Coordinated programs of gene expression drive brain development. It is unclear which transcriptional programs, in which cell-types, are affected in neuropsychiatric disorders such as schizophrenia. Here we integrate human genetics with transcriptomic data from differentiation of human embryonic stem cells into cortical excitatory neurons. We identify transcriptional programs expressed during early neurogenesis in vitro and in human foetal cortex that are down-regulated in DLG2−/− lines. Down-regulation impacted neuronal differentiation and maturation, impairing migration, morphology and action potential generation. Genetic variation in these programs is associated with neuropsychiatric disorders and cognitive function, with associated variants predominantly concentrated in loss-of-function intolerant genes. Neurogenic programs also overlap schizophrenia GWAS enrichment previously identified in mature excitatory neurons, suggesting that pathways active during prenatal cortical development may also be associated with mature neuronal dysfunction. Our data from human embryonic stem cells, when combined with analysis of available foetal cortical gene expression data, de novo rare variants and GWAS statistics for neuropsychiatric disorders and cognition, reveal a convergence on transcriptional programs regulating excitatory cortical neurogenesis.
Genetic studies robustly implicate perturbation of DLG2-scaffolded mature postsynaptic signalling complexes in schizophrenia. Here we study in vitro cortical differentiation of DLG2 -/human embryonic stem cells via integrated phenotypic, gene expression and disease genetic analyses. This uncovers a developmental role for DLG2 in the regulation of neural stem cell proliferation and adhesion, and the activation of transcriptional programs during early excitatory corticoneurogenesis. Down-regulation of these programs in DLG2 -/lines delays expression of cell-type identity and causes marked deficits in neuronal migration, morphology and active properties. Genetic risk factors for neuropsychiatric and neurodevelopmental disorders converge on these neurogenic programs, each disorder displaying a distinct pattern of enrichment. These data unveil an intimate link between neurodevelopmental and mature signalling deficits contributing to disease -suggesting a dual role for known synaptic risk genes -and reveal a common pathophysiological framework for studying the neurodevelopmental origins of Mendelian and genetically complex mental disorders. Results Knockout generation and validationTwo DLG2 -/lines were created from H7 hESCs using the CRISPR/Cas9-D10A nickase system targeting the first PDZ domain ( Figure S1). Sequencing revealed no off-target mutations (see Methods, Figure S2 & Table S1). A significant decrease in DLG2 mRNA was observed for exons spanning the first PDZ domain, with a similar decrease inferred for PDZ-containing transcripts, indicating degradation of DLG2 -/transcripts via nonsense-mediated decay ( Figure S3A, B). Quantitative mass spectrometry-based proteomic analysis of peptide-affinity pulldowns using the NMDA receptor NR2 subunit PDZ peptide ligand (Husi and Grant, 2001) confirmed the presence of DLG2 in pulldowns from WT but not DLG2 -/lines ( Figure S3C-F & Table S2). Genotyping revealed no CNVs in either DLG2 -/line relative to WT ( Figure S4A). Both DLG2 -/lines expressed pluripotency markers OCT4, SOX2 and NANOG at 100% of WT levels ( Figure S4B-E). Cells were extensively characterised for their cortical identity using western blotting and immunocytochemistry from day 20 to 60 ( Figure S5). Over 90% of day 20 cells were positive for FOXG1, PAX6 and SOX2 confirming their dorsal forebrain fate ( Figure S5A-B). DLG2 regulates neural stem-cell proliferation and adhesionRNA was extracted in triplicate from each line at 4 timepoints spanning cortical excitatory neuron development (Figure 1A, B) and gene expression quantified. To robustly identify genes dysregulated by DLG2 knockout, expression data from the 2 DLG2 -/lines were pooled and compared to a WT sister line at each timepoint (see Methods). Disruption of DLG2 had a profound effect: of the >13,000 protein-coding genes expressed at each timepoint, ~7% were differentially expressed between DLG2 -/and WT at day 15, rising to 40-60% between days 20 and 30 then decreasing to ~25% by day 60 ( Figure 1C). Strikingly, the 3 genes with the strongest ...
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