U.S. patent application number 12/387884 was filed with the patent office on 2009-09-17 for mage-c2 antigenic peptides and uses therefor.
Invention is credited to Thierry Boon-Falleur, Pierre Coulie, Catherine Germeau, Wenbin Ma, Benoit Van Den Eynde.
Application Number | 20090233315 12/387884 |
Document ID | / |
Family ID | 32045888 |
Filed Date | 2009-09-17 |
United States Patent
Application |
20090233315 |
Kind Code |
A1 |
Ma; Wenbin ; et al. |
September 17, 2009 |
MAGE-C2 antigenic peptides and uses therefor
Abstract
This invention relates to isolated peptides derived from
MAGE-C2, nucleic acid molecules that encode MAGE-C2 and the
isolated peptides derived from MAGE-C2, expression vectors
comprising the nucleic acid molecules, host cells transformed or
transfected with the nucleic acid molecules or the expression
vectors, and to tetramers comprising the peptides, HLA molecules,
.E-backward..sub.2 microglobulin and a first and second binding
partner. This invention also relates to methods for using the
peptides, nucleic acid molecules, expression vectors, tetramers and
complexes of this invention as well as to cytolytic T cells which
recognize the peptides in complex with an HLA molecule.
Inventors: |
Ma; Wenbin; (Brussels,
BE) ; Van Den Eynde; Benoit; (Brussels, BE) ;
Boon-Falleur; Thierry; (Brussels, BE) ; Germeau;
Catherine; (Brussels, BE) ; Coulie; Pierre;
(Brussels, BE) |
Correspondence
Address: |
FULBRIGHT & JAWORSKI, LLP
666 FIFTH AVE
NEW YORK
NY
10103-3198
US
|
Family ID: |
32045888 |
Appl. No.: |
12/387884 |
Filed: |
May 8, 2009 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10670472 |
Sep 26, 2003 |
7547517 |
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12387884 |
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60413844 |
Sep 27, 2002 |
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60433983 |
Dec 18, 2002 |
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60459263 |
Apr 2, 2003 |
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Current U.S.
Class: |
435/7.2 ;
530/328 |
Current CPC
Class: |
A61P 35/00 20180101;
A61P 37/04 20180101; A61K 38/00 20130101; C07K 14/4748
20130101 |
Class at
Publication: |
435/7.2 ;
530/328 |
International
Class: |
G01N 33/567 20060101
G01N033/567; C07K 7/06 20060101 C07K007/06 |
Claims
1-44. (canceled)
45. An isolated peptide consisting of amino acid sequence of
XLFGLALIEV (SEQ ID NO: 88), wherein X is any amino acid.
46. The isolated peptide of claim 45, wherein X is L.
47. A method for determining if a cell presents an HLA-A2 molecule
on its surface comprising contacting a sample containing said cell
with the peptide of claim 46 and determining binding therebetween,
said binding being indicative of HLA-A2 on the surface of said
cell.
48. A method for detecting presence of a cytolytic T cell (CTL)
specific for a peptide consisting of the amino acid sequence of SEQ
ID NO: 88 in a CTL containing sample, comprising contacting said
sample with a tetramer comprising four biotinylated complexes of
said peptide, a .beta..sub.2 microglobulin molecule and an HLA-A2
molecule, each of which is bound to an avidin molecule, and
measuring release of tumor necrosis factor (TNF) released by a CTL,
wherein an increase in level of TNF by said CTL containing sample,
as compared to level of TNF release by said CTL containing sample
in the absence of said tetramer, indicates presence of a CTL in
said sample that is specific for said peptide.
49. An isolated tetramer comprising four biotinylated complexes of
a peptide consisting of the amino acid sequence of SEQ ID NO: 88, a
P microglobulin molecule, and an HLA-A2 molecule, each of which is
bound to an avidin molecule.
50. The isolated complex of claim 49, further comprising a
label.
51. A composition comprising the isolated tetramer of claim 49, and
a carrier.
Description
RELATED APPLICATIONS
[0001] This application is a divisional of U.S. application Ser.
No. 10/670,472 filed Sep. 26, 2003, which claims priority of U.S.
Provisional Applications No. 60/413,844 filed Sep. 27, 2002, U.S.
Provisional Application No. 60/433,983 filed Dec. 18, 2002 and
60/459,263 filed Apr. 2, 2003, are all incorporated herein by
reference.
FIELD OF THE INVENTION
[0002] This invention relates to isolated peptides which bind to
HLA, particularly HLA-A2, and uses thereof. The peptides are
derived from members of the MAGE family of tumor rejection antigen
precursors. This invention also relates to nucleic acid molecules
encoding the peptides, complexes of the peptides and HLA molecule,
and to cells expressing the HLA/peptide complexes on their
surfaces, as well as uses of the nucleic acid molecules, the
HLA/peptide complexes, and the cells expressing the complexes in
the diagnosis and treatment of pathological conditions.
BACKGROUND
[0003] The process by which the mammalian immune system recognizes
and reacts to foreign or alien materials is a complex one. An
important facet of the system is the T cell response. This response
requires that T cells recognize and interact with complexes of cell
surface molecules, referred to as human leukocyte antigens
("HLAs"), or major histocompatibility complexes ("MHCs"), and
peptides. The peptides are derived from larger molecules which are
processed by the cells which also present the HLA/MHC molecule. See
in this regard Male et al., Advanced Immunology (J. P. Lipincott
Company, 1987), especially chapters 6-10. The interaction of T cell
and complexes of HLA/peptide is restricted, requiring a T cell
specific for a particular combination of an HLA molecule and a
peptide. If a specific T cell is not present, there is no T cell
response even if its partner complex is present. Similarly, there
is no response if the specific complex is absent, but the T cell is
present. This mechanism is involved in the immune system's response
to foreign materials, in autoimmune pathologies, and in responses
to cellular abnormalities. Much early work focused on the
mechanisms by which proteins are processed into the HLA binding
peptides. See, in this regard, Barinaga, Science 257: 880 (1992);
Fremont et al., Science 257: 919 (1992); Matsumura et al., Science
257: 927 (1992); Latron et al., Science 257: 964 (1992).
[0004] The mechanism by which T cells recognize cellular
abnormalities has also been implicated in cancer. For example, PCT
application PCT/US92/04354, filed May 22, 1992, published on Nov.
26, 1992, and incorporated by reference, discloses a family of
genes that are processed into peptides which, in turn, are
expressed on cell surfaces and lead to lysis of the tumor cells by
specific CTLs. The genes are said to code for "tumor rejection
antigen precursors" or "TRAP" molecules, and the peptides derived
therefrom are referred to as "tumor rejection antigens" or "TRAs".
See Traversari et al., Immunogenetics 35: 145 (1992); van der
Bruggen et al., Science 254: 1643 (1991) and U.S. Pat. No.
5,342,774 and U.S. Pat. No. 5,462,871.
[0005] Other families of genes encoding TRAPs are also known in the
art, see e.g., U.S. Pat. No. 5,629,166 for information relating to
MAGE-1 TRAP and TRAs; Lucas et al., Cancer Res., 58(4):743-52
(1998), Chen et al., PNAS, 95(12):6919-23 (1998), Jungbluth et al.,
Int. J. Canc. 94(2):252-6 (2001), Jungbluth et al., Int J. Canc.
99(6):839-45 (2002), Chomez et al., An overview of the MAGE gene
family with the identification of all human members of the family.
Cancer Res. 2001 Jul. 15; 61(14):5544-51, Rimoldi et al., cDNA and
protein characterization of human MAGE-10. Int J Cancer. September
9; 82(6):901-7 (1999), Lurquin et al., Two members of the human
MAGE-B gene family located in Xp21.3 are expressed in tumors of
various histological origins. Genomics. December 15; 46(3):397-408
(1997), De Plaen et al., Structure, chromosomal localization, and
expression of 12 genes of the MAGE family. Immunogenetics.
40:360-269 (1994), U.S. Pat. No. 5,997,872 issued Dec. 7, 1999,
PCT/US98/08493 filed Apr. 24, 1998 and U.S. patent application Ser.
No. 09/501,104 filed Feb. 9, 2000 for information relating to
MAGE-C1, MAGE C2, MAGE-C3, MAGE-B1, MAGE B2, MAGE-B3, MAGE-B5,
MAGE-B6, MAGE-A10 and MAGE All TRAPs and TRAs; U.S. Pat. No.
5,571,711 issued Jan. 5, 1996 for information relating to BAGE
TRAPs and TRAs; U.S. Pat. No. 5,571,711 issued Jan. 5, 1996 for
information relating to tyrosinase TRAP and TRAs; U.S. patent
application Ser. No. 08/096,039 and Ser. No. 08/250,162, for
information relating to GAGE TRAP and TRA, and; U.S. application
Ser. No. 08/316,231 filed Sep. 30, 1994, (DAGE TRAPs), all the
foregoing applications and patents are incorporated by reference in
their entirety.
[0006] U.S. Pat. No. 5,405,940, incorporated by reference,
describes the MAGE-1 gene coding for a tumor rejection antigen
precursor that is processed to nonapeptides, which are presented by
the HLA-A1 molecule. The nonapeptides which bind to HLA-A1 follow a
"rule" for binding in that a motif is satisfied. In this regard,
see, e.g., PCT/US93/07421; Falk et al., Nature 351:290-296 (1991);
Engelhard, Ann Rev. Immunol. 12:181-207 (1994); Ruppert et al.,
Cell 74:929-937 (1993); Rotzschke et al., Nature 348:252-254
(1990); Bjorkman et al., Nature 329:512-518 (1987); Traversari et
al., J. Exp. Med. 176:1453-1457 (1992). Because different
individuals possess different HLA phenotypes, identification of a
particular peptide as being a partner for a particular HLA molecule
has diagnostic and therapeutic ramifications, only for individuals
with that particular HLA phenotype. Thus, there is a need for
further work in the area, because cellular abnormalities are not
restricted to one particular HLA phenotype, and targeted therapy
requires some knowledge of the phenotype of the abnormal cells at
issue.
BRIEF DESCRIPTION OF THE FIGURES
[0007] FIG. 1 depicts the specific lysis of autologous melanoma
cell line EB81-MEL.2 by CTL clone 606 C/22.2. The indicated target
cells were labeled with chromium and incubated with CTL at
different effector-to-target ratios. Chromium release was measured
after 4 hours.
[0008] FIG. 2 demonstrates the HLA restriction of CTL clone 606
C/22.2. Autologous melanoma cell line EB81-MEL.2 was used to
stimulate CTL 606 C/22.2 in the absence or in the presence of
monoclonal antibodies to different HLA molecules. After 18 hours of
coculture, the production of TNF by CTL was measured by testing the
toxicity of the supernatants to TNF-sensitive cell line
WEHI-164.13.
[0009] FIG. 3 depicts the recognition of different cell lines by
CTL 606 C/22.2 LB37-NSCLC is a non-small-cell lung carcinoma cell
line. LB129-SCLC is a small cell lung carcinoma cell line.
LB39-MEL, SK23-MEL, AVL3-MEL, LB373-MEL are melanoma cell lines.
U266 is a myeloma cell line. All of the cell lines aforementioned
are HLA-A2 positive. MZ2-MEL.43/A2 is a melanoma cell line
transfected with HLA-A2. LB831-BLC is a bladder carcinoma cell
line, which was HLA-A2 negative, and was transiently transfected
with HLA-A2 before adding CTL. Tumor cells and CTL were incubated
over 18 hours, and the production of TNF by the CTL was measured by
testing the toxicity of the supernatants to the TNF-sensitive
WEHI-164.13 cells.
[0010] FIG. 4A depicts a comparison of the MAGE-C2 and MAGE-C2 cDNA
(version M) and the region coding for the antigenic peptide
recognized by CTL 606 C/22.2 (ALKDVEERV SEQ ID NO: 3). The
minigenes prepared to identify the region encoding the antigenic
peptide are also shown. Exons (E1, E2, E3, (SEQ ID NO: 75) E4)
appear as open boxes, introns as lines, and the open reading frame
(ORF) is shown as a black box. The results of CTL stimulation with
the minigene-transfected Cos-7 cells are indicated as "-" and
"+".
[0011] FIG. 4B depicts the results of stimulating CTL 606 C/22.2
with Cos-7 cells transfected with HLA-A2 and minigene constructs.
CTL or EB81-MEL.2 alone were used as negative controls, and
EB81-MEL.2 with CTL as a positive control. Transfected cells or
EB81-MEL.2 were incubated with CTL for 18 hours, and the
concentration of TNF was measured in the supernatant.
[0012] FIG. 5A demonstrates that the peptide ALKDVEERV (SEQ ID NO:
3) stimulates 606 C/22.2 release of TNF. HLA-A2-transfected Cos-7
cells were incubated with the indicated concentrations of peptide
for 30 min at 37.degree. C., and CTL 606 C/22.2 was added. After 18
hours, the supernatant was collected and its TNF content was
measured.
[0013] FIG. 5B demonstrates that the peptide ALKDVEERV (SEQ ID NO:
3) stimulates lysis of antigen presenting cells by CTL 606 C/22.2
in a lysis assay. Chromium-labeled EB81-EBV cells were incubated
for 30 min with the indicated concentrations of peptide ALKDVEERV
(SEQ ID NO: 3), ALKDVEER (SEQ ID NO: 4), or LKDVEERV (SEQ ID NO:
2). CTL 606 C/22.2 was added at an E/T ratio of 10, and chromium
release was measured after 4 hours.
[0014] FIG. 6 demonstrates HLA-A2-expressing cells transfected with
a nucleic acid molecule encoding MAGE-C2 stimulate CTL 606
C/22.2.
[0015] FIG. 7 depicts the clinical evolution of metastatic melanoma
patient EB81 after vaccination with a recombinant ALVAC virus (ALV)
and with MAGE peptides (P). The CTL/CD8 frequencies for the CTL
clone recognizing the MAGE-3 A1 peptide and for the anti-MAGE-C2 A1
CTL clone 606 C/22.2 are depicted.
[0016] FIG. 8 depicts the cDNA sequences encoding the TCR V and the
TCR 3 chains of CTL clone 606 C/22.2 and the primers used for the
clonotypic PCR amplifications. Sequences from top to bottom are SEQ
ID NO: 93, 94, 95, 96, 97, 98, 99, 100, 101.
[0017] FIG. 9. Specific lysis of autologous melanoma cell line
EB81-MEL.2 by CTL 606 C/21.7. Autologous EBV transformed B cell
line EB81-EBV, peptide Mage 3-A1 pulsed EB81-EBV cells, and K562
cells were used as control targets. Target cells were labeled with
chromium and incubated with CTL at different effector-to-target
ratios. .sup.51Cr release was measured after 4 hours.
[0018] FIG. 10. HLA restriction of CTL clone 606 C/21.7. Autologous
melanoma cell line EB81-MEL.2, incubated or not with the indicated
antibodies, were used to stimulate CTL 606 C/21.7. After 18 hours
of coculture, production of TNF by the CTL was measured by testing
the toxicity of the supernatants for TNF-sensitive cell line
WEHI-164 cl13.
[0019] FIG. 11. Recognition of different cell lines by CTL 606
C/21.7. Different HLA-A2 cell lines were used to stimulate CTL 606
C/21.7. Among them, LB37-NSCLC is a non-small-Cell lung carcinoma
cell line, AVL3-MEL and LB373-MEL are melanoma cell lines, U266 is
a myeloma cell line. After 18 hours of coculture, the production of
TNF by CTL was measured by testing the toxicity of the supernatants
for TNF-sensitive cell line WEHI-164 cl13.
[0020] FIG. 12A. Stimulation of CTL 606 C/21.7 with COS-7 cells
transfected with HLA-A2 and various minigenes derived from Mage C2
(SEQ ID NO: 72)(See FIG. 12B). CTL alone and EB81-MEL.2 without CTL
were used as negative controls and EB81-MEL.2 with CTL as positive
control. Transfected cells or EB81-MEL.2 were incubated with CTL
for 18 hours, production of TNF by the CTL was then measured by
testing the toxicity of the supernatants for TNF-sensitive cell
line WEHI-164 cl 13.
[0021] FIG. 12B. Identification of the region coding for the
antigenic peptide recognized by CTL 606 C/21.7. Position 1 depicts
the ATG start codon of the open reading (ORF) of MAGE-C2 cDNA and
corresponds to position 330 in SEQ ID NO: 72. Minigene 14=SEQ ID
NO: 81.
[0022] FIG. 13. Lysis by CTL 606C/21.7 of autologous
EBV-transformed B cell line EB81-EBV pulsed with various peptides
(LLFGLALIEV, SEQ ID NO: 77; LFGLALIEV, SEQ ID NO: 78; LLFGLALIE,
SEQ ID NO: 79; LLFGLALI, SEQ ID NO: 80). .sup.51Cr labeled target
cells EB81-EBV were pulsed for 30 minutes with various
concentrations of the indicated peptides. CTL 606C/21.7 was then
added at an E/T ratio of 10. .sup.51Cr release was measured after 4
hours. The negative control, EB81-EBV cells, which were not pulsed
with peptide, produced a level of 15%.
[0023] FIG. 14. Lysis by CTLs 606C/18.6, 606C/19.3 and 606A/16.2 of
autologous EBV-transformed B cell line EB81-EBV pulsed with various
peptides (LLFGLALIEV, SEQ ID NO: 77; LFGLALIEV, SEQ ID NO: 78;
LLFGLALIE, SEQ ID NO: 79; LLFGLALI, SEQ ID NO: 80). .sup.51Cr
labeled target cells EB81-EBV were pulsed for 30 minutes with
various concentrations of the indicated peptides. CTLs were then
added at an E/T ratio of 10. .sup.51Cr release was measured after 4
hours.
[0024] FIG. 15. Specific lysis of autologous melanoma cell line
EB81-MEL.2 by CTL 606C/17.3.
[0025] FIG. 16. HLA restriction of CTL clone 606 C/17.3.
[0026] FIG. 17. Recognition of COS 7 cells transiently transfected
with MAGE-C2 and HLA-B57 or HLA-C6 cDNA by CTL 606 C/17.3.
[0027] FIG. 18. Recognition of different cell lines by CTL 606
C/17.3.
[0028] FIG. 19A. Recognition by CTL 606C/17.3 of COS 7 cells
transfected with HLA-B57 and MAGE-C2 minigenes.
[0029] FIG. 19B. Identification of the region coding for the
antigenic peptide recognized by CTL 606 C/17.3. The sequence in the
figure corresponds to amino acid positions 41 and 103 of SEQ ID NO:
71.
[0030] FIG. 20. Lytic activity of CTL 606C/17.3 against
peptide-pulsed autologous EBV-transformed B cell line EB81-EBV. The
sequences of the peptides from top to bottom are SEQ ID NO: 90, 89,
91 and 92.
SUMMARY OF THE INVENTION
[0031] Disclosed herein is the identification of peptides derived
from MAGE-C2 that bind to HLA molecules, particularly HLA-A2
molecules. Also disclosed are nucleic acid molecules that encode
the peptides, complexes of the peptides and HLA molecules and
methods for using the peptides and complexes comprising the
peptides in diagnostic and therapeutic assays.
[0032] This invention relates to isolated peptides consisting of
the amino acid sequence ALKDVEERX (SEQ ID NO: 1) or LKDVEERV (SEQ
ID NO: 2), particularly an isolated peptide consisting of the amino
acid sequence ALKDVEERX wherein X may be any amino acid, preferably
a hydrophobic amino acid, more preferably X is Ala, Val, Leu, Ile,
Pro, Phe, Met, Trp or Glu and most preferably X is an valine (SEQ
ID NO: 3) or alanine (SEQ ID NO: 5).
[0033] This invention also relates to the isolated peptides recited
in Table 2, infra.
[0034] This invention also relates to isolated peptides consisting
of the amino acid sequence XLFGLALIEV (SEQ ID NO: 88) wherein X may
be absent or may be any amino acid, preferably a hydrophobic amino
acid, more preferably X is Ala, Val, Leu, Ile, Pro, Phe, Met, Trp
or Glu and most preferably X is a leucine (SEQ ID NO: 77).
[0035] This invention also relates to isolated peptides consisting
of the amino acid sequence ASSTLYLVF (SEQ ID NO: 89).
[0036] This invention relates to a composition useful in provoking
a cytolytic T cell response comprising the isolated peptide
consisting of the amino acid sequences ALKDVEERX (SEQ ID NO: 1),
wherein X is any amino acid, preferably X is a hydrophobic amino
acid, more preferably X is Ala, Val, Leu, Ile, Pro, Phe, Met, Trp
or Glu and most preferably X is an alanine (SEQ ID NO: 5) or a
valine (SEQ ID NO: 3) or the isolated peptide consists of the amino
acid sequence LKDVEERV (SEQ ID NO: 2), particularly the composition
comprises an isolated peptide consisting of the amino acid sequence
ALKDVEERV (SEQ ID NO: 3) and an adjuvant. The composition may
comprise at least one additional peptide.
