SUMMARY Autism spectrum disorder (ASD) is a disorder of brain development. Most cases lack a clear etiology or genetic basis, and the difficulty of reenacting human brain development has precluded understanding of ASD pathophysiology. Here we use three-dimensional neural cultures (organoids) derived from induced pluripotent stem cells (iPSCs) to investigate neurodevelopmental alterations in individuals with severe idiopathic ASD. While no known underlying genomic mutation could be identified, transcriptome and gene network analyses revealed upregulation of genes involved in cell proliferation, neuronal differentiation, and synaptic assembly. ASD-derived organoids exhibit an accelerated cell cycle and overproduction of GABAergic inhibitory neurons. Using RNA interference, we show that overexpression of the transcription factor FOXG1 is responsible for the overproduction of GABAergic neurons. Altered expression of gene network modules and FOXG1 are positively correlated with symptom severity. Our data suggest that a shift towards GABAergic neuron fate caused by FOXG1 is a developmental precursor of ASD.

Human induced pluripotent stem cells (hiPSCs) are emerging as a tool for understanding human brain development at cellular, molecular, and genomic levels. Here we show that hiPSCs grown in suspension in the presence of rostral neuralizing factors can generate 3D structures containing polarized radial glia, intermediate progenitors, and a spectrum of layer-specific cortical neurons reminiscent of their organization in vivo. The hiPSC-derived multilayered structures express a gene expression profile typical of the embryonic telencephalon but not that of other CNS regions. Their transcriptome is highly enriched in transcription factors controlling the specification, growth, and patterning of the dorsal telencephalon and displays highest correlation with that of the early human cerebral cortical wall at 8-10 wk after conception. Thus, hiPSC are capable of enacting a transcriptional program specifying human telencephalic (pallial) development. This model will allow the study of human brain development as well as disorders of the human cerebral cortex.human embryonic stem cell | embryo | differentiation | cortical layer E merging data highlight the complexity and dynamic nature of gene expression in the central nervous system (CNS) and the divergence between human and other mammalian species, which is especially pronounced in the developing brain (1-4). Exploring such differences may reveal the genetic underpinnings of the larger size and complex architecture of the human brain and elucidate the molecular and cellular substrates of higher cognitive functions, as well as of our vulnerability to neurodevelopmental and neurodegenerative disorders. To understand the genetic programs that drive cell specification and differentiation in the human brain, it is important to develop model systems that recapitulate dynamic aspects of neural development, in addition to making inferences from commonly used models of lower mammalian species.Recapitulating human neural development in vitro using human induced pluripotent stem cells (hiPSCs) can provide our first understanding of how genetic variation and disease-causing mutations influence neural development. Human iPSCs generated from reprogrammed cells can be differentiated into any tissue, including the CNS, while maintaining the genetic background of the individual of origin. These critical features have been exploited to model monogenic forms of neurodevelopmental disorders, such as Rett and Timothy syndromes, and even psychiatric disorders with complex inheritance, such as schizophrenia (5-7). The brain and spinal cord develop according to distinct differentiation programs from the earliest stages of CNS development (i.e., at the progenitor stage during gastrulation) (8, 9). Regional differences in gene expression within stem and progenitor cells appear at the onset of the formation of both mouse (10, 11) and human CNS, as shown by recent studies of the human transcriptome using postmortem tissue (4).Neural cells are thought to differentiate by "default" into an anterior, for...

Recent research on disparate psychiatric disorders has implicated rare variants in genes involved in global gene regulation and chromatin modification, as well as many common variants located primarily in regulatory regions of the genome. Understanding precisely how these variants contribute to disease will require a deeper appreciation for the mechanisms of gene regulation in the developing and adult human brain. The PsychENCODE project aims to produce a public resource of multidimensional genomic data using tissue- and cell type–specific samples from approximately 1,000 phenotypically well-characterized, high-quality healthy and disease-affected human post-mortem brains, as well as functionally characterize disease-associated regulatory elements and variants in model systems. We are beginning with a focus on autism spectrum disorder, bipolar disorder and schizophrenia, and expect that this knowledge will apply to a wide variety of psychiatric disorders. This paper outlines the motivation and design of PsychENCODE.

Genes implicated in neuropsychiatric disorders are active in human fetal brain, yet difficult to study in a longitudinal fashion. We demonstrate that organoids from human pluripotent cells model cerebral cortical development on the molecular level before 16 weeks post-conception. A multi-omics analysis revealed differentially active genes and enhancers with the greatest changes occurring at transition from stem cells to progenitors. Networks of converging gene and enhancer modules were assembled into six and four global patterns of expression/activity across time. A pattern with progressive downregulation was enriched with human-gained enhancers, suggesting their importance in early human brain development. A few convergent gene and enhancer modules were enriched in autism-associated genes and genomic variants in autistic children. The organoid model helps identify functional elements that may drive disease onset.