RNA-Seq analysis of chondrocyte transcriptome reveals genetic heterogeneity in LG/J and SM/J murine strains

Summary Objective To investigate the transcriptomic differences in chondrocytes from LG/J (large, healer) and SM/J (small, non-healer) murine strains in an attempt to discern the molecular pathways implicated in cartilage regeneration and susceptibility to osteoarthritis (OA). Design We performed RNA-sequencing on chondrocytes derived from LG/J (n=16) and SM/J (n=16) mice. We validated the expression of candidate genes and compared SNPs between the two mouse strains. We also examined gene expression of positional candidates for ear pinna regeneration and long bone length QTLs that display differences in cartilaginous expression. Results We observed a distinct genetic heterogeneity between cells derived from LG/J and SM/J mouse strains. We found that gene ontologies representing cell development, cartilage condensation, and regulation of cell differentiation were enriched in LG/J chondrocytes. In contrast, gene ontologies enriched in the SM/J chondrocytes were mainly related to inflammation and degeneration. Moreover, we found that multiple validated genes vary in sequence between LG/J and SM/J in coding and highly conserved noncoding regions. Finally, we showed that most QTLs have 20-30% of their positional candidates displaying differential expression between the two strains. Conclusions While the enrichment of pathways related to cell differentiation, cartilage development and cartilage condensation infers superior healing potential of LG/J strain, the enrichment of pathways related to cytokine production, immune cell activation and inflammation entails greater susceptibility of SM/J strain to OA. These data provide novel insights into chondrocyte transcriptome and aid in identification of the quantitative trait genes and molecular differences underlying the phenotypic differences associated with individual QTLs.