Transcriptomic profiling and structural characterization reveal UQCRC1 and COX4I1 as key mitochondrial regulators associated with oxidative stress in multiple sclerosis.

Multiple sclerosis (MS) is a chronic immune-mediated disorder of the central nervous system characterized by inflammatory demyelination, progressive neurodegeneration, and irreversible disability. While immune dysregulation initiates disease pathology, the molecular mechanisms linking chronic inflammation to mitochondrial dysfunction and oxidative stress remain incompletely understood. An integrative, multi-layered systems biology approach was applied to four independent RNA-sequencing datasets derived from MS white matter lesions, lesion-border microglia/macrophages, and Epstein-Barr virus-associated B cells. Differential gene expression analysis was combined with targeted prioritization of mitochondrial and oxidative stress-related genes using curated databases. Protein-protein interaction network construction, hub gene identification, Gene Ontology, and KEGG pathway enrichment analyses were performed to identify prioritized mitochondrial genes and enriched biological pathways. Independent validation was conducted using CNS-specific TNMplot expression profiling, and prognostic relevance was assessed through immunogenomic survival analysis. Structural and functional impacts of prioritized variants were evaluated using in silico pathogenicity prediction, protein stability analysis, secondary structure modeling, and three-dimensional structural assessment, including MutPred2 and HOPE analyses. Transcriptomic integration revealed consistent dysregulation of gene expression profiles across all datasets. Functional enrichment analyses identified mitochondrial oxidative phosphorylation as the most significantly enriched biological process, suggesting an association between altered mitochondrial respiratory pathways and MS-related molecular signatures. Network and enrichment analyses consistently prioritized UQCRC1 and COX4I1 as key mitochondrial hub genes, corresponding to core subunits of respiratory chain complexes III and IV, respectively. These genes were recurrently enriched across biological processes, cellular components, molecular functions, and neurodegeneration-related pathways. CNS-restricted validation confirmed their differential expression, while immunogenomic analysis demonstrated that higher expression levels were associated with improved overall survival. Variant-level analysis identified UQCRC1 (G235R, L197R) and COX4I1 (G155C, P152R) as deleterious substitutions predicted to destabilize protein structure, disrupt domain interactions, and impair electron transport efficiency. Functional predictions further indicated altered catalytic activity, metal binding, and structural integrity, supporting their potential functional relevance to mitochondrial biology. This study demonstrates that mitochondrial respiratory chain-related pathways, particularly those involving complexes III and IV, are consistently associated with the transcriptomic alterations observed in multiple sclerosis. UQCRC1 and COX4I1 emerged as prioritized mitochondrial hub genes supported by integrated transcriptomic, network, prognostic, and structural analyses. These findings provide evidence that mitochondrial bioenergetics and redox homeostasis may contribute to MS pathobiology and warrant further experimental investigation as potential biomarkers and therapeutic targets.