Multi-omics mendelian randomization identifies ferroptosis-related genetic variants linked to NAFLD risk

Ferroptosis, an iron-dependent cell death, contributes to non-alcoholic fatty liver disease (NAFLD), but causal genes remain unclear. This study identifies ferroptosis-related genes driving NAFLD to fill this gap. Summary data-based Mendelian Randomization (SMR) analyzed 564 ferroptosis-related genes for causal links to NAFLD by integrating mQTL/eQTL/pQTL data with GWAS, validated in FinnGen and the GWAS Catalog. To further substantiate our findings, expression of lead candidate genes was validated in independent human liver tissue datasets from the Gene Expression Omnibus (GEO). HepG2 cells were used to assess candidate gene expression, oxidative stress, and ferroptosis under free fatty acids (FFA) treatment. We evaluated cell viability, lipid ROS levels, gene expression, protein levels, and oxidative stress markers. SMR analysis revealed an association between SLC2A6 methylation/expression and NAFLD risk. Hypermethylation at cg02257517 was associated with increased NAFLD risk (OR=1.032, 95 % CI=1.013–1.051), while higher SLC2A6 expression correlated with lower risk (OR=0.919, 95 % CI=0.87–0.97). Multi-omics analysis confirmed an inverse relationship between SLC2A6 expression and cg02257517 methylation (OR=0.741, 95 % CI=0.66–0.832), suggesting hypermethylation downregulates SLC2A6 , increasing NAFLD susceptibility. Those results were further validated in HepG2 cells, where the candidate gene demonstrated a protective role against FFA-induced oxidative stress and ferroptosis. Overexpression of the gene significantly mitigated these pathological effects, supporting its potential as a therapeutic target. Multi-omics Mendelian randomization identified SLC2A6 hypermethylation as a causal NAFLD risk factor by suppressing its expression. Functional validation in disease-relevant models revealed SLC2A6-mediated protection against oxidative stress and ferroptosis, highlighting its potential as a therapeutic target for NAFLD through epigenetic or gene-based interventions.