK 0.030 8 SQKLKRIKK 0.015 3 FLPCISQKL 0.010 6
CISQKLKRI 0.010 9 QKLKRIKKG 0.000
[1232]
33TABLE IX Start Subsequence Score V8-HLA-A1-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
FLEEGMGGTI 0.900 2 KSQFLEEGMG 0.015 3 SQFLEEGMGG 0.007 8 EGMGGTIPHV
0.005 9 GMGGTIPHVS 0.005 5 LEEGMGGTIP 0.005 7 EEGMGGTIPH 0.003 4
QFLEEGMGGT 0.001 10 MGGTIPHVSP 0.001 1 EKSQFLEEGM 0.001
V13-HLA-A1-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 LSETFLPNGI 1.350 10 FLPNGINGIK 0.200 8
ETFLPNGING 0.125 4 KSLSETFLPN 0.075 5 SLSETFLPNG 0.020 1 GSPKSLSETF
0.015 9 TFLPNGINGI 0.005 7 SETFLPNGIN 0.001 2 SPKSLSETFL 0.000 3
PKSLSETFLP 0.000 V14-HLA-A1-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 29; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 1 ENLPLRLFTF 1.250 8 FTFWRGPVVV 0.050
3 LPLRLFTFWR 0.013 2 NLPLRLFTFW 0.010 6 RLFTFWRGPV 0.010 7
LFTFWRGPVV 0.001 4 PLRLFTFWRG 0.000 10 FWRGPVVVAI 0.000 5
LRLFTFWRGP 0.000 9 TFWRGPVVVA 0.000 V21-HLA-A1-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
TQEQKTKHCM 0.135 4 LTQEQKTKHC 0.025 3 KLTQEQKTKH 0.010 2 SKLTQEQKTK
0.010 9 KTKHCMFSLI 0.003 10 TKHCMFSLIS 0.003 1 LSKLTQEQKT 0.002 7
EQKTKHCMFS 0.001 6 QEQKTKHCMF 0.001 8 QKTKHCMFSL 0.000
V25-HLA-A1-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 7 CISQKLKRIK 0.200 4 FLPCISQKLK 0.200 2
ILFLPCISQK 0.200 8 ISQKLKRIKK 0.150 5 LPCISQKLKR 0.125 1 IILFLPCISQ
0.050 3 LFLPCISQKL 0.005 6 PCISQKLKRI 0.001 9 SQKLKRIKKG 0.000 10
QKLKRIKKGW 0.000
[1233]
34TABLE X Start Subsequence Score V8-A0201-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
GMGGTIPHV 115.534 4 FLEEGMGGT 2.689 1 KSQFLEEGM 0.056 2 SQFLEEGMG
0.004 5 LEEGMGGTI 0.003 3 QFLEEGMGG 0.001 9 MGGTIPHVS 0.000 7
EGMGGTIPH 0.000 6 EEGMGGTIP 0.000 V13-A0201-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 9
FLPNGINGI 110.379 4 SLSETFLPN 0.581 6 SETFLPNGI 0.203 3 KSLSETFLP
0.007 2 PKSLSETFL 0.004 5 LSETFLPNG 0.000 8 TFLPNGING 0.000 7
ETFLPNGIN 0.000 1 SPKSLSETF 0.000 V14-A0201-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 7
FTFWRGPVV 6.741 1 NLPLRLFTF 0.994 8 TFWRGPVVV 0.164 5 RLFTFWRGP
0.071 2 LPLRLFTFW 0.032 6 LFTFWRGPV 0.011 3 PLRLFTFWR 0.003 4
LRLFTFWRG 0.001 9 FWRGPVVVA 0.000 V21-A0201-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
KTKHCMFSL 0.485 5 QEQKTKHCM 0.097 2 KLTQEQKTK 0.052 1 SKLTQEQKT
0.038 4 TQEQKTKHC 0.032 9 TKHCMFSLI 0.028 3 LTQEQKTKH 0.007 7
QKTKHCMFS 0.001 6 EQKTKHCMF 0.000 V25-A0201-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 3
FLPCISQKL 98.267 6 CISQKLKRI 3.299 1 ILFLPCISQ 0.094 9 QKLKRIKKG
0.001 4 LPCISQKLK 0.000 2 LFLPCISQK 0.000 8 SQKLKRIKK 0.000 7
ISQKLKRIK 0.000 5 PCISQKLKR 0.000 V8-HLA-A0201-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
FLEEGMGGTI 1.637 8 EGMGGTIPHV 0.290 3 SQFLEEGMGG 0.028 4 QFLEEGMGGT
0.023 9 GMGGTIPHVS 0.022 1 EKSQFLEEGM 0.000 2 KSQFLEEGMG 0.000 10
MGGTIPHVSP 0.000 7 EEGMGGTIPH 0.000 6 LEEGMGGTIP 0.000
V13-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 5 SLSETFLPNG 2.670 9 TFLPNGINGI 0.062 2
SPKSLSETFL 0.027 4 KSLSETFLPN 0.012 6 LSETFLPNGI 0.007 10
FLPNGINGIK 0.004 8 ETFLPNGING 0.000 1 GSPKSLSETF 0.000 7 SETFLPNGIN
0.000 3 PKSLSETFLP 0.000 V14-HLA-A0201-10mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 29; each start position is specified,
the length of peptide is 10 amino acids, and the end position for
each peptide is the start position plus nine. 6 RLFTFWRGPV 33.455 8
FTFWRGPVVV 6.741 2 NLPLRLFTFW 0.779 3 LPLRLFTFWR 0.074 7 LFTFWRGPVV
0.034 9 TFWRGPVVVA 0.027 1 ENLPLRLFTF 0.002 4 PLRLFTFWRG 0.002 10
FWRGPVVVAI 0.001 5 LRLFTFWRGP 0.000 V21-HLA-A0201-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
TQEQKTKHCM 0.135 4 LTQEQKTKHC 0.025 3 KLTQEQKTKH 0.025 2 SKLTQEQKTK
0.010 9 KTKHCMFSLI 0.003 10 TKHCMFSLIS 0.003 1 LSKLTQEQKT 0.002 7
EQKTKHCMFS 0.001 6 QEQKTKHCMF 0.001 8 QKTKHCMFSL 0.000
V25-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 2 ILFLPCISQK 0.216 3 LFLPCISQKL 0.093 4
FLPCISQKLK 0.069 1 IILFLPCISQ 0.013 6 PCISQKLKRI 0.003 9 SQKLKRIKKG
0.001 10 QKLKRIKKGW 0.000 7 CISQKLKRIK 0.000 8 ISQKLKRIKK 0.000 5
LPCISQKLKR 0.000
[1234]
35TABLE XII Start Subsequence Score V8-HLA-A3-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
GMGGTIPHV 1.350 4 FLEEGMGGT 0.068 1 KSQFLEEGM 0.003 2 SQFLEEGMG
0.001 5 LEEGMGGTI 0.001 7 EGMGGTIPH 0.000 3 QFLEEGMGG 0.000 9
MGGTIPHVS 0.000 6 EEGMGGTIP 0.000 V13-HLA-A3-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 9
FLPNGINGI 0.900 4 SLSETFLPN 0.180 1 SPKSLSETF 0.020 6 SETFLPNGI
0.002 3 KSLSETFLP 0.001 7 ETFLPNGIN 0.001 5 LSETFLPNG 0.000 8
TFLPNGING 0.000 2 PKSLSETFL 0.000 V14-HLA-A3-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight.
NLPLRLFTF 9.000 3 PLRLFTFWR 3.600 7 FTFWRGPVV 0.050 5 RLFTFWRGP
0.030 2 LRLRLFTFW 0.009 9 FWRGPVVVA 0.001 8 TFWRGPVVV 0.001 4
LRLFTFWRG 0.000 6 LFTFWRGPV 0.000 V21-HLA-A3-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 2
KLTQEQKTK 30.000 8 KTKHCMFLS 0.405 6 EQKTKHCMF 0.018 3 LTQEQKTKH
0.015 4 TQEQKTKHC 0.003 9 TKHCMFSLI 0.002 5 QEQKTKHCM 0.001 1
SKLTQEQKT 0.000 7 QKTKHCMFS 0.000 V25-HLA-A3-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
SQKLKRIKK 1.200 3 FLPCISQKL 0.900 1 ILFLPCISQ 0.300 4 LPCISQKLK
0.100 2 LFLPCISQK 0.068 6 CISQKLKRI 0.045 5 PCISQKLKR 0.012 7
ISQKLKRIK 0.010 9 QKLKRIKKG 0.000
[1235]
36TABLE XIII Start Subsequence Score V8-HLA-A3-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 9
GMGGTIPHVS 0.270 5 FLEEGMGGTI 0.270 3 SQFLEEGMGG 0.006 7 EEGMGGTIPH
0.000 8 EGMGGTIPHV 0.000 4 QFLEEGMGGT 0.000 5 LEEGMGGTIP 0.000 2
KSQFLEEGMG 0.000 1 EKSQFLEEGM 0.000 10 MGGTIPHVSP 0.000
V13-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 10 FLPNGINGIK 9.000 5 SLSETFLPNG 0.135 1
GSPKSLSETF 0.030 2 SPKSLSETFL 0.006 6 LSETFLPNGI 0.003 8 ETFLPNGING
0.003 4 KSLSETFLPN 0.003 9 TFLPNGINGI 0.002 7 SETFLPNGIN 0.000 3
PKSLSETFLP 0.000 V14-HLA-A3-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 29; each start position is specified, the length of
peptide is 10 amino acids, and the end position for each peptide is
the start position plus nine. 6 RLFTFWRGPV 0.900 2 NLPLRLFTFW 0.600
3 LPLRLFTFWR 0.540 8 FTFWRGPVVV 0.050 4 PLRLFTFWRG 0.018 1
ENLPLRLFTF 0.012 9 TFWRGPVVVA 0.005 10 FWRGPVVVAI 0.005 7
LFTFWRGPVV 0.000 5 LRLFTFWRGP 0.000 V21-HLA-A3-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 3
KLTQEQKTKH 0.600 9 KTKHCMFSLI 0.270 2 SKLTQEQKTK 0.015 4 LTQEQKTKHC
0.007 6 QEQKTKHCMF 0.006 5 TQEQKTKHCM 0.006 8 QKTKHCMFSL 0.003 7
EQKTKHCMFS 0.001 1 LSKLTQEQKT 0.001 10 TKHCMFSLIS 0.000
V25-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 2 ILFLPCISQK 150.000 4 FLPCISQKLK 10.000 8
ISQKLKRIKK 0.200 7 CISQKLKRIK 0.200 5 LPCISQKLKR 0.080 1 IILFLPCISQ
0.009 3 LFLPCISQKL 0.002 5 PCISQKLKRI 0.001 9 SQKLKRIKKG 0.000 10
QKLKRIKKGW 0.000
[1236]
37TABLE XIV Start Subsequence Score V8-HLA-A1101-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
GMGGTIPHV 1.350 4 FLEEGMGGT 0.068 1 KSQFLEEGM 0.003 2 SQFLEEGMG
0.001 5 LEEGMGGTI 0.001 7 EGMGGTIPH 0.000 3 QFLEEGMGG 0.000 9
MGGTIPHVS 0.000 6 EEGMGGTIP 0.000 V13-HLA-A1101-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 9
FLPNGINGI 0.004 1 SPKSLSETF 0.002 4 SLSETFLPN 0.001 7 ETFLPNGIN
0.001 8 TFLPNGING 0.001 5 SETFLPNGI 0.001 3 KSLSETFLP 0.000 2
PKSLSETFL 0.000 5 LSETFLPNG 0.000 V14-HLA-A1101-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 3
PLRLFTFWR 0.024 7 FTFWRGPVV 0.020 1 NLPLRLFTF 0.012 8 TFWRGPVVV
0.004 2 LRLRLFTFW 0.003 6 LFTFWRGPV 0.002 5 RLFTFWRGP 0.000 9
FWRGPVVVA 0.000 4 LRLFTFWRG 0.000 V21-HLA-A1101-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 2
KLTQEQKTK 0.600 8 KTKHCMFSL 0.090 3 LTQEQKTKH 0.010 6 EQKTKHCMF
0.002 5 QEQKTKHCM 0.001 4 TQEQKTKHC 0.000 9 TKHCMFSLI 0.000 7
QKTKHCMFS 0.000 1 SKLTQEQKT 0.000 V25-HLA-A1101-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
SQKLKRIKK 1.200 2 LFLPCISQK 0.300 4 LPCISQKLK 0.100 5 PCISQKLKR
0.012 3 FLPCISQKL 0.004 7 ISQKLKRIK 0.002 6 CISQKLKRI 0.002 1
ILFLPCISQ 0.002 9 QKLKRIKKG 0.000
[1237]
38TABLE XV Start Subsequence Score V8-HLA-A11-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
FLEEGMGGTI 0.004 3 SQFLEEGMGG 0.002 9 GMGGTIPHVS 0.001 7 EEGMGGTIPH
0.000 4 QFLEEGMGGT 0.000 8 EGMGGTIPHV 0.000 2 KSQFLEEGMG 0.000 5
LEEGMGGTIP 0.000 1 EKSQFLEEGM 0.000 10 MGGTIPHVSP 0.000
V13-HLA-A11-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 10 FLPNGINGIK 0.400 9 TFLPNGINGI 0.003 2
SPKSLSETFL 0.002 8 ETFLPNGING 0.001 1 GSPKSLSETF 0.001 5 SLSETFLPNG
0.000 6 LSETFLPNGI 0.000 4 KSLSETFLPN 0.000 7 SETFLPNGIN 0.000 3
PKSLSETFLP 0.000 V14-HLA-A11-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 29; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 3 LPLRLFTFWR 0.180 6
RLFTFWRGPV 0.024 8 FTFWRGPVVV 0.020 9 TFWRGPVVVA 0.004 2 NLPLRLFTFW
0.004 7 LFTFWRGPVV 0.002 1 ENLPLRLFTF 0.001 10 FWRGPVVVAI 0.000 4
PLRLFTFWRG 0.000 5 LRLFTFWRGP 0.000 V21-HLA-A11-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 9
KTKHCMFSLI 0.030 2 SKLTQEQKTK 0.015 3 KLTQEQKTKH 0.012 5 TQEQKTKHCM
0.006 8 QKTKHCMFSL 0.001 6 QEQKTKHCMF 0.001 4 LTQEQKTKHC 0.001 7
EQKTKHCMFS 0.000 10 TKHCMFSLIS 0.000 1 LSKLTQEQKT 0.000
V25-HLA-A11-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 2 ILFLPCISQK 0.800 4 FLPCISQKLK 0.200 5
LPCISQKLKR 0.080 8 ISQKLKRIKK 0.040 7 CISQKLKRIK 0.040 3 LFLPCISQKL
0.003 1 IILFLPCISQ 0.001 9 SQKLKRIKKG 0.000 10 QKLKRIKKGW 0.000 6
PCISQKLKRI 0.000
[1238]
39TABLE XVI Start Subsequence Score V8-HLA-A24-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
KSQFLEEGM 1.800 4 FLEEGMGGT 0.180 5 LEEGMGGTI 0.150 9 MGGTIPHVS
0.140 8 GMGGTIPHV 0.100 3 QFLEEGMGG 0.090 7 EGMGGTIPH 0.015 2
SQFLEEGMG 0.010 6 EEGMGGTIP 0.001 V13-HLA-A24-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
SPKSLSETF 2.400 9 FLPNGINGI 1.800 4 SLSETFLPN 0.144 6 SETFLPNGI
0.144 7 ETFLPNGIN 0.100 8 TFLPNGING 0.090 2 PKSLSETFL 0.040 3
KSLSETFLP 0.030 5 LSETFLPNG 0.015 V14-HLA-A24-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
NLPLRLFTF 3.000 8 TFWRGPVVV 0.500 6 LFTFWRGPV 0.500 2 LPLRLFTFW
0.216 7 FTFWRGPVV 0.100 9 FWRGPVVVA 0.100 5 RLFTFWRGP 0.020 4
LRLFTFWRG 0.002 3 PLRLFTFWR 0.001 V21-HLA-A24-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
KTKHCMFSL 8.000 6 EQKTKHCMF 2.000 4 TQEQKTKHC 0.150 9 TKHCMFSLI
0.120 5 QEQKTKHCM 0.075 2 KLTQEQKTK 0.020 1 SLKTQEQKT 0.020 3
LTQEQKTKH 0.020 7 QKTKHCMFS 0.010 V25-HLA-A24-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 3
FLPCISQKL 11.088 6 CISQKLKRI 1.000 2 LFLPCISQK 0.090 7 ISQKLKRIK
0.018 8 SQKLKRIKK 0.011 1 ILFLPCISQ 0.010 4 LPCISQKLK 0.010 9
QKLKRIKKG 0.002 5 PCISQKLKR 0.002
[1239]
40TABLE XVII Start Subsequence Score V8-HLA-A24-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
FLEEGMGGTI 1.800 4 QFLEEGMGGT 0.900 8 EGMGGTIPHV 0.150 9 GMGGTIPHVS
0.140 1 EKSQFLEEGM 0.060 2 KSQFLEEGMG 0.030 10 MGGTIPHVSP 0.010 3
SQFLEEGMGG 0.010 6 LEEGMGGTIP 0.002 7 EEGMGGTIPH 0.001
V13-HLA-A24-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 9 TFLPNGINGI 10.800 2 SPKSLSETFL 4.000 1
GSPKSLSETF 3.600 6 LSETFLPNGI 2.160 4 KSLSETFLPN 0.360 10
FLPNGINGIK 0.021 5 SLSETFLPNG 0.012 7 SETFLPNGIN 0.010 8 ETFLPNGING
0.010 3 PKSLSETFLP 0.000 V14-HLA-A24-10mers-98P4B6 Each peptide is
a portion of SEQ ID NO: 29; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 1 ENLPLRLFTF 3.600 10
FWRGPVVVAI 1.400 7 LFTFWRGPVV 0.500 9 TFWRGPVVVA 0.500 2 NLPLRLFTFW
0.216 6 RLFTFWRGPV 0.200 8 FTFWRGPVVV 0.100 3 LPLRLFTFWR 0.015 5
LRLFTFWRGP 0.002 4 PLRLFTFWRG 0.001 V21-HLA-A24-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 9
KTKHCMFSLI 2.400 5 TQEQKTKHCM 0.750 8 QKTKHCMFSL 0.400 6 QEQKTKHCMF
0.300 4 LTQEQKTKHC 0.180 1 LSKLTQEQKT 0.132 7 EQKTKHCMFS 0.100 3
KLTQEQKTKH 0.022 10 TKHCMFSLIS 0.010 2 SKLTQEQKTK 0.002
V25-HLA-A24-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 3 LFLPCISQKL 66.528 6 PCISQKLKRI 0.150 10
QKLKRIKKGW 0.021 8 ISQKLKRIKK 0.017 4 FLPCISQKLK 0.015 1 IILFLPCISQ
0.015 7 CISQKLKRIK 0.012 9 SQKLKRIKKG 0.011 5 LPCISQKLKR 0.011 2
ILFLPCISQK 0.010
[1240]
41TABLE XVIII Start Subsequence Score V8-HLA-B7-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
KSQFLEEGM 1.000 8 GMGGTIPHV 0.200 7 EGMGGTIPH 0.030 4 FLEEGMGGT
0.030 9 MGGTIPHVS 0.020 5 LEEGMGGTI 0.012 2 SQFLEEGMG 0.010 6
EEGMGGTIP 0.001 3 QFLEEGMGG 0.001 V13-HLA-B7-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 9
FLPNGINGI 0.400 1 SPKSLSETF 0.400 6 SETFLPNGI 0.040 2 PKSLSETFL
0.040 7 ETFLPNGIN 0.030 4 SLSETFLPN 0.020 3 KSLSETFLP 0.010 5
LSETFLPNG 0.003 8 TFLPNGING 0.001 V14-HLA-B7-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 2
LPLRLFTFW 0.400 7 FTFWRGPVV 0.200 9 FWRGPVVVA 0.150 6 LFTFWRGPV
0.030 8 TFWRGPVVV 0.020 1 NLPLRLFTF 0.020 3 PLRLFTFWR 0.010 5
RLFTFWRGP 0.010 4 LRLFTFWRG 0.001 V21-HLA-B7-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
KTKHCMFSL 4.000 5 QEQKTKHCM 0.100 9 TKHCMFSLI 0.040 4 TQEQKTKHC
0.030 6 EQKTKHCMF 0.020 3 LTQEQKTKH 0.010 1 SKLTQEQKT 0.010 2
LKTQEQKTK 0.010 7 QKTKHCMFS 0.002 V25-HLA-B7-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 3
FLPCISQKL 4.000 6 CISQKLKRI 0.400 4 LPCISQKLK 0.200 8 SQKLKRIKK
0.015 1 ILFLPCISQ 0.015 7 ISQKLKRIK 0.010 9 QKLKRIKKG 0.001 2
LFLPCISQK 0.001 5 PCISQKLKR 0.001
[1241]
42TABLE XIX Start Subsequence Score V8-HLA-B7-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 8
EGMGGTIPHV 0.600 5 FLEEGMGGTI 0.120 1 EKSQFLEEGM 0.100 9 GMGGTIPHVS
0.020 10 MGGTIPHVSP 0.015 4 QFLEEGMGGT 0.010 3 SQFLEEGMGG 0.010 2
KSQFLEEGMG 0.010 7 EEGMGGTIPH 0.001 6 LEEGMGGTIP 0.000
V13-HLA-B7-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 2 SPKSLSETFL 80.000 6 LSETFLPNGI 0.120 9
TFLPNGINGI 0.040 1 GSPKSLSETF 0.020 4 KSLSETFLPN 0.020 10
FLPNGINGIK 0.010 5 SLSETFLPNG 0.010 8 ETFLPNGING 0.010 7 SETFLPNGIN
0.003 3 PKSLSETFLP 0.000 V14-HLA-B7-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 29; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 10 FWRGPVVVAI 0.400 6
RLFTFWRGPV 0.300 8 FTFWRGPVVV 0.200 3 LPLRLFTFWR 0.200 2 NLPLRLFTFW
0.020 7 LFTFWRGPVV 0.020 1 ENLPLFLFTF 0.020 9 TFWRGPVVVA 0.015 4
PLRLFTFWRG 0.010 5 LRLFTFWRGP 0.001 V21-HLA-B7-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 9
KTKHCMFSLI 0.400 8 QKTKHCMFSL 0.400 5 TQEQKTKHCM 0.300 1 LSKLTQEQKT
0.100 4 LTQEQKTKHC 0.100 7 EQKTKHCMFS 0.020 3 KLTQEQKTKH 0.010 10
TKHCMFSLIS 0.002 6 QEQKTKHCMF 0.002 2 SKLTQEQKTK 0.001
V25-HLA-B7-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 3 LFLPCISQKL 0.400 5 LPCISQKLKR 0.200 6
PCISQKLKRI 0.040 8 ISQKLKRIKK 0.015 1 IILFLPCISQ 0.015 7 CISQKLKRIK
0.010 4 FLPCISQKLK 0.010 9 SQKLKRIKKG 0.010 2 ILFLPCISQK 0.010 10
QKLKRIKKGW 0.002
[1242]
43TABLE XX Start Subsequence Score V8-HLA-B3501-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
KSQFLEEGM 20.000 8 GMGGTIPHV 0.200 9 MGGTIPHVS 0.100 4 FLEEGMGGT
0.060 2 SQFLEEGMG 0.015 5 LEEGMGGTI 0.012 7 EGMGGTIPH 0.010 3
QFLEEGMGG 0.003 6 EEGMGGTIP 0.001 V13-HLA-B3501-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 1
SPKSLSETF 60.000 9 FLPNGINGI 0.400 4 SLSETFLPN 0.200 3 KSLSETFLP
0.150 7 ETFLPNGIN 0.100 6 SETFLPNGI 0.040 5 LSETFLPNG 0.015 2
PKSLSETFL 0.010 8 TFLPNGING 0.001 V14-HLA-B3501-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 2
LRLRLFTFW 10.000 1 NLPLRLFTF 1.000 7 FTFWRGPVV 0.200 9 FWRGPVVVA
0.030 6 LFTFWRGPV 0.020 5 RLFTFWRGP 0.020 8 TFWRGPVVV 0.020 3
PLRLFTFWR 0.003 4 LRLFTFWRG 0.001 V21-HLA-B3501-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 8
KTKHCMFSL 6.000 6 EQKTKHCMF 3.000 5 QEQKTKHCM 0.200 9 TKHCMFSLI
0.040 2 KLTQEQKTK 0.030 4 TQEQKTKHC 0.030 3 LTQEQKTKH 0.020 7
QKTKHCMFS 0.010 1 SKLTQEQKT 0.010 V25-HLA-B3501-9mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. 3
FLPCISQKL 1.000 6 CISQKLKRI 0.400 4 LPCISQKLK 0.200 7 ISQKLKRIK
0.050 8 SQKLKRIKK 0.030 1 ILFLPCISQ 0.010 9 QKLKRIKKG 0.001 2
LFLPCISQK 0.001 5 PCISQKLKR 0.001
[1243]
44TABLE XXI Start Subsequence Score V14-HLA-B3501-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus nine. 1
ENLPLRLFTF 1.000 2 NLPLRLFTFW 0.500 6 RLFTFWRGPV 0.400 8 FTFWRGPVVV
0.200 3 LPLRLFTFWR 0.200 10 FWRGPVVVAI 0.120 7 LFTFWRGPVV 0.020 9
TFWRGPVVVA 0.010 4 PLRLFTFWRG 0.003 5 LRLFTFWRGP 0.001
V21-HLA-B3501-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptide is 10
amino acids, and the end position for each peptide is the start
position plus nine. 9 KTKHCMFSLI 2.400 1 LSKLTQEQKT 1.500 5
TQEQKTKHCM 0.600 7 EQKTKHCMFS 0.300 4 LTQEQKTKHC 0.200 6 QEQKTKHCMF
0.100 8 QKTKHCMFSL 0.100 3 KLTQEQKTKH 0.020 10 TKHCMFSLIS 0.010 2
SLKTQEQKTK 0.002 V25-HLA-B35-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 51; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus nine. 5 LPCISQKLKR 0.200 3
LFLPCISQKL 0.100 8 ISQKLKRIKK 0.050 10 QKLRIKKGW 0.050 6 PCISQKLKRI
0.040 9 SQKLKRIKKG 0.030 4 FLPCISQKLK 0.010 7 CISQKLKRIK 0.010 2
ILFLPCISQK 0.010 1 IILFIPCISQ 0.010
[1244]
45TABLE XXII Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-A1-9mers-98P4B6 158 PKDASRQVY 27 419
FEEEYYRFY 27 405 ISTFHVLIY 26 221 SLATFFFLY 23 263 AITLLSLVY 23 392
SFIQSTLGY 23 276 LAAAYQLYY 22 280 YQLYYGTKY 21 244 QSDFYKIPI 19 101
LWDLRHLLV 18 189 PIDLGSLSS 18 198 AREIENLPL 18 231 FVRDVIHPY 18 240
ARNQQSDFY 18 275 LLAAAYQLY 18 311 FFAMTHVAY 18 90 FVAIHREHY 17 117
SNNMRINQY 17 327 RSERYLFLN 17 388 WREFSFIQS 17 427 YTPPNFVLA 17 443
ILDLLQLCR 17 444 LDLLQLCRY 17 46 TIRLIRCGY 16 66 ASEFFPHVV 16 124
QYPESNAEY 16 200 EIENLPLRL 16 330 RYLFLNMAY 16 352 EEVWRIEMY 16 272
LAGLLAAAY 15 323 LPMRRSERY 15 351 EEEVWRIEM 15 415 WKRAFEEEY 15 416
KRAFEEEYY 15 13 LSETCLPNG 14 38 SGDFAKSLT 14 98 YTSLWDLRH 14 178
VIELARQLN 14 406 STFHVLIYG 14 94 HREHYTSLW 13 135 SLFPDSLIV 13 137
FPDSLIVKG 13 251 PIEIVNKTL 13 396 STLGYVALL 13
V2-HLA-A1-9mers-98P4B6 23 LSLPSSWDY 23 36 PCPADFFLY 20 17 FTPFSCLSL
13 28 SWDYRCPPP 12 Each peptide is a portion of SEQ ID NO; 11; each
start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. Pos 123456789 score V5A-HLA-A1-9mers-98P4B6 7 FTFWRGPVV
9 9 FWRGPVVVA 5 V5B-HLA-A1-9mers-98P4B6 21 ELEFVFLLT 24 1 WREFSFIQI
17 17 QTELELEFV 16 13 FADTQTELE 15 19 ELELEFVFL 14 Each peptide is
a portion of SEQ ID NO: 13; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V6-HLA-A1-9mers-98P4B6 34 FLEEGIGGT 14 28 GWEKSQFLE 12 35 LEEGIGGTI
12 29 WEKSQFLEE 11 41 GTIPHVSPE 11 1 VLPSIVILG 9 9 GKIILFLPC 9 19
SRKLKRIKK 9 2 LPSIVILGK 8 6 VILGKIILF 8 16 PCISRKLKR 8 7 ILGKIILFL
7 37 EGIGGTIPH 7 46 VSPERVTVM 7 3 PSIVILGKI 6 5 IVILGKIIL 6 12
ILFLPCISR 6 Each peptide is a portion of SEQ ID NO: 15; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V7A-HLA-A1-9mers-98P4B6 5 LSETFLPNG 14 4
SLSETFLPN 12 8 TFLPNGING 9 7 ETFLPNGIN 8 3 KSLSETFLP 6
V7B-HLA-A1-9mers-98P4B6 5 AYQQSTLGY 22 9 STLGYVALL 13
V7C-HLA-A1-9mers-98P4B6 59 WTEEAGATA 17 90 VTEDDEAQD 17 99
SIDPPESPD 17 167 KLETIILSK 17 32 LSEIVLPIE 16 51 STPPPPAMW 14 154
WSLGEFLGS 14 5 ILDLSVEVL 13 69 AQESGIRNK 13 9 SVEVLASPA 12 38
PIEWQQDRK 12 60 TEEAGATAE 12 66 TAEAQESGI 12 93 DDEAQDSID 12 104
ESPDRALKA 12 105 SPDRALKAA 12 123 HTNGVGPLW 12 130 LWEFLLRLL 12 96
AQDSIDPPE 11 102 PPESPDRAL 11 128 GPLWEFLLR 11 143 ASGTLSLAF 11 156
LGEFLGSGT 11 42 QQDRKIPPL 10 78 SSSSSQIPV 10 82 SQIPVVGVV 10 91
TEDDEAQDS 10 92 EDDEAQDSI 10 115 SWRNPVLPH 10 176 LTEQEQKSKH 10 177
TQEQKSKHC 10 26 NILRGGLSE 9 50 LSTPPPPAM 9 79 SSSSQIPVV 9 131
WEFLLRLLK 9 2 SIVILDLSV 8 7 DLSVEVLAS 8 21 KCLGANILR 8 31 GLSEIVLPI
8 81 SSQIPVVGV 8 124 TNGVGPLWE 8 132 EFLLRLLKS 8 141 QAASGTLSL 8
162 SGTWMKLET 8 169 ETIILSKLT 8 Each peptide is a portion of SEQ ID
NO: 17; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V8-HLA-A1-9mers-98P4B6 4
FLEEGMGGT 14 5 LEEGMGGTI 12 7 EGMGGTIPH 7 Each peptide is a portion
of SEQ ID NO: 27; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V13-HLA-A1-9mers-98P4B6 5 LSETFLPNG 14 4 SLSETFLPN 12 8 TFLPNGING 9
7 ETFLPNGIN 8 3 KSLSETFLP 6 Each peptide is a portion of SEQ ID NO:
29; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V14-HLA-A1-9mers-98P4B6 7
FTFWRGPVV 9 9 FWRGPVVVA 5 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V21-HLA-A1-9mers-98P4B6 3
LTQEQKTKH 10 4 TQEQKTKHC 10 1 SKLTQEQKT 6 8 KTKHCMFSL 6 9 TKHCMFSLI
5 Each peptide is a portion of SEQ ID NO: 51; each start position
is specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V25-HLA-A1-9mers-98P4B6 5 PCISQKLKR 10 8 SQKLKRIKK
9 1 ILFLPCISQ 6 2 LFLPCISQK 4 3 FLPCISQKL 4 7 ISQKLKRIK 4
[1245]
46TABLE XXIII Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-A0201-9mers-98P4B6 365 IMSLGLLLSL 29 271
YLAGLLAAA 28 433 VLALVLPSI 28 227 FLYSFVRDV 27 360 YISFGIMSL 27 396
STLGYVALL 27 17 CLPNGINGI 26 100 SLWDLRHLL 26 135 SLFPDSLIV 26 203
NLPRLFTL 26 402 ALLISTFHV 26 436 LVLPSIVIL 26 128 SNAEYLASL 25 140
SLIVKGFNV 25 187 FIPIDLGSL 25 210 TLWRGPVVV 25 261 IVAITLLSL 25 403
LLISTFHVL 25 5 SMMGSPKSL 24 264 ITLLSLVYL 24 274 GLLAAAYQL 24 307
LLSFFFAMV 24 369 GLLSLLAVT 24 48 RLIRCGYHV 23 49 LIRCGYHVV 23 141
LIVKGFNVV 23 313 AMVHVAYSL 23 374 LAVTSIPSV 23 393 FIQSTLGYV 23 441
IVILDLLQL 23 106 HLLVGKILI 22 180 ELARQLNFI 22 254 IVNKTLPIV 22 258
TLPIVAITL 22 262 VAITLLSLV 22 265 TLLSLVYLA 22 267 LSLVYLAGL 22 268
SLVYLAGLL 22 333 FLNMAYQQV 22 378 SIPSVSNAL 22 404 LISTFHVLI 21 435
ALVLPSIVI 21 107 LLVGKILID 20 108 LVGKILIDV 20 112 ILIDVSNNM 20 173
QARQQVIEL 20 184 QLNFIPIDL 20 368 LGLLSLLAV 20 65 FASEFFPHV 19 83
LTKTNIIFV 19 133 KLASLFPDSL 19 177 QVIELARQL 19 257 KTLPIVAIT 19
306 GLLSFFFAM 19 366 MSLGLLSLL 19 434 LALVLPSIV 19 27 DARKVTVGV 18
196 SSAREIENL 18 209 FTLWRGPVV 18 259 LPIVAITLL 18 367 SLGLLSLLA 18
371 LSLLAVTSI 18 397 TLGYVALLI 18 41 FAKSLTIRL 17 81 DALTKTNII 17
85 KTNIIFVAI 17 103 DLRHLLVGK 17 104 LRHLLVGKI 17 153 ALQLGPKDA 17
155 QLGPKDASR 17 212 WRGPVVVAI 17 250 IPIEIVNKT 17 253 EIVNKTLPI 17
363 FGIMSLGLL 17 370 LLSLLAVTS 17 410 VLIYGWKRA 17 428 TPPNFVLAL 17
438 LPSIVILDL 17 442 VILDLLQLC 17 25 IKDARKVTV 16 68 EFFPHVVDV 16
88 IIFVAIHRE 16 93 IHREHYTSL 16 99 TSLWDLRHL 16 132 YLASLFPDS 16
148 VVSAWALQL 16 171 NIQARQQVI 16 190 IDLGSLSSA 16 200 EIENLPLRL 16
372 SLLAVTSIP 16 12 SLSETCLPN 15 44 SLTIRLIRC 15 50 IRCGYHVVI 15
111 KILIDVSNN 15 211 LWRGPVVVA 15 217 VVAISLATF 15 221 SLATFFFLY 15
247 FYKIPIEIV 15 249 KIPIEIVNK 15 251 PIEIVNKTL 15 256 NKTLPIVAI 15
270 VYLAGLLAA 15 299 LQCRKQLGL 15 324 PMRRSERYL 15 331 YLFLNMAYQ 15
335 NMAYQQVHA 15 385 ALNWREFSF 15 400 YVALLISTF 15 437 VLPSIVILD 15
23 NGIKDARKV 14 37 GSGDFAKSL 14 39 GDFAKSLTI 14 42 AKSLTIRLI 14 164
QVYICSNNI 14 166 YICSNNIQA 14 220 ISLATFFFL 14 223 ATFFFLYSF 14 266
LLSLVYLAG 14 275 LLAAAYQLY 14 278 AAYQLYYGT 14 300 QCRKQLGLL 14 309
SFFFAMVHV 14 362 SFGIMSLGL 14 373 LLAVTSIPS 14 395 QSTLGYVAL 14 411
LIYGWKRAF 14 427 YTPPNFVLA 14 443 ILDLLQLCR 14 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V2-HLA-A0201-9mers-98P4B6 5 GLQALSLSL 25 1 SGSPGLQAL 21 8 ALSLSLSSG
18 17 FTPFSCLSL 17 10 SLSLSSGFT 16 3 SPGLQALSL 15 12 SLSSGFTPF 14
15 SGFTPFSCL 14 24 SLPSSWDYR 12 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V5A-HLA-A0201-9mers-98P4B6
7 FTFWRGPVV 17 1 NLPLRLFTF 16 8 TFWRGPVVV 15 9 FWRGPVVVA 14 5
RLFTFWRGP 13 3 PLRLFTFWR 10 6 LFTFWRGPV 10
V5B-HLA-A0201-9mers-98P4B6 20 LELEFVFLL 21 22 LEFVFLLTL 21 24
FVFLLTLLL 20 19 ELELEFVFL 18 12 SFADTQTEL 17 17 QTELELEFV 17 8
QIFCSFADT 15 6 FIQIFCSFA 14 14 ADTQTELEL 14 23 EFVFLLTLL 11 21
ELEFVFLLT 10 Each peptide is a portion of SEQ ID NO: 13; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V6-HLA-A0201-9mers-98P4B6 7 ILGKIILFL 27 38
GIGGTIPHV 26 10 KIILFLPCI 25 14 FLPCISRKL 23 34 FLEEGIGGT 23 5
IVILGKIIL 20 17 CISRKLKRI 20 45 HVSPERVTV 20 4 SIVILGKII 18 6
VILGKIILF 18 12 ILFLPCISR 16 1 VLPSIVILG 15 27 KGWEKSQFL 15 3
PSIVILGKI 13 35 LEEGIGGTI 13 41 GTIPHVSPE 13 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V7A-HLA-A0201-9mers-98P4B6 9 FLPNGINGI 27 4 SLSETFLPN 15
V7B-HLA-A0201-9mers-98P4B6 9 STLGYVALL 27 3 NMAYQQSTL 21 6
YQQSTLGYV 16 8 QSTLGYVAL 14 V7C-HLA-A0201-9mers-98P- 4B6 27
ILRGGLSEI 30 4 VILDLSVEV 27 5 ILDLSVEVL 26 31 GLSEIVLPI 26 129
PLWEFLLRL 26 148 SLAFTSWSL 25 2 SIVILDLSV 24 141 QAASGTLSL 23 155
SLGEFLGSG 21 163 GTWMKLETI 21 81 SSQIPVVGV 20 82 SQIPVVGVV 20 119
PVLPHTNGV 19 133 FLLRLLKSQ 19 165 WMKLETIIL 19 24 GANILRGGL 18 57
AMWTEEAGA 18 112 AANSWRNPV 18 126 GVGPLWEFL 18 12 VLASPAAAW 17 79
SSSSQIPVV 17 134 LLRLLKSQA 17 167 KLETILLSK 17 168 LETIILSKL 17 171
IILSKLTQE 17 172 ILSKLTQEQ 17 42 QQDRKIPPL 16 142 AASGTLSLA 16 160
LGSGTWMKL 16 7 DLSVEVLAS 15 17 AAAWKCLGA 15 22 CLGANILRG 15 26
NILRGGLSE 15 28 LRGGLSEIV 15 130 LWEFLLRLL 15 136 RLLKSQAAS 15 137
LLKSQAASG 15 159 FLGSGTWMK 15 185 CMFSLISGS 15 83 QIPVVGVVT 14 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V8-HLA-A0201-9mers-98P4B6 8 GMGGTIPHV 26 4
FLEEGMGGT 19 5 LEEGMGGTI 13 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V13-HLA-A0201-9mers-98P4B6
9 FLPNGINGI 27 4 SLSETFLPN 15 Each peptide is a portion of SEQ ID
NO: 29; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V14-HLA-A0201-9mers-98P4B6
7 FTFWRGPVV 17 1 NLPLRLFTF 16 8 TFWRGPVVV 15 9 FWRGPVVVA 14 5
RLFTFWRGP 13 3 PLRLFTFWR 10 6 LFTFWRGPV 10 Each peptide is a
portion of SEQ ID NO: 43; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V21-HLA-A0201-9mers-98P4B6 8 KTKHCMFSL 16 2 KLTQEQKTK 11 1
SKLTQEQKT 10 3 LTQEQKTKH 10 9 TKHCMFSLI 8 Each peptide is a portion
of SEQ ID NO: 51; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V25-HLA-A0201-9mers-98P4B6 3 FLPCISQKL 23 6 CISQKLKRI 20 1
ILFLPCISQ 16
[1246]
47 TABLE XXIV Pos 123456789 score V1-HLA-A0203-9mers-98P4B6 No
Results Found. V2-HLA-A0203-9mers-98P4B6 No Results Found.
V5A-HLA-A0203-9mers-98P4B6 No Results Found.
V5B-HLA-A0203-9mers-98P4B6 No Results Found.
V6-HLA-A0203-9mers-98P4B6 No Results Found.
V7A-HLAA0203-9mers-98P4B6 No Results Found.
V7B-HLA-A0203-9mers-98P4B6 No Results Found.
V7C-HLA-A0203-9mers-98P4B6 No Results Found.
V8-HLA-A0203-9mers-98P4B6 No Results Found.
V13-HLA-A0203-9mers-98P4B6 No Results Found.
V14-HLA-A0203-9mers-98P4B6 No Results Found.
V21-HLA-A0203-9mers-98P4B6 No Results Found.
V25-HLA-A0203-9mers-98P4B6 No Results Found.