[0037] This invention also relates to compositions useful for
provoking a CTL response comprising an adjuvant and an isolated
peptide of Table 2, infra. The composition may comprise an
additional peptide.
[0038] This invention also relates to compositions useful for
provoking a CTL response comprising an adjuvant and an isolated
peptide consisting of the amino acid sequence of XLFGLALIEV (SEQ ID
NO: 88) wherein X may be absent or may be any amino acid,
preferably a hydrophobic amino acid, more preferably X is Ala, Val,
Leu, Ile, Pro, Phe, Met, Trp or Glu and most preferably X is a
leucine (SEQ ID NO: 77). The composition may comprise at least one
additional peptide.
[0039] This invention relates to compositions useful for provoking
a CTL response comprising an adjuvant and an isolated peptide
consisting of the amino acid sequence of ASSTLYLVF (SEQ ID NO: 89).
The composition may comprise at least one additional peptide.
[0040] This invention also relates to an isolated nucleic acid
molecule comprising a nucleotide sequence which encodes the peptide
of SEQ ID NO: 1, 2, 88, 78 or 89 or the peptides recited in Table
2, infra, preferably SEQ ID NO: 1, 2, 88, 78, or 89, with the
proviso that the isolated nucleic acid molecule which encodes the
peptide does not encode MAGE-C1 (SEQ ID NO: 73) or MAGE-C2 (SEQ ID
NO: 71). The isolated nucleic acid molecule may consist of a
nucleotide sequence that encodes a peptide consisting of the amino
acid sequence ALKDVEERX (SEQ ID NO: 1) wherein X may be any amino
acid, preferably any hydrophobic amino acid, more preferably X is
Ala, Val, Leu, Ile, Pro, Phe, Met, Trp or Glu and most preferably X
is an valine (SEQ ID NO: 3) or alanine (SEQ ID NO: 5), or the
nucleic acid molecule may consist of a nucleotide sequence that
encodes a peptide consisting of the amino acid sequence LKDVEERV
(SEQ ID NO: 2). The isolated nucleic acid molecule may consist of a
nucleotide sequence that encodes a peptide consisting of the amino
acid sequence XLFGLALIEV (SEQ ID NO: 88) wherein X is absent or any
other amino acid particularly leucine (SEQ ID NO: 77), or the
isolated nucleic acid molecule may consist of a nucleotide sequence
that encodes a peptide consisting of the amino acid sequence
ASSTLYLVF (SEQ ID NO: 89). The isolated nucleic acid molecule may
consist of a nucleotide sequence that encodes a peptide consisting
of an amino acid sequence recited in Table 2, infra. Those of skill
in the art appreciate that there is degeneracy in the genetic code
and thus more than one codon my encode a single amino acid. Those
of skill in the art also appreciate that once provided with the
amino acid sequence of a peptide it would take routine effort using
standard techniques to generate all the nucleotide sequences that
would encode a particular peptide and generate nucleic acid
molecules that encode the particular peptide without listing all
those sequences herein. Such nucleic acid molecules, which encode
the particular peptides of this invention, are also a part of this
invention.
[0041] Also an aspect of this invention is an expression vector
comprising a plurality of nucleotide sequences which encode
peptides which bind to MHC molecules, wherein at least one of said
peptides is the peptide consisting of the amino acid sequences
ALKDVEERX (SEQ ID NO: 1), wherein the X may be any amino acid
preferably any hydrophobic amino acid, more preferably X is Ala,
Val, Leu, Ile, Pro, Phe, Met, Trp or Glu and most preferably X is
valine, ALKDVEERV (SEQ ID NO: 3), or alanine (SEQ ID NO: 5) or at
least one of the peptides consists of the amino acid sequence set
forth in SEQ ID NO: 2 (LKDVEERV). At least one of the nucleotide
sequences which encodes a peptide which binds to MHC molecules may
also be a nucleotide sequence that encodes XLFGLALIEV (SEQ ID NO:
88), wherein X may be absent or any amino acid, preferably X is
leucine (SEQ ID NO: 77) or LFGLALIEV (SEQ ID NO: 78). The
nucleotide sequence which encodes a peptide which binds to the MHC
molecules may be a nucleotide sequence that encodes ASSTLYLVF (SEQ
ID NO: 89).
[0042] This invention relates to a recombinant cell transformed or
transfected with an isolated nucleic acid molecule comprising a
nucleotide sequence which encodes a peptide comprising the amino
acid sequence ALKDVEERX (SEQ ID NO: 1), wherein X may be any amino
acid, preferably any hydrophobic amino acid and more preferably X
is an alanine (SEQ ID NO: 5) or a valine (SEQ ID NO: 3),
particularly the isolated nucleic acid molecule encodes a peptide
comprising the amino acid sequence ALKDVEERV (SEQ ID NO: 3), or the
peptide comprises the sequence LKDVEERV (SEQ ID NO: 2), with the
proviso that the isolated nucleic acid molecule does not encode
MAGE-C1 (SEQ ID NO: 73) or MAGE-C2 (SEQ ID NO: 71). The recombinant
host cell may also be transformed or transfected with a nucleic
acid molecule that encodes an HLA molecule, particularly an HLA-A2
molecule.
[0043] The invention relates to a recombinant cell transformed or
transfected with an isolated nucleic acid molecule comprising a
nucleotide sequence which encodes a peptide comprising an amino
acid sequence recited in Table 2, infra. The recombinant host cell
may be transformed or transfected with a nucleic acid molecule that
encodes an HLA molecule, particularly HLA-A2.
[0044] This invention relates to a recombinant cell transformed or
transfected with an isolated nucleic acid molecule comprising a
nucleotide sequence which encodes a peptide comprising the amino
acid sequence XLFGLALIEV (SEQ ID NO: 88), wherein X may be absent
or may be any amino acid, preferably X is leucine, or LFGLALIEV
(SEQ ID NO: 78), with the proviso that the isolated nucleic acid
molecule does not encode MAGE-C1 (SEQ ID NO: 73) or MAGE-C2 (SEQ ID
NO: 71). The isolated nucleic acid molecule may consist of a
nucleotide sequence that consists of the amino acid sequence
XLFGLALIEV (SEQ ID NO: 88), wherein X may be absent or may be any
amino acid, preferably X is leucine, or LFGLALIEV (SEQ ID NO: 78),
with the proviso that the isolated nucleic acid molecule does not
encode MAGE-CL (SEQ ID NO: 73) or MAGE-C2 (SEQ ID NO: 71). The
recombinant host cell may also be transformed or transfected with a
nucleic acid molecule that encodes an HLA molecule, particularly an
HLA-A2 molecule.
[0045] This invention also relates to a recombinant cell
transformed or transfected with an isolated nucleic acid molecule
comprising a nucleotide sequence which encodes a peptide comprising
the amino acid sequence ASSTLYLVF (SEQ ID NO: 89) with the proviso
that the isolated nucleic acid molecule does not encode MAGE-C1
(SEQ ID NO: 73) or MAGE-C2 (SEQ ID NO: 71) or the nucleic acid
molecule may consist of a sequence that encodes a peptide
consisting of the amino acid sequence ASSTLYLVF (SEQ ID NO: 89).
The recombinant host cell may also be transformed or transfected
with a nucleic acid molecule that encodes an HLA molecule,
particularly an HLA-B57 molecule.
[0046] A further aspect of this invention is a recombinant cell
transformed or transfected with an expression vector comprising a
nucleic acid molecule that encodes one or more peptides that bind
to HLA molecules in operable linkage with a promoter, wherein at
least one of said peptides consists of the amino acid sequence
XLFGLALIEV (SEQ ID NO: 88), wherein X is absent or any other amino
acid, particularly leu (SEQ ID NO: 77), or ALKDVEERX (SEQ ID NO: 1)
or LKDVEERV (SEQ ID NO: 2). The final amino acid X in SEQ ID NO: 1
may be any amino acid, preferably X is any hydrophobic amino acid,
and more preferably X is alanine (SEQ ID NO: 5) or valine, e.g.,
ALKDVEERV (SEQ ID NO: 3). The recombinant host cell may also be
transformed or transfected with a nucleic acid molecule that
encodes an HLA molecule, particularly an HLA-A2 molecule, in
operable linkage with a promoter. The nucleic acid molecules that
encode the peptide and the HLA molecule may be within a single
vector or may be on separate vectors.
[0047] This invention relates to a recombinant cell transformed or
transfected with an expression vector comprising a nucleic acid
molecule that encodes one or more peptides that bind to HLA
molecules inoperable linkage with a promoter, wherein at least one
of said peptide consists of amino acid sequence recited in Table 2,
infra. The recombinant host cell may be transformed or transfected
with a nucleic acid molecule that encodes an HLA molecule,
particularly an HLA-A2. The nucleic acid molecules that encode the
HLA and peptide may be within a single vector or separate
vectors.
[0048] Another aspect of this invention is a recombinant cell
transformed or transfected with an expression vector comprising a
nucleic acid molecule that encodes one or more peptides that bind
to HLA molecules in operable linkage with a promoter, wherein at
least one of said peptides consists of the amino acid sequence
ASSTLYLVF (SEQ ID NO: 89) with the proviso that the isolated
nucleic acid molecule does not encode MAGE-CL (SEQ ID NO: 73) or
MAGE-C2 (SEQ ID NO: 71). The recombinant host cell may also be
transformed or transfected with a nucleic acid molecule that
encodes an HLA molecule, particularly an HLA-B57 molecule, in
operable linkage with a promoter. The nucleic acid molecules that
encode the peptide and the HLA molecule may be within a single
vector or may be on separate vectors.
[0049] Also an aspect of this invention are methods for determining
if a cell presents an HLA molecule, particularly an HLA-A2
molecule, on its surface comprising contacting a sample containing
said cell with a peptide consisting of the amino acid sequence
ALKDVEERX (SEQ ID NO: 1), wherein X may be any amino acid,
preferably any hydrophobic amino acid and more preferably alanine
(SEQ ID NO: 5) or valine (SEQ ID NO: 3), or a peptide consisting of
the amino acid sequence LKDVEERV (SEQ ID NO: 2), and determining
binding therebetween, wherein said binding is indicative of the HLA
molecule, e.g., HLA-A2 on the surface of said cell. Methods of this
invention for determining if a cell presents a particular HLA
molecule, e.g. an HLA-A2 molecule, on its surface also comprise
contacting a sample containing the cell to be tested with a peptide
consisting of the amino acid sequence XLFGLALIEV (SEQ ID NO: 88),
wherein X may be absent or any amino acid, particularly leucine
(SEQ ID NO: 77). The binding of the peptide to the HLA molecule,
e.g., HLA-A2, may be determined by contacting the cells with a CTL
which recognizes a complex of the peptide and the HLA, e.g.,
HLA-A2, and assaying for cell lysis by the CTLs, proliferation of
the CTLs or release of TNF-.A-inverted. by the CTLs by using
standard assays.
[0050] Also an aspect of this invention are methods for determining
if a cell presents an HLA molecule, particularly an HLA-57
molecule, on its surface comprising contacting a sample containing
said cell with a peptide consisting of the amino acid sequence
ASSTLYLVF (SEQ ID NO: 89). The binding of the peptide to the HLA
molecule may be determined by contacting the cells with a CTL which
recognizes a complex of the peptide and the HLA, e.g., HLA-B57, and
assaying for cell lysis by the CTLs, proliferation of the CTLs or
release of TNF-.A-inverted. by the CTLs by using standard
assays.
[0051] This invention also relates to an isolated polytope
molecule, wherein at least a portion of which comprises the amino
acid sequence consisting of ALKDVEERX (SEQ ID NO: 1) wherein X may
be any amino acid, preferably any hydrophobic amino acid and more
preferably X is alanine (SEQ ID NO: 5) or valine (SEQ ID NO: 3), or
the amino acid sequence consisting of LKDVEERV (SEQ ID NO: 2), or,
a portion of the polytope may comprise the amino acid sequence
consisting of XLFGLALIEV (SEQ ID NO: 88), wherein the X is absent
or any amino acid particularly leucine (SEQ ID NO: 77) or a portion
of the polytope may comprise the amino acid sequence consisting of
ASSTLYLVF (SEQ ID NO: 89). The invention also related to polytopes,
wherein at least a portion of which comprises an amino acid
sequence recited in Table 2, infra.
[0052] Also a part of this invention is a nucleic acid molecule
that encodes the polytopes of this invention, expression vectors
that comprise the nucleic acid molecules of this invention in
operable linkage with a promoter and host cells transformed or
transfected with the vectors.
[0053] This invention relates to methods for determining if a
cytolytic T cell (CTL) specific for complexes of an HLA-A2 molecule
and a peptide is present in a sample, comprising admixing said
sample with an HLA-A2 molecule and a peptide consisting of
ALKDVEERX (SEQ ID NO: 1), preferably X is any hydrophobic amino
acid and more preferably X is a valine (SEQ ID NO: 3) or an alanine
(SEQ ID NO: 5), or a peptide consisting of the sequence LKDVEERV
(SEQ ID NO: 2), or a peptide consisting of the sequence XLFGLALIEV
(SEQ ID NO: 88), wherein X may be absent or any amino acid,
particularly leucine (SEQ ID NO: 77) and determining an interaction
between the CTL and complexes of the HLA-A2 molecule and the
peptide to determine the specificity of the CTL.
[0054] This invention relates to methods for determining if a
cytolytic T cell (CTL) specific for complexes of an HLA-B57
molecule and a peptide is present in a sample, comprising admixing
said sample with an HLA-B57 molecule and a peptide consisting of
ASSTLYLVF (SEQ ID NO: 89) and determining an interaction between
the CTL and complexes of the HLA-B57 molecule and the peptide to
determine the specificity of the CTL.
[0055] Another aspect of this invention is an isolated complex
useful in isolating a cytolytic T cell. The isolated complex
comprises a first and second binding partner which are specific to
each other, wherein the second binding partner is bound to a
plurality of "tetramers" of an HLA-A2 molecule, a 82 microglobulin
molecule, and a peptide consisting of ALKDVEERX (SEQ ID NO: 1)
wherein X is any amino acid, preferably X is an alanine (SEQ ID NO:
5) or valine (SEQ ID NO: 3) or the peptide consists of LKDVEERV
(SEQ ID NO: 2). Preferably the peptide consists of the amino acid
sequence ALKDVEERX (SEQ ID NO: 1) and more preferably the peptide
consists of the amino acid sequence ALKDVEERV (SEQ ID NO: 3). The
peptide in the plurality of tetramers may also consist of the
sequence XLFGLALIEV (SEQ ID NO: 88) wherein X is absent or is any
other amino acid, particularly leucine (SEQ ID NO: 77). Preferably
the first binding partner is avidin and the second binding partner
is biotin.
[0056] Another aspect of this invention is an isolated complex
useful in isolating a cytolytic T cell. The isolated complex
comprises a first and second binding partner which are specific to
each other, wherein the second binding partner is bound to a
plurality of "tetramers" of an HLA-B57 molecule, a 12 microglobulin
molecule, and a peptide consisting of ASSTLYLVF (SEQ ID NO: 89).
Preferably, the first binding partner is avidin and the second
binding partner is biotin.
[0057] The construction of such tetramers is disclosed in U.S.
patent application Ser. No. 09/275,993 filed Mar. 24, 1999
incorporated herein by reference, see also Dunbar et al., Curr.
Biol. 8:4132-416 (1998) incorporated herein by reference. The first
binding partner may be e.g., avidin or streptavidin and the second
binding partner may be e.g., biotin. The HLA molecule and
.E-backward..sub.2 microglobulin refold into a complex which is
then biotinylated with biotin holoenzyme synthase and then combined
with labeled streptavidin or labeled avidin to produce tetrameric
structures. The tetrameric structures are mixed with the particular
peptides and the multicomponent complex ("tetramer") is then used
to identify CTL cells that are specific for the complex of HLA and
peptide. The tetramers in some circumstances may also stimulate the
CTL cells to release cytokines or proliferate. The complex may
further comprise a label. For example the first or second binding
partner may be labeled with a radiolabel, a fluorescent label or a
peptide tag such as a c-myc or His6 peptide. Methods for labeling
peptides and proteins are known in the art. See e.g., Evan et al.
Mol. Cell. Biol., 5:3610-3616 (1985) and Mukhija, "High level
production and one-step purification of biologically active human
growth hormone in Escherichia coli", Gene 165:303-306 (1995);
Goldenberg "Current status of cancer imaging with radiolabeled
antibodies, Cancer Res. Clin. Oncol., 113: 203-208 (1987); Carter
and Merchant, "Engineering antibodies for imaging and therapy",
Curr. Opin. Biotechnol., 8:449-454 (1997), and; Bailey, "Labeling
of peptides and proteins by radioiodination", Method Mol. Biol.,
32:441-448 (1994) (all incorporated herein by reference) for a
general discussion of methods useful for labeling antibody
molecules and other polypeptides for identification or isolation
purposes.
[0058] Compositions comprising the tetramers are also part of this
invention, as are methods for using the tetramers to identify CTLs
which recognize specific HLA/peptide complexes and to methods of
stimulating the CTLs with the tetramers. The composition may also
comprise a carrier, and/or an adjuvant. The carrier and adjuvant
may be any that are pharmaceutically acceptable and routinely used
in the art. E.g. the carrier may be DMSO and the adjuvant may be
GM-CSF or IL-12.
[0059] A further aspect of this invention are methods for
identifying or isolating cytolytic T cells in a sample, comprising
admixing the sample with the complex described above, and
identifying or isolating CTLs which bind thereto. Methods for
determining the presence of a CTL in a sample are well known in the
art. For example, one may assay for proliferation of the CTL cells
in response to exposure to the complex or one may assay the sample
admixed with the complex for lysis of cells expressing a complex of
the peptide and an HLA molecule or one may assay for the release of
TNF by the CTLs. See e.g. Herin et al., Int. J. Cancer 39: 390-396
(1987); Been et al. J. Exp. Med. 152: 1184-1193 (1980) and;
Traversari et al., Immunogenetics 35:145-152 (1992) all
incorporated herein by reference.
[0060] Still another aspect of this invention is a method for
monitoring status of a tumor presenting complexes of a peptide and
an HLA molecule, particularly the peptides of this invention and
HLA-A2 or HLA-B57, comprising contacting a sample taken from a
patient with a tumor with the isolated complexes described above
and assaying the level of CTL response in the sample. That response
is then compared to a control, e.g., the CTL response measured in a
sample from a patient having tumors presenting the complexes and
having a known status or a sample from a patient who has no
detectable tumors. By monitoring the magnitude of the response by
the CTLs in the sample from the test patient as compared to the
controls one may monitor the status of the tumor in the test
patient.
[0061] The peptides of this invention either alone or in complex
with an HLA molecule, e.g. HLA-A2 or HLA-B57, are useful for
inducing an immune response in a subject in need thereof, e.g., the
production of antibodies or the stimulation of CTLs, which result
in tumor regression or in slowing the progression of the tumor
wherein the tumors present complexes of peptide and HLA. Methods
for inducing an immune response in a subject may comprise
administering a composition comprising a peptide of this invention
or complexes of the peptide and HLA molecules, e.g., cells
presenting an HLA/peptide complex on their surfaces or tetramers as
described above, to a subject wherein the amount of the composition
administered is sufficient to induce an immune response, either
humoral or cellular, which results in tumor regression or in
slowing the progression of the tumor.
[0062] If cells expressing the peptide are administered to a
subject they should be cells that do not have harmful effects on
the subject, e.g., the cells may be irradiated such that they do
not proliferate in the subject but still display the complex of HLA
and peptide, and the cells should be non-tumorigenic. The cells may
be autologous and may be transfected with a nucleic acid molecule
that encodes the peptide or may be transfected with a nucleic acid
molecule that encodes the HLA molecule, e.g., HLA-A2 or HLA-B57.
The cells may also be transfected with a nucleic acid molecule that
encodes both the peptide and the HLA molecule.
[0063] An agent that provokes a response by a CTL specific for the
peptide HLA complexes described herein, e.g., the peptides,
polytope or tetramer complexes of the peptides and HLA molecules of
this invention, compositions comprising the peptides, polytopes or
complexes of this invention, or cells expressing the complex of HLA
and peptide, e.g., cells transfected with nucleic acid molecules
that encode the HLA and/or the peptide, preferably a MAGE-C2 or
MAGE-C1 derived peptide, or the protein, preferably MAGE-C2 or
MAGE-C1, that is processed into the peptides, may be used in
treating a subject with a disorder. Preferably the disorder is
characterized by the presence of complexes of an HLA molecule,
particularly an HLA-A2 or HLA-B57 molecule, and a peptide of this
invention, particularly a peptide having an amino acid sequence
selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2,
SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID
NO: 88 and SEQ ID NO: 89, presented on cell surfaces.
