Prostate cancer risk regions at 8q24 and 17q24 are differentially associated with somatic TMPRSS2:ERG fusion status

Molecular and epidemiological differences have been described between TMPRSS2:ERG fusion-positive and fusion-negative prostate cancer (PrCa). Assuming two molecularly distinct subtypes, we have examined 27 common PrCa risk variants, previously identified in genome-wide association studies, for subtype specific associations in a total of 1221 TMPRSS2:ERG phenotyped PrCa cases. In meta-analyses of a discovery set of 552 cases with TMPRSS2:ERG data and 7650 unaffected men from five centers we have found support for the hypothesis that several common risk variants are associated with one particular subtype rather than with PrCa in general. Risk variants were analyzed in case-case comparisons (296 TMPRSS2:ERG fusion-positive versus 256 fusion-negative cases) and an independent set of 669 cases with TMPRSS2:ERG data was established to replicate the top five candidates. Significant differences (P < 0.00185) between the two subtypes were observed for rs16901979 (8q24) and rs1859962 (17q24), which were enriched in TMPRSS2:ERG fusion-negative (OR = 0.53, P = 0.0007) and TMPRSS2:ERG fusion-positive PrCa (OR = 1.30, P = 0.0016), respectively. Expression quantitative trait locus analysis was performed to investigate mechanistic links between risk variants, fusion status and target gene mRNA levels. For rs1859962 at 17q24, genotype dependent expression was observed for the candidate target gene SOX9 in TMPRSS2:ERG fusion-positive PrCa, which was not evident in TMPRSS2:ERG negative tumors. The present study established evidence for the first two common PrCa risk variants differentially associated with TMPRSS2:ERG fusion status. TMPRSS2:ERG phenotyping of larger studies is required to determine comprehensive sets of variants with subtype-specific roles in PrCa.

Amplification of the 9p13.3 chromosomal region in prostate cancer

Amplification of the 9p13.3 chromosomal region occurs in a subset of prostate cancers (PCs); however, the target gene or genes of this amplification have remained unidentified. The aim of this study was to investigate the 9p13.3 amplification in more detail to identify genes that are potentially advantageous for cancer cells. We narrowed down the minimally amplified area and assessed the frequency of the 9p13.3 amplification. Of the clinical samples from untreated PCs that were examined (n = 134), 9.7% showed high-level amplification, and 32.1% showed low-level amplification. Additionally, in clinical samples from castration-resistant PCs (n = 70), high- and low-level amplification was seen in 14.3% and 44.3% of the samples, respectively. We next analyzed the protein-coding genes in this chromosomal region for both their expression in clinical PC samples as well as their potential as growth regulators in PC cells. We found that the 9p13.3 amplification harbors several genes that are able to affect the growth of PC cells when downregulated using siRNA. Of these, UBAP2 was the most prominently upregulated gene in the clinical prostate tumor samples. © 2016 Wiley Periodicals, Inc.

A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer

Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of > 10 million SNPs in 43,303 prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three new susceptibility loci were identified at association P < 5 × 10(-8); 15 variants were identified among men of European ancestry, 7 were identified in multi-ancestry analyses and 1 was associated with early-onset prostate cancer. These 23 variants, in combination with known prostate cancer risk variants, explain 33% of the familial risk for this disease in European-ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the usefulness of combining ancestrally diverse populations to discover risk loci for disease.

Loss of PTEN is associated with aggressive behavior in ERG-positive prostate cancer

BACKGROUND

The associations of ERG overexpression with clinical behavior and molecular pathways of prostate cancer are incompletely known. We assessed the association of ERG expression with AR, PTEN, SPINK1, Ki-67, and EZH2 expression levels, deletion, and mutations of chromosomal region 3p14 and TP53, and clinicopathologic variables.

METHODS

The material consisted of 326 prostatectomies, 166 needle biopsies from men treated primarily with endocrine therapy, 177 transurethral resections of castration-resistant prostate cancers (CRPC), and 114 CRPC metastases obtained from 32 men. Immunohistochemistry, FISH, and sequencing was used for the measurements.

RESULTS

ERG expression was found in about 45% of all patient cohorts. In a multivariate analysis, ERG expression showed independent value of favorable prognosis (P = 0.019). ERG positivity was significantly associated with loss of PTEN expression in prostatectomy (P = 0.0348), and locally recurrent CRPCs (P = 0.0042). Loss of PTEN expression was associated (P = 0.0085) with shorter progression-free survival in ERG-positive, but not in negative cases. When metastases in each subject were compared, consistent ERG, PTEN, and AR expression as well as TP53 mutations were found in a majority of subjects.

