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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Sorted Bulk and KK10-specific CD8+ T cells from HLA-B*2705 HIV chronic progressors before and after KK10 peptide stimulation

ABSTRACT: CD8+ T cells from HLA-B*2705 HIV+ chronic progressors Hi and Lo samples are CD8+ T cells bound by an HLA-B*2705 tetramer specific for the Gag p24 peptide KK10 PBMCs were incubated in the presence and absence of KK10 peptide for 6 days, and CD8+ and KK10-specific CD8+ T cell were sorted by flow cytometry

ORGANISM(S): Homo sapiens

SUBMITTER: Gaurav Gaiha

PROVIDER: E-GEOD-56775 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Dysfunctional HIV-specific CD8+ T cell proliferation is associated with increased caspase-8 activity and mediated by necroptosis.

Gaiha Gaurav D GD McKim Kevin J KJ Woods Matthew M Pertel Thomas T Rohrbach Janine J Barteneva Natasha N Chin Christopher R CR Liu Dongfang D Soghoian Damien Z DZ Cesa Kevin K Wilton Shannon S Waring Michael T MT Chicoine Adam A Doering Travis T Wherry E John EJ Kaufmann Daniel E DE Lichterfeld Mathias M Brass Abraham L AL Walker Bruce D BD

Immunity 20141208 6

Decreased HIV-specific CD8(+) T cell proliferation is a hallmark of chronic infection, but the mechanisms of decline are unclear. We analyzed gene expression profiles from antigen-stimulated HIV-specific CD8(+) T cells from patients with controlled and uncontrolled infection and identified caspase-8 as a correlate of dysfunctional CD8(+) T cell proliferation. Caspase-8 activity was upregulated in HIV-specific CD8(+) T cells from progressors and correlated positively with disease progression and ...[more]

PMID: 25526311

Similar Datasets

Sorted Bulk and KK10-specific CD8+ T cells from HLA-B*2705 HIV elite controllers before and after KK10 peptide stimulation

Project description:CD8+ T cells from HLA-B*2705 HIV+ elite controllers Hi and Lo samples are CD8+ T cells bound by an HLA-B*2705 tetramer specific for the Gag p24 peptide KK10 PBMCs were incubated in the presence and absence of KK10 peptide for 6 days, and CD8+ and KK10-specific CD8+ T cell were sorted by flow cytometry

2014-04-23 | E-GEOD-56971 | biostudies-arrayexpress

Sorted Bulk and KK10-specific CD8+ T cells from HLA-B*2705 HIV chronic progressors before and after KK10 peptide stimulation

Project description:CD8+ T cells from HLA-B*2705 HIV+ chronic progressors Hi and Lo samples are CD8+ T cells bound by an HLA-B*2705 tetramer specific for the Gag p24 peptide KK10

2014-04-15 | GSE56775 | GEO

Expression analysis of G9C8 clone and NOD.G9C8 tg CTLs

Project description:Diabetogenic CD8+ G9C8 clone cells and the T cells from a transgenic mouse bearing the same TCR as the clone, displayed differences in their ability to induce disease in vivo.Microarray analysis was done to identify the molecular basis for such differences between the two sets of CD8 T cells. Microarray analysis was done to identify the molecular basis for such differences between the two sets of CD8 T cells 3 vials of frozen G9C8 clone cells and spleen cells from 2 NOD.G9C8 transgenic mice were similarly peptide stimulated for 3 days and rested in IL2 for 2 days in order to obtain uniformly activated cells for analysis.

2012-12-04 | E-GEOD-31726 | biostudies-arrayexpress

Role of GM-NM-1(olf) in Familial and Sporadic Adult-Onset Primary Dystonia

Project description:Gene expression studies were performed to identify pathways possibly dysregulated by mutant in the gene GM-NM-1(olf). These experiments employed RNA derived from lymphoblastoid cell lines established for 4 affected carriers and 4 non-carriers. In comparison to endogenous control and other dystonia-associated genes, GNAL was expressed at relatively low levels in lymphoblastoid cell lines. Comparison of whole blood expression profiles of mutation carrying dystonia patients with normal controls

