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.人类类器官（organoids）可用于研究细胞增殖、谱系特化及三维组织发育过程。本研究报道了一项在诱导多能干细胞（induced pluripotent stem cell，iPSC）衍生的肾脏类器官中开展的全基因组CRISPR筛选（genome-wide CRISPR screen）。通过结合诱导型基因组编辑、纵向采样以及对肾小管细胞和基质细胞的终点分选，本研究构建了一套高质量的复杂数据集，揭示了覆盖从早期发育至‘成熟’上皮形态发生全过程的丰富深刻生物学机制。本研究的功能数据集可用于优化基于ROCK抑制的中胚层诱导方案，涵盖单基因及复杂性状肾病相关基因，验证了另外两个先天性肾与泌尿系统异常（congenital anomalies of the kidney and urinary tract，CAKUT）相关基因（CCDC170与MYH7B），并提供了一份庞大的纤毛病（ciliopathy）相关候选基因列表。最后，本研究鉴定出JAGGED1通过顺式抑制效应调控上皮细胞增殖的现象，阐明了混合池CRISPR筛选中的镶嵌型敲除如何助力发现复杂组织内异质性细胞群体间的信号交流机制。总体而言，本数据集既可作为肾脏研究领域的宝贵资源，也可作为未来基于诱导多能干细胞衍生类器官的CRISPR筛选研究的基准参照。