Liver enhancer signature and regulatory network of non-alcoholic steatohepatitis resistance in humans with obesity

Non-alcoholic fatty liver disease (NAFLD), which often co-occurs with obesity and type 2 diabetes, is the most common cause of chronic liver disease worldwide. A subset of patients with NAFLD progress to the severe form known as non-alcoholic steatohepatitis (NASH), which increases the risk of developing hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. The molecular underpinnings of the progression from NAFLD to NASH in patients is poorly understood. Active enhancer landscapes are known to determine cell states and can point to key transcription factors (TF), genes, and pathways in disease pathogenesis or resistance. Also, while super-enhancers have helped reveal key disease drivers in several cancer types, they remain undefined in NASH. To define the enhancer signature of NASH-prone (NP) and NASH-resistant (NR) phenotypes in humans, we performed chromatin run-on sequencing (ChRO-seq) analysis on liver biopsies of individuals with severe obesity who were stratified into either the NP or NR group. We defined the active enhancer signature, super-enhancer linked genes, and the candidate TF networks in human NP and NR livers. Notably, we showed that NR-activated genes that are linked to NR-specific enhancers/super-enhancers are involved in serine and glycine biosynthesis (SHMT, BHMT) as well as glycine utilization (GLYAT, GATM). Overall, this study has defined for the first time the active enhancer/super-enhancer landscape and the underlying TF programs of NASH resistance in humans with obesity.