A single cell pooling framework for deciphering the regulatory wiring of allergy in pathophysiologic contexts

变态反应是一项重大的世界卫生挑战，影响着25%的人，发病率正在上升。花生过敏 仅此一项就影响了美国2.2%的学龄儿童，并可能危及生命。过敏是一种复杂的疾病， 遗传和环境因素都是导致风险的因素。为了找出潜在的遗传风险 变种，全基因组关联研究(GWAS)已经在数十万个 患者和对照，识别&gt；100个相关基因座。绝大多数的点击量都是在注释不佳的情况下 基因组的非编码区，被认为影响基因调控。面临的一个重大挑战 了解过敏(和所有复杂的疾病)就是找出原因变量(S)并定义分子 机械装置。所需的广泛的后续工作往往没有进行，因此过敏反应很少发生 有助于我们对疾病病因的理解。为了挖掘丰富的人类疾病资源 与其他协会一样，需要有新的方法来系统地诠释监管效果。现有的目录是 稀疏和偏向于特定的细胞类型(血液)、上下文(稳定状态条件)、分子 机制(基因表达的扰动)和种群(高加索人)。考虑到高度的细胞类型和 基因调控的特定于上下文的性质，这个有限的窗口不太可能足以识别 大多数人类风险变种。到目前为止，绘制调控效应图的最全面努力是基因型- 组织表达计划(GTEx)，在54个组织中定位影响基因表达的基因座(EQTL) 使用了数百名健康人的尸检样本。尽管其范围很广，但到目前为止，GTEx目录 只解释了11%的复杂疾病的遗传风险，建议额外的分析和样本 需要挖掘出导致疾病的大多数监管效应。在本申请中，我提出了一种 一种创新的方法来系统地编目基因变异对大规模 在不同的过敏相关细胞类型和患者样本中进行扩展。至关重要的是，这种可伸缩的方法可以 适应细胞刺激条件(例如，过敏原挑战)，包括不同的人类祖先 可在稀少的人体组织和血液样本上部署。通过利用单个细胞 在这一框架下，我们能够探索作为疾病介体发挥重要作用的稀有细胞群。这就做 将该方法应用于过敏相关的GTEx组织以及代表过敏的大规模生物库 异质性病例。这项研究有望极大地扩大对遗传生物学的了解。 与过敏相关的基因座并阐明多组单细胞方法的潜力，病理生理学 刺激，和患者的生物标本，以发现遗漏的复杂疾病的遗传性。

Allergy is a major world health challenge affecting 25% of people with a rising incidence. Peanut allergy alone affects 2.2% of school children in the US and can be life-threatening. Allergy is a complex disease, with both genetic and environmental factors contributing to risk. In order to pinpoint the underlying genetic risk variants, genome-wide association studies (GWAS) have been performed on hundreds of thousands of patients and controls, identifying >100 associated loci. The vast majority of hits are in poorly annotated noncoding regions of the genome and are thought to influence gene regulation. A major challenge for understanding allergy (and all complex diseases) is pinpointing the causal variant(s) and defining molecular mechanisms. The extensive follow up work required is often not undertaken and thus allergy GWAS rarely contribute to our understanding of disease etiology. In order to mine the rich resource of human disease associations, new methods are needed to systematically annotate regulatory effects. Existing catalogs are sparse and biased toward specific cell types (blood), contexts (steady state conditions), molecular mechanisms (perturbation of gene expression), and populations (Caucasians). Given the highly cell type and context specific nature of gene regulation, this limited window is unlikely to be sufficient for identifying most human risk variants. The most comprehensive effort to date to map regulatory effects is the Genotype- Tissue Expression Project (GTEx), which mapped loci that influence gene expression (eQTLs) in 54 tissues using autopsy specimens from hundreds of healthy individuals. Despite its scope, the GTEx catalog thus far explains only 11% of the genetic risk of complex disease, suggesting additional assays and specimens are needed to unearth the majority of regulatory effects contributing to disease. In this application I propose an innovative approach to systematically catalog the gene regulatory effects of genetic variants on a massive scale across diverse allergy-relevant cell types and patient specimens. Crucially, this scalable approach can accommodate cell stimulation conditions (e.g., allergen challenge), inclusion of diverse human ancestry groups, and is deployable on scant human tissue and blood specimens. By leveraging a single cell framework, we are able to probe rare cell populations that play essential roles as mediators of disease. I will apply this method to allergy relevant GTEx tissues as well as a large-scale allergy biobank representing heterogenous cases. This study is expected to provide a greatly expanded window into the biology of genetic loci linked to allergy and elucidate the potential of multi-omic single cell approaches, pathophysiological stimuli, and patient biospecimens to unearth missing complex disease heritability.