Contributions of autophagy-related genes in lupus

自噬相关基因在狼疮中的贡献

• 批准号: 10682136
• 负责人: Swapan K. Nath
• 金额: $ 75.26万
• 依托单位: OKLAHOMA MEDICAL RESEARCH FOUNDATION
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-18 至 2027-07-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10682136
• 关键词: 3-Dimensional; Acceleration; Address; Affect; African American; African American population; Age; Algorithms; Alleles; Animal Model; Antigen-Antibody Complex; Asian; Asian Americans; Asian population; Autoantibodies; Autoimmune Diseases; Autoimmunity; Autophagocytosis; B-Lymphocytes; Biochemical; Biological; Biological Assay; Biology; CDKN1B gene; Catabolic Process; Cell Line; Cell physiology; Cells; Cellular biology; Chromatin; Chronic; Clinical; Clustered Regularly Interspaced Short Palindromic Repeats; Crohn' s disease; Cytoplasm; DNA Resequencing; Data; Deposition; Diagnosis; Disease; Drug Targeting; Ethnic Origin; Ethnic Population; Etiology; European; European ancestry; Follow-Up Studies; Gender; Genes; Genetic; Genetic Heterogeneity; Genetic Transcription; Genetic study; Genotype; Gifts; Heritability; High Prevalence; Hispanic Americans; Hispanic Populations; Homeostasis; Human; IGA Glomerulonephritis; Immune; Immune System Diseases; Individual; Inflammation; Inflammatory; Intervention; Kidney; Knowledge; Lead; Life; Link; Linkage Disequilibrium; Lupus; Lupus Nephritis; Lymphocyte; Lysosomes; Maps; Mediating; Metabolic stress; Minority Groups; Molecular; Molecular Mechanisms of Action; Morbidity - disease rate; Multiple Sclerosis; Nephritis; Nucleic Acid Regulatory Sequences; Organ; Organelles; Pathogenesis; Pathogenicity; Pathway interactions; Patients; Play; Population Heterogeneity; Predisposition; Process; Production; Regulation; Regulatory Element; Reporting; Research; Resources; Risk; Role; Sampling; Signal Transduction; Single Nucleotide Polymorphism; Skin; Structure; Susceptibility Gene; System; Systemic Lupus Erythematosus; T-Lymphocyte; Targeted Resequencing; Tissues; Translating; Variant; Woman; autoreactivity; base editing; causal variant; chronic autoimmune disease; clinical heterogeneity; curative treatments; disease phenotype; effective therapy; ethnic diversity; ethnic minority; follow-up; genome wide association study; kidney cell; knockout gene; misfolded protein; mortality; multi-ethnic; multiorgan damage; novel; pathogenic autoantibodies; podocyte; protein degradation; rare variant; response; risk variant; sex; synergism

ABSTRACT Lupus or systemic lupus erythematosus (SLE) is a potentially fatal autoimmune disease with a substantial genetic basis. SLE is characterized by abnormal T- and B-cell responses, production of numerous pathogenic autoantibodies, and immune complex deposition, leading to various clinical manifestations including multi-organ damage (e.g., kidneys, skin). SLE has disproportionate impacts based on gender and ethnicity. Approximately 90% of those affected are women. In addition, SLE has a 3-5-fold higher prevalence in Asian, African-American, and Hispanic individuals compared to those with European ancestry, as well as more severe clinical manifesta- tions, including organ damage (e.g., nephritis). Evidence from genetics, cell biology, and animal models suggests that autophagy, a major pathway for organelle and protein turnover, plays a pivotal role in SLE pathogenesis. Autophagy is a highly conserved lysosome-mediated catabolic process that removes unwanted cytoplasmic components (e.g., long-lived and/or misfolded proteins) and damaged organelles. This process maintains cellular homeostasis and survival under metabolic stress. Recent genome-wide association studies (GWAS) have linked autoimmune diseases, including SLE, to autophagy-related genes. However, there is currently a huge gap in defining causal relationships between associated variants and molecular mechanisms underlying SLE. This lack of knowledge about pathogenic effects underlying GWAS signals hinders translating GWAS discoveries into diagnosis and treatment. To address this issue, we selected six highly ranked, well-replicated loci; four of them were initially discovered in Asian populations, two we previously reported as novel loci for SLE susceptibility. We have assembled a research team with the expertise and resources to discover and mechanistically characterize functional variants linked to SLE. We hypothesize that at each GWAS locus, both common and rare variants contribute to SLE risk by affecting expression of autophagy genes through tissue-specific regulatory elements. Aim 1 will identify SLE-predisposing variants using a comprehensive imputation-based analysis of combined novel resequencing data from SLE patients and controls in addition to our previous fine-mapping of four ethnically diverse populations. Functional variants will be prioritized by allele-specific expression, open chromatin, and 3D interaction data from immune cells. We will elucidate genetic and clinical heterogeneity of SLE by assessing association of identified variants with SLE and its clinical manifestations and autoantibody profiles. Associated variants, especially imputed and rare variants, will be validated through follow-up genotyping. Aim 2 will define the mechanistic and functional consequences of SLE-predisposing variants using appropriate functional assays, including CRISPR-based gene knock-out and base-editing in cell lines (Jurkat, Toledo, podocyte, HEK293) and primary immune cells (T- and B-cells) relevant to SLE. Thus, we will uncover functional variants underlying SLE association signals, and illuminate mechanisms by which these variants contribute to lupus and its clinical manifestations. Through this approach, our analysis should yield novel targets for potential clinical interventions.

