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， 这种疾病影响妇女，在非白人人群中，这种疾病往往更为严重，并伴有终末器官损伤。几 SLE存在有效的治疗方法，主要是因为病因学不完全清楚;然而， 疾病很可能发生在遗传易感的个体中，由环境触发。多基因组 广泛关联研究（GWAS）和复制研究已经确定了约100种（80种已发表，20种在 SLE易感基因座（P<5x 10 -8），主要使用欧洲和亚洲来源的人群。 我们最近的韩国GWAS和其他已发表的亚洲人研究涉及一些自噬- 与其他几种自身免疫性疾病相似。自噬是一种细胞内过程 它将受损的细胞质细胞器、大分子聚集体或细胞内病原体转运到 溶酶体降解和回收。自噬与免疫系统和对照的交叉对话 通过对各种免疫细胞的作用来调节免疫稳态并调节宿主 的防御合作.精细定位与SLE相关的自噬相关基因位点对于理解SLE是必要的 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SLE治疗的新药物靶点。由于连锁不平衡（LD），每个风险位点包含 多种变异，在某些情况下，多种基因可能影响与SLE相关的生物学功能 发病机制在目标1中，我们建议利用亚洲和非洲衍生的LD结构差异， 祖先进行跨种族精细定位和生物信息学分析的七个SLE风险基因座相关， 自噬（ATG 16 L2-FCHSD 2-P2 RY 2、PRDM 1-ATG 5、DRAM 1、CDKN 1B、CLEC 16 A、NCF 2和HIP 1）， 全球筛查阵列（GSA），其中包含SLE病例和对照组中定制变体的净空， 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，我们将获得最佳可信的变量集，以进一步研究。在目标2中， 将通过生物信息学和分子方法来确定功能变体，从而完善可靠的变体列表。 这将包括从100名AA SLE患者和100名AA对照（年龄匹配）中分选免疫细胞亚群 和性别）进行RNA-seq和qRT-PCR，以将等位基因型与差异基因表达相关联， 剪接以及进行分子生物学测定。最佳候选人将在目标3中接受进一步测试， 进行免疫表型分析，RNA-seq和自噬功能测定，以评估基因的后果， 编辑的免疫细胞系和诱导多能干细胞（iPSC），这将决定相关的细胞 从SLE患者和对照的子集进行自噬功能测定以确认基因型 方面的影响.我们的研究结果将确定潜在的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SLE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.