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Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer

Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in c...

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Autores principales: Siegel, Erin M., Riggs, Bridget M., Delmas, Amber L., Koch, Abby, Hakam, Ardeshir, Brown, Kevin D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380427/
https://www.ncbi.nlm.nih.gov/pubmed/25826459
http://dx.doi.org/10.1371/journal.pone.0122495
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author Siegel, Erin M.
Riggs, Bridget M.
Delmas, Amber L.
Koch, Abby
Hakam, Ardeshir
Brown, Kevin D.
author_facet Siegel, Erin M.
Riggs, Bridget M.
Delmas, Amber L.
Koch, Abby
Hakam, Ardeshir
Brown, Kevin D.
author_sort Siegel, Erin M.
collection PubMed
description Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97–1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated.
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spelling pubmed-43804272015-04-09 Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer Siegel, Erin M. Riggs, Bridget M. Delmas, Amber L. Koch, Abby Hakam, Ardeshir Brown, Kevin D. PLoS One Research Article Aberrant DNA methylation has been observed in cervical cancer; however, most studies have used non-quantitative approaches to measure DNA methylation. The objective of this study was to quantify methylation within a select panel of genes previously identified as targets for epigenetic silencing in cervical cancer and to identify genes with elevated methylation that can distinguish cancer from normal cervical tissues. We identified 49 women with invasive squamous cell cancer of the cervix and 22 women with normal cytology specimens. Bisulfite-modified genomic DNA was amplified and quantitative pyrosequencing completed for 10 genes (APC, CCNA, CDH1, CDH13, WIF1, TIMP3, DAPK1, RARB, FHIT, and SLIT2). A Methylation Index was calculated as the mean percent methylation across all CpG sites analyzed per gene (~4-9 CpG site) per sequence. A binary cut-point was defined at >15% methylation. Sensitivity, specificity and area under ROC curve (AUC) of methylation in individual genes or a panel was examined. The median methylation index was significantly higher in cases compared to controls in 8 genes, whereas there was no difference in median methylation for 2 genes. Compared to HPV and age, the combination of DNA methylation level of DAPK1, SLIT2, WIF1 and RARB with HPV and age significantly improved the AUC from 0.79 to 0.99 (95% CI: 0.97–1.00, p-value = 0.003). Pyrosequencing analysis confirmed that several genes are common targets for aberrant methylation in cervical cancer and DNA methylation level of four genes appears to increase specificity to identify cancer compared to HPV detection alone. Alterations in DNA methylation of specific genes in cervical cancers, such as DAPK1, RARB, WIF1, and SLIT2, may also occur early in cervical carcinogenesis and should be evaluated. Public Library of Science 2015-03-31 /pmc/articles/PMC4380427/ /pubmed/25826459 http://dx.doi.org/10.1371/journal.pone.0122495 Text en © 2015 Siegel et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Siegel, Erin M.
Riggs, Bridget M.
Delmas, Amber L.
Koch, Abby
Hakam, Ardeshir
Brown, Kevin D.
Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
title Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
title_full Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
title_fullStr Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
title_full_unstemmed Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
title_short Quantitative DNA Methylation Analysis of Candidate Genes in Cervical Cancer
title_sort quantitative dna methylation analysis of candidate genes in cervical cancer
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380427/
https://www.ncbi.nlm.nih.gov/pubmed/25826459
http://dx.doi.org/10.1371/journal.pone.0122495
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