Detection of Gastric Cancer with Novel Methylated DNA Markers: Discovery, Tissue Validation, and Pilot Testing in Plasma

Abstract

Gastric adenocarcinoma is the third most common cause of cancer mortality worldwide. Accurate and affordable noninvasive detection methods have potential value for screening and surveillance. Herein, we identify novel methylated DNA markers (MDM) for gastric adenocarcinoma, validate their discrimination for gastric adenocarcinoma in tissues from geographically separate cohorts, explore marker acquisition through the oncogenic cascade, and describe distributions of candidate MDMs in plasma from gastric adenocarcinoma cases and normal controls. Following discovery by unbiased whole-methylome sequencing, candidate MDMs were validated by blinded methylation-specific PCR in archival case-control tissues from U.S. and South Korean patients. Top MDMs were then assayed by an analytically sensitive method (quantitative real-time allele-specific target and signal amplification) in a blinded pilot study on archival plasma from gastric adenocarcinoma cases and normal controls. Whole-methylome discovery yielded novel and highly discriminant candidate MDMs. In tissue, a panel of candidate MDMs detected gastric adenocarcinoma in 92% to 100% of U.S. and South Korean cohorts at 100% specificity. Levels of most MDMs increased progressively from normal mucosa through metaplasia, adenoma, and gastric adenocarcinoma with variation in points of greatest marker acquisition. In plasma, a 3-marker panel ( detected 86% (95% CI, 71-95) of gastric adenocarcinomas at 95% specificity. Novel MDMs appear to accurately discriminate gastric adenocarcinoma from normal controls in both tissue and plasma. The point of aberrant methylation during oncogenesis varies by MDM, which may have relevance to marker selection in clinical applications. Further exploration of these MDMs for gastric adenocarcinoma screening and surveillance is warranted. .

A four-DNA methylation signature as a novel prognostic biomarker for survival of patients with gastric cancer

“…Aging, diet, obesity, H. pylori and Epstein Barr virus infection are all associated with gene methylation in GC [15]. Studies confirmed the involvement of DNA methylation in the transformation of the normal gastric mucosa to GC [16]. The tumor-related genes are hypermethylated in precancerous lesions and intestinal metaplasia [17,18], and inhibiting DNA methylation reduces the incidence of GC in animal models [19,20], DNA methylation could be used as a biomarker for diagnosis, treatment and prognosis of GC [15,21].…”

A DNA Methylation-based Test for Esophageal Cancer Detection

“…Interestingly, we showed that ZNF569me levels could discriminate between ECa and normal esophagus with high speci city, regardless of the histotype, con rming and extending those previous reports. Furthermore, ZNF569me was shown to play a tumor suppressive role in head and neck squamous cell carcinoma (29) and a DNA-methylation based panel, which included ZNF569, discriminated gastric adenocarcinoma from normal mucosa (30).…”

A DNA Methylation-based Test for Esophageal Cancer Detection

“…Interestingly, we showed that ZNF569me levels could discriminate between ECa and normal esophagus with high speci city, regardless of the histotype, extending those previous reports. Furthermore, ZNF569me was shown to play a tumor-suppressive role in head and neck squamous cell carcinoma (36) and a DNA-methylation based panel, which included ZNF569me, discriminated gastric adenocarcinoma from normal mucosa (37).…”