Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA183689 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Integrative transcriptomic and proteomic analysis of osteocytic cells exposed to fluid flow reveals novel mechano-sensitive signaling pathways
2015-07-08 | E-GEOD-42874 | ExpressionAtlas
Project description:Bone adaptation to mechanical loading is regulated via signal transduction by mechano-sensing osteocytes. Mineral-embedded osteocytes experience strain-induced interstitial fluid flow and fluid shear stress, and broad shifts in gene expression are key components in the signaling pathways that regulate bone turnover. RNA sequencing analysis, or RNA-Seq, enables more complete characterization of mechano-sensitive transcriptome regulation than previously possible. We hypothesized that RNA-Seq of osteocytic MLO-Y4 cells reveals both expected and novel gene transcript regulation in cells previously fluid flowed and analyzed using gene microarrays (Govey et al., J Biomech, 2014). MLO-Y4 cells were flowed for 2 h with 1 Pa oscillating fluid shear stress and post-incubated 2 h. RNA-Seq of original samples detected 58 fluid flow-regulated gene transcripts (p-corrected<0.05) versus 65 transcripts detected by microarray. However, RNA-Seq demonstrated greater dynamic range, with all 58 transcripts >1.5 fold-change whereas 10 of 65 met this cut-off by microarray. Analyses were complimentary in patterns of regulation, though only 6 transcripts were significant in both analyses: Cxcl5, Cxcl1, Zc3h12a, Ereg, Slc2a1, and Egln1. As part of a broad inflammatory response inferred by gene ontology analyses, we again observed greatest up-regulation of inflammatory C-X-C motif chemokines, and newly implicated HIF-1? and AMPK signaling pathways. Importantly, we detected both expected mechano-sensitive transcripts (e.g. Nos2, Ptgs2, Ccl7) and transcripts not previously identified as mechano-sensitive, e.g. Ccl2. We found RNA-Seq advantageous over microarrays because of its ability to analyze unbiased estimation of gene expression, informing our understanding of osteocyte signaling.
2017-07-23 | GSE70667 | GEO
Project description:Osteocytes, positioned within boneâs interstitial space, are subject to fluid flow upon whole bone loading. Such fluid flow is widely theorized to be a mechanical signal transduced by osteocytes, initiating a poorly understood cascade of signaling events mediating bone metabolism. The objective of this study was to utilize high-throughput approaches to examine the time course of flow-induced changes in osteocyte gene transcript and protein levels. Microarray analysis demonstrated fluid flow regulation of genes consistent with known anabolic loading responses, including Ptgs2, NF-κB inhibitors, MAP3 kinases, and Wnt/β-catenin pathway signaling molecules. However, two of the most highly up-regulated gene productsâCxcl1 and Cxcl2, confirmed by qPCRâhave not previously been reported to be responsive to fluid flow. Gene ontology analysis suggested a highly significant inflammatory and immune response, with cellular functions including trafficking, cell-to-cell signaling, and tissue development. Proteomic analysis of the same samples demonstrated greatest up-regulation of the ATP-producing enzyme NDK, calcium-binding Calcyclin, and G protein-coupled receptor kinase 6. An integrative pathway analysis merging fold changes in transcript and protein levels predicted signaling nodes not directly detected at the sampled time points, including STAT3 and c-Myc. These results extend our knowledge of the osteocytic response to fluid flow, most notably up-regulation of Cxcl1 and Cxcl2 as a possible paracrine agent for osteoblastic and osteoclastic recruitment. Osteocyte-like MLO-Y4 cells were subjected to 2 hours of 10 dyn/cm2 oscillating fluid flow in parallel-plate fluid flow chambers and harvested for analysis at 0, 2, 8, and 24 hours post-flow incubation. Parallel control samples from sham treated cells were also collected at each time point.
2013-07-01 | E-GEOD-42874 | biostudies-arrayexpress
Project description:Mechano-sensitive Gene Expression with RNA-Seq: Revisiting the Osteocytic Cell Response to Fluid Flow
| PRJNA289315 | ENA
Project description:Osteocytes, positioned within bone’s interstitial space, are subject to fluid flow upon whole bone loading. Such fluid flow is widely theorized to be a mechanical signal transduced by osteocytes, initiating a poorly understood cascade of signaling events mediating bone metabolism. The objective of this study was to utilize high-throughput approaches to examine the time course of flow-induced changes in osteocyte gene transcript and protein levels. Microarray analysis demonstrated fluid flow regulation of genes consistent with known anabolic loading responses, including Ptgs2, NF-κB inhibitors, MAP3 kinases, and Wnt/β-catenin pathway signaling molecules. However, two of the most highly up-regulated gene products—Cxcl1 and Cxcl2, confirmed by qPCR—have not previously been reported to be responsive to fluid flow. Gene ontology analysis suggested a highly significant inflammatory and immune response, with cellular functions including trafficking, cell-to-cell signaling, and tissue development. Proteomic analysis of the same samples demonstrated greatest up-regulation of the ATP-producing enzyme NDK, calcium-binding Calcyclin, and G protein-coupled receptor kinase 6. An integrative pathway analysis merging fold changes in transcript and protein levels predicted signaling nodes not directly detected at the sampled time points, including STAT3 and c-Myc. These results extend our knowledge of the osteocytic response to fluid flow, most notably up-regulation of Cxcl1 and Cxcl2 as a possible paracrine agent for osteoblastic and osteoclastic recruitment.
2013-07-01 | GSE42874 | GEO
Project description:Renal epithelial cells are exposed to mechanical forces due to flow-induced shear stress within the nephrons. We applied RNA sequencing to get a comprehensive overview of fluid-shear regulated genes and pathways in the immortalized renal proximal tubular epithelial cell line. Cells were exposed to laminar fluid shear stress (1.9 dyn/cm2) in a cone-plate device and compared to static controls.
