MIPOL1-ETV1 gene rearrangements

• US 10,167,517 B2
• Filed: 06/30/2017
• Issued: 01/01/2019
• Est. Priority Date: 07/06/2007
• Status: Active Grant

• Current Assignee: Board of Regents of the University of Michigan (University of Michigan)
• Original Assignee: Board of Regents of the University of Michigan (University of Michigan)
• Inventors: Chinnaiyan, Arul M., Tomlins, Scott, Dhanasekaran, Saravana Mohan
• Primary Examiner(s): Horlick, Kenneth R
• Application Number:
  US15/639,583
• Publication Number:
  US 20170327901A1
• Time in Patent Office: 550 Days
• Field of Search: None
• 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 2600/136 Screening for pharmacological compounds
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Compositions and methods associated with recurrent MIPOL1-ETV1 genetic rearrangements that are useful for cancer diagnosis and therapy are disclosed.

Claims

1. A method for detecting a MIPOL1-ETV1 genetic rearrangement and one or more markers associated with prostate cancer in a biological sample, the method comprising:

a) contacting a biological sample with;

i) a probe directly labeled with a detectable label and comprising a sequence that is complementary to a junction at which an ETV1 gene is inserted into a MIPOL1 gene;

or

ii) a first probe directly labeled with a detectable label and comprising a sequence complementary to a MIPOL1 gene and a second probe directly labeled with a detectable label and comprising a sequence complementary to an ETV1 gene;

or

iii) a first amplification oligonucleotide comprising a sequence complementary to a MIPOL1 gene, a second amplification oligonucleotide comprising a sequence complementary to an ETV1 gene, and a probe directly labeled with a detectable label and comprising a sequence complementary to the product produced from the first and second primers; and

b) detecting in the biological sample expression of a marker selected from the set of markers consisting of AMACR/P504S, PCA3, PCGEM1, prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P, prostate specific antigen (PSA), prostatic acid phosphatase (PAP), prostate binding protein (PBP), ABCC5(MDR5), ADAMTS1, AMACR, ANNEXINA11, ANNEXINA1, ANNEXINA4, APP, ARHB, ASNS, ATF2, C1S, C4BPA, C7, CATHEPSINB, CATHEPSINH, CAVEOLIN2, CCND2, CFLAR, CLUSTERIN, COL15A1, COL1A2, COL3A1, c-terminal binding protein, CTBP1, CTBP2, CYSTATINC, E2EPF, EDNRB, EGR1, EPHA1, ETS2, EZH2, FASN, FAT, FHL1, FIBRONECTIN1, FKBP5, FLS353, FOLH1, FOSB, FZD7, GELSOLIN, GP73, GSTM1, GSTM3, GSTM5, GSTP1, HEPSIN, HEVIN, IGFBP3, IGFBP5, IL1R1, IL1R2, ITGA1, ITGB4, ITM2C, JUN, KERATIN5, LIMK1, LUMICAN, MADH4, MAP3K10, MAPK6, MCAM, MEIS1, MEIS2, MMECD10, MOESIN, MPDZ, MTA1, MYBL2, MYLK, NBL1, NCK1, NRAS, PCM1, pim-1, PLA2G2A, PP1CB, PPP2CB, PRKCL2, PSG9, RAB2, RAB5A, RAP2, RIG, S100A11, SCYA2, SEPP1, SGK, SKI, SLUG, TACC1, TASTIN, TBXA2F, TBXA2R, TFCP2, THROMBOSPONDIN1, TIMP2, TNFS10, TNFSF10, TOP2A, TRAF4, TRAP1, UBCH10, VAV2, VIMENTIN, VINCULIN, and YWHAB.

2. The method of claim 1 wherein the marker is a protein.

3. The method of claim 1 wherein the marker is a messenger RNA.

4. The method of claim 1 wherein the marker is a messenger RNA and detecting expression of the marker comprises producing a complementary DNA.

5. The method of claim 1 wherein the amount of the marker is quantified.

6. The method of claim 1 wherein detecting the MIPOL1-ETV1 genetic rearrangement and the one or more markers is associated with the stage, aggressiveness, or progression of prostate cancer or the presence or risk of metastasis in a subject that was the source of the biological sample.

