Alterations in cellular expression in EBV infected epithelial cell lines and tumors

The Epstein Barr virus (EBV) is linked to the development of two major epithelial malignancies, gastric carcinoma and nasopharyngeal carcinoma. This study evaluates the effects of EBV on cellular expression in a gastric epithelial cell line infected with or without EBV and a nasopharyngeal carcinoma cell line containing EBV. The cells were grown in vitro and as tumors in vivo. The effects on cellular expression were determined using both 2D DIGE proteomics and high throughput RNA sequencing. The data identify multiple pathways that were uniquely activated in vitro. RNA sequences mapping to the mouse genome were identified in both the EBV positive and negative tumor samples in vivo, although, differences between the EBV positive and negative cells were not apparent. However, the tumors appeared to be grossly distinct. The majority of the identified canonical pathways based on two fold changes in expression had decreased activity within the tumors in vivo. Identification of the predicted upstream regulating factors revealed that in vitro the regulating factors were primarily protein transcriptional regulators. In contrast, in vivo the predicted regulators were frequently noncoding RNAs. Hierarchical clustering distinguished the cell lines and tumors, the EBV positive tumors from the EBV negative tumors, and the NPC tumors from the gastric tumors and cell lines. The delineating genes were changed greater than 4 fold and were frequently regulated by protein transcription factors. These data suggest that EBV distinctly affects cellular expression in gastric tumors and NPC and that growth in vivo requires activation of fewer cellular signaling pathways. It is likely that the broad changes in cellular expression that occur at low levels are controlled by regulatory viral and cellular RNAs while major changes are affected by induced protein regulators.
Author summary This study analyzes the effects of the Epstein Barr virus on cellular RNA expression in epithelial cells that were grown in culture dishes or were inoculated into immunodeficient mice to form tumors. The presence of EBV induced many changes in expression and affected the appearance of the tumors which were very bloody with EBV and solid and white without EBV. Multiple cellular pathways that were activated during growth in culture were decreased when grown as tumors. Many of the cellular genes that were affected and were changed approximately two fold were predicted to be regulated by noncoding RNAs. The clustering expression analysis identified greater changes in expression and these changes distinguished tumors from the cell lines, the gastric cells from the nasopharyngeal cancer cells, and those that contained EBV from the EBV negative cells. These findings indicate that EBV alters cell growth through major effects on cellular RNA transcription and that these changes can be induced by both noncoding RNAs and cellular transcription factors.