Mutating genes to detect cancer

By identifying the sequence in which genetic mutations that drive oesophageal cancer development occur, the large team from the International Cancer Genome Consortium have identified two genes that could be used to distinguish between the precancerous stages and the final cancerous stage.

More common in men, oesophageal cancer is one of the most common cancers in the world and can be triggered by many factors, including acid reflux, obesity and smoking. The current method of detection for oesophageal cancer is an endoscopic test, which is often not effective at detecting cancer.

The discovery phase of the research project involved whole-genome sequencing of 22 tumours removed from patients with oesophageal adenocarcinoma. This was followed by targeted amplicon sequencing on a further 90 samples from patients with oesophageal adenocarcinoma and on 109 biopsies from 79 people with two key transition points on the way to developing malignant oesophageal adenocarcinoma – 66 biopsies from people with benign metaplastic never-dysplastic Barrett’s oesophagus and 43 biopsies from people with high-grade dysplasia.

This comparison of genetic mutations in oesophageal cancer with mutations in samples from earlier stages of the disease uncovered that some mutations in a gene called TP53 were present in patients with early signs of cancer but not in patients with an earlier premalignant precursor of oesophageal cancer called Barrett’s oesophagus.

Another gene, SMAD4, only mutated in the cancerous samples (oesophageal adenocarcinoma).

Next, the team used a technique called Multiplex PCR Assay to examine mutations of the TP53 gene in a further 89 people, including 23 controls (samples with no Barrett’s oesophagus), 44 samples with never-dysplastic Barrett’s oesophagus and 22 samples with high-grade dysplasia.

These samples to examine the TP53 gene were gathered using a new non-endoscopic relatively non-invasive device called the Cytosponge, which gathered oesophageal cells from the mucous lining the oesophagus.

In summarising their results, the researchers wrote that Barrett’s oesophagus is the only known precursor lesion of oesophageal adenocarcinoma, occurring in more than 80% of cases. However, the majority of individuals with Barrett’s oesophagus will never progress to invasive disease. “There is therefore a need for sensitive and specific biomarkers that can identify those who are at risk of progression.”

“Unexpectedly, the majority of recurrently mutated genes in EAC [oesophageal adenocarcinoma] were also mutated in NDBE [never-dysplastic Barrett’s oesophagus]. Only TP53 and SMAD4 mutations occurred in a stage-specific manner, confined to HGD [high-grade dysplasia] and EAC, respectively. Finally, we applied this knowledge to identify high-risk Barrett’s oesophagus in a new non-endoscopic test. In conclusion, mutations in EAC driver genes generally occur exceptionally early in disease development with profound implications for diagnostic and therapeutic strategies.”

“The Cytosponge provides a representative sample of the entire oesophageal mucosa and, coupled with high-throughput sequencing, is capable of sensitive and objective detection of HGD. This approach could be readily adapted as understanding of the genetic basis for this disease evolves. Furthermore, our systematic molecular approach to identify key mutations involved in the steps distinguishing preinvasive from invasive disease has applicability to other epithelial cancers amenable to early detection,” the researchers concluded.

The research was published in the August 2014 edition of Nature Genetics.