Monocyte-derived dendritic cells stimulated with LPS, Poly(I:C), CD40L or a combination of IL-1-b, IL-6, TNF-a and PGE2
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE10316 | GEO | 2009/01/29
SECONDARY ACCESSION(S): PRJNA108547
REPOSITORIES: GEO
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Project description:The ubiquitin proteasome system (UPS) is known to possess important regulatory functions in the immune response. To gain a better and first comprehensive insight into the mechanisms underlying the conversion of immature to mature DC in terms of the expression of UPS related genes, we undertook a comparative gene expression profiling during DC maturation in response to four different prototypic maturation stimuli. Experiment Overall Design: Monocyte-derived DC were harvested at 3 different periods of time following stimulation for RNA extraction and hybridization on Affymetrix microarrays.
2009-02-09 | E-GEOD-10316 | biostudies-arrayexpress
Project description:Generation of human monocyte-derived DCs Peripheral blood mononuclear cells (PBMC) were isolated by Ficoll density centrifugation from buffy coats or whole blood of healthy donors and resuspended in serum-free medium (CellGro, CellGenix GmbH, Freiburg, Germany), supplemented with penicillin (50U/ml)/streptomycin (50?g/ml). Cells were plated at a density of 1-1,25 e6/cm2 in T-25 flasks and allowed to adhere for 2h at 37oC. Non-adherent cells were removed by washing twice with PBS and frozen as T cell source for stimulation experiments. Adherent monocytes were differentiated into immature DC with 1000U/ml GM-CSF and 50ng/ml IL-4 (""im DC""). Unless stated otherwise, cytokines were purchased from CellGenix GmbH, Freiburg, Germany. Cytokines were replenished on day 3. Maturation was achieved by incubation with either IL-1?; (10ng/ml), IL-6 (1000U/ml), TNF?; (10ng/ml) and PGE2 (1?g/ml, ICN, Aurora, Ohio, USA) (""PGE2-DC"") or IL-1?; (25ng/ml), IFN?; (3000U/ml, Schering-Plough, Brussels, Belgium), IFN?; (1000U/ml Strathmann Biotech AG), TNF?; (50ng/ml) and poly(I:C) (a synthetic, double-stranded RNA, 20ng/ml, Sigma-Aldrich, Taufkirchen, Germany) (""poly(I:C)-DC"") on day 6 for 48 hours Total RNA was isolated from DC before and after cytokine maturation
2008-11-01 | E-MEXP-1230 | biostudies-arrayexpress
Project description:Analysis of the specific transcriptional changes on DCs provided by direct pattern recogition receptor (PRR) or IFNAR signaling that are required for DC maturation after poly IC stimulation. Results provide important information about the intricate differentiation process of DC maturation and the importance of type I IFNs for DC immunogenicity.
2013-10-01 | GSE46478 | GEO
Project description:BACKGROUND: Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment. RESULTS: The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism. CONCLUSIONS: The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates. DC were generated from the bone marrow of C57BL/6 mice using GM-CSF, Treated with poly I:C, and RNA was isolated at 0, 1, 3, 6, 12 and 24 hours, and subjected to microarray analysis. Two independent replicate experiments were performed.
2010-08-26 | E-GEOD-21033 | biostudies-arrayexpress
Project description:Analysis of the specific transcriptional changes on DCs provided by direct pattern recogition receptor (PRR) or IFNAR signaling that are required for DC maturation after poly IC stimulation. Results provide important information about the intricate differentiation process of DC maturation and the importance of type I IFNs for DC immunogenicity. WT/IFNA-/- or WT/PRR-/- mixed-chimera mice were injected with 50 ug Poly-IC i.p. in vivo 4 and 14 hr later, wild type and KO CD11chi CD3- DX5- B220- DCs were FACS sorted based on CD45.2 expression. Total RNA was isolated and expression profile was compared between unstimulated and activated WT and KO DCs.
2013-10-01 | E-GEOD-46478 | biostudies-arrayexpress
Project description:BACKGROUND: Dendritic cells (DC) play a central role in primary immune responses and become potent stimulators of the adaptive immune response after undergoing the critical process of maturation. Understanding the dynamics of DC maturation would provide key insights into this important process. Time course microarray experiments can provide unique insights into DC maturation dynamics. Replicate experiments are necessary to address the issues of experimental and biological variability. Statistical methods and averaging are often used to identify significant signals. Here a novel strategy for filtering of replicate time course microarray data, which identifies consistent signals between the replicates, is presented and applied to a DC time course microarray experiment. RESULTS: The temporal dynamics of DC maturation were studied by stimulating DC with poly(I:C) and following gene expression at 5 time points from 1 to 24 hours. The novel filtering strategy uses standard statistical and fold change techniques, along with the consistency of replicate temporal profiles, to identify those differentially expressed genes that were consistent in two biological replicate experiments. To address the issue of cluster reproducibility a consensus clustering method, which identifies clusters of genes whose expression varies consistently between replicates, was also developed and applied. Analysis of the resulting clusters revealed many known and novel characteristics of DC maturation, such as the up-regulation of specific immune response pathways. Intriguingly, more genes were down-regulated than up-regulated. Results identify a more comprehensive program of down-regulation, including many genes involved in protein synthesis, metabolism, and housekeeping needed for maintenance of cellular integrity and metabolism. CONCLUSIONS: The new filtering strategy emphasizes the importance of consistent and reproducible results when analyzing microarray data and utilizes consistency between replicate experiments as a criterion in both feature selection and clustering, without averaging or otherwise combining replicate data. Observation of a significant down-regulation program during DC maturation indicates that DC are preparing for cell death and provides a path to better understand the process. This new filtering strategy can be adapted for use in analyzing other large-scale time course data sets with replicates.
