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.

Figure 1.

(A) Box plot for normalized gene expression data. The medians (black lines) are almost at the same level, indicating a good performance of normalization. (B) Venn diagram of differentially expressed genes identified from the NP and AF of degenerative intervertebral discs. NP, nucleus pulposus; AF, annulus fibrosus.

Figure 2.

Enriched GO terms for differentially expressed genes from the (A) nucleus pulposus and (B) annulus fibrosus. GO, Gene Ontology.

Figure 3.

KEGG pathway enrichment analysis for differentially expressed genes from the (A) nucleus pulposus and (B) annulus fibrosus. ECM, extracellular matrix. KEGG, Kyoto Encyclopedia of Genes and Genomes.

Figure 4.

(A) Enriched protein interaction network modules in a directly acyclic graph. (B) Visualization of input genes and their direct neighbors in an enriched module using a node-link diagram. adjP, P-value following adjustment with the Benjamini-Hochberg correction method; IFIT, interferon-induced protein with tetratricopeptide repeats.

Figure 5.

The integrated DEG-microRNA regulatory and DEG-DEG interaction network. DEGs, differentially expressed genes; miR, microRNA; COL6A2, collagen type VI α2; RAP1A, RAP1A, member of RAS oncogene family; FOXF2, forkhead box F2.