[1247]
48TABLE XXV Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-A3-9mers-98P4B6 103 DLRHLLVGK 27 56
VVIGSRNPK 26 249 KIPIEIVNK 26 3 SISMMGSPK 25 155 QLGPKDASR 25 263
AITLLSLVY 25 210 TLWRGPVVV 24 48 RLIRCGYHV 23 142 IVKGFNVVS 23 217
VVAISLATF 23 400 YVALLISTF 23 177 QVIELARQL 22 205 PLRLFTLWR 22 281
QLYYGTKYR 22 370 LLSLLAVTS 22 441 IVILDLLQL 22 35 VIGSGDFAK 21 77
THHEDALTK 21 148 VVSAWALQL 21 231 FVRDVIHPY 21 269 LVYLAGLLA 21 375
AVTSIPSVS 21 385 ALNWREFSF 21 274 GLLAAAYQL 20 322 CLPMRRSER 20 409
HVLIYGWKR 20 443 ILDLLQLCR 20 46 TIRLIRCGY 19 87 NIIFVAIHR 19 90
FVAIHREHY 19 258 TLPIVAITL 19 261 IVAITLLSL 19 275 LLAAAYQLY 19 279
AYQLYYGTK 19 369 GLLSLLAVT 19 372 SLLAVTSIP 19 411 LIYGWKRAF 19 436
LVLPSIVIL 19 34 GVIGSGDFA 18 92 AIHREHYTS 18 140 SLIVKGFNV 18 191
DLGSLSSAR 18 221 SLATFFFLY 18 435 ALVLPSIVI 18 22 INGIKDARK 17 49
LIRCGYHVV 17 82 ALTKTNIIF 17 111 KILIDVSNN 17 112 ILIDVSNNM 17 135
SLFPDSLIV 17 153 ALQLGPKDA 17 164 QVYICSNNI 17 203 NLPLRLFTL 17 271
YLAGLLAAA 17 304 QLGLLSFFF 17 381 SVSNALNWR 17 397 TLGYVALLI 17 403
LLISTFHVL 17 432 FVLALVLPS 17 32 TVGVIGSGD 16 107 LLVGKILID 16 151
AWALQLGPK 16 171 NIQARQQVI 16 189 PIDLGSLSS 16 216 VVVAISLAT 16 219
AISLATFFF 16 234 DVIHPYARN 16 266 LLSLVYLAG 16 302 RKQLGLLSF 16 402
ALLISTFHV 16 12 SLSETCLPN 15 21 GINGIKDAR 15 24 GIKDARKVT 15 30
KVTVGVIGS 15 121 RINQYPESN 15 136 LFPDSLIVK 15 179 IELARQLNF 15 268
SLVYLAGLL 15 356 RIEMYISFG 15 367 SLGLLSLLA 15 410 VLIYGWKRA 15 433
VLALVLPSI 15 25 IKDARKVTV 14 44 SLTIRLIRC 14 57 VIGSRNPKF 14 61
RNPKFASEF 14 106 HLLVGKILI 14 141 LIVKGFNVV 14 180 ELARQLNFI 14 207
RLFTLWRGP 14 227 FLYSFVRDV 14 235 VIHPYARNQ 14 241 RNQQSDFYK 14 251
PIEIVNKTL 14 272 LAGLLAAAY 14 294 WLETWLQCR 14 303 KQLGLLSFF 14 307
LLSFFFAMV 14 330 RYLFLNMAY 14 331 YLFLNMAYQ 14 340 QVHANIENS 14 353
EVWRIEMYI 14 364 GIMSLGLLS 14 17 CLPNGINGI 13 18 LPNGINGIK 13 26
KDARKVTVG 13 43 KSLTIRLIR 13 55 HVVIGSRNP 13 70 FPHVVDVTH 13 100
SLWDLRHLL 13 113 LIDVSNNMR 13 147 NVVSAWALQ 13 158 PKDASRQVY 13 184
QLNFIPIDL 13 200 EIENLPLRL 13 211 LWRGPVVVA 13 215 PVVVAISLA 13 253
EIVNKTLPI 13 260 PIVAITLLS 13 306 GLLSFFFAM 13 311 FFAMVHVAY 13 314
MVHVAYSLC 13 333 FLNMAYQQV 13 360 YISFGIMSL 13 392 SFIQSTLGY 13 408
FHVLIYGWK 13 440 SIVILDLLQ 13 Each peptide is a portion of SEQ ID
NO: 5; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V2-HLA-A3-9mers-98P4B6 8
ALSLSLSSG 19 12 SLSSGFTPF 18 5 GLQALSLSL 17 22 CLSLPSSWD 15 24
SLPSSWDYR 15 10 SLSLSSGFT 13 23 LSLPSSWDY 11 33 CPPPCPADF 11 3
SPGLQALSL 10 7 QALSLSLSS 9 9 LSLSLSSGF 9 11 LSLSSGFTP 9 21
SCLSLPSSW 9 37 CPADFFLYF 9 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V5A-HLA-A3-9mers-98P4B6 1
NLPLRLFTF 21 3 PLRLFTFWR 19 5 RLFTFWRGP 14 8 TFWRGPVVV 14 9
FWRGPVVVA 13 V5B-HLA-A3-9mers-98P4B6 19 ELELEFVFL 15 21 ELEFVFLLT
14 24 FVFLLTLLL 14 8 QIFCSFADT 13 6 FIQIFCSFA 12 18 TELELEFVF 11 5
SFIQIFCSF 10 9 IFCSFADTQ 9 2 REFSFIQIF 8 16 TQTELELEF 8 22
LEFVFLLTL 7 Each peptide is a portion of SEQ ID NO: 13; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V6-HLA-A3-9mers-98P4B6 45 HVSPERVTV 22 23
KRIKKGWEK 20 12 ILFLPCISR 19 5 IVILGKIIL 18 13 LFLPCISRK 18 6
VILGKIILF 17 21 KLKRIKKGW 17 2 LPSIVILGK 15 7 ILGKIILFL 15 10
KIILFLPCI 15 18 ISRKLKRIK 15 19 SRKLKRIKK 15 24 RIKKGWEKS 15 34
FLEEGIGGT 14 4 SIVILGKII 13 11 IILFLPCIS 13 26 KKGWEKSQF 13 42
TIPHVSPER 13 15 LPCISRKLK 12 16 PCISRKLKR 12 17 CISRKLKRI 12 37
EGIGGTIPH 11 1 VLPSIVILG 10 14 FLPCISRKL 10 35 LEEGIGGTI 10 38
GIGGTIPHV 10 Each peptide is a portion of SEQ ID NO: 15; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V7A-HLA-A3-9mers-98P4B6 4 SLSETFLPN 15 9
FLPNGINGI 13 1 SPKSLSETF 10 8 TFLPNGING 8 V7B-HLA-A3-9mers-98P4B6 1
FLNMAYQQS 13 5 AYQQSTLGY 12 8 QSTLGYVAL 10 7 QQSTLGYVA 9 3
NMAYQQSTL 8 9 STLGYVALL 8 4 MAYQQSTLG V7C-HLA-A3-9mers-98P4B6 167
KLETIILSK 28 175 KLTQEQKSK 25 109 ALKAANSWR 24 3 IVILDLSVE 23 26
NILRGGLSE 23 159 FLGSGTWMK 23 27 ILRGGLSEI 22 83 QIPVVGVVT 22 13
LASPAAAWK 20 35 IVLPIEWQQ 20 134 LLRLLKSQA 20 136 RLLKSQAAS 20 11
EVLASPAAA 19 137 LLKSQAASG 19 170 TIILSKLTQ 19 12 VLASPAAAW 18 38
PIEWQQDRK 18 73 GIRNKSSSS 18 5 ILDLSVEVL 17 9 SVEVLASPA 17 45
RKIPPLSTP 17 103 PESPDRALK 17 133 FLLRLLKSQ 17 171 IILSKLTQE 17 2
SIVILDLSV 15 4 VILDLSVEV 15 22 CLGANILRG 15 46 KIPPLSTPP 15 69
AQESGIRNK 15 99 SIDPPESPD 15 119 PVLPHTNGV 15 120 VLPHTNGVG 15 131
WEFLLRLLK 15 155 SLGEFLGSG 15 173 LSKLTQEQK 15 7 DLSVEVLAS 14 31
GLSEIVLPI 14 36 VLPIEWQQD 14 85 PVVGVVTED 14 129 PLWEFLLRL 14 146
TLSLAFTSW 14 148 SLAFTSWSL 14 25 ANILRGGLS 13 82 SQIPVVGVV 13 126
GVGPLWEFL 13 Each peptide is a portion of SEQ ID NO: 17; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 1234567789 score V8-HLA-A3-9mers-98P4B6 4 FLEEGMGGT 14 5
LEEGMGGTI 10 3 QFLEEGMGG 9 7 EGMGGTIPH 8 6 EEGMGGTIP 6 Each peptide
is a portion of SEQ ID NO: 27; each start position is specified,
the length of peptide is 9 amino acids, and the end position for
each peptide is the start position plus eight. Pos 123456789 score
V13-HLA-A3-9mers-98P4B6 4 SLSETFLPN 15 9 FLPNGINGI 13 1 SPKSLSETF
10 8 TFLPNGING 8 Each peptide is a portion of SEQ ID NO: 29; each
start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. Pos 123456789 score V14-HLA-A3-9mers-98P4B6 1 NLPLRLFTF
21 3 PLRLFTFWR 19 5 RLFTFWRGP 14 8 TFWRGPVVV 14 9 FWRGPVVVA 13 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V21-HLA-A3-9mers-98P4B6 2 KLTQEQKTK 27 Each peptide
is a portion of SEQ ID NO: 51; each start position is specified,
the length of peptide is 9 amino acids, and the end position for
each peptide is the start position plus eight. Pos 123456789 score
V25-HLA-A3-9mers-98P4B6 2 LFLPCISQK 21 1 ILFLPCISQ 15 8 SQKLKRIKK
15 7 ISQKLKRIK 12 4 LPCISQKLK 11 3 FLPCISQKL 10 5 PCISQKLKR 10
[1248]
49TABLE XXVI Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-A26-9mers-98P4B6 352 EEVWRIEMY 29 75
DVTHHEDAL 28 441 IVILDLLQL 28 177 QVIELARQL 26 223 ATFFFLYSF 25 231
FVRDVIHPY 25 400 YVALLISTF 25 200 EIENLPLRL 24 261 IVAITLLSL 24 217
VVAISLATF 23 436 LVLPSIVIL 23 96 EHYTSLWDL 22 234 DVIHPYARN 22 353
EVWRIEMYI 22 390 EFSFIQSTL 22 396 STLGYVALL 21 90 FVAIHREHY 20 148
VVSAWALQL 20 253 EIVNKTLPI 20 264 ITLLSLVYL 20 15 ETCLPNGIN 19 68
EFFPHVVDV 19 115 DVSNNMRIN 19 215 PVVVAISLA 19 296 ETWLQCRKQ 19 31
VTVGVIGSG 18 187 FIPIDLGSL 18 216 VVVAISLAT 18 406 STFHVLIYG 18 439
PSIVILDLL 18 2 ESISMMGSP 17 45 LTIRLIRCG 17 46 TIRLIRCGY 17 108
LVGKILIDV 17 263 AITLLSLVY 17 360 YISFGIMSL 17 363 FGIMSLGLL 17 30
KVTVGVIGS 16 117 SNNMRINQY 16 128 SNAEYLASL 16 259 LPIVAITLL 16 355
WRIEMYISF 16 392 SFIQSTLGY 16 405 ISTFHVLIY 16 432 FVLALVLPS 16 32
TVGVIGSGD 15 34 GVIGSGDFA 15 72 HVVDVTHHE 15 147 NVVSAWALQ 15 257
KTLPIVAIT 15 268 SLVYLAGLL 15 329 ERYLFLNMA 15 340 QVHANIENS 15 375
AVTSIPSVS 15 378 SIPSVSNAL 15 381 SVSNALNWR 15 428 TPPNFVLAL 15 55
HVVIGSRNP 14 56 VVIGSRNPK 14 57 VIGSRNPKF 14 83 LTKTNIIFV 14 131
EYLASLFPD 14 138 PDSLIVKGF 14 180 ELARQLNFI 14 214 GPVVVAISL 14 218
VAISLATFF 14 254 IVNKTLPIV 14 302 RKQLGLLSF 14 303 KQLGLLSFF 14 316
HVAYSLCLP 14 365 IMSLGLLSL 14 366 MSLGLLSLL 14 430 PNFVLALVL 14 444
LDLLQLCRY 14 Each peptide is a portion of SEQ ID NO: 5; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V2-HLA-A26-9mers-98P4B6 17 FTPFSCLSL 18 1
SGSPGLQAL 15 15 SGFTPFSCL 14 3 SPGLQALSL 11 5 GLQALSLSL 11 9
LSLSLSSGF 11 18 TPFSCLSLP 11 23 LSLPSSWDY 11 12 SLSSGFTPF 10 36
PCPADFFLY 10 37 CPADFFLYF 10 33 CPPPCPADF 9 35 PPCPADFFL 9 30
DYRCPPPCP 8 34 PPPCPADFF 8 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V5A-HLA-A26-9mers-98P4B6 1
NLPLRLFTF 13 7 FTFWRGPVV 13 V5B-HLA-A26-9mers-98P4B6 23 EFVFLLTLL
27 24 FVFLLTLLL 24 15 DTQTELELE 20 19 ELELEFVFL 18 22 LEFVFLLTL 18
2 REFSFIQIF 17 5 SFIQIFCSF 16 16 TQTELELEF 14 20 LELEFVFLL 14 3
EFSFIQIFC 13 Each peptide is a portion of SEQ ID NO: 13; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V6-HLA-A26-9mers-98P4B6 5 IVILGKIIL 23 6
VILGKIILF 18 41 GTIPHVSPE 18 7 ILGKIILFL 15 37 EGIGGTIPH 15 30
EKSQFLEEG 14 3 PSIVILGKI 12 10 KIILFLPCI 12 45 HVSPERVTV 12 4
SIVILGKII 11 14 FLPCISRKL 11 27 KGWEKSQFL 11 36 EEGIGGTIP 11 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V7A-HLA-A26-9mers-98P4B6 7 ETFLPNGIN 23 1 SPKSLSETF
12 V7B-HLA-A26-9mers-98P4B6 9 STLGYVALL 21 5 AYQQSTLGY 11 3
NMAYQQSTL 10 8 QSTLGYVAL 10 V7C-HLA-A26-9mers-98P4B6 169 ETIILSKLT
23 34 EIVLPIEWQ 22 11 EVLASPAAA 21 151 FTSWSLGEF 21 179 EQKSKHCMF
21 126 GVGPLWEFL 20 3 IVILDLSVE 19 85 PVVGVVTED 18 168 LETIILSKL 17
125 NGVGPLWEF 16 132 EFLLRLLKS 16 95 EAQDSIDPP 15 129 PLWEFLLRL 15
7 DLSVEVLAS 14 35 IVLPIEWQQ 14 68 EAQESGIRN 14 88 GVVTEDDEA 14 89
VVTEDDEAQ 14 98 DSIDPPESP 14 122 PHTNGVGPL 14 163 GTWMKLETI 14 9
SVEVLASPA 13 42 QQDRKIPPL 13 92 EDDEAQDSI 13 104 ESPDRALKA 13 130
LWEFLLRLL 13 2 SIVILDLSV 12 5 ILDLSVEVL 12 59 WTEEAGATA 12 152
TSWSLGEFL 12 176 LTQEQKSKH 12 8 LSVEVLASP 11 45 RKIPPLSTP 11 51
STPPPPAMW 11 62 EAGATAEAQ 11 65 ATAEAQESG 11 71 ESGIRNKSS 11 82
SQIPVVGVV 11 119 PVLPHTNGV 11 141 QAASGTLSL 11 143 ASGTLSLAF 11 145
GTLSLAFTS 11 158 EFLGSGTWM 11 170 TIILSKLTQ 11 171 IILSKLTQE 11 185
CMFSLISGS 11 Each peptide is a portion of SEQ ID NO: 17; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V8-HLA-A26-9mers-98P4B6 6 EEGMGGTIP 11 7
EGMGGTIPH 11 2 SQFLEEGMG 7 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V13-HLA-A26-9mers-98P4B6 7
ETFLPNGIN 23 1 SPKSLSETF 12 Each peptide is a portion of SEQ ID NO:
29; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V14-HLA-A26-9mers-98P4B6 1
NLPLRLFTF 13 7 FTFWRGPVV 13 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V21-HLA-A26-9mers-98P4B6 6
EQKTKHCMF 20 8 KTKHCMFSL 17 3 LTQEQKTKH 11 Each peptide is a
portion of SEQ ID NO: 51; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V25-HLA-A26-9mers-98P4B6 3 FLPCISQKL 11 6 CISQKLKRI 9 2 LFLPCISQK 7
5 PCISQKLKR 7 1 ILFLPCISQ 6 9 QKLKRIKKG 5
[1249]
50TABLE XXVII Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-B0702-9mers-98P4B6 428 TPPNFVLAL 24 438
LPSIVILDL 24 259 LPIVAITLL 21 291 FPPWLETWL 21 125 YPESNAEYL 20 214
GPVVVAISL 20 250 IPIEIVNKT 18 62 NPKFASEFF 17 211 LWRGPVVVA 17 429
PPNFVLALV 17 157 GPKDASRQV 16 326 RRSERYLFL 16 148 VVSAWALQL 15 198
AREIENLPL 15 365 IMSLGLLSL 15 426 FYTPPNFVL 15 93 IHREHYTSL 14 220
ISLATFFFL 14 261 IVAITLLSL 14 287 KYRRFPPWL 14 379 IPSVSNALN 14 396
STLGYVALL 14 5 SMMGSPKSL 13 10 PKSLSETCL 13 137 FPDSLIVKG 13 173
QARQQVIEL 13 200 EIENLPLRL 13 264 ITLLSLVYL 13 289 RRFPPWLET 13 300
QCRKQLGLL 13 315 VHVAYSLCL 13 362 SFGIMSLGL 13 390 EFSFIQSTL 13 395
QSTLGYVAL 13 430 PNFVLALVL 13 436 LVLPSIVIL 13 441 IVILDLLQL 13 18
LPNGINGIK 12 27 DARKVTVGV 12 50 IRCGYHVVI 12 70 FPHVVDVTH 12 105
RHLLVGKIL 12 128 SNAEYLASL 12 133 LASLFPDSL 12 188 IPIDLGSLS 12 202
ENLPLRLFT 12 204 LPLRLFTLW 12 212 WRGPVVVAI 12 219 AISLATFFF 12 256
NKTLPIVAI 12 299 LQCRKQLGL 12 313 AMVHVAYSL 12 324 PMRRSERYL 12 360
YISFGIMSL 12 366 MSLGLLSLL 12 403 LLISTFHVL 12 435 ALVLPSIVI 12 25
IKDARKVTV 11 37 GSGDFAKSL 11 41 FAKSLTIRL 11 68 EFFPHVVDV 11 75
DVTHHEDAL 11 85 KTNIIFVAI 11 96 EHYTSLWDL 11 100 SLWDLRHLL 11 134
ASLFPDSLI 11 146 FNVVSAWAL 11 196 SSAREIENL 11 237 HPYARNQQS 11 253
EIVNKTLPI 11 267 LSLVYLAGL 11 271 YLAGLLAAA 11 274 GLLAAAYQL 11 292
PPWLETWLQ 11 297 TWLQCRKQL 11 323 LPMRRSERY 11 328 SERYLFLNM 11 378
SIPSVSNAL 11 394 IQSTLGYVA 11 425 RFYTPPNFV 11 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V2-HLA-B0702-9mers-98P4B6 3 SPGLQALSL 23 35 PPCPADFFL 22 34
PPPCPADFF 20 37 CPADFFLYF 20 33 CPPPCPADF 18 1 SGSPGLQAL 14 15
SGFTPFSCL 14 5 GLQALSLSL 13 17 FTPFSCLSL 12 25 LPSSWDYRC 12 12
SLSSGFTPF 11 31 YRCPPPCPA 11 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V5A-HLA-B0702-9mers-98P4B6
9 FWRGPVVVA 17 2 LPLRLFTFW 13 7 FTFWRGPVV 9 8 TFWRGPVVV 9 6
LFTFWRGPV 8 V5B-HLA-B0702-9mers-98P4B6 19 ELELEFVFL 15 14 ADTQTELEL
14 24 FVFLLTLLL 13 12 SFADTQTEL 12 22 LEFVFLLTL 12 23 EFVFLLTLL 12
20 LELEFVFLL 11 21 ELEFVFLLT 10 10 FCSFADTQT 9 8 QIFCSFADT 8 16
TQTELELEF 8 1 WREFSFIQI 7 2 REFSFIQIF 7 5 SFIQIFCSF 7 6 FIQIFCSFA 7
17 QTELELEFV 7 18 TELELEFVF 7 Each peptide is a portion of SEQ ID
NO: 13; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V6-HLA-B0702-9mers-98P4B6
43 IPHVSPERV 17 7 ILGKIILFL 16 2 LPSIVILGK 14 27 KGWEKSQFL 12 45
HVSPERVTV 12 5 IVILGKIIL 11 15 LPCISRKLK 11 14 FLPCISRKL 10 38
GIGGTIPHV 10 44 PHVSPERVT 10 35 LEEGIGGTI 9 46 VSPERVTVM 9 6
VILGKIILF 8 10 KIILFLPCI 8 17 CISRKLKRI 8 26 KKGWEKSQF 8 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V7A-HLA-B0702-9mers-98P4B6 1 SPKSLSETF 16 2
PKSLSETFL 14 V7B-HLA-B0702-9mers-98P4B6 9 STLGYVALL 14 8 QSTLGYVAL
13 3 NMAYQQSTL 11 7 QQSTLGYVA 10 2 LNMAYQQST 8 6 YQQSTLGYV 6
V7C-HLA-B0702-9mers-98P4B6 102 PPESPDRAL 24 15 SPAAAWKCL 22 52
TPPPPAMWT 20 55 PPAMWTEEA 18 105 SPDRALKAA 18 101 DPPESPDRA 16 113
ANSWRNPVL 16 5 ILDLSVEVL 14 47 IPPLSTPPP 14 84 IPVVGVVTE 14 118
NPVLPHTNG 14 141 QAASGTLSL 14 160 LGSGTWMKL 14 29 RGGLSEIVL 13 42
QQDRKIPPL 13 49 PLSTPPPPA 13 121 LPHTNGVGP 13 126 GVGPLWEFL 13 128
GPLWEFLLR 13 31 GLSEIVLPI 12 48 PPLSTPPPP 12 50 LSTPPPPAM 12 54
PPPAMWTEE 12 61 EEAGATAEA 12 81 SSQIPVVGV 12 122 PHTNGVGPL 12 129
PLWEFLLRL 12 139 KSQAASGTL 12 142 AASGTLSLA 12 143 ASGTLSLAF 12 152
TSWSLGEFL 12 17 AAAWKCLGA 11 24 GANILRGGL 11 27 ILRGGLSEI 11 44
DRKIPPLST 11 53 PPPPAMWTE 11 125 NGVGPLWEF 11 148 SLAFTSWSL 11 158
EFLGSGTWM 11 165 WMKLETIIL 11 181 KSKHCMFSL 11 Each peptide is a
portion of SEQ ID NO: 17; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V8-HLA-B0702-9mers-98P4B6 8 GMGGTIPHV 10 5 LEEGMGGTI 9 1 KSQFLEEGM
7 4 FLEEGMGGT 6 7 EGMGGTIPH 6 6 EEGMGGTIP 4 Each peptide is a
portion of SEQ ID NO: 27; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V13-HLA-B0702-9mers-98P4B6 1 SPKSLSETF 16 2 PKSLSETFL 14 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V14-HLA-B0702-9mers-98P4B6 9 FWRGPVVVA 17 2
LPLRLFTFW 13 7 FTFWRGPVV 9 8 TFWRGPVVV 9 6 LFTFWRGPV 8 Each peptide
is a portion of SEQ ID NO: 43; each start position is specified,
the length of peptide is 9 amino acids, and the end position for
each peptide is the start position plus eight. Pos 123456789 score
V21-HLA-B0702-9mers-98P4B6 8 KTKHCMFSL 11 5 QEQKTKHCM 7 6 EQKTKHCMF
7 9 TKHCMFSLI 7 1 SKLTQEQKT 6 Each peptide is a portion of SEQ ID
NO: 51; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V25-HLA-B0702-9mers-98P4B6
3 FLPCISQKL 10 4 LPCISQKLK 10 6 CISQKLKRI 8 1 ILFLPCISQ 4
[1250]
51TABLE XXVIII Each peptide is a portion of SEQ ID NO: 3; each
start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. Pos 123456789 score V1-HLA-B08-9mers-98P4B6 41
FAKSLTIRL 25 203 NLPLRLFTL 25 62 NPKFASEFF 22 173 QARQQVIEL 22 253
EIVNKTLPI 22 57 VIGSRNPKF 20 81 DALTKTNII 20 285 GTKYRRFPP 20 299
LQCRKQLGL 20 326 RRSERYLFL 20 385 ALNWREFSF 20 93 IHREHYTSL 19 140
SLIVKGFNV 19 268 SLVYLAGLL 19 9 SPKSLSETC 18 28 ARKVTVGVI 18 100
SLWDLRHLL 18 171 NIQARQQVI 18 214 GPVVVAISL 18 259 LPIVAITLL 18 428
TPPNFVLAL 18 39 GDFAKSLTI 17 107 LLVGLILID 17 157 GPKDASRQV 17 274
GLLAAAYQL 17 291 FPPWLETWL 17 378 SIPSVSNAL 17 438 LPSIVILDL 17 24
GIKDARKVT 16 44 SLTIRLIRC 16 125 YPESNAEYL 16 155 QLGPKDASR 16 184
QLNFIPIDL 16 200 EIENLPLRL 16 237 HPYARNQQS 16 239 YARNQQSDF 16 251
PIEIVNKTL 16 258 TLPIVAITL 16 283 YYGTKYRRF 16 287 KYRRFPPWL 16 300
QCRKQLGLL 16 324 PMRRSERYL 16 403 LLISTFHVL 16 133 LASLFPDSL 15 159
KDASRQVYI 15 179 IELARQLNF 15 187 FIPIDLGSL 15 322 CLPMRRSER 15 360
YISFGIMSL 15 106 HLLVGKILI 14 128 SNAEYLASL 14 180 ELARQLNFI 14 197
SAREIENLP 14 245 SDFYKIPIE 14 298 WLQCRKQLG 14 323 LPMRRSERY 14 433
VLALVLPSI 14 5 SMMGSPKSL 13 17 CLPNGINGI 13 82 ALTKTNIIF 13 91
VAIHREHYT 13 103 DLRHLLVGK 13 142 IVKGFNVVS 13 146 FNVVSAWAL 13 196
SSAREIENL 13 205 PLRLFTLWR 13 264 ITLLSLVYL 13 304 QLGLLSFFF 13 395
QSTLGYVAL 13 396 STLGYVALL 13 397 TLGYVALLI 13 435 ALVLPSIVI 13 37
GSGDFAKSL 12 60 SRNPKFASE 12 96 EHYTSLWDL 12 105 RHLLVGKIL 12 109
VGKILIDVS 12 177 QVIELARQL 12 247 FYKIPIEIV 12 325 MRRSERYLF 12 362
SFGIMSLGL 12 365 IMSLGLLSL 12 390 EFSFIQSTL 12 414 GWKRAFEEE 12 426
FYTPPNFVL 12 436 LVLPSIVIL 12 441 IVILDLLQL 12 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V2-HLA-B08-9mers-98P4B6 3 SPGLQALSL 19 5 GLQALSLSL 17 35 PPCPADFFL
16 12 SLSSGFTPF 14 1 SGSPGLQAL 13 15 SGFTPFSCL 12 33 CPPPCPADF 12
34 PPPCPADFF 12 37 CPADFFLYF 12 17 FTPFSCLSL 11 28 SWDYRCPPP 11 10
SLSLSSGFT 9
[1251]
52TABLE XXIX Each peptide is a portion of SEQ ID NO: 11; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V5A-HLA-B08-9mers-98P4B6 1 NLPLRLFTF 21 3
PLRLFTFWR 13 V5B-HLA-B08-9mers-98P4B6 19 ELELEFVFL 20 12 SFADTQTEL
13 20 LELEFVFLL 13 23 EFVFLLTLL 12 24 FVFLLTLLL 12 14 ADTQTELEL 11
22 LEFVFLLTL 11 16 TQTELELEF 9 Each peptide is a portion of SEQ ID
NO: 13; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V6-HLA-B08-9mers-98P4B6 19
SRKLKRIKK 23 6 VILGKIILF 22 27 KGWEKSQFL 22 17 CISRKLKRI 21 7
ILGKIILFL 18 14 FLPCISRKL 17 21 KLKRIKKGW 17 22 LKRIKKGWE 16 24
RIKKGWEKS 14 4 SIVILGKII 13 5 IVILGKIIL 12 25 IKKGWEKSQ 12 46
VSPERVTVM 12 10 KIILFLPCI 11 23 KRIKKGWEK 11 29 WEKSQFLEE 11 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V7A-HLA-B08-9mers-98P4B6 1 SPKSLSETF 24 9 FLPNGINGI
14 2 PKSLSETFL 11 V7B-HLA-B08-9mers-98P4B6 8 QSTLGYVAL 13 9
STLGYVALL 13 3 NMAYQQSTL 11 1 FLNMAYQQS 7 V7C-HLA-B08-9mers-98P4B6
179 EQKSKHCMF 28 42 QQDRKIPPL 21 73 GIRNKSSSS 21 165 WMKLETIIL 21
27 ILRGGLSEI 20 181 KSKHCMFSL 20 5 ILDLSVEVL 19 15 SPAAAWKCL 19 113
ANSWRNPVL 19 129 PLWEFLLRL 18 148 SLAFTSWSL 18 102 PPESPDRAL 17 109
ALKAANSWR 17 163 GTWMKLETI 17 19 AWKCLGANI 16 31 GLSEIVLPI 16 137
LLKSQAASG 16 24 GANILRGGL 15 171 IILSKLTQE 15 17 AAAWKCLGA 14 141
QAASGTLSL 14 134 LLRLLKSQA 13 Each peptide is a portion of SEQ ID
NO: 17; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V8-HLA-B08-9mers-98P4B6 4
FLEEGMGGT 9 5 LEEGMGGTI 6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V13-HLA-B08-9mers-98P4B6 1
SPKSLSETF 24 9 FLPNGINGI 14 2 PKSLSETFL 11 Each peptide is a
portion of SEQ ID NO: 29; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V14-HLA-B08-9mers-98P4B6 1 NLPLRLFTF 21 3 PLRLFTFWR 13 Each peptide
is a portion of SEQ ID NO: 43; each start position is specified,
the length of peptide is 9 amino acids, and the end position for
each peptide is the start position plus eight. Pos 123456789 score
V21-HLA-B08-9mers-98P4B6 6 EQKTKHCMF 28 8 KTKHCMFSL 20 4 TQEQKTKHC
11 Each peptide is a portion of SEQ ID NO: 51; each start position
is specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V25-HLA-B08-9mers-98P4B6 8 SQKLKRIKK 23 6 CISQKLKRI
21 3 FLPCISQKL 17 Each peptide is a portion of SEQ ID NO: 3; each
start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. Pos 123456789 score V1-HLA-B1510-9mers-98P4B6 93
IHREHYTSL 23 96 EHYTSLWDL 21 105 RHLLVGKHL 20 315 VHVAYSLCL 20 200
EIENLPLRL 15 426 FYTPPNFVL 15 436 LVLPSIVIL 15 54 YHVVIGSRN 14 264
ITLLSLVYL 14 360 YISFGIMSL 14 365 IMSLGLLSL 14 395 QSTLGYVAL 14 77
THHEDALTK 13 99 TSLWDLRHL 13 125 YPESNAEYL 13 173 QARQQVIEL 13 177
QVIELARQL 13 236 IHPYARNQQ 13 261 IVAITLLSL 13 297 TWLQCRKQL 13 390
EFSFIQSTL 13 428 TPPNFVLAL 13 430 PNFVLALVL 13 5 SMMGSPKSL 12 37
GSGDFAKSL 12 41 FAKSLTIRL 12 71 PHVVDVTHH 12 78 HHEDALTKT 12 100
SLWDLRHLL 12 128 SNAEYLASL 12 133 LASLFPDSL 12 146 FNVVSAWAL 12 196
SSAREIENL 12 214 GPVVVAISL 12 220 ISLATFFFL 12 251 PIEIVNKTL 12 258
TLPIVAITL 12 259 LPIVAITLL 12 287 KYRRFPPWL 12 324 PMRRSERYL 12 326
RRSERYLFL 12 396 STLGYVALL 12 403 LLISTFHVL 12 438 LPSIVILDL 12 441
IVILDLLQL 12 10 PKSLSETCL 11 75 DVTHHEDAL 11 148 VVSAWALQL 11 184
QLNFIPIDL 11 198 AREIENLPL 11 201 IENLPLRLF 11 203 NLPLRLFTL 11 267
LSLVYLAGL 11 274 GLLAAAYQL 11 283 YYGTKYRRF 11 300 QCRKQLGLL 11 341
VHANIENSW 11 351 EEEVWRIEM 11 366 MSLGLLSLL 11 378 SIPSVSNAL 11 383
SNALNWREF 11 411 LIYGWKRAF 11 439 PSIVILDLL 11 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V2-HLA-B1510-9mers-98P4B6 1 SGSPGLQAL 15 35 PPCPADFFL 12 5
GLQALSLSL 11 15 SGFTPFSCL 11 3 SPGLQALSL 10 17 FTPFSCLSL 10 33
CPPPCPADF 9 12 SLSSGFTPF 8 37 CPADFFLYF 8 34 PPPCPADFF 7 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V5A-HLA-B1510-9mers-98P4B6 1 NLPLRLFTF 7 8
TFWRGPVVV 7 9 FWRGPVVVA 7 7 FTFWRGPVV 3 V5B-HLA-B1510-9mers-98P4B6
19 ELELEFVFL 14 12 SFADTQTEL 13 14 ADTQTELEL 12 20 LELEFVFLL 12 22
LEFVFLLTL 12 23 EFVFLLTLL 11 18 TELELEFVF 10 24 FVFLLTLLL 10 16
TQTELELEF 9 2 REFSFIQIF 7 5 SFIQIFCSF 7 Each peptide is a portion
of SEQ ID NO: 13; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V6-HLA-B1510-9mers-98P4B6 44 PHVSPERVT 15 5 IVILGKIIL 14 7
ILGKIILFL 14 14 FLPCISRKL 12 27 KGWEKSQFL 11 46 VSPERVTVM 10 6
VILGKIILF 8 26 KKGWEKSQF 7 45 HVSPERVTV 7 Each peptide is a portion
of SEQ ID NO: 15; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V7A-HLA-B1510-9mers-98P4B6 2 PKSLSEFTL 11 1 SPKSLSETF 7
V7B-HLA-B1510-9mers-98P4B6 8 QSTLGYVAL 14 3 NMAYQQSTL 12 9
STLGYVALL 12 V7C-HLA-B1510-9mers-98P4B6 122 PHTNGVGPL 22 5
ILDLSVEVL 15 102 PPESPDRAL 15 113 ANSWRNPVL 14 126 GVGPLWEFL 13 129
PLWEFLLRL 13 130 LWEFLLRLL 13 24 GANILRGGL 12 29 RGGLSEIVL 12 42
QQDRKIPPL 12 50 LSTPPPPAM 12 141 QAASGTLSL 12 160 LGSGTWMKL 12 15
SPAAAWKCL 11 20 WKCLGANIL 11 139 KSQAASGTL 11 148 SLAFTSWSL 11 152
TSWSLGEFL 11 181 KSKHCMFSL 11 127 VGPLWEFLL 10 165 WMKLETIIL 10 168
LETIILSKL 10 183 KHCMFSLIS 10 Each peptide is a portion of SEQ ID
NO: 17; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V8-HLA-B1510-9mers-98P4B6
1 KSQFLEEGM 6 4 FLEEGMGGT 4 8 GMGGTIPHV 4 5 LEEGMGGTI 3 7 EGMGGTIPH
3 9 MGGTIPHVS 3 6 EEGMGGTIP 2 Each peptide is a portion of SEQ ID
NO: 27; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V13-HLA-B1510-9mers-98P4B6
2 PKSLSETFL 11 1 SPKSLSETF 7 Each peptide is a portion of SEQ ID
NO: 29; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V14-HLA-B1510-9mers-98P4B6
1 NLPLRLFTF 7 8 TFWRGPVVV 7 9 FWRGPVVVA 7 7 FTFWRGPVV 3 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V21-HLA-B1510-9mers-98P4B6 8 KTKHCMFSL 11 5
QEQKTKHCM 8 6 EQKTKHCMF 7 4 TQEQKTKHC Each peptide is a portion of
SEQ ID NO: 51; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V25-HLA-B1510-9mers-98P4B6 3 FLPCISQKL 10 7 ISQKLKRIK 6 6 CISQKLKRI
4
[1252]
53TABLE XXX Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-B2705-9mers-98P4B6 326 RRSERYLFL 26 424
YRFYTPPNF 26 355 WRIEMYISF 26 198 AREIENLPL 24 240 ARNQQSDFY 22 325
MRRSERYLF 22 47 IRLIRCGYH 21 50 IRCGYHVVI 21 104 LRHLLVGKI 21 289
RRFPPWLET 21 416 KRAFEEEYY 21 212 WRGPVVVAI 20 302 RKQLGLLSF 20 417
RAFEEEYYR 20 28 ARKVTVGVI 19 61 RNPKFASEF 19 182 ARQLNFIPI 19 199
REIENLPLR 19 249 KIPIEIVNK 19 303 KQLGLLSFF 19 53 GYHVVIGSR 18 105
RHLLVGKIL 18 179 IELARQLNF 18 214 GPVVVAISL 18 241 RNQQSDFYK 18 274
GLLAAAYQL 18 282 LYYGTKYRR 18 436 LVLPSIVIL 18 21 GINGIKDAR 17 174
ARQQVIELA 17 223 ATFFFLYSF 17 259 LPIVAITLL 17 264 ITLLSLVYL 17 330
RYLFLNMAY 17 360 YISFGIMSL 17 365 IMSLGLLSL 17 366 MSLGLLSLL 17 400
YVALLISTF 17 430 PNFVLALVL 17 441 IVILDLLQL 17 22 INGIKDARK 16 39
GDFAKSLTI 16 40 DFAKSLTIR 16 43 KSLTIRLIR 16 56 VVIGSRNPK 16 112
ILIDVSNNM 16 175 RQQVIELAR 16 177 QVIELARQL 16 196 SSAREIENL 16 206
LRLFTLWRG 16 218 VAISLATFF 16 225 FFFLYSFVR 16 233 RDVIHPYAR 16 313
AMVHVAYSL 16 319 YSLCLPMRR 16 396 STLGYVALL 16 418 AFEEEYYRF 16 443
ILDLLQLCR 16 37 GSGDFAKSL 15 82 ALTKTNIIF 15 87 NIIFVAIHR 15 93
IHREHYTSL 15 96 EHYTSLWDL 15 155 QLGPKDASR 15 173 QARQQVIEL 15 295
LETWLQCRK 15 297 TWLQCRKQL 15 329 ERYLFLNMA 15 390 EFSFIQSTL 15 401
VALLISTFH 15 409 HVLIYGWKR 15 411 LIYGWKRAF 15 438 LPSIVILDL 15 5
SMMGSPKSL 14 10 PKSLSETCL 14 18 LPNGINGIK 14 33 VGVIGSGDF 14 41
FAKSLTIRL 14 57 VIGSRNPKF 14 60 SRNPKFASE 14 77 THHEDALTK 14 120
MRINQYPES 14 128 SNAEYLASL 14 136 LFPDSLIVK 14 146 FNVVSAWAL 14 162
SRQVYICSN 14 167 ICSNNIQAR 14 193 GSLSSAREI 14 200 EIENLPLRL 14 201
IENLPLRLF 14 217 VVAISLATF 14 258 TLPIVAITL 14 261 IVAITLLSL 14 263
AITLLSLVY 14 267 LSLVYLAGL 14 280 YQLYYGTKY 14 281 QLYYGTKYR 14 299
LQCRKQLGL 14 301 CRKQLGLLS 14 308 LSFFFAMVH 14 318 AYSLCLPMR 14 363
FGIMSLGLL 14 392 SFIQSTLGY 14 395 QSTLGYVAL 14 426 FYTPPNFVL 14 439
PSIVILDLL 14 444 LDLLQLCRY 14 35 VIGSGDFAK 13 98 YTSLWDLRH 13 99
TSLWDLRHL 13 103 DLRHLLVGK 13 113 LIDVSNNMR 13 117 SNNMRINQY 13 124
QYPESNAEY 13 129 NAEYLASLF 13 138 PDSLIVKGF 13 148 VVSAWALQL 13 151
AWALQLGPK 13 191 DLGSLSSAR 13 203 NLPLRLFTL 13 220 ISLATFFFL 13 229
YSFVRDVIH 13 239 YARNQQSDF 13 246 DFYKIPIEI 13 251 PIEIVNKTL 13 268
SLVYLAGLL 13 279 AYQLYYGTK 13 283 YYGTKYRRF 13 287 KYRRFPPWL 13 291
FPPWLETWL 13 300 QCRKQLGLL 13 304 QLGLLSFFF 13 306 GLLSFFFAM 13 315
VHVAYSLCL 13 337 AYQQVHANI 13 348 SWNEEEVWR 13 371 LSLLAVTSI 13 378
SIPSVSNAL 13 388 WREFSFIQS 13 403 LLISTFHVL 13 408 FHVLIYGWK 13 435
ALVLPSIVI 13 17 CLPNGINGI 12 70 FPHVVDVTH 12 71 PHVVDVTHH 12 80
EDALTKTNI 12 86 TNIIFVAIH 12 89 IFVAIHREH 12 106 HLLVGKILI 12 114
IDVSNNMRI 12 133 LASLFPDSL 12 134 ASLFPDSLI 12 164 QVYICSNNI 12 184
QLNFIPIDL 12 187 FIPIDLGSL 12 205 PLRLFTLWR 12 219 AISLATFFF 12 231
FVRDVIHPY 12 232 VRDVIHPYA 12 256 NKTLPIVAI 12 272 LAGLLAAAY 12 288
YRRFPPWLE 12 317 VAYSLCLPM 12 322 CLPMRRSER 12 328 SERYLFLNM 12 349
WNEEEVWRI 12 352 EEVWRIEMY 12 362 SFGIMSLGL 12 381 SVSNALNWR 12 383
SNALNWREF 12 385 ALNWREFSF 12 428 TPPNFVLAL 12 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V2-HLA-B2705-9mers-98P4B6 5 GLQALSLSL 17 9 LSLSLSSGF 15 15
SGFTPFSCL 15 1 SGSPGLQAL 14 3 SPGLQALSL 14 12 SLSSGFTPF 14 23
LSLPSSWDY 14 17 FTPFSCLSL 13 31 YRCPPPCPA 12 33 CPPPCPADF 12 34
PPPCPADFF 12 35 PPCPADFFL 12 24 SLPSSWDYR 11 37 CPADFFLYF 11 2
GSPGLQALS 9 36 PCPADFFLY 8 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V5A-HLA-B2705-9mers-98P4B6
4 LRLFTFWRG 15 1 NLPLRLFTF 13 3 PLRLFTFWR 11 5 RLFTFWRGP 7
V5B-HLA-B2705-9mers-98P4B6 2 REFSFIQIF 20 1 WREFSFIQI 19 5
SFIQIFCSF 16 22 LEFVFLLTL 16 24 FVFLLTLLL 16 12 SFADTQTEL 15 14
ADTQTELEL 15 18 TELELEFVF 15 23 EFVFLLTLL 15 16 TQTELELEF 14 20
LELEFVFLL 14 19 ELELEFVFL 13 Each peptide is a portion of SEQ ID
NO: 13; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V6-HLA-B2705-9mers-98P4B6
23 KRIKKGWEK 29 19 SRKLKRIKK 25 6 VILGKIILF 19 13 LFLPCISRK 19 5
IVILGKIIL 18 7 ILGKIILFL 18 12 ILFLPCISR 18 16 PCISRKLKR 16 26
KKGWEKSQF 16 2 LPSIVILGK 15 18 ISRKLKRIK 15 27 KGWEKSQFL 15 37
EGIGGTIPH 15 14 FLPCISRKL 14 42 TIPHVSPER 14 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V7A-HLA-B2705-9mers-98P4B6 2 PKSLSETFL 14 1 SPKSLSETF 13 9
FLPNGINGI 12 6 SETFLPNGI 8 7 ETFLPNGIN 6 8 TFLPNGING 6
V7B-HLA-B2705-9mers-98P4B6 9 STLGYVALL 16 3 NMAYQQSTL 14 8
QSTLGYVAL 14 5 AYQQSTLGY 13 4 MAYQQSTLG 7 V7C-HLA-B2705-9mers-98P4-
B6 21 KCLGANILR 18 29 RGGLSEIVL 18 69 AQESGIRNK 18 167 KLETIILSK 18
175 KLTQEQKSK 18 74 IRNKSSSSS 17 125 NGVGPLWEF 17 128 GPLWEFLLR 17
107 DRALKAANS 16 131 WEFLLRLLK 16 5 ILDLSVEVL 15 20 WKCLGANIL 15 37
LPIEWQQDR 15 42 QQDRKIPPL 15 67 AEAQESGIR 15 100 IDPPESPDR 15 126
GVGPLWEFL 15 129 PLWEFLLRL 15 135 LRLLKSQAA 15 158 EFLGSGTWM 15 160
LGSGTWMKL 15 168 LETIILSKL 15 24 GANILRGGL 14 27 ILRGGLSEI 14 28
LRGGLSEIV 14 38 PIEWQQDRK 14 113 ANSWRNPVL 14 116 WRNPVLPHT 14 139
KSQAASGTL 14 141 QAASGTLSL 14 143 ASGTLSLAF 14 173 LSKLTQEQK 14 13
LASPAAAWK 13 31 GLSEIVLPI 13 44 DRKIPPLST 13 109 ALKAANSWR 13 122
PHTNGVGPL 13 148 SLAFTSWSL 13 151 FTSWSLGEF 13 159 FLGSGTWMK 13 165
WMKLETIIL 13 176 LTQEQKSKH 13 181 KSKHCMFSL 13 39 IEWQQDRKI 12 102
