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. This series includes only single nucleus RNA Sequencing. The TCR-seq data were submitted to dbGaP.