The overarching goal of our work this year was to find new loci associated with PrCa risk, particularly men who go on to have very aggressive disease. We explored specific genes such as HOXB13 and continued with larger meta analysis. We worked to develop a set of single nucleotide polymorphisms (SNPs) for screening. We collaborated with NCI to study PrCa in men of African Ancestry. We also participated in studies of expression and methylation and PrCa (PrCa) risk. Finally, we began new studies aimed at exome sequencing of families, followed by analysis for putative mutations and then examination of those in two population based case controls studies. Lethal Prostate Cancer In a study lead by Ostrander lab Staff Scientist Danielle Karyadi, we sought to determine if genetic variants were associated with lethal PrCa in our cohort of men from hereditary PrCa families (Karyadi et al., 2015). For this study, a cohort of 957 PCa patients from 270 hereditary PrCa families of European ancestry was genotyped for a panel of 22 PCSM-associated SNPs. Families were collected by close collaborator Dr. Janet Stanford from the Fred Hutchinson Cancer Research Center. Mixed-effect Cox proportional hazards models were used to assess survival according to genotypes, accounting for relatedness and clinicopathological factors. Within this cohort, 98 PCa deaths were confirmed over an average follow-up period of 12.7 years after diagnosis. Variant allele carriers for three SNPs had significantly altered risk for PCSM rs635261 at RNASEL, hazard ratio (HR), 0.35, 95% CI, 0.18-0.66; rs915927 in XRCC1, HR, 1.91, 95% CI, 1.21-3.02; and rs2494750 at AKT1, HR, 0.45, 95% CI, 0.23-0.90). These results confirm the association of genetic variation in three genes with PCa lethality in a cohort of men with an inherited susceptibility to the disease and provide validation that germline SNPs provide prognostic information for PCa patients. We conclude that development of a panel of germline biomarkers with clinical utility for distinguishing patients at detection who have an increased risk for fatal PCa is warranted. In a larger study, with the National Cancer Institute (NCI) SPORE working group, we sought to determine if there were associations of PrCa risk variants with disease aggressiveness (Helfand et al., 2015). The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which, at the time, had been validated to be associated with PC risk from 25,674 cases with PC. After adjusting for multiple testing, only PrCa-risk SNP rs2735839 (G) was significantly and inversely associated with aggressive (OR = 0.77; 95 % CI 0.69-0.87) and high-grade disease (OR = 0.77; 95 % CI 0.68-0.86) in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels (<4.0 ng/mL) in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. HoxB13 We examined the role of HOXB13 as part of a PRACTICAL study, a gene which has been implicated in PrCa (Saunders et al., 2014). We identified a cluster of highly correlated common variants situated within or closely upstream of HOXB13 that were significantly associated with PrCa risk. We also worked with the ICPCG to14 loci in 12,506 samples (9,560 PrCa cases, 3,368 with aggressive disease, and 2,946 controls from 2,283 pedigrees (Teerlink et al., 2014). We analyzed all familial PrCa cases and the subset of aggressive cases. For the familial PrCa phenotype, 20 of the 25 SNPs were at least nominally associated with PrCa and 16 remained significant after multiple testing correction. This year we also summarized all of the available data for the community in a review (Decker and Ostrander, 2014). Screening With an eye towards developing tools for screening we worked with the PRACTICAL Consortium to determine if existing variants found in genome wide association studies (GWAS) could can be used to stratify individuals by their risk of PrCa. A total of 25 PrCa susceptibility loci were genotyped in 40,414 individuals and a polygenic risk score (PRS) was calculated. The estimated empirical odds ratios (OR) for PrCa associated with different risk strata defined by PRS and derived age-specific absolute risks of developing PrCa were sorted by PRS stratum and family history. Specifically, PrCa risk for men in the top 1% of the PRS distribution was 30.6 (95% CI,16.4-57.3) fold compared with men in the bottom 1%, and 4.2 (95% CI, 3.2-5.5) fold compared with the median risk. The absolute risk of PrCa by age of 85 years was 65.8% for a man with family history in the top 1% of the PRS distribution, compared with 3.7% for a man in the bottom 1%. The study thus concludes that risk profiling can identify men at substantially increased or reduced risk of PrCa. The effect size, measured by OR per unit PRS, was higher in men at younger ages and in men with family history of PrCa (Al Olama et al., 2015). PrCa in Men of African Ancestry In the past year we were fortunate to play a small role in a collaboration with Dr. Stephen Chanock at NCI regarding PrCa in men of African Ancestry (Bendt et al., 2015). Most men diagnosed with PrCa will experience indolent disease; hence, discovering genetic variants that distinguish aggressive from nonaggressive PrCa is of critical clinical importance. In a multistage, case-only genome-wide association study of 12,518 PrCa cases, the study identify two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49 10(-9)) and rs78943174 at 3q26.31 (NAALADL2, P=4.18 10(-8)). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive PrCa (P=8.85 10(-5)) with no association for nonaggressive PrCa compared with controls (P=0.57). The proximity of these loci to genes involved in vascular disease suggests potential biological mechanisms worthy of further investigation. Gene Expression Studies As part of the Pacific Northwest SPORE we had the opportunity to participate in a study of cell cycle regulated genes and PrCa progression (Rubicz et al., 2015). Gene expression data were generated from tumor tissues obtained at radical prostatectomy for 383 population-based patients (12.3-years average follow-up). The overall mean and individual transcript levels of 30 selected cell cycle genes was compared between patients with no evidence of recurrence (73%) and those who recurred (27%) or died (7%) from PCa. We found that mean expression level for 30 selected cell cycle-regulated genes was unrelated to recurrence risk, but was associated with a twofold increase in risk of lethal PCa. Also, transcript levels for several genes in the panel were significantly overexpressed in lethal versus non-recurrent PCa. Whole Exome Seqencing Our collaborative group previously undertook whole exome sequencing (WES) study of 80 affected and 11 unaffected men from 19 HPC (PROGRESS) families with aggressive and/or early onset disease (FitzGerald et al., 2013). This study is being continued with an expanded data set of 75 families this year in an effort led by Dr. Karyadi. We are analyzing sequence data across families to find putative risk loci. Those that appear significant are being analyzed in two population-based, case-control studies to determine their relevance for men in the general population. This work is ongoing.
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