E-MTAB-4937
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-4937 | ExpressionAtlas | 2016-07-13
REPOSITORIES: ExpressionAtlas
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2019-04-22 | ST001178 | MetabolomicsWorkbench
Project description:BACKGROUND: Neutrophils are phagocytic innate immune cells that play essential roles in host defence, but are also implicated in inflammatory diseases such as rheumatoid arthritis (RA) where they contribute to systemic inflammation and joint damage. Transcriptomic analysis of neutrophils has revealed significant changes in gene expression in neutrophils activated in vitro by cytokines and in vivo during inflammation in RA. However, there are no reports on the global metabolomic changes that occur during neutrophil activation. The aim of this study was to establish protocols for the study changes in the metabolome of human neutrophils using 1H NMR spectroscopy.
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Project description:Regulation of TLR8-activated gene expression in human neutrophils
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Project description:To combat virus infections, which are major human killers, a deeper understanding of how viruses reprogram their hosts to create optimal production of progeny is needed. Most knowledge on the regulation of cellular gene expression during adenovirus infection is derived from studies of mRNA expression. Here, we investigated the changes in cellular protein expression during the early phase of adenovirus type 2 (Ad2) infection of primary human cells by stable isotope labeling in cell culture (SILAC) with subsequent liquid chromatography-high resolution tandem mass spectrometric (LC-MS/MS) analysis using a Q-Exactive Orbitrap instrument. Cells were in-depth evaluated 6 and 12 hours post infection (hpi) and two biological replicates were investigated using swapped labeling. In total, 2027 and 2150 proteins were quantified at 6 and 12 hpi, respectively. Among them, 431 and 544 were deregulated more than 1.5-fold at the two time points. For the deregulated proteins the change in protein expression was compared with that of late phase of infection (see PXD004095). Pathway analysis showed that De novo purine and pyrimidine biosynthesis, Glycolysis and Cytoskeletal regulation by Rho GTPase pathways are activated early during the infection, while the inactivation of the Integrin signalling pathway starts between 6 and 12 hpi. The transcription factor MYC was predicted to be activated with time, and the phosphopeptide analysis revealed the up-regulation of phosphosites related with glycolysis or cytoskeletal reorganization. These results complement the previous knowledge obtained from transcriptomic data, and show novel and specific aspects of how adenovirus influence host cell gene expression at the protein level.The results contribute to our understanding of host cell gene regulation during infection at a deeper level.
2018-10-04 | PXD008980 | Pride
Project description:Among the most important regulators of gene expression in bacteria are 'nucleoid-associated proteins'. These proteins alter the topology of the bound DNA by bending, wrapping or bridging it, thus having multiple effects, including transcriptional regulation, on the bacterial cell. Among the best-studied nucleoid proteins are H-NS and Fis, which bind to specific sequences on the DNA. H-NS is a global repressor of gene expression. Fis alters the global conformation of the DNA by introducing branched structures in it; but its effect on gene expression on a genomic scale remains largely unclear. Several bacterial transcriptional regulators including H-NS and Fis have been studied using ChIP-chip. However, the higher resolution and dynamic range offered by ChIP-Seq have not been exploited for any bacterial species. By performing ChIP-Seq of these two proteins, we present the first such study in a bacterium. In addition to providing a proof-of-principle for the use of this technology for bacteria, we perform our study at multiple time-points during growth in rich medium, thus generating new insights into how these proteins function under different cellular conditions. Further, by analysing our data in conjunction with newly-generated gene expression and RNA polymerase-chromosome interaction data we provide new interpretation of the genome-scale patterns of the interactions of these proteins to the DNA. ArrayExpress Release Date: 2010-07-29 Person Roles: submitter Person Last Name: Sai Narain Seshasayee Person First Name: Aswin Person Mid Initials: Person Email: aswin@ebi.ac.uk Person Phone: Person Address: Person Affiliation: EBI
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Project description:Global intron retention mediated gene regulation during CD4+ T cell activation
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Project description:Global gene expression changes during human Angiomyolipoma xenograft propagation
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Project description:Regulation of TLR8-activated gene expression in human neutrophils [ChIP-seq]
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Project description:Progastrin is a pro-hormone that, in physiological conditions, is maturated in gastrin in G cells of the stomach. The role of the gastrin is to stimulate the secretion of gastric acids during digestion. It is also important for the regulation of cell growth of the gastric mucosal.
In a healthy person, progastrin is not detectable in the peripheral blood. However, progastrin is abnormally released in the blood of patients with different cancers (colorectal, gastric, ovarian, breast, cervix uterus, melanoma...) The gene GAST coding for progastrin is a direct target gene of the WNT/ß-catenin oncogenic pathway. The activation of this oncogenic pathway is an early event in cancer development.
Chronic activation of the WNT/ß-catenin oncogenic pathway occurs in almost all human solid tumors and is a central mechanism in cancer biology that induces cellular proliferation, blocking of differentiation leading to primary tumor growth and metastasis formation.
Progastrin measured in the peripheral blood of patients on treatments, could be a new powerful marker for diagnosis and prognosis at different stages.
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