Prostate cancer-specific alterations in ERG gene expression and detection and treatment methods based on those alterations

• US 20080269157A1
• Filed: 04/10/2008
• Published: 10/30/2008
• Est. Priority Date: 10/10/2006
• Status: Active Grant

• Current Assignee: Henry M Jackson Foundation For The Advancement of Military Medicine Incorporated
• Original Assignee: Henry M Jackson Foundation For The Advancement of Military Medicine Incorporated
• Inventors: Sun, Chen, Srivastava, Shiv, Sreenath, Taduru, Dobi, Albert, Petrovics, Gyorgy
• Granted Patent: US 9,206,481 B2
• Time in Patent Office: Days
• US Class Current: 514/44
• CPC Class Codes: A61P 13/08 of the prostate
• CPC Class Codes: A61P 31/00 Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 43/00 Drugs for specific purposes, not provided for in groups A61P1/00-A61P41/00
• CPC Class Codes: C12N 15/1135 against oncogenes or tumor suppressor genes
• CPC Class Codes: C12N 2310/11 Antisense
• CPC Class Codes: C12N 2310/14 interfering N.A.
• CPC Class Codes: C12N 2320/30 Special therapeutic applications
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Alterations in ERG gene expression can be observed in patients with prostate cancer. Specific ERG isoforms are associated with, or involved in, prostate cancer. Compositions comprising these isoforms provide therapeutic benefit and can be used in methods of detecting, diagnosing, prognosing, and treating prostate cancer. These compositions provide biomarkers for detecting the expression of combinations of the PSA/KLK3, PMEPA1, NKX3.1, ODC1, AMD1, and ERG genes.

Claims

1. A method of detecting prostate cancer in a biological sample comprising:

(a) combining the biological sample with at least a first and a second oligonucleotide primer under hybridizing conditions, wherein the first oligonucleotide primer contains a sequence that hybridizes to a first sequence in a target sequence from ERG8, EPC1, or EPC2 and the second oligonucleotide primer contains a sequence that hybridizes to a second sequence in a nucleic acid strand complementary to the target sequence, wherein the first sequence does not overlap with the second sequence;

(b) amplifying a plurality of amplification products when the target sequence is present in the biological sample by adding at least one polymerase activity to the biological sample containing the first and second oligonucleotide primers;

(c) immobilizing the plurality of amplification products;

(d) combining an oligonucleotide probe with the immobilized plurality of amplification products to thereby permit the probe to hybridize to at least one immobilized amplification product; and

(e) detecting whether a signal results from hybridization between the oligonucleotide probe and at least one amplification product, wherein detection of the signal indicates the expression of ERG8, EPC1, or EPC2 and the presence of prostate cancer in the biological sample.

2. The method of claim 1, wherein the target sequence comprises nucleotides 75 to 1168 of SEQ ID NO:

1, nucleotides 61 to 1019 of SEQ ID NO;

3, or a nucleic acid molecule comprising SEQ ID NO;

5.

3. The method of claim 2, wherein the target sequence comprises nucleotides 75 to 1168 of SEQ ID NO:

1.

4. The method of claim 2, wherein the target sequence comprises nucleotides 803 to 1168 of SEQ ID NO:

1.

5. The method of claim 2, wherein the target sequence comprises nucleotides 61 to 1019 of SEQ ID NO:

3.

6. The method of claim 2, wherein the target sequence comprises nucleotides 788 to 1019 of SEQ ID NO:

3.

7. The method of claim 2, wherein the target sequence is a nucleic acid molecule comprising SEQ ID NO:

5.

8. The method of claim 2, wherein the target sequence comprises nucleotides 127 to 807 of SEQ ID NO:

5.

9. The method of claim 2, wherein the target sequence comprises nucleotides 992 to 1096 of SEQ ID NO:

46.

10. The method of claim 2, wherein the target sequence comprises nucleotides 1335 to 1424 of SEQ ID NO:

46.

11. The method of claim 2, wherein the target sequence comprises nucleotides 1501 to 1591 of SEQ ID NO:

46.

12. An isolated nucleic acid molecule comprising SEQ ID NO:

46, a biologically active fragment thereof, or the complement thereof.

13. An isolated nucleic acid encoding the amino acid sequence set forth in SEQ ID NO:

4 (EPC1), or the complement thereof.

14. An isolated polypeptide comprising the amino acid sequence set forth in SEQ ID NO:

4 (EPC1).

15. An isolated antibody that binds the polypeptide of claim 14.

16. The antibody of claim 15, wherein the antibody binds an epitope comprising the amino acids 217 to 220 of SEQ ID NO:

4.

17. An isolated nucleic acid encoding the amino acid sequence set forth in SEQ ID NO:

6 (EPC2), or the complement thereof.

18. An isolated polypeptide comprising the amino acid sequence set forth in SEQ ID NO:

6 (EPC2).

19. An isolated antibody that binds the polypeptide of claim 18.

20. The antibody of claim 19, wherein the antibody binds an epitope comprising amino acids 28 to 97 of SEQ ID NO:

6.

21. A method of treating prostate cancer comprising destabilizing a prostate cancer-specific ERG gene transcript in prostate cancer cells.

22. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 75 to 168 of SEQ ID NO:

1.

23. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 803 to 1168 of SEQ ID NO:

1.

24. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 61 to 1019 of SEQ ID NO:

3.

25. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 788 to 1019 of SEQ ID NO:

3.

26. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises SEQ ID NO:

5.

27. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 127 to 807 of SEQ ID NO:

5.

28. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 843-861 of SEQ ID NO:

46.

29. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 970-988 of SEQ ID NO:

46.

30. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 1261-1279 of SEQ ID NO:

46.

31. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 1398-1416 of SEQ ID NO:

46.

32. The method of claim 21, wherein the prostate cancer-specific ERG gene transcript comprises nucleotides 1581-1599 of SEQ ID NO:

46.

33. The method of any of claims 21 to 32, wherein the destabilization comprises administering an interfering RNA.

34. The method of any of claims 21 to 32, wherein the destabilization comprises administering an antisense nucleic acid.

35. A method of treating prostate cancer comprising administering to a subject in need thereof an expression vector comprising a polynucleotide encoding a cytotoxic or cytostatic gene product operably linked to a promoter sequence comprising SEQ ID NO:

7 or a fragment of the nucleotide sequence set forth in SEQ ID NO;

7 that is sufficient to support expression of an operatively linked reporter gene in prostate cancer cells.

37. The method of claim 35 or 36, wherein the cytotoxic or cytostatic gene product is chosen from bacterial toxins, tumor suppressor gene products, apoptosis-inducing proteins, and drug metabolizing enzymes that convert a pro-drug into a cytotoxic product.

36. A method of reducing the growth of a prostate cancer cell comprising administering to the cell an expression vector comprising a polynucleotide encoding a cytotoxic or cytostatic gene product operably linked to a promoter sequence comprising SEQ ID NO:

7 or a fragment of the nucleotide sequence set forth in SEQ ID NO;

7 that is sufficient to support expression of an operatively linked reporter gene in prostate cancer cells.

38. An isolated nucleic acid, comprising at least about 15 contiguous nucleotides of nucleotides 788 to 1019 of SEQ ID NO:

3, wherein the nucleic acid is capable of hybridizing to SEQ ID NO;

3, or the complement thereof, under conditions of high stringency but not to ERG1, ERG2, ERG3, ERG4, ERG5, ERG6, ERG7, ERG8, ERG9, EPC2, or TMPRSS2.

39. The isolated nucleic acid of claim 38, wherein the nucleic acid is up to about 50 nucleotides long.

40. The isolated nucleic acid of claim 38, wherein the conditions of high stringency comprise hybridization for 12 hours at 65°

C. in 6×

SSC followed by a wash in 0.1×

SSC at 50°

C. for 45 minutes.

41. An isolated nucleic acid, comprising at least about 15 contiguous nucleotides of nucleotides 127 to 807 of SEQ ID NO:

5, wherein the nucleic acid is capable of hybridizing to SEQ ID NO;

5, or the complement thereof, under conditions of high stringency but not to ERG1, ERG2, ERG3, ERG4, ERG5, ERG6, ERG7, ERG8, ERG9, EPC1, or TMPRSS2.

42. The isolated nucleic acid of claim 41, wherein the nucleic acid is up to about 50 nucleotides long.

43. The isolated nucleic acid of claim 41, wherein the conditions of high stringency comprise hybridization for 12 hours at 65°

C. in 6×

SSC followed by a wash in 0.1×

SSC at 50°

C. for 45 minutes.

44. An isolated nucleic acid molecule, comprising at least about 15 contiguous nucleotides of SEQ ID NO:

46, wherein the nucleic acid is capable of hybridizing to SEQ ID NO;

46, or the complement thereof, under conditions of high stringency but not to ERG1, ERG2, ERG3, ERG4, ERG5, ERG6, ERG7, ERG9, EPC1, EPC2, or TMPRSS2.

45. The isolated nucleic acid of claim 44, wherein the nucleic acid is up to about 50 nucleotides long.

46. The isolated nucleic acid of claim 44, wherein the conditions of high stringency comprise hybridization for 12 hours at 65°

C. in 6×

SSC followed by a wash in 0.1×

SSC at 50°

C. for 45 minutes.

47. A method of prognosing prostate cancer, comprising:

(a) detecting or measuring in a biological sample from an individual the expression of two or more of genes chosen from PSA/KLK3, PMEPA1, NKX3.1, ODC1, AMD1, and ERG; and

(b) comparing, for the expression of each gene detected or measured in (a), the results obtained in (a) with the expression of the same gene in a control sample.

48. The method of claim 47, wherein the biological sample is chosen from serum, plasma, whole blood, urine, and prostatic fluid.

49. The method of claim 47, wherein reduced expression of the genes detected or measured in (a) indicates a reduced disease-free survival time following prostatectomy in the individual.

50. The method of claim 49, wherein a serum PSA level equal or higher than 0.2 ng/ml after prostatectomy indicates disease recurrence.

51. The method of claim 49, wherein reduced expression of the genes detected or measured in (a) indicates a predisposition to or the presence of advanced prostate cancer in the individual.

52. The method of claim 51, wherein the advanced prostate cancer is stage pT3 or higher.

53. The method of claim 47, wherein the genes comprise PSA/KLK3, PMEPA1, and ERG.

54. A method of evaluating the status of androgen receptor signaling in vivo, comprising:

(a) detecting or measuring in a biological sample comprising prostate cells the expression of two or more of genes chosen from PSA/KLK3, PMEPA1, NKX3.1, ODC1, AMD1, and ERG; and

(b) comparing, for the expression of each gene detected or measured in (a), the results obtained in (a) with the expression of the same gene in a control sample.

55. The method of claim 54, wherein reduced expression of the genes detected or measured in (a) indicates compromised androgen receptor signaling in the prostate cells.

56. The method of claim 55, wherein the biological sample is chosen from serum, plasma, whole blood, urine, and prostatic fluid.

57. The method of claim 54, wherein the genes comprise PSA/KLK3, PMEPA1, and ERG.