Age-associated repression of HNF4α is a driver and potential therapeutic target in liver metabolic dysfunction
Aging is a major risk factors for metabolic dysfunction-associated steatotic liver disease (MASLD). However, the mechanisms by which aging disrupts hepatocyte transcriptional networks to drive metabolic dysfunction remain poorly understood. Hepatocyte nuclear factor 4 alpha (HNF4) is a master regulator of hepatocyte identity and metabolic homeostasis, but its role in liver aging has not been defined. Here, we perform a comprehensive multi-omic profiling of young and aged mouse livers combined with targeted HNF4 functional studies to define how aging remodels HNF4-dependent gene regulation and whether HNF4 can be a target to reverse age-associated liver dysfunction. Despite preserved HNF4 expression with age, aging was associated with reduced HNF4 chromatin occupancy and transcriptional activity, accompanied by epigenetic remodeling, including changes in histone acetylation, chromatin accessibility, and DNA methylation. Integration and comparison of HNF4 CUT&RUN with hepatocyte-specific Hnf4a deletion in young and aged livers identified high-confidence overlapping but distinct young- and old- specific HNF4 target gene networks. In young hepatocytes, HNF4 coordinates two complementary transcriptional programs: activation of genes governing hepatocyte identity, lipid metabolism, and metabolic function, while simultaneously inhibiting alternative developmental, proliferative, and inflammatory programs. Spatial transcriptomic analyses further revealed zone-specific specialization of HNF4-dependent gene programs. Aging selectively disrupted these regulatory networks, resulting in compromised liver identity and metabolic gene programs, de-repression of inflammatory pathways and alternative cellular identity programs and disrupted hepatocyte zonation, consistent with age-dependent lipidomic and metabolic changes, hepatic fat accumulation, and immune infiltration. Hepatocyte-specific Hnf4a deletion in young mice recapitulated key features of liver aging, including impaired hepatocyte identity, metabolic dysfunction, steatosis, inflammatory activation and altered hepatic immune-cell composition, while deletion in aged mice further exacerbated steatosis, inflammation, and hepatic dysfunction. Conversely, hepatocyte-specific HNF4 restoration in aged mice significantly reduced hepatic steatosis and lipid accumulation, restored fatty acid metabolic programs, and partially reversed age-associated transcriptional changes. However, inflammatory and interferon-associated programs were not uniformly reversed, revealing differential responsiveness of metabolic and inflammatory pathways to HNF4 restoration. Together, these findings identify age-associated impairment of HNF4 activity as a functional contributor to liver aging, linking dysregulation of hepatocyte identity, metabolic homeostasis, and inflammatory control to age-associated hepatic dysfunction. Importantly, the selective reversibility of metabolic defects following HNF4 restoration establishes HNF4 as a promising strategy for preserving hepatocyte homeostasis and reversing age-associated hepatic metabolic dysfunction.