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.

巴雷特食管 (BE) 是食管腺癌 (EAC) 的唯一已知前兆，食管腺癌是一种高度致命的癌症。发病率上升且中位生存期<1 年的癌症已投入大量医疗资源。胃食管反流引起的下食管损伤和治疗。慢性炎症是 BE 发展的关键驱动因素，但潜在风险的分子途径尚不清楚最近由我们团队成员领导的全基因组关联研究 (GWAS) 发现了超过 20 项新发现。 BE/EAC 的遗传易感性位点，为风险的遗传成分提供了新的见解。然而，与其他 GWAS 一致，在桥接生物学方面取得的进展很少。复杂疾病，所有BE指数变异都映射到非编码区，缺乏明显的生物学功能，并且处于与许多其他 SNP 的连锁不平衡，其中任何一个都可能是因果性的。据信，潜在的 GWAS 信号可以映射并改变调节元件的活动，包括增强子以等位基因特异性的方式，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。用于实验审讯的功能变体，我们开发了定制的信息学评分管道使用来自多个公共资源的综合计算机注释，我们选择了四个高分 BE。使用荧光素酶报告基因检测对食管细胞系进行评估的风险位点，发现四个中的两个两个区域都表现出等位基因特异性增强子活性。受这些成功的启发，我们寻求与几个候选风险基因的下调相关的位点。扩展我们的综合框架来阐明 BE 相关遗传变异的功能后果。认为这种变异是通过转录调控的改变在生物学上表达的我们的目标是识别功能变异、风险增强子和靶基因。潜在的 BE 风险，利用独特的资源和互补的统计/实验方法。目标 1，我们将使用世界上最大的 BE GWAS 通过贝叶斯精细映射来定义候选因果变体 - 广泛，并通过功能潜力分数进一步优先考虑领先候选人。在目标 2 中，我们将执行新的任务。对暴露于反流的胃食管连接组织和组成细胞进行转录组分析，并鉴定在目标 3 中，我们将通过 eQTL 共定位和基于网络的分析来确定候选 BE 风险基因和途径。使用荧光素酶报告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 影响风险增强子并询问途径；通过 CRISPR 介导的基因敲低/过度表达和 RNA- 确定目标 2 和 3 中的优先目标基因这项研究将把非编码 GWAS 信号推进为功能性生物特征并支持未来努力为 BE/EAC 制定新的预防/干预策略。