Fig. 1

Comparative phenotypic analysis of the CNS myeloid cells in NAWM and active lesions of PMS. a The overlaid t-SNE plots of 8 NAWM (grey dot) and 7 active lesions (red dot). The 2D t-SNE maps were generated based on expression levels of all markers of Exp-I (Supplementary Table 8). b The overlaid t-SNE plot of all samples. The coloring indicates 12 clusters representing diverse myeloid cell phenotypes, defined by the FlowSOM algorithm. c Heat map cluster demonstrates the expression levels of all 36 markers used for the cluster analysis. Asterisk indicates differentially abundant clusters. Heat colors of expression levels have been scaled for each marker individually (to the 1st and 5th quintiles) (red, high expression; blue, low expression). d Pie charts showing the proportions of 12 defined clusters in the two groups. Four differentially abundant clusters (C1, C3, C8, and C11) between active lesions and NAWM were found. An FDR-adjusted p value < 0.05 was considered statistically significant, determined using GLMM (*p < 0.05; **p < 0.01, adjusted). Box-plots show frequencies (%) of all defined clusters. Boxes extend from the 25th to 75th percentiles. Whisker plots show the min (smallest) and max (largest) values. The line in the box denotes the median. Each dot represents the value of each sample. e Reduced-dimensional single-cell t-SNE maps highlight all four differentially abundant clusters. In the lower panel, t-SNE maps show the expression of TMEM119, TNF, CD14 and P2Y₁₂. Color spectrum indicates expression levels of the marker (red, high expression; blue, low expression)