Screening RNA from human uninfected macrophages, activated macrophages and T cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE28928 | GEO | 2011/04/29
SECONDARY ACCESSION(S): PRJNA139875
REPOSITORIES: GEO
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Project description:The Fox laboratory studies the SIV infection of rhesus monkeys as a model for HIV/AIDS, focusing on central nervous system infection, immunity, and brain dysfunction that develops following infection. Previous Fox lab data shows that virions derived from macrophages and T-cells differ in infectivity in a manner based solely on their cellular origin, and that these differences can be influenced by the removal of various glycans from the surface proteins present on the virion. This study examines the glycosylation pathways functioning in human macrophages and T-cells, in the context of examining how differences in the glycosylation pathways in these cell types might influence the infectivity of viral particles derived from macrophages vs. those derived from T-cells. RNA was prepared from uninfected, activated a) human macrophages and b) T-cells and sent to Microarray Core (E). Samples were prepared in triplicate, with 3 biological replicates from each cell type. The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays. Data was analyzed to determine the active glycosylation pathways in these cell types.
2011-04-29 | E-GEOD-28928 | biostudies-arrayexpress
Project description:Our lab has previously used the Glyco v3 gene-chip to analyze RNA from human macrophages and T-cells, as part of a project examining the effect of cellular origin on the viral infectivity of HIV/SIV. Our experiments have led us to hypothesize that the different glycosylation pathways present in macrophages and T-cells result in the production of virions with differently glycosylated viral proteins and different glycans present on the virion surface. Furthermore, studies with glycosidases using the Glyco v3 gene-chip have indicated that these differences in the glycosylation profiles of virions derived from different cell types may influence viral infectivity.
2011-06-14 | GSE29924 | GEO
Project description:Our lab has previously used the Glyco v3 gene-chip to analyze RNA from human macrophages and T-cells, as part of a project examining the effect of cellular origin on the viral infectivity of HIV/SIV. Our experiments have led us to hypothesize that the different glycosylation pathways present in macrophages and T-cells result in the production of virions with differently glycosylated viral proteins and different glycans present on the virion surface. Furthermore, studies with glycosidases using the Glyco v3 gene-chip have indicated that these differences in the glycosylation profiles of virions derived from different cell types may influence viral infectivity. Here we used glyco v3 chips for identifying the enzymes active in the glycosylation pathways of 174xCEM and 293 cells, which are cell types commonly used in HIV and SIV research. These analyses will allow us a better understanding of the role of glycans and glycosylation in cell-type specific effects on viral infectivity because there is a much larger amount of data on virus derived from these cell types and we will be able to relate our studies more directly to previous work in our lab and other labs. RNA from 174xCEM and HEK293 cells, cell types commonly used in HIV and SIV research, was isolated and sent to Microarray Core (E). RNA was prepared in duplicate, totaling 4 samples. Samples were labeled and hybridized to the GLYCOv3 array and gene expression patterns were used to identify enzymes active in glycosylation pathways.
2011-06-14 | E-GEOD-29924 | biostudies-arrayexpress
Project description:We previously looked the differences in glyco genes using the CFG microarray in normal macrophages and T cells, in conjunction with our studies on effects of glycosylation on HIV/SIV infectivity. In the review of a submitted manuscript, the question arose on the effect of HIV infection on the gene expression. To address this interesting question, we looked at RNA samples derived from macrophages (derived from the sample donor), either infected or not with HIV (in vitro) at different time points. RNA preparations of infected and un-infected Human macrophage at three different time points (5, 7, and 10 days)were sent to the Microarray Core (E). The RNA was amplified, labeled, and hybridized to the GLYCOv3 microarrays.
2011-04-29 | E-GEOD-28944 | biostudies-arrayexpress
Project description:Zaire ebolavirus (ZEBOV) infections are associated with high lethality in primates. ZEBOV primarily targets mononuclear phagocytes, which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis. The characterization of the responses of target cells to ZEBOV infection may therefore not only further understanding of pathogenesis but also suggest possible points of therapeutic intervention. Gene expression profiles of primary human macrophages exposed to ZEBOV were determined using DNA microarrays and quantitative PCR to gain insight into the cellular response immediately after cell entry. Significant changes in mRNA concentrations encoding for 88 cellular proteins were observed. Most of these proteins have not yet been implicated in ZEBOV infection. Some, however, are inflammatory mediators known to be elevated during the acute phase of disease in the blood of ZEBOV-infected humans. Interestingly, the cellular response occurred within the first hour of Ebola virion exposure, i.e. prior to virus gene expression. This observation supports the hypothesis that virion binding or entry mediated by the spike glycoprotein (GP1,2) is the primary stimulus for an initial response. Indeed, ZEBOV virions, LPS, and virus-like particles consisting of only the ZEBOV matrix protein VP40 and GP1,2 (VLPVP40-GP) triggered comparable responses in macrophages, including pro-inflammatory and pro-apoptotic signals. In contrast, VLPVP40 (particles lacking GP1,2) caused an aberrant response. Notably, some cellular interferon-inducible genes were upregulated six hours after exposure to virions and LPS, but not after exposure to VLPVP40-GP. This suggests that GP1,2 binding to macrophages plays an important role in the immediate cellular response. Primary human macrophages from three donors (D1, D2, D3) were harvested at 1 h and 6 h after in vitro exposure to purified Ebola virions and compared to RNA from mock-exposed cells derived from the same donors.
