Genetic Control of Airway Epithelium Gene Expression in Childhood Asthmatics

 描述（由申请人提供）：哮喘是儿童中最常见的慢性疾病。包括哮喘在内的复杂人类疾病的基因图谱研究结果表明，大多数相关变异是非编码的，而不是蛋白质编码的。这些非编码风险变体中的许多可能存在于影响基因表达的调控元件中。这表明在相关组织中鉴定的表达数量性状基因座（eQTL）变体将呈现富集哮喘疾病变体的变体库。支气管气道上皮细胞通过影响气道免疫应答、产生堵塞气道的粘液以及向影响气道重塑的气道间充质发出信号而参与哮喘发病机制。我们的目标是确定气道上皮eQTL，赋予不同人群的儿童哮喘的风险。鼻气道上皮是支气管气道上皮的容易接近的替代物，并且鼻气道转录组非常接近支气管气道转录组。我们假设许多哮喘遗传易感性基因座的功能基础涉及气道上皮基因表达的顺式调节。我们将测试我们的假设，有三个具体的目标：目标1：确定顺式调节基因和他们的eQTLs内的哮喘GWAS基因座在原发性气道上皮细胞从波多黎各儿童哮喘和对照。我们将使用靶向RNA-seq来确定定位于21个已确定的哮喘的所有159个基因的总/等位基因表达水平。 750名波多黎各哮喘患者和对照者鼻气道上皮中的GWAS位点。将使用全基因组基因型数据和等位基因不平衡分析通过eQTL分析确定顺式调节基因。eQTL的精细作图将使用来自所有受试者的靶向DNA-seq的完整变体数据来完成。目标二：通过对波多黎各儿童哮喘患者和对照的原发性气道上皮进行全转录组eQTL分析，鉴定新的哮喘相关eQTL。所有750名受试者的全转录组表达将用于鉴定在哮喘中差异表达且为顺式调节的基因，如目标1中所述。DNA-seq将用于生成哮喘相关顺式调节基因的完整变异数据，以进行eQTL精细作图。目的3：在不同的哮喘人群中，描述鼻哮喘eQTLs的下气道、临床和生物学意义。我们将在100名哮喘患者的支气管气道上皮中描述最强的鼻哮喘eQTL。我们将在7200名波多黎各、墨西哥和非洲裔美国儿童中确定目标1和2中确定的最强精细定位气道eQTL是否易患哮喘和相关性状。改变的生物学机制将通过气道eQTL调控的哮喘相关基因的途径分析来确定。

 DESCRIPTION (provided by applicant): Asthma is the most common chronic disease among children. Results from gene mapping studies of complex human diseases including asthma have indicated that most associated variants are non-coding, rather than protein coding. Many of these non-coding risk variants likely reside in regulatory elements that affect gene expression. This suggests expression quantitative trait loci (eQTL) variants identified in a relevant tissue will present a variant pool enriched for asthma disease variants. The bronchial airway epithelium contributes to asthma pathogenesis by affecting airway immune responses, through the production of mucus that plugs airways, and by signaling to the airway mesenchyme which influences airway remodeling. Our goal is to identify airway epithelium eQTLs which confer risk of childhood asthma in diverse populations. The nasal airway epithelium is an easily accessible alternative to bronchial airway epithelium and the nasal airway transcriptome closely approximates the bronchial airway transcriptome. We hypothesize the functional underpinnings of many asthma genetic susceptibility loci involve cis-regulation of airway epithelium gene expression. We will test our hypothesis with three specific aims: Aim 1: Identify cis-regulated genes and their eQTLs within asthma GWAS loci in primary airway epithelium from Puerto Rican childhood asthmatics and controls. We will use targeted RNA-seq to determine total/allelic expression levels of all 159 genes localized to the 21 identified asthma GWAS loci in the nasal airway epithelium of 750 Puerto Rican asthmatics and controls. Cis-regulated genes will be determined by eQTL analyses using genome-wide genotype data and allelic imbalance analyses. Finemapping of eQTLs will be accomplished with complete variant data from targeted DNA-seq of all subjects. Aim 2: Identify novel asthma-related eQTLs by whole transcriptome eQTL analysis of primary airway epithelium from Puerto Rican childhood asthmatics and controls. Whole transcriptome expression on all 750 subjects will be used to identify genes that are both differentially expressed in asthma and are cis-regulated, as in Aim 1. DNA-seq will be used to generate complete variant data at the asthma-related, cis-regulated genes to perform eQTL finemapping. Aim 3: Characterize the lower airway, clinical, and biological significance of identified nasal asthma eQTLs in diverse populations of asthmatics. We will characterize the strongest nasal asthma eQTLs in the bronchial airway epithelium of 100 asthmatics. We will determine if the strongest finemapped airway eQTLs identified in Aims 1 and 2 predispose to asthma and related traits in 7200 Puerto Rican, Mexican, and African American children. Altered biologic mechanisms will be identified by pathway analysis of asthma-associated genes regulated by airway eQTLs.