Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression in human CD4+ T-lymphocytes infected with VSVG-pseudotyped HIV-1 viruses lacking Env, Vpr, and Nef

ABSTRACT: The high mutation rate of HIV is linked to the generation of viruses expressing proteins with altered function whose impact on disease progression is unknown. We investigated the effects of HIV-1 viruses lacking Env, Vpr and Nef on CD4+ T cell gene expression using high-density DNA microarray analysis and functional assays. Keywords: three independent donors

ORGANISM(S): Homo sapiens

PROVIDER: GSE12963 | GEO | 2008/10/02

SECONDARY ACCESSION(S): PRJNA110953

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling by array of human CD4+ T-lymphocytes infected with VSVG-pseudotyped HIV-1 viruses lacking Env, Vpr, and Nef

Project description:The high mutation rate of HIV is linked to the generation of viruses expressing proteins with altered function whose impact on disease progression is unknown. We investigated the effects of HIV-1 viruses lacking Env, Vpr and Nef on CD4+ T cell gene expression using high-density DNA microarray analysis and functional assays. Experiment Overall Design: Human activated CD4+ T-lymphocytes from three independent donors were infected with HIV-1 viruses that lack Env and Nef (pNL4-3.eGFP.R+E- or HIVD2GFP) or Env, Vpr and Nef. (pNL4-3.eGFP.R-E- or HIVD3GFP) were pseudotyped with VSVG envelope. As a control, CD4+ T-lymphocytes were infected with VSVG-pseudotyped eGFP. CD4+ T-cells were sorted 48 hours after infection using GFP as a marker of infectivity. RNA was isolated 10 hours after sorting, labeled, and prepared for microarray analysis.

2008-10-26 | E-GEOD-12963 | biostudies-arrayexpress

Massive Proteome Remodelling by HIV Vpr

Project description:Viruses target host proteins for degradation to enhance their replication and transmission, and identifying these targets has provided key insights into the host-pathogen interaction1-3. Here, we use complementary unbiased mass spectrometry-based approaches to dissect the widespread proteomeic remodelling seen in HIV-1 infected T-cells. Remarkably, the HIV accessory protein Vpr is both necessary and sufficient to cause the vast majority of these changes. Protein regulation requires recruitment of the DCAF1/DDB1/CUL4 E3 ubiquitin ligase complex, and pulsed-Stable Isotope Labelling with Amino Acids in Cell Culture (SILAC) and immunoprecipitation-mass spectrometry (IP-MS) identified at least 38 cellular proteins directly targeted for degradation by Vpr. Whilst other HIV-1 accessory proteins downregulate a small number of specific host factors, Vpr depletes multiple protein targets, causing systems-level changes to the cellular proteome. A subset of the novel cellular targets identified in this study are depleted by Vpr variants from across HIV-1/SIVcpz and other primate lentiviral lineages, confirming their biological importance in vivo.

2019-05-01 | PXD013221 | Pride

E-GEOD-12963

Project description:Transcription profiling by array of human CD4+ T-lymphocytes infected with VSVG-pseudotyped HIV-1 viruses lacking Env, Vpr, and Nef

2015-08-18 | E-GEOD-12963 | ExpressionAtlas

Expression data from human monocyte derived macrophages infected with adenovirus expressing HIV-1 Vpr

Project description:HIV-1 Vpr protein is a multifunctional protein which perturbs human transcriptome and interacts with a number of cellular proteins. In this study, we have attempted to explore the efffects of Vpr on human transcriptome and have identified several genes which are involved in innate immune respone and cell signaling pathways. We used the microarray analysis to elucidate the differnetail expression pattern of differnet genes in human macrophages infected with HIV-1 Vpr. As result we found that HIV-1 Vpr protein leads to the induction of various interferon stimualted genes (ISGs) and chemokines in human macrophages. Human monocytes-derived macrophages (MDMs) were isolated from peripheral blood mononuclear cells (PBMCs) from two healthy donors and were infected with recombinant adenoviruses either expressing HIV-1 Vpr or ZsGreen1 as a control. At 48 hours post-infection, RNA was isolated and subjected to microarray analysis.

