Spatially Resolved Panoramic in vivo CRISPR Screen via Perturb-DBiT [Spatial Transcriptomics]

However, current methods are mostly for small perturbation panels and the detection of a subset of protein-coding RNAs. We present Perturb-DBiT, a versatile approach for the simultaneous co-sequencing of spatial total RNA whole-transcriptome and single-guide RNAs (sgRNAs), base-by-base, on the same tissue section.

This method enables unbiased discovery of how genetic perturbations influence RNA regulation, cellular dynamics, and tissue architecture in situ. Applying Perturb-DBiT to a human cancer metastatic colonization model, we mapped large panels of sgRNAs across tumor colonies in multiple consecutive tissue sections alongside their corresponding total RNA transcriptomes, providing insights into how perturbations affect long non-coding RNA (lncRNA) co-variation, microRNA–mRNA interactions, and distinct amino acid-specific tRNA alterations linked to tumor migration and growth.