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

基本信息

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
项目类别：
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

项目摘要

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.

项目概要超过 8% 的美国人口患有自身免疫性疾病，但是，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。开始为了解决这个问题，全基因组关联研究（GWAS）已经识别出数千种遗传变异跟踪疾病，使自身免疫领域能够专注于关键的致病区域基因组。然而，大多数这些关联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，我首先将丰富已知 T 细胞致病的疾病（包括多发性硬化症）的可能致病变异， I 型糖尿病、类风湿性关节炎、牛皮癣和炎症性肠病。我将使用高吞吐量测试报告基因表达中 20,000 个变体的等位基因偏差的方法。此外，对于 4 个非常重要的 GWAS位点（每个位点与10多个疾病关联），我将筛选改变基因的调控区域表达以及这些区域内与疾病相关的变异。通过这两种方法（和其他基因组数据，例如染色质可及性和等位基因特异性转录因子 ChIP-seq），我会对原代细胞基因组中的工程变体进行优先排序，并确定这些变体的影响改造等位基因影响 T 细胞的表达、激活和极化。该项目将带来详尽的与 5 种重要自身免疫性疾病相关的变异特征，阐明调控机制 4 个高度重要的疾病位点的结构，以及 10 个假定因果变异的实验验证通过将它们编辑到原代 T 细胞的基因组中。这项工作将为 GWAS 后续研究，帮助该领域更深入地了解路径和监管架构参与疾病，并为确定新的自身免疫靶向治疗方法提供信息。