U.S. patent application number 10/253867 was filed with the patent office on 2003-07-31 for anticancer vaccine and diagnostic methods and reagents.
This patent application is currently assigned to University of Pittsburgh of the Commonwealth System of Higher Education. Invention is credited to Finn, Olivera J., Hunt, Donald, Kao, Henry, Marto, Jarrod A..
Application Number | 20030143647 10/253867 |
Document ID | / |
Family ID | 23263637 |
Filed Date | 2003-07-31 |
United States Patent
Application |
20030143647 |
Kind Code |
A1 |
Finn, Olivera J. ; et
al. |
July 31, 2003 |
Anticancer vaccine and diagnostic methods and reagents
Abstract
The invention provides a method of priming T cells against tumor
antigens comprising by obtaining nave CD4.sup.+ or CD8.sup.+ T
cells from at least one healthy individual, obtaining at least one
protein or peptide from at least one cancerous cell; obtaining
antigen presenting cells (APCs), culturing the APCs with the at
least one protein or peptide, and adding the T cells to the culture
of the APCs. The primed T cells can then be employed to identify
the antigens or therapeutically as prophylaxis or treatment for
cancers. The invention also provides cyclin molecules, and
fragments derived from cyclin molecules, as tumor antigens. The
invention provides a method for diagnosing a malignant or
pre-malignant condition within a patient. The invention also
provides a method for vaccinating a patient against malignancies
comprising introducing a protein or peptide consisting essentially
of all or an immunogenic fragment of a cyclin protein into the
patient.
Inventors: |
Finn, Olivera J.;
(Pittsburgh, PA) ; Kao, Henry; (St. Louis, MO)
; Hunt, Donald; (Charlottesville, VA) ; Marto,
Jarrod A.; (Charlottesville, VA) |
Correspondence
Address: |
LEYDIG VOIT & MAYER, LTD
TWO PRUDENTIAL PLAZA, SUITE 4900
180 NORTH STETSON AVENUE
CHICAGO
IL
60601-6780
US
|
Assignee: |
University of Pittsburgh of the
Commonwealth System of Higher Education
200 Gardner Steel Conference Center
Pittsburgh
PA
15260
|
Family ID: |
23263637 |
Appl. No.: |
10/253867 |
Filed: |
September 24, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
60324450 |
Sep 24, 2001 |
|
|
|
Current U.S.
Class: |
435/7.23 |
Current CPC
Class: |
C07K 14/4738 20130101;
A61K 39/00 20130101; G01N 33/57484 20130101; A61K 39/0011 20130101;
A61K 2039/5158 20130101; A61P 37/04 20180101 |
Class at
Publication: |
435/7.23 |
International
Class: |
G01N 033/574; A61K
039/00 |
Goverment Interests
[0001] This invention was made in part with Government support
under grant number DAMD 17-9-1-7057 awarded by the United States
Department of Defense and grant numbers 2R37 AI33993 and 5PO1CA
73743 awarded by the United States National Institutes of Health.
The United States Government may have certain rights in this
invention.
Claims
What is claimed is:
1. A method for diagnosing a malignant or pre-malignant condition
within a patient comprising assaying for the expression of a cyclin
molecule within the patient, whereby deregulated cyclin expression
supports a diagnosis of a malignant or pre-malignant condition.
2. The method of claim 1, wherein the condition is diagnosed within
a biopsy comprising tissue excised from the patient.
3. The method of claim 1, wherein the condition is lung cancer or
precancer, breast cancer or precancer, pancreatic cancer or
precancer, or colon cancer or precancer.
4. The method of claim 1, wherein the condition is a malignancy or
premalignancy associated with altered or absent p53 production.
5. The method of claim 1, wherein the cyclin molecule is cyclin
B1.
6. A method for diagnosing a malignant or pre-malignant condition
within a patient comprising assaying for immunoreactivity to a
cyclin molecule within the patient, whereby the presence of
immunoreactivity supports a diagnosis of a malignant or
pre-malignant condition.
7. The method of claim 6, where the immunoreactivity is humoral
immunoreactivity.
8. The method of claim 6, where the immunoreactivity is cellular
immunoreactivity.
9. The method of claim 6, comprising assaying for the serum titer
of antibodies specific for a cyclin molecule within the patient,
whereby elevated antibody titer expression supports a diagnosis of
a malignant or pre-malignant condition.
10. The method of claim 9, wherein the assay is accomplished by
ELISA.
11. The method of claim 6, wherein the condition is lung cancer or
precancer, breast cancer or precancer, pancreatic cancer or
precancer, or colon cancer or precancer.
12. The method of claim 6, wherein the condition is a malignancy or
premalignancy associated with altered or absent p53 production.
13. The method of claim 6, wherein the cyclin molecule is cyclin
B1.
14. A method for vaccinating a patient against malignancies
comprising introducing a peptide consisting essentially of all or
an immunogenic fragment of a cyclin protein into a patient under
conditions sufficient for the patient to develop an immune response
to the cyclin protein.
15. The method of claim 14, wherein the peptide consists
essentially of all or an immunogenic fragment of a cyclin A, D1,
B1, or E protein.
16. The method of claim 14, wherein the peptide consists
essentially of a mature cyclin B1 protein.
17. The method of claim 14, wherein the peptide consists
essentially of a fragment of from about 5 to about 15 contiguous
amino acids of a wild-type human cyclin B1 peptide and which has
from 0 to about 5 single amino acid substitutions relative to the
wild-type sequence.
18. The method of claim 14, wherein the peptide comprises an amino
acid sequence as set forth in SEQ ID NOs: 1-8.
19. A method of priming T cells against tumor antigens comprising,
obtaining nave CD4.sup.+ or CD8.sup.+ T cells from at least one
healthy individual, obtaining at least one protein or peptide from
at least one cancerous cell; obtaining antigen presenting cells
(APCs), culturing the APCs with the at least one protein or
peptide, and adding the T cells to the culture of the APCs, whereby
the T cells are primed against the at least one protein or
peptide.
20. The method of claim 19, wherein the T cells are CD4.sup.+ T
cells
21. The method of claim 19, wherein the at least one protein or
peptide is obtained by lysing the cancerous cell to obtain a lysate
and extracting the protein or peptide from the lysate.
22. The method of claim 19, wherein the T cells are CD8.sup.+ T
cells.
23. The method of claim 19, wherein the at least one protein or
peptide is obtained by extracting HLA class I molecules from the
cancerous cell and eluting the protein or peptide from the
extracted HLA class I molecules.
24. The method of claim 19, wherein the at least one protein or
peptide is fractionated.
25. The method of claim 19, wherein the at least one protein or
peptide is obtained from a tumor comprising the at least one
cancerous cell.
26. The method of claim 19, wherein the APCs are dendritic
cells.
27. The method of claim 26, wherein the dendritic cells are
generated in vitro.
28. The method of claim 19, wherein the APCs are cultured with the
at least one protein or peptide in the presence of tumor necrosis
factor .alpha..
29. The method of claim 19, wherein the T cells are added to the
culture of the APCs in the presence of one or more cytokines.
30. The method of claim 29, wherein the cytokines are selected from
the group of cytokines consisting of IL-1.beta., IL-2, and IL-4,
and IL-7.
31. The method of claim 19, wherein the T cell/APC culture is
restimulated by introducing autologous macrophages, loaded with the
at least one protein or peptide, or irradiated cancerous cells.
32. The method of claim 19, wherein the T cell/APC culture is
restimulated more than one time at intervals of from about 7 to
about 10 days.
33. A method of identifying tumor antigens comprising, obtaining
nave CD4.sup.+ or CD8.sup.+ T cells from at least one healthy
individual, obtaining at least one protein or peptide from at least
one cancerous cell; obtaining antigen presenting cells (APCs),
culturing the APCs with the at least one protein or peptide, and
adding the T cells to the culture of the APCs, whereby the T cells
are primed against the at least one protein or peptide, and
assessing the peptide sequence of the stimulatory molecules.
34. The method of claim 33, wherein the T cells are CD4.sup.+ T
cells
35. The method of claim 33, wherein the at least one protein or
peptide is obtained by lysing the cancerous cell to obtain a lysate
and extracting the protein or peptide from the lysate.
36. The method of claim 33, wherein the T cells are CD8.sup.+ T
cells.
37. The method of claim 33, wherein the at least one protein or
peptide is obtained by extracting HLA class I molecules from the
cancerous cell and eluting the protein or peptide from the
extracted HLA class I molecules.
38. The method of claim 33, wherein the at least one protein or
peptide is fractionated.
39. The method of claim 33, wherein the at least one protein or
peptide is obtained from a tumor comprising the at least one
cancerous cell.
40. The method of claim 33, wherein the APCs are dendritic
cells.
41. The method of claim 41, wherein the dendritic cells are
generated in vitro.
42. The method of claim 33, wherein the APCs are cultured with the
at least one protein or peptide in the presence of tumor necrosis
factor .alpha..
43. The method of claim 33, wherein the T cells are added to the
culture of the APCs in the presence of one or more cytokines.
44. The method of claim 43, wherein the cytokines are selected from
the group of cytokines consisting of IL-1.beta., IL-2, and IL-4,
and IL-7.
45. The method of claim 33, wherein the T cell/APC culture is
restimulated by introducing autologous macrophages, loaded with the
at least one protein or peptide, or irradiated cancerous cells.
46. The method of claim 33, wherein the T cell/APC culture is
restimulated more than one time at intervals of from about 7 to
about 10 days.
Description
FIELD OF THE INVENTION
[0002] This invention pertains to methods and reagents for
diagnosing and vaccinating against cancer.
BACKGROUND OF THE INVENTION
[0003] Successful immunotherapy against tumors relies in part on
the discovery of tumor-specific antigens that are able to stimulate
effective immune responses in the host. Several approaches have
been developed over the years for the identification of such
tumor-specific antigens. The "genetic approach" uses tumor cDNA
libraries transfected into target cells expressing appropriate HLA
molecules. The "peptide elution approach" uses peptides eluted from
tumor HLA and loaded on target cells bearing the same HLA
molecules. The "reverse immunology approach" uses peptide sequences
derived from already known oncogenes or other putative tumor
associated genes that contain desired HLA anchor motifs. All these
approaches depend on the availability of tumor-specific T from
cancer patients cell lines or clones derived from cancer patients
used to recognize the new targets. Most recently, the SEREX
approach has been used in which tumor cDNA expression libraries are
screened with sera from cancer patients. Existing methods of
identifying tumor antigens pose several concerns. For example, many
such methods rely on T cells from cancer patients or use tumor
cells as antigen presenting cells (APCs). However, T cells from
cancer patients often are defective, and tumor cells are often poor
APCs (Kiessling et al., Springer Seminars in Immunopathology, 18,
227-42 (1996); Ostrand-Rosenberg, Cur. Opin. Immunol., 6, 722-27
(1994)).
