Extended Data Fig. 3: C1q-dependent synapse proteome changes in P301S mice.
(a,b) Volcano plots showing the comparison between A) C1qKO vs WT and B) P301S;C1qKO vs P301S synapse fraction proteomes at 6 and 9 months. 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. Significantly up- and downregulated proteins (p-value < 0.05, log2FC ± 0.5) are shown in blue and red circles, respectively. Selected differentially expressed proteins are labeled with their protein or gene name. (c) KEGG pathways significantly downregulated in synapses from 6 months old C1qKO mice and 9 months old P301S;C1qKO vs P301S mice. (d) Scatterplot comparison of PSD proteomes from 9 months old P301S vs WT mice (x-axis) and P301S;C1qKO vs WT mice (y-axis). Note that protein changes in this comparison are larger in P301S compared to P301S;C1qKO synapse fractions, suggesting that C1q deletion blunts changes in P301S mice. Red indicates significantly different (p-value <0.05) in P301S vs. WT, but not significantly different in P301S;C1qKO vs WT (97 proteins), green indicates significantly different in P301S;C1qKO vs WT, but not significantly different in P301S vs. WT (only C1qC), and blue indicates significantly different in both comparisons (12 proteins). P-values and fold changes were calculated by MSStats, as described in methods. (e) Schematic representation of an excitatory synapse with the localization of selected proteins grouped by their function. Heatmaps show protein log2 fold-changes for individual genotype and age comparison. (f) SynGO analysis of downregulated proteins in P301S vs WT and P301S;C1qKO vs WT synapse proteomes at 9 months. (g) Heatmaps of normalized protein expression of annexins across genotypes in synapses at 6 and 9 months. The annexin protein set score is shown below. In g) each dot shows data from one mouse. 2–3 mice/genotype were used. Two-way ANOVA with Šidak’s test. All data are presented as mean ± SEM.
