Analysis of haploinsufficiency in human neural progenitor cells: insights into early molecular effects of autism-related genes

Haploinsufficiency describes a phenomenon where one functional allele of a gene in a diploid cell or organism is insufficient for a normal phenotype. There are several neurodevelopmental disorders (NDD) affected by the haploinsufficiency phenomenon, and many of them are related to autism spectrum disorder (ASD). Here, we aim to identify genes involved in the early stages of neural differentiation when one of the two alleles is lost. We thus differentiated a genome-wide heterozygous loss-of-function CRISPR library into neural progenitor cells (NPCs) and defined about 250 genes essential for neural differentiation in a haploinsufficient manner. We were able to identify NDD-related dosage-sensitive pathways and pinpoint specific molecular processes affected by ASD-related genes. By comparing the molecular phenotypes of homozygote and heterozygote mutations, we could illuminate overlapping and distinct transcriptional pathways affected in the two mutant models, along with partial chemical rescue of some of these phenotypes. Our work provides a comprehensive framework for exploring dosage-sensitive regulation in early neural development and offers new insights into the embryonic molecular basis of ASD and other NDDs driven by gene dosage imbalance.