Single cell RNA sequencing of kidney tubuloids and the tissue that the tubuloids were derived from
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA421423 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6356580_1.fastq.gz | Fastqsanger.gz | |||
| SRR6356580_2.fastq.gz | Fastqsanger.gz | |||
| SRR6356571_1.fastq.gz | Fastqsanger.gz | |||
| SRR6356571_2.fastq.gz | Fastqsanger.gz | |||
| SRR6356581_1.fastq.gz | Fastqsanger.gz |
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Project description:Adult Stem Cell (ASC )-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney tubular epithelial organoids (‘tubuloids’). Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). The structures retain a normal number of chromosomes. Human tubuloids represent proximal as well as distal nephron segments, as evidenced by gene expression, immunofluorescence and tubular functional analyses. BK virus infection of tubuloids recapitulates in vivo phenomena. "Tumoroids" can be established from Wilms nephroblastoma. Kidney tubuloids from urine from a subject with Cystic Fibrosis (CF) allows ex vivo assessment of treatment efficacy. Finally, tubuloids cultured on microfluidic organ-on-a-chip plates adopt a tubular conformation and display active (trans-)epithelial transport function. Adult kidney-derived epithelial tubuloids allow studies of hereditary, infectious and malignant kidney disease in a personalized fashion.
2018-12-20 | GSE107794 | GEO
Project description:Adult Stem Cell (ASC )-derived organoids are 3D epithelial structures that recapitulate essential aspects of their organ of origin. We have developed conditions for the long-term growth of primary kidney tubular epithelial organoids (‘tubuloids’). Cultures can be established from mouse and human kidney tissue, as well as from urine and can be expanded for at least 20 passages (> 6 months). The structures retain a normal number of chromosomes. Human tubuloids represent proximal as well as distal nephron segments, as evidenced by gene expression, immunofluorescence and tubular functional analyses. BK virus infection of tubuloids recapitulates in vivo phenomena. "Tumoroids" can be established from Wilms nephroblastoma. Kidney tubuloids from urine from a subject with Cystic Fibrosis (CF) allows ex vivo assessment of treatment efficacy. Finally, tubuloids cultured on microfluidic organ-on-a-chip plates adopt a tubular conformation and display active (trans-)epithelial transport function. Adult kidney-derived epithelial tubuloids allow studies of hereditary, infectious and malignant kidney disease in a personalized fashion.
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Project description:Kidney organoids generated from induced pluripotent stem cells (iPSC) have proven valuable for studies of kidney development, disease, and therapeutic screening. However, specific applications have been hampered by limited expansion capacity, immaturity, off-target cells, and inability to access the apical side. Here, we apply recently developed tubuloid protocols to purify and propagate kidney epithelium from d7+18 (post nephrogenesis) iPSC-derived organoids. The resulting ‘iPSC organoid-derived (iPSCod)’ tubuloids can be exponentially expanded for at least 2.5 months, while retaining expression of important tubular transporters and segment-specific markers. This approach allows for selective propagation of the mature tubular epithelium, as immature cells, stroma, and undesirable off-target cells rapidly disappeared. iPSCod tubuloids provide easy apical access, which enabled functional evaluation and demonstration of essential secretion and electrolyte reabsorption processes. In conclusion, iPSCod tubuloids provide a different, complementary human kidney model that unlocks opportunities for functional characterization, disease modeling, and regenerative nephrology.
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Project description:Single-cell RNA sequencing of differentiated human iPSC organoid-derived kidney tubuloids (iPSCod tubuloids)
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Project description:Bulk RNA sequencing of kidney tubuloids and the tissue that the tubuloids were derived from
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Project description:The goal of this study was to analyse the effects of the SFPQ-TFE3 fusion by transforming kidney tubuloids with the construct. Samples without the construct (luciferase only) and overexpressing the partner only (TFE3) were also used as controls. Furthermore, transformed organoids were also transferred into mice PDX models to check their tumorigenic potential; tumors derived from the organoids were subsequently used for sequencing.
