Breast cancer antigens

Abstract

The invention provides methods for diagnosing cancer including breast cancer, based on the identification of certain breast cancer-associated polypeptides as antigens that elicit immune responses in breast cancer. The identified antigens can be utilized as markers for diagnosing breast cancer, and for following the course of treatment of breast cancer.

Description

FIELD OF THE INVENTION

[0002] The invention relates to use of novel breast cancer-associated nucleic acid molecules and the polypeptides they encode as markers for cancer, including breast cancer. The invention also relates to the use of a panel of breast cancer-associated nucleic acid molecules and the polypeptides they encode and their use as markers for breast cancer. In addition, the invention relates to the use of such nucleic acid molecules and the polypeptides they encode for diagnosing breast cancer, and monitoring the breast cancer's response to treatment.

BACKGROUND OF THE INVENTION

[0003] Breast cancer is a malignant proliferation of epithelial cells lining the ducts or lobules of the breast (Harrison's Principles of Internal Medicine, 14/e, McGraw-Hill Companies, New York, 1998). Although much progress has been made toward understanding the biological basis of breast cancer and in its diagnosis and treatment, it is still one of the leading causes of death among women in the United States. Inherent difficulties in the diagnosis and treatment of cancer include among other things, the existence of many different subgroups of cancer and the concomitant variation in appropriate treatment strategies to maximize the likelihood of positive patient outcome.

[0004] The traditional method of breast cancer diagnosis and staging is through the use of biopsy examination, for example, histological examination of a tissue sample. Once a diagnosis is made, the treatment options traditionally include surgical intervention, chemotherapy, radiotherapy, and adjuvant systemic therapies. Surgical therapy may be lumpectomy or more extensive mastectomy. Adjuvants may include but are not limited to chemotherapy, radiotherapy, and endocrine therapies such as castration; administration of LHRH agonists, antiestrogens, such as tamoxifen, high-dose progestogens; adrenalectomy; and/or aromatase inhibitors (Harrison's Principles of Internal Medicine, 14/e, McGraw Hill Companies, New York, 1998).

[0005] An accurate diagnostic test for breast cancer is critical to allow patients to receive appropriate cancer treatment when such treatment may be less invasive (e.g. the cancer is smaller) and has a high likelihood of successfully eliminating the cancer. Currently available tests are useful, but may require expensive procedures, such as mammography, followed by surgical biopsy. A less invasive and less expensive diagnostic test for breast cancer would allow better access to diagnostic services for more women, and may increase the likelihood of successful outcome for breast cancer patients.

[0006] Another element of key importance in the successful treatment of breast cancer is the selection and implementation of an appropriate combination of therapeutic approaches. For example, depending on a breast cancer patient's prognosis, therapy may include surgical intervention in combination with adjuvant therapy or it may only include surgical intervention. In addition, for some patients pretreatment with chemotherapy or radiotherapy is utilized prior to surgical intervention, but in other patients adjuvant therapies are used following surgical intervention.

[0007] Determination of appropriate treatment for an individual cancer patient is complex with a wide variety of treatments and possible treatment combinations. For example, chemotherapy is a common method of cancer treatment, with more than 50 different chemotherapeutic agents available. These therapeutic agents can be used in a wide range of dosages both singly and in combinational therapies with other chemotherapeutic agents, surgery, and/or radiotherapy. The available methods for designing strategies for treating breast cancer patients are complex and inexact. Therefore it is important to monitor the impact of the treatment on the cancer. By monitoring the effectiveness of a treatment strategy, the treatment can be modified as necessary to improve the chances for long-term patient survival.

[0008] Because of the importance of selecting appropriate treatment regimens for breast cancer patients, and for following their progress, the development of methods to monitor treatment as well as to sensitively diagnose breast cancer is of key interest to those in the medical community and their patients. Although available diagnostic procedures for breast cancer may be partially successful, the methods for detecting breast cancer and monitoring its treatment remain unsatisfactory. There is a critical need for diagnostic tests that can detect breast cancer at its early stages, when appropriate treatment may substantially increase the likelihood of positive outcome for the patient. It is also important that breast cancer treatment be monitored to allow the treatment to be adapted as necessary to best serve the patient's clinical needs. Such diagnostic and monitoring methods will enable medical care professionals to identify breast cancer, select optimal treatment regimens for individual patients, and to assess the cancer before, during, and after treatment.

SUMMARY OF THE INVENTION

[0009] The invention provides methods for diagnosing breast cancer based on the identification of certain breast cancer-associated polypeptides and the encoding nucleic acid molecules that encode the polypeptides. The polypeptides or fragments thereof, are, antigens that elicit immune responses in breast cancer. The identified antigens and/or the nucleic acid molecules that encode them can be utilized as markers for diagnosing breast cancer, for following the course of treatment of breast cancer, and for assessing breast cancer treatments.

[0010] According to one aspect of the invention, method for diagnosing breast cancer in a subject are provided. The methods include obtaining a biological sample from a subject, contacting the sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, and determining specific binding between the breast cancer-associated polypeptides and agents in the sample, wherein the presence of specific binding is diagnostic for breast cancer in the subject. In some embodiments, the biological sample is contacted with at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the methods further include contacting the biological sample with a breast cancer-associated polypeptide other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0011] According to yet another aspect of the invention, methods for determining onset, progression, or regression, of breast cancer in a subject are provided. The methods include obtaining from a subject a first biological sample, contacting the first sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81, and determining specific binding between agents in the first sample and the at least two different breast cancer-associated polypeptides. The methods also include obtaining from the subject a second biological sample, contacting the second biological sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between agents in the second sample and the at least two different breast cancer-associated polypeptides, and comparing the determination of binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of the breast cancer. In some embodiments, binding is determined between the agents and at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the methods also include determining binding between the agents and a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0012] According to another aspect of the invention, methods for selecting a course of treatment of a subject having or suspected of having breast cancer are provided. The methods include obtaining from the subject a biological sample, contacting the sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81, determining specific binding between agents in the sample that are differentially expressed in different types of cancer, and the breast cancer-associated polypeptides, and selecting a course of treatment appropriate to the cancer of the subject. In some embodiments, the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptides. In certain embodiments, the antibodies are labeled with one or more cytotoxic agents. In come embodiments, the sample is contacted with at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments the methods also include contacting the sample with a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81.

[0013] According to another aspect of the invention, methods for diagnosing cancer in a subject are provided. The methods include obtaining a biological sample from a subject, contacting the sample with a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:19, 20, 21, 22, 23, 24, 33, 36, 39, and 81 and determining specific binding between the breast cancer-associated polypeptide and agents in the sample, wherein the presence of specific binding is diagnostic for cancer in the subject. In some embodiments, the cancer is breast cancer.

[0014] According to another aspect of the invention, methods for determining onset, progression, or regression, of cancer in a subject are provided. The methods include obtaining from a subject a first biological sample, contacting the first sample with a breast cancer associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81 determining specific binding between agents in the first sample and the breast cancer-associated, obtaining from a subject a second biological sample, contacting the second sample with a breast cancer associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between agents in the second sample and the breast cancer-associated polypeptide, and comparing the determination of binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of cancer. In some embodiments, the cancer is breast cancer.

[0015] According to another aspect of the invention, methods for selecting a course of treatment of a subject having or suspected of having cancer are provided. The methods include obtaining from the subject a biological sample, contacting the sample with a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between agents in the sample that are differentially expressed in different types of cancer, and the breast cancer-associated polypeptide, and selecting a course of treatment appropriate to the cancer of the subject. In some embodiments, the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptide. In certain embodiments, the antibodies are labeled with one or more cytotoxic agents. In some embodiments, the cancer is breast cancer.

[0016] In some embodiments of the foregoing methods, the sample is blood. In other embodiments of the foregoing methods, the sample is lymph node fluid or breast discharge fluid. In some embodiments of the forgoing methods, the agents are antibodies or antigen-binding fragments thereof.

[0017] According to another aspect of the invention, methods for diagnosing breast cancer in a subject are provided. The methods include obtaining a biological sample from a subject, contacting the sample with antibodies or antigen-binding fragments thereof, that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, and determining specific binding between the antibodies or antigen-binding fragments thereof and breast cancer-associated polypeptides in the sample, wherein the presence of specific binding is diagnostic for breast cancer in the subject. In some w embodiments, the biological sample is contacted with antibodies or antigen-binding fragments thereof, that bind specifically to at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the methods also include contacting the biological sample with an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0018] According to another aspect of the invention, methods for determining onset, progression, or regression, of breast cancer in a subject are provided. The methods include obtaining from a subject a first biological sample, contacting the first sample with antibodies or antigen-binding fragments thereof, that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between breast cancer-associated polypeptides in the first sample and the antibodies or antigen-binding fragments thereof. The methods also include obtaining from the subject a second biological sample, contacting the second sample with antibodies or antigen-binding fragments thereof, that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between breast cancer-associated polypeptides in the second sample and the antibodies or antigen-binding fragments thereof, and comparing the determination of specific binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of breast cancer. In some embodiments, binding is determined between the breast cancer-associated polypeptides and antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the methods also include determining binding between the breast cancer-associated polypeptide and an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0019] According to yet another aspect of the invention methods for selecting a course of treatment of a subject having or suspected of having breast cancer are provided. The methods include obtaining from the subject a biological sample, contacting the sample with antibodies or antigen-binding fragments thereof that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between breast cancer-associated polypeptides in the sample that are differentially expressed in different types of cancer, and the antibodies or antigen-binding fragments thereof, and selecting a course of treatment appropriate to the cancer of the subject.

[0020] In some embodiments, the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptides. In certain embodiments, the antibodies are labeled with one or more cytotoxic agents. In some embodiments, the sample is contacted with antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the methods also include contacting the sample with an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81.

[0021] According to yet another aspect of the invention, methods for diagnosing cancer in a subject are provided. The methods include obtaining a biological sample from a subject, contacting the sample with an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, and determining specific binding between the antibody or antigen-binding fragment thereof and the breast cancer-associated polypeptide in the sample, wherein the presence of specific binding is diagnostic for cancer in the subject. In some embodiments, the cancer is breast cancer.

[0022] According to another aspect of the invention, methods for determining onset, progression, or regression, of cancer in a subject, are provided. The methods include obtaining from a subject a first biological sample, contacting the first sample with antibodies or antigen-binding fragments thereof, that bind specifically to a breast cancer-associated polypeptides encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81 determining specific binding between breast cancer-associated polypeptides in the first sample and the antibodies or antigen-fragments thereof, obtaining from a subject a second biological sample, contacting the second sample with antibodies or antigen-binding fragments thereof, that bind specifically to a breast cancer-associated polypeptides encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between breast cancer-associated polypeptides in the second sample and the antibodies or antigen-binding fragments thereof, and comparing the determination of specific binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of cancer. In some embodiments, the cancer is breast cancer.

[0023] According to yet another aspect of the invention, methods for selecting a course of treatment of a subject having or suspected of having cancer are provided. The methods include obtaining from the subject a biological sample, contacting the sample with antibodies or antigen-binding fragments thereof that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between breast cancer-associated polypeptides in the sample that are differentially expressed in different types of cancer, and the antibodies or antigen-binding fragments thereof, and selecting a course of treatment appropriate to the cancer of the subject. In some embodiments, the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptide. In certain embodiments, the antibodies are labeled with one or more cytotoxic agents. In some embodiments, the cancer is breast cancer.

[0024] In some embodiments of the foregoing methods, the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid. In certain embodiments of the foregoing methods, the tissue is breast tissue. In other embodiments the tissue is lymph node tissue. In other embodiments of the foregoing methods, the cells are from lymph node fluid or breast discharge fluid. In some embodiments of the foregoing methods, the antibodies are monoclonal or polyclonal antibodies. In some embodiments of the foregoing methods, the antibodies are chimeric, human, or humanized antibodies. In certain embodiments, the antibodies are single chain antibodies. In some embodiments of the foregoing methods, the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

[0025] According to another aspect of the invention, kits for the diagnosis of breast cancer in a subject are provided. The kits include at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 1-40, and 81, one or more control antigens, and instructions for the use of the polypeptides in the diagnosis of breast cancer. In some embodiments, the breast cancer-associated polypeptides are bound to a substrate. In certain embodiments, the one or more agents are antibodies or antigen-binding fragments thereof. In some embodiments, the kit comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the kits also include a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0026] According to yet another aspect of the invention, kits for the diagnosis of breast cancer in a subject are provided. The kits include antibodies or antigen-binding fragments thereof that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81, one or more control agents, and instructions for the use of the agents in the diagnosis of breast cancer. In some embodiments, the one or more agents are antibodies or antigen-binding fragments thereof. In some embodiments, the one or more agents are bound to a substrate. In some embodiments, the kit comprises antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments the kits also include an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0027] According to another aspect of the invention, protein microarrays are provided. The protein microarrays include at least two different breast cancer-associated polypeptides, wherein the breast cancer-associated polypeptides are encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 1-40, and 81, fixed to a solid substrate. In some embodiments, the microarray comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments the protein microarray also includes a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81. In some embodiments, the protein microarray includes at least one control polypeptide molecule.

[0028] According to yet another aspect of the invention, protein microarrays are provided. The protein microarrays include antibodies or antigen-binding fragments thereof, that specifically bind at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs:1-40, and 81, fixed to a solid substrate. In some embodiments, the microarray comprises antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81. In certain embodiments, the microarray also includes an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In some embodiments, the protein microarray also includes at least one control polypeptide molecule. In some embodiments, the antibodies are monoclonal or polyclonal antibodies. In other embodiments, the antibodies are chimeric, human, or humanized antibodies. In some embodiments, the antibodies are single chain antibodies. In some embodiments, the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

[0029] According to yet another aspect of the invention, nucleic acid microarrays are provided. The nucleic acid microarrays include at least two nucleic acids selected from the group consisting of SEQ ID NOs:1-40, and 81, fixed to a solid substrate. In some embodiments, the microarray comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81. In certain embodiments, the nucleic acid microarray also includes a nucleic acid molecule other than those selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the nucleic acid microarray also includes at least one control nucleic acid molecule.

