Oncotarget

Research Papers:

Comprehensive analysis of differentially expressed profiles of lncRNAs and circRNAs with associated co-expression and ceRNA networks in bladder carcinoma

Mengge Huang _, Zhenyu Zhong, Mengxin Lv, Jing Shu, Qiang Tian and Junxia Chen

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Oncotarget. 2016; 7:47186-47200. https://doi.org/10.18632/oncotarget.9706

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Abstract

Mengge Huang1,*, Zhenyu Zhong2,*, Mengxin Lv3, Jing Shu4, Qiang Tian5, Junxia Chen3

1College of Clinical Medicine, Southwest Medical University, Luzhou 646000, China

2The First Clinical College, Chongqing Medical University, Chongqing 400016, China

3Department of Cell Biology and Genetics, Chongqing Medical University, Chongqing 400016, China

4Department of Clinical Laboratory, The Affiliated Hospital of Southwest Medical University, Luzhou 646000, China

5Department of Cell Biology and Genetics, Southwest Medical University, Luzhou 646000, China

*These authors have contributed equally to this work

Correspondence to:

Qiang Tian, email: [email protected]

Junxia Chen, email: [email protected]

Keywords: lncRNA, circRNA, ceRNA, microarray, bladder carcinoma

Received: February 10, 2016     Accepted: May 16, 2016     Published: May 30, 2016

ABSTRACT

Accumulating evidences indicate that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) play important roles in tumorigenesis. However, the mechanisms remain largely unknown. To explore lncRNAs and circRNAs expression profiling and their biological functions in bladder cancer, we surveyed the lncRNA/circRNA and mRNA expression profiles of bladder cancer and para-cancer tissues using microarray for four patients. Thousands of significantly changed lncRNAs and mRNAs as well as hundreds of circRNAs were identified. Five dysregulated lncRNAs and four mRNAs were confirmed by quantitative real-time PCR in 30 pairs of samples. GO and KEGG pathway enrichment analyses were executed to determine the principal functions of the significantly deregulated genes. Further more, we constructed correlated expression networks including coding-noncoding co-expression (CNC), competing endogenous RNAs (ceRNA), cis regulation, lncRNAs-transcription factor (TF)-mRNA with bioinformatics methods. Co-expression analysis showed lncRNA APLP2 expression is correlated with apoptosis-related genes, including PTEN and TP53INP1. CeRNA network inferred that lncRNA H19 and circRNA MYLK could bind competitively with miRNA-29a-3p increasing target gene DNMT3B, VEGFA and ITGB1 expressions. Moreover, the nearby genes pattern displayed that overexpressing ADAM2 and C8orf4 are cis-regulated by lncRNA RP11-359E19.2, involving in progression of bladder cancer. In addition, lncRNAs-TF-mRNA diagram indicated that lncRNA BC041488 could trans-regulate CDK1 mRNA expression through SRF transcription factor. Taken together, these results suggested lncRNAs and circRNAs could implicate in the pathogenesis and development of bladder cancer. Our findings provide a novel perspective on lncRNAs and circRNAs and lay the foundation for future research of potential roles of lncRNAs and circRNAs in bladder carcinoma.


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