Regenerative landscape of intestinal organoids (bulk RNA-Seq 1)

Development of intestinal organoids from single intestinal stem cells is driven by the regenerative capacity of the intestinal epithelium. To unravel molecular mechanisms orchestrating organoid formation and self-organization, we developed a high-content image-based screening assay for an annotated compound library. We generated multivariate feature profiles for hundreds of thousands of individual organoids to quantitatively describe the phenotypic landscape of organoid development. Generated phenotypic fingerprints were then used to infer regulatory genetic interactions from a single screen, establishing a novel paradigm in genetic interaction screening applied to an emergent system. This allowed the identification of novel modules of genes that regulate cell identity transitions and maintain the balance between regeneration and homeostasis. We then characterized a crucial role of retinoic acid nuclear receptors in controlling the exit from the regenerative state and in driving enterocyte differentiation. By combining quantitative imaging with RNA sequencing we confirmed the role of endogenous retinoic acid signaling and metabolism in initiating transcriptional programs guiding intestinal epithelium cell fate transitions and identified a small molecule inhibitor of retinoid x receptor, RXR, that improved intestinal regeneration in vivo. We use RNA sequencing to describe transcriptional changes induced in intestinal organoids cultured in presence of retinoic signaling modulators.