Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis

Zhenxin Huo; Hao Li; Lijun Tian; Jianhua Li; Kaihui Zhang; Zhenhua Li; Guowang Li; Lilong Du; Haiwei Xu; Baoshan Xu

doi:10.1155/2021/8352683

Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis

Biomed Res Int. 2021 Aug 4:2021:8352683. doi: 10.1155/2021/8352683. eCollection 2021.

Authors

Zhenxin Huo^{1

2}, Hao Li^{1

2}, Lijun Tian^{2

3}, Jianhua Li⁴, Kaihui Zhang^{1

2}, Zhenhua Li^{1

2}, Guowang Li^{1

2}, Lilong Du^{1

2}, Haiwei Xu^{1

2}, Baoshan Xu^{1

2}

Affiliations

¹ Department of Minimally Invasive Spine Surgery, Tianjin Hospital, 406. No, Jiefangnan Road, Hexi District, Tianjin, China 300211.
² Graduate School, Tianjin Medical University, 22 Qixiangtai Road, Tianjin, China.
³ The First Affiliated Hospital of Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, Inner Mongolia, China 014010.
⁴ Department of Orthopaedics, Tianjin Haihe Hospital, Tianjin 300350, China.

Abstract

Background: The competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms are known to play a pivotal role in intervertebral disc degeneration (IDD). Our research intended to establish a ceRNA regulatory network related to IDD through bioinformatics analyses.

Methods: The expression profiles of circRNA, miRNA, and mRNA were obtained from the public Gene Expression Omnibus (GEO) datasets. Then, we use sequence-based bioinformatics methods to select differentially expressed mRNAs (DEmRNAs), microRNAs (DEmiRNAs), or circRNAs (DEcircRNAs) related to IDD. We used ChEA3 to verify the targets of transcription factors (TFs). Then, we used DAVID to annotate the DEmRNAs. Finally, we constructed a potentially circRNA-miRNA-mRNA network related to IDD by predicting in the database (ENCORI, TargetScan, miRecords, miRmap, and circBank).

Results: We identified 31 common DEmRNAs by Venn analysis, of which MMP2 was regarded as the key hub genes. Simultaneously, miR-423-5p and miR-185-5p were predicted as the upstream molecules of MMP2. Furthermore, a total of six DEcircRNAs were predicted as the upstream circRNAs of miR-423-5p and miR-185-5p. Then, a potential circRNA-miRNA-mRNA network related to IDD was constructed by bioinformatics analysis.

Conclusion: A comprehensive ceRNA regulatory network was constructed, which was found to be significant in IDD progression.

MeSH terms

Computational Biology / methods*
Disease Progression
Gene Expression Profiling
Gene Regulatory Networks
Humans
Intervertebral Disc Degeneration / genetics*
Matrix Metalloproteinase 2 / genetics*
MicroRNAs / genetics*
Molecular Sequence Annotation
RNA, Circular / genetics*
RNA, Messenger / genetics

Substances

MIRN185 microRNA, human
MIRN423 microRNA, human
MicroRNAs
RNA, Circular
RNA, Messenger
MMP2 protein, human
Matrix Metalloproteinase 2