Defining the molecular mechanisms of COPA syndrome through computational modeling and functional studies

通过计算模型和功能研究定义 COPA 综合征的分子机制

基本信息

批准号：
10388222
负责人：
Anthony Shum
金额：
$ 18.84万
依托单位：
UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
依托单位国家：
美国
项目类别：
财政年份：
2021
资助国家：
美国
起止时间：
2021-04-08 至 2023-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10388222
关键词：
Affect Amino Acids Antineutrophil Cytoplasmic Antibodies Antinuclear Antibodies Arthritis Autoantibodies Autoimmune Diseases Awareness Base Pairing Binding Binding Proteins Binding Sites Biological Assay C-terminal Childhood Chronic Childhood Arthritis Clinical Coat Protein Complex I Code Computer Models Crystallization Data Defect Diagnosis Disease Dose Early Diagnosis Endoplasmic Reticulum Enrollment Family Fibrosis Genes Golgi Apparatus Grant Immunoprecipitation Immunosuppression Impairment In Vitro Inflammatory Arthritis Interferon Type I Interferon-beta International Interstitial Lung Diseases Joints Lead Life Location Lung Lung diseases Mediating Missense Mutation Molecular Molecular Disease Movement Mutation Mutation Analysis Pathogenicity Pathway interactions Patients Pediatric cohort Peptides Phenotype Prognosis Proteins Publishing Registries Research Research Project Grants Retrieval Rheumatoid Factor Serum Signal Transduction Structure Suggestion Syndrome Uncertainty Up-Regulation Validation Variant Vasculitis WD Repeat Work arthropathies base cohort exome exome sequencing functional disability genetic testing inflammatory lung disease insight laboratory experiment molecular dynamics mutant novel protein function screening variant of unknown significance

项目摘要

PROJECT SUMMARY: Our lab recently discovered COPA syndrome, an autoimmune disease affecting the lungs and joints caused by dominant mutations in the coatomer subunit alpha (COPA) gene. COPA syndrome typically presents in childhood with either inflammatory arthritis or lung disease that manifests as pulmonary capillaritis or interstitial lung disease. Although genetic testing is used to confirm the diagnosis, uncertainty can arise when sequencing uncovers COPA variants of unknown significance (VUS). This occurs relatively frequently because verified mutations lie within a ~50 base pair (bp) region that spans less than 1% of the full coding sequence of the gene. COPA is a subunit of coat protein complex I (COPI) that mediates retrograde movement of proteins from the Golgi apparatus to the endoplasmic reticulum (ER). Established COPA mutations alter the protein’s WD40 domain and impair binding of COPA to cargo proteins marked for ER retrieval by a C-terminal dilysine motif. In this grant, we will employ molecular dynamics simulations and eigenvector centrality analysis to resolve how mutations alter the allosteric binding site of COPA and to predict novel mutations. We will functionally validate mutants through complementary experimental approaches based on our recent discovery that mutant COPA impairs retrieval of STING from the Golgi and leads to type I interferon signaling. We have identified several COPA variants of unknown significance in patients that require further functional analysis and have been contacted by clinicians throughout the world with VUS for us to study. We will search for novel COPA variants by performing whole exome sequencing in subjects enrolled in the PedVas initiative registry, the largest cohort of pediatric vasculitis patients in the world. Subjects will be identified for sequencing using screening criteria of common pulmonary and extra-pulmonary features delineated in a recently published international cohort of COPA syndrome patients. In subjects without COPA variants, we will search for novel genes suspected to cause COPA syndrome based on the cellular and molecular pathways implicated in disease. Our grant will use computational modeling and functional studies to provide insight into the basic mechanisms of COPA function by analyzing how pathogenic mutations impair binding of COPA to the C-terminal dilysine motif of cargo. This work will allow us to accurately predict whether a mutation causes COPA syndrome and has the potential to expand the molecular definition of the disease. We will perform whole exome sequencing in patients suspected to have COPA syndrome to identify new disease-causing COPA variants or identify novel genes that lead to inflammatory lung and joint disease.

项目概要：我们的实验室最近发现了 COPA 综合征，这是一种影响肺部和关节的自身免疫性疾病 COPA 综合征通常由 α 涂层亚基 (COPA) 基因显性突变引起。儿童时期患有炎症性关节炎或肺部疾病，表现为肺毛细血管炎或间质性肺病尽管基因检测可用于确认诊断，但测序时可能会出现不确定性。发现未知意义的 COPA 变体 (VUS) 由于经过验证，这种情况发生得相对频繁。突变位于大约 50 个碱基对 (bp) 的区域内，该区域的长度不到基因完整编码序列的 1%。 COPA 是外壳蛋白复合物 I (COPI) 的一个亚基，介导蛋白质从蛋白质逆行运动高尔基体到内质网 (ER) 的 COPA 突变会改变蛋白质的 WD40。域并损害 COPA 与通过 C 端二赖氨酸基序标记为 ER 检索的货物蛋白的结合。这笔资助，我们将采用分子动力学模拟和特征向量中心性分析来解决如何突变会改变 COPA 的变构结合位点并预测新的突变。基于我们最近发现突变 COPA 的补充实验方法损害高尔基体中 STING 的恢复并导致 I 型干扰素信号传导。患者中意义不明的 COPA 变异需要进一步的功能分析，并且已被世界各地的指挥官与 VUS 联系以供我们研究新的 COPA 变体。通过对 PedVas 计划登记处登记的受试者进行全外显子组测序，这是最大的队列世界上的儿童血管炎患者将使用筛选标准进行测序。最近发表的国际队列描述了常见的肺部和肺外特征在没有 COPA 变异的受试者中，我们将寻找疑似引起 COPA 综合征的新基因。 COPA 综合征基于与疾病有关的细胞和分子途径。我们的资助将使用计算模型和功能研究来深入了解基本原理通过分析致病性突变如何损害 COPA 与 C 末端的结合来了解 COPA 功能的机制这项工作将使我们能够准确预测突变是否会导致 COPA 综合征。并有可能扩大该疾病的分子定义我们将进行全外显子组测序。在疑似患有 COPA 综合征的患者中识别新的致病 COPA 变异或识别新的导致炎症性肺部和关节疾病的基因。