Fig. 3: Spatial profiling of human CAMs in situ and their cellular interactions.
From: Multiomic spatial landscape of innate immune cells at human central nervous system borders
a, Representative immunofluorescence across human CNS interfaces. DAPI (4′,6-diamidino-2-phenylindole) and collagen IV show positions of nuclei and basal lamina. Filled arrowheads indicate double-positive cells and empty arrowheads indicate single-positive cells. b, In situ quantification of selected markers across different compartments. Crossbars indicate medians. Outlier values confirmed by the Grubbs’s test were removed, resulting in at least n = 7 and at most n = 18 biologically independent samples analyzed per compartment and reaction. Each dot represents a patient. Indicated P values were derived from pairwise two-sided Mann–Whitney U-tests with pvMΦ as the reference cell type. MG, microglia; pvMΦ, perivascular macrophage; cpMΦ, choroir plexus macrophage; CP epi, epiplexus macrophage/Kolmer cells; lmMΦ, leptomengeal macrophage; dmMΦ, dura mater macrophage. c, Dendrogram showing the hierarchical clustering of the analyzed cell types based on average expression of CD206, SIGLEC1, CD163, S100A6 and CD1C. d, Spatial plot of a control section (frontal cortex) analyzed using ISS. Color coding represents different cell types. On the right, the different anatomical regions are annotated. The bar plot on the bottom shows the cell-type distribution in the PC and LM. Representative of cortical sections analyzed from four individuals. Astro, astrocytes; Oligo, oligodendrocytes. e, Heat map, color coded for the neighborhood enrichment scores of the different cell types calculated with a permutation-based test36. The color coding of the cell types is consistent with d. f, Heat map, color coded for the cell-type interaction scores in LM (left) and PC/PV (right). Color coding is consistent with d. g, Spatial plot of a tissue section (occipital cortex) analyzed using Nanostring CosMx. Color coding is consistent with d and e. Representative of 14 analyzed fields of view from 4 control samples. h, Dot plot showing the spatial cell–cell interactions of the dataset from f. The y axis indicates receiving cell types. The x axis labels show the ligand expressed by neighboring cells followed by the receptor. Color scale represents the average expression of ligand–receptor pairs. The dot size represents the percentage of cells expressing the receptor.
