The regulation and function of Epstein-Barr virus-encoded BamHI-A rightward transcripts

Abstract

Nasopharyngeal carcinoma (NPC) is prevalent in southern China and Southeast Asia. Epstein-Barr virus (EBV) is a major etiological factor for NPC in addition to genetic and environmental factors. EBV maintains a stringent latency by expressing very few viral proteins in NPC cells, presumably to evade immune detection. However, EBV expresses high levels of a family of BamHI-A rightward transcripts (BARTs) in NPC cells. BARTs encode two clusters of microRNAs (miRNAs) and multiple species of alternatively spliced long non-coding RNAs (lncRNAs), which are found in all forms of EBV latency. While BART miRNAs have been reported to prevent apoptosis, contribute to immune evasion, and promote cancer growth in EBV-infected cells, the role of BART lncRNA remains unknown as well as the cause of the abundant expression of BARTs in NPC. This study aims to investigate these questions to further understand EBV pathogenesis in NPC. In this thesis, I conducted systematic experiments to demonstrate that NF-κB binds and activates the BART promoters, whereas the introduction of mutations into putative NF-κB binding half-sites abolishes activation of BART P1 promoter by NF-κB. I found that expression of BART miRNAs and lncRNAs correlated with NF-κB activity in EBV-infected epithelial cells, while treatment of EBV-harboring NPC C666-1 cells with aspirin and PS-1145 inhibited NF-κB activity and downregulated BART expression. To further verify the hypothesis that expression of BARTs is regulated by NF-κB signaling, I found that expression of LMP1, but not an LMP1 mutant with impaired NF-κB activation ability, activated both BART promoters. LMP1 expression is tightly regulated in NPC cells and this study confirmed the ability of BART miRNA to downregulate LMP1 expression, suggesting a feedback loop between BART miRNA and LMP1 mediated NF-κB activation in the NPC setting. Notably, this study also identified an NF-κB binding site in the EBV Qp region and provided evidence to show that NF-κB signaling plays a role in regulating Qp for expression of EBNA1. Conversely, mutations in the putative NF-κB binding site abolished activation of Qp by p50 and p65. Taken together, the findings from this study suggest a general mechanism for regulation of EBV latency through NF-κB signaling in EBV-associated tumors. This thesis presents direct evidence showing nuclear localization of BART lncRNAs in EBV-infected epithelial and lymphoid cells by FISH analysis, confirming BART RNAs function as nuclear lncRNAs. More importantly, this study identified CREB-binding protein (CBP) as a novel target of BART lncRNA and showed that BART lncRNA is able to modulate expression of host genes involved in the innate immune response through a mechanism independent of conventional activation of the NF-κB or IRF-3 pathways. This is the first study to identify a BART lncRNA target, leading the way for further characterization of BART lncRNA functions in EBV associated-tumors.

In summary, this thesis provides new insights into the mechanism underlying the regulation of BARTs in NPC, identifies a regulatory loop through which BARTs support EBV latency in NPC, and characterizes BART lncRNAs as potential immune regulators through their interaction with CBP.