Simultaneous and systematic analysis of cellular and viral gene expression during Enterovirus 71-induced host shutoff
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE103308 | GEO | 2018/05/03
REPOSITORIES: GEO
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Project description:Virus infection may shut off host protein synthesis in order to achieve the replicative advantage over host cells. It is well known that human pathogenic viruses, particularly the picornaviruses, can block host protein synthesis by cleavage or inhibition of eukaryotic initiation factors (eIFs). In this study we found a novel mechanism that microRNA (miRNA) is involved in viral pathogenesis. Infection of enteroviruses can disturb the expression of host miRNAs, in which miR-141 is up-regulated and inhibits host protein synthesis by post-transcriptional repression of the target gene eIF4E, a key element for cap-dependent translation of host proteins. Knockdown of miR-141 by a specific siRNA, antagomiR-141, could restore host eIF4E expression, delay the occurrence of cytopathic effect (CPE), and impair virus propagation. We demonstrated that EV71 infection could increase early growth response 1 (EGR1) expression which induced miR-141 causing the eIF4E suppression; while silencing of EGR1 attenuated virus production. Our results suggest that enterovirus infection causes the EGR1-mediated upregulation of host miR-141, further lead to the translational switch from cap-dependent to cap-independent protein synthesis in the host cells, an environmental beneficial for viral propagation. This novel mechanism may highlight a new approach for future development of antiviral therapy. Enteroviruses in the Picornaviridae family are important human pathogens which can cause fatal diseases, including cardiopulmonary failure, aseptic meningitis, paralysis, myocarditis, and encephalomyelitis. Virus infection may induce shutoff of host protein synthesis, particularly in picornavirus, whose protein translation is cap-independent. It is known that poliovirus 2A protease cleaves eIF4G, a scaffold component of mammalian cell translational complex, leading to the shut down of host protein synthesis. Nevertheless, the cleavage of eIF4G may not be sufficient for the complete shutoff of host protein synthesis. Previous studies showed that cleavage of polyA-binding protein (PABP) by viral protease 3C and dephosphorylation of the translational repressor, eIF4E binding protein 1 (4E-BP1), also contribute to this process. The cap-binding protein, eIF4E, is the most crucial factor in determining whether cap-dependent or -independent translation takes place. The mechanism by which viral infection modulates host cell protein synthesis through interfering eIF4E expression is not yet known. miRNAs are a newly discovered class of small non-protein-coding RNAs that may act via endogenous RNA interference. Our understanding of its role in the dynamic interplay between virus and host components is quite limited. Since both virus infection and miRNAs could hinder cellular protein synthesis, whether miRNAs are involved during virus infection in shutting off host protein synthesis is still unknown. To address this issue, we analyze the altered gene and microRNA expression after EV71 infection. ***This submission represents the mRNA expression component of the study only***
2011-01-03 | E-GEOD-15323 | biostudies-arrayexpress
Project description:We have previously shown that Heparin (Hep) significantly inhibited Enterovirus 71 (EV71) infection and binding in both Vero and a human neural cell line, SK-N-SH, in vitro. Therefore, in this study we intended to gain insight into the cellular and molecular mechanisms of action of Hep against clinical EV71 infection in SK-N-SH cells. Instead of stating a long list of gene functions and pathways, we tried to select for EV71-induced genes that were exclusively affected by antiviral activity of Hep through a multi-level comparison and characterization. Overall, our microarray analysis may suggest that Hep might exert its anti-EV71 activity in SK-N-SH cells, at least in part, through the following mechanisms: i. Reduction of the down-regulation effect of EV71 on TOX that would lead to an increased population of effective, mature T-cells and NK-cells; ii. Reduction of the up-regulation effect of EV71 on GIP, that in turn, would reduce recruiting different GPCRs, leading to a reduced viral infection in host cells; iii. Partially neutralization of the EV71-mediated apoptosis through expression of CARP2 that acts as an anti-apoptosis ubiquitin protein ligase (E3). EV71 is a neurovirological virus that can sometimes cause severe and fatal CNS complications in infected patients. Since still there is no approved drug for prophylaxis of EV71-casued disease, discovering a molecular drug target(s) for EV71 infection would be crucial. This was the first study to report direct assessment of mechanisms of action of antivirals against EV71 infection. SK-N-SH cells were infected with a clinical EV71 isolate followed by treatment with 125 µg/mL of Hep. At 72 hours post infection, antiviral activity and cytotoxicity of Hep at 125 µg/mL in 12-well plates were carried out at the same time as RNA extraction. This way, we could ensure that we would assess transcript profiles of the host cells under the same condition and time as assessment of antiviral activity and cytotoxicity for the same replicates. Changes in expression profiles of the host cells were comparatively assessed under four conditions: cell control (neither infection nor treatment, designated CC), treated only with Hep (compound control, designated Cyto), EV71-infected cells treated with Hep (treatment, designated H), and infected with EV71 without treatment with Hep (virus control, designated V). All experiments were applied in triplicate, and totally twelve GeneChip® Human Gene 1.0 ST arrays were purchased from Affymetrix and processed. Then, the following five contrasts were made: Hep vs. CC; VC vs. CC; Cyto vs CC; Hep vs. VC; and Hep vs. Cyto. For each contrast, only samples from the two target groups were included. The statistical parameters of ANOVAs, p values, multiple test corrections, and fold changes were calculated within each contrast. Then, a multi-level selection and analysis procedure was employed in order to attribute changes in the gene transcription level to antiviral activity of Hep.
