Cancer-testis antigens

FIELD OF THE INVENTION

[0002] The invention relates to nucleic acids and encoded polypeptides which are novel cancer-testis antigens expressed in a variety of cancers. The invention also relates to agents which bind the nucleic acids or polypeptides. The nucleic acid molecules, polypeptides coded for by such molecules and peptides derived therefrom, as well as related antibodies and cytolytic T lymphocytes, are useful, inter alia, in diagnostic and therapeutic contexts.

BACKGROUND OF THE INVENTION

[0003] It is a little acknowledged fact that the discipline of tumor immunology has been the source of many findings of critical importance in cancer-related as well as cancer-unrelated fields. For example, it was the search for tumor antigens that led to the discovery of the CD8 T cell antigen (1) and the concept of differentiation antigens (2) (and the CD system for classifying cell surface antigens), and to the discovery of p53 (3). The immunogenetic analysis of resistance to viral leukemogenesis provided the first link between the MHC and disease susceptibility (4), and interest in the basis for non-specific immunity to cancer gave rise to the discovery of TNF (5).

[0004] Another area of tumor immunology that holds great promise is the category of antigens referred to as cancer/testis (CT) antigens, first recognized as targets for CD8 T cell recognition of autologous human melanoma cells (6, 7). The molecular definition of these antigens was a culmination of prior efforts to establish systems and methodologies for the unambiguous analysis of humoral (8) and cellular (9) immune reactions of patients to autologous tumor cells (autologous typing), and this approach of autologous typing also led to the development of SEREX (serological analysis of cDNA expression libraries) for defining the molecular structure of tumor antigens eliciting a humoral immune response (10).

[0005] Although the usefulness of the known CT antigens in the diagnosis and therapy of cancer is accepted, the expression of these antigens in tumors of various types and sources is not universal. Accordingly, there is a need to identify additional CT antigens to provide more targets for diagnosis and therapy of cancer, and for the development of pharmaceuticals useful in diagnostic and therapeutic applications.

SUMMARY OF THE INVENTION

[0006] Bioinformatic analysis of sequence databases has been applied to identify sequences having expression characteristics that fit the profile of cancer/testis antigens. Several novel cancer/testis antigens and cancer associated antigens have been identified. The invention provides, inter alia, isolated nucleic acid molecules, expression vectors containing those molecules and host cells transfected with those molecules. The invention also provides isolated proteins and peptides, antibodies to those proteins and peptides and CTLs which recognize the proteins and peptides. Fragments and variants of the foregoing also are provided. Kits containing the foregoing molecules additionally are provided. The foregoing can be used in the diagnosis, monitoring, research, or treatment of conditions characterized by the expression of one or more cancer-testis and/or cancer associated antigens.

[0007] Prior to the present invention, only a handful of cancer/testis antigens had been identified in the past 20 years. The invention involves the surprising discovery of several sequence clusters (UniGene) in sequence databases that have expression patters that fit the profile of cancer-testis antigens. Other sequence clusters fit the profile of cancer associated antigens. The knowledge that these sequence clusters have these certain expression patterns makes the sequences useful in the diagnosis, monitoring and therapy of a variety of cancers.

[0008] The invention involves the use of a single material, a plurality of different materials and even large panels and combinations of materials. For example, a single gene, a single protein encoded by a gene, a single functional fragment thereof, a single antibody thereto, etc. can be used in methods and products of the invention. Likewise, pairs, groups and even panels of these materials and optionally other CT antigen genes and/or gene products can be used for diagnosis, monitoring and therapy. The pairs, groups or panels can involve 2, 3, 4, 5 or more genes, gene products, fragments thereof or agents that recognize such materials. A plurality of such materials are not only useful in monitoring, typing, characterizing and diagnosing cells abnormally expressing such genes, but a plurality of such materials can be used therapeutically. An example of the use of a plurality of such materials for the prevention, delay of onset, amelioration, etc. of cancer cells, which express or will express such genes prophylactically or acutely. Any and all combinations of the genes, gene products, and materials which recognize the genes and gene products can be tested and identified for use according to the invention. It would be far too lengthy to recite all such combinations; those skilled in the art, particularly in view of the teaching contained herein, will readily be able to determine which combinations are most appropriate for which circumstances.

[0009] As will be clear from the following discussion, the invention has in vivo and in vitro uses, including for therapeutic, diagnostic, monitoring and research purposes. One aspect of the invention is the ability to fingerprint a cell expressing a number of the genes identified according to the invention by, for example, quantifying the expression of such gene products. Such fingerprints will be characteristic, for example, of the stage of the cancer, the type of the cancer, or even the effect in animal models of a therapy on a cancer. Cells also can be screened to determine whether such cells abnormally express the genes identified according to the invention.

[0010] According to one aspect of the invention, methods of diagnosing a disorder characterized by expression of a human CT antigen precursor coded for by a nucleic acid molecule are provided. The methods include contacting a biological sample isolated from a subject with an agent that specifically binds to the nucleic acid molecule, an expression product thereof, a fragment of an expression product thereof complexed with an HLA molecule, or an antibody that binds to the expression product, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67, and determining the interaction between the agent and the nucleic acid molecule or the expression product as a determination of the disorder.

[0011] In some embodiments the agent is selected from the group consisting of (a) nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67 or a fragment thereof, (b)an antibody that binds to an expression product of a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67, (c)an agent that binds to a complex of an HLA molecule and a fragment of an expression product of a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67, and (d) an expression product of a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67 that binds an antibody. Preferred sequences include SEQ ID NO: 1, SEQ ID NO: 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0012] In other embodiments the disorder is characterized by expression of a plurality of human CT antigen precursors and wherein the agent is a plurality of agents, each of which is specific for a different human CT antigen precursor, and wherein said plurality of agents is at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, or at least 8, at least 9 or at least 10 such agents. Preferably the disorder is cancer.

[0013] According to another aspect of the invention, methods for determining regression, progression or onset of a condition characterized by expression of abnormal levels of a protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67 are provided. The methods include monitoring a sample, from a patient who has or is suspected of having the condition, for a parameter selected from the group consisting of (i)the protein, (ii)a peptide derived from the protein, (iii) an antibody which selectively binds the protein or peptide, and (iv) cytolytic T cells specific for a complex of the peptide derived from the protein and an MHC molecule, as a determination of regression, progression or onset of said condition. Preferably the sample is assayed for the peptide. Preferred sequences include SEQ ID NO: 1, SEQ ID NO: 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0014] In certain embodiments, the sample is a body fluid, a body effusion, cell or a tissue. In other embodiments, the step of monitoring comprises contacting the sample with a detectable agent selected from the group consisting of (a) an antibody which selectively binds the protein of (i), or the peptide of (ii), (b)a protein or peptide which binds the antibody of (iii), and (c) a cell which presents the complex of the peptide and MHC molecule of (iv). Preferably, the antibody, the protein, the peptide or the cell is labeled with a radioactive label or an enzyme.

[0015] In other embodiments, the protein is a plurality of proteins, the parameter is a plurality of parameters, each of the plurality of parameters being specific for a different of the plurality of proteins, at least one of which is a CT antigen protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67. In further embodiments, the protein is a plurality of proteins, at least one of which is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67, and wherein the parameter is a plurality of parameters, each of the plurality of parameters being specific for a different of the plurality of proteins.

[0016] According to a further aspect of the invention, pharmaceutical preparations for a human subject are provided. The pharmaceutical preparations include an agent which when administered to the subject enriches selectively the presence of complexes of an HLA molecule and a human CT antigen peptide, and a pharmaceutically acceptable carrier, wherein the human CT antigen peptide is a fragment of a human CT antigen encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67.

[0017] In some embodiments, the agent comprises a plurality of agents, each of which enriches selectively in the subject complexes of an HLA molecule and a different human CT antigen peptide, wherein at least one of the human CT antigens is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67. Preferably the plurality is at least two, at least three, at least four or at least five different such agents.

[0018] In still other embodiments, the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3 and the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), or the agent comprises a plurality of agents, at least one of which is a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67, or an expression product thereof, each of which enriches selectively in the subject complexes of an HLA molecule and a different human CT antigen.

[0019] In other preferred embodiments, the agent is selected from the group consisting of (1) an isolated polypeptide comprising the human CT antigen peptide, or a functional variant thereof, (2) an isolated nucleic acid operably linked to a promoter for expressing the isolated polypeptide, or functional variant thereof, (3) a host cell expressing the isolated polypeptide, or functional variant thereof, and (4) isolated complexes of the polypeptide, or functional variant thereof, and an HLA molecule.

[0020] Preferred pharmaceutical preparations also include an adjuvant.

[0021] In still other embodiments, the agent is a cell expressing an isolated polypeptide comprising the human CT antigen peptide or a functional variant thereof, and wherein the cell is nonproliferative, or the agent is a cell expressing an isolated polypeptide comprising the human CT antigen peptide or a functional variant thereof, and wherein the cell expresses an HLA molecule that binds the polypeptide. Preferably the isolated polypeptide comprises a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0022] In certain other embodiments, the agent is at least two, at least three, at least four or at least five different polypeptides, each coding for a different human CT antigen peptide or functional variant thereof, wherein at least one of the human CT antigen peptides is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67. Preferably the at least one of the human CT antigen peptides is a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO: 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67, or a fragment thereof.

[0023] In yet other embodiments, the agent is a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence set forth as SEQ ID NO: 1, a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence set forth as SEQ ID NO: 3, a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence set forth as the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), SEQ ID NOs: 63, 65 or 67.

[0024] Preferred cells express one or both of the polypeptide and HLA molecule recombinantly, or are nonproliferative.

[0025] In still another aspect of the invention, compositions of matter are provided that include an isolated agent that binds selectively a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67. In some embodiments the agent binds selectively a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence set forth as SEQ ID NO: 1, or SEQ ID NO: 3, or SEQ ID NO: 5, or SEQ ID NO: 7, or SEQ ID NO: 9, or the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), or SEQ ID NOs: 63, 65 or 67.

[0026] In other embodiments, the agent is a plurality of different agents that bind selectively at least two, at least three, at least four, or at least five different such polypeptides. Preferably the at least one of the polypeptides is a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67, or a fragment thereof.

[0027] In further embodiments, the agent is an antibody.

[0028] According to another aspect of the invention, composition of matters including a conjugate of the foregoing agents and a therapeutic or diagnostic agent are provided. Preferably the therapeutic or diagnostic is a toxin.

[0029] According to yet another aspect of the invention, pharmaceutical compositions are provided. The compositions include an isolated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67, and a pharmaceutically acceptable carrier. Preferably, the isolated nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0030] In some embodiments, the isolated nucleic acid molecule comprises at least two isolated nucleic acid molecules coding for two different polypeptides, each polypeptide comprising a different human CT antigen, and preferably at least one of the nucleic acid molecules comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0031] In other embodiments, the pharmaceutical compositions further include an expression vector with a promoter operably linked to the isolated nucleic acid molecule or a host cell recombinantly expressing the isolated nucleic acid molecule.

[0032] According to another aspect of the invention, pharmaceutical compositions are provided that include an isolated polypeptide comprising a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67, and a pharmaceutically acceptable carrier.

[0033] In certain embodiments, the isolated polypeptide comprises a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67. Preferably the isolated polypeptide comprises at least two different polypeptides, each comprising a different human CT antigen. More preferably at least one of the polypeptides is a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67. In other preferred embodiments, the compositions include an adjuvant.

[0034] According to still another aspect of the invention, protein microarrays are provided that include at least one polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67, or an antigenic fragment thereof.

[0035] According to another aspect of the invention, protein microarrays are provided that include an antibody or an antigen-binding fragment thereof that specifically binds at least one polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67, or an antigenic fragment thereof.

[0036] According to still another aspect of the invention, nucleic acid microarrays are provided that include at least one nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67, or a fragment thereof of at least 20 nucleotides that selectively hybridizes to its complement in a biological sample.

[0037] Also provided according to the invention are, isolated fragments of a human CT antigen which, or a portion of which, binds a HLA molecule or a human antibody, wherein the CT antigen is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67. In some embodiment, the fragment is part of a complex with the HLA molecule, or the fragment is between 8 and 12 amino acids in length.

[0038] According to another aspect of the invention, kits for detecting the expression of a human CT antigen are provided. The kits include a pair of isolated nucleic acid molecules each of which consists essentially of a molecule selected from the group consisting of (a) a 12-32 nucleotide contiguous segment of the nucleotide sequence of any of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67 and (b) complements of (a), wherein the contiguous segments are nonoverlapping.

[0039] In some embodiments, the pair of isolated nucleic acid molecules is constructed and arranged to selectively amplify an isolated nucleic acid molecule selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0040] According to yet another aspect of the invention, methods for treating a subject with a disorder characterized by expression of a human CT antigen are provided. The methods include administering to the subject an amount of an agent, which enriches selectively in the subject the presence of complexes of a HLA molecule and a human CT antigen peptide, effective to ameliorate the disorder, wherein the human CT antigen peptide is a fragment of a human CT antigen encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67. In some embodiments, the disorder is characterized by expression of a plurality of human CT antigens and wherein the agent is a plurality of agents, each of which enriches selectively in the subject the presence of complexes of an HLA molecule and a different human CT antigen peptide, wherein at least one of the human CT antigens is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67. Preferably, at least one of the human CT antigen peptides is a polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56) and SEQ ID NOs: 63, 65 and 67, or a fragment thereof. In other embodiments, the plurality is at least 2, at least 3, at least 4, or at least 5 such agents. In certain other embodiments, the agent is an isolated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67. Preferably, the disorder is cancer.

[0041] According to another aspect of the invention, methods for treating a subject having a condition characterized by expression of a human CT antigen in cells of the subject are provided. The methods include (i) removing an immunoreactive cell containing sample from the subject, (ii) contacting the immunoreactive cell containing sample to the host cell under conditions favoring production of cytolytic T cells against a human CT antigen peptide that is a fragment of the human CT antigen, (iii) introducing the cytolytic T cells to the subject in an amount effective to lyse cells which express the human CT antigen, wherein the host cell is transformed or transfected with an expression vector comprising an isolated nucleic acid molecule operably linked to a promoter, wherein the isolated nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67. Preferably the host cell recombinantly or endogenously expresses an HLA molecule which binds the human CT antigen peptide.

[0042] According to still another aspect of the invention, methods for treating a subject having a condition characterized by expression of a human CT antigen in cells of the subject are provided. The methods include (i) identifying a nucleic acid molecule expressed by the cells associated with said condition, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67; (ii) transfecting a host cell with a nucleic acid selected from the group consisting of (a) the nucleic acid molecule identified, (b) a fragment of the nucleic acid identified which includes a segment coding for a human CT antigen, (c) deletions, substitutions or additions to (a) or (b), and (d) degenerates of (a), (b), or (c); (iii) culturing said transfected host cells to express the transfected nucleic acid molecule, and; (iv) introducing an amount of said host cells or an extract thereof to the subject effective to increase an immune response against the cells of the subject associated-with the condition. Preferably the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67.

[0043] In some embodiments, the method also includes identifying an MHC molecule which presents a portion of an expression product of the nucleic acid molecule, wherein the host cell expresses the same MHC molecule as identified and wherein the host cell presents an MHC binding portion of the expression product of the nucleic acid molecule.

[0044] In other embodiments, the immune response comprises a B-cell response or a T cell response. Preferably, the immune response is a T-cell response which comprises generation of cytolytic T-cells specific for the host cells presenting the portion of the expression product of the nucleic acid molecule or cells of the subject expressing the human CT antigen.

[0045] In still other embodiments, the nucleic acid molecule is selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67. In certain other embodiments, the methods include treating the host cells to render them non-proliferative.

[0046] According to another aspect of the invention, methods for treating or diagnosing or monitoring a subject having a condition characterized by expression of a protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS: 1, 3, 5, 7, 9, 63, 65 and 67 in cells or tissues other than testis, fetal ovary or placenta are provided. The methods include administering to the subject an antibody which specifically binds to the protein or a peptide derived therefrom, the antibody being coupled to a therapeutically useful agent, in an amount effective to treat the condition. Preferably the antibody is a monoclonal antibody, particularly a human monoclonal, a chimeric antibody or a humanized antibody.

[0047] According to a further aspect of the invention, methods for treating a condition characterized by expression of a protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67 in cells or tissues other than testis, fetal ovary or placenta are provided. The methods include administering to a subject a pharmaceutical composition of any one of claims 16-31 and 44-54 in an amount effective to prevent, delay the onset of, or inhibit the condition in the subject. Preferably the condition is cancer. In some embodiments the methods also include first identifying that the subject expresses in a tissue abnormal amounts of the protein.

[0048] According to another aspect of the invention, methods for treating a subject having a condition characterized by expression of a protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67 in cells or tissues other than testis, fetal ovary or placenta are provided. The methods include (i) identifying cells from the subject which express abnormal amounts of the protein; (ii) isolating a sample of the cells; (iii) cultivating the cells, and (iv) introducing the cells to the subject in an amount effective to provoke an immune response against the cells. In some embodiments, the methods also include rendering the cells non-proliferative, prior to introducing them to the subject.

[0049] According to still another aspect of the invention, methods for treating a pathological cell condition characterized by expression of a protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67 in cells or tissues other than testis, fetal ovary or placenta are provided. The methods include administering to a subject in need thereof an effective amount of an agent which inhibits the expression or activity of the protein. Preferably the agent is an inhibiting antibody which selectively binds to the protein and wherein the antibody is a monoclonal antibody, a chimeric antibody, a humanized antibody or an antibody fragment, or an antisense nucleic acid molecule which selectively binds to the nucleic acid molecule which encodes the protein. In preferred embodiments, the nucleic acid molecule comprises a nucleotide sequence set forth as SEQ ID NO: 1, or SEQ ID NO: 3 or the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), or SEQ ID NOs: 63, 65 or 67.

[0050] According to another aspect of the invention, compositions of matter useful in stimulating an immune response to a plurality of a proteins encoded by nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67 are provided. The compositions include a plurality of peptides derived from the amino acid sequences of the proteins, wherein the peptides bind to one or more MHC molecules presented on the surface of cells which are not testis, fetal ovary or placenta. In some embodiments, at least a portion of the plurality of peptides bind to MHC molecules and elicit a cytolytic response thereto. In other embodiments, at least one of the proteins is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, the nucleotide sequence of RXF4-C amplified by the C1 primer pair (SEQ ID NOs: 55, 56), and SEQ ID NOs: 63, 65 and 67. Preferably the compositions further include an adjuvant, particularly a saponin, GM-CSF, or an interleukin.

[0051] In other embodiments, the compositions include at least one peptide useful in stimulating an immune response to at least one protein which is not encoded by SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67, wherein the at least one peptide binds to one or more MHC molecules.

[0052] According to another aspect of the invention, an isolated antibody is provided which selectively binds to a complex of: (i) a peptide derived from a protein encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5, 7, 9, 63, 65 and 67 and (ii) and an MHC molecule to which binds the peptide to form the complex, wherein the isolated antibody does not bind to (i) or (ii) alone. Preferably the antibody is a monoclonal antibody, a chimeric antibody, a humanized antibody, or a fragment thereof.

[0053] According to yet another aspect of the invention, methods for identifying nucleic acids that encode a CT antigen are provided. The methods include screening sequence database records for sequences that are expressed in a first set of samples consisting of cancers of at least two tissues and are expressed in a second set of samples consisting of at least one tissue selected from the group consisting of testis, ovary and placenta, and identifying as CT antigens the sequences that match the expression criteria. In preferred embodiments, the second tissue is testis only, or ovary only (preferably fetal ovary).

[0054] In other aspects of the invention, the expression criteria include cancer-specific expression and any one of: gamete-specific gene products, gene products associated with meiosis, and trophoblast-specific gene products.

[0055] In preferred embodiments of the screening methods, the sequences are expressed in cancers at least three tissues. In embodiments of the foregoing screening methods, it is preferred that the methods include a step of verification of the expression pattern of the sequences in normal tissue samples and/or tumor samples. Preferably the expression pattern is verified by nucleic acid amplification or nucleic acid hybridization.

[0056] According to a further aspect of the invention, isolated nucleic acid molecules are provided. The molecules include a nucleotide selected from the group consisting of (a) a nucleotide sequence selected from the group consisting of SEQ ID NOs: 63, 65 and 67, which encodes a RFX4 protein, (b) a nucleotide sequence that differs from the sequence of (a) due to the degeneracy of the genetic code, and (c) complements of (a) and (b). In preferred embodiments, the nucleotide sequence is at least about 90% identical to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 63, 65 and 67. More preferably, the nucleotide sequence is at least about 95%, 96%, 97%, 98%, 99% or 99.5% identical to a nucleotide sequence selected from the group consisting of SEQ ID NOs: 63, 65 and 67.

[0057] In individual embodiments of the foregoing isolated nucleic acid molecules, the nucleotide sequence comprises the coding region of SEQ ID NO: 63, the coding region of SEQ ID NO: 65, or the coding region of SEQ ID NO: 67.

[0058] In another aspect of the invention, isolated nucleic acid molecules that include RFX4 exon 1a are provided. In other aspects, the invention provides expression vectors comprising the foregoing isolated nucleic acid molecules, and host cells that include the foregoing isolated nucleic acid molecules or the foregoing expression vectors.

[0059] According to still another aspect of the invention, isolated polypeptides that are encoded by the foregoing isolated nucleic acid molecules are provided. Preferred polypeptides are those that include the amino acid sequence of SEQ ID NO: 64, the amino acid sequence of SEQ ID NO: 66, the amino acid sequence of SEQ ID NO: 68 or the amino acid sequence of SEQ ID NO: 69.

[0060] In a further aspect of the invention, isolated antibodies that specifically bind the foregoing isolated polypeptides, but which do not specifically bind RFX4-A or RFX4-B proteins, are provided. In certain embodiments, the antibodies are coupled to a therapeutically useful agent. Preferably the antibody is a monoclonal antibody, particularly a human monoclonal, a chimeric antibody or a humanized antibody. Antigen-binding fragments of the antibodies, having the same binding specificity as the antibodies, also are provided, as are method for treating cancer using the antibodies or fragments, in which an amount of the antibodies or fragments effective to treat the cancer, preferably coupled to a therapeutically useful agent, is administered to a subject.

[0061] According to yet another aspect of the invention, methods for diagnosing astrocytoma are provided. The method include obtaining a biological sample from a subject suspected of having astrocytoma, and determining the expression of RFX4-D and/or RFX4-E nucleic acid molecules or polypeptides. The expression of RFX4-D and/or RFX4-E nucleic acid molecules or polypeptides is indicative of the presence of astrocytoma in the subject. The methods are carried out using techniques similar to other diagnostic methods described herein.

[0062] In another aspect of the invention, methods for staging astrocytoma are provided. The methods include isolating from a subject a biological sample containing astrocytoma cells, and determining the expression of RFX4-D and RFX4-E nucleic acid molecules or polypeptides. The expression of RFX4-D and RFX4-E nucleic acid molecules or polypeptides is indicative of the presence of Grade III and IV astrocytoma in the sample, and the presence of RFX4-D but not RFX4-E nucleic acid molecules or polypeptides is indicative of the presence of Grade III and IV astrocytoma in the sample. In certain embodiments, the RFX4-D nucleic acid and polypeptide comprise SEQ ID NO: 65 and SEQ ID NO: 66, respectively. In some embodiments, the RFX4-E nucleic acid comprises SEQ ID NO: 67 and the RFX4-E polypeptide comprises SEQ ID NO: 68 or SEQ ID NO: 69. The methods are carried out using techniques similar to other diagnostic methods described herein.

[0063] According to still another aspect of the invention, methods for diagnosing ovarian cancer are provided. The methods include obtaining a biological sample from a subject suspected of having ovarian cancer, and determining the expression of AKAP3 nucleic acid molecules or polypeptides, wherein the expression of AKAP3 nucleic acid molecules or polypeptides is indicative of the presence of ovarian cancer in the subject. The methods are carried out using techniques similar to other diagnostic methods described herein.

[0064] In certain embodiments, the step of determining the expression of AKAP3 nucleic acid molecules or polypeptides includes contacting the biological sample with an agent that specifically binds to the nucleic acid molecule, an expression product thereof, a fragment of an expression product thereof complexed with an HLA molecule, or an antibody that binds the expression product thereof. In these embodiments, the nucleic acid molecule includes the nucleotide sequence set forth as SEQ ID NO: 3.

[0065] The methods of this embodiment further include determining the interaction between the agent and the nucleic acid molecule, the expression product or the antibody as an indication of ovarian cancer. In certain preferred embodiments, the agent is selected from the group consisting of (a) a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 3 or a fragment thereof, (b) an antibody that binds to an expression product of a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 3, (c) an agent that binds to a complex of an HLA molecule and a fragment of an expression product of a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 3, and (d) an expression product of a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NO: 3, that binds an antibody. In other embodiments, expression of AKAP 3 that is greater than about 6% of the level of expression of G2PDH is indicative of ovarian cancer.

[0066] According to a further aspect of the invention, methods for staging ovarian cancer are provided. The methods include isolating from a subject a biological sample containing ovarian cancer cells, and determining the expression of AKAP3 nucleic acid molecules or polypeptides. The expression of AKAP3 nucleic acid molecules or polypeptides is indicative of the presence of Grade III and/or IV ovarian cancer in the sample. The methods are carried out using techniques similar to other diagnostic methods described herein.

[0067] In some embodiments, expression of AKAP 3 that is greater than about 6% of the level of expression of G2PDH is indicative of the presence of Grade III and/or IV ovarian cancer in the sample.

