Investigating anti-tumour T cell responses in nasopharyngeal carcinoma to refine vaccine-based immunotherapies

Nasopharyngeal carcinoma (NPC) is a type of cancer that occurs at the back of the nose. It is unusually common in some parts of the world, including countries like Malaysia where it constitutes a very significant health problem. NPC can be cured, but in many cases the cancer comes back and this is usually fatal. Furthermore, patients who do survive are often left with significant long-term side effects caused by the toxic treatments. Therefore, new treatments are needed to reduce deaths from NPC and improve the quality of life for survivors. All patients with NPC have a virus, known as the Epstein-Barr virus, or EBV for short, in their tumour cells. We have developed a vaccine that can recognise EBV with the aim of boosting the patients' own immune response to the tumour. Early tests of our vaccine in people show that it is safe and that it can boost immunity against the virus. In this proposal we want to understand more about immunity to EBV in patients with NPC so that we can modify how we deliver our vaccine and eventually combine it with other drugs to improve its therapeutic effects. To do this we will be using new sequencing technologies to probe how patient's T cells, the body's main weapon against virus-infected cells, respond to EBV, for example before and after treatment, enabling us to 'track' individual T cell responses over time. At the same time, we will explore the nature of potential inhibitory pathways present in the tumour so that we might eventually target these in combination with our vaccine making it more effective.

We have developed a therapeutic vaccine, known as MVA-EBNA1/LMP2, that expresses a fusion protein encoding almost all known CD4 T-cell targets in EBNA1 and multiple CD8 T-cell epitopes from LMP2. This vaccine has already been shown to be safe and to exhibit promising therapeutic activity in early phase clinical trials. Knowledge of the factors in the blood and tumour tissues of NPC patients that might limit T cell responses will be required not only to maximize the therapeutic efficacy of our vaccine, but also to identify biomarkers of likely treatment response for eventual patient stratification.

To address these gaps in knowledge we will first use multiplex immunohistochemistry to provide a detailed characterisation of the immune micro-environment of NPC, including the expression of immune checkpoints. We will use our established EBV-specific T cell clones and NPC cells, including lines we have recently established that more faithfully recapitulate primary disease, to explore the activity of these checkpoints, initially focusing on those mediated by fibroblasts. Finally, we will use next generation sequencing to describe how the TCR repertoire in the blood of NPC patients varies throughout the course of disease, and how it compares to the TCR repertoire we observe in tumour tissues. Importantly, using our cultured immune assays we will be able to interrogate these data to define T cell responses to relevant EBV and cellular tumour antigens.

This study will reveal new insights into the immune pathogenesis of nasopharyngeal carcinoma (NPC), a disease that is very common in South East Asia, including Malaysia. The Bidayuh natives in Sarawak have the highest incidence of NPC in the world, and NPC is the most common cancer among Sarawakian men. The cancer disproportionately affects the vulnerable groups, with the lowest social class reported to have 4 fold higher risk of the disease. NPC is associated with significant mortality and morbidity which result in a major impact on the immediate and extended families as over 90% of the patients supported households in some way. This study will specifically document the existence and function of immune checkpoints in biopsies from NPC patients and describe for the first time how T-cell receptor (TCR) specificities vary in the blood of NPC patients during the course of their disease and how they compare to the TCR repertoire we identify in the tumour; importantly, we will also be able to interrogate these data to define T cell responses to specific tumour antigens in both compartments. This knowledge will not only be important for our understanding of the pathogenesis of NPC, but will also help refine T cell therapies being developed for NPC patients, including our own therapeutic EBV vaccine, currently in early phase clinical trials.

A further impact of this project will be the transfer of scientific knowledge, generic and specific research skills, and technologies in the field of cancer immunology and EBV immunotherapy from the UK to Malaysia. We expect that this, coupled with the enhancement of our research network in Malaysia, will provide opportunities to translate our findings into better treatments for patients in Malaysia.

We also expect the outputs of this research to be relevant to the pharmaceutical industry and to biotech companies. The EBV vaccine is being developed for commercial use by Cancer Research Technology, who manage all IP. Eventually, this should lead to the development of additional new therapeutic agents, for example, drugs which will improve the efficacy of our vaccine when used in combination. New, more effective, therapies for patients with NPC will reduce the burden of disease, particularly for the vulnerable groups and will have a significant economic impact in Malaysia and in other parts of the world where NPC is common.