Integrative Genetic and Genomic Analyses in the Inflammatory Bowel Disease

 描述（由申请人提供）：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群的不适当定向炎症反应引起。全基因组关联研究（GWAS）已将163种特异性单核苷酸多态性（SNP）与IBD疾病发病机制联系起来。在这些相关基因座内，有超过5000个额外的SNP与所鉴定的SNP处于连锁不平衡（LD），并且不知道这些SNP中的哪些促成IBD。这些SNP中的大多数映射到基因组的非编码区，表明许多变体通过修饰基因调控元件活性而促成IBD。环境因素如肠道微生物群在IBD炎症的起始和持续中的作用是无可争议的。具体而言，固有层（LP）巨噬细胞对肠道微生物群的耐受性的丧失是慢性肠道炎症的起始和进展中的中心事件。我们推测，DNA变异，影响基因调控元件的活动显着贡献的差异主机之间的微生物刺激正常和IBD个体的反应。这项提案的主要目标是确定遗传，调节活动和基因表达的变化，显着有助于 IBD在分子和临床水平。核小体缺失的开放染色质的基因组区域已经与所有类型的调控元件相关联，并且现在可以使用全基因组测定来检测这些调控元件。在目标1中，我们将确定从升结肠的非炎症部分获得的一组全面表型的CD和UC患者组织样本的开放染色质状态、转录水平和基因型。将生成非IBD对照的相似数据以进行比较。利用这些数据，我们将确定在一系列临床和分子IBD表型中具有遗传驱动的差异活性的调控元件。在目标2中，我们将通过确定目标1中CD和UC患者亚组和非IBD对照组中固有层（LP）巨噬细胞之间活性基因调控元件和基因表达水平的变化，揭示CD中LP巨噬细胞耐受性丧失的分子基础。为了了解这些差异如何转化为对细菌的炎症反应的改变，我们将确定CD，UC和非IBD患者的LP巨噬细胞中染色质状态和表达的变化，当这些细胞用粘附侵袭性E.大肠杆菌（AIEC）菌株分离自CD患者，并分别与E.粪便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这种变异最终如何导致IBD的能力之间的差距; 2）为IBD研究人员提供独特的数据资源，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.