HLA and KIR Genomics in Inflammatory Bowel Disease

描述（由申请人提供）：两种常见的炎症性肠病（IBD），克罗恩病（CD）和溃疡性结肠炎（UC）是胃肠道的慢性复发缓解性疾病。相关研究已经确定了这两种疾病的一些易感基因，涉及适应性和先天免疫对肠道微生物的反应，以及CD，疾病易感性中的自噬途径。与几乎所有的自身免疫性和炎症性疾病一样，HLA I类和II类基因座的等位基因变异与UC和CD均相关。基于我们以前的工作，特定的HLA单倍型（例如，DRB 1 *0103-DQB 1 *0301）特别强，并且基于我们最近的GWAS，最强的SNP关联是与特定的临床亚型（例如DRB 1 * 0103-DQB 1 *0301）。医学难治性UC）。天然杀伤细胞（NK）在先天免疫中对IBD风险的贡献尚未得到很好的研究。NK细胞由编码细胞表面受体的几个基因家族控制。刺激性和/或抑制性KIR受体使用HLA I类上的多态性表位作为其同源配体。在最近的CD研究中，我们发现抑制性KIR杂合子（KIR 2DL 2/KIR 2DL 3）在其HLA配体（CI）缺失时与保护显著相关，并且在CI配体纯合性存在时与易感性显著相关。我们建议通过研究HLA和KIR等位基因、单倍型和KIR基因-HLA配体对在临床明确定义的高加索人和西班牙裔波多黎各人的CD和UC队列中的作用来扩展这项工作。我们将使用我们新开发的Roche 454 GS FLX测序系统进行等位基因HLA解析，并将完成我们的KIR（16基因）454检测试剂盒的开发和验证，以对我们队列中的两种基因复合物进行测序。将检查高加索人（1300例患者/550例对照和100个家庭三人组）和波多黎各人（300例患者/200例对照）CD队列，以及高加索人（300例难治性疾病患者/550例对照）和波多黎各人（200例患者/200例对照）UC队列。我们还将开发生物信息学工具来处理高度多态性HLA和KIR基因的复杂分析，并通过NIAID与BISC合作的ImmPort提供这些数据管理和分析工具。

DESCRIPTION (provided by applicant): The two common inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing, remitting conditions of the gastrointestinal tract. Association studies have identified a number of susceptibility genes for both diseases, implicating both adaptive and innate immunity in response to intestinal microbes and, for CD, the autophagy pathway in disease susceptibility. As with virtually all autoimmune and inflammatory disease, allelic variation at the HLA class I and class II loci has been associated with both UC and CD. Based on our previous work, the association of specific HLA haplotypes (eg. DRB1*0103-DQB1*0301) is particularly strong and, based on our recent GWAS, the strongest SNP association is with particular clinical subtypes (eg. medically refractory UC). The contribution of the natural killer cells (NK) in innate immunity to the risk of IBD has not been as well examined. NK cells are controlled by several gene families that encode cell surface receptors. The stimulatory and/or inhibitory KIR receptors use polymorphic epitopes on HLA class I as their cognate ligands. In a recent study of CD, we found inhibitory KIR heterozygotes (KIR2DL2/KIR2DL3) significantly associated with protection in the absence of their HLA ligand (CI), and predisposing in the presence of CI ligand homozygosity. We propose to expand this work by examining the role of HLA and KIR alleles, haplotypes and KIR gene-HLA ligand pairs with clinically well-defined CD and UC cohorts of Caucasian and Hispanic-Puerto Rican ancestry. We will use our newly developed Roche 454 GS FLX sequencing system for allelic HLA resolution, and will finish development and validation on our KIR (16 gene) 454 assays to sequence both gene complexes in our cohorts. Caucasian (1300 patients/550 controls and 100 family trios) and Puerto Rican (300 patients/200 controls) CD cohorts, and Caucasian (300 patients with medically refractory disease/550 controls) and Puerto Rican (200 patients/200 controls) UC cohorts will be examined. We will also develop bioinformatic tools to deal with the complex analysis of the highly polymorphic HLA and KIR genes, and make these data management and analysis tools available through NIAID's ImmPort in partnership with BISC.