BRAIN ORGANOID MODELLING OF HUMAN CORTICOGENESIS:THE PARADIGM OF WEAVER SYNDROME

Multiple strategies of brain organoidogenesis have enabled the investigation of human cerebral corticogenesis in-vitro with increasing accuracy. However, little is yet known about how closely the gene co-expression patterns seen in brain organoids (BO) match those of fetal cortex. Here we benchmarked BO against fetal corticogenesis by integrating transcriptomes from in-house differentiated cortical BO (CBO), other BO systems, human fetal brain samples processed in-house, and pre-natal cortices from the BrainSpan Atlas. We identified and ranked co-expression patterns and hubs of corticogenesis and CBO differentiation, highlighting well-preserved and variable trends across BO protocols, and we found heterochronicity of differentiation across BO models compared to fetal cortex. Once performed this benchmarking, we used CBO for disease-modelling of Weaver syndrome (WS), a rare disease characterized by intellectual disability. WS is associated with mutations in Polycomb repressive complex 2, a repressor of gene expression through H3K27me3. We differentiated patient-derived CBO and profiled their transcriptome and epigenome at different time-points, revealing upregulation of genes involved in neuronal maturation and migration as well as alteration of glucose metabolism in WS. Intersection of differentially expressed genes between WS- and control-CBO across stages with H3K27me3 ChIP-seq peaks, DNA-methylation profiles and dysregulated genes in CBO from a CRISPR/Cas9-engineered EZH2 KO revealed a set of PRC2 targets possibly mediating the WS intellectual disability phenotype. Our approach identified commonalities and divergences between state-of-the-art BO systems, providing a resource to query when modelling human corticogenesis, and identified molecular phenotypes and targets relevant for WS, generating the framework for future potential therapeutic intervention.