[0030] According to another aspect of the invention, methods for diagnosing breast cancer in a subject are provided. The methods include obtaining from the subject a biological sample, and determining the expression of at least two breast cancer-associated nucleic acid molecules or expression products thereof in the sample, wherein the nucleic acid molecules comprise a nucleotide sequence selected from the group consisting of: SEQ ID NO: 1-40, and 81, wherein the expression is diagnosis of the breast cancer in the subject. In some embodiments, expression is determined for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,36,37,38,39, or 40 nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments the method also includes determining expression of a breast cancer-associated nucleic acid molecule other than those comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In some embodiments, the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid. In some embodiments, the tissue is breast tissue. In other embodiment, the tissue is lymph node tissue. In some embodiments, the cells are from lymph node fluid or breast discharge fluid. In some embodiments, the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. In certain embodiments, the hybridization is performed using a nucleic acid microarray.

[0031] According to another aspect of the invention, methods for determining onset, progression, or regression, of breast cancer in a subject are provided. The methods include obtaining from a subject a first biological sample, determining a level of expression of at least two breast cancer-associated nucleic acid molecules or expression products thereof in the first sample, wherein the nucleic acid molecules are selected from the group consisting of: SEQ ID NOs: 1-40, and 81, obtaining from the subject a second biological sample, determining a level of expression of at least two breast cancer-associated nucleic acid molecules or expression products thereof in the second sample, wherein the nucleic acid molecules are selected from the group consisting of: SEQ ID NOs: 1-40, and 81, and comparing the level of expression in the first sample to the level of expression in the second sample as a determination of the onset, progression, or regression of the breast cancer. In some embodiments, expression is determined for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleic acid molecules selected from the group consisting of SEQ ID NOs:1-40, and 81. In certain embodiments, the method also includes determining expression for a breast cancer-associated nucleic acid molecule other than those comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81. In some embodiments, the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood and breast discharge fluid. In some embodiments, the tissue is breast tissue. In other embodiments, the tissue is lymph node tissue. In some embodiments, the cells are from lymph node fluid or breast discharge fluid. In some embodiments, the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. In certain embodiments, the hybridization is performed using a nucleic acid microarray.

[0032] According to another aspect of the invention, kits for the diagnosis of cancer in a subject are provided. The kits include a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39; and 81, one or more control antigens; and instructions for the use of the polypeptide and control antigens in the diagnosis of cancer. In some embodiments, the breast cancer-associated polypeptide is bound to a substrate. In certain embodiments, the one or more agents are antibodies or antigen-binding fragments thereof. In some embodiments the cancer is breast cancer.

[0033] According to another aspect of the invention, kits for the diagnosis of cancer in a subject are provided. The kits include antibodies or antigen-binding fragments thereof that bind specifically to a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81 one or more control agents; and instructions for the use of the antibodies, antigen-binding fragments, and agents in the diagnosis of cancer. In some embodiments, the one or more agents are antibodies or antigen-binding fragments thereof. In certain embodiments the one or more agents are bound to a substrate. In some embodiments, the cancer is breast cancer.

[0034] According to yet another aspect of the invention, protein microarrays are provided. The protein microarrays include a breast cancer-associated polypeptide, wherein the breast cancer-associated polypeptide is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, fixed to a solid substrate. In some embodiments, the protein microarray also includes at least one control polypeptide molecule.

[0035] According to another aspect of the invention, protein microarrays are provided. The protein microarrays include antibodies or antigen-binding fragments thereof, that specifically bind a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, fixed to a solid substrate. In some embodiments, the protein microarray also includes at least one control polypeptide molecule. In certain embodiments, the antibodies are monoclonal or polyclonal antibodies. In some embodiments, the antibodies are chimeric, human, or humanized antibodies. In certain embodiments, the antibodies are single chain antibodies. In some embodiments, the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

[0036] According to another aspect of the invention, nucleic acid microarrays are provided. The nucleic acid microarrays include a nucleic acid selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, fixed to a solid substrate. In some embodiments, the nucleic acid microarray also includes at least one control nucleic acid molecule.

[0037] According to another aspect of the invention, methods for diagnosing cancer in a subject are provided. The methods include obtaining from the subject a biological sample, and determining the expression of a breast cancer-associated nucleic acid molecule or expression product thereof in the sample, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: SEQ ID NO: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, wherein the expression is diagnostic of cancer in the subject. In some embodiments, the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid. In certain embodiments, the tissue is breast tissue. In other embodiments, the tissue is lymph node tissue. In some embodiments, the tissue is cells from lymph node fluid or breast discharge fluid. In some embodiments, the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. In certain embodiments, the hybridization is performed using a nucleic acid microarray. In some embodiments, the cancer is breast cancer.

[0038] According to yet another aspect of the invention, methods for determining onset, progression, or regression, of cancer in a subject are provided. The methods include obtaining from a subject a first biological sample, determining a level of expression of a breast cancer-associated nucleic acid molecule or expression products thereof in the first sample, wherein the nucleic acid molecule is selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, obtaining from the subject a second biological sample, determining a level of expression of a breast cancer-associated nucleic acid molecule or expression product thereof in the second sample, wherein the nucleic acid molecule is selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, and comparing the level of expression in the first sample to the level of expression in the second sample as a determination of the onset, progression, or regression of the cancer. In some embodiments, the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid. In certain embodiments, the tissue is breast tissue. In some embodiments, the tissue is lymph node tissue. In other embodiments, the tissue is cells from lymph node fluid or breast discharge fluid. In some embodiments, the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. In certain embodiments, the hybridization is performed using a nucleic acid microarray. In some embodiments, the cancer is breast cancer.

[0039] In preferred embodiments of the foregoing methods and compositions, the breast cancer-associated antigens encoded by SEQ ID NOs:1-40, and 81 are polypeptides comprising, respectively, the amino acid sequences set forth in SEQ ID NOs:41-80, and 82, or fragments thereof containing an epitope amino acid sequence.

[0040] In certain embodiments of the foregoing methods and compositions, nucleic acid molecules that are fragments of SEQ ID NOs:1-40, and 81, are included. Preferred fragments are those that encode fragments of SEQ ID NOs:41-80, and 82 that include epitopes. Certain preferred fragments include 20 or more contiguous nucleotides of SEQ ID NOs:1-40, and 81 more preferably 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 400, 500, or more contiguous nucleotides.

[0041] According to another aspect of the invention, methods for diagnosing cancer in a subject are provided. The methods include obtaining a non-testis biological sample from a subject, determining the level of expression of one or more cancer-associated nucleic acid molecule comprising a nucleotide sequences selected from the group consisting of SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81, comparing the level of expression of the nucleic acid molecule in the subject sample to a level of expression of the nucleic acid molecule in a control tissue, wherein a determination that the level of expression of the nucleic acid in the sample from the subject is greater than about three times the level of expression of the nucleic acid in the control tissue, indicates cancer in the subject. In some embodiments, the level of expression of the nucleic acid in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue. In certain embodiments, expression is determined for at least 2, 3, 4, 5, 6, or 7 nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81. In some embodiments, the sample is selected from the group consisting of: tissue and cells. In some embodiments, the cancer is breast cancer. In certain embodiments, the tissue is breast tissue. In some embodiments, the expression of cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. In some embodiments, the hybridization is performed using a nucleic acid microarray. In other embodiments, the nucleic acid amplification is real-time RT-PCR or RT-PCR.

[0042] According to yet another aspect of the invention, methods for determining onset, progression, or regression, of cancer in a subject are provided. The methods include obtaining from a subject a first and a second biological sample, wherein the samples comprise the same tissue type and are obtained at different times, determining a level of expression of one or more cancer-associated nucleic acid molecules or expression products thereof in the first and second biological samples, wherein the nucleic acid molecules comprise nucleotide sequences selected from the group consisting of: SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81, comparing the level of expression of one or more cancer-associated nucleic acid molecules in the first and the second biological samples to the level of expression of the one or more cancer-associated nucleic acid molecules in a control sample, wherein a higher level of expression of the one or more cancer-associated nucleic acid molecules in the first sample than in the second sample indicates regression of cancer, wherein a lower level of expression of the one or more cancer-associated nucleic acid molecules in the first sample than the second sample indicates progression of cancer, and wherein a level of expression of the cancer-associated nucleic acid molecule in the first sample that is less than three times higher than the level of expression of the cancer-associated nucleic acid molecule in the control sample and a level of expression of the cancer-associated nucleic acid molecules in the second sample that is three or more times higher than the level in the control sample, indicates onset of cancer. In some embodiments the level of expression of the one or more nucleic acid molecules in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue. In certain embodiments, expression is determined for at least 2, 3, 4, 5, 6, or 7 nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81. In some embodiments, the sample is selected from the group consisting of: tissue and cells. In certain embodiments, the cancer is breast cancer. In some embodiments, the tissue is breast tissue.

[0043] According to another aspect of the invention, methods for diagnosing cancer in a subject are provided. The methods include obtaining a biological sample from a subject, determining the level of expression of a cancer-associated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 33 and 81, and comparing the level of expression of the nucleic acid molecule in the subject sample to a level of expression of the nucleic acid in a control tissue, wherein a determination that the level of expression of the nucleic acid in the sample from the subject is greater than about three times of the level of expression of the nucleic acid in the control tissue, indicates cancer in the subject. In some embodiments, the level of expression of the nucleic acid in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue. In certain embodiments, the sample is selected from the group consisting of: tissue and cells. In some embodiments, the cancer is colon cancer. In some embodiments, the tissue is colorectal tissue. In some embodiments, the expression of cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification. In certain embodiments, the hybridization is performed using a nucleic acid microarray. In other embodiments, the nucleic acid amplification is real-time RT-PCR or RT-PCR.

[0044] According to yet another aspect of the invention, methods for determining onset, progression, or regression, of cancer in a subject are provided. The methods include obtaining from a subject a first and a second biological sample, wherein the samples comprise the same tissue type and are obtained at different times, determining a level of expression of a cancer-associated nucleic acid molecule or expression product thereof in the first and second biological samples, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 33 and 81, and comparing the level of expression of the cancer-associated nucleic acid molecule of the first and the second biological samples to the level of expression of the cancer-associated nucleic acid molecule in a control sample, wherein a higher level of expression of the cancer-associated nucleic acid molecule in the first sample than in the second sample indicates regression of cancer, wherein a lower level of expression of the cancer-associated nucleic acid molecule in the first sample than the second sample indicates progression of cancer, and wherein a level of expression of the cancer-associated nucleic acid molecule in the first sample that is less than three times higher than the level of expression of the cancer-associated nucleic acid molecule in the control sample, and a level of expression of the cancer-associated nucleic acid molecules in the second sample that is three or more times higher than the level in the control sample, indicates onset of cancer. In some embodiments, the level of expression of the one or more nucleic acid molecules in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue. In certain embodiments, the sample is selected from the group consisting of: tissue and cells. In some embodiments, the cancer is colon cancer. In some embodiments, the tissue is colorectal tissue.

[0045] The use of the foregoing nucleic acid molecules and polypeptides in the preparation of medicaments also is embraced by the invention. In preferred embodiments, the medicaments are useful in the treatment of cancer, and particularly breast cancer.

BRIEF DESCRIPTION OF THE DRAWINGS

[0046] FIG. 1 shows mRNA expression pattern of three antigens associated with a breast cancer-related serological response. FIG. 1A shows real-time analysis of the level of NY-BR-41 mRNA expression (femtograms (fg) of homologous cDNA±S.E.M.). FIG. 1B shows real-time analysis of the level of mRNA encoding NY-BR-62 showing low-level ubiquitous expression (±S.E.M.). FIG. 1C shows real-time analysis of the level of mRNA encoding NY-BR-85 showing low-level ubiquitous expression (±S.E.M).

DETAILED DESCRIPTION OF THE INVENTION

[0047] The invention described herein relates to the identification of polypeptides that elicit specific immune responses in subjects with cancer, particularly breast cancer. Breast cancer-associated polypeptides have been identified through SEREX screening of patients with cancer. The SEREX method (serological analysis of antigens by recombinant expression cloning), has been described by Sahin et al. (Proc. Natl. Acad. Sci. USA 92:11810-11813, 1995). The newly identified breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof may be used as markers for cancer, including breast cancer, and may be used in the diagnosis and treatment assessment of breast cancer in humans. In addition, sets of at least two breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof, may be used as markers in the diagnosis and treatment assessment of breast cancer in humans.

[0048] Polypeptides that elicit specific immune responses in breast cancer have now been identified and this identification allows use of these newly identified breast cancer-associated polypeptides or the encoding nucleic acids molecules thereof in cancer diagnostic assays and kits. In addition, sets of at least two of these new or previously identified polypeptides or the encoding nucleic acid molecules thereof, may be used in breast cancer diagnostic assays and kits. Such assays and kits are useful to detect breast cancer in human subjects, and for staging the progression, regression, or onset of breast cancer in subjects. The methods and kits described herein may also be used to evaluate treatments for breast cancer.

[0049] As used herein, “breast cancer-associated polypeptides” means polypeptides that elicit specific immune responses in animals having breast cancer and thus, include breast cancer-associated antigens and fragments of breast cancer-associated antigens, that are recognized by the immune system (e.g., by antibodies and/or T lymphocytes). The invention also relates to the use of the nucleic acid molecules that encode the breast cancer-associated polypeptides. In all embodiments, human breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof, are preferred. As used herein, the “encoding nucleic acid molecules thereof” means the nucleic acid molecules that code for the polypeptides.

[0050] As used herein, a subject is preferably a human, non-human primate, cow, horse, pig, sheep, goat, dog, cat, or rodent. In all embodiments, human subjects are preferred. In some embodiments, the subject is suspected of having cancer and in preferred embodiments the subject is suspected of having breast cancer. In some embodiments the subject has been diagnosed with cancer, and in preferred embodiments the subject has been diagnosed with breast cancer.

[0051] As used herein, “different types” of cancer may include different histological types, different tumor types (e.g., invasive ductal carcinoma, invasive pleomorphic lobular carcinoma), different cell types, and different stages of cancer (e.g., primary tumor or metastatic growth).

[0052] Methods for identifying subjects suspected of having breast cancer may include but are not limited to: manual examination, biopsy, subject's family medical history, subject's medical history, or a number of imaging technologies such as mammography, magnetic resonance imaging, magnetic resonance spectroscopy, or positron emission tomography. Diagnostic methods for breast cancer and the clinical delineation of breast cancer diagnoses are well-known to those of skill in the medical arts.

[0053] As used herein, a biological sample includes, but is not limited to: tissue, cells, or body fluid (e.g. blood, lymph node fluid, or nipple discharge fluid). The fluid sample may include cells and/or fluid. The tissue and cells may be obtained from a subject or may be grown in culture (e.g. from a cell line).

