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Interferon inhibits a model RNA virus via a limited set of inducible effector genes [ISG_CRISPR_Screen]

ABSTRACT: Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). An ISG-targeted CRISPR screen using IFN beta-treated U-2 OS cells was performed to determine which ISGs were required in order for host cells to suppress Venezuelan equine encephalitis virus (VEEV) infection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE233196 | GEO | 2023/05/26

REPOSITORIES: GEO

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Interferon inhibits a model RNA virus via a limited set of inducible effector genes [GW_CRISPR_Screen]

Project description:Host cells produce interferon (IFN) in response to viral infections. Secreted interferon results in the transcription and production of hundreds of interferon-stimulated genes (ISGs). A genome-wide CRISPR screen using IFN beta-treated U-2 OS cells was performed to determine which ISGs were required in order for host cells to suppress Venezuelan equine encephalitis virus (VEEV) infection.

2023-05-26 | GSE233195 | GEO

Characterization of genetic variability of Venezuelan equine encephalitis viruses

Project description:We performed whole genome single nucleotide polymorphism (SNP) based analysis of all available Venezuelan equine encephalitis (VEE) virus antigenic complex genomes and developed a high resolution genome-wide SNP microarray. We used the SNP microarray to analyze a broad panel of VEEV isolates, found excellent concordance between array and sequence based genotypes for previously sequenced strains, and genotyped unsequenced strains.

2016-03-24 | GSE79530 | GEO

The transcriptional landscape of Venezuelan equine encephalitis virus infection

Project description:No vaccines or antivirals are approved against Venezuelan equine encephalitis virus (VEEV) infection in humans. To improve our understanding of VEEV-host interactions, we simultaneously profiled host transcriptome and viral RNA (vRNA) in thousands of single cells during infection of human astrocytes. Host transcription was suppressed, and “superproducer cells” with extreme vRNA abundance and altered transcriptome emerged during the first viral life cycle. Cells with increased structural-to-nonstructural transcript ratio demonstrated upregulation of trafficking genes at later time points. Loss- and gain-of-function experiments confirmed pro- and antiviral host factors. Single-cell deep sequencing analysis identified a viral E3 protein mutation altering host gene expression. Lastly, comparison with data from other viruses highlighted common and unique pathways perturbed by infection across evolutionary scales. This study provides a high-resolution characterization of the cellular response to VEEV infection, identifies candidate targets for antivirals, and establishes a comparative single-cell approach to study the evolution of virus-host interactions.

2020-02-25 | GSE145815 | GEO

Gene expression in the brains of different strains of laboratory mice upon intranasal infection with vaccine strain (TC83) of Venezuelan equine encephalitis virus

Project description:Differing from other experimental models, intranasal infection with vaccine strain of Venezuelan equine encephalitis virus, VEEV, (TC83) caused high titer infection in the brain and 90–100% mortality in the C3H/HeN murine model. Intranasal infection with VEEV (TC83) caused persistent viral infection in the brains of mice without functional αβ T-cells (αβ-TCR -/-). While wild-type C57BL/6 mice clear infectious virus in the brain by 13 dpi, αβ-TCR -/- maintain infectious virus in the brain to 92 dpi. To better characterize the susceptibility to disease development in different strains of mice, we have analyzed the gene transcriptomes in the brains of infected mice.

2016-12-10 | GSE91074 | GEO

The interferon-induced exonuclease, ISG20, exerts antiviral activity through upregulation of type I interferon response proteins

Project description:Type I interferon-stimulated genes (ISGs) have critical roles in inhibiting virus replication and dissemination. Despite advances in understanding the molecular basis of ISG restriction, the antiviral mechanisms of many remain unclear. The 20 kDa ISG, ISG20, is a nuclear 3'-5'exonuclease with preference for single stranded RNA (ssRNA) and has been implicated in the IFN-mediated restriction of several RNA viruses. Although the exonuclease activity of ISG20 has been shown to degrade viral RNA in vitro, evidence has yet to be presented that virus inhibition in cells requires this activity. Here, we utilized a combination of an inducible, ectopic expression system and newly generated Isg20−/− mice to investigate mechanisms and consequences of ISG20-mediated restriction. Ectopically expressed ISG20 localized primarily to Cajal bodies in the nucleus and restricted replication of chikungunya and Venezuelan equine encephalitis viruses. Although restriction by ISG20 was associated with inhibition of translation of infecting genomic RNA, degradation of viral RNAs was not observed. Instead, translation inhibition of viral RNA was associated with ISG20-induced upregulation of over 100 other genes, many of which encode known antiviral effectors. ISG20 modulated the production of IFIT1, an ISG that suppresses translation of alphavirus RNAs. Consistent with this observation, the pathogenicity of IFIT1-sensitive alphaviruses was increased in Isg20−/− mice compared to wild-type viruses, but not in ISG20 ectopic-expressing cells. Our findings establish an indirect role for ISG20 in the early restriction of RNA virus replication by regulating expressionof other ISGs that inhibit translation and possibly other activities in the replication cycle.