[0064] This invention relates to a method for treating a subject
with a disorder characterized by the presence of complexes of an
HLA molecule, particularly an HLA-A2 molecule, and a peptide of
this invention, particularly a peptide having an amino acid
sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID
NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78,
SEQ ID NO: 88 and SEQ ID NO: 89, presented on cell surfaces by
administering the peptides of this invention to the subject in an
amount that is sufficient to stimulate CTLs specific for complexes
of an HLA and the peptide in sufficient numbers to alleviate the
disorder. The peptide may be administered in conjunction with an
adjuvant or may also be a part of a composition comprising one or
more additional HLA-binding peptides. The generation and
proliferation of the CTLs may be monitored by any means known in
the art.
[0065] This invention further relates to a method for treating a
subject with a disorder characterized by the presence of complexes
of an HLA molecule, particularly HLA-A2 or HLA-B57, and a peptide
of this invention, particularly one selected from the group
consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO:
5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 or SEQ ID NO: 89, on
cell surfaces by administering an amount of cytolytic T cells,
which are specific for the complexes of the HLA molecule and the
peptide, to the subject wherein the amount of CTLs is sufficient to
alleviate the disorder.
[0066] This invention also relates to methods for monitoring or
detecting CTLs in a sample that are specific for a complex of the
peptides of this invention, particularly SEQ ID NO: 1, SEQ ID NO:
2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID
NO: 88 or SEQ ID NO: 89 and an HLA molecule, e.g., HLA-A2 or
HLA-B57 molecule. One method for detecting a CTL specific for a
such complexes may comprise: (a) contacting a cytolytic T
cell-containing sample with a composition comprising cells
presenting a complex of the HLA molecule, e.g. an HLA-A2 or HLA-B57
molecule, and the isolated peptide and (b) determining if a CTL in
the CTL containing sample recognizes the cells presenting the
complex of HLA and the isolated peptide, wherein recognition of the
complex indicates the presence of a CTL specific for that complex.
Recognition of the complex by a CTL may be manifested by lysis of
the presenting cells, proliferation of CTLs in the sample or by
release of TNF.A-inverted. by CTLs in the sample. The CTL
containing sample may be from a subject having, or suspected of
having, a disorder characterized by the presentation of the
peptide/HLA complexes on the surfaces of cells associated with the
disorder.
[0067] The cells which express the HLA/peptide complex on their
surfaces may be transfected or transformed with a nucleic acid
molecule which encodes the peptide. Alternatively, the cells may be
transfected with a single expression vector comprising a nucleic
acid molecule that encodes the peptide and a nucleic acid molecule
that encodes the HLA molecule, e.g. an HLA-A2 or HLA-B57 molecule.
Alternatively the cells may be transfected with separate expression
vectors encoding the HLA molecule or the peptide.
[0068] Another aspect of this invention are polytopes comprising
one or more of the peptides of this invention. Polytopes are groups
of two or more potentially immunogenic or immune stimulating
peptides, which can be joined together in various ways, to
determine if this type of molecule will stimulate and/or provoke an
immune response. Preferably the polytope comprises a peptide
consisting of the amino acid sequence set forth in SEQ ID NO: 1,
SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO:
78, SEQ ID NO: 88 or SEQ ID NO: 89, or the polytope comprises a
peptide consisting of the amino acid sequence set forth in SEQ ID
NO: 1, a peptide consisting of the amino acid sequence set forth in
SEQ ID NO: 2, and a peptide consisting of the amino acid sequence
set forth in SEQ ID NO: 3, a peptide consisting of the amino acid
sequence set forth in SEQ ID NO: 5, a peptide consisting of the
amino acid sequence set forth in SEQ ID NO: 77, a peptide
consisting of the amino acid sequence set forth in SEQ ID NO: 78,
and a peptide consisting of the amino acid sequence set forth in
SEQ ID NO: 88 and a peptide consisting of the amino acid sequence
set forth in SEQ ID NO: 89.
[0069] Also a part of the invention are so-called "minigenes,"
i.e., nucleic acid molecules consisting of a nucleotide sequence
that encodes the peptide of interest. The peptides of this
invention are of a length that permits simple construction of all
degenerate nucleotide sequences that encode the epitope of
interest. The nucleic acid molecules consisting of these degenerate
nucleotide sequences are also part of this invention and can be
made a part of an extended "polytopic" sequence, using methods well
known in the art, and can be incorporated into coding vectors where
the minigene or genes of interest are operably linked to a
promoter, for expression in a host cell.
[0070] The minigenes can also be used in concert with nucleotide
sequences that encode an HLA molecule of interest, such as HLA-A2
or HLA-B57, coding sequence. The two sequences can constitute part
of a single vector, or a pair of vectors, which are then used in a
kit or some other combination that permits the skilled artisan to
use them to stimulate a T cell response, and so forth.
[0071] Similarly, one can envision treatment methods that employ
dendritic cells, pulsed with the peptides of this invention, as
well as cells which have been treated so as to present relevant
complexes on their surfaces, see for example U.S. Pat. No.
6,251,603 issued Jun. 26, 2001 incorporated herein by reference.
Such cells may be transformed or transfected with a tumor rejection
antigen precursor TRAP gene, e.g., MAGE-C2 or a TRAP "minigene" or
"minigenes", which encodes only relevant HLA-binding peptides such
as tumor rejection antigens, and/or may be transfected or
transformed with a relevant HLA-molecule encoding sequence, such as
HLA-A2 or HLA-B57. If appropriate, such cells may be irradiated
prior to administration.
[0072] Also an aspect of this invention are "functional variants"
of the peptides of this invention, particularly functional variants
of the MAGE-C2 HLA class I-binding peptide consisting of the
sequence set forth in SEQ ID NO: 1, 2, 3, 5, 77, 78, 88 or 89. As
used herein, a "functional variant" or "variant" of the peptides of
this invention, particularly a peptide consisting of the sequence
set forth in SEQ ID NO: 1, 2, 3, 5, 77, 78, 88 and 89 is a peptide
which contains one or more modifications to the primary amino acid
sequence of the peptide, and yet has similar HLA class I and T cell
receptor binding properties as compared to the unmodified peptide.
The modifications may be an alteration in the amino acid sequence
of the peptide such that the sequence differs from the unmodified
peptide and yet the variant has similar HLA binding properties and
a similar ability to induce a CTL response. The modifications may
also be a chemical modification of the peptide, e.g., a moiety may
be added to either end of the peptide to inhibit proteolytic
degradation or a peptidic bond may be altered to enhance resistance
to proteolysis. A further aspect of this invention are nucleic acid
molecules which encode the functional variants, expression vectors
comprising the nucleic acid molecules encoding the variants and to
the cells transformed or transfected with a nucleic acid molecule
which encodes the variant as well as method for producing the
variants synthetically or recombinantly.
DETAILED DESCRIPTION OF THE INVENTION
[0073] This invention relates to peptides of MAGE-C2, particularly
peptides consisting of an amino acid sequence selected from the
group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 (which
is SEQ ID NO: 1 wherein X is an valine), or SEQ ID NO: 5 (which is
SEQ ID NO: 1 wherein X is alanine), SEQ ID NO SEQ ID NO: 88, SEQ ID
NO: 77 (which is SEQ ID NO: 88 wherein X is leucine), SEQ ID NO: 78
(which is SEQ ID NO: 88 wherein X is absent) and SEQ ID NO: 89. The
peptides may be produced synthetically using standard techniques
known in the art e.g., manufactured by good manufactorial practice
guidelines (Multiple Systems, San Diego), or may be produced
recombinantly using an expression vector that comprises a nucleic
acid molecule that encodes the peptide in operable linkage with a
promoter.
[0074] This invention also relates to nucleic acid molecules
encoding the peptides of this invention. Oligonucleotides encoding
the peptides of this invention can be easily prepared using methods
that are standard in the art. Expression vectors comprising the
isolated nucleic acid molecule of this invention in operable
linkage with a promoter are also contemplated herein. The
expression vector may be any that is known in the art, e.g., a
plasmid, a cosmid, a bacteriophage or a viral vector. The nucleic
acid molecule may be operatively linked to any promoter known in
the art. Those of skill in the art are well-versed in recombinant
DNA technologies and would appreciate that many different promoters
are available and the choice of promoter should be one that is
compatible with a particular host environment.
[0075] Also a part of this invention are host cells transformed or
transfected with the nucleic acid molecules and expression vectors
of this invention. Host cells may be any that are used routinely in
the art, e.g. bacterial cells, e.g., E. coli, insect cells,
mammalian cells, e.g., mouse, hamster, rat, cat, dog, horse, pig,
monkey or human, avian cells, e.g., chicken, duck or goose, or
plant cells, e.g. soy bean, tobacco, rice, wheat or corn. Methods
for the transformation or transfection of particular host cells are
well known in the art and need not be described in detail
herein.
[0076] The peptides of this invention may be incorporated into
polytopes. Two or more peptides of this invention can be joined
together directly, or via the use of flanking sequences. See
Thompson et al., Proc. Natl. Acad. Sci. USA 92(13): 5845-5849
(1995), teaching the direct linkage of relevant epitopic sequences.
The use of polytopes as vaccines is well known. See, e.g. Gilbert
et al., Nat. Biotechnol. 15(12): 1280-1284 (1997); Thomson et al.,
supra; Thomson et al., J. Immunol. 157(2): 822-826 (1996); Tam et
al., J. Exp. Med. 171(1): 299-306 (1990), all of which are
incorporated by reference. The Tam reference in particular shows
that polytopes, when used in a mouse model, are useful in
generating both antibody and protective immunity. Further, the
reference shows that the polytopes, when digested, yield peptides
which can be and are presented by HLAs. Tam demonstrates this by
showing recognition of individual epitopes processed from polytope
`strings` via CTLs. This approach can be used, e.g., in determining
how many epitopes can be joined in a polytope and still provoke
recognition and also to determine the efficacy of different
combinations of epitopes. Different combinations may be
`tailor-made` for patients expressing particular subsets of tumor
rejection antigens. These polytopes can be introduced as
polypeptide structures, or via the use of nucleic acid delivery
systems. To elaborate, the art has many different ways available to
introduce DNA encoding an individual epitope, or a polytope such as
is discussed supra. See, e.g., Allsopp et al., Eur. J. Immunol.
26(8); 1951-1959 (1996), incorporated by reference. Adenovirus,
pox-virus, Ty-virus like particles, plasmids, bacteria, etc., can
be used. One can test these systems in mouse models to determine
which system seems most appropriate for a given, parallel situation
in humans. They can also be tested in human clinical trials.
[0077] The peptides of this invention either alone or in complex
with an HLA molecule, particularly HLA-A2 or HLA-B57, are useful
for inducing an immune response in a subject, either humoral or
cellular. The peptides may induce an immune response that may be
either protective, diagnostic or therapeutic. The methods for
inducing an immune response in a subject comprise administering a
composition comprising an amount of a peptide of this invention in
an amount that is sufficient to induce an immune response. The
composition may comprise complexes of the inventive peptides and an
HLA molecule, or e.g., the composition may comprise cells which
present the peptides in complex with an HLA molecule. Methods for
immunizing a subject with a composition are well known in the art,
see e.g., Jager et al. PNAS 97(9): 12198-12203 (Oct. 24, 2000)
incorporated herein by reference. The composition may comprise one
or more additional peptides that bind to HLA molecules. The
additional peptide may be one that binds to a Class I or a Class II
major histocompatibility molecule (MHC).
[0078] If cells presenting a complex the HLA and the inventive
peptides are administered to a subject, they should be cells that
do not have harmful effects on the subject, e.g., the cells may be
irradiated to insure they do not proliferate or the cells may be
non-tumorigenic. The cells expressing the HLA/peptide may be
autologous and may be transfected with a nucleic acid molecule that
encodes the peptide. If the presenting cells do not naturally
express a particular HLA molecule, e.g. HLA-A2 or HLA-B57, the
cells may also be transfected with a nucleic acid molecule that
encodes the HLA. Alternatively the presenting cells may be
transfected with a nucleic acid molecule that encodes both the
peptide and HLA molecule. Likewise the polytopes and peptide
analogs of this invention, which form complexes with the HLA that
are recognized by the CTLs that recognize complexes of the HLA and
a peptide having an amino acid sequence of SEQ ID NO: 1, SEQ ID NO:
2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID
NO: 88 or SEQ ID NO: 89, may also be used to induce an immune
response in a subject, preferably a subject with a disorder
characterized by the presentation of an HLA and a peptide having
the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2,
SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID
NO: 88 and SEQ ID NO: 89. For example the subject may have a
cancer, or suspected of having cancer, wherein the cancer cells
express the HLA/peptide complex on their surfaces.
[0079] Compositions which comprise the peptides, peptide analogs,
polytopes, tetramer complexes or CTLs of this invention may further
comprise a carrier, and/or an adjuvant. The carrier and adjuvant
may be any that are routinely used in the art and are
pharmaceutically acceptable. E.g. the carrier may be DMSO and the
adjuvant may be GM-CSF or IL-12. A pharmaceutically or
therapeutically acceptable or suitable carrier is preferably one
that does not interfere with the effectiveness of the biological
activity of the active components and which is not toxic to the
subject.
[0080] The immunogenicity of peptides may be assayed by a variety
of methods routinely used by one of skill in the art, see e.g.,
Jager et al. PNAS, 97(9):4760-4765 (Apr. 25, 2000) incorporated
herein by reference and Jager et al., (Oct. 24, 2000) supra. The
immunogenicity may be assayed in vitro by their ability to
stimulate peripheral blood lymphocytes that are positive for the
desired HLA molecule, e.g., HLA-A2 or HLA-B57. The peripheral blood
lymphocytes are preferably from healthy HLA-A2 or HLA-B57 donors.
Many assays are known in the art for determining if a CTL cell is
stimulated by a cell that is presenting an HLA/peptide complex,
e.g., ELISPOT, cytotoxicity assays and DTH assays (Jager et al.
(April 2000) supra and Jager et al. (October 2000) supra). When a
CTL cell recognizes a particular HLA-peptide complex it is
activated and this activation is manifested by, e.g., CTL
proliferation, lysis of cells presenting a complex of HLA, e.g.,
HLA-A2 or HLA-B57, and the peptide by the activated CTL, and
release of cytokines by the activated CTLs. The release of
cytokines may be assayed by e.g., ELISPOT. The activation of the
CTLs may also be detected by admixing the CTL cell containing
sample with a tetramer, as described supra, that is composed of a
the peptide of this invention, an HLA molecule, particularly an
HLA-A2 or HLA-B57 molecule, a .E-backward..sub.2-microglobulin and
biotin, which may then be labeled with a molecule such as e.g.
avidin or streptavidin (see U.S. application Ser. No. 09/725,993,
incorporated herein by reference, for a description of the
generation and use of such tetramers.) Preferably the tetramer
comprises HLA-A2 or HLA-B57, a peptide of this invention,
particularly a peptide consisting of the sequence set forth in SEQ
ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77,
SEQ ID NO: 78, SEQ ID NO: 88 and SEQ ID NO: 89, and biotin. Such
tetramers, as well as compositions comprising the tetramers and
methods for their use are also aspects of this invention.
[0081] In a method for identifying T cells, such as CTLs which are
specific for a peptide/HLA complex, where the peptide derives from
a protein of interest, a sample believed to contain relevant CTLs
is contacted to an antigen presenting cell, such as a dendritic
cell, which has been infected with a first viral vector that
encodes the protein of interest. Following this contact, the CTLs
are then contacted with a second population of antigen presenting
cells which have been, e.g., infected with a second viral vector
which also encodes the protein of interest, where the second viral
vector is different from the first viral vector. One benefit
derived from this approach is that any immune response can be more
refined in that it is targeted to the antigen rather than any
aspect of the viruses. Preferably, the first viral vector is an
adenovirus vector, preferably one that is non replicative, and the
second vector is a vaccinia vector. It will be understood, however,
that these may be reversed, and that only one of these two choices
can be used, in combination with a second virus that differs from
one of these two choices. The method requires an antigen presenting
cell, such as a dendritic cell, or some other cell type capable of
presenting complexes of an HLA molecule and a peptide on its
surface. In practice, the method preferably involves the use of
autologous cells, i.e., antigen presenting cells and CTLs from the
same patient, but the method can be carried out with allogeneic
cells as well. Use of the method permits one to identify epitopes
that are restricted by their presenting HLA molecule.
[0082] The methods of this invention are particularly useful for
detecting the presence of, and monitoring the proliferation of,
CTLs in a cell sample taken from a subject having a disorder, or
suspected of having a disorder, e.g., a cancer, associated with the
presentation of complexes of HLA and a peptide having an amino acid
sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ
ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 or SEQ ID NO:
89 on the surfaces of cells associated with that disorder, wherein
the CTLs are specific for the complex an HLA molecule, e.g. HLA-A2
or HLA-B57, and a peptide having an amino acid sequence set forth
in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID
NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 or SEQ ID NO: 89. The subject
may be monitored for the generation and proliferation of CTLs by
assaying cell samples from the subject at various times to
determine the number of CTLs that are specific for a particular
complex of the HLA and peptide and to determine if that number is
increasing or decreasing over time. In particular, the peptide of
this invention may be administered to the subject and then the
subject may be monitored for a response by CTLs and for their
subsequent proliferation. The peptide may be administered to the
subject in a form where it is not in complex with an HLA molecule
or it may be administered in complex with the HLA molecule,
particularly HLA-A2 or HLA-B57. The peptide may be administered
with any pharmaceutically suitable carrier, and may also be
administered with a pharmaceutically acceptable adjuvant, e.g.,
GM-CSF or IL-12. Intact cells or cell parts that present the
complex of HLA and peptide on their surface may be administered to
the subject in a pharmaceutically acceptable carrier. The method is
particularly useful for a subject who has cancer cells that express
a MAGE, particularly MAGE-C2, and particularly one whose cells
express HLA-A2 or HLA-B57 as well.
[0083] CTLs per se that are specific for a complex of an HLA,
particularly HLA-A2 or HLA-B57, and a peptide having an amino acid
sequence as set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3,
SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 or SEQ ID
NO: 89, are also an aspect of this invention. The CTLs are useful
in adoptive transfer wherein the CTLs are administered to a subject
in need thereof in an amount that is sufficient for the CTLs to
recognize cells presenting the complex and lysing the cells. The
CTLs are also useful for identifying cells that present complexes
of HLA, e.g. HLA-A2 or HLA-B57, and the peptides or peptide analogs
of this invention.
[0084] This invention also relates to a method for treating a
subject with a disorder characterized by the presence of complexes
of an HLA molecule, e.g. HLA-A2 or HLA-B57 molecules, and a peptide
having an amino acid sequence consisting of an amino acid sequence
selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 2,
SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID
NO: 88 and SEQ ID NO: 89, on the surfaces of cells associated with
the disorder. The method comprises administering to the subject an
amount of cytolytic T cells, which are specific for complexes of
the HLA molecules and the peptide, wherein the amount is sufficient
to alleviate the disorder. The peptides, peptide analogs or
polytopes may be administered to the subject in an amount that is
sufficient to stimulate CTLs and alleviate the symptoms of the
disorder.
[0085] Therapeutically or pharmaceutically effective amount as it
is applied to the peptides, functional variants of the peptide,
tetramers, compositions and CTLs of this invention refers to the
amount of the peptides, functional variants of the peptides,
tetramers, compositions and CTLs of this invention that is
sufficient to induce a desired biological result. The biological
result may be the alleviation of the signs, symptoms or causes of a
disease, or any other desired alteration of a biological system. In
the present invention that amount may be sufficient to induce an
immune response such as the production of antibodies specific for
the peptides or peptide analogs of this invention or a response by
CTL cells, e.g., their proliferation or their lysis of target cells
expressing an appropriate HLA/peptide complex, or sufficient to
alleviate the symptoms of a disorder characterized by the
expression of a complex of HLA, particularly HLA-A2 or HLA-B57, and
a peptide consisting of the amino acid sequence set forth in SEQ ID
NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ
ID NO: 78, SEQ ID NO: 88 or SEQ ID NO: 89.
[0086] An analysis of other members of the MAGE family, e.g.,
MAGE-C1, A10, A11, B1, B3 and B4 reveal peptide sequences that are
homologous to the ALKDVEERV MAGE-C2 peptide described herein. Table
1 presents several of these peptides, their amino acid sequence and
ligation strength to HLA-A*0201.
