Homo sapiens
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-12963
PROVIDER: PRJNA110953 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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. Keywords: three independent donors
2008-10-02 | GSE12963 | GEO
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
Project description:Viruses manipulate host cells to enhance their replication, and the identification of host factors targeted by viruses has led to key insights in both viral pathogenesis and cellular physiology. We previously described global changes in cellular protein levels during human immunodeficiency virus (HIV) infection using transformed CEM-T4 T cells as a model. In this study, we develop an HIV reporter virus displaying a streptavidin-binding affinity tag at the surface of infected cells, allowing facile one-step selection with streptavidin-conjugated magnetic beads. We use this system to obtain pure populations of HIV-infected primary human CD4+ T cells for detailed proteomic analysis, including quantitation of >9,000 proteins across 4 different donors, and temporal profiling during T cell activation. Remarkably, amongst 650 cellular proteins significantly perturbed during HIV infection of primary T cells (q<0.05), almost 50% are regulated directly or indirectly by the viral accessory proteins Vpr, Vif, Nef and Vpu. The remainder have not been previously characterised, but include novel Vif-dependent targets FMR1 and DPH7, and 192 targets not identified and/or regulated in T cell lines, such as AIRD5A and PTPN22. We therefore provide a high-coverage functional proteomic atlas of HIV infection, and a mechanistic account of HIV-dependent changes in its natural target cell.
2019-03-08 | PXD012263 | Pride
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
Project description:Herein expression trends of host miRNA were measured in CEMx174 lymphocytes infected with HIV-1NL4-3 or derivative strains deficient in Tat RSS activity (RSS) or vif-/vpr (VV), or unexposed to virus. As expected from previous studies, miRNA trends were different in naive and HIV-1 infected cells. Moreover, miRNA expression trends were similar for HIV-1 and vif-/vpr-deficient HIV-1, but diverged for RSS. Rather than generalized changes in miRNA levels, HIV-1 bearing the Tat K51A RSS mutation changed the steady state of a subset of miRNAs. The results are attributable to reduction in miRNA stability or change in miRNAs activity that altered steady state expression. Comparison of the miRNA expression trends in patient PBMC and the CEMx174 lymphocytes determined >50% overlap with a subset of miRNAs identified in patients, supporting the utility of HIV-1 cell culture model to refine experimental design with patient samples, which represent miRNA profiles of co-isolated infected and uninfected cells. Our results indicate that ablation of Tat RNA silencing suppressor activity in HIV-1 changes the steady state of a subset of host mature miRNA. The observation reinforces the concept of active HIV-1 interplay with host small RNAs that modulate replication and spread. The study validated the utility of derivative HIV-1 strains to explore the interface of viral genes with host small RNA activity. In this study the microRNA profiles of CEMx174 cells infected with HIV-1 NL4-3 or derivative viruses deficient in Vif/Vpr or Tat RNA silencing suppressor activity were compared to mock infected cells. The samples were analyzed in duplicate.
2011-03-01 | E-GEOD-21892 | biostudies-arrayexpress
Project description:To determine changes of gene expression in human CD4+ T cells (Jurkat) infected with HIV-1 and treated with digoxin. Cells were infected (MOI 0.01) with a single cycle HIV-1 delta env expressing GFP and pseudotyoed with VSV-G in the presence of 400nM digoxin or DMSO. Cells were harvested 36 hours post-infection and processed for RNAseq
2017-08-19 | E-MTAB-5982 | biostudies-arrayexpress
Project description:HIV-1 infection selectively alters gene expressions of CD4 T cells. To understand the effects of HIV to the expressions of CDK and caspase pathway genes in the presence and absence of Nef, we infected CD8-depleted PBMC from healthy donors with HIV-1 BAL in the presence of BB-94, PD-0332991, QVD-OPH or DMSO control, or with Nef-sufficient, Nef-deficient Vpu-sufficient, Vpu-deficient NL4-3 strain of HIV-1. On day 6 of infection, cells were enriched for CD4 T cells for gene expression profile analyses by RNA sequencing. We then performed gene expression profiling analysis using data obtained from RNA-seq of 16 different treated CD4 T cells.
2023-11-23 | GSE218175 | GEO
Project description:Using microRNA array analyses of in vitro HIV-1-infected CD4+ cells, we find that several host microRNAs are significantly up- or downregulated around the time HIV-1 infection peaks in vitro. While microRNA-223 levels were significantly enriched in HIV-1-infected CD4+CD8? PBMCs, microRNA-29a/b, microRNA-155 and microRNA-21 levels were significantly reduced. Based on the potential for microRNA binding sites in a conserved sequence of the Nef-3?-LTR, several host microRNAs potentially could affect HIV-1 gene expression. Among those microRNAs, the microRNA-29 family has seed complementarity in the HIV-1 3?-UTR, but the potential suppressive effect of microRNA-29 on HIV-1 is severely blocked by the secondary structure of the target region. Our data support a possible regulatory circuit at the peak of HIV-1 replication which involves downregulation of microRNA-29, expression of Nef, the apoptosis of host CD4 cells and upregulation of microRNA-223. Time course of HIV infection on CD4 cells
2012-12-05 | E-GEOD-42737 | biostudies-arrayexpress
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