Towards understanding T cell-mediated killing of cancers: Characteristics of neoantigen-specific T cell recognition in therapeutic settings

The immune system plays an active role in containing and eliminating cancers. Following tumor immune escape, the use of immunotherapy including immune checkpoint blockade (ICB) has shown immense potentials for reactivating the silenced adaptive immune system to combat cancer. However, despite the promising developments within immunotherapy, there is a need for improved knowledge of the immunological components that drive anti-tumor immunity. This is important in order to understand why a large portion of patients still fails to respond to treatment.
The overall goal of the research presented in this PhD thesis is to characterize T cell recognition of tumor mutation-derived neoepitopes in clinical settings, to enhance the insight into how T cells recognize cancers. In Manuscript I, the study interrogates longitudinal neoepitope recognition by CD8 T cells in the peripheral blood of patients with metastatic urothelial carcinoma (mUC) treated with Programmed Death-Ligand 1 (PD-L1) blockade. ICB has proven highly effective in treatment of mUC, but how this is governed by T cells remains unclear. We investigate the importance of the overall neoepitope recognition landscape prior to, during and after treatment. Further, we apply this to differentiate patients that respond to treatment from those that do not. We show that patients with disease control elicited a rapid increase in the width of the neoepitope reactive T cell repertoire during the initial weeks of therapy, compared to patients with progressive disease. By evaluating these dynamics, we provide novel insight into the characteristics of neoepitope recognizing T cells, with kinetics that were previously shown only for bulk CD8 T cells populations. We further investigate the phenotypic characteristics of such neoepitope recognizing T cells. These express an activated, proliferative phenotype early during ICB, enhanced for patients with benefit from treatment. Additionally, we illustrate that neoepitope specific T cells in the blood can be distinguished from other CD8 T cells by CD39 expression, previously only evident inside the tumor environment. Collectively, this shows that neoepitope reactive T cells not only recognize tumor specific antigens, but also are functionally activated and display an effector T cell phenotype with proliferative capacities.
In Manuscript II, the molecular recognition patterns of a T cell receptor (TCR) that recognizes a mutation-derived neoepitope is investigated. The TCR have previously shown functional activity towards the mutated neoepitope, while avoiding interaction with the wild type (WT) peptide. In this manuscript, we interrogate this difference in recognition in vitro. We find that both structural interaction and functional activation is impaired when comparing the WT peptide to the neopeptide. While structural requirements of TCR recognition are primarily governed by importance of central residues, the reduced TCR affinity to the WT peptide also restricts full functional T cell activation. These observations illustrate the critical parameters for TCR peptide recognition on a molecular level, for this individual neoepitope specific TCR. Lastly, in the Additional Results chapter, the molecular recognition patterns of two additional TCRs derived from a Type-1 diabetes context are interrogated and compared by evaluating the promiscuity in recognizing closely resembling peptides.
Together, the studies presented in this PhD thesis provide insight into the kinetics and characteristics of neoepitope recognition by CD8 T cell in immunotherapeutic settings. The findings contribute to an improved foundation for a better understanding of the mechanisms that define T cell driven elimination of cancer. Fully defining such rules is critical in order to improve the outcome of immunotherapeutic interventions in the future.