Fig. 1. Quantitative membrane proteomics reveals disrupted synaptic and epilepsy-associated protein networks in the 16p11.2^dup/+ mouse model.

a Procedure for SILAM-based quantitative proteomic profiling of cortical membranes from 16p11.2^+/+ (n = 5 mice) and 16p11.2^dup/+ (n = 5 mice) mice using ¹⁵N-enriched brains as internal standards. b Graphical display of proteomic dysregulation in cortical membranes of 16p11.2^dup/+ mice. Each protein is plotted by Z-ratio (from −150 to +150 for clarity) and ordered by chromosome to visualize the extent of dysregulation across the proteome. We identified 659 upregulated proteins (Z-ratio >1.96) and 1024 downregulated proteins (Z-ratio < −1.96) (full dataset available in Supplementary Data 1). Membrane proteins PRRT2 and SEZ6L2 within the syntenic 16p11.2 region (murine 7q4) are indicated. c Gene ontology (GO) analysis reveals an upregulation of synaptic signaling and ion transport proteins. Representative terms from the top GO clusters are presented d Molecular risk profile of the 16p11.2^dup/+ mouse model. Comparison of dysregulated proteins from the proteomic profiling to gene sets of de novo variants identified through large-scale exome sequencing studies or the OMIM database. Products of genes impacted by de novo variants in epilepsy are highly over-represented in the upregulated protein dataset. Data shows percentage enrichment and p-values from a two-sided hypergeometic test (Upregulated: control, p = 0.2954; EE, p = 0.0011; ID, p = 0.0059; SZ, p = 0.0660; ASD, p = 0.0094; Epi (OMIM), p = 0.0001; ID (OMIM), p = 0.0374. Downregulated: control, p = 0.1687; EE, p = 0.1922; ID, p = 0.0073; SZ, p = 0.0235; ASD, p = 0.0028; Epi (OMIM), p = 0.2965; ID (OMIM), p = 0.2922). e Schematic showing the 110 dysregulated proteins associated with epilepsy used to seed the protein interaction network. f The epilepsy-associated protein interaction network (Epilepsy subnetwork) discovered in the 16p11.2^dup/+ mouse model. Nodes are colored by Z-ratio. g GO analysis of the epilepsy subnetwork reveals a strong enrichment of synaptic proteins (one-sided Fisher’s Exact test with Benjamini-Hochberg correction). Abbreviations: ^*p < 0.05, ^**p < 0.01, ^***p < 0.001, EE epileptic encephalopathy, Epi epilepsy, ID intellectual disability, SZ schizophrenia, ASD autism spectrum disorder, RE Rolandic epilepsy, BD bipolar disorder, P_corr, Benjamini-Hochberg corrected p-value.