Functional validation of Rheumatoid Arthritis-associated distal regulatory SNPs i

类风湿关节炎相关远端调节 SNP 的功能验证 i

• 批准号: 8810054
• 负责人: Raymond David Hawkins
• 金额: $ 43.63万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-03-01 至 2019-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8810054
• 关键词: Address; Asthma; Autoimmune Diseases; Autoimmune Process; Automobile Driving; Binding; Biological Assay; CD4 Positive T Lymphocytes; Cataloging; Catalogs; Categories; Cells; ChIP-seq; Chromatin; Code; Crohn' s disease; Disease; Distal; Enhancers; Equilibrium; Etiology; Evaluation; Gene Expression; Gene Targeting; Genes; Genetic Risk; Goals; Health; Helper-Inducer T-Lymphocyte; Human; Immune system; Insulin-Dependent Diabetes Mellitus; Intercistronic Region; Introns; Light; Maps; Mediating; Methods; Multiple Sclerosis; Mutation; National Human Genome Research Institute; Nucleic Acid Regulatory Sequences; Pathogenesis; Play; Process; Psoriasis; Regulation; Regulatory Element; Reporter; Research; Rheumatoid Arthritis; Role; Series; Single Nucleotide Polymorphism; T cell differentiation; T cell regulation; T-Lymphocyte; Technology; Testing; Time; Twin Studies; Ulcerative Colitis; Validation; base; cell type; epigenomics; genome wide association study; genome-wide; high throughput screening; innovation; next generation sequencing; risk variant; trait; transcription factor

 DESCRIPTION (provided by applicant): Genome-wide association studies (GWASs) have produced large numbers of disease associated single-nucleotide polymorphisms (SNPs). However, many of these studies have failed to identify causative mutations. This may be due to the complexity of the disease; or in part, due to many associated SNPs lying outside of gene coding regions. A recent assessment of GWASs illustrated that 45% of disease or trait associated SNPs fell in introns, while 43% lie in intergenic regions. Global methods for determining chromatin states have shown that associated SNPs can overlap regulatory regions. We have constructed enhancer maps based H3K4me1 localization in isolated, human T cells, which were activated, or polarized toward Th1 or Th2 lineages. We focused on an early time point of polarization to determine the cis-regulome of early T cell differentiation and regulation f T cell fate commitment. To determine if rheumatoid arthritis-associated SNPs are potentially rSNPs, we analyzed the vicinities of associated SNPs from the NHGRI GWAS catalog for overlap with our global T helper cell enhancer predictions. Goal: Having identified 440 potential regulatory SNPs within enhancers driving early T cell fates, our goal is to functionally validate RA-associated rSNPs through a series of high-throughput assays and systematic evaluation to determine the most functionally relevant rSNPs. Through this process we will also determine the target genes of enhancers harboring rSNPs in order to identify new genes important in the etiology of RA pathogenesis. We will do so through the following specific aims. Specific Aim 1. Determine the effect of rSNPs on enhancer activity. Specific Aim 2. Identification of TFs and their disrupted binding at enhancer SNPs. Specific Aim 3. Identification of target genes for enhancers harboring associated SNPs

 描述（由申请人提供）：全基因组关联研究（GWAS）已经产生了大量与疾病相关的单核苷酸多态性（SNP）。然而，许多这些研究未能确定致病突变。这可能是由于疾病的复杂性；或者部分是由于许多相关的 SNP 位于基因编码区之外。最近的 GWAS 评估表明，45% 的疾病或性状相关 SNP 落在内含子中，而 43% 位于基因间区域。用于确定染色质状态的全局方法表明，相关的 SNP 可以与调控区域重叠。我们在分离的人类 T 细胞中构建了基于 H3K4me1 定位的增强子图谱，这些细胞被激活或极化为 Th1 或 Th2 谱系。我们专注于极化的早期时间点，以确定早期 T 细胞分化和调节 T 细胞命运承诺的顺式调控组。为了确定类风湿性关节炎相关的 SNP 是否可能是 rSNP，我们分析了 NHGRI GWAS 目录中相关 SNP 的邻近区域，以与我们的全球 T 辅助细胞增强子预测重叠。目标：在驱动早期 T 细胞命运的增强子内确定了 440 个潜在的调节 SNP，我们的目标是通过一系列高通量测定和系统评估来功能验证 RA 相关 rSNP，以确定功能最相关的 rSNP。通过这个过程，我们还将确定含有 rSNP 的增强子的靶基因，以便识别在 RA 发病机制中重要的新基因。我们将通过以下具体目标来实现这一目标。具体目标 1. 确定 rSNP 对增强子活性的影响。具体目标 2. 识别 TF 及其在增强子 SNP 处的破坏结合。具体目标 3. 鉴定含有相关 SNP 的增强子的靶基因