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

• 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
• 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

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.

巴雷特氏食道(BE)是已知的唯一食管腺癌(EAC)的先兆，食管腺癌是一种高度致命的疾病 癌症发病率上升，中位生存期1年。大量的卫生保健资源被投入到 筛查、监测和治疗。胃食道反流性下段食管壁损伤 慢性炎症是BE发生的关键驱动因素，但潜在风险的分子途径并不很好 已定义。最近由我们团队成员领导的全基因组关联研究(GWAS)确定了&gt；20小说 BE/EAC的遗传易感基因座，为风险的遗传遗传成分提供了新的见解。 然而，在将联系与生物学联系起来方面取得的进展甚微。与其他国家的GWA保持一致 复杂的疾病，都是映射到非编码区的索引变体，缺乏明显的生物功能，正在 与许多其他SNP的连锁不平衡，其中任何一个都可能是因果的。绝大多数职能部门 据信，潜在的GWAS信号变体映射并改变了调控元件的活性，包括 增强子以一种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，这种调节效应可能是特定于组织和条件的。开始确定候选人的优先顺序 针对实验性审讯的功能变体，我们开发了一个定制的信息学评分管道 使用来自多个公共资源的全面的电子邮件注释。我们选出了四个高分的BE 在食道细胞系中使用荧光素酶报告分析评估风险基因，并发现四个中的两个 区域显示出等位基因特异性的增强子活性。CRISPR介导的两个增强子区域的缺失 基因座与几个候选风险基因的下调相关。在这些成功的激励下，我们寻求 扩展我们的综合框架，以阐明Be相关基因变异的功能后果。我们 假设这种变异是通过转录调控和转录调控的改变在生物学上表达的 下游基因表达。我们的目标是识别功能变异、风险增强剂和靶向基因 潜在的BE风险，利用独特的资源和互补的统计/实验方法。在……里面 目标1，我们将通过贝叶斯精细映射来定义候选因果变量，使用最大的BE GWAS世界- 广泛，并进一步根据功能潜力得分对领先候选人进行优先排序。在目标2中，我们将表演新的 反流暴露的胃食道交界处组织和组成细胞的转录组图谱，并鉴定 通过eQTL共定位和基于网络的分析，候选为风险基因和途径。在《目标3》中，我们将 使用荧光素酶报告增强子活性分析验证候选功能变异体；确定目标基因 通过CRISPR介导的增强子缺失和RNA-Seq；以及受影响的询问途径对风险增强剂的影响 通过CRISPR介导的基因敲除/过表达和RNA重组，在AIMS 2和AIMS 3中优先选择靶基因 序列号。这项研究将把非编码的Gwas信号推进到功能生物学特征中，并支持未来 努力为BE/EAC制定新的预防/干预策略。