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Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation

OBJECTIVES. The BRAF(V600E) mutation is a major driver mutation in papillary thyroid cancer. The aim of this study was to elucidate the correlation between DNA methylation and gene expression changes induced by the BRAF(V600E) mutation in thyroid cells. METHODS. We used Nthy/BRAF cell lines generate...

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Autores principales: Yi, Jin Wook, Ha, Seong Yun, Jee, Hyeon-Gun, Kim, Kwangsoo, Kim, Su-jin, Chai, Young Jun, Choi, June Young, Lee, Kyu Eun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Korean Society of Otorhinolaryngology-Head and Neck Surgery 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9441509/
https://www.ncbi.nlm.nih.gov/pubmed/35538718
http://dx.doi.org/10.21053/ceo.2022.00206
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author Yi, Jin Wook
Ha, Seong Yun
Jee, Hyeon-Gun
Kim, Kwangsoo
Kim, Su-jin
Chai, Young Jun
Choi, June Young
Lee, Kyu Eun
author_facet Yi, Jin Wook
Ha, Seong Yun
Jee, Hyeon-Gun
Kim, Kwangsoo
Kim, Su-jin
Chai, Young Jun
Choi, June Young
Lee, Kyu Eun
author_sort Yi, Jin Wook
collection PubMed
description OBJECTIVES. The BRAF(V600E) mutation is a major driver mutation in papillary thyroid cancer. The aim of this study was to elucidate the correlation between DNA methylation and gene expression changes induced by the BRAF(V600E) mutation in thyroid cells. METHODS. We used Nthy/BRAF cell lines generated by transfection of Nthy/ori cells with the wild-type BRAF gene (Nthy/WT cells) and the V600E mutant-type BRAF gene (Nthy/V600E cells). We performed gene expression microarray and DNA methylation array analyses for Nthy/WT and Nthy/V600E cells. Two types of array data were integrated to identify inverse correlations between methylation and gene expression. The results were verified in silico using data from The Cancer Genome Atlas (TCGA) and in vivo through pyrosequencing and quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS. In the Nthy/V600E cells, 199,821 probes were significantly hypermethylated, and 697 genes showed a “hypermethylation-downregulation” pattern in Nthy/V600E. Tumor suppressor genes and apoptosis-related genes were included. In total, 66,446 probes were significantly hypomethylated, and 227 genes showed a “hypomethylation-upregulation” pattern in Nthy/V600E cells. Protooncogenes and developmental protein-coding genes were included. In the TCGA analysis, 491/697 (70.44%) genes showed a hypermethylation-downregulation pattern, and 153/227 (67.40%) genes showed a hypomethylation-upregulation pattern. Ten selected genes showed a similar methylation-gene expression pattern in pyrosequencing and qRT-PCR. CONCLUSION. Induction of the BRAF(V600E) mutation in thyroid cells led to frequent hypermethylation. Anticancer genes, such as those involved in tumor suppression or apoptosis, were downregulated by upstream hypermethylation, whereas carcinogenic genes, such as protooncogenes, were upregulated by hypomethylation. Our results suggest that the BRAF(V600E) mutation in thyroid cells modulates DNA methylation and results in cancer-related gene expression.
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spelling pubmed-94415092022-09-12 Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation Yi, Jin Wook Ha, Seong Yun Jee, Hyeon-Gun Kim, Kwangsoo Kim, Su-jin Chai, Young Jun Choi, June Young Lee, Kyu Eun Clin Exp Otorhinolaryngol Original Article OBJECTIVES. The BRAF(V600E) mutation is a major driver mutation in papillary thyroid cancer. The aim of this study was to elucidate the correlation between DNA methylation and gene expression changes induced by the BRAF(V600E) mutation in thyroid cells. METHODS. We used Nthy/BRAF cell lines generated by transfection of Nthy/ori cells with the wild-type BRAF gene (Nthy/WT cells) and the V600E mutant-type BRAF gene (Nthy/V600E cells). We performed gene expression microarray and DNA methylation array analyses for Nthy/WT and Nthy/V600E cells. Two types of array data were integrated to identify inverse correlations between methylation and gene expression. The results were verified in silico using data from The Cancer Genome Atlas (TCGA) and in vivo through pyrosequencing and quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS. In the Nthy/V600E cells, 199,821 probes were significantly hypermethylated, and 697 genes showed a “hypermethylation-downregulation” pattern in Nthy/V600E. Tumor suppressor genes and apoptosis-related genes were included. In total, 66,446 probes were significantly hypomethylated, and 227 genes showed a “hypomethylation-upregulation” pattern in Nthy/V600E cells. Protooncogenes and developmental protein-coding genes were included. In the TCGA analysis, 491/697 (70.44%) genes showed a hypermethylation-downregulation pattern, and 153/227 (67.40%) genes showed a hypomethylation-upregulation pattern. Ten selected genes showed a similar methylation-gene expression pattern in pyrosequencing and qRT-PCR. CONCLUSION. Induction of the BRAF(V600E) mutation in thyroid cells led to frequent hypermethylation. Anticancer genes, such as those involved in tumor suppression or apoptosis, were downregulated by upstream hypermethylation, whereas carcinogenic genes, such as protooncogenes, were upregulated by hypomethylation. Our results suggest that the BRAF(V600E) mutation in thyroid cells modulates DNA methylation and results in cancer-related gene expression. Korean Society of Otorhinolaryngology-Head and Neck Surgery 2022-08 2022-05-04 /pmc/articles/PMC9441509/ /pubmed/35538718 http://dx.doi.org/10.21053/ceo.2022.00206 Text en Copyright © 2022 by Korean Society of Otorhinolaryngology-Head and Neck Surgery https://creativecommons.org/licenses/by-nc/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0 (https://creativecommons.org/licenses/by-nc/4.0/) ) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Article
Yi, Jin Wook
Ha, Seong Yun
Jee, Hyeon-Gun
Kim, Kwangsoo
Kim, Su-jin
Chai, Young Jun
Choi, June Young
Lee, Kyu Eun
Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation
title Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation
title_full Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation
title_fullStr Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation
title_full_unstemmed Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation
title_short Induction of the BRAF(V600E) Mutation in Thyroid Cells Leads to Frequent Hypermethylation
title_sort induction of the braf(v600e) mutation in thyroid cells leads to frequent hypermethylation
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9441509/
https://www.ncbi.nlm.nih.gov/pubmed/35538718
http://dx.doi.org/10.21053/ceo.2022.00206
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