TABLE-US-00001 TABLE 1 Mage-C2 Peptide Homologs Ligation SEQ ID
Protein Peptide strength* NO: Mage-C2 ALKDVEERV 22 3 Mage-C1
ALKDVEERA 16 5 Mage-A10 ALKDEEERA 17 6 Mage-A11 ALREEGEGV 25 7
Mage-B1, -B4 ALRDEEERA 17 8 Mage-B3 ALRDEEERV 23 9 *Ligation
strength to HLA-A*0201 according to the SYFPEITHI database. (see,
Rammensee et al., SYFPEITHI: database for MHC ligands and peptide
motifs. Immunogenetics. 1999 Nov; 50(3-4): 213-9 and
syfpeithi.bmi-heidelberg.com both incorporated herein by
reference)
[0087] Interestingly, the MAGE-C1 and C2 peptides differ by only a
single amino acid, i.e., the 9.sup.th residue is valine in the
MAGE-C2 peptide and alanine in the MAGE-C1 peptide. Thus, we
predict that an HLA complex comprising the MAGE-C1 peptide will be
recognized by the CTL clone 606 C/22.2. It has previously been
shown that for the NY-ESO-1 tumor antigen a T-cell clone retained
its recognition after an amino acid substitution at position 9 of
the peptide.
[0088] Since the MAGE family are known antigens with appropriate
tumor expression profiles it follows that homologous peptides
derived from these antigens might also be recognized by T cells, as
has been observed with other homologous MAGE peptides from Mage-A1
(EADPTGHSY SEQ ID NO: 10) and MAGE-A3 (EVDPIGHLY SEQ ID NO: 11),
see U.S. Pat. No. 5,405,940.
[0089] A MAGE-C2 peptide (SEQ ID NO: 3) is naturally processed and
presented by HLA-A2 on the surface of tumor cells and recognized by
specific T cells. Thus it is expected that the homologous MAGE-C1
peptide (SEQ ID NO: 5) which has a single conservative substitution
at the C-terminal residue (position 9), would also be presented by
HLA-A2 and recognized by T cells. Gure et al. and Chen et al. infra
demonstrate that some cancer patients display both a T cell
response to MAGE-C2 (CT10) (SEQ ID NO: 71) or to MAGE-C1 (CT7) (SEQ
ID NO: 73) and a humoral response to the proteins (Gure et al.,
Int. J. Canc. 85:726-732 (2002) and Chen et al. PNAS
95(12):6919-6923 (1998)) demonstrating the strong immunogenic
properties of the proteins. Based on the disclosure herein, we
expect additional homologous peptides derived from other members of
the MAGE family (SEQ ID No: 6 to 9, Table 1) to form HLA/peptide
complexes that are targets for cytolytic T cells. As such the
peptides disclosed in Table 1 and their use in diagnostic and
therapeutic assays as disclosed herein are also a part of this
invention.
[0090] An analysis of the peptide sequences listed in Table 1
identified an immunogenic motif, i.e., ALXXXXEXX (SEQ ID NO: 12)
where the X's represent two alternative amino acids: X at position
3 is Arg (R) or Lys (K), X at position 4 is Asp (D) or Glu (E), X
at position 5 is Val (V) or Glu (E), X at position 6 is Glu (E) or
Gly (G), X at position 8 is Gly (G) or Arg (R) and X at position 9
is Ala or Val. A list of all 64 possible peptides is shown in Table
2.
TABLE-US-00002 TABLE 2 Possible peptides from the immunogenic
motif. Peptide SEQ ID NO Peptide SEQ ID NO ALRDVEERV 13 3 ALRDVEERA
14 ALKDVEERA 5 ALRDVEEGA 15 ALKDVEEGA 42 ALRDVEEGV 16 ALKDVEEGV 43
ALRDVGERV 17 ALKDVGERV 44 ALRDVGERA 18 ALKDVGERA 45 ALRDVGEGA 19
ALKDVGEGA 46 ALRDVGEGV 20 ALKDVGEGV 47 ALRDEEERV 9 ALKDEEERV 48
ALRDEEERA 8 ALKDEEERA 6 ALRDEEEGA 21 ALKDEEEGA 49 ALRDEEEGV 22
ALKDEEEGV 50 ALRDEGERV 23 ALKDEGERV 51 ALRDEGERA 24 ALKDEGERA 52
ALRDEGEGA 25 ALKDEGEGA 53 ALRDEGEGV 26 ALKDEGEGV 54 ALREVEERV 27
ALKEVEERV 55 ALREVEERA 28 ALKEVEERA 56 ALREVEEGA 29 ALKEVEEGA 57
ALREVEEGV 30 ALKEVEEGV 58 ALREVGERV 31 ALKEVGERV 59 ALREVGERA 32
ALKEVGERA 60 ALREVGEGA 33 ALKEVGEGA 61 ALREVGEGV 34 ALKEVGEGV 62
ALREEEERV 35 ALKEEEERV 63 ALREEEERA 36 ALKEEEERA 64 ALREEEEGA 37
ALKEEEEGA 65 ALREEEEGV 38 ALKEEEEGV 66 ALREEGERV 39 ALKEEGERV 67
ALREEGERA 40 ALKEEGERA 68 ALREEGEGA 41 ALKEEGEGA 69 ALREEGEGV 7
ALKEEGEGV 70 The MAGE-C2 peptide is indicated in bold italics and
other peptides from Table 1 are indicated with italics.
[0091] Recent analysis suggests that homologous peptides which bind
to more than one HLA molecules will induce a T cell response. This
has been demonstrated for the MAGE-A1 (EADPTGHSY SEQ ID NO: 10) and
MAGE-A3 (EVDPIGHLY SEQ ID NO: 11) peptides and the HLA molecule
HLA-A1 and HLA-B35, see U.S. Pat. No. 5,405,940, Schultz E. et al.
Tissue Antigens. 2001 February; 57(2):103-9 and Luiten R. et al.
Tissue Antigens. 2000 July; 56(1):77-81 all incorporated herein by
reference. Thus the peptide(s) in Table 1 which bind to other HLA
molecules in addition to HLA-A2, such as HLA-A1, A3, A26, B7, B8,
B15, B27, B44, or B51 are likely to be peptides that stimulate a
CTL response. Methods for determining if a peptide binds to a
particular HLA molecule are well known in the art.
[0092] Also an aspect of this invention are "functional variants"
of the peptides of this invention, particularly functional variants
of the MAGE-C2 HLA class I-binding peptide consisting of the
sequence set forth in SEQ ID NO: 1, 2, 3, 5, 77, 78, 88 or 89. As
used herein, a "functional variant" or "variant" of the peptides of
this invention, particularly a peptide consisting of the sequence
set forth in SEQ ID NO: 1, 2, 3, 5, 77, 78, 88 or 89 is a peptide
which contains one or more modifications to the primary amino acid
sequence of an unmodified peptide, and yet has similar HLA class I
and T cell receptor binding properties as compared to the
unmodified peptide. Thus another aspect of this invention is the
modification of MAGE-C2 HLA class I binding peptides to generate
variants which have, e.g., (1) an enhanced stability in a
preselected expression system or enhanced stability of
protein-protein binding, such as HLA-peptide binding, as compared
to the unmodified peptide; (2) a novel activity or property, e.g.,
a variant of a MAGE-C2 HLA class I-binding peptide which contains
an antigenic epitope or a detectable moiety; or (3) a different
amino acid sequence as compared to the unmodified peptide yet
displays the same or similar T cell stimulatory properties as the
unmodified MAGE-C2 HLA class I-binding peptide. Modified MAGE-C2
HLA class I binding peptides can be obtained by mutating a nucleic
acid molecule that encodes the unmodified form of the peptide by
e.g., introducing deletions, point mutations, or insertions, which
result in a truncated peptide, or a peptide having an altered amino
acid sequence, e.g., deletions, insertions or substitutions of one
or more amino acids as compared to the unmodified peptide.
Alternatively, modified MAGE-C2 HLA-class I binding peptides can be
generated by directly modifying the peptide, e.g., by cleaving the
peptide, adding a linker molecule, adding a detectable moiety,
e.g., biotin, adding a fatty acid, substituting one amino acid for
another and the like. Variants of the peptides also embrace fusion
proteins comprising all or part of the MAGE-C2 HLA class I binding
peptide amino acid sequence and a fusion partner.
[0093] The variants of the peptides include for example, peptides
that do not have the sequence set forth in SEQ ID NO: 1, SEQ ID NO:
2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID
NO: 88 or SEQ ID NO: 89, and yet form complexes with HLA molecules,
particularly an HLA-A2 or HLA-B57 molecule, and stimulate cytolytic
T cells (CTLs) that are specific for complexes of the HLA and a
peptide consisting of an amino acid sequence selected from the
group consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ
ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 and SEQ ID
NO: 89. The peptides may be, e.g., from 8-11 amino acids in length
and preferably comprise at least 8 contiguous amino acids of the
sequences set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3,
SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 and SEQ
ID NO: 89.
[0094] The amino acid sequence of MAGE-C2 HLA class I binding
peptides may be of natural or non-natural origin, that is, they may
comprise a natural MAGE-C2 HLA class I binding peptide molecule or
may comprise a modified sequence as long as the amino acid sequence
retains the ability to stimulate T cells when presented and retains
the property of binding to an HLA class I molecule such as an
HLA-A2 or HLA-B57 molecule. For example, MAGE-C2 HLA class I
binding peptides in this context may be fusion proteins of a
MAGE-C2 HLA class I binding peptide and unrelated amino acid
sequences, synthetic peptides of amino acid sequences of MAGE C2
set forth in SEQ ID NO: 71 or the MAGE-C2 peptides sequences set
forth in SEQ ID NO: 3 and SEQ ID NO: 77, labeled peptides, peptides
isolated from patients with a MAGE-C2 expressing cancer, peptides
isolated from cultured cells which express MAGE-C2, peptides
coupled to nonapeptide molecules (for example in certain drug
delivery systems) and other molecules which include the amino acid
sequences of the MAGE-C2 peptides set forth in SEQ ID NO: 3 and SEQ
ID NO: 77.
[0095] Preferably, MAGE-C2 HLA class I binding peptides are
non-hydrolyzable. To provide such peptides, one may select MAGE-C2
HLA class I binding peptides from a library of non-hydrolyzable
peptides, such as peptides containing one or more D-amino acids or
peptides containing one or more non-hydrolyzable peptide bonds
linking amino acids. Many non-hydrolyzable peptide bonds are known
in the art, along with procedures for synthesis of peptides
containing such bonds. Non-hydrolyzable bonds include
.THETA.(CH.sub.2NH)-reduced amide peptide bonds,
.THETA.(COCH.sub.2)-- ketomethylene peptide bonds,
.THETA.(CH(CN)NH)-(cyanomethylene)amino peptide bonds,
.THETA.(CH.sub.2CH(OH))-hydroxyethylene peptide bonds,
.THETA.(CH.sub.2O)-peptide bonds, and
.THETA.(CH.sub.2S)-thiomethylene peptide bonds. Methods for
determining such functional variants are provided in U.S. Pat. No.
6,087,441, incorporated herein by reference.
[0096] Among the variants having a change in an amino acid of
MAGE-C2 set forth in SEQ ID No: 71 or the MAGE-C2 peptides set
forth in SEQ ID NO: 3 and SEQ ID NO: 77, functional variants of the
MAGE-C2 HLA class I binding peptide having conservative amino acid
substitutions are preferred, i.e., substitutions which retain a
property of the original amino acid such as charge, hydrophobicity,
conformation, etc. Examples of conservative substitutions of amino
acids include substitutions made amongst amino acids within the
following groups: (a) Met, Ile, Leu, Val; (b) Phe, Tyr, Trp; (c)
Lys, Arg, H is; (d) Ala, Gly; (e) Ser, Thr; (f) Gln, Asn; and (g)
Glu, Asp.
[0097] The peptides of this invention may be chemically modified
with protective groups at one or both ends, or one or more peptide
bonds may be replaced with non-peptide bonds to produce variants
that are less susceptible to proteolytic cleavage than the
non-modified peptides. For example, one or more peptide bonds may
be replaced with an alternative type of covalent bond (e.g., a
carbon-carbon bond or an acyl bond). Where proteolytic degradation
of the peptide following administration to a subject is a problem,
the sensitive peptide bonds may be replaced to increase the
stability of the peptide and increase its usefulness as a
therapeutic. Peptidase sensitive bonds may be determined by
standard methods, see for example, application 60/290,646
incorporated herein by reference. Methods of incorporating various
types of bonds into peptides, are well known in the art and need
not be described in detail here. Peptide analogs may also be
generated by incorporating amino-terminal or carboxyl terminal
blocking groups such as t-butyloxycarbonyl, acetyl, alkyl,
succinyl, methoxysuccinyl, suberyl, adipyl, azelayl, dansyl,
benzyloxycarbonyl, fluorenyl methoxycarbonyl, methoxyazelayl,
methoxyadipyl, methoxysuberyl, and 2,4-dinitrophenyl, thereby
rendering the peptide analog or mimetic less susceptible to
proteolysis. Non-peptide bonds and carboxyl- or amino-terminal
blocking groups can be used singly or in combination to render the
peptide analog less susceptible to proteolysis than the
corresponding peptide. Peptide with modifications such as
.E-backward.-a.a. (.E-backward.-amino acid), d-a.a., Me-a.a. or
.alpha.NMe-a.a. may be synthesized by incorporation of a
corresponding modified amino acid. Many modified amino acids are
commercially available (see, e.g., Bachem A G, Budendorf,
Switzerland (NMe-a.a.), Fluka Chemie GmbH, Bush, Switzerland
(.alpha.-a.a.), Acros Organic France, Noisy-Le-Grand, France
(dMe-a.a). Me amino acid are often sold in a racemic form, and as a
consequence, peptides with Me modification may also be produced in
a racemic form.
[0098] The peptides of this invention may comprise a modification
such as for example a methylation of an carboxy group (Me-peptide)
methylation of a nitrogen engaged in peptidic bond formation
(NMe-peptide), acetylation of a terminal nitrogen (acetyl peptide),
amidation of a terminal carboxylic group (amide-peptide), reduced
bond (.PSI.1-2(CH.sub.2--NH), .beta.-amino acid (aa), e.g.,
.beta.-alanine, .beta.-glutamic acid, D-amino acid (d-aa),
hydroxylation of a terminal nitrogen (NOH-peptide), retro-inverso
peptide bond (.psi.1-2(CO--NH.sub.2), and cyclic amino acid, e.g.,
pyro-glutamic a.a. See e.g., U.S. patent application Ser. No.
09/114,002 filed Jul. 10, 1998 and incorporated herein by reference
for examples of methods for modifying peptides to increase their
resistance to proteolytic cleavage and for assays of peptide
stability. A reduced bond .psi. (CH.sub.2--NH) can be formed by the
reductive alkylation of a free amino group with a Fmoc protected
amino aldehyde performed according to the method developed by
Fehrentz and Castro (Fehrentz and Castro, Synthesis, 676-678 (1983)
incorporated herein by reference). Peptides may be purified by
reverse-phase high-pressure liquid chromatography (RP-HPLC) on a C8
column (Aquapore (Brownlee)). Identity of the purified peptides can
be confirmed by mass spectrometry using electrospray ionisation
(ESI-MS). Peptide stock solutions may be adjusted to appropriate
peptide concentration in, e.g., 100% dimethylsulfoxide (DMSO), and
stored at -20.degree. C. N-terminal-hydroxy peptides can be
synthesized according to methods disclosed in e.g., Bianco et al.,
J. Peptide Sci., 4: 471-478 (1998), Guichard et al., J. Med. Chem.,
39: 2030-2039 (1996) and Durr et al., Angew. Chem. Int. Ed. Engl.,
31(6): 785-787 (1992), all incorporated herein by reference. The
peptides of this invention may be synthesized by any method known
in the art, e.g. the solid-phase method using the Fmoc chemistry
and DIPC/HOAt (N,N
diispropylcarbodiimmide/N-hydroxyaza-benzothiazole) coupling
procedure.
[0099] Methods for identifying functional variants of the MAGE-C2
HLA class I binding peptides are provided in a U.S. Pat. Nos.
6,277,956 and 6,326,200 and published PCT application WO0136453 and
U.S. application Ser. Nos. 09/440,621, 09/514,036, 09/676,005 all
incorporated herein by reference. In general, the methods include
selecting an unmodified MAGE-C2 HLA class I binding peptide, an HLA
class I binding molecule which binds the MAGE-C2 HLA class I
binding peptide, and a T cell which is stimulated by the unmodified
MAGE-C2 HLA class I binding peptide presented by the HLA class I
binding molecule. Preferably, the unmodified MAGE-C2 HLA class I
binding peptide comprises the amino acid sequence of SEQ ID NO: 1
or SEQ ID NO: 88. More preferably, the unmodified peptide consists
of the amino acid sequence set forth in SEQ ID NO: 3 or SEQ ID NO:
77. A first amino acid residue of the MAGE-C2 HLA class I binding
peptide is mutated to prepare a modified peptide. Any method for
preparing modified peptides can be employed, such as chemical
synthesis of the modified peptide, recombinantly producing the
modified peptide using a mutated nucleic acid molecule, and the
like.
[0100] The binding of a modified peptide to HLA class I binding
molecule and the stimulation of a T cell are then determined
according to standard procedures wherein binding of the variant
peptide to the HLA class I binding molecule and stimulation of the
T cell by the variant peptide presented by the HLA class I binding
molecule indicates that the variant peptide is a functional
variant. For example, the peptide to be assayed can be contacted
with an antigen presenting cell, which contains the HLA class I
molecule known to bind to a particular MAGE-C2 peptide, to form a
complex of the modified peptide and the HLA class I molecule. The
cells presenting this complex can then be contacted with a T cell
that recognizes a complex of the particular unmodified MAGE-C2
peptide and the HLA class I binding molecule. Such T cells can be
obtained from a patient having a condition characterized by
expression of MAGE-C2. Recognition of the complex of modified
peptide and HLA class I molecule by the T cells can be determined
by measuring any indicator of T cell stimulation known in the art.
Binding of the modified peptide to the HLA class I binding molecule
and stimulation of the T cell by the modified peptide presented by
the HLA class I binding molecule indicates that the modified
peptide is a functional variant.
[0101] It is also possible to evaluate the effectiveness of the
functional variant on the stimulation of T cells by comparing the
stimulation of the T cell by complexes of the HLA and unmodified
peptide with the stimulation of the T cell by complexes of HLA and
the functional variant. By comparing the stimulation levels,
peptides with increased T cell stimulatory properties can be
identified.
[0102] Variants of the MAGE-C2 HLA class I binding peptides
prepared by any of the foregoing methods can be sequenced, if
necessary, using standard techniques to determine the amino acid
sequence and thus deduce the nucleotide sequence which encodes such
variants.
[0103] Also an aspect of this invention are combinatorial libraries
of modified peptides which are screened for variants of peptides
having an amino acids of the sequences set forth in SEQ ID NO: 1,
SEQ ID NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO:
78, SEQ ID NO: 88 or SEQ ID NO: 89. The modified peptides may be
generated by the systematic substitution, deletion or modification
of one or more amino acids of the sequences set forth in SEQ ID NO:
1, SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 5, SEQ ID NO: 77, SEQ
ID NO: 78, SEQ ID NO: 88 or SEQ ID NO: 89.
[0104] The peptides and libraries may be constructed using well
known methods. See, e.g., Merrifield, R. B., "Solid phase peptide
synthesis. I. The synthesis of a tetrapeptide", J. Am. Chem. Soc.
85:2149-2154 (1963); M. Bodanszky, "Principles of Peptide
Synthesis", Springer-Verlag p. 21-27 (1984); Jung et al., "Multiple
Peptide Synthesis Methods and Their Applications" Angew. Chem. Int.
Ed. Engl., vol. 31, No. 4, pp. 367-383 (April 1992); Janda, K. D.,
"Tagged versus untagged libraries: Methods for the generation and
screening of combinatorial chemical libraries", Proc. Natl. Acad.
Sci. USA, vol. 91, pp. 10779-10785 (November 1994), and Barbas et
al., Phage Display: A Laboratory Manual, Cold Spring Harbor
Laboratory Press, Cold Spring Harbor N.Y. (2001) (all incorporated
herein by reference). For example, oligonucleotides that encode
modified peptides may be generated by synthesizing oligonucleotides
using mixtures of two or more of the four nucleoside triphosphates
rather than pure preparations of the nucleoside triphosphates. The
mixtures of nucleosides introduce changes into the oligonucleotide
sequence and these changed oligonucleotides encode modified
peptides that differ in only a few residues from the initial
peptide. Libraries of modified peptides may also be prepared, for
example, by using a pII or a pVIII based peptides on phage system,
and combinatorial libraries can be screened to identify a phage
that presents a variant that binds to an HLA molecule and the DNA
of the phage screened to determine the sequence of the variant
displayed on the surface of the phages. Additional methods for
generating libraries of peptides are also disclosed in, e.g., U.S.
Pat. No. 5,932,546, incorporated herein by reference.
