Integrative Genomics in Asthmatics of African Descent

描述（由申请人提供）：哮喘是一种复杂的疾病，其强大的遗传基础已经牢固建立。哮喘患病率与长期暴露于某些环境因素，特别是与室内灰尘有关的环境因素所引发的免疫反应密切相关。哮喘的表现依赖于T细胞的活性，特别是T细胞的CD4+ Th2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，但相对较少的研究集中在这个代表性不足的少数群体。全基因组关联研究（GWAS）已经成功地鉴定了与哮喘风险增加相关的基因，但GWAS发现的单核苷酸多态性（SNP）关联与了解这些基因座如何控制疾病之间存在实质性差距。由于大多数GWAS关联涉及基因间或内含子区域的snp，因此调控元件的多态性似乎可以解释哮喘遗传缺失的很大一部分。为了验证这一假设，我们提出了一系列研究，将非洲血统人群中最全面的GWAS数据库之一与下一代测序技术（RNA-Seq）和eQTL定位相结合，以阐明非洲加勒比地区特应性哮喘患者和非特应性、非哮喘对照组中分离的CD4+ T细胞基因表达定量水平差异的遗传变异。这个来自巴巴多斯的种群已经被广泛地表型化，并被跟踪了大约20年。该应用程序的具体目标建立在具有不同但高度集成的专业领域的国际研究小组的基础设施上，包括以下内容：(i)识别顺式和反式效应

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.