Integrative Genomics of the Asthma-COPD Overlap

摘要 具有持续性症状的哮喘患者极有可能发展为固定性呼吸道阻塞(AO)。这个 这一建议的首要假设是，哮喘患者的这一亚群具有最大的发病风险 这种易感性是由特定的遗传和表观遗传变异引起的，这些变异影响了 主要哮喘和慢性阻塞性肺疾病易感基因在支气管上皮中的表达，包括 HHIP和FAM13A、TSLP和ORMDL3。我们认为，对这些目标的描述(和定义 其他候选者)将促进更多定向疗法的开发，以对抗 呼吸道重塑。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 易感哮喘患者外周血中mRNAs和miRNA的转录谱 特征队列：(I)cAMP中肺生长正常的哮喘患者与肺发育异常的患者 发育或早期衰退；(Ii)肺功能正常(GOLD 0)与肺功能异常的哮喘患者的COPD基因 功能(黄金II-III)。将使用Illumina Hi-Seq 2000生成RNA-Seq表达谱(n=175)。 我们假设肺功能减退的哮喘患者与保存肺功能的患者相比有所下降。 功能，表现出BE基因表达的特定模式，包括ORMDL3和TSLP增加 抑制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 将使用一种综合基因组学方法来定位影响Key表达的遗传变异 哮喘-COPD共表达网络的核心基因。这些研究将在BE中进行 在Aim 1收集的样本，并由哮喘桥(n=1548)和eclipse(n=200)队列补充， 有可用的基因组数据(基因、表达、甲基化)。将对已确定的监管变种进行测试 COPD基因与COPD易感基因的关联(n=10,300)和cAMP中固定的AO的决定因素 968例。在目标3中，我们将描述候选基因失控的功能后果。 气液界面模型。我们将比较抵抗和吸烟患者的细胞对香烟烟雾的反应。 气液界面易感受试者(每组6人，共24个样本) 阵营和COPD基因队列。我们将比较shRNA介导的基因敲除后的这些反应 候选基因(ORMDL3、TSLP、HHIP和FAM13A)，并正式测试这些响应是否 哮喘和慢性阻塞性肺病的症状相似。我们推测，在cAMP和COPD基因衍生的样本中，我们都会 在易感受试者中看到与正常哮喘患者不同的相似细胞反应 肺功能，提供了对这些基因影响肺功能的机制的关键见解。

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.