Identifying the Key Genes Regulating Mesenchymal Stem Cells Chondrogenic Differentiation: an in virto study

Mesenchymal stem cells (MSCs) possess the potential of differentiating into chondrocytes, which makes it an ideal source in healing cartilage defects. Here, we want to find out the key genes that participate in MSCs chondrogenesis. Human MSCs were induced for chondrogenesis for 7, 14, and 21 days using high-density micromass culture system and RNA was extracted for RNA-seq. A total of 6247 differentially expressed gene (DEGs) were identified at day 7, and 85 DEGs were identified at day 14. However, no significant DEGs was identified in day 21. The top 30 DEGs at day 7, including COL9A3, COL10A1, and CILP2, are closely related to extracellular matrix organization. While the top 30 DEGs at day 14 revealed that genes related to inflammation were enriched, including CXCL8, TLR2, and CCL20. We also conducted protein-protein interaction (PPI) networks analysis using search tool for the retrieval of interacting genes (STRING) database and identified key hub genes including CXCL8, TLR2, CCL20, and MMP3. The transcriptional factors were also analyzed, and identified top 5 TFs: LEF1, FOXO1, RORA, BHLHE41, SOX5. We demonstrated one particular TF, RORA, in promoting early MSCs chondrogenesis. Taken together, our result suggested that these DEGs may have a complex effect on MSCs chondrogenesis both synergistically and solitarily. Comparative gene expression profiling analysis of RNA-seq data for the chondrogenesis process of human mesenchymal stem cells