Three Dimensional Modeling of Biologically Relevant Fluid Shear Stress in Human Renal Proximal Tubule Cells Mimics In Vivo Transcriptional Profiles
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PROVIDER: PRJNA721940 | ENA |
REPOSITORIES: ENA
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Project description:We performed RNA-sequencing of human RPTEC/TERT1 cells in a microfluidic chip-based 3D model to determine transcriptomic changes. We measured transcriptional changes following the treatment of cells in this device at three different fluidic shear stress. We observed that FSS changes the expression of proximal tubule cell (PTC)-specific genes and impacted genes previously associated with renal diseases in genome-wide association studies (GWAS). At a physiological FSS level, we observed cell morphology, enhanced polarization, presence of cilia, and transport functions using albumin reabsorption via endocytosis and efflux transport. Here, we present a dynamic view of human PTCs response to FSS with increasing fluidic shear stress conditions and provide insight into hPTCs cellular function under biologically relevant conditions.
2021-07-15 | GSE172062 | GEO
Project description:The kidney proximal tubule is the primary site for solute reabsorption, secretion and where kidney diseases can originate, including drug-induced toxicity. Two-dimensional cell culture systems of the human proximal tubule cells (hPTCs) are often used to study these processes. However, these systems fail to model the interplay between filtrate flow, fluid shear stress (FSS), and functionality essential for understanding renal diseases and drug toxicity. The impact of FSS exposure on gene expression and effects of FSS at differing rates on gene expression in hPTCs has not been thoroughly investigated. Here, we performed RNA-sequencing of human RPTEC/TERT1 cells in a microfluidic chip-based 3D model to determine transcriptomic changes. We measured transcriptional changes following treatment of cells in this device at three different fluidic shear stress. We observed that FSS changes the expression of PTC-specific genes and impacted genes previously associated with renal diseases in genome-wide association studies (GWAS). At a physiological FSS level, we observed cell morphology, enhanced polarization, presence of cilia, and transport functions using albumin reabsorption via endocytosis and efflux transport. Here, we present a dynamic view of hPTCs response to FSS with increasing fluidic shear stress conditions and provide insight into hPTCs cellular function under biologically relevant conditions.
| S-EPMC8263711 | biostudies-literature
Project description:Drug-induced nephrotoxicity is a leading cause of drug attrition, partly due to the limited relevance of pre-clinical models of the proximal tubule. Culturing proximal tubule epithelial cells (PTECs) under fluid flow to mimic physiological shear stress has been shown to improve select phenotypes, but existing flow systems are expensive and difficult to implement by non-experts in microfluidics. Here, we designed and fabricated an accessible and modular flow system for culturing PTECs under physiological shear stress, which induced native-like cuboidal morphology, downregulated pathways associated with hypoxia, stress, and injury, and upregulated xenobiotic metabolism pathways. We also compared the expression profiles of shear-dependent genes in our in vitro PTEC tissues to that of ex vivo proximal tubules and observed stronger clustering between ex vivo proximal tubules and PTECs under physiological shear stress relative to PTECs under negligible shear stress. Together, these data illustrate the utility of our user-friendly flow system and highlight the role of shear stress in promoting native-like morphological and transcriptomic phenotypes in PTECs in vitro, which is critical for developing more relevant pre-clinical models of the proximal tubule for drug screening or disease modeling.
2022-12-31 | GSE221871 | GEO
Project description:We previously demonstrated that OK cells cultured under orbital shear stress have morphological and functional features that more closely resemble the proximal tubule in vivo. This study was designed to identify progressive transcriptional changes with increasing exposure time to shear stress and to compare the transcriptome of cells cultured under shear stress vs static conditions.
2020-09-29 | GSE155315 | GEO
Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation.
2013-05-06 | GSE39997 | GEO
Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation.
2013-05-06 | GSE39996 | GEO
Project description:Several organisms belonging to diverse animal groups have retained Dnmt2 as their only bona fide DNA methyltransferase gene. However, recent studies have shown that Dnmt2 functions as a tRNA methyltransferase, which prompted us to analyze the methylomes of Dnmt2-only organisms at single-base resolution. Using whole-genome bisulfite sequencing we show here that the genomes of Schistosoma mansoni and Drosophila melanogaster lack detectable DNA methylation patterns. Residual unconverted cytosine residues shared many attributes with bisulfite deamination artifacts and were observed at comparable levels in a Dnmt2-deficient fly strain. Furthermore, genetically modified mouse embryonic stem cells that had retained Dnmt2 as their only bona fide DNA methyltransferase gene, did not show any detectable DNA methylation patterns. Our results thus uncover fundamental differences among animal methylomes and suggest that Dnmt2-only organisms lack biologically relevant DNA methylation patterns.
2013-05-06 | GSE42170 | GEO
Project description:Porcine endothelial cells were preconditioned by a basal level shear stress of 15 ± 15 dynes/cm2 at 1 Hz for 24 hours, and an acute increase in shear stress frequency (2 Hz) was then applied. The transcriptomics studies using microarray identified genes that were sensitive to the elevated shear frequency. keywords: adaptation, shear stress, frequency, microarray, gene expression Porcine endothelial cells were preconditioned by a basal level shear stress of 15 ± 15 dynes/cm2 at 1 Hz for 24 hours, and an acute increase in shear stress magnitude (2 Hz) was then applied. Gene expression at multiple time points was measured using microarray.
2011-12-01 | E-GEOD-26513 | biostudies-arrayexpress
Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation. Whole genome methylation analysis of S. mansoni. One sample was analyzed, containing DNA from adult male worms.
2013-05-06 | E-GEOD-39997 | biostudies-arrayexpress
Project description:Dnmt2 is a widely conserved protein, which is closely related to eukaryotic DNA methyltransferases. However, Dnmt2 shows a robust tRNA methyltransferase activity and only limited activity towards DNA. Interestingly, a recent study has provided evidence for a biologically important function of Dnmt2-dependent DNA methylation in the blood fluke Schistosoma mansoni, which seemed to contradict the weak activity of the enzyme in other organisms. We now used whole-genome bisulfite sequencing to comprehensively analyze the methylome of adult worms and could not detect any evidence for biologically relevant DNA methylation patterns. We also characterized the methylome of Drosophila melanogaster embryos and did not find any evidence for DNA methylation. Unconverted cytosine residues were detectable only at very low levels and shared many attributes with bisulfite deamination artifacts. Our results thus strongly argue against a DNA methyltransferase activity of Dnmt2 and suggest that Dnmt2-dependent phenotypes are caused by reduced tRNA methylation. Whole genome methylation analysis of D. melanogaster. Two samples were analyzed, one sample containing DNA from WT embryos, one sample containing DNA from Dnmt2-/- embryos.
2013-05-06 | E-GEOD-39996 | biostudies-arrayexpress