PPESPDRAL 12 103 PESPDRALK 12 130 LWEFLLRLL 12 136 RLLKSQAAS 12 163
GTWMKLETI 12 178 QEQKSKHCM 12 19 AWKCLGANI 11 45 RKIPPLSTP 11 50
LSTPPPPAM 11 108 RALKAANSW 11 115 SWRNPVLPH 11 127 VGPLWEFLL 11 152
TSWSLGEFL 11 157 GEFLGSGTW 11 164 TWMKLETII 11 179 EQKSKHCMF 11 15
SPAAAWKCL 10 30 GGLSEIVLP 10 76 NKSSSSSQI 10 92 EDDEAQDSI 10 75
RNKSSSSSQ 8 85 PVVGVVTED 8 145 GTLSLAFTS 8 171 IILSKLTQE 8 185
CMFSLISGS 8 Each peptide is a portion of SEQ ID NO: 17; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V8-HLA-B2705-9mers-98P4B6 7 EGMGGTIPH 13 1
KSQFLEEGM 11 5 LEEGMGGTI 9 8 GMGGTIPHV 9 Each peptide is a portion
of SEQ ID NO: 27; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V13-HLA-B2705-9mers-98P4B6 2 PKSLSETFL 14 1 SPKSLSETF 13 9
FLPNGINGI 12 6 SETFLPNGI 8 7 ETFLPNGIN 6 8 TFLPNGING 6 Each peptide
is a portion of SEQ ID NO: 29; each start position is specified,
the length of peptide is 9 amino acids, and the end position for
each peptide is the start position plus eight. Pos 123456789 score
V14-HLA-B2705-9mers-98P4B6 4 LRLFTFWRG 15 1 NLPLRLFTF 13 3
PLRLFTFWR 11 5 RLFTFWRGP 7 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V21-HLA-B2705-9mers-98P4B6
2 KLTQEQKTK 18 3 LTQEQKTKH 14 8 KTKHCMFSL 13 5 QEQKTKHCM 11 6
EQKTKHCMF 11 Each peptide is a portion of SEQ ID NO: 51; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V25-HLA-B2705-9mers-98P4B6 2 LFLPCISQK 18 5
PCISQKLKR 16 7 ISQKLKRIK 15 8 SQKLKRIKK 15 3 FLPCISQKL 14 4
LPCISQKLK 13 6 CISQKLKRI 12 9 QKLKRIKKG 9 1 ILFLPCISQ 8
[1253]
54TABLE XXXI Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-B2709-9mers-98P4B6 326 RRSERYLFL 25 198
AREIENLPL 22 424 YRFYTPPNF 22 212 WRGPVVVAI 21 28 ARKVTVGVI 20 50
IRCGYHVVI 20 325 MRRSERYLF 19 104 LRHLLVGKI 19 182 ARQLNFIPI 19 355
WRIEMYISF 19 274 GLLAAAYQL 18 289 RRFPPWLET 18 105 RHLLVGKIL 16 193
GSLSSAREI 15 214 GPVVVAISL 15 441 IVILDLLQL 15 37 GSGDFAKSL 14 39
GDFAKSLTI 14 48 RLIRCGYHV 14 264 ITLLSLVYL 14 306 GLLSFFFAM 14 313
AMVHVAYSL 14 425 RFYTPPNFV 14 430 PNFVLALVL 14 436 LVLPSIVIL 14 47
IRLIRCGYH 13 61 PNPKFASEF 13 68 EFFPHVVDV 13 99 TSLWDLRHL 13 135
SLFPDSLIV 13 148 VVSAWALQL 13 177 QVIELARQL 13 179 IELARQLNF 13 206
LRLFTLWRG 13 220 ISLATFFFL 13 287 KYRRFPPWL 13 297 TWLQCRKQL 13 302
RKQLGLLSF 13 396 STLGYVALL 13 41 FAKSLTIRL 12 85 KTNIIFVAI 12 96
EHYTSLWDL 12 114 IDVSNNMRI 12 120 MRINQYPES 12 125 YPESNAEYL 12 146
FNVVSAWAL 12 157 GPKDASRQV 12 159 KDASRQVYI 12 200 EIENLPLRL 12 223
ATFFFLYSF 12 227 FLYSFVRDV 12 232 VRDVIHPYA 12 261 IVAITLLSL 12 267
LSLVYLAGL 12 268 SLVYLAGLL 12 303 KQLGLLSFF 12 315 VHVAYSLCL 12 317
VAYSLCLPM 12 329 ERYLFLNMA 12 365 IMSLGLLSL 12 366 MSLGLLSLL 12 395
QSTLGYVAL 12 403 LLISTFHVL 12 416 KRAFEEEYY 12 426 FYTPPNFVL 12 428
TPPNFVLAL 12 439 PSIVILDLL 12 Each peptide is a portion of SEQ ID
NO: 5; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V2-HLA-B2709-9mers-98P4B6
5 GLQALSLSL 14 3 SPGLQALSL 12 15 SGFTPFSCL 12 1 SGSPGLQAL 11 9
LSLSLSSGF 11 17 FTPFSCLSL 11 31 YRCPPPCPA 11 35 PPCPADFFL 11 12
SLSSGFTPF 9 33 CPPPCPADF 9 34 PPPCPADFF 9 37 CPADFFLYF 9 32
RCPPPCPAD 6 Each peptide is a portion of SEQ ID NO: 11; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V5A-HLA-B2709-9mers-98P4B6 4 LRLFTFWRG 13 7
FTFWRGPVV 11 6 LFTFWRGPV 9 8 TFWRGPVVV 9 1 NLPLRLFTF 8 5 RLFTFWRGP
6 V5B-HLA-B2709-9mers-98P4B6 1 WREFSFIQI 19 2 REFSFIQIF 15 14
ADTQTELEL 13 20 LELEFVFLL 13 22 LEFVFLLTL 13 24 FVFLLTLLL 13 19
ELELEFVFL 11 23 EFVFLLTLL 11 5 SFIQIFCSF 10 12 SFADTQTEL 10 16
TQTELELEF 10 18 TELELEFVF 10 Each peptide is a portion of SEQ ID
NO: 13; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V6-HLA-B2709-9mers-98P4B6
7 ILGKIILFL 13 23 KRIKKGWEK 13 5 IVILGKIIL 12 10 KIILFLPCI 12 27
KGWEKSQFL 12 38 GIGGTIPHV 12 14 FLPCISRKL 11 26 KKGWEKSQF 11 3
PSIVILGKI 10 6 VILGKIILF 10 19 SRKLKRIKK 10 31 KSQFLEEGI 10 43
IPHVSPERV 10 45 HVSPERVTV 10 4 SIVILGKII 9 17 CISRKLKRI 9 35
LEEGIGGTI 9 46 VSPERVTVM 9 20 RKLKRIKKG 6 41 GTIPHVSPE 6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V7A-HLA-B2709-9mers-98P4B6 2 PKSLSETFL 10 1
SPKSLSETF 9 6 SETFLPNGI 9 9 FLPNGINGI 8 3 KSLSETFLP 5 8 TFLPNGING
V7B-HLA-B2709-9mers-98P4B6 9 STLGYVALL 13 8 QSTLGYVAL 12 3
NMAYQQSTL 10 6 YQQSTLGYV 9 V7C-HLA-B2709-9mers-98P4B6 28 LRGGLSEIV
18 29 RGGLSEIVL 14 31 GLSEIVLPI 14 126 GVGPLWEFL 14 24 GANILRGGL 13
5 ILDLSVEVL 12 107 DRALKAANS 12 113 ANSWRNPVL 12 116 WRNPVLPHT 12
122 PHTNGVGPL 12 129 PLWEFLLRL 12 135 LRLLKSQAA 12 139 KSQAASGTL 12
141 QAASGTLSL 12 168 LETIILSKL 12 181 KSKHCMFSL 12 4 VILDLSVEV 11
20 WKCLGANIL 11 42 QQDRKIPPL 11 44 DRKIPPLST 11 50 LSTPPPPAM 11 74
IRNKSSSSS 11 82 SQIPVVGVV 11 102 PPESPDRAL 11 119 PVLPHTNGV 11 152
TSWSLGEFL 11 163 GTWMKLETI 11 2 SIVILDLSV 10 15 SPAAAWKCL 10 19
AWKCLGANI 10 76 NKSSSSSQI 10 79 SSSSQIPVV 10 81 SSQIPVVGV 10 112
AANSWRNPV 10 127 VGPLWEFLL 10 130 LWEFLLRLL 10 143 ASGTLSLAF 10 148
SLAFTSWSL 10 158 EFLGSGTWM 10 160 LGSGTWMKL 10 165 WMKLETIIL 10 27
ILRGGLSEI 9 39 IEWQQDRKI 9 78 SSSSSQIPV 9 125 NGVGPLWEF 9 179
EQKSKHCMF 9 66 TAEAQESGI 8 92 EDDEAQDSI 8 151 FTSWSLGEF 8 164
TWMKLETII 8 178 QEQKSKHCM 8 182 SKHCMFSLI 8 Each peptide is a
portion of SEQ ID NO: 17; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V8-HLA-B2709-9mers-98P4B6 8 GMGGTIPHV 12 1 KSQFLEEGM 10 5 LEEGMGGTI
8 Each peptide is a portion of SEQ ID NO: 27; each start position
is specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V13-HLA-B2709-9mers-98P4B6 2 PKSLSETFL 10 1
SPKSLSETF 9 6 SETFLPNGI 9 9 FLPNGINGI 8 3 KSLSETFLP 5 8 TFLPNGING 4
Each peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V14-HLA-B2709-9mers-98P4B6 4 LRLFTFWRG 13 7
FTFWRGPVV 11 6 LFTFWRGPV 9 8 TFWRGPVVV 9 1 NLPLRLFTF 8 5 RLFTFWRGP
6 Each peptide is a portion of SEQ ID NO: 43; each start position
is specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V21-HLA-B2709-9mers-98P4B6 8 KTKHCMFSL 12 5
QEQKTKHCM 8 6 EQKTKHCMF 8 9 TKHCMFSLI 8 Each peptide is a portion
of SEQ ID NO: 51; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V25-HLA-B2709-9mers-98P4B6 3 FLPCISQKL 11 6 CISQKLKRI 9 2 LFLPCISQK
4
[1254]
55TABLE XXXII Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V1-HLA-B4402-9mers-98P4B6 352 EEVWRIEMY 26 201
IENLPLRLF 24 179 IELARQLNF 23 14 SETCLPNGI 21 419 FEEEYYRFY 21 357
IEMYISFGI 20 42 AKSLTIRLI 18 436 LVLPSIVIL 18 117 SNNMRINQY 17 144
KGFNVVSAW 17 259 LPIVAITLL 17 441 IVILDLLQL 17 5 SMMGSPKSL 16 138
PDSLIVKGF 16 177 QVIELARQL 16 199 REIENLPLR 16 203 NLPLRLFTL 16 219
AISLATFFF 16 223 ATFFFLYSF 16 256 NKTLPIVAI 16 263 AITLLSLVY 16 290
RFPPWLETW 16 392 SFIQSTLGY 16 403 LLISTFHVL 16 428 TPPNFVLAL 16 439
PSIVILDLL 16 67 SEFFPHVVD 15 79 HEDALTKTN 15 100 SLWDLRHLL 15 130
AEYLASLFP 15 182 ARQLNFIPI 15 196 SSAREIENL 15 200 EIENLPLRL 15 212
WRGPVVVAI 15 231 FVRDVIHPY 15 252 IEIVNKTLP 15 297 TWLQCRKQL 15 363
FGIMSLGLL 15 378 SIPSVSNAL 15 389 REFSFIQST 15 390 EFSFIQSTL 15 396
STLGYVALL 15 400 YVALLISTF 15 421 EEYYRFYTP 15 430 PNFVLALVL 15 438
LPSIVILDL 15 17 CLPNGINGI 14 37 GSGDFAKSL 14 82 ALTKTNIIF 14 85
KTNIIFVAI 14 96 EHYTSLWDL 14 105 RHLLVGKIL 14 148 VVSAWALQL 14 198
AREIENLPL 14 204 LPLRLFTLW 14 218 VAISLATFF 14 221 SLATFFFLY 14 258
TLPIVAITL 14 264 ITLLSLVYL 14 272 LAGLLAAAY 14 303 KQLGLLSFF 14 313
AMVHVAYSL 14 351 EEEVWRIEM 14 355 WRIEMYISF 14 360 YISFGIMSL 14 365
IMSLGLLSL 14 366 MSLGLLSLL 14 383 SNALNWREF 14 385 ALNWREFSF 14 395
QSTLGYVAL 14 411 LIYGWKRAF 14 426 FYTPPNFVL 14 435 ALVLPSIVI 14 28
ARKVTVGVI 13 46 TIRLIRCGY 13 99 TSLWDLRHL 13 126 PESNAEYLA 13 129
NAEYLASLF 13 133 LASLFPDSL 13 134 ASLFPDSLI 13 146 FNVVSAWAL 13 158
PKDASRQVY 13 180 ELARQLNFI 13 184 QLNFIPIDL 13 240 ARNQQSDFY 13 251
PIEIVNKTL 13 253 EIVNKTLPI 13 268 SLVYLAGLL 13 274 GLLAAAYQL 13 286
TKYRRFPPW 13 287 KYRRFPPWL 13 302 RKQLGLLSF 13 311 FFAMVHVAY 13 323
LPMRRSERY 13 326 RRSERYLFL 13 328 SERYLFLNM 13 330 RYLFLNMAY 13 341
VHANIENSW 13 347 NSWNEEEVW 13 380 PSVSNALNW 13 407 TFHVLIYGW 13 418
AFEEEYYRF 13 420 EEEYYRFYT 13 424 YRFYTPPNF 13 444 LDLLQLCRY 13 10
PKSLSETCL 12 39 GDFAKSLTI 12 41 FAKSLTIRL 12 57 VIGSRNPKF 12 61
RNPKFASEF 12 75 DVTHHEDAL 12 81 DALTKTNII 12 94 HREHYTSLW 12 125
YPESNAEYL 12 128 SNAEYLASL 12 173 QARQQVIEL 12 187 FIPIDLGSL 12 214
GPVVVAISL 12 217 VVAISLATF 12 220 ISLATFFFL 12 261 IVAITLLSL 12 267
LSLVYLAGL 12 280 YQLYYGTKY 12 283 YYGTKYRRF 12 299 LQCRKQLGL 12 300
QCRKQLGLL 12 324 PMRRSERYL 12 325 MRRSERYLF 12 350 NEEEVWRIE 12 353
EVWRIEMYI 12 362 SFGIMSLGL 12 404 LISTFHVLI 12 405 ISTFHVLIY 12
Each peptide is a portion of SEQ ID NO: 5; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V2-HLA-B4402-9mers-98P4B6 1 SGSPGLQAL 18 15
SGFTPFSCL 15 33 CPPPCPADF 15 3 SPGLQALSL 14 23 LSLPSSWDY 14 12
SLSSGFTPF 13 21 SCLSLPSSW 13 35 PPCPADFFL 13 36 PCPADFFLY 13 37
CPADFFLYF 13 17 FTPFSCLSL 12 34 PPPCPADFF 12 5 GLQALSLSL 11 9
LSLSLSSGF 11 Each peptide is a portion of SEQ ID NO: 11; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V5A-HLA-B4402-9mers-98P4B6 1 NLPLRLFTF 16 2
LPLRLFTFW 13 V5B-HLA-B4402-9mers-98P4B6 2 REFSFIQIF 25 22 LEFVFLLTL
25 20 LELEFVFLL 23 18 TELELEFVF 22 5 SFIQIFCSF 16 24 FVFLLTLLL 16
19 ELELEFVFL 15 14 ADTQTELEL 14 23 EFVFLLTLL 14 12 SFADTQTEL 12
Each peptide is a portion of SEQ ID NO: 13; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V6-HLA-B4402-9mers-98P4B6 35 LEEGIGGTI 21 6
VILGKIILF 17 5 IVILGKIIL 15 7 ILGKIILFL 15 21 KLKRIKKGW 15 3
PSIVILGKI 14 10 KIILFLPCI 14 14 FLPCISRKL 14 17 CISRKLKRI 13 26
KKGWEKSQF 12 29 WEKSQFLEE 12 36 EEGIGGTIP 12 4 SIVILGKII 11 27
KGWEKSQFL 11 Each peptide is a portion of SEQ ID NO: 15; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V7A-HLA-B4402-9mers-98P4B6 6 SETFLPNGI 21 9
FLPNGINGI 14 1 SPKSLSETF 12 2 PKSLSETFL 12
V7B-HLA-B4402-9mers-98P4B6 5 AYQQSTLGY 15 9 STLGYVALL 15 8
QSTLGYVAL 14 3 NMAYQQSTL 12 V7C-HLA-B4402-9mers-98P4B6 33 SEIVLPIEW
26 157 GEFLGSGTW 24 168 LETIILSKL 23 39 IEWQQDRKI 20 143 ASGTLSLAF
17 51 STPPPPAMW 16 70 QESGIRNKS 16 103 PESPDRALK 16 113 ANSWRNPVL
16 131 WEFLLRLLK 16 42 QQDRKIPPL 15 5 ILDLSVEVL 14 61 EEAGATAEA 14
10 VEVLASPAA 13 12 VLASPAAAW 13 15 SPAAAWKCL 13 20 WKCLGANIL 13 29
RGGLSEIVL 13 60 TEEAGATAE 13 67 AEAQESGIR 13 91 TEDDEAQDS 13 102
PPESPDRAL 13 108 RALKAANSW 13 125 NGVGPLWEF 13 126 GVGPLWEFL 13 127
VGPLWEFLL 13 130 LWEFLLRLL 13 146 TLSLAFTSW 13 160 LGSGTWMKL 13 165
WMKLETIIL 13 31 GLSEIVLPI 12 122 PHTNGVGPL 12 123 HTNGVGPLW 12 129
PLWEFLLRL 12 139 KSQAASGTL 12 141 QAASGTLSL 12 151 FTSWSLGEF 12 179
EQKSKHCMF 12 Each peptide is a portion of SEQ ID NO: 17; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V8-HLA-B4402-9mers-98P4B6 5 LEEGMGGTI 20 6
EEGMGGTIP 12 Each peptide is a portion of SEQ ID NO: 27; each start
position is specified, the length of peptide is 9 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 123456789 score V13-HLA-B4402-9mers-98P4B6 6 SETFLPNGI 21 9
FLPNGINGI 14 1 SPKSLSETF 12 2 PKSLSETFL 12 Each peptide is a
portion of SEQ ID NO: 29; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V14-HLA-B4402-9mers-98P4B6 1 NLPLRLFTF 16 2 LPLRLFTFW 13 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V21-HLA-B4402-9mers-98P4B6 6 EQKTKHCMF 13 5
QEQKTKHCM 11 8 KTKHCMFSL 11 9 TKHCMFSLI 10 Each peptide is a
portion of SEQ ID NO: 51; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V25-HLA-B4402-9mers-98P4B6 3 FLPCISQKL 13 6 CISQKLKRI 12 2
LFLPCISQK 8 9 QKLKRIKKG 8
[1255]
56TABLE XXXIIII Each peptide is a portion of SEQ ID NO: 3; each
start position is specified, the length of peptide is 9 amino
acids, and the end position for each peptide is the start position
plus eight. Pos 123456789 score V1-HLA-B5101-9mers-98P4B6 81
DALTKTNII 29 27 DARKVTVGV 26 65 FASEFFPHV 23 374 LAVTSIPSV 23 434
LALVLPSIV 23 438 LPSIVILDL 22 246 DFYKIPIEI 21 262 VAITLLSLV 21 368
LGLLSLLAV 21 428 TPPNFVLAL 21 429 PPNFVLALV 21 23 NGIKDARKV 20 157
GPKDASRQV 20 214 GPVVVAISL 20 259 LPIVAITLL 20 41 FAKSLTIRL 19 125
YPESNAEYL 19 133 LASLFPDSL 19 173 QARQQVIEL 19 250 IPIEIVNKT 19 291
FPPWLETWL 19 50 IRCGYHVVI 18 228 LYSFVRDVI 17 336 MAYQQVHAN 17 371
LSLLAVTSI 17 28 ARKVTVGVI 16 39 GDFAKSLTI 16 70 FPHVVDVTH 16 104
LRHLLVGKI 16 141 LIVKGFNVV 16 160 DASRQVYIC 16 204 LPLRLFTLW 16 227
FLYSFVRDV 16 237 HPYARNQQS 16 317 VAYSLCLPM 16 52 CGYHVVIGS 15 137
FPDSLIVKG 15 164 QVYICSNNI 15 171 NIQARQQVI 15 193 GSLSSAREI 15 210
TLWRGPVVV 15 212 WRGPVVVAI 15 276 LAAAYQLYY 15 349 WNEEEVWRI 15 363
FGIMSLGLL 15 397 TLGYVALLI 15 425 RFYTPPNFV 15 18 LPNGINGIK 14 25
IKDARKVTV 14 114 IDVSNNMRI 14 152 WALQLGPKD 14 209 FTLWRGPVV 14 222
LATFFFLYS 14 242 NQQSDFYKI 14 258 TLPIVAITL 14 278 AAYQLYYGT 14 379
IPSVSNALN 14 386 LNWREFSFI 14 398 LGYVALLIS 14 401 VALLISTFH 14 404
LISTFHVLI 14 433 VLALVLPSI 14 435 ALVLPSIVI 14 Each peptide is a
portion of SEQ ID NO: 5; each start position is specified, the
length of peptide is 9 amino acids, and the end position for each
peptide is the start position plus eight. Pos 123456789 score
V2-HLA-B5101-9mers-98P4B6 3 SPGLQALSL 18 35 PPCPADFFL 16 15
SGFTPFSCL 15 1 SGSPGLQAL 13 7 QALSLSLSS 13 18 TPFSCLSLP 13 25
LPSSWDYRC 13 37 CPADFFLYF 13 33 CPPPCPADF 12 34 PPPCPADFF 12 17
FTPFSCLSL 10 4 PGLQALSLS 9 5 GLQALSLSL 8 Each peptide is a portion
of SEQ ID NO: 11; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V5A-HLA-B5101-9mers-98P4B6 2 LPLRLFTFW 16 8 TFWRGPVVV 15 7
FTFWRGPVV 13 6 LFTFWRGPV 10 9 FWRGPVVVA 8 4 LRLFTFWRG 7
V5B-HLA-B5101-9mers-98P4B6 20 LELEFVFLL 14 1 WREFSFIQI 13 22
LEFVFLLTL 13 13 FADTQTELE 12 12 SFADTQTEL 9 17 QTELELEFV 9 24
FVFLLTLLL 9 14 ADTQTELEL 8 18 TELELEFVF 8 19 ELELEFVFL 8 23
EFVFLLTLL 8 15 DTQTELELE 6 Each peptide is a portion of SEQ ID NO:
13; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V6-HLA-B5101-9mers-98P4B6
43 IPHVSPERV 23 2 LPSIVILGK 16 27 KGWEKSQFL 16 35 LEEGIGGTI 15 15
LPCISRKLK 14 17 CISRKLKRI 14 3 PSIVILGKI 13 39 IGGTIPHVS 13 38
GIGGTIPHV 12 4 SIVILGKII 11 7 ILGKIILFL 11 10 KIILFLPCI 11 14
FLPCISRKL 11 45 HVSPERVTV 11 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V7A-HLA-B5101-9mers-98P4B6
9 FLPNGINGI 14 1 SPKSLSETF 12 6 SETFLPNGI 12 2 PKSLSETFL
V7B-HLA-B5101-9mers-98P4B- 6 4 MAYQQSTLG 16 6 YQQSTLGYV 12 9
STLGYVALL 12 3 NMAYQQSTL 9 8 QSTLGYVAL 7 V7C-HLA-B5101-9mers-98P4B6
66 TAEEAQSGI 22 101 DPPESPDRA 20 112 AANSWRNPV 19 15 SPAAAWKCL 18
160 LGSGTWMKL 18 29 RGGLSEIVL 17 84 IPVVGVVTE 17 102 PPESPDRAL 17
141 QAASGTLSL 17 24 GANILRGGL 16 39 IEWQQDRKI 16 31 GLSEIVLPI 15 68
EAQESGIRN 15 82 SQIPVVGVV 15 108 RALKAANSW 15 149 LAFTSWSLG 15 163
GTWMKLETI 15 5 ILDLSVEVL 14 27 ILRGGLSEI 14 37 LPIEWQQDR 14 47
IPPLSTPPP 14 48 PPLSTPPPP 14 54 PPPAMWTEE 14 121 LPHTNGVGP 14 127
VGPLWEFLL 14 128 GPLWEFLLR 14 4 VILDLSVEV 13 13 LASPAAAWK 13 18
AAWKCLGAN 13 52 TPPPPAMWT 13 53 PPPPAMWTE 13 62 EAGATAEAQ 13 95
EAQDSIDPP 13 142 AASGTLSLA 13 164 TWMKLETII 13 17 AAAWKCLGA 12 64
GATAEAQES 12 76 NKSSSSSQI 12 79 SSSSQIPVV 12 92 EDDEAQDSI 12 105
SPDRALKAA 12 111 KAANSWRNP 12 118 NPVLPHTNG 12 129 PLWEFLLRL 12 182
SKHCMFSLI 12 16 PAAAWKCLG 11 28 LRGGLSEIV 11 56 PAMWTEEAG 11 81
SSQIPVVGV 11 119 PVLPHTNGV 11 168 LETIILSKL 11 19 AWKCLGANI 10 23
LGANILRGG 10 30 GGLSEIVLP 10 55 PPAMWTEEA 10 78 SSSSSQIPV 10 113
ANSWRNPVL 10 130 LWEFLLRLL 10 Each peptide is a portion of SEQ ID
NO: 17; each start position is specified, the length of peptide is
9 amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V8-HLA-B5101-9mers-98P4B6
5 LEEGMGGTI 16 8 GMGGTIPHV 12 9 MGGTIPHVS 12 7 EGMGGTIPH 8 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V13-HLA-B5101-9mers-98P4B6 9 FLPNGINGI 14 1
SPKSLSETF 12 6 SETFLPNGI 12 2 PKSLSETFL 8 Each peptide is a portion
of SEQ ID NO: 29; each start position is specified, the length of
peptide is 9 amino acids, and the end position for each peptide is
the start position plus eight. Pos 123456789 score
V14-HLA-B5101-9mers-98P4B6 2 LPLRLFTFW 16 8 TFWRGPVVV 15 7
FTFWRGPVV 13 6 LFTFWRGPV 10 9 FWRGPVVVA 8 4 LRLFTFWRG 7 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptide is 9 amino acids, and the end
position for each peptide is the start position plus eight. Pos
123456789 score V21-HLA-B5101-9mers-98P4B6 9 TKHCMFSLI 13 3
LTQEQKTKH 7 8 KTKHCMFSL 6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptide is 9
amino acids, and the end position for each peptide is the start
position plus eight. Pos 123456789 score V25-HLA-B5101-9mers-98P4B6
4 LPCISQKLK 14 6 CISQKLKRI 14 3 FLPCISQKL 10 9 QKLKRIKKG 7
[1256]
57TABLE XXXIV Each peptide is a portion of SEQ ID NO: 3; each start
position is specified, the length of peptide is 10 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 1234567890 score V1-HLA-A1-10mers-98P4B6 351 EEEVWRIEMY 26 391
FSFIQSTLGY 26 418 AFEEEYYRFY 26 443 ILDLLQLCRY 26 220 ISLATFFFLY 24
262 VAITLISLVY 23 327 RSERYLFLNM 23 45 LTIRLIRCGY 22 275 LLAAAYQLYY
22 404 LISTFHVLIY 22 116 VSNNMRINQY 20 123 NQYPESNAEY 20 271
TLAGLLAAAY 19 279 AYQLYYGTKY 19 427 YTPPNFVLAL 19 38 SGDFAKSLTI 18
274 GLLAAAYQLY 18 101 LWDLRHLLVG 17 157 GPKDASRQVY 17 178
VIELARQLNF 17 230 SFVRDVIHPY 17 239 YARNQQSDFY 17 396 STLGYVALLI 17
66 ASEFFPHVVD 16 89 IFVAIHREHY 16 94 HREHYTSLWD 16 129 NAEYLASLFP
16 310 FFFAMVHVAY 16 322 CLPMRRSERY 16 329 ERYLFLNMAY 16 350
NEEEVWRIEM 15 414 GWKRAFEEEY 15 415 WKRAFEEEYY 15 13 LSETCLPNGI 14
125 YPESNAEYLA 14 244 QSDFYKIPIE 14 257 KTLPIVAITL 14 76 VTHHEDALTK
13 198 AREIENLPLR 13 366 MSLGLLSLLA 13 420 EEEYYRFYTP 13 25
IKDARKVTVG 12 135 SLFPDSLIVK 12 137 FPDSLIVKGF 12 200 EIENLPLRLF 12
221 SLATFFFLYS 12 251 PIEIVNKTLP 12 268 SLVYLAGLLA 12 419
FEEEYYRFYT 12 439 PSIVILDLLQ 12 Each peptide is a portion of SEQ ID
NO: 5; each start position is specified, the length of peptide is
10 amino acids, and the end position for each peptide is the start
position plus eight. Pos 1234567890 score V2-HLA-A1-10mers-98P4B6
35 PPCPADFFLY 24 22 CLSLPSSWDY 16 28 SWDYRCPPPC 12 2 GSPGLQALSL 11
Each peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus eight. Pos
1234567890 score V5A-HLA-A1-10mers-98P4B6 8 FTFWRGPVVV 8 1
ENLPLRLFTF 4 2 NLPLRLFTFW 4 4 PLRLFTFWRG 4 10 FWRGPVVVAI 3
V5B-HLA-A1-10mers-98P4B- 6 14 FADTQTELEL 17 18 QTELELEFVF 17 22
ELEFVFLLTL 17 20 ELELEFVFLL 14 16 DTQTELELEF 12 21 LELEFVFLLT 11 2
WREFSFIQIF 10 5 FSFIQIFCSF 8 24 EFVFLLTLLL 8 Each peptide is a
portion of SEQ ID NO: 13; each start position is specified, the
length of peptide is 10 amino acids, and the end position for each
peptide is the start position plus eight. Pos 1234567890 score
V6-HLA-A1-10mers-98P4B6 29 GWEKSQELEF 19 35 FLEEGIGGTI 13 36
LEEGIGGTIP 12 1 LVLPSIVILG 11 19 ISRKLKRIKK 11 42 GTIPHVSPER 10 9
LGKIILFLPC 9 Each peptide is a portion of SEQ ID NO: 15; each start
position is specified, the length of peptide is 10 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 1234567890 score V7A-HLA-A1-10mers-98P4B6 6 LSETFLPNGI 14 4
KSLSETFLPN 13 8 ETFLPNGING 11 V7B-HLA-A1-10mers-98P4B6 5 MAYQQSTLGY
21 10 STLGYVALLI 17 V7C-HLA-A1-10mers-98P4B6 131 LWEFLLRLLK 19 33
LSEIVLPIEW 18 91 VTEDDEAQDS 17 60 WTEEAGATAE 16 100 SIDPPESPDR 16
70 AQESGIRNKS 14 94 DDEAQDSIDP 14 6 ILDLSVEVLA 13 103 PPESPDRALK 13
124 HTNGVGPLWE 13 168 KLETIILSKL 13 10 SVEVLASPAA 12 39 PIEWQQDRKI
12 43 QQDRKIPPLS 12 52 STPPPPAMWT 12 104 PESPDRALKA 12 106
SPDRALKAAN 12 128 VGPLWEFLLR 12 170 ETIILSKLTQ 12 97 AQDSIDPPES 11
115 NSWRNPVLPH 11 154 SWSLGEFLGS 11 2 PSIVILDLSV 10 61 TEEAGATAEA
10 67 TAEAQESGIR 10 92 TEDDEAQDSI 10 93 EDDEAQDSID 10 157
LGEFLGSGTW 10 162 GSGTWMKLET 10 178 TQEQKSKHCM 10 51 LSTPPPPAMW 9
146 GTLSLAFTSW 9 182 KSKHCMFSLI 9 Each peptide is a portion of SEQ
ID NO: 17; each start position is specified, the length of peptide
is 10 amino acids, and the end position for each peptide is the
start position plus eight. Pos 1234567890 score
V8-HLA-A1-10mers-98P4B6 5 FLEEGMGGTI 13 6 LEEGMGGTIP 12 Each
peptide is a portion of SEQ ID NO: 27; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus eight. Pos
1234567890 score V13-HLA-A1-10mers-98P4B6 6 LSETFLPNGI 14 4
KSLSETFLPN 13 8 ETFLPNGING 11 Each peptide is a portion of SEQ ID
NO: 29; each start position is specified, the length of peptide is
10 amino acids, and the end position for each peptide is the start
position plus eight. Pos 1234567890 score V14-HLA-A1-10mers-98P4B6
8 FTFWRGPVVV 8 1 ENLPLRLFTF 4 2 NLPLRLFTFW 4 4 PLRLFTFWRG 4 10
FWRGPVVVAI 3 Each peptide is a portion of SEQ ID NO: 43; each start
position is specified, the length of peptide is 10 amino acids, and
the end position for each peptide is the start position plus eight.
Pos 1234567890 score V21-HLA-A1-10mers-98P4B6 9 KTKHCMFSLI 11 5
TQEQKTKHCM 10 1 LSKLTQEQKT 6 4 LTQEQKTKHC 6 10 TKHCMFSLIS 6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptide is 10 amino acids, and the end
position for each peptide is the start position plus eight. Pos
1234567890 score V25-HLA-A1-10mers-98P4B6 8 ISQKLKRIKK 11 5
LPCISQKLKR 8 3 LFLPCISQKL 6
[1257]
58TABLE XXXV Pos 1234567890 score V1-HLA-A0201-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 373
LLAVTSIPSV 31 266 LLSLVYLAGL 29 107 LLVGKILIDV 28 367 SLGLLSLLAV 28
435 ALVLPSIVIL 28 364 GIMSLGLLSL 27 132 YLASLFPDSL 26 370
LLSLLAVTSI 26 437 VLPSIVILDL 26 82 ALTKTNIIFV 25 100 SLWDLRHLLV 25
140 SLIVKGFNVV 25 263 AITLLSLVYL 25 306 GLLSFFFAMV 25 402
ALLISTFHVL 25 440 SIVILDLLQL 25 258 TLPIVAITLL 24 365 IMSLGLLSLL 24
403 LLISTFHVLI 24 427 YTPPNFVLAL 24 24 GIKDARKVTV 23 48 RLIRCGYHVV
23 103 DLRHLLVGKI 23 433 VLALVLPSIV 23 92 AIHREHYTSL 22 260
PIVAITLLSL 22 261 IVAITLLSLV 22 298 WLQCRKQLGL 22 432 FVLALVLPSI 22
207 RLFTLWRGPV 21 210 TLWRGPVVVA 21 257 KTLPIVAITL 21 385
ALNWREFSFI 21 49 LIRCGYHVVI 20 98 YTSLWDLRHL 20 172 IQARQQVIEL 20
186 NFIPIDLGSL 20 219 AISLATFFFL 20 227 FLYSFVRDVI 20 249
KTPIEIVNKT 20 253 EIVNKTLPIV 20 12 SLSETCLPNG 19 135 SLFPDSLIVK 19
142 IVKGFNVVSA 19 197 SAREIENLPL 19 209 FTLWRGPVVV 19 211
LWRGPVVVAI 19 271 YLAGLLAAAY 19 312 FAMVHVAYSL 19 396 STLGYVALLI 19
16 TCLPNGINGI 18 65 FASEFFPHVV 18 67 SEFFPHVVDV 18 113 LIDVSNNMRI
18 359 MYISFGIMSL 18 392 SFIQSTLGYV 18 106 HLLVGKILID 17 179
IELARQLNFI 17 202 ENLPLRLFTL 17 250 IPIEIVNKTL 17 264 ITLLSLVYLA 17
269 LVYLAGLLAA 17 348 SWNEEEVWRI 17 361 ISFGLMSLGL 17 369
GLLSLLAVTS 17 401 VALLISTFHV 17 26 KDARKVTVGV 16 41 FAKSLTIRLI 16
111 KILIDVSNNM 16 112 ILIDVSNNMR 16 127 ESNAEYLASL 16 195
LSSAREIENL 16 223 ATFFFLYSFV 16 226 FFLYSFVRDV 16 268 SLVYLAGLLA 16
299 LQCRKIQLGLL 16 356 RIEMYISFGI 16 362 SFGIMSLGLL 16 377
TSWSVSNAL 16 428 TPPNFVLALV 16 434 LALVLPSIVI 16 438 LPSIVILDLL 16
443 ILDLLQLCRY 16 27 DARKVTVGVI 15 36 IGSGDFAKSL 15 44 SLTIRLIRCG
15 47 IRLIRCGYHV 15 147 NVVSAWALQL 15 166 YICSNNIQAR 15 189
PLDLGSLSSA 15 199 REIENLPLRL 15 221 SLATFFFLYS 15 255 VNKTLPIVAI 15
273 AGLLAAAYQL 15 275 LLAAAYQLYY 15 314 MVHVAYSLCL 15 335
NMAYQQVHAN 15 336 MAYQQVHANI 15 345 IENSWNEEEV 15 394 IQSTLGYVAL 15
395 QSTLGYVALL 15 404 LISTFHVLIY 15 411 LIYGWKRAFE 15
V2-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
5; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 2 GSPGLQALSL 16 5 GLQALSLSLS 15 16 GFTPFSCLSL
15 10 SLSLSSGFTP 14 8 ALSLSLSSGF 13 12 SLSSGFTPFS 13 24 SLPSSWDYRC
13 4 PGLQALSLSL 12 7 QALSLSLSSG 12 14 SSGFTPFSCL 11 22 CLSLPSSWDY
10 9 LSLSLSSGFT 8 17 FTPFSCLSLP 8 6 LQALSLSLSS 7 34 PPPCPADFFL 7
V5A-HLA-A0201-10mers-98- P4B6 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptides is
10 amino acids, and the end position for each peptide is the start
position plus nine. 6 RLFTFWRGPV 21 8 FTFWRGPVVV 18 10 FWRGPVVVAI
18 7 LFTFWRGPVV 11 9 TFWRGPVVVA 11 2 NLPLRLFTFW 10
V5B-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 22 ELEFVFLLTL 22 20 ELELEFVFLL 20 14 FADTQTELEL
18 23 LEFVFLLTLL 17 19 TELELEFVFL 16 17 TQTELELEFV 15 12 CSFADTQTEL
13 9 QIFCSFADTQ 11 21 LELEFVFLLT 11 1 NWREFSFIQI 10 7 FIQIFCSFAD 10
V6-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
13; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 7 VILGKIILFL 28 35 FLEEGIGGTI 22 5 SIVILGKIIL
20 14 LFLPCISRKL 18 43 TIPHVSPERV 18 2 VLPSIVILGK 17 13 ILFLPCLSRK
17 3 LPSLVILGKI 16 8 ILGKIILFLP 16 10 GKIILFLPCI 16 38 EGIGGIPWHV
16 1 LVLPSIVILG 14 46 HVSPERVTVM 14 12 IILFLPCISR 13 34 QFLEEGIGGT
13 V7A-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
10 amino acids, and the end position for each peptide is the start
position plus nine. 5 SLSETFLPNG 19 9 TFLPNGINGI 18 2 SPKSLSFTFL 11
6 LSETFLPNGI 11 10 FLPNGINGIK 11 V7B-HLA-A0201-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 10
STLGYVALLI 19 2 FLNMAYQQST 18 6 AYQQSTLGYV 16 3 LNMAYQQSTL 15 9
QSTLGYVALL 15 8 QQSTLGYVAL 13 4 NMAYQQSTLG 9
V7C-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 5 VILDLSVEVL 26 168 KLETIILSKL 26 27 NILRGGLSEI
24 28 ILRGGLSEIV 24 130 PLWEFLLRLL 24 160 FLGSGTWMKL 23 4
IVILDLSVEV 22 66 ATAEAQESGI 19 81 SSSQIPVVGV 19 156 SLGEFLGSGT 19 6
ILDLSVEVLA 18 32 GLSFIVLPIE 18 112 KAANSWRNPV 18 113 AANSWRNPVL 18
129 GPLWEFLLRL 18 8 DLSVEVLASP 17 19 AAWKCLGANI 17 79 SSSSSQIPVV 17
127 GVGPLWEFLL 17 134 FLLRLLKSQA 17 135 LLRLLKSQAA 17 141
SQAASGTLSL 17 31 GGLSEIVLPI 16 42 WQQDRKIPPL 16 58 AMWTEEAGAT 16 82
SSQIPVVGVV 16 84 QIPVVGVVTE 16 122 LPHTNGVGPL 16 137 RLLKSQAASG 16
138 LLKSQAASGT 16 148 LSLAFTSWSL 16 3 VLASPAAAWK 15 23 CLGANILRGG
15 24 LGANILRGGL 15 152 FTSWSLGEFL 15 163 SGTWMKLETI 15 3
SIVILDLSVE 14 29 LRGGLSEIVL 14 39 PIEWQQDRKI 14 121 VLPHTNGVGP 14
139 LKSQAASGTL 14 142 QAASGTLSLA 14 164 GTWMKLETII 14 171
TIILSKLTQE 14 172 IILSKLTQEQ 14 18 AAAWKCLGAN 13 50 PLSTPPPPAM 13
100 SIDPPESPDR 13 149 SLAFTSWSLG 13 2 PSIVILDLSV 12 20 AWKCLGANIL
12 47 KIPPLSTPPP 12 52 STPPPPAMWT 12 83 SQIPVVGVVT 12 102
DPPESPDRAL 12 119 NPVLPHTNGV 12 126 NGVGPLWEFL 12 144 ASGTLSLAFT 12
173 ILSKLTQEQK 12 176 KLTQEQKSKII 12 181 QKSKHCMIFSL 12
V8-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
17; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 5 FLEEGMGGTI 22 8 EGMGGTIPHV 15 9 GMGGTIPHVS 12
V13-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 5 SLSETFLPNG 19 9 TFLPNGINGI 18 2 SPKSLSETFL 11
6 LSETFLPNGI 11 10 FLPNGINGIK 11 V14-HLA-A0201-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 6
RLFTFWRGPV 21 8 FTFWRGPVVV 18 10 FWRGPVVVAI 18 7 LFTFWRGPVV 11 9
TFWRGPVVVA 11 2 NLPLRLFTFW 10 V21-HLA-A0201-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 43; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 3
KITQEQKTKH 12 9 KTKHCMFSLI 12 8 QKTKHCMFSL 11 1 LSKLTQEQKT 7 4
LTQEQKTKHC 7 2 SKLTQEQKTK 5 V25-HLA-A0201-10mers-98P- 4B6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 3
LFLPCISQKL 18 2 ILFLPCLSQK 17 1 IILFLPCISQ 13 4 FLPCISQKIK 10 6
PCISQKLKRI 10 7 CISQKLKRIK 8
[1258]
59XXXVI V1-HLA-A0203-10mers-98P4B6 Each peptide is a portion of SEQ
ID NO: 3; each start position is specified, the length of peptides
is 10 amino acids, and the end position for each peptide is the
start position plus nine. 270 VYLAGLLAAA 27 269 LVYLAGLLAA 19 144
KGFNVVSAWA 18 271 YLAGLLAAAY 17 V2-HLA-A0203-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 5; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 30
DYRCPPPCPA 10 31 YRCPPPCPAD 9 1 SGSPGLQALS 8 32 RCPPPCPADF 8
V5A-HLA-A0203-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 9 TFWRGPVVVA 10 10 FWRGPVVVAI 9
V5B-HLA-A0203-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 SFIQIFCSFA 10 7 FIQIFCSFAD 9 8 IQIFCSFADT 8
V6-HLA-A0203-10mers-98P4B6 NoResultsFound.
