3D Methodology for Interpreting Disease-Associated Genomic Variation in RAG2

解释 RAG2 中疾病相关基因组变异的 3D 方法

• 批准号: 10724152
• 负责人: Michael T Zimmermann
• 金额: $ 15.6万
• 依托单位: MEDICAL COLLEGE OF WISCONSIN
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10724152
• 关键词: 3-Dimensional; Address; Adult; Affinity; Award; B cell repertoire; B-Cell Development; B-Lymphocytes; Basic Science; Binding; Biochemical; Biochemistry; Chromatin; Complex; Computational Technique; DNA; DNA Sequence Alteration; Data; Development; Diagnosis; Dimensions; Disease; Enzymes; Evaluation; Follow-Up Studies; Functional disorder; Future; Gene Activation; Gene Mutation; Generations; Genes; Genetic; Genetic Databases; Genetic Diseases; Genetic Recombination; Genetic Variation; Genome; Genomics; Health; Hereditary Disease; Histones; Human; Human Genetics; Immune; Immune Tolerance; Immune system; Immunity; Immunologic Deficiency Syndromes; In Vitro; Individual; Infection; Intervention; Joints; Lymphocyte; Lymphoid; Measures; Mechanics; Methodology; Methods; Methylation; Modeling; Molecular; Mutate; Mutation; Nucleosome Core Particle; PH Domain; Pathogenesis; Patients; Peptide Signal Sequences; Peptides; Phenotype; Plants; Population Database; Population Genetics; Predisposition; Property; Proteins; Rag1 Mouse; Reaction; Reading; Research; Resolution; Severe Combined Immunodeficiency; Structure; Structure-Activity Relationship; Subgroup; System; T-Lymphocyte; Tail; Testing; Variant; adaptive immunity; cancer cell; computerized tools; gain of function; gene function; genetic variant; genomic variation; homeodomain; improved; innovation; loss of function; machine learning classifier; molecular mechanics; molecular modeling; monomer; multidisciplinary; negative affect; next generation; novel; novel strategies; precision medicine; protein structure function; recombinase; structural biology; thermostability; tool; variant of unknown significance

PROJECT SUMMARY The current proposal seeks to advance mechanisms of interpretation of genomic variation found in RAG2. We leverage advanced computational techniques with existing and new experimental data, to develop a novel approach for characterizing and interpreting inter-individual genetic variation, and mutations observed in patients with immunodeficiency syndromes. Our central hypothesis is that structural calculations predict functional changes for RAG2 mutations via capture of specific biochemical and molecular mechanic features. Our approach investigates RAG2 mutations in a domain-specific manner, where each Aim investigates one of the two RAG2 structured domains: 1) we interrogate the effects of β-domain mutations on the RAG heterotetramer complex across its enzymatic cycle; 2) we computationally and functionally characterize how mutations in the plant homeodomain alter stability and chromatin binding capacity. Thus, between the two domains, we will investigate alteration of the RAG enzyme and its ability to be regulated by differentially targeting to the correct places in the genome, via its histone reading function. Our Aims are independent (using different approaches for different domains), yet synergistic due to each providing new information about RAG2 mutations observed in immunodeficiency patients. Both domains will be characterized in structure-dynamics-function paradigm, to elucidate details for each mutation in high-resolution, and to identify subgroups of mutations that have similar effects on RAG function. The subgroups we anticipate identifying will serve for follow-up studies into cellular effects and how to potentially address each type of dysfunction. When completed, the proposed studies will generate new data with clear biomedical relevance for diagnosis of immunodeficiency syndromes and enabling future research in how to differently address each group of mutations that modulate specific dimensions of RAG complex function. At a higher level, our proposal addresses a broad unmet need in genomics for new computational approaches to mechanistically interpret the wide landscape of human variation. We anticipate that the approach used here, will be generalizable to other proteins for how the computational tools can be applied in a robust manner to determine the underlying protein structure-function relationship for interpreting the structural biology of genetic disease pathogenesis. The data generated in this pilot award will thereby seed future applications by the current scientific and multi-disciplinary team, to further expand our understanding of RAG genetic variation and its effects on the immune system.

项目概要 当前的提案旨在推进 RAG2 基因组变异的解释机制。 利用先进的计算技术与现有和新的实验数据，开发一种新颖的 表征和解释个体间遗传变异以及在患者中观察到的突变的方法 我们的中心假设是结构计算预测功能。 我们的方法是通过捕获特定的生化和分子力学特征来改变 RAG2 突变。 以域特异性方式研究 RAG2 突变，其中每个目标研究两个 RAG2 之一 结构域：1）我们探讨 β 结构域突变对 RAG 异四聚体复合物的影响 整个酶循环；2）我们通过计算和功能描述了植物中的突变方式 同源结构域会改变稳定性和染色质结合能力，因此，我们将研究这两个结构域之间的关系。 RAG 酶的改变及其通过差异靶向正确位置来调节的能力 基因组，通过其组蛋白读取功能，我们的目标是独立的（针对不同的情况使用不同的方法）。 域），但由于每个域都提供了有关 RAG2 突变的新信息，因此具有协同作用 免疫缺陷患者的两个领域都将在结构-动力学-功能范式中进行表征，以 以高分辨率阐明每个突变的详细信息，并识别具有相似特征的突变亚组 我们预计确定的亚组将用于细胞的后续研究。 影响以及如何潜在地解决每种类型的功能障碍 完成后，拟议的研究将。 生成具有明确生物医学相关性的新数据，用于诊断免疫缺陷综合征并启用 未来研究如何以不同的方式解决调节 RAG 特定维度的每组突变 在更高的层面上，我们的建议解决了基因组学中对新功能的广泛未满足的需求。 我们预计，机械地解释人类变异的广泛景观的计算方法。 这里使用的方法将推广到其他蛋白质，以了解如何应用计算工具 以稳健的方式确定潜在的蛋白质结构-功能关系以解释 该试点奖项中产生的数据将为遗传疾病发病机制的结构生物学奠定基础。 当前科学和多学科团队的应用，进一步扩大我们对 RAG 的理解 遗传变异及其对免疫系统的影响。