Unveiling how circular RNAs shape virus-host interactions during β-herpesvirus infection

Background

Each individual human is estimated to harbour at least three of the nine known herpesviruses. Herpesviruses are classified in three types: ɑ-, β-, and γ-herpesviruses, with varying target cells and pathogenesis. β- and γ- herpesviruses infect immune cells for the life of host. Evidence indicating the need to control both β- and γ-HHVs is accumulating: HHV-6 and HHV-7 were frequently integrated into the human genome at the telomere regions in EBV-infected B cells; HHV-6A and EBV are co-risk factors for multiple sclerosis; and β-/γ-HHVs often reactivate in transplant patients, risking rejection. These may be particularly relevant locally in Scotland, as chromosomally integrated HHV-6 was congenitally transmitted at a higher rate (2.7%) than in the general population (< 1 %). 

It is known that herpesviruses are able to remain in host cells, avoiding immune response, by utilizing the hosts’ gene-regulatory RNAs. This includes a recently discovered RNA type, circular RNAs (circRNAs). We identified the first example of herpesvirus-regulating circRNAs, some of which regulates γ-herpesvirus virus production [1-3], but β-herpesvirus circRNAs remain largely unexplored.

Aims

This research aim to detrmine circRNAs that play key roles in β-herpesvirus, as well γherpesvirus, infection. Using publicly available dataset, we recently observed that ~60 human circRNAs were regulated by both β- and γ-herpesviruses, suggesting the existence of crucial circRNAs during infection with multiple human herpesviruses. Utilising in vitro primary infection model fo human immune cell lines, we will first use novel long-read sequencing technology to holisticly profile β-herpesvirus-induced circRNAs and to detect whether β-herpesvirus generates its own viral circRNAs. Second, to determine most crucial host and viral circRNAs to regulate the infection and host cell, single cell resolution screening of circRNAs will be performed. Both methods have not been utilised in herpesvirus circRNA research and are expected to produce unprecedent depth and resolution. For candidate circRNAs, we will combine omics, RNA biology, virological, and immunological approaches to determine the mechanism by which circRNAs control infection and pathogenesis. As an extended approach, using cells infected with two or more HHVs to reveal the relevance of HHV-regulated circRNAs in pathogenesis.

Training outcomes

The student will aim to identify crucial, co-regulated circRNAs by multiple herpesviruses and novel viral circRNAs, placing the student at the forefront of this emerging field of herpesvirus-host interactions. This proposed research is foundational not only to understand circRNAs regulation of each HHV but also to reveal potential cooperative effects of HHVs in pathogenesis. Throughout the research, the student will master techniques in various discipline including virology, RNA biology, and immunology. As the research requires various omics techniques, ability to process, analyse, and think critically about the big data produced from high-throughput analysis. The identified infection-regulating circRNAs may present novel biomarkers or druggable targets. Recently, a secreted HHV6-encoded microRNA was found to be a potential biomarkers[4]. Although circRNAs were also secreted and stable in circulation, their potential as biomarkers has not been tested in HHV6-infected individuals. Working with Scottish National Blood Transfusion Service (SNBTS), the student may have a chance to quantitate candidate circRNAs from human blood-originated samples. In sum, the student will be trained to interdiscplinery researcher with expertise both in wet and dry science in the filed of infectious disease.

References

1. Tagawa T, Gao S, Koparde VN, Gonzalez M, Spouge JL, Serquiña AP, et al. Discovery of Kaposi’s sarcoma herpesvirus-encoded circular RNAs and a human antiviral circular RNA. Proc National Acad Sci. 2018;115: 201816183. doi:10.1073/pnas.1816183115
2. Tagawa T, Oh D, Dremel S, Mahesh G, Koparde VN, Duncan G, et al. A virus-induced circular RNA maintains latent infection of Kaposi’s sarcoma herpesvirus. Proc National Acad Sci. 2023;120: e2212864120. doi:10.1073/pnas.2212864120
3. Tagawa T, Oh D, Santos J, Dremel S, Mahesh G, Uldrick TS, et al. Characterizing Expression and Regulation of Gamma-Herpesviral Circular RNAs. Front Microbiol. 2021;12: 670542. doi:10.3389/fmicb.2021.670542 4. Chan C, Loh JXY, Sin W-X, Teo DBL, Tan NKZ, Nagarajan C, et al. Extracellular viral microRNAs as biomarkers of virus infection in human cells. Mol Ther - Nucleic Acids. 2025;36: 102444. doi:10.1016/j.omtn.2024.102444