Spatial CRISPR maps gene effects in the brain

Spatial Perturb-seq enables pooled in vivo CRISPR screening with single-cell, whole-transcriptome readouts preserved within intact tissue architecture. Applied to the mouse hippocampus, the technology uncovers both cell-autonomous and microenvironmental effects of gene knockouts linked to neurodegenerative disease.

Conventional Perturb-seq – which pairs pooled CRISPR screens with single-cell RNA sequencing – disrupts native tissue morphology and loses spatial and cell-cell interaction information. Spatial Perturb-Seq handles this by delivering a pooled AAV library carrying barcoded CRISPR-Cas9 guide RNAs intracranially into Cas9-expressing mice, targeting 18 genes associated with Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis via GWAS. By deliberately keeping the multiplicity of infection low, perturbed cells end up surrounded by unedited neighbours, allowing the effects of a knockout to be teased apart from those it exerts on the cell itself.

The platform works with both sequencing-based (Stereo-seq) and probe-based (Xenium) spatial technologies, and across four mice, it captured data from more than 229,000 cells. Knockout of Lrrk2 – a key Parkinson's disease gene – produced the largest cell-autonomous transcriptomic response, including downregulation of the dendritic lncRNA Bc1, and microenvironmental changes involving Sparc, Dock10, and Map2k6, confirmed across three independent datasets. Cell-cell communication analysis, moreover, identified disrupted Lrp1 signalling in the vicinity of Lrrk2-knockout neurons, pointing to a potential mechanistic link with α-synuclein pathology.

The study was led by Kimberle Shen and Wei Leong Chew at the Genome Institute of Singapore. It was published on 21 February 2026 in Nature Communications (https://doi.org/10.1038/s41467-026-69677-6).