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The construction and analysis of ceRNA networks in invasive breast cancer: a study based on The Cancer Genome Atlas

Authors Gao C, Li H, Zhuang J, Zhang H, Wang K, Yang J, Liu C, Liu L, Zhou C, Sun C

Received 3 August 2018

Accepted for publication 24 October 2018

Published 17 December 2018 Volume 2019:11 Pages 1—11

DOI https://doi.org/10.2147/CMAR.S182521

Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Colin Mak

Peer reviewer comments 2

Editor who approved publication: Dr Beicheng Sun


Chundi Gao,1,* Huayao Li,1,* Jing Zhuang,2,3 HongXiu Zhang,4 Kejia Wang,5 Jing Yang,2 Cun Liu,6 Lijuan Liu,2,3 Chao Zhou,2,3 Changgang Sun2,3

1College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People’s Republic of China; 2Department of Oncology, Weifang Traditional Chinese Hospital, Weifang 261041, People’s Republic of China; 3Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang 261031, People’s Republic of China; 4Institute of Virology, Jinan Center for Disease Control and Prevention, Jinan 250021, People’s Republic of China; 5College of Basic Medicine, Qingdao University, Qingdao 266071, People’s Republic of China; 6College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250014, People’s Republic of China

*These authors contributed equally to this work

Background: Studies have shown that long noncoding RNAs (lncRNAs) make up the major proportion of the ceRNA network and can regulate gene expression by competitively binding to miRNAs. This reveals the existence of an RNA-miRNA regulatory pathway and is of great biological significance. CeRNAs, as competitive endogenous RNAs, have revealed a new mechanism of interaction between RNAs. Until now, the role of lncRNA-mediated ceRNAs in breast cancer and their regulatory mechanisms have been elucidated to some extent.
Purpose: In this study, comprehensive analysis of large-scale invasive breast cancer samples in TCGA were conducted to further explore the developmental mechanism of invasive breast cancer and the potential predictive markers for invasive breast cancer prognosis in the ceRNA network.
Methods: Abnormal expression profiles of invasive breast cancer associated mRNAs, lncRNAs and miRNAs were obtained from the TCGA database. Through further alignment and prediction of target genes, an abnormal lncRNA-miRNA-mRNA ceRNA network was constructed for invasive breast cancer. Through the overall survival analysis, Identification prognostic biomarkers for invasive breast cancer patients,In addition, we used Cytoscape plug-in BinGo for the different mRNA performance functional cluster analysis.
Results: Differential analysis revealed that 1059 lncRNAs, 86 miRNAs, and 2138 mRNAs were significantly different in invasive breast cancer samples versus normal samples. Then we construct an abnormal lncRNA-miRNA-mRNA ceRNA network for invasive breast cancer, consisting of 90 DElncRNAs, 18 DEmiRNAs and 26 DEmRNAs.Further, 4 out of 90 lncRNAs, 3 out of 26 mRNAs, and 2 out of 18 miRNAs were useful as prognostic biomarkers for invasive breast cancer patients (P value < 0.05). It is worth noting that based on the ceRNA network, we found that the LINC00466-Hsa-mir-204- NTRK2 LINC00466-hsa-mir-204-NTRK2 axis was present in 9 RNAs associated with the prognosis of invasive breast cancer.
Conclusion:
This study provides an effective bioinformatics basis for further understanding of the molecular mechanism of invasive breast cancerand for predicting outcomes, which can guide the use of invasive breast cancerdrugs and subsequent related research.

Keywords: invasive breast cancer, cancer genome atlas, lncRNA–miRNA–mRNA ceRNA network, bioinformatics, diagnosis and prognosis biomarkers

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