[0004] Existing approaches have led to the identification of a
panel of tumor antigens (Wang et al., Immunol. Rev. 170:, 85-100
(1999)), primarily in melanomas (Boel et al., Immunity, 2, 167-75
(1995); Gaugler et al., J. Exp. Med., 179, 921-30 (1994); Herman et
al., Immunogenetics, 43, 377-83 (1996).; Traversari et al., J. Exp.
Med., 176, 1453-57 (1992); Van den Eynde et al., J. Exp. Med., 182,
689-98 (1995); van der Bruggen et al., Eur. J Immunol., 24, 3038-43
(1994); van der Bruggen el al., Eur. J. Immunol., 24, 2134-40
(1994)). Very few tumor-specific antigens have been described in
epithelial tumors, the best know being the Her-2/neu derived
peptides (Disis et a., Cri.t Rev. Immunol. 18, 37-45 (1998)) and
the core peptides of the MUC-1 tandem repeat (Barratt-Boyes et al.,
Cancer Immunology, Immunotherapy, 43, 142-51 (1996)).
[0005] In light of the foregoing, there remains a need for an
improved method for discovering tumor antigens and also for
additional tumor antigens.
BRIEF SUMMARY OF THE INVENTION
[0006] The invention provides a method of priming T cells against
tumor antigens comprising by obtaining nave CD4.sup.+ or CD8.sup.+
T cells from at least one healthy individual, obtaining at least
one protein or peptide from at least one cancerous cell; obtaining
antigen presenting cells (APCs), culturing the APCs with the
protein(s) or peptide(s), and adding the T cells to the culture of
the APCs. The primed T cells can then be employed to identify the
antigens or used as prophylaxis or treatment for cancers.
[0007] The invention also provides cyclin molecules, and fragments
derived from cyclin molecules, as tumor antigens. The invention
provides a method for diagnosing a malignant or pre-malignant
condition within a patient. The invention also provides a method
for vaccinating a patient against malignancies comprising
introducing a protein or peptide consisting essentially of all or
an immunogenic fragment of a cyclin protein into the patient.
[0008] These and other aspects of the invention will become
apparent upon reading the following detailed description in
conjunction with the accompanying drawings.
BRIEF DESCRIPTION OF THE DRAWINGS
[0009] FIG. 1 shows the results of experiments identifying of 12
primed CD8.sup.+ T cell cultures that recognized the original
tumor, MS-A2, from which the tumor peptides were derived. The
primed T cells were tested after the fourth restimulation. E:T
ratio was at 100:1. The Raji cell line (A3, B15, C7) was a control
for alloreactivity.
[0010] FIG. 2 presents the results of experiments in which
CD8.sup.+ T cells primed with peptide fraction # 32 from MS-A2
tumor recognized a shared tumor antigen on a lung tumor cell line,
201T-A2. CD8.sup.+ T cells generated from priming to eluted
peptides from Fraction # 32 were used in a CTL assay after the
fifth restimulation.
[0011] FIG. 3 presents the results of experiments in which
CD8.sup.+ T cells primed with pooled peptide fractions recognized
the original tumor and were HLA Class I-restricted. A) CD8.sup.+ T
cells primed with peptide fractions #41-46 recognized the original
tumor, MS-A2 and were blocked by the anti-MHC Class I antibody,
W6/32. B) CD8.sup.+ T cells primed with peptide fractions #61-65
recognized the original tumor (MS-A2), and not an HLA-matched
tumor, Mel 624.
[0012] FIG. 4 presents the results of experiments which identified
of 12 primed CD4.sup.+ T cell cultures that recognized the original
tumor, MS, from which the proteins were obtained. The primed
CD4.sup.+ T cells were tested in a proliferation assay using
macrophages loaded with UV-B induced apoptotic tumor
(20:1=T:macrophages) after the second restimulation.
[0013] FIG. 5 presents the results of experiments in which
CD4.sup.+ T cell cultures primed with protein fractions recognize
autologous macrophages loaded with tumor lysate. 2.times.10.sup.6
autologous macrophages were loaded with .about.1.75.times.10.sup.8
cell equivalents of tumor lysate for 2 hours and used as
stimulators of primed CD4.sup.+ T cell cultures in a proliferation
assay. T cell cultures were pooled as indicated. T cells were added
at a T cell macrophage ratio of 10:1.
[0014] FIG. 6 presents the results of SDS PAGE and functional
analysis of subfractions # 44.1-# 44.10 according to which 33% of
each sub-fraction was loaded onto 5.times.10.sup.4 macrophages
overnight and added to T cells primed to Fraction # 44 with a
T:stimulator ratio of 1:1 for a 5-day proliferation assay.
[0015] FIG. 7 presents HLA Class I-restricted T cell response of a
healthy donor to cyclin B1 peptides. CD8.sup.+ T cells generated in
vitro by priming to synthetic cyclin B1 peptides were used in an
IFN-.gamma. assay after the fourth restimulation. Number of T cells
per well is indicated in parenthesis.
[0016] FIG. 8 presents HLA Class I-restricted T cell responses to
cyclin B1 peptides in HLA-A2+ breast cancer patients. PBMCs from
breast cancer patients were tested for recognition of cyclin B1
peptides after one in vitro stimulation (A, B, E, F) or no in vitro
stimulation (C, D) in an IFN-.gamma. assay. Number of T cells per
well is indicated in parenthesis.
[0017] FIG. 9 presents HLA Class I-restricted T cell responses to
cyclin B1 peptides in HLA-A2.1+SCCHN patients. PBMCs were tested
for recognition of cyclin B1 peptides after one (A) or two in vitro
stimulations (B, C, D) in an IFN-.gamma. ELISPOT assay.
[0018] FIG. 10 presents the results of experiments that reveal that
T cells from an HLA-A2.1+SCCHN patient restimulated to cyclin B1
peptides in vitro are able to kill the original tumor. T cells
restimulated with A) P4, and B) CB9 for 5 days and tested in a CTL
assay.
[0019] FIG. 11 presents data from experiments revealing the
presence of cyclin B1 antibody in the sera of cancer patients.
[0020] FIG. 12 presents data from experiments revealing the
presence of cyclin B1 antibody in the sera of cancer patients.
[0021] FIG. 13 presents data from experiments revealing the
presence of cyclin B1 antibody in the sera of cancer patients.
[0022] FIG. 14 presents data concerning the expression of Cyclin B1
from lung cancer patients and five healthy individuals.
[0023] FIG. 15 presents data concerning the expression of Cyclin B1
from patients with adinocarcinomas.
[0024] FIG. 16 presents data concerning the expression of Cyclin B1
in cigarette smokers and non-smokers.
DETAILED DESCRIPTION OF THE INVENTION
[0025] In one embodiment, the invention provides a method of
priming T cells (e.g., cytotoxic or helper cells) against tumor
antigens. The method involves obtaining nave CD4.sup.+ or CD8.sup.+
T cells from at least one healthy individual, obtaining at least
one protein or peptide from at least one cancerous cell, and
obtaining APCs. The APCs then are cultured with the protein(s) or
peptide(s) from the cancer cell(s). Following this period of
culturing the APCs with the protein(s) or peptide(s) from the
cancer cell(s), the T cells then are added to the culture, and they
can be thus cultured for several weeks. Eventually, the T cells
become primed against at least one protein(s) or peptide(s) from
the cancer cell(s), e.g., they become cytotoxic to or activated by
(e.g., to produce cytokines such as IFN-.gamma.) tumor cells (or
other cells) expressing or having such protein(s) or peptide(s).
Where the method further comprises assessing the peptide sequence
of the stimulatory molecules (e.g., the protein(s) or peptide(s)).
The method can be used to identify the antigenic protein(s) or
peptide(s).
[0026] In accordance with the method, nave CD4.sup.+ or CD8.sup.+ T
cells are obtained from at least one healthy individual. In this
context, "healthy" is taken to indicate an individual who has not
been diagnosed with a malignant condition. The nave CD4.sup.+ or
CD8.sup.+ T cells can be obtained from such a healthy individual by
methods such as are known in the art or as set forth below in the
Examples. Of course, using such methods, one of skill in the art is
able to obtain a population of CD4.sup.+ T cells, a population of
CD8.sup.+ T cells, or a mixed population, as desired.
[0027] Once the population of CD4.sup.+ or CD8.sup.+ T cells is
obtained, at least one protein or peptide is obtained from at least
one cancerous cell, typically a tumor or cell line containing more
than one (and potentially numerous) such cancer cells. While the
protein(s) or peptide(s) can be obtained by any suitable method, it
is desirable to employ certain methods depending on the type of T
cell. In this regard, CD4.sup.+ T cells typically respond more
favorably to larger peptides or mature proteins, whereas CD8.sup.+
tend to respond more favorably to shorter peptides. Thus, where the
T cells are CD4.sup.+ T cells, the protein(s) or peptide(s)
preferably is/are obtained by a method that can extract large
peptides or even whole proteins from the cell(s). According to one
exemplary method, the cancerous cell(s) can be lysed to obtain a
lysate from which the protein(s) or peptide(s) can be extracted. Of
course, such extraction can produce a "whole protein" extract,
representing all proteins separated from the rest of the lysate.
However, if desired, a particular class of protein can be extracted
(e.g., by size, gel motility, etc.) from the lysate. Conversely,
where the T cells are CD8.sup.+ T cells, the protein(s) or
peptide(s) is/are obtained by a method that can extract smaller
peptides from the cell(s). For example, the cancerous cell(s) can
be treated to extract HLA class I molecules (which can include type
A, B, C, or any allele of HLA class I molecules), which typically
are complexed with processed peptides. Such proteins can be
obtained from the cell(s) or tumor(s) by methods known in the art
(see, e.g., Hunt et al., Science, 255, 1261-63 (1992); Henderson et
al., Science, 255, 1264-66 (1992)). The HLA class I molecules then
can be treated to release the complexed peptides, which then can be
exposed to the CD8.sup.+ T cells in accordance with the inventive
method.
[0028] However obtained, the protein(s) or peptide(s) can be
fractionated (e.g., using HPLC, and especially RP-HPLC), and even
further sub-fractioned as desired, prior to exposure to the
CD4.sup.+ or CD8.sup.+ T cells. Fractionation (and if desired,
sub-fractionation) facilitates identification of the antigen within
the fraction of protein(s) or peptide(s), as described herein.
