Project 2: High Resolution Mutation Spectra and Multi-Omics for Deducing Etiology and Predicting Disease

项目2：高分辨率突变谱和多组学用于推断病因和预测疾病

• 批准号: 10687979
• 负责人: JOHN M ESSIGMANN
• 金额: $ 48.05万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10687979
• 关键词: Acute; Address; Affect; Air Pollution; Animal Model; Animals; Biological; Biological Markers; Catchment Area; Cell Culture System; Cell Culture Techniques; Cell model; Cells; Cessation of life; Characteristics; Chemical Exposure; Chemicals; Collaborations; Communities; Complex Mixtures; Custom; DNA Adduction; DNA Adducts; DNA Damage; DNA Repair; DNA Repair Gene; DNA sequencing; Data; Data Analyses; Data Set; Detection; Dimethylnitrosamine; Disease; Disease Outcome; Dose; Elderly; Embryo; Environment; Environmental Exposure; Environmental Risk Factor; Epidemiology; Etiology; Excision; Exposure to; Female; Fibroblasts; Gene Expression; Genetic; Genetic Engineering; Genetically Engineered Mouse; Genomics; Goals; Hazardous Chemicals; Hazardous Substances; Health; Human; Human Genome; Individual; Industrialization; Inflammation; Informatics; Intervention; Intraperitoneal Injections; Investigation; Kinetics; Knowledge; Learning; MGMT gene; Maine; Malignant Neoplasms; Mammalian Cell; Measurable; Methods; Modeling; Molecular; Molecular Epidemiology; Mus; Mutagens; Mutation; Mutation Spectra; N-nitrosodimethylamine; Nitrosamines; Nitroso Compounds; Passamaquoddy Tribe of Maine; Pathology; Pathway interactions; Pattern; Persons; Phenotype; Phosphorylation; Predisposition; Prevention; Probiotics; Procedures; Process; Propylamines; Protein Analysis; Proteins; Proteome; Proteomics; Public Health; Records; Regimen; Research; Resolution; Risk; Risk Assessment; Risk Reduction; Sampling; Screening procedure; Signal Recognition Particle; Signal Transduction; Site; Source; Superfund; System; Techniques; Technology; Testing; The Cancer Genome Atlas; Tissues; Toxic Environmental Substances; Toxic effect; Toxicology; Toxin; Tribal group; Water; Water Pollution; Work; World Health Organization; animation; biological systems; burden of illness; carcinogenicity; community engagement; data management; data streams; disorder prevention; drinking water; early onset; efficacy evaluation; environmental chemical; gene environment interaction; genome integrity; genotoxicity; high throughput screening; human data; human disease; insight; male; member; mouse model; multiple omics; novel; overexpression; phosphoproteomics; programs; remediation; response; screening; stressor; superfund chemical; superfund site; tool; toxicant; transcriptomics; tumor; welfare

