Fig. 3: CITE-seq analysis shows pathogenic and activated features for CCR6⁺CCR2⁺CD4⁺ T cells in the CSF of patients with multiple sclerosis.

a UMAP and clustering of single cells based on RNA expression data from CITE-Seq of cells isolated from the cerebrospinal fluid of eight healthy controls and 19 MS patients (Batches 1 and 2, see text). Each dot represents an individual cell, color-coded according to its cluster identity. b Violin plots illustrating the expression of surface CCR6 and CCR2 across the UMAP clusters using antibody-derived data from Batches 1 and 2. c Bar graph showing percentages of CCR2⁺CCR6⁺CD4⁺ T cells in each cluster, using antibody-derived data from Batch 2. The red, horizontal line indicates the percentage of all cells that are CCR6⁺CCR2⁺. d Pie chart showing the proportions of the CCR6⁺CCR2⁺ cells that are found in each cluster, using antibody-derived data from Batch 2. e Proportions of UMAP clusters (a) in cells from control and MS participants. f Violin plots illustrating the expression of surface CD161, PD1, CD69, CD38 and ICOS across the UMAP clusters in (a), using antibody-derived data from Batches 1 and 2. g Dot plot visualizing the expression of key pathogenic Th17-associated genes across UMAP clusters in (a) where the size of a dot indicates the percentage of cells in a cluster expressing the indicated gene and the shading represents the average expression level of the gene in the clusters’ cells. h Dot plot visualizing the expression of key pathogenic Th17-associated genes for the cells from MS versus control (CON) participants analyzed according to surface expression of CCR6 and CCR2, using antibody-derived data from Batch 2, where dots represent the data as in (g).