[0068] According to still another aspect of the invention, methods for predicting the survival of a subject who has ovarian cancer are provided. The methods include isolating from a subject a biological sample containing ovarian cancer cells, and determining the expression of AKAP3 nucleic acid molecules or polypeptides, wherein the expression of AKAP3 nucleic acid molecules or polypeptides is indicative of a good prognosis for survival of the subject. In certain preferred embodiments, expression of AKAP 3 that is greater than about 6% of the level of expression of G2PDH is indicative of a good prognosis for survival of the subject. The methods are carried out using techniques similar to other diagnostic methods described herein.

[0069] The invention also involves the use of the genes, gene products, fragments thereof, agents which bind thereto, and so on in the preparation of medicaments. A particular medicament is for treating cancer.

[0070] These and other aspects of the invention will be described in further detail in connection with the detailed description of the invention.

BRIEF DESCRIPTION OF FIGURES

[0071]
FIG. 1 depicts the two-step real-time RT-PCR performed to determine expression of NY-ESO-1, and sperm protein mRNAs in 16 normal tissues using ABI PRISM 7700 Sequence Detection System. FIG. 1A shows the real-time amplification plot. Shown is Rn (the normalized reporter signal minus the base line signal) as a function of PCR cycle number. Duplicate samples for each tissue were examined. Lines indicate each sample. The horizontal line is the threshold for detection. FIG. 1B provides the Ct (threshold cycles) values for normal tissues obtained in FIG. 1A were plotted.

[0072]
FIG. 2 provides the relative mRNA expression values (n) in normal tissues standardized by the expression of β-actin. Testis specific expression was observed with NY-ESO-1, SP-10, SP17, acrosin, PH-20, OY-TES-1, AKAP110, ASP, ropporin, and NYD-sp10. Ubiquitous expression was observed with CS-1 and SPAG9.

[0073]
FIG. 3 is a diagram of the genomic structure of RFX4 and alternatively spliced transcripts. Exons and introns are shown in boxes and lines, respectively. The exon/intron structure is determined according to the NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map). In alternatively spliced transcripts, the open reading frames are shown. RFX4-A (GenBank accession number AB044245) (SEQ ID NO: 9, 10) is described by Morotomi-Yano et al. (J. Biol. Chem. 277(1): 836-842, 2002). RFX4-B (SEQ ID NO: 7, 8) is also known as NYD-sp10 (GenBank accession number AF332192). Primers used for PCR amplification are indicated by arrows.

[0074]
FIG. 4 is a schematic representation of the RFX4 proteins. The DNA binding domain (DBD), the dimerization domains (DIM) and two additional conserved regions B and C are indicated.

[0075]
FIGS. 5A and 5B are digitized photographs of agarose gels that depict the RT-PCR analysis of RFX4 mRNA in normal tissues (FIG. 5A) and tumors (FIG. 5B). RT-PCR was performed using the common primer pair (NYD-S and NYD-AS, shown in FIG. 3) at 30 cycle amplification. PCR products were analyzed by agarose gel electrophoresis. The same cDNA samples were tested for β-actin as an internal control.

[0076]
FIG. 6 provides the expression level of RFX4 splice variants in glioma. Primer pairs A1, A2, B1, B2, and C1 (see FIG. 3 and Table 7) were used to analyze the expression of three alternatively spliced transcripts in gliomas and normal testis. Representative results for 3 astrocytomas G III, 3 astrocytomas G IV, and a normal testis sample are shown.

[0077]
FIG. 7 is a schematic representation of RFX4 genomic structure and alternatively spliced variants. Exons are shown in boxes. Open reading frames are shown in hatched boxes. Primers used in this study is indicated by arrows.

[0078]
FIG. 8 is a schematic representation of RFX4 proteins. Five RFX4 isoforms and ER-RFX4 protein are shown.

[0079]
FIG. 9 shows the nucleotide and deduced amino acid sequence of RFX4-D (FIG. 9A; SEQ ID NOs: 65, 66) and RFX4-E (FIG. 9B; SEQ ID NOs: 67-69). In FIG. 9A, DBD, B, C and DIM domains are shown in boxes. In FIG. 9B, ORFI represents a 126 amino acid gene product (SEQ ID NO: 68) with an incomplete DBD domain. ORF2 represents a 110 amino acid gene product (SEQ ID NO: 69).

[0080]
FIG. 10 depicts the alignment of portions of RFX4-B (SEQ ID NO: 78), RFX4-D (SEQ ID NO: 79) and RFX4-E (SEQ ID NO: 79) proteins. The DBD domain is shown in boxes. The asterisk indicates a stop codon.

[0081]
FIG. 11 shows RT-PCR analysis of mRNA expression of the different RFX4 variants in normal tissues. FIG. 11A, agarose gel electrophoresis by ethidium bromide staining. FIG. 11B, mRNA expression in whole brain, pancreas and testis was analyzed by a capillary electrophoresis, and expressed as percent GAPDH expression in the same tissues.

[0082]
FIG. 12 shows RT-PCR analysis of different RFX4 variants in astrocytomas.

[0083]
FIG. 13 shows real-time RT-PCR analysis of RFX4-D (FIG. 13A) and RFX4-E (FIG. 13B) expression in astrocytomas. The amount of RFX4 variants was expressed as n-fold differences relative to the mean values in 4 normal brains and 5 normal tissues from grade II astrocytoma.

[0084]
FIG. 14 depicts the results of RT-PCR analysis of AKAP3 mRNA. FIG. 14A shows agarose gel electrophoresis or PCR products stained with ethidium bromide. mRNA from normal ovary (lanes 1-2), LPM (lanes 3-4), well and moderately differentiated tumor (lanes 5-6), poorly differentiated tumor (lanes 7-10), and normal testis (control; lane 11) was examined. FIG. 14B shows electrophoregram of selected specimens shown in FIG. 14A by capillary electrophoresis by Agilent 2100 Bioanalyzer. A=AKAP3; G=G3PDH.

[0085]
FIG. 15 shows AKAP3 mRNA expression in normal ovaries, low potential malignancies (LPM), well and moderately differentiated tumors, and poorly differentiated tumors. Percent expression of AKAP3 mRNA to the expression of G3PDH was calculated by the eletrophoregram shown in FIG. 14. Statistical analysis of differences in distribution between each groups was performed by Kruskal-Wallis test.

[0086]
FIG. 16 is a Kaplan-Meier survival curve in all ovarian cancer patients according to AKAP3 mRNA expression. FIG. 16A shows overall survival; FIG. 16B shows progression-free survival. Statistical analysis of prognostic survival was done by the log-rank test.

[0087]
FIG. 17 is a Kaplan-Meier survival curve in patients with poorly differentiated ovarian cancer according to AKAP3 mRNA expression. FIG. 17A shows overall survival; FIG. 17B shows progression-free survival. Statistical analysis of prognostic survival was done by the log-rank test.

DETAILED DESCRIPTION OF THE INVENTION

[0088] As a consequence of T cell epitope cloning and SEREX analysis, a growing number of cancer-testis (CT) antigens have now been defined. See Table 1 and references cited therein. There are now 14 genes or gene families identified that code for presumptive cancer-testis antigens.

1GenesChromosomeDetectionCT*System#LocationSystem**Refs.1MAGE16Xq28/Xp21T, Ab7, 10, 12, 132BAGE2UnknownT143GAGE9Xp11T15, 164SSX>5Xp11Ab10, 175NY-ESO-12Xq28Ab, T, RDA18, 19LAGE-16SCP-131p12-p13Ab207CT7/1Xq26Ab, RDA21, 22MAGE-C18CT81UnknownAb239CT911pAb2410CT10/1Xq27RDA, Ab25, 26MAGE-C211CT11p1Xq26-Xq27***2712SAGE1Xq28RDA2813cTAGE-1118p11Ab2914OY-TES-1212p12-p13Ab30*Numbered according to the CT nomenclature proposed by Old & Chen (11). **Ab = Antibody, T = CD8+ T cell, RDA = representational difference analysis. *** Defined by differential mRNA expression in a parental vs. metastatic melanoma cell variant.

[0089] A thorough analysis of these gene reveals that they encode products with the following characteristics.

[0090] i) mRNA expression in normal tissues is restricted to testis, fetal ovary, and placenta, with little or no expression detected in adult ovary.

[0091] ii) mRNA expression in cancers of diverse origin is common—up to 30-40% of a number of different cancer types, e.g., melanoma, bladder cancer, sarcoma express one or more CT antigens.

[0092] iii) The X chromosome codes for the majority of CT antigens, but a number of more recently defined CT coding genes have a non-X chromosomal locus.

[0093] iv) In normal adult testis, expression of CT antigens is primarily restricted to immature germ cells—, e.g., spermatogonia (31). However, a recently defined CT antigen, OY-TES-1, is clearly involved in late stages of sperm maturation (see below). In fetal ovary, immature germ cells (oogonia/primary oocytes) express CT antigens, whereas oocytes in the resting primordial follicles do not (32). In fetal placenta, both cytotrophoblast and syncytiotrophoblast express CT antigens, but in term placenta, CT antigen expression is weak or absent (33).

[0094] v) A highly variable pattern of CT antigen expression is found in different cancers, from tumors showing only single positive cells or small cluster of positive cells to other tumors with a generally homogeneous expression pattern (31, 34).

[0095] vi) The function of most CT antigens is unknown, although some role in regulating gene expression appears likely. Two CT antigens, however, have known roles in gamete development—SCP-1, the synaptonemal complex protein, is involved in chromosomal reduction during meiosis (35), and OY-TES-1 is a proacrosin binding protein sp32 precursor thought to be involved in packaging acrosin in the acrosome in the sperm head (36).

[0096] vii) There is increasing evidence that CT expression is correlated with tumor progression and with tumors of higher malignant potential. For instance, a higher frequency of MAGE mRNA expression is found in metastatic vs. primary melanoma (37) and in invasive vs. superficial bladder cancer (38), and NY-ESO-1 expression in bladder cancer is correlated with high nuclear grade (39).

[0097] viii) There appears to be considerable variation in the inherent immunogenicity of different CT antigens as indicated by specific CD8+T cell and antibody responses in patients with antigen positive tumors. To date, NY-ESO-1 appears to have the strongest spontaneous immunogenicity of any of the CT antigens—e.g., up to 50% of patients with advanced NY-ESO-1+ tumors develop humoral and cellular immunity to NY-ESO-1 (40, 41).

[0098] These characteristics indicate the desirability of cancer-testis antigens for use in diagnostics and therapeutics. These characteristics also provide a basis for the identification of additional cancer-testis antigens.

[0099] While others have attempted to identify cancer related sequences in public databases by the use of bioinformatics techniques, (e.g., database mining plus rapid screening by fluorescent-PCR expression, Loging et al., Genome Res 10(9):1393-402, 2000), these techniques have not focused on the identification of nucleic acid sequences that fit the preferred cancer-testis antigen profile. In particular, the present invention includes the identification of cancer-testis sequences by more stringent criteria. The database analysis criteria for identifying cancer-testis antigen sequences include the requirement that the sequences are expressed in cancers from at least two different tissues, and preferably are expressed in cancers from at least three different tissues. In addition, the sequences preferably have normal tissue expression restricted to one or more tissue selected from the group consisting of testis, placenta and ovary (preferably only fetal ovary).

[0100] In the above summary and in the ensuing description, lists of sequences are provided. The lists are meant to embrace each single sequence separately, two or more sequences together where they form a part of the same gene, any combination of two or more sequences which relate to different genes, including and up to the total number on the list, as if each and every combination were separately and specifically enumerated. Likewise, when mentioning fragment size, it is intended that a range embrace the smallest fragment mentioned to the full-length of the sequence (less one nucleotide or amino acid so that it is a fragment), each and every fragment length intended as if specifically enumerated. Thus, if a fragment could be between 10 and 15 in length, it is explicitly meant to mean 10, 11, 12, 13, 14, or 15 in length.

[0101] The summary and the claims mention antigen precursors and antigens. As used in the summary and in the claims, a precursor is substantially the full-length protein encoded by the coding region of the isolated nucleic acid and the antigen is a peptide which complexes with MHC, preferably HLA, and which participates in the immune response as part of that complex. Such antigens are typically 9 amino acids long, although this may vary slightly.

[0102] As used herein, a subject is a human, non-human primate, cow, horse, pig, sheep, goat, dog, cat or rodent. In all embodiments human cancer antigens and human subjects are preferred.

[0103] The present invention in one aspect involves the identification of human CT antigens using autologous antisera of subjects having cancer. The sequences representing CT antigen genes identified according to the methods described herein are presented in the attached Sequence Listing. The nature of the sequences as encoding CT antigens recognized by the immune systems of cancer patients is, of course, unexpected.

[0104] The invention thus involves in one aspect CT antigen polypeptides, genes encoding those polypeptides, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as diagnostics and therapeutics relating thereto.

[0105] Homologs and alleles of the CT antigen nucleic acids of the invention can be identified by conventional techniques. Thus, an aspect of the invention is those nucleic acid sequences which code for CT antigen precursors.

[0106] The term “stringent conditions” as used herein refers to parameters with which the art is familiar. Nucleic acid hybridization parameters may be found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, or Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. More specifically, stringent conditions, as used herein, refers, for example, to hybridization at 65° C. in hybridization buffer (3.5×SSC, 0.02% Ficoll, 0.02% polyvinyl pyrrolidone, 0.02% Bovine Serum Albumin, 2.5mM NaH2PO4(pH7), 0.5% SDS, 2 mM EDTA). SSC is 0.15M sodium chloride/0.15M sodium citrate, pH7; SDS is sodium dodecyl sulphate; and EDTA is ethylenediaminetetracetic acid. After hybridization, the membrane upon which the DNA is transferred is washed, for example, in 2×SSC at room temperature and then at 0.1-0.5×SSC/0.1×SDS at temperatures up to 68° C.

[0107] There are other conditions, reagents, and so forth which can be used, which result in a similar degree of stringency. The skilled artisan will be familiar with such conditions, and thus they are not given here. It will be understood, however, that the skilled artisan will be able to manipulate the conditions in a manner to permit the clear identification of homologs and alleles of CT antigen nucleic acids of the invention (e.g., by using lower stringency conditions). The skilled artisan also is familiar with the methodology for screening cells and libraries for expression of such molecules which then are routinely isolated, followed by isolation of the pertinent nucleic acid molecule and sequencing.

[0108] In general homologs and alleles typically will share at least 75% nucleotide identity and/or at least 90% amino acid identity to the sequences of CT antigen nucleic acid and polypeptides, respectively, in some instances will share at least 90% nucleotide identity and/or at least 95% amino acid identity and in still other instances will share at least 95% nucleotide identity and/or at least 99% amino acid identity. The homology can be calculated using various, publicly available software tools developed by NCBI (Bethesda, Md.) that can be obtained through the internet (ftp:/ncbi.nlm.nih.gov/pub/). Exemplary tools include the BLAST software available at http://www.ncbi.nlm.nih.gov, using default settings. Pairwise and ClustalW alignments (BLOSUM30 matrix setting) as well as Kyte-Doolittle hydropathic analysis can be obtained using the MacVector sequence analysis software (Oxford Molecular Group). Watson-Crick complements of the foregoing nucleic acids also are embraced by the invention.

[0109] In screening for CT antigen genes, a Southern blot may be performed using the foregoing conditions, together with a radioactive probe. After washing the membrane to which the DNA is finally transferred, the membrane can be placed against X-ray film to detect the radioactive signal. In screening for the expression of CT antigen nucleic acids, Northern blot hybridizations using the foregoing can be performed on samples taken from cancer patients or subjects suspected of having a condition characterized by expression of CT antigen genes. Amplification protocols such as polymerase chain reaction using primers which hybridize to the sequences presented also can be used for detection of the CT antigen genes or expression thereof.

[0110] The invention also includes degenerate nucleic acids which include alternative codons to those present in the native materials. For example, serine residues are encoded by the codons TCA, AGT, TCC, TCG, TCT and AGC. Each of the six codons is equivalent for the purposes of encoding a serine residue. Thus, it will be apparent to one of ordinary skill in the art that any of the serine-encoding nucleotide triplets may be employed to direct the protein synthesis apparatus, in vitro or in vivo, to incorporate a serine residue into an elongating CT antigen polypeptide. Similarly, nucleotide sequence triplets which encode other amino acid residues include, but are not limited to: CCA, CCC, CCG and CCT (proline codons); CGA, CGC, CGG, CGT, AGA and AGG (arginine codons); ACA, ACC, ACG and ACT (threonine codons); AAC and AAT (asparagine codons); and ATA, ATC and ATT (isoleucine codons). Other amino acid residues may be encoded similarly by multiple nucleotide sequences. Thus, the invention embraces degenerate nucleic acids that differ from the biologically isolated nucleic acids in codon sequence due to the degeneracy of the genetic code.

[0111] The invention also provides modified nucleic acid molecules which include additions, substitutions and deletions of one or more nucleotides. In preferred embodiments, these modified nucleic acid molecules and/or the polypeptides they encode retain at least one activity or function of the unmodified nucleic acid molecule and/or the polypeptides, such as antigenicity, enzymatic activity, receptor binding, formation of complexes by binding of peptides by MHC class I and class II molecules, etc. In certain embodiments, the modified nucleic acid molecules encode modified polypeptides, preferably polypeptides having conservative amino acid substitutions as are described elsewhere herein. The modified nucleic acid molecules are structurally related to the unmodified nucleic acid molecules and in preferred embodiments are sufficiently structurally related to the unmodified nucleic acid molecules so that the modified and unmodified nucleic acid molecules hybridize under stringent conditions known to one of skill in the art.

[0112] For example, modified nucleic acid molecules which encode polypeptides having single amino acid changes can be prepared. Each of these nucleic acid molecules can have one, two or three nucleotide substitutions exclusive of nucleotide changes corresponding to the degeneracy of the genetic code as described herein. Likewise, modified nucleic acid molecules which encode polypeptides having two amino acid changes can be prepared which have, e.g., 2-6 nucleotide changes. Numerous modified nucleic acid molecules like these will be readily envisioned by one of skill in the art, including for example, substitutions of nucleotides in codons encoding amino acids 2 and 3, 2 and 4, 2 and 5, 2 and 6, and so on. In the foregoing example, each combination of two amino acids is included in the set of modified nucleic acid molecules, as well as all nucleotide substitutions which code for the amino acid substitutions. Additional nucleic acid molecules that encode polypeptides having additional substitutions (i.e., 3 or more), additions or deletions (e.g., by introduction of a stop codon or a splice site(s)) also can be prepared and are embraced by the invention as readily envisioned by one of ordinary skill in the art. Any of the foregoing nucleic acids or polypeptides can be tested by routine experimentation for retention of structural relation or activity to the nucleic acids and/or polypeptides disclosed herein.

[0113] The invention also provides isolated fragments of CT antigen nucleic acid sequences or complements thereof, and in particular unique fragments. A unique fragment is one that is a ‘signature’ for the larger nucleic acid. It, for example, is long enough to assure that its precise sequence is not found in molecules within the human genome outside of the CT antigen nucleic acids defined above (and human alleles). Those of ordinary skill in the art may apply routine procedures to determine if a fragment is unique within the human genome, such as the use of publicly available sequence comparison software to selectively distinguish the sequence fragment of interest from other sequences in the human genome, although in vitro confirmatory hybridization and sequencing analysis may be performed.

[0114] Fragments can be used as probes in Southern and Northern blot assays to identify CT antigen nucleic acids, or can be used in amplification assays such as those employing PCR. As known to those skilled in the art, large probes such as 200, 250, 300 or more nucleotides are preferred for certain uses such as Southern and Northern blots, while smaller fragments will be preferred for uses such as PCR. Fragments also can be used to produce fusion proteins for generating antibodies or determining binding of the polypeptide fragments, or for generating immunoassay components. Likewise, fragments can be employed to produce nonfused fragments of the CT antigen polypeptides, useful, for example, in the preparation of antibodies, and in immunoassays. Fragments further can be used as antisense molecules to inhibit the expression of CT antigen nucleic acids and polypeptides, particularly for therapeutic purposes as described in greater detail below.

[0115] As mentioned above, this disclosure intends to embrace each and every fragment of each sequence, beginning at the first nucleotide, the second nucleotide and so on, up to 8 nucleotides short of the end, and ending anywhere from nucleotide number 8, 9, 10 and so on for each sequence, up to the entire length of the disclosed sequence. Preferred fragments are those useful as amplification primers, e.g., typically between 12 and 32 nucleotides (e.g. 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31 and 32) in length.

[0116] Those skilled in the art are well versed in methods for selecting such sequences, typically on the basis of the ability of the fragment to selectively distinguish the sequence of interest from other sequences in the human genome of the fragment to those on known databases typically is all that is necessary, although in vitro confirmatory hybridization and sequencing analysis may be performed.

[0117] Especially preferred fragments include nucleic acids encoding a series of epitopes, known as “polytopes”. The epitopes can be arranged in sequential or overlapping fashion (see, e.g., Thomson et al., Proc. Natl. Acad. Sci. USA 92:5845-5849, 1995; Gilbert et al., Nature Biotechnol. 15:1280-1284, 1997), with or without the natural flanking sequences, and can be separated by unrelated linker sequences if desired. The polytope is processed to generated individual epitopes which are recognized by the immune system for generation of immune responses.

[0118] Thus, for example, peptides derived from a polypeptide having an amino acid sequence encoded by one of the nucleic acid disclosed herein, and which are presented by MHC molecules and recognized by CTL or T helper lymphocytes, can be combined with peptides from one or more other CT antigens (e.g. by preparation of hybrid nucleic acids or polypeptides) to form “polytopes”. The two or more peptides (or nucleic acids encoding the peptides) can be selected from those described herein, or they can include one or more peptides of previously known CT antigens. Exemplary cancer associated peptide antigens that can be administered to induce or enhance an immune response are derived from tumor associated genes and encoded proteins including MAGE-A1, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-A5, MAGE-A6, MAGE-A7, MAGE-A8, MAGE-A9, MAGE-A10, MAGE-A11, MAGE-A12, GAGE-1, GAGE-2, GAGE-3, GAGE-4, GAGE-5, GAGE-6, GAGE-7, GAGE-8, GAGE-9, BAGE-1, RAGE-1, LB33/MUM-1, PRAME, NAG, MAGE-B2, MAGE-B3, MAGE-B4, tyrosinase, brain glycogen phosphorylase, Melan-A, MAGE-C1, MAGE-C2, MAGE-C3, MAGE-C4, MAGE-C5, NY-ESO-1, LAGE-1, SSX-1, SSX-2 (HOM-MEL-40), SSX-4, SSX-5, SCP-1 and CT-7. See, for example, PCT application publication no. WO96/10577. Other examples will be known to one of ordinary skill in the art and can be used in the invention in a like manner as those disclosed herein. Other examples of HLA class I and HLA class II binding peptides will be known to one of ordinary skill in the art. For example, see the following references: Coulie, Stem Cells 13:393-403, 1995; Traversari et al., J. Exp. Med. 176:1453-1457, 1992; Chaux et al., J. Immunol. 163:2928-2936, 1999; Fujie et al., Int. J. Cancer 80:169-172, 1999; Tanzarella et al., Cancer Res. 59:2668-2674, 1999; van der Bruggen et al., Eur. J. Immunol. 24:2134-2140, 1994; Chaux et al., J. Exp. Med. 189:767-778, 1999; Kawashima et al, Hum. Immunol. 59:1-14, 1998; Tahara et al., Clin. Cancer Res. 5:2236-2241, 1999; Gaugler et al., J. Exp. Med. 179:921-930, 1994; van der Bruggen et al., Eur. J Immunol. 24:3038-3043, 1994; Tanaka et al., Cancer Res. 57:4465-4468, 1997; Oiso et al., Int. J. Cancer 81:387-394, 1999; Herman et al., Immunogenetics 43:377-383, 1996; Manici et al., J. Exp. Med. 189:871-876, 1999; Duffour et al., Eur. J Immunol. 29:3329-3337, 1999; Zorn et al., Eur. J Immunol. 29:602-607, 1999; Huang et al., J. Immunol.162:6849-6854, 1999; Boël et al., Immunity 2:167-175, 1995; Van den Eynde et al., J. Exp. Med. 182:689-698, 1995; De Backer et al., Cancer Res. 59:3157-3165, 1999; Jäger et al., J. Exp. Med. 187:265-270, 1998; Wang et al., J. Immunol. 161:3596-3606, 1998; Aamoudse et al., Int. J. Cancer 82:442-448, 1999; Guilloux et al., J. Exp. Med. 183:1173-1183, 1996; Lupetti et al., J. Exp. Med. 188:1005-1016, 1998; Wölfel et al., Eur. J Immunol. 24:759-764, 1994; Skipper et al., J. Exp. Med. 183:527-534, 1996; Kang et al., J. Immunol. 155:1343-1348, 1995; Morel et al., Int. J. Cancer 83:755-759, 1999; Brichard et al., Eur. J. Immunol. 26:224-230, 1996; Kittlesen et al., J. Immunol. 160:2099-2106, 1998; Kawakami et al., J. Immunol. 161:6985-6992, 1998; Topalian et al., J. Exp. Med. 183:1965-1971, 1996; Kobayashi et al., Cancer Research 58:296-301, 1998; Kawakami et al., J. Immunol. 154:3961-3968, 1995; Tsai et al., J. Immunol. 158:1796-1802, 1997; Cox et al., Science 264:716-719, 1994; Kawakami et al., Proc. Natl. Acad. Sci. USA 91:6458-6462, 1994; Skipper et al., J. Immunol. 157:5027-5033, 1996; Robbins et al., J. Immunol. 159:303-308, 1997; Castelli et al, J. Immunol. 162:1739-1748, 1999; Kawakami et al., J. Exp. Med. 180:347-352, 1994; Castelli et al., J. Exp. Med. 181:363-368, 1995; Schneider et al., Int. J. Cancer 75:451-458, 1998; Wang et al., J. Exp. Med. 183:1131-1140, 1996; Wang et al., J. Exp. Med. 184:2207-2216, 1996; Parkhurst et al., Cancer Research 58:4895-4901, 1998; Tsang et al., J. Natl Cancer Inst 87:982-990, 1995; Correale et al., J Natl Cancer Inst 89:293-300, 1997; Coulie et al., Proc. Natl. Acad. Sci. USA 92:7976-7980, 1995; Wölfel et al., Science 269:1281-1284, 1995; Robbins et al., J. Exp. Med. 183:1185-1192, 1996; Brandle et al., J. Exp. Med. 183:2501-2508, 1996; ten Bosch et al., Blood 88:3522-3527, 1996; Mandruzzato et al., J. Exp. Med. 186:785-793, 1997; Guéguen et al., J. Immunol. 160:6188-6194, 1998; Gjertsen et al., Int. J Cancer 72:784-790, 1997; Gaudin et al., J. Immunol. 162:1730-1738, 1999; Chiari et al., Cancer Res. 59:5785-5792, 1999; Hogan et al., Cancer Res. 58:5144-5150, 1998; Pieper et al., J. Exp. Med. 189:757-765, 1999; Wang et al., Science 284:1351-1354, 1999; Fisk et al., J. Exp. Med. 181:2109-2117, 1995; Brossart et al., Cancer Res. 58:732-736, 1998; Röpke et al., Proc. Natl. Acad. Sci. USA 93:14704-14707, 1996; Ikeda et al., Immunity 6:199-208, 1997; Ronsin et al., J. Immunol. 163:483-490, 1999; Vonderheide et al., Immunity 10:673-679,1999.

