Extended Data Fig. 4: Trem1 deficiency alters gene expression in aged peripheral MΦ with minimal changes in aged brain microglia.
a Venn diagram of DEGs (all genes q < 0.05) in pairwise comparisons of microglia isolated from aged (18 - 20 mo) vs young (3 mo) mice and pairwise comparisons of microglia isolated from aged Trem1-/- vs aged WT mice (18–20 mo). Blue indicates number of downregulated genes while red indicates the number of upregulated genes (n = 3 microglial samples (2 pooled male mice per sample) per group). b KEGG Pathway enrichment analysis of upregulated genes in aged compared to young microglia; there were no enriched pathways in the comparison of aged WT vs aged Trem1-/- microglia. c Venn diagrams showing the number of DEGs (all genes q < 0.05) in pairwise comparisons of primary mouse MΦ from young WT (2 mo), aged WT (25 mo) and aged Trem1-/- (25 mo) mice. Blue indicates number of downregulated genes while red indicates the number of upregulated genes (n = 3–4 male mice per group). d Pathway enrichment analysis of upregulated genes in aged MΦ vs young and in aged Trem1-/- vs aged WT MΦ. e Heatmap of DEGs (q < 0.05) comprising the Coordinated Lysosomal Expression and Regulation (CLEAR) network. Lysosomal functional categories are indicated for each gene. Aged Trem1-/- mice cluster with the young WT mice. Scale represents z-score values from FPKM. n = 3–4 male mice per group.
