Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

49 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling by array of dendritic cells from three different human donors to characterize the impact of differential HIV opsonization on dendritic cell modulation

ABSTRACT: The aim of this study was to characterize the impact of differential HIV opsonization on DC modulation. DCs are the most potent antigen-presenting cells and among the first cells HIV is attaching to. HIV spontaneously activates the complement system even in the absence of specific antibodies and is therefore found opsonized with complement fragments from the beginning of infection. Gene expression profiles of DCs from three different human donors and treated for 24 hrs with 100 ng/ml LPS, 300 ng/ml non-opsonized HIV (HIV-MC), or 300 ng/ml complement-opsonized (HIV-C) were compared to those of untreated immature DCs.

ORGANISM(S): Homo sapiens

SUBMITTER: Hubert Hackl

PROVIDER: E-MEXP-3706 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Immediate T-Helper 17 Polarization Upon Triggering CD11b/c on HIV-Exposed Dendritic Cells.

Wilflingseder Doris D Schroll Andrea A Hackl Hubert H Gallasch Ralf R Frampton Dan D Lass-Flörl Cornelia C Pancino Gianfranco G Saez-Cirion Asier A Lambotte Olivier O Weiss Laurence L Kellam Paul P Trajanoski Zlatko Z Geijtenbeek Teunis T Weiss Günter G Posch Wilfried W

The Journal of infectious diseases 20150112 1

Early on in human immunodeficiency virus (HIV) type 1 infection, gut T-helper (Th) 17 cells are massively depleted leading eventually to compromised intestinal barrier function and excessive immune activation. In contrast, the functional Th17 cell compartment of the gut is well-maintained in nonpathogenic simian immunodeficiency virus infection as well as HIV-1 long-term nonprogressors. Here, we show that dendritic cells (DCs) loaded with HIV-1 bearing high surface complement levels after incuba ...[more]

PMID: 25583169

Similar Datasets

Effect of HIV infection on co-stimulatory capacity of dendritic cells

Project description:HIV uses dendritic cells as a carrier to infect its target CD4+ T cells. At the same time, it also hampers DCs function in terms of their T cell stimulatory capacity and cytokine secretion. We have shown that HIV causes reduction in the expression of co-stimulatory molecules, CD80 and CD86 by DCs at the mRNA level irrespective of the viral subtype or the mode in DC-HIV interaction. The microarray experiments were performed to understand the changes in the transcription factor profile of HIV infected DCs which may in turn lead to reduced CD80/CD86 expression as well as the effect of HIV infection on other co-stimulatory molecules on DCs. The data suggests that TFs NFKB1, NFKB2, REL and MYB may be responsible for the observed decrease in CD80 and CD86 expression and that HIV infection also hampers the expression of other co-stimulatory molecules like CD70, CD30, 4-1BB, OX40L etc. The total RNA was isolated from LPS matured DCs (positive control) and HIV infected DCs using Qiagen RNeasy Minikit. Agilent Quick-Amp Labelling kit (p/n 5190-0444) was used to synthesize the labeled cDNA from 3 ug of total RNA and further process the hybridized cDNA on the array. All the steps were carried out according to manufacturerM-bM-^@M-^Ys instructions (www.agilent.com/chem/dnamauals-protocol). The array slides were scanned immediately using high throughput Agilent scanner with SureScan technology. Agilent feature extraction software was used for normalization and statistical analysis,. Pathway and gene ontology analysis was done using Genespring GX v 10.0 and biointerpreter software. The experiments were performed on DCs cultured from two independent donors. The differential expression was considered if the Log 2 mean of at least -1 for the down regulated genes and +1 for the upregulated genes. We considered only the genes that were differentially regulated genes in both the donors.

2011-03-15 | E-GEOD-21017 | biostudies-arrayexpress

Gene expression profiling of CD4 T cells in treatment-naive HIV

Project description:In this study, treatment-naive HIV, HCV mono-/co-infected individuals with CD4+ T cell counts >300/?l were recruited and their global gene expression profiles were investigated. By gene set enrichment analysis (GSEA), we revealed that gene sets of cell cycle progression, innate immune response and some transcription factors in CD4+ T cells were affected mainly by HIV; while genes associated with extracellular matrix (ECM), Beta cell development and insulin synthesis and secretion were the major targets of HCV. For metabolic pathways, it was modulated by both viruses. Besides, for the first time, our data uncovered the importance of GPCR signaling pathway during HCV, HIV infections. These data for the first time offer genetic basis for HCV/HIV mono-/co- infections, which will facilitate the understanding of the interaction of HCV/HIV in vivo and how they subvert the human gene machinery at the individual cell type level.

2012-07-01 | E-MEXP-3601 | biostudies-arrayexpress

Expression data from in vitro HIV-1-infected macrophages responding to phagocytic stimuli

Project description:We used microarrays to detail the global programme of gene expression in human macrophages infected in vitro with HIV-1 and then subjected to phagocytic stimuli; we identified distinct classes of differentially regulated genes during this process Primary human macrophages from 3 different donors were infected with HIV-1ADA WT or mock-infected for 8 days. They were incubated or not (basal) with IgG-SRBCs (FcR) or Salmonella Typhimurium (4/74 strain) during 1 hour at 37Â°C, then lysed and RNA of each sample was analyzed with microarrays.

