Efficient identification of new targets to treat human disease requires a scalable way to link genotype to phenotype directly in the target organ. Pooled CRISPR screening with single-cell RNA sequencing as a readout (Perturb-seq) has emerged as a method for functional genomics but is typically applied in vitro and is limited in scale. Here, we combine in vivo Perturb-seq via adeno-associated virus (AAV)-mediated delivery with a statistical framework allowing for signal deconvolution after multiple random perturbations per cell (compressed Perturb-seq), to develop in vivo compressed AAV-Perturb-seq, a scalable way to perform high-throughput, cell-autonomous functional genomics in a desired target organ. We apply this approach to study the effect of 585 gene knockouts on the cardiomyocyte transcriptome. We identify that alterations in the mitochondrial transcriptome are a common response to genetic perturbation, a finding independently validated across species and perturbation modalities. We identify very few synergistic perturbations, despite observing frequent combinatorial effects. Broadly, our work establishes a platform to facilitate in vivo functional genomics in a target organ with direct applicability to identifying therapeutic targets for the treatment of human disease.
Kuznetsov, I. A., Li, K., Yang, Y., Zhao, W., Zhou, W., Zhu, W., Liang, J., Li, J., Edwards, J. J., Arany, Z.
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