Department of Orthopedic Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, PR China; Department of Orthopaedic Surgery, School of Medicine, Duke University, Durham, NC, USA.
Department of Orthopedic Surgery, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan Province, PR China.
Osteoarthritis Cartilage. 2022 Mar;30(3):475-480. doi: 10.1016/j.joca.2021.12.007. Epub 2021 Dec 29.
OBJECTIVES: To reveal the heterogeneity of different cell types of osteoarthritis (OA) synovial tissues at a single-cell resolution, and determine by novel methodology whether bulk-RNA-seq data could be deconvoluted to create in silico scRNA-seq data for synovial tissue analyses. METHODS: OA scRNA-seq data (102,077 synoviocytes) were provided by 17 patients undergoing total knee arthroplasty; 9 tissues with matched scRNA-seq and bulk RNA-seq data were used to evaluate six in silico gene deconvolution tools. Predicted and observed cell types and proportions were compared to identify the best deconvolution tool for synovium. RESULTS: We identified seven distinct cell types in OA synovial tissues. Gene deconvolution identified three (of six) platforms as suitable for extrapolating cellular gene expression from bulk RNA-seq data. Using paired scRNA-seq and bulk RNA-seq data, an "arthritis" specific signature matrix was created and validated to have a significantly better predictive performance for synoviocytes than a default signature matrix. Use of the machine learning tool, Cell-type Identification By Estimating Relative Subsets of RNA Transcripts x (CIBERSORTx), to analyze rheumatoid arthritis (RA) and OA bulk RNA-seq data yielded proportions of T cells and fibroblasts that were similar to the gold standard observations from RA and OA scRNA-seq data, respectively. CONCLUSION: This novel study revealed heterogeneity of synovial cell types in OA and the feasibility of gene deconvolution for synovial tissue.
目的:以单细胞分辨率揭示骨关节炎(OA)滑膜组织中不同细胞类型的异质性,并通过新方法确定批量 RNA-seq 数据是否可以进行去卷积,以创建滑膜组织分析的虚拟 scRNA-seq 数据。
方法:OA scRNA-seq 数据(102077 个滑膜细胞)由 17 名接受全膝关节置换术的患者提供;使用 9 个具有匹配 scRNA-seq 和批量 RNA-seq 数据的组织来评估六种虚拟基因去卷积工具。比较预测和观察到的细胞类型和比例,以确定用于滑膜的最佳去卷积工具。
结果:我们在 OA 滑膜组织中鉴定出七种不同的细胞类型。基因去卷积确定了三个(六个中的三个)平台适合从批量 RNA-seq 数据推断细胞基因表达。使用配对的 scRNA-seq 和批量 RNA-seq 数据,创建并验证了一个“关节炎”特异性特征矩阵,该矩阵对滑膜细胞具有比默认特征矩阵更好的预测性能。使用机器学习工具 Cell-type Identification By Estimating Relative Subsets of RNA Transcripts x(CIBERSORTx)分析类风湿关节炎(RA)和 OA 批量 RNA-seq 数据,得出的 T 细胞和成纤维细胞比例分别与 RA 和 OA scRNA-seq 数据的金标准观察结果相似。
结论:这项新研究揭示了 OA 滑膜细胞类型的异质性以及滑膜组织基因去卷积的可行性。
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