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

1. A method for identifying a patient with small-cell lung carcinoma or a lymphoma as eligible to receive N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl) piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide therapy or an anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L comprising:

(a) providing a tissue sample from a patient;

(b) determining if expression of a Bcl-x L gene is amplified relative to a baseline control level determined before the administration of N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide;

(c) identifying the patient as eligible to receive N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide or the anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L if the Bcl-x L gene is not amplified; and

(d) administering N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide or the anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L to the patient identified as being eligible to receive N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide or the anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L .

2. The method of claim 1 , wherein amplification of the Bcl-x L gene correlates with an increase in expression of Bcl-x L polypeptide.

3. The method of claim 1 , 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.

4. The method of claim 1 , wherein the determining step comprises in situ hybridization.

5. The method of claim 4 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled.

6. The method of claim 4 , 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.

7. The method of claim 1 , wherein determining comprises a polymerase chain reaction.

8. The method of claim 7 , 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.

9. The method of claim 1 , wherein the determining step comprises a nucleic acid microarray assay.

10. A method for identifying a patient with small-cell lung carcinoma or a lymphoma as eligible to receive N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide therapy or an anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L comprising:

(a) providing a test sample from a patient;

(b) determining in the test sample:

(i) if a Bcl-x L gene is amplified relative to a baseline control level determined before the administration of N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide; 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 than the amount of Bcl-x L in a control, wherein the control is a level determined before the administration of N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl) sulfonyl)benzenesulfonamide; and

(d) identifying the patient as eligible to receive N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide or the anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L 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; and

(e) administering N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide or the anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L to the patient identified as being eligible to receive N-(4-(4-((2-(4-chlorophenyl)-5,5-dimethyl-1-cyclohex-1-en-1-yl)methyl)piperazin-1-yl)benzoyl)-4-(((1R)-3-(morpholin-4-yl)-1-((phenylsulfanyl)methyl)propyl)amino)-3-((trifluoromethyl)sulfonyl)benzenesulfonamide or the anti-sense agent designed to bind to one of Bcl-2, Bcl-w, and Bcl-x L .

11. The method of claim 10 , wherein the test 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.

12. The method of claim 10 , wherein determining amplification of the Bcl-x L gene comprises in situ hybridization.

13. The method of claim 12 , wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled.

14. The method of claim 12 , 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.

15. The method of claim 10 , wherein determining amplification of the Bcl-x L gene comprises a polymerase chain reaction.

16. The method of claim 15 , 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.

17. The method of claim 10 , wherein the determining step comprises a nucleic acid microarray assay.

18. The method of claim 10 , wherein the determining step (b)(ii) is performed by immunoassay.

19. The method of claim 18 , wherein the immunoassay is a sandwich immunoassay.

20. The method of claim 18 , wherein the immunoassay is an ELISA.

21. The method of claim 18 , wherein the determining step (b)(ii) is performed on an automated immunoassay instrument.

22. The method of claim 10 , wherein the determining step (b)(ii) is performed by measuring Bcl-x L mRNA.