Machine learning combining external validation to explore the immunopathogenesis of diabetic foot ulcer and predict therapeutic drugs

• Published in: PloS one Vol. 20; no. 8; p. e0328906
• Main Authors: Lu, Zhongwen, An, Na, Sheng, Shouwei, Hong, Mao, Deng, Pin, Wu, Junde, Zhang, Shengji, Chen, Zhaojun
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.08.2025; Public Library of Science (PLoS)
• Subjects: Algorithms; Amputation; Beta cells; Biology and Life Sciences; Chemotaxis; Computer and Information Sciences; CXCL13 protein; Datasets; Development and progression; Diabetes; Diabetes mellitus; Diabetic foot; Diabetic Foot - drug therapy; Diabetic Foot - genetics; Diabetic Foot - immunology; Diabetic Foot - pathology; Diagnosis; Drug therapy; Drugs; Encyclopedias; Feet; Fibroblast growth factor receptor 2; Fibroblast growth factor receptors; Foot diseases; Gene expression; Gene Expression Profiling; Gene Regulatory Networks; Genes; Genomes; Health aspects; Humans; Hyperglycemia; Immune response; Immunological memory; Immunopathogenesis; Immunosuppressive agents; Infiltration analysis; Keratinocytes; Learning algorithms; Leg ulcers; Leukocytes (neutrophilic); Machine Learning; Macrophages; Mast cells; Medicine and Health Sciences; Memory cells; Molecular docking; Molecular Docking Simulation; Network analysis; Neutrophils - immunology; Neutrophils - metabolism; Nomograms; Ontology; Pathogenesis; Pharmacology; Physical Sciences; Plantar ulcers; Selegiline; Signal Transduction; Software; Ulcers; Wound healing; Wound infection; China
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0328906

Diabetic foot ulcer (DFU) is a severe complication of diabetes, often leading to amputation due to poor wound healing and infection. The immune-related pathogenesis of DFU remains unclear, and therapeutic drugs are limited. This study aimed to explore the immune mechanisms of DFU and identify potential therapeutic drugs using machine learning and single-cell approaches. Through differential expression analysis of Gene Expression Omnibus (GEO) datasets, we identified 287 differentially expressed genes (DEGs), which were significantly enriched in IL-17 signaling and neutrophil chemotaxis pathways. Weighted gene co-expression network analysis (WGCNA) further pinpointed disease-associated modules containing 1,693 regulatory genes. Machine learning algorithms prioritized seven core genes—CCL20, CXCL13, FGFR2, FGFR3, PI3, PLA2G2A, and S100A8—with validation in an external dataset GSE147890 and single-cell sequencing revealing their predominant expression in neutrophils and keratinocytes. Immune infiltration analysis demonstrated significant dysregulation in DFU patients, characterized by elevated proportions of memory B cells, M0 macrophages, activated mast cells, and neutrophils. Potential therapeutic compounds were identified using the Connectivity Map database and tested through molecular docking and dynamics simulations. The study pinpointed selegiline, L-BSO, flunisolide, PP-30, and fluocinolone as promising therapeutic agents, offering new insights into the pathogenesis of diabetic foot ulcers (DFU) and potential therapeutic strategies.