[0054] As used herein, a biological sample is tissue or cells obtained (e.g., from a breast tissue biopsy or aspiration) using methods well-known to those of ordinary skill in the related medical arts. In some embodiments, the tissue is breast tissue, in other embodiments, the tissue is colorectal tissue. The phrase “suspected of being cancerous” as used herein means a breast cancer tissue sample believed by one of ordinary skill in the medical arts to contain cancerous cells. Methods for obtaining the sample from the biopsy include gross apportioning of a mass, microdissection, laser-based microdissection, or other art-known cell-separation methods.

[0055] Because of the variability of the cell types in diseased-tissue biopsy material, and the variability in sensitivity of the diagnostic methods used, the sample size required for analysis may range from 1, 10, 50, 100, 200, 300, 500, 1000, 5000, 10,000, to 50,000 or more cells. The appropriate sample size may be determined based on the cellular composition and condition of the biopsy and the standard preparative steps for this determination and subsequent isolation of the nucleic acid for use in the invention are well known to one of ordinary skill in the art. An example of this, although not intended to be limiting, is that in some instances a sample from the biopsy may be sufficient for assessment of RNA expression without amplification, but in other instances the lack of suitable cells in a small biopsy region may require use of RNA conversion and/or amplification methods or other methods to enhance resolution of the nucleic acid molecules. Such methods, which allow use of limited biopsy materials, are well known to those of ordinary skill in the art and include, but are not limited to: direct RNA amplification, reverse transcription of RNA to cDNA, amplification of cDNA, or the generation of radio-labeled nucleic acids.

[0056] In some embodiments, the breast cancer-associated nucleic acid molecules from the group of nucleic acid sequences numbered 1 through 40, and 81 in Table 8 (SEQ ID NOs: 1-40, and 81) and the breast cancer-associated polypeptides encoded by SEQ ID NOs: 1-40, and 81, are the group of polypeptide sequences SEQ ID NOs: 41 through 80 and 82 in Table 8. In some embodiments, breast cancer-associated polypeptides may include polypeptides other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

[0057] The level of expression of some cancer-associated nucleic acid molecules or cancer-associated polypeptide molecules of the invention can be used to diagnose cancer (e.g. breast cancer or colon cancer) in a subject. In these tissues a determination of the level of expression of the cancer-associated nucleic acids and/or polypeptides 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. For example, the baseline level of a cancer-associated molecule used in the diagnosis of breast cancer, would be the level of expression of that cancer-associated molecule in normal breast control tissue and the baseline level of a cancer-associated molecule used in the diagnosis of colon cancer, would be the level of expression of that cancer-associated molecule in normal colorectal control tissue. The level of expression of a cancer-associated molecule in a tissue sample from a subject can be compared to the baseline level of expression of the cancer associated molecules in control tissue samples as a determination and diagnosis of cancer in the subject.

[0058] In some cases, levels of expression of one or more cancer-associated molecules that are preferably about three or more times higher than the level of expression of those cancer-associated molecules in a normal control tissue indicates cancer in the tissue. In other cases, e.g. BR-41 (SEQ ID NO: 27) a lower level of expression (preferably less than about 20% of the control level), of a cancer-associated molecule in a subject tissue sample as compared to the level in a normal control tissue indicates breast cancer in that patient sample. Thus, in some tissues there is a baseline level of expression of a cancer-associated molecule of the invention, and it is that baseline level that determines the level above (or below) which expression indicates cancer in the tissue. Therefore, as described herein, in some tissues, the level of expression of the nucleic acid molecules of the invention or the polypeptides they encode indicate cancer in the tissue when the level of expression of the nucleic acid molecule is greater than about three times the level in a control tissue sample of that type of tissue. A level of nucleic acid expression of greater than 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 24, 30, 40, 50 or more times the level of nucleic acid expression in the control tissue indicates cancer in the tissue.

[0059] The invention involves in some aspects diagnosing or monitoring cancer by determining the level of expression of one or more cancer-associated nucleic acid molecules and/or determining the level of expression of one or more cancer-associated 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 cancer-associated nucleic acid molecules or for the level of expression of one or more cancer-associated polypeptides encoded by the nucleic acid molecules of the invention.

[0060] 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.

[0061] 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.

[0062] The invention involves in some embodiments, diagnosing or monitoring breast cancer in subjects by determining the presence of an immune response to at least two breast cancer-associated polypeptides. In some embodiments, cancer, such as breast cancer, in subjects may be diagnosed or monitored by determining the presence of an immune response to one of the novel breast cancer-associated polypeptides described herein. In preferred embodiments, this determination is performed by assaying a bodily fluid obtained from the subject, preferably blood, lymph node fluid, or breast discharge fluid, for the presence of antibodies against at least two breast cancer-associated polypeptides or the nucleic acid molecules that encode the cancer-associated polypeptides, or for the presence of antibodies against one of the novel breast cancer-associated polypeptides or the encoding nucleic acid molecules thereof as described herein. This determination may also be performed by assaying a tissue or cells from the subject for the presence of at least two breast cancer-associated polypeptides and/or the encoding nucleic acid molecules thereof, or assaying a tissue or cells from the subject for the presence of one of the novel breast cancer-associated polypeptides or the encoding nucleic acid molecules thereof as described herein.

[0063] Measurement of the immune response against one of the novel breast cancer-associated polypeptides described herein, or at least two breast cancer-associated polypeptides in a subject 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 blood, lymph node fluid, or breast discharge fluid, may be obtained from a subject, tested for an immune response to one of the novel breast cancer-associated polypeptides or may be tested for an immune response to at least two breast cancer-associated polypeptides and at a second, subsequent time, another sample, such as blood, may be obtained from the subject and similarly tested. The results of the first and second (subsequent) tests can be compared as a measure of the onset, regression or progression of breast cancer, or, if breast-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.

[0064] The invention also involves in some embodiments diagnosing or monitoring breast cancer by determining the presence of at least two breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof, or by determining the presence of one of the novel breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof as described herein. In some important embodiments, this determination is performed by assaying a tissue sample from subject, preferably one believed to be cancerous, for the presence of at least two breast cancer-associated polypeptides or the encoding nucleic acid molecules thereof, or for the presence of one of the novel breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof as described herein.

[0065] In all embodiments, treatment for breast cancer may include, but is not limited to: surgical intervention, chemotherapy, radiotherapy, and adjuvant systemic therapies. In a preferred embodiment, treatment may include administering antibodies that specifically bind to the breast cancer-associated antigen. Optionally, an antibody can be linked to one or more detectable markers, antitumor agents or immunomodulators. 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.

[0066] The cytotoxic radionuclide or radiotherapeutic isotope may be an alpha-emitting isotope such as 225Ac, 211At, 212Bi, or 213Bi. Alternatively, the cytotoxic radionuclide may be a beta-emitting isotope such as 186Rh, 188Rh, 90Y, 131I or 67Cu. Further, the cytotoxic radionuclide may emit Auger and low energy electrons such as the isotopes 125I, 123I or 77Br.

[0067] Suitable chemical toxins or chemotherapeutic agents include members of the enediyne family of molecules, such as chalicheamicin 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-fluorouaracil. Other chemotherapeutic agents are known to those skilled in the art.

[0068] Agents that act on the tumor neovasculature can include tubulin-binding agents such as combrestatin A4 (Griggs et al., Lancet Oncol. 2:82, 2001) and angiostatin and endostatin (reviewed in Rosen, Oncologist 5:20, 2000, incorporated by reference herein). Immunomodulators may also be conjugated to breast cancer-associated antibodies.

[0069] The invention thus involves in one aspect, breast cancer-associated polypeptides, genes encoding those polypeptides, functional modifications and variants of the foregoing, useful fragments of the foregoing, as well as diagnostics relating thereto, and diagnostic uses thereof. In some embodiments, the breast cancer-associated polypeptide genes correspond to SEQ ID NOs: 1-40, and 81. Encoded polypeptides (e.g., proteins), peptides and antisera thereto are also preferred for diagnosis and correspond to SEQ ID NOs: 41-80, and 82. In some embodiments, the method or kit may include breast cancer-associated polypeptide genes in addition to those corresponding to SEQ ID NOs. 1-40, and 81 and the encoded polypeptides (e.g. proteins), peptides, and antisera thereto in addition to those corresponding to SEQ ID NOs:41-80, and 82.

[0070] Some of the amino acid sequences identified by SEREX as breast cancer-associated polypeptides, and the nucleotide sequences encoding them, are newly identified and some are sequences deposited in databases such as GenBank. The use of the newly identified sequences in diagnostic assays for cancer is novel, as is the use of sets of at least two of the sequences in breast cancer diagnostic assays and kits. Homologs and alleles of the breast cancer-associated polypeptide nucleic acids of the invention can be identified by conventional techniques. Thus, an aspect of the invention is those nucleic acid sequences that code for breast cancer-associated antigens and antigenic fragments thereof. As used herein, a homolog to a breast cancer-associated polypeptide is a polypeptide from a human or other animal that has a high degree of structural similarity to the identified breast cancer-associated polypeptides.

[0071] Identification of human and other organism homologs of breast cancer-associated polypeptides will be familiar to those of skill in the art. In general, nucleic acid hybridization is a suitable method for identification of homologous sequences of another species (e.g., human, cow, sheep), which correspond to a known sequence. Standard nucleic acid hybridization procedures can be used to identify related nucleic acid sequences of selected percent identity. For example, one can construct a library of cDNAs reverse transcribed from the mRNA of a selected tissue (e.g., breast) and use the nucleic acids that encode breast cancer-associated polypeptide identified herein to screen the library for related nucleotide sequences. The screening preferably is performed using high-stringency conditions to identify those sequences that are closely related by sequence identity. Nucleic acids so identified can be translated into polypeptides and the polypeptides can be tested for activity.

[0072] The term “high stringency” as used herein refers to parameters with which the art is familiar. Nucleic acid hybridization parameters may be found in references that 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, high-stringency 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, 2.5 mM NaH2PO4(pH 7), 0.5% SDS, 2 mM EDTA). SSC is 0.15M sodium chloride/0.015M sodium citrate, pH 7; 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.

[0073] There are other conditions, reagents, and so forth that 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 breast cancer-associated polypeptide 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.

[0074] In general, homologs and alleles typically will share at least 90% nucleotide identity and/or at least 95% amino acid identity to the sequences of breast cancer-associated antigen, antigenic fragment thereof, and antigen precursor thereof nucleic acid and polypeptides, respectively, in some instances will share at least 95% nucleotide identity and/or at least 97% amino acid identity, and in other instances will share at least 97% 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. Exemplary tools include the BLAST system available from the website of the National Center for Biotechnology Information (NCBI) at the National Institutes of Health. 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.

[0075] In screening for breast cancer-associated polypeptide genes, a Southern blot may be performed using the foregoing conditions, together with a detectably labeled probe (e.g. radioactive or chemiluminescent probes). After washing the membrane to which the DNA is finally transferred, the membrane can be placed against X-ray film or a phosphorimager to detect the radioactive or chemiluminescent signal. In screening for the expression of breast cancer-associated polypeptide nucleic acids, Northern blot hybridizations using the foregoing conditions can be performed on samples taken from breast cancer patients or subjects suspected of having a condition characterized by abnormal cell proliferation or neoplasia of the breast of lymph node tissues. Amplification protocols such as polymerase chain reaction using primers that hybridize to the sequences presented also can be used for detection of the breast cancer-associated polypeptide genes or expression thereof.

[0076] Identification of related sequences can also be achieved using polymerase chain reaction (PCR) and other amplification techniques suitable for cloning related nucleic acid sequences. Preferably, PCR primers are selected to amplify portions of a nucleic acid sequence believed to be conserved (e.g., a catalytic domain, a DNA-binding domain, etc.). Again, nucleic acids are preferably amplified from a tissue-specific library (e.g., breast). One also can use expression cloning utilizing the antisera described herein to identify nucleic acids that encode related antigenic proteins in humans or other species using the SEREX procedure to screen the appropriate expression libraries. (See: Sahin et al. Proc. Natl. Acad. Sci. USA 92:11810-11813, 1995).

[0077] The invention also includes degenerate nucleic acids that 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 breast cancer-associated 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.

[0078] The invention also provides modified nucleic acid molecules, which include additions, substitutions and deletions of one or more nucleotides (preferably 1-20 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, receptor binding, 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.

[0079] For example, modified nucleic acid molecules that 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 that 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.

[0080] The invention also provides nucleic acid molecules that encode antigenic fragments of breast cancer-associated proteins.

[0081] Fragments, can be used as probes in Southern and Northern blot assays to identify such 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 breast cancer-associated polypeptides, useful, for example, in the preparation of antibodies, and in immunoassays. Preferred fragments are antigenic fragments, which are recognized by agents that specifically bind to breast cancer-associated polypeptides. As used herein, breast cancer-associated antibodies, are antibodies that specifically bind to breast cancer-associated polypeptides.

[0082] The invention also permits the construction of breast cancer-associated polypeptide gene “knock-outs” or “knock-ins” in cells and in animals, providing materials for studying certain aspects of breast cancer and immune system responses to breast cancer by regulating the expression of breast cancer-associated polypeptides. For example, a knock-in mouse may be constructed and examined for clinical parallels between the model and a breast cancer-infected mouse with upregulated expression of a breast cancer-associated polypeptide, which may be useful to trigger an immune reaction to the polypeptide. Such a cellular or animal model may also be useful for assessing treatment strategies for breast cancer.

[0083] Alternative types of animal models for breast cancer may be developed based on the invention. Stimulating an immune response to a breast cancer-associated polypeptide in an animal may provide a model in which to test treatments, and assess the etiology of breast cancers.

[0084] The invention also provides isolated polypeptides (including whole proteins and partial proteins) encoded by the foregoing breast cancer-associated nucleic acids. Such polypeptides are useful, for example, alone or as fusion proteins to generate antibodies, and as components of an immunoassay or diagnostic assay. Breast cancer-associated 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, such as breast cancer-associated antigen fragments including antigenic peptides also can be synthesized chemically using well-established methods of peptide synthesis.

