Figure 1.
ATM-like microglia accumulate at the embryonic CSA and CSB
(A) Single-cell transcriptomic uniform manifold approximation and projection (UMAP) plot of embryonic microglial cells (n = 1,711) extracted from the La Manno dataset,30 showing cycling MG (orange), non-cycling MG (purple), and embryonic ATM-like MG (green).
(B) Projection of the post-natal ATM signature (top-enriched differentially expressed genes [DEGs]) from the Hammond dataset22 onto (A).
(C) Proportion of cycling (orange), non-cycling (purple), and embryonic ATM-like MG (green) at different embryonic stages.
(D) Venn diagram showing the overlap between embryonic and post-natal ATM DEGs, respectively, identified from La Manno30 and Hammond22 datasets (fold change [FC] > 1.5, Bonferroni-adjusted p < 1e−10).
(E) Immunolabeling of brain sections from E14.5 or E15 Cx3cr1gfp/+ or CD11c-EYFP embryos showing co-expression of microglia and ATM markers at the CSA. CSA close ups are delineated by dotted lines. GFP-positive microglia in Cx3cr1gfp/+ brains fully colocalized with the microglial marker P2Y12 receptor, and IBA1 was used to label microglia in CD11c-EYFP brains (performed on brain sections of at least three mice from two different litters).
(F) Immunolabeling of coronal brain sections from E18.5 Cx3cr1gfp/+ or CD11c-EYFP embryos showing co-expression of microglia and ATM markers at the cortico-septal boundary (CSB), below the corpus callosum (CC). CSB close ups are delineated by dotted lines. GFP-positive microglia in Cx3cr1gfp/+ brains fully colocalized with the IBA1 marker, which was used to label all microglia in CD11c-EYFP brains (performed on brain sections of at least three mice from two different litters).
Graphs show means ± SEM. Scale bars: 500 μm in (E, upper left); 200 μm in (E, lower); 100 μm in (E, upper right) and (F); and 20 μm (E insets).
ATM, axon-tract-associated microglia; ATM-like, axon-tract-associated-like microglia; CC, corpus callosum; CSA, cortico-striato-amygdalar boundary; CSB, cortico-septal boundary; DEGs, differentially expressed genes; MG, microglia; Ncx, neocortex; Se, Septum; Str, striatum.