[0119] One of ordinary skill in the art can prepare polypeptides comprising one or more CT antigen peptides and one or more of the foregoing cancer associated peptides, or nucleic acids encoding such polypeptides, according to standard procedures of molecular biology.

[0120] Thus polytopes are groups of two or more potentially immunogenic or immune response stimulating peptides which can be joined together in various arrangements (e.g. concatenated, overlapping). The polytope (or nucleic acid encoding the polytope) can be administered in a standard immunization protocol, e.g. to animals, to test the effectiveness of the polytope in stimulating, enhancing and/or provoking an immune response.

[0121] The peptides can be joined together directly or via the use of flanking sequences to form polytopes, and the use of polytopes as vaccines is well known in the art (see, e.g., Thomson et al., Proc. Acad. Natl. Acad. Sci USA 92(13):5845-5849, 1995; Gilbert et al., Nature Biotechnol. 15(12):1280-1284, 1997; Thomson et al., J. Immunol. 157(2):822-826, 1996; Tam et al., J. Exp. Med. 171(1):299-306, 1990). For example, Tam showed that polytopes consisting of both MHC class I and class II binding epitopes successfully generated antibody and protective immunity in a mouse model. Tam also demonstrated that polytopes comprising “strings” of epitopes are processed to yield individual epitopes which are presented by MHC molecules and recognized by CTLs. Thus polytopes containing various numbers and combinations of epitopes can be prepared and tested for recognition by CTLs and for efficacy in increasing an immune response.

[0122] It is known that tumors express a set of tumor antigens, of which only certain subsets may be expressed in the tumor of any given patient. Polytopes can be prepared which correspond to the different combination of epitopes representing the subset of tumor rejection antigens expressed in a particular patient. Polytopes also can be prepared to reflect a broader spectrum of tumor rejection antigens known to be expressed by a tumor type. Polytopes can be introduced to a patient in need of such treatment as polypeptide structures, or via the use of nucleic acid delivery systems known in the art (see, e.g., Allsopp et al., Eur. J. Immunol. 26(8):1951-1959, 1996). Adenovirus, pox viruses, Ty-virus like particles, adeno-associated virus, alphaviruses, plasmids, bacteria, etc. can be used in such delivery. One can test the polytope delivery systems in mouse models to determine efficacy of the delivery system. The systems also can be tested in human clinical trials.

[0123] In instances in which a human HLA class I molecule presents tumor rejection antigens derived from CT antigens, the expression vector may also include a nucleic acid sequence coding for the HLA molecule that presents any particular tumor rejection antigen derived from these nucleic acids and polypeptides. Alternatively, the nucleic acid sequence coding for such a HLA molecule can be contained within a separate expression vector. In a situation where the vector contains both coding sequences, the single vector can be used to transfect a cell which does not normally express either one. Where the coding sequences for a CT antigen precursor and the HLA molecule which presents it are contained on separate expression vectors, the expression vectors can be cotransfected. The CT antigen precursor coding sequence may be used alone, when, e.g. the host cell already expresses a HLA molecule which presents a CT antigen derived from precursor molecules. Of course, there is no limit on the particular host cell which can be used. As the vectors which contain the two coding sequences may be used in any antigen-presenting cells if desired, and the gene for CT antigen precursor can be used in host cells which do not express a HLA molecule which presents a CT antigen. Further, cell-free transcription systems may be used in lieu of cells.

[0124] As mentioned above, the invention embraces antisense oligonucleotides that selectively bind to a nucleic acid molecule encoding a CT antigen polypeptide, to reduce the expression of CT antigens. This is desirable in virtually any medical condition wherein a reduction of expression of CT antigens is desirable, e.g., in the treatment of cancer. This is also useful for in vitro or in vivo testing of the effects of a reduction of expression of one or more CT antigens.

[0125] As used herein, the term “antisense oligonucleotide” or “antisense” describes an oligonucleotide that is an oligoribonucleotide, oligodeoxyribonucleotide, modified oligoribonucleotide, or modified oligodeoxyribonucleotide which hybridizes under physiological conditions to DNA comprising a particular gene or to an mRNA transcript of that gene and, thereby, inhibits the transcription of that gene and/or the translation of that mRNA. The antisense molecules are designed so as to interfere with transcription or translation of a target gene upon hybridization with the target gene or transcript. Those skilled in the art will recognize that the exact length of the antisense oligonucleotide and its degree of complementarity with its target will depend upon the specific target selected, including the sequence of the target and the particular bases which comprise that sequence. It is preferred that the antisense oligonucleotide be constructed and arranged so as to bind selectively with the target under physiological conditions, i.e., to hybridize substantially more to the target sequence than to any other sequence in the target cell under physiological conditions. Based upon the sequences of nucleic acids encoding CT antigens, or upon allelic or homologous genomic and/or cDNA sequences, one of skill in the art can easily choose and synthesize any of a number of appropriate antisense molecules for use in accordance with the present invention. Molecules for generating RNA interference (RNAi) also can be prepared based on the sequences provided herein.

[0126] In order to be sufficiently selective and potent for inhibition, such antisense oligonucleotides should comprise at least 10 and, more preferably, at least 15 consecutive bases which are complementary to the target, although in certain cases modified oligonucleotides as short as 7 bases in length have been used successfully as antisense oligonucleotides (Wagner et al., Nature Biotechnol. 14:840-844, 1996). Most preferably, the antisense oligonucleotides comprise a complementary sequence of 20-30 bases.

[0127] Although oligonucleotides may be chosen which are antisense to any region of the gene or mRNA transcripts, in preferred embodiments the antisense oligonucleotides correspond to N-terminal or 5′ upstream sites such as translation initiation, transcription initiation or promoter sites. In addition, 3′-untranslated regions may be targeted. Targeting to mRNA splicing sites has also been used in the art but may be less preferred if alternative mRNA splicing occurs. In addition, the antisense is targeted, preferably, to sites in which mRNA secondary structure is not expected (see, e.g., Sainio et al., Cell Mol. Neurobiol. 14(5):439-457, 1994) and at which proteins are not expected to bind. Suitable antisense molecules can be identified by a “gene walk” experiment in which overlapping oligonucleotides corresponding to the CT antigen nucleic acid are synthesized and tested for the ability to inhibit expression, cause the degradation of sense transcripts, etc. Finally, although the listed sequences are cDNA sequences, one of ordinary skill in the art may easily derive the genomic DNA corresponding to the cDNA of a CT antigen. Thus, the present invention also provides for antisense oligonucleotides which are complementary to the genomic DNA corresponding to nucleic acids encoding CT antigens. Similarly, antisense to allelic or homologous cDNAs and genomic DNAs are enabled without undue experimentation.

[0128] In one set of embodiments, the antisense oligonucleotides of the invention may be composed of “natural” deoxyribonucleotides, ribonucleotides, or any combination thereof. That is, the 5′ end of one native nucleotide and the 3′ end of another native nucleotide may be covalently linked, as in natural systems, via a phosphodiester internucleoside linkage. These oligonucleotides may be prepared by art recognized methods which may be carried out manually or by an automated synthesizer. They also may be produced recombinantly by vectors.

[0129] In preferred embodiments, however, the antisense oligonucleotides of the invention also may include “modified” oligonucleotides. That is, the oligonucleotides may be modified in a number of ways which do not prevent them from hybridizing to their target but which enhance their stability or targeting or which otherwise enhance their therapeutic effectiveness.

[0130] The term “modified oligonucleotide” as used herein describes an oligonucleotide in which (1) at least two of its nucleotides are covalently linked via a synthetic internucleoside linkage (i.e., a linkage other than a phosphodiester linkage between the 5′ end of one nucleotide and the 3′ end of another nucleotide) and/or (2) a chemical group not normally associated with nucleic acids has been covalently attached to the oligonucleotide. Preferred synthetic internucleoside linkages are phosphorothioates, alkylphosphonates, phosphorodithioates, phosphate esters, alkylphosphonothioates, phosphoramidates, carbamates, carbonates, phosphate triesters, acetamidates, carboxymethyl esters and peptides.

[0131] The term “modified oligonucleotide” also encompasses oligonucleotides with a covalently modified base and/or sugar. For example, modified oligonucleotides include oligonucleotides having backbone sugars which are covalently attached to low molecular weight organic groups other than a hydroxyl group at the 3′ position and other than a phosphate group at the 5′ position. Thus modified oligonucleotides may include a 2′-O-alkylated ribose group. In addition, modified oligonucleotides may include sugars such as arabinose instead of ribose. Base analogs such as C-5 propyne modified bases also can be included (Nature Biotechnol. 14:840-844, 1996). The present invention, thus, contemplates pharmaceutical preparations containing modified antisense molecules that are complementary to and hybridizable with, under physiological conditions, nucleic acids encoding the CT antigen polypeptides, together with pharmaceutically acceptable carriers.

[0132] Antisense oligonucleotides may be administered as part of a pharmaceutical composition. Such a pharmaceutical composition may include the antisense oligonucleotides in combination with any standard physiologically and/or pharmaceutically acceptable carriers which are known in the art. The compositions should be sterile and contain a therapeutically effective amount of the antisense oligonucleotides in a unit of weight or volume suitable for administration to a patient. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients. The term “physiologically acceptable” refers to a non-toxic material that is compatible with a biological system such as a cell, cell culture, tissue, or organism. The characteristics of the carrier will depend on the route of administration. Physiologically and pharmaceutically acceptable carriers include diluents, fillers, salts, buffers, stabilizers, solubilizers, and other materials which are well known in the art, as further described below.

[0133] As used herein, a “vector” may be any of a number of nucleic acids into which a desired sequence may be inserted by restriction and ligation for transport between different genetic environments or for expression in a host cell. Vectors are typically composed of DNA although RNA vectors are also available. Vectors include, but are not limited to, plasmids, phagemids and virus genomes. A cloning vector is one which is able to replicate autonomously or integrated in the genome in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut in a determinable fashion and into which a desired DNA sequence may be ligated such that the new recombinant vector retains its ability to replicate in the host cell. In the case of plasmids, replication of the desired sequence may occur many times as the plasmid increases in copy number within the host bacterium or just a single time per host before the host reproduces by mitosis. In the case of phage, replication may occur actively during a lytic phase or passively during a lysogenic phase. An expression vector is one into which a desired DNA sequence may be inserted by restriction and ligation such that it is operably joined to regulatory sequences and may be expressed as an RNA transcript. Vectors may further contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transfected with the vector. Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., β-galactosidase, luciferase or alkaline phosphatase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein). Preferred vectors are those capable of autonomous replication and expression of the structural gene products present in the DNA segments to which they are operably joined.

[0134] As used herein, a coding sequence and regulatory sequences are said to be “operably” joined when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably joined if induction of a promoter in the 5′ regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein. Thus, a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript might be translated into the desired protein or polypeptide.

[0135] The precise nature of the regulatory sequences needed for gene expression may vary between species or cell types, but shall in general include, as necessary, 5′ non-transcribed and 5′ non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. Especially, such 5′ non-transcribed regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences may also include enhancer sequences or upstream activator sequences as desired. The vectors of the invention may optionally include 5′ leader or signal sequences. The choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art.

[0136] Expression vectors containing all the necessary elements for expression are commercially available and known to those skilled in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. Cells are genetically engineered by the introduction into the cells of heterologous DNA (RNA) encoding a CT antigen polypeptide or fragment or variant thereof. That heterologous DNA (RNA) is placed under operable control of transcriptional elements to permit the expression of the heterologous DNA in the host cell.

[0137] Preferred systems for mRNA expression in mammalian cells are those such as pRc/CMV or pcDNA3.1 (available from Invitrogen, Carlsbad, Calif.) that contain a selectable marker such as a gene that confers G418 resistance (which facilitates the selection of stably transfected cell lines) and the human cytomegalovirus (CMV) enhancer-promoter sequences. Additionally, suitable for expression in primate or canine cell lines is the pCEP4 vector (Invitrogen), which contains an Epstein Barr Virus (EBV) origin of replication, facilitating the maintenance of plasmid as a multicopy extrachromosomal element. Another expression vector is the pEF-BOS plasmid containing the promoter of polypeptide Elongation Factor 1α, which stimulates efficiently transcription in vitro. The plasmid is described by Mishizuma and Nagata (Nuc. Acids Res. 18:5322, 1990), and its use in transfection experiments is disclosed by, for example, Demoulin (Mol. Cell. Biol. 16:4710-4716, 1996). Still another preferred expression vector is an adenovirus, described by Stratford-Perricaudet, which is defective for E1 and E3 proteins (J. Clin. Invest. 90:626-630, 1992). The use of the adenovirus as an Adeno.P1A recombinant for the expression of an antigen is disclosed by Warnier et al., in intradermal injection in mice for immunization against P1A (Int. J. Cancer, 67:303-310, 1996).

[0138] The invention also embraces so-called expression kits, which allow the artisan to prepare a desired expression vector or vectors. Such expression kits include at least separate portions of a vector and one or more of the previously discussed CT antigen nucleic acid molecules. Other components may be added, as desired, as long as the previously mentioned nucleic acid molecules, which are required, are included. The invention also includes kits for amplification of a CT antigen nucleic acid, including at least one pair of amplification primers which hybridize to a CT antigen nucleic acid. The primers preferably are 12-32 nucleotides in length and are non-overlapping to prevent formation of “primer-dimers”. One of the primers will hybridize to one strand of the CT antigen nucleic acid and the second primer will hybridize to the complementary strand of the CT antigen nucleic acid, in an arrangement which permits amplification of the CT antigen nucleic acid. Selection of appropriate primer pairs is standard in the art. For example, the selection can be made with assistance of a computer program designed for such a purpose, optionally followed by testing the primers for amplification specificity and efficiency.

[0139] The invention also permits the construction of CT antigen gene “knock-outs” and “knock-ins” in cells and in animals, providing materials for studying certain aspects of cancer and immune system responses to cancer.

[0140] The invention also provides isolated polypeptides (including whole proteins and partial proteins) encoded by the foregoing CT antigen nucleic acids. Such polypeptides are useful, for example, alone or as fusion proteins to generate antibodies, as components of an immunoassay or diagnostic assay or as therapeutics. CT antigen polypeptides can be isolated from biological samples including tissue or cell homogenates, and can also be expressed recombinantly in a variety of prokaryotic and eukaryotic expression systems by constructing an expression vector appropriate to the expression system, introducing the expression vector into the expression system, and isolating the recombinantly expressed protein. Short polypeptides, including antigenic peptides (such as are presented by MHC molecules on the surface of a cell for immune recognition) also can be synthesized chemically using well-established methods of peptide synthesis.

[0141] A unique fragment of a CT antigen polypeptide, in general, has the features and characteristics of unique fragments as discussed above in connection with nucleic acids. As will be recognized by those skilled in the art, the size of the unique fragment will depend upon factors such as whether the fragment constitutes a portion of a conserved protein domain. Thus, some regions of CT antigens will require longer segments to be unique while others will require only short segments, typically between 5 and 12 amino acids (e.g. 5, 6, 7, 8, 9, 10, 11 or 12 or more amino acids including each integer up to the full length).

[0142] Fragments of a CT antigen polypeptide preferably are those fragments which retain a distinct functional capability of the polypeptide. Functional capabilities which can be retained in a fragment of a polypeptide include interaction with antibodies, interaction with other polypeptides or fragments thereof, selective binding of nucleic acids or proteins, and enzymatic activity. One important activity is the ability to act as a signature for identifying the polypeptide. Another is the ability to complex with HLA and to provoke in a human an immune response. Those skilled in the art are well versed in methods for selecting unique amino acid sequences, typically on the basis of the ability of the fragment to selectively distinguish the sequence of interest from non-family members. A comparison of the sequence of the fragment to those on known databases typically is all that is necessary.

[0143] The invention embraces variants of the CT antigen polypeptides described above. As used herein, a “variant” of a CT antigen polypeptide is a polypeptide which contains one or more modifications to the primary amino acid sequence of a CT antigen polypeptide. Modifications which create a CT antigen variant can be made to a CT antigen polypeptide 1) to reduce or eliminate an activity of a CT antigen polypeptide; 2) to enhance a property of a CT antigen polypeptide, such as protein stability in an expression system or the stability of protein-protein binding; 3) to provide a novel activity or property to a CT antigen polypeptide, such as addition of an antigenic epitope or addition of a detectable;,moiety; or 4) to provide equivalent or better binding to an HLA molecule. Modifications to a CT antigen polypeptide are typically made to the nucleic acid which encodes the CT antigen polypeptide, and can include deletions, point mutations, truncations, amino acid substitutions and additions of amino acids or non-amino acid moieties. Alternatively, modifications can be made directly to the polypeptide, such as by cleavage, addition of a linker molecule, addition of a detectable moiety, such as biotin, addition of a fatty acid, and the like. Modifications also embrace fusion proteins comprising all or part of the CT antigen amino acid sequence. One of skill in the art will be familiar with methods for predicting the effect on protein conformation of a change in protein sequence, and can thus “design” a variant CT antigen polypeptide according to known methods. One example of such a method is described by Dahiyat and Mayo in Science 278:82-87, 1997, whereby proteins can be designed de novo. The method can be applied to a known protein to vary a only a portion of the polypeptide sequence. By applying the computational methods of Dahiyat and Mayo, specific variants of a CT antigen polypeptide can be proposed and tested to determine whether the variant retains a desired conformation.

[0144] In general, variants include CT antigen polypeptides which are modified specifically to alter a feature of the polypeptide unrelated to its desired physiological activity. For example, cysteine residues can be substituted or deleted to prevent unwanted disulfide linkages. Similarly, certain amino acids can be changed to enhance expression of a CT antigen polypeptide by eliminating proteolysis by proteases in an expression system (e.g., dibasic amino acid residues in yeast expression systems in which KEX2 protease activity is present).

[0145] Mutations of a nucleic acid which encode a CT antigen polypeptide preferably preserve the amino acid reading frame of the coding sequence, and preferably do not create regions in the nucleic acid which are likely to hybridize to form secondary structures, such a hairpins or loops, which can be deleterious to expression of the variant polypeptide.

[0146] Mutations can be made by selecting an amino acid substitution, or by random mutagenesis of a selected site in a nucleic acid which encodes the polypeptide. Variant polypeptides are then expressed and tested for one or more activities to determine which mutation provides a variant polypeptide with the desired properties. Further mutations can be made to variants (or to non-variant CT antigen polypeptides) which are silent as to the amino acid sequence of the polypeptide, but which provide preferred codons for translation in a particular host. The preferred codons for translation of a nucleic acid in, e.g., E. coli, are well known to those of ordinary skill in the art. Still other mutations can be made to the noncoding sequences of a CT antigen gene or cDNA clone to enhance expression of the polypeptide. The activity of variants of CT antigen polypeptides can be tested by cloning the gene encoding the variant CT antigen polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the variant CT antigen polypeptide, and testing for a functional capability of the CT antigen polypeptides as disclosed herein. For example, the variant CT antigen polypeptide can be tested for binding to antibodies or T cells. Preferred variants are those that compete for binding with the original polypeptide for binding to antibodies or T cells. Preparation of other variant polypeptides may favor testing of other activities, as will be known to one of ordinary skill in the art.

[0147] The skilled artisan will also realize that conservative amino acid substitutions may be made in CT antigen polypeptides to provide functionally equivalent variants of the foregoing polypeptides, i.e., the variants retain the functional capabilities of the CT antigen polypeptides. As used herein, a “conservative amino acid substitution” refers to an amino acid substitution which does not alter the relative charge or size characteristics of the protein in which the amino acid substitution is made. Variants can be prepared according to methods for altering polypeptide sequence known to one of ordinary skill in the art such as are found in references which compile such methods, e.g. Molecular Cloning: A Laboratory Manual, J. Sambrook, et al., eds., Second Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 1989, or Current Protocols in Molecular Biology, F. M. Ausubel, et al., eds., John Wiley & Sons, Inc., New York. Exemplary functionally equivalent variants of the CT antigen polypeptides include conservative amino acid substitutions in the amino acid sequences of proteins disclosed herein. Conservative substitutions of amino acids include substitutions made amongst amino acids within the following groups: (a) M, I, L, V; (b) F, Y, W; (c) K, R, H; (d) A, G; (e) S, T; (f) Q, N; and (g) E, D.

[0148] For example, upon determining that a peptide derived from a CT antigen polypeptide is presented by an MHC molecule and recognized by CTLs (e.g., as described in the Examples), one can make conservative amino acid substitutions to the amino acid sequence of the peptide, particularly at residues which are thought not to be direct contact points with the MHC molecule, i.e., the anchor residues that confer MHC binding. One of ordinary skill in the art will know these residues and will preferentially substitute other amino acid residues in the peptides in making variants. It is possible also to use other members of the consensus amino acids for a particular anchor residue. For example, consensus anchor residues for HLA-B35 are P in position 2 and Y, F, M, L or I in position 9. Therefore, if position 9 of a peptide was tyrosine (Y), one could substitute phenylalanine (F), methionine (M), leucine (L) or isoleucine (I) and maintain a consensus amino acid at the anchor residue positions of the peptide.

[0149] In general, it is preferred that fewer than all of the amino acids are changed when preparing variant polypeptides. Where particular amino acid residues are known to confer function, such amino acids will not be replaced, or alternatively, will be replaced by conservative amino acid substitutions. Preferably, 1, 2, 3, 4, 5, 6, 7, 8, and so on up to one fewer than the length of the peptide are changed when preparing variant polypeptides. It is generally preferred that the fewest number of substitutions is made. Thus, one method for generating variant polypeptides is to substitute all other amino acids for a particular single amino acid, then assay activity of the variant, then repeat the process with one or more of the polypeptides having the best activity.

[0150] As another example, methods for identifying functional variants of HLA class II binding peptides are provided in a published PCT application of Strominger and Wucherpfennig (PCT/US96/03182). Peptides bearing one or more amino acid substitutions also can be tested for concordance with known HLA/MHC motifs prior to synthesis using, e.g. the computer program described by D'Amaro and Drijfhout (D'Amaro et al., Human Immunol. 43:13-18, 1995; Drijfhout et al., Human Immunol. 43:1-12, 1995). The substituted peptides can then be tested for binding to the MHC molecule and recognition by CTLs when bound to MHC. These variants can be tested for improved stability and are useful, inter alia, in vaccine compositions.

[0151] Conservative amino-acid substitutions in the amino acid sequence of CT antigen polypeptides to produce functionally equivalent variants of CT antigen polypeptides typically are made by alteration of a nucleic acid encoding a CT antigen polypeptide. Such substitutions can be made by a variety of methods known to one of ordinary skill in the art. For example, amino acid substitutions may be made by PCR-directed mutation, site-directed mutagenesis according to the method of Kunkel (Kunkel, Proc. Nat. Acad. Sci. U.S.A. 82: 488-492, 1985), or by chemical synthesis of a gene encoding a CT antigen polypeptide. Where amino acid substitutions are made to a small unique fragment of a CT antigen polypeptide, such as an antigenic epitope recognized by autologous or allogeneic sera or cytolytic T lymphocytes, the substitutions can be made by directly synthesizing the peptide. The activity of functionally equivalent fragments of CT antigen polypeptides can be tested by cloning the gene encoding the altered CT antigen polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the altered CT antigen polypeptide, and testing for a functional capability of the CT antigen polypeptides as disclosed herein. Peptides which are chemically synthesized can be tested directly for function, e.g., for binding to antisera recognizing associated antigens.

