Functional Genomics of Alopecia Areata

 描述(申请人提供)：斑秃(AA)是美国最常见的自身免疫性疾病之一，终生风险为1.7%，影响所有种族约530万人。我们最近进行了一项全基因组关联研究，以确定导致再生障碍性贫血风险的常见等位基因，并确定了几个包含潜在易感基因的基因组区域。在我们的初步研究中，我们已经使用几种方法在斑秃患者样本中产生了重要和独特的基因组和遗传数据集资源，包括对1000个人进行GWAS基因分型，对&gt；400个人进行免疫芯片分析，对&gt；50个家系进行连锁分析，对100个人进行基因表达谱分析，对124个人进行GWAS区的定向重测序，以及对从连锁家系中选择的10个斑秃患者的整个外显子组进行测序。这些强大和高度集成的数据集提供了丰富的基础，在这一创新提议的背景下，可以从这些基础上询问AA候选基因的变异的功能意义。作为理解这些结果的生物学意义的第一步，我们现在必须对这些区域进行深入的测序分析，以确定驱动标签SNP关联的因果变异。常见疾病遗传结构的新图景包含了普通和罕见变异独立或协同作用以影响表型的小环境。了解这些变异在疾病发病机制中的影响是迈向新的再生障碍性贫血治疗的关键一步。这些研究非常及时，将使我们能够将再生障碍性贫血置于其他自身免疫性疾病的背景下，在这些疾病中，GWAS和深度测序已经在进行中。我们推测候选基因中的因果变异是发生再障的易感性的基础。这笔赠款的重点是进行深入的测序研究，以确定候选基因中的新变异，然后是几种体外条件下的变异的功能基因组学，这将使我们能够确定：1)导致再生障碍性贫血易感性的特定变异的性质；以及2)它们促进疾病发病的机制(S)。在这项提案中，我们将进行Exome-plus测序，并在我们之前的GWA区进行浓缩，以确定因果变异。然后，我们将询问在毛囊和免疫细胞中表达的候选基因中的变异的功能后果，重点是NKG2D途径。

 DESCRIPTION (provided by applicant): Alopecia Areata (AA) is one of the most common autoimmune diseases in the US, with a lifetime risk of 1.7%, it affects approximately 5.3 million individuals across all ethnic groups. We recently carried out a genome-wide association study (GWAS) to identify common alleles that contribute to risk of AA, and identified several genomic regions harboring potential susceptibility genes. In our Preliminary Studies, we have generated a significant and unique resource of genomic and genetic datasets in alopecia areata patient samples using several approaches, including GWAS genotyping on >1000 individuals, ImmunoChip on >400 individuals, Linkage analysis on >50 families, Gene expression profiling on >100 individuals, Targeted resequencing in GWAS regions in 124 individuals, and Whole exome sequencing in >10 alopecia areata probands selected from linkage families. These robust and highly integrated datasets provide a rich foundation from which to interrogate the functional significance of variants in AA candidate genes in the context of this innovative proposal. As a first step towards understanding the biological significance of these results, we must now perform deep sequencing analysis in these regions to identify causal variants that are driving the association of tagSNPs. The emerging picture of the genetic architecture of common diseases contains niches for both common and rare variants acting independently or in concert to influence phenotypes. Understanding the impact of these variants in disease pathogenesis is the first key step in moving toward novel therapies for AA. These studies are extremely timely, and will allow us to place AA into the context of other autoimmune diseases in which GWAS and deep sequencing is already underway. We postulate that causal variants in candidate genes underlie the susceptibility to develop AA. This grant is focused on carrying out deep sequencing studies to identify new variants in candidate genes, followed by functional genomics of variants in several in vitro contexts, which will allow us to determine: 1) the nature of the specific variats contributing to AA susceptibility; and 2) the mechanism(s) by which they contribute to disease pathogenesis. In this proposal, we will carry out Exome-plus sequencing with enrichment in our previous GWAS regions to identify causal variants. We will then interrogate the functional consequences of variants within candidate genes expressed in both the hair follicle and immune cells, with an emphasis on the NKG2D pathway.