Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis
Prostate adenocarcinoma (PRAD) is the most pervasive carcinoma diagnosed in men with over 170,000 new cases every year in the United States and is the second leading cause of death from cancer in men despite its indolent clinical course. Prostate-specific antigen testing, which is the most commonly...
Main Authors: | , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2021-04-01
|
Series: | Frontiers in Oncology |
Subjects: | |
Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2021.647253/full |
id |
doaj-195b2e160a0a4b8c9a3b6fb3f1abfd90 |
---|---|
record_format |
Article |
spelling |
doaj-195b2e160a0a4b8c9a3b6fb3f1abfd902021-04-01T05:11:00ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2021-04-011110.3389/fonc.2021.647253647253Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network AnalysisYaxin Hou0Yaxin Hou1Junyi Hu2Junyi Hu3Lijie Zhou4Lijie Zhou5Lilong Liu6Lilong Liu7Ke Chen8Ke Chen9Xiong Yang10Department of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaShenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, ChinaDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaShenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, ChinaDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaShenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, ChinaDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaShenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, ChinaDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaShenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, ChinaDepartment of Urology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, ChinaProstate adenocarcinoma (PRAD) is the most pervasive carcinoma diagnosed in men with over 170,000 new cases every year in the United States and is the second leading cause of death from cancer in men despite its indolent clinical course. Prostate-specific antigen testing, which is the most commonly used non-invasive diagnostic method for PRAD, has improved early detection rates in the past decade, but its effectiveness for monitoring disease progression and predicting prognosis is controversial. To identify novel biomarkers for these purposes, we carried out weighted gene co-expression network analysis of the top 10,000 variant genes in PRAD from The Cancer Genome Atlas in order to identify gene modules associated with clinical outcomes. Methylation and copy number variation analysis were performed to screen aberrantly expressed genes, and the Kaplan–Meier survival and gene set enrichment analyses were conducted to evaluate the prognostic value and potential mechanisms of the identified genes. Cyclin E2 (CCNE2), rhophilin Rho GTPase-binding protein (RHPN1), enhancer of zeste homolog 2 (EZH2), tonsoku-like DNA repair protein (TONSL), epoxide hydrolase 2 (EPHX2), fibromodulin (FMOD), and solute carrier family 7 member (SLC7A4) were identified as potential prognostic indicators and possible therapeutic targets as well. These findings can improve diagnosis and disease monitoring to achieve better clinical outcomes in PRAD.https://www.frontiersin.org/articles/10.3389/fonc.2021.647253/fullbioinformatics analysisprostate adenocarcinomabiomarkerprognosistherapeutic target |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yaxin Hou Yaxin Hou Junyi Hu Junyi Hu Lijie Zhou Lijie Zhou Lilong Liu Lilong Liu Ke Chen Ke Chen Xiong Yang |
spellingShingle |
Yaxin Hou Yaxin Hou Junyi Hu Junyi Hu Lijie Zhou Lijie Zhou Lilong Liu Lilong Liu Ke Chen Ke Chen Xiong Yang Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis Frontiers in Oncology bioinformatics analysis prostate adenocarcinoma biomarker prognosis therapeutic target |
author_facet |
Yaxin Hou Yaxin Hou Junyi Hu Junyi Hu Lijie Zhou Lijie Zhou Lilong Liu Lilong Liu Ke Chen Ke Chen Xiong Yang |
author_sort |
Yaxin Hou |
title |
Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis |
title_short |
Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis |
title_full |
Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis |
title_fullStr |
Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis |
title_full_unstemmed |
Integrative Analysis of Methylation and Copy Number Variations of Prostate Adenocarcinoma Based on Weighted Gene Co-expression Network Analysis |
title_sort |
integrative analysis of methylation and copy number variations of prostate adenocarcinoma based on weighted gene co-expression network analysis |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Oncology |
issn |
2234-943X |
publishDate |
2021-04-01 |
description |
Prostate adenocarcinoma (PRAD) is the most pervasive carcinoma diagnosed in men with over 170,000 new cases every year in the United States and is the second leading cause of death from cancer in men despite its indolent clinical course. Prostate-specific antigen testing, which is the most commonly used non-invasive diagnostic method for PRAD, has improved early detection rates in the past decade, but its effectiveness for monitoring disease progression and predicting prognosis is controversial. To identify novel biomarkers for these purposes, we carried out weighted gene co-expression network analysis of the top 10,000 variant genes in PRAD from The Cancer Genome Atlas in order to identify gene modules associated with clinical outcomes. Methylation and copy number variation analysis were performed to screen aberrantly expressed genes, and the Kaplan–Meier survival and gene set enrichment analyses were conducted to evaluate the prognostic value and potential mechanisms of the identified genes. Cyclin E2 (CCNE2), rhophilin Rho GTPase-binding protein (RHPN1), enhancer of zeste homolog 2 (EZH2), tonsoku-like DNA repair protein (TONSL), epoxide hydrolase 2 (EPHX2), fibromodulin (FMOD), and solute carrier family 7 member (SLC7A4) were identified as potential prognostic indicators and possible therapeutic targets as well. These findings can improve diagnosis and disease monitoring to achieve better clinical outcomes in PRAD. |
topic |
bioinformatics analysis prostate adenocarcinoma biomarker prognosis therapeutic target |
url |
https://www.frontiersin.org/articles/10.3389/fonc.2021.647253/full |
work_keys_str_mv |
AT yaxinhou integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT yaxinhou integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT junyihu integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT junyihu integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT lijiezhou integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT lijiezhou integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT lilongliu integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT lilongliu integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT kechen integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT kechen integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis AT xiongyang integrativeanalysisofmethylationandcopynumbervariationsofprostateadenocarcinomabasedonweightedgenecoexpressionnetworkanalysis |
_version_ |
1724176791067688960 |