Methods and compositions for identifying, classifying and monitoring subject having bcl-2 family inhibitor-resistant tumors and cancers

Abstract

The invention is directed to methods and kits that allow for identifying, classifying, and monitoring cancer patients for Bcl-2 family inhibitor therapies. The methods and compositions of the invention are directed to determining amplification of Bcl-x L and in cancer or tumor cells, or elevated Bcl-x L polypeptide expression.

We claim: 
     
         1 . A method of classifying a patient having a cancer that is resistant to a Bcl-2 family inhibitor, comprising:
 (a) providing a tissue sample from a patient;   (b) determining if a Bcl-x L  gene is amplified; and   (c) classifying the patient as resistant to the Bcl-2 small molecule inhibitor if the Bcl-x L  gene is amplified.   
     
     
         2 . A method for identifying a patient with cancer as eligible to receive a Bcl-2-family inhibitor therapy comprising:
 (a) providing a tissue sample from a patient;   (b) determining if expression of a Bcl-x L  gene is amplified; and   (c) classifying the patient as eligible to receive the Bcl-2 family inhibitor if the Bcl-x L  gene is not amplified.   
     
     
         3 . The method of  claim 1  or  2 , wherein the Bcl-2 family inhibitor is ABT-263. 
     
     
         4 . The method of  claim 1  or  2 , wherein amplification of the Bcl-x L  gene correlates with an increase in expression of Bcl-x L  polypeptide. 
     
     
         5 . The method of  claim 1  or  2 , wherein the tissue sample comprises a peripheral blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a bone marrow sample, a lymph node sample, a urine sample, an ascites sample, a lavage sample, an esophageal brushing sample, a bladder or lung wash sample, a spinal fluid sample, a brain fluid sample, a ductal aspirate sample, a nipple discharge sample, a pleural effusion sample, a fresh frozen tissue sample, a paraffin embedded tissue sample or an extract or processed sample produced from any of a peripheral blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a bone marrow sample, a urine sample, an ascites sample, a lavage sample, an esophageal brushing sample, a bladder or lung wash sample, a spinal fluid sample, a brain fluid sample, a ductal aspirate sample, a nipple discharge sample, a pleural effusion sample, a fresh frozen tissue sample or a paraffin embedded tissue sample. 
     
     
         6 . The method of  claim 1  or  2 , wherein the determining step comprises in situ hybridization. 
     
     
         7 . The method of  claim 8 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled. 
     
     
         8 . The method of  claim 8 , wherein the in situ hybridization is performed with a nucleic acid probe or peptide nucleic acid probe that specifically hybridizes to at least part of the Bcl-x L  gene. 
     
     
         9 . The method of  claim 1  or  2 , wherein determining comprises a polymerase chain reaction. 
     
     
         10 . The method of  claim 11 , wherein the polymerase chain reaction is performed with at least one primer that specifically hybridizes to at least part of a nucleic acid sequence of the Bcl-x L  gene. 
     
     
         11 . The method of  claim 1  or  2 , wherein the determining step comprises a nucleic acid microarray assay. 
     
     
         12 . The method of  claim 1  or  2 , wherein the tissue sample is from a patient with a cancer selected from the group consisting of small-cell lung carcinoma and a lymphoma. 
     
     
         13 . The method of  claim 2 , wherein the patient is classified as eligible to receive an anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L . 
     
     
         14 . A method for monitoring a patient being treated with an anti-Bcl-2-family agent comprising:
 (a) providing a test sample from a cancer patient;   (b) identifying in or extracting from the test sample tumor or cancer cells;   (c) determining in the tumor or cancer cells if a Bcl-x L  gene is amplified; and   (d) comparing number of tumor or cancer cells having an amplified Bcl-x L  gene to baseline level of such tumor or cancer cells determined before or at onset of therapy.   
     
     
         15 . The method of  claim 14 , wherein the cancer is selected from the group consisting of small cell lung carcinoma and a lymphoma. 
     
     
         16 . The method of  claim 14 , wherein the patient is being treated with ABT-263. 
     
     
         17 . The method of  claim 14 , wherein amplification of the Bcl-x L  gene correlates with an increase in expression of Bcl-x L  polypeptide. 
     
     
         18 . The method of  claim 17 , wherein the patient is being treated with an anti-sense agent designed to bind to at least one of Bcl-2, Bcl-w, and Bcl-x L . 
     
     
         19 . The method of  claim 14 , wherein the determining step comprises in situ hybridization. 
     
     
         20 . The method of  claim 19 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled. 
     
     
         21 . The method of  claim 14 , wherein the tumor cells are circulating tumor cells. 
     