2013-01-26 | E-GEOD-43771 | biostudies-arrayexpress

CD8+ T cell gene expression after different antigen dose stimulations

Project description:This study aimed to identify the human T cell response toward different antigen doses. Fresh isolated CD8+ T cells from peripheral blood mononuclear cells (PBMCs) were stimulated with influenza M1 peptide-loaded autologous monocyte-derived dendritic cells for 2 weeks. A high M1 peptide antigen dose (10uM on moDC, HD1-5) and an optimal antigen dose (10nM on moDC OD1-5) were used. M1-specific CD8 T cells were tetramer sorted at the end of the 2 weeks. RNA was extracted and analyzed for gene expression using Agilent 8X60K gene expression microarrays. 5 independent samples from 3 different HLA A2+ blood donors.

2013-12-01 | E-GEOD-39761 | biostudies-arrayexpress

Effects of neonatal stress and morphine on murine hippocampal gene expression

Project description:Critically ill preterm infants experience multiple stressors while hospitalized. Morphine is commonly prescribed to ameliorate their pain and stress. We hypothesized that neonatal stress will have a dose-dependent effect on hippocampal gene expression, and these effects will be altered by morphine treatment. Male C57BL/6 mice were exposed to 5 treatment conditions between postnatal day 5 and 9: 1) Control, 2) mild stress + saline, 3) mild stress + morphine, 4) severe stress + saline and 5) severe stress + morphine. Hippocampal RNA was extracted and analyzed using Affymetrix Mouse Gene 1.0 ST Arrays. Single gene analysis and gene set analysis were used to compare groups with validation by qPCR. Stress resulted in enrichment of genes sets related to fear response, oxygen carrying capacity and NMDA receptor synthesis. Morphine downregulated gene sets related to immune function. Stress plus morphine resulted in enrichment of mitochondrial electron transport gene sets, and down-regulation of gene sets related to brain development and growth. We conclude that neonatal stress alone influences hippocampal gene expression, morphine alters a subset of stress-related changes in gene expression and influences other gene sets. Stress plus morphine show interaction effects not present with either stimulus alone. These changes may alter neurodevelopment. Male mice were exposed to 5 treatment conditions between postnatal day (P)5 and P9 (n=3/group), with birth recorded as P1. Litters were culled to n=7 maximum per dam. Groups included: 1) Untreated controls (CC), 2) mild stress + saline (MSS), 3) mild stress + morphine (MSM), 4) severe stress + saline (SSS) and 5) severe stress + morphine (SSM).

2013-08-30 | E-GEOD-50382 | biostudies-arrayexpress

Gestational Age-Dependent Changes in Gene Expression of Metabolic Enzymes and Transporters in Pregnant Mice

Project description:Knowing the gene expression profiles of drug-metabolizing enzymes and transporters throughout gestation is important for understanding the mechanisms of pregnancy-induced changes in drug pharmacokinetics. In this study, we compared gene expression of drug-metabolizing enzymes and transporters in the maternal liver, kidney, small intestine, and placenta of pregnant mice throughout gestation by microarray analysis. Specifically, we investigated cytochrome P450 (Cyp), UDP-glucuronosyltranserase (Ugt), and sulfotransferase (Sult), as well as ATP-binding cassette (Abc) and solute carrier (Slc) transporters. We found that relatively few Ugt and Sult genes were impacted by pregnancy in maternal tissues and placenta. Cyp1a2, most Cyp2 isoforms, Cyp3a11, and Cyp3a13 in the liver were down-regulated, with the greatest changes occurring on gestation days (gd) 15 and 19 compared to non-pregnant controls (gd 0). However, Cyp2d40, Cyp3a16, Cyp3a41a, Cyp3a41b, and Cyp3a44 in the liver were induced throughout pregnancy. Cyp expression in mid-gestation placenta (gd 10 and 15) was generally greater than that in term placenta (gd 19). There were also notable changes in Abc and Slc transporters. Abcc3 in the liver was down-regulated by 60%, and Abcb1a, Abcc4, and Slco4c1 in the kidney were down-regulated by 30-60% on gd 15 and 19 versus gd 0. Abcc5 in the placenta was induced 3-fold on gd 10 versus gd 15 and 19, whereas Slc22a3 expression in the placenta on gd 10 was 90% lower than that on gd 15 and 19. Overall, this study demonstrates important gestational age-dependent expression of drug-metabolizing enzymes and transporter genes, which may have mechanistic relevance to human pregnancy. Ninety pregnant mice at gestational days 0, 7.5, 10, 15, and 19 (n = 5-6 per gestational age) were used for the maternal liver, kidney, small intestine and placenta. The placentas were collected on gestational days 10, 15, and 19.

