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Changes in gene expression within the skin caused by antigen-specific memory CD4+ T cells during Vaccinia virus infection.

ABSTRACT: To investigate the mechanisms used by memory CD4+ T cells to protect the skin from poxvirus infection, we infected LCMV immune mice with VacV on the right ear skin and VacV expressing the dominant MHC-II restricted epitope from LCMV (VacV-Ii-GP61) on the left ear skin. On day 3 after the co-infection, RNA from whole skin was isolated and gene expression was analyzed using RNA sequencing.

ORGANISM(S): Mus musculus

PROVIDER: GSE227917 | GEO | 2023/03/24

REPOSITORIES: GEO

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Profiling whole-tissue metabolic reprogramming during cutaneous poxvirus infection and clearance

Project description:Background Vaccinia virus (VACV) infection induces prominent changes in host cell metabolism. Little is known about the global metabolic reprogramming that takes place in the whole tissue during viral infection. Here, we performed an unbiased longitudinal metabolomics study in VACV-infected mice to investigate metabolic changes in the tissue during infection. We assessed metabolites in homogenized skin over time in the presence or absence of antigen-specific T cells using untargeted mass spectrometry. VACV infection induced several significant metabolic changes, including in the levels of nucleic acid metabolites (reflecting the impact of viral replication on the skin metabolome). Furthermore, monocyte- and antiviral T cell-produced metabolites, including itaconic acid, glutamine, and glutathione, were significantly increased following infection, highlighting the immune response’s contribution to the global skin metabolome. Additional RNA-Seq of infected skin tissue recapitulated transcriptional changes identified via metabolomics. Overall, our study reveals the metabolic balance of viral replication and the antiviral immune response in the skin and identifies metabolic pathways that could contribute to cutaneous poxvirus control in vivo.

2023-11-09 | GSE236603 | GEO

Selective modulation of cell surface proteins during vaccinia infection: a resource for identifying viral immune evasion strategies

Project description:The interaction between immune cells and virus-infected targets involves multiple plasma membrane (PM) proteins. A systematic study of PM protein modulation by vaccinia virus (VACV), the paradigm of host regulation, has the potential to reveal not only novel viral immune evasion mechanisms, but also novel factors critical in host immunity. Here, >1000 PM proteins were quantified throughout VACV infection, revealing selective downregulation of known T and NK cell ligands including HLA-C, downregulation of cytokine receptors including IFNAR2, IL-6ST and IL-10RB, and rapid inhibition of expression of certain protocadherins and ephrins, candidate activating immune ligands. Downregulation of most PM proteins occurred via a proteasome-independent mechanism. Upregulated proteins included a decoy receptor for TRAIL. Twenty VACV-encoded PM proteins were identified, of which five were not recognised previously as such. Collectively, this dataset constitutes a valuable resource for future studies on antiviral immunity, host-pathogen interaction, poxvirus biology, vector-based vaccine design and oncolytic therapy.

2022-06-01 | PXD033407 | Pride

Diversity in the polyadenylation and decay of human cellular microRNAs during Vaccinia virus infection

Project description:Vaccinia virus (VACV) is a large cytoplasmic dsDNA virus that causes dramatic alterations to many cellular pathways including microRNA biogenesis. Here we use small RNA sequencing to comprehensively quantify the impact of VACV infection on the expression of endogenous small non-coding RNAs (sncRNAs) at both early (6 h) and late (24 h) times post infection. Non-coding RNAs (sncRNAs) were assessed at 6 hours and 24 hours, in naive and VACV-infected HeLa cells, in the presence or absence of the inhibitor AraC. There were three replicates for each of the eight groups.

2015-07-15 | E-GEOD-54235 | biostudies-arrayexpress

Quantitative temporal proteomic analysis of vaccinia virus infection reveals regulation of histone deacetylases by an interferon antagonist

Project description:Vaccinia virus (VACV) has numerous immune evasion strategies, including multiple mechanisms of inhibition of IRF-3, NF-κB and type I interferon (IFN) signaling. Here, we used highly multiplexed proteomics to quantify >8,000 cellular proteins and ~80% of viral proteins over seven time points spanning the whole course of VACV infection. This identified multiple novel viral targets, including putative natural killer cell ligands and IFN-stimulated genes. The class II histone deacetylase HDAC5 was selectively degraded early during VACV infection. Use of cell lines in which HDAC5 was overexpressed or knocked out showed that HDAC5 restricted replication of both VACV and herpes simplex virus type 1 (HSV-1). By generating a protein-based temporal classification of VACV gene expression, we identified the early protein C6, a multifunctional IFN antagonist, as the factor that targets HDAC5 for proteasomal degradation. Our approach thus identifies both a novel restriction factor and a viral mechanism of innate immune evasion.

