Functional Genomic Approaches to Dissect COPD GWAS Loci

解析 COPD GWAS 位点的功能基因组方法

• 批准号: 8803806
• 负责人: Edwin K Silverman
• 金额: $ 22.22万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-03-01 至 2016-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8803806
• 关键词: Affect; Affinity; Air; Alleles; Apoptosis; Binding; Biological; Biological Assay; Breathing; Cause of Death; Cell Death; Cell Line; Cells; Chromatin; Chromosomes; Chronic Obstructive Airway Disease; Complex; Disease; Disease susceptibility; Electrophoretic Mobility Shift Assay; Enhancers; Epithelial Cells; Erinaceidae; Formaldehyde; Gene Expression; Gene Expression Regulation; Gene Proteins; Gene Silencing; Genes; Genetic; Genetic Determinism; Genetic Enhancer Element; Genetic Predisposition to Disease; Genomic approach; Health; Human; Injury; Investigation; Lead; Libraries; Luciferases; Measures; Molecular; Molecular Conformation; Pathogenesis; Pathway interactions; Phase; Phenotype; Proteins; Public Health; Reading; Regulation; Regulatory Element; Reporter; Reverse Transcriptase Polymerase Chain Reaction; Risk; Role; Small Interfering RNA; Smoke; Smoker; Smoking; Testing; Therapeutic; Toxin; Transfection; Translating; Untranslated RNA; Validation; Variant; abstracting; bindin; cell injury; cell type; chromatin immunoprecipitation; cigarette smoke-induced; cigarette smoking; cigarette smoking; clinically relevant; functional genomics; genetic variant; genome wide association study; high throughput screening; in vitro Model; in vivo; insight; novel; promoter; risk variant; screening; therapeutic target; transcription factor

DESCRIPTION (provided by applicant): Chronic obstructive pulmonary disease (COPD), the third leading cause of death in the U.S, is strongly influenced by cigarette smoking and genetic predisposition. The primary objectives of this proposal are to identify functional genetic variants in two COPD genome-wide association (GWAS) loci, HHIP and FAM13A regions, and to define the molecular mechanisms by which these functional variants alter gene expression and cellular phenotypes relevant to COPD. We hypothesize that functional variants in these two loci are regulatory variants that can be measured by quantifying enhancer activity in human bronchial epithelial cells. Furthermore, we hypothesize that functional variants, through differential bindin to specific transcription factors, regulate HHIP or FAM13A gene expression, thus affecting cellular sensitivity to smoke-induced cell injury. To test these hypotheses, in the R21 phase of the project, we will apply recently developed massively parallel reporter assays (MPRA) to identify functional variants that show allele-specific enhancer activity in Beas-2B cells exposed to either room air or cigarette smoke (CS), followed by validation in reporter assays. We will also confirm allele- specific open chromatin in primary human bronchial epithelial cells (HBE) using FAIRE, and we will assess long-range interactions of identified regulatory elements with the relevant promoters using chromosome conformation capture assays. In the R33 phase of the project, we will determine the role of the functional variants in smoke-induced cell death in both Beas-2B cells and HBE. Subsequently, we will apply an siRNAs library targeting 1529 known human transcription factors (TFs) to identify TFs that bind to the identified enhancer elements with differential affinity to genetic variants (by EMSA and ChIP), alter enhancer activity (using co-transfection and reporter assays), and regulate HHIP or FAM13A expression (by RT-PCR following gene silencing) in Beas-2B cells. To demonstrate the clinical relevance of these mechanistic studies, we will perform in vivo validation in HBE cells from smokers with established COPD vs. smoking controls. Ultimately, these functional characterizations will identify biological pathways with potential therapeutic implications.

描述（由申请人提供）：慢性阻塞性肺疾病（COPD）是美国第三大死亡原因，受吸烟和遗传易感性的强烈影响。该提案的主要目标是确定功能性遗传变异 在两个COPD全基因组关联（GWAS）位点，HHIP和FAM 13 A区域，并确定这些功能变异改变COPD相关基因表达和细胞表型的分子机制。我们假设这两个基因座的功能变异是调节变异，可以通过定量增强子在人支气管上皮细胞中的活性来测量。此外，我们假设功能变异，通过差异bindin特定的转录因子，调节HHIP或FAM 13 A基因的表达，从而影响细胞的敏感性，烟雾诱导的细胞损伤。为了验证这些假设，在该项目的R21阶段，我们将应用最近开发的大规模平行报告基因测定（MPRA）来鉴定暴露于室内空气或香烟烟雾（CS）的Beas-2B细胞中显示等位基因特异性增强子活性的功能变体，然后在报告基因测定中进行验证。我们还将 使用FAIRE证实原代人支气管上皮细胞（HBE）中等位基因特异性开放染色质，我们将使用染色体构象捕获分析评估鉴定的调控元件与相关启动子的长程相互作用。在该项目的R33阶段，我们将确定功能变体在Beas-2B细胞和HBE中烟雾诱导的细胞死亡中的作用。随后，我们将应用靶向1529种已知人类转录因子（TF）的siRNA文库来鉴定与所鉴定的增强子元件结合的TF，这些TF对遗传变体具有不同的亲和力（通过EMSA和ChIP），改变增强子活性（使用共转染和报告基因测定），并调节Beas-2B细胞中HHIP或FAM 13 A的表达（通过基因沉默后的RT-PCR）。为了证明这些机制研究的临床相关性，我们将在来自已确定COPD吸烟者的HBE细胞与吸烟对照中进行体内验证。最终，这些功能表征将确定具有潜在治疗意义的生物学途径。