Defining the causality & biologic impact of genes within ulcerative colitis loci.

定义因果关系

• 批准号: 8439917
• 负责人: John D. Rioux
• 金额: $ 59.7万
• 依托单位: MONTREAL HEART INSTITUTE
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-15 至 2017-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8439917
• 关键词: Adolescent; Affect; Age; Alleles; Bioinformatics; Biological; Biological Assay; Biological Markers; Biological Process; Biology; Biometry; Biopsy; Candidate Disease Gene; Cell model; Cells; Chromosomes; Chronic; Clinical; Colon; Complement; Complex; Crohn' s disease; Custom; DNA; Data; Detection; Development; Diagnosis; Disease; Dose; Education; Environmental Risk Factor; Etiology; Family; Functional disorder; Gastrointestinal tract structure; Gene Expression Profiling; Genes; Genetic; Genetic Predisposition to Disease; Genetic Risk; Genetic Transcription; Genetic Variation; Genomics; Genotype; Guidelines; Health; Heritability; IL12B gene; Individual; Inflammation; Inflammatory Bowel Diseases; Inflammatory disease of the intestine; International; Investigation; JAK2 gene; Knowledge; Lead; Life; Light; Link; Modality; Molecular; Molecular Genetics; Morbidity - disease rate; Nature; Pathogenesis; Pathway interactions; Patient Care; Patients; Pharmaceutical Preparations; Phenotype; Play; Prevention strategy; Process; Publishing; RNA Interference; RNA Splicing; Relapse; Research; Research Personnel; Risk; Risk Factors; Role; STAT3 gene; Sampling; Signal Transduction Pathway; Social Welfare; Stress; System; Technology; Time; Ulcerative Colitis; Variant; Work; base; career; case control; cell type; cohort; disease classification; disorder risk; disorder subtype; falls; foot; genetic risk factor; genetic variant; genome wide association study; health economics; improved; innovation; insight; new therapeutic target; next generation sequencing; novel; protein expression; public health relevance; research study; small hairpin RNA; success; tool; young adult

DESCRIPTION (provided by applicant): Background: Genome-wide association studies (GWAS) have identified numerous loci for complex diseases. This success has been most notable for the inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC), where ~100 genetic risk factors have been discovered, some that are phenotype-specific and others that are common to more than one disease. But, how do disease-associated genes and their corresponding alleles exert their influence on the biology of health and disease? The genetic data indicates that IBD can emerge from the perturbations of distinct signal transduction pathways, resulting from the dysregulation of disease-causative genes. Hypothesis and specific aims: Although there has been tremendous success for identifying IBD genetic risk loci using GWAS, this approach primarily leads to the identification of common variants, most of which have modest genetic effect. We postulate that rare variants within these loci might be responsible for the effects observed. To tackle this issue, we propose to perform targeted re-sequencing of validated IBD loci to identify the causal (rare) variation. With the advent of next-generation sequencing technologies and access to well-phenotyped cohorts, we are now able to use this innovative approach, which is complementary to our previous work using GWAS, and sequence UC-associated loci to identify rare variants of greater genetic effect. These rarer, more penetrant, alleles are expected to have a more significant biological impact thus increasing the feasibility and relevance of performing allele-specific functional studies as we propose herein. Intestinal inflammation is a complex process involving an interplay genetic predisposition and environmental factors and can be the result of the dysregulation of different biological processes involving specific cell types. In an attempt to dissect this interplay between genetics and environmental factors and understand the complexity of UC pathogenesis, we will complement our genomics approach with a systematic approach to functionally characterize UC-associated genes in conjunction with different environmental stresses. Given the diverse expertise of our teams, we will combine several functional approaches, including gene-expression analysis, shRNA and allele-specific rescue experiments in different cell types to place the genes and their variants under study in functional pathways in the relevant cell type and environmental context. We anticipate that these studies will point to a subset of key pathways that are perturbed in UC to define disease-mechanism clusters and will provide a more complete picture of the complex biological networks involved in UC. Our specific aims are: Aim 1) To identify risk and protective alleles within UC-associated regions identified by GWAS We want to (1A) identify novel uncommon and rare variants by deep re-sequencing in samples from patients and controls and (1B) validate these novel variants by genotyping large cohorts. Aim 2) To determine the function of UC-candidate genes We propose to take a systematic stepwise approach to place UC-associated genes within biological pathways. We will: (2A) Determine the RNA and protein expression of confirmed UC genes in primary cells and colon biopsies from UC patients and control individuals; (2B) Perform targeted over- expression and RNA interference (RNAi) screens using cell-based functional assays (2C) Determine the biological impact of selected genes (and their variants) at a cell-specific context. Impact: Understanding the mechanisms through which genetic variation contributes to UC, although challenging, offers exciting and promising advances in biomedicine, both by providing new insights into the genetic and molecular basis of UC pathophysiology and by helping to improve diagnosis and therapy. The investigation of causal genes (and their variants) linked to UC combined with our high-throughput and cell-type specific functional analysis will provide a mechanistic understanding of the role of genetic factors in UC. The identification of causal genetic variants linked to UC and their functional implications could provide new guidelines for drug dose adjustment, for changes in treatment modalities and for prevention strategies.

背景：全基因组关联研究（GWAS）已经确定了许多复杂疾病的基因座。这一成功在炎症性肠病（IBD）、克罗恩病（CD）和溃疡性结肠炎（UC）中最为显著，在这些疾病中已经发现了约100种遗传风险因素，其中一些是表型特异性的，而另一些是不止一种疾病所共有的。但是，疾病相关基因及其对应的等位基因是如何对健康和疾病的生物学产生影响的呢？遗传数据表明，IBD可由致病基因失调引起的不同信号转导途径的扰动引起。假设和具体目的：尽管使用GWAS识别IBD遗传风险位点已经取得了巨大的成功，但这种方法主要是识别常见变异，其中大多数具有适度的遗传效应。我们假设这些基因座内的罕见变异可能是观察到的影响的原因。为了解决这个问题，我们建议对经过验证的IBD基因座进行靶向重测序，以确定原因（罕见）变异。随着下一代测序技术的出现和获得表型良好的队列，我们现在能够使用这种创新的方法，这是对我们以前使用GWAS的工作的补充，并对uc相关位点进行测序，以识别具有更大遗传效应的罕见变异。这些更罕见、更具渗透性的等位基因有望产生更显著的生物学影响，从而增加了我们在此提出的进行等位基因特异性功能研究的可行性和相关性。肠道炎症是一个复杂的过程，涉及遗传易感性和环境因素的相互作用，可能是涉及特定细胞类型的不同生物过程失调的结果。试图剖析这种相互作用