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

The genes significantly correlated with FLC-specific enhancers and those significantly associated with FLC-specific enhancer hotspots represent those genes that likely drive key oncogenic attributes of FLC cells. To further refine this list and identify high-confidence candidates, we integrated our ChRO-seq results with RNA-seq data from 23 FLC samples (Table S1 , S6), ten of which also underwent ChRO-seq analysis. We first selected genes that were identified as both significantly correlated with FLC-specific enhancers ( Fig. 4G ) and linked to FLCspecific enhancer hotspots (Fig. 5B ). These genes were then filtered to identify genes that are both highly transcribed (ChRO-seq: TPM ³ 25, fold change ³ 5, FDR < 0.2) and expressed (RNA-seq: normalized counts ³ 100, fold change ³ 5, FDR < 0.2) in FLC relative to NML. Integration of both ChRO-seq and RNA-seq data ensures that the transcriptional changes of these genes are maintained at the steady state RNA level. The final list harbored 16 genes (Fig. 6A , Table S6 ). We noticed that over half of these genes have been previously implicated in drug resistance (CA12, COL4A1, HSPA1B, IRF4, KIF26B, LINC00473, SLC16A14, TESC, and VCAN) and 10 of them are connected to elevated MAPK/ERK activity (BACE2, CA12, COL4A1, FAM19A5, HSPA1B, IRF4, KIF26B, LINC00473, TESC, and VCAN; Table S6 ).