Data-Driven Models of the Dynamic Proteome in NAFLD

NAFLD 动态蛋白质组的数据驱动模型

• 批准号: 9233740
• 负责人: Takhar Kasumov
• 金额: $ 31.27万
• 依托单位: UNIVERSITY OF TEXAS MED BR GALVESTON
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-04-01 至 2019-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9233740
• 关键词: ATP Synthesis Pathway; ATP phosphohydrolase; Affect; Agreement; Algorithms; Animal Model; Animals; Bayesian Analysis; Bayesian Modeling; Bioinformatics; Biological; Cells; Cessation of life; Cholesterol; Chromatography; Cirrhosis; Citric Acid Cycle; Code; Complex; Computer software; Coupled; Data; Deuterium; Deuterium Oxide; Development; Diabetes Mellitus; Disease; Electron Transport; Evaluation; Fatty acid glycerol esters; Feedback; Fibrosis; Food; Functional disorder; Gaussian model; Generations; Genome; Genomics; Goals; Health; Hepatic; High Fat Diet; Isotopes; Knockout Mice; Knowledge; Label; Lead; Licensing; Life Cycle Stages; Light; Link; Lipid Peroxidation; Lipid Peroxides; Liquid Chromatography; Liver Failure; Liver Mitochondria; Mass Spectrum Analysis; Measures; Membrane Potentials; Messenger RNA; Metabolic; Metabolic syndrome; Metabolism; Methodology; Methods; Mitochondria; Mitochondrial DNA; Mitochondrial Proteins; Modeling; Oxidative Stress; Pathway Analysis; Peptides; Pharmacology; Play; Population; Prevention approach; Preventive; Process; Production; Proteins; Proteome; Proteomics; Public Health; Reactive Oxygen Species; Respiratory physiology; Role; Safety; Source; Steatohepatitis; Stochastic Processes; Techniques; Testing; Therapeutic; Time; United States; Water; Work; base; cost; experimental study; fatty acid oxidation; human data; in vivo; innovation; insight; lipid metabolism; liver metabolism; mathematical model; metabolome; metabolomics; mitochondrial dysfunction; mitochondrial membrane; mouse model; nervous system disorder; non-alcoholic fatty liver; novel; oxidative damage; protein degradation; public health relevance; signal processing; stable isotope; targeted treatment; tool; virtual; western diet

 DESCRIPTION (provided by applicant): Non-alcoholic fatty liver disease (NAFLD) is very common, with estimates that it affects 30% of the United States' population. Although NAFLD has been clearly linked to metabolic syndrome, no specific targeted therapies are currently available. As a result, this disease often progresses to cirrhosis and liver failure. Mitochondria are the major cellular source of reactive oxygen species (ROS) in NAFLD, yet very little is known about the life cycle of hepatic mitochondria and its role in this disease. Our long-term goal is to combine mathematical modeling with high-throughput proteomic, genomic and metabolomic approaches to determine how accelerated mitochondrial ROS production leads to mitochondrial dysfunction in NAFLD. Our central hypothesis is that the accelerated ROS production causes enhanced degradation of electron transport chain (ETC) and ATPase subunits. Our studies of mitochondrial dynamics using dynamic proteomics will shed new light on the mechanisms underlying oxidative stress in NAFLD through the following three specific aims, to: 1) develop the methodology and software for global 2H2O-proteome dynamic studies in vivo, using Bayesian modeling to avoid overfitting of isotopomers to the experimental isotope profiles; 2) determine protein turnover rates using a novel nonparametric, data-driven stochastic model; and 3) apply the newly developed bioinformatic tools to determine the influence of high fat diet-induced hepatic oxidative stress on the synthesis of ETC and ATPase subunits in a mouse model of NAFLD by evaluating mitochondrial respiratory function, oxidative stress, oxidative mtDNA damage, and proteome expression and dynamics. Once it is known how proteins involved in the ETC and ATP synthesis are affected by ROS, it should ultimately be possible to modulate their expression levels pharmacologically, resulting in new and innovative approaches to the prevention and treatment of NAFLD. This project will produce novel bioinformatic tools for quantifying protein turnover rates, including a model of protein networks i heavy water (2H2O)-proteome dynamics that are fundamentally statistical and will be applicable to different labeling strategies. The use of 2H2O for metabolic labeling has several advantages, including safety, increased sensitivity (due to the incorporation of multiple copies of 2H into the analyzed peptides) and lower cost. Liquid chromatography coupled to mass spectrometry of metabolic labeling over a time course will provide quantitative information about the relative incorporation levels of different isotopes. The development of new bioinformatic methods for stochastic modeling of the turnover rates, and de- convolving isotope profiles of co-eluting species, will permit large-scale, automated evaluation of the protein turnover rates. As a result, this work will significantly advance and expand dynamic proteome studies quantifying protein decay and synthesis in vivo. This can then be used to investigate such other diseases as diabetes and neurological disorders.

 描述（由申请人提供）：非酒精性脂肪性肝病（NAFLD）非常常见，估计影响美国30%的人口。虽然NAFLD与代谢综合征有明确的联系，但目前还没有具体的靶向治疗方法。因此，这种疾病通常进展为肝硬化和肝功能衰竭。线粒体是NAFLD中活性氧（ROS）的主要细胞来源，但对肝脏线粒体的生命周期及其在这种疾病中的作用知之甚少。我们的长期目标是将联合收割机数学建模与高通量蛋白质组学、基因组学和代谢组学方法相结合，以确定加速的线粒体ROS产生如何导致NAFLD中的线粒体功能障碍。我们的中心假设是，加速的ROS产生导致电子传递链（ETC）和ATP酶亚基的降解增强。我们的动态蛋白质组学研究将通过以下三个具体目标为NAFLD中氧化应激的潜在机制提供新的线索：1）开发用于体内2 H2O-蛋白质组动态研究的方法和软件，使用贝叶斯模型来避免同位素异构体对实验同位素谱的过拟合; 2）使用新的非参数、数据驱动的随机模型确定蛋白质周转率;以及3）应用新开发的生物信息学工具来确定高脂肪饮食的影响-通过评估线粒体呼吸功能、氧化应激、氧化性mtDNA损伤以及蛋白质组表达和动力学，在NAFLD小鼠模型中诱导肝脏氧化应激对ETC和ATP酶亚基合成的影响。一旦知道参与ETC和ATP合成的蛋白质如何受到ROS的影响，最终应该有可能调节它们的表达水平，从而产生预防和治疗NAFLD的新的创新方法。该项目将产生新的生物信息学工具，用于量化蛋白质周转率，包括蛋白质网络模型中的重水（2 H2O）-蛋白质组动力学，从根本上统计，并将适用于不同的标记策略。使用2 H2O进行代谢标记具有几个优点，包括安全性、增加的灵敏度（由于将多个拷贝的2 H掺入到代谢物中）、以及增加的灵敏度。 分析的肽）和更低的成本。液相色谱法与质谱法联用，在一段时间内进行代谢标记，将提供有关不同同位素相对掺入水平的定量信息。开发新的生物信息学方法用于周转率的随机建模和共洗脱物质的去卷积同位素谱，将允许大规模自动评价蛋白质周转率。因此，这项工作将显着推进和扩大动态蛋白质组研究定量蛋白质的衰变和合成在体内。然后，这可以用于研究糖尿病和神经系统疾病等其他疾病。