Method of diagnosing, treating and determining progression and survival of cancer cells using bcl-2 antagonist of cell death (bad) pathway gene signature

Abstract

The present invention relates to the BAD pathway's influence on development, progression, chemo-sensitivity, and overall survival for multiple human cancers and its potential as a therapeutic target to increase chemo-sensitivity. BAD pathway expression was associated with the development and/or progression of breast, colon, and endometrial cancers, relapse-free survival from breast cancer, and overall survival from ovarian, colon, and brain cancers. Expression was also associated with in vitro sensitivity to a range of cytotoxic agents. pBAD levels were higher in cancer versus immortalized normal cells and chemo-resistant versus—sensitive cancer cells and associated with increased cell proliferation.

What is claimed is: 
     
         1 . A method of treating breast cancer comprising:
 obtaining a sample suspected of being cancerous or pre-cancerous from a patient;   obtaining an expression level of BAD pathway genes PPP3CC, YWHAB, CDC2 and PPP2CA.   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2′+ t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   calculating a median BPGES score using a highest and a lowest value of the expression levels of the BAD pathway genes obtained in the sample;   determining if the cancerous or pre-cancerous cells of the patient will be sensitive to carboplatin by comparing the BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous to the median BPGES score;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the median BPGES score is indicative of chemosensitive breast cancer; and   administering carboplatin to the patient having the high BPGES score.   
     
     
         2 . A method of treating leukemia comprising:
 obtaining a sample suspected of being cancerous or pre-cancerous from a patient;   obtaining an expression level of BAD pathway genes SHC1, EGFR, MAPK8, BAX and PRKAR2A.   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2′+ t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   calculating a median BPGES score using a highest and a lowest value of the expression levels of the BAD pathway genes obtained in the sample;   determining if the cancerous or pre-cancerous cells of the patient will be sensitive to carboplatin by comparing the BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous to the median BPGES score;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the median BPGES score is indicative of chemosensitive leukemia; and   administering carboplatin to the patient having the high BPGES score   
     
     
         3 . A method of treating leukemia comprising:
 obtaining a sample suspected of being cancerous or pre-cancerous from a patient;   obtaining an expression level of at least five BAD pathway genes selected from the group consisting of SHC1, EGFR, MAPK8, BAX, PRKAR2A, PRKACB, PPP3CB, IRS1, AKT2, GNB5, GNG5, PPP3CA, CDC2, GNG7, MAPK1, PIK3CB, RPS6KA2, RPS6KB1, PIK3R3, AKT3, BCL2, GNB2, AKT1, PPP3CC, GRB2, BAD, SFN, YWHAQ, GNG3, YWHAZ, and PPP2CB;   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   calculating a median BPGES score using a highest and a lowest value of the expression levels of the at least five BAD pathway genes obtained in the sample;   determining if the cancerous or pre-cancerous cells of the patient will be sensitive to gemcitabine by comparing the BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous to the median BPGES score;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the median BPGES score is indicative of chemosensitive leukemia; and   administering gemcitabine to the patient having the high BPGES score.   
     
     
         4 . The method of  claim 3 , wherein the genes are SHC1, EGFR, MAPK8, BAX, and PRKAR2A. 
     
     
         5 . A method of treating cancer comprising:
 obtaining a sample suspected of being cancerous or pre-cancerous from a patient;   obtaining an expression level of at least five BAD pathway genes selected from the group consisting of SHC1, IRS1, BCL2, AKT3, GNB1, PIK3R3, PPM1B, YWHAE, GNB2, AKT1, PPP3CC, GRB2, BAD, SFN, YWHAQ, GNG3, YWHAZ, and PPP2CB;   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   calculating a median BPGES score using a highest and a lowest value of the expression levels of the at least five BAD pathway genes obtained in the sample;   determining if the cancerous or pre-cancerous cells of the patient will be sensitive to paclitaxel by comparing the BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous to the median BPGES score;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the median BPGES score is indicative of chemosensitive cancer; and   administering paclitaxel to the patient having the high BPGES score wherein the cancer is colon cancer or melanoma.   
     
     
         6 . The method of  claim 5 , wherein the genes are SHC1, IRS1, BCL2, AKT3, GNB1. 
     
     
         7 . The method of  claim 6 , wherein the cancer is colon cancer. 
     
     
         8 . The method of  claim 5 , wherein the genes are PIK3R3, AKT1, PPM1B, PPP3CC, and YWHAE. 
     
     
         9 . The method of  claim 8 , wherein the cancer is melanoma. 
     
     
         10 . A method of treating breast cancer comprising:
 obtaining a sample suspected of being cancerous or pre-cancerous from a patient;   obtaining an expression level of BAD pathway genes PTPN11, EGFR, YWHAZ, PPP3CA, PRKACB, and GNB3;   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   calculating a median BPGES score using a highest and a lowest value of the expression levels of the BAD pathway genes obtained in the sample;   determining if the cancerous or pre-cancerous cells of the patient will be sensitive to topotecan by comparing the BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous to the median BPGES score;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the median BPGES score is indicative of chemosensitive breast cancer; and   administering topotecan to the patient having the high BPGES score.   
     
