Spatial perturb-seq: single-cell functional genomics within intact tissue architecture

We develop Spatial Perturb-Seq, an in vivo CRISPR technology that interrogates multiple genes within single cells of intact tissues, compatible with both sequencing-based and probe-based spatial technologies. We apply Spatial Perturb-Seq to knock out risk genes for neurodegenerative diseases in the mouse brain, uncovering cell autonomous and cell-cell microenvironmental effects within the spatially intact tissue. Spatial Perturb-Seq functionally screens multiple genes in situ and in vivo, bypasses cell processing steps that skew cell type representation, identifies intracellular and intercellular effects of knockouts, and identifies candidate genes underlying dysregulated neuronal intercellular communication pathways. Spatial CRISPR screens probe the functional impact of mutations within intact tissues. Here, authors present Spatial Perturb-Seq, a technology that localizes CRISPR perturbations and cell identities in situ, uncovers communication between cells, and shows how genes act beyond their cellular borders.