Integrated Bioinformatics-Based Identification and Validation of Neuroinflammation-Related Hub Genes in Primary Open-Angle Glaucoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39125762", "kind": "science-record", "revision": 3, "content_hash": "sha256:e25b59a18fe9e57a4e9b79c4bf4b5e62919be5746d7ddf35edd09e545839ed34", "created_at": "2026-11-01T20:29:13Z", "updated_at": "2026-11-01T22:12:26Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics-Based Identification and Validation of Neuroinflammation-Related Hub Genes in Primary Open-Angle Glaucoma.", "doi": "10.3390/ijms25158193", "pmid": "39125762", "authors": ["Zakir Ullah", "Yuanyuan Tao", "Jufang Huang"], "journal": "International journal of molecular sciences", "year": 2024, "abstract": "Glaucoma is a leading cause of permanent blindness, affecting 80 million people worldwide. Recent studies have emphasized the importance of neuroinflammation in the early stages of glaucoma, involving immune and glial cells. To investigate this further, we used the GSE27276 dataset from the GEO (Gene Expression Omnibus) database and neuroinflammation genes from the GeneCards database to identify differentially expressed neuroinflammation-related genes associated with primary open-angle glaucoma (POAG). Subsequently, these genes were submitted to Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes for pathway enrichment analyses. Hub genes were picked out through protein-protein interaction networks and further validated using the external datasets (GSE13534 and GSE9944) and real-time PCR analysis. The gene-miRNA regulatory network, receiver operating characteristic (ROC) curve, genome-wide association study (GWAS), and regional expression analysis were performed to further validate the involvement of hub genes in glaucoma. A total of 179 differentially expressed genes were identified, comprising 60 upregulated and 119 downregulated genes. Among them, 18 differentially expressed neuroinflammation-related genes were found to overlap between the differentially expressed genes and neuroinflammation-related genes, with six genes (SERPINA3, LCN2, MMP3, S100A9, IL1RN, and HP) identified as potential hub genes. These genes were related to the IL-17 signaling pathway and tyrosine metabolism. The gene-miRNA regulatory network showed that these hub genes were regulated by 118 miRNAs. Notably, GWAS data analysis successfully identified significant single nucleotide polymorphisms (SNPs) corresponding to these six hub genes. ROC curve analysis indicated that our genes showed significant accuracy in POAG. The expression of these genes was further confirmed in microglia, Müller cells, astrocytes, and retinal ganglion cells in the Spectacle database. Moreover, three hub genes, SERPINA3, IL1R1, and LCN2, were validated as potential diagnostic biomarkers for high-risk glaucoma patients, showing increased expression in the OGD/R-induced glaucoma model. This study suggests that the identified hub genes may influence the development of POAG by regulation of neuroinflammation, and it may offer novel insights into the management of POAG.", "claims": [{"id": "claim-method", "statement": "Comparison between the two groups was determined using the Student’s t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39125762", "locator": "sections[26] \"4.12. 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Diagnostic Value Validation\" paragraph 2", "quote": "The AUC values of SERPINA3, LCN2, MMP3, S100A9, IL1RN, and HP were 1.00, 0.88, 1.00, 0.97, 0.86, and 0.98, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Six neuroinflammation-related hub genes—SERPINA3, LCN2, MMP3, S100A9, IL1RN, and HP—were identified as potential diagnostic biomarkers associated with primary open-angle glaucoma, with reported AUC values of 1.00, 0.88, 1.00, 0.97, 0.86, and 0.98, respectively.", "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:39125762"], "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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