Maintenance of chronic neuroinflammation in multiple sclerosis via interferon signaling and CD8 T-cell-mediated cytotoxicity

Maintenance of chronic neuroinflammation in multiple sclerosis via interferon signaling and CD8 T-cell-mediated cytotoxicity | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Biological Sciences - Article Maintenance of chronic neuroinflammation in multiple sclerosis via interferon signaling and CD8 T-cell-mediated cytotoxicity Syed Ali Raza, Yoshimi Enose-Akahata, Anna Blazier, Lauren Guerra, and 16 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7633686/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Chronic neuroinflammation and neurodegeneration are critical but unresolved drivers of disability accumulation in progressive multiple sclerosis (MS). Chronic active white matter lesions, identifiable radiologically as paramagnetic rim lesions (PRL), indicate progression-relevant chronic neuroinflammation. Using single-cell transcriptomics (scRNAseq) and T-cell receptor sequencing (scTCR-seq), we profiled cerebrospinal fluid (CSF) and blood immune cells of 34 radiologically characterized adults with MS (17 untreated, 6 treated with B-cell-depletion) and 5 healthy controls. Coupled with proteomics, we found PRL-associated enrich-ment of interferon (IFN) signaling and upregulation of TCR signaling in CSF and blood. This was accompanied by clonal expansion of CD8+ T effector memory (TEM) cells, with the highly expanded clonal cells exhibiting T helper type 1 (TH1)-like and cytotoxic profiles. Validating the cytotoxic immune profile in blood using flow cytometry, we identified a cellular correlate of PRL exhibiting features of CD8+ TEMRA cells. Despite chronic B-cell depletion, PRL-associated neuroinflammation, driven by myeloid activation and CD8+ T-cell cytotoxicity, persisted. Serum and CSF proteomic networks showed PRL-pertinent signatures, including networks unaffected by B-cell depletion. CSF:serum protein ratios revealed compartmentalized myeloid activation in cases with PRL. Using in silico perturbation, we nominated therapeutic targets, including MYD88, TNF, MYC, TYK2, JAK2, and BTK, for alleviating chronic neuroinflammation in MS. Our findings highlight mechanisms of chronic neuroinflammation in MS and point to potential biomarkers for monitoring disease progression. Biological sciences/Immunology/Autoimmunity Biological sciences/Immunology/Neuroimmunology Biological sciences/Molecular biology/Transcriptomics Biological sciences/Molecular biology/Proteomics Biological sciences/Neuroscience/Neuroimmunology Full Text Additional Declarations Yes there is potential Competing Interest. Declaration if interests are mentioned Supplementary Files SupplementaryFile1.xlsx Dataset 1 SupplementaryFile2.xlsx Dataset 2 SupplementaryFile3.xlsx Dataset 3 SupplementaryFile4.xlsx Dataset 4 SupplementaryFile5.pdf Serum proteome modules and iGraphs SupplementaryFile6.pdf CSF proteome modules and iGraphs SupplementaryFile7.pdf Perturbed pathways with in silico gene KO in CSF SupplementaryFile8.xlsx Dataset 5 SupplementaryInformationsupplementaryfigsar20250916sardsr.pdf Supplementary Information Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7633686","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Biological Sciences - Article","associatedPublications":[],"authors":[{"id":519967941,"identity":"9fccde94-38a0-4382-be40-9b590ef7765b","order_by":0,"name":"Syed Ali Raza","email":"","orcid":"https://orcid.org/0000-0003-4782-2100","institution":"National Institute of Neurological Disorders and Stroke, National Institutes of Health","correspondingAuthor":false,"prefix":"","firstName":"Syed","middleName":"Ali","lastName":"Raza","suffix":""},{"id":519967942,"identity":"057678da-0e09-4c4b-b1dc-ca26f0ac1c0b","order_by":1,"name":"Yoshimi 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Chronic active white matter lesions, identifiable radiologically as paramagnetic rim lesions (PRL), indicate progression-relevant chronic neuroinflammation. Using single-cell transcriptomics (scRNAseq) and T-cell receptor sequencing (scTCR-seq), we profiled cerebrospinal fluid (CSF) and blood immune cells of 34 radiologically characterized adults with MS (17 untreated, 6 treated with B-cell-depletion) and 5 healthy controls. Coupled with proteomics, we found PRL-associated enrich-ment of interferon (IFN) signaling and upregulation of TCR signaling in CSF and blood. This was accompanied by clonal expansion of CD8+ T effector memory (TEM) cells, with the highly expanded clonal cells exhibiting T helper type 1 (TH1)-like and cytotoxic profiles. Validating the cytotoxic immune profile in blood using flow cytometry, we identified a cellular correlate of PRL exhibiting features of CD8+ TEMRA cells. 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