Microarray analysis of primary melanoma patient cells, melanoma cell lines, and HL cell lines
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Kerstin Brinkmann
PROVIDER: E-GEOD-44973 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Comparative gene expression analysis (PIQOR Immunology) Human Vg9Vd2 T cells amplified (soluble phosphoantigen) from ex vivo fresh PBMC of healthy human donors 3 weeks of culture in the presence of either IL-2 or IL-2+IL-21 Total RNA extracted from resting purified gamma delta T cells PIQOR microarrays PIQOR Human Immunology Service Topic-defined microarrays (Miletnyi Biotec) Comparison IL-2+IL-21 (Cy5) versus IL-2(Cy3) T7-amplified RNA
2008-12-19 | E-GEOD-13912 | biostudies-arrayexpress
Project description:The initiation of donor derived dendritic cell (DC) adhesion and migration are one of the key events mediated by ischemia reperfusion injury (IRI) following solid organ transplantation. Recently we have been able to demonstrate that a single donor treatment with the synthetic metalloporphyrin cobalt protoporphyrin (CoPPIX) for heme oxygenase 1 (HO-1) induction results in the reduction of donor-derived DCs following IRI thus leading to the preservation of graft long-term function. Gene expression analysis in murine liver revealed the up-regulation of the signal transducer and activator of transcription 3 (STAT3) after CoPPIX treatment. Since it has been shown that CoPPIX is able to inhibit DC maturation, we could demonstrate that DC (-LPS) induced maturation guided by the secretion of pro-inflammatory cytokines and alloreactive T cell proliferation is dependent of STAT3 phosphorylation and independent of HO-1 activity. These observations highlight the immunomodulatory capacity of STAT3 which might be of further interest for the inhibition of immune response. Keywords: dendritic cells, heme oxygenase-1 (HO-1), STAT3, cobalt protoporphyrin For the analysis of gene expression profiles in vivo C57BL/6 mice were treated either with 5 mg/kg CoPPIX, i.p., 50 mg/kg MC, p.o. and 500 ppm CO for 6 or 24 hrs (3 animals in each group). Untreated C57BL/6 mice were used as controls (n=9). After 6 or 24 hrs of treatment animals were sacrificed and whole livers were harvested for analysis.
2010-05-18 | E-GEOD-8452 | biostudies-arrayexpress
Project description:Dengue represents one of the most serious life-threatening vector-borne infectious diseases that afflict ~50 million people across the globe annually. Whilst symptomatic infections are frequently reported, asymptomatic dengue largely remain unnoticed. The immune correlates conferring protection to individuals that remain clinically asymptomatic have seldom been investigated. We determined the gene expression profiles of host immune factors in individuals with asymptomatic infections, and whose cognate household members showed symptoms and signs consistent to clinical dengue infection. Results provide insight in association of certain host genes to protection against clinical dengue. Blood samples were collected from Dengue Fever (DF) and Dengue Haemorrhagic Fever (DHF) patients in Malaysia who were admitted to university of Malaya Medical Centre (UMMC), Ampang Hospital (AmpangHospital), and Hospital Tengku Ampuan Rahimah (HTAR) Klang. Blood from their asymptomatic household members were also collected. Their peripheral blood mononuclear cells (PBMCs) were isolated. 29 sample pairs (SP) of dengue patients and their accompanying asymptomatic household members were chosen on the following basis for two-channel microarray experiments: patients who have shown positive results for DENV infection with at least 2 diagnostics tests indicating positivity. Positive results for the IgM-captured ELISA were P/N ratio more than 2.0, while total antibody titer of more than 1:2560 or 4 fold increase from acute to convalescence phase was considered positive in HI assay. PRNT, a neutralization test, was used as a measure for levels of neutralizing antibodies and was considered high when it was more than 1:640, based on a reduction neutralization of 50%.
2013-09-06 | E-GEOD-50634 | biostudies-arrayexpress
Project description:The aim of the study was to compare the global transcriptional responses elicited in NHDF cells by three different strains of Borrelia burgdorferi ss (the agent of Lyme borreliosis), representative of different stages in the life cycle of Borrelia: one reference strain isolated from a tick (strain N40), and two invasive strains isolated from skin biopsy of erythema migrans (strain Pbre c4) and acrodermatitis chronica atrophians skin lesions (strain 1408 c1). Three different experimental conditions have been tested: (1) unstimulated NHDF vs NHDF stimulated by Borrelia strain N40 / (2) unstimulated NHDF vs NHDF stimulated by Borrelia strain Pbre c4 / (3)M-BM- unstimulated NHDF vs NHDF stimulated by Borrelia strain 1408 c1. There is 2 biological replicates for each condition. All NHDF stimulation have been performed in independent experiments.
