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.

系统性红斑狼疮 (SLE) 是一种慢性、异质性自身免疫性疾病，影响女性，并且在非白人人群中，这种疾病往往更严重，伴有终末器官损伤。很少 SLE 存在有效的治疗方法，主要是因为其病因尚不完全清楚；然而，在环境触发下，遗传易感个体可能会发生疾病。多基因组广泛关联研究 (GWAS) 和复制研究已确定约 100 项（其中 80 项已发表，20 项已在出版过程）SLE 易感位点 (P<5x10-8) 主要使用欧洲和亚洲人群。我们最近的韩国 GWAS 和其他发表的针对亚洲人的研究表明，许多自噬- SLE 中的相关基因位点，与其他几种自身免疫性疾病类似。自噬是细胞内的过程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至溶酶体用于降解和回收。自噬与免疫系统和控制相互作用通过影响各种免疫细胞来调节免疫稳态和调节宿主而产生炎症防御。精细定位与 SLE 相关的自噬相关基因位点对于获得了解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，可能作为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 相关的生物功能发病。在目标 1 中，我们建议利用亚洲和非洲衍生的 LD 结构差异祖先对与以下疾病相关的七个 SLE 风险位点进行跨种族精细定位和生物信息学分析使用自噬（ATG16L2-FCHSD2-P2RY2、PRDM1-ATG5、DRAM1、CDKN1B、CLEC16A、NCF2 和 HIP1）全局筛选阵列 (GSA)，其中包含 SLE 病例和对照中自定义变异的空间非白人少数族裔（4000 名亚洲人和 3000 名非裔美国人 [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体集以进行进一步的研究。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异来完善可靠的变异列表。这将包括对来自 100 名 AA SLE 患者和 100 名 AA 对照（年龄匹配）的免疫细胞子集进行分类和性别）用于 RNA-seq 和 qRT-PCR，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。最好的候选人将在目标 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- 编辑免疫细胞系和诱导多能干细胞 (iPSC)，这将确定相关细胞来自 SLE 患者和对照的子集进行自噬功能测定以确认基因型影响。我们的结果将识别 SLE 风险位点及其分子/细胞的遗传变异导致自噬途径失调的机制，有助于 SLE 的发展。