Development of diagnostic and prognostic tests for esophageal adenocarcinoma

抽象的。这项提议的主要目标是开发新的分子方法来早期检测 食管腺癌(EAC)。EAC产生于胃食道反流病(GERD)和 Barrett‘s食道(BE)；GERD引起的化生改变。这一知识推动了内窥镜检查 对GERD和BE患者的筛查和监测建议，但遵从性低， 绝大多数新的EAC病例仍在晚期确诊，此时肿瘤无法手术，预后 非常穷。在过去的6-8年里，我们开发了高度协作、多机构和多部门的 学科团队专注于EAC临床有用生物标记物的开发。这项建议将建立 关于我们以前资助的项目以及我们通过这些项目获得的临床和技术资源 研究，以评价两种不同的早期检测EAC的方法。第一种方法是基于 食道细胞学标本中体细胞突变和DNA拷贝数异常特征的检测 已发表的研究和我们自己正在进行的工作有力地表明，体细胞突变和 主要的染色体重排推动了从BE到EAC的进展。我们认为，这些变化 可以用来识别可以在细胞学样本中检测到的进展的基因组签名 使用有针对性的下一代测序(NGS)测试。对基因组签名的鉴定正在进行中 我们小组通过对EAC和癌前组织样本进行大规模比较测序。评估 这个签名在识别进展方面的有效性，我们目前正在收集~350个食道 细胞学样本使用一种名为EsophaCap™的封装海绵。这种设备还没有商业化。 可用，但已根据与CapNostics LLC的安排提供给我们，目前已批准用于 在美国和加拿大进行的调查测试。这些独特的数据和组织资源将用于特定的 目的1评价食道细胞学样本靶向NGS分析的敏感性和特异性。 发现异型增生和早期EAC。第二种方法也利用了我们的大规模测序数据和 靶向测序分析，但在这种情况下，我们将评估循环中、无细胞的突变检测 从血浆中提取DNA作为EAC的生物标志物。我们目前正在收集所有 吞下EsophaCap™设备，这为测试检测提供了一个极好的组织资源 循环肿瘤DNA(CtDNA)。为了帮助检测ctDNA，我们开发了一种超灵敏的NGS- 一种检测多个基因座突变的方法，灵敏度低至0.05%(1/2000)的突变等位基因 分数。这些资源将用于具体目标2，以评估 CtDNA用于检测I、II期EAC最后，研究表明ctdna检测可能对预后有预测作用。 价值。在特定的目标3中，我们将评估ctDNA在I期和II期EAC患者中的预后价值 希望这对指导这些患者的新辅助治疗有帮助。

Abstract. The primary goal of this proposal is to develop novel molecular approaches for early detection of esophageal adenocarcinoma (EAC). EAC arises in the setting of gastroesophageal reflux disease (GERD) and Barrett's esophagus (BE); a metaplastic change resulting from GERD. This knowledge has driven endoscopic screening and surveillance recommendations for individuals with GERD and BE but compliance is low and the vast majority of new EAC cases are still diagnosed at late stage, when the tumor is inoperable and prognosis is extremely poor. Over the past 6-8 years, we have developed a highly collaborative, multi-institutional and multi- disciplinary team focused on the development of clinically useful biomarkers for EAC. This proposal will build on our previously funded projects and the clinical and technical resources available to us through these studies, in order to evaluate two different approaches to early detection of EAC. The first approach is based on detection of somatic mutation and DNA copy number abnormality signatures in esophageal cytology samples. Published studies and our own ongoing work strongly indicate that accumulation of somatic mutations and major chromosomal rearrangements drive the progression from BE to EAC. We believe that these changes can be leveraged to identify a genomic signature for progression that can be detected in cytology samples using a targeted next-generation sequencing (NGS) test. Identification of the genomic signature is ongoing in our group through large-scale comparative sequencing of EAC and pre-neoplastic tissue samples. To evaluate the effectiveness of this signature in identifying progression, we are currently collecting ~350 esophageal cytology samples using an encapsulated sponge called the EsophaCap™. This device is not yet commercially available, but has been provided to us under arrangement with CapNostics LLC and is currently approved for investigational testing in the USA and Canada. These unique data and tissue resources will be used in Specific Aim 1 to evaluate the sensitivity and specificity of a targeted NGS analysis of esophageal cytology samples to detect dysplasia and early EAC. The second approach also leverages our large-scale sequencing data and targeted sequencing assays, but in this case we will evaluate the detection of mutations in circulating, cell-free DNA isolated from plasma as a biomarker for EAC. We are currently collecting plasma from all patients who swallow the EsophaCap™ device and this provides an excellent tissue resource in which to test detection of circulating tumor DNA (ctDNA). To aid in the detection of ctDNA, we have developed an ultra-sensitive NGS- based assay that can detect mutations at multiple loci with sensitivity as low as 0.05% (1/2000) mutant allele fraction. These resources will be used in Specific Aim 2 in order to evaluate the sensitivity and specificity of ctDNA for detection of stage I and II EAC. Finally, studies indicate that ctDNA detection may have prognostic value. In Specific Aim 3 we will evaluate the prognostic value of ctDNA in stage I and II EAC patients with the hope that this may prove useful for directing neoadjuvant therapy in these patients.