Flora Vaccarino, Professor, Child Study Center & Neuroscience, Yale University, “Gene regulation in telencephalic organoids in development and disease”

Topic: Gene regulation in telencephalic  organoids in development and disease

Abstract: Risk variants for complex developmental disorders are often located in noncoding regions of the genome, containing putative gene regulatory elements. The mapping and functional analysis of these elements, such as enhancers, is challenging, as enhancer’s activity is development- and tissue-specific and polymorphic across individuals. To examine the location and activity of gene regulatory elements (regulome) in early cortical development, we performed longitudinal analyses in human induced pluripotent stem cells (hiPSC)-derived cerebral cortical organoids with an integrated set of experimental approaches, including ChIP-seq for 3 histone marks; chromatin conformation analyses (Hi-C) to map putative enhancers to their target genes; and RNA-seq, to assess the effect of differential enhancer activity on gene expression.

Comparative transcriptome analyses of organoids with isogenic human brain tissue and external large datasets of human brain tissue placed organoids at very early stages of cortical development, before 16 weeks post-conception.  Globally, a total of 96,375 active enhancers were found to be associated with 22,835 protein-coding or lincRNA target genes. Furthermore, about 50% of the enhancers active in organoids were no longer active in fetal cortex. In organoids, more enhancers changed activities during the transition from neural stem cells to progenitors, as opposed to the transition from progenitors to neurons (15,485 vs 4,871; p-value < 0.0001 by Chi-square test).  Networks of correlated gene and enhancer modules could be assembled by K-means clustering of eigengene matrices into six and four global patterns of expression/activity across time. A pattern with progressive downregulation was enriched with enhancers whose activity is increased in recent human evolution, suggesting their relevance for human neural stem cells. Using WGS data of 242 families with autism spectrum disorder (ASD) from the Simons Simplex collection (SSC), we found that early enhancers, expressed only in organoids, were significantly enriched in inherited low allele frequency SNPs found in probands relative to their siblings (t-test, p-value < 0.003, 95% CI). In conclusions, hiPSC-derived organoids model embryonic to early fetal human brain development, stages that are difficult to study using postmortem tissue.  The organoid system promises to unravel genes and regulatory elements driving the onset of neurodevelopmental disorders.

About Dr. Vaccarino: I lead a multidisciplinary research group working towards new directions for the study of mammalian brain development, particularly human, using stem cell biology and genomics as tools. I have been studying brain development in animal models for over 20 years, and I have contributed fundamental work on the role of growth factor receptor signaling in the regulation of stem cell proliferation and cortical morphogenesis. We recently developed a “cortical organoid” model, where human induced pluripotent stem cells (hiPSCs)-derived cells grown in tri-dimensional culture recapitulate the early development of the human cerebral cortex (Mariani et al, 2012, 2015). We have been characterizing cellular phenotypes, transcriptomes and regulatory elements of hiPSCs and their neuronal derivatives using next-gen sequencing techniques. I am part of the PsychENCODE consortium (http://psychencode.org/), where my group’s role is to use organoids and fetal human brains to provide an in depth understanding of gene regulatory mechanisms in early stages of cortical development, when neural stem cell commit to diverse neuronal types. We are also using patient-derived organoid models to study the relevance of these early regulatory mechanisms for the pathophysiology of autism and Tourette syndrome. Another area of interest is the study of somatic mosaicism normal brain development and cell lineage formation (Bae et al, 2018). I am part of the Brain Somatic Mosaicism Network (BSMN), a multi-site consortium that studies somatic mosaicism and its implication for disease (https://www.synapse.org/bsmn), where our role is to study somatic mutations in Tourette syndrome (TS). Ultimately, we hope to use both animal and human tissue and experimental models to elucidate normal development and the pathophysiology of childhood neuropsychiatric disorders.