Integrative Genomics in Asthmatics of African Descent

描述(申请人提供)：哮喘是一种复杂的疾病，其强大的遗传基础已被牢固地建立起来。哮喘患病率与长期暴露于某些环境因素，特别是与房屋灰尘有关的因素而引发的免疫反应密切相关。哮喘的表现取决于T细胞的活动，特别是T细胞的CD4Th2亚群。非洲血统的哮喘患者往往比欧洲血统的人有更严重的哮喘和更严重的临床症状，但相对较少的研究关注这一代表不足的少数群体。全基因组关联研究已经成功地识别了与哮喘风险增加相关的基因，但在基因组全关联研究发现的单核苷酸多态(SNP)关联和了解这些基因座如何控制疾病之间存在着巨大的差距。由于大多数Gwas关联涉及基因间或内含子区域的SNPs，似乎调控元件的多态可能解释了哮喘缺失遗传性的很大一部分原因。为了验证这一假设，我们提出了一系列研究，将关于非洲血统人群的最全面的GWAS数据库之一与下一代测序技术(RNA-Seq)和eQTL图谱相结合，以阐明从非洲加勒比特应性哮喘患者和非特应性非哮喘对照组分离的CD4T细胞基因表达水平差异的遗传变异，这些细胞生活在一个均匀的、特征良好的环境中。这些来自巴巴多斯的人已经广泛地进行了表型分析，并被跟踪了20年。这一应用程序的具体目标建立在一个国际调查小组的基础上，该小组拥有不同但高度整合的专门知识领域，并包括以下内容：(1)确定顺势和反动效应 通过对250名特应性哮喘患者分离的CD4T细胞进行RNA-Seq，然后进行eQTL分析，确定了在转录组中发现的变体；(Ii)通过比较特应性哮喘患者和250名非特应性哮喘对照人员的转录本，确定特应性哮喘特有的eQTL模式，并探索与哮喘患者CD4T细胞调节失调相关的调控网络；以及(Iii)利用预先存在的哮喘Gwas数据，整合哮喘患者(SA1)与非哮喘患者(SA2)之间的新型eQTL。最强的eQTL将通过使用纳米串计数器技术测量150名独立的特应性哮喘患者和150名非特应性非哮喘对照的转录变化来验证。我们将把这项研究的结果与来自哮喘患者和非哮喘患者的CD4T细胞的公开eQTL数据进行比较，以评估泛化，并探索基因网络。通过挖掘公开可用的GWAS数据库，我们将确定在CD4T细胞中发现的新的eQTL和转录表达是否有助于哮喘易感性，并可能解释先前发现的GWAS相关性。这些研究将极大地促进我们对哮喘分子基础的理解。

DESCRIPTION (provided by applicant): Asthma is a complex disease for which a strong genetic basis has been firmly established. Asthma prevalence is closely related to an immune response initiated by chronic exposure to certain environmental factors, especially those associated with house dust. Manifestations of asthma depend on T cell activities, particularly the CD4+ Th2 subset of T cells. Asthmatics of African ancestry tend to have more severe asthma and more severe clinical symptoms than individuals of European ancestry, but relatively few studies have focused on this underrepresented minority group. Genome-wide association studies (GWAS) have been successful in identifying genes associated with increased risk of asthma, but there is a substantial gap between single nucleotide polymorphism (SNP) associations discovered by GWAS and understanding how these loci control disease. Because most GWAS associations involve SNPs in intergenic or intronic regions, it seems likely polymorphisms in regulatory elements may account for a large portion of the missing heritability of asthma. To test this hypothesis, we propose a series of studies to integrate one of the most comprehensive GWAS databases on an African ancestry population with next-generation sequencing technology (RNA-Seq) and eQTL mapping, to elucidate the genetic variation underpinning differences in quantitative levels of gene expression of CD4+ T cells isolated from African Caribbean atopic asthmatics and non-atopic, non-asthmatic controls living in a homogeneous, well-characterized environment. This population from Barbados has been extensively phenotyped and followed for >20 years. The specific aims of this application build upon the infrastructure of an international group of investigators with diverse but highly integrated areas of expertise, and include the following: (i) to identify cis- and trans-effects of variants identified in the transcriptome from isolated CD4+ T cells from 250 atopic asthmatics by performing RNA-Seq followed by eQTL analyses; (ii) to identify eQTL patterns from CD4+ T cells specific to atopic asthma by comparing the transcriptomes of atopic asthmatics to that of 250 non-atopic, non-asthmatic controls, and explore regulatory networks associated with dysregulation of CD4+ T cells in asthma; and (iii) to integrate novel eQTLs among asthmatics (SA1) compared to non-asthmatics (SA2) with pre-existing asthma GWAS data. The strongest eQTLs will be validated by measuring the change in transcription in 150 independent atopic asthmatics and 150 non-atopic, non- asthmatic controls using NanoString nCounter technology. We will compare results generated from this study to publicly available eQTL data on CD4+ T cells from asthmatics and non-asthmatics generated from microarray assays to assess generalization, and explore networks of genes. By mining publicly available GWAS databases we will determine whether the novel eQTLs and transcript expression identified in CD4+ T cells contribute to asthma susceptibility and perhaps explain previously identified GWAS associations. These studies should substantially advance our understanding of the molecular basis for asthma.