Potential diagnostic markers and therapeutic targets for DM2 and periodontitis based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40173189", "kind": "science-record", "revision": 4, "content_hash": "sha256:9ce50281265d4b505f51e86cc53dcb1b296a3bde8042b879ee117afd4efc8c51", "created_at": "2026-11-01T20:30:21Z", "updated_at": "2026-11-01T22:56:19Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Potential diagnostic markers and therapeutic targets for DM2 and periodontitis based on bioinformatics analysis.", "doi": "10.1371/journal.pone.0320061", "pmid": "40173189", "authors": ["Rong Luo", "Zhenye Liang", "Huijun Chen", "Dandan Bao", "Xinlu Lin"], "journal": "PloS one", "year": 2025, "abstract": "BACKGROUND: Diabetes Mellitus type 2 (DM2) is thought to have a bidirectional relationship with Periodontitis (PD). However, the complex molecular interactions between DM2 and PD remain unclear. This study aimed to explore the shared genes and common signatures of DM2 and PD via bioinformatic analysis.\nMETHODS: Firstly, using bioinformatic methods to investigate common genes. The series matrix files of GSE6751 for DM and GSE15932 for PD were downloaded from the Gene Expression Omnibus (GEO) database. The data was normalized using the R package, and the limma package was utilized to identify the Differentially Expressed Genes (DEGs). Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of DEGs were performed using the \"clusterProfiler\" package in the R software. The protein-protein network was constructed to analyze the potential relationship among the proteins. CytoHubba, a plugin for the Cytoscape software, was used to identify the hub genes. The validation datasets selected for DM2 and PD were GSE10334 and GSE7014, respectively. Receiver Operating Characteristic (ROC) curve analysis was performed to obtain the area under the ROC curve. Lipopolysaccharide (LPS) + high glucose-induced DM-related PD was simulated to verify the three hub genes through quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) and Western blot (WB).\nRESULTS: In total, 44 common DEGs were identified. ITGAM, H2BC21, S100A9 was identified as he hub genes of DM2 and PD, with all of them were up-regulated. In addition, the area under the curve of all three hub genes was more than 0.65. In-vitro experiments revealed that the relative expression of S100A9 was increased after the treatment with LPS + high glucose. Besides, TLR4 and p-NF-κB levels were also improved in model group.\nCONCLUSION: S100A9 was identified as the hub gene of DM2 and PD. S100A9 could trigger TLR4 signaling way to promote disease development, which can be the potential targets for diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "The R package was utilized to normalize the data, and the limma package was used to identify the DEGs of PD/DM2 and control samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40173189", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The R package was utilized to normalize the data, and the limma package was used to identify the DEGs of PD/DM2 and control samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data are available in the manuscript and/or supporting information files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40173189", "locator": "sections[27] \"Data Availability\" paragraph 2", "quote": "All data are available in the manuscript and/or supporting information files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 44 common differentially expressed genes between periodontitis and type 2 diabetes, with ITGAM, H2BC21, and S100A9 identified as upregulated hub genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40173189", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In total, 44 common DEGs were identified."}, {"asset": "source:pmid:40173189", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "ITGAM, H2BC21, S100A9 was identified as he hub genes of DM2 and PD, with all of them were up-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 44 common differentially expressed genes between periodontitis and type 2 diabetes, with ITGAM, H2BC21, and S100A9 identified as upregulated hub genes.", "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:40173189"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE10334"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE10334"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40173189", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0320061", "sha256": 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RESULTS: In total, 44 common DEGs were"], "order_basis": "paper_text_order:1426", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The R package was utilized to normalize the data, and the limma package was used to identify the DEGs of PD/DM2 and control samples."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}