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Constructing an evolutionary atlas of the immune landscape in lung cancer

Periodic Reporting for period 1 - TRACERxTME (Constructing an evolutionary atlas of the immune landscape in lung cancer)

Reporting period: 2019-04-01 to 2021-03-31

Lung cancer is the leading cause of cancer-related deaths worldwide, accounting for 1.8 million deaths globally in 2020. This is largely due to the fact that lung tumours change over time by acquiring new mutations, making treatment difficult. This is called tumour evolution, and through an increased understanding of this process we will be able to better treat patients by tailoring treatments to individuals. TRACERx (TRAcking Cancer Evolution through therapy (Rx)) is a prospective clinical trial that aims to do just that by following over 800 lung cancer patients starting from diagnosis through surgery and relapse. This study has uncovered that the more diverse a patient’s tumour at time of surgery, the worse their outcome. Diversity can be thought of as the number of tumour cell lineages that have evolved to result in the mass detected at diagnosis. From Darwinian principles, we know the environment plays a large part in shaping the evolution of species. This project aimed to increase our understanding of how the immune system acts as an environmental force to shape the evolution of lung tumours.

At the Francis Crick Institute, with the support of the European Commission and Bristol Myers Squibb, we have developed a method to look at lung cancer cells in their native environment in unprecedented detail. We have used this method to understand whether the immune system is activated or repressed and how it changes over time. We were also able to integrate detailed clinical and genetic information to understand the relationship between particular subtypes of lung cancer, lung cancer diversity, and the corresponding immune response. The outputs of this work will help inform the rational design of new therapies with the goal of activating the immune system to ultimately improve lung cancer patient outcomes.
This project began with the development of our method for the visualisation of and analysis of cancer and immune cells and how they are organised. More specifically, we were able to identify what types of immune cells were present and whether any cells expressed proteins that enhance or repress the immune response. Several of these proteins are drug targets meaning that if we can understand the circumstances in which they are expressed we can better select patients for specific therapies.

Through applying our method to our lung cancer patient cohort, we have found that the immune response can be as diverse as the tumours themselves with half of cases showing different responses in different regions of a patient’s tumour. These changes sometimes reflected the different lineages of tumour cells that had evolved within a given tumour ecosystem. We found that two prevalent subtypes of lung cancer showed different immune responses to cancer cell mutations, which could impact how patients are selected for therapies. We also observed that the immune-related proteins that can be targeted by drugs are expressed on a wide variety of cell types, meaning that certain immunotherapies may be impacting previously unappreciated cell types. Future work is needed to determine the impact of treatment on these other immune cell types.
Ultimately, we aim to carry forward our improved understanding of how the immune system shapes lung tumour evolution to inform novel preclinical and clinical studies. Our method can now be applied beyond this project to support research on our growing cohort of lung cancer patients. These larger cohorts will be critical in order to solidify findings that could improve how clinicians select the best treatment for their patients and ultimately improve patient outcome.