High throughput functional studies of IBD-associated GWAS variants

项目摘要/摘要 炎症性肠病(IBD)、克罗恩病(CD)和溃疡性结肠炎(UC)是慢性疾病 无法治愈的胃肠道炎症性疾病。全基因组关联研究(GWAS)已经 发现了与IBD相关的250个基因组基因座，但对IBD发病机制的贡献各不相同 疾病预后仍不明朗。每个基因座通常包含数十到数百个变种， 其中大部分位于非编码区，表明在基因调控中发挥了作用。对于大多数基因座来说，因果变异， 受影响的调控元件和被调控的靶基因是未知的。我们假设 调控变异体通过改变驱动表型的基因转录程序而导致IBD表型 异质性。我们建议使用两个正交的、高吞吐量的方法来识别假定的临时调控变体 分析。目的1：染色质可及性(CaQTL)和转录的调控数量性状基因座(QTL) 因子结合(TfQTL)将遗传变异与调节活性的改变联系在一起。对于GWAS中的变种 这些分析将确定可能对疾病相关的调控做出贡献的调控变异 细胞类型和组织。目标2：或者，大规模平行报告分析(MPRA)系统地询问 等位基因对数千种基因变异转录调控的影响。利用人DNA载体进行MPRA分析 含有感兴趣的IBD相关变体的调控元件可以在小鼠细胞或器官中执行 由于人类和小鼠之间转录因子基序的保守性很好。我们将使用 MPRA确定改变结肠、回肠和肠系膜淋巴结调节活性的变体 正常和内毒素刺激的炎症状态。目标3：整合QTL和MPRA分析的结果，我们将 筛选高可信的IBD调节性变异体，用于肠上皮细胞功能验证 患者来源的2D肠道单层系统。这个项目的长期目标是：1)填补这一空白 我们检测与IBD相关的遗传、基因调控和基因表达变异的能力与我们的能力 解释该变异最终如何导致IBD；以及2)为IBD提供独特的数据资源 调查人员可以访问他们自己的研究。

PROJECT SUMMARY/ABSTRACT The Inflammatory bowel diseases (IBD), Crohn’s disease (CD) and ulcerative colitis (UC), are chronic inflammatory diseases of the gastrointestinal tract with no cure. Genome-wide association studies (GWAS) have found >250 genomic loci associated with IBD, but variant contributions to mechanisms driving IBD pathogenesis and disease prognosis remain unclear. Each locus typically contains tens to hundreds of variants, the vast majority of which are in non-coding regions suggesting a role in gene regulation. For most loci, the causal variant, the affected regulatory element, and the target gene being regulated are unknown. We hypothesize that regulatory variants contribute to IBD phenotypes by altering gene transcriptional programs driving phenotypic heterogeneity. We propose to identify putative casual regulatory variants using two, orthogonal, high-throughput analyses. Aim 1: Regulatory quantitative trait loci (QTL) for chromatin accessibility (caQTL) and transcription factor binding (tfQTL) associate genetic variation with alterations in regulatory activity. For variants in GWAS loci, these analyses will identify regulatory variants with potential contributions to regulation in disease-relevant cell types and tissues. Aim 2: Alternatively, massively parallel reporter assays (MPRA) systematically interrogate allelic effects on transcriptional regulation of thousands of genetic variants. MPRA using vectors of human DNA regulatory elements containing IBD associated variants of interest can be performed in mouse cells or organs due to the well-established conservation of transcription factor motifs between human and mouse. We will use MPRA to determine variants that alter regulatory activity in colon, ileum, and mesenteric lymph nodes under both normal and LPS-stimulated inflammatory states. Aim 3: Integrating results from QTL and MPRA assays, we will select high confidence putative IBD regulatory variants for intestinal epithelial cell focused functional validation in patient derived 2D intestinal monolayer systems. The long-term goals of this project are: 1) To fill the gap between our ability to detect genetic, gene regulatory, and gene expression variation linked to IBD and our ability to explain how that variation ultimately contributes to IBD; and 2) To provide a unique data resource for IBD investigators to access for their own studies.