Identify Diagnostic Biomarkers Related to Taurine Metabolism in Diabetic Foot Ulcers Using Bulk RNA-seq and ScRNA-seq Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41503916", "kind": "science-record", "revision": 4, "content_hash": "sha256:7d97744bf7abc7885827f4e8ed901e13914d344c8c970ced63770ffc386dc026", "created_at": "2026-11-01T20:31:29Z", "updated_at": "2026-11-01T22:57:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identify Diagnostic Biomarkers Related to Taurine Metabolism in Diabetic Foot Ulcers Using Bulk RNA-seq and ScRNA-seq Analysis.", "doi": "10.1111/1753-0407.70166", "pmid": "41503916", "authors": ["Mengrong He", "Jiamin Chen"], "journal": "Journal of diabetes", "year": 2026, "abstract": "BACKGROUND: Diabetic foot ulcers (DFU) are severe complications with complex pathogenesis involving inflammation and impaired healing. Taurine, a key antioxidant amino acid, shows therapeutic potential in diabetes, but its role in DFU remains unclear and warrants investigation.\nMETHODS: This integrated multi-omics study analyzed DFU using GEO transcriptomics data (training: GSE68183/GSE80178; validation: GSE37265/GSE134431; scRNA-seq: GSE223964). Limma identified DEGs that intersected with taurine metabolism -related genes. Key modules (MCODE) and a LASSO-based diagnostic signature were established. Immune infiltration was profiled via ssGSEA, CIBERSORT, and MCP-Counter. Regulatory networks (TFs/miRNAs) were predicted (miRNet/NetworkAnalyst), and therapeutic agents were screened (DSigDB). Seurat-processed scRNA-seq defined nine cell types, with CellChat analyzing intercellular communication.\nRESULTS: This study identified a three-gene diagnostic signature (HMOX1, MAPK3, TXN) for DFU with near-perfect accuracy (training AUC = 1, validation AUC ≥ 0.98). Multi-omics analyses revealed significant immune dysregulation (increased B cells/CD8+T cells/M1 macrophages in DFS), collagen-centric signaling dominance, and two molecular subtypes. Single-cell RNA-seq uncovered cell-type-specific dysfunction: fibroblasts and endothelial cells expanded in DFS, while HMOX1 localized to Mono-macrophages and MAPK3 to endothelium.\nCONCLUSION: This study deeply analyzed DFU immune microenvironment characteristics, intercellular communication networks, and molecular regulatory mechanisms, revealing a dysregulated metabolic-immune repair network framework, providing new insights for understanding DFU pathological mechanisms and developing targeted diagnostic and therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "Differential analysis between the DFS and NFS was performed using the limma package with thresholds of adj.p.Val < 0.05 and |log2FC| > 0.585", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41503916", "locator": "sections[5] \"Differential Analysis and Identification of Key Modules\" paragraph 2", "quote": "Differential analysis between the DFS and NFS was performed using the limma package with thresholds of adj.p.Val < 0.05 and |log2FC| > 0.585"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data and materials in the current study are available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41503916", "locator": "sections[32] \"Data Availability Statement\" paragraph 2", "quote": "The data and materials in the current study are available from the corresponding author on reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "This study identified a three-gene diagnostic signature (HMOX1, MAPK3, TXN) for DFU with near-perfect accuracy, including a training AUC of 1 and validation AUCs of at least 0.98.", "kind": "quantitative", "target": {"value": 1.0, "unit": "auc", "tolerance": null, "source": "This study identified a three‐gene diagnostic signature (HMOX1, MAPK3, TXN) for DFU with near‐perfect accuracy (training AUC = 1, validation AUC ≥ 0.98)."}, "evidence": [{"asset": "source:pmid:41503916", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "This study identified a three‐gene diagnostic signature (HMOX1, MAPK3, TXN) for DFU with near‐perfect accuracy (training AUC = 1, validation AUC ≥ 0.98)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "This study identified a three-gene diagnostic signature (HMOX1, MAPK3, TXN) for DFU with near-perfect accuracy, including a training AUC of 1 and validation AUCs of at least 0.98.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41503916"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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