Multiplexed analysis of gene expression and chromatin accessibility of human umbilical cord blood using scRNA-Seq and scATAC-Seq

• Published in: Molecular immunology 2022-12, Vol.152, p.207-214
• Main Authors: Hou, Xianliang, Wang, Ying-Lan, Shi, Wei, Hu, Wenlong, Zeng, Zhipeng, Liu, Jiayi, Li, Lian, Cai, Wanxia, Tang, Donge, Dai, Yong
• Format: Article
• Language: English
• Subjects: Gestational week; Single cell ATAC sequencing; Single cell RNA sequencing; Umbilical cord blood
• ISSN: 0161-5890; 1872-9142
• DOI: 10.1016/j.molimm.2022.10.013

Nowadays, umbilical cord blood (UCB) cells has been increasingly replacing fetal and adult-derived cells in adoptive cell therapy. However, gene expression and chromatin accessibility in umbilical cord blood cells has not yet been fully elucidated. In this study, we used an integration of scRNA-seq with the scATAC-seq technology to perform unbiased analysis of UCBCs over developmental time from 31 gestational week (GW) to 37 GW in humans. We identified several distinct cell types (erythroid cell, T cell, B cell, erythroid precursor cells, NK cell, and endothelial progenitor cell) and subpopulations (6 different clusters of erythroid cells) in UCB cells. In addition, we also identified a series of differentially expressed genes and chromatin accessibility in each cell type between different gestational weeks. Interestingly, the gene expression pattern of umbilical cord blood cells from normal fetuses of similar gestational weeks were more consistent. In conclusion, our analysis presents a better understanding of the chromatin landscape and regulatory networks in UCB cells. •Gene expression level of each cell type different in UCB of different GWs.•The gene expression pattern of UCB cells from similar GWs were more consistent.•Chromatin accessibility of each cell type different in UCB of different GWs.