Recurrent gene fusions in prostate cancer

Patent metadata

Field	Value
Publication number	US-10041123-B2
Application number	US-82555207-A
Country	US
Kind code	B2
Filing date	Jul 6, 2007
Priority date	Sep 12, 2005
Publication date	Aug 7, 2018
Grant date	Aug 7, 2018

Abstract

Recurrent gene fusions in prostate cancer of androgen regulated genes or housekeeping genes and ETS family member genes are described. Compositions and methods having utility in prostate cancer diagnosis, research, and therapy are also provided.

First claim

We claim:

1. An in vitro method for detecting a gene fusion in a human biological sample comprising prostate tissue, prostate cells, prostate secretions, or fractions thereof, the method comprising:
(a) forming a hybridized structure comprising:
i) a nucleic acid comprising a gene fusion, wherein said gene fusion comprises a 5′ portion fused to a 3′ portion at a fusion junction and said gene fusion is selected from the group consisting of:
(1) a transmembrane protease, serine 2 (TMPRSS2):ETV5 gene fusion wherein the 5′ portion of the gene fusion comprises exon 1 of TMPRSS2 and the 3′ portion of the gene fusion comprises exon 2 of ETVS5;
(2) a solute carrier family 45, member 3 (SLC45A3):ETV5 gene fusion wherein the 5′ portion of the gene fusion comprises exon 1 of SLC45A3 and the 3′ portion of the gene fusion comprises exon 8 of ETV5;
(3) a SLC45A3:ETV1 gene fusion wherein the 5′ portion comprises exon 1 of SLC45A3 and the 3′ portion of the gene fusion comprises exon 5 of ETV1;
(4) a HERV-K_22q11.23:ETV1 gene fusion wherein the 5′ portion comprises nucleotides 1-362 of SEQ ID NO:421 and the 3′ portion comprises exon 5 of ETV1; and
(5) a C15ORF21:ETV1 gene fusion wherein the 5′ portion comprises exons 1-2 of C15ORF21 and the 3′ portion of the gene fusion comprises exon 6 of ETV1; and

ii) a detectably labeled probe specifically hybridized to said nucleic acid and spanning said fusion junction; and

(b) detecting the gene fusion in the human biological sample by detecting said hybridized structure in said biological sample.

2. The method of claim 1 , wherein the 5′ portion of the gene fusion further comprises a promoter region.

3. The method of claim 1 , wherein the nucleic acid comprising the gene fusion is a genomic DNA.

4. The method of claim 1 , wherein the nucleic acid comprising the gene fusion is a chimeric mRNA.

5. The method of claim 1 , wherein the human biological sample is a sample selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions, and prostate cells.

6. The method of claim 1 , wherein detecting said hybridized structure comprises using a technique selected from the group consisting of in situ hybridization (ISH), microarray, Southern blot, and northern blot.

7. The method of claim 1 , wherein the nucleic acid comprising the gene fusion is produced using an amplification technique selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification.

8. An in vitro method for detecting a gene fusion in a human biological sample comprising prostate tissue, prostate cells, prostate secretions, or fractions thereof, the method comprising:
(a) forming a hybridized structure comprising:
i) a nucleic acid comprising a gene fusion, wherein said gene fusion comprises a 5′ portion fused to a 3′ portion at a fusion junction, and said gene fusion is selected from the group consisting of:
(1) a TMPRSS2:ETV5 gene fusion wherein the 5′ portion of the gene fusion comprises exon 1 of TMPRSS2 and the 3′ portion of the gene fusion comprises exon 2 of ETV5;
(2) a SLC45A3:ETV5 gene fusion wherein the 5′ portion of the gene fusion comprises exon 1 of SLC45A3 and the 3′ portion of the gene fusion comprises exon 8 of ETVS5;
(3) a SLC45A3:ETV1 gene fusion wherein the 5′ portion comprises exon 1 of SLC45A3 and the 3′ portion of the gene fusion comprises exon 5 of ETV1;
(4) a HERV-K_22q11.23:ETV1 gene fusion wherein the 5′ portion comprises nucleotides 1-362 of SEQ ID NO:421 and the 3′ portion comprises exon 5 of ETV1; and
(5) a C15ORF21:ETV1 gene fusion wherein the 5′ portion comprises exons 1-2 of C15ORF21 and the 3′ portion of the gene fusion comprises exon 6 of ETV1; and

ii) a first detectably labeled probe specifically hybridized to the 5′ portion of the gene fusion and a second detectably labeled probe specifically hybridized to the 3′ portion of the gene fusion; and

(b) detecting the gene fusion in the human biological sample by detecting said hybridized structure in said biological sample.

