Analyses of penetrant mutations and transcriptome studies implicate transcriptional dysregulation within the fetal cerebral cortex in the pathophysiology of autism spectrum disorders (ASD). However, the implicated regulatory elements, their target genes and their roles in development remain unclear.

Flora Vaccarino’s laboratory recently provided evidence that induced pluripotent stem cell (iPSC)-derived organoids offer a platform to study gene regulation in cortical development¹. Vaccarino proposes to use organoids derived from individuals with idiopathic ASD and unaffected family controls to analyze transcriptome and enhancer activity in single cells. The overarching aim of these studies is to investigate whether transcriptional dysregulation of specific cell types during early development represents a convergent pathophysiology in ASD.

One hypothesis is that this early dysregulation might affect the balance of excitatory and inhibitory neuron number, differentiation or function. The hypothesis will be tested using three convergent and complementary approaches, comparing cells from 20 individuals with idiopathic ASD and 20 unaffected family controls to assess: 1) genome-wide differentially active enhancers, 2) genome-wide differential expression of genes during development and 3) the enrichment of ASD-associated mutations within these genes and enhancer regions.

Specifically, Vaccarino’s laboratory and her collaborators will develop data sets of differentially active enhancers and differentially expressed transcripts in specific cell groups using single-cell ATAC-seq and RNA-seq experiments at three time points, marking transitions between neural stem cells, progenitors and post-mitotic neurons. Enhancer locations will be identified by supplementing data with the laboratory’s existing data set of 96,375 gene-linked developmental enhancers¹. Integrative analyses will then be carried out with the goal of understanding whether gene targets of differentially active enhancers are differentially expressed between individuals with ASD and controls, and whether dysregulated enhancers are active in specific cell types.

By further intersecting these findings with genomic data from various ASD cohorts (i.e., the Simons Simplex Collection, SPARK, MSSNG), Vaccarino’s team and her collaborators will determine whether differentially active genes and enhancers harbor ASD-associated mutations. The successful completion of this project will provide insights into the role that transcriptional dysregulation within specific cell types during early development plays in the pathophysiology of ASD.

1. Amiri A. et al. Science 362, eaat6720 (2018) PubMed