[0085] Fragments of a polypeptide preferably are those fragments that retain a distinct functional capability of the polypeptide. Functional capabilities that can be retained in a fragment of a polypeptide include interaction with antibodies (e.g. antigenic fragments), interaction with other polypeptides or fragments thereof, selective binding of nucleic acids or proteins, and enzymatic activity. One important activity is the ability to provoke in a subject an immune response. As will be recognized by those skilled in the art, the size of the fragment will depend upon factors such as whether the epitope recognized by an antibody is a linear epitope or a conformational epitope. Thus, some antigenic fragments of breast cancer-associated polypeptides will consist of longer segments while others will consist of shorter segments, (e.g. 5, 6, 7, 8, 9, 10, 11 or 12 or more amino acids long, including each integer up to the full length of the breast cancer-associated polypeptide). Those skilled in the art are well versed in methods for selecting antigenic fragments of proteins. The skilled artisan will also realize that conservative amino acid substitutions may be made in breast cancer-associated polypeptides to provide functionally equivalent variants, or homologs of the foregoing polypeptides, i.e, the variants retain the functional capabilities of the breast cancer-associated antigen polypeptides. As used herein, a “conservative amino acid substitution” refers to an amino acid substitution that 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 that 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 or homologs of the breast cancer-associated polypeptides include conservative amino acid substitutions of 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.

[0086] For example, upon determining that a peptide is a breast cancer-associated polypeptide, one can make conservative amino acid substitutions to the amino acid sequence of the peptide, and still have the polypeptide retain its specific antibody-binding characteristics.

[0087] Conservative amino-acid substitutions in the amino acid sequence of breast cancer-associated polypeptides to produce functionally equivalent variants of breast cancer-associated polypeptides typically are made by alteration of a nucleic acid encoding a breast cancer-associated 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 breast cancer-associated polypeptide. Where amino acid substitutions are made to a small unique fragment of a breast cancer-associated 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 breast cancer-associated polypeptides can be tested by cloning the gene encoding the altered breast cancer-associated polypeptide into a bacterial or mammalian expression vector, introducing the vector into an appropriate host cell, expressing the altered polypeptide, and testing for a functional capability of the breast cancer-associated polypeptides as disclosed herein. Peptides that are chemically synthesized can be tested directly for function, e.g., for binding to antisera recognizing associated antigens.

[0088] The invention as described herein has a number of uses, some of which are described elsewhere herein. First, the invention permits isolation of the breast cancer-associated protein molecules. A variety of methodologies well-known to the skilled practitioner can be utilized to obtain isolated breast cancer-associated polypeptide molecules. The polypeptide may be purified from cells that 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 breast cancer-associated polypeptides. These include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immune-affinity chromatography.

[0089] The isolation and identification of breast cancer-associated polypeptides also permits the artisan to diagnose a disorder characterized by expression of breast cancer-associated polypeptides, and characterized preferably by an immune response against the breast cancer-associated polypeptides.

[0090] The methods related to breast cancer-associated polypeptide immune responses involve determining the immune response (antibody or cellular) against one or more breast cancer-associated polypeptides. The immune response can be assayed by any of the various immunoassay methodologies known to one of ordinary skill in the art. For example, the antigenic breast cancer-associated polypeptides can be used as a target to capture antibodies from a sample, such as a blood sample drawn from a patient in an ELISA assay.

[0091] The methods related to breast cancer-associated polypeptide expression involve determining expression of one or more breast cancer-associated nucleic acids, and/or encoded breast cancer-associated polypeptides and/or peptides derived therefrom and comparing the expression with that in a breast cancer-free subject. Such determinations 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.

[0092] The invention also makes it possible to isolate proteins that specifically bind to breast cancer-associated antigens as disclosed herein, including antibodies and cellular binding partners of the breast cancer-associated polypeptides. Additional uses are described further herein.

[0093] The invention also involves agents such as polypeptides that bind to breast cancer-associated polypeptides. Such binding agents can be used, for example, in screening assays to detect the presence or absence of breast cancer-associated polypeptides and complexes of breast cancer-associated polypeptides and their binding partners and in purification protocols to isolate breast cancer-associated polypeptides and complexes of breast cancer-associated polypeptides and their binding partners. Such agents also may be used to inhibit the native activity of the breast cancer-associated polypeptides, for example, by binding to such polypeptides.

[0094] The invention, therefore, embraces peptide binding agents which, for example, can be antibodies or fragments of antibodies having the ability to selectively bind to breast cancer-associated polypeptides. Antibodies include polyclonal and monoclonal antibodies, prepared according to conventional methodology.

[0095] 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 Modern Immunology Wiley & Sons, Inc., New York; Roitt, I. (1991) Essential Immunology, 7th Ed., Blackwell Scientific Publications, Oxford). The pFc′ and Fc 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.

[0096] 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.

[0097] 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.

[0098] Fully human monoclonal antibodies also can be prepared by immunizing mice transgenic for large portions of human immunoglobulin heavy and light chain loci. 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.

[0099] 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.

[0100] Thus, the invention involves polypeptides of numerous size and type that bind specifically to breast cancer-associated polypeptides, and complexes of both breast cancer-associated 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.

[0101] 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 breast cancer-associated polypeptide. This process can be repeated through several cycles of reselection of phage that bind to the breast cancer-associated 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 breast cancer-associated 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 breast cancer-associated polypeptides.

[0102] Thus, the breast cancer-associated polypeptides of the invention, including fragments thereof, can be used to screen peptide libraries, including phage display libraries, to identify and select peptide binding partners of the breast cancer-associated polypeptides of the invention. Such molecules can be used, as described, for screening assays, for purification protocols, for interfering directly with the functioning of breast cancer-associated polypeptides and for other purposes that will be apparent to those of ordinary skill in the art. For example, isolated breast cancer-associated 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 that can interact with breast cancer-associated polypeptides is present in the solution, then it will bind to the substrate-bound breast cancer-associated polypeptide. The binding partner then may be isolated.

[0103] 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 breast cancer-associated polypeptides 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.

[0104] The invention also includes methods to monitor the onset, progression, or regression of breast cancer in a subject by, for example, obtaining samples at sequential times from a subject and assaying such samples for the presence and/or absence of an antigenic response that is a marker of the condition. A subject may be suspected of having breast cancer or may be believed not to have breast cancer and in the latter case, the sample may serve as a normal baseline level for comparison with subsequent samples.

[0105] Onset of a condition is the initiation of the changes associated with the condition in a subject. Such changes may be evidenced by physiological symptoms, or may be clinically asymptomatic. For example, the onset of breast cancer may be followed by a period during which there may be breast cancer-associated physiological changes in the subject, even though clinical symptoms may not be evident at that time. The progression of a condition follows onset and is the advancement of the physiological elements of the condition, which may or may not be marked by an increase in clinical symptoms. In contrast, the regression of a condition is a decrease in physiological characteristics of the condition, perhaps with a parallel reduction in symptoms, and may result from a treatment or may be a natural reversal in the condition.

[0106] A marker for breast cancer may be the specific binding of a breast cancer-associated polypeptide with an antibody. Onset of a breast cancer condition may be indicated by the appearance of such a marker(s) in a subject's samples where there was no such marker(s) determined previously. For example, if marker(s) for breast cancer are determined not to be present in a first sample from a subject, and breast cancer marker(s) are determined to be present in a second or subsequent sample from the subject, it may indicate the onset of cancer.

[0107] Progression and regression of a breast cancer condition may be generally indicated by the increase or decrease, respectively, of marker(s) in a subject's samples over time. For example, if marker(s) for breast cancer are determined to be present in a first sample from a subject and additional marker(s) or more of the initial marker(s) for breast cancer are determined to be present in a second or subsequent sample from the subject, it may indicate the progression of cancer. Regression of cancer may be indicated by finding that marker(s) determined to be present in a sample from a subject are not determined to be found, or found at lower amounts in a second or subsequent sample from the subject.

[0108] The progression and regression of a breast cancer condition may also be indicated based on characteristics of the breast cancer-associated polypeptides determined in the subject. For example, some breast cancer-associated polypeptides may be abnormally expressed at specific stages of breast cancer (e.g. early-stage breast cancer-associated polypeptides; mid-stage breast cancer-associated polypeptides; and late-stage breast cancer-associated polypeptides). Another example, although not intended to be limiting, is that breast cancer-associated polypeptides may be differentially expressed in primary tumors versus metastases, thereby allowing the stage and/or diagnostic level of the disease to be established, based on the identification of selected breast cancer-associated polypeptides in a subject sample.

[0109] Another method of staging breast cancer may be based on variation in a subject's immune response to breast cancer-associated polypeptides, which may or may not be abnormally expressed in the subject. Variability in the immune response to the polypeptides may be used to indicate the stage of breast cancer in a subject, for example, some breast cancer-associated polypeptides may trigger an immune response at different stages of the breast cancer than that triggered by other breast cancer-associated polypeptides.

[0110] Different types of breast cancer, including, but not limited to: ductal carcinoma in situ (DCIS), invasive ductal carcinoma (IDC), invasive lobular carcinoma (ILC), invasive pleomorphic lobular carcinoma, inflammatory breast cancer, medullary carcinoma, mucinous carcinoma (also known as colloid carcinoma), Paget's disease of the nipple, Phyllodes tumor, tubular carcinoma, and adenocarcinoma, may express different breast cancer-associated polypeptides and the encoding nucleic acid molecules thereof, or may have different spatial or temporal expression patterns. Such variations may allow cancer-specific diagnosis and subsequent treatment tailored to the patient's specific condition. These breast cancer-specific diagnoses may also be based on the variations in immune responses to the different breast cancer-associated polypeptides.

[0111] The invention includes kits for assaying the presence of breast cancer-associated polypeptides and/or antibodies that specifically bind to breast cancer-associated polypeptides. An example of such a kit may include the above-mentioned polypeptides bound to a substrate, for example a dipstick, which is dipped into a blood or body fluid sample of a subject. The surface of the substrate may then be processed using procedures well known to those of skill in the art, to assess whether specific binding occurred between the polypeptides and agents (e.g. antibodies) in the subject's sample. For example, procedures may include, but are not limited to, contact with a secondary antibody, or other method that indicates the presence of specific binding.

[0112] Another example of a kit may include an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide. The antibody or antigen-binding fragment thereof, may be applied to a tissue or cell sample from a patient with breast cancer and the sample then processed to assess whether specific binding occurs between the antibody and a polypeptide or other component of the sample. In addition, the antibody or antigen-binding fragment thereof, may be applied to a body fluid sample, such as breast discharge fluid or lymph node fluid, from a subject, either suspected of having breast cancer, diagnosed with breast cancer, or believed to be free of breast cancer. As will be understood by one of skill in the art, such binding assays may also be performed with a sample or object contacted with an antibody and/or breast cancer-associated polypeptide that is in solution, for example in a 96-well plate or applied directly to an object surface.

[0113] The foregoing kits can include instructions or other printed material on how to use the various components of the kits for diagnostic purposes.

[0114] The invention further includes nucleic acid or protein microarrays with breast cancer-associated peptides or nucleic acids encoding such polypeptides. In this aspect of the invention, standard techniques of microarray technology are utilized to assess expression of the breast cancer-associated polypeptides 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 breast cancer-associated peptides, also can be used for diagnostic applications, such as for identifying subjects that have a condition characterized by breast cancer-associated polypeptide expression.

[0115] 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.

[0116] 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). 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.

[0117] 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.

[0118] 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 more than two of the breast cancer-associated polypeptide nucleic acid molecules set forth herein, or one of the novel breast cancer-associated polypeptide nucleic acid molecules as described 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.

[0119] 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.

[0120] 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.

[0121] 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.

[0122] 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).

[0123] 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.

[0124] In some embodiments, one or more control 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.

EXAMPLES

Example 1

[0125] Methods

[0126] Construction of cDNA Libraries

[0127] Tumor samples from breast cancer patients 184 (invasive ductal carcinoma), 297 (invasive ductal carcinoma), 257 (invasive ductal carcinoma), and 263 (invasive pleomorphic lobular carcinoma) were obtained as surgical specimens and used in the construction of cDNA libraries. A cDNA library was also prepared from the SK-BR-3 breast cancer cell line (ATCC #HTB-30). Total RNA was prepared by the guanidinium thiocyanate method and purified to poly A+ RNA using the Dynabeads mRNA Purification Kit (Dynal, Lake Success, N.Y. Two bacteriophage expression vectors were utilized; the lambda ZAP vector (Stratagene, La Jolla, Calif.) was used for cDNA derived from the tumor of patient 184 and the SK-BR-3 cell line, and the lambda TRIPLX vector (Clontech Laboratories Inc., Palo Ala, Calif.) was used for cDNA derived from the tumors of patients 297, 257 and 263). Manufacturers' protocols were used for cDNA synthesis and ligation into appropriate vectors. Following in vitro packaging, libraries containing 1-2×106 primary recombinants were obtained. cDNA libraries were not amplified prior to immunoscreening.

[0128] Immunoscreening

[0129] Sera were obtained from individuals undergoing diagnostic or therapeutic procedures.

[0130] To remove antibodies reactive with vector-related antigens, sera (1:10 dilution) were absorbed by passage through columns containing Sepharose 4B coupled to lysates of E. coli Y1090 and bacteriophage infected E. coli BNN97 (5 Prime→3 Prime, Inc., Boulder, Colo.), followed by a 15 hour incubation with nitrocellulose filters precoated with proteins derived it from E. coli and E.coli/phage lysates (mock experimental membranes). Library screenings W were performed as described in Scanlan, et al., Int. J. Cancer 76:652-658 (1998) and Scanlan, et al., Int. J. Cancer 83:456-64, (1999), using preabsorbed patient sera at a dilution of 1:200. A total of 5-6×105 recombinants were screened per cDNA library. Serum reactive phage clones were converted to plasmid forms by in vivo excision. Plasmid DNA was sequenced at the Cornell University DNA Service (Ithaca, N.Y.) using an ABI Prism automated DNA sequencer (Applied Biosystems, Foster City, Calif.).

[0131] Two assays were employed to determine allogeneic serum reactivity. In the case of allogeneic sera derived from breast cancer patients and normal individuals, a previously described plaque assay was used (See Scanlan, et al., Int. J. Cancer 76:652-658 1998; Scanlan, et al., Int. J. Cancer 83:456-64, 1999). Briefly, 1500 pfu of monoclonal phage encoding individual serologically defined breast cancer antigens were mixed with an equal number of negative control phage (phage without cDNA inserts) and used to infect exponentially growing E. coli XL-1 Blue MRF′ (Stratagene). Following a 15 hour amplification phase, plaque-derived proteins were transferred to 47 mm nitrocellulose membrane discs and tested for reactivity with individual serum samples (1:200 dilution).

