Methods for detecting cancer and monitoring cancer progression

• US 20060281089A1
• Filed: 06/14/2004
• Published: 12/14/2006
• Est. Priority Date: 06/12/2003
• Status: Active Grant

• Current Assignee: Province of Manitoba
• Original Assignee: University of Manitoba
• Inventors: Gibson, Spencer B, Eisenstat, David D.
• Granted Patent: US 7,393,637 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07K 14/4747 Apoptosis related proteins
• CPC Class Codes: C07K 16/30 from tumour cells
• 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 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 2510/00 Detection of programmed cell death, i.e. apoptosis
• CPC Class Codes: G01N 33/57496 involving intracellular compounds

Abstract

Mutant BNIP3 plays a functionally important role in the development of solid tumors and in resistance to chemotherapy and radiation treatments. The invention relates to methods of detecting cancer, methods of monitoring the progression of cancer, methods of identifying patients with cancer that is resistant to chemotherapy or radiation treatments, and diagnostic kits for performing the methods of the invention.

Claims

1. A method of detecting cancer in a patient comprising:

(a) testing a sample from the patient for the presence of mutant BNIP3, wherein the presence of mutant BNIP3 indicates that the patient has cancer.

2. A method according to claim 1 wherein the mutant BNIP3 comprises any mutation that results in elimination of the transmembrane domain in the BNIP3 protein.

3. A method according to claim 2 wherein the mutation comprises a mutation in the PEST domain that results in elimination of the transmembrane domain in the BNIP3 protein.

4. A method according to claim 3 wherein the mutation in the PEST domain comprises the insertion of adenosine at nucleotide 235 as shown in SEQ ID NO:

5.

5. A method according to claim 2 wherein the mutation comprises a mutation in the CD domain that results in elimination of the transmembrane domain in the BNIP3 protein.

6. A method according to claim 5 wherein the mutation in the CD domain comprises the deletion of adenosine at nucleotide 356 as shown in SEQ ID NO:

3.

7. A method according to claim 1 wherein the sample is tissue or blood.

8. A method according to claim 1 wherein the cancer is brain cancer.

9. A method according to claim 1 wherein the cancer is ovarian cancer.

10. A method according to claim 1 wherein the sample is tested for the presence of nucleic acid molecules encoding mutant BNIP3 in step (a).

11. A method according to claim 10 wherein the sample is tested for the presence of mutant BNIP3 mRNA.

12. A method according to claim 1 wherein the presence of mutant BNIP3 protein is determined in step (a).

13. A method according to claim 12 wherein the mutant BNIP3 protein has the sequence shown in SEQ ID NO:

4.

14. A method according to claim 12 wherein the mutant BNIP3 protein has the sequence shown in SEQ ID NO:

6.

15. A method according to claim 12 wherein an antibody is used to determine the levels of the mutant BNIP3 protein.

29. A kit for detecting cancer in a patient comprising (i) reagents for conducting a method according to claim 1 and (ii) instructions for its use.

30. A kit according to claim 29 wherein the reagents comprise nucleic acid primers for amplifying mRNA coding for mutant BNIP3 in a reverse transcriptase polymerase chain reaction.

31. A kit according to claim 29 wherein the reagents comprise antibodies specific to mutant BNIP3 protein.

32. A kit according to claim 29 wherein the reagents comprise antibodies that recognize both wild type and mutant BNIP3 proteins, and antibodies specific to wild type BNIP3 protein.

16. A method of identifying patients with cancer that is resistant to chemotherapy or radiation treatments comprising:

(a) testing a sample from a patient for the presence of mutant BNIP3, wherein the presence of mutant BNIP3 indicates that the patient has chemotherapy- or radiation-resistant cancer.

17. A method according to claim 16 wherein the mutant BNIP3 comprises any mutation that results in elimination of the transmembrane domain in the BNIP3 protein.

18. A method according to claim 17 wherein the mutation comprises a mutation in the PEST domain that results in elimination of the transmembrane domain in the BNIP3 protein.

19. A method according to claim 18 wherein the mutation in the PEST domain comprises the insertion of adenosine at nucleotide 235 as shown in SEQ ID NO:

5.

20. A method according to claim 17 wherein the mutation comprises a mutation in the CD domain that results in elimination of the transmembrane domain in the BNIP3 protein.

21. A method according to claim 20 wherein the mutation in the CD domain comprises the deletion of adenosine at nucleotide 356 as shown in SEQ ID NO:

3.

22. A method according to claim 16 wherein the sample is tissue or blood.

23. A method according to claim 16 wherein the cancer is brain cancer.

24. A method according to claims 16 wherein the cancer is ovarian cancer.

25. A method according to claim 16 wherein the sample is tested for the presence of nucleic acid molecules encoding mutant BNIP3 in step (a).

26. A method according to claim 25 wherein the sample is tested for the presence of mutant BNIP3 mRNA.

27. A method according to claim 16 wherein the sample is tested for the presence of mutant BNIP3 protein in step (a).

28. A method according to claim 27 wherein an antibody is used to detect the presence of mutant BNIP3 protein.

33. A kit for identifying patients with cancer that is resistant to chemotherapy or radiation treatments comprising (i) reagents for conducting a method according to claim 16 and (ii) instructions for its use.

34. A kit according to claim 33 wherein the reagents comprise nucleic acid primers for amplifying mRNA coding for mutant BNIP3 in a reverse transcriptase chain reaction.

35. A kit according to claim 33 wherein the reagents comprise antibodies specific to a mutant BNIP3 protein.

36. A kit according to claim 33 wherein the reagents comprise antibodies that recognize both wild type and mutant BNIP3 proteins, and antibodies specific to wild type BNIP3 protein.

37. An isolated nucleic acid sequence encoding a BNIP3 mutant having the sequence shown in SEQ ID NO:

4.

38. An isolated nucleic acid sequence according to claim 37 having the sequence shown in SEQ ID NO:

3.

39. An isolated nucleic acid sequence encoding a BNIP3 mutant having the sequence shown in SEQ ID NO:

6.

40. An isolated nucleic acid sequence according to claim 39 having the sequence shown in SEQ ID NO:

5.

41. An isolated BNIP3 mutant having the amino acid sequence shown in SEQ ID NO:

4.

42. An isolated BNIP3 mutant having the amino acid sequence shown in SEQ ID NO:

6.