V7A-HLA-A0203-10mers-98P4B6 NoResultsFound.
V7B-HLA-A0203-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 7 YQQSTLGYVA 10 8 QQSTLGYVAL 9 9 QSTLGYVALL 8
V7C-HLA-A0201-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 11 VEVLASPAAA 27 10 SVEVLASPAA 19 105
ESPDRALKAA 19 135 LLRLLKSQAA 19 57 PAMWTEEAGA 18 59 MWTEEAGATA 18
61 TEEAGATAEA 18 12 EVLASPAAAW 17 106 SPDRALKAAN 17 136 LRLLKSQAAS
17 V8-HLA-A0203-10mers-98P4B6 NoResultsFound.
V13-HLA-A0203-10mers-98P4B6 NoResultsFound.
V14-HLA-A0203-10mers-98P4B6 9 TFWRGPVVVA 10 10 FWRGPVVVAI 9
V21-HLA-A0203-10mers-98P4B6 NoResultsFound.
V25-HLA-A0203-10mers-98P4B6 NoResultsFound.
[1259]
60TABLE XXXVII Pos 1234567890 score V1-HLA-A3-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 135
SLFPDSLIVK 28 34 GVIGSGDFAK 26 271 YLAGLLAAAY 26 48 RLIRCGYIIVV 24
21 GLNGIKDARK 23 216 VVVAISLATF 23 369 GLLSLLAVTS 23 17 CLPNGINGIK
22 17 HVVIGSRNPK 22 275 LLAAAYQLYY 22 278 AAYQLYYGTK 22 307
LLSFFFAMVH 22 112 ILIDVSNNMR 21 142 IVKGFNVVSA 21 155 QLGPKDASRQ 21
210 TLWRGPVVVA 21 76 VTHHEDALTK 20 217 VVAISLATFF 20 248 YKIPIEIVNK
20 274 GLLAAAYQLY 20 281 QLYYGTKYRR 20 294 WLETWLQCRK 20 402
ALLISTFHVL 20 2 ESISMMGSPK 19 7 LIRCGYHVVI 19 7 VVIGSRNPKF 19 102
WDLRHLLVGK 19 147 NVVSAWALQL 19 7 FLYSFVRDVI 19 269 LVYLAGLLAA 19
375 AVTSIPSVSN 19 443 ILDLLQLCRY 19 24 GIKDARKVTV 18 140 SLIVKGFNVV
18 333 FLNMAYQQVH 18 410 VLIYGWKRAF 18 411 LIYGWKRAFE 18 435
ALVLPSIVIL 18 442 VILDLLQLCR 18 46 TLRLIRCGYH 17 92 AIHREHYTSL 17
164 QVYICSNNIQ 17 177 QVIELARQLN 17 254 IVNKTLPIVA 17 261
IVAITLLSLV 17 268 SLVYLAGLLA 17 331 YLFLNMAYQQ 17 400 YVALLISTFH 17
403 LLISTFHVLI 17 404 LISTFHVLIY 17 30 KVTVGVIGSG 16 123 NQYPESNAEY
16 141 LIVKGFNVVS 16 178 VIELARQLNF 16 207 RLFTLWRGPV 16 234
DVIHPYARNQ 16 262 VAITLLSLVY 16 263 AITLLSLVYL 16 265 TLLSLVYLAG 16
306 GLLSFFFAMV 16 322 CLPMRRSERY 16 340 QVHANIENSW 16 367
SLGLLSLLAV 16 385 ALNWREFSFI 16 432 FVLALVLPSI 16 433 VLALVLPSIV 16
440 SIVILDLLQL 16 441 IVILDLLQLC 16 32 TVGVIGSGDF 15 100 SLWDLRHLLV
15 106 HLLVGKILID 15 121 RINQYPESNA 15 153 ALQLGPKDAS 15 187
FIPIDLGSLS 15 221 SLATFFFLYS 15 235 VIHPYARNQQ 15 257 KTLPIVAITL 15
260 PIVAITLLSL 15 320 SLCLPMRRSE 15 372 SLLAVTSIPS 15 393
FIQSTLGYVA 15 436 LVLPSIVILD 15 60 SRNPKFASEF 14 88 IIFVAIHREH 14
103 DLRHLLVGKI 14 108 LVGKILIDVS 14 111 KILIDVSNNM 14 132
YLASLFPDSL 14 150 SAWALQLGPK 14 171 NIQARQQVIE 14 180 ELARQLNFIP 14
189 PIDLGSLSSA 14 190 IDLGSLSSAR 14 205 PLRLFTLWRG 14 21
SPVVVAISLAT 14 231 FVRDVIHPYA 14 266 LLSLVYLAGL 14 279 AYQLYYGTKY
14 316 HVAYSLCLPM 14 370 LLSLLAVTSI 14 45 LTIRLIRCGY 13 75
DVTHHEDALT 13 82 ALTKTNIIFV 13 128 SNAEYLASLF 13 154 LQLGPKDASR 13
157 GPKDASRQVY 13 166 YICSNNIQAR 13 191 DLGSLSSARE 13 200
EIENLPLRLF 13 204 LPLRLFTLWR 13 240 ARNQQSDFYK 13 298 WLQCRKQLGL 13
304 QLGLLSFFFA 13 310 FFFAMVHVAY 13 314 MVHVAYSLCL 13 321
LCLPMRRSER 13 329 ERYLFLNMAY 13 353 EVWRIEMYIS 13 364 GIMSLGLLSL 13
373 LLAVTSIPSV 13 397 TLGYVALLIS 13 399 GYVALLISTF 13 409
HVLIYGWKRA 13 437 VLPSIVILDL 13 445 DLLQLCRYPD 13
V2-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO: 5;
each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 8 ALSLSLSSGF 21 10 SLSLSSGFTP 19 22 CLSLPSSWDY
17 5 GLQALSLSLS 15 32 RCPPPCPADF 15 12 SLSSGFTPFS 11 24 SLPSSWDYRC
11 2 GSPGLQALSL 10 33 CPPPCPADFF 10 V5A-HLA-A3-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 6
RLFTFWRGPV 16 4 PLRLFTFWRG 14 1 ENLPLRLFTF 13 2 NLPLRLFTFW 12 9
TFWRGPVVVA 11 3 LPLRLFTFWR 10 10 FWRGPVVVAI 10 8 FTFWRGPVVV 9 7
LFTFWRGPVV 7 V5B-HLA-A3-10mers-98P4B6 Each peptide is a portion of
SEQ ID NO: 11; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 9 QIFCSFADTQ 17 22 ELEFVFLLTL 17
18 QTELELEFVF 11 20 ELELEFVFLL 11 7 FIQIFCSFAD 10 8 IQIFCSFADT 8
V6-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO: 13;
each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 13 ILFLPCISRK 26 2 VLPSLVILGK 23 15 FLPCISRKLK
21 18 CISRKLKRIK 21 6 IVILGKIILF 20 22 KLKRIKKGWE 19 35 FLEEGIGGTI
19 12 IILFLPCISR 18 46 HVSPERVTVM 18 23 LKRIKKGWEK 17 11 KIILFLPCIS
16 19 ISRKLKRIKK 16 1 LVLPSIVILG 15 7 VILGKIILFL 15 25 RIKKGWEKSQ
15 26 IKKGWEKSQF 15 39 GIGGTTIHVS 15 8 ILGKIILFLP 12
V7A-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 10 FLPNGINGIK 22 5 SLSETFLPNG 12
V7B-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 5 MAYQQSTLGY 13 2 FLNMAYQQST 12 10 SILGYVALLI
11 3 LNMAYQQSTL 9 7 YQQSTLGYVA 7 8 QQSTLGYVAL 7 1 LFLNMAYQQS 6 9
QSTLGYVALL 6 V7C-HLA-A3-10mers-98P4B6 Each peptide is a portion of
SEQ ID NO: 15; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 13 VLASPAAAWK 28 173 ILSKLTQEQK 25
137 RLLKSQAASG 24 72 EVLASPAAAW 21 134 FLLRLLKSQA 21 4 IVILDLSVEV
20 36 IVLPIEWQQD 20 120 PVLPHTNGVG 20 176 KLTQEQKSKH 20 83
SQIPVVGVVT 18 84 QIPVVGVVTE 18 156 SLGEFLGSGT 18 167 MKLETIILSK 18
3 SIVILDLSVE 17 6 ILDLSVEVLA 17 28 ILRGGLSEIV 17 74 GIRNKSSSSS 17
90 VVTEDDEAQD 17 121 VLPHTNGVGP 17 138 LLKSQAASGT 17 27 NILRGGLSEI
16 100 SIDPPESPDR 16 110 ALKAANSWRN 16 168 KLETIILSKL 16 171
TIILSKLTQE 16 5 VILDLSVEVL 15 8 DLSVEVLASP 15 26 ANILRGGLSE 15 37
VLPIEWQQDR 15 135 LLRLLKSQAA 15 147 TLSLAFTSWS 15 149 SLAFTSWSLG 15
159 EFLGSGTWMK 15 175 SKLTQEQKSK 15 38 LPIEWQQDRK 14 47 KIPPLSTPPP
14 103 PPESPDRALK 14 109 RALKAANSWR 14 131 LWEFLLRLLK 14 127
GVGPLWEFLL 13 143 AASGTLSLAF 13 V8-HLA-A3-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
FLEEGMGGTI 19 V13-HLA-A3-10mers-98P4B6 Each peptide is a portion of
SEQ ID NO: 27; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 10 FLPNGINGIK 22 5 SLSETFLPNG 12
V14-HLA-A3-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
29; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 RLFTFWRGPV 16 4 PLRLFTFWRG 14 1 ENLPLRLFTF 13
2 NLPLRLFTFW 12 9 TFWRGPVVVA 11 3 LPLRLFTFWR 10 10 FWRGPVVVAI 10 8
FTFWRGPVYV 9 7 LFTFWRGPVV 7 V21-HLA-A3-10mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 43; each start position is specified,
the length of peptides is 10 amino acids, and the end position for
each peptide is the start position plus nine. 3 KLTQEQKTKH 18 2
SKLTQEQKTK 17 V25-HLA-A3-10mers-98P4B6 Each peptide is a portion of
SEQ ID NO: 51; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 2 ILFLPCISQK 29 4 FLPCISQKLK 20 7
CISQKLKRIK 18 1 IILFLPCISQ 14 V1-HLA-A26-10mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 3; each start position is specified, the
length of peptides is 10 amino acids, and the end position for each
peptide is the start position plus nine. 216 VVVALISLATF 27 296
ETWLQCRKQL 27 200 EIENLPLRLF 26 147 NVVSAWALQL 25 351 EEEVWRIEMY 25
202 ENLPLRLFTL 24 56 VVIGSRNPKF 23 127 ESNAEYLASL 23 427 YTPPNFVLAL
23 440 SIVILDLLQL 23 45 LTIRLIRCGY 22 234 DVIHPYARNQ 22 253
EIVNKTLPIV 22 260 PLVALITLLSL 22 329 ERYLFLNMAY 21 15 ETCLPNGING 20
32 TVGVIGSGDF 20 98 YTSLWDLRHL 20 353 EVWRIEMYIS 20 68 EFFPHVYDVT
19 75 DVTHIIEDALT 19 115 DVSNNMRINQ 19 186 NFIPIDLGSL 19 230
SFVRDVIHPY 19 257 KTLPIVAITL 19 314 MVHVAYSLCL 19 364 GIMSLGLLSL 19
404 LISTFHVLIY 19 217 VVAISLATFF 18 359 MYTSFGIMSL 18 399
GYVALLISTF 18 441 IVILDLLQLC 18 2 ESISMMGSPK 17 30 KVTVGVIGSG 17 40
DFAKSLTIRL 17 81 DALTKTNJIF 17 263 AITLLSLVYL 17 406 STFHVLIYGW 17
177 QVIELARQLN 16 215 PVVVAISLAT 16 269 LVYLAGLLAA 16 435
ALVLPSIVIL 16 436 LVLPSIVILD 16 34 GVIGSGDFAK 15 72 HVVDVTHHED 15
116 VSNNMRJNQY 15 142 IVKGFNVVSA 15 199 REIENLPLRL 15 250
IPIEIVNKTL 15 261 IVATTLLSLV 15 262 VAITLLSLVY 15 310 FFFAMVIIVAY
15 377 TSIPSVSNAL 15 389 REFSFIQSTL 15 391 FSFIQSTLGY 15 432
FVLALVLPSI 15 31 VTVGVIGSGD 14 55 HVVIGSRNPK 14 89 IFVAIHREHY 14
103 DLRHLLVGKI 14 108 LVGKILIDVS 14 148 VVSAWALQLG 14 222
LATFFFLYSF 14 301 CRKQLGLLSF 14 352 EEVWRIEMYI 14 362 SFGIMSLGLL 14
417 RAFEEEYYRF 14 437 VLPSIVILDL 14 443 ILDLLQLCRY 14 27 DARKVTVGVI
13 74 VDVTHHFDAL 13 92 ALHREHYTSL 13 137 FPDSLIVKGF 13 172
IQARQQVIEL 13 176 QQVIELARQL 13 178 VIELARQLNF 13 218 VAISLATFFF 13
223 ATFFFLYSFV 13 258 TLPIVAITLL 13 299 LQCRKQLGLL 13 302
RKQLGLLSFF 13 358 EMYISFUIMS 13 361 ISFGIMSLGL 13 365 IMSLGLLSLL 13
375 AVTSLPSVSN 13 376 VTSIPSVSNA 13 395 QSTLGYVALL 13 410
VLIYGWKRAF 13
[1260]
61TABLE XXXVIII Pos 1234567890 score V2-HLA-A26-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 17
FTPFSCLSLP 13 16 GFTPFSCLSL 12 35 PPCPADFFLY 11 2 GSPGLQALSL 10 4
PGLQALSLSL 10 14 SSGFTPFSCL 10 22 CLSLPSSWDY 10 8 ALSLSLSSGF 9 11
LSLSSGFTPF 9 32 RCPPPCPADF 9 33 CPPPCPADFF 9 36 PCPADFFLYF 9 30
DYRCPPPCPA 8 34 PPPCPADFFL 8 7 QALSLSLSSG 7 18 TPFSCLSLPS 7 3
SPGLQALSLS 6 V5A-HLA-A26-10mers-98P4B- 6 Each peptide is a portion
of SEQ ID NO: 11; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 1 ENLPLRLFTF 24 8 FTFWRGPVVV 12
V5B-HLA-A26-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 16 DTQTELELEF 25 22 ELEFVFLLTL 24 24 EFVFLLTLLL
23 20 ELELEFVFLL 22 18 QTELELEFVF 16 23 LEFVFLLTLL 16 4 EFSFIQIFCS
14 5 FSFIQIFCSF 13 2 WREFSFIQIF 12 12 CSFADTQTEL 12
V6-HLA-A26-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
13; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 IVILGKIILF 27 5 SIVILGKIIL 18 38 EGIGGTIPHV
18 7 VILGKIILFL 17 1 LVLPSIVILG 16 46 HVSPERVTVM 15 42 GTIPHVSPER
13 V7A-HLA-A26-10mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
10 amino acids, and the end position for each peptide is the start
position plus nine. 8 ETFLPNGING 24 V7B-HLA-A26-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 9
QSTLGYVALL 13 5 MAYQQSTLGY 11 3 LNMAYQQSTL 10 10 STLGYVALLI 10 8
QQSTLGYVAL 9 V7C-HLA-A26-10mers-98P4B6 Each peptide is a portion of
SEQ ID NO: 15; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 170 ETIILSKLTQ 24 12 EVLASPAAAW 21
35 EIVLPIEWQQ 19 102 DPPESPDRAL 19 127 GVGPLWEFLL 19 5 VILDLSVEVL
17 152 FTSWSLGEFL 17 69 EAQESGIRNK 16 105 ESPDRALKAA 16 89
GVVTEDDEAQ 15 133 EFLLRLLKSQ 15 151 AFTSWSLGEF 15 3 SLVILDLSVE 14 4
IVILDLSVEV 14 45 DRKIPPLSTP 14 86 PVVGVVTEDD 14 90 VVTEDDEAQD 14 99
DSIDPPESPD 14 130 PLWEFLLRLL 14 168 KLETIILSKL 14 171 TIILSKITQE 14
8 DLSVEVLASP 13 42 WQQDRKIPPL 13 93 LiDDEAQDSID 13 122 LPHTNGVGPL
13 125 TNGVGPLWEF 13 129 GPLWEFLLRL 13 10 SVEVLASPAA 12 36
IVLPIEWQQD 12 72 ESGIRINKSSS 12 95 DEAQDSIDPP 12 120 PVLPHTNGVG 12
126 NGVGPLWEFL 12 41 EWQQDRKJPP 11 60 WTEEAGATAE 11 62 EFAGATAEAQ
11 63 EAGATAEAQE 11 66 ATAFAQESGI 11 96 EAQDSIDPPE 11 141
SQAASGTLSL 11 159 EFLGSGTWMK 11 180 EQKSKHCMFS 11
V8-HLA-A26-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
17; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 8 EGMGGTIPHV 14 7 EEGMGGTIPH 11 1 EKSQFLEEGM 10
3 SQFLEEGMGG 6 V13-HLA-A26-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 27; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 8 ETFLPNGING 24
V14-HLA-A26-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
29; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 1 ENLPLRLFTF 24 8 FTFWRGPVVV 12
V21-HLA-A26-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 4 LTQEQKTKHC 10 7 EQKTKHCMFS 10 8 QKTKHCMFSL 10
6 QEQKTKHCMF 9 9 KTKHCMFSLI 9 V25-HLA-A26-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 2
ILFLPCISQK 10 3 LFLPCISQKL 10 6 PCISQKLKRI 9 1 IILFLPCISQ 6 9
SQKLKRIKKG 6 7 CISQKLKRIK 4
[1261]
62TBALE XXXIX Pos 1234567890 score V1-HLA-B0702-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 429
PPNFVLALVL 23 438 LPSIVILDLL 22 9 SPKSLSETCL 21 250 IPIEIVNKTL 21
323 LPMRRSERYL 21 137 FPDSLIVKGF 18 428 TPPNFVLALV 17 125
YPESNAEYLA 16 214 GPVVVAISLA 16 219 AISLATFFFL 16 394 IQSTLGYVAL 16
36 IGSGDFAKSL 15 197 SARE1ENLPL 15 325 MRRSERYLFL 15 361 ISFGIMSLGL
15 379 IPSVSNALNW 15 427 YTPPNEVLAL 15 211 LWRGPVVVAI 14 263
AITLLSLVYL 14 402 ALLISTFHVL 14 435 ALVLPSIVIL 14 40 DFAKSLTIRL 13
92 AIHREHYTSL 13 127 ESNAEYLASL i3 172 IQARQQVIEL 13 188
IP17DLGSLSS 13 195 LSSAREIENL 13 199 REIENLPLRL 13 204 LPLRLFTLWR
13 259 LPIVAITLLS 13 260 PIVAITLLSL 13 266 LLSLVYLAGL 13 290
RFPPWLETWL 13 364 GLMSLGLLSL 13 365 TMSLGLLSLL 13 4 ISMMGSPKSL 12
18 LPNGINGIKD 12 70 FPHVVDVTHH 12 98 YTSLWDLRHL 12 142 IVKGFNVVSA
12 147 NVVSAWALQL 12 157 GPKDASRQVY 12 202 ENLPLRLFTL 12 257
KTLPIVAITL 12 6273 AGLLAAAYQL 12 292 PPWLETWLQC 12 296 ETWLQCRKQL
12 298 WLQCRKQLGL 12 314 MVHVAYSLCL 12 377 TSIPSVSNAL 12 395
QSTLGYVALL 12 425 RFYTPPNFVL 12 437 VLPSIVILDL 12 440 SIVILDLLQL 12
26 KDARKVTVGV 11 27 DARKVTVGVI 11 49 LIRCGYHVVI 11 62 NPKFASEFFP 11
74 VDVTHHEDAL 11 95 REHYTSLWDL 11 99 TSLWDLRIILL 11 132 YLASLFPDSL
11 145 GFNVVSAWAL 11 183 RQLNFIPIDL 11 186 NFIPIDLGSL 11 201
IENLPLRIFT 11 213 RGPVVVAISL 11 237 HPYARNQQSD 11 252 IEIVNKTLPI 11
258 TLPIVAITLL 11 286 TKYRRFPPWL 11 291 FPPWLETWLQ 11 312
FAMVHVAYSL 11 362 SFGIMSLGLL 11 389 REFSFIQSTL 11
V2-HLA-B0702-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
5; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 34 PPPCPADFFL 21 33 CPPPCPADFF 18 2 GSPGLQALSL
14 16 GFTPFSCLSL 13 18 TPFSCLSLPS 13 4 PGLQALSLSL 12 14 SSGFTPFSCL
12 25 LPSSWDYRCP 12 35 PPCPADFFLY 12 3 SPGLQALSLS 11 8 ALSLSLSSGF
10 36 PCPADFIFLYF 10 V5A-HLA-B0702-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 11; each start position is specified, the
length of peptides is 10 amino acids, and the end position for each
peptide is the start position plus nine. 10 FWRGPVVVAI 14 3
LPLRIFTFWR 11 9 TFWRGPVVVA 10 6 RLFTFWRGPV 9 8 FTFWRGPVVV 9 1
ENLPLRLFTF 8 7 LFTFWRGPVV 8 V5B-HLA-B0702-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 11; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 19
TELELEFVFL 14 24 EFVFLLTLLL 14 14 FADIQIELEL 13 22 ELEFVFLLTL 13 12
CSFADTQTEL 12 20 ELELEFVFLL 12 23 LEFVFLLTLL 11 1 NWREFSFIQI 9 8
IQIFCSFADT 9 21 LELEFVFLLT 9 10 IFCSFADTQT 8 16 DTQTELELEF 8 5
FSFIQIFCSF 7 6 SFIQIFCSFA 7 17 TQTELELEFV 7 18 QTELELEFVF 7 2
WREFSFIQIF 6 V6-HLA-B0702-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 13; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 3 LPSIVILGKI 18 44 IPHVSPERVT 18 7
VILGKIILFL 15 27 KKGWEKSQFL 13 16 LPCISRKLKR 12 46 HVSPERVTVM 12 14
LFLPCISRKL 11 5 SIVILGKIIL 10 38 EGIGGTIPHV 10 26 IKKGWEKSQF 9 31
EKSQFLEEGI 9 45 PHVSPERVTV 9 V7A-HLA-B0702-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 2
SPKSLSETFL 22 8 QQSTLGYVAL 15 3 LNMAYQQSTL 12 9 QSTLGYVALL 12 10
STLGYVALLI 10 6 AYQQSTLGYV 8 7 YQQSTLGYVA 7
V7C-HLA-B0702-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 122 LPHTNGVGPL 22 129 GPLWEFLLRL 22 102
DPPESPDRAL 21 49 PPLSTPPPPA 18 55 PPPAMWTEEA 18 119 NPVLPHTNGV 17
141 SQAASGTLSL 15 143 AASGTLSLAF 15 29 LRGGLSEIVL 14 113 AANSWRNPVL
14 15 ASPAAAWKCL 13 48 LPPLSTPPPP 13 85 IPVVGVVTED 13 106
SPDRALKAAN 13 126 NGVGPLWEFL 13 152 FTSWSLGEFL 13 165 TWMKLETIIL 13
181 QKSKHCMFSL 13 1 LPSIVILDLS 12 5 VILDLSVFVL 12 16 SPAAAWKCLG 12
20 AWKCLGANIL 12 24 LGANTLRGGL 12 42 WQQDRKIPPL 12 54 PPPPAMWTEE 12
56 PPAMWTEEAG 12 103 PPESPDRALK 12 127 GVGPLWEFLL 12 139 LKSQAASGTL
12 28 ILRGGLSEIV 11 44 QDRKIPPLST 11 53 TPPPPAMWTE 11 81 SSSQIPVVGV
11 104 PESPDRALKA 11 144 ASGTLSLAFT 11 148 LSLAFTSWSL 11 160
FLUSGTWMKL 11 168 KLETIILSKL 11 6 ILDLSVEVLA 10 17 PAAAWKCLGA 10 19
AAWKCLGANI 10 31 GGLSEIVLPI 10 38 LPIEWQQDRK 10 50 PLSTPPPPAM 10 78
KSSSSSQIPV 10 79 SSSSSQIPVV 10 83 SQIPVVGVVT 10 112 KAANSWRNPV 10
130 PLWEFLLRLL 10 V8-HLA-B0702-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 17; each start position is specified, the
length of peptides is 10 amino acids, and the end position for each
peptide is the start position plus nine. 8 EGMGGTIPHV 11 1
EKSQFLEEGM 9 4 QFLEEGMGGT 6 5 FLEEGMGGTI 6
V13-HLA-B0702-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 2 SPKSLSETFL 22 V14-HLA-B0702-10mers-98P4B6
Each peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 10
FWRGPVVVAI 14 3 LPLRLFTFWR 11 9 TFWRGPVVVA 10 6 RLFTFWRGPV 9 8
FTFWRGPVVV 9 1 ENLPLRLFTF 8 7 LFTFWRGPVV 8
V21-HLA-B0702-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 8 QKTKHCMFSL 11 9 KTKHCMFSLI 8 6 QEQKTKHCMF 7 1
LSKITQEQKT 6 5 TQEQKTKHCM 6 V25-HLA-B0702-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 51; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 5
LPCISQKLKR 12 3 LFLPCISQKL 11 6 PCISQKLKRI 6
[1262]
63TABLE XL Pos 1234567890 score V1-HLA-B08-10mers-98P4B6
NoResultsFound. V2-HLA-B08-10mers-98P4B6 NoResultsFound.
V5A-HLA-B08-10mers-98P4B6 NoResultsFound. V5B-HLA-B08-10mers-98P4B6
NoResultsFound. V6-HLA-B08-10mers-98P4B6 NoResultsFound.
V7A-HLA-B08-10mers-98P4B6 NoResultsFound. V7B-HLA-B08-10mers-98P4B6
NoResultsFound. V7C-HLA-B08-10mers-98P4B6 NoResultsFound.
V8-HLA-B08-10mers-98P4B6 NoResultsFound. V13-HLA-B08-10mers-98P4B6
NoResultsFound. V14-HLA-B08-10mers-98P4B6 NoResultsFound.
V21-HLA-B08-10mers-98P4B6 NoResultsFound. V25-HLA-B08-10mers-98P4B6
NoResultsFound.
[1263]
64TABLE XLI Pos 1234567890 score V1-HLA-B1510-10mers-98P4B6
NoResultsFound. V2-HLA-B1510-10mers-98P4B6 NoResultsFound.
V5A-HLA-B1510-10mers-98P4B6 NoResultsFound.
V5B-HLA-B1510-10mers-98P4B6 NoResultsFound.
V6-HLA-B1510-10mers-98P4B6 NoResultsFound.
V7A-HLA-B1510-10mers-98P4B6 NoResultsFound.
V7B-HLA-B1510-10mers-98P4B6 NoResultsFound.
V7C-HLA-B1510-10mers-98P4B6 NoResultsFound.
V8-HLA-B1510-10mers-98P4B6 NoResultsFound.
V13-HLA-B1510-10mers-98P4B6 NoResultsFound.
V14-HLA-B1510-10mers-98P4B6 NoResultsFound.
V21-HLA-B1510-10mers-98P4B6 NoResultsFound.
V25-HLA-B1510-10mers-98P4B6 NoResultsFound.
V1-HLA-B2705-10mers-98P4B6 NoResultsFound.
V2-HLA-B2705-10mers-98P4B6 NoResultsFound.
V5A-HLA-B2705-10mers-98P4B6 NoResultsFound.
V5B-HLA-B2705-10mers-98P4B6 NoResultsFound.
V6-HLA-B2705-10mers-98P4B6 NoResultsFound.
V7A-HLA-B2705-10mers-98P4B6 NoResultsFound.
V7B-HLA-B2705-10mers-98P4B6 NoResultsFound.
V7C-HLA-B2705-10mers-98P4B6 NoResultsFound.
V8-HLA-B2705-10mers-98P4B6 NoResultsFound.
V13-HLA-B2705-10mers-98P4B6 NoResultsFound.
V14-HLA-B2705-10mers-98P4B6 NoResultsFound.
V21-HLA-B2705-10mers-98P4B6 NoResultsFound.
V25-HLA-B2705-10mers-98P4B6 NoResultsFound.
V1-HLA-B2709-10mers-98P4B6 NoResultsFound.
V2-HLA-B2709-10mers-98P4B6 NoResultsFound.
V5A-HLA-B2709-10mers-98P4B6 NoResultsFound.
V5B-HLA-B2709-10mers-98P4B6 NoResultsFound.
V6-HLA-B2709-10mers-98P4B6 NoResultsFound.
V7A-HLA-B2709-10mers-98P4B6 NoResultsFound.
V7B-HLA-B2709-10mers-98P4B6 NoResultsFound.
V7C-HLA-B2709-10mers-98P4B6 NoResultsFound.
V8-HLA-B2709-10mers-98P4B6 NoResultsFound.
V13-HLA-B2709-10mers-98P4B6 NoResultsFound.
V14-HLA-B2709-10mers-98P4B6 NoResultsFound.
V21-HLA-B2709-10mers-98P4B6 NoResultsFound.
V25-HLA-B2709-10mers-98P4B6 NoResultsFound.
[1264]
65TABLE XLIV Pos 1234567890 score V1-HLA-B4402-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 3; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 199
REIENLPLRL 25 351 EEEVWRIEMY 25 252 IEIVNKTLPI 23 389 REFSFIQSTL 23
95 REHYTSLWDL 21 179 IELARQLNFI 21 352 EEVWRIEMYI 20 79 HEDALTKTNI
19 377 TSIPSVSNAL 19 186 NFIPIDLGSL 18 202 ENLPLRLFTL 18 257
KTLPIVAITL 18 427 YTPPNEVLAL 18 435 ALVLPSIVIL 18 273 AGLLAAAYQL 17
289 RRFPPWLETW 17 296 ETWLQCRKQL 17 402 ALLISTFHVL 17 16 TCLPNG1NGI
16 116 VSNNMRINQY 16 200 EIENLPLRLF 16 219 AISLATFFFL 16 230
SFVRDVIHPY 16 250 IPIEIVNKTL 16 262 VAITLLSLVY 16 263 AITLLSLVYL 16
359 MYISFGIMSL 16 406 STFHVLIYGW 16 410 VLIYGWKRAF 16 36 IGSGDFAKSL
15 45 LTIRLIRCGY 15 56 VVIGSRNPKF 15 60 SRNPKFASEF 15 67 SEFFPHVVDV
15 126 PESNAEYLAS 15 130 AEYLASLFPD 15 203 NLPLRLFTLW 15 255
VNKTLPIVAI 15 258 TLPIVAITLL 15 279 AYQLYYGTKY 15 310 FFFAMVHVAY 15
329 ERYLFLNMAY 15 394 IQSTLGYVAL 15 437 VLPSIVILDL 15 4 ISMMGSPKSL
14 92 AIHREHYTSL 14 98 YTSLWDLRHL 14 99 TSLWDLRHLL 14 123
NQYPESNAFY 14 137 FPDSLLVKGF 14 147 NVVSAWALQL 14 183 RQLNFIPIDL 14
195 LSSAREIENL 14 218 VAISLATFFF 14 271 YLAGLLAAAY 14 290
RFPPWLETWL 14 346 ENSWNEEEVW 14 361 ISFGIMSLGL 14 365 IMSLGLLSLL 14
391 FSFI STLGY 14 396 STLGYVALLI 14 399 GYVALLISTF 14 404
LISTFHVLIY 14 418 AFEEEYYRFY 14 420 EEEYYRFYTP 14 440 SIVILDLLQL 14
41 FAKSLTIRLI 13 74 VDVTHHEDAL 13 80 EDALTKTNII 13 81 DALTKTNIIF 13
84 TKTNIIFVAI 13 104 LRHLLVGKIL 13 127 ESNAEYLASL 13 128 SNAEYLASLF
13 143 VKGFNVVSAW 13 145 GFNVVSAWAL 13 157 GPKDASRQVY 13 170
NNTQARQQVI 13 172 IQARQQVLEL 13 176 QQVIEILARQL 13 201 IENLPLRLFT
13 211 LWRGPVVVAI 13 213 RGPVVVAISL 13 220 ISLATFFFLY 13 245
SDFYKIPIEI 13 266 LLSLVYLAGL 13 267 LSLVYLAGLL 13 299 LQCRKQLGLL 13
303 KQLGLLSFFF 13 323 LPMRRSERYL 13 324 PMRRSERYLF 13 328
SERYLFLNMA 13 350 NEEEVWRIEM 13 362 SFGIMSLGLL 13 364 GIMSLGLLSL 13
379 IPSVSNALNW 13 384 NALNWREFSF 13 395 QSTLGYVALL 13 403
LLISTFHVLI 13 429 PPNEVLALVL 13 438 LPSIVILDLL 13 443 ILDLLQLCRY 13
38 SGDFAKSLTI 12 40 DFAKSLTIRL 12 93 IHREHYTSLW 12 105 RHLLVGKILI
12 124 QYPESNAEYL 12 178 VIELARQLNF 12 192 LGSLSSAREI 12 197
SAREIENLPL 12 216 VVVAISLATF 12 260 PIVAITLLSL 12 274 GLLAAAYQLY 12
282 LYYGTKYRRF 12 286 TKYRRFPPWL 12 295 LETWLQCRKQ 12 301
CRKQLGLLSF 12 302 RKQLGLLSFF 12 312 FAMVHVAYSL 12 357 IEMYISFGIM 12
385 ALNWREFSFI 12 417 RALFEEEYYRF 12 421 EEYYRFYTPP 12 425
RFYTPPNFVL 12 V2-HLA-B4402-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 5; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 8 ALSLSLSSGF 15 32 RCPPPCPADF 15
33 CPPPCPADFF 15 35 PPCPADFFLY 15 2 GSPGLQALSL 14 16 GFTPFSCLSL 14
36 PCPADFFLYF 13 4 PGLQALSLSL 12 11 LSLSSGFTPF 12 14 SSGFTPPFSCL 12
20 FSCLSLPSSW 12 22 CLSLPSSWDY 12 34 PPPCPADFFL 11
V5a-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
11; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 1 ENLPLRLFTF 18 2 NLPLRLFTFW 14 10 FWRGPVVVAI
13 V5B-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptides is
10 amino acids, and the end position for each peptide is the start
position plus nine. 23 LEFVFLLTLL 24 19 TELELEFVFL 23 20 ELELEFVFLL
15 22 ELEFVFLLTL 15 24 EFVFLLTLLL 15 21 LELEFVFLLT 14 2 WREFSFIQIF
13 3 REFSFIQIFC 13 5 FSFIQIFCSF 13 14 FADTQTELEL 13 1 NWREFSFIQI 12
12 CSFADTQTEL 12 16 DTQTELELEF 12 18 QTELELEFVF 12
V6-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
13; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 IVLLGKIILF 19 7 VILGKIILFL 16 14 LFLPCISRKL
16 17 PCISRKLKRI 14 37 EEGIGGTLPH 14 4 PSIVILGKIL 13 21 RKLKRIKKGW
13 5 SIVILGKLIL 12 10 GKIILFLPCI 12 26 IKKGWEKSQF 12 3 LPSIVILGKI
11 27 KKGWEKSQFL 11 30 WEKSQFLEEG 11 31 EKSQFLEEGI 11 36 LEEGIGGTW
11 35 FLEEGIGGTI 9 38 EGIGGTWHV 9 V7a-HLA-B4402-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 15; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 9
TFLPNGINGI 16 1 GSPKSLSETF 12 2 SPKSLSETFL 11 6 LSETFLPNGI 11 7
SETFLPNGIN 11 V7B-HLA-B4402-10mers-98P4B6 Each peptide is a portion
of SEQ ID NO: 15; each start position is specified, the length of
peptides is 10 amino acids, and the end position for each peptide
is the start position plus nine. 8 QQSTLGYVAL 16 10 SILGYVALLI 14 9
QSTLGYVALL 13 3 LNMAYQQSTL 12 5 MAYQQSTLGY 12
V7C-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
15; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 92 TEDDEAQDSI 20 179 QEQKSKIICMF 20 143
AASGTLSLAF 18 34 SEIVLPIEWQ 17 104 PESPDRALKA 17 12 EVLASPAAAW 16
15 ASPAAAWKCL 16 62 EFAGATAEAQ 16 132 WIBFLLRLLKS 16 20 AWKCLGANIL
15 5 VILDLSVEVL 14 11 VEVLASPAAA 14 42 WQQDRKJPPL 14 51 LSTPPPPAMW
14 68 AEAQESGIRN 14 71 QESGIRNKSS 14 102 DPPESPDRAL 14 113
AANSWRNPVL 14 127 GVGPLWEFLL 14 151 AFTSWSLGEF 14 168 KLETIILSKL 14
29 LRGGLSEIVL 13 40 IEWQQDRKTP 13 95 DEAQDSIDPP 13 108 DRALKAANSE
13 129 GPLWEFLLRL 13 130 PLWEFLLRLL 13 141 SQAASGTLSL 13 158
GEFLGSGTWM 13 165 TWMKLETIIL 13 169 LETIILSKLT 13 24 LGANILRGGL 12
27 NILRGGLSEI 12 33 LSEIVLPIEW 12 122 LPHTNGVGPL 12 123 PHTNGVGPLW
12 126 NGVGPLWEFL 12 139 LKSQAASGTL 12 146 GTLSLAFTSW 12 19
AAWKCLGANI 11 31 GGLSEIVLPI 11 61 TEEAGATAEA 11 66 ATAEAQESGI 11
125 TNGVGPLWEF 11 148 LSLAFTSWSL 11 152 FTSWSLGEFL 11 157
LGEFLGSGTW 11 160 FLGSGTWMKL 11 163 SGTWMKLETI 11 181 QKSKHCMFSL 11
182 KSKHCMIFSLI 11 39 PIEWQQDRKI 10 76 RNKSSSSSQI 9 83 SQIPVVGVVT 9
105 ESPDRALKAA 9 V8-HLA-B4402-10mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 17; each start position is specified, the
length of peptides is 10 amino acids, and the end position for each
peptide is the start position plus nine. 7 EEGMGGTIPH 14 6
LEEGMGGTIP 11 5 FLEEGMGGTI 9 8 FGMGGTIPHV 7
V13-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
27; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 9 TFLPNGINGI 16 1 GSPKSLSETF 12 2 SPKSLSETFL 11
6 LSETFLPNGI 11 7 SETFLPNGIN 11 V14-HLA-B4402-10mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 29; each start position is
specified, the length of peptides is 10 amino acids, and the end
position for each peptide is the start position plus nine. 1
ENLPLRLFTF 18 2 NLPLRLFTFW 14 10 FWRGPVVVAI 13
V21-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
43; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 6 QEQKTKHCMF 20 9 KTKHCMFSLI 11 8 QKTKHCMFSL 10
V25-HLA-B4402-10mers-98P4B6 Each peptide is a portion of SEQ ID NO:
51; each start position is specified, the length of peptides is 10
amino acids, and the end position for each peptide is the start
position plus nine. 3 LFLPCISQKL 15 6 PCISQKLKRI 14 10 QKLKIUKKGW
13 9 SQKLKRIKKG 8 2 ILFLPCISQK 7
[1265]
66TABLE XLV Pos 1234567890 score V1-HLA-B5101-10mers-98P4B6
NoResultsFound. V2-HLA-B5101-10mers-98P4B6 NoResultsFound.