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Project description:In the pursuit of pathophysiological models for assessing renal drug response, the development of kidney organoids derived from human pluripotent stem cells represents a significant step forward. However, recapitulating aging/senescence-associated pathophysiology remains challenging. Here, we present an innovative approach to generate epithelial-like structures known as “tubuloid” using primary human renal proximal tubular epithelial cells (hRPTECs) cultured from human resected kidneys, as a refined alternative. We evaluated the efficacy of tubuloids using cisplatin treatment. Tubuloids showed highly differentiated structures. Exposure to cisplatin increased γH2AX, Kidney Injury Molecule-1 (KIM-1) and Cleaved Caspase-3, markers for DNA damage response, epithelial damage and apoptosis respectively. Repeated cisplatin administration resulted in upregulation of the senescence markers. Additionally, increased secretion of inflammatory cytokines, indicating the induction of a senescence-associated secretory phenotype (SASP) were induced Supernatant collected from cisplatin-treated tubuloids induced myofibroblast activation, indicating the onset of renal fibrosis. We successfully established a tubuloid-based model of cisplatin-induced kidney injury using hRPTECs. Tubuloids can replicate cellular senescence, SASP, and fibrosis, which can recapitulate the phenotypes of chronic kidney disease (CKD). Furthermore, tubuloids provide a novel platform for studying the response of renal epithelial cells to toxins and therapeutics and offer innovative strategy for drug screening in a human-based fashion. In this study, we also performed bulk RNA sequencing on the tubuloids generated using established protocol to verify their cellular composition.
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Project description:Adult kidney organoids have been described as strictly tubular epithelial and termed tubuloids. While the cellular origin of tubuloids has remained elusive, here we report that they originate from a distinct CD24+ epithelial subpopulation. Long-term-cultured CD24+-derived tubuloids represent a functional human kidney tubule. We show that kidney tubuloids can be used to model the most common inherited kidney disease, namely autosomal dominant polycystic kidney disease (ADPKD), reconstituting the phenotypic hallmark of this disease with cyst formation. Single-cell RNA sequencing of CRISPR/Cas9 gene-edited PKD1 and PKD2 knockout tubuloids and human ADPKD and control tissue show similarities in upregulation of disease-driving genes. Furthermore, in a proof of concept, we demonstrate that tolvaptan, the only approved drug for ADPKD, shows a significant effect on cyst size in tubuloids but no effect in a pluripotent-stem-cell-derived model. Thus, tubuloids derive from a tubular epithelial subpopulation and represent an advanced model for ADPKD disease modeling.
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Project description:Tubuloids offer a powerful tool for advancing renal research and improving patient care. To facilitate this, we have established a robust biobank of 40 adult human kidney organoids derived from fresh or frozen biopsies. These organoids exhibit diverse morphologies, distal and proximal tubules, closely resembling their tissue of origin. We have extensively characterized these organoids using a combination of techniques, including histological staining, immunofluorescence, gene expression analysis (qPCR and RNA-seq), and genetic profiling (STRs). This comprehensive characterization ensures the quality and reliability of the organoids for downstream applications. Molecular analysis revealed the expression of genes characteristic of various kidney cell types. Furthermore, we have successfully cultured these organoids within microfluidic chips, demonstrating their compatibility with advanced culture systems. This platform of well-characterized, living human kidney organoids from fresh and frozen tissues provides a valuable resource for a wide range of biomedical research, including drug screening, disease modeling, and personalized medicine.
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Project description:Kidney organoids can be generated from commercially available human induced pluripotent stem cells (iPSC). They are amenable for genetic manipulation and useful for modelling development and early-onset genetic diseases. However, iPSC-derived kidney organoids lack longevity to model chronic stressors associated with chronic kidney disease. Adult epithelial kidney organoids (tubuloids) derived from nephrectomies or from renal cells suspended in urine can be passaged, expanded and cryopreserved, offering avenues to model epithelial injury and repair over longer timeframes. However, patient-derived organoids face regulatory barriers in their utilization. To leverage the benefits of both models, we establish a new protocol to generate tubuloids from iPSC-derived kidney organoids (iTubuloids). Kidney organoids were produced from iPSCs by directed differentiation then dissociated and cultured under adult organoid culture conditions. Epithelial organoids formed in less than 3 days from three distinct iPSC lines, each of which have been passaged > 12 times. Comparative analysis of gene expression profiles with RNA sequencing suggested that adult-derived tubuloids better represented the collecting duct, and iTubuloids showed increased expression of proximal and some distal markers. However, expression of proximal tubule markers was higher in iPSC-derived kidney organoids than any tubuloid model. We then evaluated the capacity of iTubuloids to model repetitive kidney injury and found exacerbation of the response and signs of failed repair as the injured progressed. Our study affirms capacity to extend the lifespan of epithelial cell types from short-lived iPSC-derived kidney organoids and reveal a need to optimise nephron cell identities in the tubuloid culture.
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