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.

人类类器官允许研究增殖、谱系规范和 3D 组织发育。在这里，我们在诱导多能干细胞 (iPSC) 衍生的肾脏类器官中展示了全基因组 CRISPR 筛选。诱导型基因组编辑、纵向采样和管状细胞和基质细胞的终点分选相结合，产生了一个复杂、高质量的数据集，揭示了从早期发育到“成人”上皮形态发生的广泛有见地的生物学。我们的功能数据集允许通过 ROCK 抑制改善中胚层诱导，包含单基因和复杂性状肾脏疾病基因，确认肾脏和泌尿道 (CAKUT) 基因（CCDC170 和 MYH7B）的另外两个先天性异常，并提供大量候选纤毛病列表-相关基因。最后，鉴定一个顺式-Jagged1 控制上皮增殖的抑制作用显示了混合 CRISPR 筛选中的马赛克敲除如何揭示复杂组织中异质细胞群之间的通信方式。这些数据为肾脏研究界提供了丰富的资源，并作为未来 iPSC 衍生的类器官 CRISPR 筛选的基准。