2018-07-01 | GSE115729 | GEO

Deep Spatial Profiling of Venezuelan Equine Encephalitis Virus Reveals Increased Genetic Diversity Amidst Neuroinflammation and Cell Death During Brain Infection

Project description:Venezuelan equine encephalitis virus (VEEV) causes a febrile illness that can progress to neurological disease with the possibility of death in human cases. The evaluation and optimization of therapeutics that target brain infections demands knowledge of the host’s response to VEEV, the dynamics of infection, and the potential for within-host evolution of the virus. We hypothesized that selective pressures during infection of the brain may differ temporally and spatially and so we investigated the dynamics of the host response, viral transcript levels, and genetic variation of VEEV TC-83 in eight areas of the brain in mice over 7 days post-infection (dpi). Viral replication increased throughout the brain until 5-6 dpi and decreased thereafter with neurons as the main site of viral replication. Low levels of genetic diversity were noted on 1 dpi, and was followed by an expansion in the genetic diversity of VEEV and nonsynonymous mutations (Ns) that peaked by 5 dpi. The proinflammatory response and the influx of immune cells mirrored the levels of virus and correlated with substantial damage to neurons by 5 dpi and increased activation of microglial cells and astrocytes. The prevalence and dynamics of Ns mutations suggests that the VEEV is under selection within the brain and that progressive neuroinflammation may play a role in acting as a selective pressure.

2023-07-21 | GSE213725 | GEO

Insect-Specific Chimeric Viruses Potentiated Antiviral Responses and Inhibited Pathogenic Alphavirus Growth in Mosquito Cells

Project description:Most alphaviruses are transmitted by mosquito vectors and infect a wide range of vertebrate hosts, with a few exceptions. Eilat virus (EILV) in this genus is characterized by a host range restricted to mosquitoes. Its chimeric viruses have been developed as safe and effective vaccine candidates and diagnostic tools. Here, we investigated the interactions between these insect-specific viruses (ISVs) and mosquito cells, unveiling their potential roles in determining vector competence and arbovirus transmission. By RNA sequencing, we found that these ISVs profoundly modified host cell gene expression profiles. Two EILV-based chimeras, consisting of EILV’s nonstructural genes and the structural genes of Chikungunya virus (CHIKV) or Venezuelan equine encephalitis virus (VEEV), namely EILV/CHIKV (E/C) and EILV/VEEV (E/V), induced more intensive transcriptome regulation than parental EILV and activated different antiviral mechanisms in host cells. We demonstrated that E/C robustly promoted antimicrobial peptide production and E/V strongly upregulated the RNA interference pathway components. This also highlighted the intrinsic divergences between CHIKV and VEEV, representatives of the Old World and New World alphaviruses. In contrast, EILV triggered a limited antiviral response. We further showed that initial chimera infections efficiently inhibited subsequent pathogenic alphavirus replication, especially in the case of E/V infection, which almost prevented VEEV and Sindbis virus (SINV) superinfections. Altogether our study provided valuable information on developing ISVs as biological control agents.

2023-01-19 | GSE220562 | GEO

Venezuelan equine encephalitis virus

Project description:Complete genome sequencing of a collection of the Venezuelan equine encephalitis viruses (VEEV).

| PRJNA157941 | ENA

Project description:Venezuelan equine encephalitis virus passaging

| PRJNA634635 | ENA

Stage-specific IFN-induced and IFN gene expression reveals convergence of type I and type II IFN and highlights their role in both acute and chronic phases of pathogenic SIV infection

Project description:Interferons (IFNs) play a major role in controlling viral infections including HIV/SIV infections. Persistent up-regulation of interferon stimulated genes (ISGs) is associated with chronic immune activation and progression in SIV/HIV infections, but the respective contribution of different IFNs is unclear. We analyzed the expression of IFN genes and ISGs in tissues of SIV infected macaques to understand the respective roles of type I and type II IFNs. Both IFN types were induced in lymph nodes during early stage of primary infection and to some extent in rectal biopsies but not in PBMCs. Induction of Type II IFN expression persisted during the chronic phase, in contrast to undetectable induction of type I IFN expression. Global gene expression analysis with a major focus on ISGs revealed that at both acute and chronic infection phases most differentially expressed ISGs were inducible by both type I and type II IFNs and displayed the highest increases, indicating strong convergence and synergy between type I and type II IFNs. These results suggest that IFN- strongly contribute to shape ISG upregulation in addition to type I IFN. The analysis of functional signatures of ISG expression revealed temporal changes in IFN expression patterns identifying phasespecific ISGs.

2017-10-30 | E-MTAB-6068 | biostudies-arrayexpress

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