[0029] The APCs for use in the inventive method can be any kind of
"professional" antigen presenting cell, such as B-cells, dendritic
cells, lymphoid fibroblasts, Langerhans cells, macrophages,
monocytes, peripheral blood fibrocytes, etc. However, dendritic
cells are particularly adept at presenting antigens, and they can
be generated in vitro by methods known in the art (see, e.g.,
Hiltbold et al., Cancer Res., 58: 5066-70 (1998)). As such,
preferably, the APCs are dendritic cells. In accordance with the
inventive method, the APCs are cultured with the protein(s) or
peptide(s) (or fraction or sub-fraction thereof) under conditions
suitable for them to present the molecules (e.g., as an MHC I or II
presented molecule). For example, with or following exposure to the
protein(s) or peptide(s) (or fraction or sub-fraction thereof), the
culture of APCs can be maintained in the presence of tumor necrosis
factor .alpha..
[0030] Following the initial incubation of the APCs with the
protein(s) or peptide(s) (or fraction or sub-fraction thereof), the
CD4.sup.+ or CD8.sup.+ T cells are added to the culture. Typically,
the T cells are added to the culture of the APCs in the presence of
one or more cytokines (e.g., IL-1b, IL-2, and IL-4, and IL-7), but
this is not necessary in all applications. Moreover, the culture
can be maintained over several weeks or months, over which period
the culture conditions can be maintained or changed, as desired. In
this regard, the T cell/APC culture can be restimulated, for
example by introducing autologous macrophages, adding or changing
the cytokine mixtures, adding additional protein(s) or peptide(s)
(or fraction or sub-fraction thereof) or irradiated cancerous cells
to the culture. Such cultures can be restimulated several times to
enhance the degree to which the T-cells are primed, typically at
intervals of from about 5 to about 15 days (e.g., from about 7 to
about 10 days). Generally, more restimulation may be desired if the
initial protein or peptide concentration is small.
[0031] Following this treatment, the CD4.sup.+ or CD8.sup.+ T-cells
can be assayed to determine if they have been primed by any
suitable method. For example, cytotoxic T-cells can be cultured
with cells from which the protein(s) or peptide(s) (or fraction or
sub-fraction thereof) was/were derived (e.g., the same tumor or
cell line). The degree to which the T-cells inhibit proliferation
of (or even kill) such cells is an indication that the T cells have
become primed to be cytotoxic against such cells or tumors.
[0032] The primed CD4.sup.+ or CD8.sup.+ T-cells can be
restimulated, such that a stable antigen-reactive T cell culture or
T cell line can be maintained for extended periods in vitro.
Therefore, T cells reactive to cancer cells can be generated
rapidly in large numbers in vitro for various therapeutic and
prophylactic applications. The antigen-reactive T cell culture or T
cell line can be stored, and used to resupply cytotoxic T cells for
long-term use. The primed T cells can be used in vitro, e.g., as
part of a diagnostic process for identifying cancers.
Alternatively, the primed cytotoxic or helper T cells can be
introduced into a patient for prophylaxis or treatment of
cancers.
[0033] For in vivo use, the invention provides a pharmaceutical
composition comprising a therapeutically or prophylactically
effective amount of primed T cells and a pharmaceutically
acceptable carrier or excipient. Such a carrier includes but is not
limited to culture medium with or without serum, buffered saline,
dextrose, water, glycerol, ethanol, and combinations thereof. The
composition, if desired, also can contain other excipients, such as
wetting agents, emulsifying agents, pH buffering agents, and the
like. The composition comprising the helper or cytotoxic cells can
be introduced into the patients systemically, or locally (e.g.,
intratumorally). Such a method can be used alone or adjunctively in
conjunction with other therapeutic regimens.
[0034] In another embodiment, the invention provides cyclin
proteins and peptide fragments thereof as antigens, such as tumor
antigens, and in particular of epithelial-associated tumors. The
cyclin molecule can comprise or consist of a mature cyclin protein,
such as cyclin A, D1, B 1, or E protein. Alternatively, the
molecule can consist essentially of such a protein or an
immunogenic peptide fragment thereof. In this regard, an antigenic
cyclin peptide can represent a fragment of from about 5 to about 15
contiguous amino acids (e.g., from about 8 to about 12 contiguous
amino acids, or even about 9 or 10 contiguous amino acids) of a
wild-type human cyclin protein. Such peptides or full length
proteins can include some variation from the native sequence, such
as having anywhere from 0 to about 5 single amino acid
substitutions relative to a wild-type sequence of about 10 amino
acids. Exemplary antigenic cyclin-derived peptides are set forth
here as SEQ ID NOs: 1-8:
[0035] SEQ ID NO: 1 AGYLMELCV
[0036] SEQ ID NO: 2 AGYLMELCM
[0037] SEQ ID NO: 3 AGYLMELCF
[0038] SEQ ID NO: 4 AGYLMELCC
[0039] SEQ ID NO: 5 AGYLMELCMA
[0040] SEQ ID NO: 6 AGYLMELCFA
[0041] SEQ ID NO: 7 AKYLMELTM
[0042] SEQ ID NO: 8 AKYLMELTML
[0043] Desirably, the cyclin peptides are able to stimulate (or
prime) helper cells or cytotoxic cells (and preferably both types
of cells) when presented to them by professional APCs, for example
as described above. Such cytotoxic or helper cells can be employed
as prophylaxis or treatment of tumors in vivo, such as epithelial
tumors (e.g., breast cancer, basal or squamous cell carcinoma,
melanoma, cutaneous lymphoma, etc.), particularly those exhibiting
deregulated cyclin expression or overexpression of cyclin
molecules. For example, activated cytotoxic T cells or helper cells
can be introduced into a patient diagnosed with such malignant
conditions, either systemically or intratumorally, for example as
discussed above or in accordance with methods known in the art
(see, e.g., U.S. Pat. No. 6,130,087). Because Cyclin B1 appears to
be overexpressed in cells that turn off the function of the tumor
suppressor protein p53 (Yu et al., Mol. Immunol., 38(12-13), 981-87
(2002)), patients with p53-negative tumors would be particularly
attractive candidates for treatment in accordance with the present
invention.
[0044] The antigenic protein or peptide can be produced by any
suitable method. For example, it can be synthesized using standard
direct peptide synthesizing techniques (Bodanszky, Principles of
Peptide Synthesis (Springer-Verlag, Heidelberg: 1984)), such as via
solid-phase synthesis (see, e.g., Merrifield, J. Am. Chem. Soc.,
85, 2149-54 (1963); Barany et al., Int. J. Peptide Protein Res.,
30, 705-739 (1987); and U.S. Pat. No. 5,424,398). Alternatively, a
gene encoding the desired protein or peptide can be subcloned into
an appropriate expression vector using well-known molecular genetic
techniques. The protein or peptide can then be produced by a host
cell and isolated from the cell. Any appropriate expression vector
(see, e.g., Pouwels et al., Cloning Vectors: A Laboratory Manual
(Elsevior, N.Y.: 1985)) and corresponding suitable host cells can
be employed for production of the desired protein or peptide.
Expression hosts include, but are not limited to, bacterial
species, mammalian or insect host cell systems including
baculovirus systems (see, e.g., Luckow et al., Bio/Technology, 6,
47 (1988)), and established cell lines such 293, COS-7, C127, 3T3,
CHO, HeLa, BHK, etc. Once isolated, protein or the peptide can be
substantially purified by standard methods and formulated into a
pharmaceutical composition (e.g., including a pharmacologically- or
physiologically-compatible carrier), lyophilized, or otherwise
employed or preserved.
[0045] Using such cyclin proteins, or peptides derived from cyclin
proteins, the invention provides a method for vaccinating a patient
against malignancies. The method can be used prophylactically or as
a treatment for many types of cancer (e.g., cancers of bladder,
bone, brain, breast, cervix, colon, epithelium, esophagus, head and
neck, kidney, liver, lung, ovary, pancreas, prostate, skin,
stomach, testicle, uterus, etc., and the various leukemias and
lymphomas). Because Cyclin B1 appears to be overexpressed in cells
that turn off the function of the tumor suppressor protein p53 (Yu
et al., Mol. Immunol., 38(12-13), 981-87 (2002)), patients with
p53-negative tumors would be particularly attractive candidates for
treatment in accordance with the present invention. Moreover, the
vaccines can have the potential or capability to prevent cancer in
individuals without cancer but who are or may become at risk of
developing cancer.
[0046] In accordance with this aspect of the invention, a protein
or peptide comprising or consisting essentially of all or an
immunogenic fragment of a cyclin protein is introduced into a
patient under conditions sufficient for the patient to develop an
immune response to the protein or peptide. Desirably, the protein
or peptide is a Cyclin B1 protein or immunogenic fragment thereof,
as set forth herein. The immune response in the patient can help
protect the patient against cancers that might develop in the
future--i.e., after the vaccination in accordance with the
inventive method. For patients diagnosed with cancer, the inventive
method can augment the patient's ability to combat the cancer. In
this regard, the inventive method can be employed alone or
adjunctively with other anticancer treatments (e.g., radiation
therapy, chemotherapy, etc.).
[0047] The protein or peptide can be introduced into a patient by
any desired method. For example, it can be formulated into a
pharmaceutical composition including, if desired, a
physiologically-compatible buffered solution and injected into the
patient (e.g., intradermally, subcutaneously, intramuscularly into
the blood stream, or other suitable route). The administration to a
patient of a vaccine in accordance with this invention for
prophylaxis and/or treatment of cancer can take place before or
after a surgical procedure to remove the cancer, before or after a
chemotherapeutic procedure for the treatment of cancer, or before
or after radiation therapy for the treatment of cancer and any
combination thereof. In addition, the vaccine can be given together
with adjuvants and/or immuno-modulators to boost the activity of
the vaccine and the patient's response.). Moreover, additional
inoculations (e.g., "booster" inoculations) can be employed as
desired. Following the inoculation(s), the patient's immune
response to the antigen can be monitored, for example, by drawing
blood from the patient and assessing the presence of
immunoglobulins reactive against the cyclin protein or peptide or
for the presence of lymphocytes reactive against the protein or
peptide.
[0048] In another embodiment, the invention provides a method for
diagnosing a pre-malignant or malignant condition within a patient.
In accordance with one aspect of the method, the patient can be
assayed for the expression of a cyclin molecule (e.g., protein or
peptide fragment thereof). For example, the method can be employed
on biopsied tissue (e.g., lung tissue, lymph nodes, epidermal
lesions, breast lesions, dysplastic nevi, colon or cervical polyps,
warts, etc.) excised from the patient. The cells of such tissues
can be fixed and inimunoassayed for the expression of the desired
cyclin molecule (e.g., cyclin A, D1, B1, E, etc.). Deregulated
cyclin expression supports a diagnosis of a pre-malignant or
malignant condition. For example, cytoplasmic staining of Cyclin
B1, rather than nuclear staining, is indicative of malignant or
pre-malignant cells within the biopsy. Overexpression of the cyclin
molecule (e.g., high levels of expression relative to adjacent or
control tissue) also can support a diagnosis of a malignant or
pre-malignant condition.
