Putative target antigens of the stereotyped intrathecal B cell response in multiple sclerosis

Abstract Intrathecal antibody production is a hallmark of multiple sclerosis (MS), yet the antigenic targets of these antibodies remain elusive. Intrathecal antibody-secreting cells in MS patients characteristically produce IgG1 antibodies carrying the G1m1 allotype and preferentially use IGHV4 heavy-chain genes paired with IGKV1 or IGKV3 light chains. This stereotyped pattern points to a common antigen-driven selection process. To test this hypothesis, we generated monoclonal antibodies from intrathecal B-lineage cells bearing this stereotyped B-cell receptor configuration and screened them against a comprehensive library of human and Epstein-Barr virus proteins. In parallel, we developed and validated an immunoprecipitation-tandem mass-spectrometry (IPMS/MS) workflow for fresh-frozen brain tissue that preserves conformational epitopes. Several proteins, like CLDN11 and PLD1, were enriched by antibodies from multiple patients. Other targets, like MED21 and GIPC2, were unique to individual patients. Our study delivers a scalable pipeline for antigen discovery in MS and nominates candidate antigens for future validation.