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，影响了生活质量和寿命 受影响的人。尽管这些疾病具有遗传成分，但根据高发病率确定 单卵双胞胎，我们仍然对遗传学如何推动每种疾病的风险和进展如何了解。 全基因组关联研究已经确定了数百个自身免疫性疾病相关区域 基因组，但在这些地区的因果和非因果变体之间通常存在紧密的联系， 大多数与疾病相关的遗传变异型在非编码区域。因此，确定变体 促进疾病及其对疾病相关的细胞类型的影响具有挑战性。一种暗示的单元格 在许多自身免疫性疾病中，是T细胞。为了响应自我抗原，自动反应性T细胞在克隆上扩展和 迁移到目标组织，在那里它们造成组织破坏。与之相关的非编码遗传变异 自身免疫性疾病在T细胞的可访问染色质中富集，这表明疾病伴侣 变体改变了可能影响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 方法可以通过测试变体来鉴定可能因果变异的方法来改变调节区域 在特定于等位基因的记者分析中的活动，并在T细胞系中使用了这种方法来发现数百种 跨基因组的预测因果变体。下一个也许最艰巨的步骤是连接变体 它们对与疾病相关的细胞类型的功能的影响。在此提案中，我们旨在确定 改变T细胞增殖和迁移的非编码调节区域。首先，我们将使用小说 CRISPR干预屏幕以识别调节T细胞增殖和迁移的变体调节区域 朝着在发炎组织中发现的趋化因子。接下来，我们将在主要t中使用单细胞筛选方法 细胞以识别由变异调节区调节的基因。然后，我们将确定变体调节性 与T细胞功能协同作用或同义方式行动的区域，从而确定关系 在单独的遗传风险基因座及其对T细胞功能的影响之间。最后，我们将确定变体是否 影响T细胞功能也与自动反应性T细胞的患病率和疾病的严重程度有关 使用大型多发性硬化队列。如果成功，这项工作将在直接链接时取得首要飞跃 在自身免疫性疾病的细胞类型中，数百个风险基因座达到细胞功能，它将提供 深入了解遗传风险如何促进疾病。因此，我们的发现可能确定具有治疗目标的 治疗自身免疫性疾病的途径。