Gene Expression Profile Alterations during Stem Cell Differentiation into Nucleus Pulposus Cells: An in- Silico Study

Although the degeneration of nucleus pulposus cells (NPCs) is one of the main causes of intervertebral disc degeneration, the molecular complications of this disease have yet to be clarified. The ability of stem cells to differentiate into different types of cells, especially NPCs, has attracted much attention. This study aimed to investigate the role of genes with differential expressions in stem cell differentiation into NPCs and to identify the salient signaling pathways involved. Since there has not been an extensive study on the important genes of NPC cell differentiation, it is necessary to investigate this process.  

RNA- sequencing raw files of stem cell samples and differentiated NPCs with the accession number GSE122429 from the GEO database. The samples were analyzed, and genes with differential expressions were isolated in the R programming language with the Limma package via logarithmic fold changes (logFC) ≠3 and adjusted   P-values < 0.05. Functional analysis was conducted on the signaling pathways and biological processes of the differentially expressed genes using the Enrichr database.

In NPCs, 170 genes were upregulated, and 102 genes were downregulated. The functional analysis revealed that the differentially expressed genes were mostly involved in the extracellular matrix organization, collagen organization, and positive cellular processes. The study of signaling pathways identified the neural crest differentiation pathway as the most significant pathway in the evaluated samples. Considering logFC ≠3, overexpression was detected in MSX2, OLIG3, WNT3A, TWIST1, PAX3, RHOB, CDH6, COL2A1, CDH1, ZIC1, PMP22, SNAI2, and MSX1, all of which are involved in the neural crest differentiation pathway.

Our results should expand the knowledge of the molecular pathways involved in stem cell differentiation into NPCs and proffer new clues to the treatment of intervertebral disc degeneration. Nonetheless, more detailed molecular studies are needed to determine the reliable biomarkers of NPCs