Wang Yuan, Kou Yan, Wang Xiaodong, Cederbaum Arthur, Wang Rong
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America.
PLoS One. 2014 Mar 21;9(3):e92504. doi: 10.1371/journal.pone.0092504. eCollection 2014.
With the use of iTRAQ technique, a multifactorial comparative proteomic study can be performed. In this study, to obtain an overview of ethanol, CYP2E1 and gender effects on liver injury and gain more insight into the underlying molecular mechanism, mouse liver proteomes were quantitatively analyzed using iTRAQ under eight conditions including mice of different genders, wild type versus CYP2E1 knockout, and normal versus alcohol diet. A series of statistical and bioinformatic analyses were explored to simplify and clarify multifactorial comparative proteomic data. First, with the Principle Component analysis, six proteins, CYP2E1, FAM25, CA3, BHMT, HIBADH and ECHS1, involved in oxidation reduction, energy and lipid metabolism and amino acid metabolism, were identified as the most differentially expressed gene products across all of the experimental conditions of our chronic alcoholism model. Second, hierarchical clustering analysis showed CYP2E1 knockout played a primary role in the overall differential protein expression compared with ethanol and gender factors. Furthermore, pair-wise multiple comparisons have revealed that the only significant expression difference lied in wild-type and CYP2E1 knockout mice both treated with ethanol. Third, K-mean clustering analysis indicated that the CYP2E1 knockout had the reverse effect on ethanol induced oxidative stress and lipid oxidation. More importantly, IPA analysis of proteomic data inferred that the gene expressions of two upstream regulators, NRF2 and PPARα, regulated by chronic alcohol feeding and CYP2E1 knockout, are involved in ethanol induced oxidative stress and lipid oxidation. The present study provides an effectively comprehensive data analysis strategy to compare multiple biological factors, contributing to biochemical effects of alcohol on the liver. The mass spectrometry proteomics data have been deposited to the ProteomeXchange with data set identifier of PXD000635.
使用iTRAQ技术，可以进行多因素比较蛋白质组学研究。在本研究中，为了全面了解乙醇、CYP2E1和性别对肝损伤的影响，并更深入地了解潜在的分子机制，在包括不同性别小鼠、野生型与CYP2E1基因敲除小鼠以及正常饮食与酒精饮食的八种条件下，使用iTRAQ对小鼠肝脏蛋白质组进行了定量分析。探索了一系列统计和生物信息学分析方法，以简化和阐明多因素比较蛋白质组学数据。首先，通过主成分分析，确定了六种参与氧化还原、能量和脂质代谢以及氨基酸代谢的蛋白质，即CYP2E1、FAM25、CA3、BHMT、HIBADH和ECHS1，它们是我们慢性酒精中毒模型所有实验条件下差异表达最显著的基因产物。其次，层次聚类分析表明，与乙醇和性别因素相比，CYP2E1基因敲除在总体差异蛋白表达中起主要作用。此外，两两多重比较显示，唯一显著的表达差异存在于均用乙醇处理的野生型和CYP2E1基因敲除小鼠中。第三，K均值聚类分析表明，CYP2E1基因敲除对乙醇诱导的氧化应激和脂质氧化具有相反的作用。更重要的是，蛋白质组学数据的IPA分析推断，由慢性酒精喂养和CYP2E1基因敲除调节的两个上游调节因子NRF2和PPARα的基因表达，参与了乙醇诱导的氧化应激和脂质氧化。本研究提供了一种有效的综合数据分析策略，用于比较多种生物学因素，有助于阐明酒精对肝脏的生化作用。质谱蛋白质组学数据已存入ProteomeXchange，数据集标识符为PXD000635。
