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Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history
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 level...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10369823/ https://www.ncbi.nlm.nih.gov/pubmed/37496025 http://dx.doi.org/10.1186/s12957-023-03099-2 |
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author | Shang, Junyi Nie, Xinran Qi, Yanan Zhou, Jing Qi, Yong |
author_facet | Shang, Junyi Nie, Xinran Qi, Yanan Zhou, Jing Qi, Yong |
author_sort | Shang, Junyi |
collection | PubMed |
description | 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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. |
format | Online Article Text |
id | pubmed-10369823 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-103698232023-07-27 Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history Shang, Junyi Nie, Xinran Qi, Yanan Zhou, Jing Qi, Yong World J Surg Oncol Research 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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. BioMed Central 2023-07-26 /pmc/articles/PMC10369823/ /pubmed/37496025 http://dx.doi.org/10.1186/s12957-023-03099-2 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Shang, Junyi Nie, Xinran Qi, Yanan Zhou, Jing Qi, Yong Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history |
title | Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history |
title_full | Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history |
title_fullStr | Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history |
title_full_unstemmed | Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history |
title_short | Short-term smoking cessation leads to a universal decrease in whole blood genomic DNA methylation in patients with a smoking history |
title_sort | short-term smoking cessation leads to a universal decrease in whole blood genomic dna methylation in patients with a smoking history |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10369823/ https://www.ncbi.nlm.nih.gov/pubmed/37496025 http://dx.doi.org/10.1186/s12957-023-03099-2 |
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