[0105] A combinatorial library of the modified peptides may be
screened for functional variant having, e.g., the following
characteristics: a peptide that does not consist of the sequence
set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID NO:
5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 or SEQ ID NO: 89 and
yet binds to an HLA molecule, preferably HLA-A2 molecule, and when
bound to the HLA molecule they form a complex that is recognized by
a cytolytic T cell that recognizes a complex of the HLA molecule,
preferably HLA-A2 or HLA-B57, and a peptide selected from the group
consisting of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3 or SEQ ID
NO: 5, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 88 or SEQ ID NO:
89. Such functional variants are useful in the methods of this
invention, e.g., for stimulating CTL cells that recognize cells
presenting a complex of an HLA molecule e.g. HLA-A2 or HLA-B57 and
a peptide selected from the group consisting of SEQ ID NO: 1, SEQ
ID NO: 2, SEQ ID NO: 3 or SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO:
78, SEQ ID NO: 88 or SEQ ID NO: 89.
[0106] Also a part of this invention are antibodies, e.g.,
polyclonal and monoclonal, and antibody fragments, e.g. Fab, Fab',
Fab'-SH, F(ab'), and Fv fragments, diabodies and any antibody
fragment that is a polypeptide having a primary structure
consisting of one uninterrupted sequence of contiguous amino acid
residues (single-chain antibody fragment or single chain
polypeptide), including without limitation; single-chain Fv (scFv)
molecules; single chain polypeptides containing only one light
chain variable domain, or a fragment thereof that contains the
three CDRs of the light chain variable domain, without an
associated heavy chain moiety; and single chain polypeptides
containing only one heavy chain variable region, or a fragment
thereof containing the three CDRs of the heavy chain variable
region, without an associated light chain moiety; and multi
specific antibodies formed from antibody fragments, that
specifically bind the peptides or HLA/peptide complexes disclosed
herein. Preferably the antibodies, the antibody fragments and T
cell receptors bind the HLA/peptide complexes in a peptide-specific
manner. Such antibodies are useful, for example, in identifying
cells presenting the HLA/peptide complexes, particularly complexes
comprising an HLA-A2, A3, A26, HLA-B7, B8, B15, B27, B35, B44, B51,
or B57 molecule, preferably HLA-A2 or B57, and a peptide consisting
essentially of the sequence set forth in SEQ ID NO: 1 (wherein X is
Ala, Val, Leu, Ile, Pro, Phe, Met, Trp or Glu, preferably Val (SEQ
ID NO: 3) or Ala (SEQ ID NO: 5)), 2, 3, 4, 5, 6, 7, 8, 9, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65,
66, 67, 68, 69, 70, 77, 78, 88 (wherein X is absent (SEQ ID NO: 78)
or any amino acid) or 89. Preferably the peptide consists of the
sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 3, SEQ
ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78 or SEQ ID NO: 89.
[0107] Such antibodies are also useful in promoting the regression
or inhibiting the progression of a tumor which expresses complexes
of the HLA and peptide. Polyclonal antisera and monoclonal
antibodies specific to the peptides or HLA/peptide complexes of
this invention may be generated according to standard procedures.
See e.g., Catty, D., Antibodies, A Practical Approach, Vol. 1, IRL
Press, Washington D.C. (1988); Klein, J. Immunology: The Science of
Cell-Non-Cell Discrimination, John Wiley and Sons, New York (1982);
Kennett, R., et al., Monoclonal Antibodies, Hybridoma, A New
Dimension In Biological Analyses, Plenum Press, New York (1980);
Campbell, A., Monoclonal Antibody Technology, in Laboratory
Techniques and Biochemistry and Molecular Biology, Vol. 13 (Burdon,
R. et al. EDS.), Elsevier Amsterdam (1984); Eisen, H. N.,
Microbiology, third edition, Davis, B. D. et al. EDS. (Harper &
Rowe, Philadelphia (1980); Kohler and Milstein, Nature, 256:495
(1975) all incorporated herein by reference.) Methods for
identifying Fab molecules endowed with the antigen-specific,
HLA-restricted specificity of T cells has been described by
Denkberg et al. Proc. Natl. Acad. Sci. 99:9421-9426 (2002) and
Cohen et al. Cancer Research 62:5835-5844 (2002) (both incorporated
herein by reference). Methods for generating and identifying other
antibody molecules, e.g., scFv and diabodies are well known in the
art, see e.g., Bird et al., Science, 242:423-426 (1988); Huston et
al., Proc. Natl. Acad. Sci., 85:5879-5883 (1988); Mallender and
Voss, J. Biol. Chem. 269:199-206 (1994); Ito and Kurosawa, J Biol
Chem 27: 20668-20675 (1993), and; Gandecha et al., Prot Express
Purif 5: 385-390 (1994)(all incorporated herein by reference).
[0108] The antibodies of this invention can be used for
experimental purposes (e.g., localization of the HLA/peptide
complexes, immunoprecipitations, Western blots, flow cytometry,
ELISA etc.) as well as diagnostic or therapeutic purposes, e.g.,
assaying extracts of tissue biopsies for the presence of
HLA/peptide complexes, targeting delivery of cytotoxic or
cytostatic substances to cells expressing the appropriate
HLA/peptide complex. The antibodies of this invention are useful
for the study and analysis of antigen presentation on tumor cells
and can be used to assay for changes in the HLA/peptide complex
expression before, during or after a treatment protocol, e.g.,
vaccination with peptides, antigen presenting cells, HLA/peptide
tetramers, adoptive transfer or chemotherapy. The antibodies and
antibody fragments of this invention may be coupled to diagnostic
labeling agents for imaging of cells and tissues that express the
HLA/peptide complexes or may be coupled to therapeutically useful
agents by using standard methods well-known in the art. The
antibodies also may be coupled to labeling agents for imaging e.g.,
radiolabels or fluorescent labels, or may be coupled to, e.g.,
biotin or antitumor agents, e.g., radioiodinated compounds, toxins
such as ricin, methotrexate, cytostatic or cytolytic drugs, etc.
Examples of diagnostic agents suitable for conjugating to the
antibodies of this invention include e.g., barium sulfate,
diatrizoate sodium, diatrizoate meglumine, iocetamic acid, iopanoic
acid, ipodate calcium, metrizamide, tyropanoate sodium and
radiodiagnostics including positron emitters such as fluorine-18
and carbon-11, gamma emitters such as iodine-123, technitium-99m,
iodine-131 and indium-111, nuclides for nuclear magnetic resonance
such as fluorine and gadolinium. As used herein, "therapeutically
useful agents" include any therapeutic molecule which are
preferably targeted selectively to a cell expressing the
HLA/peptide complexes, including antineoplastic agents,
radioiodinated compounds, toxins, other cytostatic or cytolytic
drugs. Antineoplastic therapeutics are well known and include:
aminoglutethimide, azathioprine, bleomycin sulfate, busulfan,
carmustine, chlorambucil, cisplatin, cyclophosphamide,
cyclosporine, cytarabidine, dacarbazine, dactinomycin,
daunorubicin, doxorubicin, taxol.TM. (pacitaxel), etoposide,
fluorouracil, interferon-.alpha., lomustine, mercaptopurine,
methotrexate, mitotane, procarbazine HCl, thioguanine, vinblastine
sulfate and vincristine sulfate. Additional antineoplastic agents
include those disclosed in Chapter 52, Antineoplastic Agents (Paul
Calabresi and Bruce A. Chabner), and the introduction thereto,
1202-1263, of Goodman and Gilman's "The Pharmacological Basis of
Therapeutics", Eighth Edition, 1990, McGraw-Hill, Inc. (Health
Professions Division). Toxins can be proteins such as, for example,
pokeweed anti-viral protein, cholera toxin, pertussis toxin, ricin,
gelonin, abrin, diphtheria exotoxin, or Pseudomonas exotoxin. Toxin
moieties can also be high energy-emitting radionuclides such as
cobalt-60. The antibodies may be administered to a subject having a
pathological condition characterized by the presentation of the
HLA/peptide complexes of this invention, e.g., melanoma or other
cancers, in an amount sufficient to alleviate the symptoms
associated with the pathological condition.
[0109] Soluble T cell receptors (TcR) which specifically bind to
the HLA/peptide complexes described herein are also an aspect of
this invention. In their soluble form T cell receptors are
analogous to a monoclonal antibody in that they bind to HLA/peptide
complex in a peptide-specific manner. Immobilized TcRs or
antibodies may be used to identify and purify unknown peptide/HLA
complexes which may be involved in cellular abnormalities. Methods
for identifying and isolating soluble TcRs are known in the art,
see for example WO 99/60119, WO 99/60120 (both incorporated herein
by reference) which describe synthetic multivalent T cell receptor
complex for binding to peptide-MHC complexes. Recombinant, refolded
soluble T cell receptors are specifically described. Such receptors
may be used for delivering therapeutic agents or detecting specific
peptide-MHC complexes expressed by tumor cells. WO 02/088740
(incorporated by reference) describes a method for identifying a
substance that binds to a peptide-MHC complex. A peptide-MHC
complex is formed between a predetermined MHC and peptide known to
bind to such predetermined MHC. The complex is then use to screen
or select an entity that binds to the peptide-MHC complex such as a
T cell receptor. The method could also be applied to the selection
of monoclonal antibodies that bind to the predetermined peptide-MHC
complex.
[0110] Also a part of this invention are nucleic acid molecules
encoding the antibodies and T cell receptors of this invention and
host cells, e.g., human T cells, transformed with a nucleic acid
molecule encoding a recombinant antibody or antibody fragment,
e.g., scFv or Fab, or a TcR specific for a predesignated
HLA/peptide complex as described herein, particularly a complex
wherein the HLA molecule is an HLA-A2, A3, A26, HLA-B7, B8, B15,
B27, B35, B44, B51 or B57 molecule, preferably HLA-A2 or B57, and
the peptide has a nucleotide sequence set forth in SEQ ID NO: 1
(wherein X is Ala, Val, Leu, Ile, Pro, Phe, Met, Trp or Glu,
preferably Val (SEQ ID NO: 3) or Ala (SEQ ID NO: 5)), 2, 3, 4, 5,
6, 7, 8, 9, 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, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60,
61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 77, 78, 88 (wherein X is
absent (SEQ ID NO: 78) or any amino acid) or 89. Preferably the
peptide consists of the sequence set forth in SEQ ID NO: 1, SEQ ID
NO: 2, SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78 or
SEQ ID NO: 89.
[0111] Recombinant Fab or TcR specific for a predesignated
HLA/peptide complex in T cells have been described in, e.g.,
Willemsen et al., "A phage display selected Fab fragment with MHC
class I-restricted specificity for MAGE-A1 allows for retargeting
of primary human T lymphocytes" Gene Ther. 2001 November;
8(21):1601-8. and Willemsen et al., "Grafting primary human T
lymphocytes with cancer-specific chimeric single chain and two
chain TCR". Gene Ther. 2000 August; 7(16):1369-77. (both
incorporated herein by reference) and have applications in an
autologous T cell transfer setting. The autologous T cells,
transduced to express recombinant antibody or TcR, may be infused
into a patient having an pathological condition associated with
cells expressing the HLA/peptide complex. The transduced T cells
are administered in an amount sufficient to inhibit the progression
or alleviate at least some of the symptoms associated with the
pathological condition.
[0112] This invention also relates to a method for promoting
regression or inhibiting progression of a tumor in a subject in
need thereof wherein the tumor expresses a complex of HLA and
peptide. The method comprises administering an antibody, antibody
fragment or soluble T cell receptor, which specifically binds to
the HLA/peptide complex, or by administering cells transduced so
that they express those antibodies or TcR in amounts that are
sufficient to promote the regression or inhibit progression of the
tumor expressing the HLA/peptide complex, e.g., a melanoma or other
cancer. Preferably the HLA is an HLA-A2, or B57 and the peptide is
an MAGE-C2 derived peptide preferably a peptide consisting of the
sequences set forth in SEQ ID NO: 1 (wherein X is Ala, Val, Leu,
Ile, Pro, Phe, Met, Trp or Glu, preferably Val (SEQ ID NO: 3) or
Ala (SEQ ID NO: 5)), 2, 3, 4, 5, 6, 7, 8, 9, 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, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,
69, 70, 77, 78, 88 (wherein X is absent (SEQ ID NO: 78) or any
amino acid) or 89, or their analogs, and preferably the peptide
consists of the sequence set forth in SEQ ID NO: 1, SEQ ID NO: 2,
SEQ ID NO: 3, SEQ ID NO: 5, SEQ ID NO: 77, SEQ ID NO: 78 or SEQ ID
NO: 89.
[0113] The antibodies, antibody fragments and soluble T cell
receptors may be conjugated with, or administered in conjunction
with, an antineoplastic agent, e.g., radioiodinated compounds,
toxins such as ricin, methotrexate, or a cytostatic or cytolytic
agent as discussed supra. See e.g., Pastan et al., Biochem.
Biophys. Acta, 133:C.sub.1-C.sub.6 (1997), Lode et al., Immunol.
Res. 21:279-288 (2000) and Wihoff et al. Curr. Opin. Mo. Ther.
3:53-62 (2001) (all incorporated herein by reference) for a
discussion of the construction of recombinant immunotoxins,
antibody fusions with cytokine molecules and bispecific antibody
therapy or immunogene therapy.
EXAMPLES
Example 1
[0114] An invaded lymph node of patient EB 81 was resected and
allowed to establish tumor line EB81-MEL.2. This cell line was used
to stimulate autologous T lymphocytes in a classical
mixed-lymphocyte tumor-cell culture. After cloning by limiting
dilution, cytotoxic T lymphocyte (CTL) clone 606 C/22.2 was
obtained. This clone lysed specifically EB81-MEL.2 cells, but not
autologous EBV-transformed B lymphocytes (EB8-EBV) nor K562 (FIG.
1). However, it was not directed against the peptides used for
vaccination, as it did not recognize EB81-EBV pulsed with these
peptides (FIG. 1). Anti-HLA-A2 antibody blocked the activation of
the CTL by the melanoma cells (FIG. 2) and thus the CTL was
restricted by HLA-A2. A series of allogeneic HLA-A2 tumor lines
were then tested, and several were recognized by CTL 606 C/22.2,
including melanomas AVL3-MEL, LB373-MEL and myeloma U266 (FIG. 3).
This indicated that the antigen recognized by this CTL was present
in several different tumors.
[0115] To identify the gene encoding this antigen, a cDNA library
was prepared with mRNA extracted from EB81-MEL.2 cells using
standard techniques. The library was divided into pools of about
100 bacterial clones. Plasmid DNA extracted from each pool was used
to transfect 293-EBNA cells together with plasmid DNA encoding
HLA-A2. CTL 606 C/22.2 was added to the transfected cells and TNF
production was measured. A positive pool was cloned and a new
series of transfections was performed to identify the positive cDNA
clone. The sequence of that clone proved identical to the sequence
of MAGE-C2, a cancer/germ line gene expressed in about 40% of
melanomas (Lucas et al, Int. J. Cancer, 87:55-60 (2000); Gure et
al., "CT10: A New Cancer-Testis (CT) Antigen Homologous To CT7 And
The Mage Family, Identified By Representational-Difference
Analysis" Int. J. Cancer 85:726-732 (2000); and U.S. patent
application Ser. No. 09/066,281 filed Apr. 24, 1998, now U.S. Pat.
No. 6,475,783 all incorporated herein by reference). The only
difference between this new cDNA (MAGE-C2M) and the previously
described MAGE-C2 cDNA is the presence in MAGE-C2M of a short
intronic sequence that is not spliced out. This additional exon (E3
in FIG. 4, SEQ ID NO: 75, 5'-GTTTCCCAGCAG
ACAAACTCCCTAGGAAGACAGGAGACCTGTGAGGCCCTAGAGCACCACCT
TAAGAGAAGAAGAGCT-3') is located in the 5' untranslated region and
therefore does not affect the coding sequence.
[0116] To identify the antigenic peptide, several minigenes were
constructed by amplifying different fragments of the MAGE-C2 cDNA
by PCR. PCR products were cloned into plasmid vector pcDNA3.1/H is
by TOPO T/A cloning (Invitrogen, following manufacturer's
instructions). Cos-7 cells were transfected with the different
minigenes, CTL 606 C/22.2 was added and the TNF production was
measured.
[0117] The results shown in FIGS. 4A and 4B, indicated that the
peptide-coding sequence was within the last 211 nucleotides of the
open reading frame of the MAGE-C2 DNA. Several candidate peptides
bearing the binding motif for HLA-A2 were then synthesized and
nonapeptide ALKDVEERV (SEQ ID NO: 3) was found capable of
stimulating TNF release by CTL 606/22.2 (FIG. 5A). The recognition
of this peptide by CTL 66/22.2 was then confirmed in a lysis assay
of autologous EB81-EBV cells pulsed with peptide ALKDVEERV (SEQ ID
NO: 3) or with shorter peptides ALKDVEER (SEQ ID NO: 4) and
LKDVEERV (SEQ ID NO: 2). As shown in FIG. 5B, ALKDVEERV (SEQ ID NO:
3) was recognized with half-maximal lysis at 1 ng/ml peptide.
Peptide LKDVEERV (SEQ ID NO: 2) was recognized about 30 times less
efficiently.
[0118] SK23-MEL cells express HLA-A2 but do not express MAGE-C2.
These cells were stably transfected with pcDNA3 containing a cDNA
(SEQ ID NO: 72) encoding MAGE-C2 (SEQ ID NO: 71) by
calcium-phosphate transfection. Transfected cells were selected
with G418 (500 ug/ml), and cloned by limiting dilution. CTL 606
C/22.2 was stimulated by the transfected cells for 18 hours, then
the concentration of TNF in the supernatant was measured by testing
its toxicity for WEHI-164.13 cells. FIG. 6 demonstrates the
recognition of clones of transformed SK23-MEL cells,
SK23-MEL/MAGE-C2c13, SK23-MEL/MAGE-C2c12, SK23-MEL/MAGE-C2c11 by
CTL 606C/22.2.
Example 2
Clinical Evolution of Patient EB81
[0119] EB 81 is a melanoma patient who showed complete regression
of multiple cutaneous metastases after vaccination with a
recombinant canary poxvirus (ALVAC) encoding MAGE-1.A1 and
MAGE-3.A1 peptides and with synthetic MAGE-1.A1 (EADPTGHSY, SEQ ID
NO: 10) and MAGE-3.A1 (EVDPIGHLY, SEQ ID NO: 11) peptide. The
patient expressed both HLA-A1 and HLA-A2 alleles A*0101 and *0201
and HLA-B50, HLA-B57 and HLA-C6.
[0120] In April 1999 a primary cutaneous melanoma was surgically
excised from the right ankle of patient EB81. Cutaneous metastases
appeared in patient EB81 in June 1999. One of these cutaneous
metastases was excised and found to contain melanoma cells
expressing gene MAGE-3. Because the patient was initially typed as
HLA-A1, she was vaccinated with a recombinant canarypox virus of
the ALVAC type containing a minigene encoding the MAGE-1.A1 and
MAGE-3.A1 peptides. Four injections of ALVAC, between September and
November 1999, were followed by vaccinations with peptides
MAGE-1.A1 and MAGE-3.A1, injected subcutaneously and intradermally
without adjuvant. When vaccination was initiated, the patient had
about 65 cutaneous metastases. About a third of these tumors
started to regress during vaccination with ALVAC, while the others
regressed later, during vaccination with the peptides. Two
regressing metastases were resected, and all the others were
undetectable by June and July 2000, ten months after the first
vaccination. The patient did not receive any other anti-cancer
treatment, except for a resection in April 2000 of an enlarged
inguinal lymph node (FIG. 7), which contained tumor cells
expressing genes MAGE-1 and MAGE-3. Subsequently, the remaining
lymph nodes of the same region were removed, but none of them
contained melanoma cells. As of September 2002, the patient was
still free of detectable melanoma.
Clonotypic PCR for the TCR of the Anti-MAGE-C2.A2 CTL Clone
606C/22.2.
[0121] The T cell receptor (TCR) of the anti-MAGE-C2.A2 CTL clone
606C/22.2 corresponds to V.A-inverted.2-J.A-inverted.6 and
V.beta.28-J.beta.1-6 rearranged products. Clonotypic PCRs (Coulie
et al., "A monoclonal cytolytic T-lymphocyte response observed in a
melanoma patient vaccinated with a tumor-specific antigenic peptide
encoded by gene MAGE-3" PNAS 28:10290-10295, 2001 incorporated
herein by reference) were designed to assay for each of these two
chains (FIG. 8).