7. The method of claim 1 wherein the biological sample comprises, or comprises a fraction of, a prostate biopsy sample, prostatectomy tissue sample, blood sample, urine sample, semen sample, prostatic secretion sample, plasma sample, serum sample, urine supernatant, urine cell pellet, or prostate cell sample.

8. The method of claim 1 further comprising quantifying ETV1 expression.

9. The method of claim 1 further comprising producing or receiving the biological sample.

10. The method of claim 1 further comprising reporting the presence, absence, or amount of the MIPOL1-ETV1 genetic rearrangement and one or more of the markers.

11. The method of claim 1 further comprising providing an array comprising one or more probes comprising a sequence complementary to the MIPOL1-ETV1 genetic rearrangement and one or more probes comprising a sequence complementary to the set of markers.

12. The method of claim 6 further comprising treating the subject that was the source of the biological sample.

13. A kit for detecting a MIPOL1-ETV1 genetic rearrangement and one or more markers associated with prostate cancer in a biological sample, the kit comprising:

a) a first component selected from the group consisting of;

i) a probe directly labeled with a detectable label and comprising a sequence that is complementary to a junction at which an ETV1 gene is inserted into a MIPOL1 gene;

ii) a first probe directly labeled with a detectable label and comprising a sequence complementary to a MIPOL1 gene and a second probe directly labeled with a detectable label and comprising a sequence complementary to an ETV1 gene; and

iii) a first amplification oligonucleotide comprising a sequence complementary to a MIPOL1 gene, a second amplification oligonucleotide comprising a sequence complementary to an ETV1 gene, and a probe directly labeled with a detectable label and comprising a sequence complementary to the product produced from the first and second primers; and

b) a second component comprising a probe directly labeled with a detectable label and for detecting a marker selected from the set of markers consisting of AMACR/P504S, PCA3, PCGEM1, prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P, prostate specific antigen (PSA), prostatic acid phosphatase (PAP), prostate binding protein (PBP), ABCC5(MDR5), ADAMTS1, AMACR, ANNEXINA11, ANNEXINA1, ANNEXINA4, APP, ARHB, ASNS, ATF2, C1S, C4BPA, C7, CATHEPSINB, CATHEPSINH, CAVEOLIN2, CCND2, CFLAR, CLUSTERIN, COL15A1, COL1A2, COL3A1, c-terminal binding protein, CTBP1, CTBP2, CYSTATINC, E2EPF, EDNRB, EGR1, EPHA1, ETS2, EZH2, FASN, FAT, FHL1, FIBRONECTIN1, FKBP5, FLS353, FOLH1, FOSB, FZD7, GELSOLIN, GP73, GSTM1, GSTM3, GSTM5, GSTP1, HEPSIN, HEVIN, IGFBP3, IGFBP5, IL1R1, IL1R2, ITGA1, ITGB4, ITM2C, JUN, KERATIN5, LIMK1, LUMICAN, MADH4, MAP3K10, MAPK6, MCAM, MEIS1, MEIS2, MMECD10, MOESIN, MPDZ, MTA1, MYBL2, MYLK, NBL1, NCK1, NRAS, PCM1, pim-1, PLA2G2A, PP1CB, PPP2CB, PRKCL2, PSG9, RAB2, RAB5A, RAP2, RIG, S100A11, SCYA2, SEPP1, SGK, SKI, SLUG, TACC1, TASTIN, TBXA2F, TBXA2R, TFCP2, THROMBOSPONDIN1, TIMP2, TNFS10, TNFSF10, TOP2A, TRAF4, TRAP1, UBCH10, VAV2, VIMENTIN, VINCULIN, and YWHAB.

14. The kit of claim 13 wherein the probe is a nucleic acid comprising a sequence complementary to the marker.

15. The kit of claim 13 wherein the probe is an antibody specific for the marker.

16. The kit of claim 13 wherein the first component comprises a probe or a pair of probes and an array comprises the first and second components.

