LXR and RAR activation modulate TREM-1 expression in dendritic cells
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Cristina Battaglia
PROVIDER: E-MTAB-6224 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Abstract Two major dendritic cell (DC) subsets have been described in the islets of mice: The immunogenic CD8α-CD11b+ DCs and the tolerogenic CD8α+CD103+ DCs. We have recently reported on reduced numbers of the minor population of tolerogenic CD8α+CD103+ DCs in the pancreas of 5 week old pre-diabetic non-obese diabetic (NOD) mice. Aim: To analyze also the larger subset of CD11c+CD8α- DCs isolated from the pancreas of pre-diabetic NOD mice 1) for maturation and tolerance inducing molecules found abnormally expressed on CD8α+CD103+ DCs, and 2) for genome-wide gene expression to further elucidate abnormalities in underlying gene expression networks. Methods: CD11c+CD8α- DCs were isolated from 5 week old C57BL/6 and NOD pancreas. Expression of cell surface markers including CD86, CCR5, CD11b, CD103, Clec9a, CD24 and CD200R3 were measured by FACS. Genome-wide gene expression by microarray was assessed during the steady state and after in vitro LPS stimulation. Results: The steady state pancreatic CD11c+ CD8α- DCs during the pre-diabetic stage showed: 1) A reduced expression of several gene networks important for the prime functions of the cell, such as for cell renewal, immune stimulation and immune tolerance induction, for migration and for the provision of growth factors for beta cell regeneration. This general deficiency state was corroborated by a reduced in vivo proliferation (BrdU incorporation) of the cells and the reduced expression in FACS analysis of CD86, CCR5, CD103, Clec9a, CD24 and CD200R3 on the cells. 2) A hyper reactivity of these cells to LPS correlated with an enhanced pro-inflammatory state characterized by altered expression of a number of classical pro-inflammatory factors and cytokines. Conclusion: The NOD CD11c+CD8α- DCs seem to be Janus-faced depending on the conditions: Deficient in steady state with reduced immune stimulation capabilities also for tolerance induction; over-inflammatory with a molecular profile suggesting a preferential stimulatory capacity for Th1 cells when encountering a Pathogen-Associated Molecular Pattern (PAMP) in the form of LPS. We used microarray gene expression analysis to explain the abnormal expression of several cell surface markers involved in tolerace, migration and maturation in the steady-state and to measure the effect of a PAMP such as LPS We isolated RNA from FACS sorted CD11c+CD8α- DCs in 10 pooled pancreases from pre-diabetic NOD and non-diabetic C57BL/6 mice at 5 weeks. In addition, we treated in another experiment the isolated pancreas DCs with LPS (and PBS), incubated for 18h and measured gene expression. We compared gene expression between strains NOD vs C57BL/6 under steady-state and after in-vitro LPS/PBS stimulation.
2014-07-01 | E-GEOD-45028 | biostudies-arrayexpress
Project description:Small molecule ligands often have multiple effects on the transcriptional program of a cell: they trigger a receptor specific response and additional, indirect responses ("side effects"). Distinguishing those responses is important for understanding secondary effects of drugs and for elucidating molecular mechanisms of toxic chemicals. We addressed this problem by exposing cells to the environmental contaminant benzo-a-pyrene (B[a]P). B[a]P exposure activates the aryl hydrocarbon receptor (Ahr) and causes toxic stress resulting in transcriptional changes that are not regulated through Ahr. We sought to distinguish these two types of responses based on a time course of expression changes measured after B[a]P exposure. Using Random Forest machine learning we classified 81 direct Ahr targets and 1,308 genes regulated as secondary exposure effects. Subsequent weighted clustering gave further insight into the connection between expression pattern, mode of regulation, and biological function. Finally, the accuracy of the predictions was supported through extensive experimental validation. This study presents a strategy for distinguishing receptor dependent and secondary responses based on expression time courses. 36 samples were analyzed in total. Time-course data for four different time points, two different benzo(a)pyrene concentrations, including a vehicle control for each time points. Three biological replicates were generated for each treatment and time point.
