Effects of bromodomain inhibitors on CD4 T+ cells under Th17-promoting conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Paul Bowness
PROVIDER: E-GEOD-71231 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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2021-03-19 | PXD008563 | Pride
Project description:In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS. We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS. Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with TGF-β (1 ng/mL), IL-1β (10 ng/mL), IL-6 (25 ng/mL), IL-21 (25 ng/mL) and IL-23 (25 ng/mL) for Th17, and TGF-β (10 ng/mL) and IL-2 (10 ng/mL) for Treg. Cells were cultured for six days in Iscoveâs modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM βâmercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th17 and Treg cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K v2 microarray kit, according to the manufactureâs instruction (Agilent Technologies).
2015-11-12 | E-GEOD-60679 | biostudies-arrayexpress
Project description:In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS. We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS. Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with plate-bound anti-CD3 (500 ng/mL), soluble anti-CD28 (500 ng/mL), in the presence of IL-12 (5 ng/mL), IL-2 (10 ng/mL) and antiâ??IL-4 (5 µg/mL) for Th1, IL-4 (10 ng/mL), IL-2 (10 ng/mL) and anti-IL-12 (5 µg/mL) and antiâ??IFN-g (5 µg/mL) for Th2. Cells were cultured for six days in Iscoveâ??s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM βâ??mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th1 and Th2 cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K microarray kit, according to the manufactureâ??s instruction (Agilent Technologies).
2015-11-12 | E-GEOD-60678 | biostudies-arrayexpress
Project description:To explore the effects of IL-4 on tumor-associated macrophagess, we first sorted CD14+ monocytes from peripheral blood mononuclear cells of healthy donors using magnetic-activated cell sorting and then induced their differentiation into macrophages by culture with M-CSF for 5 days. We then stimulated these macrophages with or without IL-4 (20 ng/ml) for 6 hours and examined gene expression using a cDNA microarray. IL-4 stimulated gene expression on monocyte-derived macrophages was measured at 6 hours after exposure to doses of 20 ng/ml IL-4.
2015-12-10 | E-GEOD-75829 | biostudies-arrayexpress
Project description:To explore the effects of sRANKL on tumor-associated macrophages, we first sorted CD14+ monocytes from peripheral blood mononuclear cells of healthy donors using magnetic-activated cell sorting and then induced their differentiation into macrophages by culture with M-CSF for 5 days. We then stimulated these macrophages with IL-4 (20 ng/ml) together with or without 100 ng/ml of sRANKL for 6 hours and examined gene expression using a cDNA microarray. sRANKL stimulated gene expression on monocyte-derived macrophages was measured at 6 hours after exposure to doses of 100 ng/ml sRANKL.
2015-08-24 | E-GEOD-72292 | biostudies-arrayexpress
Project description:CD4+ T cells that selectively produce interleukin (IL)-17, are critical for host defense and autoimmunity1-4. Crucial for T helper17 (Th17) cells in vivo5,6, IL-23 has been thought to be incapable of driving initial differentiation. Rather, IL-6 and transforming growth factor (TGF)-β1 have been argued to be the factors responsible for initiating specification7-10. Herein, we show that Th17 differentiation occurs in the absence of TGF-β signaling. Neither IL-6 nor IL-23 alone efficiently generated Th17 cells; however, these cytokines in combination with IL-1β effectively induced IL-17 production in naïve precursors, independently of TGF-β. Epigenetic modification of the Il17a/Il17f and Rorc promoters proceeded without TGF-β1, allowing the generation of cells that co-expressed Rorγt and T-bet. T-bet+Rorγt+ Th17 cells are generated in vivo during experimental allergic encephalomyelitis (EAE), and adoptively transferred Th17 cells generated with IL-23 in the absence of TGF-β1 were more pathogenic in this experimental disease. These data suggest a new model for Th17 differentiation. Consistent with genetic data linking the IL23R with autoimmunity, our findings re-emphasize the role of IL-23 and therefore have important implications for the development of new therapies. Mouse T helper 17 cell differentiation with or without TGFB
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Project description:IL-4 and IL-13 are cytokines involved in type 2 immune responses involved in atopic asthma and other diseases. They have a partially overlapping set of cognate receptors whose roles are incompletely understood. Here we explore the effects of these cytokines on various cells related to human lung disease in order to assess the global similarities and contrasts in the genes whose expression their ligation modulates. Monocytes, monocyte-differentiated (6 days, then 24h rest) macrophages, or normal primary lung fibroblasts were cultured on matrigel and treated for 6 or 24 hours with IL-4 (10 ng/ml), IL-13 (10ng/ml), IL-10 (20 ng/ml), TGFb (10 ng/ml), or dexamethasone (0.5 uM) before harvest.