2019-05-07 | PXD012785 | Pride

Diversity in the polyadenylation and decay of human cellular microRNAs during Vaccinia virus infection

2015-07-15 | GSE54235 | GEO

Gene expression analysis of SMARTA in response to LCMV or Lm-gp61 infection

2008-01-11 | GSE10094 | GEO

Gene expression profile of WT and PD-1 -/- CD8+ T cells from murine skin (ear)

Project description:Gene expression changes were computed between naïve, WT and PD-1 -/- T Cells. WT or PD-1 -/- OT-1+ CD8+ donor T cells were sorted from the ear skin of recipient mice at day 14 after VACV-OVA skin scarification. Naïve CD8+ OT-1 T cells were isolated from lymph node and spleen of naive mice by negative selection on MACS beads

2020-12-22 | GSE130207 | GEO

Host cell gene expression profile in vaccinia virus infected mouse RAW cells at 2, 16 hours post infection

Project description:The poxviruses are a family of linear double-stranded DNA viruses about 130 to 230 kbp, that belong to the family Poxviridae. The poxviruses have an animal origin and have evolved to infect a wide host range. Variola virus (VARV), the causative agent of smallpox, is a poxvirus that infect only humans, but other poxviruses such monkey pox virus and cowpox virus have also across over from animals to infect humans. Therefor understanding the biology of poxviruses can help to devise antiviral strategies. In this study we used a system-based approach to examine the host responses to three different orthopoxviruses, CPXV, VACV and ECTV in the murine macrophage RAW 264.7 cell line.

2019-01-15 | GSE120614 | GEO

Permissivity of the NCI-60 cancer cell lines to oncolytic Vaccinia Virus GLV-1h68

Project description:Oncolytic viral therapy represents an alternative therapeutic strategy for the treatment of cancer. This therapy relies on efficient replication of virus in tumor cells in vivo with minimal or no replication in normal tissues. We recently described GLV-1h68 as a modified Vaccinia Virus (VACV) construct with exclusive in vivo tropism for tumor cells in experimental animal models. Moreover, we had previously observed a cell line-specific relationship between the ability of GLV-1h68 to replicate in vitro during the first 20 hours following infection and the in vivo ability to colonize and eliminate the corresponding tumor implant. Thus, we surveyed the in vitro permissivity to GLV-1h68 replication of the NCI-60 panel of cell lines, extensively characterized and used for the assessment of novel therapeutic modalities. All cell lines were cultured and infected in identical conditions. Pre-infection transcriptional profiling was obtained to search for correlates of permissivity to viral infection. Selected cell lines were also tested for permissivity to another VACV and a vesicular stomatitis virus (VSV) strain. We observed that permissivity to VACV infection during the first 20 hours is quite heterogeneous among cell lines but highly reproducible within each cell line. The tissue of origin of each cell line does not influence permissivity to infection with the exception of B cell derivation. Permissivity correlates between two VACV constructs and between them and VSV suggesting a common permissive phenotype. No clear transcriptional pattern predictive of permissivity to infection could be identified though weak associations were observed that suggest a multifactorial control of viral replication. This study adds to the current characterization of the NCI-60 panel to guide the design and interpretation of experimental models testing oncolytic therapies.

2012-03-24 | GSE28472 | GEO

Transcription profiling of mouse SMARTA transgenic cells in response to LCMV or Lm-gp61 infection

Project description:Following infection with LCMV, CD4+ SMARTA TCR transgenic cells (specific for the gp61-80 epitope of the LCMV glycoprotein) rapidly expand, become effector cells, and go on to form a long-lived memory population. Following infection with a recombinant Listeria monocytogenes expressing the LCMV epitope gp61-80, SMARTA cells also expand but display defective effector differentiation and fail to form memory. In an attempt to understand the signals required for CD4 T cell memory differentiation, we compared gene expression by SMARTA cells at the peak of the primary response following either Lm-gp61 or LCMV infection. Experiment Overall Design: SMARTA cells were purified at day 7 post-infection with either LCMV or Lm-gp61. SMARTA cells were sorted on the basis of Thy1.1 expression using a FACSAria. Cells were sorted through the machine twice to enhance purity. Two biological replicates of each group are provided. Each replicate represents the results of SMARTA pooled from three animals.

2008-06-11 | E-GEOD-10094 | biostudies-arrayexpress

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