RNA-seq on primary human kidney epithelial cells with oleate treatment and PLIN2 knockdown
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE206084 | GEO | 2022/10/01
REPOSITORIES: GEO
Similar Datasets
Project description:Here we investigated the transcriptomic changes induced by PPFIBP1 or PLEKHA1 siRNA treatments on human Primary Renal Proximal Tubule Epithelial Cells (RPTECs) with RNA-seq.
2024-02-15 | GSE240639 | GEO
Project description:We performed bulk RNA-seq on primary and immortalized human renal proximal tubule epithelial cells (RPTECs) subjected to siRNA mediated TNIK silencing.
2024-04-10 | GSE216015 | GEO
Project description:Multipotent progenitor cells (MPs) have been observed in human kidneys and particularly in Bowman's capsule and proximal tubules. The kidney owns the ability to repair local damage and renal MPs may play a role in the regenerative processes. Microarray technology was applied to identify differentially expressed genes among resident MPs isolated from glomeruli and tubules of normal renal tissue, renal proximal tubular epithelial cells (RPTECs) and mesenchymal stem cells (MSCs). The results of our analysis represent a starting point for further functional studies. Experiment Overall Design: This study includes three renal tissue samples which were processed to obtain 3 glomerular progenitor populations and 3 tubular ones. Three subcoltures of MSCs and RPTECs were included as well. The differences in gene expression patterns of the 4 cell types were found out.
2009-11-09 | E-GEOD-8611 | biostudies-arrayexpress
Project description:The proximal tubule plays an important role in the secretion and reabsorption of drugs in the kidney and is a major site of drug interaction and toxicity. Kidney toxicity analysis via in vitro assays is challenging as few provide appropriate proximal tubular cell function. In this study, we aimed to develop a simple and reproducible method to culture human proximal tubular epithelial cells (RPTECs), used in pharmacokinetic and toxicological evaluation by monitoring organic anion transporter (OAT)1 as a selection marker. As a result, by culturing RPTECs in spherical cellular aggregates, OAT1 protein expression, which does not increase in conventional 2D culture, increased over time and reached a similar level to that in human renal cortices from 5 different donors. The expression of proximal tubule markers, AQP1 and CDH6, was maintained, indicating that 3D RPTEC spheroids had proximal tubule characteristics. For SLC transporters, the 3D spheroid culture improved the protein expression of about 7% of the 139 transporter proteins detected and 2.3% of 4,800 proteins detected to about 5-fold that in human renal cortices. Furthermore, the protein expression levels of about 4800 proteins in 3D RPTEC spheroids (cultured for 12 days) were maintained over 20 days. Cisplatin and adefovir exhibited transporter-dependent ATP decreases in 3D RPTEC spheroids. These results indicate that the 3D RPTEC spheroid is a simple and robust in vitro experimental system for pharmacokinetic and toxicological evaluation in drug development.
2023-10-20 | GSE216153 | GEO
Project description:Fatty liver is a condition of excessive triglyceride accumulation in hepatocytes. Additionally, hepatocytes showed a high degree of fat droplet accumulation during excessive alcohol consumption and metabolic syndrome. However, the molecular mechanisms involved in fat droplet formation remain unknown. This study used an in vitro fatty liver formation model of the human liver cancer cell line HepG2 to comprehensively search for fat droplet formation-related genes whose expression changes during fat droplet formation. Microarray analysis with extracted total RNA determined the genes that are involved in fat droplet formation and confirmed their expression by real-time polymerase chain reaction after culturing HepG2 cells in a culture medium containing 0, 50, 200, and 500 μM of oleic acid for 24 h. The results revealed 142 genes demonstrating increased expressions by >2.0 fold with oleic acid treatment and 426 genes demonstrating decreased expressions. Perilipin 2 (PLIN2) was estimated as the gene most closely associated with fatty liver. Lipid droplet formation in HepG2 upregulated PLIN2 in an oleic acid-treated concentration-dependent manner. These results indicate the involvement of genes in oleate treatment-induced lipid droplet formation in HepG2, particularly PLIN2 may play an important role.
2023-12-01 | GSE248166 | GEO
Project description:Drugs and other xenobiotics are not only secreted/reabsorbed by the renal proximal tubule epithelial cells (RPTEC) but may also adversely impact kidney function. In vitro models that can afford prediction of toxic effects and model directional transport are in high demand in both drug and chemical safety; accordingly, active development of new models is underway. The objective of this study was to investigate physiological and transport function of various sources of human RPTECs under static and fluidic conditions. We tested TERT1-immortalized RPTECs, including OAT1-, OCT2- and OAT3-overexpressing variants) and two primary RPETC sources. Cells were cultured on transwell membranes in two conditions – static (24-well transwells) and fluidic (transwells placed into PhysioMimix TC12 organ-on-chip platform with 2 L/s flow). We evaluated barrier formation, transport, and gene expression. We show that primary RPTECs may not be suitable for studies of directional transport on transwell membranes because they form an inferior barrier even though they show generally more relevant expression of key transporters, especially when shear stress is present. Both TERT1 and -OAT1 and -OAT3 overexpressing cells formed robust barrier, but it was unaffected by shear stress. TERT1-OAT1 cells exhibited inhibitable pAH transport; shear stress increased pAH transport function of these cells. However, efficient tenofovir secretion and perfluorooctanoic acid (PFOA) reabsorption by TERT1-OAT1 cells were not modulated by shear stress. With respect to gene expression profiles, we found that both TERT1 and TERT1-OAT1 cells exhibited human kidney-like transcriptomes, but that shear stress did not result in an apparent enhancement of the kidney phenotype. Overall, our data show that addition of flow to in vitro studies of the renal proximal tubule may afford benefits in some aspects of kidney function, but that careful consideration of the impact such studies would have on the cost and throughput of the experiments is needed.
