A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers

Hypermethylation of CpG islands in the promoter region of tumor suppressor genes (TSGs) and their subsequent silencing is thought to be one of the main mechanisms of carcinogenesis. MBD2b enrichment coupled with a NimbleGen array was applied to examine the genome-wide CpG island methylation profile...

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Autores principales: Yang, Yuan, Zhao, Linghao, Huang, Bo, Hou, Guojun, Zhou, Beibei, Qian, Jin, Yuan, Shengxian, Xiao, Huasheng, Li, Minghui, Zhou, Weiping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2017
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5394454/
https://www.ncbi.nlm.nih.gov/pubmed/28418032
http://dx.doi.org/10.1038/srep46533
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author Yang, Yuan
Zhao, Linghao
Huang, Bo
Hou, Guojun
Zhou, Beibei
Qian, Jin
Yuan, Shengxian
Xiao, Huasheng
Li, Minghui
Zhou, Weiping
author_facet Yang, Yuan
Zhao, Linghao
Huang, Bo
Hou, Guojun
Zhou, Beibei
Qian, Jin
Yuan, Shengxian
Xiao, Huasheng
Li, Minghui
Zhou, Weiping
author_sort Yang, Yuan
collection PubMed
description Hypermethylation of CpG islands in the promoter region of tumor suppressor genes (TSGs) and their subsequent silencing is thought to be one of the main mechanisms of carcinogenesis. MBD2b enrichment coupled with a NimbleGen array was applied to examine the genome-wide CpG island methylation profile of hepatocellular carcinoma (HCC). Hypermethylated DNA of 58 pairs of HCC and adjacent tissue samples was enriched and hybridized in the same array. Aberrant hypermethylated peaks of HCC and adjacent tissues were screened and annotated after data processing using NimbleScan2.5 and our newly developed Weighting and Scoring (WAS) method, respectively. Validation using bisulfite sequencing of randomly selected ANKRD45, APC, CDX1, HOXD3, PTGER and TUBB6 genes demonstrated significant hypermethylation modification in HCC samples, consistent with the array data.
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spelling pubmed-53944542017-04-20 A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers Yang, Yuan Zhao, Linghao Huang, Bo Hou, Guojun Zhou, Beibei Qian, Jin Yuan, Shengxian Xiao, Huasheng Li, Minghui Zhou, Weiping Sci Rep Article Hypermethylation of CpG islands in the promoter region of tumor suppressor genes (TSGs) and their subsequent silencing is thought to be one of the main mechanisms of carcinogenesis. MBD2b enrichment coupled with a NimbleGen array was applied to examine the genome-wide CpG island methylation profile of hepatocellular carcinoma (HCC). Hypermethylated DNA of 58 pairs of HCC and adjacent tissue samples was enriched and hybridized in the same array. Aberrant hypermethylated peaks of HCC and adjacent tissues were screened and annotated after data processing using NimbleScan2.5 and our newly developed Weighting and Scoring (WAS) method, respectively. Validation using bisulfite sequencing of randomly selected ANKRD45, APC, CDX1, HOXD3, PTGER and TUBB6 genes demonstrated significant hypermethylation modification in HCC samples, consistent with the array data. Nature Publishing Group 2017-04-18 /pmc/articles/PMC5394454/ /pubmed/28418032 http://dx.doi.org/10.1038/srep46533 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Yang, Yuan
Zhao, Linghao
Huang, Bo
Hou, Guojun
Zhou, Beibei
Qian, Jin
Yuan, Shengxian
Xiao, Huasheng
Li, Minghui
Zhou, Weiping
A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
title A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
title_full A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
title_fullStr A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
title_full_unstemmed A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
title_short A New Approach to Evaluating Aberrant DNA Methylation Profiles in Hepatocellular Carcinoma as Potential Biomarkers
title_sort new approach to evaluating aberrant dna methylation profiles in hepatocellular carcinoma as potential biomarkers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5394454/
https://www.ncbi.nlm.nih.gov/pubmed/28418032
http://dx.doi.org/10.1038/srep46533
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