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 3D tissue development. Here we present a genome-wide CRISPR screen in induced pluripotent stem cell (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 congenital anomalies of the kidney and urinary tract (CAKUT) genes (CCDC170 and MYH7B), and provides a large candidate list of ciliopathy-related genes. Finally, identification of a cis-inhibitory effect of Jagged1 controlling epithelial proliferation shows how mosaic knockouts in pooled CRISPR screening can reveal ways of communication between heterogeneous cell populations in complex tissues. These data serve as a rich resource for the kidney research community and as a benchmark for future iPSC-derived organoid CRISPR screens.

Automated summary

Human organoids provide valuable insights into proliferation, lineage specification, and 3D tissue development. In this study, a genome-wide CRISPR screen was conducted in induced pluripotent stem cell (iPSC)-derived kidney organoids, resulting in a complex and high-quality dataset. The findings shed light on various aspects of biology, ranging from early development to adult epithelial morphogenesis. The dataset not only enhances mesoderm induction and identifies kidney disease genes, but also confirms genetic anomalies and provides a list of potential ciliopathy-related genes.