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Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers

Objective. To identify DNA methylation patterns of heavy smokers in oral rinse samples. Methods. Genome-wide DNA methylation data was imported from Gene Expression Omnibus GSE70977 using the GEOquery package. Two independent sets were analyzed: (a) 71 epigenomes of cancer-free subjects (heavy smoker...

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Autores principales: Hernández, Hernán Guillermo, Aranzazu-Moya, Gloria Cristina, Pinzón-Reyes, Efraín Hernando
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10376800/
https://www.ncbi.nlm.nih.gov/pubmed/37509437
http://dx.doi.org/10.3390/biomedicines11071797
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author Hernández, Hernán Guillermo
Aranzazu-Moya, Gloria Cristina
Pinzón-Reyes, Efraín Hernando
author_facet Hernández, Hernán Guillermo
Aranzazu-Moya, Gloria Cristina
Pinzón-Reyes, Efraín Hernando
author_sort Hernández, Hernán Guillermo
collection PubMed
description Objective. To identify DNA methylation patterns of heavy smokers in oral rinse samples. Methods. Genome-wide DNA methylation data was imported from Gene Expression Omnibus GSE70977 using the GEOquery package. Two independent sets were analyzed: (a) 71 epigenomes of cancer-free subjects (heavy smokers n = 37 vs. non-smokers n = 31); for concordance assessment (b) 139 oral-cancer patients’ epigenomes (heavy smokers n = 92 vs. non-smokers n = 47). Differential DNA methylation for CpG positions and at the regional level was determined using Limma and DMRcate Bioconductor packages. The linear model included sex, age, and alcohol consumption. The statistical threshold was set to p < 0.05. Functional gene prioritization analysis was performed for gene-targeted analysis. Results. In individuals without cancer and heavy smokers, the FAM184B gene was found with two CpG positions differentially hypermethylated (p = 0.012 after FDR adjustment), in a region of 48 bp with an absolute methylation difference >10% between groups (p = 1.76 × 10(−8)). In the analysis corresponding to oral-cancer patients, we found AHRR differentially hypomethylated cancer patients, but also in subjects without oral cancer in the targeted analyses. Remarkably, ADAMTS2 was found differentially hypermethylated in heavy smokers without a diagnosis of cancer in two consecutive probes cg05575921 (p = 3.13 × 10(−7)) and cg10208897 (p = 1.36 × 10(−5)). Conclusions: Differentially methylated AHRR, ADAMTS2, and FAM184B genes are biomarker candidates in oral rinse samples.
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spelling pubmed-103768002023-07-29 Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers Hernández, Hernán Guillermo Aranzazu-Moya, Gloria Cristina Pinzón-Reyes, Efraín Hernando Biomedicines Article Objective. To identify DNA methylation patterns of heavy smokers in oral rinse samples. Methods. Genome-wide DNA methylation data was imported from Gene Expression Omnibus GSE70977 using the GEOquery package. Two independent sets were analyzed: (a) 71 epigenomes of cancer-free subjects (heavy smokers n = 37 vs. non-smokers n = 31); for concordance assessment (b) 139 oral-cancer patients’ epigenomes (heavy smokers n = 92 vs. non-smokers n = 47). Differential DNA methylation for CpG positions and at the regional level was determined using Limma and DMRcate Bioconductor packages. The linear model included sex, age, and alcohol consumption. The statistical threshold was set to p < 0.05. Functional gene prioritization analysis was performed for gene-targeted analysis. Results. In individuals without cancer and heavy smokers, the FAM184B gene was found with two CpG positions differentially hypermethylated (p = 0.012 after FDR adjustment), in a region of 48 bp with an absolute methylation difference >10% between groups (p = 1.76 × 10(−8)). In the analysis corresponding to oral-cancer patients, we found AHRR differentially hypomethylated cancer patients, but also in subjects without oral cancer in the targeted analyses. Remarkably, ADAMTS2 was found differentially hypermethylated in heavy smokers without a diagnosis of cancer in two consecutive probes cg05575921 (p = 3.13 × 10(−7)) and cg10208897 (p = 1.36 × 10(−5)). Conclusions: Differentially methylated AHRR, ADAMTS2, and FAM184B genes are biomarker candidates in oral rinse samples. MDPI 2023-06-23 /pmc/articles/PMC10376800/ /pubmed/37509437 http://dx.doi.org/10.3390/biomedicines11071797 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hernández, Hernán Guillermo
Aranzazu-Moya, Gloria Cristina
Pinzón-Reyes, Efraín Hernando
Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers
title Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers
title_full Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers
title_fullStr Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers
title_full_unstemmed Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers
title_short Aberrant AHRR, ADAMTS2 and FAM184 DNA Methylation: Candidate Biomarkers in the Oral Rinse of Heavy Smokers
title_sort aberrant ahrr, adamts2 and fam184 dna methylation: candidate biomarkers in the oral rinse of heavy smokers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10376800/
https://www.ncbi.nlm.nih.gov/pubmed/37509437
http://dx.doi.org/10.3390/biomedicines11071797
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