Integrative Genomics in Asthmatics of African Descent
Start Date: 12/01/2014
End Date: 11/30/2018
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.