PMID- 31845522 OWN - NLM STAT- MEDLINE DCOM- 20210422 LR - 20210422 IS - 1582-4934 (Electronic) IS - 1582-1838 (Print) IS - 1582-1838 (Linking) VI - 24 IP - 2 DP - 2020 Jan TI - Identification of differentially expressed genes by single-cell transcriptional profiling of umbilical cord and synovial fluid mesenchymal stem cells. PG - 1945-1957 LID - 10.1111/jcmm.14891 [doi] AB - 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 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. CI - (c) 2019 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd. FAU - Jia, Zhaofeng AU - Jia Z AUID- ORCID: 0000-0003-2377-6277 AD - Department of Osteoarthropathy and Institute of Orthopedic Research, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University and the First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China. FAU - Wang, Shijin AU - Wang S AD - Department of Orthopaedics, Taian City Central Hospital, Taian, China. FAU - Liu, Qisong AU - Liu Q AD - Institute for Regenerative Medicine, Texas A&M Health Science Center College of Medicine, Temple, TX, USA. LA - eng PT - Journal Article PT - Research Support, Non-U.S. Gov't DEP - 20191217 PL - England TA - J Cell Mol Med JT - Journal of cellular and molecular medicine JID - 101083777 SB - IM MH - *Gene Expression Profiling MH - Gene Expression Regulation MH - Gene Ontology MH - Humans MH - Mesenchymal Stem Cells/*metabolism MH - Principal Component Analysis MH - *Single-Cell Analysis MH - Synovial Fluid/*cytology MH - *Transcription, Genetic MH - Umbilical Cord/*cytology PMC - PMC6991657 OTO - NOTNLM OT - DEGs OT - ScRNA-seq OT - hSF-MSCs OT - hUC-MSCs OT - subpopulations COIS- The authors confirm that there are no conflicts of interest. EDAT- 2019/12/18 06:00 MHDA- 2021/04/23 06:00 PMCR- 2020/01/01 CRDT- 2019/12/18 06:00 PHST- 2019/09/01 00:00 [received] PHST- 2019/11/22 00:00 [revised] PHST- 2019/11/27 00:00 [accepted] PHST- 2019/12/18 06:00 [pubmed] PHST- 2021/04/23 06:00 [medline] PHST- 2019/12/18 06:00 [entrez] PHST- 2020/01/01 00:00 [pmc-release] AID - JCMM14891 [pii] AID - 10.1111/jcmm.14891 [doi] PST - ppublish SO - J Cell Mol Med. 2020 Jan;24(2):1945-1957. doi: 10.1111/jcmm.14891. Epub 2019 Dec 17.