17. An assay composition comprising a sample from a subject and:

a) a first component selected from the group consisting of;

i) a junction probe directly labeled with a detectable label and comprising a sequence that is complementary to a junction at which an ETV1 gene is inserted into a MIPOL1 gene;

ii) a first probe directly labeled with a detectable label and comprising a sequence complementary to a MIPOL1 gene and a second probe directly labeled with a detectable label and comprising a sequence complementary to an ETV1 gene; and

iii) a first amplification oligonucleotide comprising a sequence complementary to a MIPOL1 gene, a second amplification oligonucleotide comprising a sequence complementary to an ETV1 gene, and an amplicon probe directly labeled with a detectable label and comprising a sequence complementary to the amplicon produced from the first and second primers; and

b) a second component comprising a probe directly labeled with a detectable label and for detecting a marker selected from the set of markers consisting of AMACR/P504S, PCA3, PCGEM1, prostein/P501S, P503S, P504S, P509S, P510S, prostase/P703P, P710P, prostate specific antigen (PSA), prostatic acid phosphatase (PAP), prostate binding protein (PBP), ABCC5(MDR5), ADAMTS1, AMACR, ANNEXINA11, ANNEXINA1, ANNEXINA4, APP, ARHB, ASNS, ATF2, C1S, C4BPA, C7, CATHEPSINB, CATHEPSINH, CAVEOLIN2, CCND2, CFLAR, CLUSTERIN, COL15A1, COL1A2, COL3A1, c-terminal binding protein, CTBP1, CTBP2, CYSTATINC, E2EPF, EDNRB, EGR1, EPHA1, ETS2, EZH2, FASN, FAT, FHL1, FIBRONECTIN1, FKBP5, FLS353, FOLH1, FOSB, FZD7, GELSOLIN, GP73, GSTM1, GSTM3, GSTM5, GSTP1, HEPSIN, HEVIN, IGFBP3, IGFBP5, IL1R1, IL1R2, ITGA1, ITGB4, ITM2C, JUN, KERATIN5, LIMK1, LUMICAN, MADH4, MAP3K10, MAPK6, MCAM, MEIS1, MEIS2, MMECD10, MOESIN, MPDZ, MTA1, MYBL2, MYLK, NBL1, NCK1, NRAS, PCM1, pim-1, PLA2G2A, PP1CB, PPP2CB, PRKCL2, PSG9, RAB2, RAB5A, RAP2, RIG, S100A11, SCYA2, SEPP1, SGK, SKI, SLUG, TACC1, TASTIN, TBXA2F, TBXA2R, TFCP2, THROMBOSPONDIN1, TIMP2, TNFS10, TNFSF10, TOP2A, TRAF4, TRAP1, UBCH10, VAV2, VIMENTIN, VINCULIN, and WTHAB.

18. The assay composition of claim 17 wherein the second component comprises a probe that is a nucleic acid comprising a sequence complementary to the marker.

19. The assay composition of claim 17 wherein the second component comprises an antibody that is specific for the marker.

20. The assay composition of claim 17 wherein:

a) said first component is;

(i) said junction probe and said junction probe is hybridized to said junction;

or

(ii)said first and second probes and said first probe is hybridized to the MIPOL1 gene and said second probe is hybridized to the ETV1 gene;

or

(iii) said first and second amplification oligonucleotides and said amplicon probe, and said first amplification oligonucleotide is hybridized to the MIPOL1 gene and said second amplification oligonucleotide is hybridized to the ETV1 gene; and

b)the second component is a nucleic acid hybridized to the marker.

21. The assay composition of claim 17 wherein:

a) said first component is;

(i) said junction probe and said junction probe is hybridized to said junction;

or

(ii)said first and second probes and said first probe is hybridized to the MIPOL1 gene and said second probe is hybridized to the ETV1 gene;

or

(iii) said first and second amplification oligonucleotides and said amplicon probe, and said first amplification oligonucleotide is hybridized to the MIPOL1 gene and said second amplification oligonucleotide is hybridized to the ETV1 gene; and

b) the second component is an antibody specifically bound to the marker.

22. The assay composition of claim 17 wherein the first component comprises a first amplification oligonucleotide comprising a sequence complementary to a MIPOL1 gene, a second amplification oligonucleotide comprising a sequence complementary to an ETV1 gene, a probe directly labeled with a detectable label and comprising a sequence complementary to the product produced from the first and second primers, and a polymerase.