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MRNA sequencing of wildtype versus CEP83 knockout hiPSCs at diffirent time points of differentiation to kidney organoids [bulk RNA-seq]

ABSTRACT: Centrosomal protein 83 (CEP83) is a component of the distal appendages proteins of centrioles, which is necessary for the assembly of primary cilia. Previous studies have implicated primary cilia in normal development and tissue homeostasis, including kidney development. The kidney develops from human induced pluripotent stem cell (hiPSCs) in a stepwise process involving induction of specialized Nephron progenitors (NPs) in the intermediate mesoderm (IM), followed by their differentiation into kidney epithelia. Here, we used CRISPR-cas9 technology to knockout CEP83 in hiPSCs that were differentiated versus the wildtype hiPSCs into IM followed by kidney epithelial differentiation to analyze the role of CEP83 in human kidney epithelial differentiation. We used morphological analyses, gene expression studies and immunostaining to analyze IM and nephron differentiation. Bulk RNA and single cell sequencing showed that CEP83-/- IM cells abnormally upregulate regulatory transcription factors of lateral plate mesoderm (LPM) including OSR1, FOXF1, FOXF2, HAND2 and FEDRR., and downregulate marker genes in specific NPs ncluding; PAX8, HOXB7 and EYA1. Further, wildtype hiPSCs successfully differentiated into kidney organoids that upregulate key nephron markers, including NPHS1, CUBN and GATA3. In contrast, CEP83-/- hiPSCs failed to differentiate into nephron epithelia and didn’t express nephron marker genes. In a human system modeling kidney epithelial differentiation from hiPSCs, our data provide a new insight to the essential role of CEP83 in NPs differentiation and may help to better understand the pathogenesis of CEP83-associated renal developmental defects.

ORGANISM(S): Homo sapiens

PROVIDER: GSE205976 | GEO | 2022/10/12

REPOSITORIES: GEO

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mRNA sequencing of wildtype versus CEP83 knockout hiPSCs at diffirent time points of differentiation to kidney organoids [scRNA-seq]

Project description:Centrosomal protein 83 (CEP83) is a component of the distal appendages proteins of centrioles, which is necessary for the assembly of primary cilia. Previous studies have implicated primary cilia in normal development and tissue homeostasis, including kidney development. The kidney develops from human induced pluripotent stem cell (hiPSCs) in a stepwise process involving induction of specialized Nephron progenitors (NPs) in the intermediate mesoderm (IM), followed by their differentiation into kidney epithelia. Here, we used CRISPR-cas9 technology to knockout CEP83 in hiPSCs that were differentiated versus the wildtype hiPSCs into IM followed by kidney epithelial differentiation to analyze the role of CEP83 in human kidney epithelial differentiation. We used morphological analyses, gene expression studies and immunostaining to analyze IM and nephron differentiation. Bulk RNA and single cell sequencing showed that CEP83-/- IM cells abnormally upregulate regulatory transcription factors of lateral plate mesoderm (LPM) including OSR1, FOXF1, FOXF2, HAND2 and FEDRR., and downregulate marker genes in specific NPs ncluding; PAX8, HOXB7 and EYA1. Further, wildtype hiPSCs successfully differentiated into kidney organoids that upregulate key nephron markers, including NPHS1, CUBN and GATA3. In contrast, CEP83-/- hiPSCs failed to differentiate into nephron epithelia and didn’t express nephron marker genes. In a human system modeling kidney epithelial differentiation from hiPSCs, our data provide a new insight to the essential role of CEP83 in NPs differentiation and may help to better understand the pathogenesis of CEP83-associated renal developmental defects.

2022-10-12 | GSE205977 | GEO

A modular differentiation system maps multiple human kidney lineages from pluripotent stem cells [RNA-Seq]

Project description:Recent studies using human pluripotent stem cells (hPSCs) have developed protocols to induce kidney-lineage cells and reconstruct kidney organoids. However, the separate generation of metanephric nephron progenitors (NPs), mesonephric NPs and ureteric bud (UB) cells, which constitute embryonic kidneys, in in vitro differentiation culture systems has not been fully investigated. Here we created a culture system in which these mesoderm-like cell types as well as paraxial and lateral plate mesoderm-like cells were separately generated from hPSCs. We succeeded in recapitulating nephrogenic niches from separately induced metanephric NP-like and UB-like cells, which were subsequently differentiated into glomeruli, renal tubules and collecting ducts in vitro and further vascularized in vivo. Our selective differentiation protocols should contribute to understanding the mechanisms underlying human kidney development and diseases and also supply cell sources for regenerative therapies.

2020-07-15 | GSE146117 | GEO

A modular differentiation system maps multiple human kidney lineages from pluripotent stem cells [scRNA-Seq]

2020-07-15 | GSE146118 | GEO

Tet2 and Tet3 mediated active cytosine hydroxymethylation in Six2 progenitor cells is critical for nephron progenitor differentiation and nephron endowment

Project description:Nephron endowment is a key determinant of later life hypertension and kidney disease. Here we studied whether epigenetic changes, specifically the ten–eleven translocation (Tet) DNA demethylase family, Tet1, Tet2, and Tet3-mediated active DNA hydroxymethylation is necessary for gene expression regulation and kidney differentiation. We generated mice with deletion of Tet1, Tet2 or Tet3 in Six2 positive nephron progenitors (NP). We did not observe changes in development or kidney function in mice with nephron progenitor-specific deletion of Tet1, Tet2, Tet3 or Tet1/Tet2 or Tet1/Tet3. On the other hand, mice with combined Tet2 and Tet3 loss in Six2-positive NPCs failed to form nephrons leading to kidney failure and perinatal death. Tet2 and Tet3 loss in Six2-positive NPs resulted in defect in mesenchymal to epithelial transition and renal vesicle differentiation. Whole genome bisulfite sequencing, single cell RNA sequencing, and gene and protein expression assay identified a defect in expression in genes in the WNT-β-catenin signaling pathway in absence of Tet2 and Tet3 due to a failure in demethylation of these loci. Our results indicate the key role of Tet2 and Tet3-mediated active cytosine hydroxymethylation in NPs in kidney development and nephron endowment.

