单细胞转录组测序技术在心脏发育、疾病以及医学中的应用

doi:10.13560/j.cnki.biotech.bull.1985.2020-0396

摘要/Abstract

摘要：

单细胞转录组测序（Single-cell RNA sequencing,scRNA-seq）可以在单细胞水平描绘出每个细胞同一基因的表达量在不同细胞间的表达水平差异,使得在单细胞水平重新认识各种组织器官成为可能。目前对心脏的测序研究正从传统的普通转录组水平过渡到单细胞水平,对小鼠和人的心脏的测序陆续地发表出来。概述了scRNA-seq在心脏发育、疾病以及医学中的应用,讨论了scRNA-seq 技术在胚胎心脏发育、心脏细胞的异质性以及在心脏血管方面、多能干细胞分化心血管细胞模型和先天性心脏畸形的进展和存在问题,对scRNA-seq技术对心脏发育、心脏再生、心脏病和单细胞个性化医疗等方面作出展望。

关键词: 单细胞测序, 心脏发育, 异质性, 心脏疾病

Abstract:

Single-cell RNA sequencing（scRNA-seq）can depict the difference in the expression level of the same gene between different cells at the single-cell level,enabling a new understanding of various tissues and organs at the single-cell level. At present,the sequencing research of the heart is transitioning from the bulk RNA-seq to the scRNA-seq,and research articles on the sequencing of mice’s and human’s heart have been published one after another. This article reviews the application of scRNA-seq in heart development,disease and medicine,and discusses scRNA-seq in embryonic heart development,cell heterogeneity of heart,pluripotent stem cells derived cardiovascular cell models,and congenital heart malformation. Finally,we conclude with prospects of scRNA-seq technology for heart development,heart regeneration,heart disease and single-cell precision medicine.

Key words: single-cell sequencing, heart development, heterogeneity, heart disease

朱庆元, 李天晴. 单细胞转录组测序技术在心脏发育、疾病以及医学中的应用[J]. 生物技术通报, 2021, 37(1): 145-154.

ZHU Qing-yuan, LI Tian-qing. Applications of Single-cell RNA Sequencing in Heart Development,Disease and Medicine[J]. Biotechnology Bulletin, 2021, 37(1): 145-154.

图/表 3

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发表年份	测序技术	UMI长度/bp	基因数	精度	单细胞捕获方法	扩增噪音	单个细胞成本	参考文献
2012	Smart-seq/C1	0	中	中	平板	高	高	[9]
2014	Smart-seq2	0	高	高	平板	中高	高	[11]
2014	MARS-seq	8	低	低	微流	中	高	[12]
2015	Drop-seq	8	低	中高	液滴	低	中	[14]
2016	CEL-seq2/C1	6	中	低	微流	低	高	[20]
2016	SORT-seq	4	高	高	平板	低	中	[21]
2017	10×Genomics	10	高	中	油滴	低	低	[15]
2018	mcSCRB-seq	10	中	中	平板	低	高	[22]

发表年份	测序技术	UMI长度/bp	基因数	精度	单细胞捕获方法	扩增噪音	单个细胞成本	参考文献
2012	Smart-seq/C1	0	中	中	平板	高	高	[9]
2014	Smart-seq2	0	高	高	平板	中高	高	[11]
2014	MARS-seq	8	低	低	微流	中	高	[12]
2015	Drop-seq	8	低	中高	液滴	低	中	[14]
2016	CEL-seq2/C1	6	中	低	微流	低	高	[20]
2016	SORT-seq	4	高	高	平板	低	中	[21]
2017	10×Genomics	10	高	中	油滴	低	低	[15]
2018	mcSCRB-seq	10	中	中	平板	低	高	[22]

细胞类型	共有标记基因	亚型	标记基因	结合空间转录组定位
心肌	TNNT2、TNNC1、ACTC1、TNNI3、ACTN2、NKX2-5、ENO3、COX6A2	心室肌	MYH7、MYL2、LBH、NAV1、HAND1	心室
		心房肌	MYH6、TBX5、PAM、HNF4A	心房
		小梁肌	ANGPT1、COL2A1、ITGA6、RELN、SLIT2、CRABP2
		myoz2心肌	MYOZ2、FABP3	心房和心室
		表达细胞外基质基因心肌	OPHN1、FOXK1、COL2A1、DCN
		致密化心肌
内皮	RAMP2、EMCN、PECAM1、CDH5、TIE1、TEK、HES1	冠状动脉内皮	FABP4、CD36	致密化心肌
		血管内皮	ELN、FNLN5
		瓣膜内皮	NTRK2、NFATC1
		心内膜内皮	CDH11、NPR3	小梁肌
心外膜	UPK3B、ALDH1A2、WT1、TBX18	心外膜	CFB、C3、PRG4、ITLN1	心脏最外层包绕心脏
心外膜	UPK3B、ALDH1A2、WT1、TBX18	心外膜前体细胞	KLK6、CRABP2、TCF21	房室区心外膜下间质
成纤维细胞	DCN、COL1A1、FBLN1、LUM、TCF21	骨骼肌结缔组织样成纤维		流出道、瓣膜
		小血管发育成纤维		心外膜下
		大血管发育成纤维		靠近流出道
		平滑肌样成纤维		流出道、房室区心外膜下间质
神经嵴细胞	ISL1、STMN2			纵隔间质和流出道
施旺细胞	ALDH1A1、DHH			纵隔间质和流出道房室外膜下间质
瓣膜细胞	APCDD1、EDIL3、SCRG1、SLN、NR4A2

细胞类型	共有标记基因	亚型	标记基因	结合空间转录组定位
心肌	TNNT2、TNNC1、ACTC1、TNNI3、ACTN2、NKX2-5、ENO3、COX6A2	心室肌	MYH7、MYL2、LBH、NAV1、HAND1	心室
		心房肌	MYH6、TBX5、PAM、HNF4A	心房
		小梁肌	ANGPT1、COL2A1、ITGA6、RELN、SLIT2、CRABP2
		myoz2心肌	MYOZ2、FABP3	心房和心室
		表达细胞外基质基因心肌	OPHN1、FOXK1、COL2A1、DCN
		致密化心肌
内皮	RAMP2、EMCN、PECAM1、CDH5、TIE1、TEK、HES1	冠状动脉内皮	FABP4、CD36	致密化心肌
		血管内皮	ELN、FNLN5
		瓣膜内皮	NTRK2、NFATC1
		心内膜内皮	CDH11、NPR3	小梁肌
心外膜	UPK3B、ALDH1A2、WT1、TBX18	心外膜	CFB、C3、PRG4、ITLN1	心脏最外层包绕心脏
心外膜	UPK3B、ALDH1A2、WT1、TBX18	心外膜前体细胞	KLK6、CRABP2、TCF21	房室区心外膜下间质
成纤维细胞	DCN、COL1A1、FBLN1、LUM、TCF21	骨骼肌结缔组织样成纤维		流出道、瓣膜
		小血管发育成纤维		心外膜下
		大血管发育成纤维		靠近流出道
		平滑肌样成纤维		流出道、房室区心外膜下间质
神经嵴细胞	ISL1、STMN2			纵隔间质和流出道
施旺细胞	ALDH1A1、DHH			纵隔间质和流出道房室外膜下间质
瓣膜细胞	APCDD1、EDIL3、SCRG1、SLN、NR4A2