Single-cell RNA-seq and chromatin accessibility profiling decipher the heterogeneity of mouseγδT cells  

单细胞转录组和单细胞染色质开放性图谱解析小鼠γδT细胞异质性

作　　者：Zhenhua Li Quanli Yang Xin Tang Yiming Chen Shanshan Wang Xiaojie Qi Yawen Zhang Zonghua Liu Jing Luo Hui Liu Yongbing Ba Lianxia Guo Baojian Wu Fang Huang Guangchao Cao Zhinan Yin 李振华;杨全利;唐欣;陈一铭;王闪闪;齐晓杰;张亚雯;刘宗华;骆静;刘晖;巴永兵;郭练霞;吴宝剑;黄芳;曹广超;尹芝南(Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment,Zhuhai Institute of Translational Medicine,Zhuhai People’s Hospital Affiliated with Jinan University,Jinan University,Zhuhai 519000,China;The Biomedical Translational Research Institute,Faculty of Medical Science,Jinan University,Guangzhou 510632,China;The First Affiliated Hospital,Faculty of Medical Science,Jinan University,Guangzhou 510000,China;Emergency Department,The First Affiliated Hospital of Jinan University,Jinan University,Guangzhou 510000,China;OE Biotech Co.,Ltd.,Shanghai 201114,China;Institute of Molecular Rhythm and Metabolism,Guangzhou University of Chinese Medicine,Guangzhou 510700,China;Zhuhai People’s Hospital(Zhuhai Hospital Affiliated with Jinan University),Jinan University,Zhuhai 519000,China)

机构地区：[1]Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment,Zhuhai Institute of Translational Medicine,Zhuhai People’s Hospital Affiliated with Jinan University,Jinan University,Zhuhai 519000,China [2]The Biomedical Translational Research Institute,Faculty of Medical Science,Jinan University,Guangzhou 510632,China [3]The First Affiliated Hospital,Faculty of Medical Science,Jinan University,Guangzhou 510000,China [4]Emergency Department,The First Affiliated Hospital of Jinan University,Jinan University,Guangzhou 510000,China [5]OE Biotech Co.,Ltd.,Shanghai 201114,China [6]Institute of Molecular Rhythm and Metabolism,Guangzhou University of Chinese Medicine,Guangzhou 510700,China [7]Zhuhai People’s Hospital(Zhuhai Hospital Affiliated with Jinan University),Jinan University,Zhuhai 519000,China

出　　处：《Science Bulletin》2022年第4期408-426,M0004,共20页科学通报（英文版）

基　　金：supported by the National Natural Science Foundation of China(31830021,32030036,32000615,and 32100695);the National Key Research and Development Program of China(2020YFA0803502);the 111 Project(B16021);China Postdoctoral Science Foundation(2020M683180,2019M663374,and 2020T130251);Guangdong Basic and Applied Basic Research Foundation(2020A1515111045 and 2020A1515111081)。

摘　　要：The distinct characteristics ofγδT cells determine their vital roles in the formation of local immune responses and contribute to tissue homeostasis.However,the heterogeneity ofγδT cells across tissues remains unclear.By combining transcriptional and chromatin analyses with a truly unbiased fashion,we constructed a single-cell transcriptome and chromatin accessibility landscape of mouseγδT cells in the lymph,spleen,and thymus.We also revealed the heterogeneity ofγδT1 andγδT17 cells across these tissues and inferred their potential regulatory mechanisms.In the thymus,we reconstructed the developmental trajectory and gained further insights into the signature genes from the mature stage,intermediate stage,and immature stage ofγδT cells on the basis of single-cell RNA sequencing and single-cell assay for transposase-accessible chromatin sequencing data.Notably,a novel Gzma^(+)γδT cell subset was identified with immature properties and only localized to the thymus.Finally,NR1 D1,a circadian transcription factor(TF),was validated as a key and negative regulator ofγδT17 cell differentiation by performing a combined analysis of TF motif enrichment,regulon enrichment,and Nr1 d1 knockout mice.In summary,our data represent a comprehensive mapping on the transcriptome and chromatin accessibility dynamics of mouseγδT cells,providing a valuable resource and reference for future studies onγδT cells.γδT细胞具有重要的免疫监视功能,其不同亚群在维持组织稳态和局部免疫反应中发挥不同作用,但是γδT细胞的异质性尚未完全解析.本文对小鼠胸腺、脾脏和淋巴结中的γδT细胞开展了单细胞转录和染色质开放性组学分析,系统地解析了其异质性.经典的γδT1(IFN-γ^(+))和γδT17(IL-17A;)亚群内部也存在显著的异质性,作者推断了其潜在调控机制.通过对胸腺γδT细胞进行拟时序分析,作者构建了其发育轨迹.有意思的是,作者发现胸腺中存在一群独立于γδT1和γδT17的新亚群—GZMA;γδT细胞,并且发现该亚群具有前体细胞特征.作者还通过转录子活性分析、转录因子识别基序富集发现了一个新的γδT17转录抑制因子—NR1D1,并利用基因敲除小鼠进行了验证.综上,本文构建了小鼠γδT单细胞转录图谱和单细胞染色质开放性图谱,为深入解析γδT细胞异质性和亚群调控机制提供了宝贵的资源库.

关 键 词：γδT cell scRNA-seq scATAC-seq Innate immunity HETEROGENEITY 

分 类 号：Q343[生物学—遗传学]