[0049] In accordance with another aspect of the method, the patient
can be assayed for immunoreactivity to cyclin molecules (such as
cyclin A, D1, B1, E, etc.). Such reactivity can, for example, be
humoral or cellular immunity, which can be assessed by measuring
antibody molecules (e.g., immunoglobulins) in fluid (e.g., blood
product) drawn from the patient. For example, the titer of
anti-cyclin antibodies within the serum of a patient can be
ascertained using any standard assay (e.g., ELISA). In other
embodiments, immunoreactivity to the cyclin molecule(s) can be
assessed by detecting the presence of T cells reactive to the
cyclin molecule(s) in fluid or tissue drawn from the patient. The
presence of immunoreactivity to the desired cyclin molecule (such
as, for example, a noted elevation in the titer of anti-cyclin
antibodies in comparison with a standardized baseline or in
comparison with healthy patients) can support a diagnosis of a
pre-malignant or malignant condition. Such a test can, for example,
assist in the diagnosis of lung cancer, prostate cancer, breast
cancer, as well as cancers associated with abnormal or absent p53.
Of course, the inventive method of diagnosis, however carried out,
can be employed alone or in conjunction with other diagnostic
methods or in conjunction with the evaluation of other relevant
information (such as genetic propensity, family history, identified
risk factors, and the like). Thus, for example, the detection of
elevated serum anti-cyclin antibody titer in a heavy, long-term
smoker (a known risk factor for lung cancers), can serve as an
early warning sign of an increase risk in that patient for
developing lung cancer. Such a test also can help monitor cancer
patients following treatment for the purpose of detecting
recurrence, as elevation of anti-cyclin antibody titer correlates
with the recurrence of some types of cancers (e.g., lung cancers,
adenocarcinoma, etc.).
[0050] As discussed above, various aspects of the invention involve
treatment of patients and in vivo application of reagents. Such
patients typically are mammalian, and can be human. In light of the
extensive conservation of the antigen among species, the patient
can be selected from any mammalian species (e.g., feline, canine,
bovine, porcine, equine, rodent, ungulate, primate, etc.). The
patient can be a healthy individual or diseased. In this regard,
the methods of prophylaxis can be used to help guard healthy
patients from subsequent development of cancers. Methods of
treatment can be used to attenuate tumor growth or metastasis, and
in some applications such methods can regress tumor growth or
reduce tumor size. Indeed, in some applications, the inventive
methods, alone or in conjunction with other therapeutic methods,
can eliminate tumors or cancerous cells from a patient.
EXAMPLE 1
[0051] This example demonstrates the efficacy of the inventive
method of priming T cells (e.g., cytotoxic or helper cells) against
tumor antigens.
Materials and Methods
[0052] Cell lines. MS (A3, B7, B7, C7, C7; DR15, DQ6 homozygous) is
a breast epithelial adenocarcinoma cell line derived from the
metastasis of a breast cancer patient. This cell line does not
express either MUC-1 or Her-2/neu, the two major epithelial tumor
antigens. MS-A2 is the same cell line that was stably transfected
with the HLA-A2.1 plasmid (Vega et al., Proc. Nat. Acad. Sci., 86,
2688-92 (1989)) using the calcium phosphate precipitation method
(Stratagene, La Jolla, Calif.). The B lymphoma cell line Raji (A3,
B15, C7 homozygous; DR3, DR10, DQ1, DQ2) was purchased from the
American Type Culture Collection (Manassas, Va.). The chronic
myelogenous leukemia cell line K562 was also purchased from ATCC.
The melanoma cell line Mel 624 is A2, A3, B7 homozygous. The lung
tumor cell line, 201T is A10, A29, B15, B44, also was transfected
with the HLA-A2.1 plasmid (designated 201T-A2). Nave CD4.sup.+ ,
CD8.sup.+ T cells, dendritic cells, and macrophages were derived
from a leukophoresis product of a healthy platelet donor (A2, A29,
B7, B44, C7, C7; DR15, DR7, DQ6, DQ2).
[0053] Antibodies. Mouse anti-human HLA-DR (L243), CD3 (Leu-4), CD4
(Leu-3a), CD8 (Leu-2a), and CD56 (Leu-19) were purchased from
Becton Dickinson (San Jose, Calif.). Mouse anti-human CD45RO
(UCHL1) and CD20 were purchased from DAKO (Carpinteria, Calif.).
Goat anti-mouse IgG antibodies were obtained from Zymed
Laboratories, Inc. (South San Francisco, Calif.). W6/32, a mouse
anti-human MHC Class I antibody, was produced by the W/632
hybridoma obtained from ATCC (Manassas, Va.) and purified via a
Protein A-Sepharose column (Sigma, St. Louis, Mo.) in the
laboratory.
[0054] Isolation of tumor HLA Class I-bound peptides. Preparation
of HLA Class I-associated peptides was similar to previously
described methods (Hunt et al., Science, 255, 1261-63 (1992),
Henderson et al., Science, 255, 1264-66 (1992)). MS-A2 tumor cells
were grown in 10-chamber cell factories (Nalge Nunc, Naperville,
Ill.), and expanded weekly until >1.5.times.10.sup.10 cells were
obtained. The cells were washed three times in ice-cold PBS,
pelleted and stored at -800 C. for later use. Detergent lysis
buffer (1% CHAPS) and a cocktail of protease inhibitors (2 mM PMSF,
100 mM Iodoacetamide, 5 mg/ml Aprotinin, 10 mg/ml Leupeptin, 10
mg/ml Pepstatin A, 3 ng/ml EDTA, and 0.04% sodium azide) (Sigma,
St. Louis, Mo.) were used to solubilize the cells at 4.degree. C.
for 1 hr. The cell lysate was spun at 100,000.times. g for 1 hour
to remove insoluble proteins, and the supernatant was filtered
through a 0.22 mm filter (Millipore, Bedford, Mass.) to further
remove debris from the suspension. The supernatant was then passed
through a Protein A-Sepharose anti-class I (W6/32) column (BioRad,
Hercules, Calif.) overnight. The column then was washed 30 times
sequentially with low salt (150 mM NaCl, 20 mM Tris pH 8.0), high
salt (1 M NaCl, 20 mM Tris pH 8.0), and Tris buffer (20 mM Tris pH
8.0). Class I molecules then were eluted from the column using 0.2N
acetic acid, and peptides were extracted from the Class I molecules
by boiling in 10% acetic acid for 5 minutes. The released peptides
were further purified using 5 kD cut-off microconcentrators
(Amicon, Bedford, Mass.), vacuum centrifuged to reduce the volume,
and frozen at -800.degree. C.
[0055] Fractionation of peptide extracts. The peptide extracts were
fractionated by reverse phase HPLC on a Rainin HPLC separation
system (Varian, Woburn, Mass.). The peptide extracts were
concentrated to 150 ml via vacuum centrifugation, and injected into
a Brownlee Aquapore (Applied Systems Inc., San Jose, Calif.) C18
column (column dimensions: 2.1 mm.times.3 cm, pore size: 300 .ANG.,
particle size: 7 mm) on the HPLC. The peptides were eluted with a
65 minute trifluoracetic acid/acetonitrile gradient [v/v 0-15% for
5 minutes, 15-60% for 50 minutes, and 60-100% for 10 minutes
solvent B (60% acetonitrile in 0.085% TFA) in solvent A (De-ionized
water in 0.1% TFA) with a flow rate of 200 ml/min]. Two hundred
microliter fractions were collected at one minute intervals,
concentrated via vacuum centrifugation to 40 ml, and divided into 4
aliquots, 3 for the use in T cell stimulation and 1 for mass
spectrometry analysis.
[0056] Fractionation of protein extracts. >1.times.10.sup.9 MS
tumor cells were lysed in detergent buffer, spun at 100,000.times.
g, and then filtered using a 0.22 mm filter as above. The
supernatant was dialyzed overnight in Tris Buffered Saline pH 7.2
(TBS) (Sigma) to remove detergent. The protein extract was
concentrated by vacuum centrifugation, and one-tenth of the extract
(.about.1.times.10.sup.8 cell equivalents) was fractionated by
reverse-phase HPLC using a Phenomenex Jupiter C4 column (column
dimensions: 4.6 mm.times.150 mm, pore size: 300 .ANG., particle
size: 7 mm) (Torrence, Calif.). The proteins were eluted with a 60
minute TFA/acetonitrile gradient (10-80% acetonitrile in 60
minutes) at a flow rate of 500 ml/min. Five hundred microliter
fractions were collected at one minute intervals, concentrated by
vacuum centrifugation to 100 ml, and divided into 4 aliquots each
for later use. All solvents were HPLC grade and were obtained from
VWR Scientific Products (West Chester, Pa.).
[0057] Sub-Fractionation of protein fractions. 25% of a specific
protein fraction obtained from the primary fractionation was
further sub-fractionated by reverse-phase HPLC using a Phenomenex
Jupiter C4 column (column dimensions: 4.6 mm.times.150 mm, pore
size: 300 .ANG., particle size: 7 mm) (Torrence, Calif.). The
proteins were eluted with a shallow gradient (55-62% acetonitrile
in 10 minutes) at a flow rate of 500 ml/min, and fractions were
collected at one minute intervals. The sub-fractions were then
further concentrated by vacuum centrifugation, with 33% of the
material loaded onto a 15% SDS-PAGE gel and visualized using a
silver stain analysis kit (BioRad), and 33% was loaded onto
macrophages and used in a proliferation assay.
[0058] Generation of dendritic cells (DCs) in vitro. DCs were
cultured in vitro for 7 days as described previously (Hiltbold et
al., Cancer Res., 58, 5066-70 (1998)). PBMCs from a healthy donor
were isolated after centrifugation over Lymphocyte Separation
Medium (Organon Teknika, Durham, N.C.) and washed extensively with
PBS to eliminate residual platelets. The cells were plated in a
T-75 flask for two hours in serum-free AIM-V (Life Technologies,
Grand Island, N.Y.) medium, after which the non-adherent cells were
removed and used as the source of nave T cells. The adherent cells
were treated with 1000 U/ml GM-CSF and 26 ng/ml IL-4 (Schering
Plough, Kenilworth, N.J.) for 7 days in serum-free AIM-V (Life
Technologies) medium supplemented with 2 mM L-glutamine and
penicillin/streptomycin. DCs were fed with additional media and
cytokines on Day 4 of culture, and purified on Day 7 by negative
selection of contaminating T, B, and NK cells. The cells were
stained with anti-CD3, -CD19, and -CD56 antibodies for 45 minutes
in cold PBS and washed in PBS supplemented with 5% human AB serum
(Gemini Products, Calabasas, Calif.). Magnetic DYNAL beads (Lake
Success, N.Y.) coated with goat anti-mouse IgG were then added to
the cells for 45 minutes, and the contaminating cells were removed
by magnetic separation. Flow cytometry analysis of the remaining
cells showed they were high HLA-DR+ and B7-2+.
