Functional investigation and two-sample Mendelian randomization study of non-alcoholic fatty liver disease hub genes obtained by WGCNA

Aims: Non-alcoholic fatty liver disease (NAFLD) poses significant health risks with progression to severe liver pathologies, while its molecular mechanisms remain unclear. This study aimed to identify NAFLD hub genes and evaluate their clinical and causal value. Methods: We performed differential expression analysis and weighted gene co-expression network analysis (WGCNA) on GSE89632 to screen NAFLD-related modules and hub genes, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. A nomogram model and Receiver Operating Characteristic (ROC) curves were constructed for diagnostic efficacy assessment, and the correlation between FOS (Fos proto-oncogene) expression and immune cell infiltration was analyzed. Two-sample Mendelian randomization (MR) was used to verify the causal relationship between FOS and NAFLD susceptibility. Results: 115 key genes were obtained from the intersection of WGCNA module genes and differentially expressed genes (DEGs), enriched in fat cell differentiation, Tumor necrosis factor (TNF)/Mitogen-activated protein kinase (MAPK) signaling pathways, etc. The top 10 upregulated hub genes were FOS, JUN, Nuclear receptor subfamily 4 group A member 1 (NR4A1), JunB proto-oncogene, AP-1 transcription factor subunit (JUNB), Early growth response 1 (EGR1), MYC proto-oncogene, bHLH transcription factor (MYC), Interleukin 1 beta (IL1B), C-C motif chemokine ligand 2 (CCL2), C-X-C motif chemokine ligand 8 (CXCL8), Prostaglandin-endoperoxide synthase 2 (PTGS2). The nomogram model had good NAFLD prediction performance, and FOS, JUN, MYC had an AUC of 1.000 for diagnosis. FOS expression correlated with immune cell infiltration in NAFLD. The Mendelian randomization analysis found no causal link between FOS and NAFLD risk (OR = 0.997, 95% CI = 0.947–1.049, p = 0.898). Conclusion: We identified 10 NAFLD-associated hub genes. These genes support early NAFLD diagnosis. They clarify NAFLD molecular mechanisms.