Project description:The addition of 5uM retinoic acid to kidney organoids at day 12 (day 7+5). This data is from the same experimental batch as data within GSE119561.
Project description:To define retinoic acid-responsive transcriptional programs in the intestinal stem cells, we performed RNA sequencing on stem cell-enriched intestinal organoids following 24-hour retinoic acid treatment. This dataset provides a resource for examining gene expression changes associated with retinoic acid signaling in intestinal stem cell-enriched epithelial cultures.
Project description:Retinoic acid promotes the in vitro growth, patterning and improves the cellular composition of human pluripotent stem-cell-derived intestinal organoids
Project description:During kidney development, an intermediate mesoderm (IM) give rise to distinct structures: the ureteric bud (UB) and the metanephric mesenchyme (MM). These structures differentiate further into the collecting duct and nephron, forming a mature kidney. Generating functional kidney organoids has been challenging due to incomplete development of the UB. Researchers have overcome this limitation by differentiating UB and MM separately and co-culturing them to generate kidney organoids. However, this study developed a co-culture-free method using retinoic acid (RA), plays important role in the anterior IM differentiation and BMP7 secreted by UB in vivo development. This protocol provided not only simplifies the complexity of kidney organoid generation but also advances our understanding of the crucial signaling pathways involved in kidney development.
Project description:During kidney development, an intermediate mesoderm (IM) give rise to distinct structures: the ureteric bud (UB) and the metanephric mesenchyme (MM). These structures differentiate further into the collecting duct and nephron, forming a mature kidney. Generating functional kidney organoids has been challenging due to incomplete development of the UB. Researchers have overcome this limitation by differentiating UB and MM separately and co-culturing them to generate kidney organoids. However, this study developed a co-culture-free method using retinoic acid (RA), plays important role in the anterior IM differentiation and BMP7 secreted by UB in vivo development. This protocol provided not only simplifies the complexity of kidney organoid generation but also advances our understanding of the crucial signaling pathways involved in kidney development.
Project description:Epiblast cells ingress into the primitive streak, undergoing mesendoderm (MES) specification, which subsequently gives rise to the mesoderm and endoderm. Although recent advances in human organoid technology facilitating the study of early post-implantation development, robust human models that accurately recapitulate MES specification and primitive streak (PS) formation remain lacking. Here, we showed that human induced pluripotent stem cells (iPSCs) can be employed to generate three-dimensional (3D) MES organoids that closely mimic in vivo human MES specification, particularly the cells from the anterior region of primitive streak. We revealed that formation of MES organoids depended on the appearance of PTEN, and PTEN abrogation potently impaired the MES organoids-derived definitive endoderm and mesoderm specification. To elucidate the molecular mechanisms underlying the defects induced by PTEN loss, we performed integrative multi-omic analyses‒including RNA sequencing (RNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and phospho‒proteomics‒on WT and PTEN−/− MES cells. These analyses indicated retinoic acid (RA) signalling as a critical pathway suppressed by PTEN during MES lineage specification. Moreover, we identified CYP26A1, a RA-degrading enzyme, as a key downstream effector of PTEN in MES cell generation. Notably, our results demonstrated that excessive RA was detrimental, while an optimal level of RA was indispensable for MES cell generation. Overall, our MES organoids provide a valuable platform for investigating human MES specification, and our findings demonstrated PTEN as a driver of MES lineage commitment through the inhibition of RA signalling.