Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes

We generated 64 epigenomic datasets using ChIP-seq and ATAC-seq profiling on 28 fresh bladder cancer (BLCA) specimens of luminal and basal-squamous expression subtypes. An integrated analysis of core regulatory circuitry, enhancer activity and transcription factor expression specificity nominated 23 luminal-specific and 14 basal-squamous-specific candidate master transcription factors (MTFs), including established regulators like FOXA1, PPARG, and GATA3 for luminal BLCA, and TP63 for basal-squamous BLCA, as well as new basal-squamous MTF candidates SNAI2 and CEBPB. GRHL2, a regulator of subtype differentiation, was identified as a common MTF to luminal and basal-squamous BLCA. Cis-regulatory elements were enriched up to 80-fold for bladder cancer risk variants. Keratinization pathways were enriched in genetically-determined basal-squamous sites, while carcinogen glucuronidation pathways were enriched in luminal sites. Integrating germline variation and epigenomics through a cistrome-wide association study identified a new BLCA risk locus upstream of SPINK1, and linked 10/19 BLCA risk loci to regulatory elements from a 350,000-sample genome-wide association study (GWAS). Implications: Overall, this integrative computational analysis provides comprehensive insights into the epigenomic underpinnings of BLCA subtypes, nominates candidate master regulators of cellular identity for future experimental validation, and reveals how regulatory elements harboring inherited germline variation may contribute to BLCA risk and biology.