MSMB-gene based diagnosis, staging and prognosis of prostate cancer

• US 20090203010A1
• Filed: 01/21/2009
• Published: 08/13/2009
• Est. Priority Date: 01/18/2008
• Status: Abandoned Application

• Current Assignee: Katholieke Universiteit Leuven
• Original Assignee: Katholieke Universiteit Leuven
• Inventors: Beke, Lijs, van Eynde, Aleyde, Beullens, Monique, Bollen, Mathieu, Litovkin, Kyrylo, Nuytten, Mieke
• Application Number:
  US12/321,583
• Publication Number:
  US 20090203010A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2600/154 Methylation markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

This invention relates generally to a method of diagnosis for distinguishing between a benign prostate hyperplasia and a prostate cancer and between a hormone-sensitive and a hormone-refractory prostate cancer condition and specifically to identification of a hypermethylated (on CpG and non-CpG dinucleotides) CpG island in the beta-microseminoprotein (MSMB) regulatory regions surrounding the transcriptional start site of the MSMB gene as a diagnostic indicator of prostate cancer (PrCa) and for distinguishing androgen-refractory from androgen-sensitive prostate cancer.

Claims

1. A method of identifying a prostate cell proliferative disorder in a human male subject, the method comprising:

providing a sample comprising prostatic tissue, prostatic cells, fluid of the prostate from a human patient susceptible to a prostate cancer, and

analyzing the sample for the level DNA methylation of the regulatory region surrounding the transcription start site (TSS) of a beta-microseminoprotein gene (MSMB gene), wherein hypermethylation in this region indicates the presence of prostate cancer cells or is indicative of prostate cancer.

2. The method according to claim 1, wherein the region comprises one or more CpG islands and extends from about 3.0 kb upstream to about 2.2 kb downstream from the TSS of the MSMB gene.

3. The method according to claim 1, wherein the region extends from −

3128 bp to −

2817 bp upstream from the transcription start site of the MSMB gene.

4. The method according to claim 1, wherein the region extends from −

3533 bp to −

2734 bp upstream from the transcription start site of the MSMB gene.

5. The method according to claim 1, wherein the region extends from −

452 bp upstream to +150 bp downstream from the transcription start site of the MSMB gene.

6. The method according to claim 1, wherein the region extends from 2180 bp to 2390 bp downstream from the transcription start site of the MSMB gene.

7. The method according to claim 1, wherein the region between −

13877 and −

13583 or between −

10528 and −

10254 or between −

3920 to −

3673 or between −

3471 and −

3141 or −

3128 and −

2817 base pairs upstream from the transcription start site of the MSMB gene is analyzed for hypermethylation.

8. The method according to claim 1, wherein the region between 1671 and 1996 or between 2180 and 2390 between 5236 and 5616 or between 7670 and 8030 or between 11432 and 11754 or base pairs downstream from the transcription start site of the MSMB gene is analysed for hypermethylation.

9. The method according to claim 1, wherein the presence of hypermethylation of CpG and non-CpG dinucleotides in this regulatory region surrounding the transcription start site indicates the presence of prostate cancer cells or is indicative of prostate cancer.

10. The method according to claim 1, wherein the method comprises:

analyzing the level DNA methylation of the regulatory region surrounding the TSS of a beta-MSMB gene in a biological sample isolated from the subject;

whereby non-CpG methylation or non-CpG hypermethylation in the regulatory regions surrounding the transcriptional start site of the MSMB gene is an indication of prostate cancer or for prostate cancer cells'"'"' presence.

11. The method according to claim 1, wherein the method comprises:

analyzing the level DNA methylation of the regulatory region surrounding the TSS of a beta-MSMB gene in a biological sample isolated from the subject, and further comprises comparing the DNA methylation with the DNA methylation in a control sample and/or a benign prostate hyperplasia sample;

whereby increased non-CpG methylation in the regulatory regions surrounding the transcriptional start site of the MSMB gene is an indication for prostate cancer or for the presence of prostate cancer cells.

12. The method according to claim 1, wherein the method comprises:

analyzing the level DNA methylation of the regulatory region surrounding the TSS of a beta-MSMB gene in a biological sample isolated from the subject, and further comprises comparing the DNA methylation with the DNA methylation in a control sample;

whereby increased CpG methylation in the regulatory regions surrounding the transcriptional start site of the MSMB gene is an indication for prostate cancer or for the presence of prostate cancer cells.

13. The method according to claim 1, wherein the method comprises:

analyzing the level DNA methylation of the regulatory region surrounding the TSS of a beta-MSMB gene in a biological sample isolated from the subject, and further comprises comparing the DNA methylation with the DNA methylation in a sample of androgen sensitive prostate cancer;

whereby increased level methylation of the CpG dinucleotides in the regulatory region surrounding the transcriptional start site of the MSMB gene relative to the androgen sensitive prostate cancer is an indication of an hormone refractory prostate cancer, androgen-independent prostate cancer (AIPC) or androgen-independent metastatic prostate cancer.