V2-HLA-B5101-10mers-98P4B6 NoResultsFound.
V5A-HLA-B5101-10mers-98P4B6 NoResultsFound.
V5B-HLA-B5101-10mers-98P4B6 NoResultsFound.
V6-HLA-B5101-10mers-98P4B6 NoResultsFound.
V7A-HLA-B5101-10mers-98P4B6 NoResultsFound.
V7B-HLA-B5101-10mers-98P4B6 NoResultsFound.
V7C-HLA-B5101-10mers-98P4B6 NoResultsFound.
V8-HLA-B5101-10mers-98P4B6 NoResultsFound.
V13-HLA-B5101-10mers-98P4B6 NoResultsFound.
V21-HLA-B5101-10mers-98P4B6 NoResultsFound.
V25-HLA-B5101-10mers-98P4B6 NoResultsFound.
[1266]
67TABLE XLVI Pos 123456789012345 score
V1-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 3; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 143 VKGFNVVSAWALQLG 266 LLSLVYLAGLLAAAY 33
367 SLGLLSLLAVTSIPS 32 1 MESISMMGSPKSLSE 31 130 AEYLASLFPDSLIVK 30
30 KVTVGVIGSGDFAKS 29 431 NFVLALVLPSIVILD 29 206 LRLFTLWRGPVVVAI 28
215 PVVVAISLATFFFLY 28 370 LLSLLAVTSIPSVSN 28 438 LPSIVILDLLQLCRY
28 101 LWDLRHLLVGKILID 27 185 LNFIPIDLGSLSSAR 27 356
RIEMYISFGIMSLGL 27 360 YISFGIMSLGLLSLL 27 397 TLGYVALLISTFHVL 27
421 EEYYRFYTPPNFVLA 27 38 SGDFAKSLTRLIRC 26 102 WDLRHLLVGKILIDV 26
122 INQYPESNAEYLASL 26 149 VSAWALQLGPKDASR 26 244 QSDFYKTPIEIVNKT
26 249 KIPIEIYNKTLPIVA 26 256 NKTLPIVAITLLSLV 26 261
LVAITLLSLVYLAGL 26 298 WLQCRKQLGLLSFFF 26 368 LGLLSLLAVTSIPSV 26
109 VGKILIDVSNNMRIN 25 137 FPDSLIVKGFNVVSA 25 145 GFNVVSAWALQLGPK
25 198 AREIENLPLRLFTLW 25 222 LATFFFLYSFVRDVI 25 252
IEIVNKTLPIVAITL 25 264 ITLLSLVYLAGLLAA 25 302 RKQLGLLSFFFAMVH 25
309 SFFFAMVHVAYSLCL 25 354 VWRJEMYISFGIMSL 25 362 SFGIMSLGLLSLLAV
25 365 IMSLGLLSLLAVTSI 25 51 RCGYHVVIGSRNPKLF 24 98 YTSLWDLRHLLVGKJ
24 106 HLLVGKILIDVSNNM 24 150 SAWALQLGPKDASRQ 24 184
QLNFIPIDLGSLSSA 24 205 PLRLFTLWRGPVVVA 24 229 YSFVRDVIHPYARNQ 24
269 LVYLAGLLAAAYQLY 24 330 RYLFLNMAYQQVHAN 24 335 NMAYQQVHANTENSW
24 388 WREFSFIQSTLGYVA 24 391 FSFIQSTLGYVALLL 24 398
LGYVALLISTFHVLI 24 427 YTPPNFVLALVLPSI 24 430 PNFVLALVLPSIVIL 24 52
CGYHVVIGSRNPKFA 23 55 HVVIGSRNPKLFASEF 23 186 NFIPIDLGSLSSARE 23
214 GPVVVAISLATFFFL 23 258 TLPIVAITLLSLVYL 23 351 EEEVWRIEMYISFGI
23 352 EEVWPJEMYISFGIM 23 127 ESNAEYLASLFPDSL 22 178
VIELARQLNFIPIDL 22 189 PIDLGSLSSARFIEN 22 211 LWRGPVVVAISLATF 22
216 VVVAISLATFFFLYS 22 255 VNKTLPIVAITLLSL 22 301 CRKQLGLLSFFFAMV
22 312 FMAVHVAYSLCLPMR 22 359 MYISFGIMSLGLLSL 22 364
GIMSLGLLSLLAVTS 22 395 QSTLGYVALLISTFH 22 432 FVLALVLPSIVILDL 22
435 ALVLPSIVILDLLQL 22 20 NGINGIKDARKVTVG 21 117 SNNMRTNQYPESNAE 21
161 ASRQVYICSNNIQAR 21 174 ARQQVIELARQLNEI 21 277 AAAYQLYYGTKYRRF
21 373 LLAVTSPSVSNALN 21 399 GYVALLISTFHVLIY 21 407 TFHVLIYGWKRAFEE
21 31 VTVGVIGSGDFAKSL 20 142 IVKGFNVVSAWALQL 20 209 FTLWRGPVVVAISLA
20 346 ENSWNEEEVWRIEMY 20 385 ALNWREFSFIQSTLG 20 429
PPNFVLALVLPSIVI 20 45 LTIRLIRCGYHVVIG 19 80 EDALTKTNIIFVAIH 19 95
REHYTSLWDLRHLLV 19 135 SLFPDSLIVKGFNVV 19 139 DSLIVKGFNVVSAWA 19
224 TFFFLYSFVRDVIHP 19 259 LPIVAITLLSLVYLA 19 280 YQLYYGTKYRRFPPW
19 281 QLYYGTKYRRLFPPWL 19 288 YRRFPPWLETWLQCR 19 307
LLSFFFAMVHVAYSL 19 322 CLPMRRSERYLFLNM 19 328 SERYLFLNMAYQQVH 19
357 IEMYISFGIMSLGLL 19 400 YVALLISTFHVLIYG 19 424 YRFYTPPNFVLALVL
19 7 MGSPKSLSETCLPNG 18 25 IKDARKVTVGVIGSG 18 27 DARKVTVGVIGSGDF 18
39 GDFAKSLTIRLIRCG 18 47 IRLIRCGYHVVIGSR 18 62 NPKFASEFFPHVVDV 18
129 NAEYLASLFPDSLW 18 163 RQVYICSNNIQARQQ 18 167 ICSNNIQARQQVIEL 18
179 IELARQLNFIPIDLG 18 190 IDLGSLSSAREIENL 18 236 IHPYARNQQSDFYKI
18 267 LSLVYLAGLLAAAYQ 18 268 SLVYLAGLLAAAYQL 18 285
GTKYRRFPPWLETWL 18 296 ETWLQCRKQLGLLSF 18 299 LQCRKQLGLLSFFFA 18
326 RRSERYLFLNMAYQQ 18 380 PSVSNALNWREFSFI 18 383 SNALNWREFSFIQST
18 390 EFSFIQSTLGYVALL 18 405 ISTFHVLLYGWKRAF 18 410
VLIYGWKRAFEEFYY 18 423 YYRFYTPPNFVLALV 18 433 VLAIVLPSIVILDLL 18 22
INGIKDARKVTVGVI 17 29 RKVTVGVIGSGDFAK 17 33 VGVIGSGDFAKSLTI 17 34
GVIGSGDFAKSLTIR 17 44 SLTIRLIRCGYHVVI 17 46 TIRLIRCGYHVVIGS 17 54
YHVVIGSRNPKFASE 17 58 IGSRNPKFASEFFPH 17 77 THHEDALTKTNTIFV 17 87
NIIFVAIHREHYTSL 17 90 FVAIHREHYTSLWDL 17 105 RHLLVGKILIDVSNN 17 119
NMRINQYPESNAEYL 17 138 PDSLIVKGFNVVSAW 17 140 SLIVKGFNVVSAWAL 17
151 AWALQLGPKDASRQV 17 154 LQLGPKDASRQVYIC 17 176 QQVIELARQLNFIPI
17 187 FIPIDLGSLSSAREI 17 195 LSSAREIENLPLRLF 17 217
VVAISLATFFFLYSF 17 226 FFLYSFVRDVIHPYA 17 232 VRDVIHPYARNQQSD 17
251 PIEIVNKTLPIVAIT 17 253 EIVNKTLPIVAUTLL 17 270 VYLAGLLAAAYQLYY
17 271 YLAGLLAAAYQLYYG 17 305 LGLLSFFFAMVHVAY 17 316
HVAYSLCLPMRRSER 17 317 VAYSLCLPMRRSERY 17 329 ERYLFLNMAYQQVHA 17
361 ISFGIMSLGLLSLLA 17 363 FGIMSLGLLSLLAVT 17 389 REFSFIQSTLGYVAL
17 392 SFIQSTLGYVALLIS 17 406 STFHVLIYGWKRAFE 17 408
FHVLIYGWKRAFEFE 17 436 LVLPSIVLLDLLQLC 17 2 ESISMMGSPKSLSET 16 3
SISMMGSPKSLSETC 16 8 GSPKSLSETCLPNGI 16 11 KSLSETCLPNGINGI 16 16
TCLPNGNGIKDARK 16 24 GIKDARKVTVGVIGS 16 59 GSRNPKFASEFFPHV 16 67
SEFFPHVVDVTHHED 16 71 PHVVDVTHHEDALTK 16 103 DLRIILLVGKJLIDVS 16
111 KILIDVSNNMRIINQY 16 126 PESNAEYLASLFPDS 16 153 ALQLGPKDASRQVYI
16 166 YICSNNIQARQQVIE 16 171 NTQARQQVIIELARQL 16 175
RQQVIELARQLNFIP 16 182 ARQLNFIPIDLGSLS 16 200 FIENLPLRLFTLWRG 16
208 LFTLWRGPVVVAISL 16 219 AISLATFFFLYSFVR 16 225 FFFLYSFVRDVIHPY
16 263 AITLLSLVYLAGLLA 16 265 TLLSLVYLAGLLAAA 16 294
WLETWLQCRKQLGLL 16 304 QLGLLSFFFAMVHVA 16 308 LSFFFAMVHVAYSLC 16
310 FFFAMVHVAYSLCLP 16 314 MVHVAYSLCLPMRRS 16 371 LSLLAVTSIPSVSNA
16 394 IQSTLGYVALLISTF 16 401 VALLISTFHVLIYGW 16 420
EEEYYRFYTPPNFVL 16 428 TPPNFVLALVLPSIV 16 440 SLVILDLLQLCRYPD 16
V2-HLA-DRB1-0101-15mers-98- P4B6 Each peptide is a portion of SEQ
ID NO: 5; each start position is specified, the length of peptides
is 15 amino acids, and the end position for each peptide is the
start position plus fourteen. 17 FTPFSCLSLPSSWDY 26 28
SWDYRCPPPCPADFF 26 6 LQALSLSLSSGFTPF 25 8 ALSLSLSSGFTPFSC 25 3
SPGLQALSLSLSSGF 24 10 SLSLSSGFTPFSCLS 22 14 SSGFTPFSCLSLPSS 19 26
PSSWDYRCPPPCPAD 16 31 YRCPPPCPADFFLYF 16 1 SGSPGLQALSLSLSS 15 4
PGLQALSLSLSSGFT 15 20 FSCLSLPSSWDYRCP 15 2 GSPGLQALSLSLSSG 14 7
QALSLSLSSGFTPFS 14 13 LSSGFTPFSCLSLPS 14 16 GFTPFSCLSLPSSWD 14 19
PFSCLSLPSSWDYRC 14 27 SSWDYRCPPPCPADF 14 30 DYRCPPPCPADFFLY 14
V5A-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 11 LRLFTFWRGPVVVAI 28 3 AREIENLPLRLFTFW 25
16 FWRGPVVVAISLATF 22 14 FTFWRGPVVVAISLA 20 13 LFTFWRGPVVVAISL 18 5
EIENLPLRLFTFWRG 16 10 PLRLFTFWRGPVVVA 16 12 RLFTFWRGPVVVAIS 15 2
SAREIENLPLRLFTF 14 7 ENLPLRLFTFWRGPV 14 15 TFWRGPVVVAISLAT 14
V5B-HLA-DRB1-0101-15mers-98P4B- 6 Each peptide is a portion of SEQ
ID NO: 11; each start position is specified, the length of peptides
is 15 amino acids, and the end position for each peptide is the
start position plus fourteen. 7 WREFSFIQIFCSFAD 25 9
EFSFIQIFCSFADTQ 24 4 ALNWREFSFIQIFCS 20 2 SNALNWREFSFIQLF 18 20
ADTQTELELEFVFLL 18 8 REFSFIQTFCSFADT 17 10 FSFIQIFCSFADTQT 17 22
TQTELELEFVFLLTL 17 23 QTELELEFVFLLTLL 17 12 FIQIFCSFADTQTEL 16 16
FCSFADTQTELELEF 16 17 CSFADTQTELELEFV 14
V6-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 13; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 1 NFVLALVLPSIVILG 29 8 LPSIVILGKIILFLP 29
46 GGTIPHVSPERVTVM 28 17 LILFLPCISRKLKRI 26 11 IVILGKIILFLPCIS 24
38 SQFLEEGIGGTIPHV 24 39 QFLEEGIGGTIPHVS 24 7 VLPSIVILGKIILFL 23 14
LGKIILFLPCISRKL 23 2 FVLALVLPSIVILGK 22 42 EEGIGGTIPHVSPER 22 13
ILGKIILFLPCISRK 19 3 VLALVLPSIVILGKI 18 6 LVLPSIVILGKIILF 18 9
PS1YILGKIILFLPC 17 15 GKIILFLPCISRKLK 17 5 ALVLPSLVILGKIIL 16 10
SIVILGKIILFLPCI 16 18 ILFLPCISRKLKRIK 15 25 SRKLKRIKKGWEKSQ 15 30
RIKKGWEKSQFLEEG 14 43 EGIGGTIPHVSPFRV 14
V7A-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 12 SETFLPNGINGIKDA 21 5 MGSPKSLSETFLPNG 18
1 SISMMGSPKSLSETF 16 4 MMGSPKSLSETFLPN 16 6 GSPKSLSETFLPNGI 16 9
KSLSETFLPNGINGI 16 14 TFLPNGTNGIKDARK 16 2 ISMMGSPKSLSETFL 14 15
FLPNGINGIKDARKV 13 10 SLSETFLPNGINGIK 10
V7B-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 4 RYLFLNMAYQQSTLG 24 14 QSTLGYVALLISTFH 22
7 FLNMAYQQSTLGYVA 21 2 SERYLFLNMAYQQST 19 9 NMAYQQSTLGYVALL 18 3
ERYLFLNMAYQQSTL 17 11 AYQQSTLGYVALLIS 17 10 MAYQQSTLGYVALLI 16 13
QQSTLGYVALLISTF 16 8 LNMAYQQSTLGYVAL 14
V7C-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 23 AAAWKCLGANILRGG 36 168 SGTWMKLETIILSKL
35 138 EFLLRLLKSQAASGT 33 13 DLSVEVLASPAAAWK 30 50 DRKIPPLSTPPPPAM
30 28 CLGAMLRGGLSEIV 28 62 PAMWTEEAGATAEAQ 27 110 ESPDRALKAANSWRN
26 124 NPVLPHTNGVGPLWE 26 141 LRLLKSQAASGTLSL 25 8 SIVILDLSVEVLASP
24 31 ANTLRGGLSELVLPI 24 42 VLPIEWQQDRKIPPL 24 77 ESGIRNKSSSSSQIP
24 130 TNGVGPLWEFLLRLL 24 137 WEFLLRLLKSQAASG 24 7 PSIVILDLSVEVLAS
23 12 LDLSVEVLASPAAAW 23 150 SGTLSLAETSWSLGE 23 171 WMKLETIILSKLTQE
23 3 ALVLPSIVILDLSVE 22 53 IPPLSTPPPPAMWTE 22 157 FTSWSLGEFLGSGTW
22 89 QIIPVVGVVTEDDEAQ 21 6 LPSIVILDLSVEVLA 20 58 TPPPPAMWTEEAGAT
20 97 TEDDEAQDSIDPPES 20 100 DEAQDSIDPPESPDR 20 134 GPLWEFLLRLLKSQA
19 154 SLAFTSWSLGEFLGS 19 1 VLALVLPSIVILDLS 18 22 PAAAWKCLGANTLRG
18 44 PIE WQQDRKIPPLST 18 122 WRNPVLPHTNGVGPL 18 135
PLWEFLLRLLKSQAA 18 140 LLRLLKSQAASGTLS 18 148 AASGTLSLAFTSWSL 18
159 SWSLGEFLGSGTWMK 18 161 SLGEFLGSGTWMKLE 18 169 GTWMKLETIILSKLT
18 176 TIILSKLTQEQKSKH 18 4 LVLPSIVILDLSVEV 17 9 IVILDLSVEVLASPA 17
30 GANILRGGLSEIVLP 17 61 PPAMWTEEAGATAEA 17 67 EEAGATAEAQESGIR 17
94 GVVTEDDEAQDSIDP 17 101 EAQDSIDPPESPDRA 17 107 DPPESPDRALKAANS 17
133 VGPLWEFLLRLLKSQ 17 143 LLKSQAASGTLSLAE 17 162 LGEFLGSGTWMKLET
17 163 GEFLGSGTWMKLETI 17 172 MKLETIILSKLTQEQ 17
V8-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 17; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 8 SQFLEEGMGGTLPHV 24 9 QFLEEGMGGTWHVS 24 12
EEGMGGTWHVSPER 22 13 EGMGGTIPHVSPERV 14 7 KS FLEEGMGGTIPH 13 2
KKGWEKSQFLEEGMG 12 6 EKSQFLEEGMGGTIP 12
V13-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 27; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 12 SETFLPNGINGIKDA 21 5 MGSPKSLSETFLPNG 18
1 SISMMGSPKSLSETF 16 4 MMGSPKSLSETFLPN 16 6 GSPKSLSETFLPNGI 16 9
KSLSETFLPNGINGI 16 14 TFLPNGINGIKDARK 16 2 ISMMGSPKSLSETFL 14 15
FLPNGINGIKDARKV 13 10 SLSETFLPNGINGIK 10
V14-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 29; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 10 LRLFTFWRGPVVVAI 28 2 AREIENLPLRLFTFW 25
15 FWRGPVVVALISLATF 22 13 FTFWRGPVVVAISLA 20 12 LFTFWRGPVVVAISL 18
4 EIENLPLRLFTFWRG 16 9 PLRLFTFWRGPVVVA 16 11 RLFTFWRGPVVVAJS 15 1
SAREIENLPLRLFTF 14 6 ENLPLRLFTFWRGPV 14 14 TFWRGPVVVAISLAT 14 8
LPLRLFTFWRGPVVV 12 V21-HLA-DRB1-0101-15mers-98P4B6 Each peptide is
a portion of SEQ ID NO: 15; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 3 TIILSKLTQEQKTKH 18 2
ETIILSKLTQEQKTK 14 7 SKLTQEQKTKHCMFS 13 6 LSKLTQEQKTKHCMF 11 11
QEQKTKHCMFSLISG 11 1 LETIILSKLTQEQKT 10 9 LTQEQKTKHCMFSLI 10 10
TQEQKTKHCMFSLIS 9 12 EQKTKHCMFSLISGS 9 5 ILSKLTQEQKTKHCM 8 8
KLTQEQKTKHCMFSL 8 V25-HLA-DRB1-0101-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 51; each start position is specified, the
length of peptides is 15 amino acids, and
the end position for each peptide is the start position plus
fourteen. 6 IILFLPCISQKLKRI 25 3 LGKIILFLPCISQKL 23 2
ILGKIILFLPCISQK 19 4 GKIILFLPCISQKLK 17 7 ILFLPCISQKLKRIK 15 9
FLPCISQKLKRIKKG 15 14 SQKLKRIKKGWEKSQ 15 15 QKLKRIKKGWEKSQF 13
[1267]
68TABLE XLVII Pos 123456789012345 score
V1-HLA-DRB1-0301-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 3; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 97 HYTSLWDLRJJLLVGK 28 176 QQVIELARQLNFIPI
27 228 LYSFVRDVIHPYARN 27 322 CLPMRRSERYLFLNM 27 54
YHVVIGSRINPKFASE 26 296 ETWLQCRKQLGLLSF 26 408 FHVLLYGWKRAFEEE 26
273 AGLLAAAYQLYYGTK 25 439 PSIVILDLLQLCRYP 25 109 VGKILIDVSNNMRIN
24 288 YRRFPPWLETWLQCR 24 87 NIIFVAIHREHYTSL 23 423 YYRFYTPPNFVLALV
23 133 LASLFPDSLIVKGFN 22 185 LNFIPIDLGSLSSAR 22 261
IVAITLLSLVYLAGL 22 272 LAGLLAAAYQLYYGT 22 433 VLALVLPSIVILDLL 22
145 GFNVVSAWALQLGPK 21 214 GPVVVAISLATFFFL 21 269 LVYLAGLLAAAYQLY
21 362 SFGTMSLGLLSLLAV 21 363 FGIMSLGLLSLLAVT 21 175
RQQVIELARQLNFIP 20 198 AREIENLPLRLFTLW 20 258 TLPIVAITLLSLVYL 20
264 ITLLSLVYLAGLLAA 20 376 VTSIPSVSNALNWRE 20 400 YVALLISTFHVLIYG
20 435 ALVLPSIVILDLLQL 20 438 LPSLVILDLLQLCRY 20 440
SIVILDLLQLCRYPD 20 30 KVTVGVIGSGDFAKS 19 53 GYHVVIGSRNPKFAS 19 110
GMUDVSNNMRIINQ 19 130 AEYLASLFPDSLIVK 19 151 AWALQLGPKDASRQV 19 215
PVVVAISLATFFFLY 19 217 VVAISLATFFFLYSF 19 256 NKTLPIVAITLLSLV 19
312 FAMVIIVAYSLCLPM 19 320 SLCLPMRRSERYLFL 19 402 ALLISTFHVLIYGWK
19 3 SISMMGSPKSLSETC 18 22 INGIKDARKVTVGVI 18 34 GVIGSGDFAKSLTIR 18
90 FVAIHREHYTSLWDL 18 119 NMRINQYPESNAEYL 18 139 DSLIVKGFNVVSAWA 18
143 VKGFNVVSAWALQLG 18 162 SRQVYICSNNTQARQ 18 184 QLNFIPIDLGSLSSA
18 195 LSSAREIENLPLRLF 18 233 RDVIHPYARNQQSDF 18 308
LSFFFAMVHVAYSLC 18 331 YLFLNMAYQQVHANI 18 360 YISFGIMSLGLLSLL 18
409 HVLIYGWKRAFEEEY 18 7 MGSPKSLSETCLPNG 17 21 GINGIKDARKVTVGV 17
38 SGDFAKSLTIRLIRC 17 113 LIDVSNNMRINQYPE 17 121 RINQYPESNAEYLAS 17
155 QLGPKDASRQVYICS 17 169 SNNIQARQQVIELAR 17 178 VIELARQLNFIPIDL
17 192 LGSLSSAREIENLPL 17 225 FFFLYSFVRDVIHPY 17 249
KIPIEIVNKTLPIVA 17 292 PPWLETWLQCRKQLG 17 318 AYSLCLPMRRSERYL 17
327 RSERYLFLNMAYQQV 17 338 YQQVHANIENSWNEE 17 379 IPSVSNALNWREFSF
17 416 KRAFEEEYYRFYTPP 17 15 ETCLPNGINGLKDAR 16 72 HVVDVTHHEDALTKT
16 79 HEDALTKTNTIFVAI 16 88 ILFVAIHREHYTSLW 16 111 KILIDVSNNMRTNQY
16 205 PLRLFTLWRGPVVVA 16 248 YKIPIEIVNKTLPIV 16 279
AYQLYYGTKYRRFPP 16 342 HANIENSWNEEEVWR 16 382 VSNALNWREFSFIQS 16
413 YGWKRAFEEEYYRFY 16 43 KSLTIRLIRCGYHVV 15 263 AITLLSLVYLAGLLA 15
294 WLETWLQCRKQLGLL 15 321 LCLPMkRSERYLFLN 15 367 SLGLLSLLAVTSIPS
15 387 NWREFSFIQSTLGYV 15 412 IYGWKRAFEEEYYRF 15 73 VVDVTHHEDALTKTN
14 104 LRHLLVGKILIDVSN 14 236 IHPYARNQQSDFYKI 14 267
LSLVYLAGLLAAAYQ 14 304 QLGLLSFFFAMVHVA 14 365 IMSLGLLSLLAVTSI 14
373 LLAVTSWSVSNALN 14 401 VALLISTFHVLIYGW 14 434 LALVLPSIVILDLLQ 14
1 MESISMMGSPKSLSE 13 4 ISMMGSPKSLSFTCL 13 32 TVGVIGSGDFAKSLT 13 33
VGVIGSGDFAKSLTI 13 101 LWDLRHLLVGKILID 13 138 PDSL1YKGFNVVSAW 13
164 QVYICSNNIQARQQV 13 189 PIDLGSLSSAREIEN 13 201 IENLPLRLFTLWRGP
13 213 RGPVVVAISLATFFF 13 266 LLSLVYLAGLLAAAY 13 407
TFHVLIYGWKRAEEE 13 V2-HLA-DR1-0301-15mers-98P- 4B6 Each peptide is
a portion of SEQ ID NO: 5; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 6 LQALSLSLSSGFTPF 20
14 SSGFTPFSCLSLPSS 20 20 FSCLSLPSSWDYRCP 20 24 SLPSSWDYRCPPPCP 16 2
GSPGLQALSLSLSSG 12 3 SPGLQALSLSLSSGF 12 8 ALSLSLSSGFTPFSC 12 9
LSLSLSSGFTPFSCL 12 10 SLSLSSGFTPFSCLS 11 22 CLSLPSSWDYRCPPP 11 30
DYRCPPPCPADFFLY 10 31 YRCPPPCPADFFLYF 10 12 SLSSGFTPFSCLSLP 9 17
FTPFSCLSLPSSWDY 9 V5A-HLA-DR1-0301-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 11; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 3 AREIENLPLRLFTFW 20
10 PLRLFTFWRGPVVVA 16 2 SAREIENLPLRLFTF 12 6 IENLPLRLFTFWRGP 12 8
NLPLRLFTFWRGPVV 12 5 EIENLPLRLFTFWRG 11 13 LFTFWRGPVVVAISL 10 4
REIENLPLRLFTFWR 9 11 LRLFTFWRGPVVVAI 9
V5B-HLA-DR1-0301-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 15 IFCSFADTQTELELE 24 23 QTELELEFVFLLTLL 20
1 VSNALNWREFSFIQI 16 19 FADTQTELELEFVFL 16 21 DTQTELELEFVFLLT 16 17
CSFADTQTELELEFV 15 22 TQTELELEFVFLLTL 13 2 SNALNWREFSFIQIF 11 10
FSFIQWCSFADTQT 11 V6-HLA-DR1-0301-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 13; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 8 LPSIVILGKIILFLP 26 3
VLALVLPSIVILGKI 22 9 PSIVILGKIILFLPC 22 10 SIVILGKIILFLPCI 21 17
IILFLPCISRKLKRI 20 18 ILFLPCISRKLKRIK 18 25 SRKLKRLKKGWEKSQ 18 21
LPCISRKLKRIKKGW 17 28 LKRIKKGWEKSQFLE 17 29 KRIKKGWEKSQFLEE 16 4
LALVLPSIVILGKII 14 14 LGKIILFLPCISRKL 13 15 GKIILFLPCISRKLK 13 1
NFVLALVLPSIVILG 12 5 ALVLPSIVILGKIIL 12 37 KSQFLEEGIGGTIPH 12
V7A-HLA-DR1-0301-15mers-98P4- B6 Each peptide is a portion of SEQ
ID NO: 15; each start position is specified, the length of peptides
is 15 amino acids, and the end position for each peptide is the
start position plus fourteen. 1 SISMMGSPKSLSETF 18 5
MGSPKSLSFTFLPNG 17 13 ETFLPNGINGIKDAR 16 2 ISMMGSPKSLSETFL 13 12
SETFLPNGINGIKDA 13 8 PKSLSETFLPNGING 12 4 MMGSPKSLSETFLPN 9 10
SLSETFLPNGINGIK 8 V7B-HLA-DR1-0301-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 15; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 5 YLFLNMAYQQSTLGY 18 1
RSERYLFLNMAYQQS 17 6 LFLNMAYQQSTLGYV 14 12 YQQSTLGYVALLIST 12 3
ERYLFLNMAYQQSTL 11 4 RYLFLNMAYQQSTLG 11 7 FLNMAYQQSTLGYVA 11 11
AYQQSTLGYVALLIS 11 14 QSTLGYVALLISTFH 11 8 LNMAYQQSTLGYVAL 10
V7C-HLA-DR1-0301-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 93 VGVVTEDDEAQDSID 29 130 TNGVGPLWEFLLRLL
26 7 PSIVILDLSVEVLAS 24 1 VLALVLPSIVILDLS 22 8 SIVILDLSVEVLASP 21
133 VGPLWEFLLRLLKSQ 21 3 ALVLPSLVILDLSVE 20 163 GEFLGSGTWMKLETI 20
9 IVILDLSVEVLASPA 19 123 RNPVLPHTNGVGPLW 19 137 WEFLLRLLKSQAASG 19
154 SLAFTSWSLGEFLGS 19 171 WMKLETIILSKLTQE 19 38 LSEIVLPIEWQQDRK 18
179 LSKLTQEQKSKHCMF 18 40 EIVLPIEWQQDRKIP 17 44 PIEWQQDRKIPPLST 16
90 WXTVGVVTEDDEAQD 16 176 TIILSKLTQEQKSKH 16 15 SVEVLASPAAAWKCL 15
27 KCLGANILRGGLSEL 15 32 NTLRGGLSE1VLPIE 15 39 SEIVLPIEWQQDRKI 15
116 LKAANSWRNPVLPHT 15 138 EFLLRLLKSQAASGT 15 175 ETIILSKLTQEQKSK
15 2 LALVLPSIVILDLSV 14 V8-HLA-DR1-0301-15mers-98P4- B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptides is 15 amino acids, and the end
position for each peptide is the start position plus fourteen. 7
KSQFLEEGMGGTIPH 12 8 SQFLEEGMGGTIPHV 11 12 EEGMGGTIPHVSPER 10 1
IKKGWEKSQFLEEGM 9 4 GWEKSQFLEEGMGGT 7 5 WEKSQFLEEGMGGTI 7
V13-HLA-DR1-0301-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 27; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 1 SISMMGSPKSLSETF 18 5 MGSPKSLSETFLPNG 17
13 ETFLPNGINGIKDAR 16 2 ISMMGSPKSLSETFL 13 12 SETFLPNGINGIKDA 13 8
PKSLSETFLPNGING 12 4 MMGSPKSLSETFLPN 9 10 SLSETFLPNGINGIK 8
V14-HLA-DR1-0301-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 29; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 2 AREIENLPLRLFTFW 20 9 PLRLFTFWRGPVVVA 16 1
SAREIENLPLRLFTF 12 5 IENLPLRLFTFWRGP 12 7 NLPLRLFTFWRGPVV 12 4
EIENLPLRLFTFWRG 11 12 LFTFWRGPVVVAISL 10 3 REIENLPLRLFTFWR 9 10
LRLFTFWRGPVVVAI 9 V21-HLA-DR1-0301-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 43; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 6 LSKLTQEQKTKHCMF 18 3
TIILSKLTQEQKTKH 16 2 ETIILSKLTQEQKTK 15 1 LETIILSKLTQEQKT 13 4
IILSKLTQEQKTKHC 10 5 ILSKLTQEQKTKHCM 9 9 LTQEQKTKHCMFSLI 9 11
QEQKTKHCMFSLISG 9 V25-HLA-DR1-0301-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 51; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 6 IILFLPCISQKLKRI 21 7
ILFLPCISQKLKRIK 18 14 SQKLKRIKKGWEKSQ 18 10 LPCISQKLKRJKKGW 17 3
LGKIILFLPCISQKL 13 4 GKIILFLPCISQKLK 13 5 KIILFLPCISQKLKR 11
[1268]
69TABLE XLVIII Pos 123456789012345 score
V1-HLA-DR1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 3; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 420 EEEYYRFYTPPNFVL 28 98 YTSLWDLRIILLVGKI
26 109 VGKILIDVSNNMRIN 26 175 RQQVIELARQLNFIP 26 205
PLRLFTLWRGPVVVA 26 213 RGPVVVAISLATFFF 26 225 FFFLYSFVRDVIHPY 26
229 YSFVRDVIHPYARNQ 26 312 FAMVHVAYSLCLPMR 26 370 LLSLLAVTSIPSVSN
26 373 LLAVTSIPSVSNALN 26 376 VTSIPSVSNALNWRE 26 38 SGDFAKSLTIRLIRC
22 51 RCGYHVVIGSRNPKF 22 62 NPKIFASEFFPHVVDV 22 87 NTIFVALHREHYTSL
22 143 VKGFNVVSAWALQLG 22 163 RQVYICSNNIQARQQ 22 184
QLNFIPIDLGSLSSA 22 222 LATFFFLYSFVRDVI 22 244 QSDFYKIPIEIVNKT 22
307 LLSFFFAMVHVAYSL 22 309 SFFFAMVHVAYSLCL 22 328 SERYLFLNMAYQQVH
22 346 ENSWNEEEVWRIEMY 22 357 IEMYISFGIMSLGLL 22 385
ALNWREFSFIQSTLG 22 388 WREFSFIQSTLGYVA 22 405 ISTFHVLIYGWKRAF 22
423 YYRFYTPPNFVLALV 22 429 PPNFVLALVLPSIVI 22 1 MESISMMGSPKSLSE 20
15 ETCLPNGINGIKDAR 20 19 PNGINGIKDARKVTV 20 22 INGLKDARKVTVGVI 20
30 KVTVGVIGSGDFAKS 20 47 IRLIRCGYHVVIGSR 20 53 GYHVVIGSRNPKFAS 20
70 FPHVVDVTHHEDALT 20 71 PHVVDVTHHEDALTK 20 86 TNIIFVAIHREHYTS 20
90 FVAJHREHYTSLWDL 20 101 LWDLRHLLVGKJLID 20 106 HLLVGKILIDVSNNM 20
110 GKILIDVSNNMRINQ 20 111 KILIDVSNNMRINQY 20 113 LIDVSNNMRINQYPE
20 130 AEYLASLFPDSLIVK 20 133 LASLFPDSLIVKGFN 20 139
DSLLVKGFNVVSAWA 20 140 SLIVKGFNVVSAWAL 20 145 GFNVVSAWALQLGPK 20
162 SRQVYICSNNIQARQ 20 176 QQVIELARQLNELPI 20 185 LNFLPIDLGSLSSAR
20 189 PIDLGSLSSAREIEN 20 192 LGSLSSAREIENLPL 20 217
VVAISLATFFFLYSF 20 219 AISLATFFFLYSFVR 20 233 RDVIHPYARNQQSDF 20
247 FYKLPIEIYNKTLPI 20 256 NKTLPIVAITLLSLV 20 258 TLPIVAITLLSLVYL
20 261 IVAITLLSLVYLAGL 20 264 ITLLSLVYLAGLLAA 20 266
LLSLVYLAGLLAAAY 20 267 LSLVYLAGLLAAAYQ 20 273 AGLLAAAYQLYYGTK 20
292 PPWLETWLQCRKQLG 20 302 RKQLGLLSFFFAMVH 20 304 QLGLLSFFFAMVHVA
20 331 YLFLNMAYQQVHANI 20 351 EEEVWRIEMYISFGI 20 354
VWRIEMYISFGIMSL 20 362 SFGIMSLGLLSLLAV 20 365 IMSLGLLSLLAVTSI 20
367 SLGLLSLLAVTSIPS 20 368 LGLLSLLAVTSIPSV 20 379 IPSVSNALNWREFSF
20 395 QSTLGYVALLISTFH 20 398 LGYVALLISTFHVLI 20 401
VALLISTFHVLIYGW 20 430 PNFVLALVLPSIVIL 20 431 NFVLALVLPSIVILD 20
435 ALVLPSIVLLDLLQL 20 438 LPSIVILDLLQLCRY 20 440 SIVILDLLQLCRYPD
20 12 SLSETCLPNGINGIK 18 21 GINGIKDAThVTVGV 18 36 IGSGDFAKSLTIRLL
18 76 VTHHEDALTKTNIIF 18 97 HYTSLWDLRHLLVGK 18 142 IVKGFNVVSAWALQL
18 154 LQLGPKDASRQVYIC 18 161 ASRQVYICSNNTQAR 18 168
CSNNTQARQQVIELA 18 186 NFIPIDLGSLSSARE 18 195 LSSAREIENLPLRLF 18
234 DVIHPYARNQQSDFY 18 248 YKJPIELVNKTLPIV 18 257 KTLPIVAITLLSLVY
18 289 RRFPPWLETWLQCRK 18 339 QQVHANTENSWNEEE 18 348
SWNEEEVWRIEMYIS 18 359 MYISFGIMSLGLLSL 18 364 GIMSLGLLSLLAVTS 18
384 NALNWREFSFIQSTL 18 387 NWREFSFIQSTLGYV 18 399 GYVALLISTFHVLIY
18 432 FVLALVLPSIVILDL 18 66 ASEFFPHVVDVTHHE 16 67 SEFFPHVVDVTHHED
16 95 REHYTSLWDLRIILLV 16 122 INQYPESNAEYLASL 16 129
NAEYLASLFPDSLIV 16 206 LRLFTLWRGPVVVAI 16 209 FTLWRGPVVVAISLA 16
224 TFFFLYSFVRDVIHP 16 226 FFLYSFVRDVIHPYA 16 228 LYSFVRDVIHPYARN
16 236 IHPYARNQQSDFYKJ 16 245 SDFYKIPIEIVNKTL 16 268
SLVYLAGLLAAAYQL 16 285 GTKYRRFPPWLETWL 16 288 YRRFPPWLETWLQCR 16
308 LSFFFAMVHVAYSLC 16 330 RYLFLNMAYQQVHAN 16 335 NMAYQQVHANIENSW
16 352 EEVWRIEMYISFGIM 16 360 YISFGIMSLGLLSLL 16 390
EFSFIQSTLGYVALL 16 397 TLGYVALLISTFHVL 16 412 IYGWKRAFEEEYYRF 16
416 KRAFEEEYYRFYTPP 16 424 YRFYTPPNFVLALVL 16 296 ETWLQCRKQLGLLSF
15 3 SISMMGSPKSLSETC 14 4 ISMMGSPKSLSETCL 14 32 TVGVIGSGDFAKSLT 14
33 VGVIGSGDFAKSLTI 14 44 SLTIRLIRCGYHVVI 14 46 TIRLIRCGYHVVIGS 14
54 YHVVIGSRNPKEASE 14 73 VVDVTHHEDALTKTN 14 80 EDALTKTNTIFVAIH 14
85 KTNIIFVAIHREHYT 14 88 IIFVAIHREHYTSLW 14 117 SNNMRINQYPESNAE 14
119 NMIUNQYPESNAEYL 14 151 AWALQLGPKDASRQV 14 178 VIELARQLNFIPIDL
14 182 ARQLNFIPIDLGSLS 14 187 FIPIDLGSLSSAREI 14 198
AREIENLPLRLFTLW 14 203 NLPLRLFTLWRGPVV 14 208 LFTLWRGPVVVAISL 14
214 GPVVVAISLATFFFL 14 232 VRDVIHPYARNQQSD 14 249 KIPIEIVNKTLPIVA
14 252 IE1VNKTLPIVAITL 14 259 LPIVAITLLSLVYLA 14 263
AITLLSLVYLAGLLA 14 269 LVYLAGLLAAAYQLY 14 272 LAGLLAAAYQLYYGT 14
305 LGLLSFFFAMVHVAY 14 311 FFAMVHVAYSLCLPM 14 314 MVHVAYSLCLPMRRS
14 318 AYSLCLPMRRSERYL 14 322 CLPMRRSERYLFLNM 14 329
ERYLFLNMAYQQVHA 14 333 FLNMAYQQVHANIEN 14 342 HANIENSWNEEEVWR 14
356 RIEMYISFGIMSLGL 14 363 FGIMSLGLLSLLAVT 14 371 LSLLAVTSIPSVSNA
14 391 FSFIQSTLGYVALLI 14 400 YVALLISTFHVLIYG 14 402
ALLISTFHVLIYGWK 14 407 TFHVLIYGWKRAFEE 14 409 HVLIYGWKRAFEEEY 14
433 VLALVLPSIVILDLL 14 439 PSIVILDLLQLCRYP 14
V5A-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 14 SSGFTPFSCLSLPSS 22 17 FTPFSCLSLPSSWDY 22
3 SPGLQALSLSLSSGF 20 10 SLSLSSGFTPFSCLS 20 2 GSPGLQALSLSLSSG 18 7
QALSLSLSSGFTPFS 18 28 SWDYRCPPPCPADFF 16 6 LQALSLSLSSGFTPF 14 20
FSCLSLPSSWDYRCP 14 4 PGLQALSLSLSSGFT 12 13 LSSGFTPFSCLSLPS 12 16
GFTPFSCLSLPSSWD 12 19 PFSCLSLPSSWDYRC 12 24 SLPSSWDYRCPPPC 12
V5B-HLA-DRB1-0401-15mers-98P4- B6 Each peptide is a portion of SEQ
ID NO: 11; each start position is specified, the length of peptides
is 15 amino acids, and the end position for each peptide is the
start position plus fourteen. 4 ALNWREFSFIQIFCS 22 7
WREFSFIQIFCSFAD 22 9 EFSFIQIFCSFADTQ 22 13 IQIFCSFADTQTELE 22 10
FSFIQIFCSFADTQT 20 23 QTELELEFVFLLTLL 20 3 NALNWREFSFIQIFC 18 15
IFCSFADTQTELELE 18 16 FCSFADTQTELELEF 16 12 FIQIFCSFADTQTEL 14 6
NWREFSFIQIFCSFA 12 14 QIFCSFADTQTELEL 12 20 ADTQTELELEFVFLL 12 22
TQTELELEFVFLLTL 12 24 TELELEFVFLLTLLL 12
V6-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 13; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 18 ILFLPCISRKLKRIK 26 17 IILFLPCISRKLKRI 22
37 KSQFLEEGIGGTIPH 22 1 NFVLALVLPSIVILG 20 5 ALVLPSIVILGKIIL 20 8
LPSIVTLGKIILFLP 20 14 LGKIILFLPCISRKL 20 46 GGTIPHVSPERVTVM 20 2
FVLALVLPSIVILGK 18 22 PCISRKLKRIKKGWE 18 30 RJKKGWEKSQFLEEG 18 3
VLALVLPSIVILGKI 14 11 IVILGKIILFLPCIS 14 15 GKIILFLPCLSRKLK 14 16
KIILFLPCISRKLKR 14 25 SRKLKRIKKGWEKSQ 14 28 LKRIKKGWEKSQFLE 14 38
SQFLEEGIGGTIPHV 14 42 EEGIGGTIPHVSPER 14 6 LVLPSIVILGKIILF 12 7
VLPSIVILGKIILFL 12 13 ILGKIILFLPCISRK 12 34 GWEKSQFLEEGIGGT 12 43
EGIGGTIPHVSPERV 12 V7A-HLA-DRB1-0401-15mers-98P4B6 Each peptide is
a portion of SEQ ID NO: 15; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 13 ETFLPNGINGIKDAR 20
10 SLSETFLPNGINGIK 18 12 SETFLPNGINGIKDA 16 1 SISMMGSPKSLSETF 14 2
ISMMGSPKSLSETFL 14 5 MGSPKSLSETFLPNG 12 7 SPKSLSETFLPNGIN 12 9
KSLSETFLPNG1NGI 12 V7B-HLA-DRB1-0401-15mers-98P4B6 Each peptide is
a portion of SEQ ID NO: 15; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 5 YLFLNMAYQQSTLGY 26 2
SERYLFLNMAYQQST 22 14 QSTLGYVALLISTFH 20 4 RYLFLNMAYQQSTLG 16 9
NMAYQQSTLGYVALL 16 3 ERYLFLNMAYQQSTL 14 7 FLNMAYQQSTLGYVA 14 1
RSERYLFLNMAYQQS 12 6 LFLNMAYQQSTLGYV 12 11 AYQQSTLGYVALLIS 12 15
STLGYVALLISTFHV 12 V7C-HLA-DRB1-0401-15mers-98P4B6 Each peptide is
a portion of SEQ ID NO: 15; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 134 GPLWEFLLRLLKSQA 28
168 SGTWMKLETIWSKL 28 7 PSIVILDLSVEVLAS 26 13 DLSVEVLASPAAAWK 26
113 DRALKAANSWRNPVL 26 138 EFLLRLLKSQAASGT 26 150 SGTLSLAFTSWSLGE
26 176 TIILSKLTQEQKSKH 26 23 AAAWKCLGANTLRGG 22 62 PAMWTEEAGATAEAQ
22 162 LGEFLGSGTWMKLET 22 3 ALVLPSIVILDLSVE 10 8 SIVILDLSVEVLASP 20
31 ANTLRGGLSEIVLPI 20 40 EIVLPIEWQQDRKIP 20 50 DRKIPPLSTPPPPAM 20
61 PPAMWTEEAGATAFA 20 89 QIPVVGVVTEDDEAQ 20 92 VVGVVTEDDEAQDSI 20
130 TNGVGPLWEFLLRLL 20 133 VGPLWEFLLRLLKSQ 20 137 WEFLLRLLKSQAASG
20 159 SWSLGEFLGSGTWMK 20 169 GTWMKLETIILSKLT 20 171
WMKLETIILSKLTQE 20 27 KCLGANILRGGLSFI 18 74 EAQESGIRNKSSSSS 18 95
VVTEDDEAQDSIDPP 18 142 RLLKSQAASGTLSLA 18 151 GTLSLAFTSWSLGEF 18
172 MKLETIILSKLTQEQ 18 44 PIEWQQDRKIPPLST 16 119 ANSWRNPVLPHTNGV 16
157 FTSWSLGEFLGSGTW 16 77 ESGIIRNKSSSSSQIP 15 175 BTIILSKLTQEQKSK
15 1 VLALVLPSIVILDLS 14 6 LPSIVILDLSVEVLA 14 9 IVILDLSVEVLASPA 14
11 ILDLSVEVLASPAAA 14 16 VEVLASPAAAWKCLG 14 30 GANTLRGGLSEIVLP 14
35 RGGLSEIVLPIEWQQ 14 38 LSEIVLPIFWQQDRK 14 39 SEIVLPIEWQQDRKI 14
42 VLPIEWQQDRKIPPL 14 53 IPPLSTPPPPAMWTE 14 87 SSQIPVVGVVTEDDE 14
90 IPVVGVVTEDDEAQD 14 93 VGVVTEDDEAQDSID 14 103 QDSIDPPESPDRALK 14
123 RNPVLPHTNGVGPLW 14 141 LRLLKSQAASGTLSL 14 163 GEFLGSGTWMKLETI
14 179 LSKLTQEQKSKHCMF 14 V8-HLA-DRB1-0401-15mers-98P4B6 Each
peptide is a portion of SEQ ID NO: 17; each start position is
specified, the length of peptides is 15 amino acids, and the end
position for each peptide is the start position plus fourteen. 7
KSQFLEEGMGGTIPH 22 8 SQFLEFGMGGTIPHV 14 12 EEGMGGTIPIIVSPER 14 4
GWEKSQFLEEGMGGT 12 13 EGMGGTIPHVSPERV 12 2 KKGWEKSQFLEEGMG 10
V8-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 17; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 13 ETFLPNGINGIKDAR 20 10 SLSETFLPNGINGIK 18
12 SETFLPNGINGIKDA 16 1 SISMMGSPKSLSETF 14 2 ISMMGSPKSLSETFL 14 5
SPKSLSETFLPNGIN 12 7 KSLSETFLPNGINGI 12 9 KSLSETFLPNGINGI 12
V14-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 29; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 9 PLRLFTFWRGPVVVA 26 10 LRLFTFWRGPVVVAJ 16
12 LFTFWRGPVVVAISL 16 13 FTFWRGPVVVAISLA 16 2 AREIENLPLRLFTFW 14 7
NLPLRLFTFWRGPVV 14 3 REIENLPLRLFTFWR 12 6 ENLPLRLFTFWRGPV 12 14
TFWRGPVVVAISLAT 12 15 FWRGPVVVAISLATF 12
V21-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 3 TIILSKLTQEQKTKH 26 2 ETIILSKLTQEQKTK 15 6
LSKLTQEQKTKHCMF 14 5 ILSKITQEQKTKHCM 12
V25-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 51; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 7 ILFLPCISQKLKRIK 26 6 IWFLPCISQKLKRI 22 3
LGKIILFLPCISQKL 20 4 GKIILFLPCISQKLK 20 11 PCISQKLKRIKKGWE 18 5
KIILFLPCLSQKIKR 14 14 SQKLKRIKKGWEKSQ 14 2 ILGKIILFLPCISQK 12
[1269]
70TABLE XLIX Pos 123456789012345 score
V1-HLA-DRB1-0401-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 3; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 249 KIPIEIVNKTLPIVA 27 308 LSFFFAMVHVAYSLC
27 229 YSFVRDVIHPYARNQ 26 281 QLYYGTKYRRFPPWL 25 295
LETWLQCRKQLGLLS 25 87 NIIFVAIHREHYTSL 24 388 WREFSFIQSTLGYVA 23 309
SFFFAMVHVAYSLCL 22 3 SISMMGSPKSLSETC 21 71 PHVVDVTHHEDALTK 21 98
YTSLWDLRIILLVGKI 21 175 RQQVIELARQLNFIP 21 205 PLRLFTLWRGPVVVA 21
70 FPHVVDVTHHEDALT 20 95 REHYTSLWDLRHLLV 20 151 AWALQLGPKDASRQV 20
263 AITLLSLVYLAGLLA 20 1 MESISMMGSPKSLSE 19 51 RCGYHVVIGSRNPKF 19
106 HLLVGKILIDVSNNM 19 182 ARQLNFIPHJLGSLS 19 266 LLSLVYLAGLLAAAY
19 351 EEEVWRIEMYISFGI 19 395 QSTLGYVALLISTFH 19 424
YRFYTPPNEVLALVL 19 67 SEFFPHVVDVTHHED 18 222 LATFFFLYSFVRDVI 18 302
RKQLGLLSFFFAMVH 18 307 LLSFFFAMVHVAYSL 18 367 SLGLLSLLAVTSIPS 18
370 LLSLLAVTSIPSVSN 18 28 ARKVTVGVIGSGDFA 17 86 TNIIFVAIHREHYTS 17
99 TSLWDLRIILLVGKIL 17 134 ASLFPDSLIVKGFNV 17 143 VKGFNVVSAWALQLG
17 225 FFFLYSFVRDVIHPY 17 226 FFLYSFVRDVIHPYA 17 244
QSDFYKIPIEIVNKT 17 335 NMAYQQVHANIENSW 17 360 YISFGIMSLGLLSLL 17
405 ISTFHVLIYGWKRAF 17 136 LFPDSLLVKGFNVVS 16 163 RQVYICSNNLQARQQ
16 184 QLNFIPIDLGSLSSA 16 268 SLVYLAGLLAAAYQL 16 279
AYQLYYGTKYRRFPP 16 282 LYYGTKYRRFPPWLE 16 328 SERYLFLNMAYQQVH 16
330 RYLFLNMAYQQVHAN 16 385 ALNWREFSFIQSTLG 16 397 TLGYVALLLSTFHVL