     
         11 . A method of treating colon cancer comprising:
 obtaining a sample suspected of being cancerous or pre-cancerous from a patient;   obtaining an expression level of BAD pathway genes SHC1, IRS1, BCL2, AKT3 and GNB1;   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   calculating a median BPGES score using a highest and a lowest value of the expression levels of the BAD pathway genes obtained in the sample;   determining if the cancerous or pre-cancerous cells of the patient will be sensitive to docetaxel by comparing the BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous to the median BPGES score;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the median BPGES score is indicative of chemosensitive colon cancer; and   administering docetaxel to the patient having the high BPGES score.   
     
     
         12 . A method of diagnosing cancer comprising:
 obtaining an expression level of at least one Bcl-2 antagonist of cell death (BAD) pathway gene selected from the group consisting of those genes listed in  FIGS. 6 and 7  in a sample suspected of being cancerous or pre-cancerous;   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i , is score, p i  is loading coefficient, and E is residual matrix;   obtaining an expression level of a control;   using the expression level of the control to obtain a BAD Pathway Gene Expression Signature (BPGES) score of the control;   comparing the BPGES score of the sample suspected of being cancerous or pre-cancerous to the BPGES score of the control sample;   wherein a higher BAD Pathway Gene Expression Signature (BPGES) score for the sample suspected of being cancerous or pre-cancerous as compared to the control sample is indicative of cancer; and   administering a chemotherapeutic to the patient if a high BPGES score is obtained;   wherein the cancer is selected from the group consisting of breast cancer, ovarian cancer, endometrial cancer, colon cancer, lung cancer, leukemia, brain cancer and melanoma.   
     
     
         13 . The method of  claim 12 , wherein the chemotherapeutic is carboplatin, cyclophosphamide, topotecan, docetaxel, paclitaxel, or gemcitabine. 
     
     
         14 . A method of determining survival from cancer comprising:
 identifying at least one BAD pathway gene differentially expressed in cells sensitive to at least one chemotherapeutic versus cells resistant to the at least one chemotherapeutic wherein the at least one BAD pathway gene is selected from the group consisting of genes listed in  FIGS. 6 and 7 ; and   comparing the least one BAD pathway gene in a sample suspected of being cancerous or pre-cancerous to a control sample;   wherein a lower differential expression of the at least one BAD pathway gene of the sample suspected of being cancerous or pre-cancerous as compared to the control sample is indicative of cancer non-survival;   wherein the cancer is selected from the group consisting of breast cancer, ovarian cancer, endometrial cancer, colon cancer, lung cancer, leukemia, brain cancer and melanoma.   
     
     
         15 . The method of  claim 14 , wherein the chemotherapeutic is carboplatin, cyclophosphamide, topotecan, docetaxel, paclitaxel, or gemcitabine. 
     
     
         16 . A method of identifying cancer sensitivity to chemotherapeutics comprising:
 obtaining an expression level of at least one Bcl-2 antagonist of cell death (BAD) pathway gene selected from the group consisting of those genes listed in  FIGS. 6 and 7  in a sample suspected of being cancerous or pre-cancerous;   determining a BAD Pathway Gene Expression Signature (BPGES) score of the sample suspected of being cancerous or pre-cancerous wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   obtaining an expression level of at least one Bcl-2 antagonist of cell death (BAD) pathway gene from a control sample;   determining a BPGES score of the control sample;   comparing the BPGES score of the sample suspected of being cancerous or pre-cancerous to the BPGES score of the control sample;   wherein the BAD Pathway Gene Expression Signature (BPGES) score identifies the chemosensitivity of cancerous or pre-cancerous cells to at least one chemotherapeutic;   wherein a high BAD Pathway Gene Expression Signature (BPGES) score as compared to the control BPGES score is indicative of chemosensitive cancer; and   administering a chemotherapeutic to the patient if a high BPGES is obtained.   
     
     
         17 . The method of  claim 16 , wherein the chemotherapeutic is carboplatin, topotecan, docetaxel, gemcitabine and paclitaxel. 
     
     
         18 . A method of monitoring neoplasia progression from one biological state to another in a tumor sample comprising:
 obtaining an expression level of at least one Bcl-2 antagonist of cell death (BAD) pathway gene selected from the group consisting of those genes listed in  FIGS. 6 and 7  in a tumor sample;   determining a first BAD Pathway Gene Expression Signature (BPGES) score of the tumor sample at a first timepoint wherein the BPGES score is determined by principal component analysis (PCA) in which X=t 1 *p 1 ′+t 2 *p 2 ′+t 3 *p 3 ′+ . . . +t A *p A ′+E, where X is gene expression value, t i  is score, p i  is loading coefficient, and E is residual matrix;   obtaining a second BPGES score from the tumor sample at a second timepoint wherein the second timepoint is at a given interval after the first timepoint; and   comparing the first and the second BPGES score to each other;   wherein a decrease in the second BPGES score as compared to the first BPGES score is indicative of neoplasia progression and an increase in the second BPGES score as compared to the first BPGES score is indicative of neoplasia regression; and   administering a chemotherapeutic to the patient if the second BPGES score is increased as compared to the first BPGES score;   wherein the neoplasia is selected from the group consisting of breast cancer, ovarian cancer, endometrial cancer, colon cancer, lung cancer, leukemia, brain cancer and melanoma.   
     
     
         19 . The method of  claim 18 , wherein the neoplasia progression being monitored is normal tissue to pre-cancerous tissue, normal to pre-invasive cancerous tissue, pre-cancerous tissue to pre-invasive cancerous tissue, or pre-invasive cancerous tissue to invasive cancerous tissue.