[0132] Subsequent screening of serum samples from patients with other forms of cancer (lung, colon, ovarian, esophageal) was carried out using a modification of the plaque assay, termed a spot assay. In this method, 80×120 mm nitrocellulose membranes were precoated with a film of NZY/0.7% Agarose/2.5 mM IPTG and placed on a reservoir layer of NZY/0.7% Agarose in a 86×128 mm Omni Tray (Nalge Nunc International Corp., Naperville, Ill.). Approximately 1.0×105 pfu of monoclonal phage encoding individual serologically defined breast cancer antigens, in a volume of 20 μl, were mixed with 20 μl of exponentially growing E. coli XL-1 Blue MRF and spotted (0.7 μl aliquots) on the precoated nitrocellulose membranes. Membranes were incubated for 15 hours at 37° C. A total of 46 different serologically defined breast cancer antigens were spotted in duplicate per nitrocellulose membrane. The agarose film was then removed from the membrane and the filters were processed for reactivity with individual serum samples (1:200 dilution), as described in Scanlan, et al., Int. J. Cancer 76:652-658 (1998) and Scanlan, et al., Int. J. Cancer 83:456-64, (1999). Serum reactivity detected by the spot assay was verified in the plaque assay, and both assays appear to have comparable specificity and sensitivity.

[0133] Northern Blot Analysis and Standard Reverse Transcription (RT)-PCR

[0134] Northern blots containing normal tissue poly A+ RNA (2 μg/lane) were obtained commercially (Clontech Laboratories, Inc., Palo Alto, Calif.). Random-primed 32P labeled probes consisting of 300-600 bp PCR products from coding sequences of selected seroreactive cDNA clones were hybridized for 1.5 hours in ExpressHyb (Clontech Laboratories) at 68° C., and washed at high stringency (2 times, 30 min. each, 0.1×SSC/0.1% SDS at 65° C.). The resultant Northern blots were developed with Biomax MS autoradiography films (Eastman Kodak Co., Rochester, N.Y.).

[0135] The mRNA expression pattern of a selected set of serologically defined breast cancer antigens was also determined by standard RT-PCR, using a panel of normal tissue RNA from lung, testis, small intestine, breast, liver, and placenta (Clontech Laboratories). The cDNA preparations used as templates in the RT-PCR reactions were synthesized using MuLV reverse transcriptase as described in Scanlan, et al., Int. J. Cancer 83:456-64, (1999). As a control for genomic DNA contamination, all cDNA synthesis reactions were set up in duplicate with additional samples lacking reverse transcriptase. The cDNA was then amplified by PCR (30 cycles), using gene specific primers (Gibco, BRL, Grand Island, N.Y.) and AmpliTaq Gold DNA polymerase (Applied Biosystems, Foster City, Calif.), as described in Scanlan, et al., Int. J. Cancer 83:456-64, (1999).

[0136] Real-Time Quantitative Reverse Transcription-PCR

[0137] Total RNA from ten different breast cancer specimens was prepared by the guanidinium thiocyanate method using standard procedures. Total RNA from normal breast consisted of a pool of RNA from two healthy individuals (Clontech Laboratories). RNA (1 μg) was reverse transcribed into cDNA using the TaqMan EZ RT-PCR kit (PE Biosystems). As a control for genomic DNA contamination, all cDNA synthesis reactions were set up in duplicate with additional samples lacking reverse transcriptase. Reagents were purchased from Applied Biosystems, except where noted. Multiplex PCR reactions were prepared using 2.5 μl of cDNA diluted in TaqMan Universal PCR Master Mix supplemented with VIC—(Applied Biosystems proprietary dye) labeled human beta glucuronidase endogenous control probe/primer mix, 200 nM FAM (6-carboxy-fluorescein) labeled gene-specific TaqMan probe, and a predetermined, optimum concentration of corresponding gene-specific forward and reverse primers (300-900 nM). Triplicate PCR reactions were prepared for each cDNA sample. PCR consisted of 40 cycles of 95° C. denaturation (15 seconds) and 60° C. annealing/extension (60 seconds). Thermal cycling and fluorescent monitoring were performed using an ABI 7700 sequence analyzer (Applied Biosystems). The point at which the PCR product was first detected above a fixed threshold, termed cycle threshold (Ct), was determined, and normalized against the Ct value of the endogenous control product (ΔCt=Ct FAM−Ct VIC). The quantity of gene-specific transcripts present in the breast cancer cDNA samples relative to normal breast tissue was calculated by comparing the normalized cycle thresholds in tumor with non-malignant breast tissue (ΔΔCt=ΔCt of tumor−ΔCt of normal breast), and determining the relative concentration (Relative Concentration=2−ΔΔCt).

[0138] In addition, a selected set of FAM-labeled gene-specific TaqMan probe/primer combinations were used to amplify a panel of 14 normal tissue cDNA preparations, which had been normalized against 6 housekeeping genes and purported to be virtually free of genomic DNA (Clontech Laboratories). The relative abundance of gene-specific transcripts in normal tissues was determined by comparison with a standard curve generated from the Ct values of known concentrations of plasmid DNA containing the relevant gene. Because cDNA derived from normal breast tissue was not included in the commercially obtained panel, a cDNA preparation derived from normal breast tissue (see above) was normalized according to the Ct values for beta glucuronidase, and the concentration of gene-specific transcripts in normal breast tissue was also calculated relative to its expression in testis, using the formula described above.

[0139] Results

[0140] Identification of Human Breast Cancer Antigens by SEREX Analysis

[0141] Serum samples from six individuals with breast cancer were used to immunoscreen tumor-derived cDNA expression libraries via the SEREX method. In four of the six cases, autologous patient sera were used to screen cDNA libraries prepared from the corresponding primary breast cancer. In the other two cases, allogeneic patient sera were used to screen a cDNA library prepared from the SK-BR-3 cell line. As shown in Table 1, ninety-four serologically defined breast cancer antigens were identified. They were designated NY-BR-8 through NY-BR-101.

TABLE 1
Immunoscreening of cDNA Expression Libraries from Breast Cancer with
Autologous and Allogeneic Patient Sera (SEREX)
				Antigens with	Antigens with
			Number of	Non-Cancer	Cancer-
		Breast Cancer	Distinct Antigens	Related	related
		cDNA Library	Identified by SEREX	Serological	Serological
Tumor Type	Serum Source	Designation	(Known1/Novel2)	Profiles	Profiles
Invasive ductal carcinoma	Autologous	184	17 (12/5)	13	4
Invasive ductal carcinoma	Autologous	297	6 (6/0)	5	1
Invasive ductal carcinoma	Autologous	257	9 (8/1)	4	5
Invasive pleomorphic	Autologous	263	13 (9/4)	5	8
lobular carcinoma
SK-BR-3 (established	Allogeneic-1	9993	34 (27/7)	14	20
breast cancer cell line)
SK-BR-3	Allogeneic-2	9993	15 (12/3)	9	6
Totals			94 (74/20)	50	44
1Identical to GenBank Entries.
2Identities limited to expressed sequence tags (ESTs)

[0142] These 94 antigens (Tables 2 through 4) represent 74 known gene products and 17 novel proteins, and could be categorized on the basis of cellular localization, subcellular targeting motifs, known function, or sequence similarities.

TABLE 2
SEREX-Defined Breast Cancer Antigens: Reactivity with Sera From Normal Individuals
			Reactivity	Reactivity
NY-BR-		SEREX Database ID Number1 of	with	with Breast
Antigen	Identity/Similarities (Unigene cluster)	Equivalent Isolate (Tumor Source2)	Normal Sera	Cancer Sera
Known Gene Products
8	H2K binding factor 2 (Hs.278573)	439 (RC), 1201 (MEL), 8 (GC)	1/16	2/10
13	Zuotin related factor 1 (Hs.82254)	6 (GC)	3/12	3/10
17	NP220 (Hs.169984)	1531 (OC)	1/12	2/10
22	Protein phosphatase 1B (Hs.5687)		1/12	1/10
23	DKFZp434L0117 (Hs.63795)		1/12	1/10
27	MHC Class 1 HLA Cw-0304 (Hs.277477)		4/25	2/25
29	Proteosome subunit p112 (Hs.3887)		6/12	4/10
30	GPDH (Hs.169476)		4/12	3/10
32	Ribosomal protein L34 (Hs.250895)		2/25	2/25
35	VEGFB (Hs.78781)		1/12	2/10
36	COL6A2 (Hs.4217)		4/19	6/20
42	Vacuolar sorting protein 45B (Hs.6650)		1/17	1/25
43	Defender against cell death-1 (Hs.82890)		8/25	5/25
50	Sphingosine-1-phosphate lyase 1 (Hs.186613)		7/12	5/10
60	HIP-55 (Hs.180766)		2/25	1/25
61	TGFB1 anti-apoptotic factor-1 (Hs.75822)	1057 (BC)	1/25	2/25
66	FBI-1 (Hs.104640)		1/20	2/20
68	Heme oxygenase 2 (Hs.63908)		2/20	2/20
70	KIAA0713 protein (Hs.88756)	159 (LC)	1/20	4/20
71	KIAA1002 protein (Hs.102483)		2/20	4/20
74	U2 snRNP auxiliary factor-2 (Hs.103962)	786 (HD), 430 (RC)	5/16	1/20
78	RNA helicase-related protein (Hs.8765)		3/25	1/25
80	TCP1 ring complex pp 5 (Hs.1708)		1/20	1/20
82	KIAA0801 protein (Hs.17585)		1/20	3/20
88	Talin (Hs.278559)	608 (PC)	1/20	1/20
89	Candidate of metastasis 1 (Hs.8603)		1/20	1/20
90	NAP-22 (Hs.79516)		1/20	2/20
95	KIAA0376 protein (Hs.4791)	1777 (CC), 357 (RC), 551 (GC), 955 (BC)	11/20	11/20
100	BRACA-1 AP 2 (Hs.122764)	1785 (CC), 1158 (RC), 190 (PC), 1616 (OC), 807 (BC)	2/19	2/20
Novel Gene Products
15	Putative nuclear protein (Hs.178175)		1/12	1/10
16	Similar to Ankyrin (Hs.190251)	1792 (CC)	4/12	6/10
18	RNA splicing factor similarity (Hs.11065)		2/12	1/10
20	Similar to calmodulin (Hs.239812)		1/12	1/10
24	Similar to CDC 10 proteins (Hs.99741)		1/12	1/10
40	None (Hs.149190)		1/12	2/10
81	Phospholipase C beta similarity (Hs.75280)		1/20	1/20
86	Oxysterol binding protein similarity (Hs.233495)	319 (GC)	2/17	2/20
87	2 possible reading frames (Hs.18946)		1/25	1/25
1SEREX database ID number from http://www.licr.org/SEREX.html.
2Abbreviations: BC, breast cancer; CC, colon cancer; HD, Hodgkin's disease; GC, gastric cancer; LC, lung cancer; MEL, melanoma; OC, ovarian cancer; PC, prostate cancer; RC, renal cancer

[0143]

TABLE 3
SEREX-Defined Breast Cancer Antigens: Antigens Associated with Autoimmune Disease
					Reactivity
				Reactivity	with
NY-				with	Breast
BR-		SEREX Database ID Number1	Autoimmunue	Normal	Cancer
Antigen	Identity (Unigene Cluster)	of Equivalent Isolate (Tumor Source2)	Disease Associations3	Sera	Sera
9	Ifn inducible autoantigen 16 (Hs.155530)		SLE	1/12	1/10
12	RNA pol. II 23kDa subunit (Hs.24301)		SLE, PSS	1/12	1/10
14	Proteasome activator subunit 3/Ki		SLE	1/12	1/10
	nuclear autoantigen (Hs.152978)
28	Glutathione S-transferase theta-1 (Hs.77490)		AH	1/12	2/10
31	Ribosomal phosphoprotein P1 (Hs.177592)		SLE	5/25	2/25
39	DBI-related protein (Hs.15250)	244 (RC), 1328 (GC), 1031 (BC)	AD	1/16	1/12
47	Dynamin 1-like protein (Hs.180628)		Sclero	0/20	1/20
58	Aldolase A (Hs.273415)	79 (LC)	RA	0/20	1/20
59	PARP (Hs.177766)	432 (CC), 698 (RC) 939 (BC)	SLE, SS, RA, PSS	1/18	1/20
64	Alanyl-tRNA synthetase (Hs.75102)	471 (RC)	PM	0/20	1/20
65	Nuclear matrix protein 238 (Hs.272822)		PM, AH	0/20	1/20
69	Centromere protein F (Hs.77204)	626 (PC), 1557 (EC), 809 (BC)	SLE, Sclero	8/20	1/20
91	U1 snRNP (Hs.180789)	24 (GC), 349 (CC), 1267 (RC), 751 (BC)	SLE, SS, RA, PM, Sclero	3/20	6/20
93	Human autoantigen (Hs.75682)		SS, SLE, Sclero, RA	0/20	1/20
97	Sjogren syndrome antigen A1 (Hs.1042)		SS, SLE	0/20	1/20
101	Vinculin (Hs.75350)	1288 (BC)	thrombocytopenia	0/20	1/20
1 SEREX database ID number from http://www.licr.org/SEREX.html.
2 Tumor tissue abbreviations: BC, breast cancer; CC, colon cancer; EC, esophageal cancer; GC, gastric cancer; LC, lung cancer;           , no additional isolates; PC, prostate cancer; RC, renal cancer.
3 Autoimmune disease abbreviations; AH, autoimmune hepatitis; AD, autoimmune diabetes; PM, polymyositis; PSS, Progressive Systemic Sclerosis; RA, Rheumatoid Arthritis; Sclero, scleroderma; SLE, systemic lupus erythematosus; SS, Sjogren's Syndrome

[0144]

TABLE 4
SEREX-Defined Breast Cancer Antigens: Antigens Detected
with Sera from a Single Breast Cancer Patient1
NY-BR-Antigen Identity/Similarities/Motifs (Unigene cluster)
Known Gene Products
10            Desmoplakin I (Hs.74316)
11            RING 3 gene product (Hs.75243)
19            CGI-149 protein (Hs.241266)
21            KIAA0708 (Hs.117177)
26            Modulator recognition factor (Hs.920)
33            GSPTI (Hs.2707)
37            HRIHFB2157 gene product (Hs.4552)
44            BMAL1e protein (Hs.74515)
48            Sorting nexin 6 (Hs.76127)
52            Transcriptional activator SRCAP (Hs.87908)
54            SOM172 gene product (Hs.100623)
67            TIS11D gene product (Hs.78909)
76            MAGE A3 (Hs.36978)
77            SMRT corepressor (Hs.120980)
83            KIAA0081 protein. (Hs.78871)
92            Ribosomal protein L10 (Hs.29797)
Novel Gene Products
38            SCR repeat domain (not clustered)
46            None (not clustered)
49            Ankyrin repeat domain (Hs.55565)
51            None (Hs.128685)
73            Similar to coatomer proteins (Hs.217001)
85            Nuclear localization signals (Hs.105153)
84            Transmembrane domain (Hs.206196)
99            RNA splicing factors similarity (Hs.183438)
1                    Antigens reacted with sera from single breast cancer patients (1/25), but not with sera from normal individuals (0/25), colon cancer patients (0/19), lung cancer patients (0/15), ovarian cancer patients (0/15) or esophageal cancer patients (0/15), and no equivalent isolates of these antigens were found in the SEREX database.

