Research ArticleOpen Access

Microarray Analysis of Differentially Expressed LncRNAs with Associated Co-Expression and CeRNA Networks in Coronary Heart Disease

Volume 3 - Issue 2

Yi Sun¹,a, Shuna Huang¹,a, Qing Huang¹,a, Guiqing Wu¹, Qishuang Ruan¹, Shaowei Lin¹, Tingxing Zhang³, Huangyuan Li⁴, Siying Wu¹

Author Information Open or Close
- ¹Department of Epidemiology and Health Statistics, the Key Laboratory of Environment and Health among Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, China
- ²Department of Orthopedics, Fujian Medical University Union Hospital
- ³Department of Cardiology, The First Affiliated Hospital of Fujian Medical University, China
- ⁴Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, China
- ^aThese authors contributed equally to this work
*Corresponding author: Siying Wu, Department of Epidemiology and Health Statistics, the Key Laboratory of Environment and Health among Universities and Colleges in Fujian, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, China

*Corresponding author: Huangyuan Li, Department of Preventive Medicine, Fujian Provincial Key Laboratory of Environmental Factors and Cancer, School of Public Health, Fujian Medical University, Minhou County, Fuzhou, China

Received: February 28, 2018; Published: March 26, 2018

DOI: 10.26717/BJSTR.2018.03.000886

Full Text PDF

To view the Full Article Peer-reviewed Article PDF

Abstract

Objectives: The present study aims to explore the expression profiles and biological functions of long-chain noncoding RNA (lncRNA) in coronary heart disease (CHD) and to construct a lncRNA/microRNA (miRNA)/messenger RNA (mRNA) network for mechanism exploration.

Methods: Ten human blood samples (five each from the CHD and control groups) were included. The differentially expressed lncRNAs, miRNAs, and mRNAs were evaluated using microarray. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis for differentially expressed lncRNAs–mRNAs was performed. The miRNAs that interact with differentially expressed lncRNAs were predicted using the miRanda package, whereas the mRNAs with clear biological functions and regulated by miRNAs were predicted using miRWalk2.0. Expression networks, including coding/noncoding gene co-expression, cis-regulation, and lncRNAs-transcription factors (TFs), were constructed using bioinformatics methods and were then combined to form a lncRNA-miRNA-mRNA network..

Results: A total of 320 lncRNAs, 25 miRNAs, and 953 mRNAs were differentially expressed in CHD and healthy control cases. GO and KEGG pathway analysis reveal the role of these differentially regulated lncRNAs. Co-expression analysis showed that hundreds of lncRNAs, including lncRNA HIT000066433, ENST00000450016.1, and NR_028272.1, were correlated with CHD. Cis-regulation indicated that uc003qsf.4 had maximum adjacent coding genes called SOD2 and MYADM. The lncRNA-TF diagram indicated that lncRNA HIT000066433 can regulate mRNA expression through Nkx2-5 TF. Finally, the constructed lncRNA-miRNA-mRNA network confirmed that the RNA interactions show a novel perspective for the mechanisms of CHD.

Conclusion: LncRNAs harbor miRNA response elements and are involved in the pathogenesis and development of CHD.

Keywords: LncRNA-miRNA-mRNA network; Functional enrichment; Co-expression; Microarray analysis; Coronary heart disease

Abbreviations: LncRNA: Long-Chain Non-Coding RNA; CHD: Coronary Heart Disease; miRNA: MicroRNA; mRNA: Messenger RNA; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; DAVID: Database for Annotation Visualization and Integrated Discovery; TFs: lncRNAs-Transcription Factors; ceRNA: Competing Endogenous RNA; MREs: miRNA Response Elements; CNC: Coding-Noncoding Gene Co- Expression