[0152] The invention also provides, in certain embodiments, “dominant negative” polypeptides derived from CT antigen polypeptides. A dominant negative polypeptide is an inactive variant of a protein, which, by interacting with the cellular machinery, displaces an active protein from its interaction with the cellular machinery or competes with the active protein, thereby reducing the effect of the active protein. For example, a dominant negative receptor which binds a ligand but does not transmit a signal in response to binding of the ligand can reduce the biological effect of expression of the ligand. Likewise, a dominant negative catalytically-inactive kinase which interacts normally with target proteins but does not phosphorylate the target proteins can reduce phosphorylation of the target proteins in response to a cellular signal. Similarly, a dominant negative transcription factor which binds to a promoter site in the control region of a gene but does not increase gene transcription can reduce the effect of a normal transcription factor by occupying promoter binding sites without increasing transcription.

[0153] The end result of the expression of a dominant negative polypeptidd in a cell is a reduction in function of active proteins. One of ordinary skill in the art can assess the potential for a dominant negative variant of a protein, and using standard mutagenesis techniques to create one or more dominant negative variant polypeptides. For example, given the teachings contained herein of CT antigens, especially those which are similar to known proteins which have known activities, one of ordinary skill in the art can modify the sequence of the CT antigens by site-specific mutagenesis, scanning mutagenesis, partial gene deletion or truncation, and the like. See, e.g., U.S. Pat. No. 5,580,723 and Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. The skilled artisan then can test the population of mutagenized polypeptides for diminution in a selected and/or for retention of such an activity. Other similar methods for creating and testing dominant negative variants of a protein will be apparent to one of ordinary skill in the art.

[0154] The invention as described herein has a number of uses, some of which are described elsewhere herein. First, the invention permits isolation of the CT antigen protein molecules. A variety of methodologies well-known to the skilled practitioner can be utilized to obtain isolated CT antigen molecules. The polypeptide may be purified from cells which naturally produce the polypeptide by chromatographic means or immunological recognition. Alternatively, an expression vector may be introduced into cells to cause production of the polypeptide. In another method, mRNA transcripts may be microinjected or otherwise introduced into cells to cause production of the encoded polypeptide. Translation of mRNA in cell-free extracts such as the reticulocyte lysate system also may be used to produce polypeptide. Those skilled in the art also can readily follow known methods for isolating CT antigen polypeptides. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography and immune-affinity chromatography.

[0155] The invention also makes it possible to isolate proteins which bind to CT antigens as disclosed herein, including antibodies and cellular binding partners of the CT antigens. Additional uses are described further herein.

[0156] The isolation and identification of CT antigen genes also makes it possible for the artisan to diagnose a disorder characterized by expression of CT antigens. These methods involve determining expression of one or more CT antigen nucleic acids, and/or encoded CT antigen polypeptides and/or peptides derived therefrom. In the former situation, such determinations can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction, or assaying with labeled hybridization probes. In the latter two situations, such determinations can be carried out by immunoassays including, for example, ELISAs for the CT antigens, immunohistochemistry on tissue samples, and screening patient antisera for recognition of the polypeptide.

[0157] The invention also involves diagnosing or monitoring cancer in subjects by determining the presence of an immune response to one or more molecules of the invention. In preferred embodiments, this determination is performed by assaying a bodily fluid obtained from the subject, preferably serum, blood, or lymph node fluid for the presence of antibodies against the antigens described herein. This determination may also be performed by assaying a tissue or cells from the subject for the presence of one or more CT antigens (or nucleic acid molecules that encode these antigens) described herein. In another embodiment, the presence of antibodies against at least one additional cancer antigen is determined for diagnosis of cancer. The additional antigen may be a antigen as described herein or may be some other cancer-associated antigen. This determination may also be performed by assaying a tissue or cells from the subject for the presence of the molecules described herein.

[0158] Measurement of the immune response against one of the molecules over time by sequential determinations permits monitoring of the disease and/or the effects of a course of treatment. For example, a sample, such as serum, blood, or lymph node fluid, may be obtained from a subject, tested for an immune response to one of the molecules, and at a second, subsequent time, another sample, may be obtained from the subject and similarly tested. The results of the first and second (or subsequent) tests can be compared as a measure of the onset, regression or progression of cancer, or, if cancer treatment was undertaken during the interval between obtaining the samples, the effectiveness of the treatment may be evaluated by comparing the results of the two tests. In preferred embodiments the molecules (e.g., CT antigens) are bound to a substrate. In other preferred embodiments the immune response of the biological sample to the antigens is determined with ELISA. Other methods will be apparent to one of skill in the art.

[0159] Diagnostic methods of the invention also involve determining the aberrant expression of one or more of the polypeptides described herein or the nucleic acid molecules that encode them. Such determinations can be carried out via any standard nucleic acid assay, including the polymerase chain reaction or assaying with hybridization probes, which may be labeled, or by assaying biological samples with binding partners (e.g., antibodies) for these polypeptides.

[0160] The diagnostic methods of the invention can be used to detect the presence of a disorder associated with aberrant expression of a molecule of the invention, as well as to assess the progression and/or regression of the disorder such as in response to treatment (e.g., chemotherapy, radiation). According to this aspect of the invention, the method for diagnosing a disorder characterized by aberrant expression of a molecule involves detecting expression of a molecule in a first biological sample obtained from a subject, wherein differential expression of the molecule compared to a control sample indicates that the subject has a disorder characterized by aberrant expression of a molecule, such as cancer.

[0161] As used herein, “aberrant expression” of a molecule of the invention is intended to include any expression that is statistically significant from the expected amount of expression. For example, expression of a molecule (i.e., the polypeptides described herein or the nucleic acid molecules that encode them) in a tissue that is not expected to express the molecule would be included in the definition of “aberrant expression”. Likewise, expression of the molecule that is determined to be expressed at a significantly higher or lower level than expected is also included. Therefore, a determination of the level of expression of one or more of the polypeptides and/or the nucleic acids that encode them is diagnostic of cancer if the level of expression is above a baseline level determined for that tissue type. The baseline level of expression can be determined using standard methods known to those of skill in the art. Such methods include, for example, assaying a number of histologically normal tissue samples from subjects that are clinically normal (i.e. do not have clinical signs of cancer in that tissue type) and determining the mean level of expression for the samples.

[0162] The level of expression of the nucleic acid molecules of the invention or the polypeptides they encode can indicate cancer in the tissue when the level of expression is significantly more in the tissue than in a control sample. In some embodiments, a level of expression in the tissues that is at least about 5%, 6%, 7%, 8%, 9%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 150%, 200%, 250%, 300%, 400 %, or 500% more than the level of expression in the control tissue indicates cancer in the tissue.

[0163] As used herein the term “control” means predetermined values, and also means samples of materials tested in parallel with the experimental materials. Examples include samples from control populations or control samples generated through manufacture to be tested in parallel with the experimental samples.

[0164] As used herein the term “control” includes positive and negative controls which may be a predetermined value that can take a variety of forms. The control(s) can be a single cut-off value, such as a median or mean, or can be established based upon comparative groups, such as in groups having normal amounts of molecules of the invention and groups having abnormal amounts of molecules of the invention. Another example of a comparative group is a group having a particular disease, condition and/or symptoms and a group without the disease, condition and/or symptoms. Another comparative group is a group with a family history of a particular disease and a group without such a family history of the particular disease. The predetermined control value can be arranged, for example, where a tested population is divided equally (or unequally) into groups, such as a low-risk group, a medium-risk group and a high-risk group or into quadrants or quintiles, the lowest quadrant or quintile being individuals with the lowest risk or lowest expression levels of a molecule of the invention that is up-regulated in cancer and the highest quadrant or quintile being individuals with the highest risk or highest expression levels of a molecule of the invention that is up-regulated in cancer.

[0165] The predetermined value of a control will depend upon the particular population selected. For example, an apparently healthy population will have a different “normal” molecule expression level range than will a population which is known to have a condition characterized by aberrant expression of the molecule. Accordingly, the predetermined value selected may take into account the category in which an individual falls. Appropriate ranges and categories can be selected with no more than routine experimentation by those of ordinary skill in the art. Typically the control will be based on apparently healthy individuals in an appropriate age bracket. As used herein, the term “increased expression” means a higher level of expression relative to a selected control.

[0166] The invention involves in some aspects diagnosing or monitoring cancer by determining the level of expression of one or more nucleic acid molecules of the invention and/or determining the level of expression of one or more polypeptides they encode. In some important embodiments, this determination is performed by assaying a tissue sample from a subject for the level of expression of one or more nucleic acid molecules or for the level of expression of one or more polypeptides encoded by the nucleic acid molecules of the invention.

[0167] The expression of the molecules of the invention may be determined using routine methods known to those of ordinary skill in the art. These methods include, but are not limited to: direct RNA amplification, reverse transcription of RNA to cDNA, real-time RT-PCR, amplification of cDNA, hybridization, and immunologically based assay methods, which include, but are not limited to immunohistochemistry, antibody sandwich capture assay, ELISA, and enzyme-linked immunospot assay (EliSpot assay). For example, the determination of the presence of level of nucleic acid molecules of the invention in a subject or tissue can be carried out via any standard nucleic acid determination assay, including the polymerase chain reaction, or assaying with labeled hybridization probes. Such hybridization methods include, but are not limited to microarray techniques.

[0168] These methods of determining the presence and/or level of the molecules of the invention in cells and tissues may include use of labels to monitor the presence of the molecules of the invention. Such labels may include, but are not limited to radiolabels or chemiluminescent labels, which may be utilized to determine whether a molecule of the invention is expressed in a cell or tissue, and to determine the level of expression in the cell or tissue. For example, a fluorescently labeled or radiolabeled antibody that selectively binds to a polypeptide of the invention may be contacted with a tissue or cell to visualize the polypeptide in vitro or in vivo. These and other in vitro and in vivo imaging methods for determining the presence of the nucleic acid and polypeptide molecules of the invention are well known to those of ordinary skill in the art.

[0169] The invention further includes nucleic acid or protein microarrays with CT antigens or nucleic acids encoding such polypeptides. In this aspect of the invention, standard techniques of microarray technology are utilized to assess expression of the CT antigens and/or identify biological constituents that bind such polypeptides. The constituents of biological samples include antibodies, lymphocytes (particularly T lymphocytes), and the like. Protein microarray technology, which is also known by other names including: protein chip technology and solid-phase protein array technology, is well known to those of ordinary skill in the art and is based on, but not limited to, obtaining an array of identified peptides or proteins on a fixed substrate, binding target molecules or biological constituents to the peptides, and evaluating such binding. See, e.g., G. MacBeath and S. L. Schreiber, “Printing Proteins as Microarrays for High-Throughput Function Determination,” Science 289(5485):1760-1763, 2000. Nucleic acid arrays, particularly arrays that bind CT antigens, also can be used for diagnostic applications, such as for identifying subjects that have a condition characterized by CT antigen expression.

[0170] Microarray substrates include but are not limited to glass, silica, aluminosilicates, borosilicates, metal oxides such as alumina and nickel oxide, various clays, nitrocellulose, or nylon. The microarray substrates may be coated with a compound to enhance synthesis of a probe (peptide or nucleic acid) on the substrate. Coupling agents or groups on the substrate can be used to covalently link the first nucleotide or amino acid to the substrate. A variety of coupling agents or groups are known to those of skill in the art. Peptide or nucleic acid probes thus can be synthesized directly on the substrate in a predetermined grid. Alternatively, peptide or nucleic acid probes can be spotted on the substrate, and in such cases the substrate may be coated with a compound to enhance binding of the probe to the substrate. In these embodiments, presynthesized probes are applied to the substrate in a precise, predetermined volume and grid pattern, preferably utilizing a computer-controlled robot to apply probe to the substrate in a contact-printing manner or in a non-contact manner such as ink jet or piezo-electric delivery. Probes may be covalently linked to the substrate.

[0171] Targets are peptides or proteins and may be natural or synthetic. The tissue may be obtained from a subject or may be grown in culture (e.g. from a cell line).

[0172] In some embodiments of the invention one or more control peptide or protein molecules are attached to the substrate. Preferably, control peptide or protein molecules allow determination of factors such as peptide or protein quality and binding characteristics, reagent quality and effectiveness, hybridization success, and analysis thresholds and success.

[0173] In other embodiments, one or more control peptide or nucleic acid molecules are attached to the substrate. Preferably, control nucleic acid molecules allow determination of factors such as binding characteristics, reagent quality and effectiveness, hybridization success, and analysis thresholds and success.

[0174] Nucleic acid microarray technology, which is also known by other names including: DNA chip technology, gene chip technology, and solid-phase nucleic acid array technology, is well known to those of ordinary skill in the art and is based on, but not limited to, obtaining an array of identified nucleic acid probes on a fixed substrate, labeling target molecules with reporter molecules (e.g., radioactive, chemiluminescent, or fluorescent tags such as fluorescein, Cye3-dUTP, or Cye5-dUTP), hybridizing target nucleic acids to the probes, and evaluating target-probe hybridization. A probe with a nucleic acid sequence that perfectly matches the target sequence will, in general, result in detection of a stronger reporter-molecule signal than will probes with less perfect matches. Many components and techniques utilized in nucleic acid microarray technology are presented in The Chipping Forecast, Nature Genetics, Vol.21, January 1999, the entire contents of which is incorporated by reference herein.

[0175] According to the present invention, nucleic acid microarray substrates may include but are not limited to glass, silica, aluminosilicates, borosilicates, metal oxides such as alumina and nickel oxide, various clays, nitrocellulose, or nylon. In all embodiments a glass substrate is preferred. According to the invention, probes are selected from the group of nucleic acids including, but not limited to: DNA, genomic DNA, cDNA, and oligonucleotides; and may be natural or synthetic. Oligonucleotide probes preferably are 20 to 25-mer oligonucleotides and DNA/cDNA probes preferably are 500 to 5000 bases in length, although other lengths may be used. Appropriate probe length may be determined by one of ordinary skill in the art by following art-known procedures. In one embodiment, preferred probes are sets of two or more of the CT antigen nucleic acid molecules set forth herein. Probes may be purified to remove contaminants using standard methods known to those of ordinary skill in the art such as gel filtration or precipitation.

[0176] In one embodiment, the microarray substrate may be coated with a compound to enhance synthesis of the probe on the substrate. Such compounds include, but are not limited to, oligoethylene glycols. In another embodiment, coupling agents or groups on the substrate can be used to covalently link the first nucleotide or olignucleotide to the substrate. These agents or groups may include, for example, amino, hydroxy, bromo, and carboxy groups. These reactive groups are preferably attached to the substrate through a hydrocarbyl radical such as an alkylene or phenylene divalent radical, one valence position occupied by the chain bonding and the remaining attached to the reactive groups. These hydrocarbyl groups may contain up to about ten carbon atoms, preferably up to about six carbon atoms. Alkylene radicals are usually preferred containing two to four carbon atoms in the principal chain. These and additional details of the process are disclosed, for example, in U.S. Pat. No. 4,458,066, which is incorporated by reference in its entirety.

[0177] In one embodiment, probes are synthesized directly on the substrate in a predetermined grid pattern using methods such as light-directed chemical synthesis, photochemical deprotection, or delivery of nucleotide precursors to the substrate and subsequent probe production.

[0178] In another embodiment, the substrate may be coated with a compound to enhance binding of the probe to the substrate. Such compounds include, but are not limited to: polylysine, amino silanes, amino-reactive silanes (Chipping Forecast, 1999) or chromium. In this embodiment, presynthesized probes are applied to the substrate in a precise, predetermined volume and grid pattern, utilizing a computer-controlled robot to apply probe to the substrate in a contact-printing manner or in a non-contact manner such as ink jet or piezo-electric delivery. Probes may be covalently linked to the substrate with methods that include, but are not limited to, UV-irradiation. In another embodiment probes are linked to the substrate with heat.

[0179] Targets for microarrays are nucleic acids selected from the group, including but not limited to: DNA, genomic DNA, cDNA, RNA, mRNA and may be natural or synthetic. In all embodiments, nucleic acid target molecules from human tissue are preferred. The tissue may be obtained from a subject or may be grown in culture (e.g. from a cell line).

[0180] In embodiments of the invention one or more control nucleic acid molecules are attached to the substrate. Preferably, control nucleic acid molecules allow determination of factors such as nucleic acid quality and binding characteristics, reagent quality and effectiveness, hybridization success, and analysis thresholds and success. Control nucleic acids may include but are not limited to expression products of genes such as housekeeping genes or fragments thereof.

[0181] In some embodiments, one or more control peptide or nucleic acid molecules are attached to the substrate. Preferably, control nucleic acid molecules allow determination of factors such as binding characteristics, reagent quality and effectiveness, hybridization success, and analysis thresholds and success.

[0182] Expression of CT antigen polypeptides can also be determined using protein measurement methods. Preferred methods of specifically and quantitatively measuring proteins include, but are not limited to: mass spectroscopy-based methods such as surface enhanced laser desorption ionization (SELDI; e.g., Ciphergen ProteinChip System, Ciphergen Biosystems, Fremont Calif.), non-mass spectroscopy-based methods, and immunohistochemistry-based methods such as two-dimensional gel electrophoresis.

[0183] SELDI methodology may, through procedures known to those of ordinary skill in the art, be used to vaporize microscopic amounts of tumor protein and to create a “fingerprint” of individual proteins, thereby allowing simultaneous measurement of the abundance of many proteins in a single sample. Preferably SELDI-based assays may be utilized to classify tumor samples with respect to the expression of a variety of CT antigens. Such assays preferably include, but are not limited to the following examples. Gene products discovered by RNA microarrays may be selectively measured by specific (antibody mediated) capture to the SELDI protein disc (e.g., selective SELDI). Gene products discovered by protein screening (e.g., with 2-D gels), may be resolved by “total protein SELDI” optimized to visualize those particular markers of interest from among CT antigens.

[0184] Tumors can be classified based on the measurement of multiple CT antigens. Classification based on CT antigen expression can be used to stage disease, monitor progression or regression of disease, and select treatment strategies for the cancer patients.

[0185] The invention also involves agents such as polypeptides which bind to CT antigen polypeptides. Such binding agents can be used, for example, in screening assays to detect the presence or absence of CT antigen polypeptides and complexes of CT antigen polypeptides and their binding partners and in purification protocols to isolated CT antigen polypeptides and complexes of CT antigen polypeptides and their binding partners. Such agents also can be used to inhibit the native activity of the CT antigen polypeptides, for example, by binding to such polypeptides.

[0186] The invention, therefore, embraces peptide binding agents which, for example, can be antibodies or fragments of antibodies having the ability to selectively bind to CT antigen polypeptides. Antibodies include polyclonal and monoclonal antibodies, prepared according to conventional methodology.

[0187] Significantly, as is well-known in the art, only a small portion of an antibody molecule, the paratope, is involved in the binding of the antibody to its epitope (see, in general, Clark, W. R. (1986) The Experimental Foundations of Modem Immunology Wiley & Sons, Inc., New York; Roitt, I. (1991) Essential Immunology, 7th Ed., Blackwell Scientific Publications, Oxford). The pFc′ and Fe regions, for example, are effectors of the complement cascade but are not involved in antigen binding. An antibody from which the pFc′ region has been enzymatically cleaved, or which has been produced without the pFc′ region, designated an F(ab′)2 fragment, retains both of the antigen binding sites of an intact antibody. Similarly, an antibody from which the Fc region has been enzymatically cleaved, or which has been produced without the Fc region, designated an Fab fragment, retains one of the antigen binding sites of an intact antibody molecule. Proceeding further, Fab fragments consist of a covalently bound antibody light chain and a portion of the antibody heavy chain denoted Fd. The Fd fragments are the major determinant of antibody specificity (a single Fd fragment may be associated with up to ten different light chains without altering antibody specificity) and Fd fragments retain epitope-binding ability in isolation.

[0188] Within the antigen-binding portion of an antibody, as is well-known in the art, there are complementarity determining regions (CDRs), which directly interact with the epitope of the antigen, and framework regions (FRs), which maintain the tertiary structure of the paratope (see, in general, Clark, 1986; Roitt, 1991). In both the heavy chain Fd fragment and the light chain of IgG immunoglobulins, there are four framework regions (FR1 through FR4) separated respectively by three complementarity determining regions (CDR1 through CDR3). The CDRs, and in particular the CDR3 regions, and more particularly the heavy chain CDR3, are largely responsible for antibody specificity.

[0189] It is now well-established in the art that the non-CDR regions of a mammalian antibody may be replaced with similar regions of conspecific or heterospecific antibodies while retaining the epitopic specificity of the original antibody. This is most clearly manifested in the development and use of “humanized” antibodies in which non-human CDRs are covalently joined to human FR and/or Fc/pFc′ regions to produce a functional antibody. See, e.g., U.S. Pat. Nos. 4,816,567, 5,225,539, 5,585,089, 5,693,762 and 5,859,205.

[0190] Fully human monoclonal antibodies also can be prepared by immunizing mice transgenic for large portions of human immunoglobulin heavy and light chain loci. See, e.g., U.S. Pat. Nos. 5,545,806, 6,150,584, and references cited therein. Following immunization of these mice (e.g., XenoMouse (Abgenix), HuMAb mice (Medarex/GenPharm)), monoclonal antibodies can be prepared according to standard hybridoma technology. These monoclonal antibodies will have human immunoglobulin amino acid sequences and therefore will not provoke human anti-mouse antibody (HAMA) responses when administered to humans.

[0191] Thus, as will be apparent to one of ordinary skill in the art, the present invention also provides for F(ab′)2, Fab, Fv and Fd fragments; chimeric antibodies in which the Fc and/or FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric F(ab′)2 fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; chimeric Fab fragment antibodies in which the FR and/or CDR1 and/or CDR2 and/or light chain CDR3 regions have been replaced by homologous human or non-human sequences; and chimeric Fd fragment antibodies in which the FR and/or CDR1 and/or CDR2 regions have been replaced by homologous human or non-human sequences. The present invention also includes so-called single chain antibodies.

[0192] Accordingly, the invention involves polypeptides of numerous size and type that bind specifically to CT antigen polypeptides, and complexes of both CT antigen polypeptides and their binding partners. These polypeptides may be derived also from sources other than antibody technology. For example, such polypeptide binding agents can be provided by degenerate peptide libraries which can be readily prepared in solution, in immobilized form or as phage display libraries. Combinatorial libraries also can be synthesized of peptides containing one or more amino acids. Libraries further can be synthesized of peptoids and non-peptide synthetic moieties.

[0193] Phage display can be particularly effective in identifying binding peptides useful according to the invention. Briefly, one prepares a phage library (using e.g. m13, fd, or lambda phage), displaying inserts from 4 to about 80 amino acid residues using conventional procedures. The inserts may represent, for example, a completely degenerate or biased array. One then can select phage-bearing inserts which bind to the CT antigen polypeptide. This process can be repeated through several cycles of reselection of phage that bind to the CT antigen polypeptide. Repeated rounds lead to enrichment of phage bearing particular sequences. DNA sequence analysis can be conducted to identify the sequences of the expressed polypeptides. The minimal linear portion of the sequence that binds to the CT antigen polypeptide can be determined. One can repeat the procedure using a biased library containing inserts containing part or all of the minimal linear portion plus one or more additional degenerate residues upstream or downstream thereof. Yeast two-hybrid screening methods also may be used to identify polypeptides that bind to the CT antigen polypeptides. Thus, the CT antigen polypeptides of the invention, or a fragment thereof, can be used to screen peptide libraries, including phage display libraries, to identify and select peptide binding partners of the CT antigen polypeptides of the invention. Such molecules can be used, as described, for screening assays, for purification protocols, for interfering directly with the functioning of CT antigen and for other purposes that will be apparent to those of ordinary skill in the art.

[0194] As detailed herein, the foregoing antibodies and other binding molecules may be used for example to identify tissues expressing protein or to purify protein. Antibodies also may be coupled to specific diagnostic labeling agents for imaging of cells and tissues that express CT antigens or to therapeutically useful agents according to standard coupling procedures. Diagnostic agents include, but are not limited to, barium sulfate, iocetamic acid, iopanoic acid, ipodate calcium, diatrizoate sodium, diatrizoate meglumine, 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. Other diagnostic agents useful in the invention will be apparent to one of ordinary skill in the art.

[0195] As used herein, “therapeutically useful agents” include any therapeutic molecule which desirably is targeted selectively to a cell expressing one of the cancer antigens disclosed herein, including antineoplastic agents, radioiodinated compounds, toxins, other cytostatic or cytolytic drugs, and so forth. Antineoplastic therapeutics are well known and include: aminoglutethimide, azathioprine, bleomycin sulfate, busulfan, carmustine, chlorambucil, cisplatin, cyclophosphamide, cyclosporine, cytarabidine, dacarbazine, dactinomycin, daunorubicin, doxorubicin, taxol, etoposide, fluorouracil, interferon-α, 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.

[0196] The antibodies (and antigen-binding fragments thereof) can be linked not only to a detectable marker but also an antitumor agent or an immunomodulator. Antitumor agents can include cytotoxic agents and agents that act on tumor neovasculature. Detectable markers include, for example, radioactive or fluorescent markers. Cytotoxic agents include cytotoxic radionuclides, chemical toxins and protein toxins.

[0197] The cytotoxic radionuclide or radiotherapeutic isotope preferably is an alpha-emitting isotope such as 225Ac, 211At, 212Bi, 213Bi, 212Pb, 224Ra or 223Ra. Alternatively, the cytotoxic radionuclide may a beta-emitting isotope such as 186Rh, 188Rh, 177Lu, 90Y, 131I, 67Cu, 64Cu, 153Sm or 166Ho. Further, the cytotoxic radionuclide may emit Auger and low energy electrons and include the isotopes 125I, 123I or 77Br.

