Integrated bioinformatics analysis and mouse validation identify C7 and MFAP4 as candidate genes associated with type 2 diabetes and atherosclerosis

Type 2 diabetes mellitus (T2DM) is closely associated with accelerated atherosclerosis (AS), but the molecular features linking these two conditions remain incompletely understood. This study aimed to identify candidate genes associated with T2DM and AS and to explore their potential biological relevance. Public GEO transcriptomic datasets were analysed. GSE38642 and GSE100927 were used as T2DM and AS training datasets, while GSE41762 and GSE57691 were used for validation. Differentially expressed genes were identified using limma, and disease-associated modules were screened by weighted gene co-expression network analysis. Candidate genes were obtained by intersecting differentially expressed genes with module genes, followed by protein-protein interaction analysis, cytoHubba-MCC, and MCODE screening. Expression validation, receiver operating characteristic analysis, cross-validation, permutation testing, GeneMANIA, GSEA, ssGSEA-based immune infiltration analysis, regulatory network construction, and exploratory drug-gene enrichment analysis were performed. Selected genes were further examined in mouse models. 21 overlapping genes were identified, and six candidate hub genes were further screened. Among them, C7 and MFAP4 showed reproducible but disease-context-dependent expression patterns and exploratory discriminatory performance across the training and validation datasets. Functional analyses suggested that C7 and MFAP4 were associated with inflammatory response, complement activation, TNF-α/NF-κB signaling, oxidative phosphorylation, extracellular matrix remodeling, and immune-related alterations. Additional robustness analyses supported the exploratory relevance of these two genes, particularly MFAP4, while also indicating that the findings should be interpreted cautiously. In mouse models, C7 and MFAP4 showed disease-associated expression changes, supporting their potential relevance to metabolic stress and vascular remodeling. This integrated bioinformatics and experimental validation study identified C7 and MFAP4 as exploratory candidate genes associated with T2DM and AS.