Abstract：
BACKGROUND: Mesenchymal stem cells (MSCs) possess the potential to differentiate into chondrocytes, which makes them an ideal source for healing cartilage defects. Here, we seek to identify the essential genes participating in MSCs chondrogenesis.
METHODS: Human MSCs were induced for chondrogenesis for 7, 14, and 21 days using a high-density micromass culture system, and RNA was extracted for RNA-seq.
RESULTS: A total of 6247 differentially expressed genes (DEGs) were identified on day 7, and 85 DEGs were identified on day 14. However, no significant DEGs was identified on 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 inflammation-related genes were enriched, including CXCL8, TLR2, and CCL20. We also conducted protein-protein interaction (PPI) networks analysis using the 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, identifying the top 5 TFs: LEF1, FOXO1, RORA, BHLHE41, and SOX5. We demonstrated one particular TF, RORA, in promoting early MSCs chondrogenesis.
CONCLUSIONS: Taken together, our results suggested that these DEGs may have a complex effect on MSCs chondrogenesis both synergistically and solitarily.
METHODS: Human MSCs were induced for chondrogenesis for 7, 14, and 21 days using a high-density micromass culture system, and RNA was extracted for RNA-seq.
RESULTS: A total of 6247 differentially expressed genes (DEGs) were identified on day 7, and 85 DEGs were identified on day 14. However, no significant DEGs was identified on 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 inflammation-related genes were enriched, including CXCL8, TLR2, and CCL20. We also conducted protein-protein interaction (PPI) networks analysis using the 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, identifying the top 5 TFs: LEF1, FOXO1, RORA, BHLHE41, and SOX5. We demonstrated one particular TF, RORA, in promoting early MSCs chondrogenesis.
CONCLUSIONS: Taken together, our results suggested that these DEGs may have a complex effect on MSCs chondrogenesis both synergistically and solitarily.
摘要：
背景：间充质干细胞（MSCs）具有分化为软骨细胞的潜能，这使得它们成为治疗软骨缺陷的理想来源。这里,我们试图鉴定参与MSCs软骨形成的重要基因。
方法：使用高密度微团培养系统诱导人MSCs软骨形成7、14和21天，并提取RNA用于RNA-seq。
结果:在第7天鉴定了总共6247个差异表达基因(DEGs),在第14天鉴定了85个DEGs。然而,在第21天未发现显著的DEGs。第7天的前30个DEGs，包括COL9A3，COL10A1和CILP2，与细胞外基质组织密切相关。虽然第14天的前30个DEG显示炎症相关基因被富集，包括CXCL8、TLR2和CCL20。我们还使用搜索工具进行了蛋白质-蛋白质相互作用（PPI）网络分析，以检索相互作用基因（STRING）数据库并确定关键枢纽基因，包括CXCL8、TLR2、CCL20和MMP3。还分析了转录因子，确定前5个TF：LEF1、FOXO1、RORA、BHLHE41和SOX5。我们展示了一个特定的TF，罗拉,促进早期MSCs软骨形成。
结论：综合来看，我们的结果表明，这些DEGs可能对MSCs软骨形成具有协同和孤立的复杂作用。
方法：使用高密度微团培养系统诱导人MSCs软骨形成7、14和21天，并提取RNA用于RNA-seq。
结果:在第7天鉴定了总共6247个差异表达基因(DEGs),在第14天鉴定了85个DEGs。然而,在第21天未发现显著的DEGs。第7天的前30个DEGs，包括COL9A3，COL10A1和CILP2，与细胞外基质组织密切相关。虽然第14天的前30个DEG显示炎症相关基因被富集，包括CXCL8、TLR2和CCL20。我们还使用搜索工具进行了蛋白质-蛋白质相互作用（PPI）网络分析，以检索相互作用基因（STRING）数据库并确定关键枢纽基因，包括CXCL8、TLR2、CCL20和MMP3。还分析了转录因子，确定前5个TF：LEF1、FOXO1、RORA、BHLHE41和SOX5。我们展示了一个特定的TF，罗拉,促进早期MSCs软骨形成。
结论：综合来看，我们的结果表明，这些DEGs可能对MSCs软骨形成具有协同和孤立的复杂作用。