16 429 PPNFVLALVLPSIVI 16 42 AKSLTIRLIRCGYHV 15 47 IRLIRCGYHVVIGSR
15 103 DLRHLLVGKILIDVS 15 142 IVKGFNVVSAWALQL 15 210
TLWRGPVVVAISLAT 15 317 VAYSLCLPMRRSERY 15 318 AYSLCLPMRRSERYL 15
322 CLPMRRSERYLFLNM 15 401 VALLISTFHVLIYGW 15 408 FHVLIYGWKRAFEEE
15 428 TPPNFVLALVLPSIV 15 19 PNGINGLKDARKVTV 14 22 INGIKDARKVTVGVI
14 43 KSLTIRLIRCGYHVV 14 52 CGYHVVIGSRNPKFA 14 53 GYHVVIGSRNPKEAS
14 56 VVIGSRNPKFASEFF 14 66 ASEFFPHVVDVTHHE 14 77 THHEDALTKTNIIFV
14 85 KTNIIFVAIHREHYT 14 89 IFVAIHREHYTSLWD 14 113 LIDVSNNMRINQYPE
14 189 PIDLGSLSSAREIEN 14 198 AREIENLPLRLFTLW 14 203
NLPLRLFTLWRGPVV 14 212 WRGPVVVAISLATFF 14 233 RDVIHPYARNQQSDF 14
261 LVAITLLSLVYLAGL 14 319 YSLCLPMRRSERYLF 14 348 SWNEEEVWRIEMYIS
14 373 LLAVTSIPSVSNALN 14 381 SVSNALNWREFSFIQ 14 407
TFHVLIYGWKRAFEE 14 409 HVLIYGWKRAFEEEY 14 430 PNFVLALVLPSIVIL 14
435 ALVLPSIVILDLLQL 14 30 KVTVGVIGSGDFAKS 13 33 VGVIGSGDFAKSLTI 13
101 LWDLRHLLVGKILID 13 139 DSLIVKGFNVVSAWA 13 146 FNVVSAWALQLGPKD
13 178 VIELARQLNFIPIDL 13 185 LNFIPIDLGSLSSAR 13 206
LRLFTLWRGPVVVAI 13 208 LFTLWRGPVYVAISL 13 223 ATFFFLYSFVRDVIH 13
252 IEIVNKTLPIVAITL 13 256 NKTLPIVAITLLSLV 13 280 YQLYYGTKYRRFPPW
13 311 FFAMVHVAYSLCLPM 13 358 EMYISFGIMSLGLLS 13 364
GIMSLGLLSLLAVTS 13 376 VTSIPSVSNALNWRE 13 391 FSFIQSTLGYVALLI 13
431 NFVLALVLPSIVILD 13 V2-HLA-DRB1-1101-15mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 5; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 17 FTPFSCLSLPSSWDY 22
3 SPGLQALSLSLSSGF 19 28 SWDYRCPPPCPADFF 16 24 SLPSSWDYRCPPPCP 14 5
GLQALSLSLSSGFTP 12 8 ALSLSLSSGFTPFSC 12 10 SLSLSSGFTPFSCLS 12 14
SSGFTPFSCLSLPSS 12 26 PSSWDYRCPPPCPAD 10
V5A-HLA-DRB1-1101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 11; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 13 LFTFWRGPVVVAISL 17 10 PLRLFTFWRGPVVVA 15
15 TFWRGPVVVAISLAT 15 3 AREIENLPLRLFTFW 14 8 NLPLRLFTFWRGPVV 14 11
LRLFTFWRGPVVVAI 13 14 FTFWRGPVVVAISLA 12 16 FWRGPVVVAISLATF 9 4
RELENLPLRLFTFWR 8 V5B-HLA-DRB1-1101-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 11; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 7 WREFSFIQIFCSFAD 22 9
EFSFIQIFCSFADTQ 22 16 FCSFADTQTELELEF 11 4 ALNWREFSFIQIFCS 10 13
IQIFCSFADTQTELE 10 V6-HLA-DRB1-1101-15mers-98P4B6 Each peptide is a
portion of SEQ ID NO: 13; each start position is specified, the
length of peptides is 15 amino acids, and the end position for each
peptide is the start position plus fourteen. 8 LPSIVILGKIILFLP 21
18 ILFLPCISRKLKRID 21 25 SRKLKRIKKGWEKSQ 20 43 EGIGGTIPHVSPERV 20
11 IVILGKIILFLPCIS 19 21 LPCISRKLKRIKKGW 16 22 PCISRKLKRIKKGWE 15 5
ALVILPSIVILGKIIL 14 46 GGTIPHVSPERVTVM 14 1 NFVLALVLPSIVILG 13 4
LALVLPSIVILGKII 13 14 LGKIILFLPCISRKI 13 35 WEKSQFLEEGIGGTI 13 39
QFLEEGIGGTIPHVS 13 42 EEGIGGTWHVSPER 13 15 GKIILFLPCISRKLK 12 17
IILFLPCISRKILKRI 12 32 KKGWEKSQFLEEGIG 10 37 KSQFLEEGIGGTIPH 10
V7A-HLA-DRB1-1101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 15; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 1 SISMMGSPKSLFETF 21 8 PKSLSETFLPNGING 12
12 SETFLPNGINGIKDA 10 V7B-HLA-DRB1-1101-15mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 15; each start position is specified,
the length of peptides is 15 amino acids, and the end position for
each peptide is the start position plus fourteen. 4 RYLFLNMAYQQSTLG
22 14 QSTLGYVALLISTFH 19 2 SERYLFLNMAYQQST 16 7 FLNMAYQQSTLGYVA 13
9 NMAYQQSTLGYVALL 10 V7C-HLA-DRB1-1101-15mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 15; each start position is specified,
the length of peptides is 15 amino acids, and the end position for
each peptide is the start position plus fourteen. 137
WEFLLRLLKSQAASG 26 134 GPLWEFLLRLLKSQA 25 44 PIEWQQDRKIPPLST 24 121
SWRNPVLPHTNGVGP 21 13 DLSVEVLASPAAAWK 19 50 DRKIPPLSTPPPPAM 18 62
PAMWTEEAGATAEAQ 18 138 EFLLRLLKSQAASGT 18 23 AAAWKCLGANTLRGG 17 168
SGTWMKLETIILSKL 17 179 LSKLTQEQKSKHCMF 17 157 FTSWSLGEFLGSGTW 16 9
IVILDLSVEVLASPA 15 11 ILDLSVEVLASPAAA 15 19 LASPAAAWKCLGANI 15 35
RGGLSEIVLPIEWQQ 15 43 LPIEWQQDRKLPPLS 15 73 AEAQESGIRNKSSSS 15 3
ALVLPSIVILDLSVE 14 27 KCLGANILRGGLSEI 14 75 AQESGIRNKSSSSSQ 14 89
QIPVVGVVTEDDFAQ 14 135 PLWEFLLRILKSQAA 14 173 KLETIILSKLTQEQK 14 4
LVLPSIVILDLSVEV 13 6 LPSIVILDLSVEVLA 13 8 SIVILDLSVEVLASP 13 26
WKCLGANILRGGLSE 13 28 CLGANILRGGLSEIV 13 87 SSQIPVVGVVTEDDE 13 90
TPVVGVVTEDDEAQD 13 123 RNPVLPHTNGVGPLW 13 130 TNGVGPLWEFLLRLL 13
152 TLSLAFTSWSLGEFL 13 156 AFTSWSLGEFLGSGT 13 169 GTWMKLETHLSKLT 13
171 WIVIKLETIILSKLTQE 13 10 VILDLSVEVLASPAA 12 12 LDLSVEVLASPAAAW
12 39 SEIVLPIEWQQDRKI 12 58 TPPPPAMWTEEAGAT 12 74 EAQESGIRNKSSSSS
12 77 ESGIRNKSSSSSQIP 12 100 DEAQDSIDPPESPDR 12 110 ESPDRALKAANSWRN
12 119 ANSWRNPVLPHTNGV 12 124 NPVLPHTNGVGPLWE 12 140
LLRLLKSQAASGTLS 12 150 SGTLSLAFTSWSLGE 12 154 SLAFTSWSLGEFLGS 12
176 TIILSKLTQEQKSKH 12 V8-HLA-DRB1-1101-15mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 17; each start position is specified,
the length of peptides is 15 amino acids, and the end position for
each peptide is the start position plus fourteen. 13
EGMGGTIPHVSPERV 20 9 QFLEEGMGGTIPHVS 13 12 EEGMGGTIPHVSPER 13 5
WEKSQFLEEGMGGTI 12 2 KKGWEKSQFLEEGMG 10 7 KSPFLEEGMGGTIPH 10
V13-HLA-DRB1-1101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 27; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 1 SISMMGSPKSLSETF 21 8 PKSLSETFLPNGING 12
12 SETFLPNGINGIKDA 10 V14-HLA-DRB1-1101-15mers-98P4B6 Each peptide
is a portion of SEQ ID NO: 29; each start position is specified,
the length of peptides is 15 amino acids, and the end position for
each peptide is the start position plus fourteen. 12
LFTFWRGPVVVAISL 17 9 PLRLFTFWRGPVVVA 15 14 TFWRGPVVVAISLAT 15 2
AREIENLPLRLFTFW 14 7 NLPLRLFTFWRGPVV 14 10 LRLFTFWRGPVVVAI 13 13
FTFWRGPVVVAISLA 12 15 FWRGPVVVAISLATF 9 3 REIENLPLRLFTFWR 8
V21-HLA-DRB1-1101-15mers-98P- 4B6 Each peptide is a portion of SEQ
ID NO: 43; each start position is specified, the length of peptides
is 15 amino acids, and the end position for each peptide is the
start position plus fourteen. 6 LSKLTQEQKTKHCMF 17 3
TIILSKLTQEQKTKH 12 8 KLTQEQKTKHCMFSL 8 9 LTQEQKTKHCMFSLI 8
V25-HLA-DRB1-1101-15mers-98P4B6 Each peptide is a portion of SEQ ID
NO: 51; each start position is specified, the length of peptides is
15 amino acids, and the end position for each peptide is the start
position plus fourteen. 14 SQKLKRIKKGWEKSQ 20 10 LPCISQKLKRIKKGW 16
11 PCISQKLKRIKKGWE 15 3 LGKIILFLPCISQKL 13 7 ILFLPCISQKLKRIK 13 4
GKIILFLPCISQKLK 12 6 IILFLPCISQKLKRI 11 8 LFLPCISQKLKRIKK 9
[1270]
71TABLE L Properties of 98P4B6 Bioinformatic Program URL Outcome
V.1 ORF ORF finder Protein length 454 aa Transmembrane region TM
Pred http://www.ch.embnet.org/ 6TM, aa 214-232, 261-286, 304-325,
359-379, 393-415, 426-447, N- term inside HMMTop
http://www.enzim.hu/hmmtop/ 6TM, aa 215-232 261-279 306-325 360-379
396-415 428-447 N- term out Sosui http://www.genome.ad.jp/SOSui/
6TM, aa 206-228, 255-277, 304-325, 359-381, 393-415, 428-450 TMHMM
http://www.cbs.dtu.dk/services/TMHMM 6TM, aa 210-232, 262-284,
304-323, 360-382, 392-414, 427-449 Signal Peptide Signal P
http://www.cbs.dtu.dk/services/SignalP/ none pI pI/MW tool
http://www.expasy.ch/tools/ pI 8.74 Molecular weight pI/MW tool
http://www.expasy.ch/tools/ 52.0 kD Localization PSORT
http://psort.nibb.ac.jp/ Plasma membrane 60%, golgi 40% PSORT II
http://psort.nibb.ac.jp/ Endoplasmic reticulum 39%, plasma membrane
34% Motifs Pfam http://www.sanger.ac.uk/- Pfam/ no known motifs
Prints http://www.biochem.ucl.ac.uk/ pyridine nucleotide reductase
ProDom http://prodes.toulouse.inra.f Dudulin, oxidoreductase Blocks
http://www.blocks.fhcrc.org/ adenosyl-L- homocysteine hydrolase V.2
ORF ORF finder Protein length 45 aa Transmembrane region TM Pred
http://www.ch.embnet.org/ 1 TM, aa 5-23, N-term inside HMMTop
http://www.enzim.hu/hmmto- p/ no TM Sosui
http://www.genome.ad.jp/SOSui/ souble protein TMHMM
http://www.cbs.dtu.dk/services/TMHMM no TM Signal Peptide Signal P
http://www.cbs.dtu.dk/services/SignalP/ none pI pI/MW tool
http://www.expasy.ch/tools/ pI 4.2 Molecular weight pI/MW tool
http://www.expasy.ch/tools/ 4.84 kD Localization PSORT
http://psort.nibb.ac.jp/ Ouside 37%, microbody 32% PSORT II
http://psort.nibb.ac.jp/ Extracellular 33%, nuclear 33% Motifs Pfam
http://www.sanger.ac.uk/Pfam/ no known motifs Prints
http://www.biochem.ucl.ac.uk/ no known motifs Blocks
http://www.blocks.fhcrc.org/ no known motifs V.5 ORF ORF finder
Protein length 419 aa Transmembrane region TM Pred
http://www.ch.embnet.org/ 4TM, aa 214-232, 261-286, 304-325,
359-379 N-term inside HMMTop http://www.enzim.hu/hmmtop- / 4TM, aa
215-232, 259-278, 305-324, 360-379 N-term outside Sosui
http://www.genome.ad.jp/SOSui/ 4TM, aa 209-231, 255-277, 304-325,
356-379 TMHMM http://www.cbs.dtu.dk/s- ervices/TMHMM 4TM, aa
210-232, 262-284, 304-323, 360-382 Signal Peptide Signal P
http://www.cbs.dtu.dk/services/SignalP/ none pI pI/MW tool
http://www.expasy.ch/tools/ pI 8.1 Molecular weight pI/MW tool
http://www.expasy.ch/tools/ 47.9 kD Localization PSORT
http://psort.nibb.ac.jp/ Plasma membrane 60%, golgi 40% PSORT II
http://psort.nibb.ac.jp/ Endoplasmic reticulum 44%, plasma membrane
22% Motifs Pfam http://www.sanger.ac.uk/Pfam/ no known motifs
Prints http://www.biochem.ucl.ac.uk/ no known motifs ProDom
http://prodes.toulouse.inra.f Dudulin, oxidoreductase Blocks
http://www.blocks.fhcrc.org/ no known motifs V.6 ORF ORF finder
Protein length 490 aa Transmembrane region TM Pred
http://www.ch.embnet.org/ 6TM, aa 214-232, 261-286, 304-325,
359-379, 393-415, 432-455 HMMTop http://www.enzim.hu/hmmtop/ 7TM,
aa 140-158, 214-232, 259-280, 305-323, 361-383, 396-413, 432-455,
N-term out Sosui http://www.genome.ad.jp/SOSui/ 6TM, aa 206-228,
255-277, 304-325, 359-381, 393-415, 428-450 TMHMM
http://www.cbs.dtu.dk/services/TMHMM 6TM, aa 210-232, 262-284,
304-323, 360-382, 392-414, 427-449 Signal Peptide Signal P
http://www.cbs.dtu.dk/services/SignalP/ none pI pI/MW tool
http://www.expasy.ch/tools/ pI 9.2 Molecular weight pI/MW tool
http://www.expasy.ch/tools/ 55.9 kD Localization PSORT
http://psort.nibb.ac.jp/ Plasma membrane 60%, golgi 40% PSORT II
http://psort.nibb.ac.jp/ Endoplasmic reticulum 39%, plasma membrane
34% Motifs Pfam http://www.sanger.ac.uk/- Pfam/ no known motifs
Prints http://www.biochem.ucl.ac.uk/ pyridine nucleotide reductase
ProDom http://prodes.toulouse.inra.f Dudulin, oxidoreductase Blocks
http://www.blocks.fhcrc.org/ adenosyl-L- homocysteine hydrolase V.7
ORF ORF finder Protein length 576 aa Transmembrane region TM Pred
http://www.ch.embnet.org/ 6TM, aa 214-232, 262-280, 306-322,
331-360, 371-393, 525-544. N- term out HMMTop
http://www.enzim.hu/hmmtop/ 5TM, aa 215-232, 261-279, 306-325,
342-359, 378-397 N -term out Sosui http://www.genome.ad.jp/SOSui/ 5
TM, aa 206-228, 255-277, 304-325, 339-360, 380-402 TMHMM
http://www.cbs.dtu.dk/services/TMHMM 4TM, aa 210-232, 262-284,
304-323, 343-360 Signal Peptide Signal P
http://www.cbs.dtu.dk/services/SignalP/ none pI pI/MW tool
http://www.expasy.ch/tools/ pI 8.5 Molecular weight pI/MW tool
http://www.expasy.ch/tools/ 64.5 kD Localization PSORT
http://psort.nibb.ac.jp/ Plasma membrane 60%, golgi 40% PSORT II
http://psort.nibb.ac.jp/ Endoplasmic reticulum 44%, plasma membrane
22% Motifs Pfam http://www.sanger.ac.uk/- Pfam/ no known motifs
Prints http://www.biochem.ucl.ac.uk/ pyridine nucleotide reductase
ProDom http://prodes.toulouse.inra.f Dudulin, oxidoreductase Blocks
http://www.blocks.fhcrc.org/ Ets domain, adenosyl- L-homocysteine
hydrolase
[1271]
72TABLE LI Exon boundaries of transcript 98P4B6 v.1 Exon Number
Start End Length 1 23 321 299 2 322 846 525 3 847 1374 528 4 1375
1539 165 5 1540 1687 148 6 1688 2453 766
[1272]
73TABLE LII(a) Nucleotide sequence (partial, 5' open) of transcript
variant 98P4B6 v.2 (SEQ ID NO: 153) agtggatccc ccgggctgca
ggctctctct ctctctctct cttccgggtt cacgccattc 60 tcctgcctca
gcctcccgag tagctgggac tacaggtgcc cgccaccatg cccggctgat 120
ttctttttgt atttttagta cagacggagt ttcaccgtgt tagccaggat ggtctcgatc
180 tcctgacctc gtgatccgcc cgccttggcc tccaaagtgc tgggattaca
ggtgtgagct 240 accgcgcccg gcctattatc ttgtactttc taactgagcc
ctctattttc tttattttaa 300 taatatttct ccccacttga gaatcacttg
ttagttcttg gtaggaattc agttgggcaa 360 tgataacttt tatgggcaaa
aacattctat tatagtgaac aaatgaaaat aacagcgtat 420 tttcaatatt
ttcttattcc ttaaattcca ctcttttaac actatgctta accacttaat 480
gtgatgaaat attcctaaaa gttaaatgac tattaaagca tatattgttg catgtatata
540 ttaagtagcc gatactctaa ataaaaatac cactgttaca gataaatggg
gcctttaaaa 600 atatgaaaaa caaacttgtg aaaatgtata aaagatgcat
ctgttgtttc aaatggcact 660 atcttctttt cagtactaca aaaacagaat
aattttgaag ttttagaata aatgtaatat 720 atttactata attctaaatg
tttaaatgct tttctaaaaa tgcaaaacta tgatgtttag 780 ttgctttatt
ttacctctat gtgattattt ttcttaattg ttatttttta taatcattat 840
ttttctgaac cattcttctg gcctcagaag taggactgaa ttctactatt gctaggtgtg
900 agaaagtggt ggtgagaacc ttagagcagt ggagatttgc tacctggtct
gtgttttgag 960 aagtgcccct tagaaagtta aaagaatgta gaaaagatac
tcagtcttaa tcctatgcaa 1020 aaaaaaaatc aagtaattgt tttcctatga
ggaaaataac catgagctgt atcatgctac 1080 ttagctttta tgtaaatatt
tcttatgtct cctctattaa gagtatttaa aatcatattt 1140 aaatatgaat
ctattcatgc taacattatt tttcaaaaca tacatggaaa tttagcccag 1200
attgtctaca tataaggttt ttatttgaat tgtaaaatat ttaaaagtat gaataaaata
1260 tatttatagg tatttatcag agatgattat tttgtgctac atacaggttg
gctaatgagc 1320 tctagtgtta aactacctga ttaatttctt ataaagcagc
ataaccttgg cttgattaag 1380 gaattctact ttcaaaaatt aatctgataa
tagtaacaag gtatattata ctttcattac 1440 aatcaaatta tagaaattac
ttgtgtaaaa gggcttcaag aatatatcca atttttaaat 1500 attttaatat
atctcctatc tgataactta attcttctaa attaccactt gccattaagc 1560
tatttcataa taaattctgt acagtttccc ccaaaaaaag agatttattt atgaaatatt
1620 taaagtttct aatgtggtat tttaaataaa gtatcataaa tgtaataagt
aaatatttat 1680 ttaggaatac tgtgaacact gaactaatta ttcctgtgtc
agtctatgaa atccctgttt 1740 tgaaataagt aaacagccta aaatgtgttg
aaattatttt gtaaatccat gacttaaaac 1800 aagatacata catagtataa
cacacctcac agtgttaaga tttatattgt gaaatgagac 1860 accctacctt
caattgttca tcagtgggta aaacaaattc tgatgtacat tcaggacaaa 1920
tgattagccc taaatgaaac tgtaataatt tcagtggaaa ctcaatctgt ttttaccttt
1980 aaacagtgaa ttttacatga atgaatgggt tcttcacttt ttttttagta
tgagaaaatt 2040 atacagtgct taattttcag agattctttc catatgttac
taaaaaatgt tttgttcagc 2100 ctaacatact gagttttttt taactttcta
aattattgaa tttccatcat gcattcatcc 2160 aaaattaagg cagactgttt
ggattcttcc agtggccaga tgagctaaat taaatcacaa 2220 aagcagatgc
ttttgtatga tctccaaatt gccaacttta aggaaatatt ctcttgaaat 2280
tgtctttaaa gatcttttgc agctttgcag atacccagac tgagctggaa ctggaatttg
2340 tcttcctatt gactctactt ctttaaaagc ggctgcccat tacattcctc
agctgtcctt 2400 gcagttaggt gtacatgtga ctgagtgttg gccagtgaga
tgaagtctcc tcaaaggaag 2460 gcagcatgtg tcctttttca tcccttcatc
ttgctgctgg gattgtggat ataacaggag 2520 ccctggcagc tgtctccaga
ggatcaaagc cacacccaaa gagtaaggca gattagagac 2580 cagaaagacc
ttgactactt ccctacttcc actgcttttt cctgcattta agccattgta 2640
aatctgggtg tgttacatga agtgaaaatt aattctttct gcccttcagt tctttatcct
2700 gataccattt aacactgtct gaattaacta gactgcaata attctttctt
ttgaaagctt 2760 ttaaaggata atgtgcaatt cacattaaaa ttgattttcc
attgtcaatt agttatactc 2820 attttcctgc cttgatcttt cattagatat
tttgtatctg cttggaatat attatcttct 2880 ttttaactgt gtaattggta
attactaaaa ctctgtaatc tccaaaatat tgctatcaaa 2940 ttacacacca
tgttttctat cattctcata gatctgcctt ataaacattt aaataaaaag 3000
tactatttaa tgatttaaaa aaaaaaaaaa aaaaaaaaaa a 3041
[1273]
74TABLE LIII(a) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 154) and 98P4B6 v.2 (SEQ ID NO: 155) Score = 1429 bits (743),
Expect = 0.0Identities = 750/751 (99%), Gaps = 1/751 (0%) Strand =
Plus/Plus V.1: 1687
gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt 1746
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline. V.2: 2291
gatcttttgcagctttgcagatacccagactgagctggaactgga- atttgtcttcctatt 2350
V.1: 1747 gactctacttctttaaaagcggctgcc-
cattacattcctcagctgtccttgcagttaggt 1806 .vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline. V.2: 2351
gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt 2410
V.1: 1807 gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagc-
atgtg 1866 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.2: 2411
gtacatgtgactgagtgttggccagtga- gatgaagtctcctcaaaggaaggcagcatgtg 2470
V.1: 1867
tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc 1926
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.2: 2471
tcctttttcatcccttcatcttgctgctgggattgtggatataaca- ggagccctggcagc 2530
V.1: 1927 tgtctccagaggatcaaagccacaccca-
aagagtaaggcagattagagaccagaaagacc 1986 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.2: 2531
tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc 2590
V.1: 1987 ttgactacttccctacttccactgctttt-cctgcatttaagccattgtaaatct-
gggtg 2045 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.2: 2591
ttgactacttccctacttccactgcttt- ttcctgcatttaagccattgtaaatctgggtg 2650
V.1: 2046
tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt 2105
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.2: 2651
tgttacatgaagtgaaaattaattctttctgcccttcagttcttta- tcctgataccattt 2710
V.1: 2106 aacactgtctgaattaactagactgcaa-
taattctttcttttgaaagcttttaaaggata 2165 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.2: 2711
aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata 2770
V.1: 2166 atgtgcaattcacattaaaattgattttccattgtcaattagttatactcatttt-
cctgc 2225 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.2: 2771
atgtgcaattcacattaaaattgatttt- ccattgtcaattagttatactcattttcctgc 2830
V.1: 2226
cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt 2285
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.2: 2831
cttgatctttcattagatattttgtatctgcttggaatatattatc- ttctttttaactgt 2890
V.1: 2286 gtaattggtaattactaaaactctgtaa-
tctccaaaatattgctatcaaattacacacca 2345 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.2: 2891
gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca 2950
V.1: 2346 tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtacta-
tttaa 2405 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.2: 2951
tgttttctatcattctcatagatctgcc- ttataaacatttaaataaaaagtactatttaa 3010
V.1: 2406 tgatttaaaaaaaaaaaaaaaaaaaaaaaaa 2436
.vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline. V.2:
3011 tgatttaaaaaaaaaaaaaaaaaaaaaaaaa 3041 NOTE: THERE WAS A SINGLE
NUCLEOTIDE INSERTION OF A SINGLE BASE AT 2620 OF V.2.
[1274]
75TABLE LIV(a) Peptide sequences (partial) of protein coded by
98P4B6 v.2 (SEQ ID NO: 156) SGSPGLQALS LSLSSGFTPF SCLSLPSSWD
YRCPPPCPAD 45 FFLYF
[1275]
76TABLE LV(a) Amino acid sequence alignment of 98P4B6 v.1 and
98P4B6 v.2 NO SIGNIFICANT HOMOLOGY
[1276]
77TABLE LII(b) Nucleotide sequence of transcript variant 98P486 v.3
(SEQ ID NO: 157) ttctgctata gagatggaac agtatatgga aagctcccaa
gaaagtgaag agaggaaatt 60 ggaaaattgt gagtggacct tctgatactg
ctcctccttg cgtggaaaag gggaaagaac 120 tgcatgcata ttattcagcg
tcctatattc aaaggatatt cttggtgatc ttqgaagtgt 180 ccgtatcatq
gaatcaatct ctatgatggg aagccctaag agccttaqtg aaacttgttt 240
acctaatggc ataaatggta tcaaagatgc aaggaaggtc actgtaggtg tgattggaag
300 tggagatttt gccaaatcct tgaccattcg acttattaga tgcggctatc
atgtggtcat 360 aggaagtaga aatcctaagt ttgcttctga attttttcct
catgtggtag atgtcactca 420 tcatgaagat gctctcacaa aaacaaatat
aatatttgtt gctatacaca gagaacatta 480 tacctccctg tgggacctga
gacatctgct tgtgggtaaa atcctgattg atgtgagcaa 540 taacatgagg
ataaaccagt acccagaatc caatgctgaa tatttggctt cattattccc 600
agattctttg attgtcaaag gatttaatgt tgtctcagct tgggcacttc agttaggacc
660 taaggatgcc agccggcagg tttatatatg cagcaacaat attcaagcgc
gacaacaggt 720 tattgaactt gcccgccagt tgaatttcat tcccattgac
ttgggatcct tatcatcagc 780 cagagagatt gaaaatttac ccctacgact
ctttactctc tggagagggc cagtggtggt 840 agctataagc ttggccacat
tttttttcct ttattccttt gtcagagatg tqattcatcc 900 atatgctaga
aaccaacaga gtgactttta caaaattcct atagagattg tgaataaaac 960
cttacctata gttgccatta ctttgctctc cctagtatac cttgcaggtc ttctggcagc
1020 tgcttatcaa ctttattacg gcaccaagta taggagattt ccaccttggt
tggaaacctg 1080 gttacagtgt agaaaacagc ttggattact aagttttttc
ttcgctatgg tccatgttgc 1140 ctacagcctc tgcttaccga tgagaaggtc
agagagatat ttgtttctca acatggctta 1200 tcagcaggtt catgcaaata
ttgaaaactc ttggaatgag gaagaagttt ggagaattga 1260 aatgtatatc
tcctttggca taatgagcct tggcttactt tccctcctgg cagtcacttc 1320
tatcccttca gtgagcaatg ctttaaactg gagagaattc agttttattc agtctacact
1380 tggatatgtc gctctgctca taagtacttt ccatgtttta atttatggat
ggaaacgagc 1440 ttttgaggaa gagtactaca gattttatac accaccaaac
tttgttcttg ctcttgtttt 1500 gccctcaatt gtaattctgg atcttttgca
gctttgcaga tacocagact gagctggaac 1560 tggaatttgt cttcctattg
actctacttc tttaaaagcg gctgcccatt acattcctca 1620 gctgtccttg
cagttaggtg tacatgtgac tgagtgttgg ccagtgagat gaagtctcct 1680
caaaggaagg cagcatgtgt cctttttcat cccttcatct tgctgctggg attgtggata
1740 taacaggagc cctggcagct gtctccagag gatcaaagcc acacccaaag
agtaaggcag 1800 attagagaca agaaagacct tgactacttc cctacttcca
ctgctttttc ctgcatttaa 1860 gccattgtaa atctgggtgt gttacatgaa
gtgaaaatta attctttctg cccttcagtt 1920 ctttatcctg ataccattta
acactgtctg aattaactag actgcaataa ttctttcttt 1980 tgaaagcttt
taaaggataa tgtgcaattc acattaaaat tgattttcca ttgtcaatta 2040
gttatactca ttttcctgcc ttgatctttc attagatatt ttgtatctgc ttggaatata
2100 ttatcttctt tttaactgtg taattggtaa ttactaaaac tctgtaatct
ccaaaatatt 2160 gctatcaaat tacacaccat gttttctatc attctcatag
atctgcctta taaacattta 2220 aataaaaaqt actatttaat gatttaactt
ctgttttgaa aaaaaaaaaa aaaaaaaaaa 2280
[1277]
78TABLE LIII(b) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 158) and 98P4B6 v.3 (SEQ ID NO: 159) Score = 4013 bits (2087),
Expect = 0.0Identities = 2116/2128 (99%), Gaps = 1/2128 (0%) Strand
= Plus/Plus V.1: 320
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa 379
.vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline. V.3: 153 aggatattcttggtgatcttggaagtgtccgtatcatggaa-
tcaatctctatgatgggaa 212 V.1: 380 gccctaagagccttagtgaaact-
tgtttacctaatggcataaatggtatcaaagatgcaa 439
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.3: 213 gccctaagagccttagtgaaacttgtttacctaatggcataaatggt-
atcaaagatgcaa 272 V.1: 440 ggaaggtcactgtaggtgtgattggaagt-
ggagattttgccaaatccttgaccattcgac 499 .vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline. V.3: 273
ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac 332
V.1: 500 ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttc-
tgaat 559 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 333 ttattagatgcggctatcatgtggtcat-
aggaagtagaaatcctaagtttgcttctgaat 392 V.1: 560
tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa 619
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 393 tttttcctcatgtggtagatgtcactcatcatgaagatgctctcac-
aaaaacaaatataa 452 V.1: 620 tatttgttgctatacacagagaacatta-
tacctccctgtgggacctgagacatctgcttg 679 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 453
tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg 512
V.1: 680 tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccaga-
atcca 739 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 513 tgggtaaaatcctgattgatgtgagcaa-
taacatgaggataaaccagtacccagaatcca 572 V.1: 740
atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg 799
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 573 atgctgaatatttggcttcattattcccagattctttgattgtcaa-
aggatttaatgttg 632 V.1: 800 tctcagcttgggcacttcagttaggacc-
taaggatgccagccggcaggtttatatatgca 859 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 633
tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca 692
V.1: 860 gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaattt-
cattc 919 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 693 gcaacaatattcaagcgcgacaacaggt-
tattgaacttgcccgccagttgaatttcattc 752 V.1: 920
ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct 979
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 753 ccattgacttgggatccttatcatcagccagagagattgaaaattt-
acccctacgactct 812 V.1: 980 ttactctctggagagggccagtggtggt-
agctataagcttggccacattttttttccttt 1039 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 813
ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt 872
V.1: 1040 attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgactt-
ttaca 1099 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 873 attcctttgtcagagatgtgattcatcc-
atatgctagaaaccaacagagtgacttttaca 932 V.1: 1100
aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc 1159
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 933 aaattcctatagagattgtgaataaaaccttacctatagttgccat-
tactttgctctccc 992 V.1: 1160 tagtataccttgcaggtcttctggcagc-
tgcttatcaactttattacggcaccaagtata 1219 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 993
tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata 1052
V.1: 1220 ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggatt-
actaa 1279 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 1053
ggagatttccaccttggttggaaacctg- gttacagtgtagaaaacagcttggattactaa 1112
V.1: 1280
gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag 1339
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 1113
gttttttcttcgctatggtccatgttgcctacagcctctgcttacc- gatgagaaggtcag 1172
V.1: 1340 agagatatttgtttctcaacatggctta-
tcagcaggttcatgcaaatattgaaaactctt 1399 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 1173
agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt 1232
V.1: 1400 ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgag-
ccttc 1459 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 1233
ggaatgaggaagaagtttggagaattga- aatgtatatctcctttggcataatgagccttg 1292
V.1: 1460
gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga 1519
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 1293
gcttactttccctcctggcagtcacttctatcccttcagtgagcaa- tgctttaaactgga 1352
V.1: 1520 gagaattcagttttattcagtctacact-
tggatatgtcgctctgctcataagtactttcc 1579 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 1353
gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc 1412
V.1: 1580 atgttttaatttatggatggaaacgagcttttgaggaagagtactacagatttta-
tacac 1639 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 1413
atgttttaatttatggatggaaacgagc- ttttgaggaagagtactacagattttatacac 1472
V.1: 1640
caccaaactttgttcttgctcttgttttgccctcaattgtaattctggatcttttgcagc 1699
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 1473
caccaaactttgttcttgctcttgttttgccctcaattgtaattct- ggatcttttgcagc 1532
V.1: 1700 tttgcagatacccagactgagctggaac-
tggaatttgtcttcctattgactctacttctt 1759
.vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 1533
tttgcagatacccagactgagctggaactggaatttgtcttcctattgactctacttctt 1592
V.1: 1760 taaaagcggctgcccattacattcctcagctgtccttgcagttaggtgtacatgt-
gactg 1819 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 1593
taaaagcggctgcccattacattcctca- gctgtccttgcagttaggtgtacatgtgactg 1652
V.1: 1820
agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtgtcctttttcatcc 1879
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 1653
agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgt- gtcctttttcatcc 1712
V.1: 1880 cttcatcttgctgctgggattgtggata-
taacaggagccctggcagctgtctccagagga 1939 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 1713
cttcatcttgctgctgggattgtggatataacaggagccctggcagctgtctccagagga 1772
V.1: 1940 tcaaagccacacccaaagagtaaggcagattagagaccagaaagaccttgactac-
ttccc 1999 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 1773
tcaaagccacacccaaagagtaaggcag- attagagaccagaaagaccttgactacttccc 1832
V.1: 2000
tacttccactgcttttacctgcatttaagccattgtaaatctgggtgtgttacatgaagt 2058
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 1833
tacttccactgctttttcctgcatttaagccattgtaaatctgggt- gtgttacatgaagt 1892
V.1: 2059 gaaaattaattctttctgcccttcagtt-
dtttatcctgataccatttaacactgtctgaa 2118 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 1893
gaaaattaattctttctgcccttcagttctttatcctgataccatttaacactgtctgaa 1952
V.1: 2119 ttaactagactgcaataattctttcttttgaaagcttttaaaggataatgtgcaa-
ttcac 2178 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 1953
ttaactagactgcaataattctttcttt- tgaaagcttttaaaggataatgtgcaattcac 2012
V.1: 2179
attaaaattgattttccattgtcaattagttatactcattttcctgccttgatctttcat 2238
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 2013
attaaaattgattttccattgtcaattagttatactcattttcctg- ccttgatctttcat 2072
V.1: 2239 tagatattttgtatctgcttggaatata-
ttatcttctttttaactgtgtaattggtaatt 2298 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.3: 2073
tagatattttgtatctgcttggaatatattatcttctttttaactgtgtaattggtaatt 2132
V.1: 2299 actaaaactctgtaatctccaaaatattgctatcaaattacacaccatgttttct-
atcat 2358 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.3: 2133
actaaaactctgtaatctccaaaatatt- gctatcaaattacacaccatgttttctatcat 2192
V.1: 2359
tctcatagatctgccttataaacatttaaataaaaagtactatttaatgatttaaaaaaa 2418
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.3: 2193
tctcatagatctgccttataaacatttaaataaaaagtactattta- atgatttaacttct 2252
V.1: 2419 aaaaaaaaaaaaaaaaaaaaaaaaaaaa 2446
.vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.
