Ubiquitination-driven fibroblast dysfunction: a multi-omics blueprint for precision diagnosis and therapy in diabetic foot ulcer

Diabetic foot ulcer (DFU) is a severe diabetes complication affecting 15–25% of patients and frequently causing lower extremity amputations. While ubiquitination regulates diverse cellular functions, ubiquitination-related genes (URGs) in DFU pathogenesis remain unexplored. We analyzed single-cell RNA sequencing data from 29 samples (19 controls, 10 DFU) and bulk RNA sequencing from 60 samples (25 controls, 35 DFU). Using 1,610 URGs from GeneCards database, we performed single-cell analysis, pseudotime analysis, and cell communication studies. Four machine learning algorithms identified diagnostic biomarkers, followed by functional enrichment, immune infiltration, and molecular docking analyses. Key gene expression patterns were further validated by quantitative real-time PCR (qPCR) in independent clinical samples (n = 6 per group). Single-cell analysis identified 12 cell types with significantly elevated URGs in DFU fibroblasts. A pathogenic fibroblast subpopulation exhibited enhanced stemness and dysregulated communication networks. Machine learning identified four key URGs (MEF2A, SKIL, MAF, KRT5) as diagnostic biomarkers, achieving optimal performance (AUC 0.957). SKIL showed strongest correlation with metabolic reprogramming. Two distinct molecular subtypes with different immune profiles were identified. Lumicolchicine and ramipril were identified as potential SKIL-targeting therapeutics. This study provides the first URGs characterization in DFU, identifying pathogenic fibroblasts and SKIL as key regulators. The diagnostic signature and therapeutic targets establish foundations for precision DFU treatment approaches. These findings support the development of URG-based diagnostic strategies and provide a translational rationale for repurposing clinically approved drugs, such as ramipril, for precision management of DFU.