Genetics and quantum chemistry as tools for unknown metabolite identification

遗传学和量子化学作为未知代谢物鉴定的工具

• 批准号: 10180966
• 负责人: ARTHUR S EDISON
• 金额: $ 85.58万
• 依托单位: UNIVERSITY OF GEORGIA
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10180966
• 关键词: Animal Model; Animals; Area; Biochemical Pathway; Biological; CRISPR/Cas technology; Caenorhabditis elegans; Chemicals; Chromatography; Complex; Computer Models; DNA sequencing; Data; Data Analytics; Development; Disease; Future; Genes; Genetic; Genetic Models; Genome; Genomic DNA; Genotype; Homologous Gene; Human; Individual; Laboratories; Malignant Neoplasms; Mass Spectrum Analysis; Measurement; Measures; Mechanics; Medical; Metabolic Pathway; Modeling; Modernization; Modification; Molecular; NMR Spectroscopy; Natural Products; Nuclear Magnetic Resonance; Other Genetics; Pathway interactions; Pattern; Phase; Population; Preparation; Property; Publishing; Resolution; Resources; Sampling; Science; Standardization; Structure; System; Techniques; Technology; Testing; Time; Translating; Validation; base; cost effective; design; genetic association; genome wide association study; human disease; improved; insight; metabolome; metabolomics; mutant; neglect; novel; precision medicine; quantum; quantum chemistry; relational database; spectroscopic data; theories; tool

Overall: Our project combines the significant advantages of a genetic model organism, sophisticated pathway mapping tools, high-throughput and accurate quantum chemistry (QM), and state-of-the-art experimental measurements. The result will be an efficient and cost-effective approach for unknown compound identification in metabolomics, which is one of the major limitations facing this growing field of medical science. Caenorhabditis elegans has several advantages for this study, including over 10,000 available genetic mutants, well-developed CRISPR/Cas9 technology, and a panel of over 500 wild C. elegans isolates with complete genomes. Half of C. elegans genes have homologs to human disease genes, making this model organism an outstanding choice to improve our understanding of metabolic pathways in human disease. We will develop an automated pipeline for sample preparation to reproducibly measure tens of thousands of unknown features by UHPLC-MS/MS. We will use the wild isolates to conduct metabolome-wide genetic association studies (m-GWAS), and SEM-path to locate unknowns in pathways using partial correlations. The relevance of the unknown metabolites to specific pathways will be tested by measuring UHPLC-MS/MS data from genetic mutants of those pathways. Molecular formula and pathway information will be the inputs for automated quantum mechanical calculations of all possible structures, which will be used to accurately calculate NMR chemical shifts that will be matched to experimental data. The correct structures will be validated by comparing them with 2D NMR data of the same compound. The validated computed structures will then be used to improve QM-based MS/MS fragment prediction, using the experimental UHPLC-MS/MS data. This project will enhance many areas of science beyond worms and model organisms. First, C. elegans is the simplest animal model available with significant homology to other animals and humans. The discoveries we make in metabolic pathways will have a direct impact on studies of several human diseases. Second, our approach is highly transferable to other genetic systems and with little modification can be applied to many other applications. Perhaps most important is the relevance to large-scale human precision medicine studies. The wild C. elegans isolates are “individuals” with diverse genomes that are a model for natural populations such as humans. It is true that we are using mutant animals that would not be available in a human precision medicine study, but the mutants are used primarily to validate pathways that are constructed entirely by wild isolate data. Once the approaches are fully developed and validated, the mutants will not be necessary. C. elegans and other genetic model organisms were instrumental in the development of modern genomics and DNA sequencing technologies. Our premise is that the worm will have a comparable impact in metabolomics.

总体而言：我们的项目结合了遗传模型有机体的重要优势，复杂的途径 映射工具，高通量和准确的量子化学（QM）以及最先进的实验 测量。结果将是未知化合物识别的有效且具有成本效益的方法 在代谢组学中，这是这一医学科学领域面临的主要局限性之一。 秀丽隐杆线虫在这项研究中具有多个优点，包括10,000多个可用的通用 突变体，发达的CRISPR/CAS9技术，以及一组超过500个野生秀丽隐杆线虫分离株 完整的基因组。一半的秀丽隐杆线虫基因对人类疾病基因具有同源性，使该模型 有机体是提高我们对人类疾病代谢途径的理解的出色选择。我们 将开发自动管道以进行样品准备，以重现数以万计的测量 UHPLC-MS/MS的未知功能。我们将使用野生分离株进行全代代谢组的通用 结合研究（M-GWAS）和SEM-Path使用部分相关在途径中定位未知数。 未知代谢物与特定途径的相关性将通过测量UHPLC-MS/MS数据来测试 来自这些途径的基因突变体。分子公式和途径信息将是 所有可能的结构的自动量子机械计算将用于准确 计算NMR化学位移将与实验数据相匹配。正确的结构将是 通过将它们与同一化合物的2D NMR数据进行比较来验证。经过验证的计算结构 然后，将使用实验性UHPLC-MS/MS用于改善基于QM的MS/MS片段预测 数据。 该项目将增强科学领域的许多领域，而不是蠕虫和模型生物。首先，秀丽隐藏是 最简单的动物模型可与其他动物和人类具有重要同源性。我们的发现 在代谢途径中的成分将对几种人类疾病的研究产生直接影响。第二，我们的 方法被高度转移到其他遗传系统，并且几乎没有修改可以应用于许多人 其他应用程序。也许最重要的是与大型人类精确医学研究的相关性。 野生秀丽隐杆线虫分离株是具有潜水基因组的“个体”，这是自然种群的模型 例如人类。的确，我们正在使用不可用人类精确度的突变动物 医学研究，但突变体主要用于验证完全由野生构建的途径 隔离数据。一旦方法得到充分开发和验证，突变体将无需。 C 秀丽隐杆线虫和其他遗传模型生物有助于现代基因组学和 DNA测序技术。我们的前提是蠕虫将对代谢组学产生可比的影响。