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: 9767153
• 负责人: ARTHUR S EDISON
• 金额: $ 85.46万
• 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 2022-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9767153
• 关键词: Animal Model; Animals; Area; Biochemical Pathway; Biological; CRISPR/Cas technology; Caenorhabditis elegans; Chemicals; Chromatography; Complex; Computer Simulation; 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生物的显着优势、复杂的途径 绘图工具、高通量和精确的量子化学 (QM) 以及最先进的实验 测量的结果将是一种有效且具有成本效益的未知化合物鉴定方法。 代谢组学，这是这个不断发展的医学科学领域面临的主要限制之一。 秀丽隐杆线虫在这项研究中具有多项优势，包括超过 10,000 个可用的遗传基因 突变体、成熟的 CRISPR/Cas9 技术以及超过 500 个野生秀丽隐杆线虫分离株 完整的基因组。秀丽隐杆线虫基因的一半与人类疾病基因具有同源性，从而形成了这个模型。 生物体是提高我们对人类疾病代谢途径的理解的绝佳选择。 将开发一个用于样品制备的自动化管道，以可重复地测量数以万计的样品 通过 UHPLC-MS/MS 检测未知特征 我们将使用野生分离株进行全代谢组遗传分析。 关联研究 (m-GWAS) 和 SEM-path 使用部分相关性来定位路径中的未知数。 将通过测量 UHPLC-MS/MS 数据来测试未知代谢物与特定途径的相关性 来自这些途径的基因突变的分子式和途径信息将作为输入。 所有可能结构的自动量子力学计算，将用于准确地 计算与实验数据相匹配的 NMR 化学位移。 通过将它们与相同化合物的 2D NMR 数据进行比较来进行验证。 然后将使用实验性 UHPLC-MS/MS 来改进基于 QM 的 MS/MS 片段预测 数据。 该项目将促进蠕虫和模式生物以外的许多科学领域的发展。首先，线虫是最重要的。 我们发现的最简单的动物模型与其他动物和人类具有显着的同源性。 代谢途径的研究将对多种人类疾病的研究产生直接影响。 该方法高度可移植到其他遗传系统，只需很少的修改即可应用于许多 其他应用也许最重要的是与大规模人类精准医学研究的相关性。 野生线虫分离株是具有不同基因组的“个体”，是自然种群的模型 确实，我们正在使用人类精度无法达到的突变动物。 医学研究，但突变体主要用于验证完全由野生动物构建的途径 分离数据。一旦这些方法得到充分开发和验证，突变体就不再是必要的了 C. 线虫和其他遗传模型生物在现代基因组学的发展中发挥了重要作用 DNA 测序技术的前提是该蠕虫将在代谢组学中产生类似的影响。