Prime Editing Models the MTARC1 A165T Variant in Human Liver Organoids, Demonstrating Reduced Steatosis, Inflammation, and Fibrosis

Abstract

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent cause of chronic liver disease. MASLD is a progressive and multifactorial disease marked initially by hepatic steatosis, which can progress to steatohepatitis, fibrosis, cirrhosis, and liver cancer. Genetic factors influence the development, progression, and complications in MASLD, and genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with altered risk. Mitochondrial amidoxime reducing component 1 (MTARC1) rs2642438 (p.A165T) variant has been identified as protective, but the role of MTARC1 and the impact of this variant in hepatocytes remains poorly understood. Here, we applied prime editing to create the rs2642438 variant in human pluripotent stem cells (hPSCs) before differentiation into human liver organoids (HLOs) to investigate the effect of the variant under conditions of steatotic and fibrotic injury. Compared to HLOs formed from hPSCs containing the MTARC1 reference sequence, HLOs with the rs2642438 variant show lower levels of MTARC1 protein and triglycerides and are protected from steatotic and fibrotic injury, as predicted by the phenotype observed in patients carrying the variant. The observed decrease in triglyceride level with the variant appears to be driven more by suppression of de novo lipogenesis rather than stimulation in {beta}-oxidation in the HLO model. While resmetirom, the thyroid hormone receptor-beta (THRB) agonist approved to treat patients with metabolic dysfunction-associated steatohepatitis (MASH) was effective in reducing triglyceride levels in the setting of steatotic injury in HLOs with the reference sequence, HLOs containing the variant did not show further reduction in triglyceride levels with exposure to resmetirom, despite increased expression of THRB. Together, this study establishes an approach to model disease-related SNPs in HLOs and provides further insights into the activity of the MTARC1 variant, and suggests that profiling SNPs may be a path to identify patients more likely to respond to therapies for MASLD.