Bioinformatics-based analysis of the microarray data on intervertebral disc degeneration / 医学研究生学报

ABSTRACT

Objective MicroRNAs (miRNA) play an important role in the development and progression of intervertebral disc degeneration (IDD), but the underlying mechanisms remain unclear. This study was to search for differentially expressed miRNAs and predict their target genes in the degenerative intervertebral disc tissue. Methods Data on the miRNA expression profile in the nucleus pulposus of the intervertebral disc were downloaded from the GEO database, involving nucleus pulposus samples from 3 cases of IDD and normal nucleus pulposus samples from another 3 patients with new traumatic lumbar fracture. Differentially expressed microRNAs were identified in the nucleus pulposus tissues of the IDD and normal control groups with the R Software, and the target genes significantly differentially expressed in the miRNAs were predicted using the miRWalk Software. The above target genes were enriched in the clusterProfiler package by GO biological function analysis and KEGG pathway analysis. Meanwhile, a protein-protein interaction network of the target genes was constructed with the STRING database and Cytoscape software, and the hub genes were identified. Based on the Pfirrmann grading of IDD, the subjects involved in the GSE23130 data were divided into a control group (≤grade 3, n = 15) and an IDD group (>grade 3, n = 8) followed by analysis of the expression levels of the hub genes. Results A total of 374 differentially expressed miRNAs were identified, 189 up-regulated and 185 down-regulated, with hsa-let-7b-5p most significantly down-regulated. Prediction of the 5 most significantly up- or down-regulated miRNAs showed the highest number of target genes in hsa-let-7b-5p, 85 in all, including GPAT4, E2F2, and PAK1. GO enrichment analysis manifested that these target genes were mainly involved in the biological processes of cell cycle G1/S phase transition and positive regulation of membrane-targeted proteins. The signaling pathways enriched in the target genes mainly included prolactin, insulin, p53 signaling pathways. Ten hub genes were identified by analysis of the PPI network, including CCND2, NRAS, E2F2, E2F6, STX3, CDCA8, RRM2, PPP2R2A, TXLNG and AKT2. The expression levels of CCND2, NRAS, E2F2, E2F6, STX3, CDCA8, RRM2, PPP2R2A and AKT2 in the degenerative intervertebral disc tissue were significantly higher than those in the control group (P < 0.05). Conclusion Significantly reduced expression of hsa-let-7b-5p in the nucleus pulposus tissue of IDD patients may play an important role in IDD by regulating its target genes CCND2, NRAS, etc.