Integrated multi-omics reveals adaptive anti-oxidant remodeling in early alcohol-associated liver disease

Abstract

Alcohol-associated liver disease (ALD) is a leading cause of liver-related morbidity and mortality. Although various omics approaches have revealed early metabolic alterations, individual datasets provide limited mechanistic insight. Here, we integrated RNA sequencing with mass spectrometry-based analyses to quantify gene expression, protein abundance, proteome and acetylome dynamics, and metabolic fluxes in livers of alcohol-fed mice. This multi-layered approach revealed extensive metabolic rewiring characterized by suppressed mitochondrial energy metabolism and compensatory upregulation of glutathione (GSH) production, utilization, and recycling, establishing a high-flux antioxidant network. These changes were coupled to epigenetic histone H3 remodeling, marked by increased permissive acetylation and decreased suppressive methylation, linking alcohol-induced metabolic and redox alterations to chromatin reprogramming. ChEA-based in silico upstream transcription factor analysis, identified hepatocyte nuclear factor 4 (HNF4) and nuclear factor erythroid 2-related factor 2 (NRF2) as key regulatory nodes. Alcohol exposure was associated with a modest HNF4 suppression alongside increased expression of NRF2, indicating a shift from HNF4-driven metabolic programs toward NRF2-mediated antioxidant responses. Despite acetylation-associated impairment of mitochondrial proteins, GSH-related enzymes were preserved, supporting a protective, high-turnover antioxidant response that limits early oxidative stress and defines an adaptive state maintaining redox homeostasis while potentially predisposing to ALD progression.