2011-12-31 | E-GEOD-29188 | biostudies-arrayexpress
Project description:Toll like receptors (TLRs) sense microbial products and initiate adaptive immune responses by activating dendritic cells (DCs). Since pathogens may contain several agonists we asked whether different TLRs may synergize in DC activation. We report that in human and mouse DC TLR3 or TLR4 potently synergize with TLR7, TLR8 or TLR9 in the induction of selected cytokine genes. Upon synergistic stimulation, IL-12, IL-23 and Delta-4 are induced at levels 50-100 fold higher than those induced by optimal concentrations of single agonists, leading to enhanced and sustained TH1 polarizing capacity. Using microarray analysis we show that only 1.5% of the transcripts induced by single TLR agonists are synergistically regulated by combinations of TLR4 and TLR8 agonists.. These results identify a combinatorial code by which DCs discriminate pathogens and provide (suggest) a rationale to design adjuvants for TH1 responses. Series_overall_design: 3 untreated, 3 treated with LPS at 2h, 3 treated with LPS at 8h, 3 treated with R848 at 2h, 3 treated with R848 at 8h, 3 treated with LPS + R848 at 2h, 3 treated with LPS + R848 at 8h
2007-09-14 | E-GEOD-2706 | biostudies-arrayexpress
Project description:Gene expression profiels in the human monocyte-derived dendritic cells (DCs) from 4 different donors (A, B, C, and D) were studied. Cells were left untreated (Group 4), activated with LPS alone (Group 1) or activated in the presence cmv IL-10 (Group 2) or human IL-10 (Group 3) for 12 hours before subjected to RNA extraction. Experiment Overall Design: Overall ranscriptional profiles of activated DCs and IL-10-exposed activated DCs were compared with untreaetd immature DCs as baseline control.
2008-06-15 | E-GEOD-7095 | biostudies-arrayexpress
Project description:DCs treated with PTX (PTX-DC) is able to induce EAE like PTX as adjuvant whereas neither LPS nor DCs treated with LPS (LPS-DC) fails to induce EAE. We want to identify genes that are responsible for EAE induction in DCs and genes that are able to toloerize EAE in DCs through the microarray. Bone marrow derived dendritic cells are either unstimulated or stimulated with LPS and PTX for 24h respectively. Cells are harveseted for RNA extraction and hybridization on Affymetrix microarrays.
2015-07-31 | E-GEOD-50779 | biostudies-arrayexpress
Project description:Dendritic cells (DCs) are a special class of leukocytes able to activate both innate and adaptive immune responses. They interact with microbes through germline-encoded pattern-recognition receptors (PRRs), which recognize molecular patterns expressed by various microorganisms. Upon antigen binding, PRRs instruct DCs for the appropriate priming of natural killer cells, followed by specific T-cell responses. Once completed the effector phase, DCs reach the terminal differentiation stage and eventually die by apoptosis. We have observed that following lipopolysaccharide (LPS)-stimulation the initiation of the apoptotic pathway in DCs is due the activation of NFAT proteins. Indeed, LPS induces Src-family kinase and phospholipase C (PLC)γ2 activation, influx of extracellular Ca2+ and calcineurin-dependent nuclear NFAT translocation. The initiation of this pathway is independent of TLR4 engagement, and dependent exclusively on CD14. According with this observation CD14-deficient DCs do not die following LPS stimulation. Nevertheless, CD14-deficient DC death following LPS activation can be restored by co-stimulating DCs with LPS and thapsigargin. Thapsigargin empties the intracellular calcium stores by blocking calcium pumping into the sarcoplasmic and endoplasmic reticulum and thereby activates plasma membrane calcium channels. This, in turn, allows an influx of calcium into the cytosol and NFAT activation. To identify the NFAT controlled apoptosis genes in LPS activated DCs we have performed a kinetic microarray analysis (0, 48 and 60 h) in conditions allowing or inhibiting NFAT activation. Four genes have been selected: Nur77, Gadd45g, Ddit3/Gadd153/Chop-10 and Tia1. To identify apoptosis genes selectively modulated by NFAT, a comparative kinetic (time points 0, 48 and 60 h) microarray analysis was performed in the following conditions: 1) wild type bone marrow derived DCs (wtBMDCs) stimulated with LPS; 2) CD14-deficient BMDCs stimulated with LPS; 3) wtBMDCs stimulated with LPS in presence of thapsigargin; 4) CD14-deficient BMDCs stimulated with LPS in presence of thapsigargin.
