Fig. 4

Altered microglial gene expression profiles in 5xFAD mice housed under GF conditions. (a) Venn diagram depicting the different regulated and overlapping genes between FACS-isolated hippocampal microglia of SPF, GF and ABX-treated 5xFAD animals compared to respective non-transgenic littermates of the same conditions (SPF/GF/ABX). (b) RNA-Seq analysis presenting mRNA expression profile of genes, whose expression was either induced or reduced with an adjusted P value < 0.0001 in hippocampal microglia of SPF, GF and ABX-treated transgenic 5xFAD animals and respective age-matched WT littermates. Representative genes are noted on the right. One column represents microglia from one individual mouse. Three to five mice were investigated per condition. Color code presents z-score (red: upregulated, blue: downregulated). Ingenuity pathway analysis (Qiagen) on differentially expressed genes in hippocampal microglia of SPF (c), GF (d) and ABX-treated (e) 5xFAD animals compared to respective WT littermates of the same housing/treatment conditions (SPF/GF/ABX) based on an RNA-sequencing analysis. Diagram depicts –log(p) value and predicted activation z-scores (red: increased activity, blue: reduced activity; grey: no predicted z-score available). (f) Heatmap of differently expressed genes attributed to the pathway ‘phagosome maturation’ of hippocampal microglia from SPF, GF and ABX-treated transgenic 5xFAD animals and respective age-matched WT littermates. Representative genes are noted on the bottom. One row represents microglia from one individual mouse. Three to five mice were investigated per condition. Color code presents z-score (red: upregulated, blue: downregulated)