In vivo perturb-seq of cancer and immune cells dissects oncologic drivers and therapy response

Abstract

AbstractGenetic perturbation screens with single cell readouts have enabled rich phenotyping of gene function and regulatory networks. These approaches have been challengingin vivo, especially in adult disease models such as cancer, which include mixtures of malignant and microenvironment cells. Here, we develop a multiplexin vivoperturb-seq CRISPRi platform for single cell genetic screens in cancer and immune cells that leverages intracranial convection enhanced delivery of sgRNA libraries into models of glioblastoma (GBM), a fatal brain cancer. Our results revealin vivospecific rewiring of genetic dependencies in response to radiotherapy, a potent yet non-curative therapy for GBM, as well as alterations of ligand-receptor interactions between microenvironment cells. In sum, we demonstrate the utility of multiplexed perturb-seq forin vivosingle cell dissection of adult tissue biology across multiple cell types in the context of therapeutic stimuli.