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Single cell RNA sequencing of Nasopharyngeal Carcinoma Cell lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation

ABSTRACT: The HK1-EBV cell line is a human nasopharyngeal carcinoma cell line (RRID:CVCL_7084) infected in vitro with recombinant Epstein-Barr virus (EBV) Akata strain expressing EGFP and neoR inserted into the BXLF1 locus (PMIDs: 16611410). This cell line has been authenticated to be free of HeLa contaminants (PMIDs: 18196576; 24991015). We used bulk RNA sequencing techniques to analyze these cell lines reactivated at the air liquid interface (ALI) in a 3D cell culture model for ALI-induced EBV reactivation.

ORGANISM(S): Homo sapiens

PROVIDER: GSE231688 | GEO | 2024/12/31

REPOSITORIES: GEO

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Bulk-RNA Sequencing of Nasopharyngeal Carcinoma Cell Lines infected with Epstein-Barr virus (EBV) subjected to air-liquid interface (ALI)-induced reactivation

Project description:The HK1-EBV cell line is a human nasopharyngeal carcinoma cell line (RRID:CVCL_7084) infected in vitro with recombinant Epstein-Barr virus (EBV) Akata strain expressing EGFP and neoR inserted into the BXLF1 locus (PMIDs: 16611410). This cell line has been authenticated to be free of HeLa contaminants (PMIDs: 18196576; 24991015). We used bulk RNA sequencing techniques to analyze these cell lines reactivated at the air liquid interface (ALI) in a 3D cell culture model for ALI-induced EBV reactivation.

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Affymetrix analysis for host cells transcriptome

Project description:Analyze possible changes in the transcriptome of host cell line infected with a recombinant EBV virus. The recombinant virus is an Akata cell-derived NeoR EBV strain, previously used in PMID: 12969959

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circRNA microarray of the Epstein-Barr virus positive Burkitt's lymphoma cell line Akata

Project description:Epstein-Barr virus positive Burkitt's lymphoma cell line Akata (+) and it's EBV-depleted subclone Akata (-) were analyzed for human circRNA expression.

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Estrogen induces the expression of EBV lytic protein ZEBRA, a marker of poor prognosis in nasopharyngeal carcinoma.

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Temporal Analysis of Cell Protein Ubiquitination during Epstein-Barr Virus Reactivation by BCR Cross-linking

Project description:Epstein-Barr virus (EBV) reactivation in latently infected B cells is essential for persistent infection and B cell receptor (BCR) activation is a physiologically relevant stimulus for EBV reactivation. Post-translational modifications, such as phosphorylation and ubiquitination, are known to be regulated by antigen binding to BCR within minutes. However, a detailed understanding of the signaling alterations at later time when EBV is being actively replicated remains elusive. To gain insights into BCR activation-mediated reprogramming of the cellular environment in both Akata-BX1 (EBV+) and Akata-4E3 (EBV-) B cells, we utilized a 3-plex stable isotope labeling by amino acid in cell culture (SILAC)-based quantitative proteomic approach to monitor the dynamic changes of protein ubiquitination during the course of immunoglobulin G (IgG) cross-linking of BCRs. We observed temporal alterations in the level of ubiquitination on approximately 150 sites in both Akata-BX1 (EBV+) and Akata-4E3 (EBV-) B cells post-IgG cross-linking compared with no cross-linking controls, with the majority of protein ubiquitination down-regulated. Our analysis revealed that IgG cross-linking plays a major role in the regulation of protein ubiquitination in both EBV+ and EBV- B cells. Bioinformatic analyses of up-regulated ubiquitination events revealed significant enrichment of proteins involved in RNA processing. Among the down-regulated ubiquitination events are proteins enriched in apoptosis and the ubiquitin-proteasome pathway. The comparative and quantitative studies provide a foundation for further understanding how BCR activation regulates cellular protein ubiquitination and how EBV utilizes or subverts BCR engagement-mediated changes to facilitate viral replication.

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Transcriptome analysis of CHAF1B depletion in Akata EBV+ Burkitt Lymphoma cells

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ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE

2012-12-31 | GSE29123 | GEO

ABBERANT GENE EXPRESSION BY EBERs IN EBV-NEGATIVE NPC HK1 CELL LINE

Project description:Differential gene expression in RNA isolated from stably-transfected EBERs-negative versus EBERs-positive HK1 cell lines We established stable transfection of EBERs in the EBV-negative NPC cell line, HK1,to elucidate the role of the EBERs in NPC pathogenesis. Microarray gene expression profiling was carried out to investigate candidate genes which expression correlates with the expression of the EBERs. Total RNA was extracted from each cell line and processed using GeneChipÂ® Whole Transcript (WT) Sense Target Labelling Assay and then analyzed with GeneChipÂ® Human Gene 1.0 ST Array, with three repeats. Candidate genes differentially expressed between the two transfected HK1 cell lines were identified using GeneSpring GX 10 (Agilent Technologies).

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Expression data from Epstein-Barr virus -positive and negative Akata Burkitt's Lymphoma Clones

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Alveolar Epithelial Cell Injury with EBV Upregulates TGF-beta1 Expression

Project description:Idiopathic pulmonary fibrosis (IPF) is a refractory and lethal interstitial lung disease characterized by alveolar epithelial cells apoptosis, fibroblast proliferation and extra-cellular matrix proteins deposition. Epstein - Barr virus (EBV) has previously been localised to alveolar epithelial cells of IPF patients. In this study we utilised a microarray based differential gene expression analysis strategy to identify potential molecular drivers of EBV associated lung fibrosis. We employed an alveolar epithelial cell line infected with EBV (A-Akata). Lytic phase infection induced in the A-Akata cells by TPA/BA treatment resulted in increase of TGFbeta1 and TIEG1 mRNA expression. Treatment of the A-Akata cells with ganciclovir, resulted in a down regulation of both TIEG1 and TGFbeta1 expression, accompanied by a suppression of the EBV early response genes, Rta and Zta. This suppression of cell turnover mediators was correlated with an increase in cell activity index. To identify a possible role for Rta in driving apoptotic gene expression, we inhibited the Rta gene expression by silencing RNA, resulting in a decrease in TGFbeta1 and TIEG1 expression. This study identifies an apoptotic role of the EBV early response genes, as enhancer factors of TIEG1 and TGFbeta1 in EBV infected alveolar epithelial cells, potentially providing a possible mechanism for the role of EBV infection in pulmonary fibrosis. Keywords: EBV lytic phase infection, epithelial cell apoptosis, oligonucleotide array analysis

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