by ecancer reporter Clare Sansom

Oesophageal adenocarcinoma is the most common form of cancer of the oesophagus; like other forms of oesophageal cancer, it is intractable mainly because it is difficult to diagnose in the early stages.

Like many epithelial cancers, this tumour develops gradually from pre-invasive lesions, with genetic changes accumulating at each step.

The pre-invasive precursor to oesophageal adenocarcinoma is a condition known as Barrett’s Oesophagus, which itself arises from exposure to gastric acid and chronic inflammation.

Individuals who have been diagnosed with Barrett’s Oesophagus are about 11 times more likely to develop any oesophageal cancer than the general population, although most people with this condition still never progress to cancer.

Oesophageal cancer is currently diagnosed using endoscopy, which is an invasive procedure that does not always give accurate results.

Barrett’s oesophagus is a tractable system in which to study the genetic evolution of tumours as Barrett’s patients are frequently monitored by sampling the oesophageal mucosa.

A large group of researchers led by Rebecca Fitzgerald of the MRC Cancer Cell Unit, University of Cambridge, UK and incorporating the UK-based OeOesophageal Cancer Clinical and Molecular Stratification (OCCAMS) consortium conducted a study to identify genes mutated in Barrett’s oesophagus that are associated with progression to malignant disease.

Firstly, paired samples of tumour and normal tissue from 22 oesphageal adenocarcinomas were subjected to whole-genome sequencing using the Illumina method.

A total of 1,086 point mutations in coding regions of the genome were confirmed as somatic, and 23 small indels were also confirmed as somatic after re-sequencing using the Sanger method.

Surprisingly, the most frequently observed mutation type was the T:A>G:C transversion.

A set of 26 frequently mutated or otherwise “interesting” genes were selected, and these genes were sequenced in a larger group of 90 tumours using targeted amplicon re-sequencing.

Fifteen genes were discovered to be mutated in four or more tumours from the complete cohort of 116: these included three - MYO18B, SEMA5A and ABCB1 – that had not previously been associated with this tumour type.

If mutations in any of these genes occur at a boundary between two stages in the gradual progression from Barrett’s oesophagus to malignant disease, the genes concerned would be both biomarker candidates and potential targets for drugs for early stage cancer.

The researchers therefore sequenced the complete set of 26 genes in biopsy samples from 79 Barrett’s oesophagus patients undergoing regular surveillance for progression to cancer.

There was no evidence of progression towards cancer in 40 of these individuals: the other 39 had already been diagnosed with high-grade dysplasia (HGD), which is the disease stage immediately preceding malignancy.

Unexpectedly, almost all genes tested were mutated at approximately the same rate in both groups of Barrett’s oesophagus samples and in the tumour samples, indicating that these mutations occurred at an extremely early stage.

Only two genes were mutated at distinctly different frequencies in the three groups: mutations in TP53 occurred disproportionately often in HGD and tumour samples, and mutations in SMAD4 in tumour samples only.

The researchers therefore considered that mutations in TP53 might be used to discriminate between low risk and high risk Barrett’s oesophagus cases, and developed a prototype diagnostic test using this gene as a biomarker.

This test used a non-endoscopic device, the Cytosponge, to collect cell samples covering the whole oesophagus length from Barrett’s oesophagus patients with and without dysplasia and healthy controls.

Amplification and sequencing of TP53 showed mutations in this gene in 19 of 22 cases of HGD but in no other samples, confirming the association between this gene and transition to high grade dysplasia.

Furthermore, the researchers concluded that the identification of many genes that are mutated very early in the progression to oesophageal adenocarcinoma is likely to have profound implications for its diagnosis and treatment.

Reference

Weaver, J.M.J., Ross-Innes, C.S., Shannon, N. and 25 others, and the OCCAMS Consortium (2014). Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nature Genetics, published online ahead of print 22 June 2014.