Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA375711 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5264430_1.fastq.gz | Fastqsanger.gz | |||
| SRR5264430_2.fastq.gz | Fastqsanger.gz | |||
| SRR5264431_1.fastq.gz | Fastqsanger.gz | |||
| SRR5264431_2.fastq.gz | Fastqsanger.gz | |||
| SRR5264432_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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Project description:Classically, connections within a complex network can be identified through systematically removing its components one at a time and observing the resulting functional changes throughout the network. We applied this concept to identify the signaling network downstream from protein kinase A (PKA) in epithelial cells expressing the Gs-coupled V2 vasopressin receptor. Both genes coding for PKA catalytic subunits (Prkaca and Prkacb) were modified using CRISPR-Cas9 to introduce indels resulting in the absence of detectable PKA catalytic subunit protein (immunoblotting and SILAC-based quantitative protein mass spectrometry). Analysis of multiple PKA double knockout (dKO) lines using SILAC-based quantitative phosphoproteomics showed that phosphorylation sites with decreased phospho-occupancy were dominated by the basophilic motif (R/K)-(R/K)-x-S, consistent with that seen for previously identified PKA targets. Overall, 233 PKA target sites were identified, the majority of which are not annotated as PKA sites in public databases. In addition, we identified a large number of sites with increased phospho-occupancy and the motif x-(S/T)-P, consistent with activation of one or more CMGC family kinases in response to PKA deletion. An unexpected finding was a complete, selective loss of expression of the Aqp2 gene (coding for a kidney-specific water channel) with PKA deletion observed both with quantitative proteomics and RNA-Seq based transcriptomics. Using large-scale data integration techniques, the quantitative proteomic, phosphoproteomic, and RNA-Seq datasets were integrated with prior data from the literature to identify a PKA signaling network that explains most of the cellular physiological responses to vasopressin in the target cells, including the regulation of Aqp2 gene transcription.
2017-11-23 | PXD005938 | Pride
Project description:Protein Kinase A (PKA) is a widely studied protein that has been viewed by most investigators as a single entity, although its catalytic subunits are coded in the genome by two separate genes, PKA catalytic alpha (Gene symbol: Prkaca) and PKA catalytic beta Gene symbol: Prkacb). At an amino-acid level, the two are 91.5 percent identical and the catalytic domains are virtually identical. (Footnote: A third entity PKA catalytic gamma, is not widely expressed and will not be considered here.) We have recently succeeded in using CRISPR-Cas9 to create disruptive mutations in both PKA genes (PKA double KO, or PKA dKO) in vasopressin-responsive kidney epithelial cells (mpkCCD cells). Here we carry out mass spectrometry based quantitative proteomics and phosphoproteomics separately in PKA catalytic-alpha and PKA catalytic-beta single knockouts address the issue of function difference between these two PKA catalytic subunits.
2020-06-01 | PXD015050 | Pride
Project description:An effective combination of multi-omic datasets can enhance our understanding of complex biological phenomena. To build a context-dependent network with multiple omic layers, i.e., a trans-omic network, we performed phosphoproteomics, transcriptomics, proteomics, and metabolomics of murine liver for 4 h after insulin administration and integrated the time series. Structural characteristics and dynamic nature of the network were analyzed to elucidate the impact of insulin. Early and prominent changes in protein phosphorylation and persistent and asynchronous changes in mRNA and protein levels through non-transcriptional mechanisms indicate enhanced crosstalk between phosphorylation-mediated signaling and protein expression regulation. Metabolic response shows different temporal regulation with transient increases at early time points across categories and enhanced response in the amino acid and nucleotide categories at later time points due to process convergence. This extensive and dynamic view of the trans-omic network elucidates prominent regulatory mechanisms that drive insulin responses through intricate interlayer coordination.
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Project description:Kidney fibrosis, characterized by excessive extracellular matrix (ECM) deposition, is a progressive disease that, despite affecting 10% of the population, lacks specific treatments and suitable biomarkers. Aimed at unraveling disease mechanisms and identifying potential therapeutic targets, this study presents a comprehensive, time-resolved multi-omics analysis of kidney fibrosis using an in vitro model system based on human kidney PDGFRβ+ mesenchymal cells. Using computational network modeling we integrated transcriptomics, proteomics, phosphoproteomics, and secretomics with imaging of the extracellular matrix (ECM). We quantified over 14,000 biomolecules across seven time points following TGF-β stimulation, revealing distinct temporal patterns in the expression and activity of known and potential novel renal fibrosis markers and modulators. The resulting time-resolved multi-omic network models allowed us to propose mechanisms related to fibrosis progression through early transcriptional reprogramming. Using siRNA knockdowns and phenotypic assays, we validated predictions and elucidated regulatory mechanisms underlying kidney fibrosis. Notably, we demonstrate that several early-activated transcription factors, including FLI1 and E2F1, act as negative regulators of collagen deposition and propose underlying molecular mechanisms. This work advances our understanding of the pathogenesis of kidney fibrosis and provides a valuable resource for the organ fibrosis research community.
