Infection of Epstein–Barr virus in a gastric carcinoma cell line induces anchorage independence and global changes in gene expression

Marquitz, Aron R.; Mathur, Anuja; Shair, Kathy H.Y.; Raab‐Traub, Nancy

doi:10.1073/pnas.1202910109

Cited by 85 publications

(104 citation statements)

References 39 publications

(45 reference statements)

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“…However, these tumors are clonally infected with EBV, suggesting that EBV infection is an early event in the formation of the tumors (3). Consistent with these observations, EBV infection of an epithelial cell line in vitro is capable of promoting growth in soft agar independent of any latent protein expression (4). EBV epithelial malignancies, nasopharyngeal and gastric carcinomas, exhibit a unique expression pattern that includes extensive transcription from the BamHI A region of the viral genome (5).…”

supporting

confidence: 64%

mentioning

confidence: 99%

“…Importantly, EBV infection of AGS cells consistently induces anchorage-independent growth and increased motility (4,15,16). Gene expression microarray analysis of a single AGS-EBV cell line compared to parental cells suggested that there are widespread changes in host transcription due to latent EBV infection and that the downregulated genes were highly enriched for BART miRNA targets (4). In the present study, multiple clonal AGS-EBV cell lines were profiled by RNA-seq, generating data that are more accurate than data obtained by microarray analysis, that account for the clonal evolution inherent in any one particular cell line, and that include an evaluation of not only host but also viral transcription.…”

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confidence: 99%

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Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region

Marquitz

Mathur

Edwards

et al. 2015

J Virol

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In Epstein-Barr virus-infected epithelial cancers, the alternatively spliced BamHI A rightward transcripts (BARTs) are the most abundant viral polyadenylated RNA. The BART introns form the template for the production of 44 microRNAs (miRNAs), and the spliced and polyadenylated exons form nuclear non-protein-coding RNAs. Analysis of host cell transcription by RNA-seq during latency in AGS cells identified a large number of reproducibly changed genes. Genes that were downregulated were enriched for BART miRNA targets. Bioinformatics analysis predicted activation of the myc pathway and downregulation of XBP1 as likely mediators of the host transcriptional changes. Effects on XBP1 activity were not detected in these cells; however, myc activation was confirmed through use of a myc-responsive luciferase reporter. To identify potential regulatory properties of the spliced, polyadenylated BART RNAs, a full-length cDNA clone of one of the BART isoforms was obtained and expressed in the Epstein-Barr virus (EBV)-negative AGS cells. The BART cDNA transcript remained primarily nuclear yet induced considerable and consistent changes in cellular transcription, as profiled by RNA-seq. These transcriptional changes significantly overlapped the transcriptional changes induced during latent EBV infection of these same cells, where the BARTs are exclusively nuclear and do not encode proteins. These data suggest that the nuclear BART RNAs are functional long noncoding RNAs (lncRNAs). The abundant expression of multiple forms of noncoding RNAs that contribute to growth regulation without expression of immunogenic proteins would be an important mechanism for viral oncogenesis in the presence of a functional immune system. IMPORTANCEInfection with Epstein-Barr virus (EBV) is nearly ubiquitous in the human population; however, it does contribute to the formation of multiple types of cancer. In immunocompromised patients, EBV causes multiple types of lymphomas by expressing viral oncogenes that promote growth and survival of infected B lymphocytes. EBV-positive gastric carcinoma does not require immune suppression, and the viral oncoproteins that are frequent targets for an immunological response are not expressed. This study demonstrates using transcriptional analysis that the expression of various classes of viral non-protein-coding RNAs likely contribute to the considerable changes in the host transcriptional profile in the AGS gastric cancer cell line. This is the first report to show that the highly expressed polyadenylated BamHI A rightward transcripts (BART) viral transcript in gastric carcinoma is in fact a functional viral long noncoding RNA. These studies provide new insight into how EBV can promote transformation in the absence of viral protein expression. L atent infection with Epstein-Barr virus (EBV), a nearly ubiquitous human herpesvirus, is responsible for multiple malignancies in the two types of cells that it infects: B lymphocytes and epithelial cells (1). The mechanism by which EBV leads to transformation dep...

