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An integrated analysis for long noncoding RNAs and microRNAs with the mediated competing endogenous RNA network in papillary renal cell carcinoma

Authors Huang CG, Yuan NJ, Wu LY, Wang XF, Dai JQ, Song P, Li FX, Xu CB, Zhao XH

Received 17 May 2017

Accepted for publication 9 July 2017

Published 14 August 2017 Volume 2017:10 Pages 4037—4050


Checked for plagiarism Yes

Review by Single-blind

Peer reviewers approved by Dr Colin Mak

Peer reviewer comments 2

Editor who approved publication: Dr XuYu Yang

Chuiguo Huang,1,* Naijun Yuan,2,* Liying Wu,3 Xiaofu Wang,1 Junqiang Dai,4 Pan Song,5 Fengxi Li,6 Changbao Xu,1 Xinghua Zhao1

1Department of Urology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 2College of Traditional Chinese Medicine of Jinan University, Institute of Integrated Traditional Chinese and Western Medicine of Jinan University, Guangzhou, 3Department of Nephrology, The Second Affiliated Hospital of Hainan Medical College, Hainan, 4Department of Neurosurgery, The Second Affiliated Hospital of Lanzhou University, Lanzhou, 5Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 6Department of General Surgery, The First Affiliated Hospital of Guangxi Medical University, Guangxi, People’s Republic of China

*These authors contributed equally to this work

Abstract: Papillary renal cell carcinoma (PRCC) is the second most common subtype of renal cell carcinoma, and it lacks effective therapeutic targets and prognostic molecular biomarkers. Attention has been increasingly focused on long noncoding RNAs (lncRNAs), which can act as competing endogenous RNA (ceRNA) to compete for shared microRNAs (miRNAs) in the tumorigenesis of human tumors. Therefore, to clarify the functional roles of lncRNAs with respect to the mediated ceRNA network in PRCC, we comprehensively integrated expression profiles, including data on mRNAs, lncRNAs and miRNAs obtained from 289 PRCC tissues and 32 normal tissues in The Cancer Genome Atlas. As a result, we identified 2,197 differentially expressed mRNAs (DEmRNAs) and 84 differentially expressed miRNAs (DEmiRNAs) using a threshold of |log2 (fold change)| >2.0 and an adjusted P-value <0.05. To determine the hub DEmRNAs that could be key target genes, a weighted gene co-expression network analysis was performed. A total of 28 hub DEmRNAs were identified as potential target genes. Seven dysregulated DEmiRNAs were identified that were significantly associated with the 28 hub potential target genes. In addition, we found that 16 differentially expressed lncRNAs were able to interact with the DEmiRNAs. Finally, we used Cytoscape software to visualize the ceRNA network with these differently expressed molecules. From these results, we believe that the identified ceRNA network plays a crucial role in the process of PRCC deterioration, and some of the identified genes are strongly related to clinical prognosis.

Keywords: papillary renal cell carcinoma, The Cancer Genome Atlas, weighted gene co-expression network analysis, long noncoding RNA, competing endogenous RNA network, survival prognosis

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