The development of intestinal organoids from single adult intestinal stem cells in vitro recapitulates the regenerative capacity of the intestinal epithelium1,2. Here we unravel the mechanisms that orchestrate both organoid formation and the regeneration of intestinal tissue, using an image-based screen to assay an annotated library of compounds. We generate multivariate feature profiles for hundreds of thousands of organoids to quantitatively describe their phenotypic landscape. We then use these phenotypic fingerprints to infer regulatory genetic interactions, establishing a new approach to the mapping of genetic interactions in an emergent system. This allows us to identify genes that regulate cell-fate transitions and maintain the balance between regeneration and homeostasis, unravelling previously unknown roles for several pathways, among them retinoic acid signalling. We then characterize a crucial role for retinoic acid nuclear receptors in controlling exit from the regenerative state and driving enterocyte differentiation. By combining quantitative imaging with RNA sequencing, we show the role of endogenous retinoic acid metabolism in initiating transcriptional programs that guide the cell-fate transitions of intestinal epithelium, and we identify an inhibitor of the retinoid X receptor that improves intestinal regeneration in vivo.

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肠道类器官再生的表型景观

从单个成体肠道干细胞体外培养出的肠道类器官概括了肠道上皮的再生能力1, 2。在这里，我们使用基于图像的屏幕来分析带注释的化合物库，从而揭示了协调类器官形成和肠道组织再生的机制。我们为数十万个类器官生成多变量特征配置文件，以定量描述它们的表型景观。然后，我们使用这些表型指纹来推断调控遗传相互作用，建立一种新方法来绘制新兴系统中的遗传相互作用。这使我们能够识别调节细胞命运转变并维持再生和体内平衡之间平衡的基因，解开以前未知的几种途径的作用，其中包括视黄酸信号。然后，我们描述了视黄酸核受体在控制退出再生状态和驱动肠细胞分化中的关键作用。通过将定量成像与 RNA 测序相结合，我们展示了内源性视黄酸代谢在启动指导肠上皮细胞命运转变的转录程序中的作用，并且我们确定了一种可改善体内肠道再生的维甲酸 X 受体抑制剂。