     
         22 . A method of classifying a patient having a cancer that is resistant to a Bcl-2 family inhibitor, comprising
 (a) providing a test sample from a patient;   (b) determining in the test sample:
 (i) if Bcl-x L  gene is amplified; and 
 (ii) an amount of Bcl-x L  in the test sample; 
   (c) determining if the amount of Bcl-x L  in the test sample is higher or lower then the amount of Bcl-x L  in a control; and   (d) classifying the patient as having a cancer that is resistant to the Bcl-2 family inhibitor based on:
 (i) amplification of the Bcl-x L  gene; and 
 (ii) the amount of Bcl-x L  is higher in the test sample than in the control. 
   
     
     
         23 . A method for identifying a patient with cancer as eligible to receive a Bcl-2-family inhibitor therapy comprising:
 (a) providing a test sample from a patient;   (b) determining in the test sample:
 (i) if Bcl-x L  gene is amplified; and 
 (ii) an amount of Bcl-x L  in the test sample; 
   (c) determining if the amount of Bcl-x L  in the test sample is higher or lower then the amount of Bcl-x L  in a control; and   (d) classifying the patient as eligible to receive the Bcl-2 family inhibitor therapy based on:
 (i) amplification of the Bcl-x L  gene; and 
 (ii) the amount of Bcl-x L  is higher in the test sample than in the control. 
   
     
     
         24 . The method of  claim 22  or  23 , wherein the Bcl-2 family inhibitor is ABT-263. 
     
     
         25 . The method of  claim 22  or  23 , wherein the tissue sample comprises a peripheral blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a bone marrow sample, a lymph node sample, a urine sample, an ascites sample, a lavage sample, an esophageal brushing sample, a bladder or lung wash sample, a spinal fluid sample, a brain fluid sample, a ductal aspirate sample, a nipple discharge sample, a pleural effusion sample, a fresh frozen tissue sample, a paraffin embedded tissue sample or an extract or processed sample produced from any of a peripheral blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a bone marrow sample, a urine sample, an ascites sample, a lavage sample, an esophageal brushing sample, a bladder or lung wash sample, a spinal fluid sample, a brain fluid sample, a ductal aspirate sample, a nipple discharge sample, a pleural effusion sample, a fresh frozen tissue sample or a paraffin embedded tissue sample. 
     
     
         26 . The method of  claim 22  or  23 , wherein determining amplification of the Bcl-x L  gene comprises in situ hybridization. 
     
     
         27 . The method of  claim 26 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled. 
     
     
         28 . The method of  claim 27 , wherein the in situ hybridization is performed with a nucleic acid probe or peptide nucleic acid probe that specifically hybridizes to at least part of the Bcl-x L  gene. 
     
     
         29 . The method of  claim 22  or  23 , wherein determining amplification of the Bcl-x L  gene comprises a polymerase chain reaction. 
     
     
         30 . The method of  claim 29 , wherein the polymerase chain reaction is performed with at least one primer that specifically hybridizes to at least part of a nucleic acid sequence of the Bcl-x L  gene. 
     
     
         31 . The method of  claim 22  or  23 , wherein the determining step comprises a nucleic acid microarray assay. 
     
     
         32 . The method of  claim 22  or  23 , wherein the tissue sample is from a patient with a cancer selected from the group consisting of small-cell lung carcinoma and a lymphoma. 
     
     
         33 . The method of  claim 23 , wherein the patient is classified as eligible to receive an anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L . 
     
     
         34 . The method of  claim 22  or  23 , wherein the determining step (b)(ii) is performed by immunoassay. 
     
     
         35 . The method of  claim 34 , wherein the immunoassay is a sandwich immunoassay. 
     
     
         36 . The method of  claim 34 , wherein the immunoassay is an ELISA. 
     
     
         37 . The method of  claim 34 , wherein the determining step (b)(ii) is performed on an automated immunoassay instrument. 
     
     
         38 . The method of  claim 22  or  23 , wherein the determining step (b)(ii) is performed by measuring Bcl-x L  mRNA. 
     
     
         39 . A method for monitoring a patient being treated with an anti-Bcl-2-family agent comprising:
 (a) providing a test sample from a cancer patient;   (b) identifying in or extracting from the sample tumor or cancer cells;   (c) determining whether the patient should continue to be treated with the Bcl-2 family inhibitor based on the presence of absence of amplification of the Bcl-x L  gene.   
     
     
         40 . The method of  claim 39 , wherein the cancer is selected from the group consisting of small cell lung carcinoma and a lymphoma. 
     
