High throughput functional studies of IBD-associated GWAS variants

IBD 相关 GWAS 变异的高通量功能研究

• 批准号: 10681060
• 负责人: Terrence S. Furey
• 金额: $ 67.13万
• 依托单位: UNIV OF NORTH CAROLINA CHAPEL HILL
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-04-01 至 2027-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10681060
• 关键词: Achievement; Affect; Alleles; Automobile Driving; Binding; Biological Assay; Brain; Cell Differentiation process; Cell physiology; Cells; Cellular biology; Chromatin; Circulation; Collaborations; Colon; Complement; Crohn' s disease; Data; Dependovirus; Diagnosis; Digestive System Disorders; Disease; Environment; Epithelial Cells; Funding; Gene Expression; Gene Expression Regulation; Genes; Genetic; Genetic Transcription; Genetic Variation; Genotype; Goals; Heart; Heterogeneity; Human; Inflammatory; Inflammatory Bowel Diseases; Intestinal Diseases; Intestines; Libraries; Link; Liver; Lung; Measures; Mus; Muscle; NF-kappa B; Organ; Pathogenesis; Patients; Permeability; Phenotype; Physiology; Proliferating; Protocols documentation; Quantitative Trait Loci; Regulation; Regulator Genes; Regulatory Element; Reporter; Research Personnel; Role; Site; System; Testing; Therapeutic Intervention; Tissue Sample; Tissues; Transcriptional Regulation; Ulcerative Colitis; Untranslated RNA; Validation; Variant; causal variant; cell type; chronic inflammatory disease; data resource; disease phenotype; disease prognosis; gene expression variation; genetic variant; genome wide association study; genomic locus; genomic variation; genotyped patients; high throughput analysis; human DNA; human genomics; ileum; intestinal epithelium; jun Oncogene; mesenteric lymph node; monolayer; programs; public health relevance; sex; time use; transcription factor; variant of interest; vector

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.

项目概要/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 全基因组关联研究（GWAS）发现无法治愈的胃肠道炎症性疾病。 发现超过 250 个与 IBD 相关的基因组位点，但对 IBD 发病机制的驱动机制有不同贡献 每个位点通常包含数十到数百个变异，数量巨大。 其中大部分区域是非编码区域，表明对于大多数基因座（因果变异）而言，具有一定的作用。 受影响的调控元件和被调控的靶基因尚不清楚。 调控变异通过改变驱动表型的基因转录程序来促进IBD表型 我们建议使用两个正交的高通量来识别假定的随意调节变异。 目标 1：染色质可及性 (caQTL) 和转录的调节数量性状位点 (QTL)。 因子结合 (tfQTL) 将遗传变异与调控活性的改变联系起来。 位点，这些分析将识别对疾病相关调控具有潜在贡献的调控变异 目标 2：或者，大规模平行报告分析 (MPRA) 有意询问。 使用人类 DNA 载体对数千种遗传变异的转录调控进行等位基因效应。 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进行 由于人类和小鼠之间转录因子基序的保守性，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异 目标 3：整合 QTL 和 MPRA 测定的结果。 选择高置信度的假定 IBD 调节变异体进行以肠上皮细胞为中心的功能验证 该项目的长期目标是：1）填补空白。 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之间的关系 解释这种变异最终如何导致 IBD；以及 2) 为 IBD 提供独特的数据资源 研究人员可以访问以进行自己的研究。