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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide mapping of IL-2 regulated target genes and IL-2 activated STAT5 binding sites in Kit225 human leukemia cells.

ABSTRACT: This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Zsuzsanna Nagy

PROVIDER: E-GEOD-40624 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome wide mapping reveals PDE4B as an IL-2 induced STAT5 target gene in activated human PBMCs and lymphoid cancer cells.

Nagy Zsuzsanna S ZS Ross Jeremy A JA Rodriguez Georgialina G Balint Balint L BL Szeles Lajos L Nagy Laszlo L Kirken Robert A RA

PloS one 20130225 2

IL-2 is the primary growth factor for promoting survival and proliferation of activated T cells that occurs following engagement of the Janus Kinase (JAK)1-3/and Signal Transducer and Activator of Transcription (STAT) 5 signaling pathway. STAT5 has two isoforms: STAT5A and STAT5B (commonly referred to as STAT5) which, in T cells, play redundant roles transcribing cell cycle and survival genes. As such, inhibition of STAT5 by a variety of mechanisms can rapidly induce apoptosis in certain lymphoi ...[more]

PMID: 23451206

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IL-2 induced gene expression changes in Kit225 human leukemia cell lines

Project description:Identify IL-2 mediated genes in Kit225 cells. IL-2 withdrawn cells were treated with IL-2 or left untreated for 3 hours and then subjected to gene expression microarray analysis.

2013-03-21 | E-GEOD-40618 | biostudies-arrayexpress

Genome-Wide STAT5 binding sites in Kit225 leukemia cells

Project description:In order to systematically map STAT5 genomic binding sites and IL-2 mediated gene expression changes we mapped STAT5 binding sites using chip-on-ChIP in IL-2 dependent Kit225 cells that were either left un-stimulated or stimulated with IL-2 for 30 minutes. Using MAT analysis we identified 1581 STAT5 binding sites. IL2-stimulated Kit225 cells ChIPed with STAT5 antibodies vs. Input

2013-03-21 | E-GEOD-40619 | biostudies-arrayexpress

Gene expression in Escherichia coli treated with human PGRP, gentamicin, and CCCP

Project description:Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Escherichia coli and bacterial defense against PGRP killing, gene expression in E. coli treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, repair of damaged proteins and DNA, methionine and histidine synthesis, energy generation, and Fe-S clusters repair. PGRP also caused marked decrease in the expression of genes for Fe uptake and motility. Gene expression microarray in E. coli exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than E. coli exposed to an aminoglycoside antibiotic and a membrane potential decoupler. E. coli was treated with PGRP (human recombinant PGLYRP4), gentamicin, or CCCP (carbonyl cyanide 3-chlorophenylhydrazone). RNA was obtained from each culture and assayed for gene expression using whole genome Affymetrix E. coli Genome 2.0 Array. Each experiment was repeated 3 times.

2014-07-25 | E-GEOD-44211 | biostudies-arrayexpress

Gene expression in Bacillus subtilis treated with human PGRP, gentamicin, and CCCP

Project description:Human Peptidoglycan Recognition Proteins (PGRPs) kill bacteria, likely by over-activating stress responses in bacteria. To gain insight into the mechanism of PGRP killing of Bacillus subtilis and bacterial defense against PGRP killing, gene expression in B. subtilis treated with a control protein (bovine serum albumin, BSA), human recombinant PGRP (PGLYRP4), gentamicin (aminoglycoside antibiotic), and CCCP (membrane potential decoupler) were compared. Each treatment induced unique and somewhat overlapping pattern of gene expression. PGRP highly increased expression of genes for oxidative and disulfide stress, detoxification and efflux of Cu, As, and Zn, several transporters, repair of damaged proteins and DNA, energy generation, histidine and cysteine synthesis, envelope lysis and remodeling, and other stress responses. PGRP also caused marked decrease in the expression of genes for phosphate uptake and utilization, Fe uptake, and motility. Gene expression microarray in B. subtilis exposed to a human bactericidal innate immunity protein, PGRP, showed induction of oxidative stress response and defense genes, with different expression pattern than B. subtilis exposed to an aminoglycoside antibiotic and a membrane potential decoupler. B. subtilis was treated with PGRP (human recombinant PGLYRP4), gentamicin, or CCCP (carbonyl cyanide 3-chlorophenylhydrazone). RNA was obtained from each culture and assayed for gene expression using custom whole genome Affymetrix 900513 GeneChip B. subtilis Genome Array. Each experiment was repeated 3 times.

2014-07-25 | E-GEOD-44212 | biostudies-arrayexpress

Expression data for naÃ¯ve IL-2 and IL-12 primed Pmel-1 CD8+ T-cells

Project description:The expansion, trafficking and functional effectiveness of adoptively transferred CD8+ T-cells play a critical role in mediating effective anti-tumor immunity. However, the mechanisms which program the highly proliferative and functional state of CD8+ T-cells are not completely understood. We hypothesized that IL-12, a cytokine commonly induced by TLR activation, could enhance T-cell priming by altering responsiveness to antigen and cytokines. Priming of tumor specific CD8+ T-cells in the presence of IL-12 induced the acquisition of a 'polyfunctional' effector response and increased the generation of memory cells. Moreover, IL-12 priming also promoted high levels of the IL-2 receptor alpha-chain (CD25) and robust IL-2 mediated activation of STAT5. This sensitivity to IL-2 translated into enhanced in vivo proliferation of adoptively transferred CD8+ T-cells. Furthermore, real-time, in vivo imaging of T-cell trafficking confirmed the ability of IL-12 priming to drive in vivo proliferation. IL-12 priming enhanced the anti-tumor function of adoptively transferred cells by reducing established subcutaneous tumor burden, and significantly increasing survival in an established intracranial tumor model. Finally, IL-12 priming of human PBMCs generates tumor specific T-cells phenotypically and functionally similar to IL-12 primed Pmel-1 T-cells. These results highlight IL-12 as an important mediator of CD8+ T-cell effector function and anti-tumor immunity. We primed Pmel-1 TCR transgenic CD8+ T-cells with cognate antigen and either IL-2 or IL-12 and compared their gene expression profiles. This was used to identify pathways or genes necessary for anti-tumor activity in vivo. RNA was isolated from Pmel-1 T-cells primed with antigen and cytokine for 6 days and hybridized to Affymetrix arrays.