     
         41 . The method of  claim 39 , wherein the patient is being treated with ABT-263. 
     
     
         42 . The method of  claim 39 , wherein amplification of the Bcl-x L  gene correlates with an increase in expression of Bcl-x L  polypeptide. 
     
     
         43 . The method of  claim 42 , wherein the patient is being treated with an anti-sense agent designed to bind to at least one of Bcl-2, Bcl-w, and Bcl-x L . 
     
     
         44 . The method of  claim 42 , wherein the determining step comprises in situ hybridization. 
     
     
         45 . The method of  claim 44 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled. 
     
     
         46 . The method of  claim 44 , wherein the in situ hybridization is performed with at least two nucleic acid probes. 
     
     
         47 . The method of  claim 46  wherein one of the nucleic acid probes is designed to hybridize to a Bcl-x L  gene. 
     
     
         48 . The method of  claim 39 , wherein the tumor cells are circulating tumor cells. 
     
     
         49 . A method for monitoring a patient being treated with an anti-Bcl-2-family agent comprising:
 (a) providing a test sample from a patient;   (b) determining in the test sample:
 (i) if Bcl-x L  gene is amplified; and 
 (ii) an amount of Bcl-x L  in the test sample; 
   (c) determining if the amount of Bcl-x L  in the test sample is higher or lower then the amount of Bcl-x L  in a control; and   (d) determining whether the patient should continue to be treated with the Bcl-2 family inhibitor based on:
 (i) if the Bcl-x L  gene is amplified; 
 (ii) if the amount of Bcl-x L  is higher in the test sample than in the control. 
   
     
     
         50 . The method of  claim 49 , wherein the Bcl-2 family inhibitor is ABT-263. 
     
     
         51 . The method of  claim 49 , wherein the tissue sample comprises a peripheral blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a bone marrow sample, a lymph node sample, a urine sample, an ascites sample, a lavage sample, an esophageal brushing sample, a bladder or lung wash sample, a spinal fluid sample, a brain fluid sample, a ductal aspirate sample, a nipple discharge sample, a pleural effusion sample, a fresh frozen tissue sample, a paraffin embedded tissue sample or an extract or processed sample produced from any of a peripheral blood sample, a tumor tissue or a suspected tumor tissue, a thin layer cytological sample, a fine needle aspirate sample, a bone marrow sample, a urine sample, an ascites sample, a lavage sample, an esophageal brushing sample, a bladder or lung wash sample, a spinal fluid sample, a brain fluid sample, a ductal aspirate sample, a nipple discharge sample, a pleural effusion sample, a fresh frozen tissue sample or a paraffin embedded tissue sample. 
     
     
         52 . The method of  claim 49 , wherein determining amplification of the Bcl-x L  gene comprises in situ hybridization. 
     
     
         53 . The method of  claim 52 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled. 
     
     
         54 . The method of  claim 53 , wherein the in situ hybridization is performed with a nucleic acid probe or peptide nucleic acid probe that specifically hybridizes to at least part of the Bcl-x L  gene. 
     
     
         55 . The method of  claim 49 , wherein determining amplification of the Bcl-x L  gene comprises a polymerase chain reaction. 
     
     
         56 . The method of  claim 55 , wherein the polymerase chain reaction is performed with at least one primer that specifically hybridizes to at least part of a nucleic acid sequence of the Bcl-x L  gene. 
     
     
         57 . The method of  claim 49 , wherein the determining step comprises a nucleic acid microarray assay. 
     
     
         58 . The method of  claim 49 , wherein the tissue sample is from a patient with a cancer selected from the group consisting of small-cell lung carcinoma and a lymphoma. 
     
     
         59 . The method of  claim 49 , wherein the patient is classified as eligible to receive an anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L . 
     
     
         60 . The method of  claim 49 , wherein the determining step (b)(ii) is performed by immunoassay. 
     
     
         61 . The method of  claim 60 , wherein the immunoassay is a sandwich immunoassay. 
     
     
         62 . The method of  claim 60 , wherein the immunoassay is an ELISA. 
     
     
         63 . The method of  claim 60 , wherein the determining step (b)(ii) is performed on an automated immunoassay instrument. 
     
     
         64 . The method of  claim 49 , wherein the determining step (b)(ii) is performed by measuring Bcl-x L  mRNA. 
     
     
         65 . A kit, comprising:
 (a) reagents to detect an amplified Bcl-x L  gene; and   (b) instructions.   
     
     
         66 . The kit of  claim 65 , wherein the reagents to detect the amplified Bcl-x L  gene comprises detectably-labeled polynucleotides that hybridize to at least a portion of the Bcl-x L  gene.