Identification of key genes associated with the effect of osmotic stimuli on intervertebral discs using microarray analysis

Abstract

Abstract. The present study aimed to explore the effect of osmotic stimuli on intervertebral discs (IVDs) using microarray analysis. Gene expression dataset GSE1648 was downloaded from the Gene Expression Omnibus database. There were 11 IVD cell samples in this dataset, which included 4 hyperosmotic stimuli samples, 3 hypoosmotic stimuli samples and 4 isosmotic stimuli samples. The differentially expressed genes (DEGs) in hyperosmotic or hypoosmotic IVD cells (designated DEGs-hyper or DEGs-hypo) were identified, compared with isosmotic cells, using the limma package of R software. The Database for Annotation, Visualization and Integrated Discovery was used to perform a Gene Ontology (GO) term enrichment analysis for the DEG sets. Protein-protein interaction (PPI) network and microRNA (miRNA) gene-regulatory network data for the DEG sets were obtained using the Human Protein Reference Database (HPRD) and the TargetScan database, respectively, and these networks were constructed and visualized using Cytoscape software. There was a total of 43 DEGs in DEGs-hyper and 9 in DEGs-hypo. Analysis of DEGs-hyper revealed that 41 GO terms were significantly enriched. In total, 376 pairs and 382 nodes were involved in the PPI network, and 1,314 miRNA-gene pairs and 422 nodes were contained in the miRNA-gene-regulated network. The results of the present study indicated that potential target genes (including NCOA3, SOS1, XPO1, ZBTB18, EFNB2 and SOBP) may be involved in the effect of osmotic stimuli on IVD, and the biological processes of apoptosis and cell death may be associated with the effect of high osmolality on IVD disease. The potential targets identified in the present study are more reliable than those identified by previous studies.

The Roles of circRNAs in Intervertebral Disc Degeneration: Inflammation, Extracellular Matrix Metabolism, and Apoptosis

“…However, at present, more researches suggested that IDD is genetically driven [11][12][13][14]. They found that there are many significantly differentially expressed genes (DEGs) in IDD tissues compared with normal tissues [15][16][17][18]. Among this, DEGs, noncoding RNAs (ncRNAs), as an important regulatory element, play critical roles in IDD [19].…”

Genomic signatures of adaptation to novel environments: hatchery and life history-associated loci in landlocked and anadromous Atlantic salmon (Salmo salar)

“…3B, 3C). ZBTB18 is a transcriptional repressor involved in a wide variety of functions including brain and muscle development (Yokoyama et al 2009; Okado 2019) and is also differentially expressed in response to hyperosmotic conditions in cell culture (Boyd et al 2005;Ni et al 2017). Differentiation at multiple SNPs within this gene between landlocked and anadromous populations may be related to differences in growth and development (e.g., age and size at maturity; Riley and Power 1987;Hutchings et al 2019) or to differences in salinity between the two environments.…”