- Ramesh, Akshaya;
- Schubert, Ryan D;
- Greenfield, Ariele L;
- Dandekar, Ravi;
- Loudermilk, Rita;
- Sabatino, Joseph J;
- Koelzer, Matthew T;
- Tran, Edwina B;
- Koshal, Kanishka;
- Kim, Kicheol;
- Pröbstel, Anne-Katrin;
- Banerji, Debarko;
- San Francisco MS-EPIC Team University of California;
- Guo, Chu-Yueh;
- Green, Ari J;
- Bove, Riley M;
- DeRisi, Joseph L;
- Gelfand, Jeffrey M;
- Cree, Bruce AC;
- Zamvil, Scott S;
- Baranzini, Sergio E;
- Hauser, Stephen L;
- Wilson, Michael R
Central nervous system B cells have several potential roles in multiple sclerosis (MS): secretors of proinflammatory cytokines and chemokines, presenters of autoantigens to T cells, producers of pathogenic antibodies, and reservoirs for viruses that trigger demyelination. To interrogate these roles, single-cell RNA sequencing (scRNA-Seq) was performed on paired cerebrospinal fluid (CSF) and blood from subjects with relapsing-remitting MS (RRMS; n = 12), other neurologic diseases (ONDs; n = 1), and healthy controls (HCs; n = 3). Single-cell immunoglobulin sequencing (scIg-Seq) was performed on a subset of these subjects and additional RRMS (n = 4), clinically isolated syndrome (n = 2), and OND (n = 2) subjects. Further, paired CSF and blood B cell subsets (RRMS; n = 7) were isolated using fluorescence activated cell sorting for bulk RNA sequencing (RNA-Seq). Independent analyses across technologies demonstrated that nuclear factor kappa B (NF-κB) and cholesterol biosynthesis pathways were activated, and specific cytokine and chemokine receptors were up-regulated in CSF memory B cells. Further, SMAD/TGF-β1 signaling was down-regulated in CSF plasmablasts/plasma cells. Clonally expanded, somatically hypermutated IgM+ and IgG1+ CSF B cells were associated with inflammation, blood-brain barrier breakdown, and intrathecal Ig synthesis. While we identified memory B cells and plasmablast/plasma cells with highly similar Ig heavy-chain sequences across MS subjects, similarities were also identified with ONDs and HCs. No viral transcripts, including from Epstein-Barr virus, were detected. Our findings support the hypothesis that in MS, CSF B cells are driven to an inflammatory and clonally expanded memory and plasmablast/plasma cell phenotype.