Investigating Genetic and Epigenetic Control of T Cell Function in Autoimmunity

摘要 在美国有2400万人患有自身免疫性疾病，影响生活质量和寿命 受影响的个体。虽然这些疾病具有遗传成分，但从#年的高发病率确定 同卵双胞胎，我们仍然对遗传如何驱动每种疾病的风险和进展知之甚少。 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，但在这些区域的因果和非因果变异之间往往存在紧密的连锁不平衡， 而且大多数与疾病相关的遗传变异都在非编码区。因此，确定 促进疾病及其对疾病相关细胞类型的影响是具有挑战性的。一种被牵连的细胞类型 在许多自身免疫性疾病中存在T细胞。作为对自身抗原的反应，自身反应性T细胞克隆扩增并 迁移到目标组织，在那里它们会导致组织破坏。与以下相关的非编码遗传变异 自身免疫性疾病在T细胞的可及染色质中丰富，这表明疾病的病因 变异体改变了可能影响T细胞功能的增强剂，使它们更具致病性。我们最近创建了一个 通过测试变异是否改变调控区域来识别可能的因果变异的方法 在等位基因特异性报告分析中的活性，并在T细胞系中使用这种方法发现了数百个 假设是基因组中的因果变异。下一步，也可能是最令人望而生畏的一步是将变种 它们对疾病相关细胞类型的功能的影响。在这项提案中，我们的目标是在 改变T细胞增殖和迁移的非编码调节区。首先，我们将用一本小说 CRISPR干扰筛选以确定调节T细胞增殖和迁移的不同调节区 在发炎组织中发现的趋化因子。接下来，我们将在初级T细胞中使用单细胞筛查方法 细胞来识别由不同的调节区调节的基因。然后我们将确定不同的监管 协同作用或以上位方式作用于T细胞功能的区域，从而识别一种关系 不同遗传风险基因座之间的关系及其对T细胞功能的影响。最后，我们将确定变种是否 影响T细胞功能的因素也与自身反应性T细胞的流行和疾病严重程度有关 使用了一个庞大的多发性硬化症队列。如果成功，这项工作将在直接链接方面迈出第一步 在自身免疫性疾病相关的细胞类型中，数百个风险基因与细胞功能有关，它将提供 对遗传风险如何促进疾病的洞察。因此，我们的发现可能确定治疗的靶向性 自身免疫性疾病的治疗途径。

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.