Title: Reshaping the mutational landscape in oesophageal squamous pre-cancer
Funder: Cancer Research UK

Abstract: Reshaping the mutational landscape in oesophageal squamous pre-cancer Background Normal human oesophagus progressively accumulates cells carrying mutations associated with cancer. Genetic evidence argues that these mutants are under Darwinian selection and that squamous cancer evolves within the population of mutated cells. However, the extent to which the normal tissue mutational landscape’ varies between individuals, the impact of common mutations on cancer risk and the genetic and environmental factors that shape the landscape are not known. This programme will investigate these issues and whether intervention can alter the mutational landscape with the goal of decreasing cancer risk. Aims 1. Map of mutations in the oesophagus in men and women aged over 65, the age group at the highest risk of developing oesophageal squamous cancer. Determine the frequency of clones carrying multiple mutations and other genomic alterations. 2. Determine how mutants of the p53, Pik3ca and Notch1 genes, which are common in normal human oesophagus, colonise normal epithelium and the impact this has on cellular and tissue function. 3. Measure how the development of the mutational landscape is altered by somatic mutation and germline mutations that predispose to squamous oesophageal cancer. 4. Test the ability of clinically applicable interventions to deplete mutations that promote squamous carcinoma development. Methods Deep targeted exome and low coverage whole genome sequencing of small samples of normal oesophageal epithelium will be used to map mutant clones in normal human oesophagus. Bespoke software will be used to detect mutations and analyse evolutionary selection. Cell tracking in transgenic mouse models and live imaging of tissue equivalents in culture will be used to study how mutant and wild type cells interact. Profiling of transcription in mutant cells will reveal candidate genes that underpin mutant cell phenotypes which will be tested by gene editing. The impact of somatic or germline mutation on the development of mutational landscape will be tested in mouse models and analysed by the same methods as used for human oesophagus. Interventions to alter the mutational landscape will be tested in long term cultures of mouse and human oesophagus and validated in vivo. How the results of this research will be used: The results will reveal the processes that shape oesophageal mutational landscape, the impact of somatic mutations on subsequent mutation and cancer risk, how germline mutants alter mutational landscape and identify interventions to deplete oncogenic mutants and reduce cancer risk that are suitable for future translational studies.

Lay abstract: Reshaping the mutational landscape in oesophageal squamous pre-cancer Background Normal human oesophagus progressively accumulates cells carrying mutations associated with cancer. Genetic evidence argues that these mutants are under Darwinian selection and that squamous cancer evolves within the population of mutated cells. However, the extent to which the normal tissue mutational landscape’ varies between individuals, the impact of common mutations on cancer risk and the genetic and environmental factors that shape the landscape are not known. This programme will investigate these issues and whether intervention can alter the mutational landscape with the goal of decreasing cancer risk. Aims 1. Map of mutations in the oesophagus in men and women aged over 65, the age group at the highest risk of developing oesophageal squamous cancer. Determine the frequency of clones carrying multiple mutations and other genomic alterations. 2. Determine how mutants of the p53, Pik3ca and Notch1 genes, which are common in normal human oesophagus, colonise normal epithelium and the impact this has on cellular and tissue function. 3. Measure how the development of the mutational landscape is altered by somatic mutation and germline mutations that predispose to squamous oesophageal cancer. 4. Test the ability of clinically applicable interventions to deplete mutations that promote squamous carcinoma development. Methods Deep targeted exome and low coverage whole genome sequencing of small samples of normal oesophageal epithelium will be used to map mutant clones in normal human oesophagus. Bespoke software will be used to detect mutations and analyse evolutionary selection. Cell tracking in transgenic mouse models and live imaging of tissue equivalents in culture will be used to study how mutant and wild type cells interact. Profiling of transcription in mutant cells will reveal candidate genes that underpin mutant cell phenotypes which will be tested by gene editing. The impact of somatic or germline mutation on the development of mutational landscape will be tested in mouse models and analysed by the same methods as used for human oesophagus. Interventions to alter the mutational landscape will be tested in long term cultures of mouse and human oesophagus and validated in vivo. How the results of this research will be used: The results will reveal the processes that shape oesophageal mutational landscape, the impact of somatic mutations on subsequent mutation and cancer risk, how germline mutants alter mutational landscape and identify interventions to deplete oncogenic mutants and reduce cancer risk that are suitable for future translational studies.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;3.3 NUTRITION AND CHEMOPREVENTION
Health categories: CANCER AND NEOPLASMS