DNA methylation in late-stage oesophageal cancer

Thesis

Oesophageal adenocarcinoma (OAC) is a cancer with unmet needs, signified by late diagnosis, poor prognosis, and ineffective screening. Recently, phase III randomized trials showed that first line combined immune checkpoint inhibitors (ICI) and chemotherapy (CTX) is superior to CTX alone in selected patients. However, patient selection is based on histologic criteria that could vary substantially between paraffin sections. Also, there is a lack of good tools for ICI treatment monitoring.

It has been reported that changes in DNA methylation are common and early events in the development of OAC. DNA methylation can also be peripherally detected in circulating cell-free DNA (cfDNA), which showed promises in early detection of cancer and disease monitoring. Therefore, I investigated whether DNA methylation is associated with prognosis in OAC after ICI+CTX, and whether tumour-specific signals can be detected in cfDNA methylation.

The LUD2015-005 study is a phase I/II trial to assess the safety and efficacy of combined ICI+CTX in OAC. Samples from 23 patients with at least 12 months of follow-up belonging to the inoperable cohort were used for whole genome sequencing (WGS), bulk RNA sequencing, and whole genome single-base resolution methylation using TET-assisted pyridine borane sequencing (TAPS).

A new statistical framework was proposed to conduct tumour purity and copy number aware analysis of the tumour DNA methylation. Global hypomethylation in late replicating regions was identified to a specific feature for all OAC and possibly Barrett's oesophagus, the pre-malignant lesion of OAC. Importantly, the tumour-specific methylation can be detected in cfDNA down to around 0.2\% tumour fraction, and changes in cfDNA tumour signal after 4 weeks of ICI can predict progression-free survival up to 1 year.

In addition, two OAC methylation subtypes were discovered, which were characterized by genomic instability and severe global hypomethylation, versus less severe global hypomethylation but more aggressive molecular phenotype. The clinical implication of these subtypes is currently unclear due to small sample size.

Finally, this thesis highlighted a possible mechanism of focal hypermethylation in cancer by linking together the crosstalk between replication timing, histone modification, and DNA methylation, which is yet to be tested with further experiments.

Authors: Xie, P

• DOI: 10.5287/ora-j25xm17nb
• Type of award: DPhil
• Level of award: Doctoral
• Awarding institution: University of Oxford
• Language: English
• Keywords: oesophageal adenocarcinoma; immunotherapy; cfDNA; DNA methylation
• Subjects: Cancer; Genomics; Epigenetics