Epstein-Barr virus (EBV) infects nearly all adults and poses significant worldwide public health burdens due to EBV-associated cancers and autoimmune diseases. Our lab is interested in understanding disease-relevant EBV-host dynamics at high resolution. We combine experimentally tractable infection models with single-cell (scRNA-seq, scATAC-seq), flow cytometry, microscopy) and spatial biology techniques to define key host-virus regulatory axes and understand how EBV reprograms host cells to pathogenic states. Through collaborations with clinicians at U-M and beyond, we are also interested in characterizing the genome-wide landscapes of EBV-associated tumors and their microenvironments. Our projects are motivated by the complementary goals of understanding fundamental host-virus genomic regulation in exquisite detail and informing better treatments for EBV-associated diseases.

Project 1: Host-Virus Epigenetic Regulation in Latent EBV Infection
We are interested in epigenetic governance of B cell fate mediated by interactions of EBV EBNA3A and EBNA3C with the cellular H3K27 histone methyltransferase EZH2. Prior studies have shown that EBNA3A and EBNA3C target EZH2-mediated H3K27me3 deposition to silence tumor suppressors (e.g., CDKN2A / p16INK4A) and genes critical for terminal B cell differentiation into non-proliferative plasma cells (e.g., PRDM1 / BLIMP1 and CDKN2C / p18INK4C). Consequently, gene regulation by the EBNA3A/3C-EZH2 axis appears to play a crucial role in sustaining proliferation of latently infected cells. EBNA3A and EBNA3C are critical mediators of infected B cell fate via gene promoter-enhancer looping, and each oncoprotein can co-repress or co-activate different target cellular genes. However, the epigenetic logic of EBNA3A/3C-mediated host gene regulation – and their relation to the balance of EBV-driven cellular fates and biological functions – remain incompletely understood. To address these gaps, we aim to apply high-dimensional assays to in vitro and in vivo (murine) models of infection using EBV strains that conditionally express EBNA3A and EBNA3C in conjunction with small molecule inhibitors of EZH2. This project will help define distinct gene regulatory mechanisms that underpin EBV-mediated transformation and depend on interactions between host and viral factors.

Project 2: Cellular Reprogramming in EBV Lytic Reactivation
While most EBV-positive B cell lymphomas predominantly exhibit latent infections, subsets of tumor cells undergo lytic reactivation. The EBV lytic cycle plays an important but poorly understood role in oncogenesis. Interestingly, horizontal infection of bystander cells with newly produced virions does not appear essential for tumorigenesis, since viral strains with late-stage replication defects induce tumors. However, expression of the master EBV lytic transcription factor Zta (aka Z, ZEBRA; encoded by the BZLF1 gene) appears critical, since humanized mice infected with BZLF1-KO virus do not develop tumors. These findings suggest that some early events of the lytic cycle or incomplete (“abortive”) reactivation may play a role in EBV-associated cancers. Notably, host cell nuclei are profoundly reorganized during both early and late stages of EBV reactivation. Moreover, time-resolved scRNA-seq studies of EBV reactivation reveal that a subset of lytic cells express genes associated with cancer “stemness” and reprogrammed plasticity. These findings imply that aberrant cellular expression in response to lytic-mediated stresses or nuclear damage may contribute to virus-associated malignancy. To further dissect pathogenic cell reprogramming during the lytic cycle, we are applying single-cell techniques to examine models of successful and defective EBV reactivation at high resolution.

Project 3: Defining spatial landscapes of virus-associated diseases
An infection does not exist in a vacuum, and its effects extend well beyond the cells that directly harbor virus. This concept is especially important for considering the role of EBV infection in conditioning virus-associated tumors and their microenvironments. The presence or absence of EBV can have significant implications for disease progression and response to therapy. However, the EBV status of DLBCL and other non-Hodgkin Lymphomas (NHLs) does not currently influence recommended therapies despite being routinely assayed in pathological workups. In a recent study of HIV-associated NHLs (HIV-NHLs), we used spatial transcriptomics to identify distinct tumor and microenvironment features stratified by EBV status. This work highlights the power of modern spatial biology technologies for discovery and investigation of viral contributions to in vivo disease presentations that may ultimately lead to tailored therapies and better outcomes. We are actively seeking collaborations to use similar and complementary spatial methods for ongoing investigations of diseases associated with EBV – and other viral pathogens.