Identification of differentially expressed genes by single-cell transcriptional profiling of umbilical cord and synovial fluid mesenchymal stem cells
Identification of differentially expressed genes by single-cell transcriptional profiling of umbilical cord and synovial fluid mesenchymal stem cells
复制标题
DOI：
10.1111/jcmm.14891
复制
发表时间：
2019-12-17
影响因子：
5.3
通讯作者：
Liu, Qisong
中科院分区：
文献类型：
--
作者：
Jia, Zhaofeng;Wang, Shijin;Liu, Qisong
本研究的目的是通过单细胞rna测序（scRNA-seq）测量人脐带源性间充质干细胞（hUC-MSCs）和人滑膜液源性间充质干细胞（hSF-MSCs）的异质性。使用Chromium （TM）技术，对通过质量控制检查的样品中的hUC-MSCs和hSF-MSCs进行scrna测序。为了确定亚群和激活途径，使用了几种生物信息学工具来分析转录组谱，包括聚类、主成分分析（PCA）、t-分布随机邻居嵌入（t-SNE）、基因集富集分析以及基因本体（GO）和京都基因与基因组百科全书（KEGG）分析。对两组样本进行scrna测序。hUC-MSCs和hSF-MSCs分别有104 761 163条和6 577 715条reads，定位率为60%。基于PCA和t-SNE分析，我们在hUC-MSCs中鉴定出11个亚群，在hSF-MSCs中鉴定出7个亚群。基因集富集分析发现，hUC-MSCs的11个亚群中差异表达基因（DEGs）分别为533、57、32、44、10、319、731、1037、90、25和230个，hSF-MSCs的7个亚群中差异表达基因（DEGs）分别为204、577、30、577、16、57和35个。scRNA-seq不仅能够识别样本集中hUC-MSCs和hSF-MSCs的亚群，而且还提供单个患者hUC-MSCs和hSF-MSCs的数字转录计数。scRNA-seq分析可以阐明MSCs的一些生物学特性，并有助于更好地理解MSCs的多向分化、免疫调节特性和组织修复能力。
The purpose of this study was to measure the heterogeneity in human umbilical cord-derived mesenchymal stem cells (hUC-MSCs) and human synovial fluid-derived mesenchymal stem cells (hSF-MSCs) by single-cell RNA-sequencing (scRNA-seq). Using Chromium (TM) technology, scRNA-seq was performed on hUC-MSCs and hSF-MSCs from samples that passed our quality control checks. In order to identify subgroups and activated pathways, several bioinformatics tools were used to analyse the transcriptomic profiles, including clustering, principle components analysis (PCA), t-Distributed Stochastic Neighbor Embedding (t-SNE), gene set enrichment analysis, as well as Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. scRNA-seq was performed on the two sample sets. In total, there were 104 761 163 reads for the hUC-MSCs and 6 577 715 for the hSF-MSCs, with >60% mapping rate. Based on PCA and t-SNE analyses, we identified 11 subsets within hUC-MSCs and seven subsets within hSF-MSCs. Gene set enrichment analysis determined that there were 533, 57, 32, 44, 10, 319, 731, 1037, 90, 25 and 230 differentially expressed genes (DEGs) in the 11 subsets of hUC-MSCs and 204, 577, 30, 577, 16, 57 and 35 DEGs in the seven subsets of hSF-MSCs. scRNA-seq was not only able to identify subpopulations of hUC-MSCs and hSF-MSCs within the sample sets, but also provided a digital transcript count of hUC-MSCs and hSF-MSCs within a single patient. scRNA-seq analysis may elucidate some of the biological characteristics of MSCs and allow for a better understanding of the multi-directional differentiation, immunomodulatory properties and tissue repair capabilities of MSCs.