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. A patient discovery set (n = 37) was used for differential methylation analysis and biomarker identification using the Infinium methylation EPIC array, on high-risk (n = 13), low-risk (n = 11), and histologically benign (n = 13) tissues. Enhancers were primarily hypermethylated. However proportionally, hypomethylated enhancers were more prominent in high-risk (n = 385, 15%) than low-risk (n = 105, 10%) disease, primarily targeting genes involved in development and enriched for oncoprotein binding motifs, including FOXA1. The clinical significance of enhancer methylation 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 large external dataset (n = 746) obtained from four publicly available prostate tissue methylation array studies was used to assess the enhancer signature through logistic regression models trained on a 2/3 training set and tested in a 1/3 test set. This delivered an area under the curve of 0.81 (95% bootstrapped CI 0.78–0.9) for selective detection of high-risk PCa, achieving a 0.71 sensitivity and 0.76 specificity. Array-wide aberrant DNA methylation at enhancers highlighted their epigenetic perturbance in high-risk disease. A clinically significant enhancer signature from this study could be used for detecting high-risk PCa.