CONCLUSIONS

A similar frequency of ERG positivity from early to late stage of the disease suggests lack of selection of ERG expression during disease progression. The prognostic significance of PTEN loss solely in ERG-positive cases indicates interaction of these pathways. The finding of consistent genetic alterations in different metastases suggests that the major genetic alterations take place in the primary tumor.

IMPACT

Interaction of PTEN and ERG pathways warrants further studies.

Abstract A28: Correlation of ERG expression with other genetic and expression abnormalities in prostate cancer

Fusion between TMPRSS2 (transmembrane protease, serine 2) and ERG (v-ets erythroblastosis virus E26 oncogene like (avian)) (TMPRSS2:ERG) is the most commonly found genetic alteration in prostate cancer and is found in 35–50% of all cases. TMPRSS2 is induced by the androgen receptor (AR). Fusion with TMPRSS2 renders ERG androgen inducible, causing most of its overexpression in prostate cancer. Studies suggest that SPINK1 (serine peptidase inhibitor, Kazal type 1) expression is exclusive to TMPRSS2:ERG fusion negative tumors, PTEN (phosphatase and tensin homolog) and TP53 (tumor protein p53) deletions are enriched in fusion positive tumors, a small region in chromosome 3p14 (including three possible tumor suppressor genes, FOX1, RYBP and SHQ1) is specifically deleted in a subset of fusion positive tumors, and that AR expression is down regulated in fusion positive tumors. Correlation with EZH2 (enhancer of zeste homolog 2 (Drosophila)) and Ki-67 (antigen identified by monoclonal antibody Ki-67) expression has also been suggested.

To confirm these correlations we used fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC) techniques in our sample material, which consisted of 330 prostatectomy samples and 150 locally recurrent castration resistant prostate cancers (CRPC).

About half of the prostatectomy (47%, 107/230) and CRPC (45%, 70/156) samples showed positive ERG staining and ERG positivity was significantly associated with longer progression-free survival (p=0.0001, Log rank test) compared to ERG negative cases. Positive SPINK1 expression was seen in 14% (34/243) of the prostatectomy samples and in 12% (17/138) of the CRPC tumors. SPINK1 was almost exclusively expressed in ERG negative tumors (in prostatectomies p&lt;0.0001 and in CRPCs p=0.0132, Fisher's exact test). High AR staining was seen in 82% (206/252) of the prostatectomy samples and in 93% (127/136) of the CRPC tumors. In prostatectomy samples, AR expression was significantly associated with ERG positivity (p&lt;0.0001, Fisher's exact test). Low PTEN expression was seen in 15% (42/282) of the prostatectomy samples and in 45% (55/122) of the CRPC tumors. In CRPC tumors, but not in prostatectomy samples, loss of PTEN expression was associated with ERG positivity (p=0.0035, Fisher's exact test). Low PTEN expression was significantly associated with shorter progression-free survival compared to PTEN positive tumors (p=0.0133, Log rank test). Deletion of TP53 was seen in 8% (19/237) of the prostatectomy samples and in 18% (25/140) of the CRPC tumors. Deletion of chromosome region 3p14 was seen in approximately 4% of both prostatectomy (8/229) and CRPC (5/118) samples. Neither of these deletions was associated with ERG positivity. Analysis of Ki-67 and EZH2 staining is ongoing.

SPINK1 was almost exclusively expressed in ERG negative samples, and the association was statistically significant in both the prostatectomy samples and the locally recurrent CRPC samples. PTEN loss of expression was associated with ERG positivity in the CRPC samples, but not in the prostatectomy samples, indicating that this late event occurs preferentially in ERG positive cases. High AR expression was statistically significantly associated with ERG positivity. Since there shouldn't be any ERG expression from TMPRSS2:ERG fusion gene without AR, the results are in line with the known regulatory mechanisms of TMPRSS2:ERG. Contrary to previous reports, the specific deletions of 3p14 or TP53 were not enriched in the ERG positive samples. TP53 deletion was more frequent in the advanced disease.

Citation Format: Katri A. Leinonen, Teuvo L.J. Tammela, Outi R. Saramäki, Tapio Visakorpi. Correlation of ERG expression with other genetic and expression abnormalities in prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr A28.