[0122] cDNA of RNA extracted with Tripure.TM. isolation reagent
(Gibco) from groups of peripheral blood mononuclear cells (PBMC),
or from cells of a microdissected tumor, was prepared using an
oligodT oligonucleotide containing a T7 promoter sequence. A
fraction ( 1/100) of the cDNA was then used as template in three
successive rounds of nested PCR using various primers to detect
either the TCR.A-inverted. or the TCR.beta. rearranged product, as
shown on FIG. 8. PCR products were visualized on ethidium
bromide-stained agarose gels using standard techniques.
[0123] The frequency of CTL 606C/22.2 to CD8 cells was determined
in samples of PBMCs collected from patient EB81 in March 2000, 6
months after the first vaccination with recombinant ALVAC and
peptides (FIG. 7). cDNA of RNA extracted from 14 groups of 66,000
PBMCs, containing 17% CD8 T lymphocytes, was prepared and used as
template in the TCR.A-inverted. and TCR.E-backward. clonotypic
PCRs. Nine groups of the PBMCs were positive in both PCRs,
indicating a frequency of anti-MAGE-C2.A2 CTL in the CD8 cells was
about 9.times.10.sup.-5. Four months later, the estimated frequency
of anti-MAGE-C2. A2 CTL in the CD8 cells was 4.times.10.sup.-5
(FIG. 7).
[0124] The presence of the anti-MAGE-C2.A2 CTL was also analyzed in
the metastatic lymph node resected in April 2000, seven months
after the first vaccination (FIG. 7). Twenty circular sections
(diameter.+-.1 mm) were microdissected from this metastatic tumor
and RNA extracted from cells of the microdissected sections was
converted to cDNA. The cDNA used as template in a quantitative PCR
for the CD8.beta. gene product, and for the two clonotypic PCRs for
CTL 606C/22.2. The results of the quantitative PCR for the
CD8.beta. gene product were used to estimate the number of CD8 T
lymphocytes present in each microdissected section. All but two of
the 20 microdissected sections contained CD8 cells, with estimated
numbers varying from 1 to more than 600 cells (Table 3). The
clonotypic PCR results indicated that CTL 606C/22.2 was present in
all the microdissected sections that contained CD8 cells, even
where the estimated number of CD8 cells in the section was lower
than 10. These results indicate that in the tumor, the frequency of
CTL 606C/22.2 in the CD8 cell population is about
10.sup.-1-10.sup.-2. This frequency corresponded to an enrichment
of at least 100-fold as compared to the frequency found in the PBMC
sample. In contrast, when the frequency of anti-MAGE-3.A1 CTL in
the CD8 cell population of the same lymph node was assayed by
clonotypic PCR, the estimated CTL frequency proved similar to that
found in the PBMC sample.
TABLE-US-00003 TABLE 3 Clonotypic PCR for CTL 606C/22.2 on
fragments of tumor sections. Microdissected Number of CD8 cells
Clonotypic section in the section PCR 1 0 - 2 3 + 3 1 + 4 10 + 5
666 + 6 32 + 7 14 + 8 0 + 9 13 + 10 16 + 11 291 + 12 6 + 13 3 + 14
141 + 15 47 + 16 3 + 17 9 + 18 0 - 19 299 + 20 421 +
Example 3
[0125] Cytotoxic T lymphocyte (CTL) clone 606 C/21.7, was obtained
by stimulating autologous CD8+ T lymphocytes with melanoma cell
line EB81-MEL.2, which was derived from a lymph node metastasis
resected from melanoma patient EB81 (HLA-A*0101, A*0201, B50, B57,
C6). This patient was vaccinated with Mage-3.A1 nonapeptide
EVDPIGHLY, SEQ ID NO: 11 and recombinant canarypoxvirus (ALVAC)
expressing this nonapeptide, and showed a complete regression of
all metastatic lesions.
[0126] Specific lysis of autologous melanoma cell line EB81-MEL.2
by CTL 606 C/21.7 is depicted in FIGS. 9 and 10. Autologous EBV
transformed B-cell line EB81-EBV, Mage 3-A1 peptide-pulsed EB81-EBV
cells, and K562 cells were labeled with chromium and incubated with
CTL at various effector-to-target ratios. .sup.51Cr release was
measured after 4 hours. In FIG. 10 autologous melanoma cell line
EB81-MEL.2, incubated with or without the indicated antibodies
(FIG. 10), were used to stimulate CTL 606 C/21.7. After 18 hours of
coculture, production of TNF.A-inverted. was measured by assaying
the toxicity of the supernatants on WEHI-164 cl13 cells, which are
TNF.A-inverted.-sensitive, using standard techniques (see
Traversari et al., Immunogenetics 35: 145-152 (1992), incorporated
herein by reference). CTL 606 C/21.7 specifically lyses EB81-MEL.2
cells, and its HLA restriction is HLA-A2.
[0127] The CTL recognizes different allogeneic tumor cell lines
expressing HLA-A2 e.g., melanoma lines AVL.3.MEL, and LB373-MEL and
a myeloma cell line U266 (FIG. 11) indicating that the antigen
recognized by CTL 606-C/21.7 is shared by those tumor cell lines. A
non-small cell lung carcinoma cell line, LB37-NSCLC was not
recognized by CTL 606 C/21.7.
[0128] To determine whether the HLA/peptide complex recognized by
CTL 606 C/21.7 was encoded by a known gene, we transfected COS-7
cells with cDNAs corresponding to various genes known to be
expressed in melanoma cells and that are known to produce antigenic
peptides recognized by various CTLs. Transfected COS-7 cells were
then assayed for their ability to induce TNF.A-inverted. production
by CTL 606 C/21.7 to determine if they presented the HLA/peptide
complex recognized by CTL 606 C/21.7. Cells transfected with cDNA
encoding MAGE C2 were positive (FIG. 12A).
[0129] To localize the antigenic peptide, we produced truncated
MAGE C2 cDNA fragments by PCR amplification using standard
techniques, sub-cloned the cDNA fragments into the expression
vector pcDNA3.1/Amp and transfected COS-7 cells with the expression
vectors. A region of MAGE C2 encoding the antigenic peptide was
comprised between positions 558 and 612 of the MAGE C2 cDNA (FIGS.
12A and 12B, wherein position 1 in the figure is the ATG start
codon at position 330 in SEQ ID NO: 72).
[0130] Several peptides were chosen in this region according to
their affinity for HLA-A2 using the SYFPEITHI database at
syfpeithi.bmi-heidelberg.com supra and the BIMAS database at
bimas.dcrt.nih.gov/molbio/hlabind/index.html (Parker, K. C., et
al., J. Immunol. 152:163., 1994). These peptides were tested for
their ability to sensitize autologous EBV transformed B cells
(EB81-EBV) such that they are lysed by CTL 606 C/21.7. Decamer
peptide-LLFGLALIEV (SEQ ID NO: 77) was best recognized, with
half-maximum lysis achieved at dose of 200 pg/ml (FIG. 13). The
negative control baseline level is 15%.
[0131] Three other independent CTL clones obtained by the same
approach from the same patient were found to recognize the same
peptide (FIG. 14). The T cell receptor sequence of the 4 clones
were different:
TABLE-US-00004 CTL T cell receptor 606A/16.2
V.E-backward.9*01-J.E-backward.2-7*01/02; 606C/18.6
V.E-backward.2*01-J.E-backward.2-7*01; 606C/19.3
V.E-backward.7-9*01-J.E-backward.2-1*01; 606C/21.7
V.E-backward.15-2*01-J.E-backward.2-3*01
TABLE-US-00005 TABLE 4 Homologs to the Mage-C2 peptide Ligation SEQ
ID Protein Peptide strength* NO: Mage-C2 LLFGLALIEV 31 77 Mage-C1
ILFGISLREV 31 82 Mage-A10 LVFGIDVKEV 24 83 Mage-C3 LIFGIALTDM 21 84
Mage-B4 LVFGLALKEV 24 85 Mage-A11 LLFGIDVKEV 30 86 Mage-B4
WFGLELNKV 25 87 *Ligation strength to HLA-A*0201 according to the
SYFPEITHI database (syfpeithi.bmi-heidelberg.com) supra. Peptide
SEQ ID NOs from top to bottom of Table 4 are SEQ ID NO: 77, 83, 84,
85, 86 and 87.
Example 4
[0132] Cytotoxic T lymphocyte (CTL) clone 606 C/17.3, was obtained
by stimulating peripheral blood CD8+ T lymphocytes with melanoma
cell line EB81-MEL.2, which was derived from a lymph node
metastasis resected from melanoma patient EB81 (HLA-A*0101, A*0201,
B50, B57, C6) as disclosed in Examples 2 and 3.
[0133] CTL 606 C/17.3 specifically lyses EB81-MEL.2 cells as
assayed by chromium release (FIG. 15). Autologous EBV transformed B
cell line EB81-EBV and K562 cells were used as control targets.
Target cells were labeled with chromium and incubated with CTL at
different effector-to-target ratios. .sup.51Cr release was measured
after 4 hours. Its HLA restriction was identified by analyzing the
inhibitory effect of specific anti-HLA monoclonal antibodies (mAbs)
on the recognition of EB81-MEL.2 cells. Autologous melanoma cell
line EB81-MEL.2, alone or treated with specific antibodies against
different HLA molecules, were used to stimulate CTL 606 C/17.3.
After 18 hours of coculture, the production of TNF by CTL was
measured by testing the toxicity of the supernatants on
TNF-sensitive cell line WEHI-164 cl13. TNF production by CTL 606
C/17.3 was only blocked by anti-HLA-A.B.C and anti-HLA-B.C in this
circumstance, but not by anti-HLA-A2 or anti-HLA-Bw6. This
demonstrates that this CTL clone is HLA-B.C restricted (FIG. 16)
and can be either HLA-B57 or HLA-C6, because HLA-B50 would be
blocked by anti-HLA-Bw6 (anti-HLA-Bw6 blocks a range of different
HLA-B types, among them HLA-B50, but not HLA-B57. See Marsh et al.,
The HLA Facts Book, Academic Press, 2000, incorporated herein by
reference).
[0134] To determine the HLA restriction of CTL 606 C/17.3 and
whether the antigen recognized by this CTL was encoded by a known
gene, we transiently transfected COS-7 cells with plasmids
containing cDNAs encoding various known proteins together with
plasmids encoding either HLA-B57 or HLA-C6. Transfected cells were
incubated with CTL for 18 hours and then the TNF in the supernatant
was measured by its toxicity on TNF-sensitive cell line
WEHI-164cl13 as a measure of their ability to stimulate CTL 606
C/17.3. Among the cDNAs assayed, a MAGE C2-encoding DNA was
positive when cotransfected with an HLA-B57-encoding cDNA (FIG.
17). MAGE-C2 is expressed in about 40% of melanomas and also other
types of tumors (S Lucas, Int. J. Cancer: 87, 55-60, 2002).
[0135] To assay recognition of different cell lines by CTL 606
C/17.3, HLA-B57 positive cell lines were used to stimulate CTL 606
C/17.3. After 18 hours of coculture, the production of TNF by CTL
was measured by assaying the toxicity of the supernatants on the
TNF-sensitive cell line WEHI-164 cl13. Gene MAGE-C2 expression in
different tumor cell lines is shown in FIG. 18 right column, with a
"+", "++" or "+++" for positive depending on the expression level
and "-" for negative. Tumor lines expressing MAGE-C2 and HLA-B57
were recognized by CTL 606 C/17.3.
[0136] To localize the antigenic peptide, we produced truncated
MAGE-C2 cDNA fragments by PCR amplification, and cloned them into
expression vector pcDNA3.1/Amp. FIG. 19B is a schematic diagram of
gene MAGE-C2, is cDNA and the minigenes constructed to identify the
region of candidate antigenic peptide. Exons (E1, E2, E3 and E4)
appear as open boxes, introns as lines, an the open reading frame
(ORF) is shown as a black box. The first and last positions of the
minigenes are indicated with numbers with the first nucleotide of
the ORF considered as 1. Results of stimulating CTL with these
minigenes-transfected COS 7 cells in TNF production assay are
indicated as "-" for negative and "+" for positive following the
name of the minigenes. The sequence of the antigenic peptide is
shown as bold letters and underlined. We transiently transfected
these minigenes into COS-7 cells together with the HLA-B57 cDNA.
The transfected cells or EB81-MEL.2 cells were incubated with CTL
for 18 hours and then TNF in the supernatants were measured by its
toxicity on TNF-sensitive cell line WEHI-163 cl13. Using this we
defined a region between nucleotide positions 120 and 309, counting
from the start ATG of the open reading frame (ORF), of the MAGE-C2
cDNA (SEQ ID NO: 72) that encodes the antigenic peptide (FIGS. 19A
and 19B).
[0137] Several peptides within the region encoded by the nucleotide
sequence between positions 120-309 of MAGE C2 (as above, counting
begins at the first ATG of the ORF of the MAGE-C2 cDNA, SEQ ID NO:
72) were assayed for their ability to sensitize autologous EBV
transformed B cells (EB81-EBV) to lysis by CTL 606 C/17.3. These
peptides were selected with the aid of the SYFPEITHI database at
syfpeithi.bmi-heidelberg.com supra. EB-81-EBV were labeled with
.sup.51Cr and then pulsed with peptides for 30 minutes at the
concentrations indicated in FIG. 20. Thereafter, CTL 606 C/17.3 was
added at an effector-to-target ratio of 10. Chromium release was
measured after 4 hours of coincubation. Nonapeptide-ASSTLYLVF (SEQ
ID NO: 89) was best recognized, with half-maximal lysis achieved at
a dose around 10 ng/ml (FIG. 20).
Sequence CWU 1
1
10519PRTHomo sapiensMISC_FEATURE(9)..(9)Xaa at position 9 may be
any amino acid 1Ala Leu Lys Asp Val Glu Glu Arg Xaa1 528PRTHomo
sapiens 2Leu Lys Asp Val Glu Glu Arg Val1 539PRTHomo sapiens 3Ala
Leu Lys Asp Val Glu Glu Arg Val1 548PRTHomo sapiens 4Ala Leu Lys
Asp Val Glu Glu Arg1 559PRTHomo sapiens 5Ala Leu Lys Asp Val Glu
Glu Arg Ala1 569PRTHomo sapiens 6Ala Leu Lys Asp Glu Glu Glu Arg
Ala1 579PRTHomo sapiens 7Ala Lys Arg Glu Glu Gly Glu Gly Val1
589PRTHomo sapiens 8Ala Leu Arg Asp Glu Glu Glu Arg Ala1 599PRTHomo
sapiens 9Ala Leu Arg Asp Glu Glu Glu Arg Val1 5109PRTHomo sapiens
10Glu Ala Asp Pro Thr Gly His Ser Tyr1 5119PRTHomo sapiens 11Glu
Val Asp Pro Ile Gly His Leu Tyr1 5129PRTArtificial
sequencePotential Binding Motif 12Ala Leu Xaa Xaa Xaa Xaa Glu Xaa
Xaa1 5139PRTArtificial SequenceAntigenic peptide 13Ala Leu Arg Asp
Val Glu Glu Arg Val1 5149PRTArtificial SequenceAntigenic Peptide
14Ala Leu Arg Asp Val Glu Glu Arg Ala1 5159PRTArtificial
SequenceAntigenic peptide 15Ala Leu Arg Asp Val Glu Glu Gly Ala1
5169PRTARTIFICIAL SEQUENCEAntigenic peptide 16Ala Leu Arg Asp Val
Glu Glu Gly Val1 5179PRTARTIFICIAL SEQUENCEAntigenic peptide 17Ala
Leu Arg Asp Val Gly Glu Arg Val1 5189PRTARTIFICIAL
SEQUENCEAntigenic peptide 18Ala Leu Arg Asp Val Gly Glu Arg Ala1
5199PRTARTIFICIAL SEQUENCEAntigenic peptide 19Ala Leu Arg Asp Val
Gly Glu Gly Ala1 5209PRTARTIFICIAL SEQUENCEAntigenic peptide 20Ala
Leu Arg Asp Val Gly Glu Gly Val1 5219PRTARTIFICIAL
SEQUENCEAntigenic peptide 21Ala Leu Arg Asp Glu Glu Glu Gly Ala1
5229PRTARTIFICIAL SEQUENCEAntigenic peptide 22Ala Leu Arg Asp Glu
Glu Glu Gly Val1 5239PRTARTIFICIAL SEQUENCEAntigenic peptide 23Ala
Leu Arg Asp Glu Gly Glu Arg Val1 5249PRTARTIFICIAL
