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 chromatin immunoprecipitation with sequencing and assay for transposase-accessible chromatin sequencing profiling on 28 fresh bladder cancer specimens of luminal and basal-squamous expression subtypes. An integrated analysis of core regulatory circuitry, enhancer activity, and transcription factor (TF) expression specificity nominated 23 luminal-specific and 14 basal-squamous-specific candidate master TFs (MTF), including established regulators like FOXA1, PPARG, and GATA3 for luminal bladder cancer and TP63 for basal-squamous bladder cancer, 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 bladder cancers. Cis-regulatory elements were enriched up to 80-fold for bladder cancer risk variants. Keratinization pathways were enriched in genetically determined basal-squamous sites, whereas carcinogen glucuronidation pathways were enriched in luminal sites. Integrating germline variation and epigenomics through a cistrome-wide association study identified a new bladder cancer risk locus upstream of SPINK1 and linked 10 of 19 bladder cancer risk loci to regulatory elements from a 350,000-sample genome-wide association study. IMPLICATIONS: Overall, this integrative computational analysis provides comprehensive insights into the epigenomic underpinnings of bladder cancer subtypes, nominates candidate master regulators of cellular identity for future experimental validation, and reveals how regulatory elements harboring inherited germline variation may contribute to bladder cancer risk and biology.