Identifying CNS-colonizing T cells as potential therapeutic targets to prevent progression of multiple sclerosis

Background: Multiple sclerosis (MS), an autoimmune disease of the central nervous system (CNS), can be suppressed in its early stages but eventually becomes clinically progressive and unresponsive to therapy. Here we investigate whether the therapeutic resistance of progressive MS can be attributed to chronic immune cell accumulation behind the blood brain barrier. Methods: We systematically track CNS-homing immune cells in the peripheral blood of 31 MS patients and 31 matched healthy individuals in an integrated analysis of 497,705 single cell transcriptomes and 355,433 surface protein profiles from 71 samples. Through spatial RNA-sequencing we localize these cells in post-mortem brain tissue of 6 progressive MS patients contrasted against 4 control brains (20 samples, 85,000 spot transcriptomes). Findings: We identify a specific pathogenic CD161+/LTB+ T cell population that resides in brains of progressive MS patients. Intriguingly, our data suggest that the colonization of the CNS by these T cells may begin earlier in the disease course, as they can be mobilized to the blood by usage of the integrin-blocking antibody natalizumab in relapsing-remitting MS patients. Conclusions: As a consequence, we lay the groundwork for a therapeutic strategy to deplete CNS-homing T cells before they can fuel treatment-resistant progression. Funding: This study was supported by funding from the University Medical Center Hamburg-Eppendorf, the Stifterverband für die Deutsche Wissenschaft, the OAK Foundation, Medical Research Council UK and Wellcome. In a primary cohort nine relapsing-remitting MS (RRMS) patients’ peripheral blood mononuclear cells (PBMC) were sampled longitudinally with and without natalizumab treatment. Two auxiliary cross-sectional cohorts consisting of eleven untreated RRMS and ten primary-progressive MS (PPMS) patients as well as 31 matched healthy individuals for all patients were included. Taken together, we performed multi-modal immunophenotyping by scRNA-seq and surface antibody staining in a total of 71 PBMC samples from 62 donors resulting in close to half a million single cell transcriptomes and around 360,000 surface protein profiles **Raw data not provided due to patient privacy concerns**