Open AccessAn lncRNA-miRNA-mRNA-ceRNA network regulates intervertebral disc degeneration: A bioinformatics study based on the dataset analysis
Author(s) -
Xutao Fan,
Guowu Chen,
Fengyu Ma,
Bao X. Qi,
Yanhu Liang,
Pihao Gopng,
Chunyang Meng
Publication year - 2021
Publication title -
general physiology and biophysics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.376
H-Index - 39
eISSN - 1338-4325
pISSN - 0231-5882
DOI - 10.4149/gpb_2021013
Subject(s) - competing endogenous rna , microrna , intervertebral disc , bioinformatics , messenger rna , computational biology , biology , rna , gene , genetics , long non coding rna , anatomy
Intervertebral disc degeneration (IDD) leads to low back pain (LBP). This study aimed to determine the regulation of IDD by competing endogenous RNAs (ceRNAs). We obtained the GSE63492, GSE124272, and GSE129789 datasets from the Gene Expression Omnibus database. The changes of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in IDD were characterized. The significantly changed mRNAs were subjected to protein-protein interaction analysis using the STRING database, and its functions and involved pathways were analyzed using the DAVID database and gene set enrichment analysis (GSEA). The significant changed lncRNAs, miRNAs and mRNAs were linked in a ceRNA network based on their interactions - predicted by Starbase and miRWalk. Differentially methylated loci of significantly changed mRNAs in early and advanced IDD were compared using the GSE129789 dataset. We identified 245 significantly changed mRNAs, 133 lncRNAs, and 228 miRNAs between patients with IDD and normal individuals. GSEA suggested that 17 pathways related to cell proliferation were activated while 35 cell signaling and immune-related pathways were suppressed in IDD. The following ceRNA network in IDD was built: LINC00665/hsa-miR-7-5p/FZD3, ZNF549; LINC00665/hsa-let-7e-5p/FZD3, ACVR2B; TRG-AS1/hsa-miR-574-5p/ACVR2B, P3H2; TRG-AS1/ hsa-let-7e-5p/FZD3, ACVR2B; and ZNF571-AS1/let-7e-5p/ACVR2B, FZD3. A lncRNA-miRNAmRNA ceRNA network which might regulate the progression of IDD was developed.