Differential expression profiling of lncRNAs related to Epstein-Barr virus infection in the epithelial cells

Epstein-Barr virus (EBV) is a prevalent γ-herpesvirus associated with a variety of cancers, including epithelial nasopharyngeal carcinoma (NPC) and gastric carcinoma (GC). Long noncoding RNAs (lncRNAs) are emerging as powerful regulators that have demonstrated to play crucial roles in cancer development. In this approach, based on genome-wide RNA sequencing, we examined the lncRNA expression profiles in four EBV genome-infected and EBV-negative 293 cells. A series of lncRNAs were found to be dysregulated in a comparative analysis. Then, eight typical lncRNAs were selected for validation of expression levels by real-time quantitative polymerase chain reaction and were detected in EBV-positive or EBV-negative GC and NPC cells. The differential expression patterns of the eight lncRNAs for validation were fundamentally identical to those revealed in RNA sequencing. Particularly, the differential expression of these lncRNAs in GC and NPC cells indicated their possible roles in EBV infection and tumorigenesis. In addition, a predicted lncRNA-microRNA-messenger RNA network suggested their potential interactions. This study reveals the first lncRNAome related to EBV infection in the epithelial cells and provides novel clues for the study of viral role in epithelial cancers through the interaction between EBV and host lncRNAs.