Exploring antiviral RNA interference in mammals

All organisms possess defence mechanisms to combat infections caused by viruses. In plants, insects and worms, one of these mechanisms is called antiviral RNA interference (RNAi). Many viruses have genetic material made of RNA, which after the virus infects a cell, will be copied into molecules called double-stranded RNAs (dsRNAs). These dsRNAs alert the cell to the presence of a virus. A protein made by the cell, called Dicer, then chops these dsRNA molecules up into small inhibitory fragments. It is these RNA fragments that then stick to all copies of the viral genetic material inside the cell and direct their destruction, thereby halting the infection.

Although mammalian cells also contain Dicer protein and other molecules needed for RNAi, they possess an additional antiviral mechanism whereby dsRNA molecules formed during viral infections trigger the production of messenger proteins called interferons (IFNs). These IFNs act on neighbouring cells to alert them of a virus attack and boost their defences to allow them to stop viral invaders. It has been proposed that antiviral RNAi has been superseded in mammals and replaced by an IFN-based defence mechanism.

However, recent data generated by myself and other labs have revealed that the RNAi-based defence system is also active in mammalian cells and might block viruses only in particular cell types. My work has shown that the RNAi pathway is antiviral in mouse embryonic stem cells. These are cells found in early stage embryos that can self-renew and be programmed to develop into all the different cell types that the body needs. Importantly, they lack an IFN-based response and so are dependent on other mechanisms to defend themselves against viruses. In virally infected mouse embryonic stem cells, Dicer efficiently chops up viral dsRNA molecules into inhibitory fragments, while in fully mature cells, Dicer's activity is greatly reduced. Why Dicer works in immature cells but not in mature cells is only beginning to be understood. Interestingly, my own work shows that in mature cells, proteins produced in response to IFNs inhibit Dicer's activity, suggestive of an incompatibility between antiviral RNAi and the IFN system in mammals.

These studies have uncovered another mechanism of innate anti-viral immunity that mammalian cells have at their disposal. The question now is how, where and when this defence mechanism works. To answer the first question I will investigate how Dicer's ability to chop viral dsRNA is controlled. For this, I will focus on three proteins produced by the cell that are known to attach to Dicer and evaluate their role in Dicer's function. My second question aims to define in which cells this RNAi-based defence matters. For this, I will test my working hypothesis that RNAi is active not only in stem cells from the embryo, but also in stem cells found in various tissues of our body. Finally, and most importantly, I will test how much RNAi helps to protect living animals from infections, since inhibitory RNA fragments produced by Dicer have previously been shown to accumulate in infected newborn mice.
There is huge scope for discovery in this field because RNAi has only recently been shown to be antiviral in mammals. This proposal tackles fundamental and exciting questions to elucidate the functional role of this ancestral mode of defence in mammalian immunology. Knowledge generated will improve our understanding and ability to boost natural antiviral mechanisms. Moreover, the results will also be relevant to deciphering the fundamental biology of stem cells and to our understanding of the evolution of the immune system.

Viruses constitute a constant threat to the human population as illustrated by pandemic outbreaks caused by Influenza virus, Zika virus and human immunodeficiency virus. To develop innovative therapeutic approaches to combact these infections, it is essential to understand the full repertoire of defences available in our cells. My research programme's fundamental aim is to explore an antiviral defense mechanism based on RNA interference (RNAi) only recently revealed in mammals, therefore the scope for impact from my research is broad.

In the short term, this research will directly influence the academic community within the innate immunity field as it will provide wide-ranging insight into how this antiviral defence mechanism works, in which type of cells it is active and how it impacts viral infection either in newborns or adults. My findings will undoubtedly have major effects on the direction of research within the virology and immunology fields and beyond in other academic research communities. My work will notably impact on stem cells research as it will help to understand how these cells are protected from viral attacks. This is important because these cells are at risk of infection as observed for instance during embryogenesis with neural progenitors cells that are targeted by Zika virus.

Beyond academica, this research programme will impact on clinical regenerative medicine. One strategy currently explored to replace cells in damaged tissues, for instance in heart disease, is to harvest progenitors cells from patients, expand them and then transplant them back into the patient to potentially regenerate the malfunctioning tissue. Given the potential risk of infection during the transplantation, a full understanding of the immune mechanisms active in these multipotent cells is important as it could precipitate new strategies to boost these defences, which will be beneficial for the patients.

In the long term, the identification of a novel antiviral mechanism active in vivo and how it is counteracted by viral proteins will impact the pharmaceutical industry by providing novel targets for antiviral drugs. One approach might be the design of drugs that specifically enhance the antiviral activity of the RNAi pathway. In addition, designing drugs that target viral proteins that suppress the RNAi defence mechanism could be a potentially highly selective approach to block infection with minimal side effects and therefore directly benefit virally-infected people.

Finally, during this multidisciplinary research programme I will acquire new skills and foster collaborations which will be essential for my development as an independent researcher and to form the optimal foundations to build up my research group. I will also train a postodoctoral researcher in various methods to analyse RNA, to work with stem cells as well as to perform a range of virological assays. During this programme, the postdoctoral researcher will also benefit from the numerous interactions with collaborators or other scientitsts in the fields of virology, immunology and stem cells.