2016-07-03 | E-GEOD-59991 | biostudies-arrayexpress

Transcriptomic analysis of CD4 T cells

Project description:Treatment-naive HIV, HCV mono-/co-infected individuals with CD4+ T cell counts >300/uL were recruited, and the global gene expression profiles of CD4+ T cells were analyzed.Equal amount of CD4+ T cells isolated from each individual were pooled to form three replicative groups. Total RNA was isolated and analyzed by Affymetrix GeneChip Array. Differentially expressed genes were identified and further confirmed by qRT-PCR. To further understand the biological meanings underlying the transcriptome data the Gene Set Enrichment Analysis was used.

2012-04-28 | E-MTAB-1014 | biostudies-arrayexpress

HIV co-receptor usage determines specific miRNA modulations in T-lymphocytes.

Project description:HIV-1 and HIV-2 are two etiological agents of Acquired Immune Deficiency Syndrome (AIDS). Several differences exist between these two retroviruses in terms of geographical distribution, replication, transmission and progression to AIDS. The molecular reasons explaining these features are largely unknown. One reason could rely on host factors able to differently counteract HIV replication. Among these factors, cellular microRNAs (miRNAs) have recently emerged as playing crucial roles. One aspect of the complex interplay between HIV and host miRNAs is the ability of HIV-1 to modulate host miRNAs and thereby to create favorable conditions for its replication. Here, we sought to compare the miRNA modulations elicited by HIV-1 and HIV-2 using an unbiased experimental strategy based on miRNA arrays. Surprisingly, we observed that these two unrelated HIVs similarly modulated the host miRNA repertoire, when utilizing CD4 and CXCR4 for entry. However, these modulations were different from the changes triggered by HIV-1 using CD4 and CCR5. In accordance with the mode of action of miRNAs, our observations were confirmed at the mRNA level. We concluded that co-receptor utilization (CXCR4 or CCR5), as opposed to genomic organization and phylogeny, is a key event determining the modulations of the host miRNA repertoire.

2012-03-06 | E-MEXP-3139 | biostudies-arrayexpress

Transcriptomic Assay of CD8 2012-05-15

Project description:In this study, Genome-wide transcriptomes of CD8+ T cells from HCV/HIV co-infected or mono-infected treatment-naive individuals were analyzed by using microarray assays. Pairwise comparisons were performed and differentially expressed genes were identified followed by quantitative real time PCR (qRT-PCR) validation. To identify the important functional categories, Directed Acyclic Graphs (DAG) from Web-based Gene SeT AnaLysis Toolkit (WebGestalt) was used to find out Gene Ontology (GO) categories with significantly enriched gene numbers. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also obtained by using the similar methods in the same website.

2012-05-17 | E-MEXP-3635 | biostudies-arrayexpress

Human Immunodeficiency Virus Tat Directly Interacts with a Specific Set of Cellular RNAs

Project description:We have used RNA immunoprecipitation to identify the set of mRNAs that HIV-1 Tat interacts with in T-cells. We have also performed measurements of relative RNA abundance to determine if Tat binding is associated with an increase in RNA abundance in Tat-expressing T-cells and during HIV infection of primary T-cells. We have also used RNA IP and ChIP-Chip to compare the RNAs with which Tat interacts with to the RNAs that RISC interacts with and the genes associated with pTEF-b.

2013-11-05 | E-MEXP-3199 | biostudies-arrayexpress

Transcription profiling of human monocyte-derived macrophages infected with HIV-1 or stimulated with interferon-beta, interferon-gamma or lipopolysaccharide

Project description:Transcriptional profiling of HIV-1 infected and that of IFNbeta, IFNgamma or LPS stimulated human monocyte derived macrophages.

2009-09-01 | E-MEXP-2032 | biostudies-arrayexpress

Determination of HOXA1 and HOXA9 target genes with inducible HOX constructs

Project description:Target genes of HOXA1 and HOXA9 were determined with the help of inducible HOX-ER constructs. For this purpose bone marrow was harvested from C57BL/6 mice and c-Kit positive progenitors were enriched by magnetic sorting (MACS technology, Miltenyi, Germany). After retroviral infection by spinoculation the cells were plated for three rounds in methylcellulose. Subsequently cells were maintained in liquid culture in RPMI1640 supplemented with murine recombinant cytokines at 100ng/ml (stem cell factor) and 10ng/ml (IL-3, IL-6, granulocyte/macrophage-colony stimulating factor) as well as 100nM 4-hydroxy-tamoxifen (TAM) for HOX activation.<br><br>For microarray analysis 4 independent cell lines were created for each HOX construct. RNA was isolated from cells in the presence of TAM and 72h after withdrawal of the inductor. Pairs of RNA replicates were pooled and two +TAM as well as two -TAM duplicates per HOX gene were hybridized to Agilent44K mouse expression arrays. Array processing and evaluation was done commercially according to Agilent specifications by ImaGenes (now SourceBioScience), Berlin, Germany.

2012-11-02 | E-MEXP-3648 | biostudies-arrayexpress

HIV Infection and Antiretroviral Therapy Have Divergent Effects on Mitochondria in Adipose Tissue

Project description:Exploratory microarray analysis identified significant changes in gene expression in adipose tissue. These included changes in genes regulating lipid and steroid metabolic processes and electron carrier activity in HIV-infected patients receiving antiretroviral therapy (ART). Additional genes involved in metabolic processes and mitochondrial function were found to be up-regulated in the adipose tissue of HIV-positive patients compared with HIV-negative controls. To identify differential gene expression in different tissues (PBMC, muscle, adipose tissue) between HIV patient groups (HIV negative, HIV positive with ART, HIV positive without ART).

2011-07-07 | E-GEOD-30310 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data