基于单细胞转录组测序分析构建花斑裸鲤三种造血器官细胞图谱  

Generating Cellular Atlases of Three Haematopoietic Organs of the Gymnocypris eckloni using Single-Cell RNA Sequencing

作　　者：寇若彬 刘丹 高强 晁燕[3] 张存芳 聂苗苗 贾军梅 谭瑾 郭守全 姚占雯 祁得林 KOU Ruo-Bin;LIU Dan;GAO Qiang;CHAO Yan;ZHANG Cun-Fang;NIE Miao-Miao;JIA Jun-Mei;TAN Jin;GUO Shou-Quan;YAO Zhan-Wen;QI De-Lin(State Key Laboratory of Plateau Ecology and Agriculture,Qinghai University,Xining 810016;College of Eco-Environmental Engineering,Qinghai University,Xining 810016;Animal Science Department of Agriculture and Animal Husbandry College,Qinghai University,Xining 810016,China)

机构地区：[1]青海大学省部共建三江源生态与高原农牧业国家重点实验室,西宁810016 [2]青海大学生态环境工程学院,西宁810016 [3]青海大学农牧学院动物科学系,西宁810016

出　　处：《动物学杂志》2025年第1期69-79,共11页Chinese Journal of Zoology

基　　金：青海省自然科学基金项目(No.2020-ZJ-907);国家自然科学基金项目(No.31960127)。

摘　　要：利用单细胞转录组测序技术在细胞水平探究花斑裸鲤(Gymnocypris eckloni)肾、肝和脾三种造血器官中的细胞组成类型,系统描绘花斑裸鲤这三种造血器官的细胞图谱,为进一步研究花斑裸鲤造血系统发育,尤其是红细胞发育积累科学数据。研究方法包括花斑裸鲤肾、肝和脾三种造血器官的单细胞悬液制备、单细胞RNA-seq文库构建、测序以及降维聚类分析、细胞注释、差异基因分析和功能富集分析。结果表明,花斑裸鲤三种造血器官内存在类型丰富的细胞,包括红细胞、中性粒细胞、T细胞、B细胞、树突状细胞、上皮细胞、巨噬细胞、血管内皮细胞、肌细胞、成纤维细胞、单核细胞和神经细胞。在三种器官中细胞分布存在较大的异质性:脾中参与发挥红细胞功能的细胞群分布占比较大;肾中参与免疫反应的细胞群分布占比较大;肝中血管内皮细胞和肌细胞分布占比较大。在功能方面,花斑裸鲤与多数硬骨鱼类相似,它的肾、脾和肝不仅参与造血及红细胞的发育,而且对于免疫系统的发育和应答等过程也发挥一定作用。本研究从单细胞角度对花斑裸鲤造血系统发育研究进行了一定的补充与完善,展现了三种造血器官中细胞分布的特征与差异,对于后续进一步预测花斑裸鲤的红细胞发育路径提供了一定的研究基础。[Objectives]Single-cell RNA sequencing was used to investigate the cellular composition of the three hematopoietic organs-kidney,liver,and spleen of Gymnocypris eckloni.The study aims to systematically map the cellular composition of these organs,and to accumulate scientific data for the study of the haematopoietic system,particularly erythropoiesis,in this species.[Methods]Single-cell suspensions were prepared and sequenced using single cell RNA sequencing software to clarify the characteristics and differences in the distribution of cells in the haematopoietic organs and to construct a preliminary cellular atlas of the haematopoietic organs of G.eckloni.[Results]Cells within the three organs of G.eckloni were initially classified into 16 subpopulations based on the sequencing results(Fig.2).This,combined with the expression of the top 20 differentially expressed genes and known marker genes for each cell population,identified a variety of cell types.These included erythrocytes,neutrophils,T cells,B cells,dendritic cells,epithelial cells,macrophages,vascular endothelial cells,myoblasts,fibroblasts,monocytes and neuronal cells.There is considerable heterogeneity in the distribution of cells in the three organs(Fig.4).The G.eckloni had a relatively large distribution of cell populations involved in erythrocyte functions,the kidney had a relatively large distribution of cell populations involved in the immune response,and the liver had a relatively large distribution of vascular endothelial cells and myocytes.[Conclusion]The similarity to the haematopoietic cell types of the Zebrafish Danio rerio demonstrates the high conservation of haematopoietic cell development and evolution.According to functional enrichment analysis,G.eckloni,like most scleractinian fishes,has kidneys,spleen and liver,which are not only involved in haematopoiesis and erythropoiesis,but also play roles in immune system development,response and other processes.Meanwhile,the present study complements and improves the study of the haematopoietic

关 键 词：单细胞转录组测序 造血系统发育 细胞图谱 花斑裸鲤 

分 类 号：Q955[生物学—动物学]