Characterizing prostate cancer risk through multi-ancestry genome-wide discovery of 187 novel risk variants

The transferability and clinical value of genetic risk scores (GRSs) across populations remain limited due to an imbalance in genetic studies across ancestrally diverse populations. Here we conducted a multi-ancestry genome-wide association study of 156,319 prostate cancer cases and 788,443 controls of European, African, Asian and Hispanic men, reflecting a 57% increase in the number of non-European cases over previous prostate cancer genome-wide association studies. We identified 187 novel risk variants for prostate cancer, increasing the total number of risk variants to 451. An externally replicated multi-ancestry GRS was associated with risk that ranged from 1.8 (per standard deviation) in African ancestry men to 2.2 in European ancestry men. The GRS was associated with a greater risk of aggressive versus non-aggressive disease in men of African ancestry (P = 0.03). Our study presents novel prostate cancer susceptibility loci and a GRS with effective risk stratification across ancestry groups.

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.

Abstract 148: Transcriptome sequencing reveals PCAT5 - new ERG-regulated non-coding transcript in prostate cancer

Background: Prostate cancer (PC) is the second most common cancer among men. Most PC-related deaths are due to invasive tumors that are treated with therapies inhibiting androgen production or androgen receptor (AR) activity. After an initial response, tumors invariably progress to castration resistant prostate cancers (CRPCs) for which no effective cure exists.

Methods and Results: We used transcriptome sequencing to study fresh-frozen tissue specimens from 12 benign prostatic hyperplasias (BPHs), 28 PCs, and 13 CRPCs. Reference-based transcriptome assembly uncovered 145 previously unannotated intergenic PC and CRPC associated long non-coding transcripts (lncRNAs) or isoforms. One third of the transcripts were CRPC-specific. We showed that one of the novel transcripts, Prostate Cancer Associated Transcript 5 (PCAT5), expressed in half of the tumors, was likely regulated by ERG, the key transcription factor in ∼50% of prostate cancers. Genome-wide expression analysis of a PCAT5-positive prostate cancer cell line after PCAT5 knockdown suggested significant alterations in proliferation pathways. In vitro validation of the pathway alterations revealed concordantly dramatic effects in phenotype: stalling of cell growth, migration, invasion, and colony forming potential, and increase in the rate of apoptosis.

Conclusions: We identified the key differences between PC and CRPC in transcriptome level, and validated the oncogenic potential of a novel lncRNA in ERG-positive prostate cancers, PCAT5. Our study presents a number of putative lncRNA biomarkers for CRPC, and opportunities for therapeutic intervention.

Citation Format: Antti Ylipää, Kati Kivinummi, Matti Annala, Annika Kohvakka, Leena Latonen, Mauro Scaravilli, Kimmo Kartasalo, Simo-Pekka Leppänen, Serdar Karakurt, Janne Seppälä, Olli Yli-Harja, Teuvo L.J. Tammela, Wei Zhang, Tapio Visakorpi, Matti Nykter. Transcriptome sequencing reveals PCAT5 - new ERG-regulated non-coding transcript in prostate cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 148. doi:10.1158/1538-7445.AM2015-148

Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer

The 2q37 and 17q12-q22 loci are linked to an increased prostate cancer (PrCa) risk. No candidate gene has been localized at 2q37 and the HOXB13 variant G84E only partially explains the linkage to 17q21-q22 observed in Finland. We screened these regions by targeted DNA sequencing to search for cancer-associated variants. Altogether, four novel susceptibility alleles were identified. Two ZNF652 (17q21.3) variants, rs116890317 and rs79670217, increased the risk of both sporadic and hereditary PrCa (rs116890317: OR = 3.3-7.8, p = 0.003-3.3 × 10(-5) ; rs79670217: OR = 1.6-1.9, p = 0.002-0.009). The HDAC4 (2q37.2) variant rs73000144 (OR = 14.6, p = 0.018) and the EFCAB13 (17q21.3) variant rs118004742 (OR = 1.8, p = 0.048) were overrepresented in patients with familial PrCa. To map the variants within 2q37 and 17q11.2-q22 that may regulate PrCa-associated genes, we combined DNA sequencing results with transcriptome data obtained by RNA sequencing. This expression quantitative trait locus (eQTL) analysis identified 272 single-nucleotide polymorphisms (SNPs) possibly regulating six genes that were differentially expressed between cases and controls. In a modified approach, prefiltered PrCa-associated SNPs were exploited and interestingly, a novel eQTL targeting ZNF652 was identified. The novel variants identified in this study could be utilized for PrCa risk assessment, and they further validate the suggested role of ZNF652 as a PrCa candidate gene. The regulatory regions discovered by eQTL mapping increase our understanding of the relationship between regulation of gene expression and susceptibility to PrCa and provide a valuable starting point for future functional research.