[0145] Thirty-nine antigens were known or predicted nuclear proteins, and include DNA binding proteins (e.g., BR-8, -21, -55, and -66), transcription factors (e.g., BR-11, -52, -77, and -79), RNA binding proteins (e.g., BR-17, -18, -74 and -91), and RNA/DNA helicases (BR-65, -78 and -82). Twenty-four antigens were known or predicted cytoplasmic proteins, and include metabolic enzymes (e.g., BR-28, -30, -39 and -58), ribosomal proteins (e.g., BR-31, -32, -64 and -92), cytoskeletal proteins (BR-10, -88 and -101), sorting proteins (e.g., BR-42, -44, -48 and -80), adaptor proteins (BR-34 and BR-41) and proteins involved in the ubiquitin pathway (BR-29 and BR-37). Six antigens localized to the plasma membrane (BR-27, -43, -56, -57, -82 and -90) and two were extracellular gene products (BR-35 and BR-36). The nucleotide sequences of all novel clones have been deposited in the GenBank database (sequential accession numbers AF308284-AF308300). The cDNA sequences coding for the 94 antigens identified in this study were also compared to sequences deposited in the SEREX database, which can be accessed at the Ludwig Institute for Cancer Research web site at: http:/www.licr.org/SEREX.html. Examination of this database revealed that 25 of the 94 breast cancer antigens defined in this study (26%) were also identified through SEREX analysis of breast cancer and other tumor types (Tables 2, 3 and 5).

TABLE 5
SEREX-Defined Breast Cancer Antigens: Antigens Reactive with Sera from Breast Cancer Patients and Patients with Other Forms of Cancer1
	SEREX Database ID	Seroreactivity
NY-BR-	Identity/Similarities/	Number2 of Equivalent	Breast	Colon	Lung	Ovarian	Esophageal
Antigen	Motifs (Unigene Cluster)	Isolate (Tumor Source3)	Cancer	Cancer	Cancer	Cancer	Cancer
25	KIAA0854 protein, (Hs.30209)	128 (RC)	1/25	1/19	0/15	1/15	0/15
34	SHB adaptor protein (Hs.173752)		1/25	0/19	0/15	1/15	0/15
41	SNT-1 adaptor (Hs.251394)		1/25	0/19	1/15	0/15	0/15
45	Kinesin 2 (Hs.117977)	332 (GC), 96 (SM), 797 (RC)	2/25	0/19	0/15	0/15	0/15
53	LAGE-14 (Hs.167379)		4/25	1/19	2/15	1/15	2/15
55	Nucleosome assembly protein-1 (Hs.179662)	126 (RC), 1137 (MEL)	1/25	1/19	1/15	0/15	0/15
56	gC1Q binding protein (Hs.78614)		2/25	0/19	0/15	0/15	0/15
57	HER2 nue/erbB2 (Hs.173664)		2/25	0/19	0/15	0/15	0/15
62	Novel, kinesin similarity (Hs.278323)		2/25	0/19	0/15	0/15	0/15
63	Tumor protein D52 (Hs.2384)		2/25	0/19	0/15	0/15	0/15
72	MAGE A6 (Hs.198263)		1/25	0/19	0/15	1/15	0/15
75	Novel (Hs.5111)	1184 (MEL)	2/25	0/19	0/15	0/15	1/15
79	Tata element modulatory factor 1 (Hs.74985)	246 (GC)	1/25	0/19	0/15	0/15	0/15
94	Tumor protein p53 (Hs.1846)	33 (CC)	1/25	3/19	0/15	1/15	2/15
96	Novel, S/T kinase domain (Hs.4789)	296 (MEL)	2/25	0/19	0/15	0/15	0/15
98	MAGE D (Hs.4943)		3/25	0/19	1/15	0/15	0/15
1Antigens did not react with sera from normal individuals (0/25).
2SEREX database ID number from http://www.licr.org/SEREX.html.
3Abbreviations: BC, breast cancer; CC, colon cancer; GC, gastric cancer; MEL, melanoma;           , no additional isolates; RC, renal cancer; SM, seminoma.
4Assays for LAGE-1 seroreactivity were performed using a recombinant phage expressing the highly homologous NY-ESO-1 protein.

[0146] Reactivity Patterns of Sera from Normal Individuals and Cancer Patients with SEREX-Defined Breast Cancer Antigens

[0147] To determine whether immune recognition of the isolated antigens was cancer related, allogeneic sera samples obtained from 25 normal blood donors and 24 additional patients with breast cancer were tested for reactivity against the panel of antigens using the plaque assay. Fifty four of the 94 antigens (57%) had a serological profile that was not restricted to cancer patients, as evidenced by their reactivity with normal sera (Tables 1 and 2), or their known association with autoimmune disease (Tables 1 and 3). The remaining 40 antigens had a cancer-related serological profile, reacting only with sera from cancer patients (Tables 1,4 and5).

[0148] The 40 antigens having a cancer-related serological profile were further tested for reactivity with serum panels from colon, lung, ovarian, and esophageal cancer patients using the spot assay, and the following seroreactivity patterns were defined: a) antigens that reacted with serum from only a single breast cancer patient; b) antigens that reacted exclusively with sera from two or more breast cancer patients; and c) antigens that reacted with sera from patients having other forms of cancer in addition to breast cancer patients. Of the 40 antigens having a cancer-related serological profile, 24 antigens reacted with sera from only one breast cancer patient, either the autologous patient or a single allogeneic patient, and are listed in Table 4. Sixteen of the 40 antigens having a cancer-related serological profile reacted with sera from more than one cancer patient (breast cancer patients and/or patients with other tumor types), and are listed in Table 5. Four of these antigens [gC1Q/BR-56, Her2neu/BR-57, BR-62, and tumor protein D52 (TPD52)/BR-63] reacted with sera from more than one breast cancer patient, but not with sera from patients with other forms of cancer. The remaining antigens listed in Table 5 react with sera from both breast cancer patients and individuals with other forms of cancer. In terms of known tumor antigens, LAGE-1/BR-53, a cancer-testis antigen highly homologous to NY-ESO-1, was isolated in the current study. In accordance with results of previous serologic surveys (see: Stockert, et al., J. Exp Med. 187:1349-54, 1998), LAGE-1/NY-ESO-1 had the highest frequency of cancer-related seroreactivity; antibody responses were detected in patients with breast (4/20), colon (1/19), lung (2/15), ovarian (1/15) and esophageal cancer (2/15). Similarly, a cancer-related serological response was also detected against p53/BR-94 (1/25 breast cancer, 3/19 colon cancer, 1/15 ovarian cancer and 2/15 esophageal cancer patients), and Her2neu/BR-57 (2/25 breast cancers patents), confirming previous surveys of seroreactivity against these antigens (see: Scanlan, et al., Int. J. Cancer 76:652-8,1998; Disis, et al., Cancer Res. 54:16-20, 1994; Labrecque, et al., Cancer Res. 53:3468-71, 1993). In addition, a new set of immunogenic breast cancer antigens was defined in this study, including known proteins such as kinesin 2/BR-45, gC1Q binding protein/BR-56, TPD52/BR-63, and MAGE-DIBR-98, as well as novel gene products such as NY-BR-62, NY-BR-75, and NY-BR-96.

[0149] Expression Patterns of mRNA Encoding Serologically Defined Breast Cancer Antigens in Normal Tissues

[0150] A preliminary in silico mRNA expression profile of all gene products identified in this study was based on the tissue distribution of expressed sequence tags (ESTs) in the human EST database. Products with no EST matches, or those having EST matches limited to tumor tissue, fetal tissue, or a single normal tissue were further examined by Northern blotting and RT-PCR. Gene products with restricted EST profiles include the three well-characterized cancer-testis antigens MAGE-A3/BR-76, MAGE-A6/BR-72 and LAGE-1/BR-53, which are expressed exclusively in normal testis and a range of different tumor types (Chen, et al., Proc. Natl. Acad. Sci. USA 94:1914-18, 1997), and four putative tissue-restricted antigens, including a known gene product, SNT-1/BR-41, and 3 novel proteins identified in this study, BR-49, -62, and -85. All seven of these antigens showed a cancer-related serological profile.

[0151] The mRNA expression profiles of BR-41, -49, -62, and -85 were examined in Northern blots of non-normalized mRNA preparations derived from 16 different human tissues. Expression of SNT-1/BR-41, BR-62 and BR-85 was restricted to testis, appearing as a 3.2 kB mRNA transcript, a 4.0 kB mRNA transcript, and 2.4 KB and 3.2 KB mRNA transcripts, respectively. Expression of BR-49 was widespread, appearing as a 4.2 kB hybridization signal in 10 of 16 normal tissues (absent in spleen, ovary, PBL, heart, brain, and skeletal muscle). The mRNA expression patterns of BR-41, -49, -62, and -85 were also analyzed by conventional RT-PCR, and transcripts for these 4 gene products were found in all normal tissues tested (lung, testis, small intestine, breast, liver, and placenta).

[0152] The detection of BR-41, -62, and -85 mRNA in normal tissues by RT-PCR but not by Northern blotting indicates low-level ubiquitous expression. To examine this further, real-time RT-PCR was used to quantify mRNA expression in a panel of normalized cDNA preparations from 15 different human tissues. PCR amplification of cDNA coding for BR-41, -62, and -85 yielded distinct values for cycle threshold (Ct), which were compared to the Ct values obtained from a set of homologous cDNA standards of known concentration. As shown in FIG. 1, the highest levels of BR-41 mRNA expression (FIG. 1 A) in the normalized cDNA panel were detected in testis (equivalent to 43.8 fg of cDNA) and peripheral blood leukocytes (equivalent to 35.4 fg of cDNA), and lower levels (less 18.0 fg of cDNA) in each of the remaining 12 normal tissues. Because cDNA from normal breast tissue was not included in this commercially obtained cDNA panel, the concentration of BR-41 mRNA in normal mammary gland was calculated relative to normal testis, and determined to be approximately 170 times higher in normal breast tissue compared to testis, and was equivalent 7300 fg of cDNA. The highest levels of BR-62 mRNA expression (FIG. 1B) were detected in normal testis (271 fg of cDNA), thymus (89 fg of cDNA), and colon (20 fg of cDNA), with lower levels (less 6 fg of cDNA) detected in each of the remaining 11 normal tissues. The concentration of BR-62 mRNA in normal breast was equivalent to 0.8 fg of cDNA. The highest levels of BR-85 mRNA expression (FIG. 1C) were detected in normal thymus (54 fg of cDNA) and testis (39 fg of cDNA), while lower levels (less than 16 fg of cDNA) were detected in each of the remaining 12 normal tissues. The concentration of BR-85 mRNA in normal breast was equivalent to 8.0 fg of cDNA.

[0153] Expression Levels of mRNA Encoding Serologically Defined Breast Cancer Antigens in Normal and Malignant Breast Tissue

[0154] The mRNA expression levels of eleven antigens associated with a cancer-related serological response (Table 5) and/or showing differential mRNA expression were measured in 10 breast cancer specimens and normal breast tissue by real-time RT-PCR. The relative level of mRNA expression in breast cancer compared to normal breast tissue was calculated on the basis of differences in normalized Ct values between the two tissues. Overexpression was defined as an mRNA expression level that is three times higher in tumor compared to normal breast tissue. As shown in Table 6, mRNA transcripts encoding 6/10 antigens, BR-56, -57, -62, -63, -85, and -98, were overexpressed in at least one breast cancer specimen. Four of these ten antigens were frequently overexpressed in breast cancer, including Her2neu/BR-57 (3/10 cases), BR-62 (6/10 cases), TPD52/BR-63 (5/10 cases), and BR-85 (9/10 cases). Exceptionally high levels of mRNA expression in breast cancer were associated with Her2neu/BR-57 (107 times that of normal breast in patient # 7), BR-62 (53 times that of normal breast in patient # 8), and TPD52/BR-63 (132 times that of normal breast in patent # 8). In contrast expression of SNT-1/BR-41 mRNA was consistently lower in breast cancer relative to normal breast tissue, with apparent down-regulated expression (defined as an expression level of less than 20% of normal breast) occurring in 7/10 cases. The remaining products, kinesin 2/BR-45, BR-75 and BR-96, had similar mRNA expression levels in tumor and normal breast tissue.

TABLE 6
Quantitative Analysis of mRNA Encoding SEREX Defined Breast Cancer Antigens in
Normal and Malignant Breast Tissue: Relation Between mRNA Level and Immunogenicity
	Ratio of mRNA in breast cancer to mRNA in normal breast
	(‘+’ indicates serum antibody reactivity1)
Antigen	1	2	3	4	5	6	7	8	9	102
BR-41	0.01	0.19	0.04	0.26	0.38	0.11	0.10	0.86	0.03	0.07
BR-45/Kinesin 2	0.50	0.35	0.41	0.25	0.34	0.27	0.43	0.85	0.23	0.57
BR-56/gC1Q	0.66	0.49	0.22	0.83	0.40	0.44	0.69	0.77	0.44	3.71 (+)
BR-57/Her2neu	0.30	1.17	2.48	2.18	1.43	65.49	107.39	5.91	0.44	1.81 (+)
BR-62	1.21	1.65	0.26	2.20	5.19	3.80	4.22	53.44	15.49	12.21 (+)
BR-63/TP D52	1.44	4.08	0.91	7.36	6.26	2.08	2.88	132.51	1.67	5.33 (+)
BR-75	2.27	0.34	0.48	0.59	0.43	0.34	0.37	0.78	0.36	1.06 (+)
BR-85	5.55	6.28	1.15	6.65	3.17	4.98	5.91	11.42	10.34	11.34 (+)
BR-96	0.53	1.09	0.45	0.65	0.39	0.33	0.56	0.81	0.31	1.26
BR-98/MAGE D	0.16	2.10	0.58	2.55	0.73 (+)	0.58	0.67 (+)	12.67	1.44	0.60
1Serum reactivity of patients # 1, 3, 5, 6, 7, 8, 9 and 10 assessed in the plaque assay.
2Patient # 10 referred to as allogeneic-1 in Table 1.

