前列腺癌风险变异通过激活增强子并在前列腺癌不同阶段形成多连接增强子-启动子枢纽来调控癌基因

Prostate cancer (PCa) is a complex disease and the second leading cause of cancer death in the US men. Clinical outcomes vary among PCa stages. PCa becomes increasingly aggressive, progressing from localized disease to metastatic PCa, then to metastatic castration-resistant PCa and ultimately to neuroendocrine PCa. Multi-ethnic genome-wide association studies have identified over a thousand of genetic variants associated with PCa risk, including variants linked to aggressive forms of the disease. Considering population-specific linkage disequilibrium patterns, we identified over 40,000 highly linked variants to PCa risk variants. However, most of these variants reside in non-coding regions, making it challenging to elucidate their roles in disease development and progression. Non-coding regions often include functional elements called regulatory elements such as promoters, enhancers, and insulators. Among regulatory elements, enhancer activities, which can be assessed by the histone modification mark H3K27ac, are tightly associated with cell fate. We therefore hypothesized that PCa risk variants affect enhancer activities at distinct disease stages, contributing to disease development and progression, and ultimately influencing clinical outcomes. In this study, we integrated over 200 H3K27ac ChIP-seq and over 550 RNA-seq datasets from prostate tissues and cell lines across PCa progression stages and found stage-specific enhancers and transcription factors (TFs) that are distinctly activated at different stages. Moreover, we found over 5,500 PCa risk variants located in enhancers containing motifs of the identified TFs. To evaluate the PCa risk variants associated with enhancer activities, we integrated patient tissue-derived H3K27ac ChIP-seq data and performed chromatin quantitative trait loci and allelic imbalance analyses. We identified over 700 variants associated with enhancer activities, including those affected by TF binding. Moreover, to identify target genes of these enhancer variants, we analyzed over 100 genome-wide chromatin interaction datasets. By integrating chromatin interaction data with epigenomic and transcriptomic data, we identified enhancer variants involved in chromatin looping to regulate transcription. Furthermore, we found over 1,700 enhancer variants located in multi-connected enhancer-promoter (E-P) hubs, including those potentially regulated by stage-specific TFs. Overall, these findings support a model in which genetic and epigenetic reprogramming converge on E-P hubs to drive transcription of oncogenes and promote disease initiation and progression in PCa.