[0059] Generation of nave CD8.sup.+ and CD4.sup.+ T cells.
Non-adherent cells obtained after plastic adherence for DC
isolation was used as the source of nave CD8.sup.+ or nave
CD4.sup.+ T cells. To purify nave CD8.sup.+ T cells, the cells were
stained with anti-CD4, -CD20, CD56, and CD45RO antibodies for 45
minutes in cold PBS and washed in PBS with 5% HAB serum. Four
100-mm petri dishes (Nunc LabTek, Naperville, Ill.) were precoated
with 10 mg/ml goat anti-mouse IgG antibodies (Zymed) in 0.05 M
Tris, pH 9.5 at room temperature for 1 hr and washed with PBS.
Cells were added to each plate and incubated at 40.degree. C. for 1
hr. The non-adherent cells collected were the CD45RA+CD8.sup.+ T
cells. The same procedure was used for purifying nave CD4.sup.+ T
cells, except that anti-CD8 antibodies are used instead. All T cell
cultures were grown in RPMI medium (ICN, Costa Mesa, Calif.)
supplemented with 10% human AB sera (Gemini Products), L-glutamine,
and penicillin/streptomycin (Life Technologies).
[0060] Priming nave CD8.sup.+ T cells to tumor peptides. To prime
nave CD8.sup.+ T cells, 2.times.10.sup.4 dendritic cells were
incubated for 2-4 hours first with 25% of each peptide containing
RP-HPLC fraction (10 ml), and then overnight in the presence of
1000 U/ml TNF-a (Genzyme, Cambridge, Mass.) in 96-well U-bottom
plates (Falcon, Franklin lakes, N.J.). 2.times.10.sup.5 autologous
nave CD8.sup.+ T cells were added the next day to the DCs in the
presence of 2 ng/ml IL-1b (R & D Systems, Minneapolis, Minn.),
20 U/ml IL-2 (DuPont, Wilmington, Del.), and 26 ng/ml IL-4
(Schering Plough). The CD8.sup.+ T cell cultures were fed every 3-4
days with 10 U/ml IL-2 and 13 ng/ml IL-4. In addition, 10 ng/ml
IL-7 (Pharmingen, San Diego, Calif.) was included in the cytokine
mixture after the 2nd restimulation. The CD8.sup.+ T cell cultures
were restimulated every 7-10 days using autologous macrophages
(obtained by plastic adherence) loaded with the individual peptide
fractions, until the third restimulation, where autologous
macrophages loaded with irradiated (12,000 Rads) MS-A2 tumors
(macrophages:tumor=1:5) were used as stimulators (T cells:loaded
macrophages=10:1).
[0061] Priming nave CD4.sup.+ T cells to tumor proteins. To prime
nave CD4.sup.+ T cells, dendritic cells were loaded with 25% of
each protein fraction (.about.25 ml), and treated the same as
described for CD8.sup.+ T cell priming above. The CD4.sup.+ T cell
cultures were restimulated every 10-14 days using autologous
macrophages loaded with the individual protein fractions (T
cells:macrophages=10:1), and fed every 4-5 days with 10 U/ml IL-2
and 13 ng/ml IL-4, depending on growth kinetics. 10 ng/ml IL-7
(Pharmingen) was added to the CD4.sup.+ T cell cultures after the
second restimulation. For the third restimulation, MS tumor was
irradiated for 7 minutes (2.18 J/cm.sup.2) using a Spectra Mini II
UV-B irradiator (Daavlin, Bryan, Ohio) and loaded onto macrophages
overnight (5:1=apoptotic tumor:macrophages) that were used as
stimulators (T:loaded macrophages 10:1) the next day.
[0062] Cytotoxicity assays. 1-2.times.10.sup.6 target cells were
labeled with 50 mCi of Na251CrO4 (Amersham, Arlington Heights,
Ill.) for 90 minutes at 37.degree. C. The labeled cells were then
washed three times and plated at 1.times.10.sup.3 cells/well in a
96-well V-bottom plate (Costar, Cambridge, Mass.) with various
numbers of effector T cells. In addition, a 50-fold excess of
unlabeled K562 (5.times.10.sup.4) was added to the wells for 15
minutes prior to the addition of T cells to prevent the detection
of lymphokine-activated killer (LAK) activity in the assay. The
plates were centrifuged and incubated for 4 hours at 37.degree. C.
All determinations were done in triplicate. Supernatants were
harvested using a Skatron harvesting press (Skatron Instruments,
Sterling, Va.) and counted on a Cobra II series auto gamma counting
system (Packard, Meriden, Conn.). Maximum release was obtained by
adding 50 ml of 1% Triton X-100 to the labeled target cells.
Spontaneous release was obtained by incubating the labeled cells in
the absence of T cells. Percent specific lysis was calculated from
the following formula: % specific lysis=100.times.(experimental
release-spontaneous release)/(maximum release-spontaneous release).
In blocking experiments, anti-MHC Class I Ab (W6/32) was added to
the labeled target cells for 30 minutes prior to the addition of
the effector T cells.
[0063] Proliferation Assays. Autologous macrophages loaded with
UV-induced apoptotic MS tumor cells (5:1=apoptotic
tumor:macrophages) were seeded in round-bottom 96-well microplates
(Costar, Cambridge, Mass.) with primed T cell cultures at a T
cell:stimulator ratio of 20:1. For proliferation assays using tumor
lysate, MS tumor cell lysate was generated as described previously,
and 1.75.times.10.sup.8 cell equivalents were loaded onto
2.times.10.sup.6 autologous macrophages for 2 hours. T cells were
added at a T cell:stimulator ratio of 10:1. For the proliferation
assay using the sub-fractions of #44, 33% of the sub-fraction was
loaded onto 5.times.10.sup.4 macrophages overnight and added to T
cells with a T:stimulator ratio of 1:1 the next day. The wells were
pulsed with [.sup.3H]TdR (Amersham, Life Science) for the last 18
hours of the 5-day period, harvested by a Skatron semiautomatic
cell harvester (Skatron Instruments), and counted on a Wallac 1205
beta plate scintillation counter (Gaithersburg, Md.). The results
are expressed as mean values of triplicate determinations.
[0064] Mass spectrometry analysis. 25% of the RP-HPLC peptide
fraction was concentrated by vacuum centrifugation to near dryness
and resuspended in 5 ml of 0.1M acetic acid. One microliter of this
material was loaded onto a microcapillary C18 column (150
mm.times.75 mm i.d.), and eluted with a 20 minute linear gradient
(v/v 0-80% solvent B (0.1 M acetic acid in 100% acetonitrile) in
solvent A (De-ionized water in 0.1 M acetic acid). Flow rates for
the nanospray probe (186 nl/min) was achieved by coupling the
Rainin HPLC system with an Accurate microflow processor (LC
Packings, San Francisco, Calif.) for flow splitting. The nanospray
probe was operated at a voltage differential of +3.2 keV. The
source temperature was maintained at 300.degree. C. Mass spectra
were obtained by scanning from 300-1500 every 3 seconds and summing
individual spectra on a Fisons Quattro II triple quadrupole mass
spectrometer (Micromass Inc., Loughborough, U.K.).
Results
[0065] Identification of HPLC fractions containing immunogenic
tumor peptides. CD8.sup.+ T cell cultures were primed and
restimulated with HPLC fractions as described above. Due to the low
amount of peptide, later restimulations were done using macrophages
loaded with irradiated MS-A2 tumor cells. Monitoring the CD8.sup.+
T cell cultures with an inverted microscope over four
restimulations clearly showed that while there was T cell
proliferation in all wells, several of the CD8.sup.+ T cell
cultures were expanding at a much higher rate, suggesting the
presence of immunostimulatory peptides in the fractions used for
priming in these wells. Most of the unstimulated CD8.sup.+ T cell
cultures reached senescence after 8 weeks in culture.
[0066] FIG. 1 shows the result of one priming experiment in which
after the fourth restimulation, all the T cell cultures could be
assayed for their ability to recognize the original tumor, MS-A2,
from which the peptides were derived. Out of the 65 CD8.sup.+ T
cell cultures primed on the individual peptide fractions, 12
(Fractions 15, 22, 30, 32, 37, 38, 43, 44, 50, 51, 52, 63)
exhibited strong cytotoxicity against the tumor. Since the PBL
donor and the tumor were mismatched at the HLA-A3 allele, the Raji
tumor cell line (which was matched only at the HLA-A3 allele with
the PBL donor) also was used to ensure that the cytotoxic CD8.sup.+
T cell cultures were not alloreactive. None of the cultures that
killed MS-A2 tumor cells recognized the Raji targets.
[0067] The 12 cytotoxic CD8.sup.+ T cell cultures also were tested
for their ability to recognize another epithelial adenocarcinoma, a
lung tumor, 201T-A2, to look for shared tumor antigens. As shown in
FIG. 2, a CD8.sup.+ T cell culture, primed with peptide fraction
#32, recognized again the original tumor, and also the lung tumor.
Since the lung tumor and the breast tumor shared only the HLA-A2.1
allele, this suggested that the peptide being recognized was a
shared antigen restricted by HLA-A2.1.
[0068] To determine the extent of reproducibility of this approach,
the acid extraction was repeated, as was the peptide fractionation
and priming procedures. Several consecutive peptide fractions were
pooled for two reasons: 1) to compensate for small shifts in
fraction number between HPLC runs, and 2) to reduce the total
number of T cell cultures in vitro, making the approach less labor
intensive. Naive CD8.sup.+ T cells were primed on pooled peptide
fractions that were composed of the positive peptide fractions
identified earlier as well as flanking peptide fractions. The
patterns of T cell stimulation and expansion induced by the pooled
peptide fractions were consistent with the patterns induced by the
immunostimulatory peptide fractions observed in the previous
priming. An example is shown in FIG. 3, in which primed CD8.sup.+ T
cell cultures were primed to fractions 41-46 (FIG. 3A) and 61-65
(FIG. 3B), and generated specificity to the original tumor, MS-A2.
This corresponded to immunostimulatory fraction #44 and fraction
#63 from the previous run, respectively (FIG. 1). CD8.sup.+ T cells
primed on fractions 41-46 also were blocked by the MHC Class I
antibody, W6/32 (FIG. 3A). Furthermore, the specific antigen was
present in the epithelial tumor, and not in the perfectly
HLA-matched melanoma, Mel 624 (FIG. 3B).
