Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity

doi:10.1016/j.gpb.2021.02.006

	Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity
	Luo, Haitao 1,2,3; Bu, Dechao 4; Shao, Lijuan 1,2,3; Li, Yang 5; Sun, Liang 4; Wang, Ce 1,2; Wang, Jing 1,2,3; Yang, Wei 1,2; Yang, Xiaofei 1,2; Dong, Jun 3; Zhao, Yi 4; Li, Furong 1,2
	2021-06-01
发表期刊	GENOMICS PROTEOMICS & BIOINFORMATICS
ISSN	1672-0229
卷号	19 期号:3 页码:377-393
摘要	The development of new biomarkers or therapeutic targets for cancer immunotherapies requires deep understanding of T cells. To date, the complete landscape and systematic characterization of long noncoding RNAs (lncRNAs) in T cells in cancer immunity are lacking. Here, by systematically analyzing full-length single-cell RNA sequencing (scRNA-seq) data of more than 20,000 libraries of T cells across three cancer types, we provided the first comprehensive catalog and the functional repertoires of lncRNAs in human T cells. Specifically, we developed a custom pipeline for de novo transcriptome assembly and obtained a novel lncRNA catalog containing 9433 genes. This increased the number of current human lncRNA catalog by 16% and nearly doubled the number of lncRNAs expressed in T cells. We found that a portion of expressed genes in single T cells were lncRNAs which had been overlooked by the majority of previous studies. Based on metacell maps constructed by the MetaCell algorithm that partitions scRNA-seq datasets into disjointed and homogenous groups of cells (metacells), 154 signature lncRNA genes were identified. They were associated with effector, exhausted, and regulatory T cell states. Moreover, 84 of them were functionally annotated based on the co-expression networks, indicating that lncRNAs might broadly participate in the regulation of T cell functions. Our findings provide a new point of view and resource for investigating the mechanisms of T cell regulation in cancer immunity as well as for novel cancer-immune biomarker development and cancer immunotherapies.
关键词	Long non-coding RNA Transcriptome assembly Metacell Immune regulation Functional annotation
DOI	10.1016/j.gpb.2021.02.006
收录类别	SCI
语种	英语
资助项目	Science and Technology Project of Shenzhen, China[JCYJ20190807145013281] ; Science and Technology Project of Shenzhen, China[JHZ20170310090257380] ; Science and Technology Project of Shenzhen, China[JCYJ20170413092711058] ; Science and Technology Project of Shenzhen, China[JCYJ20170307095822325] ; China Postdoctoral Science Foundation[2019M663369] ; National Natural Science Foundation of China[31970636]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000753148400005
出版者	ELSEVIER
引用统计	被引频次：11[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/18999
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Luo, Haitao; Dong, Jun; Zhao, Yi; Li, Furong
作者单位	1.Jinan Univ, Clin Med Coll 2, Shenzhen Peoples Hosp, Translat Med Collaborat Innovat Ctr, Shenzhen 518020, Peoples R China 2.Shenzhen Key Lab Stem Cell Res & Clin Transformat, Shenzhen 518020, Peoples R China 3.Jinan Univ, Integrated Chinese & Western Med Postdoctoral Res, Guangzhou 510632, Peoples R China 4.Chinese Acad Sci, Inst Comp Technol, Adv Comp Res Ctr, Key Lab Intelligent Informat Proc,Bioinformat Res, Beijing 100190, Peoples R China 5.Jinan Univ, Clin Med Coll 2, Shenzhen Peoples Hosp, Dept Gastrointestinal Surg, Shenzhen 518020, Peoples R China
推荐引用方式 GB/T 7714	Luo, Haitao,Bu, Dechao,Shao, Lijuan,et al. Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity[J]. GENOMICS PROTEOMICS & BIOINFORMATICS,2021,19(3):377-393.
APA	Luo, Haitao.,Bu, Dechao.,Shao, Lijuan.,Li, Yang.,Sun, Liang.,...&Li, Furong.(2021).Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity.GENOMICS PROTEOMICS & BIOINFORMATICS,19(3),377-393.
MLA	Luo, Haitao,et al."Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity".GENOMICS PROTEOMICS & BIOINFORMATICS 19.3(2021):377-393.