Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance

Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy

Our analysis reveals that transcription at distal TREs (i.e. enhancers) stratify FLC from NML samples better than transcription at proximal TREs or gene bodies, similar to previous reports (Corces et al., 2016 (Corces et al., , 2018 . These findings are consistent with other studies (Franco et al., 2018; Van Groningen et al., 2017; Ooi et al., 2016) that have shown enhancer activity is more sensitive than gene expression for sample classification (e.g., tumor-normal, tumor subtypes, cell types). Unlike other methods to identify enhancers, such as assay for transposaseaccessible chromatin using sequencing (ATAC-seq) or chromatin immunoprecipitation and sequencing (ChIP-seq) for enhancer-associated histone modifications or proteins, ChRO-seq identifies active regulatory elements as well as actively transcribed genes. This advantage allowed us to correlate enhancer and gene transcription within the same assay, as well as to provide a more direct output of enhancer function (transcription) than steady state RNA levels, which reflect cumulative effects of transcriptional, co-transcriptional, and post-transcriptional regulatory processes.