2014-04-09 | E-GEOD-56591 | biostudies-arrayexpress

Expression data from human monocyte derived dendritic cells infected with adenovirus expressing HIV-1 Vpr

Project description:HIV-1 Vpr protein is a multifunctional protein which perturbs human transcriptome and interacts with a number of cellular proteins. In this study, we have attempted to explore the efffects of Vpr on human transcriptome and have identified several genes which are involved in innate immune responses. We used the microarray analysis to elucidate the differnetail expression pattern of differnet genes in human dendritic cells infected with HIV-1 Vpr. As result we found that HIV-1 Vpr protein leads to the induction of various interferon stimualted genes (ISGs) in human monocyte derived dendritic cells. Human monocytes-derived dendritic cells (MDDCs) were isolated from peripheral blood mononuclear cells (PBMCs) from two healthy donors and were infected with recombinant adenoviruses either expressing HIV-1 Vpr or ZsGreen1 as a control. At 48 hours post-infection, RNA was isolated and subjected to microarray analysis.

2014-09-06 | E-GEOD-61171 | biostudies-arrayexpress

Expression data from human monocyte derived dendritic cells infected with adenovirus expressing HIV-1 Vpr

2014-09-06 | GSE61171 | GEO

Expression data from human monocyte derived macrophages infected with adenovirus expressing HIV-1 Vpr

2014-04-09 | GSE56591 | GEO

HIV-1 Nef changes the proteome of T cells extracellular vesicles

Project description:Extracellular vesicles (EVs) are biomolecule carriers for intercellular communication in health and disease. Nef is a human immunodeficiency virus (HIV) virulence factor that is released from cells within EVs and is present in plasma EVs of HIV-1 infected individuals. We performed a quantitative proteomic analysis to fully characterize the Nef-induced changes in protein composition of T cell-derived EVs and identify novel host targets of HIV. Several proteins with well-described roles in infection or not previously associated with HIV pathogenesis were specifically modulated by Nef in EVs. Among the downregulated proteins are the interferon-induced transmembrane 1, 2 and 3 proteins (IFITM1-3), broad-spectrum antiviral factors known to be cell-to-cell transferable by EVs. Our data establish Nef as a modulator of EVs' global protein content and as an HIV factor that antagonizes IFITMs.

2024-01-26 | PXD041028 | Pride

Gene expression profiling of CD4+ T cell line due to presence of Nef during HIV-1 infection.

Project description:We have utilized microarray technology to compare gene expression profile in presence or absence of Nef during HIV-1 infection in T cell-line. We found several genes significantly differentially regulated due to ∆nef HIV-1 infection and WT HIV-1 infection when compared to Uninfected cells and also several genes significantly dergulated due to WT HIV-1 infection as compared to ∆nef HIV-1 infection. We redistributed genes belonging to several gene ontology into broad categories like “signaling”, “apoptosis”, “transcription” and “lipid metabolism”. We selected some lipid metabolism genes to validate the Nef directed differential expression using quantitative real-time RT-PCR. Thus the present work highlights the importance of Nef directed differential gene expression in milieu of other viral proteins present during infection.

2016-12-06 | GSE76793 | GEO

CD4 T cell transcriptomic response to HIV-1 infection: effects of time, viral strain, cell subtype, Vpr, and IFNa/b R2 blocking

Project description:Analysis of gene expression in primary CD4 T cells of multiple donors, following in vitro HIV-1 infection. Gene expression was measured at 4.5, 8, 12, 24 and 48h post infection and compared to mock-infected and HIV-1 delta-Env infected cells to determine and categorise the temporal expression profiles of genes affected by HIV-1 infection. Additional experiments determined: 1) the degree to which the accessory viral protein Vpr is responsible for the observed transcriptomic changes, 2) the effect of varying the viral strain, 3) the effect on the transcriptome of specifically memory CD4 T cells, the primary target cell subtype of HIV-1, in comparison with bulk CD4 T cells, and 4) the effect of blocking the Interferon alpha/beta receptor 2 during HIV-1 infection.

2021-06-10 | GSE166375 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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