Genetic susceptibility to Barrett's esophagus: From GWAS to biology

巴雷特食管的遗传易感性：从 GWAS 到生物学

基本信息

批准号：
10674348
负责人：
Matthew Frank Buas
金额：
$ 80.18万
依托单位：
SLOAN-KETTERING INST CAN RESEARCH
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-12-21 至 2025-11-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10674348
关键词：
19p13 8p23.1 Address Affect Alleles Barrett Esophagus Bayesian Method Biological Biological Assay Biological Process Biology Biopsy Candidate Disease Gene Cell Line Cells Chromatin Chronic Chronic Disease Clustered Regularly Interspaced Short Palindromic Repeats Complex Conserved Sequence DNA Binding Data Development Disease Down-Regulation Enhancers Epidemiology Esophageal Adenocarcinoma Esophagogastric Junction Esophagus Evaluation Exhibits Future Gastroesophageal reflux disease Gene Expression Gene Targeting Genes Genetic Genetic Determinism Genetic Predisposition to Disease Genetic Variation Genotype Genotype-Tissue Expression Project Goals Healthcare Incidence Inflammation Informatics Inherited Injury Intervention Lesion Link Luciferases Malignant Neoplasms Maps Mediating Mediator Methods Molecular Mucous Membrane Network-based Pathogenesis Pathway Analysis Pathway interactions Patients Phase Predisposition Prevention Prevention strategy Preventive Probability Promoter Regions Public Health Reflux Regulatory Element Reporter Research Resources Risk Scheme Signal Transduction Susceptibility Gene System Testing The Cancer Genome Atlas Tissues Transcriptional Regulation Translating Untranslated RNA Variant Weight Work analytical tool biological specimen archives candidate identification candidate validation causal variant cell type genome wide association study genome-wide in silico indexing insight knock-down member mortality novel novel strategies overexpression premalignant prevent public health relevance risk variant screening single-cell RNA sequencing statistics success trait transcriptome sequencing transcriptomic profiling virtual

项目摘要

Barrett’s esophagus (BE) is the only known precursor for esophageal adenocarcinoma (EAC), a highly lethal cancer with rising incidence and median survival <1 year. Substantial health-care resources are devoted to BE screening, surveillance, and treatment. Gastroesophageal reflux-induced injury of the lower esophagus and chronic inflammation are key drivers of BE development, but molecular pathways underlying risk are not well defined. Recent genome-wide association studies (GWAS) led by members of our team identified >20 novel genetic susceptibility loci for BE/EAC, providing new insights into the inherited genetic component of risk. Nevertheless, little progress has been made in bridging associations to biology. Consistent with GWAS of other complex diseases, all BE index variants map to non-coding regions, lack obvious biologic function, and are in linkage disequlibrium with many other SNPs, any of which may be causal. The vast majority of functional variants underlying GWAS signals are believed to map to and alter activity of regulatory elements including enhancers, in an allele-specific manner, and in turn modulate expression of downstream genes involved in risk. Importantly, such regulatory effects may be tissue- and condition-specific. To begin prioritizing candidate functional variants for experimental interrogation, we developed a customized informatics scoring pipeline using comprehensive in-silico annotations from multiple public resources. We selected four high-scoring BE risk loci for evaluation using luciferase reporter assays in esophageal cell lines, and found that two of four regions exhibited allele-specific enhancer activity. CRISPR-mediated deletion of the enhancer region at both loci correlated with downregulation of several candidate risk genes. Motivated by these successes, we seek to expand our integrative framework for elucidating functional consequences of BE-related genetic variation. We hypothesize that such variation is biologically expressed through alterations in transcriptional regulation and downstream gene expression. Our goal is to identify functional variants, risk enhancers, and target genes underlying BE risk, leveraging unique resources and complementary statistical/experimental approaches. In Aim 1, we will define candidate causal variants via Bayesian fine-mapping, using the largest BE GWAS world- wide, and further prioritize leading candidates via functional-potential scores. In Aim 2, we will perform new transcriptome profiling of reflux-exposed gastroesophageal junction tissues and constituent cells, and identify candidate BE risk genes and pathways via eQTL colocalization and network-based analysis. In Aim 3, we will validate candidate functional variants using luciferase reporter enhancer activity assays; identify target genes of risk enhancers via CRISPR-mediated enhancer deletion and RNA-Seq; and interrogate pathways influenced by prioritized target genes in Aims 2 & 3 via CRISPR-mediated gene knockdown/overexpression and RNA- Seq. This study will advance noncoding GWAS signals into functional biological signatures and support future efforts to develop novel preventive/interventional strategies for BE/EAC.

Barrett的食道（BE）是唯一已知的食管腺癌（EAC）的先驱，这是一种高度致命的癌症的事件增加，中位生存率<1年。大量的医疗保健资源专门用于筛查，监视和治疗。胃管道反射诱导的下食道损伤和慢性炎症是发展的关键驱动因素，但是依赖风险的分子途径不好定义。我们团队成员领导的最新全基因组协会研究（GWAS）确定了> 20个小说 BE/EAC的遗传敏感性局部，为风险的遗传遗传成分提供了新的见解。然而，在与生物学的桥接关联方面取得了很少的进步。与其他GWA一致复杂疾病，都是指数变体映射到非编码区域，缺乏明显的生物学功能，并且在与许多其他SNP的连锁分解，其中任何一个可能是因果关系。绝大多数功能据信GWAS信号下的变体映射到并改变了调节元素的活动，包括增强子以特定于等位基因的方式，进而调节涉及风险的下游基因的表达。重要的是，这种调节作用可能是组织和条件特异性的。开始优先考虑候选人实验询问的功能变体，我们开发了一个定制的信息评分管道使用来自多个公共资源的综合内部注释。我们选择了四个高分使用荧光素酶记者在食管细胞系中使用荧光素酶报告基因测定的风险位置，发现四个区域暴露了等位基因特异性增强子活性。 CRISPR介导的增强剂区域的删除基因座与几个候选风险基因的下调相关。受这些成功的动机，我们试图扩展我们的综合框架，以阐明与BE相关遗传变异的功能后果。我们假设这种变异是通过转录调控和下游基因表达。我们的目标是识别功能变体，风险增强子和靶基因潜在的风险，利用独特的资源和完整的统计/实验方法。在 AIM 1，我们将使用最大的是GWAS世界来定义候选因果变体 - 通过功能潜在的得分宽，并进一步优先考虑领先的候选人。在AIM 2中，我们将执行新反射管道结构组织的转录组分析并构成细胞，并鉴定通过EQTL共定位和基于网络的分析，候选者是风险基因和途径。在AIM 3中，我们将使用荧光素酶报告基因增强子活性测定验证候选功能变体；识别靶基因通过CRISPR介导的增强子删除和RNA-seq的风险增强子；并询问受影响的途径通过CRISPR介导的基因敲低/过表达和RNA-通过AIMS 2和3中的优先靶基因 - seq。这项研究将使非编码GWAS信号成为功能性生物学特征，并支持未来为BE/EAC制定新颖的预防/介入策略的努力。