Effect of Crohn's Disease Risk Alleles on Enteric Microbiota

克罗恩病风险等位基因对肠道微生物群的影响

基本信息

批准号：
8147921
负责人：
ELLEN LI
金额：
$ 25万
依托单位：
WASHINGTON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-06-24 至 2012-05-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8147921
关键词：
Abscess Affect Age Alleles Antibiotics Bacterial Genome Bacteroidetes Biological Assay Blood Censuses Childhood Ciprofloxacin Clinic Clinical Code Collection Colorado Confounding Factors (Epidemiology)Containment Crohn&apos s disease Data Databases Discipline Disease Enteral Escherichia coli Gene Expression Genetic Genetic screening method Genome Genotype Guns Human Human Microbiome Immune response Individual Inflammatory Inflammatory Bowel Diseases Inflammatory disease of the intestine Institution Intestines Lead Link Medical center Metagenomics Mining Molecular Analysis Multivariate Analysis New Mexico North Carolina Onset of illness Operative Surgical Procedures Organism Outcome Paneth Cells Pathogenesis Patients Pharmaceutical Preparations Phase Phenotype Placebos Population Procedures Randomized Recombinant DNA Reporting Ribosomal RNA Risk Role SNP genotyping Sampling Sequence Analysis Shotgun Sequencing Shotguns Smoke Smoking Subgroup T-Lymphocyte Testing Therapeutic immunosuppression Time Tissues Universities Virulence Virulence Factors Washington base commensal microbes disorder risk genome sequencing microbial microbiome microorganism interaction novel prospective public health relevance rRNA Genes

项目摘要

DESCRIPTION: Abnormal host-microbial interactions are implicated in the pathogenesis of inflammatory Bowel disease (IBD). Crohn's disease (CD) risk alleles, such as the NOD2 and ATG16L1, have been associated with defective host containment of commensal bacteria. We hypothesize that these CD risk alleles contribute to compositional changes in intestinal microbiota. These changes in microbiota might reduce the proportion of protective commensal organisms and increase the numbers of proinflammatory organisms that incite intestinal inflammation. We propose to take a metagenomic approach towards testing this hypothesis in three Specific Aims: 1.) Analyze the effect of CD-risk alleles on mucosal associated microbiota in GI tissues collected from ileal CD, non-ileal IBD and non-IBD patients; 2. ) Develop and test novel genetic probes for pro-inflammatory commensal organisms; 3.) Expand prospective collection of GI tissues in four major IBD centers. During the UH2 pilot year, we will focus our study on 755 existing GI tissues from 364 subjects already collected at three institutions. High throughput 16S rRNA sequence analysis of the combined ileal tissues and high throughput genotyping for all highly reproducible CD risk alleles (~30, including NOD2 and ATG16L1) will be performed at Washington University. Quantitative PCR will be performed to quantify specific microbial subgroups. Multivariate analysis of the metagenomic data and the genotyping data will include potentially confounding variables such as age, disease state, medications and smoking. The adherent invasive E. coli (AIEC) are a novel group of bacterial strains that have been implicated as candidate "pathogenic" organisms that incite intestinal inflammation. Because there is limited genome information on AIEC strains, we will produce genome sequences of AIEC strains isolated from the GI tissues. During the UH3 phase of the project, prospective collection of GI tissues from 700-800 ileal CD, non-ileal IBD and non-IBD patients a year will be conducted at four major IBD centers: Washington University, University of North Carolina, Cleveland Clinic, and Mount Sinai Medical Center. Shotgun sequencing will be performed on selected fecal samples linked to the ileal tissues to identify additional, or auxiliary, or synergistic pathogenic factors or other functional changes in the microbiome that are contributed by uncultivatable organisms. Genetic probes for pathogenic commensal organisms developed by mining the bacterial genome data and shotgun sequencing data will be used to test the hypothesis that increased numbers of these organisms are associated with dysbiosis and/or CD risk alleles. Our combined expertise in multiple disciplines across multiple institutions, our demonstrated ability to collect a large number of well-phenotyped samples with longitudinal clinical information that will be linked to host response profiling and morphologic studies, and our consortium's capacity for high-throughput sequencing will be used to investigate how alterations in the human microbiome relate to CD risk alleles and CD pathogenesis. PUBLIC HEALTH RELEVANCE: We have combined expertise in multiple disciplines and the capability to collect a large number of well-phenotyped human clinical samples across six institutions (Washington University in St. Louis, University of North Carolina, University of Colorado, University of New Mexico, Mount Sinai Medical Center, and Cleveland Clinic) with the capacity for high-throughput sequencing at the Genome Center at Washington University to study how alterations in the human intestinal microbiome relate to Crohn's disease.

描述：异常的宿主 - 微生物相互作用与炎症性肠病（IBD）的发病机理有关。克罗恩病（CD）风险等位基因，例如NOD2和ATG16L1，与共生细菌的宿主遏制有缺陷有关。我们假设这些CD风险等位基因有助于肠道菌群的组成变化。微生物群的这些变化可能会减少保护性共生生物的比例，并增加促进肠道炎症的促炎生物的数量。我们建议采取一种宏基因组方法来检验这一假设的三个特定目的：1。）分析CD危险等位基因对胃CD，非回离IBD和非IBD患者的GI组织中粘膜相关微生物群的影响； 2。）开发和测试用于促炎的共生生物的新型遗传探针； 3.）扩大四个主要IBD中心的GI组织的预期收集。在UH2试点年度，我们将研究研究来自已经在三个机构收集的364名受试者的755个现有GI组织。华盛顿大学将对所有高度可重现的CD风险等位基因（包括NOD2和ATG16L1）进行高吞吐量16S rRNA序列分析和所有高度可重现的CD风险等位基因（包括〜30，包括30，包括30）的高通量基因分型分析。定量PCR将进行量化特定的微生物亚组。宏基因组数据和基因分型数据的多元分析将包括可能混淆的变量，例如年龄，疾病状态，药物和吸烟。粘附的侵入性大肠杆菌（AIEC）是一组新型的细菌菌株，这些菌株被认为是促使肠道炎症的候选“致病”生物。由于关于AIEC菌株的基因组信息有限，因此我们将产生从GI组织分离的AIEC菌株的基因组序列。在该项目的UH3阶段，将在四个主要的IBD中心（华盛顿大学，北卡罗来纳州大学，克利夫兰诊所和西奈山医疗中心）进行预期收集的GI组织，每年700-800次回肠CD，非回离IBD和非IBD患者。将对与回肠组织相关的选定粪便样品进行shot弹枪测序，以鉴定由不可培养的生物体造成的其他微生物组的其他，辅助或协同的致病因素或其他功能变化。通过挖掘细菌基因组数据和shot弹枪测序数据而开发的致病性共生生物的遗传探针将用于检验以下假设：这些生物数量增加与营养不良和/或CD风险等位基因有关。我们在多个机构的多个学科中的综合专业知识，我们证明的能力，可以收集大量具有纵向的临床信息的良好的样本，这些样本将与宿主反应分析和形态学研究以及我们的财团的高通量测序能力有关，将用于调查人类微生物与CD CD CD CD CD CD CD CYD CYCERESISOS中的变化。公共卫生相关性：我们将多个学科的专业知识结合在一起，并有能力在六家机构（华盛顿大学，圣路易斯的华盛顿大学，北卡罗来纳大学，新墨西哥州大学，新墨西哥大学，西奈山山和克利夫兰山诊所的高级统一中心置于基因组合的能力）上，在六个机构中收集大量良好的人类临床样本（华盛顿大学，华盛顿大学微生物组与克罗恩病有关。