Epstein-Barr virus lncBARTs interact with BRD4 and CTCF complex to regulate EBV latent replication and promote EBV-associated oncogenesis

Abstract

<p>The Epstein-Barr Virus (EBV) infects approximately 95% of the global population, with the majority of these infections being asymptomatic. However, EBV is strongly associated with the development of certain tumors affecting lymphoid or epithelial tissues, such as Burkitt lymphoma, Hodgkin lymphoma, nasopharyngeal carcinoma (NPC), and gastric cancer (GC). In these EBV-associated cancers, the virus maintains a latent infection and expresses only a few viral proteins. There is considerable interest in understanding how EBV maintains latency in associated tumors and the role it plays in the oncogenesis of these cancers. Increasing evidence suggests that long non-coding RNAs play crucial roles in the epigenetic reprogramming of human cancer cells. We have previously characterized a family of EBV-expressed long non-coding RNAs, known as lncBARTs, in EBV-associated nasopharyngeal and gastric carcinoma. It is important to understand how EBV replicates in infected cells, and we sought to explore the role of lncBARTs in EBV replication in infected cancer cells. Our study discovered that lncBARTs co-localize in nuclear speckles and identified BRD4 and CTCF as interacting partners of lncBARTs. EBV expressed EBNA1 is essential for EBV replication, and we further confirmed that lncBARTs interact with the EBV genome via the BRD4/CTCF/EBNA1 complex. Using a combination of functional genomic analysis and gene-editing strategy, we noted a significant reduction in the tethering of EBV episomes to cell chromosomes when lncBARTs were knocked down in EBV-infected NPC and GC cells. This supports a mechanism whereby lncBARTs facilitate EBV episome tethering to the chromosome for latent replication through interaction with the EBV latent origin of replication (Orip). Our findings suggest that the interaction of lncBARTs with the BRD4-CTCF complex could impact the epigenetic reprogramming of host cells. Importantly, ATAC and transcriptome analyses indicated that lncBARTs drive tumorigenesis by aberrantly regulating the expression of MYC and BCL2 in EBV-infected cells. These findings reveal that EBV turns off the expression of viral proteins to avoid provoking an immune response and utilizes virus-encoded lncBARTs to maintain EBV latent replication in conjunction with cancer cell division. Consequently, lncBARTs-BRD4/CTCF promotes the reprogramming of the host epigenome and drives tumorigenesis in EBV-associated epithelial tumors.</p>