The genomic and phenotypic characterisation of inflammation, injury and repair in the oesophagus

Background Recent advances in whole genome sequencing have shown that somatic mutagenesis is not unique to cancer.

Non-cancerous diseases of the oesophagus are rising in incidence with a significant effect on life expectancy and quality of life.

Repeated cycles of inflammation, injury and repair are thought to contribute to their pathogenesis and associated cancer risk, yet the process of how cells in the oesophagus respond to injury and renew remain poorly understood.

Unravelling this will advance our understanding of how tissue regenerates appropriately and how this process goes astray and contributes to the earliest steps of carcinogenesis.

Aims We aim to determine the effect on the human genome and transcriptome in the oesophagus, in the context of inflammation, injury and repair.

This will be in the context of diseased non-cancerous conditions and epithelial loss and regeneration in patients with oesophageal perforation.

We aim to delineate the somatic mutagenesis and associated effects on the transcriptome in injured and regenerated tissue, and compare this to normal epithelium and cancer development. Methods This pilot study will be divided in two groups.

Cohort 1: Diseased non-cancerous conditions (n=5) including esophagitis and achalasia; Cohort 2: Epithelial loss undergoing regenerative therapy (n=5) in cases of oesophageal perforation.

Samples will be collected using endoscopy and at surgery for Cohort 1 and a combination of endoscopy and vacuum sponge therapy for Cohort 2.

The latter involves an endoluminal vacuum sponge inserted into a hole in the cavity, connected to negative pressure and changed every three days until the cavity regenerates (median time of 21 days).

Live cell suspensions (from the enoluminal vacuum sponge), and snap frozen samples will be collected at several time-points and undergo whole genome sequencing using high resolution techniques developed at the WTSI (including Laser Capture Microscopy) and single cell RNA sequencing.

Data analysis will include mutational signatures, somatic variant and copy number calling (DNA) and gene expression analysis (RNA).

How the results of the research will be used We anticipate that this experiment will provide preliminary results for use in a larger study, for which further funding will be applied.

The changes that characterize the genome and transcriptome in the injured and regenerated oesophagus will advance our knowledge of this process, and its association with the earliest steps of carcinogenesis.

In the longer term, understanding how the oesophagus regenerates will also provide valuable information for clinical tissue engineering applications associated with cancer therapies.