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

项目3概要 食管腺癌（EAC）的发病率在过去几十年中上升了近10倍， EAC的预后仍然很差。在此期间，胃肠道微生物组经历了一个 随着抗生素的出现和幽门螺杆菌感染率的逐步下降， 越来越多的证据表明细菌在胃肠道癌症中起着重要作用。然而，贡献 食管微生物组与巴雷特食管（BE）和EAC的关系尚不清楚，可能涉及 与上皮、微环境和胃食管反流的复杂关系。填补这一空白， 知识对于制定合理的癌症预防策略至关重要;目前的模式， 依靠临床怀疑来识别患者进行内窥镜检查以筛查BE，一直不成功， 错过了大多数发展为EAC的患者。BE患者的食管微生物组中大量存在 革兰氏阴性菌，可能导致慢性炎症状态。我们发现了大量的 本课题组前期的工作表明，具核梭杆菌在EAC中的表达量明显高于具核梭杆菌。具核质具有原核性 结肠的影响。此外，在初步数据中，我们发现BE患者在特定分类群中有改变， 口腔微生物组，BE的潜在生物标志物。在项目3中，我们建议直接在项目1和项目2的基础上进行建设 为了阐明BE和EAC中微生物组、炎症和微环境之间的关系， 最终目标是开发一种基于致病因素的非内窥镜检测策略， EAC风险最高的患者。为了实现这一目标，我们将招募100名已知BE的患者（50名 不典型增生或EAC）和50名无BE的受试者接受上消化道内窥镜检查。内镜检查前，每例受试者 将接受三种微创潜在筛查和监测测试：唾液（口腔微生物组）， 呼气试验（呼出的挥发性有机化合物）和栓系胶囊海绵采样（甲基化DNA 标记）。然后，我们将讨论以下具体目标：1）评估 Barrett's中的微生物组（使用16 S rRNA基因测序）和组织炎症（使用RNA-Seq） 发展到EAC。我们还将探索口腔微生物组和呼出的挥发性有机化合物， 潜在的生物标志物。2)确定胆汁酸组成如何影响微生物组和组织 BE炎症。我们还将评估这些因素与甲基化DNA标记物之间的关系。 3)为BE制定一种非内镜、基于生物学的筛查和监测策略。我们将 结合临床和人体测量因素评估这些新的测试，以描述一种最佳的 BE筛查和监测策略。我们希望这将导致开发一种测试方法， 患者高度可接受，具有成本效益，并且可以容易地转化为非专业设置。 此外，我们预计我们的研究结果也将导致EAC化学预防的新途径。

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.