Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37496025", "kind": "science-record", "revision": 4, "content_hash": "sha256:dfac03361513d921fa087722f3f140cd62c1b3c1b3da25f7ec3440c7fbe5b24e", "created_at": "2026-11-01T19:02:16Z", "updated_at": "2026-11-01T22:09:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history.", "doi": "10.1186/s12957-023-03099-2", "pmid": "37496025", "authors": ["Junyi Shang", "Xinran Nie", "Yanan Qi", "Jing Zhou", "Yong Qi"], "journal": "World journal of surgical oncology", "year": 2023, "abstract": "BACKGROUND: Epigenetics is involved in various human diseases. Smoking is one of the most common environmental factors causing epigenetic changes. The DNA methylation changes and mechanisms after quitting smoking have yet to be defined. The present study examined the changes in DNA methylation levels before and after short-term smoking cessation and explored the potential mechanism.\nMETHODS: Whole blood and clinical data were collected from 8 patients before and after short-term smoking cessation, DNA methylation was assessed, and differentially methylated sites were analyzed, followed by a comprehensive analysis of the differentially methylated sites with clinical data. GO/KEGG enrichment and protein-protein interaction (PPI) network analyses identified the hub genes. The differentially methylated sites between former and current smokers in GSE50660 from the GEO database were detected by GEO2R. Then, a Venn analysis was carried out using the differentially methylated sites. GO/KEGG enrichment analysis was performed on the genes corresponding to the common DNA methylation sites, the PPI network was constructed, and hub genes were predicted. The enriched genes associated with the cell cycle were selected, and the pan-cancer gene expression and clinical significance in lung cancer were analyzed based on the TCGA database.\nRESULTS: Most genes showed decreased DNA methylation levels after short-term smoking cessation; 694 upregulated methylation CpG sites and 3184 downregulated methylation CpG sites were identified. The DNA methylation levels were altered according to the clinical data (body weight, expiratory, and tobacco dependence score). Enrichment analysis, construction of the PPI network, and pan-cancer analysis suggested that smoking cessation may affect various biological processes.\nCONCLUSIONS: Smoking cessation leads to epigenetic changes, mainly decreased in the decline of most DNA methylation levels. Bioinformatics further identified the biologically relevant changes after short-term smoking cessation.", "claims": [{"id": "claim-method", "statement": "Paired analysis of the methylation levels of 8 patients before and after short-term smoking cessation showed differential expression in 3878 CpG sites (P < 0.001) (Fig. 1a).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37496025", "locator": "sections[9] \"Altered DNA methylation levels before and after short-term smoking cessation\" paragraph 2", "quote": "Paired analysis of the methylation levels of 8 patients before and after short-term smoking cessation showed differential expression in 3878 CpG sites (P < 0.001) (Fig. 1a)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated during the current study are available in the Gene Expression Omnibus (GEO) with the number GSE201532.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37496025", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "The datasets generated during the current study are available in the Gene Expression Omnibus (GEO) with the number GSE201532."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Most genes showed decreased DNA methylation levels after short-term smoking cessation; 694 upregulated methylation CpG sites and 3184 downregulated methylation CpG sites were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37496025", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Most genes showed decreased DNA methylation levels after short-term smoking cessation; 694 upregulated methylation CpG sites and 3184 downregulated methylation CpG sites were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Most genes showed decreased DNA methylation levels after short-term smoking cessation; 694 upregulated methylation CpG sites and 3184 downregulated methylation CpG sites were identified.", "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:37496025"], "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:GSE201532"], "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:GSE201532"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37496025", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12957-023-03099-2", "sha256": 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