CRISPR Knockout Screens Used to Reveal Brain Development Genes

CRISPR knockout screens have identified genes essential for transforming embryonic stem cells into brain cells, shedding light on early neural development and related disorders. Researchers led by Sagiv Shifman from The Hebrew University of Jerusalem, working with Binnaz Yalcin from INSERM, used genome-wide CRISPR methods to address a core question: which genes drive proper brain cell formation? They systematically disrupted roughly 20,000 genes in embryonic stem cells and during their shift into neurons, pinpointing disruptions that halt normal neural differentiation.

The screens, detailed in a Nature Neuroscience paper, mapped critical stages of neuron differentiation, identifying 331 genes required for generating neurons. Many had not been previously linked to brain development, offering potential insights into conditions like altered brain size, autism, and developmental delay. A key finding highlighted PEDS1, a gene vital for producing plasmalogens—specialized phospholipids abundant in myelin, the insulating sheath around nerve fibers. The genetic screen revealed PEDS1's role in nerve cell formation and maintaining brain size; its absence leads to smaller brains.

In two unrelated families, rare PEDS1 mutations correlated with severe developmental delay and reduced brain volume in affected children. Experimental inactivation of PEDS1 confirmed its necessity for neuron generation and migration, directly explaining the observed clinical symptoms. Prof. Shifman explains: “By tracking the differentiation of embryonic stem cells into neural cells and systematically disrupting nearly all genes in the genome, we created a map of the genes essential for brain development. This map can help us better understand how the brain develops and identify genes linked to neurodevelopmental disorders that have yet to be discovered. Identifying PEDS1 as a genetic cause of developmental impairment in children, and clarifying its function, opens the door to improved diagnosis and genetic counseling for families, and may eventually support the development of targeted treatments.” 

The team’s “essentiality map,” which shows when genes are required during development, also helped clarify differences between the mechanisms underlying autism and developmental delay. Genes that are broadly essential were more strongly associated with developmental delay, while genes that are specifically critical during the stages of nerve cell formation were more strongly associated with autism. This helps explain how disruptions in different pathways can lead to overlapping symptoms and supports the view that changes in early brain development can contribute to autism.