2018-03-15 | E-MTAB-6640 | biostudies-arrayexpress
Project description:Pkd1-/- renal epithelial cells are exposed to mechanical forces due to flow-induced shear stress within the nephrons. We applied RNA sequencing to get a comprehensive overview of fluid-shear regulated genes and pathways in the immortalized Pkd1-/- renal proximal tubular epithelial cell line. Cells were exposed to laminar fluid shear stress (1.9 dyn/cm2) in a cone-plate device and compared to static controls.
2019-03-01 | E-MTAB-6641 | biostudies-arrayexpress
Project description:Biomechanical cues dynamically control major cellular processes but whether genetic variants actively participate in the mechano-sensing mechanisms remain unexplored. Vascular homeostasis is tightly regulated by hemodynamic forces. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constant activation of vascular endothelium contributing to the development of atherosclerosis, the major cause of coronary artery disease (CAD). Conversely, unidirectional flow promotes the anti-inflammatory and anti-permeable endothelial phenotype resistant to atherogenesis. Genome-wide association studies (GWAS) have identified chromosome 1p32.2 as one of the loci most strongly associated with CAD susceptibility; however, the causal mechanism related to this CAD locus remain unknown. PhosphoLipid PhosPhatase 3 (PLPP3) is located at 1p32.2 and encodes a phosphatase that suppresses endothelial inflammation and promotes monolayer integrity by hydrolyzing lysophosphatidic acid. Our previous studies demonstrated that PLPP3 is significantly reduced in vascular endothelium exposed to disturbed flow while unidirectional flow significantly increases endothelial PLPP3 expression in vitro and in vivo. In addition, CAD protective allele at 1p32.2 locus is associated with increased PLPP3 in an endothelium-specific manner, shown by expression quantitative trait locus (eQTL). Using Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq), H3K27ac ChIP-Seq, H3K4me2 ChIP-Seq, and luciferase assays, here we identified a mechano-sensitive endothelial enhancer in PLPP3 intron 5 that is dynamically activated by unidirectional flow. Deletion of this enhancer by CRISPR/Cas9-based genome editing causatively reduces endothelial PLPP3 expression and promotes endothelial activation, and moreover, impairs endothelial PLPP3 induction by unidirectional flow. Chromatin accessibility quantitative trait locus (caQTL) mapping, allelic imbalance assay, and luciferase assays further demonstrated that CAD protective allele at rs17114036 in the PLPP3 intron 5 confers an increased enhancer activity. ChIP-PCR and luciferase assays showed that CAD protective allele C at rs17114036 creates a binding site (CACC) for mechano-sensitive transcription factor KLF2, leading to increased enhancer activity under unidirectional flow. These results elucidate the contributory role of CAD genetic predisposition in critical endothelial mechano-transduction mechanisms and suggest that human genetic variants provide a previously unappreciated layer of regulatory control in cellular mechano-sensing mechanisms.
2018-11-19 | GSE112336 | GEO
Project description:Biomechanical cues dynamically control major cellular processes but whether genetic variants actively participate in the mechano-sensing mechanisms remain unexplored. Vascular homeostasis is tightly regulated by hemodynamic forces. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constant activation of vascular endothelium contributing to the development of atherosclerosis, the major cause of coronary artery disease (CAD). Conversely, unidirectional flow promotes the anti-inflammatory and anti-permeable endothelial phenotype resistant to atherogenesis. Genome-wide association studies (GWAS) have identified chromosome 1p32.2 as one of the loci most strongly associated with CAD susceptibility; however, the causal mechanism related to this CAD locus remain unknown. PhosphoLipid PhosPhatase 3 (PLPP3) is located at 1p32.2 and encodes a phosphatase that suppresses endothelial inflammation and promotes monolayer integrity by hydrolyzing lysophosphatidic acid. Our previous studies demonstrated that PLPP3 is significantly reduced in vascular endothelium exposed to disturbed flow while unidirectional flow significantly increases endothelial PLPP3 expression in vitro and in vivo. In addition, CAD protective allele at 1p32.2 locus is associated with increased PLPP3 in an endothelium-specific manner, shown by expression quantitative trait locus (eQTL). Using Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-Seq), H3K27ac ChIP-Seq, H3K4me2 ChIP-Seq, and luciferase assays, here we identified a mechano-sensitive endothelial enhancer in PLPP3 intron 5 that is dynamically activated by unidirectional flow. Deletion of this enhancer by CRISPR/Cas9-based genome editing causatively reduces endothelial PLPP3 expression and promotes endothelial activation, and moreover, impairs endothelial PLPP3 induction by unidirectional flow. Chromatin accessibility quantitative trait locus (caQTL) mapping, allelic imbalance assay, and luciferase assays further demonstrated that CAD protective allele at rs17114036 in the PLPP3 intron 5 confers an increased enhancer activity. ChIP-PCR and luciferase assays showed that CAD protective allele C at rs17114036 creates a binding site (CACC) for mechano-sensitive transcription factor KLF2, leading to increased enhancer activity under unidirectional flow. These results elucidate the contributory role of CAD genetic predisposition in critical endothelial mechano-transduction mechanisms and suggest that human genetic variants provide a previously unappreciated layer of regulatory control in cellular mechano-sensing mechanisms.
2018-11-19 | GSE112328 | GEO
Project description:RNA-seq technology was used to reveal the transcriptome changes of tubular epithelia in response to fluid flow and determine the role of primary cilia in this process. Many fluid flow-sensitive genes were identified, among which are those regulated by primary cilia sensing of fluid flow. These genes were further validated by RT-qPCR.
2018-01-27 | GSE109701 | GEO