2010-03-03 | E-GEOD-15720 | biostudies-arrayexpress
Project description:Background: Resveratrol has been demonstrated to exert pleiotropic health beneficial effects. Among the various mechanisms of action antioxidant, anti-inflammatory, cardio- and cancer-protective outcomes have been reported. Particularly, an important function of this natural compound against atherosclerosis has been postulated and the action of resveratrol on lipids and lipoprotein levels seems to be of relevance in this pathology, but also for other metabolic diseases. Accordingly, taking into consideration the straight contact of resveratrol with the intestine, this study aimed to gain insights into the protective effects of trans-resveratrol on enterocyte physiology and metabolism in proinflammatory conditions. For this purpose, a DNA microarray analysis was conducted in Caco-2 cells where global gene expression profile at intestinal level was screened. Cells were pretreated with 50 μÎ? of trans-resveratrol and, subsequently, lipopolysaccharide (LPS) was added for 48 h. Results: The microarray analysis revealed 121 genes differentially expressed between resveratrol-treated and non-treated cells (B> 0). Four genes, inhibitor of DNA binding 1(ID1), histidine-rich glycoprotein (HRG), NADPH oxidase (NOX1) and sprouty homolog 1 (SPRY), were upregulated by LPS treatment, but significantly downregulated with trans-resveratrol pretreatment (padj< 0.05). Moreover, genes implicated in pathways related to lipid metabolism, such as synthesis of lipids (z-score= -1.195) and concentration of cholesterol (z-score= -0.109), were markedly downregulated by trans-resveratrol. Other genes implicated in lipid metabolism, but also in cell death and survival function, such as transcription factors Krüppel-like factor 5 (KLF5) and amphiregulin (AREG), were also significantly inhibited by trans-resveratrol pretreatment. RT-qPCR-data confirmed the microarray results. Special mention deserves acyl-CoA synthetase long-chain family member 3 (ACSL3) and endothelial lipase (LIPG), which were downregulated by the stilbene and have been previously associated with fatty acid synthesis and obesity in other tissues. Conclusions: This study envisages that trans-resveratrol might exert important anti-lipogenic effect at intestinal level under proinflammatory conditions, which have not been previously described. The experiment was conducte in Caco-2 cells. There were three experimental groups (n=5), Caco-2 cells stimulated with lipopolysaccharides (LPS), Caco-2 cells stimulated with LPS and pre-treated with trans-resveratrol (LPS+RSV) and non-treated Caco-2 cells.
2016-06-30 | E-GEOD-73650 | biostudies-arrayexpress
Project description:Reports that low-intensity microwave radiation can induce heat-shock reporter gene expression in the nematode, Caenorhabditis elegans, have recently been reinterpreted as a subtle thermal effect caused by very slight heating. This study used a microwave exposure system (1.0 GHz, 0.5 W power input; SAR 0.9-3 mW kg-1 for 6-well plates) that minimises the temperature differential between sham and exposed conditions to ≤ 0.1°C. Comparable measurement and simulation studies of SAR distribution within this exposure system are presented. We compared 5 Affymetrix gene-arrays of pooled triplicate RNA populations from sham-exposed L4/adult worms against 5 gene-arrays of pooled RNA from microwave-exposed worms (taken from the same source population in each run). Few genes showed consistent expression changes across all 5 comparisons, and all such expression changes appeared modest after applying standard normalisation procedures (≤ 30% up- or down-regulated). The number of statistically significant differences in gene expression (846) was less than the false-positive rate expected by chance (1131). As one example, an apparent up-regulation of the vit-3 vitellogenin gene by microwave exposure was not mirrored by similar changes affecting the other co-regulated members of the same vit gene family. We conclude that the pattern of gene expression in L4/adult C elegans is not substantially perturbed by low-intensity microwave radiation, and that the minor changes observed in this study may well be explicable as false positives. As a check on the sensitivity of the Affymetrix gene-arrays used, we also compared RNA samples from N2 worms subjected to a sub-heat-shock treatment (28ºC) against controls kept at 26 ºC (but using only 2 gene arrays per condition). After similar normalisation, many more genes (3712) showed substantial expression changes (i.e. > 2-fold at p < 0.05), including a group of six heat-shock genes which were strongly but unexpectedly down-regulated (by > 10-fold). However, further replication and confirmation by real-time RT-PCR would be needed to establish how many of these changes might also be false positives. Experimenter name: Adam Dawe; Experimenter phone: +27 21 959 2364; adam@sanbi.ac.za; Experimenter institute: South African National Bioinformatics Institute; Experimenter address: University of Western Cape, Old Chemistry Building, University of Western Cape, Modderdam Road, Bellville 7530, Capetown; Experimenter zip/postal_code: 7530; Experimenter country: South Africa Experiment Overall Design: 14 samples were used in this experiment
2009-03-20 | E-GEOD-10787 | biostudies-arrayexpress
Project description:Dendritic cells (DCs) in tissues and lymphoid organs comprise distinct functional subsets that differentiate in situ from circulating progenitors. Tissue-specific signals that regulate DC subset differentiation are poorly understood. We report that DC-specific deletion of the Notch2 receptor caused a reduction of DC populations in the spleen. Within the splenic CD11b+ DCs, Notch signaling blockade ablated a distinct population marked by high expression of adhesion molecule Esam. The Notch-dependent Esamhi DC subset also required lymphotoxin beta receptor signaling, proliferated in situ and facilitated efficient CD4+ T cell priming. The Notch-independent Esamlo DCs expressed monocyte-related genes and showed superior cytokine responses. In addition, Notch2 deletion led to the loss of CD11b+ CD103+ DCs in the intestinal lamina propria and to the corresponding decrease of IL-17-producing CD4+ T cells in the intestine. Thus,Notch2 is a common differentiation signal for T cell-priming CD11b+ DC subsets in the spleen and intestine. We compared genome-wide expression profiles of wild-type Esam(hi) and Esam(lo) splenic CD11b+ DC populations, along with CD11b+ DCs from DC-RBPJΔ mice. Spleens from 2-3 Cx3cr1-GFP+ RBPJflox/flox CD11c-Cre+ mice or Cx3cr1-GFP+ RBPJflox/flox Cre-negative littermate controls were isolated, pooled and depleted of lymphoid and erythroid cells by negative selection on MACS columns. Live cells were stained for surface expression of CD11c, CD11b and Esam. CD11c(hi) CD11b+ DCs from control mice could be separated into Esam(lo) GFP(hi) versus Esam(hi) GFP(lo) subsets. CD11c(hi) CD11b+ DCs from RBPJ-targeted mice spleens were uniformly Esam(lo) GFP(hi). The two subsets from control mice and single Esam(lo) GFP(hi) subset from RBPJ-targeted mice were sorted using FACSAria II flow sorter and analyzed using GeneChip Mouse Gene 1.0 ST Array (Affymetrix).
2011-10-31 | E-GEOD-31551 | biostudies-arrayexpress
Project description:Dendritic cells (DCs) are pivotal for both recognition of antigens and control of an array of immune responses by recognizing microbes through distinct pattern recognition receptors (PRRs). The first microbial component to be studied in detail and known to cause septic shock is endotoxin (LPS). DCs recognize LPS via Toll-like receptor TLR-47. LPS causes many changes in the DCs, but the elicitation of cytokine production is perhaps the one with clear biologic relevance. We used microarrays to detail the global programme of gene expression underlying regulation of TLR 4 signaling and identified the upregulated and downregulated genes in response to LPS treatment in mouse dendritic cells. We use microarray to determine the conserved hematopoietic miRNAs to study their potential contribution to regulating many different immunological cellular processes and contexts. To obtain overall gene expression profile, we extracted bone marrow cells from at least 3 mice for each experiment. Purified ( 97~98% purity) mouse dendritic cells, treated with LPS or control diluent, were used for RNA extraction and hybridization on Affymetrix microarrays. To obtain overall miRNA expression profile, we extracted bone marrow cells from at least 3 mice (C57BL/6) for each experiment. Purified ( 97~98% purity for CD11C+ ) mouse dendritic cells were used for RNA extraction and hybridization on Exiqon miRCURY LNATM microRNA array.
2011-04-05 | E-GEOD-28340 | biostudies-arrayexpress