Transcriptome signatures reveal candidate key genes in the whole blood of patients with lumbar disc prolapse

Abstract

The present study aimed to investigate differentially expressed genes (DEGs) in whole blood (WB) obtained from patients with lumbar disc prolapse (LDP) and healthy volunteers. A total of 8 patients with LDP and 8 healthy volunteers were recruited. An Agilent SurePrint G3 human gene expression microarray 8×60 K was used to perform the microarray analyses. R was employed to identify DEGs, which were then subjected to bioinformatics analysis, including a Gene Ontology (GO) analysis, Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) network analysis. DEGs in the degenerative annulus fibrosis (AF) and nucleus pulposus (NP) compared with non-degenerative tissues were also identified based on microarray data and the intersections of the three were assessed. Furthermore, reverse transcription-quantitative (RT-q)PCR was performed to confirm the aberrant expression levels of selected DEGs in the WB of all subjects. A total of 161 DEGs between LDP patients and the healthy controls were identified (128 upregulated and 33 downregulated). These DEGs were enriched in 293 biological process, 36 cellular component and 21 molecular function GO terms, as well as in 24 KEGG pathways. The PPI network contained 4 submodules, and Toll-like receptor 4 had the highest degree centrality. A total of 22 DEGs were common to the three groups of DEGs. The RT-qPCR assay confirmed that the expression levels of cytochrome P450 family 27 subfamily A member 1, superoxide dismutase 2, protein disulfide isomerase family A member 4, FKBP prolyl isomerase 11 and ectonucleotide pyrophosphatase/phosphodiesterase 4 were significantly different between the patient group and the volunteer group. In conclusion, several genes were identified as potential biomarkers in WB that should be further explored in future studies to determine their potential application in the clinical treatment and diagnosis of LDP, and the present bioinformatics analysis revealed several GO terms, KEGG pathways and submodules of the PPI network that may be involved in LDP, although the exact mechanisms remain elusive.

Microarray analysis reveals an inflammatory transcriptomic signature in peripheral blood for sciatica

“…In the PPI network, TLR4 had the highest centrality degree. This finding is consistent with our previous research [ 11 ], demonstrating that TLR4 may be essential for the differential expression of genes in the whole blood of patients with lumbar disc prolapse. Of all the Toll-like receptors, TLR4 is the most studied because it plays a major role in the inflammatory response [ 23 ].…”

“…Both grouping methods have pros and cons. Second, we have performed several other similar studies [ 11 , 45 , 46 ], but the results of these studies and the present study were not much the same. All of our studies are cross-sectional studies, and due to the limitations of a cross-sectional study, the results are largely affected by the conditions at the time of the study.…”

“…Patients with any medication record within the previous 3 months were also excluded. Peripheral blood was drawn and collected as described previously [ 11 ]. From each participant, 10 mL of fasting peripheral blood was collected from the left median cubital vein between 7:00 and 7:30 AM.…”

“…Cytoscape software (V3.6.1) was used for visualization of the PPI network. Disconnected nodes were excluded, the centrality degree of the DEGs was calculated, and submodules were clustered, as previously described [ 11 ].…”

Integrated traditional Chinese medicine alleviates sciatica while regulating gene expression in peripheral blood

“…An Agilent SurePrint G3 Microarray (8 × 60 K) was used for the microarray experiment, which was performed by Shanghai Biotech Co. (Shanghai, China). These procedures were described in our previous study [ 16 ].…”