Integrative multi-omics dissection identifies ACO2, KLF5, and IMP4 as central regulators of the mitochondrial-immune axis in ulcerative colitis.

Background: Ulcerative colitis (UC) is a chronic relapsing inflammatory bowel disease characterized by persistent mucosal inflammation and epithelial barrier disruption. Emerging evidence suggests that metabolic reprogramming plays a pivotal role in regulating immune responses and epithelial homeostasis in UC. However, the key metabolic-immune regulatory genes and their cellular mechanisms remain poorly defined. Methods: We integrated publicly available genome-wide association study (GWAS) summary statistics for UC (n = 394,626), along with expression quantitative trait loci (eQTL) resources and multiple independent bulk transcriptomic datasets (total n = 215 cases and 134 controls). Summary-based Mendelian randomization (SMR), genome-wide Mendelian randomization (MR), and transcriptomic analyses were performed to systematically identify causal genes associated with UC. Cross-validation was conducted using immune infiltration analyses and single-cell RNA sequencing (scRNA-seq) datasets from human UC colonic tissues (n = 18 cases and 12 controls), as well as a dextran sulfate sodium (DSS)-induced murine colitis model. Gene set enrichment and network analyses were applied to explore potential metabolic and immune pathways. Results: Through integrative multi-omics analysis, we identified ACO2, KLF5, IMP4, and AGPS as key hub genes linking mitochondrial metabolism with immune regulation in UC. Among them, ACO2, KLF5, and IMP4 were consistently downregulated in UC tissues and negatively correlated with macrophage and dendritic cell infiltration. Although AGPS did not show consistent transcriptional changes across UC datasets, it may still contribute to lipid remodeling based on its metabolic function. Single-cell analyses revealed that ACO2 and KLF5 were primarily expressed in macrophage populations and markedly reduced in inflamed colonic regions, while IMP4 exhibited context- and cell-type-specific dynamics. In the DSS mouse model, Aco2 and Klf5 expression decreased progressively with disease severity, accompanied by metabolic pathway enrichment in oxidative phosphorylation and glycolysis. Conclusion: Our findings reveal a set of metabolic-immune regulatory genes that orchestrate mitochondrial function, epithelial integrity, and immune activation in UC. The integration of genetic, transcriptomic, and single-cell data highlights ACO2, KLF5, and IMP4 as promising biomarkers and potential therapeutic targets, offering novel insights into the immunometabolism mechanisms driving UC pathogenesis.