Single-cell Long Non-coding RNA Landscape of T Cells in Human Cancer Immunity
- Author:
Luo HAITAO
1
;
Bu DECHAO
;
Shao LIJUAN
;
Li YANG
;
Sun LIANG
;
Wang CE
;
Wang JING
;
Yang WEI
;
Yang XIAOFEI
;
Dong JUN
;
Zhao YI
;
Li FURONG
Author Information
1. Translational Medicine Collaborative Innovation Center,The Second Clinical Medical College(Shenzhen People's Hospital),Jinan University,Shenzhen 518020,China;Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation,Shenzhen 518020,China;Integrated Chinese and Western Medicine Postdoctoral Research Station,Jinan University,Guangzhou 510632,China
- Keywords:
Long non-coding RNA;
Transcriptome assembly;
Metacell;
Immune regulation;
Functional annotation
- From:
Genomics, Proteomics & Bioinformatics
2021;19(3):377-393
- CountryChina
- Language:Chinese
-
Abstract:
The development of new biomarkers or therapeutic targets for cancer immunotherapies requires deep under-standing 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.
