Virus manipulation of host non-coding RNA regulatory networks

It has been known for some years that only ~2% of the human genome encodes for proteins, whereas ~80% is actively transcribed into RNAs with no obvious coding capacities, known as non-coding RNAs (ncRNAs). The importance of this non-coding transcriptome is emphasised due to the fact that ncRNAs are frequently altered in many human diseases, including aging, cancer, auto-immunity and infections. Functional studies have shown that ncRNAs are critical regulators of gene expression. For example, a group of short ncRNAs known as microRNAs (miRNAs), modulate gene expression by binding to their target protein coding transcript, which leads either to the transcript's translation repression, cleavage or decay. As such, research in this area has mainly focussed on identifying the interaction between specific miRNAs and their target transcript(s). However, emerging evidence now suggests the existence of an unexpected interplay between different ncRNAs that strongly influences, for example, how a miRNA can bind to its target. In this case, other ncRNA species, such as circular RNAs and other long ncRNAs, function as competing endogenous RNAs, interacting with miRNAs to sponge or decoy the miRNA, thus inhibiting the miRNA from binding to the target mRNA and preventing its repression. As such, this network of ncRNA-ncRNA interactions can have a profound effect on the regulation of gene expression in many cellular processes.

We have exciting preliminary data suggesting that a herpesviruses has evolved ways to manipulate these ncRNA regulatory networks to enhance virus gene expression and modulate the host response to infection. We have demonstrated that during herpesvirus infection several circular RNAs are upregulated whereas the majority of dysregulated miRNAs are downregulated. This suggests that these virus-induced circular RNAs could sponge specific miRNAs to outcompete their binding to target protein coding transcripts and prevent their repression or degradation.

We now aim to further investigate these observations and identify the interplay between ncRNA species and their associated regulatory networks which are manipulated by the virus. Furthermore, we will determine why these regulatory networks are altered during infection by determining the role of the target protein-coding transcripts that are aberrantly expressed due to the manipulation of their respective networks. Moreover, we will investigate novel mechanisms of how a virus enhances circular RNA levels during infection. Finally, we have identified a group of miRNAs that in contrast to the majority of downregulated miRNAs are actually increased during infection, which suggests the virus enhances their production to repress or degrade cellular transcripts which are probably detrimental to virus infection. We will determine how the viruses upregulates these miRNAs and also determine the inhibitory role of their target mRNAs in virus replication.

In summary, this project will identify novel ways a virus can manipulate the host cell to enhance its own replication and provide a better understanding how the interplay between different ncRNA species can regulate gene expression. A better knowledge of these fundamental processes has the potential for far reaching impacts on our understanding of cell and developmental biology processes, the development of human disease and provide new strategies for therapeutic interventions of important human pathogens.

Non-coding RNA (ncRNAs) constitute the majority of the human transcriptome. ncRNAs play diverse roles in a multitude of cellular processes, functioning as critical regulators of gene expression. This is reinforced by ncRNA dysregulation being implicated in the development and progression of a wide range of human diseases. To date research into the mechanisms of ncRNA function has mainly focussed on the unidirectional regulation of target protein-coding transcripts, particularly by miRNAs. However, it is now evident that there exists an unexpected interplay between different ncRNA species, that strongly influence how gene expression is regulated. This hidden cross-talk of ncRNA-ncRNA interactions forms competitive regulatory networks. Notably, aberrant expression of any network component could derail the complex regulatory circuit, culminating in the development and progression of disease.

We have exciting preliminary data to suggest Kaposi's sarcoma-associated herpesvirus (KSHV) manipulates ncRNA regulatory networks to enhance virus gene expression and modulate the host response to infection. As such, this provides an excellent model to study how dysregulation of these ncRNA-based networks impact on host gene expression.

The aim of the project will determine how and why these ncRNA regulatory networks are altered during infection. We will investigate novel mechanisms of how a virus dysregulates ncRNA biogenesis during infection and determine the role of the target protein-coding transcripts aberrantly expressed due to virus-mediated manipulation of these ncRNA networks.

In summary, this project will identify novel ways viruses manipulate the host cell to enhance their replication and provide a better understanding of how the interplay between different ncRNA species can regulate gene expression and how this impacts on human disease. Moreover, it may provide new strategies for therapeutic interventions of important human pathogens.

The proposal builds upon previous novel work which has focussed on applying omic-based strategies to understanding the interactions between viruses and the host cell. The aim of this current proposal is to test the hypothesis that herpesvirus infection manipulates ncRNA regulatory networks. In particular, we aim to examine how a virus commandeers the intricate interplay between ncRNAs to enhance virus gene expression and modulate the host response to infection.

Whilst this study is fundamental in nature, the impact of the research will be wide reaching. The virus model provides an excellent tool to determine how ncRNA regulatory networks exert regulatory control on gene expression. Aberrant ncRNA processing and levels are implicated in a number of human diseases, therefore any clues as to how cellular ncRNA processing quality control checkpoints are bypassed by virus infection generated from this project will be of interest to the pharmaceutical industry. Recent advances of biological drugs have broadened the scope of therapeutic targets for a variety of human diseases. This holds true for RNA-based therapeutics, recent developments in this area have improved synthetic delivery carriers and chemical modifications to enhance their stability. These emerging drug approaches will be key in modulating ncRNA regulatory networks which are dysregulated in human diseases.

In addition, a key element of this project is the characterisation of essential virus-host cell interactions which will provide avenues for novel antiviral strategies. As numerous virus-host cell interactions are conserved in herpesviruses this approach may have generic applications for the treatment of a variety of additional human and animal diseases caused by this large family of viruses. Therefore, these discoveries may foster new collaborations with the pharmaceutical and other commercial industries to exploit these findings for new therapeutic strategies.

In the longer term, exploitation of these findings by the commercial sector may lead to new treatments for a wide range of diseases and virus infections, and this will provide benefits to the quality of life of the general public. Moreover, exploitation of the research findings by the commercial sector is also likely to have a direct impact on the prosperity of the general public of the UK, through increased investment and employment opportunities that will arise from new therapeutic drugs.