Bioinformatics analyses of a potential miRNA‒mRNA regulatory axis in lumbar degenerative disc disease

Intervertebral disc degeneration (IDD), normally characterized by a loss of nucleus pulposus cells (NPCs), is one of the leading causes of lower back pain and various degenerative spinal disorders and has been regarded as a public health issue because of its heavy social and economic consequences. However, the molecular mechanisms underlying IDD formation and progression are unclear so far, which results in the lack of existing biomarkers or treatments in targeting early degeneration effectively. Novel potential biomarkers for the early diagnosis, prevention and treatment of IDD are urgently needed. In this study, miRNA sequencing and qRT-PCR validation were performed on original clinical nucleus pulposus (NP) tissues from our own IDD patient cohort. Furthermore, we applied bioinformatics analysis to the mRNA expression profiles in NP tissues (GSE186542) and whole blood (GSE124272) from IDD patients. We screened key genes and miRNA regulators by conducting overlap analysis. The results showed that 466 differentially expressed miRNAs, 187 downregulated and 279 upregulated significantly, were identified from miRNA sequencing analysis in NP tissues. Overlap analysis with the predicted miRNA targets and the differentially expressed genes (DEGs) in the GSE186542 database exhibited 27 overlapping genes, among which copine-6 (CPNE6) and beta-1,3-glucuronyltransferase (B3GAT1) overlapped with the DEGs from the whole blood of IDD patients in the GSE124272 database. Further qRT‒PCR results revealed that CPNE6 and B3GAT1 expression was significantly upregulated, but their corresponding miRNA regulators miR-3620-5p and miR-6511b-3p were significantly downregulated in IDD patients. Moreover, cells proliferation was inhibited, but the IL-1β, IL-18 and TNF-α contents were significantly increased, in ATDC5 cells after miR-3620-5p and miR-6511b-3p inhibition. Thus, miR-3620-5p and miR-6511b-3p might be the key effectors in IDD progression by mediating the expression of CPNE6 and B3GAT1 in NP tissues. This newly discovered specific miRNA‑mRNA interactions were identified and validated using our original patient samples, with public datasets used for bioinformatic cross‑validation. It holds huge potential applications for miRNA-based therapies in early diagnosis and treatment of IDD.