Genome-wide chromatin structure alteration during Epstein-Barr virus infection (Hi-C)
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE135941 | GEO | 2020/05/23
REPOSITORIES: GEO
Similar Datasets
Project description:We analysed epigenetic alterations by EBV infection especially at enhancer regions, to elucidate their contribution to tumorigenesis. We performed ChIP-seq on H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K9me3 using gastric epithelial cells with or without EBV infection. We showed that repressive marks were redistributed after EBV infection, resulting in aberrant enhancer activation and repression. Enhancer dysfunction leads to activation of pathway related to cancer hallmarks (e.g. resisting cell death, disrupting cellular energetics, activation invasion, evading growth suppressors, sustaining proliferative signaling, angiogenesis and tumor promoting inflammation) and inactivation of tumour suppressive pathway. Dysregulation of cancer-related genes during in vitro EBV infection were also observed in EBV+ gastric cancer patients. Our analysis showed that EBV-infection associated epigenetic alteration may contribute to tumorigenesis through enhancer activation and repression.
2017-08-21 | GSE97838 | GEO
Project description:Extensive DNA methylation in promoter regions is observed in gastric cancer with Epstein-barr virus (EBV) infection and EBV infection is the cause to induce this extensive hypermethylaiton phenotype in gastric epithelial cells. From transcriptome analysis, we found that TET2, one of the demethylase enzymes, was downregulated by EBV infection in gastric epithelial cell line MKN7. TET2 was overexpressed in a gastric epithelial cell line, GES1, to see its function and the hydroxymethylation, a byproduct of DNA demethylation, acquired genes by TET2 overexpression and methylation acquired genes by EBV infection were significantly overlapped. These suggested that hydroxymethylation by TET2 could function to keep unmethylated status of genes before EBV infection, and TET2 depression could contribute to methylation acquisition of these target genes after EBV infection.
2017-04-28 | GSE84897 | GEO
Project description:Epstein-Barr virus (EBV) has a lifelong latency period after initial infection. Rarely, however, when the EBV immediate early gene BZLF1 is expressed by a specific stimulus, the virus switches to the lytic cycle to produce progeny viruses. We found that EBV infection reduced levels of various ceramide species in gastric cancer cells. As ceramide is a bioactive lipid implicated in the infection of various viruses, we assessed the effect of ceramide on the EBV lytic cycle. Treatment with C6-ceramide (C6-Cer) induced an increase in the endogenous ceramide pool and increased production of the viral product as well as BZLF1 expression. Treatment with the ceramidase inhibitor ceranib-2 induced EBV lytic replication with an increase in the endogenous ceramide pool. The glucosylceramide synthase inhibitor Genz-123346 inhibited C6-Cer-induced lytic replication. C6-Cer induced ERK1/2 and CREB phosphorylation, c-JUN expression, and accumulation of the autophagosome marker LC3B. Treatment with MEK1/2 inhibitor U0126 or autophagy initiation inhibitor 3-MA suppressed C6-Cer-induced EBV lytic replication. In contrast, the autophagosome-lysosome fusion inhibitor chloroquine induced BZLF1 expression. Transfection with siCREB reduced ERK1/2 phosphorylation and C6-Cer-induced BZLF1 expression. On the other hand, siJUN transfection did not affect BZLF1 expression. Our results show that increased endogenous ceramide and glycosyl ceramide (GlyCer) following C6-Cer treatment induce EBV lytic replication in gastric cancer cells via ERK1/2 and CREB phosphorylation and autophagosome accumulation.
2023-12-20 | MTBLS7649 | MetaboLights
Project description:Genome-wide chromatin structure alteration during Epstein-Barr virus infection (Hi-C)
| PRJNA560694 | ENA
Project description:Gene expression profile of AGS gastric carcinoma cell line infected in vitro with Epstein-Barr Virus. Some samples also contain are stably transfected with a dominant negative LMP1 construct. 8 total samples. 4 biological replicates of EBV infected cells, 2 biological replicates with EBV infected cells with LMP1DN construct, and 2 biological replicates with EBV infected cells with control vector.
