Exploring the role of ferroptosis-related genes as biomarkers in acute kidney injury.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39042632", "kind": "science-record", "revision": 4, "content_hash": "sha256:701fbfe8e0ad380abbb933e8ad9b5c5c1a26c5ae3c6a40004603a94d9b82e203", "created_at": "2026-11-01T20:29:07Z", "updated_at": "2026-11-01T22:54:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the role of ferroptosis-related genes as biomarkers in acute kidney injury.", "doi": "10.1371/journal.pone.0307472", "pmid": "39042632", "authors": ["Gang Luo", "Yi Gao", "Ziyu Zheng", "Baobao Gao", "Lini Wang", "Xuemiao Tang", "Chong Lei"], "journal": "PloS one", "year": 2024, "abstract": "INTRODUCTION: Acute kidney injury (AKI) is a severe condition with high morbidity and mortality. Innovative biomarkers and treatments are essential for improving patient outcomes. This study aims to investigate the role of ferroptosis-related genes (FRGs) in AKI for identifying potential biomarkers and therapeutic targets.\nMETHODS: We analyzed mRNA expression profiles from the Gene Expression Omnibus (GEO: GSE139061) dataset, comparing 36 AKI samples with 9 normal samples. Differentially expressed genes (DEGs) were identified using the R software package limma. Functional enrichment analyses were conducted using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Key biomarkers were validated through area under the curve (AUC) values, and immune cell infiltration was analyzed using CIBERSORT.\nRESULTS: We identified 78 differentially expressed FRGs, with 27 up-regulated and 51 down-regulated genes. Key signaling pathways included MAPK, ferroptosis, and p53. Five genes-NR4A1, GLRX5, USP35, AEBP2, and MDM4-were identified as potential biomarkers, each demonstrating AUC values greater than 0.800. Specifically, MDM4 showed significant potential by promoting the phosphorylation of p53 at Ser46, enhancing mitochondrial apoptotic activity. Immune analysis revealed a significant elevation of M0 macrophages in AKI samples compared to normal samples (P < 0.01).\nCONCLUSION: Our findings highlight the critical role of ferroptosis-related genes in AKI, identifying NR4A1, GLRX5, USP35, AEBP2, and MDM4 as key biomarkers with high diagnostic potential. These results provide novel insights into the molecular mechanisms of AKI.", "claims": [{"id": "claim-method", "statement": "The LASSO logistic regression algorithm with 10-fold cross-validation identified 8 disease-related features (Fig 3C and 3D), while the SVM-RFE algorithm selected 9 disease-related features.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39042632", "locator": "sections[15] \"Construction of the ferroptosis-related gene biomarkers in AKI\" paragraph 2", "quote": "The LASSO logistic regression algorithm with 10-fold cross-validation identified 8 disease-related features (Fig 3C and 3D), while the SVM-RFE algorithm selected 9 disease-related features."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We analyzed mRNA expression profiles from the Gene Expression Omnibus (GEO: GSE139061) dataset, comparing 36 AKI samples with 9 normal samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39042632", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We analyzed mRNA expression profiles from the Gene Expression Omnibus (GEO: GSE139061) dataset, comparing 36 AKI samples with 9 normal samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Five genes—NR4A1, GLRX5, USP35, AEBP2, and MDM4—were identified as potential biomarkers, each demonstrating AUC values greater than 0.800.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39042632", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Five genes—NR4A1, GLRX5, USP35, AEBP2, and MDM4—were identified as potential biomarkers, each demonstrating AUC values greater than 0.800."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Five genes—NR4A1, GLRX5, USP35, AEBP2, and MDM4—were identified as potential biomarkers, each demonstrating AUC values greater than 0.800.", "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:39042632"], "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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