A meta-analysis of genome-wide association studies to identify prostate cancer susceptibility loci associated with aggressive and non-aggressive disease

Genome-wide association studies (GWAS) have identified multiple common genetic variants associated with an increased risk of prostate cancer (PrCa), but these explain less than one-third of the heritability. To identify further susceptibility alleles, we conducted a meta-analysis of four GWAS including 5953 cases of aggressive PrCa and 11 463 controls (men without PrCa). We computed association tests for approximately 2.6 million SNPs and followed up the most significant SNPs by genotyping 49 121 samples in 29 studies through the international PRACTICAL and BPC3 consortia. We not only confirmed the association of a PrCa susceptibility locus, rs11672691 on chromosome 19, but also showed an association with aggressive PrCa [odds ratio = 1.12 (95% confidence interval 1.03-1.21), P = 1.4 × 10(-8)]. This report describes a genetic variant which is associated with aggressive PrCa, which is a type of PrCa associated with a poorer prognosis.

Chromosomes 4 and 8 implicated in a genome wide SNP linkage scan of 762 prostate cancer families collected by the ICPCG

BACKGROUND

In spite of intensive efforts, understanding of the genetic aspects of familial prostate cancer (PC) remains largely incomplete. In a previous microsatellite-based linkage scan of 1,233 PC families, we identified suggestive evidence for linkage (i.e., LOD ≥ 1.86) at 5q12, 15q11, 17q21, 22q12, and two loci on 8p, with additional regions implicated in subsets of families defined by age at diagnosis, disease aggressiveness, or number of affected members.

METHODS

In an attempt to replicate these findings and increase linkage resolution, we used the Illumina 6000 SNP linkage panel to perform a genome-wide linkage scan of an independent set of 762 multiplex PC families, collected by 11 International Consortium for Prostate Cancer Genetics (ICPCG) groups.

RESULTS

Of the regions identified previously, modest evidence of replication was observed only on the short arm of chromosome 8, where HLOD scores of 1.63 and 3.60 were observed in the complete set of families and families with young average age at diagnosis, respectively. The most significant linkage signals found in the complete set of families were observed across a broad, 37 cM interval on 4q13-25, with LOD scores ranging from 2.02 to 2.62, increasing to 4.50 in families with older average age at diagnosis. In families with multiple cases presenting with more aggressive disease, LOD scores over 3.0 were observed at 8q24 in the vicinity of previously identified common PC risk variants, as well as MYC, an important gene in PC biology.

CONCLUSIONS

These results will be useful in prioritizing future susceptibility gene discovery efforts in this common cancer.

Abstract A9: Androgen-regulated miR-32 targets BTG2 and is overexpressed in castration-resistant prostate cancer