9. The method of claim 8 , wherein the 5′ portion of the gene fusion further comprises a promoter region.

10. The method of claim 8 , wherein the nucleic acid comprising the gene fusion is a genomic DNA.

11. The method of claim 8 , wherein the nucleic acid comprising the gene fusion is a chimeric mRNA.

12. The method of claim 8 , wherein the human biological sample is a sample selected from the group consisting of tissue, blood, plasma, serum, urine, urine supernatant, urine cell pellet, semen, prostatic secretions, and prostate cells.

13. The method of claim 8 , wherein detecting said hybridized structure comprises using in situ hybridization (ISH).

14. The method of claim 8 , wherein the nucleic acid comprising the gene fusion is produced using an amplification technique selected from the group consisting of polymerase chain reaction, reverse transcription polymerase chain reaction, transcription-mediated amplification, ligase chain reaction, strand displacement amplification, and nucleic acid sequence based amplification.

15. The method of claim 1 , wherein the nucleic acid comprising the gene fusion is produced using a first amplification oligonucleotide that is complementary to the 5′ portion of the gene fusion and a second amplification oligonucleotide that is complementary to the 3′ portion of the gene fusion.

16. The method of claim 8 , wherein the nucleic acid comprising the gene fusion is produced using a first amplification oligonucleotide that is complementary to the 5′ portion of the gene fusion and a second amplification oligonucleotide that is complementary to the 3′ portion of the gene fusion.

17. An in vitro method for detecting a gene fusion in a human biological sample comprising prostate tissue, prostate cells, prostate secretions, or fractions thereof, the method comprising:
(a) forming a hybridized structure comprising:
i) a nucleic acid comprising a gene fusion, wherein said gene fusion comprises a 5′ portion fused to a 3′ portion at a fusion junction and said gene fusion is selected from the group consisting of:
(1) a TMPRSS2:ETV5 gene fusion wherein the 5′ portion of the gene fusion comprises exon 1 of TMPRSS2 and the 3′ portion of the gene fusion comprises exon 2 of ETV5;
(2) a SLC45A3:ETV5 gene fusion wherein the 5′ portion of the gene fusion comprises exon 1 of SLC45A3 and the 3′ portion of the gene fusion comprises exon 8 of ETV5;
(3) a SLC45A3:ETV1gene fusion wherein the 5′ portion comprises exon 1 of SLC45A3 and the 3′ portion of the gene fusion comprises exon 5 of ETV1;
(4) a HERV-K_22q11.23:ETV1 gene fusion wherein the 5′ portion comprises nucleotides 1-362 of SEQ ID NO:421 and the 3′ portion comprises exon 5 of ETV1; and
(5) a C15ORF21:ETV1 gene fusion wherein the 5′ portion comprises exons 1-2 of C15ORF21 and the 3′ portion of the gene fusion comprises exon 6 of ETV1; and

ii) a first amplification primer specifically hybridized to said 5′ component and a second amplification primer specifically hybridized to said 3′ component;

(b) amplifying a portion of the nucleic acid using a nucleic acid amplification reaction to produce an amplicon; and
(c) detecting the gene fusion in the human biological sample by detecting in vitro the amplicon.

18. The method of claim 17 wherein detecting the amplicon comprises hybridizing a directly labeled probe

Assignees

• Chinnaiyan Arul M
• Tomlins Scott
• Univ Michigan Regents

Inventors

• Chinnaiyan Arul M
• Tomlins Scott

Classifications

• G01N33/57555

  of the prostate · CPC title

• C12N9/6445

  Kallikreins (3.4.21.34; 3.4.21.35) · CPC title

• C07K14/82

  Translation products from oncogenes · CPC title

• C12N2310/14

  interfering nucleic acids [NA] · CPC title

• C12Q2600/136

  Screening for pharmacological compounds · CPC title