CHD8 haploinsufficiency alters the developmental trajectories of human excitatory and inhibitory neurons linking autism phenotypes with transient cellular defects

Abstract

Chromodomain helicase DNA-binding 8 (CHD8) is one of the most frequently mutated genes causative of autism spectrum disorder (ASD). While its phenotypic spectrum often encompasses macrocephaly and hence implicates cortical abnormalities in this form of ASD, the neurodevelopmental impact of human CHD8 haploinsufficiency remains unexplored. Here we combined human cerebral organoids and single cell transcriptomics to define the effect of ASD-linked CHD8 mutations on human cortical development. We found that CHD8 haploinsufficiency causes a major disruption of neurodevelopmental trajectories with an accelerated generation of inhibitory neurons and a delayed production of excitatory neurons alongside the ensuing protraction of the proliferation phase. This imbalance leads to a significant enlargement of cerebral organoids aligned to the macrocephaly observed in patients with CHD8 mutations. By adopting an isogenic design of patient-specific mutations and mosaic cerebral organoids, we define genotype-phenotype relationships and uncover their cell-autonomous nature. Finally, our results assign different CHD8-dependent molecular defects to particular cell types, pointing to an abnormal and extended program of proliferation and alternative splicing specifically affected in, respectively, the radial glial and immature neuronal compartments. By identifying temporally restricted cell-type specific effects of human CHD8 mutations, our study uncovers developmental alterations as reproducible endophenotypes for neurodevelopmental disease modelling.

Chromatin Remodeler CHD8 in Autism and Brain Development

“…While it is tempting to speculate that these findings might apply to individuals with mutations in CHD8 , we are not aware of any study on human brain tissues to support this hypothesis. In this respect, pluripotent stem cell-derived cerebral organoids (see below [ 76 ]) could help to bridge the gap between mice and human studies.…”

“…Embryonic stem cell (ESC) and induced pluripotent stem cell (iPSC) derived neuronal cell types exhibit genetically encoded molecular and cellular phenotypes matching human mid- to late-term brain development. Most recently, Villa et al [ 76 ] reported the effect of CHD8 mutations on human cortical development by combining the generation of ESC-derived human cerebral organoids with single cell transcriptomics. By adopting an isogenic design of patient-specific mutations, wild-type and mutated CHD8 conditions were investigated on identical genetic backgrounds.…”

Single-Cell Transcriptomics Supports a Role of CHD8 in Autism

“…Until recently, the production of cerebral organoids has been labor-intensive and plagued by high organoid-to-organoid variability. Refinements in culturing techniques [ 81 ] and progress toward fully automated high-throughput workflows for human organoid production and analysis [ 87 ] open the perspective to enlarge sample sizes in terms of the number of independent donors and genes to be investigated. Improvements in reproducibility are likewise important to cost reduction and statistical analysis [ 88 ].…”

“…In light of the importance of this compartment for human cortical growth, the authors suggested that human brain development might be more vulnerable to CHD8 dosage than the mouse. Strikingly, Villa et al [ 81 ] described in human cerebral organoids a shift in the proliferation/differentiation dynamics of neural progenitors that drove the expansion of this compartment and a subsequent increase in the number of later neurons. At the same time, however, the number of Tbr2-positive intermediate progenitors actually decreased.…”

“…Most recently, Villa et al [ 81 ] carried out sc-RNAseq of human cerebral organoids to assess the effect of various CHD8 mutations on human neocorticogenesis. CRISPR/Cas9 editing in a human ESC line was used to delete either the C-terminal helicase domain or introduce two patient-specific mutations, each resulting in a premature stop codon (i.e., S62X and E1114X; see Figure 2 ).…”