SEQUENCEAntigenic peptide 24Ala Leu Arg Asp Glu Gly Glu Arg Ala1
5259PRTARTIFICIAL SEQUENCEAntigenic peptide 25Ala Leu Arg Asp Glu
Gly Glu Gly Ala1 5269PRTARTIFICIAL SEQUENCEAntigenic peptide 26Ala
Leu Arg Asp Glu Gly Glu Gly Val1 5279PRTARTIFICIAL
SEQUENCEAntigenic peptide 27Ala Leu Arg Glu Val Glu Glu Arg Val1
5289PRTARTIFICIAL SEQUENCEAntigenic peptide 28Ala Leu Arg Glu Val
Glu Glu Arg Ala1 5299PRTARTIFICIAL SEQUENCEAntigenic peptide 29Ala
Leu Arg Glu Val Glu Glu Gly Ala1 5309PRTARTIFICIAL
SEQUENCEantigenic peptide 30Ala Leu Arg Glu Val Glu Glu Gly Val1
5319PRTARTIFICIAL SEQUENCEAntigenic peptide 31Ala Leu Arg Glu Val
Glu Glu Gly Val1 5329PRTARTIFICIAL SEQUENCEantigenic peptide 32Ala
Leu Arg Glu Val Gly Glu Arg Ala1 5339PRTARTIFICIAL
SEQUENCEAntigenic peptide 33Ala Leu Arg Glu Val Gly Glu Gly Ala1
5349PRTARTIFICIAL SEQUENCEAntigenic peptide 34Ala Leu Arg Glu Val
Gly Glu Gly Val1 5359PRTARTIFICIAL SEQUENCEAntigenic peptide 35Ala
Leu Arg Glu Glu Glu Glu Arg Val1 5369PRTARTIFICIAL
SEQUENCEAntigenic peptide 36Ala Leu Arg Glu Glu Glu Glu Arg Ala1
5379PRTARTIFICIAL SEQUENCEAntigenic peptide 37Ala Leu Arg Glu Glu
Glu Glu Gly Ala1 5389PRTARTIFICIAL SEQUENCEAntigenic peptide 38Ala
Leu Arg Glu Glu Glu Glu Gly Val1 5399PRTARTIFICIAL
SEQUENCEAntigenic peptide 39Ala Leu Arg Glu Glu Gly Glu Ala Val1
5409PRTARTIFICIAL SEQUENCEAntigenic peptide 40Ala Leu Arg Glu Glu
Gly Glu Arg Ala1 5419PRTARTIFICIAL SEQUENCEAntigenic peptide 41Ala
Leu Arg Glu Glu Gly Glu Gly Ala1 5429PRTARTIFICIAL
SEQUENCEAntigenic peptide 42Ala Leu Lys Asp Val Glu Glu Gly Ala1
5439PRTARTIFICIAL SEQUENCEAntigenic peptide 43Ala Leu Lys Asp Val
Glu Glu Gly Val1 5449PRTARTIFICIAL SEQUENCEAntigenic peptide 44Ala
Leu Lys Asp Val Gly Glu Ala Val1 5459PRTARTIFICIAL
SEQUENCEAntigenic peptide 45Ala Leu Lys Asp Val Gly Glu Arg Ala1
5469PRTARTIFICIAL SEQUENCEAntigenic peptide 46Ala Leu Lys Asp Val
Gly Glu Gly Ala1 5479PRTARTIFICIAL SEQUENCEAntigenic peptide 47Ala
Leu Lys Asp Val Gly Glu Gly Val1 5489PRTARTIFICIAL
SEQUENCEAntigenic peptide 48Ala Leu Lys Asp Glu Glu Glu Arg Val1
5499PRTARTIFICIAL SEQUENCEAntigenic peptide 49Ala Leu Lys Asp Glu
Glu Glu Gly Ala1 5509PRTARTIFICIAL SEQUENCEAntigenic peptide 50Ala
Leu Lys Asp Glu Glu Glu Gly Val1 5519PRTARTIFICIAL
SEQUENCEAntigenic peptide 51Ala Leu Lys Asp Glu Gly Glu Arg Val1
5529PRTARTIFICIAL SEQUENCEAntigenic peptide 52Ala Leu Lys Asp Glu
Gly Glu Arg Ala1 5539PRTARTIFICIAL SEQUENCEAntigenic peptide 53Ala
Leu Lys Asp Glu Gly Glu Gly Ala1 5549PRTARTIFICIAL
SEQUENCEAntigenic peptide 54Ala Leu Lys Asp Glu Gly Glu Gly Val1
55511PRTARTIFICIAL SEQUENCEAntigenic peptide 55Ala Leu Lys Glu Val
Glu Glu Arg Val Ala Asn1 5 10569PRTARTIFICIAL SEQUENCEAntigenic
peptide 56Ala Leu Lys Glu Val Glu Glu Arg Ala1 5579PRTARTIFICIAL
SEQUENCEantigenic peptide 57Ala Leu Lys Glu Val Glu Glu Gly Ala1
5589PRTARTIFICIAL SEQUENCEAntigenic peptide 58Ala Leu Lys Glu Val
Glu Glu Gly Val1 5599PRTARTIFICIAL SEQUENCEAntigenic peptide 59Ala
Leu Lys Glu Val Gly Glu Arg Val1 5609PRTARTIFICIAL
SEQUENCEAntigenic peptide 60Ala Leu Lys Glu Val Gly Glu Arg Ala1
5619PRTARTIFICIAL SEQUENCEAntigenic peptide 61Ala Leu Lys Glu Val
Gly Glu Gly Ala1 5629PRTARTIFICIAL SEQUENCEAntigenic peptide 62Ala
Leu Lys Glu Val Gly Glu Gly Val1 5639PRTARTIFICIAL
SEQUENCEAntigenic peptide 63Ala Leu Lys Glu Glu Glu Glu Arg Val1
5649PRTARTIFICIAL SEQUENCEAntigenic peptide 64Ala Leu Lys Glu Glu
Glu Glu Arg Ala1 5659PRTARTIFICIAL SEQUENCEantigenic peptide 65Ala
Leu Lys Glu Glu Glu Glu Gly Ala1 5669PRTARTIFICIAL
SEQUENCEantigenic peptide 66Ala Leu Lys Glu Glu Glu Glu Gly Val1
5679PRTARTIFICIAL SEQUENCEantigenic peptide 67Ala Leu Lys Glu Glu
Gly Glu Arg Val1 5689PRTARTIFICIAL SEQUENCEAntigenic peptide 68Ala
Leu Lys Glu Glu Gly Glu Arg Ala1 5699PRTARTIFICIAL
SEQUENCEAntigenic peptide 69Ala Leu Lys Glu Glu Gly Glu Arg Ala1
5709PRTARTIFICIAL SEQUENCEantigenic peptide 70Ala Leu Lys Glu Glu
Gly Glu Gly Val1 571373PRTHomo sapiensMISC_FEATURE(334)..(334)Xaa
at position at position 334 is Lys in MAGE-C2 and Glu in CT-10
71Met Pro Pro Val Pro Gly Val Pro Phe Arg Asn Val Asp Asn Asp Ser1
5 10 15Pro Thr Ser Val Glu Leu Glu Asp Trp Val Asp Ala Gln His Pro
Thr 20 25 30Asp Glu Glu Glu Glu Glu Ala Ser Ser Ala Ser Ser Thr Leu
Tyr Leu 35 40 45Val Phe Ser Pro Ser Ser Phe Ser Thr Ser Ser Ser Leu
Ile Leu Gly 50 55 60Gly Pro Glu Glu Glu Glu Val Pro Ser Gly Val Ile
Pro Asn Leu Thr65 70 75 80Glu Ser Ile Pro Ser Ser Pro Pro Gln Gly
Pro Pro Gln Gly Pro Ser 85 90 95Gln Ser Pro Leu Ser Ser Cys Cys Ser
Ser Phe Ser Trp Ser Ser Phe 100 105 110Ser Glu Glu Ser Ser Ser Gln
Lys Gly Glu Asp Thr Gly Thr Cys Gln 115 120 125Gly Leu Pro Asp Ser
Glu Ser Ser Phe Thr Tyr Thr Leu Asp Glu Lys 130 135 140Val Ala Glu
Leu Val Glu Phe Leu Leu Leu Lys Tyr Glu Ala Glu Glu145 150 155
160Pro Val Thr Glu Ala Glu Met Leu Met Ile Val Ile Lys Tyr Lys Asp
165 170 175Tyr Phe Pro Val Ile Leu Lys Arg Ala Arg Glu Phe Met Glu
Leu Leu 180 185 190Phe Gly Leu Ala Leu Ile Glu Val Gly Pro Asp His
Phe Cys Val Phe 195 200 205Ala Asn Thr Val Gly Leu Thr Asp Glu Gly
Ser Asp Asp Glu Gly Met 210 215 220Pro Glu Asn Ser Leu Leu Ile Ile
Ile Leu Ser Val Ile Phe Ile Lys225 230 235 240Gly Asn Cys Ala Ser
Glu Glu Val Ile Trp Glu Val Leu Asn Ala Val 245 250 255Gly Val Tyr
Ala Gly Arg Glu His Phe Val Tyr Gly Glu Pro Arg Glu 260 265 270Leu
Leu Thr Lys Val Trp Val Gln Gly His Tyr Leu Glu Tyr Arg Glu 275 280
285Val Pro His Ser Ser Pro Pro Tyr Tyr Glu Phe Leu Trp Gly Pro Arg
290 295 300Ala His Ser Glu Ser Ile Lys Lys Lys Val Leu Glu Phe Leu
Ala Lys305 310 315 320Leu Asn Asn Thr Val Pro Ser Ser Phe Pro Ser
Trp Tyr Xaa Asp Ala 325 330 335Leu Lys Asp Val Glu Glu Arg Val Gln
Ala Thr Ile Asp Thr Ala Asp 340 345 350Asp Ala Thr Val Met Ala Ser
Glu Ser Leu Ser Val Met Ser Ser Asn 355 360 365Val Ser Phe Ser Glu
370721983DNAHomo sapiensmisc_feature(1329)..(1329)n at position
1329 is "a" in MAGE-C2 and "g" in CT10 72tgggaatctg acggatcgga
ggcatttgtg aggaggcgcg aatcaagtta gcggggggaa 60gagtcttaga cctggccagt
cctcagggtg agggccctga ggaagaactg agggacctcc 120caccatagag
agaagaaacc ccggcctgta ctgcgctgcc gtgagactgg tgctccagga
180accaggtggt gacgaactgg gtgtgaggca cacagcctaa agtcagcaca
gcagaggagg 240cccaggcagt gccaggagtc aaggcctgtt ggatctcatc
atccatatcc ctgttgatac 300gtttacctgc tgctcctgaa gaagtcgtca
tgcctcccgt tccaggcgtt ccattccgca 360acgttgacaa cgactccccg
acctcagttg agttagaaga ctgggtagat gcacagcatc 420ccacagatga
ggaagaggag gaagcctcct ccgcctcttc cactttgtac ttagtatttt
480ccccctcttc tttctccaca tcctcttctc tgattcttgg tggtcctgag
gaggaggagg 540tgccctctgg tgtgatacca aatcttaccg agagcattcc
cagtagtcct ccacagggtc 600ctccacaggg tccttcccag agtcctctga
gctcctgctg ctcctctttt tcatggagct 660cattcagtga ggagtccagc
agccagaaag gggaggatac aggcacctgt cagggcctgc 720cagacagtga
gtcctctttc acatatacac tagatgaaaa ggtggccgag ttagtggagt
780tcctgctcct caaatacgaa gcagaggagc ctgtaacaga ggcagagatg
ctgatgattg 840tcatcaagta caaagattac tttcctgtga tactcaagag
agcccgtgag ttcatggagc 900ttctttttgg ccttgccctg atagaagtgg
gccctgacca cttctgtgtg tttgcaaaca 960cagtaggcct caccgatgag
ggtagtgatg atgagggcat gcccgagaac agcctcctga 1020ttattattct
gagtgtgatc ttcataaagg gcaactgtgc ctctgaggag gtcatctggg
1080aagtgctgaa tgcagtaggg gtatatgctg ggagggagca cttcgtctat
ggggagccta 1140gggagctcct cactaaagtt tgggtgcagg gacattacct
ggagtatcgg gaggtgcccc 1200acagttctcc tccatattat gaattcctgt
ggggtccaag agcccattca gaaagcatca 1260agaagaaagt actagagttt
ttagccaagc tgaacaacac tgttcctagt tcctttccat 1320cctggtacna
ggatgctttg aaagatgtgg aagagagagt ccaggccaca attgataccg
1380cagatgatgc cactgtcatg gccagtgaaa gcctcagtgt catgtccagc
aacgtctcct 1440tttctgagtg aagtctagga tagtttcttc cccttgtgtt
tgaacagggc agtttaggtt 1500ctaggtagtg gagggccagg tggggctcga
ggaacgtagt gttctttgca tttctgtccc 1560atatgggtga tgtagagatt
tacctgtttt tcagtatttt ctaaatgctt ttcctttgaa 1620tagcaggtag
ttagcttcag agtgttaatt tatgaatatt agtcgcacat gtattgctct
1680ttatctggtt taagagtaac agtttgatat tttgttaaaa aaatggaaat
accttctccc 1740ttattttgtg atctgtaaca gggtagtgtg gtattgtaat
aggcattttt tttttttttt 1800acaatgtgca ataactcagc agttaaatag
tggaacaaaa ttgaagggtg gtcagtagtt 1860tcatttcctt gtcctgctta
ttcttttgtt cttgaaaatt atatatacct ggctttgctt 1920agcttgttga
agaaagtagc agaaattaaa tcttaataaa agaaaaaaaa aaaaaaaaaa 1980agg
1983731142PRTHomo sapiens 73Met Gly Asp Lys Asp Met Pro Thr Ala Gly
Met Pro Ser Leu Leu Gln1 5 10 15Ser Ser Ser Glu Ser Pro Gln Ser Cys
Pro Glu Gly Glu Asp Ser Gln 20 25 30Ser Pro Leu Gln Ile Pro Gln Ser
Ser Pro Glu Ser Asp Asp Thr Leu 35 40 45Tyr Pro Leu Gln Ser Pro Gln
Ser Arg Ser Glu Gly Glu Asp Ser Ser 50 55 60Asp Pro Leu Gln Arg Pro
Pro Glu Gly Lys Asp Ser Gln Ser Pro Leu65 70 75 80Gln Ile Pro Gln
Ser Ser Pro Glu Gly Asp Asp Thr Gln Ser Pro Leu 85 90 95Gln Asn Ser
Gln Ser Ser Pro Glu Gly Lys Asp Ser Leu Ser Pro Leu 100 105 110Glu
Ile Ser Gln Ser Pro Pro Glu Gly Glu Asp Val Gln Ser Pro Leu 115 120
125Gln Asn Pro Ala Ser Ser Phe Phe Ser Ser Ala Leu Leu Ser Ile Phe
130 135 140Gln Ser Ser Pro Glu Ser Ile Gln Ser Pro Phe Glu Gly Phe
Pro Gln145 150 155 160Ser Val Leu Gln Ile Pro Val Ser Ala Ala Ser
Ser Ser Thr Leu Val 165 170 175Ser Ile Phe Gln Ser Ser Pro Glu Ser
Thr Gln Ser Pro Phe Glu Gly 180 185 190Phe Pro Gln Ser Pro Leu Gln
Ile Pro Val Ser Arg Ser Phe Ser Ser 195 200 205Thr Leu Leu Ser Ile
Phe Gln Ser Ser Pro Glu Arg Ser Gln Arg Thr 210 215 220Ser Glu Gly
Phe Ala Gln Ser Pro Leu Gln Ile Pro Val Ser Ser Ser225 230 235
240Ser Ser Ser Thr Leu Leu Ser Leu Phe Gln Ser Ser Pro Glu Arg Thr
245 250 255Gln Ser Thr Phe Glu Gly Phe Pro Gln Ser Pro Leu Gln Ile
Pro Val 260 265 270Ser Arg Ser Phe Ser Ser Thr Leu Leu Ser Ile Phe
Gln Ser Ser Pro 275 280 285Glu Arg Thr Gln Ser Thr Phe Glu Gly Phe
Ala Gln Ser Pro Leu Gln 290 295 300Ile Pro Val Ser Pro Ser Phe Ser
Ser Thr Leu Val Ser Ile Phe Gln305 310 315 320Ser Ser Pro Glu Arg
Thr Gln Ser Thr Phe Glu Gly Phe Pro Gln Ser 325 330 335Pro Leu Gln
Ile Pro Val Ser Ser Ser Phe Ser Ser Thr Leu Leu Ser 340 345 350Leu
Phe Gln Ser Ser Pro Glu Arg Thr Gln Ser Thr Phe Glu Gly Phe 355 360
365Pro Gln Ser Pro Leu Gln Ile Pro Gly Ser Pro Ser Phe Ser Ser Thr
370 375 380Leu Leu Ser Leu Phe Gln Ser Ser Pro Glu Arg Thr His Ser
Thr Phe385 390 395 400Glu Gly Phe Pro Gln Ser Pro Leu Gln Ile Pro
Met Thr Ser Ser Phe 405 410 415Ser Ser Thr Leu Leu Ser Ile Leu Gln
Ser Ser Pro Glu Ser Ala Gln 420 425 430Ser Ala Phe Glu Gly Phe Pro
Gln Ser Pro Leu Gln Ile Pro Val Ser 435 440 445Ser Ser Phe Ser Tyr
Thr Leu Leu Ser Leu Phe Gln Ser Ser Pro Glu 450 455 460Arg Thr His
Ser Thr Phe Glu Gly Phe Pro Gln Ser Pro Leu Gln Ile465 470 475
480Pro Val Ser Ser Ser Ser Ser Ser Ser Thr Leu Leu Ser Leu Phe Gln
485 490 495Ser Ser Pro Glu Cys Thr Gln Ser Thr Phe Glu Gly Phe Pro
Gln Ser 500 505 510Pro Leu Gln Ile Pro Gln Ser Pro Pro Glu Gly Glu
Asn Thr His Ser 515 520 525Pro Leu Gln Ile Val Pro Ser Leu Pro Glu
Trp Glu Asp Ser Leu Ser 530 535 540Pro His Tyr Phe Pro Gln Ser Pro
Pro Gln Gly Glu Asp Ser Leu Ser545 550 555 560Pro His Tyr Phe Pro
Gln Ser Pro Pro Gln Gly Glu Asp Ser Leu Ser 565 570 575Pro His Tyr
Phe Pro Gln Ser Pro Gln Gly Glu Asp Ser Leu Ser Pro 580 585 590His
Tyr Phe Pro Gln Ser Pro Pro Gln Gly Glu Asp Ser Met Ser Pro 595 600
605Leu Tyr Phe Pro Gln Ser Pro Leu Gln Gly Glu Glu Phe Gln Ser Ser
610 615 620Leu Gln Ser Pro Val Ser Ile Cys Ser Ser Ser Thr Pro Ser
Ser Leu625 630 635 640Pro Gln Ser Phe Pro Glu Ser Ser Gln Ser Pro
Pro Glu Gly Pro Val 645 650 655Gln Ser Pro Leu His Ser Pro Gln Ser
Pro Pro Glu Gly Met His Ser 660 665 670Gln Ser Pro Leu Gln Ser Pro
Glu Ser Ala Pro Glu Gly Glu Asp Ser 675 680 685Leu Ser Pro Leu Gln
Ile Pro Gln Ser Pro Leu Glu Gly Glu Asp Ser 690 695 700Leu Ser Ser
Leu His Phe Pro Gln Ser Pro Pro Glu Trp Glu Asp Ser705 710 715
720Leu Ser Pro Leu His Phe Pro Gln Phe Pro Pro Gln Gly Glu Asp Phe
725 730 735Gln Ser Ser Leu Gln Ser Pro Val Ser Ile Cys Ser Ser Ser
Thr Ser 740 745 750Leu Ser Leu Pro Gln Ser Phe Pro Glu Ser Pro Gln
Ser Pro Pro Glu 755 760 765Gly Pro Ala Gln Ser Pro Leu Gln Arg Pro
Val Ser Ser Phe Phe Ser 770 775 780Tyr Thr Leu Ala Ser Leu Leu Gln
Ser Ser His Glu Ser Pro Gln Ser785 790
795 800Pro Pro Glu Gly Pro Ala Gln Ser Pro Leu Gln Ser Pro Val Ser
Ser 805 810 815Phe Pro Ser Ser Thr Ser Ser Ser Leu Ser Gln Ser Ser
Pro Val Ser 820 825 830Ser Phe Pro Ser Ser Thr Ser Ser Ser Leu Ser
Lys Ser Ser Pro Glu 835 840 845Ser Pro Leu Gln Ser Pro Val Ile Ser
Phe Ser Ser Ser Thr Ser Leu 850 855 860Ser Pro Phe Ser Glu Glu Ser
Ser Ser Pro Val Asp Glu Tyr Thr Ser865 870 875 880Ser Ser Asp Thr
Leu Leu Glu Ser Asp Ser Leu Thr Asp Ser Glu Ser 885 890 895Leu Ile
Glu Ser Glu Pro Leu Phe Thr Tyr Thr Leu Asp Glu Lys Val 900 905
910Asp Glu Leu Ala Arg Phe Leu Leu Leu Lys Tyr Gln Val Lys Gln Pro
915 920 925Ile Thr Lys Ala Glu Met Leu Thr Asn Val Ile Ser Arg Tyr
Thr Gly 930 935 940Tyr Phe Pro Val Ile Phe Arg Lys Ala Arg Glu Phe
Ile Glu Ile Leu945 950 955 960Phe Gly Ile Ser Leu Arg Glu Val Asp
Pro Asp Asp Ser Tyr Val Phe 965 970 975Val Asn Thr Leu Asp Leu Thr
Ser Glu Gly Cys Leu Ser Asp Glu Gln 980 985 990Gly Met Ser Gln Asn
Arg Leu Leu Ile Leu Ile Leu Ser Ile Ile Phe 995 1000 1005Ile Lys
Gly Thr Tyr Ala Ser Glu Glu Val Ile Trp Asp Val Leu 1010 1015
1020Ser Gly Ile Gly Val Arg Ala Gly Arg Glu His Phe Ala Phe Gly
1025 1030 1035Glu Pro Arg Glu Leu Leu Thr Lys Val Trp Val Gln Glu
His Tyr 1040 1045 1050Leu Glu Tyr Arg Glu Val Pro Asn Ser Ser Pro
Pro Arg Tyr Glu 1055 1060 1065Phe Leu Trp Gly Pro Arg Ala His Ser
Glu Val Ile Lys Arg Lys 1070 1075 1080Val Val Glu Phe Leu Ala Met
Leu Lys Asn Thr Val Pro Ile Thr 1085 1090 1095Phe Pro Ser Ser Tyr
Lys Asp Ala Leu Lys Asp Val Glu Glu Arg 1100 1105 1110Ala Gln Ala
Ile Ile Asp Thr Thr Asp Asp Ser Thr Ala Thr Glu 1115 1120 1125Ser
Ala Ser Ser Ser Val Met Ser Pro Ser Phe Ser Ser Glu 1130 1135
1140744265DNAHomo sapiens 74gtctgaagga cctgaggcat tttgtgacga
ggatcgtctc aggtcagcgg agggaggaga 60cttatagacc tatccagtct tcaaggtgct
ccagaaagca ggagttgaag acctgggtgt 120gagggacaca tacatcctaa
aagcaccaca gcagaggagg cccaggcagt gccaggagtc 180aaggttccca
gaagacaaac cccctaggaa gacaggcgac ctgtgaggcc ctagagcacc
240accttaagag aagaagagct gtaagccggc ctttgtcaga gccatcatgg
gggacaagga 300tatgcctact gctgggatgc cgagtcttct ccagagttcc
tctgagagtc ctcagagttg 360tcctgagggg gaggactccc agtctcctct