2024-10-23 | GSE246180 | GEO
Project description:Dent disease has multiple defects attributed to proximal tubule malfunction including low molecular weight proteinuria, aminoaciduria, phosphaturia and glycosuria. In order to understand the changes in kidney function of the Clc5 transporter gene knockout mouse model of Dent disease, we examined gene expression profiles from proximal tubules of mouse kidneys. Overall 720 genes are expressed differentially in the proximal tubules of the Dent Clcn5 knockout mouse model compared to those of control wild type mice. The fingerprint of these gene changes may help us to understand the phenotype of Dent disease. Experiment Overall Design: Renal proximal tubules were dissected from wild type and Clcn5 knockout mice. Mice were anesthetized with halothane, the abdominal aorta of each animal was accessed and the left kidney was perfused with an ice-cold salt. Proximal tubule dissection was performed in an ice-cold salt solution. After dissection of approximately 80-100 segments of 2 mm in length per kidney, the RNA for 3-4 mice was combined to have enough RNA per chip. Experiment Overall Design: 3 microarrays each of wild type and knockout mouse proximal tubule were processed
2008-06-11 | E-GEOD-10162 | biostudies-arrayexpress
Project description:All mammalian cells need oxygen. Inadequate oxygen (hypoxia) triggers cellular responses for survival and the maintenance of homeostasis. A transcription factor, hypoxia-inducible factor (HIF), plays a central role in the hypoxia response; its activity is regulated by the oxygen-dependent degradation of the HIF-1a protein. Despite the ubiquity and importance of hypoxia responses, very little is known about the variation in the global transcriptional response to hypoxia among different cell types and its links to tissue and cell-specific diseases. We analyzed the temporal changes in global transcript levels in response to hypoxia in primary renal proximal tubule epithelial cells (RPTECs), breast epithelial cells, smooth muscle (SMs), and endothelial cells (ECs) with DNA microarrays. The extent of the transcriptional response to hypoxia was greatest in the renal tubule cells. This exaggerated response was associated with a uniquely high level of HIF-1a RNA in renal cells and could be diminished by reducing HIF-1a expression via RNA interference (RNAi). A gene-expression signature of the hypoxia response, derived from our studies of cultured mammary and renal tubular epithelial cells, showed coordinated variation in several human cancers, and was a strong predictor of clinical outcomes in both breast and ovarian cancers. In an analysis of a large, published gene-expression dataset from breast cancers, we found that the prognostic information in the hypoxia signature was virtually independent of that provided by the previously reported wound signature and more predictive of outcomes than any of the clinical parameters in current use. A stimulus or stress experiment design type is where that tests response of an organism(s) to stress/stimulus. e.g. osmotic stress, behavioral treatment Using regression correlation
2010-07-01 | E-GEOD-3537 | biostudies-arrayexpress
Project description:TGFbeta is the major cytokine driver of fibrosis in the kidney and other tissue. Epithelial-mesenchymal transition has been postulated to contibrute to renal fibrosis in diseases such as diabetic nephropathy. We wished to identify novel genes that were upregulated in human kidney epithelial cells in response to TGFb1.The transcriptional responses for human proximal tubule epithelial cells to 10 ng/ml TGFbeta1 was examined over 24 and 48 hr There were three treatment groups: vehicle, 24hr TGFb1, 48 hr TGFb1. Each treatment was carried out in triplicate 10 cm plates and the experiment was carried out in triplicate using consecutive passages of cells.
2011-05-30 | E-GEOD-23338 | biostudies-arrayexpress
Project description:Microphysiological systems are a promising new experimental tool for drug and chemical safety evaluation. These models are rapidly evolving, and concerns exist about the reproducibility, robustness and relative benefits when compared to traditional in vitro cultures. This study used OrganoPlate® 3-lane 40, a microfluidics-based model of the renal proximal tubule and compared it to multi-well static cultures using a number of human renal proximal tubule epithelial cell (RPTEC) types. We followed previously published protocols but adapted them to the varying cell proliferation rates of different RPTECs; primary cells required up to 7 days in culture before experiments, while some immortalized cell lines could be used in 3 days. Function of various tubule-specific transporters, permeability of small molecules (cisplatin, tenofovir and perfluorooctanoic acid) and fluorescent dextrans (60-150 kDa), basal and chemical-effected gene expression, and cell viability were tested. Different RPTEC types and culture conditions (OrganoPlate® 3-lane 40 vs multi-well plates) were compared. We found that there are advantages offered by OrganoPlate® 3-lane 40 as compared to multi-well cultures – presence of media flow, albeit intermittent, and fairly high throughput. However, this model appears to offer only limited (e.g., MRP-mediated transport) advantages in terms of either gene expression or transporter function when compared to the multi-well plate culture conditions. It can also be used to study cellular uptake and direct toxic effects of small molecules; still, it may have limited utility for studies of pharmaco-/toxico-kinetics because drug transport between blood and tubule compartments is considerably affected by the gel barrier.
2023-11-08 | GSE233406 | GEO