Genetic heterogeneity exists between cells within an individual. The accumulation of these somatic mutations can ultimately result in oncogenic transformation. Cancer development is often a multi-step process, the earliest stages of which remain incompletely understood. Recent technological advances have enabled detection of somatic mutations in healthy tissues, revealing that as we age many of our tissues are converted into a patchwork of mutant clones, despite retaining their histologically normal appearance. These clonal expansions are commonly driven by mutations in known oncogenes and tumour suppressor genes, with the driver landscape in a given tissue resembling its associated cancer.

Bladder cancer exhibits complex landscapes of clonal selection and somatic mutagenesis. In order to characterise these features in normal urothelium, we developed an approach to sequence laser-dissected microbiopsies derived from transplant donors with no history of cancer and cystectomy specimens from bladder cancer patients. Using a combination of targeted and exome sequencing, we demonstrate that the driver landscape is dominated by chromatin remodellers, with mutations occurring less frequently in other classes of canonical bladder cancer genes, and is extensively heterogeneous between individuals. Whole-genome sequencing reveals that APOBEC mutagenesis, which accounts for the majority of mutations in bladder cancer, occurs in normal urothelium, with variable exposure levels between clones. Additionally, we identify three novel mutational signatures, one of which is associated with smoking, a major risk factor for bladder cancer the molecular basis for which was previously unknown.

Overall, this dissertation provides a tantalising glimpse into the rich and diverse mutational landscape of normal urothelium. These findings may potentially contribute to the development of personalised risk models and tools for the early detection of cancer.