Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma
Abstract Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet...
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doaj-a845c54b9bd346c7a0c0abe93fe0dc6c2021-04-02T12:31:57ZengBMCBMC Medical Genomics1755-87942020-07-0113111610.1186/s12920-020-00757-2Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinomaArash Poursheikhani0Mohammad Reza Abbaszadegan1Negin Nokhandani2Mohammad Amin Kerachian3Medical Genetics Research Center, Mashhad University of Medical SciencesMedical Genetics Research Center, Mashhad University of Medical SciencesDepartment of Immunology, School of Medicine, University of Golestan Medical SciencesMedical Genetics Research Center, Mashhad University of Medical SciencesAbstract Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an urgent need to indicate promising potential diagnostic and prognostic biomarkers in COAD patients. Methods In the current study, level 3 RNA-Seq and miR-Seq data and corresponding clinical data of colon adenocarcinoma (COAD) were retrieved from the TCGA database. The “limma” package in R software was utilized to indicate the differentially expressed genes. For in silico functional analysis, GO and KEGG signaling pathways were conducted. PPI network was constructed based on the STRING online database by Cytoscape 3.7.2. A ceRNA network was also constructed by “GDCRNATools” package in R software. Kaplan-Meier survival analysis (log-rank test) and ROC curve analysis were used to indicate the diagnostic and prognostic values of the biomarkers. Results The differential expression data demonstrated that 2995 mRNAs, 205 lncRNAs, and 345 miRNAs were differentially expressed in COAD. The GO and KEGG pathway analysis indicated that the differentially expressed mRNAs were primarily enriched in canonical processes in cancer. The PPI network showed that the CDKN2A, CCND1, MYC, E2F, CDK4, BRCA2, CDC25B, and CDKN1A proteins were the critical hubs. In addition, the Kaplan-Meier analysis revealed that 215 mRNAs, 14 lncRNAs, and 39 miRNAs were associated with overall survival time in the patients. Also, the ceRNA network data demonstrated that three lncRNAs including MIR17HG, H19, SNHG1, KCNQ1OT1, MALAT1, GAS5, SNHG20, OR2A1-AS1, and MAGI2-AS3 genes were involved in the development of COAD. Conclusions Our data suggested several promising lncRNAs in the diagnosis and prognosis of patients with COAD.http://link.springer.com/article/10.1186/s12920-020-00757-2Colorectal cancerTumorigenesisLong non-coding RNAsMicroRNA |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Arash Poursheikhani Mohammad Reza Abbaszadegan Negin Nokhandani Mohammad Amin Kerachian |
spellingShingle |
Arash Poursheikhani Mohammad Reza Abbaszadegan Negin Nokhandani Mohammad Amin Kerachian Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma BMC Medical Genomics Colorectal cancer Tumorigenesis Long non-coding RNAs MicroRNA |
author_facet |
Arash Poursheikhani Mohammad Reza Abbaszadegan Negin Nokhandani Mohammad Amin Kerachian |
author_sort |
Arash Poursheikhani |
title |
Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma |
title_short |
Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma |
title_full |
Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma |
title_fullStr |
Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma |
title_full_unstemmed |
Integration analysis of long non-coding RNA (lncRNA) role in tumorigenesis of colon adenocarcinoma |
title_sort |
integration analysis of long non-coding rna (lncrna) role in tumorigenesis of colon adenocarcinoma |
publisher |
BMC |
series |
BMC Medical Genomics |
issn |
1755-8794 |
publishDate |
2020-07-01 |
description |
Abstract Background Colon adenocarcinoma (COAD) is one of the most common gastrointestinal cancers globally. Molecular aberrations of tumor suppressors and/or oncogenes are the main contributors to tumorigenesis. However, the exact underlying mechanisms of COAD pathogenesis are clearly not known yet. In this regard, there is an urgent need to indicate promising potential diagnostic and prognostic biomarkers in COAD patients. Methods In the current study, level 3 RNA-Seq and miR-Seq data and corresponding clinical data of colon adenocarcinoma (COAD) were retrieved from the TCGA database. The “limma” package in R software was utilized to indicate the differentially expressed genes. For in silico functional analysis, GO and KEGG signaling pathways were conducted. PPI network was constructed based on the STRING online database by Cytoscape 3.7.2. A ceRNA network was also constructed by “GDCRNATools” package in R software. Kaplan-Meier survival analysis (log-rank test) and ROC curve analysis were used to indicate the diagnostic and prognostic values of the biomarkers. Results The differential expression data demonstrated that 2995 mRNAs, 205 lncRNAs, and 345 miRNAs were differentially expressed in COAD. The GO and KEGG pathway analysis indicated that the differentially expressed mRNAs were primarily enriched in canonical processes in cancer. The PPI network showed that the CDKN2A, CCND1, MYC, E2F, CDK4, BRCA2, CDC25B, and CDKN1A proteins were the critical hubs. In addition, the Kaplan-Meier analysis revealed that 215 mRNAs, 14 lncRNAs, and 39 miRNAs were associated with overall survival time in the patients. Also, the ceRNA network data demonstrated that three lncRNAs including MIR17HG, H19, SNHG1, KCNQ1OT1, MALAT1, GAS5, SNHG20, OR2A1-AS1, and MAGI2-AS3 genes were involved in the development of COAD. Conclusions Our data suggested several promising lncRNAs in the diagnosis and prognosis of patients with COAD. |
topic |
Colorectal cancer Tumorigenesis Long non-coding RNAs MicroRNA |
url |
http://link.springer.com/article/10.1186/s12920-020-00757-2 |
work_keys_str_mv |
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1721568626657460224 |