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

As super enhancers have been shown to regulate key cancer drivers (Lovén et al., 2013) , we linked each FLC-specific enhancer hotspot to the closest gene that is both robustly transcribed (ChRO-seq: TPM ³ 25) and significantly increased in transcription (ChRO-seq: FDR < 0.05, log2fold change ³ 1) in FLC compared to NML. Several of these genes have been consistently linked to FLC, including CA12, SLC16A14, LINC00473, OAT, TMEM163, and TNRC6C. Others, such as FAM19A5, have not previously been reported as dysregulated in FLC and represent novel candidate oncogenes. Enrichment analysis of genes linked to FLCspecific enhancer hotspots revealed significant over-representation in the Computationally predicted gene-enhancer links, FLC-specific TREs, CREB motifs within FLCspecific TREs (blue), and FOSL2/JUN motifs within FLC-specific TREs (green) are shown below the gene diagram. FLC-specific TREs containing CREB motifs are shown in blue, those containing FOSL2/JUN motifs in green, those containing both CREB and FOSL2/JUN motifs in purple, and all others in black. Transcriptional signal from the plus and minus strand are shown in red and grey, respectively. FLC and NML show similar levels of paused polymerase for CA12 (peak at TSS), but FLC has significantly more gene body transcription. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.01.18.911297 doi: bioRxiv preprint MAPK signaling pathway (Fig. 5C ) and enrichment for MAPK1 targets (Fig. 5D ). Correlation analysis using the ARCHS4 database (Lachmann et al., 2018) demonstrated that these genes are also strongly linked to JUN expression (Fig. 5E ). This finding is consistent with our previous analysis that JUN may be critical for the transcriptional regulation of these genes.