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Stomach Cancer CNVs Point to Similar Overall Disease in Eastern, Western Populations

NEW YORK (GenomeWeb) – A new study suggests that somatic structural variants largely overlap between stomach cancers in Asia and the West, arguing against the notion that the disease differs significantly by location or population.

Researchers from the US, Italy, and Korea considered array-based copy number profiles in gastric adenocarcinoma tumors from more than 600 cases in several Asian and Western countries. Despite differences in stomach cancer prevalence, presentation, and outcomes in Eastern and Western countries, they saw recurrent copy number changes such as MYB amplification and SMARCA4 deletions across the gastric cancer cases.

The team did see a slight uptick in focal deletions in gastric adenocarcinomas from individuals in Western countries — particularly a focal deletion affecting a PTPRD gene coding for a phosphatase enzyme. But such changes were not unique to any one population, the group reported yesterday in PLOS One, and instead fell along the spectrum of molecular subtypes established for stomach cancer through efforts such as The Cancer Genome Atlas.

"[O]ur data support the supposition that Eastern and Western gastric cancers are not fundamentally distinct diseases and are consistent with emerging thinking that rather than geography or ethnicity, it is the molecular subtypes of this disease that are the primary categories we should evaluate to subdivide these tumors," Dana-Farber Cancer Institute researchers and co-corresponding authors Rameen Beroukhim, Adam Bass, and Ramesh Shivdasani, and their colleagues wrote.

The researchers profiled somatic copy number alterations ranging in size from focal changes to alterations affecting chromosome arms, using new and existing Affymetrix microarray data on gastric adenocarcinoma tumor samples from 323 individuals from Korea, Singapore, Vietnam, and other Asian countries and 334 individuals from Western countries such as Italy, Russia, and Ukraine.

Across the tumors, their analysis uncovered recurrent gains or losses involving stretches of several different chromosomes, along with dozens of focal amplifications or deletions, including focal copy number changes affecting noted oncogenes, tumor suppressor genes, and/or genes already implicated in gastric cancer.

When the team compared copy number patterns in tumors from individuals in the Eastern and Western populations, it saw somewhat more pronounced somatic changes and an uptick in chromosomal instability in cases from the West. And one change, the PTPRD deletion, was significantly more common in the West, where it turned up in more than one-quarter of the gastric adenocarcinoma tumors.

The researchers suspected some of the copy number differences in the East and West could be chalked up to a slightly higher proportion of tumors with chromosome instability in the West or to differences in the purity and tumor content of samples taken at different sites, though they noted that other factors — such as differences in Helicobacter pylori infection rates between sites — might also come into play.

But while there appeared to be potential differences in subtype representation in the East and West, the authors did not see evidence for population-specific forms of gastric adenocarcinoma based on copy number profiles in the cases considered.

"As we further explore the biology and therapeutics for these cancers in different patient populations, it will be essential to take … molecular subtypes into account to avoid comparisons that are confounded because of distinct distributions of cancer subtypes across different populations of patients," the authors concluded.