Chromatin remodeler HELLS is an epigenetic driver for hepatocellular carcinoma progression

Abstract

Hepatocellular carcinoma (HCC) is the major type of liver cancer and the second leading cause of cancer death worldwide. Every year, more than six hundred thousand people are newly diagnosed. For the advanced HCC patients, only one FDA-approved drug is currently available. Therefore, there is an urge to delineate the molecular mechanism of HCC progression for developing new therapeutics. Increasing evidence showed that epigenetic alterations play an important role in the carcinogenesis process. The epigenetic regulatory mechanism is accomplished by DNA methylation, histone modification, and chromatin remodeling. Deregulation of DNA methylation and histone modifications have recently been characterized in HCC, but the significance of chromatin remodeling in liver carcinogenesis remains to be explored. In this study, we employed RNA-seq to investigate the expression of chromatin remodelers in human HCCs. We found that HELicase, Lymphoid-Specific (HELLS), a SWI2/SNF2 chromatin remodeling enzyme, was remarkably overexpressed in HCC. Overexpression of HELLS was correlated with more aggressive clinicopathological features and poorer patient prognosis. We further showed that up-regulation of HELLS in HCC was conferred by hyper-activation of transcription factor SP1. To investigate the functions of HELLS in HCC, we generated both gain- and loss-of-function models by CRISPR activation system, lentiviral shRNA, and CRISPR/Cas9 genome editing system. We demonstrated that overexpression of HELLS augmented HCC cell proliferation and migration. In contrast, depletion of HELLS reduced HCC cell growth and motility. Moreover, inactivation of HELLS induced apoptosis in HCC cells. Coherently, ablation of HELLS also mitigated tumorigenicity and lung metastasis in vivo as demonstrated with both subcutaneous and orthotopic tumor implantation models. Mechanistically, by using RNA-seq and MNase-seq, we revealed that HELLS controls the nucleosome occupancy at gene enhancer and transcription start site (TSS). Overexpression of HELLS increased nucleosome occupancy that obstructed the accessibility of enhancers and hindered the formation of nucleosome-free region (NFR) at TSS of its target genes, thereby blocks the binding of transcription factors for activating gene expression. Consequently, though this mechanism, up-regulation of HELLS mediated epigenetic silencing of multiple tumor suppressor genes including E-Cadherin, FBP1, IGFBP3, XAF1 and CREB-H in HCC. In conclusion, our data unravel that HELLS is a key epigenetic driver of HCC. By altering the nucleosome occupancy at NFR and enhancer, HELLS epigenetically suppresses numerous tumor suppressor genes to promote HCC progression.