Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RASSF1A promotes its tumor-suppressive function via YAP1 target genes

ABSTRACT: The aim of the study was to determine the effect of the tumour suppressor RASSF1A in a stably induced YAP system, as both are members of the growth regulatory HIPPO pathway. YAP1 expression was induced by Doxycycline in stably transfected HEK293 cells. In addition the cells were transfected with RASSF1A/GFP or GFP. Transfected cells were FACS-sorted by the GFP-signal and lysed for transcriptome analysis.

ORGANISM(S): Homo sapiens

SUBMITTER: Antje Richter

PROVIDER: E-MTAB-4781 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Proteomic anlaysis of Fabry iPSC derived cardiomyocytes treated with GLA modRNA

Project description:Recent studies in non-human model systems have shown therapeutic potential of modified mRNA (modRNA) treatments for lysosomal storage diseases. Here, we assessed the efficacy of a modRNA treatment to restore the expression of the ÃŽÂ±-galactosidase (GLA) gene in a human cardiac model generated from induced-pluripotent stem cell-derived from two patients with Fabry disease. In line with the clinical phenotype, cardiomyocytes from Fabry patientÃ¢â‚¬â„¢s induced pluripotent stem cells show accumulation of the glycosphinolipid Globotriaosylceramide (GB3), which is an ÃŽÂ±-galactosidase substrate. Further, the patient-specific cardiomyocytes have significant upregulation of lysosomal associated proteins. Upon modRNA treatment, a subset of lysosomal proteins were partially restored to wildtype levels, implying the rescue of the molecular phenotype associated with the Fabry genotype. Importantly, a significant reduction of GB3 levels was observed in GLA modRNA treated cardiomyocytes demonstrating that ÃŽÂ±-galactosidase enzymatic activity was restored. Together, our results validate the utility of patient IPSC-derived cardiomyocytes as a model to study disease processes in Fabry disease and the therapeutic potential of GLA modRNA treatment to reduce GB3 accumulation in the heart.

2023-07-20 | PXD038361 | Pride

Transcriptional profiling by array of stable HeLa cell line with doxycycline-inducible transcription factor E2F7 transgene

Project description:stable dox-inducible HeLa lines expressing E2F7

2012-08-02 | E-TABM-1212 | biostudies-arrayexpress

The GlycoPaSER prototype as a real-time N-glycopeptide identification tool based on the PaSER parallel computing platform

Project description:Real-time database searching allows for simpler and automated proteomics workflows as it eliminates technical bottlenecks in high throughput experiments. Most importantly, it enables results dependent acquisition (RDA) where search results can be used to guide data acquisition during acquisition. This is especially beneficial for glycoproteomics since the wide range of physicochemical properties of glycopeptides lead to a wide range of optimal acquisition parameters. We established here the GlycoPaSER prototype by extending the Parallel Search Engine in Real-time (PaSER) functionality for real-time glycopeptide identification from fragmentation spectra. Glycopeptide fragmentation spectra were decomposed into peptide- and glycan-moiety spectra using common N-glycan fragments. Each moiety was subsequently identified by a specialized algorithm running in real-time. GlycoPaSER can keep up with the rate of data acquisition for real-time analysis with similar performance to other glycoproteomics software and produces results that are in line with literature reference data. The GlycoPaSER prototype presented here provides the first proof-of-concept for real-time glycopeptide identification that unlocks future development of RDA technology to transcend data acquisition.

2023-03-13 | PXD040716 | Pride

Ribosome profiling of harringtonine-treated SUM1315 cells

Project description:SUM1315 were treated with harringtonine, and an untreated control sample was taken. Ribosome profiling was performed on these samples. 1 treated and 1 untreated sample

2016-02-17 | E-GEOD-59815 | biostudies-arrayexpress

Dipeptidyl peptidase-IV is associated with decreased glioma growth

Project description:Effect of expression of dipeptidyl peptidase-IV (DPP-IV) in U373 cell line on uncontrolled cell proliferation and aberrant interactions with the brain extracellular matrix.

