Supplementary Figure 5: cbMg display a more immature and neurodegeneration-associated phenotype as compared to a more mature homeostatic phenotype in stMg.
From: Epigenetic regulation of brain region-specific microglia clearance activity
(a) MA plot for differential expression analysis (DESeq2, n=2/region) for each gene shows log2 (mean expression) across all samples (x-axis) and log2 (fold change) of expression of stMg over cbMg from 9mo Cx3cr1CreErt2/+;Eef1a1LSLeGFPL10a/+ mice (y-axis). 733 genes (purple) are significantly enriched in stMg, 297 genes (orange) are significantly enriched in cbMg, and genes in green are equally enriched. Pie charts show the GO-based categories of 733 stMg-enriched genes (top) and 297 cbMg-enriched genes (bottom). (b) Heatmaps show the variation in the expression levels of genes involved in engulfment, metabolism, transcription regulation, and chromatin modification from the 297 cbMg-enriched genes identified by microglia-TRAP from 9mo mice (DESeq2, n=2). Also shown: selected proinflammatory genes that are not significantly enriched. z-scored log2 RPKM of genes in cbMg and stMg of 3-,6-, and 9-month-old mice are shown. (c) Left: Venn diagrams show overlap between cbMg (orange) and stMg (purple) enriched genes with immature microglia markers10 (red; stMg: p=0.0083, OR= 1.809, χ2=7.003; cbMg: p < 0.0001, OR= 8.083, χ2=167.0) and mature microglia markers10 (blue; stMg: p < 0.0001, OR=10.45, χ2=548.1; cbMg: p=0.2416, OR=1.518, χ2=1.371). Right: Venn diagrams show overlap between cbMg (orange) and stMg (purple) enriched genes with genes up- (red; stMg: p=0.9149, OR=0.9773, χ2=0.3533; cbMg: p < 0.0001, OR=4.113, χ2=69.38) and down-regulated (blue; stMg: p < 0.0001, OR=11.41, χ2=755.2; cbMg: p=0.93, OR=1.034, χ2=0.007709) in Alzheimer’s Disease (AD)-associated microglia in mice12. (d) Venn diagrams show overlap between cbMg (orange) and stMg (purple) enriched genes with microglia associated with early response to AD11 (cluster 3; red; stMg: p =0.543, OR= 0.8897, χ2=0.37; cbMg: p < 0.0001, OR= 3.374, χ2=54.44) (cluster 7; red; stMg: p =0.7595, OR= 1.056, χ2=0.09368; cbMg: p < 0.0001, OR= 2.579, χ2=26.02) and late response to AD11 (cluster 6; red; stMg: p =0.6705, OR= 0.9227, χ2=0.181; cbMg: p < 0.0001, OR= 3.903, χ2=77.47). (c,d) Genes found in significant overlaps are indicated. p values and odds ratios of Venn diagrams (underneath each overlap) were calculated using the non-parametric χ2 test from a total of 22,706 protein-coding genes analyzed in DESeq2.
