Discovery and Validation of Plasma DNA Methylation Biomarker for Detection of Stomach Cancer

Despite markedly declining incidence in recent decades, almost one million new cases of stomach cancer were estimated to have occurred in 2012, making it the fifth most common malignancy in the world after lung, breast, colorectal, and prostate cancer. More than 70% of cases (677,000 cases) occur in developing countries, and half occur in Eastern Asia (mainly in China). Although North America is considered to be a low-risk region, 22,000 cases are diagnosed in the US each year. Five-year survival for 2005-2011 in the US was less than 30%, since stomach cancer is generally asymptomatic in early stages and has often metastasized by the time of diagnosis. In contrast, 5-year survival rates are almost 70% in South Korea and Japan where mass screening programs have been implemented and a large proportion of stomach cancer is detected in early stages. UGI endoscopy has been considered as the gold standard for diagnosis of stomach cancer but endoscopy-based mass screening may not be feasible in relatively low-risk or less developed regions. Therefore, identification of biomarkers for early stage disease is crucial to in the development of effective screening strategies. With the recent advances in cancer genetics and assay technologies, this is an opportune time to discover minimally invasive, specific, and cost-effective biomarkers.

A surprising discovery from the large scale cancer genome projects such as TCGA was the enormous variation in mutational patterns both across and within individual tumor types. Even the most commonly mutated genes were typically altered in less than half of cases of a given cancer. The two most frequently mutated driver genes in stomach cancer, TP53 (tumor protein p53) and ARID1A (AT rich interactive domain 1A), were mutated in only 44% and 17% of cases, respectively. Mutation rates for the remaining stomach cancer driver genes were even lower. Importantly, mutations of these genes are often spread across several exons which complicates detection of DNA-based sequence variation, since large numbers of samples and extensive genotyping will be required to achieve adequate sensitivity and power. In contrast, DNA methylation, which is a chemical modification of CpG dinucleotides that does not alter base pair sequence, generates a more robust signal as compared to genetic alterations. For example, methylation in the Stratifin promoter was found in 96% (24/25) of breast carcinomas, 83% (15/18) of ductal carcinoma in situ, and 38% (3/8) of benign atypical hyperplasias, but was absent in breast tissues from healthy individuals, which suggests that methylation status of this locus is an early event of breast cancer that could serve as a breast cancer biomarker. Aberrant DNA methylation occurs in an early phase of carcinogenesis and contributes to development and progression. Notably, a comprehensive molecular characterization of 295 primary stomach cancers in TCGA classified the tumors into four molecular subtypes. All four types exhibited DNA hypermethylation to various degrees, with one type more heavily methylated than any other tumor group previously analyzed in TCGA. Moreover, other studies have also suggested that aberrant methylation may be associated with various pre-malignant conditions like Helicobacter pylori infection, severe gastritis, intestinal metaplasia, and dysplasia, implying a role for an epigenetic field effect which may reflect the earliest steps in neoplastic transformation of the stomach. Importantly, hypermethylation can be detected in circulating cell-free DNA (cfDNA) which is thought to be derived from preneoplastic or tumor tissues. Efforts to discover blood-based DNA methylation markers are underway in various types of cancers. In particular, plasma methylated SEPT9 DNA has been evaluated for detection of colorectal cancer, and a commercialblood test for this is under review for approval by the US Food and Drug Administration.