Targeting Epstein-Barr virus non-coding RNA drivers of cancer hallmarks

Tumor viruses cause cancer by expression of viral proteins which can serve as oncogenes or inhibitors of host tumor suppressor proteins.

We have recently discovered that Epstein-Barr virus (EBV) can both drive oncogenes and inhibit tumor suppressor genes by expression of a single viral gene, RPMS1. This gene encodes a long non-coding RNA and 44 microRNAs. The function of these viral elements are largely unknown.

We analyzed 156 sequencing datasets from four types of EBV-associated cancers and all tumors contained high levels of RPMS1.

Analysis of single-cell sequencing datasets from 48 EBV-positive nasopharyngeal carcinomas allowed for comparison of cancer cells and healthy epithelium from the same tumor. We identified recurrently perturbed pathways in EBV-positive tumors.

In the cancer cells we observed upregulation of oncogenic hallmarks such as Myc, Kras, E2F, MTORC1 and epithelial to mesenchymal transition, as well as downregulation of p53 pathway and interferon response. These pathways were reconstituted in cell lines in which we transfected the RPMS1-encoded miRNAs.

Furthermore, the RPMS1 gene contains the origin of DNA replication from which reactivation is initiated.

With the resolution provided by the single-cell datasets, we observed that viral reactivation was coupled with upregulation of transcription within the origin.

We hypothesize that RPMS1 functions as the driver of cancer hallmarks by expression of microRNA and serves as a regulator of viral reactivation.