Genome-wide screening in human kidney organoids identifies developmental and disease-related aspects of nephrogenesis

Human organoids allow the study of proliferation, lineage specification, and three-dimensional tissue development. Here, we present a genome-wide CRISPR screen in iPSC-derived kidney organoids. The combination of inducible genome editing, longitudinal sampling and endpoint sorting of tubular and stromal cells generated a complex, high-quality dataset uncovering a broad spectrum of insightful biology from early development to ‘adult’ epithelial morphogenesis. Our functional dataset allows improving mesoderm induction by ROCK inhibition, contains monogenetic and complex trait kidney disease genes, confirms two additional CAKUT genes (CCDC170 and MYH7B), and provides a large candidate list of ciliopathy-related genes. Finally, the identification of a cis-inhibitory effect of Jagged1 controlling epithelial proliferation shows how mosaic knockouts in pooled CRISPR screening can discover ways of communication between heterogeneous cell populations in complex tissues. Collectively, these data serve both as a rich resource for the kidney community and as a benchmark for future iPSC-derived organoid CRISPR screens.