Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis
Although radiotherapy is greatly successful in the treatment of prostate cancer (PCa), radioresistance is still a major challenge in the treatment. To our knowledge, this study is the first to screen long non-coding RNAs (lncRNAs) associated with radioresponse in PCa by The Cancer Genome Atlas (TCGA...
Main Authors: | , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2020-04-01
|
Series: | Frontiers in Oncology |
Subjects: | |
Online Access: | https://www.frontiersin.org/article/10.3389/fonc.2020.00498/full |
id |
doaj-854d493aad8644b3bb237013f239678d |
---|---|
record_format |
Article |
spelling |
doaj-854d493aad8644b3bb237013f239678d2020-11-25T02:30:00ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2020-04-011010.3389/fonc.2020.00498515583Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics AnalysisMeng Xu0Shiqi Gong1Yue Li2Jun Zhou3Jun Zhou4Junhua Du5Junhua Du6Cheng Yang7Cheng Yang8Mingwei Yang9Fan Zhang10Chaozhao Liang11Chaozhao Liang12Zhuting Tong13Department of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaDepartment of Otolaryngology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, ChinaDepartment of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaDepartment of Urology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaInstitute of Urology, Anhui Medical University, Heifei, ChinaDepartment of Urology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaInstitute of Urology, Anhui Medical University, Heifei, ChinaDepartment of Urology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaInstitute of Urology, Anhui Medical University, Heifei, ChinaDepartment of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaDepartment of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaDepartment of Urology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaInstitute of Urology, Anhui Medical University, Heifei, ChinaDepartment of Radiation Oncology, The First Affiliated Hospital, Anhui Medical University, Hefei, ChinaAlthough radiotherapy is greatly successful in the treatment of prostate cancer (PCa), radioresistance is still a major challenge in the treatment. To our knowledge, this study is the first to screen long non-coding RNAs (lncRNAs) associated with radioresponse in PCa by The Cancer Genome Atlas (TCGA). Bioinformatics methods were used to identify the differentially expressed lncRNAs and protein-coding genes (PCGs) between complete response (CR) and non-complete response (non-CR) groups in radiotherapy. Statistical methods were applied to identify the correlation between lncRNAs and radioresponse as well as lncRNAs and PCGs. The correlation between PCGs and radioresponse was analyzed using weighted gene co-expression network analysis (WGCNA). The three online databases were used to predict the potential target miRNAs of lncRNAs and the miRNAs that might regulate PCGs. RT-qPCR was utilized to detect the expression of lncRNAs and PCGs in our PCa patients. A total of 65 differentially expressed lncRNAs and 468 differentially expressed PCGs were found between the two groups of PCa. After the chi-square test, LINC01600 was selected to be highly correlated with radioresponse from the 65 differentially expressed lncRNAs. Pearson correlation analysis found 558 PCGs co-expressed with LINC01600. WGCNA identified the darkred module associated with radioresponse in PCa. After taking the intersection of the darkred module of WGCNA, differentially expressed PCGs between the two groups of PCa, and the PCGs co-expressed with LINC01600, three PCGs, that is, JUND, ZFP36, and ATF3 were identified as the potential target PCGs of LINC01600. More importantly, we detected the expression of LINC01600 and three PCGs using our PCa patients, and finally verified that LINC01600 and JUND were differentially expressed between CR and non-CR groups, excluding ZFP36 and ATF3. Meantime, the potential regulation ability of LINC01600 for JUND in PCa cell lines was initially explored. In addition, we constructed the competing endogenous RNA (ceRNA) network of LINC01600—miRNA—JUND. In conclusion, we initially reveal the association of LINC01600 with radioresponse in PCa and identify its potential target PCGs for further basic and clinical research.https://www.frontiersin.org/article/10.3389/fonc.2020.00498/fulllong non-coding RNAprostate cancerradioresponsebioinformatics analysisWGCNA |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Meng Xu Shiqi Gong Yue Li Jun Zhou Jun Zhou Junhua Du Junhua Du Cheng Yang Cheng Yang Mingwei Yang Fan Zhang Chaozhao Liang Chaozhao Liang Zhuting Tong |
spellingShingle |
