Integrative Genomics of the Asthma-COPD Overlap

哮喘-慢性阻塞性肺病重叠的综合基因组学

• 批准号: 9754673
• 负责人: Benjamin Alexander Raby
• 金额: $ 41.05万
• 依托单位: BRIGHAM AND WOMEN'S HOSPITAL
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/9754673
• 关键词: Adrenal Cortex Hormones; Adult; Adverse effects; Age; Air; Airway Disease; Asthma; Candidate Disease Gene; Childhood Asthma; Chromosome Mapping; Chronic Obstructive Airway Disease; Complement; Complication; Data; Development; Diagnostic radiologic examination; Disease; Epigenetic Process; Epithelial; Epithelial Cells; Etiology; Exhibits; Expression Profiling; Gene Expression; Genes; Genetic; Genetic Determinism; Genomic approach; Genomics; Genotype; Growth; Impairment; Individual; Inflammatory; Inhalation; Joints; Lead; Link; Liquid substance; Lung; Maps; Mediating; Mediation; Mediator of activation protein; Messenger RNA; Methylation; MicroRNAs; Modeling; Network-based; Patients; Pattern; Pharmacology; Predisposition; Randomized Clinical Trials; Recording of previous events; Reproducibility; Resistance; Respiratory physiology; Risk; Sampling; Smoker; Susceptibility Gene; Systems Biology; TGFB1 gene; TSLP gene; Testing; Variant; airway obstruction; airway remodeling; asthma inhaler; asthmatic; bronchial epithelium; cigarette smoke; cohort; cytokine; differential expression; epidemiologic data; genetic variant; genomic data; imaging study; insight; knock-down; lung preservation; neutrophil; non-smoking; overexpression; persistent symptom; phenotypic data; response; small hairpin RNA; transcriptome sequencing; transcriptomics; vector; young adult

ABSTRACT Asthmatics with persistent symptoms are at great risk of developing fixed airways obstruction (AO). The overarching hypothesis of this proposal is that it is this subset of asthmatics that is at greatest risk of developing COPD and that this susceptibility is caused by specific genetic and epigenetic variants that influence the expression of key asthma- and COPD-susceptibility genes expressed in the bronchial epithelium (BE), including HHIP and FAM13A, TSLP and ORMDL3. We argue that characterization of these targets (and defining additional candidates) will facilitate the development of more directed therapies to counter the adverse effects of airway remodeling. To test these hypotheses, we propose three Specific Aims. In Aim 1, we will characterize the mRNA and miRNA transcriptomic profiles in BE of the susceptible asthmatic in subjects from two well- characterized cohorts: (i) asthmatics from CAMP who exhibit normal lung growth vs. those with abnormal growth or early decline; (ii) asthmatics in COPDGene with normal lung function (GOLD 0) vs. abnormal lung function (GOLD II-III). RNA-seq expression profiles (n=175) will be generated using the Illumina Hi-Seq 2000. We hypothesize that asthmatics with reduced lung function decline, compared to those with preserved lung function, demonstrate a specific pattern of BE gene expression, including increased ORMDL3 and TSLP expression, and reduced HHIP and FAM13A expression. We will characterize the co-expression network influenced by these genes to define additional candidates that contribute to lung function decline. In Aim 2, we will use an integrative genomics approach to map the genetic variants that influence the expression of key genes at the core of the asthma-COPD co-expression networks. These studies will be performed in the BE samples collected in Aim 1, and complemented by Asthma BRIDGE (n=1548) and ECLIPSE (n=200) cohorts, with available genomic data (genotype, expression, methylation). Identified regulatory variants will be tested for association as COPD-susceptibility loci in COPDGene (n=10,300), and as determinants of fixed AO in CAMP (n=968). In Aim 3, we will characterize the functional consequences of dysregulation of the candidate genes in an air-liquid interface model. We will compare cellular responses to cigarette smoke among resistant and susceptible subjects (n=6 per group, 24 samples total) in air liquid interface using BE derived from subjects from the CAMP and COPDGene cohorts. We will compare these responses following shRNA-mediated knockdown of candidate genes (ORMDL3, TSLP, HHIP and FAM13A) and formally test whether these responses are similar in asthma and COPD. We speculate that in both the CAMP and COPDGene derived samples, we will see similar cellular responses in the susceptible subjects that are distinct from those in asthmatics with normal lung function, providing key insights in to the mechanisms by which these genes impact lung function.

抽象的 症状持续的哮喘患者发生固定气道阻塞（AO）的风险很大。这 该提案的总体假设是，这部分哮喘患者患上哮喘的风险最大 慢性阻塞性肺病，这种易感性是由影响慢性阻塞性肺病的特定遗传和表观遗传变异引起的 支气管上皮 (BE) 中表达的关键哮喘和 COPD 易感基因的表达，包括 HHIP 和 FAM13A、TSLP 和 ORMDL3。我们认为，这些目标的特征（以及定义 其他候选者）将促进更有针对性的疗法的开发，以应对副作用 气道重塑。为了检验这些假设，我们提出了三个具体目标。在目标 1 中，我们将描述 来自两个健康状况良好的受试者中易感哮喘患者 BE 中 mRNA 和 miRNA 转录组图谱 特征队列：(i) 来自 CAMP 且肺部生长正常的哮喘患者与肺部生长异常的患者 增长或早期衰退； (ii) COPDGene 中肺功能正常 (GOLD 0) 的哮喘患者与肺功能异常的患者 功能（黄金 II-III）。 RNA-seq 表达谱 (n=175) 将使用 Illumina Hi-Seq 2000 生成。 我们假设，与保留肺功能的哮喘患者相比，肺功能降低的哮喘患者会出现衰退 功能，展示 BE 基因表达的特定模式，包括 ORMDL3 和 TSLP 增加 表达，并减少 HHIP 和 FAM13A 的表达。我们将描述共表达网络的特征 受这些基因的影响，以确定导致肺功能下降的其他候选基因。在目标 2 中，我们 将使用综合基因组学方法来绘制影响关键表达的遗传变异 哮喘-慢性阻塞性肺病共表达网络的核心基因。这些研究将在 BE 进行 在目标 1 中收集的样本，并由 Asthma BRIDGE (n=1548) 和 ECLIPSE (n=200) 队列进行补充， 具有可用的基因组数据（基因型、表达、甲基化）。将测试已确定的监管变体 作为 COPDGene (n=10,300) 中的 COPD 易感基因座的关联，以及作为 CAMP 中固定 AO 的决定因素 （n=968）。在目标 3 中，我们将描述候选基因失调的功能后果 气液界面模型。我们将比较耐药性和耐药性的细胞对香烟烟雾的反应 气液界面中的易感受试者（每组 n=6，总共 24 个样本）使用来自受试者的 BE CAMP 和 COPDGene 队列。我们将比较 shRNA 介导的敲低后的这些反应 候选基因（ORMDL3、TSLP、HHIP 和 FAM13A）并正式测试这些反应是否 哮喘和慢性阻塞性肺病的情况相似。我们推测，在 CAMP 和 COPDGene 衍生样本中，我们将 在易感受试者中观察到相似的细胞反应，这与正常哮喘患者的细胞反应不同 肺功能，提供有关这些基因影响肺功能的机制的关键见解。