2013-12-31 | E-GEOD-47538 | biostudies-arrayexpress
Project description:T cells were collected from four healthy donors using heparin anti-coagulant, diluted with equal amounts of PBS EDTA, then layered over Lymphoprep and spun to collect PBMCs. CD4+ T cells were purifed using the Miltenyi positive selection magnetic labeling kit. Cells were resuspended in RPMI (Invitrogen) with 10% FCS amd 50 U/ml IL-2 (Immunotools), and 3.5x105 plated out per well in 48 well plates, coated overnight with 2 µg/ml anti-CD3 and either anti-CD28 or anti-CD46. Purity was assessed by flow cytometry and was in all cases ⥠95%. RNA was purified from a set of unactivated cells before plating, to represent the resting, 0 hr time point samples. For early activation samples, CD28 or CD46 co-stimulated cells were harvested 2 hrs after plating. Then, 36 hours after plating, the remaining CD46-stimulated cells were harvested and labeled for IL-10 or IFN-g secretion using the Miltenyi cytokine detection kits, according to manufacturerâs instructions. Cells were then sorted into separate cytokine-secreting populations (IFN-g+/IL-10â, IFN-g+/IL-10+, and IFN-gâ/IL-10+) using a BD biosciences FACS machine.RNA from separate populations was labeled using the Hy3 microRNA (miRNA) Power labeling kit (Exiqon) and hybridised to an LNA (locked nucleic acid)-based miRCURY miRNA microarray slides (Exiqon, version 11) using a Maui hybridisation chamber (BioMicrosystems). Spot signals were acquired with an Agilent array scanner and GenePix Pro 4.1 was used for annotation (mirBase 14.0), signal processing and quantification using default background subtraction.
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Project description:Distinct metabolic programs support the differentiation of CD4+T cells into their separate lineages. In this study, we investigated metabolic mechanisms underlying the differentiation of IL-9 producing-CD4+T cells (TH9) in allergic airway inflammation and cancerous tumors. We found here that SIRT1 negatively regulates TH9 differentiation. A deficiency of SIRT1 induced by either conditional deletion in mouse CD4+T cells or the use of small interfering RNA (siRNA) in mouse or human T cells increased IL-9 production, whereas ectopic SIRT1 expression inhibited it. Notably, SIRT1-inhibited the differentiation of TH9 cells that regulated anti-tumor immunity and allergic pulmonary inflammation. Glycolytic activation through the mTOR-hypoxia-inducible factor-1α (HIF1α) pathway was required for the differentiation of the TH9 cells that confer protection against tumors and are involved in allergic airway inflammation. Our results define the essential features of a SIRT1-mTOR-HIF1α signaling-coupled glycolytic pathway in inducing TH9 cell differentiation, with implications for metabolic reprogramming as an immunotherapeutic approach. Lymphocytes were isolated from the spleen and lymph nodes of mice and sorted on a FACSAria II (Becton Dickinson). The sorted naïve T cells (CD4+TCR+CD62Lhi CD44lo) from WT or SIRT1flox/flox-CD4-Cre mice were used for in vitro culture. T cells were activated with 2 ug/ml anti-CD3 (2C11; Bio X Cell), 2 ug/ml anti-CD28 (37.51; Bio X Cell) and 100 U/ml human IL-2. For TH9 cell differentiation, cultures were supplemented with 10 ng/ml IL-4 (R&D system), 2 ng/ml TGFβ1 (R&D system). After 5-6 d culture, differentiated T cells were collected and for microarray assay.
2016-06-14 | E-GEOD-79607 | biostudies-arrayexpress
Project description:The human dataset includes the gene expression profile of CD4+ T cells isolated from blood of healthy controls and plated on TCP in RPMI-1640 containing 10% FCS, Penicillin-Streptomycin (50,000 units-50 mg) and L-glutamine (2 mM). Cells were stimulated for 4 days with 20 ng/ml of IL-1beta, 100 IU/ml of IL-2, 20 ng/ml of IL-6, 20 ng/ml IL-23 plus anti-CD2/3/28 beads at a ratio of 1 bead per 10 cells. RNA samples were isolated using the RNeasy Mini Kit (Qiagen) with on-column DNA digestion. The transcriptional profile was evaluated in three different donors using the HT12v4.1 BeadChip arrays from Illumina.
2015-07-23 | GSE71231 | GEO