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Diverse risk genes have been identified for neurodevelopmental disorders (NDDs),but how these genes converge on similar biological pathways in neurons,and thus give rise to similar phenotypes,is unclear. Here we apply a pooled CRISPR approach to successfully target 23 NDD loss-of-function genes with roles in chromatin biology and examine convergent effects on gene expression across human induced pluripotent stem cell-derived neural progenitor cells,glutamatergic neurons and GABAergic neurons. Points of convergence vary between these cell types,with the greatest number of convergent genes and strongest convergent networks in mature glutamatergic neurons,where they broadly represent synaptic,epigenetic and,unexpectedly,mitochondrial pathways. The most convergent networks were observed between NDD genes with shared biological annotations,clinical associations and co-expression patterns in human post-mortem brain. Drugs that were predicted to reverse convergent transcriptomic signatures and/or arousal and sensory processing behaviors ameliorated behavioral phenotypes in zebrafish NDD gene mutants. These results suggest that convergent effects of NDD risk genes could provide clinically useful insights. By studying 23 neurodevelopmental disorder genes across model systems and brain cell types,the authors uncovered shared downstream effects that converge on synaptic biology,epigenetic regulation and mitochondrial function. View Publication

Rett syndrome arises from loss-of-function mutations in the X-linked chromatin regulator MECP2,yet the earliest molecular derailments in development are poorly defined. Using isogenic human embryonic stem cell (hESC) models carrying three patient-derived MECP2 mutations,we followed the transcriptome from pluripotency through neuroectoderm,neural stem/progenitor stages. Developmental stage dominated transcriptional variance,but mutants shared a secondary program enriched for synaptic-membrane and extracellular matrix genes. Single-cell/bulk profiling at the embryonic stem cell (ESC) stage revealed partial naïve-like drift,marked by the up-regulation of the naïve-enriched factor ZFP42/REX1 and related markers in MECP2-mutant lines. Among convergently dysregulated genes,the cortical determinant EMX1 showed an abnormal developmental trajectory,early repression followed by overshoot,and was consistently altered across independent Rett PSC models. Single-nucleus RNA-seq of cerebral organoids uncovered allele-specific yet convergent disturbances in cortical lineage allocation. These data chart a continuous developmental trajectory for MECP2-mutant cells and nominate naïve-like drift and mis-timed EMX1 expression as tractable entry points for dissecting Rett pathogenesis. Graphical abstract Highlights•MECP2 mutations induce an early naïve-like transcriptional drift in hESCs•EMX1 shows a conserved abnormal developmental trajectory across Rett models•Shared transcriptional programs emerge during neural induction in MECP2 mutants•Rett cerebral organoids display mutation-specific shifts in lineage allocation In this article,Flamier and colleagues show that MECP2 mutations perturb human neurodevelopment from the pluripotent stage onward. Using isogenic hESC and organoid models,they identify an early naïve-like transcriptional drift,abnormal EMX1 timing,and convergent defects in cortical lineage allocation,revealing continuous developmental vulnerability in Rett syndrome. View Publication