2022-11-23 | GSE212715 | GEO

Revisiting the Role of Notch in Nephron Segmentation Confirms A Role for Proximal Fate Selection During Mouse and Human Nephrogenesis

Project description:Notch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/fate tracing, and genetically modified human iPSC to revisit this question in developing mouse kidneys and human kidney organoids. We confirmed that Notch signaling is needed for maturation of all nephron lineages, and thus mature lineage markers fail to detect a fate bias. By contrast, early markers identified a distal fate bias in cells lacking Notch2, and a concomitant increase in early proximal and podocyte fates in cells expressing hyperactive Notch1 was observed. Orthogonal support for a conserved role for Notch signaling in the distal/proximal axis segmentation is provided by the demonstration that Nicastrin-deficient hiPSCs-derived organoids differentiate into TFA2B+ distal tubule and CDH1 connecting segment progenitors, but not into HNF4A+ or LTL+ proximal progenitors.

2022-05-04 | GSE201938 | GEO

Inducible three-factor direct reprogramming to nephron progenitors using piggyBac transposons

Project description:All nephrons in the mammalian kidney arise from a transient nephron progenitor population that is lost after birth. The recreation of nephron progenitors (NPs) and/or their maintenance in culture has been a major focus of renal regenerative strategies. Using a lentiviral screening approach, we previously generated an induced nephron progenitor (iNP) state in vitro using a pool of six transcription factors (SIX1, SIX2, HOXA11, OSR1, EYA1, SNAI2). Here, using an inducible piggyBac transposon system, we demonstrate efficient reprogramming to iNPs with only three transcription factors (SNAI2, EYA1 and SIX1). Coupled with maintenance in culture conditions supportive of this progenitor state, the resulting population can contribute to developing nephrons in vitro, ex vivo and in vivo. This approach provides a rapid and efficient method for the generation of NPs from human somatic cells.

2019-11-28 | GSE107410 | GEO

Single cell RNA sequencing reveals differential cell cycle activity in key cell populations during nephrogenesis

Project description:The kidney is a complex organ composed of more than 30 terminally differentiated cell types that all are required to perform its numerous homeostatic functions. De-fects in kidney development are a significant cause of chronic kidney disease in children, which can lead to kidney failure that can only be treated by transplant or dialysis. A better understanding of molecular mechanisms that drive kidney development is important for designing strategies to enhance renal repair and regeneration. In this study, we profiled gene expression in the developing mouse kidney at embryonic day 14.5 at single cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney. Cell cycle activity distinguishes between the “primed” and “self-renewing” sub-populations of nephron progenitors, with increased expression of the cell cycle related genes Birc5, Cdca3, Smc2 and Smc4 in “primed” nephron progenitors. Augmented Birc5 expression was also detected in immature distal tubules and a sub-set of ureteric bud cells, suggesting that Birc5 might be a novel key molecule required for early events of nephron patterning and tubular fusion between the distal nephron and the collecting duct epithelia.

2021-11-24 | GSE158166 | GEO

Expression data from metanephric mesenchyme induced to convert into nephron epithelia

Project description:During kidney development segmented epithelia of the nephron derive from progenitor cells in the metanephric mesenchyme after induction by secreted molecules from the ureteric bud. We have identified three distinct inductive activities from a ureteric bud cell line. These include leukemia inhibitory factor (LIF), neutrophil gelatinase-associated lipocalin (NGAL) and an active fraction currently referred to as ANX. Each of these activities induces segmented nephron epithelia in isolated rat metanephric mesenchyme over a time period of 7 days. This study was designed to characterize the temporal sequence of gene expression in the course of the conversion process induced by each of the distinct inducers. Keywords: time course

2007-07-01 | GSE5478 | GEO

ChIP-seq of Smad3 and EZH2 binding sites in hiPSC and iPSC-derived Nephron Progenitors

Project description:Chromatin immunoprecipitation sequencing analysis of Smad3 and EZH2 binding sites in hIPSCs and iPSC-derived nephron progenitors.

2022-12-01 | E-MTAB-10910 | biostudies-arrayexpress

Transcriptional response of cap mesenchyme (undifferentiated nephron progenitors) to Wnt activation

Project description:During mammalian kidney development, mesenchymal nephron progenitors (cap mesenchyme) differentiate into the epithelial cells that go on to form the nephron. Although differentiation of nephron progenitors is triggered by activation of Wnt/b-catenin signaling, constitutive activation of Wnt/b-catenin signaling blocks epithelialization of nephron progenitors. Full epithelialization of nephron progenitors requires transient activation of Wnt/b-catenin signaling. We performed transcriptional profiling of nephron progenitors responding to constitutive or transient activation of Wnt/b-catenin signaling. Nephron progenitors were FACS-isolated from BAC transgenic Six2GFPcre-positive embryonic kidneys at E16.5. Cells were aggregated by centrifugation at 850g for 5min and incubated in 10%FBS/DMEM containing either 4uM BIO or the equal volume of DMSO for 24hrs or 48hrs.

2012-09-11 | E-GEOD-39583 | biostudies-arrayexpress

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