Single cell transcriptomic profiling of human brain organoids reveals developmental timing- and cell-type-specific vulnerabilities induced by NRXN1 CNVs in schizophrenia

De novomutations and copy number variations (CNVs) inNRXN1(2p16.3) pose a significant risk for schizophrenia (SCZ). HowNRXN1CNVs impact cortical development in a cell type-specific manner and how disease genetic background modulates these phenotypes are unclear. Here, we leveraged human pluripotent stem cell-derived brain organoid models carryingNRXN1heterozygous deletions in isogenic and SCZ patient genetic backgrounds and conducted single cell transcriptomic analysis over the course of cortical brain organoid development from 3 weeks to 3.5 months. We identified maturing glutamatergic and GABAergic neurons as being consistently impacted due toNRXN1CNVs irrespective of genetic background, contributed in part by altered gene modules in ubiquitin-mediated pathways, splicing, and synaptic signaling. Moreover, while isogenicNRXN1CNVs impact differentiation and maturation of neurons and astroglia, cell composition and developmental trajectories of early neural progenitors are affected in SCZ-NRXN1CNVs. Our study reveals developmental timing dependentNRXN1CNV-induced cellular mechanisms in SCZ at single cell resolution and highlights the emergence of disease-specific transcriptomic signatures and cellular vulnerabilities, which can arise from interaction between genetic variants and disease background. Developing forebrain organoid samples generated from a cohort of human pluripotent stem cells including 4 donor derived healthy control iPSC lines, 4 schizophrenia patient derived iPSC lines, and 1 NRXN1 cKO hESC line. NRXN1 cKO hESC line samples include 2 replicates of d50 and d100 time points. All other samples are single replicate across time points (from d22/23 to d100/101).