Autism spectrum disorders (ASDs) affect 1%-2.5% of children worldwide. We suggest that etiological and genetic heterogeneity might converge in a few neurobiological downstream pathways. We have been investigating the pathobiology of ASD with large brain volume (macrocephaly), a phenotype which confers poorer prognosis. Ongoing studies have shown that telencephalic organoids differentiated in vitro from induced pluripotent stem cells (iPSC) derived from patients with ASD and macrocephaly have increased cell proliferation, increased synaptic growth and overproduction of GABAergic inhibitory neurons, indicating an early imbalance in glutamate/GABA neuron ratio. RNA interference experiments suggested that the overproduction of GABAergic cells is attributable, at least in part, to an increase in expression of FOXG1, a master regulatory transcription factor crucial for telencephalic development. Major goals of this application are (1) to expand our analysis of the developmental pathways that are dysregulated in ASD to a larger number of families and (2) to understand to what extent developmental alterations we identified in ASD with macrocephaly also apply to ASD in general. To this end, we will obtain data on neurobiological measures, transcriptome and chromatin active regions in organoids derived from ASD patients with enlarged brain size and ASD patients with normal brain size. The altered gene regulatory network will be inferred and the two networks will be compared to understand similarities and differences in the two subgroups of ASD. To begin to understand the upstream causes of these developmental alterations, we will then investigate whether patients with ASD carry an increased burden of rare genomic variations in regions of the genome that participate in this regulatory network. Finally we will perform overexpression and RNAi knockdown experiments to examine the specific role of our current best candidate transcription factor, FOXG1, in the constellation of neurobiological and transcriptome alterations found in ASD-derived progenitors. We will assess the impact of perturbing FOXG1 gene expression on neurobiological functions (cell proliferation, glutamate/GABA neuron fate, synaptic growth), transcriptome and activity of transcription regulatory regions by RNA-seq and ChIP-seq, respectively, to gain insights into the role of a FOXG1-driven transcriptional program in the aberrant neuronal differentiation of ASD-derived neural progenitors. In summary, in this application we delineate strategies for (1) identifying gene networks and biological pathways that characterize altered development in two subgroups of ASD; (2) testing the causal role of one crucial node in such networks, the transcription factor FOXG1, which is over- active in ASD with macrocephaly; and (3) identifying regulatory factors, both genetic and epigenetic, upstream from neurobiological and gene expression abnormalities. The impact of these experiments will be the definition of a number of biological functions and molecular markers that are implicated in the neurobiology of ASD.

Public Health Relevance

In this application, we identify neurodevelopmental pathways that are altered in idiopathic autism spectrum disorders (ASD), for which no genetic cause has yet been identified, focusing on the subset of patients with a large brain size (macrocephaly) and comparing with ASD with normal brain size. Using 'organoids', which are organized structures, derived from induced pluripotent stem cells (iPSC) recapitulating forebrain development, we will obtain and integrate multiple sources of information, including the transcriptome, the activity of transcription regulatory regions and cellular phenotypes. The impact of these experiments will be the definition of a number of biological functions and molecular markers assayable in iPSCs for neurobiologically distinct subtypes of ASD, which have direct therapeutic implications insofar as they may be used to ameliorate altered neurobiology.

National Institute of Health (NIH)
National Institute of Mental Health (NIMH)
Research Project (R01)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-MDCN-P (57)R)
Program Officer
Panchision, David M
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Yale University
Schools of Medicine
New Haven
United States
Zip Code
Ardhanareeswaran, Karthikeyan; Mariani, Jessica; Coppola, Gianfilippo et al. (2017) Human induced pluripotent stem cells for modelling neurodevelopmental disorders. Nat Rev Neurol 13:265-278