摘要 狼疮或系统性红斑狼疮(SLE)是一种潜在的致命的自身免疫性疾病，具有显著的 遗传基础。系统性红斑狼疮的特点是T细胞和B细胞反应异常，产生许多致病因素 自身抗体和免疫复合物沉积，导致包括多器官在内的各种临床表现 损害(例如，肾脏、皮肤)。系统性红斑狼疮对性别和种族的影响不成比例。大致 受影响的人中有90%是女性。此外，系统性红斑狼疮在亚裔、非裔美国人、 与欧洲血统的人相比，西班牙裔人以及更严重的临床表现- 疾病，包括器官损伤(如肾炎)。来自遗传学、细胞生物学和动物模型的证据表明 自噬是细胞器和蛋白质代谢的主要途径，在SLE的发病机制中起着关键作用。 自噬是一种高度保守的溶酶体介导的分解代谢过程，它可以去除不需要的细胞质 成分(例如，长寿和/或错误折叠的蛋白质)和受损的细胞器。这一过程维持了细胞 代谢应激状态下的动态平衡和生存。最近的全基因组关联研究(GWAS)已经将 自身免疫性疾病，包括系统性红斑狼疮，与自噬相关基因有关。然而，目前在这方面存在着巨大的差距 确定相关变异和SLE潜在分子机制之间的因果关系。这种缺失 关于GWAS信号潜在致病效应的知识阻碍了将GWAS的发现转化为 诊断和治疗。为了解决这个问题，我们选择了六个排名很高、重复性很好的基因座；其中四个 最初在亚洲人群中发现，我们之前报告的两个新的SLE易感性基因座。我们 已经组建了一支拥有专业知识和资源的研究团队，以发现并机械地描述 与系统性红斑狼疮相关的功能变异。我们假设在每个GWAS基因座上，无论是常见的还是罕见的变异 通过组织特异性调控元件影响自噬基因的表达，从而增加系统性红斑狼疮风险。 目标1将使用基于联合的基于归因的综合分析来识别SLE易感变异 除了我们之前对四个种族的精细图谱外，来自SLE患者和对照的新的重新测序数据 不同的人群。功能变异将根据等位基因特定的表达、开放染色质和3D来优先处理 来自免疫细胞的相互作用数据。我们将通过评估来阐明SLE的遗传和临床异质性 已识别的变异与系统性红斑狼疮及其临床表现和自身抗体谱的相关性。关联的 变异，特别是归因于和罕见的变异，将通过后续的基因分型进行验证。目标2将定义 使用适当的功能分析的SLE易感变异体的机制和功能后果， 包括基于CRISPR的细胞系(Jurkat、Toledo、Podocyte、HEK293)的基因敲除和碱基编辑 与SLE相关的初级免疫细胞(T细胞和B细胞)。因此，我们将揭示SLE背后的功能变异 关联信号，并阐明这些变异导致狼疮及其临床的机制 表现形式。通过这种方法，我们的分析应该为潜在的临床干预提供新的靶点。