Singel Cell Analysis of Acute Inflammatory Demyelinating Syndromes Identify Cell State Enriched for MS Susceptibilty

Objective: To determine, at high resolution, the diversity of cell states found in cerebrospinal fluid (CSF) of patients with acute, non-infectious inflammatory syndromes using single cell-RNA sequencing (RNA-seq). We use this population structure to refine our understanding of the mechanism of multiple sclerosis (MS) onset. Background: Single cell RNA sequencing facilitates the discovery of rare cell types and context-specific cell states that have not been appreciated either by using bulk profiles of CSF cells, where individual profiles are averaged, or by using cytometric data, where only a limited set of selected markers are measured. Design/Methods: We successfully generated single-cell RNA-seq data from fresh CSF samples obtained from untreated individuals with optic neuritis, new onset relapsing-remitting MS, and tumefactive MS. Each cell has a transcriptome with an average of ~1200 RNA transcripts, which were used to empirically assemble clusters of cells with similar expression patterns. A reference atlas of immune cell gene expression is then used to annotate each cluster and to identify known cell populations. Results: Clustering analyses identify the expected types of CSF cells, with multiple broad myeloid classes as well as B- and T-cells. T cells predominate as anticipated, and we find substantial heterogeneity among T-cell subtypes, including combinations of genes encoding for surface proteins, transcription factors, and cell-cell signaling factors. We find differential representation of T-cell transcriptomic profiles in different donors, particularly in our case of tumefactive MS. We note the presence of an intriguing novel myeloid cell population with a mixture of monocytic and microglial features. Conclusions: We identified new cell populations such as a mixed monocyte/microglial cell type whose role needs to be better defined, and it identifies key subtypes of CD4+ and CD8+ T cells as preferentially targeted by genetic variation that contributes to MS onset, prioritizing their modulation in the development of primary prevention strategies for MS. Disclosure: Dr. Diaconu has nothing to disclose. Dr. Menon has nothing to disclose. Dr. De Jager has received personal compensation for consulting, serving on a scientific advisory board, speaking, or other activities with Biogen and Roche. Dr. De Jager has received research support from Biogen and Roche.