Project 3: Application of the Microbiome and Microenvironment to Novel Non Endoscopic Screening and Surveillance in Barrett's Esophagus

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PROJECT 3 SUMMARY The incidence of esophageal adenocarcinoma (EAC) has risen nearly ten-fold over the past several decades, and the prognosis for EAC remains poor. During this time period, the GI microbiome has undergone a significant shift with the advent of antibiotics and the progressive decline in Helicobacter pylori infection rates, and there is increasing evidence that bacteria play an important role in GI cancers. However, the contribution of the esophageal microbiome to Barrett’s esophagus (BE) and EAC is not understood, and likely involves a complex relationship with the epithelium, microenvironment and gastro-esophageal reflux. Filling this gap in knowledge is critical to the development of rational cancer prevention strategies; the current paradigm, which relies on clinical suspicion to identify patients for endoscopy to screen for BE, has been unsuccessful and misses most patients who go on to develop EAC. The esophageal microbiome in BE is heavily populated with Gram-negative bacteria, which may drive a chronic inflammatory state. We have found high abundance of Fusobacterium nucleatum in EAC, and previous work by our team showed that F. nucleatum has proneoplastic effects in the colon. Further, in preliminary data we found that BE patients have alterations in specific taxa in the oral microbiome, a potential biomarker for BE. In Project 3 we propose to build directly on Projects 1 and 2 to elucidate the relationship between the microbiome, inflammation, and the microenvironment in BE and EAC, with the end goal of developing a non-endoscopic testing strategy based on pathogenic factors to identify patients at highest risk for EAC. To accomplish this we will enroll 100 patients with known BE (50 with dysplasia or EAC) and 50 subjects without BE undergoing upper endoscopy. Prior to endoscopy each subject will undergo three minimally invasive potential screening and surveillance tests: saliva (oral microbiome), breath test (exhaled volatile organic compounds), and tethered capsule sponge sampling (methylated DNA markers). We will then address the following Specific Aims: 1) To assess the relationship between the microbiome (using 16S rRNA gene sequencing) and tissue inflammation (using RNA-Seq) in Barrett’s progression to EAC. We will also explore the oral microbiome and exhaled volatile organic compounds as potential biomarkers. 2) To determine how bile acid composition impacts the microbiome and tissue inflammation in BE. We will also assess the relationship between these factors and methylated DNA markers. 3) To develop a non-endoscopic, biologically-based screening and surveillance strategy for BE. We will evaluate these novel tests in combination with clinical and anthropometric factors to describe an optimal strategy for BE screening and monitoring. We hope that this will lead to development of a testing approach that is highly acceptable to patients, is cost-effective, and can be easily translated to the non-specialist setting. Furthermore, we anticipate that our findings will also lead to novel avenues for EAC chemoprevention.