Data-Driven Models of the Dynamic Proteome in NAFLD

NAFLD 动态蛋白质组的数据驱动模型

基本信息

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
项目类别：
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

项目摘要

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（由适用提供）：非酒精性脂肪肝病（NAFLD）非常普遍，估计它影响了美国30％的人口。尽管NAFLD已与代谢综合征明显相关，但目前尚无特定的靶向疗法。结果，这种疾病通常会发展为肝硬化和肝衰竭。线粒体是NAFLD中活性氧（ROS）的主要细胞来源，但对肝素线粒体的生命周期及其在该疾病中的作用知之甚少。我们的长期目标是将数学建模与高通量蛋白质组学，基因组和代谢组方法相结合，以确定如何加速线粒体ROS产生导致NAFLD中的线粒体功能障碍。我们的中心假设是，加速的ROS产生会导致电子传输链（ETC）和ATPase亚基的降解增强。我们使用动态蛋白质组学对线粒体动力学的研究将通过以下三个特定目的为NAFLD中的氧化应激的潜在机制提供新的启示：1）为：1）开发用于体内全球2H2O蛋白质动力学研究的方法和软件，使用贝叶斯建模，以避免使用贝叶斯建模来避免对实验型同位素型的过度使用; 2）使用新型的非参数，数据驱动的随机模型来确定蛋白质周转率； 3）应用新开发的生物信息学工具来确定高脂肪饮食诱导的肝氧化应激对NAFLD小鼠模型中ETC和ATPase亚基合成的影响，通过评估线粒体呼吸功能，氧化应激，氧化性mTDNA损伤以及蛋白质的表达和动力学。一旦知道参与ETP和ATP合成的蛋白质如何受到ROS的影响，最终应该可以通过药理学调节其表达水平，从而为预防和治疗NAFLD提供了新的和创新的方法。该项目将生产新型的生物信息学工具，用于量化蛋白质周转率，包括蛋白质网络I重水（2H2O） - 蛋白酶动力学的模型，这些动力学从根本上统计并适用于不同的标签策略。使用2H2O代谢标记具有多种优势，包括安全性，提高了灵敏度（由于将2H的多个副本掺入分析的辣椒）和较低的成本。在时间过程中，液相色谱与代谢标记的质谱法相结合将提供有关不同同位素的相对收入水平的定量信息。开发用于周转率随机建模的新生物信息学方法，以及共同洗脱物种的撤消同位素谱的开发，将允许对蛋白质周转率的大规模自动评估。结果，这项工作将显着推进和扩大量化蛋白质衰减和体内合成的动态蛋白研究。然后，这可以用于研究诸如糖尿病和神经系统疾病之类的其他疾病。