Assessing Circulating Cell-free Tumour DNA as a Potential Biomarker for Early Detection and Chemoprevention of Colorectal Cancer

Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths in the UK, and patient mortality is strongly correlated to the cancer stage at diagnosis. Circulating cell-free DNA (cfDNA) are short DNA fragments released into the blood from dying cells, and the use of cfDNA as a predictive and diagnostic biomarker for CRC patients has gained traction recently. The work undertaken in the thesis aimed to assess whether cfDNA could be a suitable biomarker for detection and monitoring of early colorectal lesions in preclinical and clinical settings. Custom qPCR and ddPCR assays were designed and implemented for quantitative cfDNA analysis and for detection of tumour-derived mutations in plasma samples. Preclinical studies investigating the cfDNA dynamics during early tumourigenesis were conducted with the Lgr5-EGFP-IRES-creERT2+/0;Apcfl/fl mouse model of CRC. In parallel, plasma cfDNA was also assessed in an adenoma patient cohort (n=76) against a ‘polyp-free’ control group (n=37). Analysis of mice failed to show a correlation between total cfDNA levels and the adenoma development in three separate preclinical studies, whereas detection of a surrogate tumour-derived mutation in animal plasma samples showed sensitivities between 16 and 25%. Similarly, total plasma cfDNA concentrations between the adenoma patient and control group showed no significant difference (p=0.1012). Targeted detection of BRAF and KRAS mutations in the plasma was achievable, but hampered by low sensitivities (0-25%). Multi-regional targeted next-generation sequencing (NGS) was performed on selected patient cases. The data unmasked extensively and previously unappreciated intra-tumour heterogeneity in colorectal adenomas. Nonetheless, identification and plasma targeting of tumour truncal mutations did not improve the detection rate. In conclusion, these results suggested that further methodological optimisation is necessary to achieve improved diagnostic sensitivity with plasma cfDNA liquid biopsy for the early detection of colorectal lesions.