Deciphering Epigenetic Regulation of Enhancers in High-Risk Prostate Cancer

Prostate cancer (PCa) is associated with widespread promoter hypermethylation. We hypothesized that aberrant DNA methylation also targets gene enhancers, modulating their activity and contributing to disease etiology. DNA methylation was assessed in a discovery set (n = 37) of primary PCa via the Infinium methylation EPIC array, using high-risk (HR; n=13), low-risk (LR; n=11), and histologically benign (n=13) tissues. A higher proportion of enhancers was hypomethylated in HR (n=385, 15%) than LR (n=105, 10%) PCa, primarily targeting genes involved in development and enriched for oncoprotein binding motifs, including FOXA1. Clinical significance was evaluated by identifying a 17 enhancer differentially methylated probe (DMP) signature using a Least Absolute Shrinkage and Selection Operator model in the discovery set. A logistic regression model was trained using the HR PCa-specific signature in a training set (n=490) and validated in a testing set (n=256). The signature had a 0.81 (95% bootstrapped CI 0.78-0.9) area under the curve, for selective detection of HR PCa, achieving a 0.71 sensitivity and 0.76 specificity (testing set). Array-wide aberrant DNA methylation at enhancers highlighted their epigenetic perturbance in HR disease. A clinically significant enhancer signature from this study could be used for detecting HR PCa. FFPE tissue samples were collected from 37 PCa patients. DNA was isolated and methylation was measured using the Illumina Infinium Human MethylationEPIC BeadChip. Normalized beta-values were used to compare methylation patterns between different risk groups.