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

Transcription factor motif enrichment analysis of conditionspecific TREs using HOMER (Heinz et al., 2010) revealed significant enrichment in FLC-specific TREs for motifs of FOSL2/JUN (AP-1) and CREB (Fig. 2D) , both of which are activated by MAPK signaling. Similar analysis of NML-specific TREs showed enrichment for HNF4A motifs (Table S3) . Additionally, analysis of the promoters of genes nearest to FLC-specific TREs using the Genomic Regions Enrichment of Annotations Tool (GREAT, McLean et al., 2010) revealed the most significant enrichment for motifs of CREB family members ATF2, CREB1, and ATF3, as well as JUN (Fig. 2E ). Separate examination of FLC-specific promoters (proximal TREs) and enhancers (distal TREs) revealed promoter enrichment of E2F6, MYB, and FOSL1 (Fig. 2F , Table S3 ) and enhancer enrichment of FOSL2/JUN and CREB (Fig. 2G ). We found that 2129 (38.2%) FLC-specific enhancers contain FOSL2/JUN motifs and 1090 (19.6%) contain CREB motifs. FLC- The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 specific TREs that did not contain FOSL2/JUN or CREB motifs were enriched in HES2 and SOX1 motifs (Table S3 ). Our results suggest that FLC is characterized by an aberrant map of regulatory elements that is strongly associated with transcription factors from the CREB, AP-1 families, E2F, and MYB families.