EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape

Abstract

The Epstein Barr virus (EBV) contributes to the tumor phenotype through a limited set of primarily non-coding viral RNAs, including 31 mature miRNAs. Here we investigated the impact of EBV miRNAs on remodeling the tumor cell transcriptome. Strikingly, EBV miRNAs displayed exceptionally abundant expression in primary EBV-associated Burkitt’s Lymphomas (BLs) and Gastric Carcinomas (GCs). To investigate viral miRNA targeting, we used the high-resolution approach, CLASH in GC and BL cell models. Affinity constant calculations of targeting efficacies for CLASH hits showed that viral miRNAs bind their targets more effectively than their host counterparts, as did Kaposi’s sarcoma-associated herpesvirus (KSHV) and murine gammaherpesvirus 68 (MHV68) miRNAs. Using public BL and GC RNA-seq datasets, we found that high EBV miRNA targeting efficacies translates to enhanced reduction of target expression. Pathway analysis of high efficacy EBV miRNA targets showed enrichment for innate and adaptive immune responses. Inhibition of the immune response by EBV miRNAs was functionally validated in vivo through the finding of inverse correlations between EBV miRNAs and immune cell infiltration and T-cell diversity in BL and GC datasets. Together, this study demonstrates that EBV miRNAs are potent effectors of the tumor transcriptome that play a role in suppressing host immune response.

MicroRNA and Other Non-Coding RNAs in Epstein–Barr Virus-Associated Cancers

“…Targets of EBV miRNAs were also shown to be enriched for genes with functions in innate and adaptive immune responses [219]. Moreover, the increased levels of the EBV miRNA correlated with reduced immune cell infiltration in both BL and GC [219]. It is noteworthy that this same study showed that EBV miRNAs form thermodynamically stable complexes with their targets at a higher efficacy than cellular miRNAs, indicating that they are likely to override any regulation of immune targets by cellular miRNA [219].…”

“…In nasal NK cell lymphoma, BART20-5p and BART8 suppress IFN-γ-STAT1 signaling [218]. Targets of EBV miRNAs were also shown to be enriched for genes with functions in innate and adaptive immune responses [219]. Moreover, the increased levels of the EBV miRNA correlated with reduced immune cell infiltration in both BL and GC [219].…”

Clinical and Therapeutic Implications of Epstein–Barr Virus in HIV-Related Lymphomas

“…In addition, miR-BART6-3p regulates the expression of the IL-6 receptor ( IL-6R ), being able to contribute to immune system evasion [ 94 ]. Furthermore, it has been postulated that EBV-miRNAs have a role in the microenvironment regulation, reducing the innate and adaptative immune response in EBV-positive tumors, similar to BL ( Figure 2 ) [ 96 ].…”

Identification and characterization of a novel Epstein-Barr Virus-encoded circular RNA from LMP-2 Gene

“…S4 ) of the top 10 miRNA-targeted genes, Toll receptor signaling pathway and CCKR signaling pathway maps are the top 2 pathways that can be potentially regulated by circ LMP-2_e5 through miRNA sponging. However, a search for potential AGO2: miRNA: circ LMP2-e5 interactions via interrogating publicly available AGO2 pulldown assay datasets from EBV-positive cell lines of different cell types and latencies 40 – 43 did not reveal clear such interaction (data not shown). We note that these datasets only encompass the latent state, hence there is still a possibility of circ LMP2-e5 functioning as a miRNA sponge during the lytic state.…”