The androgen receptor (AR) signaling pathway is central to the emergence of castration-resistant prostate cancer (CRPC). We set out to identify androgen-regulated microRNAs (miRNAs) that may contribute to the development of CRPC. We found miR-32 to be an androgen regulated miRNA which is differentially expressed in CRPC compared to benign prostate hyperplasia (BPH) according to microarray analyses. qRT-PCR analyses confirmed that miR-32 expression increases in CRPC compared to BPH, and that in untreated prostate cancer (PC) miR-32 expression is higher in tumors of stage pT3 compared to pT2. Transfection of pre-miR-32 to prostate cancer cell line LNCaP provided a significant growth advantage to the cells, and miR-32 was further demonstrated to reduce apoptosis. To identify target genes for miR-32, an mRNA microarray analysis was performed with LNCaP cells transfected with pre-miR-32. In this assay, B cell translocation gene 2 (BTG2) was identified as a novel putative target for miR-32. BTG2 was reduced both at mRNA and protein level in the cells transfected with pre-miR-32, and BTG2 was confirmed to be a miR-32 target by 3′-UTR-luciferase assay. Furthermore, BTG2 was able to partially rescue the growth advantage of miR-32 in LNCaP cells. Immunostainings of prostate cancer patient material showed a statistically significant (p &lt; 0.0001) reduction of BTG2 protein in CRPCs compared to PC. The lack of BTG2 staining was also associated (p=0.0021) with a short progression-free time in patients who underwent prostatectomy and inversely correlated to miR-32 expression levels. In conclusion, we find that miR-32 is an androgen-regulated miRNA targeting BTG2 and overexpressed in CRPC. Thus, miR-32 is a potential marker for aggressive disease and is a putative drug target in PC.

Citation Format: Sanni E. Jalava, Leena Latonen, Mauro Scaravilli, Kati K. Waltering, Janne Seppälä, Harri Lähdesmäki, Teuvo L.J. Tammela, Tapio Visakorpi. Androgen-regulated miR-32 targets BTG2 and is overexpressed in castrationresistant 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 A9.

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 A97: Risk of biochemical recurrence after radical prostatectomy among men using 5α-reductase inhibitors and alpha-blockers

Background: Previous studies have demonstrated that 5α-reductase inhibitors (5-ARIs) finasteride and dutasteride decrease overall prostate cancer risk, while the proportion of high risk tumors may be increased. We compared risk of biochemical recurrence and mortality after radical prostatectomy between users of 5-ARIs, alpha-blockers and medication non-users

Materials and Methods: A total of men 1,315 men who underwent radical prostatectomy at the Tampere University Hospital during 1995–2009 were included in the study cohort. Post-operatively, men were followed at six month intervals during the first postoperative year and yearly afterwards. Serum PSA was measured at each visit. Biochemical relapse was defined as PSA becoming detectable after the operation. Information on causes of death was obtained from the Finnish Cancer Registry. Data on medication purchases during 1995–2009 was obtained from national prescription database. Cox proportional regression was used to analyze hazard ratios (HRs) and 95% confidence intervals (95% CI) of biochemical relapse and death.

Results: A total of 117 men had used finasteride or dutasteride, while 372 had used tamsulosin or alfuzosin. During the follow-up 424 men had a biochemical relapse, while 124 died, of which 22 due to prostate cancer. The median follow-up time until biochemical relapse was 3.17 years and until death 5.08 years. Pathological T-stage and tumor Gleason score among users of either drug group did not significantly vary from non-users. However, 5-ARI and alpha-blocker users had more often local lymph node metastases and positive surgical margins. Prediagnostic PSA, Gleason grade, pathological T-stage and marginal positivity were all independent predictors of biochemical recurrence. Risk of biochemical relapse was comparable to non-users among 5–ARI users (HR 1.38; 95% CI 0.86–2.19), but elevated among alpha-blocker users (HR 1.71; 95% CI 1.31–2.25). However, this risk increase was only observed when alpha-blockers were being used after the surgery. Overall mortality and prostate cancer-specific mortality did not differ by medication usage.

Conclusions: Use of finasteride or dutasteride was not associated with prostate cancer grade in this population, although the users had more often local lymph node metastases and positive surgical margins. Nevertheless, the risk of biochemical recurrence and prostate cancer mortality were not affected by 5-ARI use. Our finding of increased risk of biochemical recurrence among alpha-blocker users likely reflects treatment of symptoms of aggressive prostate cancer with alpha-blockers.

Citation Information: Cancer Prev Res 2011;4(10 Suppl):A97.