Fig. 3: WM-microglia appear more advanced in age than GM-microglia, are elongated, and selectively express SLC15A1.

a UMAP plot of microglia/immune cells colored by Level 2 subclustering. PBMC peripheral blood mononuclear cells. b Violin plot showing the expression of genes in each subcluster (local) and in each cell class (global). c Relative abundance of microglia by coarse tissue category; n = 42 independent samples; the median is annotated (black diamond shape) and listed. d Expression of SLC15A1 in adult marmoset brain sections. Solid arrowheads, IBA1⁺/SLC15A1⁻ microglia; open arrowheads, IBA1⁺/SLC15A⁺ microglia. IBA1 is a pan microglia marker, and intense PLP1 labeling demarcates the WM area. Scale bar, 1 mm (1x and 4x), 100 μm (20x). e Box-and-whisker plot showing the number of IBA1⁺ cells from three ROI per tissue type per biological repeat (BR) that were quantified manually or by automatic image processing; n = 9 ROI from three biologically independent animals; the median is annotated (black diamond shape) and listed. ***p < 0.001, t-test, two-sided, p = 2.5E-04 (group manual), p = 5.8E-08 (group auto). f The morphology of IBA⁺ cells in GM and WM was extracted by processing IBA1/PLP1 labeled images. Experiment was repeated independently three times with similar results as quantified in g, h. g The distribution of shape factor by measuring perimeter (P) and area (A) of IBA1⁺ cells to calculate the reciprocal of circularity (P²/4 πA) with a step size of 1 grouped by tissue type. Circularity⁻¹ ranges from 1 (perfect circle) to infinity. h Violin plot summarizing the shape factor of IBA1⁺ cells. The reciprocal of circularity measured from WM cells is significantly higher than that measured from GM cells, ***p < 0.001, t-test, two-sided, p = 6.8E-07; n = 1432 cells examined over three WM areas from biologically independent animals; n = 438 cells examined over three GM areas from biologically independent animals. i UMAP plots of marmoset microglia colored by tissue type and mouse microglia from Hammond et al. 2019 colored by animal age. j Heatmap showing the expression of gene modules in seven MIC subclusters from marmoset and mouse microglia grouped by age. Gene modules enriched in GM-microglia (MIC1) of marmoset are enriched in microglia of younger mice (PG.m2/8, Knn.m6/3/5), and gene modules enriched in WM-microglia (MIC3) of marmoset are enriched in microglia of older mice (PG.m1/4/3, Knn.m1/7/2). The lower and upper hinges of the box plot in a, d, e correspond to the 25^th and 75^th percentiles, whiskers extend from the hinges to maxima or minima at most 1.5 times inter-quartile range.