2024-11-07 | E-MTAB-14521 | biostudies-arrayexpress
Project description:The Ca2+/CaM-dependent protein kinase 2-delta (CAMK2D) has been proposed to be involved in vasopressin signaling in the renal collecting duct, which controls water and salt excretion by the kidney. RNA sequancing and quantitative proteomics analyses identified the expression of multiple CAMK2 isoforms, with CAMK2D being the most abundant in collecting duct cells. To investigate the role of CAMK2D in regulating RNA expression in response to vasopressin signaling, the transcriptome of CRISPR/Cas9-mediated Camk2d knock-out mpkCCD cells was profiled using RNA-Seq in the presence of vasopressin analogue dDAVP.
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Project description:A major goal in the discovery of signaling networks is to identify regulated phosphorylation sites and map them to the protein kinases responsible for their phosphorylation. The V2 vasopressin receptor is a Galphas-coupled GPCR that is responsible for regulation of renal water excretion through control of osmotic water transport in kidney collecting duct cells. Genome editing experiments have demonstrated that virtually all vasopressin-triggered phosphorylation changes are dependent on PKA, but events downstream from PKA are obscure. Here we used: 1) TMT-based quantitative phosphoproteomics to track phosphorylation changes over time in native collecting duct cells isolated from rats; 2) a clustering algorithm to classify time course data; and 3) Bayes’ Theorem to integrate the dynamic phosphorylation data with multiple prior “omic” data sets to identify a set of protein kinases that are regulated secondary to PKA activation. The data establish three PKA-dependent protein kinase modules whose regulation mediate the physiological effects of vasopressin at a cellular level. The three modules are 1) a pathway involving several Rho/Rac/Cdc42-dependent protein kinases that control actin cytoskeleton dynamics; 2) MAP kinase and cyclin-dependent kinase pathways that control cell proliferation; and 3) calcium/calmodulin-dependent signaling. The findings provide a template for investigating signaling via other Galphas-coupled GPCRs.
2022-06-17 | PXD031332 | Pride
Project description:In this project, we cultured rat hippocampal neurons in mechanically different environments and studied electrical maturation. We compared WT neurons with two different Piezo1 knockdown conditions. These two knockdown conditions were generated in two independent CRISPR-Cas9 KD assays. Each assay is based on four different CRISPR-Cas9 guides targeting the Piezo1 gene. RNA sequencing was used to analyse the pathway leading to the stiffness dependent maturation behaviour.
2024-07-10 | E-MTAB-13503 | biostudies-arrayexpress
Project description:In this study, we coupled microarray-based transcriptomics and MS-based phosphoproteomics assay to determine mRNA, protein, and phosphopeptide expression levels from 71 autopsied temporal cortical samples, with varying degree of Alzheimer's Disease (AD)-related neurofibrillary pathology. With computational analysis, we identified disease-related transcript, protein and phosphopeptide expression patterns, associated with distinct biological processes and cell types.
2018-12-16 | GSE106241 | GEO
Project description:Vasopressin regulates renal water excretion by binding to the Gs-coupled vasopressin receptor (V2R) in collecting duct cells, resulting in cyclic AMP-dependent increases in epithelial water permeability through regulation of the aquaporin-2 (AQP2) water channel. Our prior studies showed that CRISPR-mediated deletion of protein kinase A (PKA) in cultured mpkCCD cells largely eliminates these regulatory events. These PKA-null cells provide a means of identifying PKA-independent signaling downstream from the V2 receptor. We carried out large-scale quantitative protein mass spectrometry (SILAC) to identify PKA-independent phosphorylation changes in response to V2R-selective vasopressin analog, dDAVP. The results show that V2R-mediated vasopressin signaling is predominantly, but not entirely, PKA-dependent. Target motif analysis of the phosphopeptides increased in response to dDAVP in PKA-null cells indicates that the vasopressin activates of one or more members of the AMPK/SNF1 subfamily of basophilic protein kinases. Among the upregulated phosphorylation sites were three known targets of SNF1-subfamily kinases, namely Lipe (S559), Crtc1 (S151) and Arhgef2 (S151). One of the phosphorylation sites that increased in occupancy in PKA-null cells was Ser256 of AQP2, a site critical for vasopressin-mediated trafficking of AQP2 to the cell surface. Beyond this, PKA-independent active site phosphorylation changes were also seen for protein kinases Stk39 (SPAK) and Prkci (Protein kinase C iota). Cyclic AMP levels were ~10-fold higher in PKA-null than in PKA-intact cells in the presence of phosphodiesterase inhibitor IBMX, consistent with a marked acceleration of cAMP production in PKA-null cells. The findings are indicative of substantial PKA-independent signaling downstream from the Gs-coupled V2 receptor.
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Project description:The expression profile in miR-155-/- FLT3-ITD+ AML is unknown. Using empty vector (EV) or two distinct miR-155 (S3 or S10) lentiviral CRISPR-Cas9 infected FLT3-ITD+ AML cell lines (MV4-11 cells), we performed next generation RNA sequencing to determine the expression profile in these cells dependent on miR-155. We found a number of pathways dysregulated, including STAT5 activation. RNAseq was performed on EV or miR-155 lentiviral CRISPR-Cas9 infected MV4-11 cell lines in triplicate cultures.
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