[0198] Suitable chemical toxins or chemotherapeutic agents include members of the enediyne family of molecules, such as calicheamicin and esperamicin. Chemical toxins can also be taken from the group consisting of methotrexate, doxorubicin, melphalan, chlorambucil, ARA-C, vindesine, mitomycin C, cis-platinum, etoposide, bleomycin and 5-fluorouracil. Other antineoplastic agents that may be conjugated to the anti-PSMA antibodies of the present invention include dolastatins (U.S. Pat. Nos. 6,034,065 and 6,239,104) and derivatives thereof. Of particular interest is dolastatin 10 (dolavaline-valine-dolaisoleuine-dolaproine-dolaphenine) and the derivatives auristatin PHE (dolavaline-valine-dolaisoleuine-dolaproine-phenylalanine-methyl ester) (Pettit, G. R. et al., Anticancer Drug Des. 13(4):243-277, 1998; Woyke, T. et al., Antimicrob. Agents Chemother. 45(12):3580-3584, 2001), and aurastatin E and the like. Toxins that are less preferred in the compositions and methods of the invention include poisonous lectins, plant toxins such as ricin, abrin, modeccin, botulina and diphtheria toxins. Of course, combinations of the various toxins could also be coupled to one antibody molecule thereby accommodating variable cytotoxicity. Other chemotherapeutic agents are known to those skilled in the art.

[0199] Agents that act on the tumor vasculature can include tubulin-binding agents such as combrestatin A4 (Griggs et al., Lancet Oncol. 2:82, 2001), angiostatin and endostatin (reviewed in Rosen, Oncologist 5:20, 2000, incorporated by reference herein) and interferon inducible protein 10 (U.S. Pat. No. 5,994,292). A number of antiangiogenic agents currently in clinical trials are also contemplated. Agents currently in clinical trials include: 2ME2, Angiostatin, Angiozyme, Anti-VEGF RhuMAb, Apra (CT-2584), Avicine, Benefin, BMS275291, Carboxyamidotriazole, CC4047, CC5013, CC7085, CDC801, CGP-41251 (PKC 412), CM101, Combretastatin A-4 Prodrug, EMD 121974, Endostatin, Flavopiridol, Genistein (GCP), Green Tea Extract, IM-862, ImmTher, Interferon alpha, Interleukin-12, Iressa (ZD1839), Marimastat, Metastat (Col-3), Neovastat, Octreotide, Paclitaxel, Penicillamine, Photofrin, Photopoint, PI-88, Prinomastat (AG-3340), PTK787 (ZK22584), RO317453, Solimastat, Squalamine, SU 101, SU 5416, SU-6668, Suradista (FCE 26644), Suramin (Metaret), Tetrathiomolybdate, Thalidomide, TNP-470 and Vitaxin. additional antiangiogenic agents are described by Kerbel, J. Clin. Oncol. 19(18s):45s-51s, 2001, which is incorporated by reference herein. Immunomodulators suitable for conjugation to the antibodies include α-interferon, γ-interferon, and tumor necrosis factor alpha (TNFα).

[0200] The coupling of one or more toxin molecules to the antibody is envisioned to include many chemical mechanisms, for instance covalent binding, affinity binding, intercalation, coordinate binding, and complexation. The toxic compounds used to prepare the immunotoxins are attached to the antibodies or antigen-binding fragments thereof by standard protocols known in the art.

[0201] In some embodiments, antibodies prepared according to the invention are specific for complexes of MHC molecules and the CT antigens described herein.

[0202] When “disorder” is used herein, it refers to any pathological condition where the CT antigens are expressed. An example of such a disorder is cancer, including but not limited to: biliary tract cancer; bladder cancer; breast cancer; brain cancer including glioblastomas, astrocytomas and medulloblastomas; cervical cancer; choriocarcinoma; colon cancer; endometrial cancer; esophageal cancer; gastric cancer; head and neck cancer; hematological neoplasms including acute lymphocytic and myelogenous leukemia, multiple mycloma, AIDS-associated leukemias and adult T-cell leukemia lymphoma; intraepithelial neoplasms including Bowen's disease and Paget's disease; liver cancer; lung cancer including small cell lung cancer and non-small cell lung cancer; lymphomas including Hodgkin's disease and lymphocytic lymphomas; neuroblastomas; oral cancer including squamous cell carcinoma; ovarian cancer including those arising from epithelial cells, stromal cells, germ cells and mesenchymal cells; pancreatic cancer; prostate cancer; rectal cancer; sarcomas including leiomyosarcoma, rhabdomyosarcoma, liposarcoma, fibrosarcoma, synovial sarcoma and osteosarcoma; skin cancer including melanoma, Kaposi's sarcoma, basocellular cancer, and squamous cell cancer; testicular cancer including germinal tumors such as seminoma, non-seminoma (teratomas, choriocarcinomas), stromal tumors, and germ cell tumors; thyroid cancer including thyroid adenocarcinoma and medullar carcinoma; transitional cancer and renal cancer including adenocarcinoma and Wilms tumor.

[0203] Samples of tissue and/or cells for use in the various methods described herein can be obtained through standard methods such as tissue biopsy, including punch biopsy and cell scraping, and collection of blood or other bodily fluids by aspiration or other methods.

[0204] In certain embodiments of the invention, an immunoreactive cell sample is removed from a subject. By “immunoreactive cell” is meant a cell which can mature into an immune cell (such as a B cell, a helper T cell, or a cytolytic T cell) upon appropriate stimulation. Thus immunoreactive cells include CD34+ hematopoietic stem cells, immature T cells and immature B cells. When it is desired to produce cytolytic T cells which recognize a CT antigen, the immunoreactive cell is contacted with a cell which expresses a CT antigen under conditions favoring production, differentiation and/or selection of cytolytic T cells; the differentiation of the T cell precursor into a cytolytic T cell upon exposure to antigen is similar to clonal selection of the immune system.

[0205] Some therapeutic approaches based upon the disclosure are premised on a response by a subject's immune system, leading to lysis of antigen presenting cells, such as cancer cells which present one or more CT antigens. One such approach is the administration of autologous CTLs specific to a CT antigen/MHC complex to a subject with abnormal cells of the phenotype at issue. It is within the ability of one of ordinary skill in the art to develop such CTLs in vitro. An example of a method for T cell differentiation is presented in International Application number PCT/US96/05607. Generally, a sample of cells taken from a subject, such as blood cells, are contacted with a cell presenting the complex and capable of provoking CTLs to proliferate. The target cell can be a transfectant, such as a COS cell. These transfectants present the desired complex of their surface and, when combined with a CTL of interest, stimulate its proliferation. COS cells are widely available, as are other suitable host cells. Specific production of CTL clones is well known in the art. The clonally expanded autologous CTLs then are administered to the subject.

[0206] Another method for selecting antigen-specific CTL clones has recently been described (Altman et al., Science 274:94-96, 1996; Dunbar et al., Curr. Biol. 8:413-416, 1998), in which fluorogenic tetramers of MHC class I molecule/peptide complexes are used to detect specific CTL clones. Briefly, soluble MHC class I molecules are folded in vitro in the presence of p2-microglobulin and a peptide antigen which binds the class I molecule. After purification, the MHC/peptide complex is purified and labeled with biotin. Tetramers are formed by mixing the biotinylated peptide-MHC complex with labeled avidin (e.g. phycoerythrin) at a molar ratio or 4:1. Tetramers are then contacted with a source of CTLs such as peripheral blood or lymph node. The tetramers bind CTLs which recognize the peptide antigen/MHC class I complex. Cells bound by the tetramers can be sorted by fluorescence activated cell sorting to isolate the reactive CTLs. The isolated CTLs then can be expanded in vitro for use as described herein.

[0207] To detail a therapeutic methodology, referred to as adoptive transfer (Greenberg, J. Immunol. 136(5): 1917, 1986; Riddel et al., Science 257: 238, 1992; Lynch et al, Eur. J. Immunol. 21: 1403-1410,1991; Kast et al., Cell 59: 603-614, 1989), cells presenting the desired complex (e.g., dendritic cells) are combined with CTLs leading to proliferation of the CTLs specific thereto. The proliferated CTLs are then administered to a subject with a cellular abnormality which is characterized by certain of the abnormal cells presenting the particular complex. The CTLs then lyse the abnormal cells, thereby achieving the desired therapeutic goal.

[0208] The foregoing therapy assumes that at least some of the subject's abnormal cells present the relevant HLA/CT antigen complex. This can be determined very easily, as the art is very familiar with methods for identifying cells which present a particular HLA molecule, as well as how to identify cells expressing DNA of the pertinent sequences, in this case a CT antigen sequence. Once cells presenting the relevant complex are identified via the foregoing screening methodology, they can be combined with a sample from a patient, where the sample contains CTLs. If the complex presenting cells are lysed by the mixed CTL sample, then it can be assumed that a CT antigen is being presented, and the subject is an appropriate candidate for the therapeutic approaches set forth supra.

[0209] Adoptive transfer is not the only form of therapy that is available in accordance with the invention. CTLs can also be provoked in vivo, using a number of approaches. One approach is the use of non-proliferative cells expressing the complex. The cells used in this approach may be those that normally express the complex, such as irradiated tumor cells or cells transfected with one or both of the genes necessary for presentation of the complex (i.e. the antigenic peptide and the presenting HLA molecule). Chen et al. (Proc. Natl. Acad. Sci. USA 88: 110-114,1991) exemplifies this approach, showing the use of transfected cells expressing HPVE7 peptides in a therapeutic regime. Various cell types may be used. Similarly, vectors carrying one or both of the genes of interest may be used. Viral or bacterial vectors are especially preferred. For example, nucleic acids which encode a CT antigen polypeptide or peptide may be operably linked to promoter and enhancer sequences which direct expression of the CT antigen polypeptide or peptide in certain tissues or cell types. The nucleic acid may be incorporated into an expression vector. Expression vectors may be unmodified extrachromosomal nucleic acids, plasmids or viral genomes constructed or modified to enable insertion of exogenous nucleic acids, such as those encoding CT antigen, as described elsewhere herein. Nucleic acids encoding a CT antigen also may be inserted into a retroviral genome, thereby facilitating integration of the nucleic acid into the genome of the target tissue or cell type. In these systems, the gene of interest is carried by a microorganism, e.g., a Vaccinia virus, pox virus, herpes simplex virus, retrovirus or adenovirus, and the materials de facto “infect” host cells. The cells which result present the complex of interest, and are recognized by autologous CTLs, which then proliferate.

[0210] A similar effect can be achieved by combining the CT antigen or an immune response stimulatory fragment thereof with an adjuvant to facilitate incorporation into antigen presenting cells in vivo. The CT antigen polypeptide is processed to yield the peptide partner of the HLA molecule while a CT antigen peptide may be presented without the need for further processing. Generally, subjects can receive an intradermal injection of an effective amount of the CT antigen. Initial doses can be followed by booster doses, following immunization protocols standard in the art.

[0211] The invention involves the use of various materials disclosed herein to “immunize” subjects or as “vaccines”. As used herein, “immunization” or “vaccination” means increasing or activating an immune response against an antigen. It does not require elimination or eradication of a condition but rather contemplates the clinically favorable enhancement of an immune response toward an antigen. Generally accepted animal models can be used for testing of immunization against cancer using a CT antigen nucleic acid. For example, human cancer cells can be introduced into a mouse to create a tumor, and one or more CT antigen nucleic acids can be delivered by the methods described herein. The effect on the cancer cells (e.g., reduction of tumor size) can be assessed as a measure of the effectiveness of the CT antigen nucleic acid immunization. Of course, testing of the foregoing animal model using more conventional methods for immunization include the administration of one or more CT antigen polypeptides or peptides derived therefrom, optionally combined with one or more adjuvants and/or cytokines to boost the immune response. Methods for immunization, including formulation of a vaccine composition and selection of doses, route of administration and the schedule of administration (e.g. primary and one or more booster doses), are well known in the art. The tests also can be performed in humans, where the end point is to test for the presence of enhanced levels of circulating CTLs against cells bearing the antigen, to test for levels of circulating antibodies against the antigen, to test for the presence of cells expressing the antigen and so forth.

[0212] As part of the immunization compositions, one or more CT antigens or stimulatory fragments thereof are administered with one or more adjuvants to induce an immune response or to increase an immune response. An adjuvant is a substance incorporated into or administered with antigen which potentiates the immune response. Adjuvants may enhance the immunological response by providing a reservoir of antigen (extracellularly or within macrophages), activating macrophages and stimulating specific sets of lymphocytes. Adjuvants of many kinds are well known in the art. Specific examples of adjuvants include monophosphoryl lipid A (MPL, SmithKline Beecham), a congener obtained after purification and acid hydrolysis of Salmonella minnesota Re 595 lipopolysaccharide; saponins including QS21 (SmithKline Beecham), a pure QA-21 saponin purified from Quillja saponaria extract; DQS21, described in PCT application WO96/33739 (SmithKline Beecham); QS-7, QS-17, QS-18, and QS-L1 (So et al., Mol. Cells 7:178-186, 1997); incomplete Freund's adjuvant; complete Freund's adjuvant; montanide; immunostimulatory oligonucleotides (see e.g. CpG oligonucleotides described by Kreig et al., Nature 374:546-9, 1995); vitamin E and various water-in-oil emulsions prepared from biodegradable oils such as squalene and/or tocopherol. Preferably, the,peptides are administered mixed with a combination of DQS21/MPL. The ratio of DQS21 to MPL typically will be about 1:10 to 10:1, preferably about 1:5 to 5:1 and more preferably about 1:1. Typically for human administration, DQS21 and MPL will be present in a vaccine formulation in the range of about 1 μg to about 100 μg. Other adjuvants are known in the art and can be used in the invention (see, e.g. Goding, Monoclonal Antibodies: Principles and Practice, 2nd Ed., 1986). Methods for the preparation of mixtures or emulsions of peptide and adjuvant are well known to those of skill in the art of vaccination.

[0213] Other agents which stimulate the immune response of the subject can also be administered to the subject. For example, other cytokines are also useful in vaccination protocols as a result of their lymphocyte regulatory properties. Many other cytokines useful for such purposes will be known to one of ordinary skill in the art, including interleukin-12 (IL-12) which has been shown to enhance the protective effects of vaccines (see, e.g., Science 268:1432-1434, 1995), GM-CSF and IL-18. Thus cytokines can be administered in conjunction with antigens and adjuvants to increase the immune response to the antigens.

[0214] There are a number of immune response potentiating compounds that can be used in vaccination protocols. These include costimulatory molecules provided in either protein or nucleic acid form. Such costimulatory molecules include the B7-1 and B7-2 (CD80 and CD86 respectively) molecules which are expressed on dendritic cells (DC) and interact with the CD28 molecule expressed on the T cell. This interaction provides costimulation (signal 2) to an antigen/MHC/TCR stimulated (signal 1) T cell, increasing T cell proliferation and effector function. B7 also interacts with CTLA4 (CD152) on T cells and studies involving CTLA4 and B7 ligands indicate that the B7-CTLA4 interaction can enhance antitumor immunity and CTL proliferation (Zheng P., et al. Proc. Natl. Acad. Sci. USA 95 (11):6284-6289 (1998)).

[0215] B7 typically is not expressed on tumor cells so they are not efficient antigen presenting cells (APCs) for T cells. Induction of B7 expression would enable the tumor cells to stimulate more efficiently CTL proliferation and effector function. A combination of B7/IL-6/IL-12 costimulation has been shown to induce IFN-gamma and a Th1 cytokine profile in the T cell population leading to further enhanced T cell activity (Gajewski et al., J. Immunol, 154:5637-5648 (1995)). Tumor cell transfection with B7 has been discussed in relation to in vitro CTL expansion for adoptive transfer immunotherapy by Wang et al., (J. Immunol., 19:1-8 (1986)). Other delivery mechanisms for the B7 molecule would include nucleic acid (naked DNA) immunization (Kim J., et al. Nat Biotechnol., 15:7:641-646 (1997)) and recombinant viruses such as adeno and pox (Wendtner et al., Gene Ther., 4:7:726-735 (1997)). These systems are all amenable to the construction and use of expression cassettes for the coexpression of B7 with other molecules of choice such as the antigens or fragment(s) of antigens discussed herein (including polytopes) or cytokines. These delivery systems can be used for induction of the appropriate molecules in vitro and for in vivo vaccination situations. The use of anti-CD28 antibodies to directly stimulate T cells in vitro and in vivo could also be considered. Similarly, the inducible co-stimulatory molecule ICOS which induces T cell responses to foreign antigen could be modulated, for example, by use of anti-ICOS antibodies (Hutloff et al., Nature 397:263-266, 1999).

[0216] Lymphocyte function associated antigen-3 (LFA-3) is expressed on APCs and some tumor cells and interacts with CD2 expressed on T cells. This interaction induces T cell IL-2 and IFN-gamma production and can thus complement but not substitute, the B7/CD28 costimulatory interaction (Parra et al., J. Immunol., 158:637-642 (1997), Fenton et al., J. Immunother., 21:2:95-108 (1998)).

[0217] Lymphocyte function associated antigen-1 (LFA-1) is expressed on leukocytes and interacts with ICAM-1 expressed on APCs and some tumor cells. This interaction induces T cell IL-2 and IFN-gamma production and can thus complement but not substitute, the B7/CD28 costimulatory interaction (Fenton et al., J. Immunother., 21:2:95-108 (1998)). LFA-1 is thus a further example of a costimulatory molecule that could be provided in a vaccination protocol in the various ways discussed above for B7.

[0218] Complete CTL activation and effector function requires Th cell help through the interaction between the Th cell CD40L (CD40 ligand) molecule and the CD40 molecule expressed by DCs (Ridge et al., Nature, 393:474 (1998), Bennett et al., Nature, 393:478 (1998), Schoenberger et al., Nature, 393:480 (1998)). This mechanism of this costimulatory signal is likely to involve upregulation of B7 and associated IL-6/IL-12 production by the DC (APC). The CD40-CD40L interaction thus complements the signal 1 (antigen/MHC-TCR) and signal 2 (B7-CD28) interactions.

[0219] The use of anti-CD40 antibodies to stimulate DC cells directly, would be expected to enhance a response to tumor antigens which are normally encountered outside of a inflammatory context or are presented by non-professional APCs (tumor cells). In these situations Th help and B7 costimulation signals are not provided. This mechanism might be used in the context of antigen pulsed DC based therapies or in situations where Th epitopes have not been defined within known TRA precursors.

[0220] A CT antigen polypeptide, or a fragment thereof, also can be used to isolate their native binding partners. Isolation of such binding partners may be performed according to well-known methods. For example, isolated CT antigen polypeptides can be attached to a substrate (e.g., chromatographic media, such as polystyrene beads, or a filter), and then a solution suspected of containing the binding partner may be applied to the substrate. If a binding partner which can interact with CT antigen polypeptides is present in the solution, then it will bind to the substrate-bound CT antigen polypeptide. The binding partner then may be isolated.

[0221] It will also be recognized that the invention embraces the use of the CT antigen cDNA sequences in expression vectors, as well as to transfect host cells and cell lines, be these prokaryotic (e.g., E. coli), or eukaryotic (e.g., dendritic cells, B cells, CHO cells, COS cells, yeast expression systems and recombinant baculovirus expression in insect cells). Especially useful are mammalian cells such as human, mouse, hamster, pig, goat, primate, etc. They may be of a wide variety of tissue types, and include primary cells and cell lines. Specific examples include keratinocytes, peripheral blood leukocytes, bone marrow stem cells and embryonic stem cells. The expression vectors require that the pertinent sequence, i.e., those nucleic acids described supra, be operably linked to a promoter.

[0222] The invention also contemplates delivery of nucleic acids, polypeptides or peptides for vaccination. Delivery of polypeptides and peptides can be accomplished according to standard vaccination protocols which are well known in the art. In another embodiment, the delivery of nucleic acid is accomplished by ex vivo methods, i.e. by removing a cell from a subject, genetically engineering the cell to include a CT antigen, and reintroducing the engineered cell into the subject. One example of such a procedure is the use of dendritic cells as delivery and antigen presentation vehicles for the administration of CT antigens in vaccine therapies. Another example of such a procedure is outlined in U.S. Pat. No. 5,399,346 and in exhibits submitted in the file history of that patent, all of which are publicly available documents. In general, it involves introduction in vitro of a functional copy of a gene into a cell(s) of a subject, and returning the genetically engineered cell(s) to the subject. The functional copy of the gene is under operable control of regulatory elements which permit expression of the gene in the genetically engineered cell(s). Numerous transfection and transduction techniques as well as appropriate expression vectors are well known to those of ordinary skill in the art, some of which are described in PCT application WO95/00654. In vivo nucleic acid delivery using vectors such as viruses and targeted liposomes also is contemplated according to the invention.

[0223] In preferred embodiments, a virus vector for delivering a nucleic acid encoding a CT antigen is selected from the group consisting of adenoviruses, adeno-associated viruses, poxviruses including vaccinia viruses and attenuated poxviruses, Semliki Forest virus, Venezuelan equine encephalitis virus, retroviruses, Sindbis virus, and Ty virus-like particle. Examples of viruses and virus-like particles which have been used to deliver exogenous nucleic acids include: replication-defective adenoviruses (e.g., Xiang et al., Virology 219:220-227, 1996; Eloit et al., J. Virol. 7:5375-5381, 1997; Chengalvala et al., Vaccine 15:335-339, 1997), a modified retrovirus (Townsend et al., J. Virol. 71:3365-3374, 1997), a nonreplicating retrovirus (Irwin et al., J. Virol. 68:5036-5044, 1994), a replication defective Semliki Forest virus (Zhao et al., Proc. Natl. Acad. Sci. USA 92:3009-3013, 1995), canarypox virus and highly attenuated vaccinia virus derivative (Paoletti, Proc. Natl. Acad. Sci. USA 93:11349-11353, 1996), non-replicative vaccinia virus (Moss, Proc. Natl. Acad. Sci. USA 93:11341-11348, 1996), replicative vaccinia virus (Moss, Dev. Biol. Stand. 82:55-63, 1994), Venzuelan equine encephalitis virus (Davis et al., J. Virol. 70:3781-3787, 1996), Sindbis virus (Pugachev et al., Virology 212:587-594, 1995), and Ty virus-like particle (Allsopp et al., Eur. J. Immunol 26:1951-1959, 1996). In preferred embodiments, the virus vector is an adenovirus or an alphavirus.

[0224] Another preferred virus for certain applications is the adeno-associated virus, a double-stranded DNA virus. The adeno-associated virus is capable of infecting a wide range of cell types and species and can be engineered to be replication-deficient. It further has advantages, such as heat and lipid solvent stability, high transduction frequencies in cells of diverse lineages, including hematopoietic cells, and lack of superinfection inhibition thus allowing multiple series of transductions. The adeno-associated virus can integrate into human cellular DNA in a site-specific manner, thereby minimizing the possibility of insertional mutagenesis and variability of inserted gene expression. In addition, wild-type adeno-associated virus infections have been followed in tissue culture for greater than 100 passages in the absence of selective pressure, implying that the adeno-associated virus genomic integration is a relatively stable event. The adeno-associated virus can also function in an extrachromosomal fashion.

[0225] In general, other preferred viral vectors are based on non-cytopathic eukaryotic viruses in which non-essential genes have been replaced with the gene of interest. Non-cytopathic viruses include retroviruses, the life cycle of which involves reverse transcription of genomic viral RNA into DNA with subsequent proviral integration into host cellular DNA. Adenoviruses and retroviruses have been approved for human gene therapy trials. In general, the retroviruses are replication-deficient (i.e., capable of directing synthesis of the desired proteins, but incapable of manufacturing an infectious particle). Such genetically altered retroviral expression vectors have general utility for the high-efficiency transduction of genes in vivo. Standard protocols for producing replication-deficient retroviruses (including the steps of incorporation of exogenous genetic material into a plasmid, transfection of a packaging cell lined with plasmid, production of recombinant retroviruses by the packaging cell line, collection of viral particles from tissue culture media, and infection of the target cells with viral particles) are provided in Kriegler, M., “Gene Transfer and Expression, A Laboratory Manual,” W. H. Freeman Co., New York (1990) and Murry, E. J. Ed. “Methods in Molecular Biology,” vol. 7, Humana Press, Inc., Cliffton, N.J. (1991).

[0226] Preferably the foregoing nucleic acid delivery vectors: (1) contain exogenous genetic material that can be transcribed and translated in a mammalian cell and that can induce an immune response in a host, and (2) contain on a surface a ligand that selectively binds to a receptor on the surface of a target cell, such as a mammalian cell, and thereby gains entry to the target cell.

[0227] Various techniques may be employed for introducing nucleic acids of the invention into cells, depending on whether the nucleic acids are introduced in vitro or in vivo in a host. Such techniques include transfection of nucleic acid-CaPO4 precipitates, transfection of nucleic acids associated with DEAE, transfection or infection with the foregoing viruses including the nucleic acid of interest, liposome mediated transfection, and the like. For certain uses, it is preferred to target the nucleic acid to particular cells. In such instances, a vehicle used for delivering a nucleic acid of the invention into a cell (e.g., a retrovirus, or other virus; a liposome) can have a targeting molecule attached thereto. For example, a molecule such as an antibody specific for a surface membrane protein on the target cell or a ligand for a receptor on the target cell can be bound to or incorporated within the nucleic acid delivery vehicle. Preferred antibodies include antibodies which selectively bind a CT antigen, alone or as a complex with a MHC molecule. Especially preferred are monoclonal antibodies. Where liposomes are employed to deliver the nucleic acids of the invention, proteins which bind to a surface membrane protein associated with endocytosis may be incorporated into the liposome formulation for targeting and/or to facilitate uptake. Such proteins include capsid proteins or fragments thereof tropic for a particular cell type, antibodies for proteins which undergo internalization in cycling, proteins that target intracellular localization and enhance intracellular half life, and the like. Polymeric delivery systems also have been used successfully to deliver nucleic acids into cells, as is known by those skilled in the art. Such systems even permit oral delivery of nucleic acids.

