Assessing the function of tumour specific and bystander T-cells in relation to clinical outcomes of melanoma patients

Abstract

CD8+ T cells are immune cells that can specifically target and kill cancer cells. Immune checkpoint inhibitors (ICIs) that boost CD8+ T cell activity in tumours have greatly reduced melanoma recurrence rates. Yet, over 40% of metastatic melanoma patients still recur following therapy, and mechanisms of ICI response remain unclear. As such, biomarkers for ICI response are urgently needed. CD8+ T cells could act as such, yet markers of tumour antigen specificity in CD8+ T cells remain unproven. Furthermore, recent investigations are finding that many CD8+ T cells in the tumour microenvironment (TME) do not recognise cancer cells, raising questions as to their function. In this thesis, we assess potential markers of antigen specificity in CD8+ T cells to determine their function and associations with patient outcomes. Tissue from primary and stage III melanomas was analysed using flow cytometry and multiplex fluorescent immunohistochemistry (mIHC) to identify CD8+ T cell populations and other immune cells. We identify intratumoural CD39+CD103+ CD8+ T cell populations as biomarkers for recurrence-free survival in both primary melanoma and ICI-treated stage III melanoma. Detailed spatial analysis suggests the anti-tumour reactivity of these populations. Neighbourhood analysis provides a computational method for the identification of B cell aggregates in primary melanoma, and finds them associated with improved patient outcomes. Finally, we detail future work utilising a combination of techniques including scRNAseq to assess the gene expression profile of antigen-specific CD8+ T cells in the tumour and blood of stage III melanoma patients. This thesis identifies specific CD8+ T cell populations as biomarkers for outcome in multiple stages and treatment contexts for melanoma. These findings have significant clinical and therapeutic implications, particularly for patient selection and treatment enhancement in current and upcoming immunotherapies.