Spatial modelling and quantification of T cell exhaustion in the tumour microenvironment of oesophageal cancer

Background. Recently, immunotherapy of oesophageal adenocarcenoma (OAC) with immune checkpoint inhibitors has been shown to improve depth and durability of therapeutic responses for a significant minority of treated patients. Successful control and elimination of a cancer by the immune system requires the trafficking and infiltration of activated tumour antigen specific cytotoxic T lymphocytes into tumours, followed by recognition and killing of cancer cells, as described in the cancer-immunity cycle. This process can be disrupted at multiple points, leading to the breakdown and prevention of effective lymphocyte-driven destruction of cancer. Prominent among these is the influence of a suppressive microenvironment that can inhibit tumour-specific, activated, cytotoxic CD8+ T lymphocytes from expanding, migrating to the tumour, and killing cancer cells; and the impact of lymphocyte exhaustion. These immunological "checkpoints" prevent an anti-tumour response from developing and frustrate immunotherapeutic activation of the anti-tumour response. Thus, identifying the mechanisms underlying primary resistance to targeted immunotherapies is vital for progress. Multiple immunosuppressive networks have been described, including interactions with regulatory T cells (T-regs) and cancer assisted fibroblasts (CAFs). In OAC, bulk counts of T cell infiltration correlate poorly with clinical outcomes, and CAFs are strongly implicated in cytotoxic T cell suppression. Together, these observations suggest that spatial relations between different types of T cells and CAFs are important for understanding immunosuppression in OAC. The aim of this project is to analyse and quantify spatial domains involving immune cells from patients with OAC in order to develop new metrics, based on spatial statistics, that will improve diagnostics, prognostics, and immunotherapeutic strategies. Novelty of research methodology. We will develop a spatially-resolved, multiscale computational model describing the in vivo growth of OAC and its interactions with CAFs and different T cell subtypes, adapting an existing model. Subcellular variables will represent each T cell's level of exhaustion as a continuous value, which will determine its efficacy for killing OAC cells. In turn, T cell exhaustion will be altered through interactions with CAFs and T regs and immunotherapy. Simulation outputs will be described quantitatively using a suite of spatial statistical analysis tools. These tools will also be applied to mIHC images of OAC, generated by the Elliott lab, with existing panel optimised for CD8+ subsets, T-regs and CAFs. direct quantitative comparison will therefore be possible between biomedical images and ABM simulations. We will identify combinations of spatial statistics which distinguish between simulations generated via different parameters, and apply these to IHC samples to predict patient outcomes and responses to therapy. Proposed outcomes. The project will deliver a versatile multiscale computational model that simulates interactions between immune cell subsets and OAC, and that generates synthetic spatial data for comparison with mIHC images. The model will provide new mechanistic understanding of processes driving T cell exhaustion and immunosuppression within OAC and also serve as tool for identifying potential new immunotherapies. By comparing model outcomes with mIHC data, we will identify statistical descriptions of cell colocalization which act as imaging biomarkers and which can distinguish patients who would benefit from immunotherapeutic treatments from those who would not. Professor Tim Elliott's lab at the Nuffield Department of Medicine will be collaborating to provide Multiplex Immunohistological (Vectra) images of OAC. This project falls within the EPSRC Mathematical Biology research area.

The main impact of the SABS CDT will be the difference made by the scientists trained within it, both during their DPhils and throughout their future careers.

The impact of the students during their DPhil should be measured by the culture change that the centre engenders in graduate training, in working at the interface between mathematical/physical sciences and the biomedical sciences, and in cross sector industry/academia working practices.

Current SABS projects are already changing the mechanisms of industry academic collaboration, for example as described by one of our Industrial Partners

"UCB and Roche are currently supervising a joint DPhil project and have put in two more joint proposals, which would have not been possible without the connections and the operational freedom offered by SABS-IDC and its open innovation culture, a one-of-the-kind in UK's CDTs."

New collaborations are also being generated: over 25% of current research projects are entirely new partnerships brokered by the Centre. The renewal of SABS will allow it to continue to strengthen and broaden this effect, building new bridges and starting new collaborations, and changing the culture of academic industrial partnerships. It will also continue to ensure that all of its research is made publically available through its Open Innovation structure, and help to create other centres with similar aims.

For all of our partners however, the students themselves are considered to be the ultimate output: as one our partners describes it,

"I believe the current SABS-IDC has met our original goals of developing young research scientists in a multidisciplinary environment with direct industrial experience and application. As a result, the graduating students have training and research experience that is directly applicable to the needs of modern lifescience R&D, in areas such as pharmaceuticals and biotechnology."

However, it is not only within the industrial realm that students have impact; in the later years of their DPhils, over 40% of SABS students, facilitated by the Centre, have undertaken various forms of public engagement. This includes visiting schools, working alongside Zooniverse to develop citizen science projects, and to produce educational resources in the area of crystal images. In the new Centre all students will be required to undertake outreach activities in order to increase engagement with the public.

The impact of the students after they have finished should be measured by how they carry on this novel approach to research, be it in the sector or outside it. As our industrial letters of support make clear, though no SABS students have yet completed their DPhils, there is a clear expectation that they will play a significant role in shaping the UK economy in the future. For example, as one of our partners comments about our students

"UCB has been in constant search for such talents, who would thrive in pharmaceutical research, but they are rare to find in conventional postgraduate programmes. Personally I am interested in recruiting SABS-IDC students to my group once they are ready for the job market."

To demonstrate the type of impact that SABS alumni will have, we consider the impact being made by the alumni of the i-DTC programmes from which this proposal has grown. Examples include two start-up companies, both of which already have investment in the millions. Several students also now hold senior positions in industry and in research facilities and institutes. They have also been named on 30 granted or pending patents, 15 of these arising directly from their DPhil work.

The examples of past success given above indicate the types of impact we expect the graduates from SABS to achieve, and offer clear evidence that SABS students will become future research leaders, driving innovation and changing research culture.