[0228] When administered, the therapeutic compositions of the present invention can be administered in pharmaceutically acceptable preparations. Such preparations may routinely contain pharmaceutically acceptable concentrations of salt, buffering agents, preservatives, compatible carriers, supplementary immune potentiating agents such as adjuvants and cytokines and optionally other therapeutic agents.

[0229] The therapeutics of the invention can be administered by any conventional route, including injection or by gradual infusion over time. The administration may, for example, be oral, intravenous, intraperitoneal, intramuscular, intracavity, subcutaneous, or transdermal. When antibodies are used therapeutically, a preferred route of administration is by pulmonary aerosol. Techniques for preparing aerosol delivery systems containing antibodies are well known to those of skill in the art. Generally, such systems should utilize components which will not significantly impair the biological properties of the antibodies, such as the paratope binding capacity (see, for example, Sciarra and Cutie, “Aerosols,” in Remington's Pharmaceutical Sciences, 18th edition, 1990, pp. 1694-1712; incorporated by reference). Those of skill in the art can readily determine the various parameters and conditions for producing antibody aerosols without resort to undue experimentation. When using antisense preparations of the invention, slow intravenous administration is preferred.

[0230] The compositions of the invention are administered in effective amounts. An “effective amount” is that amount of a CT antigen composition that alone, or together with further doses, produces the desired response, e.g. increases an immune response to the CT antigen. In the case of treating a particular disease or condition characterized by expression of one or more CT antigens, such as cancer, the desired response is inhibiting the progression of the disease. This may involve only slowing the progression of the disease temporarily, although more preferably, it involves halting the progression of the disease permanently. This can be monitored by routine methods or can be monitored according to diagnostic methods of the invention discussed herein. The desired response to treatment of the disease or condition also can be delaying the onset or even preventing the onset of the disease or condition.

[0231] Such amounts will depend, of course, on the particular condition being treated, the severity of the condition, the individual patient parameters including age, physical condition, size and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment. It will be understood by those of ordinary skill in the art, however, that a patient may insist upon a lower dose or tolerable dose for medical reasons, psychological reasons or for virtually any other reasons.

[0232] The pharmaceutical compositions used in the foregoing methods preferably are sterile and contain an effective amount of CT antigen or nucleic acid encoding CT antigen for producing the desired response in a unit of weight or volume suitable for administration to a patient. The response can, for example, be measured by determining the immune response following administration of the CT antigen composition via a reporter system by measuring downstream effects such as gene expression, or by measuring the physiological effects of the CT antigen composition, such as regression of a tumor or decrease of disease symptoms. Other assays will be known to one of ordinary skill in the art and can be employed for measuring the level of the response.

[0233] The doses of CT antigen compositions (e.g., polypeptide, peptide, antibody, cell or nucleic acid) administered to a subject can be chosen in accordance with different parameters, in particular in accordance with the mode of administration used and the state of the subject. Other factors include the desired period of treatment. In the event that a response in a subject is insufficient at the initial doses applied, higher doses (or effectively higher doses by a different, more localized delivery route) may be employed to the extent that patient tolerance permits.

[0234] In general, for treatments for eliciting or increasing an immune response, doses of CT antigen are formulated and administered in doses between 1 ng and 1 mg, and preferably between 10 ng and 100 μg, according to any standard procedure in the art. Where nucleic acids encoding CT antigen or variants thereof are employed, doses of between 1 ng and 0.1 mg generally will be formulated and administered according to standard procedures. Other protocols for the administration of CT antigen compositions will be known to one of ordinary skill in the art, in which the dose amount, schedule of injections, sites of injections, mode of administration (e.g., intra-tumoral) and the like vary from the foregoing. Administration of CT antigen compositions to mammals other than humans, e.g. for testing purposes or veterinary therapeutic purposes, is carried out under substantially the same conditions as described above.

[0235] Where CT antigen peptides are used for vaccination, modes of administration which effectively deliver the CT antigen and adjuvant, such that an immune response to the antigen is increased, can be used. For administration of a CT antigen peptide in adjuvant, preferred methods include intradermal, intravenous, intramuscular and subcutaneous administration. Although these are preferred embodiments, the invention is not limited by the particular modes of administration disclosed herein. Standard references in the art (e.g., Remington's Pharmaceutical Sciences, 18th edition, 1990) provide modes of administration and formulations for delivery of immunogens with adjuvant or in a non-adjuvant carrier.

[0236] When administered, the pharmaceutical preparations of the invention are applied in pharmaceutically-acceptable amounts and in pharmaceutically-acceptable compositions. The term “pharmaceutically acceptable” means a non-toxic material that does not interfere with the effectiveness of the biological activity of the active ingredients. Such preparations may routinely contain salts, buffering agents, preservatives, compatible carriers, and optionally other therapeutic agents. When used in medicine, the salts should be pharmaceutically acceptable, but non-pharmaceutically acceptable salts may conveniently be used to prepare pharmaceutically-acceptable salts thereof and are not excluded from the scope of the invention. Such pharmacologically and pharmaceutically-acceptable salts include, but are not limited to, those prepared from the following acids: hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic, acetic, salicylic, citric, formic, malonic, succinic, and the like. Also, pharmaceutically-acceptable salts can be prepared as alkaline metal or alkaline earth salts, such as sodium, potassium or calcium salts.

[0237] A CT antigen composition may be combined, if desired, with a pharmaceutically-acceptable carrier. The term “pharmaceutically-acceptable carrier” as used herein means one or more compatible solid or liquid fillers, diluents or encapsulating substances which are suitable for administration into a human. The term “carrier” denotes an organic or inorganic ingredient, natural or synthetic, with which the active ingredient is combined to facilitate the application. The components of the pharmaceutical compositions also are capable of being co-mingled with the molecules of the present invention, and with each other, in a manner such that there is no interaction which would substantially impair the desired pharmaceutical efficacy.

[0238] The pharmaceutical compositions may contain suitable buffering agents, including: acetic acid in a salt; citric acid in a salt; boric acid in a salt; and phosphoric acid in a salt.

[0239] The pharmaceutical compositions also may contain, optionally, suitable preservatives, such as: benzalkonium chloride; chlorobutanol; parabens and thimerosal.

[0240] The pharmaceutical compositions may conveniently be presented in unit dosage form and may be prepared by any of the methods well-known in the art of pharmacy. All methods include the step of bringing the active agent into association with a carrier which constitutes one or more accessory ingredients. In general, the compositions are prepared by uniformly and intimately bringing the active compound into association with a liquid carrier, a finely divided solid carrier, or both, and then, if necessary, shaping the product.

[0241] Compositions suitable for oral administration may be presented as discrete units, such as capsules, tablets, lozenges, each containing a predetermined amount of the active compound. Other compositions include suspensions in aqueous liquids or non-aqueous liquids such as a syrup, elixir or an emulsion.

[0242] Compositions suitable for parenteral administration conveniently comprise a sterile aqueous or non-aqueous preparation of CT antigen polypeptides or nucleic acids, which is preferably isotonic with the blood of the recipient. This preparation may be formulated according to known methods using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation also may be a sterile injectable solution or suspension in a non-toxic parenterally-acceptable diluent or solvent, for example, as a solution in 1,3-butane diol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil may be employed including synthetic mono-or di-glycerides. In addition, fatty acids such as oleic acid may be used in the preparation of injectables. Carrier formulation suitable for oral, subcutaneous, intravenous, intramuscular, etc. administrations can be found in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa.

[0243] As used herein with respect to nucleic acids, the term “isolated” means: (i) amplified in vitro by, for example, polymerase chain reaction (PCR); (ii) recombinantly produced by cloning; (iii) purified, as by cleavage and gel separation; or (iv) synthesized by, for example, chemical synthesis. An isolated nucleic acid is one which is readily manipulable by recombinant DNA techniques well known in the art. Thus, a nucleotide sequence contained in a vector in which 5′ and 3′ restriction sites are known or for which polymerase chain reaction (PCR) primer sequences have been disclosed is considered isolated but a nucleic acid sequence existing in its native state in its natural host is not. An isolated nucleic acid may be substantially purified, but need not be. For example, a nucleic acid that is isolated within a cloning or expression vector is not pure in that it may comprise only a tiny percentage of the material in the cell in which it resides. Such a nucleic acid is isolated, however, as the term is used herein because it is readily manipulable by standard techniques known to those of ordinary skill in the art. An isolated nucleic acid as used herein is not a naturally occurring chromosome.

[0244] As used herein with respect to polypeptides, “isolated” means separated from its native environment and present in sufficient quantity to permit its identification or use. Isolated, when referring to a protein or polypeptide, means, for example: (i) selectively produced by expression cloning or (ii) purified as by chromatography or electrophoresis. Isolated proteins or polypeptides may, but need not be, substantially pure. The term “substantially pure” means that the proteins or polypeptides are essentially free of other substances with which they may be found in nature or in vivo systems to an extent practical and appropriate for their intended use. Substantially pure polypeptides may be produced by techniques well known in the art. Because an isolated protein may be admixed with a pharmaceutically acceptable carrier in a pharmaceutical preparation, the protein may comprise only a small percentage by weight of the preparation. The protein is nonetheless isolated in that it has been separated from the substances with which it may be associated in living systems, i.e. isolated from other proteins.

EXAMPLES

Example 1

[0245] Identification of CT Antigens

[0246] Much attention has been given to the potential of CT antigens as targets for cancer vaccine development, and, other than mutational antigens and virus encoded antigens, they clearly represent the most specific tumor antigens discovered to date. However, the CT antigens also provide a new way to think about cancer and its evolution during the course of the disease.

[0247] The starting point for this view is the fact that CT antigen expression is restricted to early germ cell development and cancer. Germ cells give rise to gametes (oocytes and spermatocytes) and trophoblastic cells that contribute to the formation of the chorion and the placenta. Primitive germ cells arise in the wall of the yolk sack and during embryogenesis migrate to the future site of the gonads. In oogenesis, the process begins before birth, with oogonia differentiating into primary oocytes. The primary oocytes, which reach their maximal numbers during fetal development, are arrested at the initial phase of meiosis, and do not renew and complete meiosis until ovulation and fertilization. In contrast, spermatogenesis begins at puberty and is a continuous process of mitosis to maintain the spermatogonia pool and meiosis to generate the mature sperm population. CT antigens, like SCP-1 and OY-TES-1, the proacrosomal binding protein precursor, are clearly important in gametogenesis, and it is likely that the other CT antigens with their restricted expression in gametes and trophoblasts also play a critical role in early germ cell development.

[0248] One possibility to account for aberrant CT expression in cancer relates to the global demethylation associated with certain cancers (42). The promoter region of the MAGE gene has binding sites for transcriptional activators and these sites are methylated in normal somatic cells but demethylated in MAGE-expressing cancer cells and testis. Although cancer-associated demethylation could therefore account for CT (MAGE) expression in tumors, it does not easily accommodate the usual observation of non-coordinate expression patterns (sets) of different CT antigens in most tumors. Also, the marked heterogeneity in CT expression in some tumors (34, 43) is also not easily explicable by a global demethylation process.

[0249] Another mechanism for reactivating CT expression in cancer has to do with mutations in regulatory regions of the CT genes. Although no mutations in CT genes have been found to date, more extensive sequencing, particularly in the promoter region, needs to be done before this can be excluded. However, mutation of CT genes is unlikely to be a common mechanism for the induction of CT expression in cancer.

[0250] Another possibility to account for the appearance of CT antigens in cancer is the induction or activation of a gametogenic program in cancer. According to this view, the different CT sets seen in cancer would replicate the corresponding sets of CT antigens normally expressed during different stages of gametogenesis or trophoblast development. Triggering events for inducing the gametogenic program could be a mutation in an as yet unidentified master switch in germ cell development, or an activation of this master switch by threshold mutations in oncogenes, suppressor genes, or other genes in cancer. It is also possible that activation of a single CT gene could be the switch for activating other genes in the gametogenic program. Supporting evidence for this idea comes from the study of synovial sarcoma, where a translocation event involving the SYT gene on chromosome 18 and the SSX-1 or SSX-2 gene on chromosome X is associated with high expression of unrelated CT antigens, such as NY-ESO-1 and MAGE (44, 45). Extending this line of reasoning and relating it to the role of demethylation in the appearance of CT antigens, a demethylation state in cancer (whatever its cause) could induce the gametogenic program and result in the activation of silent CT genes. Alternatively, demethylation may be an intrinsic part of the gametogenic program and therefore a consequence, not a cause, of switching on the gametogenic program and CT genes in cancer.

[0251] In addition to questions about mechanisms for reactivating CT antigen expression in cancer, another important issue is whether expression of these genes in the cancer cell contributes to its malignant behavior. The finding that gametes, trophoblasts and cancers share a battery of antigens restricted to these cell types suggests extending the search for other shared characteristics.

[0252] It was a similarity in the biological features of trophoblasts and cancer cells that prompted the Scottish embryologist John Beard at the turn of the last century to propose his trophoblastic theory of cancer (46, 47). In his view, cancers arise from germ cells that stray or are arrested in their trek to the gonads. Under the influence of carcinogenic stimuli, such cells undergo a conversion to malignant trophoblastic cells. These malignant trophoblastic cells take on features of the resident cell types in different organs, but the resulting cancers, no matter their site of origin or how distinct they appear morphologically, are of trophoblastic origin. Beard ascribed the invasive, destructive and metastatic features of cancer to functions normally displayed by trophoblastic cells, e.g., invasion of blood vessels, growth into the uterine wall, and spread beyond the uterus. From a contemporary perspective, Beard's idea that cancers are derived from arrested germ cells seems incompatible with our growing knowledge of serological and molecular markers that distinguish different pathways of normal differentiation and their preservation in cancer. Beard's insight that trophoblasts and cancer cells share common features is better explained by the induction of a gametogenic program in resident cancer cells, rather than the derivation of cancer from an aberrant germ cell. The end result, however, would be the same—selected features of cells undergoing gametogenesis and trophoblast development being imposed on transformed somatic cells.

[0253] In addition to CT antigens, other features shared by germ cells and cancer are identified. For example, SCP-1, a critical element in the meiotic program, is expressed in non-germ cell cancers. The induction of a meiotic program in a somatic cell, normal or malignant, likely leads to chromosomal anarchy, a prime feature of advanced cancers. Accordingly, other proteins uniquely associated with meiosis and expressed in cancer cells also are identified as candidate CT antigens.

[0254] OY-TES-1, the proacrosin binding protein precursor that is part of the unique program leading to the formation of spermatozoa, has been identified as a CT antigen. Accordingly, other mature sperm-specific gene products that are expressed in cancer cells also are identified as candidate CT antigens.

[0255] In addition, expression of CT antigens by trophoblasts sheds new light on an old issue—the much studied sporadic production of human chorionic gonadotropin (HCG) and other trophoblastic hormones by human cancers (e.g., 48, 49, 50). The production of HCG by cancer cells has been generally viewed as yet another indication of the genetic instability of cancer cells, resulting in the random and aberrant activation of silent genes during carcinogenesis and tumor progression. However, it can also be viewed as a consequence of the induction of a gametogenic/trophoblastic program in cancer, one that would also result in the semi-coordinate expression of CT antigens. Activation of this program would also confer other properties of germ cells, gametes, and trophoblasts on cancer cells, but these are more difficult to relate in any precise fashion. Nonetheless, immortalization, invasion, lack of adhesion, migratory behavior, induction of blood vessels, demethylation, and downregulation of MHC, are some features shared by cancer and by cells undergoing germ cell/gamete/trophoblast differentiation pathways. The metastatic properties of cancer may also have counterparts in the migratory behavior of germ cells, and in the propensity of normal trophoblast cells to migrate to other organs, such as the lung, during normal pregnancy, but then to undergo involution at term.

[0256] In pursing the idea of a program change in cancer leading to the expression of gametogenic features, a hypothesis termed “Gametogenic Program Induction in Cancer” (GPIC), it might be well to distinguish at least four different pathways involved in germ cell development: A) germ cell→germ cell, B) germ cell→oogonia→oocytes, C) germ cell→spermatogonia→sperm, and D) germ cell→trophoblast. The meiotic program would be common to B and C, proteins like OY-TES-1 would be restricted to C, and HCG would be a characteristic of D. The reason for distinguishing these pathways and ultimately stages in each pathway is that the variety of patterns or sets of CT antigens observed in different cancers may be a reflection of the germ cell program, e.g., pathway and stage that has been induced in these cancers.

[0257] With this background and framework of thinking about the relation of gametogenesis and cancer development, there are a number of approaches to be taken to identify additional CT antigens.

[0258] 1. The search for new CT antigens is accomplished using several methodologies, including SEREX (see, for example, ref. 10), particularly with libraries from testis, normal or malignant trophoblasts, or tumors or tumor cell lines (growing with or without demethylating agents) that express a range of CT antigens, and by extending the use of representational difference analysis. Bioinformatics and chip technology are used for mining databanks for transcripts that show cancer/gamete/trophoblast specificity (e.g., screening annotation of sequence records).

[0259] 2. The expression pattern of known CT antigens in normal gametogenesis and trophoblast development is determined to identify markers that distinguish different pathways and stages in the normal gametogenic program. This information provides a basis for interpreting the complex patterns of CT expression in cancers in relation to gametogenic pathways/stages, and provides new ways to classify cancer on the basis of CT phenotypes.

[0260] 3. The frequency of expression of individual CT antigens in different tumor types has been defined for those CT antigens known to date. In addition to analyzing frequency of expression for CT antigens identified by the methods described herein, additional information is gathered about the composite CT phenotype of individual tumors, and how frequently these composite CT patterns are seen in tumors of different origin. Databases of clinical, genotypic, phenotypic and CT antigen expression data for individual tumors are established to compare the properties of individual tumors and establish correlations between the data. With this information, correlations of CT expression with other biological features of the tumor, e.g., growth rate, local vs. invasive, primary vs. metastatic, different metastatic deposits in the same patient, etc. can be established.

[0261] 4. Determining which stage in the life history of cancer that CT (gametogenic) features are induced can be approached in model systems in the mouse, in vitro systems with human cells, or with naturally occurring tumors in man that show incremental stages in tumor progression. As discussed above, there is evidence that CT expression is a sign of greater malignancy.

[0262] 5. The heterogeneous expression of CT antigens in a large proportion of human cancers needs to be understood. This may reflect a quantitative difference in levels of mRNA/protein in CT+ and CT− cells, or there may be a qualitative distinction between CT+ and CT− cells in CT mRNA/protein expression. Laser dissection microscopy may be one way to analyze this question and cloning of tumor cells from a tumor with heterogeneous CT expression is another approach to understand heterogeneous expression. There is a growing impression that established human cancer cell lines show a higher frequency of CT antigen expression than what would be expected from CT typing of the corresponding tumor type, particularly tumors with a low frequency of CT expression. This could be a secondary consequence of in vitro culture, or it could be that CT+ cells (even if they represent only a minority population of the tumor) have a growth advantage for propagating in vitro, and possibly also in vivo.

[0263] 6. Although CT antigens provide a strong link between the gametogenic program and cancer, it is determined whether other distinguishing features of gamete development are expressed by cancer and whether their expression is correlated with CT antigen expression. The many reports over the last three decades of HCG production by certain human cancers provides a specific starting point to explore this issue and ask whether the production of HCG is correlated with CT antigen expression, particularly a unique pattern of CT expression, such as a pattern reflecting the trophoblast program.

[0264] 7. Transgenic and knock-out approaches using mouse CT counterparts, and transfection analysis with CT coding genes in normal and malignant human cells are performed to define the role of CT antigens in gametogenesis and trophoblast development and their functional significance in cancer.

Example 2

[0265] Identification of Testis-specific Gene as Novel CT Antigens Expressed in Multiple Tumors

[0266] Materials and Methods

[0267] Sperm Proteins

[0268] A number of proteins have been identified as sperm-specific gene products in the literature. These include the proteins listed in Table 2. These are proteins involved in sperm-egg interaction, enzymes present in sperm, and others. SPAN-X was shown to be homologous to the known CT antigen CTp11 (17), and not analyzed in this study.

2TABLE 2Sperm ProteinsAntigensSpeciesFunction/CharacteristicsProteins involved insperm-egg interactionSP-10HumanAcrosomal antigenSP17Human, rabbit,Zona pellucida (ZP) binding inmousevitroNZ-1MouseZP binding, tyrosinephosphorylation activityNZ-2HumanZP binding, tyrosinephosphorylation activityFA-1MouseZP binding, sperm capacitationEnzyme presentin spermAcrosinHuman, mouseSerine protease localized in spermacrosomePH-20Guinea pig,Hyaluronidase activity, spermhumanpenetration of the layer of cumuluscells surrounding oocyteLDH-C4MouseLactate dehydrogenase-C4OthersSP32 (OY-TES-1)Human, mouse,Proacrosin binding proteinguinea pig, pigAKAP110Human, mouseA-kinase anchoring proteinASPHumanAKAP-associated proteinRopporinHumanAKAP-associated proteinCS-1HumanCleavage signal proteinSPAG9 (HSS)HumanSperm surface proteinNYD-sp10HumanSPAN-X/CTp11HumanNuclear protein

[0269] mRNA Isolation and cDNA Synthesis

[0270] mRNA from malignant tissues was purified using the QuickPrep Micro mRNA Purification Kit (Amersham Pharmacia, Piscataway, N.J.). mRNA was reverse transcribed into single strand cDNA using Moloney murine leukemia virus reverse transcriptase and oligo (dT)15 as a primer (Amersham Pharmacia). cDNAs were tested for integrity by amplification of G3PDH transcripts in a 30 cycle reaction.

[0271] Reverse Transcription-PCR (RT-PCR)

[0272] To amplify cDNA segments from normal tissue (Multiple Tissue cDNA panel, lo CLONTECH, Palo Alto, Calif.) and malignant tissues, the primers for the respective genes were designed (Table 3). To avoid amplification of contaminating genomic DNA, primers were placed in different exons. RT-PCR was performed by using 30 amplification cycles and followed by a 10-min elongation step at 72° C. The PCR products were analyzed by agarose gel electrophoresis and capillary electrophoresis on a microtip device (DNA 7500 LabChip, Caliber Technologies, Mountain View, Calif.) by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.) and assessed for a single amplification product of the correct size.

[0273] Real-time Quantitative PCR

[0274] A two-step real-time RT-PCR was used to determine relative expression levels of sperm protein mRNA using ABI Prism 7700 Sequence Detection System (Perkin-Elmer Applied Biosystems, Foster City, Calif.). Primer pairs specific for NY-ESO-1, OY-TES-1, SP17, acrosin, PH-20, AKAP110, ASP, CS-1 and SPAG9 used were listed in Table 3. For SP-10, ropporin and NYD-sp10, newly designed primer pairs were used: SP-10-5′: 5′-CCAGAGGAACATCAAGTCAGC-3′ (SEQ ID NO: 11); SP-10-3′: 5′-ATATTGTGCCTGTAGATGTG-3′ (SEQ ID NO: 12), product size 515 bp; ropporin-5′: 5′-TGCCGAAAATGCTGAAGGAG-3′ (SEQ ID NO: 13); ropporin-3′: 5′-GTAGACAAACTGGAAGGTGC-3′ (SEQ ID NO: 14), product size 455 bp; NYD-sp10-5′: 5′-TACATTGAGTGGCTGGATAC-3′ (SEQ ID NO: 15); NYD-sp10-3′: 5′-AGGTAGAGCACGTAGTCATC-3′ (SEQ ID NO: 16), product size 212 bp. PCR was performed using SYBR Green PCR Core Reagent kit (Perkin-Elmer Applied Biosystems). The thermal cycling conditions comprised an initial denaturation step at 95° C. for 10 min and 40 cycles at 95° C. for 15 sec and 60° C. for 1 min. The house keeping gene β-actin was used for internal normalization. Experiments were performed in duplicate for each data point. Final results, expressed as n-fold differences in sperm protein gene expression relative to β-actin gene and normal testis (the calibrator) were determined in exponent as follows:

[0275] n=2−(ΔCt sample−ΔCt calibrator)

[0276] where ΔCt values of the sample and calibrator are determined by subtracting the average Ct value of the sperm gene from the average Ct value of the β-actin gene.

3TABLE 3Primer pairs used in this studyAnnealing temperaturePCRSEQ IDGeneSequence of primer pair1(° C.)Product size (bp)NO:NY-ESO-1CACACAGGATCCATGGATGCTGCAGATGCGG6035317CACACAAAGCTTGGCTTAGCGCCTCTGCCCTG18SP-10CCAGAGGAACATCAAGTCAGC6496419GAGAAAGAGTTGGAGCAGGGAA20SP17GGCAGTTCTTACCAAGAAGAT6049421GGAGGTAAAACCAGTGTCCTC22AcrosinTGCATGACTGGAGACTGGTT6056523CAGTTCAGATAAGGCCAGGT24PH-20AGAGGCCACTGAGAAAGCAA6057425GGCTGCTAGTGTGACGTTGA26OY-TES-1/sp32AAGGACAGGGGACTAAGGAG6260427CCGTACAAATCCAGCCCGTA28AKAP110CTAACTTCGGCCTTCCCAGA6046129AGTGGGGTTGCCGATTACAG30ASPAAGCAATTCACCAAGGCTGC6055231ACCTATCATGCCGTTCTTCC32RopporinAGGTTCTACTGCTCTCCTTC6063133GTAGAGAAACTGGAAGGTGC34CS-1ATGGGAATGTGTGGCAGTAGA6058135CCACTTACAATTTCCCGTCTG36SPAG9ACTCCCACCAAAGGCATAGA6051537CGAATCATCTCTGTCCATCG38NYD-sp10TGTGTGACTCCATCCTCTAC6064039AGGTAGAGCACGTAGTCATC401Forward primer sequence is shown in top and reverse primer sequence in bottom for each gene. Sequence is 5′-3′ for both primers.

