Interpreting molecular role of DNA variants associated with Crohn's Disease through integrative analysis of open chromatin, epigenome and transcriptome data in diverse and relevant tissues and cells

描述（由申请人提供）：克罗恩病（CD）是两种主要炎症性肠病之一，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CD疾病发病机制联系起来。在这些区域内，有超过5600个额外的SNP与标签SNP处于连锁不平衡（LD），并且不知道这些SNP中的哪些促成CD。大多数这些SNPs映射到基因组的非编码区，表明致病变异通过修饰基因调控元件活性而导致CD。重要的第一步是鉴定在受影响和未受影响个体之间的CD相关肠组织（包括结肠）和细胞（即上皮细胞和免疫细胞）中具有差异调节活性的基因组区域。为此，我们已经产生了遗传，开放染色质，和转录组数据从结肠组织和免疫细胞获得的27 CD患者和14正常对照，并从巨噬细胞，T细胞和上皮细胞分离的5 CD患者和5正常对照的结肠。开放染色质测定鉴定与所有类型的调控元件（包括启动子、增强子和沉默子）相关的核小体耗尽的基因组区域。虽然这些测定提供了所有调节元件在特定组织或细胞样品中的位置的最完整注释，但缺点是它们不能确定所有调节元件在特定组织或细胞样品中的位置。 确定每个调控元件的精确功能（启动子、增强子、沉默子）。表观基因组学路线图项目和ENCODE项目已经在CD相关组织和免疫细胞中生成了组蛋白修饰数据，当与我们的数据整合时，将提供关键的监管注释，并有助于解释这些可变元件的功能。我们的长期目标是阐明遗传变异导致CD的基因组区域和分子机制。该提案将通过以下具体目标来促进这一目标：1）鉴定在CD患者的结肠组织和免疫细胞中具有遗传驱动的差异调节活性的基因组区域。将GWAS数据与我们来自基因分型CD患者和对照的开放染色质和转录组数据整合，我们将确定一组基于证据的CD患者中具有差异调节活性的基因组区域; 2）整合来自表观基因组学路线图项目（ERP）和ENCODE项目的表观遗传数据，以注释CD相关调节区域的功能。ERP和ENCODE已经从广泛的组织（包括结肠粘膜）和细胞类型（包括单核细胞、T细胞、上皮细胞和非免疫细胞群）中生成了数据。我们将使用这些数据来更好地表征CD相关细胞的调节活性以及该活性的细胞特异性。该项目将有助于填补我们检测与CD相关的遗传、染色质和转录变异的能力与解释该变异最终如何导致CD的能力之间的差距。

DESCRIPTION (provided by applicant): Crohn's disease (CD), one of the two major inflammatory bowel diseases, results 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 CD disease pathogenesis. Within these regions, there are over 5600 additional SNPs that are in linkage disequilibrium (LD) with the tag SNPs, and it is not known which of these contribute to CD. Most of these SNPs map to non-coding regions of the genome, suggesting that causal variants contribute to CD by modifying gene regulatory element activity. An important first step is to identify genomic regions that have differential regulatory activity in CD-relevant intestinal tissues, including colon, and cells, namely epithelial and immune cells, between affected and unaffected individuals. Towards this end, we have generated genetic, open chromatin, and transcriptome data from the colon tissue and immune cells obtained from 27 CD patients and 14 normal controls, and from macrophages, T cells and epithelial cells isolated from the colons of 5 CD patients and 5 normal controls. Open chromatin assays identify nucleosome-depleted genomic regions that are associated with all types of regulatory elements, including promoters, enhancers, and silencers. While these assays provide the most complete annotation of where all regulatory elements are in a particular tissue or cell sample, a weakness is their inability to identify the precise function (promoter, enhancer, silencer) of each regulatory element. The Epigenomics Roadmap Project and ENCODE Project has generated histone modification data in CD-relevant tissues and immune cells that when integrated with our data will provide critical regulatory annotations and will help explain the functions of these variable elements. Our long-term goal is to elucidate the genomic regions and molecular mechanisms by which genetic variation contributes to CD. This proposal will contribute to this goal through the following specific aims: 1) To identify genomic regions with genetically-driven differential regulatory activity in colon tissue and immune cells of CD patients. Integrating GWAS data with our open chromatin and transcriptome data from genotyped CD patients and controls, we will determine an evidence-based set of genomic regions with differential regulatory activity in CD patients; 2) To integrate epigenetic data from the Epigenomics Roadmap Project (ERP) and the ENCODE project to annotate functions of CD-associated regulatory regions. The ERP and ENCODE have generated data from a wide range of tissues, including colon mucosa, and cell types, including monocytes, T cells, epithelial, and non-immune cell populations. We will use these data to better characterize regulatory activity in CD-relevant cells, and the cell-specificity of this activity. Tis project will help fill the gap between our ability to detect genetic, chromatin, and transcriptiona variation linked to CD and our ability to explain how that variation ultimately contributes to CD.