V.3: 2253 gttttgaaaaaaaaaaaaaaaaaaaaaa 2280 NOTE: AN INSERTION OF A
SINGLE BASE AT 1845 OF V.3
[1278]
79TABLE LV(b) Peptide sequences of protein coded by 98P4B6 v.3 (SEQ
ID NO: 160) MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD FAKSLTIRLI
RCGYHVVIGS 60 RNPKFASEFF PHVVDVTHHE DALTKTNIIF VAIHREHYTS
LWDLRHLLVG KILIDVSNNM 120 RINQYPESNA EYLASLFPDS LIVKGFNVVS
AWALQLGPKD ASRQVYICSN NIQARQQVIE 180 LARQLNFIPI DLGSLSSARE
IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA 240 RNQQSDFYKI
PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ 300
CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN EEKVWRIEMY
360 ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY VALLISTFHV
LIYGWKRAFE 420 EEYYRFYTPP NFVLALVLPS IVILDLLQLC RYPD 454
[1279]
80TABLE LV(b) Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 161) and 98P4B6 v.3 (SEQ ID NO: 162) Score = 910 bits (2351),
Expect = 0.0Identities = 454/454 (100%), Positives = 454/454 (100%)
V.1: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
60 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVICSGDFAKSLTIRLIRCGYHVVIGS
V.3: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIR-
CGYHVVIGS 60 V.1: 61 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHR-
EHYTSLWDLRHLLVGKILIDVSNNM 120 RNPKFASEFFPHVVDVTHHEDALTKT-
NIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM V.3: 61
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM 120
V.1: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQ-
VIE 180 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYIC-
SNNIQARQQVIE V.3: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQL-
GPKDASRQVYICSNNIQARQQVIE 180 V.1: 181
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA 240
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA V.3:
181 LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFV- RDVIHPYA
240 V.1: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLL-
AAAYQLYYCTKYRRFPPWLETWLQ 300 RNQQSDFYKIPIEIVNKTLPIVAITLL-
SLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ V.3: 241
RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ 300
V.1: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRI-
EMY 360 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENS-
WNEEEVWRIEMY V.3: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNM-
AYQQVHANIENSWNEEEVWRIEMY 360 V.1: 361
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE 420
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE V.3:
361 ISFGIMSLGLLSLLAVTSIPSVSNALNWREESFIQSTLGYVALLISTEHVLI- YGWKRAFE
420 V.1: 421 EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD 454
EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD V.3: 421
EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD 454
[1280]
81TABLE LII(c) Nucleotide sequence of transcript variant 98P4B6 v.4
(SEQ ID NO: 163) cccacgcgtc cgcggacgcg tgggcggacg cgtgggttcc
tcgggccctc ggcgccacaa 60 gctgtccggg cacgcagccc ctagcggcgc
gtcgctgcca agccggcctc cgcgcgcctc 120 cctccttcct tctcccctgg
ctgttcgcga tccagcttgg gtaggcgggg aagcagctgg 180 agtgcgaccg
ccacggcagc caccctgcaa ccgccagtcg gagagctaag ggcaagtcct 240
gaggttgggc ccaggagaaa gaaggcaagg agacattgtc ccaggatatt cttggtgatc
300 ttggaagtgt ccgtatcatg gaatcaatct ctatgatggg aagccctaag
agccttagtg 360 aaacttgttt acctaatggc ataaatggta tcaaagatgc
aaggaaggtc actgtaggtg 420 tgattggaag tggagatttt gccaaatcct
tgaccattcg acttattaga tgcggctatc 480 atgtggtcat aggaagtaga
aatcctaagt ttgcttctga attttttcct catgtggtag 540 atgtcactca
tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca 600
gagaacatta tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg
660 atgtgagcaa taacatgagg ataaaccagt acccagaatc caatgctgaa
tatttggctt 720 cattattccc agattctttg attgtcaaag gatttaatgt
tgtctcagct tgggcacttc 780 agttaggacc taaggatgcc agccggcagg
tttatatatg cagcaacaat attcaagcgc 840 gacaacaggt tattgaactt
gcccgccagt tgaatttcat tcccattgac ttgggatcct 900 tatcatcagc
cagagagatt gaaaatttac ccctacgact ctttactctc tggagagggc 960
cagtggtggt agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg
1020 tgattcatcc atatgctaga aaccaacaga gtgactttta caaaattcct
atagagattg 1080 tgaataaaac cttacctata gttgccatta ctttgctctc
cctagtatac cttgcaggtc 1140 ttctggcagc tgcttatcaa ctttattacg
gcaccaagta taggagattt ccaccttggt 1200 tggaaacctg gttacagtgt
agaaaacagc ttggattact aagttttttc ttcgctatgg 1260 tccatgttgc
ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca 1320
acatggctta tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt
1380 ggagaattga aatgtatatc tcctttggca taatgagcct tggcttactt
tccctcctgg 1440 cagtcacttc tatcccttca gtgagcaatg ctttaaactg
gagagaattc agttttattc 1500 agtctacact tggatatgtc gctctgctca
taagtacttt ccatgtttta atttatggat 1560 ggaaacgagc ttttgaggaa
gagtactaca gattttatac accaccaaac tttgttcttg 1620 ctcttgtttt
gccctcaatt gtaattctgg atcttttgca gctttgcaga tacccagact 1680
gagctggaac tggaatttgt cttcctattg actctacttc tttaaaagcg gctgcccatt
1740 acattcctca gctgtccttg cagttaggtg tacatgtgac tgagtgttgg
ccagtgagat 1800 gaagtctcct caaaggaagg cagcatgtgt cctttttcat
cccttcatct tgctgctggg 1860 attgtggata taacaggagc cctggcagct
gtctccagag gatcaaagcc acacccaaag 1920 agtaaggcag attagagacc
agaaagacct tgactacttc cctacttcca ctgcttttcc 1980 tgcatttaag
ccattgtaaa tctgggtgtg ttacatgaag tgaaaattaa ttctttctgc 2040
ccttcagttc tttatcctga taccatttaa cactgtctga attaactaga ctgcaataat
2100 tctttctttt gaaagctttt aaaggataat gtgcaattca cattaaaatt
gattttccat 2160 tgtcaattag ttatactcat tttcctgcct tgatctttca
ttagatattt tgtatctgct 2220 tggaatatat tatcttcttt ttaactgtgt
aattggtaat tactaaaact ctgtaatctc 2280 caaaatattg ctatcaaatt
acacaccatg ttttctatca ttctcataga tctgccttat 2340 aaacatttaa
ataaaaagta ctatttaatg attt 2374
[1281]
82TABLE LIII(c) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 164) and 98P4B6 v.4 (SEQ ID NO: 165) Score = 404 bits (210),
Expect = e-109Identities = 210/210 (100%) Strand = Plus/Plus V.1: 1
ggacgcgtgggcggacgcgtggg- ttcctcgggccctcggcgccacaagctgtccgggcac 60
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 14
ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagc- tgtccgggcac 73
V.1: 61 gcagcccctagcggcgcgtcgctgccaagccgg-
cctccgcgcgcctccctccttccttct 120 .vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline. V.4: 74
gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttccttct 133
V.1: 121 cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgacc-
gcca 180 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.4: 134
cccctggctgttcgcgatccagcttgggtag- gcggggaagcagctggagtgcgaccgcca 193
V.1: 181 cggcagccaccctgcaaccgccagtcggag 210
.vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline. V.4: 194
cggcagccaccctgcaaccgccagtcggag 223 Score = 4022 bits (2092), Expect
= 0.0Identities = 2092/2092 (100%) Strand = Plus/Plus V.1: 320
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatc- tctatgatgggaa 379
.vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline. V.4: 283
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa 342
V.1: 380 gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagat-
gcaa 439 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.4: 343
gccctaagagccttagtgaaacttgtttacc- taatggcataaatggtatcaaagatgcaa 402
V.1: 440
ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac 499
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 403
ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatcct- tgaccattcgac 462
V.1: 500 ttattagatgcggctatcatgtggtcatagg-
aagtagaaatcctaagtttgcttctgaat 559 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.4: 463
ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat 522
V.1: 560 tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaat-
ataa 619 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.4: 523
tttttcctcatgtggtagatgtcactcatca- tgaagatgctctcacaaaaacaaatataa 582
V.1: 620
tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg 679
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 583
tatttgttgctatacacagagaacattatacctccctgtgggacctga- gacatctgcttg 642
V.1: 680 tgggtaaaatcctgattgatgtgagcaataa-
catgaggataaaccagtacccagaatcca 739 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.4: 643
tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca 702
V.1: 740 atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaat-
gttg 799 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.4: 703
atgctgaatatttggcttcattattcccaga- ttctttgattgtcaaaggatttaatgttg 762
V.1: 800
tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca 859
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 763
tctcagcttgggcacttcagttaggacctaaggatgccagccggcagg- tttatatatgca 822
V.1: 860 gcaacaatattcaagcgcgacaacaggttat-
tgaacttgcccgccagttgaatttcattc 919 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.4: 823
gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc 882
V.1: 920 ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacga-
ctct 979 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.4: 883
ccattgacttgggatccttatcatcagccag- agagattgaaaatttacccctacgactct 942
V.1: 980
ttactctctggagagggccagtggtggtagctataagcttggccacattttttttccttt 1039
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 943
ttactctctggagagggccagtggtggtagctataagcttggccacat- tttttttccttt 1002
V.1: 1040 attcctttgtcagagatgtgattcatccat-
atgctagaaaccaacagagtgacttttaca 1099 .vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline. V.4: 1003
attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca 1062
V.1: 1100 aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgct-
ctccc 1159 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 1063
aaattcctatagagattgtgaataaaacc- ttacctatagttgccattactttgctctccc 1122
V.1: 1160
tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagtata 1219
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 1123
tagtataccttgcaggtcttctggcagctgcttatcaactttattac- ggcaccaagtata 1182
V.1: 1220 ggagatttccaccttggttggaaacctgg-
ttacagtgtagaaaacagcttggattactaa 1279 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 1183
ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa 1242
V.1: 1280 gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaag-
gtcag 1339 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 1243
gttttttcttcgctatggtccatgttgcc- tacagcctctgcttaccgatgagaaggtcag 1302
V.1: 1340
agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactctt 1399
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 1303
agagatatttgtttctcaacatggcttatcagcaggttcatgcaaat- attgaaaactctt 1362
V.1: 1400 ggaatgaggaagaagtttggagaattgaa-
atgtatatctcctttggcataatgagccttg 1459 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 1363
ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg 1422
V.1: 1460 gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaa-
ctgga 1519 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 1423
gcttactttccctcctggcagtcacttct- atcccttcagtgagcaatgctttaaactgga 1482
V.1: 1520
gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtactttcc 1579
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 1483
gagaattcagttttattcagtctacacttggatatgtcgctctgctc- ataagtactttcc 1542
V.1: 1580 atgttttaatttatggatggaaacgagct-
tttgaggaagagtactacagattttatacac 1639 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 1543
atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac 1602
V.1: 1640 caccaaactttgttcttgctcttgttttgccctcaattgtaattctggatctttt-
gcagc 1699 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 1603
caccaaactttgttcttgctcttgttttg- ccctcaattgtaattctggatcttttgcagc 1662
V.1: 1700
tttgcagatacccagactgagctggaactggaatttgtcttcctattgactctacttctt 1759
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 1663
tttgcagatacccagactgagctggaactggaatttgtcttcctatt- gactctacttctt 1722
V.1: 1760 taaaagcggctgcccattacattcctcag-
ctgtccttgcagttaggtgtacatgtgactg 1819 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 1723
taaaagcggctgcccattacattcctcagctgtccttgcagttaggtgtacatgtgactg 1782
V.1: 1820 agtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtgtccttttt-
catcc 1879 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 1783
agtgttggccagtgagatgaagtctcctc- aaaggaaggcagcatgtgtcctttttcatcc 1842
V.1: 1880
cttcatcttgctgctgggattgtggatataacaggagccctggcagctgtctccagagga 1939
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 1843
cttcatcttgctgctgggattgtggatataacaggagccctggcagc- tgtctccagagga 1902
V.1: 1940 tcaaagccacacccaaagagtaaggcaga-
ttagagaccagaaagaccttgactacttccc 1999 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 1903
tcaaagccacacccaaagagtaaggcagattagagaccagaaagaccttgactacttccc 1962
V.1: 2000 tacttccactgcttttcctgcatttaagccattgtaaatctgggtgtgttacatg-
aagtg 2059 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 1963
tacttccactgcttttcctgcatttaagc- cattgtaaatctgggtgtgttacatgaagtg 2022
V.1: 2060
aaaattaattctttctgcccttcagttctttatcctgataccatttaacactgtctgaat 2119
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 2023
aaaattaattctttctgcccttcagttctttatcctgataccattta- acactgtctgaat 2082
V.1: 2120 taactagactgcaataattctttcttttg-
aaagcttttaaaggataatgtgcaattcaca 2179 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 2083
taactagactgcaataattctttcttttgaaagcttttaaaggataatgtgcaattcaca 2142
V.1: 2180 ttaaaattgattttccattgtcaattagttatactcattttcctgccttgatctt-
tcatt 2239 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.4: 2143
ttaaaattgattttccattgtcaattagt- tatactcattttcctgccttgatctttcatt 2202
V.1: 2240
agatattttgtatctgcttggaatatattatcttctttttaactgtgtaattggtaatta 2299
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.4: 2203
agatattttgtatctgcttggaatatattatcttctttttaactgtg- taattggtaatta 2262
V.1: 2300 ctaaaactctgtaatctccaaaatattgc-
tatcaaattacacaccatgttttctatcatt 2359 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.4: 2263
ctaaaactctgtaatctccaaaatattgctatcaaattacacaccatgttttctatcatt 2322
V.1: 2360 ctcatagatctgccttataaacatttaaataaaaagtactatttaatgattt 2411
.vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline. V.4: 2323
ctcatagatctgccttataaacatttaaataaaaagtact- atttaatgattt 2374
[1282]
83TABLE LIV(c) Peptide sequences of protein coded by 98P4B6 v.4
(SEQ ID NO: 166) MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD
FAKSLTIRLI RCGYHVVIGS 60 RNPKFASEFF PHVVDVTHHE DALTKTNIIF
VAIHREHYTS LWDLRHLLVG KILIDVSNNM 120 RINQYPESNA EYLASLFPDS
LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE 180 LARQLNFIPI
DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA 240
RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ
300 CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN
EEEVWRIEMY 360 ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY
VALLISTFHV LIYGWKRAFE 420 EEYYRFYTPP NFVLALVLPS IVILDLLQLC RYPD
454
[1283]
84TABLE LV(c) Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 167) and 98P4B6 v.4 (SEQ ID NO: 168) Score = 910 bits (2351),
Expect = 0.0Identities = 454/454 (100%), Positives = 454/454 (100%)
V.1: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
60 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
V.4: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGY-
HVVIGS 60 V.1: 61 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYT-
SLWDLRHLLVGKILIDVSNNM 120 RNPKFASEFFPHVVDVTHHEDALTKTNIIFV-
AIHREHYTSLWDLRHLLVGKILIDVSNNM V.4: 61
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM 120
V.1: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQ-
VIE 180 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICS-
NNIQARQQVIE V.4: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLG-
PKDASRQVYICSNNIQARQQVIE 180 V.1: 181
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA 240
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA V.4:
181 LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVR- DVIHPYA
240 V.1: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLA-
AAYQLYYGTKYRRFPPWLETWLQ 300 RNQQSDFYKIPIEIVNKTLPIVAITLLSL-
VYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ V.4: 241
RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLETWLQ 300
V.1: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRI-
EMY 360 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSW-
NEEEVWRIEMY V.4: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMA-
YQQVHANIENSWNEEEVWRIEMY 360 V.1: 361
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE 420
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE V.4:
361 ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIY- GWKRAFE
420 V.1: 421 EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD 454
EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD V.4: 421
EEYYRFYTPPNFVLALVLPSIVILDLLQLCRYPD 454
[1284]
85TABLE LII(d) Nucleotide sequence of transcript variant 98P4B6 v.5
(SEQ ID NO: 169) cccacgcgtc cgcggacgcg tgggcggacg cgtgggttcc
tcgggccctc ggcgccacaa 60 gctgtccggg cacgcagccc ctagcggcgc
gtcgctgcca agccggcctc cgcgcgcctc 120 cctccttcct tctcccctgg
ctgttcgcga tccagcttgg gtaggcgggg aagcagctgg 180 agtgcgaccg
ctacggcagc caccctgcaa ccgccagtcg gagagctaag ggcaagtcct 240
gaggttgggc ccaggagaaa gaaggcaagg agacattgtc ccaggatatt cttggtgatc
300 ttggaagtgt ccgtatcatg gaatcaatct ctatgatggg aagccctaag
agccttagtg 360 aaacttgttt acctaatggc ataaatggta tcaaagatgc
aaggaaggtc actgtaggtg 420 tgattggaag tggagatttt gccaaatcct
tgaccattcg acttattaga tgcggctatc 480 atgtggtcat aggaagtaga
aatcctaagt ttgcttctga attttttcct catgtggtag 540 atgtcactca
tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca 600
gagaacatta tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg
660 atgtgagcaa taacatgagg ataaaccagt acccagaatc caatgctgaa
tatttggctt 720 cattattccc agattctttg attgtcaaag gatttaatgt
tgtctcagct tgggcacttc 780 agttaggacc taaggatgcc agccggcagg
tttatatatg cagcaacaat attcaagcgc 840 gacaacaggt tattgaactt
gcccgccagt tgaatttcat tcccattgac ttgggatcct 900 tatcatcagc
cagagagatt gaaaatttac ccctacgact ctttactttc tggagagggc 960
cagtggtggt agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg
1020 tgattcatcc atatgctaga aaccaacaga gtgactttta caaaattcct
atagagattg 1080 tgaataaaac cttacctata gttgccatta ctttgctctc
cctagtatac cttgcaggtc 1140 ttctggcagc tgcttatcaa ctttattacg
gcaccaagta taggagattt ccaccttggt 1200 tggaaacctg gttacagtgt
agaaaacagc ttggattact aagttttttc ttcgctatgg 1260 tccatgttgc
ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca 1320
acatggctta tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt
1380 ggagaattga aatgtatatc tcctttggca taatgagcct tggcttactt
tccctcctgg 1440 cagtcacttc tatcccttcg gtgagcaatg ctttaaactg
gagagaattc agttttattc 1500 agatcttttg cagctttgca gatacccaga
ctgagctgga actggaattt gtcttcctat 1560 tgactctact tctttaaaag
cggctgccca ttacattcct cagctgtcct tgcagttagg 1620 tgtacatgtg
actgagtgtt ggccagtgag atgaagtctc ctcaaaggaa ggcagcatgt 1680
gtcctttttc atcccttcat cttgctgctg ggattgtgga tataacagga gccctggcag
1740 ctgctccaga ggatcaaagc cacacccaaa gagtaaggca gattagagac
cagaaagacc 1800 ttgactactt ccctacttcc actgcttttt cctgcattta
agccattgta aatctgggtg 1860 tgttacatga agtgaaaatt aattctttct
gcccttcagt tctttatcct gataccattt 1920 aacactgtct gaattaacta
gactgcaata attctttctt ttgaaagctt ttaaaggata 1980 atgtgcaatt
cacattaaaa ttgattttcc attgtcaatt agttatactc attttcctgc 2040
cttgatcttt cattagatat tttgtatctg cttggaatat attatcttct ttttaactgt
2100 gtaattggta attactaaaa ctctgtaatc tccaaaatat tgctatcaaa
ttacacacca 2160 tgttttctat cattctcata gatctgcctt ataaacattt
aaataaaaag tactatttac 2220 caaaaaaaaa aaaaaaaaaa aaaaaaaaa 2249
[1285]
86TABLE LIII(d) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 170) and 98P4B6 v.5 (SEQ ID NO: 171) Score = 398 bits (207),
Expect = e-107Identities = 209/210 (99%) Strand = Plus / Plus V.1:
1 ggacgcgtgggcggacgcgtgggttcctcggg- ccctcggcgccacaagctgtccgggcac 60
.vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.5: 14
ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac 73
V.1: 61 gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttcct-
tct 120 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.5: 74
gcagcccctagcggcgcgtcgctgccaagccgg- cctccgcgcgcctccctccttccttct 133
V.1: 121
cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca 180
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 134
cccctggctgttcgcgatccagcttgggtaggcggggaagcagctgga- gtgcgaccgcta 193
V.1: 181 cggcagccaccctgcaaccgccagtcggag 210
.vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline. V.5: 194 cggcagccaccctgcaaccgccagtcggag 223 Score
= 2334 bits (1214), Expect = 0.0Identities = 1218/1220 (99%) Strand
= Plus / Plus V.1: 320
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa 379
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.5: 283
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatc- tctatgatgggaa 342
V.1: 380 gccctaagagccttagtgaaacttgtttac-
ctaatggcataaatggtatcaaagatgcaa 439 .vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline. V.5: 343
gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa 402
V.1: 440 ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccatt-
cgac 499 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.5: 403
ggaaggtcactgtaggtgtgattggaagtgg- agattttgccaaatccttgaccattcgac 462
V.1: 500
ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat 559
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 463
ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagt- ttgcttctgaat 522
V.1: 560 tttttcctcatgtggtagatgtcactcatca-
tgaagatgctctcacaaaaacaaatataa 619 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.5: 523
tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa 582
V.1: 620 tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctg-
cttg 679 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.5: 583
tatttgttgctatacacagagaacattatac- ctccctgtgggacctgagacatctgcttg 642
V.1: 680
tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca 739
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 643
tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagt- acccagaatcca 702
V.1: 740 atgctgaatatttggcttcattattcccaga-
ttctttgattgtcaaaggatttaatgttg 799 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.5: 703
atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg 762
V.1: 800 tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatata-
tgca 859 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.5: 763
tctcagcttgggcacttcagttaggacctaa- ggatgccagccggcaggtttatatatgca 822
V.1: 860
gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc 919
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 823
gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagt- tgaatttcattc 882
V.1: 920 ccattgacttgggatccttatcatcagccag-
agagattgaaaatttacccctacgactct 979 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.5: 883
ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct 942
V.1: 980 ttactctctggagagggccagtggtggtagctataagcttggccacattttttttc-
cttt 1039 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.5: 943
ttactttctggagagggccagtggtggtagc- tataagcttggccacattttttttccttt 1002
V.1: 1040
attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca 1099
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 1003
attcctttgtcagagatgtgattcatccatatgctagaaaccaacag- agtgacttttaca 1062
V.1: 1100 aaattcctatagagattgtgaataaaacc-
ttacctatagttgccattactttgctctccc 1159 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1063
aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc 1122
V.1: 1160 tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaa-
gtata 1219 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.5: 1123
tagtataccttgcaggtcttctggcagct- gcttatcaactttattacggcaccaagtata 1182
V.1: 1220
ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa 1279
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 1183
ggagatttccaccttggttggaaacctggttacagtgtagaaaacag- cttggattactaa 1242
V.1: 1280 gttttttcttcgctatggtccatgttgcc-
tacagcctctgcttaccgatgagaaggtcag 1339 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1243
gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag 1302
V.1: 1340 agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaa-
ctctt 1399 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.5: 1303
agagatatttgtttctcaacatggcttat- cagcaggttcatgcaaatattgaaaactctt 1362
V.1: 1400
ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg 1459
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 1363
ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggc- ataatgagccttg 1422
V.1: 1460 gcttactttccctcctggcagtcacttct-
atcccttcagtgagcaatgctttaaactgga 1519 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1423
gcttactttccctcctggcagtcacttctatcccttcggtgagcaatgctttaaactgga 1482
V.1: 1520 gagaattcagttttattcag 1539
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1483
gagaattcagttttattcag 1502 Score 1375 bits (715), Expect =
0.0Identities = 741/749 (98%), Gaps = 2/749 (0%) Strand = Plus /
Plus V.1: 1687 gatcttttgcagctttgcagatacccagactgagctggaactggaatttgt-
cttcctatt 1746 .vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline. V.5: 1502
gatcttttgcagctttgcagatac- ccagactgagctggaactggaatttgtcttcctatt 1561
V.1: 1747
gactctacttctttaaaagcggctgcccattacattcctcagctgtccttgcagttaggt 1806
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 1562
gactctacttctttaaaagcggctgcccattacattcctcagctgtc- cttgcagttaggt 1621
V.1: 1807 gtacatgtgactgagtgttggccagtgag-
atgaagtctcctcaaaggaaggcagcatgtg 1866 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1622
gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg 1681
V.1: 1867 tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctg-
gcagc 1926 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.5: 1682
tcctttttcatcccttcatcttgctgctg- ggattgtggatataacaggagccctggcagc 1741
V.1: 1927
tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaaagacc 1986
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 1742
tg-ctccagaggatcaaagccacacccaaagagtaaggcagattaga- gaccagaaagacc 1800
V.1: 1987 ttgactacttccctacttccactgctttt-
-cctgcatttaagccattgtaaatctgggtg 2045 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1801
ttgactacttccctacttccactgctttttcctgcatttaagccattgtaaatctgggtg 1860
V.1: 2046 tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgatac-
cattt 2105 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.5: 1861
tgttacatgaagtgaaaattaattctttc- tgcccttcagttctttatcctgataccattt 1920
V.1: 2106
aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaaggata 2165
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 1921
aacactgtctgaattaactagactgcaataattctttcttttgaaag- cttttaaaggata 1980
V.1: 2166 atgtgcaattcacattaaaattgattttc-
cattgtcaattagttatactcattttcctgc 2225 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 1981
atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc 2040
V.1: 2226 cttgatctttcattagatattttgtatctgcttggaatatattatcttcttttta-
actgt 2285 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.5: 2041
cttgatctttcattagatattttgtatct- gcttggaatatattatcttctttttaactgt 2100
V.1: 2286
gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattacacacca 2345
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.5: 2101
gtaattggtaattactaaaactctgtaatctccaaaatattgctatc- aaattacacacca 2160
V.1: 2346 tgttttctatcattctcatagatctgcct-
tataaacatttaaataaaaagtactatttaa 2405 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.5: 2161
tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttac 2220
V.1: 2406 tgatttaaaaaaaaaaaaaaaaaaaaaaa 2434
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline.
V.5: 2221 caaaaaaaaaaaaaaaaaaaaaaaaaaaa 2249 NOTE: A SNP AT 192 AND
AT 1510, A DELETION AT 1742-1743, AND AN INSERTION OF SINGLE BASE
AT 1830 OF V.5.
[1286]
87TABLE LIV(d) Peptide sequences of protein coded by 98P4B6 v.5
(SEQ ID NO: 172) MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD
FAKSLTIRLI RCGYHVVIGS 60 RNPKFASEFF PHVVDVTHHE DALTKTNIIF
VAIHREHYTS LWDLRHLLVG KILIDVSNNM 120 RINQYPESNA EYLASLFPDS
LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE 180 LARQLNFIPI
DLGSLSSARE IENLPLRLFT FWRGPVVVAI SLATFFFLYS FVRDVIHPYA 240
RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ
300 CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN
EEEVWRIEMY 360 ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQIFCSF
ADTQTELELE FVFLLTLLL 419
[1287]
88TABLE LV(d) Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 173) and 98P4B6 v.5 (SEQ ID NO: 174) Score = 788 bits (2036),
Expect = 0.0Identities = 394/395 (99%), Positives = 394/395 (99%)
V.1: 1 MESISMMGSPKSLSETCLPNGINGIK-
DARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS 60
MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS V.5: 1
MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS 60
V.1: 61 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRH-
LLVGKILIDVSNNM 120 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHY-
TSLWDLRHLLVGKILIDVSNNM V.5: 61 RNPKFASEFFPHVVDVTHHEDALTKTN-
IIFVAIHREHYTSLWDLRHLLVGKILIDVSNNM 120 V.1: 121
RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE 180
RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQARQQVIE V.5:
121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPKDASRQVYICSNNIQ- ARQQVIE
180 V.1: 181 LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVV-
VAISLATFFFLYSFVRDVIHPYA 240 LARQLNFIPIDLGSLSSAREIENLPLRLF- T
WRGPVVVAISLATFFFLYSFVRDVIHPYA V.5: 181
LARQLNFIPIDLGSLSSAREIENLPLRLFTFWRGPVVVAISLATFFFLYSFVRDVIHPYA 240
V.1: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPPWLET-
WLQ 300 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYR-
RFPPWLETWLQ V.5: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLA-
AAYQLYYGTKYRRFPPWLETWLQ 300 V.1: 301
CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY 360
CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEEVWRIEMY V.5:
301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQVHANIENSWNEEE- VWRIEMY
360 V.1: 361 ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ 395
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ V.5: 361
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ 395 NOTE: A SNP CAUSED A SINGEL
AMINO ACID DIFFERENCE AT 211.
[1288]
89TABLE LII(e) Nucleotide sequence of transcript variant 98P4B6 v.6
(SEQ ID NO: 175) cccacgcgtc cgcggacgcg tgggcggacg cgtgggttcc
tcgggccctc ggcgccacaa 60 gctgtccggg cacgcagccc ctagcggcgc
gtcgctgcca agccggcctc cgcgcgcctc 120 cctccttcct tctcccctgg
ctgttcgcga tccagcttgg gtaggcgggg aagcagctgg 180 agtgcgaccg
ccacggcagc caccctgcaa ccgccagtcg gagagctaag ggcaagtcct 240
gaggttgggc ccaggagaaa gaaggcaagg agacattgtc ccaggatatt cttggtgatc
300 ttggaagtgt ccgtatcatg gaatcaatct ctatgatggg aagccctaag
agccttagtg 360 aaacttgttt acctaatggc ataaatggta tcaaagatgc
aaggaaggtc actgtaggtg 420 tgattggaag tggagatttt gccaaatcct
tgaccattcg acttattaga tgcggctatc 480 atgtggtcat aggaagtaga
aatcctaagt ttgcttctga attttttcct catgtggtag 540 atgtcactca
tcatgaagat gctctcacaa aaacaaatat aatatttgtt gctatacaca 600
gagaacatta tacctccctg tgggacctga gacatctgct tgtgggtaaa atcctgattg
660 atgtgagcaa taacatgagg ataaaccagt acccagaatc caatgctgaa
tatttggctt 720 cattattccc agattctttg attgtcaaag gatttaatgt
tgtctcagct tgggcacttc 780 agttaggacc taaggatgcc agccggcagg
tttatatatg cagcaacaat attcaagcgc 840 gacaacaggt tattgaactt
gcccgccagt tgaatttcat tcccattgac ttgggatcct 900 tatcatcagc
cagagagatt gaaaatttac ccctacgact ctttactctc tggagagggc 960
cagtggtggt agctataagc ttggccacat tttttttcct ttattccttt gtcagagatg
1020 tgattcatcc atatgctaga aaccaacaga gtgactttta caaaattcct
atagagattg 1080 tgaataaaac cttacctata gttgccatta ctttgctctc
cctagtatac cttgcaggtc 1140 ttctggcagc tgcttatcaa ctttattacg
gcaccaagta taggagattt ccaccttggt 1200 tggaaacctg gttacagtgt
agaaaacagc ttggattact aagttttttc ttcgctatgg 1260 tccatgttgc
ctacagcctc tgcttaccga tgagaaggtc agagagatat ttgtttctca 1320
acatggctta tcagcaggtt catgcaaata ttgaaaactc ttggaatgag gaagaagttt
1380 ggagaattga aatgtatatc tcctttggca taatgagcct tggcttactt
tccctcctgg 1440 cagtcacttc tatcccttca gtgagcaatg ctttaaactg
gagagaattc agttttattc 1500 agtctacact tggatatgtc gctctgctca
taagtacttt ccatgtttta atttatggat 1560 ggaaacgagc ttttgaggaa
gagtactaca gattttatac accaccaaac tttgttcttg 1620 ctcttgtttt
gccctcaatt gtaattctgg gtaagattat tttattcctt ccatgtataa 1680
gccgaaagct aaaacgaatt aaaaaaggct gggaaaagag ccaatttctg gaagaaggta
1740 ttggaggaac aattcctcat gtctccccgg agagggtcac agtaatgtga
tgataaatgg 1800 tgttcacagc tgccatataa agttctactc atgccattat
ttttatgact tctacgttca 1860 gttacaagta tgctgtcaaa ttatcgtggg
ttgaaacttg ttaaatgaga tttcaactga 1920 cttagtgata gagttttctt
caagttaatt ttcacaaatg tcatgtttgc caatatgaat 1980 ttttctagtc
aacatattat tgtaatttag gtatgttttg ttttgttttg cacaactgta 2040
accctgttgt tactttatat ttcataatca gacaaaaata cttacagtta ataatataga
2100 tataatgtta aaaacaattt gcaaaccagc agaattttaa gcttttaaaa
taattcaatg 2160 gatatacatt tttttctgaa gattaagatt ttaattattc
aacttaaaaa gtagaaatgc 2220 attattatac atttttttaa gaaaggacac
gttatgttag catctaggta aggctgcatg 2280 atagcattcc tatatttctc
tcataaaata ggatttgaag gatgaaatta attgtatgaa 2340 gcaatgtgat
tatatgaaga gacacaaatt aaaaagacaa attaaacctg aaattatatt 2400
taaaatatat ttgagacatg aaatacatac tgataataca tacctcatga aagattttat
2460 tctttattgt gttacagagc agtttcattt tcatattaat atactgatca
ggaagaggat 2520 tcagtaacat ttggcttcca aaactgctat ctctaatacg
gtaccaatcc taggaactgt 2580 atactagttc ctacttagaa caaaagtatc
aagtttgcac acaagtaatc tgccagctga 2640 cctttgtcgc accttaacca
gtcaccactt gctatggtat aggattatac tgatgttctt 2700 tgagggattc
tgatgtgcta ggcatggttc taagtacttt acttgtatta tcccatttaa 2760
tacttagaac aaccccgtga gataagtagt tattatcctc attttacaca tgagggaccg
2820 aaggatagaa aagttatttt tcaaaggtct tgcagttaat aaatggcaga
gtgagcattc 2880 aagtccaggt agtcatattc cagaggccac ggttttaacc
actaggctct agagctcccg 2940 ccgcgcccct atgcattatg ttcacaatgc
caatctagat gcttcctctt ttgtataaag 3000 tcactgacat tctttagagt
gggttgggtg catccaaaaa tgtataaaaa tattattata 3060 ataaacttat
tactgcttgt agggtaattc acagttactt accctattct tgcttggaac 3120
atgagcctgg agacccatgg cagtccatat gcctccctat gcagtgaagg gccctagcag
3180 tgttaacaaa ttgctgagat cccacggagt ctttcaaaaa tctctgtaga
gttagtcttc 3240 tccttttctc ttcctgagaa gttctcctgc ctgcataacc
attcattagg gagtacttta 3300 caagcatgaa ggatattagg gtaagtggct
aattataaat ctactctaga gacatataat 3360 catacagatt attcataaaa
tttttcagtg ctgtccttcc acatttaatt gcattttgct 3420 caaactgtag
aatgccctac attcccccca ccccaatttg ctatttcctt attaaaatag 3480
aaaattatag gcaagataca attatatgcg ttcctcttcc tgaaattata acatttctaa
3540 acttacccac gtagggacta ctgaatccaa ctgccaacaa taaaaagact
tttatttagt 3600 agaggctacc tttcccccca gtgactcttt ttctacaact
gccttgtcag tttggtaatt 3660 cacttatgat tttctaatgt tctcttggtg
aattttatta tcttggaccc tctttttttt 3720 tttttttaaa gacagagtct
tgctctgtca ccca 3754
[1289]
90TABLE LIII(e) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 176) and 98P4B6 v.6 (SEQ ID NO: 177) Score = 404 bits (210),
Expect = e-109Identities = 210/210 (100%) Strand = Plus / Plus V.1:
1 ggacgcgtgggcggacgcgtgggttcctcgg- gccctcggcgccacaagctgtccgggcac 60
.vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline. V.6: 14
ggacgcgtgggcggacgcgtgggttcctcgggccctcggcgccacaagctgtccgggcac 73
V.1: 61 gcagcccctagcggcgcgtcgctgccaagccggcctccgcgcgcctccctccttcct-
tct 120 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.6: 74
gcagcccctagcggcgcgtcgctgccaagccgg- cctccgcgcgcctccctccttccttct 133
V.1: 121
cccctggctgttcgcgatccagcttgggtaggcggggaagcagctggagtgcgaccgcca 180
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 134
cccctggctgttcgcgatccagcttgggtaggcggggaagcagctgga- gtgcgaccgcca 193
V.1: 181 cggcagccaccctgcaaccgccagtcggag 210
.vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline. V.6: 194 cggcagccaccctgcaaccgccagtcggag 223 Score
= 2630 bits (1368), Expect = 0.0Identities = 1368/1368 (100%)
Strand = Plus / Plus V.1: 320
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaa 379
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.6: 283
aggatattcttggtgatcttggaagtgtccgtatcatggaatcaatc- tctatgatgggaa 342
V.1: 380 gccctaagagccttagtgaaacttgtttac-
ctaatggcataaatggtatcaaagatgcaa 439 .vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline. V.6: 343
gccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaa 402
V.1: 440 ggaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccatt-
cgac 499 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.6: 403
ggaaggtcactgtaggtgtgattggaagtgg- agattttgccaaatccttgaccattcgac 462
V.1: 500
ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaat 559
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 463
ttattagatgcggctatcatgtggtcataggaagtagaaatcctaagt- ttgcttctgaat 522
V.1: 560 tttttcctcatgtggtagatgtcactcatca-
tgaagatgctctcacaaaaacaaatataa 619 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.6: 523
tttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataa 582
V.1: 620 tatttgttgctatacacagagaacattatacctccctgtgggacctgagacatctg-
cttg 679 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.6: 583
tatttgttgctatacacagagaacattatac- ctccctgtgggacctgagacatctgcttg 642
V.1: 680
tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatcca 739
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 643
tgggtaaaatcctgattgatgtgagcaataacatgaggataaaccagt- acccagaatcca 702
V.1: 740 atgctgaatatttggcttcattattcccaga-
ttctttgattgtcaaaggatttaatgttg 799 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.6: 703
atgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttg 762
V.1: 800 tctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatata-
tgca 859 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.6: 763
tctcagcttgggcacttcagttaggacctaa- ggatgccagccggcaggtttatatatgca 822
V.1: 860
gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattc 919
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 823
gcaacaatattcaagcgcgacaacaggttattgaacttgcccgccagt- tgaatttcattc 882
V.1: 920 ccattgacttgggatccttatcatcagccag-
agagattgaaaatttacccctacgactct 979 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.6: 883
ccattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactct 942
V.1: 980 ttactctctggagagggccagtggtggtagctataagcttggccacattttttttc-
cttt 1039 .vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline. V.6: 943
ttactctctggagagggccagtggtggtagc- tataagcttggccacattttttttccttt 1002
V.1: 1040
attcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttaca 1099
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 1003
attcctttgtcagagatgtgattcatccatatgctagaaaccaacag- agtgacttttaca 1062
V.1: 1100 aaattcctatagagattgtgaataaaacc-
ttacctatagttgccattactttgctctccc 1159 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.6: 1063
aaattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccc 1122
V.1: 1160 tagtataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaa-
gtata 1219 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.6: 1123
tagtataccttgcaggtcttctggcagct- gcttatcaactttattacggcaccaagtata 1182
V.1: 1220
ggagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaa 1279
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 1183
ggagatttccaccttggttggaaacctggttacagtgtagaaaacag- cttggattactaa 1242
V.1: 1280 gttttttcttcgctatggtccatgttgcc-
tacagcctctgcttaccgatgagaaggtcag 1339 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.6: 1243
gttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcag 1302
V.1: 1340 agagatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaa-
ctctt 1399 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.6: 1303
agagatatttgtttctcaacatggcttat- cagcaggttcatgcaaatattgaaaactctt 1362
V.1: 1400
ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttg 1459
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 1363
ggaatgaggaagaagtttggagaattgaaatgtatatctcctttggc- ataatgagccttg 1422
V.1: 1460 gcttactttccctcctggcagtcacttct-
atcccttcagtgagcaatgctttaaactgga 1519 .vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.6: 1423
gcttactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactgga 1482
V.1: 1520 gagaattcagttttattcagtctacacttggatatgtcgctctgctcataagtac-
tttcc 1579 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.6: 1483
gagaattcagttttattcagtctacactt- ggatatgtcgctctgctcataagtactttcc 1542
V.1: 1580
atgttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacac 1639
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.6: 1543
atgttttaatttatggatggaaacgagcttttgaggaagagtactac- agattttatacac 1602
V.1: 1640 caccaaactttgttcttgctcttgttttg- ccctcaattgtaattctgg 1687
.vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline.