2010-08-26 | GSE21033 | GEO
Project description:The ubiquitin proteasome system (UPS) is known to possess important regulatory functions in the immune response. To gain a better and first comprehensive insight into the mechanisms of remodelling of UPS related gene expression inresponse to interferon-gamma, we undertook a comparative gene expression profiling during interferon-gamma stimulation at very early time points. Keywords: time course
2010-05-11 | GSE21760 | GEO
Project description:Background Dendritic cells (DC) represent the major cell type leading to polarized T helper (Th) cell responses in vivo. The current data indicate that DC maturation under inflammatory conditions or by helminth infections induce only incomplete DC maturation bearing a partially tolerogenic potential. Such semi-mature DC promoted a Th2 profile with increasing proportions of regulatory IL-10 producing T cells (Tr-1) upon restimulation. Methodology/Principal Findings Here we asked whether the instruction of DC by the proinflammatory cytokine TNF is qualitatively different from maturation by two types of variant surface glycoproteins (VSGs) of Trypanosoma brucei. We tested differentially matured murine bone marrow (BM)-derived DC for changes in surface markers or cytokines, by microarray analyses, for their induction of Th2 responses and their capacity to influence the disease models asthma for Th2 immunity and experimental autoimmune encephalomyelitis (EAE) for a Th1/Th17 response. Conclusions/Significance Together, our data suggest that the partial maturation signatures induced by TNF and VSG antigens are highly similar and result in comparable Th2/Tr1 profiles, effects on asthma and EAE. This is remarkable since the responses resulting from endogenous inflammatory TNF-receptor signals or exogenous pathogenic MyD88 ligands are comparable. total samples analysed are 5
2012-03-19 | E-GEOD-28231 | biostudies-arrayexpress
Project description:Background Dendritic cells (DC) represent the major cell type leading to polarized T helper (Th) cell responses in vivo. The current data indicate that DC maturation under inflammatory conditions or by helminth infections induce only incomplete DC maturation bearing a partially tolerogenic potential. Such semi-mature DC promoted a Th2 profile with increasing proportions of regulatory IL-10 producing T cells (Tr-1) upon restimulation. Methodology/Principal Findings Here we asked whether the instruction of DC by the proinflammatory cytokine TNF is qualitatively different from maturation by two types of variant surface glycoproteins (VSGs) of Trypanosoma brucei. We tested differentially matured murine bone marrow (BM)-derived DC for changes in surface markers or cytokines, by microarray analyses, for their induction of Th2 responses and their capacity to influence the disease models asthma for Th2 immunity and experimental autoimmune encephalomyelitis (EAE) for a Th1/Th17 response. Conclusions/Significance Together, our data suggest that the partial maturation signatures induced by TNF and VSG antigens are highly similar and result in comparable Th2/Tr1 profiles, effects on asthma and EAE. This is remarkable since the responses resulting from endogenous inflammatory TNF-receptor signals or exogenous pathogenic MyD88 ligands are comparable.
2012-03-19 | GSE28231 | GEO
Project description:XCR1+ dendritic cells (DC) have been shown to excel in antigen cross-presentation for the activation of naïve CD8 T cells. This property was reported to be associated to the subset of the XCR1+ DC expressing IL-12b upon ex vivo stimulation for 24 h with a mixture of CpG, IFN-γ, and GM-CSF (Lin ML et al. Proc Natl Acad Sci USA. 2008. PMID: 18272486). DC found in the steady-state non-lymphoid tissues undergo an homeostatic, tolerogenic, maturation and migrate to the draining lymph nodes to interact with naive autoreactive T cells and induction their peripheral tolerance. In contrast, spleen DC are thought to exist solely in an immature state. The aim of this study was to re-examine heterogeneity within steady state spleen XCR1+ DC, in particular examining whether this population encompass a fraction of mature DCs as assessed through their expression of CCR7 and/or the Il12b gene. Indeed, we show that a small fraction of XCR1+ spleen DC constitutively mature into two distinct but likely successive activation stages characterized as CCR7+ and CCR7+Il12b+ respectively, and correlated with increasing ability to cross-present antigen to naïve CD8 T cells. Transcriptomic analysis of the subsets of XCR1+ DC found in steady state spleen unexpectedly showed that their homeostatic maturation was unexpectedly associated with up-regulated of many genes thought to drive pro-inflammatory T-cell responses and previously found to be commonly induced upon maturation of distinct DC subsets in response to stimulation by various microbial-type stimuli (Vu Manh TP et al. Eur J Immunol. 2013. PMID: 23553052). Thus, our results reveal that spleen XCR1+ DC undergo constitutive maturation and emphasize the common mechanisms operating upon homeostatic, tolerogenic, DC maturation versus microbial-type stimuli-induced, immunogenic, DC maturation. DC were isolated from the spleen of untreated Il12b-EYFP reporter mice (Reinhardt RL et al. J Immunol. 2006. PMID:16849470) mice as previously described (Robbins SH et al. Genome Biol. 2008. PMID: 18218067; Baranek T et al. Cell Host Microbe. 2012. PMID: 23084923). DC subsets were sorted by flow cytometry according to the marker combinations described in the âcharacteristics: phenotypeâ field for each sample.
2016-08-22 | E-GEOD-71167 | biostudies-arrayexpress