Abstract 3060: Target genes of chromosomal 9p13.3 amplification in prostate cancer

The development and progression of cancer is caused by alterations that accumulate in the genome of malignant cells. We are studying genetic alterations occurring in prostate cancer, the most common male malignancy in Western countries. We have previously identified a frequent (39%) gain at 9p13-q21 in 13 prostate cancer xenografts and 5 cell lines by aCGH (Saramäki et al., Int J Cancer 119:1322-1329, 2006). Preliminary results indicate that in clinical prostatectomy samples, gains and amplifications are found in approximately 30% and 10% of the cases, respectively, and that the amplification frequency seems to increase with disease progression to hormone-refractory stage. The 9p13.3 amplification is also found from several breast cancer cell lines, raising the possibility that the amplification target gene(s) in this area may take part in breast cancer formation in addition to prostate cancer.

We aim at identifying the target gene of the 9p13.3 amplification in prostate cancer. A minimal region for the 9p13.3 amplification, determined by fluorescence in situ hybridisation (FISH), spans nearly 3.5 Mb and contains more than 40 known and hypothetical protein-coding genes. We initially screened mRNA expression levels by quantitative RT-PCR and chromosomal copy number alterations by FISH for these genes in 7 prostate cancer cell lines and 19 prostate cancer xenografts. Thus, we narrowed down the list of amplification target candidates to eight protein-coding genes (C9orf25, GALT, PIGO, UBAP1, UBAP2, UBE2R2, UNC13B and VCP). We have performed siRNA-mediated downregulation of these genes in cell lines with either a normal copy number status or a gain/amplification in 9p13.3 (prostate cancer cell lines PC-3 and 22Rv1; breast cancer cell lines MCF-7 and BT-474). Downregulation of several of these genes decrease the proliferation rate of the cells significantly (GALT, PIGO, UBAP1, UBAP2, VCP). As decreased levels of VCP induce cell death in PC-3 cells, downregulation of UBAP1 induces a cell cycle arrest in the G2/M phase. In addition, invasion of PC-3 cells in Boyden chamber assay is affected by knock-down of GALT and PIGO. Genes exhibiting alterations in the siRNA assays have been further analyzed for their expression in clinical prostate cancer tumor material by qRT-PCR and immunohistochemistry. These genes are also studied by overexpressing their cDNAs in cell lines with normal 9p13.3 copy number status and screening for altered cellular growth, survival and invasion in vitro. We aim at identifying a novel diagnostic and/or prognostic marker for prostate cancer, and potentially also a target for new cancer therapies, from the 9p13.3 region.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3060. doi:10.1158/1538-7445.AM2011-3060

Association of SPINK1 expression and TMPRSS2:ERG fusion with prognosis in endocrine-treated prostate cancer

PURPOSE

The aim of the study was to examine whether TMPRSS2:ERG fusion or SPINK1 protein expression is associated with hormone responsiveness of prostate cancer and can thus be used as a biomarker.

EXPERIMENTAL DESIGN

Diagnostic needle biopsies from prostate cancer patients primarily treated by endocrine therapy were evaluated for TMPRSS2:ERG fusion with fluorescence in situ hybridization and SPINK1 protein expression with immunohistochemistry.

RESULTS

The frequency of TMPRSS2:ERG fusion in 178 biopsies of hormonally treated patients was 34%. Of the fusion-positive cases, 71% showed deletion between the two genes, and 23% showed gain of the fusion. The fusion was associated with high Ki-67 staining (P=0.001), age at diagnosis (P=0.024), and tumor area (P=0.006), but not with Gleason score, T stage, M stage, prostate-specific antigen (PSA), or progression-free survival. Strong positive SPINK1 expression was found in 11% (21 of 186) of the biopsies. SPINK1-positive cases had significantly shorter progression-free survival compared with SPINK1-negative cases (P=0.001). The expression was not associated with any other clinicopathologic variables studied. In a multivariate analysis, SPINK1 expression showed independent prognostic value, with a relative risk of 2.3 (95% confidence interval, 1.1-4.6). SPINK1 expression and the fusion were not associated with each other.

CONCLUSIONS

There was no association between TMPRSS2:ERG fusion and prognosis, suggesting that TMPRSS2:ERG rearrangement does not implicate hormone dependence of the cancer. SPINK1 expression, found in approximately 10% of prostate cancers, was associated with aggressive form of the disease and could serve as a biomarker in endocrine-treated prostate cancer.