Abstract 2290: DNA methylation markers for sensitive detection of circulating tumor DNA in plasma from patients with gastroesophageal adenocarcinomas
Authors: Iden Cecilie Riis , Øgaard Nadia , Jensen Sarah Østrup , Mustafa Salah Mohammad , Ahlborn Lise Barlebo , Hasselby Jane Preuss , Rohrberg Kristoffer Staal , Achiam Michael Patrick , Andersen Claus Lindbjerg , Mau-Sørensen Morten 
Published: June 2023

Abstract
Background: We have previously shown that detection of methylated ctDNA in the three genes c9orf50, KCNQ5, and CLIP4 is a highly sensitive method (named the TriMeth assay) to discriminate patients with colorectal cancer from healthy individuals (1). The publicly available Infinium HumanMethylation450K BreadChip DNA methylation array indicates that these three markers are also highly methylated in gastric and esophageal cancer. In this study, we investigate the ability of the TriMeth assay to detect ctDNA in patients with gastric and gastroesophageal junction (GEJ) adenocarcinomas.
Methods: Purified DNA was extracted from tumor tissue and plasma from 63 patients with gastric/GEJ adenocarcinomas. Sodium bisulfite conversion was performed to distinguish methylated from unmethylated cytosines. Droplet digital PCR (ddPCR) with methylation-specific primers and probes was performed to detect hypermethylated sites in the three genes c9orf50, KCNQ5, and CLIP4. The TriMeth assay was considered positive if at least two out of three markers were methylated according to a predefined cut-off. Eleven plasma samples from healthy individuals were used as negative controls.Results: In tumor tissue, methylated copies were detected in all 29 surgical samples (100% sensitivity), with varying allele frequencies. In plasma, methylated copies were detected in 14 out of 18 samples (78% sensitivity) from patients with advanced disease, with varying sensitivity amongst the three markers (AUC for the three markers CLIP4, C9orf50, and KCNQ5 was 0.61, 0.86, and 0.94, respectively). In plasma from patients with resectable disease, methylated copies were detected in 10 of 17 samples (59% sensitivity), although only 7/17 (41% sensitivity) were positive according to the predefined cut-off. All 11 controls were negative for methylation signals (100% specificity).
Conclusion and Further Perspectives: Using a pre-defined cut-off value, the TriMeth assay detected methylated DNA in all tumor samples. The sensitivity of the TriMeth assay in plasma was 78% in advanced disease and 41% in resectable disease. Further investigations of the TriMeth assay in patients with resectable gastric and GEJ adenocarcinomas are needed. We plan to validate the sensitivity of the TriMeth assay for treatment monitoring and detection of residual disease.
References: 1. Jensen, S.Ø., et al. Novel DNA methylation biomarkers show high sensitivity and specificity for blood-based detection of colorectal cancer—a clinical biomarker discovery and validation study. Clin Epigenet 11, 158 (2019). https://doi.org/10.1186/s13148-019-0757-3
Citation Format: Cecilie Riis Iden, Nadia Øgaard, Sarah Østrup Jensen, Salah Mohammad Mustafa, Lise Barlebo Ahlborn, Jane Preuss Hasselby, Kristoffer Staal Rohrberg, Michael Patrick Achiam, Claus Lindbjerg Andersen, Morten Mau-Sørensen. DNA methylation markers for sensitive detection of circulating tumor DNA in plasma from patients with gastroesophageal adenocarcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2290.