14. The method according to claim 1, wherein the method comprises:

analyzing the level DNA methylation of regulatory region surrounding the TSS of a beta-MSMB gene in a biological sample isolated from the subject, and further comprises comparing the DNA methylation with the DNA methylation in a control sample or a benign prostate hyperplasia sample;

whereby increased non-CpG methylation in the regulatory regions surrounding the transcriptional start site of the MSMB gene relative to a control sample is an indication for prostate cancer and comparing the DNA methylation with the DNA methylation in a androgen sensitive prostate cancer sample; and

whereby an increased level methylation of the CpG dinucleotides in the regulatory region surrounding the transcriptional start site of the MSMB gene relative to a control sample is an indication of an hormone refractory prostate cancer, androgen-independent prostate cancer (AIPC) or androgen-independent metastatic prostate cancer.

15. The method according to claim 1, wherein the method comprises:

analyzing histone acetylation or deacetylation of the MSMB gene in the sample.

16. The method according to claim 14, wherein the method comprises:

analyzing histone acetylation or deacetylation of the MSMB gene in the sample.

17. The method according to claim 1, wherein an androgen-independent metastatic prostate cancer in a prostate cell or prostate tissue is diagnosed.

18. The method according to claim 14, wherein an androgen-independent metastatic prostate cancer in a prostate cell or prostate tissue is diagnosed.

19. The method according to claim 1, further comprising:

carrying out a prostate cancer grading or prostate cancer staging.

20. The method according to claim 14, further comprising:

carrying out a prostate cancer grading or prostate cancer staging.

21. The method according to claim 1, further comprising:

deciding on a treatment or medicament of the prostate disease state.

22. The method according to claim 14, further comprising:

deciding on a treatment or medicament of the prostate disease state.

23. The method according to claim 1, wherein hypermethylation is determined using PCR or other amplification technique.

24. The method according to claim 1, wherein hypermethylation is determined by bisulfite genomic sequencing PCR analysis.

25. The method according to claim 1, wherein hypermethylation is determined by Methylation-Specific PCR analysis or other amplification technique.

26. The method according to claim 1, wherein hypermethylation is determined by a diagnostic array, the array comprising primers for assessing the presence of hypermethylation in a regulatory region surrounding the TSS of the MSMB gene.

27. The method according to claim 1 which utilizes at least one primer of the group consisting of methylated specific primers (SEQ ID NOs:

13, 14, 17, 19, 20, 21, 22, 26, 28, 29, 38, 39, 42, 43, 50, 51, 57, 58, 61, and

     62) and of the group consisting of unmethylated specific primers (SEQ ID NO'"'"'s 15, 16, 18, 23, 24, 25, 27, 30, 31, 40, 41, 44, 45, 52, 53, 59, 60, 63 and

     64).

28. The method according to claim 1 which utilizes at least one primer of the group consisting of bisulfite sequencing primers (SEQ ID NO:

9, 10, 11, 12, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 54, 55, 56, 65, 66, 67, 68, 69 and

     70).

29. The method according to claim 1, wherein distinguishing between methylated and non-methylated CpG dinucleotide sequences within the target sequence comprises utilizing at least one primer in each case a contiguous sequence at least 16 nucleotides in length that is complementary to, or hybridizes under stringent conditions to a bisulfite-converted sequence (SEQ ID NO:

6 and

     8) derived from a sequence selected from the SEQ ID NO;

5 and 7.

30. The method according to claim 1 wherein PCR analysis is performed on polynucleotide materials of cells derived from prostatic tissue.

31. The method according to claim 1 wherein PCR analysis is performed on polynucleotide materials of the cells derived from seminal fluid or from ejaculate.

32. The method according to claim 1 wherein PCR analysis is performed on polynucleotide materials of the cells derived from body fluids selected from the group consisting of blood, urine, ejaculates, prostate secretions, and combinations thereof.

33. The method according to claim 1 wherein PCR analysis is performed on polynucleotide materials of the cells derived from prostate tissue from histological slides or biopsies or paraffin-embedded tissue.

34. The method according to claim 1 wherein PCR analysis is performed on polynucleotide materials of the cells of prostatic tissue from biopsy or from surgical resection.

35. The method according to claim 1, comprising:

obtaining a biological sample from the subject;

determining the methylation state of CpG island upstream and/or downstream of the transcriptional start site of the MSMB gene in the subject'"'"'s sample; and

identifying hypermethylation of one or more CpG islands of the regulatory region surrounding the transcription start site of the MSMB gene, wherein detection of hypermethylation is indicative of a predisposition to, or the incidence of prostate cancer.

36. The method according to claim 1, wherein differential methylation is observed when compared to the methylation status of the regulatory region surrounding the transcription start site of the MSMB gene from a androgen-sensitive prostate cancer cell or a normal cell, which differential methylation is hypermethylation and is indicative for androgen-refractory prostate cancer.

37. The method according to claim 1, wherein detection of hypermethylation is indicative for the grade and/or stage of the prostate proliferative disorder.

38. The method according to claim 1, wherein detection of hypermethylation is indicative for decided about a treatment with a DNA methylation inhibitor.

39. The method according to claim 1, wherein detection of hypermethylation is indicative for decided about the initiation or continuation of treating with a compound in an effective amount to reduce male hormones.

40. The method according to claim 1, further comprising analyzing acetylation of the MSMB gene histones for distinguishing between an androgen-independent or androgen-refractory prostate cancer and/or an androgen-sensitive prostate cancer.

41. A nucleic acid molecule consisting essentially of a sequence at least 16 continuous bases in length of a sequence selected from the sequence group consisting of SEQ ID NOS:

6 and 8.