V.6: 1603 caccaaactttgttcttgctcttgttttgccctcaattgtaattctgg 1650
[1290]
91TABLE LIV(e) Peptide sequences of protein coded by 98P4B6 v.6
(SEQ ID NO: 178) MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD
FAKSLTIRLI RCGYHVVIGS 60 RNPKFASEFF PHVVDVTHHE DALTKTNIIF
VAIHREHYTS LWDLRHLLVG KILIDVSNNM 120 RINQYPESNA EYLASLFPDS
LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE 180 LARQLNFIPI
DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA 240
RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ
300 CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN
EEEVWRIEMY 360 ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY
VALLISTFHV LIYGWKRAFE 420 EEYYRFYTPP NFVLALVLPS IVILGKIILF
LPCISRKLKR IKKGWEKSQF LEEGIGGTIP 480 HVSPERVTVM 490
[1291]
92TABLE LV(e) Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 179) and 98P4B6 v.6 (SEQ ID NO: 180) Score = 888 bits (2294),
Expect = 0.0Identities = 444/444 (100%), Positives = 444/444 (100%)
V.1: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
60 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
V.6: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
60 V.1: 61
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVS- NNM 120
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVS- NNM V.6:
61 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILID- VSNNM
120 V.1: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPK-
DASRQVYICSNNIQARQQVIE 180 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPK-
DASRQVYICSNNIQARQQVIE V.6: 121
RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQL- GPKDASRQVYICSNNIQARQQVIE 180
V.1: 181
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA 240
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA V.6:
181 LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
240 V.1: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPP-
WLETWLQ 300 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPP-
WLETWLQ V.6: 241
RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRR- FPPWLETWLQ 300
V.1: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFL-
NMAYQQVHANIENSWNEEEVWRIEMY 360 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFL-
NMAYQQVHANIENSWNEEEVWRIEMY V.6: 301
CRKQLGLLSFFFAMVHVAYSLCLPMRRSERY- LFLNMAYQQVHANIENSWNEEEVWRIEMY 360
V.1: 361
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE 420
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE V.6:
361 ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE
420 V.1: 421 EEYYRFYTPPNFVLALVLPSIVIL 444 EEYYRFYTPPNFVLALVLPSIVIL
V.6: 421 EEYYRFYTPPNFVLALVLPSIVIL 444
[1292]
93TABLE LII(f) Nucleotide sequence of transcript variant 98P4B6 v.7
(SEQ ID NO: 181) ggagaaaatt tacagaaacc cagagccaaa ggtgctctca
ggggatcccc tgaaacattc 60 aaagccattg cggccccaga agcttgggta
ggcggggaag cagctggagt gcgaccgccg 120 cggcagccac cctgcaaccg
ccagtcggag gtgcagtccg taggccctgg cccccgggtg 180 ggcccttggg
gagtcggcgc cgctcccggg gagctgcaag gctcgcccct gcccggcgtg 240
gagggcgcgg ggggcgcgga ggatattctt ggtgatcttg gaagtgtccg tatcatggaa
300 tcaatctcta tgatgggaag ccctaagagc cttagtgaaa cttttttacc
taatggcata 360 aatggtatca aagatgcaag gaaggtcact gtaggtgtga
ttggaagtgg agattttgcc 420 aaatccttga ccattcgact tattagatgc
ggctatcatg tggtcatagg aagtagaaat 480 cctaagtttg cttctgaatt
ttttcctcat gtggtagatg tcactcatca tgaagatgct 540 ctcacaaaaa
caaatataat atttgttgct atacacagag aacattatac ctccctgtgg 600
gacctgagac atctgcttgt gggtaaaatc ctgattgatg tgagcaataa catgaggata
660 aaccagtacc cagaatccaa tgctgaatat ttggcttcat tattcccaga
ttctttgatt 720 gtcaaaggat ttaatgttgt ctcagcttgg gcacttcagt
taggacctaa ggatgccagc 780 cggcaggttt atatatgcag caacaatatt
caagcgcgac aacaggttat tgaacttgcc 840 cgccagttga atttcattcc
cattgacttg ggatccttat catcagccag agagattgaa 900 aatttacccc
tacgactctt tactctctgg agagggccag tggtggtagc tataagcttg 960
gccacatttt ttttccttta ttcctttgtc agagatgtga ttcatccata tgctagaaac
1020 caacagagtg acttttacaa aattcctata gagattgtga ataaaacctt
acctatagtt 1080 gccattactt tgctctccct agtatacctc gcaggtcttc
tggcagctgc ttatcaactt 1140 tattacggca ccaagtatag gagatttcca
ccttggttgg aaacctggtt acagtgtaga 1200 aaacagcttg gattactaag
ttttttcttc gctatggtcc atgttgccta cagcctctgc 1260 ttaccgatga
gaaggtcaga gagatatttg tttctcaaca tggcttatca gcagtctaca 1320
cttggatatg tcgctctgct cataagtact ttccatgttt taatttatgg atggaaacga
1380 gcttttgagg aagagtacta cagattttat acaccaccaa actttgttct
tgctcttgtt 1440 ttgccctcaa ttgtaattct ggatctgtct gtggaggttc
tggcttcccc agctgctgcc 1500 tggaaatgct taggtgctaa tatcctgaga
ggaggattgt cagagatagt actccccata 1560 gagtggcagc aggacaggaa
gatcccccca ctctccaccc cgccgccacc ggccatgtgg 1620 acagaggaag
ccggggcgac cgccgaggcc caggaatccg gcatcaggaa caagtctagc 1680
agttccagtc aaatcccggt ggttggggtg gtgacggagg acgatgaggc gcaggattcc
1740 attgatcccc cagagagccc tgatcgtgcc ttaaaagccg cgaattcctg
gaggaaccct 1800 gtcctgcctc acactaatgg tgtggggcca ctgtgggaat
tcctgttgag gcttctcaaa 1860 tctcaggctg cgtcaggaac cctgtctctt
gcgttcacat cctggagcct tggagagttc 1920 cttgggagtg ggacatggat
gaagctggaa accataattc tcagcaaact aacacaggaa 1980 cagaaatcca
aacactgcat gttctcactg ataagtggga gttgaacaat gagaacacat 2040
ggacacaggg aggggaacgt cacacaccag ggcctgtcgg gggtgggagg cctagcaatt
2100 cattagaatt acctgtgaag cttttaaaat gtaaggtttg gatggaatgc
tcagacccta 2160 ccttagaccc aattaagccc acagctttga gg 2192
[1293]
94TABLE LIII(f) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 182) and 98P4B6 v.7 (SEQ ID NO: 183) Score = 2350 bits (1222),
Expect = 0.0Identities = 1230/1234 (99%) Strand = Plus/Plus V.1:
141 agcttgggtaggcggggaagcagc- tggagtgcgaccgccacggcagccaccctgcaaccg
200 .vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline.
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline. V.7: 81
agcttgggtaggcggggaagcagctggagtgcgaccgccgcggcagccaccctgcaaccg 140
V.1: 201 ccagtcggaggtgcagtccgtaggccctggcccccgggtgggcccttggggagtcgg-
cgc 260 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.7: 141
ccagtcggaggtgcagtccgtaggccctggcc- cccgggtgggcccttggggagtcggcgc 200
V.1: 261
cgctcccgaggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgcgga 320
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline.
.vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.
V.7: 201 cgctcccggggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgc-
gga 260 V.1: 321 ggatattcttggtgatcttggaagtgtccgtatcatggaat-
caatctctatgatgggaag 380 .vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline. V.7: 261
ggatattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaag 320
V.1: 381 ccctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgc-
aag 440 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline.
.vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline. V.7: 321
ccctaagagccttagtgaaacttttttacctaatggcataa- atggtatcaaagatgcaag 380
V.1: 441 gaaggtcactgtaggtgtgattgga-
agtggagattttgccaaatccttgaccattcgact 500 .vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline. V.7: 381
gaaggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgact 440
V.1: 501 tattagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctga-
att 560 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.7: 441
tattagatgcggctatcatgtggtcataggaa- gtagaaatcctaagtttgcttctgaatt 500
V.1: 561
ttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataat 620
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.7: 501
ttttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaa- aacaaatataat 560
V.1: 621 atttgttgctatacacagagaacattatacct-
ccctgtgggacctgagacatctgcttgt 680 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.7: 561
atttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttgt 620
V.1: 681 gggtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatc-
caa 740 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.7: 621
gggtaaaatcctgattgatgtgagcaataaca- tgaggataaaccagtacccagaatccaa 680
V.1: 741
tgctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttgt 800
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.7: 681
tgctgaatatttggcttcattattcccagattctttgattgtcaaagg- atttaatgttgt 740
V.1: 801 ctcagcttgggcacttcagttaggacctaagg-
atgccagccggcaggtttatatatgcag 860 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.7: 741
ctcagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgcag 800
V.1: 861 caacaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcat-
tcc 920 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.7: 801
caacaatattcaagcgcgacaacaggttattg- aacttgcccgccagttgaatttcattcc 860
V.1: 921
cattgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactctt 980
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.7: 861
cattgacttgggatccttatcatcagccagagagattgaaaatttacc- cctacgactctt 920
V.1: 981 tactctctggagagggccagtggtggtagcta-
taagcttggccacattttttttccttta 1040 .vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline. V.7: 921
tactctctggagagggccagtggtggtagctataagcttggccacattttttttccttta 980
V.1: 1041 ttcctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgactttt-
acaa 1100 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.7: 981
ttcctttgtcagagatgtgattcatccata- tgctagaaaccaacagagtgacttttacaa 1040
V.1: 1101
aattcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccct 1160
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.7: 1041
aattcctatagagattgtgaataaaaccttacctatagttgccatt- actttgctctccct 1100
V.1: 1161 agtataccttgcaggtcttctggcagct-
gcttatcaactttattacggcaccaagtatag 1220 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline.
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline. V.7: 1101
agtatacctcgcaggtcttctggcagctgcttatcaactttattacggcaccaagtatag 1160
V.1: 1221 gagatttccaccttggttggaaacctggttacagtgtagaaaacagcttggatta-
ctaag 1280 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.7: 1161
gagatttccaccttggttggaaacctgg- ttacagtgtagaaaacagcttggattactaag 1220
V.1: 1281
ttttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcaga 1340
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.7: 1221
ttttttcttcgctatggtccatgttgcctacagcctctgcttaccg- atgagaaggtcaga 1280
V.1: 1341 gagatatttgtttctcaacatggcttat- cagcag 1374
.vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline.
V.7: 1281 gagatatttgtttctcaacatggcttatcagcag 1314 Score = 298 bits
(155), Expect = 2e-77Identities = 155/155 (100%) Strand = Plus/Plus
V.1: 1537 cagtctacacttggatatgtcgctctgctcataagtactttcca-
tgttttaatttatgga 1596 .vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline. V.7: 1312
cagtctacacttggatatgtcgctctgctcataagtactttccatgttttaatttatgga 1371
V.1: 1597 tggaaacgagcttttgaggaagagtactacagattttatacaccaccaaactttg-
ttctt 1656 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.7: 1372
tggaaacgagcttttgaggaagagtact- acagattttatacaccaccaaactttgttctt 1431
V.1: 1657 gctcttgttttgccctcaattgtaattctggatct 1691
.vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline. V.7: 1432
gctcttgttttgccctcaattgtaa- ttctggatct 1466
[1294]
95TABLE LIV(f) Peptide sequences of protein coded by 98P4B6 v.7
(SEQ ID NO: 184) MESISMMGSP KSLSETFLPN GINGIKDARK VTVGVIGSGD
FAKSLTIRLI RCGYHVVIGS 60 RNPKFASEFF PHVVDVTHHE DALTKTNIIF
VAIHREHYTS LWDLRHLLVG KILIDVSNNM 120 RINQYPESNA EYLASLFPDS
LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE 180 LARQLNFIPI
DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA 240
RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ
300 CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ STLGYVALLI
STFHVLIYGW 360 KRAFEEEYYR FYTPPNFVLA LVLPSIVILD LSVEVLASPA
AAWKCLGANI LRGGLSEIVL 420 PIEWQQDRKI PPLSTPPPPA MWTEEAGATA
EAQESGIRNK SSSSSQIPVV GVVTEDDEAQ 480 DSIDPPESPD RALKAANSWR
NPVLPHTNGV GPLWEFLLRL LKSQAASGTL SLAFTSWSLG 540 EFLGSGTWMK
LETIILSKLT QEQKSKHCMF SLISGS 576
[1295]
96TABLE LV(f) Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 185) and 98P4B6 v.7 (SEQ ID NO: 186) Score = 753 bits (1944),
Expect = 0.0Identities = 390/446 (87%), Positives = 390/446 (87%),
Gaps = 55/446 (12%) V.1: 1
MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS 60
MESISMMGSPKSLSET LPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS V.7: 1
MESISMMGSPKSLSETFLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS 60
V.1: 61 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGK-
ILIDVSNNM 120 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGK-
ILIDVSNNM V.7: 61
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLV- GKILIDVSNNM 120
V.1: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWA-
LQLGPKDASRQVYICSNNIQARQQVIE 180 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWA-
LQLGPKDASRQVYICSNNIQARQQVIE V.7: 121
RINQYPESNAEYLASLFPDSLIVKGFNVVS- AWALQLGPKDASRQVYICSNNIQARQQVIE 180
V.1: 181
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA 240
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA V.7:
181 LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
240 V.1: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPP-
WLETWLQ 300 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPP-
WLETWLQ V.7: 241
RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRR- FPPWLETWLQ 300
V.1: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFL-
NMAYQQVHANIENSWNEEEVWRIEMY 360 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFL-
NMAYQQ V.7: 301
CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFLNMAYQQ------------ --------- 340
V.1: 361 ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQ-
STLGYVALLISTFHVLIYGWKRAFE 420 STLGYVALLISTFHVLIYGWKRAFE V.7: 341
-------------------------------- ----STLGYVALLISTFHVLIYGWKRAFE 365
V.1: 421 EEYYRFYTPPNFVLALVLPSIVILDL 446 EEYYRFYTPPNFVLALVLPSIVILDL
V.7: 366 EEYYRFYTPPNFVLALVLPSIVILDL 391
[1296]
97TABLE LII(g) Nucleotide sequence of transcript variant 98P4B6 v.8
(SEQ ID NO: 187) gccccctccg agctccccga ctcctccccg cgctccacgg
ctcttcccga ctccagtcag 60 cgttcctcgg gccctcggcg ccacaagctg
tccgggcacg cagcccctag cggcgcgtcg 120 ctgccaagcc ggcctccgcg
cgcctccctc cttccttctc ccctggctgt tcgcgatcca 180 gcttgggtag
gcggggaagc agctggagtg cgaccgccac ggcagccacc ctgcaaccgc 240
cagtcggagg tgcagtccgt aggccctggc ccccgggtgg gcccttgggg agtcggcgcc
300 gctcccgagg agctgcaagg ctcgcccctg cccggcgtgg agggcgcggg
gggcgcggag 360 gatattcttg gtgatcttgg aagtgtccgt atcatggaat
caatctctat gatgggaagc 420 cctaagagcc ttagtgaaac ttgtttacct
aatggcataa atggtatcaa agatgcaagg 480 aaggtcactg taggtgtgat
tggaagtgga gattttgcca aatccttgac cattcgactt 540 attagatgcg
gctatcatgt ggtcatagga agtagaaatc ctaagtttgc ttctgaattt 600
tttcctcatg tggtagatgt cactcatcat gaagatgctc tcacaaaaac aaatataata
660 tttgttgcta tacacagaga acattatacc tccctgtggg acctgagaca
tctgcttgtg 720 ggtaaaatcc tgattgatgt gagcaataac atgaggataa
accagtaccc agaatccaat 780 gctgaatatt tggcttcatt attcccagat
tctttgattg tcaaaggatt taatgttgtc 840 tcagcttggg cacttcagtt
aggacctaag gatgccagcc ggcaggttta tatatgcagc 900 aacaatattc
aagcgcgaca acaggttatt gaacttgccc gccagttgaa tttcattccc 960
attgacttgg gatccttatc atcagccaga gagattgaaa atttacccct acgactcttt
1020 actctctgga gagggccagt ggtggtagct ataagcttgg ccacattttt
tttcctttat 1080 tcctttgtca gagatgtgat tcatccatat gctagaaacc
aacagagtga cttttacaaa 1140 attcctatag agattgtgaa taaaacctta
cctatagttg ccattacttt gctctcccta 1200 gtataccttg caggtcttct
ggcagctgct tatcaacttt attacggcac caagtatagg 1260 agatttccac
cttggttgga aacctggtta cagtgtagaa aacagcttgg attactaagt 1320
tttttcttcg ctatggtcca tgttgcctac agcctctgct taccgatgag aaggtcagag
1380 agatatttgt ttctcaacat ggcttatcag caggttcatg caaatattga
aaactcttgg 1440 aatgaggaag aagtttggag aattgaaatg tatatctcct
ttggcataat gagccttggc 1500 ttactttccc tcctggcagt cacttctatc
ccttcagtga gcaatgcttt aaactggaga 1560 gaattcagtt ttattcagtc
tacacttgga tatgtcgctc tgctcataag tactttccat 1620 gttttaattt
atggatggaa acgagctttt gaggaagagt actacagatt ttatacacca 1680
ccaaactttg ttcttgctct tgttttgccc tcaattgtaa ttctgggtaa gattatttta
1740 ttccttccat gtataagccg aaagctaaaa cgaattaaaa aaggctggga
aaagagccaa 1800 tttctggaag aaggtatggg aggaacaatt cctcatgtct
ccccggagag ggtcacagta 1860 atgtgatgac aaatggtgtt cacagctgcc
atataaagtt ctactcatgc cattattttt 1920 atgacttcta cgttcagtta
caagtatgct gtcaaattat cgtgggttga aacttgttaa 1980 atgagatttc
aactgactta gtgatagagt tttcttcaag ttaattttca caaatgtcat 2040
gtttgccaat atgaattttt ctagtcaaca tattattgta atttaggtat gttttgtttt
2100 gttttgcaca actgtaaccc tgttgttact ttatatttca taatcaggca
aaaatactta 2160 cagttaataa tatagatata atgttaaaaa caatttgcaa
accagcagaa ttttaagctt 2220 ttaaaataat tcaatggata tacatttttt
tctgaagatt aagattttaa ttattcaact 2280 taaaaagtag aaatgcatta
ttatacattt ttttaagaaa ggacacgtta tgttagcatc 2340 taggtaaggc
tgcatgatag cattcctata tttctctcat aaaataggat ttgaaggatg 2400
aaattaattg tatgaagcaa tgtgattata tgaagagaca caaattaaaa agacaaatta
2460 aacctgaaat tatatttaaa atatatttga gacatgaaat acatactgat
aatacatacc 2520 tcatgaaaga ttttattctt tattgtgtta cagagcagtt
tcattttcat attaatatac 2580 tgatcaggaa gaggattcag taacatttgg
cttccaaaac tgctatctct aatacggtac 2640 caatcctagg aactgtatac
tagttcctac ttagaacaaa agtatcaagt ttgcacacaa 2700 gtaatctgcc
agctgacctt tgtcgcacct taaccagtca ccacttgcta tggtatagga 2760
ttatactgat gttctttgag ggattctgat gtgctaggca tggttctaag tactttactt
2820 gtattatccc atttaatact tagaacaacc ccgtgagata agtagttatt
atcctcattt 2880 tacacatgag ggaccgaagg atagaaaagt tatttttcaa
aggtcttgca gttaataaat 2940 ggcagagtga gcattcaagt ccaggtagtc
atattccaga ggccacggtt ttaaccacta 3000 ggctctagag ctcccgccgc
gcccctatgc attatgttca caatgccaat ctagatgctt 3060 cctcttttgt
ataaagtcac tgacattctt tagagtgggt tgggtgcatc caaaaatgta 3120
taaaaatatt attataataa acttattact gcttgtaggg taattcacag ttacttaccc
3180 tattcttgct tggaacatga gcctggagac ccatggcagt ccatatgcct
ccctatgcag 3240 tgaagggccc tagcagtgtt aacaaattgc tgagatccca
cggagtcttt caaaaatctc 3300 tgtagagtta gtcttctcct tttctcttcc
tgagaagttc tcctgcctgc ataaccattc 3360 attagggagt actttacaag
catgaaggat attagggtaa gtggctaatt ataaatctac 3420 tctagagaca
tataatcata cagattattc ataaaatttt tcagtgctgt ccttccacat 3480
ttaattgcat tttgctcaaa ctgtagaatg ccctacattc cccccacccc aatttgctat
3540 ttccttatta aaatagaaaa ttataggcaa gatacaatta tatgcgttcc
tcttcctgaa 3600 attataacat ttctaaactt acccacgtag gtactactga
atccaactgc caacaataaa 3660 aagactttta tttagtagag gctacctttc
ccaccagtga ctctttttct acaactgcct 3720 tgtcagtttg gtaattcact
tatgattttc taatgttctc ttggtgaatt ttattatctt 3780 gtaccctctt
tttttttttt ttttttttta aagacagagt cttgctctgt cacccaggct 3840
ggagtgcagt ggcacgatct cggctcactg caagctctgc ctcccgggtt cacgccattc
3900 tcctgcctca gcctcccgag tagctgggac tacaggtgcc cgccaccatg
cccggctgat 3960 ttctttttgt atttttagta gagacggagt ttcaccgtgt
tagccaggat ggtctcgatc 4020 tcctgacctc gtgatccgcc cgccttggcc
tccaaagtgc tgggattaca ggtgtgagct 4080 accgcgcccg gcctattatc
ttgtactttc taactgagcc ctctattttc tttattttaa 4140 taatatttct
ccccacttga gaatcacttg ttagttcttg gtaggaattc agttgggcaa 4200
tgataacttt tatgggcaaa aacattctat tatagtgaac taatgaaaat aacagcgtat
4260 tttcaatatt ttcttattcc ttaaattcca ctcttttaac actatgctta
accacttaat 4320 gtgatgaaat attcctaaaa gttaaatgac tattaaagca
tatattgttg catgtatata 4380 ttaagtagcc gatactctaa ataaaaatac
cactgttaca gataaatggg gcctttaaaa 4440 atatgaaaaa caaacttgtg
aaaatgtata aaagatgcat ctgttgtttc aaatggcact 4500 atcttctttt
cagtactaca aaaacagaat aattttgaag ttttagaata aatgtaatat 4560
atttactata attctaaatg tttaaatgct tttctaaaaa tgcaaaacta tgatgtttag
4620 ttgctttatt ttacctctat gtgattattt ttcttaattg ttatttttta
taatcattat 4680 ttttctgaac cattcttctg gcctcagaag taggactgaa
ttctactatt gctaggtgtg 4740 agaaagtggt ggtgagaacc ttagagcagt
ggagatttgc tacctggtct gtgttttgag 4800 aagtgcccct tagaaagtta
aaagaatgta gaaaagatac tcagtcttaa tcctatgcaa 4860 aaaaaaaaat
caagtaattg ttttcctatg aggaaaataa ccatgagctg tatcatgcta 4920
cttagctttt atgtaaatat ttcttatgtc tcctctatta agagtattta aaatcatatt
4980 taaatatgaa tctattcatg ctaacattat ttttcaaaac atacatggaa
atttagccca 5040 gattgtctac atataaggtt tttatttgaa ttgtaaaata
tttaaaagta tgaataaaat 5100 atatttatag gtatttatca gagatgatta
ttttgtgcta catacaggtt ggctaatgag 5160 ctctagtgtt aaactacctg
attaatttct tataaagcag cataaccttg gcttgattaa 5220 ggaattctac
tttcaaaaat taatctgata atagtaacaa ggtatattat actttcatta 5280
caatcaaatt atagaaatta cttgtgtaaa agggcttcaa gaatatatcc aatttttaaa
5340 tattttaata tatctcctat ctgataactt aattcttcta aattaccact
tgccattaag 5400 ctatttcata ataaattctg tacagtttcc ccccaaaaaa
gagatttatt tatgaaatat 5460 ttaaagtttc taatgtggta ttttaaataa
agtatcataa atgtaataag taaatattta 5520 tttaggaata ctgtgaacac
tgaactaatt attcctgtgt cagtctatga aatccctgtt 5580 ttgaaatacg
taaacagcct aaaatgtgtt gaaattattt tgtaaatcca tgacttaaaa 5640
caagatacat acatagtata acacacctca cagtgttaag atttatattg tgaaatgaga
5700 caccctacct tcaattgttc atcagtgggt aaaacaaatt ctgatgtaca
ttcaggacaa 5760 atgattagcc ctaaatgaaa ctgtaataat ttcagtggaa
actcaatctg tttttacctt 5820 taaacagtga attttacatg aatgaatggg
ttcttcactt tttttttagt atgagaaaat 5880 tatacagtgc ttaattttca
gagattcttt ccatatgtta ctaaaaaatg ttttgttcag 5940 cctaacatac
tgagtttttt ttaactttct aaattattga atttccatca tgcattcatc 6000
caaaattaag gcagactgtt tggattcttc cagtggccag atgagctaaa ttaaatcaca
6060 aaagcagatg cttttgtatg atctccaaat tgccaacttt aaggaaatat
tctcttgaaa 6120 ttgtctttaa agatcttttg cagctttgca gatacccaga
ctgagctgga actggaattt 6180 gtcttcctat tgactctact tctttaaaag
cggctgccca ttacattcct cagctgtcct 6240 tgcagttagg tgtacatgtg
actgagtgtt ggccagtgag atgaagtctc ctcaaaggaa 6300 ggcagcatgt
gtcctttttc atcccttcat cttgctgctg ggattgtgga tataacagga 6360
gccctggcag ctgtctccag aggatcaaag ccacacccaa agagtaaggc agattagaga
6420 ccagaaagac cttgactact tccctacttc cactgctttt tcctgcattt
aagccattgt 6480 aaatctgggt gtgttacatg aagtgaaaat taattctttc
tgcccttcag ttctttatcc 6540 tgataccatt taacactgtc tgaattaact
agactgcaat aattctttct tttgaaagct 6600 tttaaaggat aatgtgcaat
tcacattaaa attgattttc cattgtcaat tagttatact 6660 cattttcctg
ccttgatctt tcattagata ttttgtatct gcttggaata tattatcttc 6720
tttttaactg tgtaattggt aattactaaa actctgtaat ctccaaaata ttgctatcaa
6780 attacacacc atgttttcta tcattctcat agatctgcct tataaacatt
taaataaaaa 6840 gtactattta atgattt 6857
[1297]
98TABLE LIII(g) Nucleotide sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 188) and 98P4B6 v.8 (SEQ ID NO: 189) Score = 3201 bits (1665),
Expect = 0.0Identities = 1665/1665 (100%) Strand = Plus/Plus V.1:
23 gttcctcgggccctcggcgccaca- agctgtccgggcacgcagcccctagcggcgcgtcgc
82 .vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline. V.8: 62
gttcctcgggccctcggcgccacaagctgtccgggcacgcagcccctagcggcgcgtcgc 121
V.1: 83 tgccaagccggcctccgcgcgcctccctccttccttctcccctggctgttcgcgatcc-
ag 142 .vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline. V.8: 122
tgccaagccggcctccgcgcgcctccctccttc- cttctcccctggctgttcgcgatccag 181
V.1: 143
cttgggtaggcggggaagcagctggagtgcgaccgccacggcagccaccctgcaaccgcc 202
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.8: 182
cttgggtaggcggggaagcagctggagtgcgaccgccacggcagccac- cctgcaaccgcc 241
V.1: 203 agtcggaggtgcagtccgtaggccctggcccc-
cgggtgggcccttggggagtcggcgccg 262 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.8: 242
agtcggaggtgcagtccgtaggccctggcccccgggtgggcccttggggagtcggcgccg 301
V.1: 263 ctcccgaggagctgcaaggctcgcccctgcccggcgtggagggcgcggggggcgcgg-
agg 322 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.8: 302
ctcccgaggagctgcaaggctcgcccctgccc- ggcgtggagggcgcggggggcgcggagg 361
V.1: 323
atattcttggtgatcttggaagtgtccgtatcatggaatcaatctctatgatgggaagcc 382
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.8: 362
atattcttggtgatcttggaagtgtccgtatcatggaatcaatctcta- tgatgggaagcc 421
V.1: 383 ctaagagccttagtgaaacttgtttacctaat-
ggcataaatggtatcaaagatgcaagga 442 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.8: 422
ctaagagccttagtgaaacttgtttacctaatggcataaatggtatcaaagatgcaagga 481
V.1: 443 aggtcactgtaggtgtgattggaagtggagattttgccaaatccttgaccattcgac-
tta 502 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.8: 482
aggtcactgtaggtgtgattggaagtggagat- tttgccaaatccttgaccattcgactta 541
V.1: 503
ttagatgcggctatcatgtggtcataggaagtagaaatcctaagtttgcttctgaatttt 562
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.8: 542
ttagatgcggctatcatgtggtcataggaagtagaaatcctaagtttg- cttctgaatttt 601
V.1: 563 ttcctcatgtggtagatgtcactcatcatgaa-
gatgctctcacaaaaacaaatataatat 622 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.8: 602
ttcctcatgtggtagatgtcactcatcatgaagatgctctcacaaaaacaaatataatat 661
V.1: 623 ttgttgctatacacagagaacattatacctccctgtgggacctgagacatctgcttg-
tgg 682 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.8: 662
ttgttgctatacacagagaacattatacctcc- ctgtgggacctgagacatctgcttgtgg 721
V.1: 683
gtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacccagaatccaatg 742
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.8: 722
gtaaaatcctgattgatgtgagcaataacatgaggataaaccagtacc- cagaatccaatg 781
V.1: 743 ctgaatatttggcttcattattcccagattct-
ttgattgtcaaaggatttaatgttgtct 802 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.8: 782
ctgaatatttggcttcattattcccagattctttgattgtcaaaggatttaatgttgtct 841
V.1: 803 cagcttgggcacttcagttaggacctaaggatgccagccggcaggtttatatatgca-
gca 862 .vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline. V.8: 842
cagcttgggcacttcagttaggacctaaggat- gccagccggcaggtttatatatgcagca 901
V.1: 863
acaatattcaagcgcgacaacaggttattgaacttgcccgccagttgaatttcattccca 922
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline. V.8: 902
acaatattcaagcgcgacaacaggttattgaacttgcccgccagttga- atttcattccca 961
V.1: 923 ttgacttgggatccttatcatcagccagagag-
attgaaaatttacccctacgactcttta 982 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.8: 962
ttgacttgggatccttatcatcagccagagagattgaaaatttacccctacgactcttta 1021
V.1: 983 ctctctggagagggccagtggtggtagctataagcttggccacattttttttcctt-
tatt 1042 .vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline. V.8: 1022
ctctctggagagggccagtggtggtagct- ataagcttggccacattttttttcctttatt 1081
V.1: 1043
cctttgtcagagatgtgattcatccatatgctagaaaccaacagagtgacttttacaaaa 1102
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 1082
cctttgtcagagatgtgattcatccatatgctagaaaccaacagag- tgacttttacaaaa 1141
V.1: 1103 ttcctatagagattgtgaataaaacctt-
acctatagttgccattactttgctctccctag 1162 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.8: 1142
ttcctatagagattgtgaataaaaccttacctatagttgccattactttgctctccctag 1201
V.1: 1163 tataccttgcaggtcttctggcagctgcttatcaactttattacggcaccaagta-
tagga 1222 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.8: 1202
tataccttgcaggtcttctggcagctgc- ttatcaactttattacggcaccaagtatagga 1261
V.1: 1223
gatttccaccttggttggaaacctggttacagtgtagaaaacagcttggattactaagtt 1282
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 1262
gatttccaccttggttggaaacctggttacagtgtagaaaacagct- tggattactaagtt 1321
V.1: 1283 ttttcttcgctatggtccatgttgccta-
cagcctctgcttaccgatgagaaggtcagaga 1342 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.8: 1322
ttttcttcgctatggtccatgttgcctacagcctctgcttaccgatgagaaggtcagaga 1381
V.1: 1343 gatatttgtttctcaacatggcttatcagcaggttcatgcaaatattgaaaactc-
ttgga 1402 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.8: 1382
gatatttgtttctcaacatggcttatca- gcaggttcatgcaaatattgaaaactcttgga 1441
V.1: 1403
atgaggaagaagtttggagaattgaaatgtatatctcctttggcataatgagccttggct 1462
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 1442
atgaggaagaagtttggagaattgaaatgtatatctcctttggcat- aatgagccttggct 1501
V.1: 1463 tactttccctcctggcagtcacttctat-
cccttcagtgagcaatgctttaaactggagag 1522 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.8: 1502
tactttccctcctggcagtcacttctatcccttcagtgagcaatgctttaaactggagag 1561
V.1: 1523 aattcagttttattcagtctacacttggatatgtcgctctgctcataagtacttt-
ccatg 1582 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.8: 1562
aattcagttttattcagtctacacttgg- atatgtcgctctgctcataagtactttccatg 1621
V.1: 1583
ttttaatttatggatggaaacgagcttttgaggaagagtactacagattttatacaccac 1642
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 1622
ttttaatttatggatggaaacgagcttttgaggaagagtactacag- attttatacaccac 1681
V.1: 1643 caaactttgttcttgctcttgttttgcc- ctcaattgtaattctgg 1687
.vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline. V.8: 1682
caaactttgttcttgctcttgttttgccctcaattgtaattctgg 1726 Score = 1381
bits (718), Expect = 0.0Identities = 725/726 (99%), Gaps = 1/726
(0%) Strand = Plus/Plus V.1: 1687 gatcttttgcagctttgcagataccc-
agactgagctggaactggaatttgtcttcctatt 1746 .vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline. V.8:
6132 gatcttttgcagctttgcagatacccagactgagctggaactggaatttgtcttcctatt
6191 V.1: 1747 gactctacttctttaaaagcggctgcccattacattcctcagctgtcctt-
gcagttaggt 1806 .vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline. V.8: 6192
gactctacttctttaaaagcggc- tgcccattacattcctcagctgtccttgcagttaggt 6251
V.1: 1807
gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaaggaaggcagcatgtg 1866
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 6252
gtacatgtgactgagtgttggccagtgagatgaagtctcctcaaag- gaaggcagcatgtg 6311
V.1: 1867 tcctttttcatcccttcatcttgctgct-
gggattgtggatataacaggagccctggcagc 1926 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.8: 6312
tcctttttcatcccttcatcttgctgctgggattgtggatataacaggagccctggcagc 6371
V.1: 1927 tgtctccagaggatcaaagccacacccaaagagtaaggcagattagagaccagaa-
agacc 1986 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.8: 6372
tgtctccagaggatcaaagccacaccca- aagagtaaggcagattagagaccagaaagacc 6431
V.1: 1987
ttgactacttccctacttccactgctttt-cctgcatttaagccattgtaaatctgggtg 2045
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline.
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line. V.8: 6432
ttgactacttccctacttccactgctttttcctgcatttaagccattgtaa- atctgggtg 6491
V.1: 2046 tgttacatgaagtgaaaattaattctttctgcc-
cttcagttctttatcctgataccattt 2105 .vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline. V.8: 6492
tgttacatgaagtgaaaattaattctttctgcccttcagttctttatcctgataccattt 6551
V.1: 2106 aacactgtctgaattaactagactgcaataattctttcttttgaaagcttttaaa-
ggata 2165 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.8: 6552
aacactgtctgaattaactagactgcaa- taattctttcttttgaaagcttttaaaggata 6611
V.1: 2166
atgtgcaattcacattaaaattgattttccattgtcaattagttatactcattttcctgc 2225
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 6612
atgtgcaattcacattaaaattgattttccattgtcaattagttat- actcattttcctgc 6671
V.1: 2226 cttgatctttcattagatattttgtatc-
tgcttggaatatattatcttctttttaactgt 2285 .vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline..vertline..vertline-
..vertline..vertline..vertline..vertline..vertline..vertline..vertline..ve-
rtline..vertline..vertline..vertline..vertline..vertline..vertline..vertli-
ne..vertline..vertline..vertline..vertline..vertline..vertline..vertline..-
vertline..vertline..vertline..vertline..vertline..vertline..vertline..vert-
line..vertline..vertline..vertline..vertline..vertline. V.8: 6672
cttgatctttcattagatattttgtatctgcttggaatatattatcttctttttaactgt 6731
V.1: 2286 gtaattggtaattactaaaactctgtaatctccaaaatattgctatcaaattaca-
cacca 2345 .vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline. V.8: 6732
gtaattggtaattactaaaactctgtaa- tctccaaaatattgctatcaaattacacacca 6791
V.1: 2346
tgttttctatcattctcatagatctgccttataaacatttaaataaaaagtactatttaa 2405
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline..vertline..vertline..vertline..vertline..vertline..vertline..ver-
tline..vertline..vertline..vertline..vertline..vertline..vertline..vertlin-
e..vertline..vertline..vertline..vertline..vertline..vertline..vertline..v-
ertline..vertline..vertline..vertline..vertline..vertline..vertline..vertl-
ine..vertline..vertline..vertline..vertline..vertline..vertline..vertline.-
.vertline. V.8: 6792
tgttttctatcattctcatagatctgccttataaacatttaaataa- aaagtactatttaa 6851
V.1: 2406 tgattt 2411
.vertline..vertline..vertline..vertline..vertline..vertline. V.8:
6852 tgattt 6857
[1298]
99TABLE LIV(g) Peptide sequences of protein coded by 98P4B6 v.8
(SEQ ID NO: 190) MESISMMGSP KSLSETCLPN GINGIKDARK VTVGVIGSGD
FAKSLTIRLI RCGYHVVIGS 60 RNPKFASEFF PHVVDVTHHE DALTKTNIIF
VAIHREHYTS LWDLRHLLVG KILIDVSNNM 120 RINQYPESNA EYLASLFPDS
LIVKGFNVVS AWALQLGPKD ASRQVYICSN NIQARQQVIE 180 LARQLNFIPI
DLGSLSSARE IENLPLRLFT LWRGPVVVAI SLATFFFLYS FVRDVIHPYA 240
RNQQSDFYKI PIEIVNKTLP IVAITLLSLV YLAGLLAAAY QLYYGTKYRR FPPWLETWLQ
300 CRKQLGLLSF FFAMVHVAYS LCLPMRRSER YLFLNMAYQQ VHANIENSWN
EEEVWRIEMY 360 ISFGIMSLGL LSLLAVTSIP SVSNALNWRE FSFIQSTLGY
VALLISTFHV LIYGWKRAFE 420 EEYYRFYTPP NFVLALVLPS IVILGKIILF
LPCISRKLKR IKKGWEKSQF LEEGMGGTIP 480 HVSPERVTVM 490
[1299]
100TABLE LV(g) Amino acid sequence alignment of 98P4B6 v.1 (SEQ ID
NO: 191) and 98P4B6 v.8 (SEQ ID NO: 192) Score = 888 bits (2294),
Expect = 0.0Identities = 444/444 (100%), Positives = 444/444 (100%)
V.1: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
60 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
V.8: 1 MESISMMGSPKSLSETCLPNGINGIKDARKVTVGVIGSGDFAKSLTIRLIRCGYHVVIGS
60 V.1: 61
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVS- NNM 120
RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILIDVS- NNM V.8:
61 RNPKFASEFFPHVVDVTHHEDALTKTNIIFVAIHREHYTSLWDLRHLLVGKILID- VSNNM
120 V.1: 121 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPK-
DASRQVYICSNNIQARQQVIE 180 RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQLGPK-
DASRQVYICSNNIQARQQVIE V.8: 121
RINQYPESNAEYLASLFPDSLIVKGFNVVSAWALQL- GPKDASRQVYICSNNIQARQQVIE 180
V.1: 181
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA 240
LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA V.8:
181 LARQLNFIPIDLGSLSSAREIENLPLRLFTLWRGPVVVAISLATFFFLYSFVRDVIHPYA
240 V.1: 241 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPP-
WLETWLQ 300 RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRRFPP-
WLETWLQ V.8: 241
RNQQSDFYKIPIEIVNKTLPIVAITLLSLVYLAGLLAAAYQLYYGTKYRR- FPPWLETWLQ 300
V.1: 301 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFL-
NMAYQQVHANIENSWNEEEVWRIEMY 360 CRKQLGLLSFFFAMVHVAYSLCLPMRRSERYLFL-
NMAYQQVHANIENSWNEEEVWRIEMY V.8: 301
CRKQLGLLSFFFAMVHVAYSLCLPMRRSERY- LFLNMAYQQVHANIENSWNEEEVWRIEMY 360
V.1: 361
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE 420
ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE V.8:
361 ISFGIMSLGLLSLLAVTSIPSVSNALNWREFSFIQSTLGYVALLISTFHVLIYGWKRAFE
420 V.1: 421 EEYYRFYTPPNFVLALVLPSIVIL 444 EEYYRFYTPPNFVLALVLPSIVIL
V.8: 421 EEYYRFYTPPNFVLALVLPSIVIL 444
* * * * *
References