Epstein-barr virus infected gastric adenocarcinoma expresses latent and lytic viral transcripts and has a distinct human gene expression profile

<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>EBV DNA is found within the malignant cells of 10% of gastric cancers. Modern molecular technology facilitates identification of virus-related biochemical effects that could assist in early diagnosis and disease management.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, RNA expression profiling was performed on 326 macrodissected paraffin-embedded tissues including 204 cancers and, when available, adjacent non-malignant mucosa. Nanostring nCounter probes targeted 96 RNAs (20 viral, 73 human, and 3 spiked RNAs).</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infected<jats:italic>versus</jats:italic>uninfected cancers, and in malignant<jats:italic>versus</jats:italic>adjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels of<jats:italic>EBER1</jats:italic>and<jats:italic>EBER2</jats:italic>RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs,<jats:italic>EBNA1</jats:italic>from the Q promoter and<jats:italic>BRLF1</jats:italic>were highly expressed while<jats:italic>EBNA2</jats:italic>levels were low positive in only 6/14 infected cancers. Concomitant upregulation of cellular factors implies that virus is not an innocent bystander but rather is linked to NFKB signaling (<jats:italic>FCER2, TRAF1</jats:italic>) and immune response<jats:italic>(TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC)</jats:italic>, with<jats:italic>PPARG</jats:italic>expression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressed<jats:italic>INHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS</jats:italic>, three collagens, the cell proliferation markers<jats:italic>MYC</jats:italic>and<jats:italic>PCNA</jats:italic>, and EBV<jats:italic>BLLF1</jats:italic>while they lacked<jats:italic>CDH1 (E-cadherin), CLDN18</jats:italic>,<jats:italic>PTEN, SDC1</jats:italic>(CD138),<jats:italic>GAST</jats:italic>(gastrin) and its downstream effector<jats:italic>CHGA</jats:italic>(chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressed<jats:italic>CLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG</jats:italic>, and<jats:italic>CDH17</jats:italic>while they had diminished levels of<jats:italic>IFITM1</jats:italic>and<jats:italic>HIF1A</jats:italic>. The druggable targets ERBB2 (Her2), MET, and the HIF pathway, as well as several other potential pharmacogenetic indicators (including EBV infection itself, as well as<jats:italic>SPARC, TYMS, FCGR2B</jats:italic>and<jats:italic>REG4</jats:italic>) were identified in some tumor specimens.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>This study shows how modern molecular technology applied to archival fixed tissues yields novel insights into viral oncogenesis that could be useful in managing affected patients.</jats:p></jats:sec>