Endoscopic Collection and Analysis of Gastric Fluid DNA: A Liquid Biopsy Methodology for Tumor Biomarker Discovery

Gastric cancer remains a major global health challenge, and reliable prognostic biomarkers are urgently needed to guide treatment decisions. Here, we present a simple and efficient protocol for a novel liquid biopsy approach based on quantifying gastric fluid DNA (gfDNA) collected during routine esophagogastroduodenoscopy (EGD). We have previously shown that gfDNA carries gastric cancer-derived mutations; moreover, its concentration increases with tumor progression and varies according to cancer prognosis. This empirically observed increase in gfDNA may mechanistically stem from enhanced cellular turnover, tissue disorganization, dysbiosis of the local microbiota, and/or fluctuations in immune cell infiltrates. Surprisingly, however, in patients diagnosed with gastric cancer, elevated gfDNA levels were also associated with improved survival. This paradoxical finding may be reconciled by an increased anti-tumor immune cell response in treatment-responsive gastric cancers, as well as by the contribution of non-tumoral DNA from inflammatory processes within the microenvironment of the stomach. Here, we detail a standardized protocol for gastric fluid collection and processing, designed to support downstream gfDNA quantification among other potential molecular applications. Key features • A novel liquid biopsy approach for discovering potential biomarkers in human gastric cancer. • Translation of simple gfDNA concentration analysis for the diagnosis and prognosis of gastric cancer. • gfDNA cutoff metrics that discriminate between groups and enable tumor prognostic classification. • gfDNA as a source for downstream profiling of genetic mutations and microbiome-related studies.