Autism genes converge on asynchronous development of shared neuron classes

Abstract

Genetic risk for autism spectrum disorders (ASD) is associated with hundreds of genes spanning a wide range of biological functions 1-6 . The alterations in the human brain resulting from mutations in these genes remain unclear. Furthermore, their phenotypic manifestation varies across individuals 6,7 . Here, we leveraged organoid models of the human cerebral cortex to identify cell type-specific developmental abnormalities resulting from haploinsufficiency in three ASD risk genes, SUV420H1 (KMT5B), ARID1B, and CHD8, in multiple cell lines from different donors, using single-cell RNA-seq (scRNA-seq) of over 745,000 cells and proteomic analysis of individual organoids, to identify phenotypic convergence. Each of the three mutations demonstrates asynchronous development of two main cortical neuronal lineages, GABAergic neurons and deep-layer excitatory projection neurons, but acts through largely distinct molecular pathways. Although these phenotypes are consistent across cell lines, their expressivity is influenced by the individual genomic context, in a manner that is dependent on both the risk gene and the developmental defect. Calcium imaging in intact organoids shows that these early-stage developmental changes are followed by abnormal circuit activity. This work uncovers cell typespecific neurodevelopmental abnormalities shared across ASD risk genes that are finely modulated Paulsen et al.

Single-cell multiomics atlas of organoid development uncovers longitudinal molecular programs of cellular diversification of the human cerebral cortex

“…To begin to understand the regulatory logic that underlies this cellular diversification, we investigated gene-regulatory changes across organoid development. We generated single-cell Assay for Transposase Accessible Chromatin Using Sequencing (scATAC-seq) (Corces et al ., 2017; Satpathy et al ., 2019) profiles of 38,017 nuclei, combining our previously published dataset (Paulsen et al ., 2022) with an additional 11,551 newly-profiled cells from 1, 3, and 6 month organoids, spanning amplification of neural progenitors, the peak of excitatory neuron diversity, and the emergence of astroglia and interneurons, respectively (Figure 1C and S3, n = 3 individual organoids per timepoint). To classify cell types, we integrated the expression profiles from scRNA-seq with inferred gene activity scores from scATAC-seq clusters by label transfer from scRNA-seq (Figure S3A-F), and refined assignments by looking at genes near differentially accessible regions (DARs).…”

“…To investigate the molecular characteristics and reproducibility of corticogenesis in human brain organoids, we built a longitudinal single-cell atlas comprising 8 timepoints across 6 months of organoid development, spanning processes from early stages of progenitor amplification to later astroglia production (Figure 1A). We profiled a total of 532,414 cells by single-cell RNA sequencing (scRNA-seq), combining our previously published datasets (Velasco et al ., 2019; Paulsen et al ., 2022) with an additional 218,240 newly-profiled cells from multiple timepoints. We analyzed organoids derived from multiple stem cell lines (2-6 lines per stage) and differentiation batches (n = 2-7 per line and stage; Figures 1A and S1A).…”

“…Human brain organoids have emerged as a powerful experimental system to investigate human brain development and neurodevelopmental diseases (Lancaster et al ., 2013; Mariani et al ., 2015; Bershteyn et al ., 2017; Birey et al ., 2017; Kanton et al ., 2019; Klaus et al ., 2019; Esk et al ., 2020; Khan et al ., 2020; Paulsen et al ., 2022). Organoids generate a large diversity of cell types resembling those that populate the human developing cortex (Camp et al ., 2015; Quadrato et al ., 2017; Velasco et al ., 2019; Yoon et al ., 2019), and they are capable of doing so in a reproducible fashion (Velasco et al ., 2019).…”

Benchmarking brain organoid recapitulation of fetal corticogenesis

“…BO are thus becoming central to the investigation of how genetic vulnerabilities or environmental perturbations can alter physiological neurodevelopment and seed the unfolding of psychiatric and neurological conditions 1,2 . As we and others recently demonstrated, the exposure of specific windows of vulnerability is proving of particular value, highlighting how temporally defined or even transient alterations in neurodevelopmental trajectories can bring about major mental health outcomes, from language delay to ASD [3][4][5] . Indeed, a growing body of literature testifies to the edge that BO are bringing to the modelling of complex neuropsychiatric disorders, from autism spectrum disorder to schizophrenia, bipolar disorder and beyond [6][7][8] .…”

CellDrift: Inferring Perturbation Responses in Temporally-Sampled Single Cell Data

“…Nowadays, researchers are increasingly considering the impact of time when designing experiments. For example, the genetic effects of autism risk genes have been studied during the development of the nervous system using brain organoids [13,14]. Additionally, influenza vaccination effects have been evaluated by monitoring immune responses over multiple follow-up periods [15].…”