Hells (LSH) Controls Gene Expression in T-Cell Lymphomas By Regulating RNA Polymerase II with a Bimodal Function

Chromatin modifiers are emerging as determinants of many types of cancer, including anaplastic large cell lymphoma (ALCL), a family of highly heterogeneous T-cell lymphomas for which therapeutic options are still limited. We recently identified the DNA helicase HELLS - a member of the SWI/SNF2 family- as a genetic vulnerability of ALK - ALCLs. HELLS is a multifunctional chromatin remodeler that affects genomic instability. Although its transcriptional function has been suggested, no clues on how HELLS controls transcription are currently available. To explore its transcriptional function in ALCLs, we integrated HELLSChromatin immunoprecipitation‐sequencing (ChIP‐seq) analysis in the TLBR-2 cell line with RNA-sequencing data TLBR-2 HELLS KD and control cells. Out of 729 genes significantly affected by HELLS KD, 467 genes (64% of the total) resulted directly bound by HELLS. We termed these genes HELLS-direct genes (HDGs). Analysis of HELLS binding profile at HDGs site showed that 67% of HELLS binding sites at HDGs has intragenic localization being associated with promoters, introns, and exons. Gene-set enrichment analysis of HDGs revealed several pathogenic processes associated with deregulated genes including JAK/STAT signaling pathway, inflammation mediated by chemokines, and cytokines signaling pathway. To assess the contribution of HELLS to the transcription of its HDGs, the distribution of RNA‐PolymeraseII (RNAPII) was investigated by ChIP‐seq in TLBR-2 HELLS KD and control cells. We observed that HELLSdepletion caused a bimodal alteration of RNAPII. On genes belonging to biological processes involved in the dysregulation of circuitries that controls T-cells dependent host interactions (n=195, 40% of HDG promoters), the depletion of HELLS caused a significant impairment of RNAPII recruitment suggesting that HELLS partakes in transcription regulation of these pathways acting as a co-transcriptional factor. Whereas, on the remaining 60% of HDGs (n=272), which are enriched for selective biological functions including cytoskeleton regulation and DNA metabolic processes, we observed a selective loss of RNAPII signal in the regions immediately downstream of the TSS coherent with a potential proximal promoter pausing of RNAPII. Target analysis of phospho-CTD modification ser2P of RNAPII confirmed the RNAPII pausing after HELLS depletion. Stacked RNAPII during elongation drives DNA-RNA hybrids (R-loops) formation and it is a primary source of DNA break accumula