Gene expression profile identifies potential biomarkers for human intervertebral disc degeneration

Abstract

The present study aimed to reveal the potential genes associated with the pathogenesis of intervertebral disc degeneration (IDD) by analyzing microarray data using bioinformatics. Gene expression profiles of two regions of the intervertebral disc were compared between patients with IDD and controls. GSE70362 containing two groups of gene expression profiles, 16 nucleus pulposus (NP) samples from patients with IDD and 8 from controls, and 16 annulus fibrosus (AF) samples from patients with IDD and 8 from controls, was downloaded from the Gene Expression Omnibus database. A total of 93 and 114 differentially expressed genes (DEGs) were identified in NP and AF samples, respectively, using a limma software package for the R programming environment. Gene Ontology (GO) function enrichment analysis was performed to identify the associated biological functions of DEGs in IDD, which indicated that the DEGs may be involved in various processes, including cell adhesion, biological adhesion and extracellular matrix organization. Pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) demonstrated that the identified DEGs were potentially involved in focal adhesion and the p53 signaling pathway. Further analysis revealed that there were 35 common DEGs observed between the two regions (NP and AF), which may be further regulated by 6 clusters of microRNAs (miRNAs) retrieved with WebGestalt. The genes in the DEG-miRNA regulatory network were annotated using GO function and KEGG pathway enrichment analysis, among which extracellular matrix organization was the most significant disrupted biological process and focal adhesion was the most significant dysregulated pathway. In addition, the result of protein-protein interaction network modules demonstrated the involvement of inflammatory cytokine interferon signaling in IDD. These findings may not only advance the understanding of the pathogenesis of IDD, but also identify novel potential biomarkers for this disease.

Effect of optimized collagenase digestion on isolated and cultured nucleus pulposus cells in degenerated intervertebral discs

“…NP comprises mainly of proteoglycans, collagen type II, water, and NP cells, which are responsible for the homeostasis of the NP matrix. [ 5 , 6 ] Furthermore, NP is derived from mid-mesoderm notochordal structures, and has been reported to be affected by age-associated IVDD, [ 7 – 9 ] combined with decreased cellularity and water content, loss of proteoglycans in the extracellular matrix, and increased matrix stiffness. [ 10 ]…”

β‑ecdysterone protects against apoptosis by promoting autophagy in nucleus pulposus cells and ameliorates disc degeneration

“…β-ecdysterone regulates the expression of degeneration-associated genes via autophagy. Decrease in ECM proteins including aggrecan, collagen II and other factors often results in IDD (26,27). To additionally explore the degeneration of nucleus pulposus cells, the expression levels of major ECM synthesis genes (Col2a1 and aggrecan) and ECM degrading genes (MMP-3 and Adamts5) in nucleus pulposus cells were examined.…”

Peer Review #1 of "Identification of hub genes and small-molecule compounds related to intracerebral hemorrhage with bioinformatics analysis (v0.2)"

“…We downloaded the series matrix file dataset of GSE24265, and subsequently transformed the gene probes of the platform to gene names by referencing the GPL570 platform. Both the normalization of the data and screening of the DEGs were performed using the limma package in the R language (version 3.5.1) (Guo et al 2017). To identify the genes with significant differences in the fold change of expression, we set the screening criteria to filter genes with a fold change (FC) value of (|log2FC|) > 2 and a P-value of < 0.05.…”