Deciphering the T cell receptor repertoire and immune checkpoint landscape in tumours with a high mutational load

The advent of checkpoint immunotherapy has revolutionised the treatment of solid cancers, resulting in durable responses in a number of patients. However the majority of patients do not respond to treatment, underscoring the need to better understand the mechanisms that underlie the immunological response to cancer. T cell receptor (TCR) repertoire analysis and immune checkpoint mapping are powerful tools to study the anti-tumoural immune response. This thesis explores the TCR repertoire and immune checkpoint landscape in muscle invasive bladder cancer (MIBC), non-small cell lung carcinoma (NSCLC) and metastatic melanoma. In patients with MIBC, immune checkpoint mapping and TCR repertoire analysis revealed similarities between lymphocytes in the urine and bladder tumour microenvironment. Urine-derived lymphocytes may therefore provide a non-invasive immune biomarker to track the evolution of the immune landscape in MIBC. The lung TRACERx study is a prospective study exploring the cancer genome evolution of early stage NSCLC. The TCR repertoire of multi-region tumour specimens was found to be distinct to non-tumour lung and PBMC. TCR repertoire heterogeneity amongst TCRs preferentially expanded in the tumour, was correlated to intratumoural genomic heterogeneity. Intratumoural TCR expansion enriched for a tumour reactive T cell phenotype. These observations suggest a dynamic intra-tumoural T cell response related to the mutational landscape of NSCLC. The immune checkpoint landscape of treatment naive and anti-PD-1 treated metastatic melanoma patients was assessed by multiparametric flow cytometry. The checkpoint phenotype of PD-1 expressing tumour infiltrating lymphocytes (TILs) in treatment naive samples was heterogeneous. Drug bound effector TILs in anti-PD-1 treated melanoma co-expressed multiple immune checkpoint molecules that may have contributed to treatment resistance. Immune checkpoint mapping of CD8+ and CD4+FoxP3- cells and CD4+FoxP3+ (regulatory T cells) revealed differences in the expression level and frequencies of key co-inhibitory and co-stimulatory molecules. TCR repertoire analysis and T cell immune checkpoint mapping provide valuable and complementary tools for analysis of the immune response to solid cancers.