Extended Data Fig. 5: Abundance of glial proteins at synapses and expression of their corresponding genes.
(a) Cell-type-specific expression of genes that encode the most highly decreased proteins in P301S synapses at 9 months. Percentage of gene expression was calculated based on pseudobulk analysis of scRNAseq data from P301S mice. (b) Volcano plot comparing P301S and WT synapse proteomes highlighting increased proteins that are selectively expressed by glial cells (<5% gene expression by neurons) and their annotated subcellular localization. MSStats was used to calculate log2(fold change) and standard error utilizing a linear mixed-effects model that considered quantification from each peptide and biological replicate per protein. P values were then calculated by comparing the model-based test statistic to a two-sided Student t-test distribution. (c) Heatmap showing z-scores from bulk RNAseq across genotypes for astrocyte and microglia specific genes encoding proteins in Fig 3c. The glial gene set score is shown on the right. (d) Mitochondrial proteins (blue dots) highlighted in volcano plots comparing 9 months old P301S vs WT synapse proteomes. Statistical tests were done as in panel B. The most highly up- or downregulated mitochondrial proteins are labeled using their gene or protein name. (e) Gene set score for mitochondrial proteins that are significantly increased in P301S synapses are shown across genotypes and age as indicated. (f) Cell-type-specific expression of genes encoding mitochondrial proteins that are up- or down-regulated in P301S PSDs at 9 months. Percentage of gene expression was calculated based on pseudobulk analysis of scRNAseq data from P301S mice. (g) Gene set score for peroxisome proteins that are significantly increased in P301S synapses are shown across genotypes and age as indicated. (h) Cell-type-specific expression of genes encoding peroxisome proteins that are up- or down-regulated in P301S PSDs at 9 months. Each dot shows data from one mouse. 2–5 mice/genotype were used. In c one-way ANOVA with Tukey multiple comparison test and in e, g two-way ANOVA with Tukey multiple comparison test was used. Percentage of gene expression in a, f and h is based on scRNAseq data from P301S mice.
