Machine learning-based transcriptmics analysis reveals BMX, GRB10, and GADD45A as crucial biomarkers and therapeutic targets in sepsis.

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This study leverages transcriptomics and machine learning (ML) to identify critical biomarkers and therapeutic targets in sepsis. Analyzing microarray data from the Gene Expression Omnibus (GEO) datasets GSE28750, GSE26440, GSE13205, and GSE9960, we discovered three pivotal biomarkers that BMX (bone marrow tyrosine kinase gene on chromosome X), GRB10 (growth factor receptor bound protein 10), and GADD45A (growth arrest and DNA damage inducible alpha), exhibiting exceptional diagnostic accuracy (AUC >0.9). Functional enrichment analyses revealed that these genes play key roles in reactive oxygen species metabolism and immune response regulation. Specifically, GADD45A was positively correlated with eosinophils and inversely associated with activated NK cells, CD8 T cells, and activated memory CD4 T cells. BMX showed positive correlations with eosinophils, mast cells, and neutrophils, while GRB10 was linked to eosinophils and M2 macrophages. Additionally, we constructed a comprehensive mRNA-miRNA-lncRNA regulatory network, identifying key interactions that may drive sepsis pathogenesis. Molecular docking and dynamics simulations validated Bendroflumethiazide, Cianidanol, and Hexamidine as promising therapeutic agents targeting these biomarkers. In conclusion, this integrated approach provides profound insights into the molecular mechanisms underlying sepsis, pinpointing BMX, GRB10, and GADD45A as pivotal biomarkers and therapeutic targets. These findings significantly enhance our understanding of sepsis pathophysiology and lay the groundwork for developing personalized diagnostic and therapeutic strategies aimed at improving patient outcomes.", "claims": [{"id": "claim-method", "statement": "To identify gene modules associated with sepsis, we performed weighted gene co-expression network analysis (WGCNA) using the “WGCNA” package in R (Langfelder and Horvath, 2008).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40230692", "locator": "sections[4] \"Screening of potential hub biomarkers in sepsis\" paragraph 2", "quote": "To identify gene modules associated with sepsis, we performed weighted gene co-expression network analysis (WGCNA) using the “WGCNA” package in R (Langfelder and Horvath, 2008)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. 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These data can be found here: https://www.ncbi.nlm.nih.gov/geo/, using accession numbers GSE28750, GSE26440, GSE13205, and GSE9960."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Analysis of four GEO microarray datasets using transcriptomics and machine learning identified BMX, GRB10, and GADD45A as pivotal sepsis biomarkers with diagnostic AUC values above 0.9.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40230692", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Analyzing microarray data from the Gene Expression Omnibus (GEO) datasets GSE28750, GSE26440, GSE13205, and GSE9960, we discovered three pivotal biomarkers that BMX (bone marrow tyrosine kinase gene on chromosome X), GRB10 (growth factor receptor bound protein 10), and GADD45A (growth arrest and DNA damage inducible alpha), exhibiting exceptional diagnostic accuracy (AUC >0.9)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Analysis of four GEO microarray datasets using transcriptomics and machine learning identified BMX, GRB10, and GADD45A as pivotal sepsis biomarkers with diagnostic AUC values above 0.9.", "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:40230692"], "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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