2012-05-07 | E-GEOD-37753 | biostudies-arrayexpress
Project description:The prototypic gammaherpesvirus Epstein-Barr virus (EBV) is carried by over 90% of the adult human population. Although infection often proceeds asymptomatically, the virus is causally involved in infectious mononucleosis and various malignancies. Like all herpesviruses, EBV establishes a lifelong latent infection in its human host. To successfully establish a persistent infection and spread to new hosts, EBV needs to avoid clearance by the host immune system. In addition to ~100 proteins, some of which perform immunomodulatory functions, EBV encodes over 40 mature miRNAs. Cellular miRNAs regulate diverse cellular processes, but the functions of the EBV miRNAs remain poorly understood. In this study, we identify EBV-encoded miR-BART16 as a novel viral immune evasion factor that interferes with host type I IFN responses. miR-BART16-5p downregulates the cellular histone acetyltransferase CBP (CREBB-binding protein) by directly targeting the CBP-encoding mRNA. CBP plays an important role in the type I IFN signaling pathway. Inhibiting endogenously expressed miR-BART16 in EBV-transformed B cells and gastric carcinoma cells results in increased CBP levels. Consistent with the important role of CBP in type I IFN signaling, miR-BART16 expression interferes with ISRE-promoter activity and production of interferon-stimulated genes in response to IFN-α treatment. These combined data show that EBV employs miRNAs to modify IFN-induced gene transcription. Given the importance of the host IFN system in the antiviral defence, obstructing this response may provide a way for EBV to favour viral replication and could play an etiological role in EBV-associated malignancies.
2017-04-05 | GSE69697 | GEO
Project description:Aberrant promoter methylation is known to be deeply involved in human gastric carcinogenesis, while association of Epstein-Barr virus (EBV) to the aberrant methylation has not been fully clarified. We analyzed promoter methylation in clinical gastric cancer cases using illumina's Infinium beadarray, and hierarchical clustering analysis classified gastric cancer into three subgroups: low and high methylation epigenotypes in EBV-negative cases, and markedly higher methylation epigenotype that was completely matched to EBV-positive cases. Three epigenotypes were characterized by three groups of genes: genes methylated specifically in the EBV-positive epigenotype (EBV(+)-markers, e.g. CXXC4, TIMP2, PLXND1), genes methylated both in EBV-positive and high epigenotypes (High-markers, e.g. COL9A2, EYA1, ZNF365), and genes methylated all in EBV-positive, high and low epigenotypes of gastric cancer (Common-markers, e.g. AMPH, SORCS3, AJAP1). Polycomb repressive complex (PRC)-target genes in ES cells were significantly enriched in High- and Common-markers (P=2x10-15 and 2x10-34, respectively), but not in EBV(+)-markers (P=0.2), suggesting a different cause for EBV(+)-marker methylation. Recombinant EBV was infected to low epigenotype gastric cancer cell, MKN7. In all the three independently established clones, DNA methylation was induced in High- and EBV(+)-markers after 18 weeks, demonstrating that EBV-positive epigenotype should involve methylation of Common-, High-, and EBV(+)-markers simultaneously. The de novo methylated genes were overlapped well among the three clones, and the methylation caused gene repression. In summary, gastric cancer was classified into three DNA methylation epigenotypes, EBV-positive gastric cancer showed markedly high methylation epigenotype expanding to non-PRC target genes, and EBV infection per se could induce the EBV-positive epigenotype.
