Identification and validation of diagnostic biomarkers for temporal lobe epilepsy related to ferroptosis and potential therapeutic targets.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39930056", "kind": "science-record", "revision": 3, "content_hash": "sha256:89d366875b5810daba40fa909ea9edd1fb64173faae643caba2848aec0288777", "created_at": "2026-11-01T20:30:12Z", "updated_at": "2026-11-01T22:13:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of diagnostic biomarkers for temporal lobe epilepsy related to ferroptosis and potential therapeutic targets.", "doi": "10.1038/s41598-025-89390-6", "pmid": "39930056", "authors": ["Dai Shi", "Jingxuan Li", "Zhenpeng Niu", "Likun Wang", "Siying Ren", "Wen Gu", "Hui Yang", "Hong Xue", "Guofeng Wu"], "journal": "Scientific reports", "year": 2025, "abstract": "Ferroptosis pathway activation is potentially correlated with temporal lobe epilepsy (TLE). However, the diagnostic significance and mechanism of ferroptosis-related genes (FRGs) in TLE require further investigation. A comprehensive analysis of the GSE134697 dataset from the Gene Expression Omnibus (GEO) database using Weighted gene co-expression network analysis (WGCNA) identified 3,212 differentially expressed genes (DEGs) between temporal lobe epilepsy (TLE) and control groups, with a critical focus on the turquoise module. Through intersection of DEGs and key module genes, correlation analyses with functional-related genes (FRG), protein-protein interactions (PPI), least absolute shrinkage and selection operator (LASSO), and machine learning methods, five potential biomarkers of ferroptosis (CBS, SHMT1, RIN3, QDPR, and PLPP4) were isolated. A nomogram was constructed using these markers, and enrichment analyses revealed their links to T-cell activation, allograft rejection, and glial differentiation. Variations in 13 immune cell types were also noted. Upregulation of CBS, RIN3, QDPR, and PLPP4 in TLE was confirmed through RT-qPCR and Western blot assays. Additionally, five SHMT1-targeting and one CBS-targeting drugs were predicted using the Drug-Gene Interaction Database (DGIdb). These findings provide new insights into the potential pathogenesis of TLE and suggest new targets for future research.", "claims": [{"id": "claim-method", "statement": "To further analyze the association between the 437 candidate genes and TLE, five key genes were identified through 10-fold cross-validation using LASSO.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39930056", "locator": "sections[5] \"Identification of five biomarkers in candidate genes\" paragraph 2", "quote": "To further analyze the association between the 437 candidate genes and TLE, five key genes were identified through 10-fold cross-validation using LASSO."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analysed during the current study are available in the GSE134697 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134697), FerrDb database (http://www.zhounan.org/ferrdb/current/), and BioGPS database (http://biogps.org/#goto=welcome).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39930056", "locator": "sections[31] \"notes\" paragraph 1", "quote": "The datasets analysed during the current study are available in the GSE134697 dataset (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE134697), FerrDb database (http://www.zhounan.org/ferrdb/current/), and BioGPS database (http://biogps.org/#goto=welcome)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Through intersection of DEGs and key module genes, correlation analyses with functional-related genes (FRG), protein-protein interactions (PPI), least absolute shrinkage and selection operator (LASSO), and machine learning methods, five potential biomarkers of ferroptosis (CBS, SHMT1, RIN3, QDPR, and PLPP4) were isolated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39930056", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Through intersection of DEGs and key module genes, correlation analyses with functional-related genes (FRG), protein-protein interactions (PPI), least absolute shrinkage and selection operator (LASSO), and machine learning methods, five potential biomarkers of ferroptosis (CBS, SHMT1, RIN3, QDPR, and PLPP4) were isolated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Through intersection of DEGs and key module genes, correlation analyses with functional-related genes (FRG), protein-protein interactions (PPI), least absolute shrinkage and selection operator (LASSO), and machine learning methods, five potential biomarkers of ferroptosis (CBS, SHMT1, RIN3, QDPR, and PLPP4) were isolated.", "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:39930056"], "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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