[0277] To determine the specificity of these sperm-specific gene products as CT antigens, the expression of the corresponding genes in normal tissues was determined by RT-PCR of a panel of normal tissues. RT-PCR was conducted as described above.

[0278] Results

[0279] Sperm Protein mRNA Expression in Normal Tissues by Conventional RT-PCR.

[0280] We investigated expression of sperm protein genes in normal tissues by RT-PCR analysis at 30 cycles. Eleven sperm protein genes (see Table 2) and well-defined control NY-ESO-1 were amplified with 16 normal tissue cDNA templates (Multiple Tissue cDNA panel, CLONTECH). PCR products were analyzed by agarose gel electrophoresis and capillary electrophoresis on a microtip device by Agilent 2100 Bioanalyzer. As shown in Table 4, acrosin, PH-20, OY-TES-1, AKAP110 and NYD-sp10 mRNAs were amplified only in testis. SP-10 and ropporin mRNA were amplified in testis and, to a lesser extent, in pancreas. SP17, CS-1 and SPAG9 mRNAs were amplified in most tissues.

[0281] Real-time RT-PCR Analysis of Sperm Protein Genes in Normal Tissues

[0282] To further analyze sperm protein mRNA expression in normal tissues, real-time RT-PCR analysis was performed. As shown in FIG. 1, CS-1 and SPAG9 showed mRNA expression in normal tissues ubiquitously, whereas other genes showed variable expression. Among tissues, the highest expression was consistently observed in testis. The gene with the highest expression in testis was SP17. Its threshold cycle (Ct) value (i.e. the cycle at which the fluorescence of the reaction first arises above the background) was 21.8 for testis. Ct values of SP17 for other tissues, except skeletal muscle, were also rather high (26.9-30.4) (FIG. 1). The results were consistent with the above results obtained by conventional RT-PCR analysis.

[0283] The relative mRNA expression (n value, as described above) was determined. As shown in FIG. 2, NY-ESO-1, SP-10, SP17, acrosin, PH-20, OY-TES-1, AKAP110, ASP, ropporin, and NYD-sp10 mRNA expression was 102 to 107 fold higher in testis than in other tissues. CS-1 mRNA was expressed 1.37, 1.63, and 8.13 fold higher in liver, placenta and pancreas, respectively, to that in testis. SPAG9 mRNA expression in various tissues was 0.6-27% of that found in the testis.

4TABLE 4mRNA expression of sperm proteins in normal human tissuesGenesOY-TES-1Tissues(sp32)SP-1OSP17AcrosinPH-20AKAP11OASPRopporinCS-1SPAG9NYD-sp10Brain−−+−−−−−++−Heart−−+−−−−−+±−Kidney−−+−−−−−−−−Liver−−+−−−−−++−Lung−−+−−−−−+±−Pancreas−−+−−−±++±−Placenta−−+−−−−−+−−Skeletal−−+−−−−−+−−MuscleColon−−+−−−−−++−Ovary−−+−−−−−+−−PBL−−−−−−+−++−Prostate−−+−−−−−+−−Small−−+−−−−−+−−IntestineSpleen−−+−−−−−+±−Testis+++++++++++Thymus−−+−−−−−−−−

[0284] mRNA Expression of Selected Sperm Proteins in Tumors

[0285] Because of highly restricted mRNA expression in normal tissues, acrosin, PH-20, OY-TES-1, AKAP110, NYD-sp10, SP-10, and ropporin were chosen for mRNA expression analysis in malignant tissues by RT-PCR. The expression of the foregoing gene products was determined by RT-PCR of a panel of human tumor tissues. Samples of nine different types of cancer (bladder, breast, liver, lung, colon, stomach, renal, ovarian and glioma) were tested. As shown in Table 5, AKAP110 mRNA was most frequently expressed in a variety of tumors. It was expressed in 26% (6/23) of bladder cancer samples, 20% (1/5) of liver cancer samples, 27% (4/15) of colon cancer samples, 40% (4/10) of renal cancer samples, and 39% (7/18) of ovarian cancer samples. No expression was observed in breast or stomach cancer samples. Acrosin was expressed in 5% (1/22) of bladder cancer samples, 20% (1/5) of breast cancer samples, 40% (2/5) of liver cancer samples, and 20% (1/5) of lung cancer samples. No expression of acrosin mRNA was observed in colon, stomach, renal and ovarian cancer samples. SP-10, ropporin, PH-20 and NYD-sp10 showed infrequent expression patterns in tumors.

[0286] These results indicated that five of the sperm proteins were specifically expressed in testis only: PH-20 (e.g., GenBank accession number XM—004865; SEQ ID NO: 1, 2), AKAP110 (e.g., GenBank accession number AF093408; SEQ ID NO: 3, 4), acrosin (e.g., GenBank accession number XM—010064; SEQ ID NO: 5, 6), NYD-sp10 (e.g., GenBank accession number AF332192; SEQ ID NO: 7, 8) and OY-TES-1 (previously determined to be a CT antigen (Ono et al., Proc. Nat'l. Acad. Sci. USA 98:3282-3287, 2001); e.g., GenBank accession number AB051833 (SEQ ID NO: 41,42). In addition, two proteins, SP10 (e.g., GenBank accession number M82968 (SEQ ID NO: 43, 44) and ropporin (e.g., GenBank accession number NM—017578 (SEQ ID NO: 45, 46), were expressed in only testis and pancreas.

[0287] According to the expression pattern in normal and cancer tissues, the sperm-specific gene products PH-20, AKAP110, acrosin and NYD-sp10 were classified as additional CT antigens.

5TABLE 5mRNA expression of sperm specific proteins in human cancerGenesTumor typeSP-10AcrosinPH-20OY-TES-1/sp32AKAP110RopporinNYD-sp10Bladder cancer0/28 (0%)1/22 (5%)0/23 (0%)11/39 (28%) 6/23 (26%)N.D 0/22 0%)Breast cancer 0/5 (0%) 1/5 (20%) 0/5 (0%) 2/5 (40%) 0/5 (0%) 0/5 (0%) 0/5 (0%)Liver cancer 0/5 (0%) 2/5 (40%) 0/5 (0%) 2/5 (40%) 1/5 (20%) 0/5 (0%) 0/4 (0%)Lung cancer 1/5 (20%) 1/5 (20%) 0/5 (0%) 1/5 (20%)N.D 2/5 (40%) 1/5 (20%)Colon cancer0/15 (0%)0/15 (0%)0/15 (0%) 2/13 (15%) 4/15 (27%)0/15 (0%) 0/15 (0%)Stomach cancer 0/5 (0%) 0/5 (0%) 0/5 (0%) 0/5 (0%) 0/5 (0%) 0/5 (0%) 0/5 (0%)Renal cancer0/10 (0%)0/10 (0%)0/10 (0%) 0/10 (0%) 4/10 (40%)0/10 (0%) 0/10 (0%)Ovarian cancer0/18 (0%)0/18 (0%)3/18 (17%) 4/18 (22%) 7/18 (39%)0/18 (0%) 1/18 (6%)Glioma7/34 (21%)N.D.1/34 (3%)19/34 (56%)16/34 (47%)1/34 (3%)21/37 (57%)

Example 3

[0288] Expression of RFX4 Alternatively Spliced Variants in Gliomas as Cancer/Testis Antigens

[0289] Materials and Methods

[0290] Tissues

[0291] Tumor tissues were obtained from patients who visited at Okayama University Medical School Hospital. Tumor specimens investigated in this study are listed in Table 6. For histological diagnosis of brain tumor specimens, World Health Organization (WHO) classification was used.

6TABLE 6.RFX4 mRNA expression in glioma and other tumorsTumor typemLRNA, positive/totalGlioblastoma21/37 (57%)Astrocytoma G II 3/9 (33%)Astrocytoma G III 8/11 (73%)Astrocytoma G IV 7/12 (58%)Mixed glioma 1/2 (50%)Ependymoma 2/3 (67%)Meningioma 0/8 (0%)Lung cancer 1/5 (20%)Ovarian cancer 1/20 (5%)Cervical cancer 1/16 (6%)Breast cancer 0/5 (0%)Renal cancer 0/10 (0%)Bladder cancer 0/22 (0%)Liver cancer 0/4 (0%)Colon cancer 0/15 (0%)Stomach cancer 0/5 (0%)

[0292] mRNA Isolation and cDNA Synthesis

[0293] mRNA from frozen tumor tissues was purified using the QuickPrep Micro mRNA Purification Kit (Amersham Pharmacia, Piscataway, N.J.). mRNA was reverse transcribed into single strand cDNA using Moloney murine leukemia virus reverse transcriptase and oligo (dT)15 as a primer (Amersham Pharmacia). cDNAs were tested for integrity by amplification of β-actin transcripts in a 30 cycle reaction.

[0294] Reverse-transcription PCR (RT-PCR)

[0295] To amplify cDNA segments from normal tissues (Multiple Tissue cDNA panels, CLONTECH, Palo Alto, Calif.) and tumors, the gene specific primers listed in Table 7 were used. RT-PCR was performed by using 30 amplification cycles and followed by a 10-mi n elongation step at 72° C. The PCR products were analyzed by using conventional agarose gel electrophoresis.

[0296] Rapid Amplification of cDNA Ends (RACE)

[0297] 5′ RACE was performed to identify the 5′ end sequence of RFX4-C using the 5′RACE System for Rapid Amplification kit (Gibco BRL, Rockville, Md.). Total RNA was isolated from RFX4-C positive glioma specimens using the RNeasy kit (Qiagen GmbH, Hilden, Germany) and used as a template. The first-strand of cDNA was synthesized using the specific primer, GSP1-R1 (5′-CCCGAGTCTTCTGGTGGTTA-3′) (SEQ ID NO: 59). dC-tailed cDNA was amplified using a gene-specific nested primer GSP2-R1 (5′-AGCATTGACAGGTTGGGTATC-3′) (SEQ ID NO: 60) and an abridged universal anchor primer (5′-GGCCACGCGTCGACTAGTAC-3′) (SEQ ID NO: 61). The RACE product was sequenced with the sequence primer, RS1 (5′-AGTTCTCCTCCAGCCAT-3′) (SEQ ID NO: 62).

7TABLE 7Primer pairs used in this studyAnnealingPCRSEQtemperatureproductIDPrimer pairsSequence of primers(° C.)size (bp)NO:A1A1-SGCAATGGCTGGAGGAGAACT6270647A1-ASAGCCACTTTTAGCCACTTCATC48A2NYD-STGTGTGACTCCATCCTCTAC6298449A2-ASGTCTGGCTTTTTGTGTGTGTG50B1B1-SGAAGACACGGAAGGCACAGA6268251A1-ASAGCCACTTTTAGCCACTCATC52B2B2-SACCGGAAACTCATCACCCCAAT62105553B2-ASGTAAGCAAAGCCAGGAAAGTG54C1A1-SGCAATGGCTGGAGGAGAACT62159055C1-ASTAAACTGGTATCCTGTGTGTGA56commonNYD-STGTGTGACTCCATCCTCTAC6064057NYD-ASAGGTAGAGCACGTAGTCATC58Forward primer sequence is shown in top and reverse primer sequence in bottom for each primer pair. Sequence is 5′-3′ for both primers.

[0298] Results

[0299] Expression of RFX4 mRNA in Normal and Malignant Tissues

[0300] RFX4 gene is located on chromosome 12q24 and spans ˜164-kb composed of 19 exons according to the NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map) (FIG. 3). Two alternatively spliced variants have been described. RFX4-A (SEQ ID NO: 9, 10) that was originally described as RFX4 by Morotomi-Yano et al. (51) and designated here as such is composed of exons 1-5, and 7-16, containing a DNA binding domain (DBD) encoded by exons 3, 4, 5 and 7 (FIGS. 3 and 4). RFX4-B, which was reported as NYD-sp10 (SEQ ID NO: 7, 8) (GenBank accession number AF332192), is composed of exons 6-19 lacking DBD. Both products share evolutionarily conserved B, C regions and dimerization domain.

[0301] We investigated RFX4 mRNA expression in adult normal tissues (Multiple Tissue cDNA panels, CLONTECH) and various tumors by RT-PCR using common primers for RFX4-A and RFX4-B (primer pair NYD-S and NYD-AS). As shown in FIG. 5, no expression of RFX4 mRNA was observed in adult normal tissues except for testis. On the other hand, in tumors, a high level of RFX4 mRNA expression was observed in gliomas. RFX4 mRNA was detected in 33% (3/9) of astrocytoma G II, 73% (8/11) of astrocytoma G III, 58% (7/12) of astrocytoma G IV, 50% (1/2) of mixed glioma, and 67% (2/3) of ependymoma (FIG. 5 and Table 6). No expression was observed in meningiomas. In other tumors, RFX4 mRNA was detected in 20% (1/5) of lung cancer, 5% (1/20) of ovarian cancer, and 6% (1/16) of cervical cancer. No expression of RFX4 mRNA was observed in breast, renal, bladder, liver, colon, and stomach cancer.

[0302] Expression of RFX4 Alternatively Spliced Variants in Glioma

[0303] We further investigated the expression of alternatively spliced variants RFX4-A and B in gliomas using primer pairs as shown in FIG. 3 and Table 7. With 5′ primer pairs A1 and B1, amplification was observed only with A1 in all 21 specimens of 37 gliomas that were positive for RFX4 using common primers. However, with 3′ primer pairs A2 and B2, amplification was observed by B2 only in the same 21 specimens. Amplification by primer pair A2 was observed in three tumor specimens. These results suggested that there is another splice variant in gliomas, designated RFX4-C (SEQ ID NOs: 63 and 64 represent the nucleotide and amino acid sequences, respectively), spanning the 5′ end of RFX4-A to the 3′ end of RFX4-B (FIG. 3).

[0304] We examined the expression of RFX4-C in gliomas using the RFX4-C specific primer pair C1 shown in FIG. 3. As shown in FIG. 6 and Table 8, all glioma specimens that were positive for RFX4 using common primers also expressed RFX4-C. Expression of the splicing variants in various tumor specimens is shown in Table 8 below. 27% (3/8) of RFX4-C mRNA positive astrocytoma G III expressed RFX4-A simultaneously. No expression of RFX4-B was observed.

[0305] In testis, expression of RFX4-A, B, and C mRNA was observed.

8TABLE 8Expression of RFX4 splicing variants in gliomaRFX4 positiveDiagnosisspecimensRFX4-ARFX4-BRFX4-CAstrocytoma G II300 3Astrocytoma G III830 8Astrocytoma G IV700 7Mixed glioma100 1Ependymoma200 2Total213 (14%)0 (0%)21 (100%)RT-PCR analysis was performed using primer pairs A1, A2, B1, B2 and C1 (FIG. 3 and Table 7) as shown in FIG. 6. All glioma specimens that were positive for RFX4 using common primers in RT-PCR were also positive for RFX4-C. Three astrocytoma G III specimens expressed both RFX4-A and C.

Example 4

[0306] Preparation of Recombinant CT Antigens

[0307] To facilitate screening of patients' sera for antibodies or T cells reactive with CT antigens, for example by ELISA, recombinant proteins are prepared according to standard procedures. In one method, the clones encoding CT antigens are subcloned into a baculovirus expression vector, and the recombinant expression vectors are introduced into appropriate insect cells. Baculovirus/insect cloning systems are preferred because post-translational modifications are carried out in the insect cells. Another preferred eukaryotic system is the Drosophila Expression System from Invitrogen. Clones which express high amounts of the recombinant protein are selected and used to produce the recombinant proteins. The recombinant proteins are tested for antibody recognition using serum from the patient which was used to isolated the particular clone, or in the case of CT antigens recognized by allogeneic sera, by the sera from any of the patients used to isolate the clones or sera which recognize the clones' gene products.

[0308] Alternatively, the CT antigen clones are inserted into a prokaryotic expression vector for production of recombinant proteins in bacteria. Other systems, including yeast expression systems and mammalian cell culture systems also can be used.

Example 5

[0309] Preparation of Antibodies to CT Antigens

[0310] The recombinant CT antigens produced as in Example 3 above are used to generate polyclonal antisera and monoclonal antibodies according to standard procedures. The antisera and antibodies so produced are tested for correct recognition of the CT antigens by using the antisera/antibodies in assays of cell extracts of patients known to express the particular CT antigen (e.g. an ELISA assay). These antibodies can be used for experimental purposes (e.g. localization of the CT antigens, immunoprecipitations, Western blots, etc.) as well as diagnostic purposes (e.g., testing extracts of tissue biopsies, testing for the presence of CT antigens).

[0311] The antibodies are useful for accurate and simple typing of cancer tissue samples for expression of the CT antigens.

Example 6

[0312] Expression of CT Antigens in Cancers of Similar and Different Origin.

[0313] The expression of one or more of the CT antigens is tested in a range of tumor samples to determine which, if any, other malignancies should be diagnosed and/or treated by the methods described herein. Tumor cell lines and tumor samples are tested for CT antigen expression, preferably by RT-PCR according to standard procedures. Northern blots also are used to test the expression of the CT antigens. Antibody based assays, such as ELISA and western blot, also can be used to determine protein expression. A preferred method of testing expression of CT antigens (in other cancers and in additional same type cancer patients) is allogeneic serotyping using a modified SEREX protocol (as described above).

[0314] In all of the foregoing, extracts from the tumors of patients who provided sera for the initial isolation of the CT antigens are used as positive controls. The cells containing recombinant expression vectors described in the Examples above also can be used as positive controls.

[0315] The results generated from the foregoing experiments provide panels of multiple cancer associated nucleic acids and/or polypeptides for use in diagnostic (e.g. determining the existence of cancer, determining the prognosis of a patient undergoing therapy, etc.) and therapeutic methods (e.g., vaccine composition, etc.).

Example 7

[0316] HLA Typing of Patients Positive for CT Antigens

[0317] To determine which HLA molecules present peptides derived from the CT antigens of the invention, cells of the patients which express the CT antigens are HLA typed. Peripheral blood lymphocytes are taken from the patient and typed for HLA class I or class II, as well as for the particular subtype of class I or class II. Tumor biopsy samples also can be used for typing. HLA typing can be carried out by any of the standard methods in the art of clinical immunology, such as by recognition by specific monoclonal antibodies, or by HLA allele-specific PCR (e.g. as described in WO97/31126).

Example 8

[0318] Characterization of CT Antigen Peptides Presented by MHC Class I and Class II Molecules.

[0319] Antigens which provoke an antibody response in a subject may also provoke a cell-mediated immune response. Cells process proteins into peptides for presentation on MHC class I or class II molecules on the cell surface for immune surveillance. Peptides presented by certain MHC/HLA molecules generally conform to motifs. These motifs are known in some cases, and can be used to screen the CT antigens for the presence of potential class I and/or class II peptides. Summaries of class I and class II motifs have been published (e.g., Rammensee et al., Immunogenetics 41:178-228, 1995). Based on the results of experiments such as those described above, the HLA types which present the individual CT antigens are known. Motifs of peptides presented by these HLA molecules thus are preferentially searched.

[0320] One also can search for class I and class II motifs using computer algorithms. For example, computer programs for predicting potential CTL epitopes based on known class I motifs has been described (see, e.g., Parker et al, J. Immunol. 152:163, 1994; D'Amaro et al., Human Immunol. 43:13-18, 1995; Drijfhout et al., Human Immunol. 43:1-12, 1995). Computer programs for predicting potential T cell epitopes based on known class II motifs has also been described (see, e.g Sturniolo et al., Nat Biotechnol 17(6):555-61, 1999). HLA binding predictions can conveniently be made using an algorithm available via the Internet on the National Institutes of Health World Wide Web site at URL http://bimas.dcrt.nih.gov. See also the website of: SYFPEITHI: An Internet Database for MHC Ligands and Peptide Motifs (access via http://www.uni-tuebingen.de/uni/kxi/ or http:H/134.2.96.221/scripts/hlaserver.dll/EpPredict.htm. Methods for determining HLA class II peptides and making substitutions thereto are also known (e.g. Strominger and Wucherpfennig (PCT/US96/03182)).

Example 9

[0321] Identification of the Portion of a Cancer Associated Polypeptide Encoding an Antigen

[0322] To determine if the CT antigens identified and isolated as described above can provoke a cytolytic T lymphocyte response, the following method is performed. CTL clones are generated by stimulating the peripheral blood lymphocytes (PBLs) of a patient with autologous normal cells transfected with one of the clones encoding a CT antigen polypeptide or with irradiated PBLs loaded with synthetic peptides corresponding to the putative protein and matching the consensus for the appropriate HLA class I molecule (as described above) to localize an antigenic peptide within the CT antigen clone (see, e.g., Knuth et al., Proc. Natl. Acad. Sci. USA 81:3511-3515, 1984; van der Bruggen et al., Eur. J. Immunol. 24:3038-3043, 1994). These CTL clones are screened for specificity against COS cells transfected with the CT antigen clone and autologous HLA alleles as described by Brichard et al. (Eur. J. Immunol. 26:224-230, 1996). CTL recognition of a CT antigen is determined by measuring release of TNF from the cytolytic T lymphocyte or by 51Cr release assay (Herin et al., Int. J. Cancer 39:390-396, 1987). If a CTL clone specifically recognizes a transfected COS cell, then shorter fragments of the CT antigen clone transfected in that COS cell are tested to identify the region of the gene that encodes the peptide. Fragments of the CT antigen clone are prepared by exonuclease III digestion or other standard molecular biology methods. Synthetic peptides are prepared to confirm the exact sequence of the antigen.

[0323] Optionally, shorter fragments of CT antigen cDNAs are generated by PCR. Shorter fragments are used to provoke TNF release or 51Cr release as above.

[0324] Synthetic peptides corresponding to portions of the shortest fragment of the CT antigen clone which provokes TNF release are prepared. Progressively shorter peptides are synthesized to determine the optimal CT antigen tumor rejection antigen peptides for a given HLA molecule.

[0325] A similar method is performed to determine if the CT antigen contains one or more HLA class II peptides recognized by T cells. One can search the sequence of the CT antigen polypeptides for HLA class II motifs as described above. In contrast to class I peptides, class II peptides are presented by a limited number of cell types. Thus for these experiments, dendritic cells or B cell clones which express HLA class II molecules preferably are used.

Example 10

[0326] Identification of New Variants of RFX4 Transcript and Their Expression in Astrocytoma

[0327] Materials and Methods

[0328] Tissues

[0329] The astrocytomas (n=40) included in this study consisted of 12 grade II, 13 grade III, and 15 grade IV astrocytomas that were surgically obtained from patients in Okayama University Hospital. Tumors were graded according to World Health Organization (WHO) criteria. Peritumoral normal tissues were obtained from 5 grade II, and 6 grade III and IV astrocytomas.

[0330] mRNA Isolation and cDNA Synthesis

[0331] mRNA from frozen tumor tissues was purified using the QuickPrep Micro mRNA Purification Kit (Amersham Pharmacia, Piscataway, N.J.). mRNA was reverse transcribed into single strand cDNA using Moloney murine leukemia virus reverse transcriptase (Ready-To-Go You-Prime First-Strand Beads, Amersham Pharmacia), and oligo (dT)15 as a primer. cDNAs were tested for integrity by amplification of G3PDH transcripts in a 30 cycle amplification and normalized on the basis of G3PDH content (5˜10ng/μl).

[0332] RT-PCR

[0333] To amplify cDNA segments from normal tissues (Multiple Tissue cDNA panels, CLONTECH, Palo Alto, Calif.) and tumors, the gene specific primers were designed. The primer pairs used in this study are shown in FIG. 7 and Table 9.

9TABLE 9Primer pairs used in this studyPrimer pairSequencesSEQ ID NOAGAAGACACGGAAGGCACAGA51AGCCACTTTTAGCCACTCATC52BACCGGAAACTCATCACCCAAT70GTCTGGCTTTTTGTGTGTGTG50A and BGCAATGGCTGGAGGAGAACT47TAAACTGGTATCCTGTGTGTGA56CGCCGTTCCACTGAGAGCTG71TAAACTGGTATCCTGTGTGTGA56DATGCATTGTGGGTTACTGGAG72TGAATATGCCACTGTCTGTTTG73D′TACATTGAGTGGCTGGATAC15AGGTAGAGCACGTAGTCATC16EGCAATGGCTGGAGGAGAACT47CCGTCATAAAGCTCTTCCATAT74Forward primer sequence is shown in top and reverse primer sequence is bottom for each primer pair. Sequence is 5′-3′ for both primers.

[0334] RT-PCR was performed by using 30 amplification cycles and followed by a 10-min elongation step at 72° C. The PCR products were analysed by using conventional agarose gel electrophoresis and capillary electrophoresis on a microtip (DNA 7500 LabChip, Caliber Technologies, Mountain View, Calif.) by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo, Alto, Calif.).

