Cargando…
Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling
DNA methylation is an important epigenetic regulatory mechanism in esophageal carcinoma (EC) and is associated with genomic instability and carcinogenesis. In the present study, we aimed to identify tumor biomarkers for predicting prognosis of EC patients. We downloaded mRNA expression profiles and...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Lippincott Williams & Wilkins
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7489726/ https://www.ncbi.nlm.nih.gov/pubmed/32925794 http://dx.doi.org/10.1097/MD.0000000000022194 |
_version_ | 1783581916680683520 |
---|---|
author | Wang, Jianlin Luo, Judong Sun, Zhiqiang Sun, Fei Kong, Ze Yu, Jingping |
author_facet | Wang, Jianlin Luo, Judong Sun, Zhiqiang Sun, Fei Kong, Ze Yu, Jingping |
author_sort | Wang, Jianlin |
collection | PubMed |
description | DNA methylation is an important epigenetic regulatory mechanism in esophageal carcinoma (EC) and is associated with genomic instability and carcinogenesis. In the present study, we aimed to identify tumor biomarkers for predicting prognosis of EC patients. We downloaded mRNA expression profiles and DNA methylation profiles associated with EC from the Gene Expression Omnibus database. Differentially expressed and differentially methylated genes between tumor tissues and adjacent normal tissue samples were identified. Functional enrichment analyses were performed, followed by the construction of protein–protein interaction networks. Data were validated based on methylation profiles from The Cancer Genome Atlas. Candidate genes were further verified according to survival analysis and Cox regression analysis. We uncovered multiple genes with differential expression or methylation in tumor samples compared with normal samples. After taking the intersection of 3 differential gene sets, we obtained a total of 232 overlapping genes. Functional enrichment analysis revealed that these genes are related to pathways such as “glutathione metabolism,” “p53 signaling pathway,” and “focal adhesion.” Furthermore, 8 hub genes with inversed expression and methylation correlation were identified as candidate genes. The abnormal expression levels of MSN, PELI1, and MTHFD2 were correlated with overall survival times in EC patients (P < .05). Only MTHFD2 was significantly associated with a pathologic stage according to univariate analysis (P = .037) and multivariate analysis (P = .043). Our study identified several novel EC biomarkers with prognostic value by integrated analysis of transcriptomic data and methylation profiles. MTHFD2 could serve as an independent biomarker for predicting prognosis and pathological stages of EC. |
format | Online Article Text |
id | pubmed-7489726 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Lippincott Williams & Wilkins |
record_format | MEDLINE/PubMed |
spelling | pubmed-74897262020-09-24 Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling Wang, Jianlin Luo, Judong Sun, Zhiqiang Sun, Fei Kong, Ze Yu, Jingping Medicine (Baltimore) 5700 DNA methylation is an important epigenetic regulatory mechanism in esophageal carcinoma (EC) and is associated with genomic instability and carcinogenesis. In the present study, we aimed to identify tumor biomarkers for predicting prognosis of EC patients. We downloaded mRNA expression profiles and DNA methylation profiles associated with EC from the Gene Expression Omnibus database. Differentially expressed and differentially methylated genes between tumor tissues and adjacent normal tissue samples were identified. Functional enrichment analyses were performed, followed by the construction of protein–protein interaction networks. Data were validated based on methylation profiles from The Cancer Genome Atlas. Candidate genes were further verified according to survival analysis and Cox regression analysis. We uncovered multiple genes with differential expression or methylation in tumor samples compared with normal samples. After taking the intersection of 3 differential gene sets, we obtained a total of 232 overlapping genes. Functional enrichment analysis revealed that these genes are related to pathways such as “glutathione metabolism,” “p53 signaling pathway,” and “focal adhesion.” Furthermore, 8 hub genes with inversed expression and methylation correlation were identified as candidate genes. The abnormal expression levels of MSN, PELI1, and MTHFD2 were correlated with overall survival times in EC patients (P < .05). Only MTHFD2 was significantly associated with a pathologic stage according to univariate analysis (P = .037) and multivariate analysis (P = .043). Our study identified several novel EC biomarkers with prognostic value by integrated analysis of transcriptomic data and methylation profiles. MTHFD2 could serve as an independent biomarker for predicting prognosis and pathological stages of EC. Lippincott Williams & Wilkins 2020-09-11 /pmc/articles/PMC7489726/ /pubmed/32925794 http://dx.doi.org/10.1097/MD.0000000000022194 Text en Copyright © 2020 the Author(s). Published by Wolters Kluwer Health, Inc. http://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 4.0 (CCBY-NC), where it is permissible to download, share, remix, transform, and buildup the work provided it is properly cited. The work cannot be used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc/4.0 |
spellingShingle | 5700 Wang, Jianlin Luo, Judong Sun, Zhiqiang Sun, Fei Kong, Ze Yu, Jingping Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
title | Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
title_full | Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
title_fullStr | Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
title_full_unstemmed | Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
title_short | Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
title_sort | identification of mthfd2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling |
topic | 5700 |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7489726/ https://www.ncbi.nlm.nih.gov/pubmed/32925794 http://dx.doi.org/10.1097/MD.0000000000022194 |
work_keys_str_mv | AT wangjianlin identificationofmthfd2asanovelprognosisbiomarkerinesophagealcarcinomapatientsbasedontranscriptomicdataandmethylationprofiling AT luojudong identificationofmthfd2asanovelprognosisbiomarkerinesophagealcarcinomapatientsbasedontranscriptomicdataandmethylationprofiling AT sunzhiqiang identificationofmthfd2asanovelprognosisbiomarkerinesophagealcarcinomapatientsbasedontranscriptomicdataandmethylationprofiling AT sunfei identificationofmthfd2asanovelprognosisbiomarkerinesophagealcarcinomapatientsbasedontranscriptomicdataandmethylationprofiling AT kongze identificationofmthfd2asanovelprognosisbiomarkerinesophagealcarcinomapatientsbasedontranscriptomicdataandmethylationprofiling AT yujingping identificationofmthfd2asanovelprognosisbiomarkerinesophagealcarcinomapatientsbasedontranscriptomicdataandmethylationprofiling |