Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses

Abstract

Identification of complex molecular networks underlying common human phenotypes is a major challenge of modern genetics. In this study, we develop a method for network-based analysis of genetic associations (NETBAG). We use NETBAG to identify a large biological network of genes affected by rare de novo CNVs in autism. The genes forming the network are primarily related to synapse development, axon targeting, and neuron motility. The identified network is strongly related to genes previously implicated in autism and intellectual disability phenotypes. Our results are also consistent with the hypothesis that significantly stronger functional perturbations are required to trigger the autistic phenotype in females compared to males. Overall, the presented analysis of de novo variants supports the hypothesis that perturbed synaptogenesis is at the heart of autism. More generally, our study provides proof of the principle that networks underlying complex human phenotypes can be identified by a network-based functional analysis of rare genetic variants.

Figure 1

Outline of the NETwork-Based Analysis of Genetic associations (NETBAG), the method used in our study to identify significant and functionally related gene networks affected by de novo CNV events. (A) A background network of human genes is constructed in which nodes indicate genes and edges represent the likelihood that two genes participate in the same genetic phenotype. (B) One or two genes are selected from each of de novo CNV region to form a cluster. The genes are mapped to the likelihood network and a combined score is calculated for each cluster based on interactions between its genes. (C) A greedy search procedure is used to identify the cluster with maximal score. (D) The significance of the cluster with maximum score is determined by comparing it to the distribution of maximal scores from randomly selected genomic regions with similar gene counts. See Figure S1 for a further description of the NETBAG approach.

Figure 2

Gene clusters found using NETBAG analysis of de novo CNV regions observed in autistic individuals. A) The highest scoring cluster obtained using the search procedure with up to one gene per each CNV region. B) The cluster obtained using the search with up to two genes per region. In the figure genes (nodes) with known functions in the brain and nervous systems are colored in orange (see Table S2 for functional information about the genes forming the cluster). Node sizes represent the importance of each gene to the overall cluster score. Edge widths are proportional to the prior likelihood that the two corresponding genes contribute to a shared genetic phenotype. For clarity, we show only edges corresponding to the two strongest connections for at least one node.

Figure 3

Genes associated with the morphogenesis of dendritic spines. Dendritic spines are dynamically forming protrusions from a neuron’s dendrite which mediate excitatory connection to axons and determine synaptic strength. The proteins shown in the figure play crucial roles in formation of physical contacts between axons and dendrites, organization of postsynaptic density (PSD), and signaling processes controlling spine morphology. Many of the signaling pathways ultimately converge on the regulation of the growth and branching of the actin filament network, which is essential for spine structural remodeling. The proteins encoded by genes from the identified functional cluster (Figure 2) are shown in yellow, other genes hit by de novo CNV from Levy et al., in blue, and genes previously implicated or discussed in the context of autism are highlighted using orange borders.