MR1-restricted T cell clonotypes are associated with “resistance” to Mycobacterium tuberculosis infection

T cells are required for protective immunity against Mycobacterium tuberculosis. We recently described a cohort of Ugandan household contacts of tuberculosis cases who appear to “resist” M. tuberculosis infection (resisters; RSTRs) and showed that these individuals harbor IFN-γ–independent T cell responses to M. tuberculosis–specific peptide antigens. However, T cells also recognize nonprotein antigens via antigen-presenting systems that are independent of genetic background, known as donor-unrestricted T cells (DURTs). We used tetramer staining and flow cytometry to characterize the association between DURTs and “resistance” to M. tuberculosis infection. Peripheral frequencies of most DURT subsets were comparable between RSTRs and latently infected controls (LTBIs). However, we observed a 1.65-fold increase in frequency of MR1-restricted T (MR1T) cells among RSTRs in comparison with LTBIs. Single-cell RNA sequencing of 18,251 MR1T cells sorted from 8 donors revealed 5,150 clonotypes that expressed a common transcriptional program, the majority of which were private. Sequencing of the T cell receptor α/T cell receptor δ (TCRα/δ) repertoire revealed several DURT clonotypes were expanded among RSTRs, including 2 MR1T clonotypes that recognized mycobacteria-infected cells in a TCR-dependent manner. Overall, our data reveal unexpected donor-specific diversity in the TCR repertoire of human MR1T cells as well as associations between mycobacteria-reactive MR1T clonotypes and resistance to M. tuberculosis infection. MR1-restricted T-cells (defined as live CD7+ MR1-5-OP-RU tetramer+ cells) were sorted from peripheral blood samples (n = 8). Surface protein expression, gene expression and paired T-cell receptor sequencing were performed on each sample. Samples from 4 ‘resistors’ (RSTR, defined as longitudinally negative for tuberculin skin test and IFNg release assay) and 4 latently infected donors (LTBI, defined as longitudinally positive for tuberculin skin test and IFNg release assay) have been included in this dataset. Samples were sequenced ex vivo without stimulation.

T细胞是抗结核分枝杆菌（Mycobacterium tuberculosis）保护性免疫所必需的。我们此前曾报道过一组乌干达结核病例的家庭接触者队列，这些个体看似能够"抵抗"结核分枝杆菌感染（以下简称抵抗者，RSTRs），且研究证实这类个体存在针对结核分枝杆菌特异性肽抗原的γ干扰素（Interferon-γ, IFN-γ）非依赖性T细胞应答。然而，T细胞还可通过不依赖遗传背景的抗原呈递系统识别非蛋白类抗原，这类T细胞被称为供体非限制性T细胞（donor-unrestricted T cells, DURTs）。我们采用四聚体染色（tetramer staining）与流式细胞术（flow cytometry），探究了供体非限制性T细胞与结核分枝杆菌感染抵抗之间的关联。多数供体非限制性T细胞亚群在外周血中的频率，在抵抗者与潜伏感染对照者（latently infected controls, LTBIs）之间无统计学差异。但相较潜伏感染对照者，抵抗者体内MR1限制性T细胞（MR1-restricted T cells, MR1Ts）的频率升高了1.65倍。我们对从8名供体中分选得到的18251个MR1限制性T细胞进行了单细胞RNA测序（single-cell RNA sequencing），共鉴定出5150个克隆型（clonotype），这些克隆型均表达一套共同的转录程序，其中绝大多数为私有克隆型（private clonotype）。对T细胞受体α/T细胞受体δ（T cell receptor α/T cell receptor δ, TCRα/δ）受体库进行测序后发现，多个供体非限制性T细胞克隆型在抵抗者体内出现扩增，其中2个MR1限制性T细胞克隆型可通过T细胞受体依赖的方式识别分枝杆菌感染的细胞。综上，我们的研究揭示了人类MR1限制性T细胞受体库中意外存在的供体特异性多样性，同时也发现了分枝杆菌反应性MR1限制性T细胞克隆型与结核分枝杆菌感染抵抗之间的关联。本数据集的样本为从外周血中分选得到的MR1限制性T细胞（定义为活的CD7+ MR1-5-OP-RU四聚体阳性细胞），共8份。对每份样本均进行了表面蛋白表达检测、基因表达分析及配对T细胞受体测序。本数据集包含4名抵抗者（RSTR，定义为结核菌素皮肤试验与γ干扰素释放试验长期呈阴性的个体）与4名潜伏感染供体（LTBI，定义为结核菌素皮肤试验与γ干扰素释放试验长期呈阳性的个体）的样本。所有样本均未经过体外刺激即进行了测序。