CHD8 regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

Abstract

Truncating mutations of chromodomain helicase DNA-binding protein 8 (CHD8), and of many other genes with diverse functions, are strong-effect risk factors for autism spectrum disorder (ASD), suggesting multiple mechanisms of pathogenesis. We explored the transcriptional networks that CHD8 regulates in neural progenitor cells (NPCs) by reducing its expression and then integrating transcriptome sequencing (RNA sequencing) with genome-wide CHD8 binding (ChIP sequencing). Suppressing CHD8 to levels comparable with the loss of a single allele caused altered expression of 1,756 genes, 64.9% of which were up-regulated. CHD8 showed widespread binding to chromatin, with 7,324 replicated sites that marked 5,658 genes. Integration of these data suggests that a limited array of direct regulatory effects of CHD8 produced a much larger network of secondary expression changes. Genes indirectly down-regulated (i.e., without CHD8-binding sites) reflect pathways involved in brain development, including synapse formation, neuron differentiation, cell adhesion, and axon guidance, whereas CHD8-bound genes are strongly associated with chromatin modification and transcriptional regulation. Genes associated with ASD were strongly enriched among indirectly down-regulated loci (P < 10 −8) and CHD8-bound genes (P = 0.0043), which align with previously identified coexpression modules during fetal development. We also find an intriguing enrichment of cancer-related gene sets among CHD8-bound genes (P < 10 −10). In vivo suppression of chd8 in zebrafish produced macrocephaly comparable to that of humans with inactivating mutations. These data indicate that heterozygous disruption of CHD8 precipitates a network of gene-expression changes involved in neurodevelopmental pathways in which many ASD-associated genes may converge on shared mechanisms of pathogenesis.he genetic architecture of autism spectrum disorder (ASD) is complex and heterogeneous. A wave of recent discoveries has identified individual genes that contribute to ASD when they suffer heterozygous inactivation by coding mutation, copy number variation, or balanced chromosomal abnormalities (1-7). Many of these genes fit neatly into current biological models of ASD involving altered synaptic structure and glutamatergic neurotransmission, but others have been surprising, with a less ready biological interpretation, including genes involved in chromatin modification, DNA methylation, cell adhesion, and global transcriptional regulation. This diversity of genes predisposing to ASD suggests either that there are many pathways that independently can result in the autism phenotype or that functionally distinct ASD-risk genes can trigger consequences that converge on a limited number of shared pathways of ASD pathogenesis. Because now experimental tools are available to reduce gene expression specifically in human neural progenitor cells (NPCs), which can mimic the impact of functional hemizygosity, we have explored this question by investigating the functional genomic consequences of suppr...

ATP-dependent chromatin remodeling during mammalian development

“…Ikaros-NuRD subunit CHD4 has a role in thymocyte development (Arenzana et al, 2015;Sridharan and Smale, 2007) NuRD has roles in cardiomyocyte proliferation (Garnatz et al, 2014) and in renal progenitor cells during kidney development (Denner and Rauchman, 2013) CHD5 CHD5 Orchestrates chromatin remodeling during neurogenesis (Thompson et al, 2003;Vestin and Mills, 2013) and sperm development ) CHD7 CHD7 Involved in charge syndrome (Bajpai et al, 2010;Janssen et al, 2012;Vissers et al, 2004), neurogenesis (Hurd et al, 2010), adult brain development (Jones et al, 2015), cardiac development (Payne et al, 2015), and proper craniofacial and tracheal development (Sperry et al, 2014) CHD8 CHD8 Involved in autism spectrum disorder (Sanders, 2015) and neural development (Bernier et al, 2014;Cotney et al, 2015;Sugathan et al, 2014) CHD9 CHD9 Associates with selective promoters of osteoprogenitors (Shur et al, 2006) *Current mouse gene symbols are listed only where they differ from protein nomenclature.…”

“…Furthermore, CHD7 is required for neurogenesis during inner ear morphogenesis (Hurd et al, 2010). CHD8, in contrast, is linked to autism spectrum disorder (ASD); reducing the Chd8 dose by half in neural progenitors downregulates genes involved in neural development, including those associated with ASD (Sugathan et al, 2014). CHD proteins are also involved during heart development.…”

A Novel Genetic Syndrome Caused by Haploinsufficiency of CHD2, a Regulator of Chromatin Structure

“…While the minimal deleted region contains CHD8 and the adjacent SUPT16H locus, the importance of abrogated CHD8 function in the phenotype of these patients is underscored by the identification of disruptive CHD8 mutations in individuals with DD or ASD [31] and recapitulation of a subset of features of the human phenotype in the zebrafish model [32]. Although other CHD proteins have yet to be linked to human genetic disease, it has been demonstrated that CHD4 and CHD5 carry out important functions in neurogenesis [33,34].…”

Chromodomain Helicase DNA-Binding Proteins in Stem Cells and Human Developmental Diseases

“…CHD proteins in autism spectrum disorder, intellectual disability, and epilepsy Application of cytogenetic and next-generation sequencing technologies to large cohorts of individuals with autism spectrum disorder (ASD), intellectual disability (ID), and/or epilepsy has uncovered de novo and inherited heterozygous frameshift, nonsense, or copy dosage mutations in several CHD genes, including CHD2, CHD6, CHD7, and CHD8 [66][67][68][69][70][71][72][73][74]. For CHD2, CHD6, and CHD7, mutations identified thus far are nonrecurrent (present in only individual cases), private mutations that account for a small fraction of ASD/ ID/epilepsy cases.…”

“…In cultured cells, CHD8 has been shown to bind CHD7 and to both bind and regulate p53 and inhibit its proapoptotic effects during development; thus, it is surprising that loss of CHD8 is not associated with broader phenotypic effects in humans [79][80][81][82]. Knockdown of Chd8 by shRNA does not alter the morphology or neural ectodermal markers of neural progenitors derived from human iPS cells, but does significantly impair their gene expression [74]. A very recent study also showed that CHD7 binds to and represses p53, suggesting some CHD proteins (at least those in the third subclass) may share common downstream mechanisms, interacting factors, and target genes [83].…”