PROJECT SUMMARY/ABSTRACT – PROJECT 2 Exposure of people to single chemicals or mixtures at Superfund sites has unquestionably occurred. The unanswered question addressed here is whether those exposures can be associated with measurable risks to genome integrity or expression, which would provide biological plausibility to the argument that the chemicals in the environment have affected human health and welfare. The compounds chosen for investigation were inspired by engagement efforts with a local community containing a Superfund site and with Tribal groups in Maine. Carcinogenic N-nitrosamines (e.g., N-nitrosodimethylamine or NDMA) as well as other toxicants are abundant in both of our catchment areas. These agents have not been studied as mutagens or proteome disruptors at the level of detail proposed here, and they certainly have not been subjected to the combined multi-omic scrutiny of this Project taken together with Project 1 (DNA damage and gene-environment interactions). The technology of Project 2 has five components: (a) We employ a genetically engineered panel of mice (Project 1) that responds to environmental toxicants in a manner that reveals underlying mechanisms that confer susceptibility to a toxicant. The pathway to toxicity involves disease initiation, concomitant complications such as tissue-destructive inflammation, through end stage pathologies such as cancers. (b) We use a newly developed high-fidelity DNA sequencing procedure that provides unprecedentedly high-resolution mutational spectra (HRMS); HRMS can be used to identify chemical-specific mutational patterns resulting from environmental exposures. (c) We use a unique proteomic platform that sensitively senses disruptions in thousands of nodes in signaling networks. (d) We use a novel computational module via the Data Management and Analysis Core that quantitatively compares HRMS and proteomic patterns from our models with the rapidly expanding human data sets of The Cancer Genome Atlas Project (TCGA), other tumor sequencing efforts, and the growing body of knowledge of proteomic patterns. (e) Lastly, we introduce mouse embryo fibroblast (MEF) lines isogenic with our mouse models that can be used as high-throughput screening tools to help find genotoxic fractions in complex mixtures (Projects 3 and 4). Our multi-omic approach centers on animal and cellular models, but we also look ahead to application of these novel tools for molecular epidemiology and for disease prevention. Regarding the latter possibility, the proteomic and mutagenic biomarkers we already see in our work can be immediately be used to assess the efficacy of probiotic mitigation of disease, via our interactions with Project 1. Regarding contributions to epidemiology, the distinctive mutational spectra we have already observed following NDMA exposure to animals and cells could eventually become valuable early-onset biomarkers that portend later life diseases. Taken together, this Project leverages basic studies on genomics, adductomics, gene expression, and systems toxicology to provide practical tools that can help detect and mitigate human diseases caused by specific environmental chemicals that both our community partners and regulators have defined as agents of concern.

项目总结/摘要-项目2 毫无疑问，人们在超级基金场所接触单一化学品或混合物的情况已经发生。的 这里要解决的一个尚未回答的问题是，这些风险是否与可衡量的风险有关， 基因组的完整性或表达，这将提供生物学上的合理性的论点， 环境影响了人类的健康和福祉。选择用于研究的化合物的灵感来自 通过与包含超级基金网站的当地社区和缅因州的部落团体的参与努力。 致癌的N-亚硝胺（例如，N-亚硝基二甲胺或NDMA）以及其他有毒物质是丰富的 在我们的两个集水区。这些试剂尚未作为诱变剂或蛋白质组干扰剂进行研究， 这里提出的详细程度，他们肯定没有受到联合多组学审查， 该项目与项目1（DNA损伤和基因-环境相互作用）一起进行。技术 项目2有五个组成部分：（a）我们采用了一组基因工程小鼠（项目1）， 环境毒物的方式，揭示了潜在的机制，赋予易感性， 有毒物质毒性的途径涉及疾病的发生、伴随的并发症，如组织破坏性 炎症，通过终末期病理如癌症。(b)我们使用一种新开发的高保真DNA 测序程序，提供前所未有的高分辨率突变谱（HRMS）; HRMS可以是 用于识别环境暴露导致的化学特定突变模式。(c)我们使用一个 独特的蛋白质组学平台，灵敏地感知信号网络中数千个节点的中断。（d）其他事项 我们通过数据管理和分析核心使用一种新的计算模块， 将我们模型中的HRMS和蛋白质组模式与快速扩展的人类数据集进行了比较。 癌症基因组图谱计划（TCGA），其他肿瘤测序工作，以及越来越多的知识， 蛋白质组模式(e)最后，我们引入了与我们的小鼠同基因的小鼠胚胎成纤维细胞（MEF）系， 可用作高通量筛选工具的模型，以帮助在复杂混合物中找到遗传毒性组分 （项目3和4）。我们的多组学方法以动物和细胞模型为中心，但我们也展望未来， 将这些新工具应用于分子流行病学和疾病预防。关于后者 可能性，我们在工作中已经看到的蛋白质组学和诱变生物标志物可以立即用于 通过我们与项目1的互动，评估益生菌缓解疾病的功效。关于捐款 流行病学，我们已经观察到的独特的突变谱后，NDMA暴露于 动物和细胞最终可能成为有价值的早期生物标志物，预示着以后的生活疾病。 总之，该项目利用基因组学，内收体学，基因表达和系统的基础研究 毒理学提供实用的工具，可以帮助检测和减轻人类疾病引起的具体 我们的社区合作伙伴和监管机构都将环境化学品定义为关注的物质。