Combining bulk and single-cell RNA-sequencing data to reveal gene expression pattern of chondrocytes in the osteoarthritic knee.
Combining bulk and single-cell RNA-sequencing data to reveal gene expression pattern of chondrocytes in the osteoarthritic knee.
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结合大量和单细胞 RNA 测序数据揭示骨关节炎膝关节软骨细胞的基因表达模式
DOI：
10.1080/21655979.2021.1903207
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发表时间：
2021-12
期刊：
影响因子：
4.9
通讯作者：
Zhao L
中科院分区：
文献类型：
--
作者：
Li X;Liao Z;Deng Z;Chen N;Zhao L
摘要骨性关节炎主要发生在膝关节、髋关节、指间关节和脊柱小关节，以软骨退变为主要特征。现有的膝关节骨关节炎软骨细胞的整体RNA测序(Bulk RNA-seq)和单细胞测序(scRNA-seq)数据分别提供了整个细胞群体和单个细胞的表达谱。在这里，我们旨在对这两种类型的测序数据进行分析，以期对OA有更全面的了解。我们分别比较了GSE114007数据集和GSE104782数据集的整体RNA-seq和scRNA-seq的分析结果，并鉴定了差异表达基因(Deg)。然后，我们试图找到关键的转录因子是一个更正规的术语(TFS)和长的非编码RNA(LncRNA)的调控。我们突出显示了这两类数据同时提示的271个基因，并提供了它们在骨性关节炎中可能的表达模式。其中TWIST2、MYBL2、relA、Jun、KLF4和Pttg1可能是271个基因的关键转录因子。我们还发现，271个基因中的8个lncRNAs以及CyTOR和Nrp1之间的lncRNA调控可能参与了膝骨性关节炎软骨的疼痛和血管化。总之，我们的研究结合了骨性关节炎软骨细胞大量RNA-seq和scRNA-seq数据的分析结果，有助于进一步阐明骨性关节炎发病的分子机制。
ABSTRACT Osteoarthritis (OA) occurs mostly in the knees, hips, finger interphalangeal joints, and spinal facet joints, and is characterized by cartilage degeneration. The existing bulk RNA sequencing (bulk RNA-seq) and single-cell sequencing (scRNA-seq) data for chondrocytes in the osteoarthritic knee joint provide the expression profiles of entire cell populations and individual cells, respectively. Here, we aimed to analyze these two types of sequencing data in order to obtain a more comprehensive understanding of OA. We compared the analysis results of bulk RNA-seq and scRNA-seq from the dataset GSE114007 and the dataset GSE104782, respectively, and identified the differentially expressed genes (DEGs). Then, we tried to find the key The transcription factor is a more fomal term (TFs) and long non-coding RNA (lncRNA) regulation. We highlighted 271 genes that were simultaneously suggested by these two types of data and provided their possible expression pattern in OA. Among the 271 genes, we identified 14 TFs, and TWIST2, MYBL2, RELA, JUN, KLF4, and PTTG1 could be the key TFs for the 271 genes. We also found that 8 lncRNAs among the 271 genes and the lncRNA regulation between CYTOR and NRP1 could contribute to the pain and vascularization of cartilage in the osteoarthritic knee. In short, our research combined the analysis results of bulk RNA-seq and scRNA-seq data for OA chondrocytes, which will contribute to further elucidation of the molecular mechanisms of OA pathogenesis.
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