2012-01-04 | GSE31788 | GEO
Project description:Aberrant promoter methylation is known to be deeply involved in human gastric carcinogenesis, while association of Epstein-Barr virus (EBV) to the aberrant methylation has not been fully clarified. We analyzed promoter methylation in clinical gastric cancer cases using illumina's Infinium beadarray, and hierarchical clustering analysis classified gastric cancer into three subgroups: low and high methylation epigenotypes in EBV-negative cases, and markedly higher methylation epigenotype that was completely matched to EBV-positive cases. Three epigenotypes were characterized by three groups of genes: genes methylated specifically in the EBV-positive epigenotype (EBV(+)-markers, e.g. CXXC4, TIMP2, PLXND1), genes methylated both in EBV-positive and high epigenotypes (High-markers, e.g. COL9A2, EYA1, ZNF365), and genes methylated all in EBV-positive, high and low epigenotypes of gastric cancer (Common-markers, e.g. AMPH, SORCS3, AJAP1). Polycomb repressive complex (PRC)-target genes in ES cells were significantly enriched in High- and Common-markers (P=2x10-15 and 2x10-34, respectively), but not in EBV(+)-markers (P=0.2), suggesting a different cause for EBV(+)-marker methylation. Recombinant EBV was infected to low epigenotype gastric cancer cell, MKN7. In all the three independently established clones, DNA methylation was induced in High- and EBV(+)-markers after 18 weeks, demonstrating that EBV-positive epigenotype should involve methylation of Common-, High-, and EBV(+)-markers simultaneously. The de novo methylated genes were overlapped well among the three clones, and the methylation caused gene repression. In summary, gastric cancer was classified into three DNA methylation epigenotypes, EBV-positive gastric cancer showed markedly high methylation epigenotype expanding to non-PRC target genes, and EBV infection per se could induce the EBV-positive epigenotype.
2012-01-04 | GSE31787 | GEO
Project description:Latent Epstein-Barr Virus (EBV) infection promotes cancers derived from B-lymphocytes and epithelial cells. EBV-encoded nuclear antigen 1 (EBNA1) is uniformly expressed in EBV-associated cancers. The MUC1 gene evolved in mammals to protect barrier tissues from viral infections. We report that MUC1 and the encoded oncogenic MUC1-C protein are upregulated in EBV-associated gastric cancers (EBVaGCs). We demonstrate that EBNA1 forms a complex with MUC1-C that regulates EBNA1 and MUC1-C expression. EBNA1 appropriates MUC1-C for (i) inducing DNA methyltransferases and DNA methylation, (ii) suppressing p21 and driving cell cycle progression, (iii) increasing survivin in promoting survival, and (iv) regulating MYC as an effector of EBV latency. MUC1-C thereby functions in maintaining EBV episomes and regulating EBV latency and lytic genes. In regard to EBVaGC progression, MUC1-C regulates expression of the SOX2 and NOTCH1-3 stemness genes, self-renewal capacity, and tumorigenicity. These findings indicate that EBNA1 co-opts MUC1-C functions that promote EBV latency and that MUC1-C is necessary for EBVaGC pathogenesis.
2024-06-28 | GSE270984 | GEO
Project description:Epstein Barr Virus (EBV) is a potentially oncogenic gammaherpesvirus that establishes a chronic, latent infection in memory B cells. The EBV genome persists in infected host cells as a chromatinized episome and is subject to chromatin-mediated regulation. Binding of the host insulator protein CTCF to the EBV genome has an established role in maintaining viral latency type. CTCF is post-translationally modified by the host enzyme PARP1. PARP1, or Poly(ADP-ribose) polymerase 1, catalyzes the transfer of a poly(ADP-ribose) (PAR) moiety from NAD+ onto acceptor proteins including itself, histone proteins, and CTCF. PARylation of CTCF by PARP1 can affect CTCF’s insulator activity, DNA binding capacity, and ability to form chromatin loops. Both PARP1 and CTCF have been implicated in the regulation of EBV latency and lytic reactivation. Thus, we predicted that pharmacological inhibition with PARP1 inhibitors would affect EBV latency type through a chromatin-specific mechanism. Here, we show that PARP1 and CTCF colocalize at specific sites throughout the EBV genome, and provide evidence to suggest that PARP1 acts to stabilize CTCF binding and maintain the open chromatin landscape at the active Cp promoter during type III latency. Further, PARP1 activity is important in maintaining latency type-specific viral gene expression. The data presented here provide a rationale for the use of PARP inhibitors in the treatment of EBV-associated cancers exhibiting type III latency, and could ultimately contribute to an EBV-specific treatment strategy for AIDS-related or post-transplant lymphomas.
2018-06-27 | GSE115829 | GEO