| dc.description.abstract | Barrett’s oesophagus (BO), a metaplasia affecting the distal oesophagus, is the only known precursor for oesophageal adenocarcinoma (OAC) which, despite advances in healthcare, continues to carry a dire prognosis. The emergence of BO has been shown to have polyclonal origins forming a mosaic of distinct geno-phenotypic clones across the space. However, the precise transformative cellular population, rate of clonal expansion and subsequent neighbouring clonal dynamics that promote a benign or malignant course remain unknown. Recent work has demonstrated the ability to use the sequence of epigenetic methylation marks, which are somatically inherited at mitosis, as a marker of clonal ancestry, mutational ordering in progression and to determine mitotic age in colorectal adenomas and cancer. Characterisation of the dynamics that underpin stem cell behaviour, which ultimately are the precursor cells for the cancer phenotype, can also be inferred by mapping methylation patterns at high resolution across epithelium. These techniques are transferrable to BO, another epithelial, glandular and clonal disease, and form the primary modus operandi of this thesis. This thesis adds to the debate regarding whether there is a particular dwell time to cancer; whether there is a mitotic age that predicts it; where and how the BO lesion expands at inception and varies over its natural history; the turnover of glandular phenotypes and whether they follow a linear or direct evolution to cancer; and how molecular diversity can be a proxy marker for cancer risk. I have designed a novel targeted allele specific methylation sequencing (ASM-Seq) array that utilises modern next generation sequencing technology to significantly enhance resolution and coverage over previous studies. Furthermore, my protocol is the first of its type in a cytosine deaminated DNA template that incorporates unique molecular identifiers (UMIs) in efforts to reduce confounders in sequencing data. Targeted ASM-Seq has the potential to reveal the intricate tissue dynamics not just of BO but any disease characterised by a clonal organisation and ancestry. Ultimately, this understanding will assist in better targeting of surveillance, clinical resources and therapies to patients deemed at risk of OAC. | en_US |
