Deregulation of bromodomain-containing proteins BRPF1 and BRD9 in hepatocellular carcinoma

Abstract

Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. HCC treatment is very challenging, which is mainly due to the lack of early diagnostic tools and limited treatment options. Accumulation of genetics and epigenetics alterations is the driving force of liver carcinogenesis. While it is difficult to correct genetic mutations, epigenetic alterations are often reversible. Therefore, epigenetic therapy that targets the deregulated epigenetic regulators becomes a new and attractive therapeutic strategy. Bromodomain inhibitors are one of the emerging groups of small molecule drugs with promising therapeutic potential. Some of them have been already studied in clinical trials on multiple cancers and metabolic diseases. Bromodomain inhibitors target specific bromodomain which recognizes histone and non-histone acetylation. Protein acetylation is of paramount importance in cell signaling and transcriptional regulation. In this study, I demonstrated that most bromodomain-containing proteins were upregulated in HCC, among these BRPF1 and BRD9 were selected for further investigation. BRPF1 is an epigenetic reader found in MOZ/MORF acetyltransferase complex. I showed that BRPF1 was frequently upregulated in human HCC and associated with poor survival of HCC patients. The upregulation of BRPF1 was caused by gene copy number gain and increased expression of transcription factor SP1. I also showed that BRPF1 inhibition by CRISPR/Cas9 knockout suppressed tumorigenicity in nude mice. I further showed that treatment of GSK5959, a BRPF1-specific inhibitor, significantly suppressed cell proliferation in HCC cell lines and tumor growth in nude mice. BRPF1 regulated various processes related to cancer growth, such as cell cycle, cellular senescence and cancer stemness. RNA-sequencing data revealed that BRPF1 was a master regulator in the expression of multiple oncogenes involved in HCC, while E2F2 and EZH2 were further validated. BRPF1 promoted the expression of E2F2 and EZH2 through MOZ/MORF-mediated H3K14 acetylation at their promoters. BRD9 is also a pure epigenetic reader which is a subunit of BAF chromatin remodeling complex. BRD9 inhibition by CRISPR/Cas9 or I-BRD9, a BRD9 specific inhibitor, reduced HCC growth in cell models and nude mice. Reversely, overexpression of BRD9 promoted HCC cell growth. BRD9 synergistically induced apoptosis with two first-line, molecular targeted drugs for HCC treatment, sorafenib and lenvatinib. RNA-sequencing further identified PHGDH and SPHK1 were the downstream targets of BRD9. Taken together, this study revealed the pathological roles of bromodomain-containing proteins in HCC development and shed light on the therapeutic potential of two bromodomain inhibitors.