Genomics of NFκB-mediated gene regulation in multiple sclerosis

摘要 多发性硬化（MS）是一种潜在的进行性、中枢神经系统的自身免疫性神经系统疾病 中枢神经系统（CNS）白色物质，推测由自身反应性CD4 + T细胞介导。这种疾病是 遗传易感性和环境因素的综合作用最近的全基因组关联研究（GWAS） 已经确定了超过100种与MS风险增加相关的遗传变异。 变异体属于有限数量的主要与免疫应答相关的信号级联， 细胞因子信号，这表明它们是遗传和环境线索 相互作用，使个体在疾病发作前易患自身免疫。但 这些变体影响免疫反应的功能机制，并最终导致 MS的发展在很大程度上尚不清楚。了解这些变异介导的疾病风险状态 将使我们能够确定MS的发病机制，并确定个体-无论遗传 负载-谁展示它，因此处于危险之中。因此，揭示这种状态对早期 诊断以及生物标志物和新治疗药物的开发。 NF κ B是先天性免疫和适应性免疫的主要调节因子， 分化和多种免疫细胞类型中的细胞因子产生，包括MS关键的CD4 + T细胞 发病机制GWAS研究已经确定NF κ B是多种肿瘤易感性的中心通路， 自身免疫性疾病，包括MS，和几个证据链支持其因果关系的作用：MS患者 显示出比对照组更高的NF κ B信号传导;许多GWAS风险变体影响NF κ B信号传导;以及几种MS 疾病调节剂抑制该途径。因此，它是一个很好的模型系统，以探讨 与疾病相关的信号级联的遗传介导的改变。在这里，我们提出一个 系统分析NF κ B信号传导的改变如何导致基因调控程序的改变， CD4 + T细胞功能，作为诱发风险状态的致病途径的原型。 为此，我们将（i）确定MS遗传变异如何改变CD 4 + T细胞中刺激依赖性NF κ B信号传导 改变基因调控;和（ii）确定NFkB结合位点中的MS风险变体如何影响 目标基因。我们将使用一种创新的、整合的全基因组基因组方法， NF κ B信号传导，其与顺式调节区的结合和伴随的激活以及产生的基因 表情因此，我们将开发一个实验范式，全面研究风险变量如何 影响基因调控导致自身免疫性疾病的风险。这些研究代表了重大创新， 他们采取综合的、无偏见的方法来理解NF κ B介导的 信号转导导致基因调控程序的改变和随后的CD4 + T细胞表型的差异。

Abstract Multiple sclerosis (MS) is a potentially progressive, autoimmune neurological disorder of the central nervous system (CNS) white matter presumably mediated by autoreactive CD4+ T cells. The disease is a consequence of both genetic predisposition and environmental triggers. Recent genome-wide association studies (GWAS) have identified over 100 genetic variants associated with increased risk of developing MS. Many of these variants fall in a limited number of signaling cascades primarily associated with immune responses and cytokine signaling, which suggests they are key biological nodes where genetic and environmental cues interact to predispose an individual towards autoimmunity, prior to the onset of disease. However, the functional mechanisms by which these variants impact immune responses, and ultimately lead to the development of MS, are largely unknown. Understanding the disease risk state mediated by these variants would allow us to determine both the pathogenesis of MS and also identify individuals – irrespective of genetic load – who exhibit it and are consequently at risk. Thus, uncovering this state has implications both for early diagnosis and the development of biomarkers and new therapeutic agents. NFκB is a master regulator of both innate and adaptive immunity, and is critical for activation, proliferation, differentiation, and cytokine production in multiple immune cell types, including the CD4+ T cells critical to MS pathogenesis. GWAS studies have identified NFκB as a central pathway in susceptibility to multiple autoimmune conditions including MS, and several strands of evidence support its causal role: MS patients exhibit higher NFκB signaling than controls; many GWAS risk variants affect NFκB signaling; and several MS disease-modifying agents inhibit this pathway. It is therefore an excellent model system to explore genetically mediated alterations in signaling cascades associated with disease. Here, we propose a systematic dissection of how alterations in NFκB signaling lead to altered gene regulatory programs and CD4+ T cell function, as an archetype of a disease-causing pathway inducing a risk state. To do so we will (i) establish how MS genetic variants alter stimulus-dependent NFκB signaling in CD4+ T cells alter gene regulation; and (ii) determine how MS risk variants in NFkB binding sites affect regulation of target genes. We will use an innovative, integrated genome-wide genomic approach simultaneously assessing NFκB signaling, its binding to and concomitant activation of cis-regulatory regions and resulting gene expression. Thus we will develop an experimental paradigm to comprehensively examine how risk variants affecting gene regulation lead to autoimmune disease risk. These studies represent significant innovation, as they take an integrative, unbiased approach to the problem of understanding how changes to NFκB-mediated signaling result in alterations to gene regulatory programs and subsequent differences CD4+ T cell phenotype.