2011-12-10 | E-GEOD-34234 | biostudies-arrayexpress
Project description:Many viruses potently inhibit host protein synthesis while employing unconventional strategies to sustain their own translation, but how and why certain cellular mRNAs continue to be translated remains unclear. Here, we show that during shutoff by Vaccinia Virus (VacV) several host mRNAs increase in polysome occupancy but few, topped by JUN, result in increased protein abundance. Translation of viral mRNAs depended on the small ribosomal protein, Receptor for Activated C Kinase 1 (RACK1) and the eukaryotic Initiation Factor, eIF3. Cryo-electron microscopy (cryo-EM) further showed that eIF3 bound to virus-modified RACK1-containing 40S subunits that exhibit altered head rotation during infection. By contrast, RACK1 and eIF3 were dispensable for JUN translation. Moreover, structurally distinct 5’ untranslated regions (5’UTRs) in viral versus JUN mRNAs conferred differential eIF3 dependencies. Altogether, we reveal how distinct modes of non-canonical initiation support the production of both host and viral proteins that facilitate poxvirus replication despite infection-induced shutoff.
2024-10-30 | GSE278320 | GEO
Project description:African swine fever is a viral disease of swine caused by the African swine fever virus (ASFV). Currently, ASFV is a serious threat to the global pig industry. A viral strategy to undermine host cell response is to establish a global shutoff of host protein synthesis (virus-induced shutoff, vhs). Here, we characterize ASFV-induced shutoff in primary porcine macrophages by measurement of relative protein synthesis rates based on stable isotope labeling with amino acids in cell culture (SILAC). The impact of ASFV infection on the synthesis of >2000 individual host proteins showed a high degree of variability ranging from complete shutoff to a strong induction of proteins that are absent from naïve cells. By GO-term enrichment analysis the cellular pathways that were most efficiently impacted by vhs were identified. The experimental setup is suitable to quantify vhs after infections with different viruses.
2023-05-31 | PXD039806 | Pride
Project description:We have previously shown that Heparin (Hep) significantly inhibited Enterovirus 71 (EV71) infection and binding in both Vero and a human neural cell line, SK-N-SH, in vitro. Therefore, in this study we intended to gain insight into the cellular and molecular mechanisms of action of Hep against clinical EV71 infection in neural cells. Instead of stating a long list of gene functions and pathways, we tried to select for EV71-induced genes that were exclusively affected by antiviral activity of Hep through a multi-level comparison and characterization. Overall, the findings of this study suggest several molecular targets by which Hep might exert its antiviral activity against clinical EV71 infection in neural cells. Mostly, Hep appeared to modulate induction effect of EV71 on several genes in a way that may benefit the host cell and inhibit the viral infection. The most important genes where expression patterns were significantly changed by Hep include genes related to; (i) cell growth, (ii) DNA repair and replication, (iii) cytoplasmic microfilaments and related apoptosis, (iv) regulation of energy metabolism and mitochondrion-related apoptosis, (v) cytoplasmic viral transport, (vi) transmembrane proteins and the related signaling pathways, (vii) phosphoribosyltransferase, (viii) transcription factors, (ix) G protein-coupled receptors and G protein-coupled receptors-interacting proteins, (x) remodeling actin filament assembly, (xi) chemokin receptors, and (xii) immunosuppression. In addition, Hep sometimes appeared to be harmful for cells, like the case in that Hep likely suppresses regulation of Metallothionein 1E. Furthermore, it should not be ignored that the Hep-caused affects seen in this microarray analysis may partially be attributed to a significant inhibitory effect of Hep on EV71 entry into the cells. In conclusion, we propose that our microarray findings may suggest new directions for further studies on molecular targets of anti-EV71 activity of Hep. EV71 is a neurovirological virus that can cause severe and fatal CNS complications in infected patients. There is no approved drug for prophylaxis of EV71-casued disease and discovering a molecular drug target(s) for EV71 infection would be beneficial. The microarray analysis reported here was a large-scale microarray pilot study and thus further confirmatory experiments such as real time RT PCR and Western blotting would be warranted in order to confirm the mode of action of Hep implied here.
2011-12-10 | GSE34234 | GEO
Project description:This study finds that EV71 has oncolytic activity against experimental human malignant gliomas. RNA-seq analysis of infected glioma cells reveals transcriptional up-regulation, notably genes in apoptosis pathways. Application of virus targeting based on brain-specific microRNA-124 enhances the safety profile. Oncolysis with EV71 may be a potentially novel treatment for malignant gliomas.
2019-08-27 | GSE136330 | GEO
Project description:This study characterizes the effects of Epstein-Barr virus (EBV) reactivation on the host and virus transcriptomes. For this work, a dual-fluorescent lytic reporter (DFLR) EBV was constructed based on the M81 EBV strain and used to transform primary B cells into lymphoblastoid cell lines (LCL). Deposited here is RNA-seq data from these DFLR LCLs that were induced by BCR crosslinking and sorted into latent, early lytic, and late lytic fractions. All samples consist of 40,000 sorted cells and include equal quantities of ERCC spike-in RNAs for normalization. We also performed the same experimental approach on a second DFLR LCL in which the EBV BGLF5 host shutoff nuclease was deleted. This allowed us to define which changes in the transcriptome during EBV replication were due to BGLF5. This approach demonstrated extensive shutoff of host genes during EBV replication and, unexpectedly, revealed that most of those changes were independent of BGLF5.
2024-07-08 | GSE271717 | GEO
Project description:shRNA knockdown of host gene for EV71 replication
2017-04-16 | GSE80407 | GEO
Project description:Enterovirus 71 (EV71) belongs to human enterovirus species A of the genus Enterovirus within the family Picornaviridae. We established transformant cells by transfection of mouse cells with genomic DNA from human cells and then detected two EV71-susceptible cell lines. Using microarray with the two cell lines we found that scavenger receptor B2 is a cellular receptor for EV71.
2009-06-21 | GSE16358 | GEO