In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

TLDR

Human genetic studies have identified far more disease risk genes and loci than can be systematically studied. The study applies in vivo Perturb‑Seq to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay de novo loss‑of‑function risk genes. CRISPR‑Cas9 was used to introduce pooled frameshift mutations into developing mouse brains in utero, and single‑cell RNA‑sequencing of perturbed cells postnatally enabled in vivo Perturb‑Seq to assess how diverse mutations affect cell types and states. The screen uncovered cell‑type‑specific, evolutionarily conserved gene modules in neuronal and glial cells, with recurrent modules and cell types affected across perturbations, highlighting shared cellular effects of ASD/ND risk genes.

Abstract

The number of disease risk genes and loci identified through human genetic studies far outstrips the capacity to systematically study their functions. We applied a scalable genetic screening approach, in vivo Perturb-Seq, to functionally evaluate 35 autism spectrum disorder/neurodevelopmental delay (ASD/ND) de novo loss-of-function risk genes. Using CRISPR-Cas9, we introduced frameshift mutations in these risk genes in pools, within the developing mouse brain in utero, followed by single-cell RNA-sequencing of perturbed cells in the postnatal brain. We identified cell type-specific and evolutionarily conserved gene modules from both neuronal and glial cell classes. Recurrent gene modules and cell types are affected across this cohort of perturbations, representing key cellular effects across sets of ASD/ND risk genes. In vivo Perturb-Seq allows us to investigate how diverse mutations affect cell types and states in the developing organism.