Identifying Rare Germline Variants Associated with Metastatic Prostate Cancer Through an Extreme Phenotype Study

Abstract Background Studies of germline variants in prostate cancer (PCa) have largely focused on their connections to cancer predisposition. However, an understanding of how heritable factors contribute to cancer progression and metastasis remain limited. Objective To identify low frequency to rare germline nonsynonymous variants associated with increased risk for metastatic PCa (mPCa), while providing functional validation. Design We assembled an extreme phenotype cohort (EPC) of 52 patients diagnosed with predominantly high-grade (Gleason Score (GS) ≥ 8) PCa and > 7 years of follow-up for which localized treatment naïve tumor tissues were available. In half of the cases, the tumor had metastasized to bone, providing an even distribution of bone mPCa and non mPCa cases. Tumor and matched distant benign DNA samples were exome sequenced and analyzed for germline variants with population-wide minor allelic frequencies σ; 2%. Findings were validated using two independent PCa germline cohorts, including a closely matched Australian study biased to aggressive disease (n = 53) and Pan Prostate Cancer Group (PPCG, n = 976). Two mPCa-promoting candidate variants in KDM6B and BRCA2 were engineered into cell lines and functionalized. Results Germline nonsynonymous rare variants (gnsRVs) identified in 25 DNA Damage Repair (DDR) genes were significantly enriched in the mPCa patients (p=4.57e-06). Conversely, the prevalence of synonymous variants at minor allele frequencies of σ; 2% were similar between the mPCa and non mPCa patients. The predictive power of variants in 53 non-DDR genes was validated in the Australian cohort (p=0.028) and correlated with high-risk PCa in PPCG (p=0.03). KDM6B K973Q showed functional significance despite being annotated as benign in ClinVar, while BRCA2 I1962T showed sensitivity to Olaparib. In total, six EPC variants related to DNA repair or epigenetics were found to alter enzymatic activity. Conclusions EPCs coupled with low frequency/rare variant analyses may advance understanding of interactions between the germline and tumor in PCa. We identified a series of germline variants that were enriched among mPCa patients. Moreover, we showed that one of these variants confers a metastatic phenotype. Our findings suggest that germline testing at diagnosis may improve treatment stratification in PCa. Patient summary The presence of specific genetic variants among men with PCa may elevate the risk of mPCa once PCa develops. Knowledge of the variant burden at time of diagnosis may enable accurate stratification of some patients for aggressive therapeutic interventions.

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