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

自噬相关 SLE 风险位点的跨祖先精细定位和功能解剖

基本信息

批准号：
9898320
负责人：
Christopher J Lessard
金额：
$ 70.12万
依托单位：
MEDICAL UNIVERSITY OF SOUTH CAROLINA
依托单位国家：
美国
项目类别：
财政年份：
2018
资助国家：
美国
起止时间：
2018-04-09 至 2023-02-28
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9898320
关键词：
Affect African African American Age Alleles Amino Acids Antigen Presentation Apoptotic Asians Autoimmune Diseases Autoimmunity Autophagocytosis B-Lymphocytes Bayesian Method Binding Proteins Bioinformatics Biological Biological Assay Biological Process CD4 Positive T Lymphocytes CDKN1B gene CRISPR/Cas technology Candidate Disease Gene Cell Cycle Progression Cell Line Cells Cellular Assay Chromatin Chronic Clathrin Codon Nucleotides Complex Crohn&apos s disease Custom Cytoplasmic Organelle Data Development Disease Dissection Endosomes Etiology European Exhibits Exposure to Functional disorder Gender Gene Expression Genes Genetic Genetic Polymorphism Genetic Variation Genetically Engineered Mouse Genomics Genotype Haplotypes Homeostasis Homologous Gene Host Defense Human Immune Immune response Immune system Immunophenotyping Individual Inflammation Koreans Link Linkage Disequilibrium Lymphocyte Lymphoid Lysosomes Mediating Microbe Minority Molecular Molecular Biology Mus Myelogenous NADPH Oxidase Odds Ratio Organ PRDM1 gene Pathogenesis Pathway interactions Patient Care Patients Phagocytes Play Pluripotent Stem Cells Population Population Control Process Proteins Public Health Publishing Quantitative Reverse Transcriptase PCR RNA Splicing Recycling Reporting Risk Role Sample Size Signal Transduction Sorting - Cell Movement Spliced Genes Stimulus Structure Susceptibility Gene System Systemic Lupus Erythematosus T-Cell Proliferation T-Lymphocyte TLR7 gene TP53 gene Testing Therapeutic Thymic epithelial cell Tissue-Specific Gene Expression Transcript Transport Process Tumor Suppressor Proteins Variant Woman autoinflammatory case control causal variant cell type chromatin protein clinical care cytokine effective therapy ethnic minority population experimental study genetic variant genome wide association study genomic locus in vivo induced pluripotent stem cell insight lupus-like lysosomal proteins member monocyte neutrophil new therapeutic target novel novel therapeutics pathogen plasma cell differentiation response risk variant screening targeted treatment tool transcriptome sequencing

项目摘要

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.

全身性红斑狼疮（SLE）是一种慢性的，异质的自身免疫性疾病，不成比例影响妇女，这种疾病通常更严重，而非白人人群的最终器官损害。很少 SLE的有效治疗方法很大程度上是因为病因未完全理解。但是，在环境触发因素的基因易感人群中可能发生疾病。多重基因组广泛的关联研究（GWAS）和复制研究已经确定了〜100（80个已发布，其中20个发布过程）SLE敏感性基因座（P <5x10-8）主要使用欧洲和亚洲衍生的人群。我们最近的韩国GWAS和其他关于亚洲人的研究暗示了许多自噬 - SLE中的相关基因基因座类似于其他几种自身免疫性疾病。自噬是一个细胞内过程将损伤的细胞质细胞器，大分子聚集体或细胞内病原体传输到溶酶体降解和回收。与免疫系统和控制的自噬交叉对话通过对各种免疫细胞的影响来调节免疫稳态并调节宿主的炎症防御。与SLE相关的精细映射自噬相关基因基因座对于获得理解是必要的这些遗传变异如何影响特定免疫细胞类型的自噬途径的不同方面，可以作为SLE治疗的新药物。由于连锁不平衡（LD），每个风险基因座都包含多种变体，在某些情况下，可能影响与SLE有关的生物学功能的多个基因发病。在AIM 1中，我们建议利用亚洲和非洲衍生的LD结构差异对与七个SLE风险基因座进行跨性细微映射和生物信息学分析的祖先与使用自噬（ATG16L2-FCHSD2-P2RY2，PRDM1-ATG5，DRAM1，CDKN1B，CLEC16A，NCF2和HIP1）全球筛选阵列（GSA），其中包含SLE案件中自定义变体的净空和控制非白人少数民族（4000名亚洲人和3000名非裔美国人[AA]）。通过比较单倍型结构和采用贝叶斯方法，我们将获得最佳的可靠变体以进一步追求。在AIM 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靠的变体列表。这将包括对100名AA SLE患者和100个AA对照的免疫细胞子集进行分类（与年龄相匹配性别）用于RNA-SEQ和QRT-PCR，将等位基因基因型与差异基因表达和剪接以及进行分子生物学测定法。最好的候选人将在AIM 3中进一步测试进行免疫表型，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），这将决定相关细胞 SLE患者和对照组的子集进行自噬功能测定以确认基因型效果。我们的结果将确定SLE SLE风险基因座及其分子/细胞的遗传变异导致自噬途径失调的机制导致SLE的发展。