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

定义因果关系

• 批准号: 8644262
• 负责人: John D. Rioux
• 金额: $ 59.33万
• 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/8644262
• 关键词: Adolescent and Young Adult; 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; rare variant; research study; risk variant; small hairpin RNA; success; tool

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.

描述（由申请人提供）： 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) 方面最为引人注目，已发现约 100 种遗传风险因素，其中一些是表型特异性的，另一些是多种疾病所共有的。但是，疾病相关基因及其相应的等位基因如何对健康和疾病的生物学产生影响？遗传数据表明，IBD 可能是由于致病基因失调导致的不同信号转导途径的扰动而引起的。假设和具体目标：尽管使用 GWAS 识别 IBD 遗传风险位点取得了巨大成功，但这种方法主要导致常见变异的识别，其中大多数变异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造成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 位点进行有针对性的重测序，以识别因果（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方法，这与我们之前使用 GWAS 的工作相补充，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预计将具有更显着的生物学影响，从而增加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，涉及遗传倾向和环境因素的相互作用，并且可能是涉及特定细胞类型的不同生物过程失调的结果。试图剖析两者之间的相互作用 遗传学和环境因素并了解 UC 发病机制的复杂性，我们将用系统方法来补充我们的基因组学方法，以结合不同的环境压力对 UC 相关基因进行功能表征。鉴于我们团队的多元化专业知识，我们将结合多种功能方法，包括不同细胞类型中的基因表达分析、shRNA 和等位基因特异性拯救实验，以将基因及其变体置于相关细胞类型和环境背景下的功能途径中进行研究。我们预计这些研究将指出 UC 中受到干扰的关键途径的子集，以定义疾病机制簇，并将提供 UC 中涉及的复杂生物网络的更完整的图景。我们的具体目标是： 目标 1) 识别 GWAS 识别的 UC 相关区域内的风险和保护性等位基因 我们希望 (1A) 通过对患者和对照样本进行深度重测序来识别新的不常见和罕见变异，并 (1B) 通过对大型队列进行基因分型来验证这些新变异。目标 2) 确定 UC 候选基因的功能 我们建议采取系统的逐步方法将 UC 相关基因置于生物途径中。我们将： (2A) 确定 UC 患者和对照个体的原代细胞和结肠活检中已确认的 UC 基因的 RNA 和蛋白质表达； (2B) 使用基于细胞的功能测定进行靶向过度表达和 RNA 干扰 (RNAi) 筛选 (2C) 确定所选基因（及其变体）在细胞特定环境下的生物学影响。影响：了解遗传变异导致 UC 的机制虽然具有挑战性，但通过提供对 UC 病理生理学的遗传和分子基础的新见解以及帮助改进诊断和治疗，为生物医学提供了令人兴奋和有希望的进展。对与 UC 相关的致病基因（及其变异体）的研究结合我们的高通量和细胞类型特异性功能分析，将为遗传因素在 UC 中的作用提供机制上的理解。识别与 UC 相关的因果遗传变异及其功能意义可以为药物剂量调整、治疗方式的改变和预防策略提供新的指导。