[0335] Rapid Amplification of cDNA Ends (RACE)

[0336] 5′ and 3′ RACE were performed using GeneRacer kit (Invitrogen, Carlsbad, Calif.). Total RNA was isolated from normal brain, testis, and astrocytoma specimens using RNeasy kit (Qiagen GmbH, Hilden, Germany) and used as templates. The first strand cDNA was synthesized using GeneRacer Oligo dT primer following the manufacturer's directions. Primers used for 5′ and 3′ RACE were R1, R2 and R3, and F1 and F2, respectively (FIG. 7). Sequence of the primers are as follows: 5′-TGAATATGCCACTGTCTGTTTGC-3′ (R1, SEQ ID NO: 75); 5′-CCCGAGTCTTCTGGTGGTTA-3′ (R2, SEQ ID NO: 59); 5′-CCGTCATAAAGCTCTTCCAT-3′ (R3, SEQ ID NO: 74); 5′-GCCACTCCACTATGCCCCTTACCA-3′ (F1, SEQ ID NO: 76); and 5′-GTAAGCACCGGACGGCCATT-3′ (F2, SEQ ID NO: 77). The RACE products were cloned into pCR 2.1 vector (Invitrogen) and sequenced by using ABI PRISM automated Sequencer (Perkin-Elmer, Foster City, Calif.).

[0337] Real-time Quantitative RT-PCR

[0338] A two-step real-time RT-PCR was performed using the SYBR Green PCR Core Reagents Kit (Perkin-Elmer Applied Biosystems) by ABI Prism 7700 Sequence Detection system (Perkin Elmer Applied Biosystems). The thermal cycling conditions comprised an initial denaturation step at 95° C. for 10 min and 40 cycles at 95° C. for 15 s and 58° C. for 1 min. G3PDH was used for internal normalization. Experiments were performed in duplicate for each data point. Real-time PCR products were separated by gel electrophoresis to verify the presence of specific products. Threshold cycle (Ct) value was determined as the cycle at which the fluorescence of the reaction first arises above the background. To determine real-time PCR efficiencies, Ct value versus the concentration of serially diluted standard solution were plotted to calculate the slope. To normalize the quantity of mRNA present in each samples, the Ct values obtained from the endogenous control were subtracted from the gene-specific Ct values (ΔCt=Ct of RFX4-D or -E-Ct of G3PDH). The mean of 9 ΔCt from normal brains including 4 normal brains purchased from clontech and 5 peritumoral normal tissues from grade II astrocytomas were calculated and used as a calibrator. The concentration of RFX4-D or -E mRNA in astrocytomas, relative to normal brain, was calculated by subtracting the mean ACt value of normal brains from ΔCt obtained with tumor samples (ΔΔCt=ΔCt of tumors−mean ΔCt of normal brains), and the relative concentration was determined as 2−ΔΔCt.

[0339] Results

[0340] Identification of Three New Variants of RFX4 Transcript

[0341] RFX4 gene is located on chromosome 12q24 and composed of 19 exons according to the NCBI Map Viewer (http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/map_search) (FIG. 7). Two alternatively spliced variants have been described. One is designated here as RFX4-A (SEQ ID NOs: 7, 8), which was reported as NYD-sp10 (GenBank accession number AF332192), and composed of exons 6-19 lacking the DNA binding domain (DBD) that is encoded by exons 3, 4, 5 and 7 (FIGS. 7 and 8). RFX4-B (SEQ ID NOs: 9, 10) is composed of exons 1-4, the 5′ end of exon 5, and exons 7-16, containing DBD. Both products share evolutionarily conserved B and C regions and the dimerization domain.

[0342] Please note that in Example 3, RFX4-B (SEQ ID NO: 7,8) was referred to as RFX-4A and RFX-4A (SEQ ID NO: 9, 10) was referred to as RFX4-B. The current nomenclature was adopted to be consistent with the nomenclature used in publicly available databases and published reports: in the NCBI database the sequence of NYD-sp10 is described as isoform a and transcript variant 1; and the gene published in J. Biol. Chem. 277: 836-842, 2002 is described as isoform b and transcript variant 2. As used in this example, RFX4-A corresponds to NYD-sp10 as isoform a, and RFX4-B corresponds to isoform b and transcript variant 2. The size of RFX4-B protein is 563 amino acids (see FIG. 8).

[0343] In the course of RFX4-A and -B mRNA expression studies, we found possible new variants amplified with primer pair A and B, that spanned from the RFX4-B specific 5′ region to the RFX4-A specific 3′ region (FIG. 7) in normal tissues and astrocytomas. To identify those new isoforms, 5′ and 3′ RACE based on the 5′ and 3′ sequences of RFX4-B and RFX4-A, respectively, were performed using cDNA from normal brain, testis, and astrocytoma specimens as templates. As shown in FIG. 7, 5′ RACE with primers R1 and R2 showed two amplification products of different sizes. One amplification product from testis was identical to the 5′ end of RFX4-B deposited in GenBank (accession number AB044245), but 30 base pairs were added to it. Another amplification product derived from normal brain and astrocytoma contained a new exon, termed exon 1 a, which was located about 18 kb upstream of exon 1. On the other hand, 3′ RACE with primer F1 revealed two different polyadenylated cDNA ends in exon 19.

[0344] With further RT-PCR using primers designed in exon 1 a, 1, and 19, full length of two new variants, designated RFX4-C and RFX4-D, were isolated. The RFX4-C cDNA spanned from 30 bp upstream to the 5′end of RFX4-B to 3′end of RFX4-A with shorter 3′ untranslated region. RFX4-C was found to be 2560 bp in length (SEQ ID NO: 63) and encoded a putative protein of 744 amino acids (SEQ ID NO: 64) (FIGS. 7 and 8). The RFX4-D cDNA contained exon 1a that spliced to exon 2. RFX4-D spanned 18 exons except for exons 1 and 6, and was 3955 bp in length (SEQ ID NO: 65) encoding a putative protein of 735 amino acids (SEQ ID NO: 66) (FIG. 9A). The difference of N-terminal amino acid sequences between RFX4-B and C, and RFX4-D, were the initial 23 and 14 amino acids corresponding to exon 1 and exon 1a, respectively (FIGS. 7-9).

[0345] Furthermore, we identified another variant, designated RFX4-E, by RACE based on the sequence of ER-RFX4 (GenBank accession number M69296) (FIG. 8) using cDNA from astrocytoma as a template. Primers used for 5′ and 3′ RACE were R3 and F2, respectively, as shown in FIG. 7. RFX4-E was found to be 2104 bp in length (SEQ ID NO: 67) and contained two possible open reading frames of 126 (SEQ ID NO: 68) and 110 amino acids (SEQ ID NO: 69) (FIG. 9B). RFX4-E transcript started from 98 base pairs downstream from translation start site of RFX4-D in exon 1a. The 3′ end was identical with ER-RFX4. RFX4-E had an incomplete DBD because of lacking downstream from exon 7 (FIGS. 7-9). FIG. 10 depicts the alignment of portions of RFX4-B (SEQ ID NO: 78), RFX4-D (SEQ ID NO: 79) and RFX4-E (SEQ ID NO: 80) proteins. The DBD domain is shown in boxes.

[0346] Expression of RFX4 mRNA Variants in Normal Tissues and Astrocytomas

[0347] We investigated the expression of RFX4 mRNA variants in normal tissues (Multiple Tissue cDNA panels, CLONTECH) and astrocytomas by RT-PCR using specific primer pairs for RFX4-A, -B, -C, -D, and -E (FIG. 7 and Table 9). The PCR products were analyzed by conventional agarose gel and also capillary electrophoresis on microtip to examine the expression of RFX4 semiquantitatively. The amount of PCR product was expressed as percent of G3PDH expressed in the same tissue. As shown in FIGS. 11A and 11B, in normal tissues, RFX4-A was the most abundantly expressed variant and the expression was 126% and 4.5% of G3PDH in testis and pancreas, respectively. Expression of RFX4-B and -C was restricted to testis and 4.2% and 7.3% of G3PDH, respectively. RFX4-D mRNA was detected only in brain at 3.5%. RFX4-E was expressed very weakly (<1.0%) in brain and testis.

[0348] On the other hand, in astrocytomas, no expression of RFX4-A, -B, and -C was observed (FIG. 12). The expression of RFX4-D and RFX4-E mRNA was observed in some astrocytomas.

[0349] Real-time RT-PCR Analysis of RFX4-D and RFX4-E mRNA Expression in Normal Brains and Astrocytomas

[0350] To investigate the RFX4-D and RFX4-E mRNA expression in normal brains (n=9) and astrocytomas (n=40) quantitatively, we performed real-time RT-PCR. Primer pairs D′ and E were used (FIG. 13 and Table 9). Primer pair D′ was designed to obtain appropriate sized amplified product. Quantity was expressed as n-fold differences in RFX4-D and RFX4-E mRNA expression relative to mean values in 4 normal brains and 5 normal tissues from grade II astrocytoma. As shown in FIGS. 13A and B, overexpression of RFX4-D and RFX4-E mRNA was observed in astrocytomas. In RFX4-D mRNA expression, significant differences were observed between normal brains and grade II astrocytomas (p=0.0028) or grade III and IV astrocytomas (p=0.0086) by Mann-Whitney U test. On the other hand, in RFX4-E mRNA expression, significant difference was observed between normal brain and grade III and IV astrocytomas (p=0.00020), but not grade II astrocytomas (p=0.13). With regard to the expression between grade II astrocyotomas and grade III and IV astrocytomas, significant difference was observed in RFX4-E (p=0.018) but not in RFX4-D (p=0.72).

[0351] The number of tissue samples that expressed RFX4-D and -E MnRNA more than 5 times of the mean value of the normal brain is shown in Table 10.

10TABLE 10RFX4-DRFX4-ENormal brain(4)00Normal tissues (G II)(5)00Astrocytoma G II(12)22Normal tissues (G III-IV)(6)01Astrocytoma G III-IV(28)912

Example 11

[0352] Analysis of AKAP3 Expression in Ovarian Cancer

[0353] Ovarian cancer represents the fifth leading cause of death in cancers for women, and the first in gynecological malignancies (52). Because of difficulties in detection, diagnosis and treatment, overall survival rate of ovarian cancer patient is still poor (53, 54). Therefore, development of diagnostics and therapeutics that overcome those difficulties is necessary.

[0354] AKAPs are a group of structurally diverse proteins that bind to the regulatory subunit of PKA. They localize in discrete sites in a cell and function for PKA to be exposed to cAMP efficiently (55). Recently, it has been demonstrated that AKAP-medicated PKA activation inhibited cell growth in the muscle (56) and T lymphocyte (57, 58). Paclitaxel, docetaxel, and vincrisine, which were shown to damage microtubules, also activate PKA and induce hyperphosphorylation of Bcl-2 caused growth arrest and apoptosis (59, 60). A paclitaxel based regimen of chemotherapy is now commonly used for treatment of postoperative ovarian cancer patients (61, 62).

[0355] In this study, we investigated AKAP3 mRNA expression in normal ovary and ovarian cancer semiquantitatively using capillar electrophoresis on a microtip. AKAP3 is also known as AKAP110, certain properties of which are reported in Example 2 above. A previous study showed that AKAP3 is a sperm protein and that mRNA expression was observed only in testis in normal adult tissues (63). We show herein that high AKAP3 mRNA expression was observed in ovarian cancer and the expression was correlated to histological grade and clinical stage of the tumor. The expression in normal ovary was only marginal. Thus, AKAP3 appears to be a cancer/testis (CT) antigen.

[0356] We also investigated the relation between AKAP3 mRNA expression and prognosis. We show herein that AKAP3 mRNA expression is an independent and favorable prognostic factor in patients with poorly differentiated ovarian cancer.

[0357] Material and Methods

[0358] Patients and Specimens

[0359] The number of patients investigated in this study was 54 and the median age at diagnosis was 54 (range 28 to 83) years old. Clinical and pathological information was documented at the time of surgery. Histological type and grade were determined according to the WHO classification and the standard criteria, respectively. 54 ovarian cancer specimens were obtained surgically under informed consent. Those specimens were 29 (54%) serous, 10 (19%) mucinous, 9 (18%) endometriod, 3 (7%) clear cell tumors. A malignant Brenner, an undifferentiated and an unclassified tumors were classified as others in Table 1. Clinical stage of the tumor was reviewed based on the International Federation of Gynecology and Obstetrics (FIGO) staging system. Tumors investigated were composed of 17 (31%) stage I, 6 (11%) stage II, 27 (50%) stage III, and 5 (9.3%) stage IV. Twenty normal ovarian specimens were obtained from 16 and 4 patients who underwent oophorectomy for myoma uteri and cervical intraepitherial neoplasia, respectively.

[0360] Reverse Transcription-polymerase Chain Reaction (RT-PCR).

[0361] Total RNA was isolated from frozen tumor specimens using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) and RNA was reverse-transcribed into single-stranded cDNA using Moloney murine leukemia virus reverse transcriptase (Ready-To-Go You-Prime First-Strand Beads, Amersham Pharmacia, Piscataway, N.J.), and oligo(dT)15 as a primer. cDNAs were tested for integrity by amplication of G3PDH transcripts in a 30-cycle reaction. Gene specific primers for AKAP3 were as follows: sense, 5′-CTAACTTCGGCCTTCCCAGA-3′(SEQ ID NO: 29); antisense, 5′-AGTGGGGTTGCCGATTACAG-3′ (SEQ ID NO: 30). The amplification program for AKAP3 was: 1 min. at 94° C., 1 min at 60° C. and 1.5 min. at 72° C. for 30 cycles after denature at 94° C. for 1 min. These cycles were followed by a 10 min elongation step at 72° C. PCR products were analyzed by 0.8% agarose gel electrophoresis.

[0362] Semiquantitative PCR Analysis

[0363] The PCR products (460 bp) were analyzed semiquantitatively by capillary electrophoresis on a microtip device (DNA 7500 LabChip, Caliber Technologies, Mountain View, Calif.) by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). The amount of PCR product was expressed as percent G3PDH expressed in the same tissue.

[0364] Nucleotide Sequencing

[0365] The PCR products were cloned into the pCR2.1 vector using an Original TA cloning Kit (Invitrogen, San Diego, Calif.). The nucleotide sequence was determined using an ABI 310 DNa Sequencer (Perkin-Elmer, Foster City, Calif.).

[0366] Statistical Analysis

[0367] AKAP3 mRNA expression level in normal ovaries and tumors was analyzed by the Kruskal-Wallis test. The relation between AKAP mRNA expression and clinical pathological variables was determined by the chi-square test and Fisher's exact test. The impact of various factors on overall and progression-free survival was calculated by the univariate and multivariate Cox proportional hazards regression model. Survival curve was represented using the method of Kaplan-Meier. The log rank test was used to examine the significance of the differences in the survival between groups. The survival analysis was repeated separately for subgoup. A value of P<0.05 was considered statistically significant.

[0368] Results

[0369] AKAP3 mRNA Expression in Normal and Malignant Ovarian Tissues

[0370] Expression of AKAP3 mRNA was analyzed by RT-PCR using a panel of normal and malignant ovarian tissue specimens. Representative results are shown in FIG. 14A. Little or no expression was observed in normal ovaries, low potential malignancies, or well and moderately differentiated ovarian cancers by ethidium bromide staining on agarose gel electrophoresis. On the other hand, AKAP3 mRNA expression was observed in some poorly differentiated ovarian cancers with variable intensity of PCR signal. To determine the AKAP3 mRNA expression semiquantitatively, the PCR product was analyzed by capillary electrophoresis on a microtip device (FIG. 14B). The amount of the PCR product was expressed as percent expression of the G3PDH expressed in the same specimen. As shown in FIG. 15, a range of 0 to 6.0% (median value, 1.1%) AKAP3 mRNA expression was observed in normal ovaries. Similarly, 0 to 6.0% (median value, 1.1%) expression was observed in low potential malignancies (LPM), and 0 to 8.5% (median value, 0%) expression was observed in well and moderately differentiated ovarian cancers. On the other hand, in poorly differentiated ovarian cancers, 0 to 100% (median value, 8.5%) AKAP3 mRNA expression was observed. AKAP3 mRNA expression in poorly differentiated ovarian cancers was significantly higher than that in normal ovaries, low potential malignancies, and well and moderately differentiated ovarian cancers (p=0.013 by Kruskal Wallis test). Difference of the median value was 7 fold.

[0371] Relationship Between AKAP3 mRNA Expression and Other Variables in Ovarian Cancer.

[0372] Based on the marginal AKAP mRNA expression in the normal ovary as described above, its expression higher than 6% of the G2PDH expressed in the same specimen was considered as significantly higher expression in ovarian cancer. Table 11 shows the AKAP3 mRNA expression in ovarian cancer specimens in relation to pathological and clinical features. High AKAP3 mRNA expression was correlated with histological grade. High AKAP3 mRNA expression was observed in significantly higher frequency in poorly differentiated tumors than well and moderately differentiated tumors (p=0.009 by Fisher's exact test). Advanced stage (III and IV) tumors also showed a higher frequency of high AKAP mRNA expression compared with early stage (I and II) tumor (p=0.014 by Fisher's exact test). No correlation was found between AKAP3 mRNA expression and other variables. Histological grade was the only factor to correlate with High AKAP3 mRNA expression in multivariate analysis using logistic regression model (p=0.019).

11TABLE 11Correlation between AKAP3 mRNA expression and pathologicaland clinical features in ovarian cancerHighPathological and clinical featuresAKAP3 expression/tumor examinedAll tumors15/54 (28%)Histological typeserous11/29 (38%)mucinous 0/10 (0%)endometrioid 2/9 (11%)clear cell 0/3 (0%)othersa 2/3 (67%)Histological gradelow potential malignancy 0/9 (0%)well and moderately differentiated 2/19 (11%)poorly differentiated13/26 (50%)FIGO stageearly (I and II) 2/22 (9%)advance (III and IV)13/32 (41%)Peritoneal cytologynegative 3/21 (14%)positive12/33 (36%)Ascites volume (ml)<100011/43 (26%) 1000 4/11 (36%)Residual tumor size (cm) 0 6/29 (21%)1-2 3/7 (43%) >2 6/18 (33%)aA malignant Brenner, an undifferentiated, and an unclassified tumors.

[0373] Survival Analysis in All Patients

[0374] Nine low potential malignancies were excluded from survival analysis because of their favorable prognosis. Of the 45 patients included in this analysis, the median follow up time after initial diagnosis was 27 months (range, 3-75 months) for all patients. The result of univariate survival analysis is shown in Table 12. No correlation was found between AKAP3 mRNA expression and overall or progression-free survival. Histological grade, FIGO stage, and residual tumor size showed a significant association with death and relapse. Peritoneal cytology and ascites volume related with a poor prognosis only in progression-free survival. However, by multivariate Cox proportional hazards regression model, only histological grade and residual tumor size remained significant both in overall and progression-free survival. The Kaplan-Meier survival curve also demonstrated no association of the AKAP3 mRNA expression with overall and progression-free survival (FIG. 16).

12TABLE 12Univariate analysis of prognostic factors in patients with ovarian cancerOverall survivalProgression-free survivalFactorsHRa95% CIbpHRa95% CIbpAKAP3 mRNA0.4750.127-1.7750.2680.8050.314-2.0600.650Age1.0330.984-1.0850.1891.0080.969-1.0500.683Histological typed1.1310.358-3.5700.8331.3610.532-3.4820.520Histological gradee11.3631.443-90.4060.021°5.5201.603-19.0100.0068FIGO stage2.5361.159-5.5520.0192.2961.265-4.1670.0063Peritoneal cytology6.1220.786-47.6960.0834.8421.102-21.2740.0367Ascites volumef2.2200.663-7.4370.1963.1321.203-8.1550.0190Residual tumor sizeg3.0761.354-6.9860.00724.0291.972-8.2320.0001aHazard ratio estimated by Cox proportional hazards regression model. bConfidence interval of the estimated HR. cHigh versus low expression. dSerous versus all other types. ePoorly differentiated versus well and moderately differentiated. fCategorized into massive ascites (>1000 ml) or not. gCategorized into 2, 1-2, and 0 (cm). °Significant p value is underlined.

[0375] Univariate and Multivariate Survival Analysis in Poorly Differentiated Ovarian Cancer.

[0376] Because high AKAP3 mRNA expression was frequently observed in poorly differentiated ovarian cancer (Table 11), survival analysis was performed on patients with poorly differentiated tumors using Cox proportional hazards regression model. As shown in Table 13, high AKAP3 mRNA expression was a strong predictor of overall and progression-free survival by both univariate and multivariate analysis. These results were also demonstrated by the Kaplan-Meier survival curves. As shown in FIG. 17, patients with high AKAP3 mRNA tumors showed more favorable overall and progression-free survival than those with low AKAP3 mRNA tumors. These results suggested that AKAP3 mRNA expression is an independent prognostic factor in patients with poorly differentiated ovarian cancer.

13TABLE 13Univariate and multivariate analysis of prognostic factors inpatients with poorly differentiated ovarian cancerOverall survivalProgression-free survivalFactorsHRa95% CIbpHRa95% CIbpUnivariate analysisAKAP3 mRNA0.0700.009-0.5570.012°0.1850.058-0.5880.0042Age0.9910.932-1.0550.7850.9720.919-1.0280.324Histological typed0.6560.198-2.1810.4911.2780.439-3.7250.652FIGO stage1.3961.159-5.5520.4331.9050.917-3.9550.084Peritoneal cytology1.9500.249-15.2680.5243.0130.391-23.2230.289Residual tumor sizeg1.8570.767-4.4980.1703.1271.317-7.4240.0098Multivariate analysisAKAP3 mRNA0.0300.002-0.5190.0150.0580.009-0.3740.0028Age1.0540.951-1.1700.3161.0200.954-1.0900.562Histological typed0.2920.056-1.5270.1440.7070.192-2.6120.603FIGO stage1.2860.328-5.5010.7181.3790.520-3.6570.518Peritoneal cytology6.2490.120-325.2820.3630.2890.023-3.6950.339Residual tumor sizee2.9180.516-16.4960.2254.7371.389-16.1490.012aHazard ratio estimated by Cox proportional hazards regression model. bConfidence interval of the estimated HR. cHigh versus low expression. dSerous versus all other types. eCategorized into 2, 1-2, and 0 (cm). °Significant p value is underlined.

[0377] Discussion

[0378] In this study, high AKAP3 mRNA expression was observed in 2 of 19 (11%) well and moderately differentiated and 13 of 26 (50%) poorly differentiated ovarian cancers. AKAP3 mRNA expression was correlated with histological grade and clinical stage of the tumor. No or only marginal AKAP3 mRNA expression was observed in 20 normal ovaries and 9 low potential malignancies. Moreover, high AKAP3 mRNA expression was shown to be a significant predictor of overall and progression-free survival and an independent prognostic factor in patients with poorly differentiated ovarian cancer.

[0379] AKAP3 is a sperm protein (63). Analysis of AKAP3 mRNA expression in a variety of normal tissues by Northern blot (63) and RT-PCR revealed that its expression was restricted to testis in adult tissues. AKAP3 mRNA expression was reinvestigated in normal ovary and no expression was confirmed with 20 normal ovaries in conventional ethidium bromide staining in agarose gel electrophoresis after 30-cycle RT-PCR. However, semiquantitative analysis by capillary electrophoresis revealed low level of AKAP3 mRNA expression in the same 20 normal ovaries ranging from 0-6% of G3PDH expressed in the same sample. Subsequent semiquantitative analysis of AKAP3 mRNA expression in ovarian cancers revealed high expression of AKAP3 ranging from 0-100% of G3PDH expressed in the same tissue. Moreover, the expression was correlated with histological grade and also FIGO stage.

[0380] Correlation between the expression of tumor antigens and histological grade and clinical stage has been shown previously. For example, NY-ESO-1 mRNA expression was correlated with histological grade in transitional cell carcinoma (39). A higher frequency of MAGE expression was observed in metastatic melonoma (37). This could result from gene expression randomly occurring as a result of mechanisms such as demethylation, etc., which occurr frequently in malignant cells. Alternatively, it could be due to specific gene expression that was involved in maintaining malignant or metastatic phenotype.

[0381] There have been a few reports studying the relation between tumor antigen expression and patient prognosis. The present study demonstrated that the AKAP3 mRNA expression was a favorable independent prognostic indicator in both overall and progression free survival in poorly differentiated tumors. The finding was confirmed with the threshold of AKAP3 mRNA expression between 5% to 15% with maximal significance (p=0.0009) at 6%. In a similar finding, it was shown previously that HER2/neu expression was correlated with better prognosis in high grade osteosarcoma (64). There are several possibilities for why prognosis was better in the patients with poorly differentiated ovarian cancers with high AKAP3 mRNA expression. Firstly, AKAP3 expressed on the tumor could be immonogenic and stimulate immune response against tumor in the patients. AKAP3 mRNA expression was mostly restricted to testis in normal adult tissues and the expression was only marginal if any in other tissues (data not shown). The finding suggested that AKAP3 belongs to a member of cancer/testis (CT) antigen.

[0382] To address this possibility, antibody production in patient sera is examined using recombinant AKAP3 protein. Furthermore, CD8 and CD4 cell responses against MHC class I and II epitope peptides, respectively, present in AKAP3 molecule is investigated. In addition, the growth inhibitory effect or induction of apoptosis of tumor cells by AKAP3 is investigated.

[0383] In this study, no mutation was observed in full length AKAP3 obtained by PCR from ovarian cancer specimens.

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[0449] Equivalents

[0450] Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. Such equivalents are intended to be encompassed by the following claims.

[0451] All references disclosed herein are incorporated by reference in their entirety.

	Number	Date	Country
	60356937	Feb 2002	US
	60285343	Apr 2001	US

	Number	Date	Country
Parent	PCT/US02/12497	Apr 2002	US
Child	10262666	Oct 2002	US

Cancer-testis antigens

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