[0069] To evaluate the content of these 12 immunostimulatory
fractions, they were analyzed by electrospray ionization nanospray
mass spectrometry. A panel of peptide species (Table 1) conforming
to mass-to-charge ratios of 700-1300 Daltons indicative of HLA
Class I-binding peptides was employed. These results showed that
peptides from HLA Class I molecules were extracted, and that there
were immunostimulatory peptides in the HPLC fractions that were
capable of stimulating nave CD8.sup.+ T cells to proliferate
and
1TABLE 1 Mass spectrometry analyses of immunostimulatory peptide
fractions.sup.a Fraction # m/z.sup.b,c 15 851.7, 879.8 22 921.3,
1061.4 30 717 32 717 37 None 38 921.3 43 949.2, 816 Fraction # m/z
44 615.2, 1229.5, 942.3, 921.4, 1061.5 50 728.1, 949.2, 1256.5 51
949 52 949, 885.9 63 805.6 .sup.aHPLC peptide fractions that tested
positive in the CTL assay were analyzed by nanospray microcapillary
HPLC mass spectrometry. .sup.bMass-to-charge ratio. .sup.cPeptide
mass to charge ratios (m/z) conforming to peptides that bind HLA
Class I molecules (700-1300 Daltons) were considered candidates for
tumor antigens.
[0070] Identification of HPLC fractions containing immunogenic
tumor proteins. CD4.sup.+ T cell cultures were primed and
restimulated, and by the third restimulation, macrophages loaded
with apoptotic MS tumor cells were used to stimulate the CD4.sup.+
T cell cultures. Similar to the CD8.sup.+ T cell cultures,
observation of the CD4.sup.+ T cell cultures with an inverted
microscope over five restimulations showed that not all the
CD4.sup.+ T cell cultures were growing equally well, suggesting
that the CD4.sup.+ T cells were responding to immunostimulatory
proteins present in some of these fractions, and not in others.
Most of the unstimulated CD4.sup.+ T cell cultures reached
senescence after 10 weeks in culture.
[0071] FIG. 4 shows the results of one priming experiment in which
after the second restimulation, all the T cell cultures were tested
for their ability to recognize the original tumor, MS, from which
the proteins were obtained. Autologous macrophages were loaded with
apoptotic tumor and used in a 5-day proliferation assay as
stimulators of the primed CD4.sup.+ T cell cultures. Out of the 52
CD4.sup.+ T cell cultures primed on the individual protein
fractions, 14 (Fractions 5, 10, 11, 12, 13, 22, 28, 35, 37, 38, 39,
40, 46, 51) proliferated in response to macrophages loaded with
apoptotic tumor. The CD4.sup.+ T cell cultures also were tested for
cytotoxicity against the original tumor via a CTL assay. None of
the T cells tested killed the original tumor. Some of the positive
CD4.sup.+ T cell cultures were also tested for their ability to
recognize autologous macrophages loaded with tumor lysate. As shown
in FIG. 5, CD4.sup.+ T cell cultures primed with protein fractions
# 5-6 and # 15 were able to proliferate to macrophages loaded with
tumor lysate, consistent with the results shown in FIG. 4.
[0072] To determine the content of the immunostimulatory protein
fractions, the protein fractions were analyzed by SDS-PAGE and
silver stain analysis. An example is shown in FIG. 6, representing
the immunostimulatory protein fraction, Fraction #44, from another
priming experiment. This fraction corresponds to Fraction #46 in
the first priming experiment (FIG. 4), but it eluted later due to
slight variations in HPLC fraction number between runs. Fraction
#44 was sub-fractioned into 10 sub-fractions and analyzed for
protein content and immunostimulatory capacity. As shown in FIG. 6,
immunostimulatory capacity was detected in 4 of the 10 subfractions
(#44.1, #44.2, #44.4, and #44.7). A silver stain analysis of the
corresponding subfractions detected two bands at 17 & 19 kD in
fraction 44.4.
EXAMPLE 2
[0073] This example demonstrates the identification of peptides
derived from Cyclin B1 as epithelial tumor associated antigens. It
also demonstrates overexpression and deregulated expression of
Cyclin B1 in epithelial cancer cells.
Materials and Methods
[0074] Cells and Tumor Cell lines. MS-A2 is an HLA-A*0201+
transfected tumor cell line derived from a breast adenocarcinoma
cell line, MS (Hiltbold et al., Cell. Immunol., 194, 143-49
(1999)). MS-A2/CD80 is the MS-A2 cell line retrovirally-transduced
with the CD80 gene obtained from Corixa Corporation, Seattle, Wash.
The lung tumor cell line, 201T, is described above. PCI-13, is a
head and neck tumor cell line (Yasumura et al., Cancer Res., 53(6),
1461-68 (1993)). T cells, dendritic cells (DCs), and macrophages
were derived from the peripheral blood of HLA-A*0201+ healthy donor
and cancer patients under an IRB approved protocol and with signed
informed consent.
[0075] Peptide Synthesis. All peptides used in this example were
synthesized with F-moc chemistry using the 432A Synergy Peptide
Synthesizer (Applied Biosystems, Foster City, Calif.). Peptides
were purified by RP-HPLC to greater than 85% purity, and dissolved
in DMSO and frozen until further use.
[0076] Antibodies. MA2.1, a mouse anti-human HLA-A2.1 antibody, was
produced by the MA2.1 hybridoma; W6/32, a mouse anti-human MHC
Class I antibody, was produced by the W6/32 hybridoma; both were
obtained from the American Tissue Culture Collection (ATCC,
Manasas, Va.). GNS-1, a mouse anti-human cyclin B1 antibody, was
purchased from BD Pharmingen, Franklin Lakes, N.J.
[0077] Mass spectrometry (MS) Data Acquisition. Active
first-dimension HPLC fractions were screened for peptide content on
a home-built Fourier transform mass spectrometer (FTMS), equipped
with a nano-flow high performance liquid chromatography
micro-electrospray ionization (nano-HPLC micro-ESI) interface
(Martin et al,. Anal. Chem. 72(18), 4266-74 (2000)). Nano-HPLC
columns were constructed from 50 mm I.D. fused silica capillaries
and packed with an 8 cm bed length of 5 mm diameter reversed phase
beads. An integrated microESI emitter tip (.about.2 mm diameter)
was located a few mm from the column bed. Typically, .about.0.75 mL
(corresponding to .about.2.3.times.10.sup.8 cell equivalents or
.about.1.5%) of an active, first-dimension HPLC fraction was loaded
onto a column and eluted directly into the mass spectrometer with a
linear, 17 minute gradient of 0-70% acetonitrile in 0.1% acetic
acid. Full scan mass spectra, over a mass-to-charge (m/z) range
300.ltoreq.m/z.ltoreq.2500, were acquired at a rate of
approximately 1 scan/second.
[0078] Mass Spectrometry/Mass Spectrometry (MS/MS) Data
Acquisition. Mass spectrometry/mass spectrometry (MS/MS) data were
acquired on a Finnigan LCQ quadrupole ion trap mass spectrometer
(Finnigan Corp., San Jose, Calif.), equipped with a nano-HPLC
micro-ESI source as described above. Typically, .about.1.5 mL
(corresponding to .about.4.5.times.10.sup.8 cell equivalents or
.about.3%) of an active, first-dimension HPLC fraction was loaded
onto a column eluted directly into the mass spectrometer with a
linear, 30 minute gradient of 0-30% acetonitrile in 0.1% acetic
acid. Data dependent spectral acquisition (Shabanowitz et al.,
"Sequencing the Primordial Soup," pages 163-177 in "Mass
Spectrometry in Biology and Medicine" A. L. Burlingame, S. A. Carr
and M. A. Baldwin, editors. Humana Press (Totowa, N.J. 2000)) was
performed as follows: A full scan mass spectrum (MS) was acquired
over the range 300.ltoreq.m/z.ltoreq.2000. The instrument control
computer then selected the top 5 most abundant ion species in the
MS scan for subsequent MS/MS analysis over the next 5 scans. After
acquiring MS/MS data on a particular ion species, its corresponding
m/z value was excluded from consideration by the instrument control
computer for a period equal to the observed chromatographic peak
width (approximately 1.5 minutes for the data herein). This data
acquisition procedure minimized redundancy and allowed MS/MS
analysis on peptide species whose abundances spanned a wide dynamic
range. After acquisition, tandem mass spectral data were searched
using SEQUEST (Eng et al., J. Am. Soc. Mass. Spectrom. 5, 976-89
(1994)), an algorithm that matches uninterpreted MS/MS spectra to
theoretical spectra for peptides generated from user-specified
databases. All data were searched against non-redundant (nr)
protein databases compiled at the National Center for Biotechnology
Information (NCBI). In addition, manual (e.g. de novo)
interpretation of MS/MS spectra was performed. Peptide sequence
information obtained in this manner was compared to sequences in
the nr protein database using the MS-TAG algorithm (Clauser et al.,
Anal Chem., 71(14), 2871-82 (1999)). Candidate peptide sequences
were subsequently confirmed by comparison of their MS/MS spectra
acquired for synthetic analogs.
[0079] HLA Class I stabilization assays. Peptide-induced
stabilization of HLA-A2.1 molecules on T2 cells was done as
previously described (Zeh et al., Hum. Immunol., 39(2), 79-86
(1994)). 2.times.10.sup.5 T2 cells were incubated with 20 mg/ml of
the indicated synthetic peptides in 3 mg/ml human B2m (Calbiochem,
La Jolla, Calif.) for 18-20 hours at room temperature. The cells
were then stained with the HLA-A2.1-specific antibody, MA2.1, for
45 minutes, washed with FACS Buffer (PBS, 5% FBS, and 0.01% sodium
azide), and stained with a secondary FITC-conjugated anti-IgG
antibody (Biosource International, Camarillo, Calif.). The cells
were fixed in 4% formaldehyde prior to flow cytometry analysis. The
negative control consisted of T2 cells without peptide. The
positive control consisted of T2 cells loaded with the Flu matrix
peptide, GILGFVFTL. Flow cytometric analysis was done using a
FACScan flow cytometer (Becton-Dickinson). Experimental results are
depicted as X-Fold increase=(Mean Fluorescent Intensity of T2 cells
loaded with peptide/Mean Fluorescent Intensity of T2 cells with no
peptide). An X-Fold Increase of >1 indicates that the peptide
binds to HLA-A2.1.
[0080] IFN-.gamma. ELISPOT Assays. IFN-g ELISPOT assays were
conducted as previously described (Herr et al., J. Immunol.
