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Generation of human kidney organoids from urine cells (scRNA-Seq)

ABSTRACT: Kidney organoids are ideal models to study the complex process of human kidney development. Here we report the generation of functional kidney organoids by reprogramming human urine epithelial cells (hUCs). RNA-seq and ATAC-seq revealed the three-stage process of the 2D U-iRO induction. Single cell RNA-seq further reveals the cell types in 2D and 3D organoids, 2D U-iRO dominated with mesenchyme and 3D U-iRO with tubule.

ORGANISM(S): Homo sapiens

PROVIDER: GSE198840 | GEO | 2022/10/18

REPOSITORIES: GEO

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Generation of human kidney organoids from urine cells

Project description:Kidney organoids are ideal models to study the complex process of human kidney development. Here we report the generation of functional kidney organoids by reprogramming human urine epithelial cells (hUCs). RNA-seq and ATAC-seq revealed the three-stage process of the 2D U-iRO induction. Single cell RNA-seq further reveals the cell types in 2D and 3D organoids, 2D U-iRO dominated with mesenchyme and 3D U-iRO with tubule.

2022-10-18 | GSE198844 | GEO

Generation of human kidney organoids from urine cells (RNA-seq)

2022-10-18 | GSE198839 | GEO

Generation of human kidney organoids from urine cells (ATAC-seq)

2022-10-18 | GSE198838 | GEO

Proximal tubule cells in blood and urine have potential as biomarkers for kidney disease biopsies

Project description:Early diagnosis and treatment is pivotal to the management of kidney disease, whereas the pathological mechanisms and minimally invasive diagnostic method still need to be investigated. In the present study, single-cell RNA sequencing (scRNA-seq) was used to evaluate the heterogeneity of kidney diseases in single cell level. Cellular gene expression profiles of cells of renal tissue, peripheral blood mononuclear cells (PBMCs) and urine from four nephritis patients were performed. Our analysis revealed 12 subsets of renal cells and leukocytes, including fibroblast cells, mesangial cells, epithelial cells, proximal tubule cells (PTCs), and 6 types of immune cells, CD8+ T cell, macrophages (MC), nature killer cells (NK), dendritic cells (DC), B cell and neutrophils. PTCs were detected in both PBMC and urine, while PTC was negative in healthy blood sample. Multiple populations of fibroblast cells, mesangial cells and PTCs demonstrated pro-inflammatory or pro-apoptotic responses. Gene expression analysis suggested that chemotactic and activating effect of inflammatory PTCs and fibroblasts on neutropils were critical for the development and progress of nephritis, which was supported by the widely overexpressed pro-inflammatory genes in these cells. Gene expression profiles of inflammatory PTCs in PBMC, urine and kidney are highly correlated, indicating the high possibility of urine and PBMC PTCs in serving as a surrogate for kidney biopsies.

2022-05-23 | GSE203406 | GEO

Generation of human kidney organoids from urine cells (scRNA-Seq)

Project description:Generation of human kidney organoids from urine cells (scRNA-Seq)

| PRJNA817165 | ENA

Generation of human kidney organoids from urine cells (RNA-seq)

Project description:Generation of human kidney organoids from urine cells (RNA-seq)

| PRJNA817166 | ENA

Generation of human kidney organoids from urine cells (ATAC-seq)

Project description:Generation of human kidney organoids from urine cells (ATAC-seq)

| PRJNA817168 | ENA

2D and 3D Madin-Darby Canine Kidney Cell Type II cell line response to hepatocyte growth factor

Project description:Analysis of 2D (transwell) and 3D (collagen type I) cultured MDCK cells and HGF (a MAPK activator). Traditional 2D cultures are fast and inexpensive but do no mimic natural niche/cell environment as well as the more laborious and costly 3D-cultures. 3D cultures, arguably, are better models for the study of developmental processes, such as tubulogenesis. Epithelial organs (such as kidney) develop via tubulogenesis, a process, at least in part, regulated by MAPK signaling. Therefore, 2D and 3D cells also treated with HGF plus MAPK inhibitors. Results provide insights into differential response to HGF-induced tubulogenesis depending on cell culture conditions (2D vs. 3D). 29 samples total: 2D and 3D control (untreated) in quadruplicate, respectively; 2D and 3D + HGF in quadruplicate, respectively; 2D + HGF + PD-98059 in quadruplicate; 3D + HGF + PD-98059 in triplicate; 2D + HGF + U0126 in triplicate; and 3D + HGF + U0126 in triplicate.

2014-03-31 | E-GEOD-49518 | biostudies-arrayexpress

Generation of human kidney organoids from urine cells

Project description:Generation of human kidney organoids from urine cells

| PRJNA817161 | ENA

Single-Cell RNA-Seq Analysis of cells from human urine

Project description:Urine passes through the entire kidney and urinary tract system starting from the glomerulus and ending to the urethra. Cells in the kidney and urinary tract could be exfoliated from the epithelium into the urine, while leukocyte could infiltrate from the local tissue into the urine, which makes the urine a useful subject for clinical evaluation of relevant diseases. We performed scRNA-seq on voided urine samples. 50–100 mL middle stream urine samples were collected from 12 Chinese healthy adults and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells. We presented the first single-cell atlas of adult human urine and identified multiple previously unrecognized cell types. Based on our scRNA-seq analysis data, a SOX9+ cell population was identified in adult human urine which we speculated to have progenitor potential.

2021-01-25 | GSE165396 | GEO

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