Fig. 4

Deeply characterizing monocyte cells in the CSF of MS and control patients. A Grouped bar plot of the absolute count of differential expressed genes (DEGs) in listed cell types in level 1 and level 2 clustering. B Dot plot of selected genes for the total Mono cluster (level 1) in MS compared to control (Ctrl). C Volcano plot showing differential expressed genes of the Mono cluster (level 1) in MS compared to Ctrl plotted as fold change (log2) against p value (-log10, FDR). Please note that yellow highlighted genes are higher expressed in the Ctrl and blue ones are more expressed in MS. The upregulation of B cell typical genes we interpret as an artifact here due to miss annotation. D  Left stacked bar plot showing the cell count of CD14⁺ and CD16⁺ monocytes in MS compared to Ctrl. Right s-tacked bar plot showing the proportion of CD14⁺ and CD16⁺ monocyte cells in MS compared to Ctrl. Both monocyte cell clusters are set to 100% irrespective of their total abundance, thereby not allowing a quantitative comparison. E Precomputed differential expressed genes by cellxgene VIP of selected genes with a focus on phagocytosis, lipid metabolism and trafficking-associated genes in CD14⁺ and F CD16⁺ monocyte cells. Color coding shows significant up- (red) or downregulation (blue), dot size encodes the fold change. Small white numbers represent the FDR. Fold change > 1.5. G Dot plot of gene expression of activation markers and anti-inflammatory cytokines in CD14⁺ and CD16⁺ monocytes in MS and Ctrl. H Dot plot depicting expression of signature genes for CNS-associated macrophages (CAM) [40, 41], microglia [53] and monocyte-derived cells [40] in CD14⁺ and CD16⁺ monocytes in Ctrl and MS