Targeting ZNRF3 and RNF43 to Restore Regeneration and Metabolic Balance in Fatty Liver Disease

MASLD and its more advanced stage, MASH, are increasingly common causes of end-stage liver disease and liver cancer. Both conditions involve defects in hepatocyte function, impaired regenerative capacity, and excess lipid buildup in the liver. Despite the liver's regenerative capacity, chronic injury in MASLD/MASH impairs this process, and safe therapeutic strategies to restore regenerative and metabolic function remain lacking. This project investigates the therapeutic potential of targeting ZNRF3 and RNF43, two endogenous inhibitors of the WNT/beta-catenin signaling pathway, to restore hepatocyte regeneration and reverse disease features in preclinical models of MASLD and MASH. Using hepatocyte-specific gene deletion strategies and RNA-seq analyses, we demonstrate that ZNRF3/RNF43 loss reactivates beta-catenin signaling in hepatocytes, reversing steatosis, inflammation, and fibrosis in two well-established dietary mouse models of MASLD/MASH: the FAT-MASH model (Western diet plus low-dose CCl4) and the GAN diet model (Gubra Amylin NASH model). Transcriptomic profiling via bulk liver RNA-seq revealed that the therapeutic benefit of ZNRF3/RNF43 deletion is mediated by beta-catenin-dependent metabolic reprogramming. Specifically, we observe selective activation of the alternative bile acid synthesis pathway (Cyp27a1 and Cyp7b1), which promotes conversion of hepatic cholesterol into detoxified, CDCA-enriched bile acids. This pathway is associated with improved hepatic lipid clearance, increased hepatocyte proliferation, and reduced hepatotoxic bile acid retention, without causing cholestasis or tumorigenesis. Knockdown of ZNRF3 and RNF43 via lipid nanoparticle (LNP)-formulated siRNA also achieved therapeutic benefits, supporting its translational potential. The RNA-seq data include transcriptomic profiles from mouse livers under FAT-MASH dietary conditions, with samples derived from two experimental groups: wild-type controls (WT; n = 3 replicates) and ZNRF3/RNF43 deletion (ZRdKO; n = 2 replicates). Sequencing was performed in paired-end format, and raw FASTQ files follow the naming convention: __R1.fq.gz and __R2.fq.gz, where R1 and R2 refer to forward and reverse reads, respectively (e.g., WT_1_R1.fq.gz and WT_1_R2.fq.gz). These datasets, derived from bulk liver tissue, provide a resource for studying liver regeneration, WNT signaling, bile acid metabolism, and transcriptional adaptation in fatty liver disease.