Meng Xu Shiqi Gong Yue Li Jun Zhou Jun Zhou Junhua Du Junhua Du Cheng Yang Cheng Yang Mingwei Yang Fan Zhang Chaozhao Liang Chaozhao Liang Zhuting Tong Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis Frontiers in Oncology long non-coding RNA prostate cancer radioresponse bioinformatics analysis WGCNA |
author_facet |
Meng Xu Shiqi Gong Yue Li Jun Zhou Jun Zhou Junhua Du Junhua Du Cheng Yang Cheng Yang Mingwei Yang Fan Zhang Chaozhao Liang Chaozhao Liang Zhuting Tong |
author_sort |
Meng Xu |
title |
Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis |
title_short |
Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis |
title_full |
Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis |
title_fullStr |
Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis |
title_full_unstemmed |
Identifying Long Non-coding RNA of Prostate Cancer Associated With Radioresponse by Comprehensive Bioinformatics Analysis |
title_sort |
identifying long non-coding rna of prostate cancer associated with radioresponse by comprehensive bioinformatics analysis |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Oncology |
issn |
2234-943X |
publishDate |
2020-04-01 |
description |
Although radiotherapy is greatly successful in the treatment of prostate cancer (PCa), radioresistance is still a major challenge in the treatment. To our knowledge, this study is the first to screen long non-coding RNAs (lncRNAs) associated with radioresponse in PCa by The Cancer Genome Atlas (TCGA). Bioinformatics methods were used to identify the differentially expressed lncRNAs and protein-coding genes (PCGs) between complete response (CR) and non-complete response (non-CR) groups in radiotherapy. Statistical methods were applied to identify the correlation between lncRNAs and radioresponse as well as lncRNAs and PCGs. The correlation between PCGs and radioresponse was analyzed using weighted gene co-expression network analysis (WGCNA). The three online databases were used to predict the potential target miRNAs of lncRNAs and the miRNAs that might regulate PCGs. RT-qPCR was utilized to detect the expression of lncRNAs and PCGs in our PCa patients. A total of 65 differentially expressed lncRNAs and 468 differentially expressed PCGs were found between the two groups of PCa. After the chi-square test, LINC01600 was selected to be highly correlated with radioresponse from the 65 differentially expressed lncRNAs. Pearson correlation analysis found 558 PCGs co-expressed with LINC01600. WGCNA identified the darkred module associated with radioresponse in PCa. After taking the intersection of the darkred module of WGCNA, differentially expressed PCGs between the two groups of PCa, and the PCGs co-expressed with LINC01600, three PCGs, that is, JUND, ZFP36, and ATF3 were identified as the potential target PCGs of LINC01600. More importantly, we detected the expression of LINC01600 and three PCGs using our PCa patients, and finally verified that LINC01600 and JUND were differentially expressed between CR and non-CR groups, excluding ZFP36 and ATF3. Meantime, the potential regulation ability of LINC01600 for JUND in PCa cell lines was initially explored. In addition, we constructed the competing endogenous RNA (ceRNA) network of LINC01600—miRNA—JUND. In conclusion, we initially reveal the association of LINC01600 with radioresponse in PCa and identify its potential target PCGs for further basic and clinical research. |
topic |
long non-coding RNA prostate cancer radioresponse bioinformatics analysis WGCNA |
url |
https://www.frontiersin.org/article/10.3389/fonc.2020.00498/full |
work_keys_str_mv |
AT mengxu identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT shiqigong identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT yueli identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT junzhou identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT junzhou identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT junhuadu identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT junhuadu identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT chengyang identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT chengyang identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT mingweiyang identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT fanzhang identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT chaozhaoliang identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT chaozhaoliang identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis AT zhutingtong identifyinglongnoncodingrnaofprostatecancerassociatedwithradioresponsebycomprehensivebioinformaticsanalysis |
_version_ |
1724830369280163840 |