[0155] The relationship between upregulation of gene expression and serological reactivity was examined in 8 breast cancer patients whose tumors and sera were available for typing (informative cases, patients #1, 3, 5, 6, 7, 8, 9, 10). Serum antibodies against BR-56, -57, -62, -63, -75, and -85 were detected in breast cancer patient #10. In this case, mRNA transcripts encoding 4/6 of these antigens were overexpressed in the autologous tumor (BR-56, -62, -63, and -85). None of the other cases showed seroreactivity against the amplified/overexpressed SEREX-defined antigens.

Example 2

[0156] Method

[0157] Real-time PCR examination of NY-BR-62 mRNA in colon cancer tissue and normal colon tissue was also performed using the methods described above. Samples of colon cancer tissue from 9 patients were tested and the ratio of NY-BR-62 mRNA in the cancer tissues to mRNA in normal tissues were compared.

[0158] Results

[0159] Results from the real-time PCR examination of NY-BR-62 mRNA in colon cancer tissue and normal tissue are shown in Table 7. Nine samples of colon cancer tissue were tested and the ratio of NY-BR-62 mRNA in the cancer tissues to mRNA in normal tissues were compared. The results indicated that NY-BR-62 gene expression was upregulated in colon cancer when compared to its expression level in normal tissue counterpart.

TABLE 7
Real-time PCR of NY-BR-62 in colon cancer tissues.
	Ratio of NY-BR-62 mRNA in cancer to mRNA
	in its normal tissue counterpart
	Pa-
Tumor	tient
Type	#1	#2	#3	#4	#5	#6	#7	#8	#9
Colon	22.39	20.04	3.54	5.82	4.93	15.98	9.81	28.27	3.57
Cancer

[0160]

TABLE 8
Sequence Identification numbers
Sequence Name	Nucleotide SEQ ID NO	Protein SEQ ID NO.
NY-BR-10	1	41
NY-BR-11	2	42
NY-BR-19	3	43
NY-BR-21	4	44
NY-BR-26	5	45
NY-BR-33	6	46
NY-BR-37	7	47
NY-BR-44	8	48
NY-BR-48	9	49
NY-BR-52	10	50
NY-BR-54	11	51
NY-BR-67	12	52
NY-BR-76	13	53
NY-BR-77	14	54
NY-BR-83	15	55
NY-BR-92	16	56
NY-BR-38	17	57
NY-BR-46	18	58
NY-BR-49	19	59
NY-BR-51	20	60
NY-BR-73	21	61
NY-BR-85	22	62
NY-BR-84	23	63
NY-BR-99	24	64
NY-BR-25	25	65
NY-BR-34	26	66
NY-BR-41	27	67
NY-BR-45	28	68
NY-BR-53	29	69
NY-BR-55	30	70
NY-BR-56	31	71
NY-BR-57	32	72
NY-BR-62	33	73
NY-BR-63	34	74
NY-BR-72	35	75
NY-BR-75	36	76
NY-BR-79	37	77
NY-BR-94	38	78
NY-BR-96	39	79
NY-BR-98	40	80
KNSL7 (Genbank No:	81	82
AB035898)

[0161] Other aspects of the invention will be clear to the skilled artisan and need not be repeated here. Each reference cited herein is incorporated by reference in its entirety.

[0162] The terms and expressions that have been employed are used as terms of description and not of limitation, and there is no intention in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, it being recognized that various modifications are possible within the scope of the invention.

Claims

1. A method for diagnosing breast cancer in a subject comprising: obtaining a biological sample from a subject, contacting the sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, and determining specific binding between the breast cancer-associated polypeptides and agents in the sample, wherein the presence of specific binding is diagnostic for breast cancer in the subject.

2. The method of claim 1, wherein the sample is blood.

3. The method of claim 1, wherein the sample is lymph node fluid or breast discharge fluid.

4. The method of claim 1, wherein the biological sample is contacted with at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOS:1-40, and 81.

5. The method of claim 1, wherein the agents are antibodies or antigen-binding fragments thereof.

6. The method of claim 1, further comprising: contacting the biological sample with a breast cancer-associated polypeptide other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

7. A method for diagnosing breast cancer in a subject comprising: obtaining a biological sample from a subject, contacting the sample with antibodies or antigen-binding fragments thereof, that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, and determining specific binding between the antibodies or antigen-binding fragments thereof and breast cancer-associated polypeptides in the sample, wherein the presence of specific binding is diagnostic for breast cancer in the subject.

8. The method of claim 7, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

9. The method of claim 8, wherein the tissue is breast tissue.

10. The method of claim 8, wherein the tissue is lymph node tissue.

11. The method of claim 8, wherein the cells are from lymph node fluid or breast discharge fluid.

12. The method of claim 7, wherein the biological sample is contacted with antibodies or antigen-binding fragments thereof, that bind specifically to at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

13. The method of claim 7, further comprising: contacting the biological sample with an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

14. The method of claim 7, wherein the antibodies are monoclonal or polyclonal antibodies.

15. The method of claim 7, wherein the antibodies are chimeric, human, or humanized antibodies.

16. The method of claim 7, wherein the antibodies are single chain antibodies.

17. The method of claim 7, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

18. A method for determining onset, progression, or regression, of breast cancer in a subject, comprising: obtaining from a subject a first biological sample, contacting the first sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between agents in the first sample and the at least two different breast cancer-associated polypeptides, obtaining from a subject a second biological sample, contacting the second biological sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between agents in the second sample and the at least two different breast cancer-associated polypeptides, and comparing the determination of binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of the breast cancer.

19. The method of claim 18, wherein the sample is a blood sample.

20. The method of claim 18, wherein the sample is a lymph node fluid or breast discharge fluid.

21. The method of claim 18, wherein binding is determined between the agents and at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

22. The method of claim 18, wherein the agents are antibodies or antigen-binding fragments thereof.

23. The method of claim 18, further comprising: determining binding between the agents and a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

24. A method for determining onset, progression, or regression, of breast cancer in a subject, comprising: obtaining from a subject a first biological sample, contacting the first sample with antibodies or antigen-binding fragments thereof, that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between breast cancer-associated polypeptides in the first sample and the antibodies or antigen-binding fragments thereof, obtaining from a subject a second biological sample, contacting the second sample with antibodies or antigen-binding fragments thereof, that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between breast cancer-associated polypeptides in the second sample and the antibodies or antigen-binding fragments thereof, and comparing the determination of specific binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of breast cancer.

25. The method of claim 24, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

26. The method of claim 25, wherein the tissue is breast tissue.

27. The method of claim 25, wherein the tissue is lymph node tissue.

28. The method of claim 25, wherein the cells are from lymph node fluid or breast discharge fluid.

29. The method of claim 24, wherein binding is determined between the breast cancer-associated polypeptides and antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

30. The method of claim 24, further comprising: determining binding between the breast cancer-associated polypeptide and an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

31. The method of claim 24, wherein the antibodies are monoclonal or polyclonal antibodies.

32. The method of claim 24, wherein the antibodies are chimeric, human, or humanized antibodies.

33. The method of claim 24, wherein the antibodies are single chain antibodies.

34. The method of claim 24, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

35. A method for selecting a course of treatment of a subject having or suspected of having breast cancer, comprising: obtaining from the subject a biological sample, contacting the sample with at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, determining specific binding between agents in the sample that are differentially expressed in different types of cancer, and the breast cancer-associated polypeptides, and selecting a course of treatment appropriate to the cancer of the subject.

36. The method of claim 35, wherein the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptides.

37. The method of claim 36, wherein the antibodies are labeled with one or more cytotoxic agents.

38. The method of claim 35, wherein the sample is a blood sample.

39. The method of claim 35, wherein the sample is lymph node fluid or breast discharge fluid.

40. The method of claim 35, wherein the agents are antibodies or antigen-binding fragments thereof.

41. The method of claim 35, wherein the sample is contacted with at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

42. The method of claim 35, further comprising: contacting the sample with a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

43. A method for selecting a course of treatment of a subject having or suspected of having breast cancer, comprising: obtaining from the subject a biological sample, contacting the sample with antibodies or antigen-binding fragments thereof that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81 determining specific binding between breast cancer-associated polypeptides in the sample that are differentially expressed in different types of cancer, and the antibodies or antigen-binding fragments thereof, and selecting a course of treatment appropriate to the cancer of the subject.

44. The method of claim 43, wherein the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptides.

45. The method of claim 44, wherein the antibodies are labeled with one or more cytotoxic agents.

46. The method of claim 43, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

47. The method of claim 46, wherein the tissue is breast tissue.

48. The method of claim 46, wherein the tissue is lymph node tissue.

49. The method of claim 46, wherein the cells are from lymph node fluid or breast discharge fluid.

50. The method of claim 43, wherein the sample is contacted with antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81.

51. The method of claim 43, further comprising: contacting the sample with an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

52. The method of claim 44, wherein the antibodies are monoclonal or polyclonal antibodies.

53. The method of claim 44, wherein the antibodies are chimeric, human, or humanized antibodies.

54. The method of claim 44, wherein the antibodies are single chain antibodies.

55. The method of claim 44, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

56. A kit for the diagnosis of breast cancer in a subject, comprising: at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 1-40, and 81, one or more control antigens, and instructions for the use of the polypeptides in the diagnosis of breast cancer.

57. The kit of claim 56, wherein the breast cancer-associated polypeptides are bound to a substrate.

58. The kit of claim 56, wherein the one or more agents are antibodies or antigen-binding fragments thereof.

59. The kit of claim 56, wherein the kit comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81.

60. The kit of claim 56, wherein the kit further comprises a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

61. A kit for the diagnosis of breast cancer in a subject, comprising: antibodies or antigen-binding fragments thereof that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81, one or more control agents, and instructions for the use of the agents in the diagnosis of breast cancer.

62. The kit of claim 61, wherein the one or more agents are antibodies or antigen-binding fragments thereof.

63. The kit of claim 61, wherein the one or more agents are bound to a substrate.

64. The kit of claim 61, wherein the kit comprises antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 1-40, and 81.

65. The kit of claim 61, wherein the kit further comprises an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

66. A protein microarray comprising at least two different breast cancer-associated polypeptides, wherein the breast cancer-associated polypeptides are encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 1-40, and 81, fixed to a solid substrate.

67. The protein microarray of claim 66, wherein the microarray comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

68. The protein microarray of claim 66, further comprising a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

69. The protein microarray of claim 66, further comprising at least one control polypeptide molecule.

70. A protein microarray comprising antibodies or antigen-binding fragments thereof, that specifically bind at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs:1-40, and 81, fixed to a solid substrate.

71. The protein microarray of claim 70, wherein the microarray comprises antibodies or antigen-binding fragments thereof, that bind specifically to least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

72. The protein microarray of claim 70, further comprising an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide other than those encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

73. The protein microarray of claim 70, further comprising at least one control polypeptide molecule.

74. The protein microarray of claim 70, wherein the antibodies are monoclonal or polyclonal antibodies.

75. The protein microarray of claim 70, wherein the antibodies are chimeric, human, or humanized antibodies.

76. The protein microarray of claim 70, wherein the antibodies are single chain antibodies.

77. The protein microarray of claim 70, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

78. A nucleic acid microarray comprising at least two nucleic acids selected from the group consisting of SEQ ID NOs: 1-40, and 81, fixed to a solid substrate.

79. The nucleic acid microarray of claim 78, wherein the microarray comprises at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 different nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

80. The nucleic acid microarray of claim 78, further comprising a nucleic acid molecule other than those selected from the group consisting of SEQ ID NOs:1-40, and 81.

81. The nucleic acid microarray of claim 78, further comprising at least one control nucleic acid molecule.

82. A method for diagnosing breast cancer in a subject comprising: obtaining from the subject a biological sample, and determining the expression of at least two breast cancer-associated nucleic acid molecules or expression products thereof in the sample, wherein the nucleic acid molecules comprise a nucleotide sequence selected from the group consisting of: SEQ ID NO: 1-40, and 81 wherein the expression is diagnosis of the breast cancer in the subject.

83. The method of claim 82, wherein expression is determined for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

84. The method of claim 82, further comprising: determining expression of a breast cancer-associated nucleic acid molecule other than those comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

85. The method of claim 82, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

86. The method of claim 85, wherein the tissue is breast tissue.

87. The method of claim 85, wherein the tissue is lymph node tissue.

88. The method of claim 85, wherein the cells are from lymph node fluid or breast discharge fluid.

89. The method of claim 82, wherein the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.

90. The method of claim 89, wherein the hybridization is performed using a nucleic acid microarray.

91. A method for determining onset, progression, or regression, of breast cancer in a subject comprising: obtaining from a subject a first biological sample, determining a level of expression of at least two breast cancer-associated nucleic acid molecules or expression products thereof in the first sample, wherein the nucleic acid molecules are selected from the group consisting of: SEQ ID NOs: 1-40, and 81, obtaining from the subject a second biological sample, determining a level of expression of at least two breast cancer-associated nucleic acid molecules or expression products thereof in the second sample, wherein the nucleic acid molecules are selected from the group consisting of: SEQ ID NOs: 1-40, and 81, and comparing the level of expression in the first sample to the level of expression in the second sample as a determination of the onset, progression, or regression of the breast cancer.

92. The method of claim 91, wherein expression is determined for at least 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, or 40 nucleic acid molecules selected from the group consisting of SEQ ID NOs:1-40, and 81.

93. The method of claim 91, further comprising: determining expression for a breast cancer-associated nucleic acid molecule other than those comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:1-40, and 81.

94. The method of claim 91, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood and breast discharge fluid.

95. The method of claim 94, wherein the tissue is breast tissue.

96. The method of claim 94, wherein the tissue is lymph node tissue.

97. The method of claim 94, wherein the cells are from lymph node fluid or breast discharge fluid.

98. The method of claim 91, wherein the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.

99. The method of claim 98, wherein the hybridization is performed using a nucleic acid microarray.

100. A method for diagnosing cancer in a subject comprising: obtaining a biological sample from a subject, contacting the sample with a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, and determining specific binding between the breast cancer-associated polypeptide and agents in the sample, wherein the presence of specific binding is diagnostic for cancer in the subject.