Methods, 191(2), 131-42 (1996)). Briefly, nitrocellulose plates
(Millipore, Bedford, Mass.) were coated with the anti-IFN-.gamma.
capture mAb 1-D1K (MabTech, Stockholm, Sweden) overnight at
4.degree. C. For assays using dendritic cells as APCs, DCs were
loaded with 10 mg of the indicated peptides for 2-6 hrs, and mixed
with autologous T cells at a DC:T ratio of 1:10 for 20 hours at
37.degree. C. For assays using autologous PBMCs as APCs, PBMCs were
irradiated at 3000 Rads, loaded with 10 mg of peptides for 4 hours,
and mixed with autologous T cells at an APC:T ratio of 1:5 for 40
hours at 37.degree. C. The T cells were seeded at
3.times.10.sup.3-1.times.10.sup.- 5 cells/well. All assays were
done in serum-free AIM-V medium (Gibco Life Technologies, Grand
Island, N.Y.). The plates were then washed in PBS+0.1% Tween and
stained with anti-IFN-.gamma. mAb 7-B6-1 (Mabtech) for 2 hours at
37.degree. C. The plates were washed, and the avidin-peroxidase
complex (Vectastain ABC Kit, Vector Laboratories) was added to the
plates for 1 hour. The plates were then developed using AEC (Sigma)
substrate, and spots were quantified microscopically with an
inverted phase-contrast microscope (Carl Zeiss, Hallbergmoos,
Germany) along with a computer-assisted image analysis system (KS
ELISPOT). For HLA Class I blocking experiments, the W6/32 antibody
was added to the APCs for 30-45 minutes prior to the incubation
with the T cells.
[0081] Priming naive CD8.sup.+ T cells from a healthy donor to
cyclin B1 peptides in vitro. Nave CD8.sup.+ T cells and in vitro
generated dendritic cells were purified as described above in
Example 1. 2.times.10.sup.4 dendritic cells were loaded overnight
with 10 mg/well peptide in 96-well U-bottom plates (Falcon,
Franklin lakes, N.J.) and mixed with 2.times.10.sup.5 autologous
nave CD8.sup.+ T cells the next day in the presence of 2 ng/ml
IL-1b ( (R & D Systems, Minneapolis, Minn.), 20 U/ml IL-2
(DuPont, Wilmington, Del.), and 10 U/ml IL-4 (Schering Plough).
Depending on growth kinetics, T cells were fed every 3-4 days with
10 U/ml IL-2 and 5 U/ml IL-4. T cells were restimulated every 7-10
days using peptide-loaded autologous macrophages.
[0082] Stimulating CD8.sup.+ T cells from breast cancer and SCCHN
patients with cyclin B1 peptides in vitro. PBMCs from cancer
patients were X-irradiated at 3000 Rads, loaded with 10 mg of the
indicated peptides for 2-4 hours, and mixed with autologous PBMCs
in the presence of 20 U/ml IL-2 (DuPont). The T cell cultures were
fed every 3-4 days with 10 U/ml IL-2, and restimulated every 10-12
days, if necessary, using peptide-loaded autologous irradiated
PBMCs. All T cell cultures were grown in RPMI medium (ICN, Costa
Mesa, Calif.) supplemented with 10% human AB sera (Gemini Products,
Calabasas, Calif.), L-glutamine, and penicillin/streptomycin (Life
Technologies).
[0083] Cytotoxicity assays. 1-2.times.10.sup.6 target cells were
labeled with 50 mCi of Na251CrO4 (Amersham, Arlington Heights,
Ill.) for 90 minutes at 37.degree. C. The labeled cells were then
washed three times and plated at 1.times.10.sup.3 cells/well in a
96-well V-bottom plate (Costar, Cambridge, Mass.) with various
numbers of effector T cells. In addition, a 50-fold excess of
unlabeled K562 (5.times.10.sup.4) was added to the wells for 30
minutes prior to the addition of T cells to minimize the detection
of lymphokine-activated killer (LAK) activity in the assay. The
plates were centrifuged and incubated for 4 hours at 37.degree. C.
All determinations were done in triplicate. Supernatants were
harvested using a Skatron harvesting press (Skatron Instruments,
Sterling, Va.) and counted on a Cobra II series auto gamma counting
system (Packard, Meriden, Conn.). Maximum release was obtained by
adding 50 ml of 1% Triton X-100 to the labeled target cells.
Spontaneous release was obtained by incubating the labeled cells in
the absence of T cells. Percent specific lysis was calculated from
the following formula: % specific lysis=100.times.(experimental
release-spontaneous release)/(maximum release-spontaneous
release).
[0084] Immunohistochemical staining of cyclin B1 in tumor cell
lines and in tumor sections. For tumor cell lines, the cells were
left to adhere overnight on poly-lysine charged slides (Fisher
Scientific) in the presence of RPMI+10% FBS (CELLGRO.RTM., Media
Tech, Inc., Herudon, Va.). The cells were then fixed for 15 minutes
on ice with either 2% Triton-X or 50% Formalin/50% acetone, blocked
with serum, and stained with the anti-cyclin B1 antibody, GNS-1
(BD-Pharmingen). The avidin-biotin peroxidase method was then
applied according to manufacturer's instructions using the
Vectastain ABC Elite.TM. staining kit (Vector Laboratories,
Burlingame, Calif.). For SCCHN sections, formalin-fixed,
paraffin-embedded tumor tissues were sectioned (3-5 mm), air-dried
overnight at 37.degree. C., deparaffinized and dehydrated and
stained with the anti-human cyclin B1 antibody. The avidin-biotin
peroxidase method was applied as above according to the
instructions supplied by the manufacturer (DAKO Corporation,
Carpinteria, Calif.)
Results
[0085] Identification of T cell stimulatory tumor-derived peptides.
Peptides were acid-extracted from immunoaffinity purified HLA Class
I molecules of an HLA-A*0201 epithelial tumor cell line,
fractionated by RP-HPLC, and loaded onto dendritic cells to prime
in vitro autologous naive CD8.sup.+ T cells from a healthy donor as
described in Example 1. One analyzed RP-HPLC fraction whose
peptides supported the growth of tumor-specific CTLs was analyzed
by nano-HPLC micro ESI tandem mass spectrometry. Analysis of the
resulting MS/MS data yielded 6 candidate peptide sequences that
corresponded to the mass range expected for HLA Class I-associated
peptides (700-1300 Da). The abundances of these candidates
represented the majority of total ion current observed in the mass
range of 700-1300 Da. Candidate peptide sequences were subsequently
confirmed by comparison of their mass spectra acquired for
synthetic analogs. All six peptides had related sequences, with
four being 9 amino acids long, and two being 10 amino acids long
(Table 2). The four 9-mers (P1-P4) were identical in the first
eight amino acids and differed at the C-terninus, where the amino
acids were valine (SEQ ID NO: 1), methionine (SEQ ID NO: 2),
phenylalanine (SEQ ID NO: 3), and cysteine (SEQ ID NO: 1). The two
10-mers, SEQ ID NOs: 5 and 6, were identical to SEQ ID NOs 2 and 3,
respectively, except for an additional alanine at the C-terminus.
When these sequences were entered into the protein database, they
were found to be homologous to a human cyclin B1 sequence derived
from HeLa cells. These sequences were also homologous to mouse and
rat cyclin B1 (Table 2).
2TABLE 2 Cyclin B1 sequences derived from the tumor and database
bind to HLA-A2.1 HLA-A2.1 Sequence.sup.a Binding.sup.b Cyclin B1
peptides from the tumor SEQ ID NO:1 AGYLMELCV 1.60 SEQ ID NO:2
AGYLMELCM 1.48 SEQ ID NO:3 AGYLMELCF 1.42 SEQ ID NO:4 AGYLMELCC
1.61 SEQ ID NO:5 AGYLMELCMA 1.58 SEQ ID NO:6 AGYLMELCFA 2.08 Cyclin
B1 peptides from the database Human cyclin B1 (SEQ ID NO:7)
AKYLMELTM 2.28 Human cyclin B1 (SEQ ID NO:8) AKYLMELTML 2.25 Mouse
cyclin B1 AKYLMELSML -- Rat cyclin B1 AKYLMELSML --
[0086] Peptides having sequences SEQ ID NOs: 1-8 were synthesized
and tested for their ability to bind HLA-A2.1 using the T2 cell
line and class I stabilization assay. Since leucine and isoleucine
have identical masses and are not distinguished by low-energy MS/MS
analysis, the peptides were synthesized with leucine at positions 4
and 7 to match leucine present at the same position in the HeLa
cyclin B1 sequence, as well as in the mouse and rat cyclin B1
sequences. All the peptides bound to HLA-A2.1, with various
affinities, as measured by increases in mean fluorescent intensity
in anti-HLA-A2.1 staining of peptide-loaded T2 cells. The
HeLa-derived cyclin B1 peptides also bound to HLA-A2.1. Affinities
of the HeLa-derived cyclin B1 peptides were higher than that of all
tumor-derived peptides, except SEQ ID NO: 6 (Table 2).
[0087] CD8.sup.+ T cells from an HLA-A*0201 healthy donor can be
primed to synthetic cyclin B1 peptide SEQ ID NO: 4. Since these
peptides were derived from a first dimension HPLC fraction that
primed tumor-specific CTLs from a HLA-A2.1+ donor, the cyclin B1
peptides were used to prime T cells from another HLA-A2.1+ donor.
Naive CD8.sup.+ T cells and autologous dendritic cells were loaded
with the individual synthetic peptides (SEQ ID NOs: 1-6). No T cell
responses were detected against the peptides in the absence of in
vitro stimulation in this donor as well as another HLA-A2.1+ donor.
However, after several rounds of restimulation, antigen-specific
IFN-.gamma. secretion by CD8.sup.+ T cells in response to SEQ ID
NO: 4 was detected, but not to other peptides (SEQ ID NOs: 1, 2, 5,
or 6) or HIV-POL (ILKEPGSHV), which is known to bind HLA-A2.1 and
serves here as the negative control (FIG. 7). The T cell response
to SEQ ID NO: 4 was blocked using the anti-Class I antibody, W6/32,
suggesting that the antigen-specific responses were HLA Class
I-restricted. However, the T cells that specifically recognized
P4-loaded DCs were unable to kill the original tumor from which the
peptides were derived. This was not unexpected considering that
these T cells were primed with high concentrations of peptide (50
mM), and are thus expected to be of low affinity and incapable of
recognizing the comparatively lower levels of the same HLA-peptide
complexes on the tumor.
