Transancestral fine mapping and functional dissection of autophagy-related SLE risk loci

系统性红斑狼疮(SLE)是一种慢性、异质性自身免疫性疾病。 影响妇女，疾病往往更严重，在非白人人群中有终末器官损害。一些 系统性红斑狼疮存在有效的治疗方法，很大程度上是因为对其病因还不完全了解；然而， 在环境的触发下，疾病很可能发生在遗传易感的个体中。多基因组 广谱关联研究和复制研究已经确定了约100个(80个已发表，20个在 发表过程)SLE易感基因座(P&lt；5x10-8)主要使用来自欧洲和亚洲的人群。 我们最近对亚洲人进行的韩国GWA和其他已发表的研究表明，存在许多自噬现象-- SLE的相关基因座，与其他几种自身免疫性疾病相似。自噬是一个细胞内的过程。 将受损的细胞器、大分子聚集体或细胞内病原体运送到 用于降解和回收的溶酶体。自噬与免疫系统和控制系统的相互作用 炎症通过作用于各种免疫细胞来调节免疫动态平衡和调节宿主 防御。对与SLE相关的自噬相关基因进行精细定位是了解SLE的必要条件 这些遗传变异如何影响特定免疫细胞类型中自噬途径的不同方面， 可能成为治疗SLE的新药靶点。由于连锁不平衡(LD)，每个风险基因包含 多个变异，在某些情况下，多个基因可能影响与SLE相关的生物功能 发病机制。在目标1中，我们建议利用亚洲人和非洲人之间的LD结构差异 祖先将对与以下疾病相关的7个SLE风险基因进行跨种族精细定位和生物信息学分析 自噬(ATG16L2-FCHSD2-P2RY2、PRDM1-ATG5、DRAM1、CDKN1B、CLEC16A、NCF2和HIP1)使用 全球筛查阵列(GSA)，包含SLE病例和对照的自定义变体的净空 非白人少数民族(4000名亚洲人和3000名非洲裔美国人[AA])。通过比较单倍型结构和 应用贝叶斯方法，我们将获得最可信的变种集以供进一步研究。在目标2中，我们 将通过使用生物信息学和分子方法来识别功能变体来完善可信的变体列表。 这将包括对100名AA SLE患者和100名AA对照组(年龄匹配)的免疫细胞亚群进行分类 和性别)用于RNA-seq和qRT-PCR来关联等位基因类型与差异基因表达和 剪接以及进行分子生物学分析。最优秀的候选人将在目标3至 进行免疫表型、RNA-seq和自噬功能分析，以评估基因- 编辑免疫细胞系和诱导多能干细胞(IPSCs)，这将确定相关的细胞 来自SLE患者和对照组的亚群进行自噬功能分析以确认基因分型 效果。我们的结果将确定SLE风险基因座的遗传变异及其分子/细胞 导致自噬途径失调的机制有助于系统性红斑狼疮的发展。

Systemic lupus erythematosus (SLE) is a chronic, heterogeneous autoimmune disease that disproportionally affects women and the disease is often more severe with end-organ damage in non-white populations. Few effective treatments exist for SLE, largely because the etiology is incompletely understood; however, the disease is likely to occur in genetically susceptible individuals upon environmental triggers. Multiple genome wide association studies (GWAS) and replication studies have identified ~100 (80 published and 20 in the publishing process) SLE susceptibility loci (P<5x10-8) using mainly European- and Asian-derived populations. Our recent Korean GWAS and other published studies of Asians have implicated a number of autophagy- related gene loci in SLE, similar to several other autoimmune diseases. Autophagy is an intracellular process that transports damage cytoplasmic organelles, macromolecular aggregates, or intracellular pathogens to the lysosome for degradation and recycling. Autophagy cross talks with the immune system and controls inflammation through effects on various immune cells to regulate immune homeostasis and to modulate host defenses. Fine mapping autophagy-related gene loci associated with SLE is necessary to gain understanding how these genetic variants affect different aspects of autophagy pathways in specific immune cell types, which may serve as a new drug target for SLE treatment. Due to linkage disequilibrium (LD), each risk locus contains multiple variants, and in some cases, multiple genes that could impact biologic functions relating to SLE pathogenesis. In Aim 1, we propose to utilize LD structure differences between Asian and African-derived ancestries to conduct transracially fine-mapping and bioinformatics analysis of seven SLE risk loci related to autophagy (ATG16L2-FCHSD2-P2RY2, PRDM1-ATG5, DRAM1, CDKN1B, CLEC16A, NCF2 and HIP1) using the Global Screening Array (GSA) that contains headroom for custom variants in SLE cases and controls of non-white minorities (4000 Asians and 3000 African Americans [AA]). By comparing haplotype structures and applying Bayesian approaches, we will obtain the best credible set of variants to pursue further. In Aim 2, we will refine credible variant list by using bioinformatics and molecular approaches to identify functional variants. This will include sorting immune cell subsets from 100 AA SLE patients and 100 AA controls (matched for age and gender) for RNA-seq and qRT-PCR to correlate allelic genotypes with differential gene expression and splicing as well as conducting molecular biology assays. The best candidates will be further tested in Aim 3 to conduct immunophenotyping, RNA-seq and autophagy functional assays to assess the consequences of gene- edited immune cell lines and induced pluripotent stem cells (iPSCs), which will determine the pertinent cell subset from SLE patients and controls to conduct autophagy functional assays for confirmation of genotypic effects. Our results will identify genetic variants underlying SLE risk loci and their molecular/cellular mechanisms leading to dysregulation of autophagy pathways contributing to the development of SLE.