101. The method of claim 100, wherein the sample is blood.

102. The method of claim 100, wherein the sample is lymph node fluid or breast discharge fluid.

103. The method of claim 100, wherein the agents are antibodies or antigen-binding fragments thereof.

104. The method of claim 100, wherein the cancer is breast cancer.

105. A method for diagnosing cancer in a subject comprising: obtaining a biological sample from a subject, contacting the sample with an antibody or antigen-binding fragment thereof, that binds specifically to a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs:19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, and determining specific binding between the antibody or antigen-binding fragment thereof and the breast cancer-associated polypeptide in the sample, wherein the presence of specific binding is diagnostic for cancer in the subject.

106. The method of claim 105, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

107. The method of claim 106, wherein the tissue is breast tissue.

108. The method of claim 106, wherein the tissue is lymph node tissue.

109. The method of claim 106, wherein the cells are from lymph node fluid or breast discharge fluid.

110. The method of claim 105, wherein the antibodies are monoclonal or polyclonal antibodies.

111. The method of claim 105, wherein the antibodies are chimeric, human, or humanized antibodies.

112. The method of claim 105, wherein the antibodies are single chain antibodies.

113. The method of claim 105, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

114. The method of claim 105, wherein the cancer is breast cancer.

115. A method for determining onset, progression, or regression, of cancer in a subject, comprising: obtaining from a subject a first biological sample, contacting the first sample with a breast cancer associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between agents in the first sample and the breast cancer-associated, obtaining from a subject a second biological sample, contacting the second sample with a breast cancer associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between agents in the second sample and the breast cancer-associated polypeptide, and comparing the determination of binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of cancer.

116. The method of claim 115, wherein the sample is a blood sample.

117. The method of claim 115, wherein the sample is lymph node fluid or breast discharge fluid.

118. The method of claim 115, wherein the agents are antibodies or antigen-binding fragments thereof.

119. The method of claim 115, wherein the cancer is breast cancer.

120. A method for determining onset, progression, or regression, of cancer in a subject, comprising: obtaining from a subject a first biological sample, contacting the first sample with antibodies or antigen-binding fragments thereof, that bind specifically to a breast cancer-associated polypeptides encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between breast cancer-associated polypeptides in the first sample and the antibodies or antigen-fragments thereof, obtaining from a subject a second biological sample, contacting the second sample with antibodies or antigen-binding fragments thereof, that bind specifically to a breast cancer-associated polypeptides encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81 determining specific binding between breast cancer-associated polypeptides in the second sample and the antibodies or antigen-binding fragments thereof, and comparing the determination of specific binding in the first sample to the determination of specific binding in the second sample as a determination of the onset, progression, or regression of cancer.

121. The method of claim 120, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

122. The method of claim 121, wherein the tissue is breast tissue.

123. The method of claim 121, wherein the tissue is lymph node tissue.

124. The method of claim 121, wherein the cells are from lymph node fluid or breast discharge fluid.

125. The method of claim 120, wherein the antibodies are monoclonal or polyclonal antibodies.

126. The method of claim 120, wherein the antibodies are chimeric, human, or humanized antibodies.

127. The method of claim 120, wherein the antibodies are single chain antibodies.

128. The method of claim 120, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

129. The method of claim 120, wherein the cancer is breast cancer.

130. A method for selecting a course of treatment of a subject having or suspected of having cancer, comprising: obtaining from the subject a biological sample, contacting the sample with a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between agents in the sample that are differentially expressed in different types of cancer, and the breast cancer-associated polypeptide, and selecting a course of treatment appropriate to the cancer of the subject.

131. The method of claim 130, wherein the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptide.

132. The method of claim 131, wherein the antibodies are labeled with one or more cytotoxic agents.

133. The method of claim 130, wherein the sample is a blood sample.

134. The method of claim 130, wherein the sample is lymph node fluid or breast discharge fluid.

135. The method of claim 130, wherein the agents are antibodies or antigen-binding fragments thereof.

136. The method of claim 130, wherein the cancer is breast cancer.

137. A method for selecting a course of treatment of a subject having or suspected of having cancer, comprising: obtaining from the subject a biological sample, contacting the sample with antibodies or antigen-binding fragments thereof that bind specifically to at least two different breast cancer-associated polypeptides encoded by nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, determining specific binding between breast cancer-associated polypeptides in the sample that are differentially expressed in different types of cancer, and the antibodies or antigen-binding fragments thereof, and selecting a course of treatment appropriate to the cancer of the subject.

138. The method of claim 137, wherein the treatment is administering antibodies that specifically bind to the breast cancer-associated polypeptide.

139. The method of claim 138, wherein the antibodies are labeled with one or more cytotoxic agents.

140. The method of claim 137, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

141. The method of claim 140, wherein the tissue is breast tissue.

142. The method of claim 140, wherein the tissue is lymph node tissue.

143. The method of claim 140, wherein the cells are from lymph node fluid or breast discharge fluid.

144. The method of claim 137, wherein the antibodies are monoclonal or polyclonal antibodies.

145. The method of claim 137, wherein the antibodies are chimeric, human, or humanized antibodies.

146. The method of claim 137, wherein the antibodies are single chain antibodies.

147. The method of claim 137, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

148. The method of claim 137, wherein the cancer is breast cancer.

149. A kit for the diagnosis of cancer in a subject, comprising: a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39 and 81; one or more control antigens; and instructions for the use of the polypeptide and control antigens in the diagnosis of cancer.

150. The kit of claim 149, wherein the breast cancer-associated polypeptide is bound to a substrate.

151. The kit of claim 149, wherein the one or more agents are antibodies or antigen-binding fragments thereof.

152. The kit of claim 149, wherein the cancer is breast cancer.

153. A kit for the diagnosis of cancer in a subject, comprising: antibodies or antigen-binding fragments thereof that bind specifically to a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, one or more control agents; and instructions for the use of the antibodies, antigen-binding fragments, and agents in the diagnosis of cancer.

154. The kit of claim 153, wherein the one or more agents are antibodies or antigen-binding fragments thereof.

155. The kit of claim 153, wherein the one or more agents are bound to a substrate.

156. The kit of claim 153, wherein the cancer is breast cancer.

157. A protein microarray comprising a breast cancer-associated polypeptide, wherein the breast cancer-associated polypeptide is encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: SEQ II) NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, fixed to a solid substrate.

158. The protein microarray of claim 157, further comprising at least one control polypeptide molecule.

159. A protein microarray comprising antibodies or antigen-binding fragments thereof, that specifically bind a breast cancer-associated polypeptide encoded by a nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, fixed to a solid substrate.

160. The protein microarray of claim 159, further comprising at least one control polypeptide molecule.

161. The protein microarray of claim 159, wherein the antibodies are monoclonal or polyclonal antibodies.

162. The protein microarray of claim 159, wherein the antibodies are chimeric, human, or humanized antibodies.

163. The protein microarray of claim 159, wherein the antibodies are single chain antibodies.

164. The protein microarray of claim 159, wherein the antigen-binding fragments are F(ab′)2, Fab, Fd, or Fv fragments.

165. A nucleic acid microarray comprising a nucleic acid selected from the group consisting of SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, fixed to a solid substrate.

166. The nucleic acid microarray of claim 165, further comprising at least one control nucleic acid molecule.

167. A method for diagnosing cancer in a subject comprising: obtaining from the subject a biological sample, and determining the expression of a breast cancer-associated nucleic acid molecule or expression product thereof in the sample, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: SEQ ID NO: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, wherein the expression is diagnostic of cancer in the subject.

168. The method of claim 167, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

169. The method of claim 168, wherein the tissue is breast tissue.

170. The method of claim 168, wherein the tissue is lymph node tissue.

171. The method of claim 168, wherein the tissue is cells from lymph node fluid or breast discharge fluid.

172. The method of claim 167, wherein the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.

173. The method of claim 172, wherein the hybridization is performed using a nucleic acid microarray.

174. The method of claim 167, wherein the cancer is breast cancer.

175. A method for determining onset, progression, or regression, of cancer in a subject comprising: obtaining from a subject a first biological sample, determining a level of expression of a breast cancer-associated nucleic acid molecule or expression products thereof in the first sample, wherein the nucleic acid molecule is selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, obtaining from the subject a second biological sample, determining a level of expression of a breast cancer-associated nucleic acid molecule or expression product thereof in the second sample, wherein the nucleic acid molecule is selected from the group consisting of: SEQ ID NOs: 19, 20, 21, 22, 23, 24, 33, 36, 39, and 81, and comparing the level of expression in the first sample to the level of expression in the second sample as a determination of the onset, progression, or regression of the cancer.

176. The method of claim 175, wherein the sample is selected from the group consisting of: tissue, cells, lymph node fluid, blood, and breast discharge fluid.

177. The method of claim 176, wherein the tissue is breast tissue.

178. The method of claim 176, wherein the tissue is lymph node tissue.

179. The method of claim 176, wherein the tissue is cells from lymph node fluid or breast discharge fluid.

180. The method of claim 175, wherein the expression of breast cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.

181. The method of claim 180, wherein the hybridization is performed using a nucleic acid microarray.

182. The method of claim 175, wherein the cancer is breast cancer.

183. A method for diagnosing cancer in a subject comprising: obtaining a non-testis biological sample from a subject, determining the level of expression of one or more cancer-associated nucleic acid molecule comprising a nucleotide sequences selected from the group consisting of SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81, comparing the level of expression of the nucleic acid molecule in the subject sample to a level of expression of the nucleic acid molecule in a control tissue, wherein a determination that the level of expression of the nucleic acid in the sample from the subject is greater than about three times the level of expression of the nucleic acid in the control tissue, indicates cancer in the subject.

184. The method of claim 183, wherein the level of expression of the nucleic acid in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue.

185. The method of claim 183, wherein expression is determined for at least 2, 3, 4, 5, 6, or 7 nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81.

186. The method of claim 183, wherein the sample is selected from the group consisting of: tissue and cells.

187. The method of claim 183, wherein the cancer is breast cancer.

188. The method of claim 186, wherein the tissue is breast tissue.

189. The method of claim 183, wherein the expression of cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.

190. The method of claim 189, wherein the hybridization is performed using a nucleic acid microarray.

191. The method of claim 189, wherein the nucleic acid amplification is real-time RT-PCR or RT-PCR.

192. A method for determining onset, progression, or regression, of cancer in a subject comprising: obtaining from a subject a first and a second biological sample, wherein the samples comprise the same tissue type and are obtained at different times, determining a level of expression of one or more cancer-associated nucleic acid molecules or expression products thereof in the first and second biological samples, wherein the nucleic acid molecules comprise nucleotide sequences selected from the group consisting of: SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81, comparing the level of expression of one or more cancer-associated nucleic acid molecules in the first and the second biological samples to the level of expression of the one or more cancer-associated nucleic acid molecules in a control sample, wherein a higher level of expression of the one or more cancer-associated nucleic acid molecules in the first sample than in the second sample indicates regression of cancer, wherein a lower level of expression of the one or more cancer-associated nucleic acid molecules in the first sample than the second sample indicates progression of cancer, and wherein a level of expression of the cancer-associated nucleic acid molecule in the first sample that is less than three times higher than the level of expression of the cancer-associated nucleic acid molecule in the control sample and a level of expression of the cancer-associated nucleic acid molecules in the second sample that is three or more times higher than the level in the control sample, indicates onset of cancer

193. The method of claim 192, wherein the level of expression of the one or more nucleic acid molecules in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue.

194. The method of claim 192, wherein expression is determined for at least 2, 3, 4, 5, 6, or 7 nucleic acid molecules comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 22, 31, 32, 33, 34, 40, and 81.

195. The method of claim 192, wherein the sample is selected from the group consisting of: tissue and cells.

196. The method of claim 192, wherein the cancer is breast cancer.

197. The method of claim 195, wherein the tissue is breast tissue.

198. A method for diagnosing cancer in a subject comprising: obtaining a biological sample from a subject, determining the level of expression of a cancer-associated nucleic acid molecule comprising a nucleotide sequence selected from the group consisting of SEQ ID NOs: 33 and 81, and comparing the level of expression of the nucleic acid molecule in the subject sample to a level of expression of the nucleic acid in a control tissue, wherein a determination that the level of expression of the nucleic acid in the sample from the subject is greater than about three times of the level of expression of the nucleic acid in the control tissue, indicates cancer in the subject.

199. The method of claim 198, wherein the level of expression of the nucleic acid in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue.

200. The method of claim 198, wherein the sample is selected from the group consisting of: tissue and cells.

201. The method of claim 198, wherein the cancer is colon cancer.

202. The method of claim 200, wherein the tissue is colorectal tissue.

203. The method of claim 198, wherein the expression of cancer-associated nucleic acid molecules is determined by a method selected from the group consisting of nucleic acid hybridization and nucleic acid amplification.

204. The method of claim 203, wherein the hybridization is performed using a nucleic acid microarray.

205. The method of claim 203, wherein the nucleic acid amplification is real-time RT-PCR or RT-PCR.

206. A method for determining onset, progression, or regression, of cancer in a subject comprising: obtaining from a subject a first and a second biological sample, wherein the samples comprise the same tissue type and are obtained at different times, determining a level of expression of a cancer-associated nucleic acid molecule or expression product thereof in the first and second biological samples, wherein the nucleic acid molecule comprises a nucleotide sequence selected from the group consisting of: SEQ ID NOs: 33 and 81, and comparing the level of expression of the cancer-associated nucleic acid molecule of the first and the second biological samples to the level of expression of the cancer-associated nucleic acid molecule in a control sample, wherein a higher level of expression of the cancer-associated nucleic acid molecule in the first sample than in the second sample indicates regression of cancer, wherein a lower level of expression of the cancer-associated nucleic acid molecule in the first sample than the second sample indicates progression of cancer, and wherein a level of expression of the cancer-associated nucleic acid molecule in the first sample that is less than three times higher than the level of expression of the cancer-associated nucleic acid molecule in the control sample, and a level of expression of the cancer-associated nucleic acid molecules in the second sample that is three or more times higher than the level in the control sample, indicates onset of cancer.

207. The method of claim 206, wherein the level of expression of the one or more nucleic acid molecules in the sample from the subject is at least about 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, or 50 times the level of expression in the control tissue.

208. The method of claim 206, wherein the sample is selected from the group consisting of: tissue and cells.

209. The method of claim 206, wherein the cancer is colon cancer.

210. The method of claim 208, wherein the tissue is colorectal tissue.