2010-10-19 | E-GEOD-22443 | biostudies-arrayexpress

DRAK2 alters IL-2 sensitivity and Treg development

Project description:Drak2¬-deficient (Drak2-/-) mice are resistant to multiple models of autoimmunity, yet effectively eliminate pathogens and tumors. Thus, DRAK2 is an ideal target to treat autoimmune diseases. However, the mechanisms by which DRAK2 contributes to autoimmunity, particularly type 1 diabetes (T1D), remain unresolved. Our data indicate that DRAK2 contributes to autoimmunity in multiple ways by regulating thymic Treg development and by impacting the sensitivity of conventional T cells to Treg-mediated suppression.

2023-02-09 | PXD037922 | Pride

The gene encoding the hematopoietic stem cell regulator CCN3 (NOV) is under direct cytokine control through the transcription factors STAT5a/b.

Project description:Cytokines control the biology of hematopoietic stem and progenitor cells in part through the transcription factors STAT5a/b. CCN3/NOV has been reported as a positive regulator of hematopoietic stem and progenitor cells. We report microarray analyses of Lineage- Sca-1+ c-Kit+ (KSL) cells in the presence and absence of STAT5a/b. Expression of the ccn3 gene was induced over 100-fold in control, but not STAT5a/b-null cells, upon stimulation with a cocktail containing IL-3, IL-6, SCF, TPO and Flt3 ligand. Among the cytokines, IL-3 elevated ccn3 mRNA level in Lineage- c-Kit+ (KL) cells and 32D cells. ChIP assays using 32D cells revealed IL-3-induced binding of STAT5a/b to a GAS site in the ccn3 gene promoter. This is the first report to link two molecules with importance in the regulation of HSCs, CCN3 and STAT5a/b. We report that the regulation and expression of the ccn3 gene is directly controlled by IL-3 through the transcription factors STAT5a/b. Six Control and Six Stat5a/b-null KSL cells, including three biological replications, were unstimulated or stimulated with a cocktail containing IL-3, IL-6, SCF, TPO and FL.

2010-08-25 | E-GEOD-20684 | biostudies-arrayexpress

Transcription profiling of mouse muscle mutant to reveals skeletal muscle growth and fiber composition in mice are regulated through the transcription factors STAT5a/b

Project description:In skeletal muscle, STAT5a/b transcription factors are critical for normal postnatal growth, whole-animal glucose homeostasis, and local IGF-1 production. These observations have led us to hypothesize that STAT5a/b are critical for maintenance of normal muscle mass and function. To investigate this, mice with a skeletal muscle-specific deletion of the Stat5a/b genes (Stat5MKO) were used. Stat5MKO mice displayed reduced muscle mass, altered fiber-type distribution and reduced activity. On a molecular level, gene expression in skeletal muscle of Stat5MKO and control mice was analyzed by microarrays and real-time PCR, both in the presence and absence of growth hormone (GH) stimulation. Several genes involved in muscle growth, fiber-type and metabolism were significantly changed. Specifically in the quadriceps, a muscle almost exclusively composed of type II fibers, the absence of STAT5a/b led to increased expression of several genes associated with type I fibers and the de novo appearance of type I fibers. Additionally, it is shown here that expression of the androgen receptor gene (Ar) is controlled by GH through STAT5a/b. The link between STAT5a/b and Ar gene is likely through direct transcriptional regulation, as chromatin immunoprecipitaion of the Ar promoter region in C2C12 myoblasts was accomplished by antibodies against STAT5a. These experiments demonstrate an important role for STAT5a/b in skeletal muscle physiology and they provide a direct link to androgen signaling. Experiment Overall Design: Total 6 WT controls and 6 stat5a/b KO mice, treated or w/o GH

2009-09-05 | E-GEOD-14710 | biostudies-arrayexpress

Gene Expression Effects of IL-13 on Primary Human Airway Epithelial Cells

Project description:Primary culture airway epithelial cells, grown under physiologic air-liquid interface conditions, with, or without IL-13 in order to study the effects of this cytokine on mucous cell metaplasia, an important feature of asthma and COPD. Keywords: IL13, mucus, goblet cell RNA was isolated from primary culture airway epithelial cells grown at air-liquid interface, treated with or without IL-13 for 21 days.

2012-12-04 | E-GEOD-37693 | biostudies-arrayexpress

Comparison of gene expression in the intestinal metaplasia in Cdx2/IL-1beta mice vs IL-1beta alone

Project description:Cdx2/IL-1beta mice have less intestinal metaplasia at the squamocolumnar junction thanIL-1beta mice alone. This study was to identify a mechanism for this effect by examining differences in gene expression patterns when Cdx2 is co-expressed. We dissected out intestinal metaplasia nodules from the squamocolumnar junction in Cdx2/IL-1beta mice and Il-1beta mice and measured gene expression on a Mouse Gene 2.0ST Affymetrix array in Oct 2013.

2016-08-01 | E-GEOD-60320 | biostudies-arrayexpress

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