Pluto Bioinformatics

GSE128490: RNA-Seq Analysis of Murine Chondrocytes Reveals Pathways Associated with Cartilage Regeneration and Degeneration

Bulk RNA sequencing

Objectives: Understanding the molecular mechanisms underlying cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). We report transcripts and pathways differentially expressed in chondrocytes obtained from genotypically and phenotypically distinct mouse strains.; ; Methods: We performed RNA-sequencing and computational analysis on chondrocytes derived from LG/J (large, healer, n=16) and SM/J (small, non-healer, n=16) mouse strains. We validated the expression of candidate genes using real-time PCR and immunostaining.; ; Results: Of those nearly 6,000 differentially expressed genes between LG/J and SM/J, 138 genes (99 protein-coding) were up-regulated and 145 (103 protein-coding) were down-regulated with log2 fold changes of 2 or more. Interestingly, we found the top up-regulated gene ontology biological pathways in the chondrocytes from the LG/J mice were related to chondrocyte development, cartilage condensation, and regulation of chondrocyte differentiation. In contrast, the top upregulated pathways in the SM/J mice were mostly inflammation related. Real-time PCR confirmed the expression pattern of a number of differentially expressed genes. Immunostaining of two candidate genes revealed that Tnfrsf23 and Car2 were respectively increased in LG/J and SM/J strains.; ; Conclusions: The enrichment of genes and pathways related chondrocyte differentiation, cartilage development and cartilage condensation in LG/J appear to be responsible for their superior healing potential. The enrichment of pathways related to cytokine production, immune cell activation and inflammation in SM/J suggests a compromised chondrocyte proliferation and/or survival ability and a higher sensitivity to inflammation and OA. Tnfrsf23 and Car2 warrant further investigation to discern their specific role(s) in chondrocyte function and OA. SOURCE: Muhammad Farooq RaiLinda Sandell Washington University School of Medicine