Function of asthma- and allergic disease-associated risk variants and genes in lung immunecells

哮喘和过敏性疾病(AAD)在美国影响着超过2500万儿童和成人，AAD 在过去的40年里，发病率一直在上升。AAD具有显著的临床异质性，其原因是 多种重叠但不同的潜在疾病机制。既有先天的也有适应性的 免疫系统在哮喘的发病机制和疾病的异质性中起着关键作用。然而，对生物多样性的研究 哮喘的免疫细胞主要依赖于外周血细胞，外周血细胞具有不同的来源、组成 受体和功能比肺中的免疫细胞更多。我们的工作与其他人的工作相结合证明了 肺T细胞、B细胞、巨噬细胞和树突状细胞亚群与其 血液和其他组织中的对应物。因此，循环免疫细胞不是以组织为基础的模型 在对AADS的研究中，应将重点转移到肺部驻留的免疫细胞。在项目2中，我们 专注于发现引导特定肺部常驻免疫细胞功能的机制以及如何 基因变异扰乱了这些机制。大多数与AAD相关的基因变异传递的前提是 它们通过改变细胞类型特定的调控元件的属性从而改变其表达而发挥作用 靶基因，意味着这些变异的表型效应应该在同源基因中研究。 特定的肺细胞群。然而，最大的公共表达数量性状基因座(EQTL) 数据库，如GTEx，采样整个肺，这代表了许多不同类型的细胞的混合。几乎所有人 已知的关于免疫细胞遗传效应的研究来自于对外周血液免疫细胞的研究。因此， 从这些资源中推断AAD风险变量的影响不太可能反映它们的影响 与AAD相关的肺免疫细胞。因此，我们的总体目标是通过利用这一点来解决这些重大差距 协作计划的独特资源，以确定i)特定的肺免疫细胞类型与AADS的相关性 对免疫反应的贡献，II)遗传变异对这些反应的影响，III)不同的肺 免疫细胞类型协调以产生免疫反应，以及AAD相关因素对免疫反应的影响 炎症状态，以及iv)对AAD因果变体及其靶基因的功能影响。我们会 通过三个目标实现我们的目标。AIM 1将使用人类淋巴和髓系肺常驻免疫细胞来 确定刺激反应基因、增强子和刺激反应染色质的图景 以及遗传变异对这些反应的影响。目标2将确定推定的因果变量如何 影响哮喘相关条件下肺免疫细胞的基因表达和下游功能。目标 3将研究通过我们的组学研究确定的遗传变异在体内对 使用CRISPR和BAC转基因技术进行过敏刺激。实现我们的目标将链接特定于细胞的 免疫调节机制、AAD的遗传风险和特定基因，最终导致治疗 哮喘和过敏性疾病。

Asthma and allergic diseases (AADs) affect over 25 million children and adults in the United States, and AAD incidence has been increasing over the last 4 decades. There is significant clinical heterogeneity in AAD due to multiple overlapping but distinct underlying mechanisms of disease. Both innate and adaptive branches of the immune system play key roles in asthma pathogenesis and the heterogeneity of the disease. Yet, studies of immune cells in asthma have rely mostly on peripheral blood cells, which have different origins, composition, receptors and function than immune cells in the lung. Our work combined with those of others demonstrated that subsets of lung T cells, B cells, macrophages and dendritic cells have substantial differences from their counterparts in blood and other tissues. Thus, circulating immune cells are a poor model for tissue-based immune cells, and focus should shift toward lung-resident immune cells in studies of AADs. In Project 2, we focus on discovering mechanisms that guide the function of specific lung-resident immune cells and how genetic variation perturbs these mechanisms. The premise that most AAD-associated genetic variants impart their effects by changing the properties of cell type-specific regulatory elements thereby altering expression of target genes, implies that the phenotypic effects of these variants should be studied in homogenous populations of specific lung cells. Nevertheless, the largest public expression quantitative trait loci (eQTL) databases, such as GTEx, sample whole lung, which represents a mix of many different cell types. Nearly all that is known about genetic effects in immune cells are from studies of peripheral blood immune cells. As such, extrapolation of the effects of AAD risk variants from these resources are not likely to reflect their effects in AAD-relevant lung immune cells. Thus, our overall goal is to address these significant gaps by leveraging this collaborative program’s unique resources to determine i) how specific lung immune cell types relevant to AADs contribute to immune responses, ii) the effects of genetic variation on these responses, iii) how different lung immune cell types coordinate to generate immune responses and how this is skewed by AAD-relevant inflammatory states, and iv) the functional effects on AAD causal variants and their target genes. We will achieve our goals through 3 Aims. Aim 1 will use human lymphoid and myeloid lung-resident immune cells to determine the landscape of stimulation-responsive genes, enhancers and stimulation-responsive chromatin and the effects of genetic variation on these responses. Aim 2 will determine how putative causal variants affect gene expression and downstream function in lung immune cells under asthma relevant conditions. Aim 3 will investigate the role of genetic variation identified through our omics studies on the in vivo response to allergic stimulation using CRISPR and BAC transgenic technology. Achieving our goals will link cells-specific mechanisms of immune regulation, genetic risk in AAD and specific genes, ultimately leading to treatments for asthma and allergic diseases.