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Background  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.    Methods  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).    Results  In 182 tissues with adequate housekeeper RNAs, distinct profiles were found in infected  versus  uninfected cancers, and in malignant  versus  adjacent benign mucosa. EBV-infected gastric cancers expressed nearly all of the 18 latent and lytic EBV RNAs in the test panel. Levels of  EBER1  and  EBER2  RNA were highest and were proportional to the quantity of EBV genomes as measured by Q-PCR. Among protein coding EBV RNAs,  EBNA1  from the Q promoter and  BRLF1  were highly expressed while  EBNA2  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 ( FCER2, TRAF1 ) and immune response  (TNFSF9, CXCL11, IFITM1, FCRL3, MS4A1 and PLUNC) , with  PPARG  expression implicating altered cellular metabolism. Compared to adjacent non-malignant mucosa, gastric cancers consistently expressed  INHBA, SPP1, THY1, SERPINH1, CXCL1, FSCN1, PTGS2 (COX2), BBC3, ICAM1, TNFSF9, SULF1, SLC2A1, TYMS , three collagens, the cell proliferation markers  MYC  and  PCNA , and EBV  BLLF1  while they lacked  CDH1 (E-cadherin), CLDN18 ,  PTEN, SDC1  (CD138),  GAST  (gastrin) and its downstream effector  CHGA  (chromogranin). Compared to lymphoepithelioma-like carcinoma of the uterine cervix, gastric cancers expressed  CLDN18, EPCAM, REG4, BBC3, OLFM4, PPARG , and  CDH17  while they had diminished levels of  IFITM1  and  HIF1A . 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  SPARC, TYMS, FCGR2B  and  REG4 ) were identified in some tumor specimens.    Conclusion  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.

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