METHODS AND COMPOSITIONS FOR IDENTIFYING, CLASSIFYING AND MONITORING SUBJECT HAVING BCL-2 FAMILY INHIBITOR-RESISTANT TUMORS AND CANCERS

• US 20100234239A1
• Filed: 02/11/2010
• Published: 09/16/2010
• Est. Priority Date: 02/11/2009
• Status: Active Grant

• Current Assignee: Abbvie Incorporated, The Walter & Eliza Hall Institute Of Medical Research
• Original Assignee: Abbott Laboratories Incorporated
• Inventors: van Delft, Mark F., Uziel, Tamar, Lesniewski, Richard R., Tse, Christin, Semizarov, Dimitri, Huang, David Ching Siang
• Granted Patent: US 9,045,800 B2
• Time in Patent Office: Days
• US Class Current: 506/9
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: G01N 2333/4703 Regulators; Modulating activity
• CPC Class Codes: G01N 33/57496 involving intracellular compounds

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.

Claims

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.

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.

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.

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.

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.

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.

7. The method of claim 8, wherein the in situ hybridization is performed with a nucleic acid probe that is detectably labeled.

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.

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.

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.

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.

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.

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.