2012-08-01 | E-GEOD-31740 | biostudies-arrayexpress
Project description:To ensure safety tolerance induction protocols are accompanied by conventional immunosuppressive drugs IS. But IS such as calcineurin inhibitors CNI can interfere with tolerance induction. We investigated the effect of an additional CNI treatment on anti-CD4 mAb-induced tolerance induction upon rat kidney transplantation. Additional CNI treatment induced deteriorated graft function and chronic rejection characterised by alloantibody production, intragraft plasma cells and C3d deposition. Microarray analysis revealed enhanced intragraft expression of the B cell chemokine CXCL13 upon additional CNI treatment. In contrast PNOC, a B cell-related gene highly expressed in operational tolerant kidney transplant recipients, was decreased in grafts of anti-CD4 mAb+CsA-treated recipients suggesting an altered balance of B regulatory genes. Transient B cell depletion or transfer of Tregs three weeks after transplantation could inhibit intragraft B cell accumulation, alloantibody production and ameliorate chronic rejection. These data represent unexpected findings and should be taken into consideration when designing new clinical trials. To safe the benefit of CNI in controlling memory T cell responses we need strategies for a therapeutic optimization. We show here that early B cell depletion or transfer of Tregs may be one approach to arrest B cell accumulation, activation and graft destruction. comparative analysis of different immunosuppressive regimens on renal allograft gene expression versus untreated allografts
2013-09-01 | E-GEOD-40454 | biostudies-arrayexpress
Project description:The TSC/mTOR (tuberous sclerosis complex/mammalian target of rapamycin) pathway has a central role in cell growth and is involved in human tumorigenesis. Here, we demonstrate an unexpected role of TSC2 and mTOR in regulating key inflammatory cytokines in monocytes, macrophages, and dendritic cells after bacterial stimulation. mTOR deficiency promoted IL-12/IL-23 and blocked IL-10 production via the transcription factor NF-kB. Conversely, loss of TSC2, a key negative regulator of mTOR, led to reduced NF-kB activity, limited IL-12 but enhanced IL-10 production. Transcriptional profiling demonstrated that mTOR additionally regulated many mediators important for inflammation and immunoregulation including PD-L1, CCR5, CCL22, and MCP-1. mTOR inhibition in vivo rescued susceptible mice from a lethal Listeria monocytogenes infection by modulating IL-12/IL-10 production. These data identify the TSC2/mTOR pathway as a novel pathway in innate immune responses by controlling NF-kB with profound clinical implications for infectious diseases, cancer, or transplantation. Keywords: inflammatory response of monocytes to LPS and rapamycin 107 CD14+ monocytes from four different donors were stimulated with 100 ng/ml LPS with or without 100 nM rapamycin for 4 hours. Cells were harvested, washed and pelleted and frozen at â80° C. Sample preparation and hybridization to a PIQORTM Immunology Microarray Human Antisense (quadrupled cDNA fragments for 1070 genes) was performed at the Miltenyi Microarray Service Unit. In brief, RNA was extracted with the TRIzol method (Sigma-Aldrich) and 1mg of total RNA was linear amplified by T7 polymerase. Total RNA from the LPS treated cells were Cy3 labeled, LPS and rapamycin treated cells were Cy5 labeled; both samples of a donor were hybridized on a single microarray. Only genes with signal intensities >2-fold above average background in one of the two channels were regarded as expressed.
2010-05-19 | E-GEOD-6002 | biostudies-arrayexpress
Project description:For the comparison of 6BG/TMZ with control sample, the predominant annotation among the upregulated genes is M-bM-^@M-^XapoptosisM-bM-^@M-^Y. The majority of the downregulated genes is assigned to heat shock proteins and proteins which bind unfolded proteins. To look at early changes in gene expression, primary human myeloid precursor cells (40 x 10^6 per sample) derived from 3 pooled CD34+ products were treated for 18 hours with control (vehicle), 6BG, TMZ, or 6BG/TMZ and cell pellets flash frozen. Total RNA were isolated at Miltenyi Biotec (Cologne, Germany) and bioinformatics analysis of four microarray datasets was performed by their Bioinformatics Group. The direct comparisons were: 6BG/TMZ vs Control, TMZ vs 6BG, 6BG/TMZ vs 6BG, 6BG/TMZ vs TMZ. A two-dye competitive hybridization of mRNAs derived from differently treated human cells in comparison to a reference mRNA derived from cells which underwent a different treatment was conducted. After treatment with two different drugs or a combination of both drugs, respectively, RNA was extracted from the cells and hybridized against the corresponding reference mRNA. As microarray platform, the PIQORM-bM-^DM-" Cell Death Microarray with 494 probes was used.
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