2011-12-31 | E-MTAB-583 | biostudies-arrayexpress

The tumor suppressor Rassf1a prevents mouse liver tumorigenesis and regulates levels of the oncogenic kinase Tbk1 and of beta tubulin gene expression in the liver

Project description:The tumor suppressor gene RASSF1A (Ras association domain family protein 1A) coding for a microtubule stabilizing protein is epigenetically silenced in most human cancers. As a binding partner of the kinases MST1 and MST2, the mammalian orthologues of the Drosophila Hippo kinase, RASSF1A is a potential regulator of the Hippo tumor suppressor pathway. RASSF1A shares these properties with the scaffold protein SAV1. The role of this pathway in human cancer has remained enigmatic because Hippo pathway components are rarely mutated. Rassf1a homozygous knockout mice developed liver tumors. However, heterozygous deletion of Sav1 or co-deletion of Rassf1a and Sav1 produced liver tumors with much higher efficiency than single deletion of Rassf1a. Analysis of RASSF1A binding partners by mass spectrometry identified the Hippo kinases MST1, MST2 and the oncogenic IkB kinase TBK1 as the most significantly enriched RASSF1A-interacting proteins. The transcriptome of Rassf1a-/- livers was more deregulated than that of Sav1+/- livers and the transcriptome of Rassf1a-/-, Sav1+/- livers was similar to that of Rassf1a-/- mice. We found that the levels of Tbk1 protein were substantially upregulated in livers lacking Rassf1a, and at the transcript level, factors regulating Tbk1 stability, including Usp2 and Dtx4, were also dysregulated. Furthermore, transcripts of several beta tubulin isoforms were increased in the Rassf1a-deficient liver genotypes presumably reflecting a role of Rassf1a as a tubulin-binding and microtubule-stabilizing protein. Our data suggest a multifactorial role of Rassf1a in suppression of liver carcinogenesis.

2016-05-31 | GSE73911 | GEO

Quantitative and dynamic catalogs of proteins released during apoptotic and necroptotic cell death

Project description:The inflammatory functions of the cytokine tumor necrosis factor (TNF) rely on its ability to induce cytokine production and to induce cell death. Caspase dependent and independent pathways Ã¢â‚¬â€œ apoptosis and necroptosis Ã¢â‚¬â€œ respectively, regulate immunogenicity by the release of distinct sets of cellular proteins. To obtain an unbiased, systems-level understanding of this important process, we here applied mass spectrometry-based proteomics to dissect protein release during apoptosis and necroptosis. We report hundreds of proteins released from human myeloid cells in time-course experiments. Both cell death types induce receptor shedding, but only apoptotic cells released nucleosome components. Conversely, necroptotic cells release lysosomal components by activating lysosomal exocytosis at early stages of necroptosis- induced membrane permeabilisation and show reduced release of conventionally secreted cytokines.

2020-07-18 | PXD014966 | Pride

PhosphoProtein-Peptide Turnover Profiling, validation

Project description:We combined pulsed stable isotope labeling of amino acids (pSILAC) with enrichment of phosphorylated peptides in a method we term PhosphoProtein-Peptide Turnover Profiling (PhosphoPPToP). We applied the method to HeLa cells to find peptides whose clearance rates differ from the protein median. Using theoretical modelling, we show that readouts from PPToP are primarily defined by the wiring of the PTM-modification network and not by effects of the PTM on a protein's proteolytic stability. Thus PPToP can be used to identify PTMs occurring, e.g., preferentially early or late in a protein's lifetime. This enables identification of, e.g., protein maturation or protein complex assembly intermediates. This dataset covers experimental testing of identified phosphosites with PPToP. Here, proteins of interest are expressed as GFP-fusion constructs in HeLa cells and subjected to a SILAC pulse. Thereafter, proteins are pulled-down with anti-GFP beads to isolate the exogenously expressed constructs. We multiplex SILAC timepoints from wild-type and mutant constructs for every given protein of interest using TMT16.

2022-12-02 | PXD032945 | Pride

Proline hydroxylation of collagens in prolyl 4-hydroxylase mutant mice

Project description:Collagen from the skin of wild type and prolyl 4-hydroxylase mutant mice was extracted and proline hydroxylation of the collagen-derived peptides were analyzed by LC-MS/MS.

2018-04-10 | PXD008802 | Pride

The tumor suppressor Rassf1a prevents mouse liver tumorigenesis and regulates levels of the oncogenic kinase Tbk1 and of beta tubulin gene expression in the liver

2016-05-31 | E-GEOD-73911 | biostudies-arrayexpress