Fig. 3

Brain macrophage heterogeneity in multiple sclerosis brain tissues. a Workflow of the experiment. b UMAP depicting 56,522 cells. Colors depict unsupervised clustering. c UMAP where colors depict donor of origin (left) or tissue region of origin (right). d UMAPs where color scales depict module scores of microglia- and CAM-enriched gene sets (top) or expression levels of S100A9 and PLP1 (bottom). e Bar plots depicting cluster distribution among donor groups with standard error. Black circles depict individual samples. C = NACT; W = NAWM; L = WML. f Dot plot depicting marker genes of each cluster. Size of the circles depicts the fraction of cells expressing the gene, color scale depicts average expression level. g Heatmap depicting enrichment scores of literature-derived gene-sets in the scRNAseq dataset. h Immunofluorescent images of stainings for FCGR2B (orange; Hs8); CLDN5 (magenta; blood vessels), Hoechst (cyan; nuclei) and IBA1 (green; macrophages) in an active and inactive lesion. Left panels: overview image. Scale bar = 25 μm. Center panel: Zoom in on parenchymal macrophages. Scale bar = 10 μm. Right panel: Zoom in on vessel-associated macrophages. i–j Quantification of immunohistochemistry for FCGR2B in parenchyma and near/on blood vessels. In (j) a subset of tissues is presented to enable visualization of differences in samples with low tissue coverage. *: p < 0.05. Abbreviations: NACT = normal appearing cortical tissue; NAWM = normal appearing white matter; WML = white matter lesion, PLWM = perilesional white matter