Extended Data Fig. 6: Transcriptional and functional analysis of ME immune cells.
From: Intestinal macrophages modulate synucleinopathy along the gut–brain axis
a, FACS gating strategy of CD3+ cells and CX3CR1hiCD11b+CD11c− duodenal ME-Macs. b, UMAP projections of 3KL vs WT ME-Macs and CD3+ cells c,d, Violin plots (c) and dot plots (d) showing marker genes in identified ME-Mac clusters and T cells. e, Pathway analysis of ME-Macs of 4 mo 3KL, data analysed using a one-sided hypergeometric test. f-g, Gating strategy for CCR2+ and CD163+ ME-Macs within live CD45+CX3CR1+F4/80+CD64+Ly6CloMHCIIhi cells in ME (f) and LP (g) and absolute cell count (h), n = 4 per condition and time point. 1 experiment per time point, 2way ANOVA (CD163+ and CCR2−CD163−), Bonferroni’s multiple comparison test (CCR2+). i-l, Confocal images and proportion of CCR2+, CD163+ and CCR2−CD163− among IBA1+duodenal ME-Macs in 3 mo WT vs 3KL (i,j) and 1 mo post-NHC-αS vs PD-αS injection (k,l), n = 6 mice for WT; n = 5 mice for 3KL; n = 5 mice for NHC-αS; n = 7 for PD-αS. 3 experiments per genotype/treatment, 2way repeated measures ANOVA (j, l), Bonferroni’s multiple comparison test (j). m,n, Reconstructed images of lysosomal s129p engulfment in CD163+ and CCR2+ duodenal ME-Macs at 1 mo post-αS injection and 3 mo WT vs 3KL (m) and quantification of engulfment at 1 mo post-αS injection (n), n = 4 per condition. 1 experiment, 2way ANOVA. Data are mean ± s.e.m.
