In vivo perturb-seq dissects oncologic drivers of glioblastoma and its microenvironment

Genetic perturbation screens with single cell readout have enabled rich phenotyping of gene function and regulatory networks. However, these approaches have been challenging in vivo and have not been achieved in cancer, which include mixtures of malignant and microenvironment cells. Here, we developed an in vivo perturb-seq platform for single cell genetic screens in glioblastoma (GBM) models that leverages convection enhanced delivery (CED) for delivery of genetic perturbations into intact tumors. Our platform reveals in vivo rewiring of transcriptional programs by radiotherapy, as well as alterations of ligand-receptor interactions between microenvironment cells thus demonstrating the utility of this platform for in vivo single cell resolution dissection of complex cancer phenotypes, such as therapeutic interventions, across multiple cell types.