Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming

Abstract

Hepatocellular carcinomas (HCC) exhibit distinct promoter hypermethylation patterns, but the epigenetic regulation and function of transcriptional enhancers remain unclear. Here, our affinity- and bisulfite-based whole-genome sequencing analyses reveal global enhancer hypomethylation in human HCCs. Integrative epigenomic characterization further pinpoints a recurrent hypomethylated enhancer of CCAAT/enhancer-binding protein-beta (C/EBPβ) which correlates with C/EBPβ over-expression and poorer prognosis of patients. Demethylation of C/EBPβ enhancer reactivates a self-reinforcing enhancer-target loop via direct transcriptional up-regulation of enhancer RNA. Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers, leading to drastic suppression of driver oncogenes and HCC tumorigenicity. Hepatitis B X protein transgenic mouse model of HCC recapitulates this paradigm, as C/ebpβ enhancer hypomethylation associates with oncogenic activation in early tumorigenesis. These results support a causal link between aberrant enhancer hypomethylation and C/EBPβ over-expression, thereby contributing to hepatocarcinogenesis through global transcriptional reprogramming.

Diversity and Emerging Roles of Enhancer RNA in Regulation of Gene Expression and Cell Fate

“…In mouse embryonic stem cells, these hypomethylated, actively transcribed regions were occupied by TET family DNA hydroxylases, which can actively demethylate CpG dinucleotides (Stadler et al, 2011). In a liver cancer model, hypomethylated DNA was shown to be necessary for eRNA production as targeted DNA demethylation through a Cas9-TET1 fusion increased eRNA production (Xiong et al, 2019). In another FIGURE 1 | eRNA transcription, elongation, and termination.…”

Epigenetics in hepatocellular carcinoma development and therapy: The tip of the iceberg

“…This was illustrated by the recurrent hypomethylation at the enhancer of C/EBPβ , resulting in the reactivation of its enhancer RNA (eRNA) and gene overexpression, leading to increased tumourigenesis. 80 Other examples of genes – with possible tumour-promoting effects – that are hypomethylated and overexpressed in HCC are summarised in Table 2 . Together, these observations provide further mechanistic links explaining the role of DNA hypomethylation in hepatocarcinogenesis.…”

A combination strategy targeting enhancer plasticity exerts synergistic lethality against BETi-resistant leukemia cells

“…Enhancer reprogramming during tumorigenesis can increase the fitness of tumor cells toward anti-tumor therapy 44,45 , and thus provide an alternative strategy for tumor cells to maintain the Murine MLL-AF9 AML BETi resistant…”