ccagattccc cagagttctc ctgagagcga 420cgacaccctg tatcctctcc
agagtcctca gagtcgttct gagggggagg actcctcgga 480tcctctccag
agacctcctg aggggaagga ctcccagtct cctctccaga ttccccagag
540ttctcctgag ggcgacgaca cccagtctcc tctccagaat tctcagagtt
ctcctgaggg 600gaaggactcc ctgtctcctc tagagatttc tcagagccct
cctgagggtg aggatgtcca 660gtctcctctg cagaatcctg cgagttcctt
cttctcctct gctttattga gtattttcca 720gagttcccct gagagtattc
aaagtccttt tgagggtttt ccccagtctg ttctccagat 780tcctgtgagc
gccgcctcct cctccacttt agtgagtatt ttccagagtt cccctgagag
840tactcaaagt ccttttgagg gttttcccca gtctccactc cagattcctg
tgagccgctc 900cttctcctcc actttattga gtattttcca gagttcccct
gagagaagtc agagaacttc 960tgagggtttt gcacagtctc ctctccagat
tcctgtgagc tcctcctcgt cctccacttt 1020actgagtctt ttccagagtt
cccctgagag aactcagagt acttttgagg gttttcccca 1080gtctccactc
cagattcctg tgagccgctc cttctcctcc actttattga gtattttcca
1140gagttcccct gagagaactc agagtacttt tgagggtttt gcccagtctc
ctctccagat 1200tcctgtgagc ccctccttct cctccacttt agtgagtatt
ttccagagtt cccctgagag 1260aactcagagt acttttgagg gttttcccca
gtctcctctc cagattcctg tgagctcctc 1320cttctcctcc actttattga
gtcttttcca gagttcccct gagagaactc agagtacttt 1380tgagggtttt
ccccagtctc ctctccagat tcctggaagc ccctccttct cctccacttt
1440actgagtctt ttccagagtt cccctgagag aactcacagt acttttgagg
gttttcccca 1500gtctcctctc cagattccta tgacctcctc cttctcctct
actttattga gtattttaca 1560gagttctcct gagagtgctc aaagtgcttt
tgagggtttt ccccagtctc ctctccagat 1620tcctgtgagc tcctctttct
cctacacttt attgagtctt ttccagagtt cccctgagag 1680aactcacagt
acttttgagg gttttcccca gtctcctctc cagattcctg tgagctcctc
1740ctcctcctcc tccactttat tgagtctttt ccagagttcc cctgagtgta
ctcaaagtac 1800ttttgagggt tttccccagt ctcctctcca gattcctcag
agtcctcctg aaggggagaa 1860tacccattct cctctccaga ttgttccaag
tcttcctgag tgggaggact ccctgtctcc 1920tcactacttt cctcagagcc
ctcctcaggg ggaggactcc ctatctcctc actactttcc 1980tcagagccct
cctcaggggg aggactccct gtctcctcac tactttcctc agagccctca
2040gggggaggac tccctgtctc ctcactactt tcctcagagc cctcctcagg
gggaggactc 2100catgtctcct ctctactttc ctcagagtcc tcttcagggg
gaggaattcc agtcttctct 2160ccagagccct gtgagcatct gctcctcctc
cactccatcc agtcttcccc agagtttccc 2220tgagagttct cagagtcctc
ctgaggggcc tgtccagtct cctctccata gtcctcagag 2280ccctcctgag
gggatgcact cccaatctcc tctccagagt cctgagagtg ctcctgaggg
2340ggaggattcc ctgtctcctc tccaaattcc tcagagtcct cttgagggag
aggactccct 2400gtcttctctc cattttcctc agagtcctcc tgagtgggag
gactccctct ctcctctcca 2460ctttcctcag tttcctcctc agggggagga
cttccagtct tctctccaga gtcctgtgag 2520tatctgctcc tcctccactt
ctttgagtct tccccagagt ttccctgaga gtcctcagag 2580tcctcctgag
gggcctgctc agtctcctct ccagagacct gtcagctcct tcttctccta
2640cactttagcg agtcttctcc aaagttccca tgagagtcct cagagtcctc
ctgaggggcc 2700tgcccagtct cctctccaga gtcctgtgag ctccttcccc
tcctccactt catcgagtct 2760ttcccagagt tctcctgtga gctccttccc
ctcctccact tcatcgagtc tttccaagag 2820ttcccctgag agtcctctcc
agagtcctgt gatctccttc tcctcctcca cttcattgag 2880cccattcagt
gaagagtcca gcagcccagt agatgaatat acaagttcct cagacacctt
2940gctagagagt gattccttga cagacagcga gtccttgata gagagcgagc
ccttgttcac 3000ttatacactg gatgaaaagg tggacgagtt ggcgcggttt
cttctcctca aatatcaagt 3060gaagcagcct atcacaaagg cagagatgct
gacgaatgtc atcagcaggt acacgggcta 3120ctttcctgtg atcttcagga
aagcccgtga gttcatagag atactttttg gcatttccct 3180gagagaagtg
gaccctgatg actcctatgt ctttgtaaac acattagacc tcacctctga
3240ggggtgtctg agtgatgagc agggcatgtc ccagaaccgc ctcctgattc
ttattctgag 3300tatcatcttc ataaagggca cctatgcctc tgaggaggtc
atctgggatg tgctgagtgg 3360aataggggtg cgtgctggga gggagcactt
tgcctttggg gagcccaggg agctcctcac 3420taaagtttgg gtgcaggaac
attacctaga gtaccgggag gtgcccaact cttctcctcc 3480tcgttacgaa
ttcctgtggg gtccaagagc tcattcagaa gtcattaaga ggaaagtagt
3540agagtttttg gccatgctaa agaataccgt ccctattacc tttccatcct
cttacaagga 3600tgctttgaaa gatgtggaag agagagccca ggccataatt
gacaccacag atgattcgac 3660tgccacagaa agtgcaagct ccagtgtcat
gtcccccagc ttctcttctg agtgaagtct 3720agggcagatt cttccctctg
agtttgaagg gggcagtcga gtttctacgt ggtggagggc 3780ctggttgagg
ctggagagaa cacagtgcta tttgcatttc tgttccatat gggtagttat
3840ggggtttacc tgttttactt ttgggtattt ttcaaatgct tttcctatta
ataacaggtt 3900taaatagctt cagaatccta gtttatgcac atgagtcgca
catgtattgc tgtttttctg 3960gtttaagagt aacagtttga tattttgtaa
aaacaaaaac acacccaaac acaccacatt 4020gggaaaacct tctgcctcat
tttgtgatgt gtcacaggtt aatgtggtgt tactgtagga 4080attttcttga
aactgtgaag gaactctgca gttaaatagt ggaataaagt aaaggattgt
4140taatgtttgc atttcctcag gtcctttagt ctgttgttct tgaaaactaa
agatacatac 4200ctggtttgct tggcttacgt aagaaagtcg aagaaagtaa
actgtaataa ataaaagtgt 4260cagtg 42657577DNAHomo sapiens
75gttcccagca gacaaactcc ctaggaagac aggagacctg tgaggcccta gagcaccacc
60ttaagagaag aagagct 77762887DNAHomo
sapiensmisc_feature(1)..(2887)MAGE-C2 gene 76tgggaatctg acggatcgga
ggcatttgtg aggaggcgcg aatcaagtta gcggggggaa 60gagtcttaga cctggccagt
cctcagggtg agggccctga ggaagaactg agggacctcc 120caccatagag
agaagaaacc ccggcctgta ctgcgctgcc gtgagactgg taggtcccag
180acagggaaat ggccccagaa gaagggagga ggtgccggcc ctctagggaa
taaataggaa 240gacactgagg agggctgggg ggaacgcccc acctcagagg
gcagattccc agagattccc 300accctgctcc tcaagtatca gccctcgtag
agctccccag tcagctcagg cggggtggca 360gccatcttat tcctgggtga
gtggcgtagg ggaggcggag gccttggtct gagggtccca 420tggcaagtca
gcacggggag ctgcctctgg ttggcagagg gaagattccc aggccctgct
480ggggataaga ctgaggagtc acatgtgcat cagaacggac gtgaggctac
cccgactgcc 540cccatggtag agtgctggga ggtggctgcc accgccctac
ctcccactgc tctcagggat 600gtggcggttg ctctgaggtt ttgccttagg
ccagcagagt ggtggaggct cggccctctc 660tgagaagccg tgaagttgct
aattaaattc tgagggggcc atgcagtcca gaactatgag 720gctctgggat
tctggccagc cccagctgtc agccctagca ggcccaagac cctacttgca
780gtctttagcc tgaggggctc cctcacttcc tcttgcaggt gctccaggaa
ccaggtggtg 840acgaactggg tgtgaggcac acagcctaaa gtcagcacag
cagaggaggc ccaggcagtg 900ccaggagtca aggtgagtgc acaccctggc
tgtgtaccaa gggccctacc cccagaaaca 960gaggagaccc cacagcaccc
ggccctaccc acctattgtc actcctgggg tctcaggctc 1020tgcctgccag
ctgtgccctg aggtgtgttc ccacatcctc ctacaggttc ccagcagaca
1080aactccctag gaagacagga gacctgtgag gccctagagc accaccttaa
gagaagaaga 1140gctgtaaggt ggcctttgtc agagccatca tgggtgagtt
tctcagctga ggccactcac 1200actgtcactc tcttccacag gcctgttgga
tctcatcatc catatccctg ttgatacgtt 1260tacctgctgc tcctgaagaa
gtcgtcatgc ctcccgttcc aggcgttcca ttccgcaacg 1320ttgacaacga
ctccccgacc tcagttgagt tagaagactg ggtagatgca cagcatccca
1380cagatgagga agaggaggaa gcctcctccg cctcttccac tttgtactta
gtattttccc 1440cctcttcttt ctccacatcc tcttctctga ttcttggtgg
tcctgaggag gaggaggtgc 1500cctctggtgt gataccaaat cttaccgaga
gcattcccag tagtcctcca cagggtcctc 1560cacagggtcc ttcccagagt
cctctgagct cctgctgctc ctctttttca tggagctcat 1620tcagtgagga
gtccagcagc cagaaagggg aggatacagg cacctgtcag ggcctgccag
1680acagtgagtc ctctttcaca tatacactag atgaaaaggt ggccgagtta
gtggagttcc 1740tgctcctcaa atacgaagca gaggagcctg taacagaggc
agagatgctg atgattgtca 1800tcaagtacaa agattacttt cctgtgatac
tcaagagagc ccgtgagttc atggagcttc 1860tttttggcct tgccctgata
gaagtgggcc ctgaccactt ctgtgtgttt gcaaacacag 1920taggcctcac
cgatgagggt agtgatgatg agggcatgcc cgagaacagc ctcctgatta
1980ttattctgag tgtgatcttc ataaagggca actgtgcctc tgaggaggtc
atctgggaag 2040tgctgaatgc agtaggggta tatgctggga gggagcactt
cgtctatggg gagcctaggg 2100agctcctcac taaagtttgg gtgcagggac
attacctgga gtatcgggag gtgccccaca 2160gttctcctcc atattatgaa
ttcctgtggg gtccaagagc ccattcagaa agcatcaaga 2220agaaagtact
agagttttta gccaagctga acaacactgt tcctagttcc tttccatcct
2280ggtacaagga tgctttgaaa gatgtggaag agagagtcca ggccacaatt
gataccgcag 2340atgatgccac tgtcatggcc agtgaaagcc tcagtgtcat
gtccagcaac gtctcctttt 2400ctgagtgaag tctaggatag tttcttcccc
ttgtgtttga acagggcagt ttaggttcta 2460ggtagtggag ggccaggtgg
ggctcgagga acgtagtgtt ctttgcattt ctgtcccata 2520tgggtgatgt
agagatttac ctgtttttca gtattttcta aatgcttttc ctttgaatag
2580caggtagtta gcttcagagt gttaatttat gaatattagt cgcacatgta
ttgctcttta 2640tctggtttaa gagtaacagt ttgatatttt gttaaaaaaa
tggaaatacc ttctccctta 2700ttttgtgatc tgtaacaggg tagtgtggta
ttgtaatagg catttttttt tttttttaca 2760atgtgcaata actcagcagt
taaatagtgg aacaaaattg aagggtggtc agtagtttca 2820tttccttgtc
ctgcttattc ttttgttctt gaaaattata tatacctggc tttgcttagc 2880ttgttga
28877710PRTHomo sapiens 77Leu Leu Phe Gly Leu Ala Leu Ile Glu Val1
5 10789PRTHomo sapiens 78Leu Phe Gly Leu Ala Leu Ile Glu Val1
5799PRTHomo sapiens 79Leu Leu Phe Gly Leu Ala Leu Ile Glu1
5808PRTHomo sapiens 80Leu Leu Phe Gly Leu Ala Leu Ile1
58116PRTARTIFICIAL SEQUENCEProtein sequence of minigene 14 Figure
12B 81Met Glu Leu Leu Phe Gly Leu Ala Leu Ile Glu Val Gly Pro Asp
His1 5 10 158210PRTHomo sapiens 82Ile Leu Phe Gly Ile Ser Leu Arg
Glu Val1 5 108310PRTHomo sapiens 83Leu Val Phe Gly Ile Asp Val Lys
Glu Val1 5 108410PRTHomo sapiens 84Leu Ile Phe Gly Ile Ala Leu Thr
Asp Met1 5 108510PRTHomo sapiens 85Leu Val Phe Gly Leu Ala Leu Lys
Glu Val1 5 108610PRTHomo sapiens 86Leu Leu Phe Gly Ile Asp Val Lys
Glu Val1 5 108710PRTHomo sapiens 87Val Val Phe Gly Leu Glu Leu Asn
Lys Val1 5 108810PRTHomo sapiensMISC_FEATURE(1)..(1)Xaa may be any
amino acid 88Xaa Leu Phe Gly Leu Ala Leu Ile Glu Val1 5
10899PRTHomo sapiens 89Ala Ser Ser Thr Leu Tyr Leu Val Phe1
59010PRTHomo sapiens 90Ser Ala Ser Ser Thr Leu Tyr Leu Val Phe1 5
10918PRTHomo sapiens 91Ser Ser Thr Leu Tyr Leu Val Phe1 5928PRTHomo
sapiens 92Ala Ser Ser Thr Leu Tyr Leu Val1 59360DNAartificial
sequenceOligodT(T7) primer 93tctagtcgac ggccagtgaa ttgtaatacg
actcactata gggcgttttt tttttttttt 609422DNAHomo sapiens 94gtgagacaca
ggttacgaat gt 229524DNAHomo sapiens 95tctggatata cggatgaaca ataa
249619DNAHomo sapiens 96gaagagtcgt ccctgctat 199721DNAHomo sapiens
97tatgtagctt cctcctgaga a 219825DNAHomo sapiens 98agagaaagtt
tttctggaat gtgtc 259920DNAHomo sapiens 99acagtgagcc tggtcccatt
2010019DNAHomo sapiens 100accccgatgc cgactagat 1910120DNAHomo
sapiens 101aggggtgaat tcgtatccaa 2010240DNAHomo
sapiensmisc_featureadditional exon in MAGE C2M 102tcccagcaga
caaactccct aggaagacag gagacctgtg 4010335DNAHomo
sapiensmisc_featureExon sequence in MAGE C2M 103aggccctaga
gcaccacctt aagagaagaa gagct 351041983DNAHomo
sapiensmisc_featureMAGE C2 cDNA sequence 104tgggaatctg acggatcgga
ggcatttgtg aggaggcgcg aatcaagtta gcggggggaa 60gagtcttaga cctggccagt
cctcagggtg agggccctga ggaagaactg agggacctcc 120caccatagag
agaagaaacc ccggcctgta ctgcgctgcc gtgagactgg tgctccagga
180accaggtggt gacgaactgg gtgtgaggca cacagcctaa agtcagcaca
gcagaggagg 240cccaggcagt gccaggagtc aaggcctgtt ggatctcatc
atccatatcc ctgttgatac 300gtttacctgc tgctcctgaa gaagtcgtca
tgcctcccgt tccaggcgtt ccattccgca 360acgttgacaa cgactccccg
acctcagttg agttagaaga ctgggtagat gcacagcatc 420ccacagatga
ggaagaggag gaagcctcct ccgcctcttc cactttgtac ttagtatttt
480ccccctcttc tttctccaca tcctcttctc tgattcttgg tggtcctgag
gaggaggagg 540tgccctctgg tgtgatacca aatcttaccg agagcattcc
cagtagtcct ccacagggtc 600ctccacaggg tccttcccag agtcctctga
gctcctgctg ctcctctttt tcatggagct 660cattcagtga ggagtccagc
agccagaaag gggaggatac aggcacctgt cagggcctgc 720cagacagtga
gtcctctttc acatatacac tagatgaaaa ggtggccgag ttagtggagt
780tcctgctcct caaatacgaa gcagaggagc ctgtaacaga ggcagagatg
ctgatgattg 840tcatcaagta caaagattac tttcctgtga tactcaagag
agcccgtgag ttcatggagc 900ttctttttgg ccttgccctg atagaagtgg
gccctgacca cttctgtgtg tttgcaaaca 960cagtaggcct caccgatgag
ggtagtgatg atgagggcat gcccgagaac agcctcctga 1020ttattattct
gagtgtgatc ttcataaagg gcaactgtgc ctctgaggag gtcatctggg
1080aagtgctgaa tgcagtaggg gtatatgctg ggagggagca cttcgtctat
ggggagccta 1140gggagctcct cactaaagtt tgggtgcagg gacattacct
ggagtatcgg gaggtgcccc 1200acagttctcc tccatattat gaattcctgt
ggggtccaag agcccattca gaaagcatca 1260agaagaaagt actagagttt
ttagccaagc tgaacaacac tgttcctagt tcctttccat 1320cctggtacaa
ggatgctttg aaagatgtgg aagagagagt ccaggccaca attgataccg
1380cagatgatgc cactgtcatg gccagtgaaa gcctcagtgt catgtccagc
aacgtctcct 1440tttctgagtg aagtctagga tagtttcttc cccttgtgtt
tgaacagggc agtttaggtt 1500ctaggtagtg gagggccagg tggggctcga
ggaacgtagt gttctttgca tttctgtccc 1560atatgggtga tgtagagatt
tacctgtttt tcagtatttt ctaaatgctt ttcctttgaa 1620tagcaggtag
ttagcttcag agtgttaatt tatgaatatt agtcgcacat gtattgctct
1680ttatctggtt taagagtaac agtttgatat tttgttaaaa aaatggaaat
accttctccc 1740ttattttgtg atctgtaaca gggtagtgtg gtattgtaat
aggcattttt tttttttttt 1800acaatgtgca ataactcagc agttaaatag
tggaacaaaa ttgaagggtg gtcagtagtt 1860tcatttcctt gtcctgctta
ttcttttgtt cttgaaaatt atatatacct ggctttgctt 1920agcttgttga
agaaagtagc agaaattaaa tcttaataaa agaaaaaaaa aaaaaaaaaa 1980agg
1983105373PRTHomo sapiensmisc_featureMAGE C2 105Met Pro Pro Val Pro
Gly Val Pro Phe Arg Asn Val Asp Asn Asp Ser1 5 10 15Pro Thr Ser Val
Glu Leu Glu Asp Trp Val Asp Ala Gln His Pro Thr 20 25 30Asp Glu Glu
Glu Glu Glu Ala Ser Ser Ala Ser Ser Thr Leu Tyr Leu 35 40 45Val Phe
Ser Pro Ser Ser Phe Ser Thr Ser Ser Ser Leu Ile Leu Gly 50 55 60Gly
Pro Glu Glu Glu Glu Val Pro Ser Gly Val Ile Pro Asn Leu Thr65 70 75
80Glu Ser Ile Pro Ser Ser Pro Pro Gln Gly Pro Pro Gln Gly Pro Ser
85 90 95Gln Ser Pro Leu Ser Ser Cys Cys Ser Ser Phe Ser Trp Ser Ser
Phe 100 105 110Ser Glu Glu Ser Ser Ser Gln Lys Gly Glu Asp Thr Gly
Thr Cys Gln 115 120 125Gly Leu Pro Asp Ser Glu Ser Ser Phe Thr Tyr
Thr Leu Asp Glu Lys 130 135 140Val Ala Glu Leu Val Glu Phe Leu Leu
Leu Lys Tyr Glu Ala Glu Glu145 150 155 160Pro Val Thr Glu Ala Glu
Met Leu Met Ile Val Ile Lys Tyr Lys Asp 165 170
175Tyr Phe Pro Val Ile Leu Lys Arg Ala Arg Glu Phe Met Glu Leu Leu
180 185 190Phe Gly Leu Ala Leu Ile Glu Val Gly Pro Asp His Phe Cys
Val Phe 195 200 205Ala Asn Thr Val Gly Leu Thr Asp Glu Gly Ser Asp
Asp Glu Gly Met 210 215 220Pro Glu Asn Ser Leu Leu Ile Ile Ile Leu
Ser Val Ile Phe Ile Lys225 230 235 240Gly Asn Cys Ala Ser Glu Glu
Val Ile Trp Glu Val Leu Asn Ala Val 245 250 255Gly Val Tyr Ala Gly
Arg Glu His Phe Val Tyr Gly Glu Pro Arg Glu 260 265 270Leu Leu Thr
Lys Val Trp Val Gln Gly His Tyr Leu Glu Tyr Arg Glu 275 280 285Val
Pro His Ser Ser Pro Pro Tyr Tyr Glu Phe Leu Trp Gly Pro Arg 290 295
300Ala His Ser Glu Ser Ile Lys Lys Lys Val Leu Glu Phe Leu Ala
Lys305 310 315 320Leu Asn Asn Thr Val Pro Ser Ser Phe Pro Ser Trp
Tyr Lys Asp Ala 325 330 335Leu Lys Asp Val Glu Glu Arg Val Gln Ala
Thr Ile Asp Thr Ala Asp 340 345 350Asp Ala Thr Val Met Ala Ser Glu
Ser Leu Ser Val Met Ser Ser Asn 355 360 365Val Ser Phe Ser Glu
370
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