2011-08-31 | E-GEOD-31747 | biostudies-arrayexpress
Project description:We previously looked the differences in glyco genes using the CFG microarray in normal macrophages and T cells, in conjunction with our studies on effects of glycosylation on HIV/SIV infectivity. In the review of a submitted manuscript, the question arose on the effect of HIV infection on the gene expression.
2011-04-29 | GSE28944 | GEO
Project description:We analyzed the incorporation of cellular microRNAs (miRNAs) into highly purified HIV-1 virions and observed that this largely, but not entirely, mirrored the level of miRNA expression in the producer CD4+ T cells. Specifically, of the 58 cellular miRNAs detected at significant levels in the producer cells, only five miRNAs were found at a 2 to 4-fold higher level in virions than predicted based on random sampling. Of note, these included two miRNAs, miR-155 and miR-92a, reported previously to at least weakly bind HIV-1 transcripts. To test whether miRNA binding induces virion incorporation, we introduced artificial miRNA target sites into the HIV-1 genome and observed a 10 to 40-fold increase in the packaging of the cognate miRNA into virions, leading to the recruitment of up to 1.6 copies into each virion. Importantly, this high level of incorporation significantly inhibited HIV-1 virion infectivity. We conclude that target sites for cellular miRNAs can inhibit RNA virus replication at two distinct steps, i.e., during infection and during viral gene expression, thus explaining why a range of different RNA viruses appear to have evolved to restrict cellular miRNA binding to their genome.
2016-12-22 | GSE89868 | GEO
Project description:The objective of this study was to identify the viral transcripts packaged into the virion particles produced from BCBL1 cells as well as virions from 293L cells containing BAC36 BACs RNA from virions were extracted and analyzed by RNA sequencing
2014-10-16 | E-GEOD-62343 | biostudies-arrayexpress
Project description:Zaire ebolavirus (ZEBOV) infections are associated with high lethality in primates. ZEBOV primarily targets mononuclear phagocytes, which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis. The characterization of the responses of target cells to ZEBOV infection may therefore not only further understanding of pathogenesis but also suggest possible points of therapeutic intervention. Gene expression profiles of primary human macrophages exposed to ZEBOV were determined using DNA microarrays and quantitative PCR to gain insight into the cellular response immediately after cell entry. Significant changes in mRNA concentrations encoding for 88 cellular proteins were observed. Most of these proteins have not yet been implicated in ZEBOV infection. Some, however, are inflammatory mediators known to be elevated during the acute phase of disease in the blood of ZEBOV-infected humans. Interestingly, the cellular response occurred within the first hour of Ebola virion exposure, i.e. prior to virus gene expression. This observation supports the hypothesis that virion binding or entry mediated by the spike glycoprotein (GP1,2) is the primary stimulus for an initial response. Indeed, ZEBOV virions, LPS, and virus-like particles consisting of only the ZEBOV matrix protein VP40 and GP1,2 (VLPVP40-GP) triggered comparable responses in macrophages, including pro-inflammatory and pro-apoptotic signals. In contrast, VLPVP40 (particles lacking GP1,2) caused an aberrant response. Notably, some cellular interferon-inducible genes were upregulated six hours after exposure to virions and LPS, but not after exposure to VLPVP40-GP. This suggests that GP1,2 binding to macrophages plays an important role in the immediate cellular response.
2011-09-01 | GSE31747 | GEO
Project description:Tuberculosis (TB) remains a prevalent and lethal infectious disease. The glycobiology associated with Mycobacterium tuberculosis infection of frontline alveolar macrophages is still unresolved. Herein, we investigated the regulation of protein N-glycosylation in human macrophages and their secreted microparticles (MPs) used for intercellular communication upon M. tb infection. LC-MS/MS-based proteomics and glycomics were performed to monitor the regulation of glycosylation enzymes and receptors and the N-glycome in in vitro-differentiated macrophages and in isolated MPs upon M. tb infection. Infection promoted a dramatic regulation of the macrophage proteome. Most notably, significant infection-dependent down-regulation (4-26 fold) of 11 lysosomal exoglycosidases e.g. β-galactosidase, β-hexosaminidases and α-/β-mannosidases was observed. Relative weak infection-driven transcriptional regulation of these exoglycosidases and a stronger augmentation of the extracellular hexosaminidase activity demonstrated that the lysosome-centric changes may originate predominantly from infection-induced secretion of the lysosomal content. The macrophages showed heterogeneous N-glycan profiles and displayed significant up-regulation of complex-type glycosylation and concomitant down-regulation of paucimannosylation upon infection. Complementary intact N-glycopeptide analysis supported a subcellular-specific manipulation of the glycosylation machinery and altered glycosylation patterns of lysosomal N-glycoproteins within infected macrophages. Interestingly, the corresponding macrophage-derived MPs displayed unique N-glycome and proteome signatures supporting a preferential packaging from plasma membranes. The MPs were devoid of infection-dependent N-glycosylation signatures, but interestingly displayed increased levels of the glyco-initiating oligosaccharyltransferase complex and associated α-glucosidases that correlated with increased formation, N-glycan precursor levels and N-glycan density of infected MPs. In conclusion, this system-wide study provides new insight into the host- and pathogen-driven N-glycoproteome manipulation of macrophages in TB.
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