Generating Patterned Kidney Organoids for Studying Development and Diseases [bulk RNA-Seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA545106 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9134800_1.fastq.gz | Fastqsanger.gz | |||
| SRR9134800_2.fastq.gz | Fastqsanger.gz | |||
| SRR9134801_1.fastq.gz | Fastqsanger.gz | |||
| SRR9134801_2.fastq.gz | Fastqsanger.gz | |||
| SRR9134802_1.fastq.gz | Fastqsanger.gz |
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Project description:Generating Patterned Kidney Organoids for Studying Development and Diseases
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Project description:Generating Patterned Kidney Organoids for Studying Development and Diseases [scRNA-Seq]
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Project description:Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. By single cell RNA-sequencing, we identify a subset of nephron progenitor cells as a potential source of the vasculature. Upon implantation into host mice, these kidney organoids undergo further structural and functional maturation, as demonstrated by the size-selective handling of dextran. Based on this differentiation platform, we establish an in vitro model of autosomal recessive polycystic kidney disease (ARPKD) by differentiating induced PSCs (iPSCs) from an ARPKD patient into 3D kidney organoids that develop tubule cysts in response to cAMP upregulation. The cystogenesis phenotype can be effectively prevented by gene correction or drug treatment. Our studies provide a versatile platform for studying human kidney development and diseases, and opens new avenues for modeling disease pathogenesis and performing patient-specific drug screening.
2019-06-01 | GSE132023 | GEO
Project description:Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental processes and tissue architectures, but the intrinsic limitations, such as variability and a lack of vasculature, have greatly hampered their application. Here we establish a highly efficient and versatile protocol for generating vascularized three-dimensional (3D) kidney organoids. We employ dynamic modulation of WNT signaling to control the relative proportion of proximal versus distal nephron segments, thereby producing a correlative level of VEGFA to define the resident vascular network. By single cell RNA-sequencing, we identify a subset of nephron progenitor cells as a potential source of the vasculature. Upon implantation into host mice, these kidney organoids undergo further structural and functional maturation, as demonstrated by the size-selective handling of dextran. Based on this differentiation platform, we establish an in vitro model of autosomal recessive polycystic kidney disease (ARPKD) by differentiating induced PSCs (iPSCs) from an ARPKD patient into 3D kidney organoids that develop tubule cysts in response to cAMP upregulation. The cystogenesis phenotype can be effectively prevented by gene correction or drug treatment. Our studies provide a versatile platform for studying human kidney development and diseases, and opens new avenues for modeling disease pathogenesis and performing patient-specific drug screening.
2019-05-29 | GSE131841 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-06-01 | GSE132026 | GEO
Project description:Loss of contractility and acquisition of an epithelial phenotype of vascular smooth muscle cells (VSMCs) are key events in proliferative vascular pathologies such as atherosclerosis and post-angioplastic restenosis. There is no proper cell culture system allowing VSMC differentiation so that it is difficult to delineate the molecular mechanism responsible for proliferative vasculopathy. We investigated whether a micro-patterned substrate could restore the contractile phenotype of VSMCs in vitro. To induce and maintain the differentiated VSMC phenotype in vitro, we introduced a micro-patterned groove substrate to modulate the morphology and function of VSMCs.
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Project description:With the rapid development of stem cell technology, the advent of three-dimensional (3D) cultured brain organoids has opened a new avenue for studying human neurodevelopment and neurological disorders. Brain organoids are stem-cell-derived 3D suspension cultures that self-assemble into an organized structure with cell types and cytoarchitectures recapitulating the developing brain. In recent years, brain organoids have been utilized in various aspects, ranging from basic biology studies, to disease modeling, and high-throughput screening of pharmaceutical compounds. In this review, we overview the establishment and development of brain organoid technology, its recent progress, and translational applications, as well as existing limitations and future directions.
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Project description:Hematopoietic stem cells (HSCs) derive from the hemogenic endothelium of the dorsal aorta, which develops in spatial and functional proximity to the heart anlagen in the human embryo. Despite the biomedical importance of HSCs, their in vitro induction and niche-like stabilization in a proper developmental context is challenging and poorly established. The underlying reasons include the poorly understood signals controlling HSC formation and the lack of unequivocal markers specifying their stages of differentiation and maturation. Our recently established human pluripotent stem cell (hPSC)-derived heart-forming organoids (HFOs) represent complex, well-patterned multi-tissue structures recapitulating key aspects of heart, foregut and vasculature development. Modulating HFO development by the stage-dependent supplementation of hemato-endothelial factors, we here report the generation of blood-generating-HFOs (BG-HFOs). While maintaining their well-patterned heart anlagen, BG-HFOs comprise a dense, mesenchyme-embedded endothelial layer giving rise to hematopoietic cells thereby resembling – in vitro - aspects of the intra-embryonic region giving rise to definitive hematopoiesis in vivo. Single cell-RNA sequencing of BG-HFOs revealed a gene expression signature of hematopoietic progenitor cells (HPCs) as well as patterns resembling hematopoietic derivatives such as erythroid, megakaryocytic and myeloid cells. Notably, BG-HFO-derived CD34pos CD43pos and CD34neg CD43pos cells display erythroid and myeloid potential in colony forming unit (CFU) assays, while CD34pos CD43neg HPCs retain lymphoid potential, observed via generation of T-cell progenitors in artificial thymic organoid (ATO)-based assays. This suggests presence of different multipotent HPCs in BG-HFOs and a potential transient downregulation of CD43 in lymphoid-restricted HPCs. Together, BG-HFOs represent the first human model of cardiac, endothelial and multipotent-hematopoietic cell co-development. The study promotes research on the multi-tissue interactions of hematopoiesis in vitro, overcoming limitations of such studies in the human embryo.
2024-08-06 | GSE239748 | GEO
Project description:Current kidney organoids model development and diseases of the nephron but not the contiguous epithelial network of the kidney's collecting duct (CD) system. Here, we report the generation of an expandable, 3D branching ureteric bud (UB) organoid culture model that can be derived from primary UB progenitors from mouse and human fetal kidneys, or generated de novo from human pluripotent stem cells. In chemically-defined culture conditions, UB organoids generate CD organoids, with differentiated principal and intercalated cells adopting spatial assemblies reflective of the adult kidney's collecting system. Aggregating 3D-cultured nephron progenitor cells with UB organoids in vitro results in a reiterative process of branching morphogenesis and nephron induction, similar to kidney development. Applying an efficient gene editing strategy to remove RET activity, we demonstrate genetically modified UB organoids can model congenital anomalies of kidney and urinary tract. Taken together, these platforms will facilitate an enhanced understanding of development, regeneration and diseases of the mammalian collecting duct system.
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Project description:In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brainin vitro. Here, we developed a method by assembling polydimethylsiloxane (PDMS) devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termedMorphogen-gradientInducedBrainOrganoids (MIBOs). At 3.5 weeks, MIBOs replicated Dorsal-Ventral patterning observed in the Ganglionic Eminence (GE). Analysis of matured MIBOs through single-cell RNA sequencing revealed distinct Dorsal GE derived CALB2+ interneurons (INs), Medium Spiny Neurons (MSNs), and MGE derived cell types. Finally, we demonstrate long term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.
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