Integrative Genetic and Genomic Analyses in the Inflammatory Bowel Disease

 描述(申请人提供)：炎症性肠病(IBD)，由克罗恩病(CD)和溃疡性结肠炎(UC)组成，由遗传易感宿主对肠道微生物区系的不适当炎症反应引起。全基因组关联研究已将163个特异性单核苷酸多态(SNPs)与IBD疾病的发病机制联系起来。在这些相关基因座中，还有5000多个SNPs与已识别的SNPs处于连锁不平衡(LD)状态，目前尚不清楚这些SNPs中哪些与IBD有关。这些SNP大多映射到基因组的非编码区，这表明许多变异通过改变基因调节元件的活性而导致IBD。环境因素，如肠道微生物区系，在IBD炎症的启动和持续中的作用是毋庸置疑的。特别是，失去固有层(LP)巨噬细胞对肠道微生物区系的耐受性是慢性肠炎发生和发展的中心事件。我们假设，影响基因调控元件活性的DNA变异显著有助于正常和IBD患者对微生物刺激的不同宿主反应。这项提案的主要目标是确定显著促进基因、调节活动和基因表达变化的基因 IBD的分子水平和临床水平。核小体耗尽的开放染色质的基因组区域已经与所有类型的调控元件联系在一起，现在已经有了全基因组检测这些元件的方法。在目标1中，我们将确定一组CD和UC患者组织样本的开放染色质状态、转录水平和基因类型，这些样本来自升结肠的非炎症部分。将为非IBD对照生成类似的数据以供比较。使用这些数据，我们将确定在多种临床和分子IBD表型中具有遗传驱动差异活性的调控元件。在目标2中，我们将通过检测CD和UC患者以及目标1中非IBD对照组的固有层(LP)巨噬细胞之间活性基因调控元件和基因表达水平的差异，揭示CD患者LP巨噬细胞丧失耐受性的分子基础。为了了解这些差异是如何转化为对细菌的炎症反应改变的，我们将确定CD、UC和非IBD患者的LP巨噬细胞在CD、UC和非IBD患者的LP巨噬细胞用先前从CD患者和粪肠球菌分离的粘附性侵袭性大肠杆菌(AIEC)株刺激时染色质状态和表达的变化。该项目的长期目标是：1)填补我们检测与IBD相关的遗传、染色质和基因表达变异的能力与我们解释该变异最终如何导致IBD之间的差距；2)为IBD研究人员提供一个独特的数据资源供他们自己的研究使用。

 DESCRIPTION (provided by applicant): The inflammatory bowel diseases (IBD), composed of Crohn's disease (CD) and ulcerative colitis (UC), result from an inappropriately directed inflammatory response to the enteric microbiota in a genetically susceptible host. Genome wide association studies (GWAS) have linked 163 specific single nucleotide polymorphisms (SNPs) to IBD disease pathogenesis. Within these associated loci, there are over 5000 additional SNPs that are in linkage disequilibrium (LD) with the identified SNPs, and it is not known which of these contribute to IBD. Most of these SNPs map to non-coding regions of the genome, suggesting that many variants contribute to IBD by modifying gene regulatory element activity. The role of environmental factors such as the enteric microbiota in the initiation and perpetuation of inflammation in IBD is incontrovertible. Specifically, loss of lamina propria (LP) macrophage tolerance to the enteric microbiota is a central event in the initiation and progression of chronic intestinal inflammation. We hypothesize that DNA variation that impacts gene regulatory element activity significantly contributes to the differential host response to microbial stimuli between normal and IBD individuals. The primary goal of this proposal is to identify genetic, regulatory activity, and gene expression changes that significantly contribute to IBD at molecular and clinical levels. Genomic regions of nucleosome-depleted, open chromatin have been linked to all types of regulatory elements, and genome-wide assays to detect these are now available. In Aim 1, we will determine open chromatin status, transcription levels, and genotypes for a panel of comprehensively phenotyped CD and UC patient tissue samples obtained from the non-inflamed section of the ascending colon. Similar data will be generated for non-IBD controls for comparison. Using these data, we will determine regulatory elements with genetically driven differential activity across a host of clinical and molecular IBD phenotypes. In Aim 2, we will uncover the molecular basis for loss of LP macrophage tolerance in CD by determining variation in active gene regulatory elements and gene expression levels between lamina propria (LP) macrophages in a subset of CD and UC patients and non-IBD controls in Aim 1. To understand how these differences translate to altered inflammatory response to bacteria, we will determine changes in chromatin status and expression in LP macrophages from CD, UC, and non-IBD patients when these cells are stimulated with an adherent-invasive E. coli (AIEC) strain previously isolated from CD patients and separately with E. faecalis. The long-term goals of this project are: 1) To fill the gap between our ability to detct genetic, chromatin, 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.