[0088] HLA Class I-restricted memory T cell responses against
cyclin B1 peptides in HLA-A*0201 breast cancer patients. PBMCs from
six breast cancer patients who had undergone surgery but no
chemotherapy were tested for their ability to recognize the cyclin
B1 peptides in an IFN-.gamma. ELISPOT assay. Four out of the six
HLA-A2+ breast cancer patients tested exhibited secondary responses
against one or more of the cyclin B1 peptides (FIG. 8). Patient A
exhibited strong HLA Class I-restricted secondary T cell responses
to three of the three peptides tested, SEQ ID NOs: 4, 7, and 8,
after only one in vitro stimulation. There was no recognition of
the HIV-POL control peptide. Patient B appeared to have a weak
secondary response to one of the three peptides tested, SEQ ID NO:
1, and only after two in vitro stimulations. This patient was later
found to be HLA-A*0206, suggesting that, if the response is real,
SEQ ID NO: 1 may also bind to HLA-A*0206.
[0089] Most interestingly, secondary responses were detected in the
absence of any in vitro stimulation. Patient C showed
peptide-specific HLA Class I-restricted T cell responses to two of
two peptides tested, SEQ ID NOs: 4 and 7. Patient D showed strong
HLA Class I-restricted T cell responses to P4 and lower responses
against both the HIV-POL peptide and SEQ ID NO: 7. However, only
the SEQ ID NO: 7 response was blocked by the anti-MHC Class I
antibody, confirming antigen-specificity. Patients E and F did not
respond to either of the two peptides tested, SEQ ID NOs: 4 and 7.
No response was detected to any peptides in an HLA-A*0201 negative
patient
[0090] HLA Class I-restricted memory T cell responses to cyclin B1
peptides in HLA-A*0201 SCCHN patients. PBMCs from five HLA-A*0201
SCCHN patients for their ability to respond to the cyclin B1
peptides was assessed in an IFN-.gamma. ELISPOT assay. HLA Class
I-restricted T cell responses to one or more of the cyclin B1
peptides were detected in four of the five patients tested (FIG.
9). Patient A exhibited HLA Class I-restricted T cell responses to
five of eight peptides after only one in vitro stimulation. For two
of these peptides, SEQ ID NOs: 4 and 7, peptide-specific T cells
also were detected in the absence of any in vitro stimulation.
[0091] Patient B exhibited HLA Class I-restricted T cell responses
to three of the five peptides (SEQ ID NOs: 3, 4, and 7), and not to
the other two (SEQ ID NOs: 1 and 2). Patient C showed heightened T
cell responses to all five peptides tested, but only responses
against SEQ ID NOs: 2 and 8 could be blocked with anti-Class I
antibody. Patient D had the same heightened T cell response that
appeared specific for three of the six peptides tested, SEQ ID NOs:
4, 5, and 9. The fifth SCCHN patient failed to show a detectable
response to any of the peptides even after three in vitro
stimulations.
[0092] T cells sensitized to SEQ ID NOs: 4 and 7 in one SCCHN
patient can lyse the tumor from which the peptides were derived. To
determine whether T cells restimulated to cyclin B1 peptides could
lyse tumor, T cells from one SCCHN patient (Patient A, FIG. 9) were
tested for their ability to kill the original tumor from which the
peptides were derived (MS-A2), and the same tumor transduced with
the CD80 gene (MS-A2/CD80) to provide "costimulation" for T cell
activation. As shown in FIG. 10A, T cells that were sensitized to
SEQ ID NO: 4 were able to lyse the MS-A2/CD80 tumor and to a lesser
extent, MS-A2 tumor, but not the untransfected MS tumor or K562,
which is a control for LAK activity. Similarly, in FIG. 10B, T
cells sensitized to SEQ ID NO: 7 were able to lyse the MS-A2/CD80
tumor and not the other tumors.
[0093] Cyclin B1 protein is overexpressed in epithelial tumor cell
lines. Cyclin B1 expression was assayed by immunohistochemistry in
the original tumor cell line MS-A2 from where they were first
isolated and identified. There was intense staining of cyclin B1
protein in the tumor cells, predominantly found in the cytoplasm.
Similar intense cytoplasmic staining of cyclin B1 was observed in a
human lung adenocarcinoma cell line 201T, also localized in the
cytoplasm. No cyclin B1 staining was observed in normal cells,
represented by primary cultures of human airway bronchoepithelial
cells.
[0094] Cyclin B1 protein is overexpressed in SCCHN tumors. To
ascertain that the intense staining of cyclin B1 observed in the
tumor cell lines was not a result of a prolonged in vitro culture,
a tumor cell line and tumor tissue sections obtained from the SCCHN
patients whom had been analyzed for cyclin B1-specific T cell
responses were examined. Intense cytoplasmic staining of cyclin B1
was observed in the tumor cell line PCI-13, which was derived from
a tumor of the SCCHN Patient A described above. Very high
expression of cyclin B1 in the cell line correlates with strong
cyclin B1-specific T cell responses observed in this patient.
Intense cytoplasmic cyclin B1 staining was also observed in the
tumor samples of two other patients who exhibited cyclin
B1-specific T cell responses (Patients C and D respectively). No
cyclin B1 staining was detected in the normal mucosa surrounding
the tumor. The tumor showed weak and diffuse cyclin B1 staining
that was not convincingly positive. Patient B from whom the tumor
was derived did have cyclin B1-specific T cell responses (FIG. 9).
The same weak staining was seen in the tumor derived from a patient
who did not exhibit any HLA Class I-restricted T cell responses
against the cyclin B1 peptides.
EXAMPLE 3
[0095] This Example demonstrates that the presence of Cyclin B1
antibody production correlates with the presence of cancers in
patients.
[0096] Purified recombinant human cyclin B1 protein was purified
from recombinant baculovirus infected insect cells and used it in
ELISA assays to screen patients' sera for antibody to Cyclin B1. 7
breast cancer patients were so screened, as were 17 pancreatic
cancer patients and 27 colon cancer patients.
[0097] Of these patients, 23% had close to normal levels (negative)
of anti-cyclin B1 antibody. However, 54% of these patients had low
to intermediate titers of antibody and 23% had very high titers of
antibody (see FIG. 11). In addition, all sera recognized, the
purified protein of a correct molecular weight.
[0098] Moreover, the intermediate and high titers of anti-Cyclin B1
antibody were observed in all three types of cancers (FIG. 12).
However the two of antibody varied depending on the type of cancer
(FIG. 13). From breast cancer patients, the predominant isotype was
observed to be IgG, while in pancreatic cancer the data suggest
that IgA (mucosal immunity) were generated. Colon cancer patients
generated predominantly IgG with some IgM.
EXAMPLE 4
[0099] This Example demonstrates that the titer of Cyclin B1
antibody correlates with the presence and recurrence of lung
cancer.
[0100] Over 100 lung cancer patients were screened as reported in
Example 3. Screening lung cancer patients without regard for tumor
type revealed that patients with recurrent disease (n=5) exhibited
a higher antibody titer than patients who were stage 4 (n=3) or
other stages (n=33) at surgery (FIG. 14). Similar results were
observed in patients with lung adenocarcinoma, in that patients
with recurrent disease (n=6) exhibited a higher antibody level than
patients who were stage 4 (n=4) or other stages (n=60) at surgery
(FIG. 15).
[0101] These results indicate that assaying for the presence of
Cyclin B1 antibodies can server as a diagnostic tool in the
detection of tumors and also tumor recurrence.
EXAMPLE 5
[0102] This Example demonstrates that the titer of Cyclin B1
antibody correlates with smoking activity, a known cancer risk.
[0103] The titer of Cyclin B1 antibody for light smokers (n=3) was
similar to non smokers (n=8) having low or negative antibody titers
to cyclin B1. Heavy smokers (n=9) and those identifying themselves
as "smokers" smokers (n=4) demonstrated increased antibody titer,
and one individual with unknown history exhibited heightened Cyclin
B1 antibody titer (see FIG. 16). These results suggest that cyclin
B1 may correlate with precancerous development, at least for lung
cancer, and may serve as an early diagnostic tool for screening
patients at risk of developing cancer.
[0104] All references, including publications, patent applications,
and patents, cited herein are hereby incorporated by reference to
the same extent as if each reference were individually and
specifically indicated to be incorporated by reference and were set
forth in its entirety herein.
[0105] The use of the terms "a" and "an" and "the" and similar
referents in the context of describing the invention (especially in
the context of the following claims) are to be construed to cover
both the singular and the plural, unless otherwise indicated herein
or clearly contradicted by context. Recitation of ranges of values
herein are merely intended to serve as a shorthand method of
referring individually to each separate value falling within the
range, unless otherwise indicated herein, and each separate value
is incorporated into the specification as if it were individually
recited herein. All methods described herein can be performed in
any suitable order unless otherwise indicated herein or otherwise
clearly contradicted by context. The use of any and all examples,
or exemplary language (e.g., "such as") provided herein, is
intended merely to better illuminate the invention and does not
pose a limitation on the scope of the invention unless otherwise
claimed. No language in the specification should be construed as
indicating any non-claimed element as essential to the practice of
the invention.
[0106] Preferred embodiments of this invention are described
herein, including the best mode known to the inventors for carrying
out the invention. Of course, variations of those preferred
embodiments will become apparent to those of ordinary skill in the
art upon reading the foregoing description. The inventors expect
skilled artisans to employ such variations as appropriate, and the
inventors intend for the invention to be practiced otherwise than
as specifically described herein. Accordingly, this invention
includes all modifications and equivalents of the subject matter
recited in the claims appended hereto as permitted by applicable
law. Moreover, any combination of the above-described elements in
all possible variations thereof is encompassed by the invention
unless otherwise indicated herein or otherwise clearly contradicted
by context.
Sequence CWU 1
1
8 1 9 PRT Artificial Sequence cyclin-derived polypeptide 1 Ala Gly
Tyr Leu Met Glu Leu Cys Val 1 5 2 9 PRT Artificial Sequence
cyclin-derived polypeptide 2 Ala Gly Tyr Leu Met Glu Leu Cys Met 1
5 3 9 PRT Artificial Sequence cyclin-derived polypeptide 3 Ala Gly
Tyr Leu Met Glu Leu Cys Phe 1 5 4 9 PRT Artificial Sequence
cyclin-derived polypeptide 4 Ala Gly Tyr Leu Met Glu Leu Cys Cys 1
5 5 10 PRT Artificial Sequence cyclin-derived polypeptide 5 Ala Gly
Tyr Leu Met Glu Leu Cys Met Ala 1 5 10 6 10 PRT Artificial Sequence
cyclin-derived polypeptide 6 Ala Gly Tyr Leu Met Glu Leu Cys Phe
Ala 1 5 10 7 9 PRT Artificial Sequence cyclin-derived polypeptide 7
Ala Lys Tyr Leu Met Glu Leu Thr Met 1 5 8 10 PRT Artificial
Sequence cyclin-derived polypeptide 8 Ala Lys Tyr Leu Met Glu Leu
Thr Met Leu 1 5 10
* * * * *