Investigating Genetic and Epigenetic Control of T Cell Function in Autoimmunity

研究自身免疫中 T 细胞功能的遗传和表观遗传控制

• 批准号: 10687531
• 负责人: John Philip Ray
• 金额: $ 155.97万
• 依托单位: BENAROYA RESEARCH INST AT VIRGINIA MASON
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-08 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10687531
• 关键词: Affect; Alleles; Area; Autoantigens; Autoimmune Diseases; Autoimmunity; Biological Assay; CRISPR interference; Cell Line; Cell physiology; Cells; Chromatin; Clonal Expansion; Disease; Enhancers; Epigenetic Process; Genes; Genetic; Genetic Risk; Genome; Goals; Incidence; Individual; Link; Linkage Disequilibrium; Longevity; Methodology; Monozygotic twins; Multiple Sclerosis; Nucleic Acid Regulatory Sequences; Pathogenicity; Pathway interactions; Persons; Prevalence; Quality of life; Reporter; Risk; Severity of illness; T-Cell Proliferation; T-Lymphocyte; Testing; Therapeutically Targetable; Tissues; United States; Untranslated RNA; Variant; Work; autoreactive T cell; causal variant; cell motility; cell type; chemokine; cohort; disorder risk; genetic variant; genome wide association study; insight; migration; novel; response; risk variant; screening

SUMMARY ~24 million people in the United States have an autoimmune disease, impacting quality of life and longevity of the affected individuals. While these diseases have a genetic component, as determined from high incidence in monozygotic twins, we still know very little about how genetics drives risk and progression for each disease. Genome-wide association studies have identified hundreds of autoimmune disease-associated regions of the genome, but there is often tight linkage disequilibrium between causal and non-causal variants in these regions, and most disease-associated genetic variants are in non-coding regions. Thus, determining the variants that promote disease and their effects on disease-relevant cell types is challenging. One cell type that is implicated in many autoimmune diseases is the T cell. In response to self-antigen, autoreactive T cells clonally expand and migrate to target tissues, where they cause tissue destruction. Non-coding genetic variants associated with autoimmune diseases are enriched within the accessible chromatin of T cells, suggesting that disease-causal variants alter enhancers that may affect T cell function, making them more pathogenic. We recently created a methodology to identify likely causal variants through testing variants for whether they alter regulatory region activity in allele-specific reporter assays and have used this methodology in a T cell line to discover hundreds of putatively causal variants across the genome. The next and perhaps most daunting step is to connect variants to their effect on the function of disease-relevant cell types. In this proposal, we aim to identify variants in non-coding regulatory regions that alter T cell proliferation and migration. First, we will use a novel CRISPR-interference screen to identify variant regulatory regions that regulate T cell proliferation and migration toward chemokines found in inflamed tissues. Next, we will use a single-cell screening approach in primary T cells to identify the genes modulated by variant regulatory regions. We will then determine variant regulatory regions that act synergistically or in an epistatic manner on T cell function, thereby identifying a relationship between separate genetic risk loci and their effects on T cell function. Finally, we will determine whether variants that influence T cell function are also associated with the prevalence of autoreactive T cells and disease severity using a large multiple sclerosis cohort. If successful, this work will take the first leap in directly linking hundreds of risk loci to a cellular function in an autoimmune disease-relevant cell type and it will provide insight into how genetic risk promotes disease. Our findings may therefore identify therapeutically targetable pathways for treatment of autoimmune diseases.

概括 美国约有 2400 万人患有自身免疫性疾病，影响着人们的生活质量和寿命 受影响的个人。虽然这些疾病具有遗传成分，但从高发病率可以看出 对于同卵双胞胎，我们对遗传学如何驱动每种疾病的风险和进展仍然知之甚少。 全基因组关联研究已经确定了数百个与自身免疫性疾病相关的区域 基因组，但这些区域的因果变异和非因果变异之间通常存在紧密的连锁不平衡， 大多数与疾病相关的遗传变异都位于非编码区。因此，确定变体 促进疾病及其对疾病相关细胞类型的影响具有挑战性。涉及的一种细胞类型 在许多自身免疫性疾病中，T细胞发挥着重要作用。为了响应自身抗原，自身反应性 T 细胞克隆扩增并 迁移到目标组织，导致组织破坏。与相关的非编码遗传变异 自身免疫性疾病在 T 细胞可及的染色质中富集，这表明致病因素 变异体改变可能影响 T 细胞功能的增强子，使其更具致病性。我们最近创建了一个 通过测试变异是否改变监管区域来识别可能的因果变异的方法 等位基因特异性报告基因检测中的活性，并在 T 细胞系中使用这种方法发现了数百个 整个基因组中假定的因果变异。下一步也许是最艰巨的步骤是连接变体 其对疾病相关细胞类型功能的影响。在这个提案中，我们的目标是识别变体 改变 T 细胞增殖和迁移的非编码调节区。首先，我们将使用一本小说 CRISPR 干扰筛选，鉴定调节 T 细胞增殖和迁移的变异调节区 针对发炎组织中发现的趋化因子。接下来，我们将在原代 T 细胞中使用单细胞筛选方法 细胞识别受变异调控区调节的基因。然后我们将确定变体监管 对 T 细胞功能具有协同作用或上位性作用的区域，从而确定关系 不同遗传风险位点及其对 T 细胞功能的影响之间的关系。最后，我们将确定是否存在变体 影响 T 细胞功能的因素还与自身反应性 T 细胞的流行和疾病严重程度相关 使用大型多发性硬化症队列。如果成功的话，这项工作将迈出直接链接的第一步 自身免疫性疾病相关细胞类型中数百个细胞功能的风险位点，它将提供 深入了解遗传风险如何促进疾病。因此，我们的研究结果可能会确定治疗目标 治疗自身免疫性疾病的途径。