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supporting

confidence: 64%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region

Marquitz

Mathur

Edwards

et al. 2015

J Virol

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“…This subset of gastric carcinoma, 8 to 10% of cases, is more prevalent in Caucasian and Hispanic patients than Asians, and it shows no association with Helicobacter pylori infection (22). In these cases, EBV appears to play a direct oncogenic role through genome-wide alteration of promoter methylation (24), microRNA (miRNA) expression, and expression of genes involved in cell motility and transformation pathways (25). The integration status of EBV in gastric carcinoma remains poorly understood.…”

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confidence: 99%

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

Khoury¹,

Tannir

Williams³

et al. 2013

J Virol

198

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Elucidation of tumor-DNA virus associations in many cancer types has enhanced our knowledge of fundamental oncogenesis mechanisms and provided a basis for cancer prevention initiatives. RNA-Seq is a novel tool to comprehensively assess such associations. We interrogated RNA-Seq data from 3,775 malignant neoplasms in The Cancer Genome Atlas database for the presence of viral sequences. Viral integration sites were also detected in expressed transcripts using a novel approach. The detection capacity of RNA-Seq was compared to available clinical laboratory data. Human papillomavirus (HPV) transcripts were detected using RNA-Seq analysis in head-and-neck squamous cell carcinoma, uterine endometrioid carcinoma, and squamous cell carcinoma of the lung. Detection of HPV by RNA-Seq correlated with detection by in situ hybridization and immunohistochemistry in squamous cell carcinoma tumors of the head and neck. Hepatitis B virus and Epstein-Barr virus (EBV) were detected using RNA-Seq in hepatocellular carcinoma and gastric carcinoma tumors, respectively. Integration sites of viral genes and oncogenes were detected in cancers harboring HPV or hepatitis B virus but not in EBV-positive gastric carcinoma. Integration sites of expressed viral transcripts frequently involved known coding areas of the host genome. No DNA virus transcripts were detected in acute myeloid leukemia, cutaneous melanoma, low-and high-grade gliomas of the brain, and adenocarcinomas of the breast, colon and rectum, lung, prostate, ovary, kidney, and thyroid. In conclusion, this study provides a large-scale overview of the landscape of DNA viruses in human malignant cancers. While further validation is necessary for specific cancer types, our findings highlight the utility of RNA-Seq in detecting tumor-associated DNA viruses and identifying viral integration sites that may unravel novel mechanisms of cancer pathogenesis.

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“…In our study, we used the 2-DE approach coupled with MS to study the differentially expressed proteins of gastric epithelial AGS cell, with and without EBV infection. The same system has previously been used to analyze differences in gene expression using cDNA microarrays (Marquitz et al, 2012). In the current study, we obtained an overview of the altered protein expressions of host cells responding to EBV infection.…”

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confidence: 99%

Proteomics Analysis of Gastric Epithelial AGS Cells Infected with Epstein-Barr Virus

Ding

Li²,

Yang³

et al. 2013

Asian Pacific Journal of Cancer Prevention

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Effects of the Epstein-Barr virus (EBV) on cellular protein expression are essential for viral pathogenesis. To characterize the cellular response to EBV infection, differential proteomes of gastric epithelial AGS cellswere analyzed with two-dimensional gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionizationtime of flight (MALDI-TOF) and liquid chromatography electrospray/ionization ion trap (LC-ESI-IT) mass spectrometry identification. Mass spectrometry identified 9 altered cellular proteins, including 5 up-regulated and 4 down-regulated proteins after EBV infection. Notably 2-DE analysis revealed that EBV infection induced increased expression of heat shock cognate 71 kDa protein, actin cytoplasmic 1, pyridoxine-5'-phosphate oxidase, caspase 9, and t-complex protein 1 subunit alpha. In addition, EBV infection considerably suppressed those cellular proteins of zinc finger protein 2, cyclin-dependent kinase 2, macrophage-capping protein, and growth/ differentiation factor 11. Furthermore, the differential expressional levels of partial proteins (cyclin-dependent kinase 2 and caspase 9) were confirmed by Western blot analysis.Thus, this work effectively provided useful protein-related information to facilitate further investigation of the mechanisms underlying EBV infection and pathogenesis.

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Infection of Epstein–Barr virus in a gastric carcinoma cell line induces anchorage independence and global changes in gene expression

Cited by 85 publications

References 39 publications

Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region

Host Gene Expression Is Regulated by Two Types of Noncoding RNAs Transcribed from the Epstein-Barr Virus BamHI A Rightward Transcript Region

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

Proteomics Analysis of Gastric Epithelial AGS Cells Infected with Epstein-Barr Virus

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