Lung resident memory CD8+ T cells during viral infections - generation and functionality regulated by localisation and type I IFNs

According to the World Health Organisation, lung infections kill ~3 million people each year, more than twice the number that die of diarrhoeal diseases, AIDS and diabetes combined. Viruses are responsible for many of these infections, but there is relatively little research investment in discovering how upper respiratory viral infections spread to the lungs and cause pneumonia. The most common viral causes of lower respiratory tract infections are respiratory syncytial virus (RSV) and influenza A virus (IAV), both frequently causing severe disease. Despite a vast effort over six decades, vaccines that elicit protection against RSV are yet to be developed. There are partially effective vaccines against IAV, but they need to be redesigned each year to match the new strains of IAV that constantly evolve. Most vaccines are given as an injection and induce protective antibodies that circulate in the bloodstream. As such, they are not optimised to specifically protect the lung or to mobilise lung-resident immune cells that help protect from severe disease.

Our understanding of how lung-resident immune cells defend us against respiratory viruses is incomplete, but recent evidence shows that a special subset of T cells, known as tissue resident memory T (Trm) cells, are critical for rapid elimination of viruses such as RSV and IAV. While it is likely that the environment in which these cells reside shapes their function and life span, it remains unclear how this happens. We believe that Trm cells are maintained in specific niches within the lung where they are nurtured by interactions with neighbouring cells.

During viral infection, essential anti-viral molecules called type I interferons (IFNs) are produced in large quantities. These cytokines can alter how T cells behave but their role in determining the function of Trm cells is not known. In this proposal we will study how type I IFNs affect the behaviour of Trm cells. To achieve this, we will use a new technique in which we study live slices of lung tissue in culture. These living slices can be re-stimulated with virus or components of the virus in the lab to enable detailed visualisation of tissue-resident cells and their responses. We will compare slices from mice and humans, investigating how type I IFNs influence Trm cells; their survival, function and localisation. Thus, this proposal will provide increased understanding of how tissue-protective T cells are regulated, which will help the development of new vaccines and treatments that harness the potentials of Trm cells to alleviate viral induced disease.

Lower respiratory tract infections are a leading cause of death globally and respiratory syncytial virus (RSV) and influenza virus together account for a large number of hospitalisations of especially children and the elderly. Absence of effective vaccines and recurrent infections throughout life demonstrate the difficulties in eliciting protective memory responses in the lung. However, recent evidence indicating the potency of protective mechanisms mediated by tissue resident T cells (Trm) suggest that these cells may be key. In human experimental RSV infection, CD8+ Trm cells correlate with improved outcome and contribute to heterosubtypic immunity against influenza viruses. However, we have limited knowledge of what these cells require in order to become resident, be maintained and function efficiently in the lung.

During respiratory viral infections, type I interferons (IFNs) drive early inflammatory responses and modulate T cell effector and memory programming. However, how type I IFNs influence Trm cells has not been investigated. We will address this using established mouse models and a new ex vivo approach involving precision cut lung slices (PCLS). We will use type I IFN receptor deficient (Ifnar1-/-) mice to study the influence of type I IFNs on Trm cell generation and function and will use PCLS to study Trm cell localisation and re-activation after ex vivo infection or antigen re-stimulation. In addition, we will use antibody-mediated blocking and gene silencing tools in PCLS to directly test the impact of type I IFN signalling on Trm cell function. Finally, we will extend PCLS to human lung tissue, providing a unique opportunity to study and manipulate human Trm cells in situ. These studies will help to understand the factors that govern Trm cell residency and function and may ultimately enhance our ability to develop vaccines that better protect against respiratory viral infections.

Severe respiratory infections, especially in infants and the elderly, are at the top of the list of causes of death worldwide. The proposed work will help to understand why certain people get severe lower respiratory tract viral infections and which pathways we need to harness in order to obtain good memory responses to natural infection or vaccination. Specifically we will learn how effective lung specific memory responses are generated and maintained to protect us from severe disease caused by viruses such as respiratory syncytial virus and influenza virus, This knowledge will impact patients, clinicians, other scientists and the biopharmaceutical industry.

Patients and clinicians:
This work will impact patients that suffer from severe respiratory infection and their families, as well as the clinicians that treat these patients. For example, the proposed work will help elucidate how lung resident T cells combat viral infection. All these findings have direct translational possibilities as in the future this new knowledge will help direct therapies and vaccine development.

Scientists and research:
This project will offer full training for a post-doctoral scientist in a range of biological techniques, including in vivo mouse models, cell culture, etc. Furthermore, the postdoc will also acquire transferable skills in terms of scientific method, science communication and project management stemming from their training in planning of experiments, data analysis, critical thinking, data presentation and writing-up of results for publication.
The work proposed in this grant spans the fields of immunology, vaccinology and virology and is therefore multi-disciplinary in nature. It will impact national and international academic research across fields and will also impact on industry as described in the Academic Beneficiaries section.

Biopharmaceutical industry and policy-makers:
In the long term the data generated from this work may influence policy-makers and commercial pharmaceutical and biotechnology companies. This work will contribute essential results important for improving health especially in children and the elderly.