Fig. 9
From: Neuronal transcriptome, tau and synapse loss in Alzheimer’s knock-in mice require prion protein
PrPC-dependent gene expression profile in neuronal and glial cell populations. A The number of positively and negatively differently expressed genes (DEGs) in neuronal and glial cell sub-populations of 10-months (left) and 20-months (right) in Prnp−/− mice as compared to WT. B Venn diagram demonstrating the number of shared DEGs between excitatory and inhibitory neuronal cell populations of 10-month-old Prnp−/− mice. C Venn diagram of significant DEGs in oligodendrocytes shared between 10- and 20-months old Prnp−/− mice. The statistical significance of gene overlap shown in B,C was assessed by Fisher’s exact test relative to the number of DEGs. D Volcano plots representing the gene expression changes in excitatory (left) and inhibitory (right) cells population showing the statistical significance (Log10(p-val adj.), y-axis) vs the Log2 Fold Change (Log2(FC), x-axis) of the Prnp−/− group as compared to WT; vertical dashed lines indicate ± 0.25 Log2(FC). A selection of significant PrPC-associated genes is labeled. DEGs are deemed significant if they exhibit an absolute Log2(FC) > 0.25, with p < 0.005 (Wilcoxon rank sum test) and are colored purple (downregulated) or teal (upregulated). For the full gene list, refer to Suppl. Table S1. E Volcano plot of gene expression changes identified in 20-month oligodendrocyte cell populations. F, G Pathway enrichment analysis of pooled significant excitatory and inhibitory DEGs between Prnp−/− versus WT mice at 10 months. G Enrichment terms (nodes), resulting from GO Molecular Functions, KEGG, and REAC Pathway analysis, organized into functional network groups which are linked by shared gene associations (edges). The intra-group significant terms (leading terms) are color highlighted with corresponding p-value and total functional group gene association count plotted in (F). H Protein–Protein interaction (PPI) evidence of gene set enrichment analysis shown in (F, G). Genes with stronger associations are connected by thicker lines with gene groups encircled based on shared functional pathways