Transcriptomic and clonal characterization of T cells in the human central nervous system

Tissues develop unique homeostatic immune states through specific recruitment of immune cells that are further shaped by the tissue environment. Here, we use single-cell RNA and TCR sequencing of healthy cerebrospinal fluid (CSF) and single-nucleus RNA sequencing of brain parenchyma to profile the T cell state in the human central nervous system (CNS). We observe a continuum of T cell states, reflecting a blood-CSF “axis”, that we use to reveal that T cells in the CSF largely exhibit a tissue-resident phenotype with a balance of co-inhibitory and effector function gene expression, including PD-1+ T cells retaining the ability to produce IFNg. Leveraging paired single-cell TCR sequencing to identify clonal T cell groups, we find that T cell phenotypes mirror the tissue where they reside and that clonally-expanded T cells reflect the most CSF-distinct state. To identify how this T cell state is perturbed during neuroinflammation, we profiled newly-diagnosed, treatment-naive patients with multiple sclerosis (MS) and observed that clonally expanded T cells are the most phenotypically different between patients and healthy controls. We then identify putative pathways of communication between T cells in the brain parenchyma and glia and neurons that may be involved in shaping T cell function. Our elucidation of the CNS T cell state provides context for understanding neuroinflammation and neurodegeneration as well as providing a framework for understanding tissue-driven T cell adaptation. Overall design: This series includes only single nucleus RNA Sequencing. The TCR-seq data were submitted to dbGaP.

组织通过特异性招募免疫细胞，形成独特的稳态免疫状态，而这些免疫细胞又会进一步受组织微环境的塑造。本研究采用健康受试者脑脊液（cerebrospinal fluid, CSF）的单细胞RNA测序与T细胞受体（TCR）测序，以及脑实质的单细胞核RNA测序，对人类中枢神经系统（CNS）中的T细胞状态进行全景表征。我们观察到一系列连续的T细胞状态，这反映了血液-脑脊液"轴"的特征；借此我们揭示，脑脊液中的T细胞大多呈现组织驻留表型，同时兼具共抑制与效应功能相关的基因表达特征，其中包括可分泌干扰素γ（IFNγ）的PD-1阳性T细胞。借助配对单细胞TCR测序鉴定克隆性T细胞群，我们发现T细胞表型与其所处组织高度匹配，且克隆扩增的T细胞呈现出与脑脊液差异最为显著的状态。为探究该T细胞状态在神经炎症过程中如何发生扰动，我们对新确诊且未接受过治疗的多发性硬化（multiple sclerosis, MS）患者进行了细胞图谱分析，发现克隆扩增的T细胞是患者与健康对照之间表型差异最为显著的细胞群。随后，我们鉴定出脑实质T细胞与胶质细胞、神经元之间的潜在信号通路，这些通路可能参与调控T细胞功能。本研究对中枢神经系统T细胞状态的解析，为理解神经炎症与神经退行性疾病提供了研究背景，同时也为解析组织驱动的T细胞适应性机制提供了理论框架。研究整体设计：本系列仅包含单细胞核RNA测序数据。TCR测序数据已提交至dbGaP数据库。