Multiple sclerosis (MS) is a complex inflammatory and neurodegenerative disease of the central nervous system (CNS) with a multifaceted pathophysiology, likely involving a variety of mechanisms and effectors. To characterize the spectrum of cellular and molecular factors involved in MS at an unprecedented level, we here performed a comprehensive analysis of cerebrospinal fluid (CSF) and peripheral blood using multiple high-dimensional technologies, including mass cytometry, metabolomics and proteomics (NULISA and Olink Explore 3072). Enriched B cells and proteins involved in B cell functions in the CSF separated MS patients from other neurological disease entities. Specific B cell subpopulations and molecular markers including gut-microbiota-derived metabolites and neurofilament light protein, a marker of neuroaxonal damage, in CSF correlated with clinical (acute vs. stable disease) and/or radiological (gadolinium enhancement) disease activity. Altogether, unbiased broad phenotyping suggests key roles of diverse B subpopulations and B cell related molecular markers in MS, which are associated with both, inflammatory and degenerative aspects of the disease and may serve as disease activity and treatment response biomarkers.

F.P. received research support from F. Hoffmann-La Roche Ltd., Alexion Pharma Germany GmbH and Horizon Therapeutics Ireland DAC.

This study was in part funded by F. Hoffmann-La Roche Ltd as part of Integrative Neuroscience Collaborations Network (INTONATE, MOGAD Precision). M. W. received the PhD scholarship from the Chinese Scholarship Council (CSC). C.B. was funded by the Deutsche Forschungsgemeinschaft (DFG, the German Research Foundation Project ID 259373024 CRC/TRR 167 (B05) and the BMBF (German Ministry of Education and Research), Foerderkennzeichen 01EJ2202A (TAhRget consortium).

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

The details of the IRB/oversight body that provided approval or exemption for the research described are given below:

The study was approved by the ethics committee of the Charite Universitaetsmedizin Berlin (Ethikkommission der Charite Universitaetsmedizin Berlin; registration number EA1/386/20) in accordance with the Declaration of Helsinki of 1964 and its later amendments. All study participants provided informed consent before any study related procedures were undertaken and did not receive a compensation.

I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.

Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.

Yes

Source data are provided with this paper as Source Data file.