Pathway analysis of smoking-induced changes in buccal mucosal gene expression.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37521848", "kind": "science-record", "revision": 3, "content_hash": "sha256:cb08b65af834f8abea706125fc3d0bef75742aa34670cc5fa8f6c525b05a0e55", "created_at": "2026-11-01T19:02:18Z", "updated_at": "2026-11-01T21:31:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Pathway analysis of smoking-induced changes in buccal mucosal gene expression.", "doi": "10.1186/s43042-022-00268-y", "pmid": "37521848", "authors": ["Anas Khaleel", "Bayan Alkhawaja", "Talal Salem Al-Qaisi", "Lubna Alshalabi", "Amneh H Tarkhan"], "journal": "The Egyptian journal of medical human genetics", "year": 2022, "abstract": "Background: Cigarette smoking is the leading preventable cause of death worldwide, and it is the most common cause of oral cancers. This study aims to provide a deeper understanding of the molecular pathways in the oral cavity that are altered by exposure to cigarette smoke.\nMethods: The gene expression dataset (accession number GSE8987, GPL96) of buccal mucosa samples from smokers (n = 5) and never smokers (n = 5) was downloaded from The National Center for Biotechnology Information's (NCBI) Gene Expression Omnibus (GEO) repository. Differential expression was ascertained via NCBI's GEO2R software, and Ingenuity Pathway Analysis (IPA) software was used to perform a pathway analysis.\nResults: A total of 459 genes were found to be significantly differentially expressed in smoker buccal mucosa (p < 0.05). A total of 261 genes were over-expressed while 198 genes were under-expressed. The top canonical pathways predicted by IPA were nitric oxide and reactive oxygen production at macrophages, macrophages/fibroblasts and endothelial cells in rheumatoid arthritis, and thyroid cancer pathways. The IPA upstream analysis predicted that the TP53, APP, SMAD3, and TNF proteins as well as dexamethasone drug would be top transcriptional regulators.\nConclusions: IPA highlighted critical pathways of carcinogenesis, mainly nitric oxide and reactive oxygen production at macrophages, and confirmed widespread injury in the buccal mucosa due to exposure to cigarette smoke. Our findings suggest that cigarette smoking significantly impacts gene pathways in the buccal mucosa and may highlight potential targets for treating the effects of cigarette smoking.\nSupplementary Information: The online version contains supplementary material available at 10.1186/s43042-022-00268-y.", "claims": [{"id": "claim-method", "statement": "The GEO2R software, which is available on the NCBI website, was used to create a list of 15,000 differentially expressed genes between smoker and never-smoker buccal samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37521848", "locator": "sections[4] \"Identification of differentially expressed (DE) genes\" paragraph 2", "quote": "The GEO2R software, which is available on the NCBI website, was used to create a list of 15,000 differentially expressed genes between smoker and never-smoker buccal samples."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The current report utilized a previously published dataset for the analysis. 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The dataset used in this work was acquired from The National Center for Biotechnology Information’s (NCBI) Gene Expression Omnibus (GEO) depository (accession number GSE8987)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 459 genes were found to be significantly differentially expressed in smoker buccal mucosa (p < 0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "A total of 459 genes were found to be significantly differentially expressed in smoker buccal mucosa (p < 0.05)."}, "evidence": [{"asset": "source:pmid:37521848", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 459 genes were found to be significantly differentially expressed in smoker buccal mucosa (p < 0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 459 genes were found to be significantly differentially expressed in smoker buccal mucosa (p < 0.05).", "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:37521848"], "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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