Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease relevant pathologies

Abstract

Autism spectrum disorder (ASD) is a genetically heterogeneous disorder. Sequencing studies have identified hundreds of risk genes for autism spectrum disorder (ASD), but the signaling networks of genes at the protein level remain largely unexplored, which can provide insight into previously unknown individual and convergent disease pathways in the brain. To address this gap, we used neuron-specific proximity-labeling proteomics (BioID) to identify protein-protein interaction (PPI) networks of 41 ASD-risk genes. Network analysis revealed the combined 41 risk gene PPI network map had more shared connectivity between unrelated ASD-risk genes than represented in existing public databases. We identified common pathways between established and uncharacterized risk genes, including synaptic transmission, mitochondrial/metabolic processes, Wnt signaling pathways, ion channel activity and MAPK signaling. Investigation of the mitochondrial and metabolic network using gene knockouts revealed a functional hub in neurons for multiple risk genes not previously associated with this pathway. Further, we identified that the uncharacterized ASD-risk gene PPP2R5D localizes to the synapse, which is disrupted by patient de novo missense mutations. Investigation of de novo missense variants of additional synaptic ASD-risk genes demonstrated that changes in PPI networks can capture synaptic transmission deficits. The neuronal 41 ASD-risk gene PPI network map also revealed enrichment for an additional 112 ASD-risk genes and human brain cell types implicated in ASD pathology. Interestingly, clustering of ASD-risk genes based on their PPI network connectivity identified multiple gene groups that correlate mutation-type to clinical behavior scores. Together, our data reveal that using PPI networks to map ASD risk genes can identify previously unknown individual and convergent neuronal signaling networks, provide a method to assess the impact of patient variants, and reveal new biological insight into disease mechanisms.

Direct control of translational elongation by TAOK2β highlights altered protein synthesis as a fundamental underlying component of autism

“…First, we performed immunoprecipitation coupled with mass spectrometry ( IP- MS ) analysis using an anti-TAOK2β antibody in cytoplasmic lysates from either mouse cortices or N2a cells transfected with wild-type TAOK2β. In parallel, we used a neuronal proximity-based proteomic system to identify protein-protein interaction ( PPI ) networks associated with TAOK2β in mouse cortical neurons (18DIV) infected with lentiviral constructs, expressing a BioID2 fusion protein (pLV-hSyn-tGFP-P2A-TAOK2β-13xLinker- BioID2-3xFLAG) 12 . Co-purified proteins from the three biological samples were involved in chloride channel activity, synaptic structure constituents and translational control based on gene ontology (GO) term analysis (Figure 1 and Supplementary Table 1).…”

“…pAAV-CAG huTAOK2β wt (plasmid encodes humanTAOK2-short variant) and pAAV-CAG-tDimer2 (plasmid encodes the A tandem dimer mutant of DsRed tagged to the RFP) were used for in utero electroporation of cortical neurons. pLV-hSyn-tGFP-P2A-POI-13xLinker-BioID2-3xFLAG construct expressing BioID2 fusion proteins and Luciferase-P2A-BioID2-3xFLAG construct as a negative control were used in neuron viral infection 12 .…”

“…to identify protein-protein interaction (PPI) in DIV18 neuron, we followed our previously described protocol 12 .…”

Integrative Functional Genomic Analysis in Multiplex Autism Families from Kazakhstan

“…According to the obtained results, ten genes clearly formed potentially important nodes in the PPI networks. Six of these genes, namely HDAC4, MECP2, TCF4, TRIM33, TTN, and TSC2, belong to the SFARI category 1-2 (highconfidence and strong candidate genes) and are widely associated with the neuropathological mechanisms of ASD [31,[52][53][54][55][56][57][58][59][60][61][62][63][64][65][66][67][68][69][70]. The CFTR, NOD2, PPP2R2B, and TTR genes were not found in the SFARI databases, and data on the role of 11 Disease Markers these genes in ASD are very sparse [71,72].…”

“…Despite a considerable genetic heterogeneity underlying ASD, there is compelling evidence that a large number of risk genes can be integrated into a much smaller number of proteinprotein interaction (PPI) networks [26]. Previous studies have shown that ASD genes functionally converge in synapse development, axon alignment, neuron motility, synaptic transmission, chromatin remodeling, transcription and translation regulation, ion transport, and cell adhesion [27][28][29][30][31][32]. As far as we know, these studies were mainly focused on investigating genes affected in children with ASD, but not in relatives with subclinical phenotypes of BAP.…”