2013-10-08 | E-GEOD-41438 | biostudies-arrayexpress

Large-scale downregulation of cytokeratins in amniotic epithelium after Group B Streptococcus choriodecidual infection in Macaca nemestrina: a pathway to PPROM

Project description:Early events leading to intrauterine infection remain poorly defined, but may hold the key to a therapeutic intervention for preterm delivery. To determine early molecular pathways associated with membrane weakening that may progress to preterm premature rupture of membranes (PPROM), we examined the effects of Group B Streptococcus (GBS) on fetal membranes after a choriodecidual infection. Ten chronically catheterized pregnant monkeys (Macaca nemestrina) at 118-125 days gestation (term=172 days) received choriodecidual inoculation of either: 1) Group B Streptococcus (n=5) or 2) saline (n=5). Cesarean section and fetal necropsy was performed in the first week after GBS or saline inoculation regardless of labor. Macaca nemestrina chorioamnion samples were obtained at the site of inocculation immediately after cesarean delivery 4 days after GBS inoculation and 7 days after saline inoculation. RNA was extracted and profiled by microarray. Results were analyzed using single gene, Gene Set, and Ingenuity Pathway Analysis. Validation was by RT-PCR and immunohistochemistry.

2014-11-18 | E-GEOD-46290 | biostudies-arrayexpress

Transcriptional impact of organophosphate and metal mixtures on olfaction: copper dominates the chlorpyrifos-induced response in adult zebrafish.

Project description:Chemical exposures in fish have been linked to loss of olfaction leading to an inability to detect predators and prey and decreased survival. However, the mechanisms underlying olfactory neurotoxicity are not well characterized, especially in environmental exposures which involve chemical mixtures. We used zebrafish to characterize olfactory transcriptional responses by two model olfactory inhibitors, the pesticide chlorpyrifos (CPF) and mixtures of CPF with the neurotoxic metal copper (Cu). 30 one-year-old adult AB strain zebrafish were exposed, in groups of three, to CPF/Cu concentrations of 0/0, 0.1/0, 0.25/0, 0.6/0, 0/0.1, 0/0.25, 0/0.6, 0.1/0.25, 0.25/0.25, 0.6/0.25.

2013-05-21 | E-GEOD-47039 | biostudies-arrayexpress

Copper-induced deregulation of microRNA expression in the zebrafish olfactory system

Project description:Although environmental trace metals, such as copper (Cu), can disrupt normal olfactory function in fish, the underlying molecular mechanisms of metal-induced olfactory injury have not been elucidated. Current research has suggested the involvement of epigenetic modifications. To address this hypothesis, we analyzed microRNA (miRNA) profiles in the olfactory tissues of Cu-exposed zebrafish. Our data revealed 2, 10, and 28 differentially expressed miRNAs in a dose response pattern to three increasing Cu concentrations. Numerous deregulated miRNAs were involved in neurogenesis (let-7, miR-7a, miR-128 and miR-138), indicating a role for Cu-mediated toxicity via interference with olfactory neurogenesis. Putative gene targets of deregulated miRNAs were identified when interrogating our previously published microarray database, including those involved in olfactory cell growth and proliferation, cell death, and cell morphology. Moreover, several miRNAs (miR-203a, miR-199*, miR-16a, miR-16c, and miR-25) were inversely correlated with the depression of key genes within olfactory signal transduction pathways, which likely contributed to the inhibition of olfactory function. Our findings provide novel insight into the epigenetic regulatory mechanisms of metal-induced neurotoxicity of fish olfactory system, and identify novel miRNA biomarkers of metal exposures. 12 one-year-old adult AB strain zebrafish were exposed to Cu concentrations of 0, 6.3, 16 and 40 ppb Cu.

2014-04-30 | E-GEOD-46891 | biostudies-arrayexpress

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