Prioritizing and Characterizing T Cell-Relevant Genetic Variants Associated with Autoimmune Diseases

优先考虑和表征与自身免疫性疾病相关的 T 细胞相关遗传变异

• 批准号: 10040566
• 负责人: John Philip Ray
• 金额: $ 16.2万
• 依托单位: BENAROYA RESEARCH INST AT VIRGINIA MASON
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-12-18 至 2022-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10040566
• 关键词: Address; Affect; Alleles; Architecture; Autoimmune Diseases; Autoimmunity; BACH2 gene; Biological Assay; CRISPR interference; Cell Line; Cell physiology; Cells; ChIP-seq; Chromatin; Clustered Regularly Interspaced Short Palindromic Repeats; Complex; Disease; Disease susceptibility; Elements; Engineering; Epigenetic Process; Fluorescence-Activated Cell Sorting; Follow-Up Studies; Gene Expression; Genes; Genetic; Genetic Determinism; Genetic Variation; Genome; IRF1 gene; Immune; Immunohistochemistry; Inflammatory Bowel Diseases; Insulin-Dependent Diabetes Mellitus; Linkage Disequilibrium; Mediating; Multiple Sclerosis; Nucleic Acid Regulatory Sequences; Pathogenesis; Pathogenicity; Pathway interactions; Patients; Population; Psoriasis; Psoriatic Arthritis; Reading; Regulatory Element; Reporter; Rest; Rheumatoid Arthritis; STAT4 gene; T-Cell Activation; T-Lymphocyte; Testing; Therapeutic; United States; Untranslated RNA; Validation; Variant; Work; base; causal variant; cell type; exhaustion; follow-up; genetic variant; genome resource; genome wide association study; genomic data; insight; mRNA Expression; new therapeutic target; novel therapeutics; protein expression; response; transcription factor

PROJECT SUMMARY Greater than 8% of the United States population suffers from autoimmune disease, but, due to complex non- Mendelian inheritance, the genetic determinants of autoimmune disease are difficult to parse. To begin to address this problem, genome-wide association studies (GWAS) have identified thousands of genetic variants that track with disease, allowing the field of autoimmunity to focus on key disease-causal regions of the genome. However, the exact causal genetic variants for most of these associations remain unidentified, and thus the genes and pathways they alter remain poorly understood. To tackle this problem, I first will enrich for likely causal variants for diseases in which T cells are known to be pathogenic, including multiple sclerosis, type I diabetes, rheumatoid arthritis, psoriasis, and inflammatory bowel disease. I will use a high-throughput approach to test 20,000 variants for allelic skew in reporter expression. Furthermore, for 4 highly important GWAS loci (each with more than 10 disease associations), I will screen for regulatory regions that alter gene expression and the disease-associated variants that lie within these regions. With these two approaches (and other genomic data, such as chromatin accessibility and allele-specific transcription factor ChIP-seq), I will prioritize variants for engineering in the genomes of primary cells, and determine the effects of these engineered alleles on expression, activation, and polarization of T cells. This project will result in exhaustive characterization of variants associated to 5 important autoimmune diseases, elucidation of the regulatory architecture of 4 highly important disease loci, and experimental validation of 10 putatively causal variants through editing them into the genome of primary T cells. This work will provide an extensive resource for GWAS follow-up studies, help bring the field closer to understanding the pathways and regulatory architecture involved in disease, and inform approaches for identifying new targeted therapeutics for autoimmunity.

项目总结 超过8%的美国人口患有自身免疫性疾病，但由于复杂的非 孟德尔遗传，自身免疫性疾病的遗传决定因素很难解析。开始，开始 为了解决这个问题，全基因组关联研究(GWAS)已经确定了数千种遗传变异 它跟踪疾病，使自身免疫领域能够专注于 基因组。然而，这些关联中大多数的确切因果遗传变异仍未确定，并且 因此，它们改变的基因和途径仍然知之甚少。为了解决这个问题，我首先将丰富 T细胞已知是致病的疾病的可能原因变异，包括多发性硬化症， I型糖尿病、类风湿性关节炎、牛皮癣和炎症性肠病。我将使用高吞吐量的 测试20,000个变种在报告表达中的等位基因偏斜的方法。此外，对于4个非常重要的 Gwas基因座(每个都有10个以上的疾病关联)，我将筛选改变基因的调节区 表达和位于这些区域内的与疾病相关的变体。使用这两种方法(和 其他基因组数据，如染色质可及性和等位基因特异转录因子芯片序列)，我将 对原代细胞基因组中的工程变体进行优先排序，并确定这些变体的效果 基因工程等位基因对T细胞表达、激活和极化的影响。这个项目将导致详尽的 与5种重要的自身免疫性疾病相关的变异的特征、调控机制的阐明 4个高度重要的疾病基因座的结构，以及10个假定的因果变异的实验验证 通过将它们编辑到初级T细胞的基因组中。这项工作将为 GWAS后续研究，有助于使该领域更接近于了解路径和监管架构 与疾病有关，并为确定自身免疫的新靶向治疗方法提供信息。