The overall goal of this proposal is to help define key metabolic changes in the liver metabolome to aid research into a variety of diseases including hepatic steatosis, inflammation, and drug toxicity. These diseases of the liver are an increasing burden on the healthcare system with growing prevalence of obesity, type II diabetes, and drug and alcohol abuse. Metabolomics, or the study of chemical fingerprints that biological processes leave behind, is a rapidly advancing discipline that has great promise to improve our understanding of these pathological conditions. However, there remain significant gaps in our understanding of how extraction methodologies and separation approaches influence the data used in downstream chemometric analyses. Therefore, we have designed the four specific aims that address fundamentally essential aspects of any metabolomic study based on liquid chromatography coupled with mass spectrometry: extraction, separation, and identification with specific reference to the mammalian liver. We hypothesize that reproducible extraction and separation methodologies can be developed that are independent of disease state. To date, there has not been an organized, concerted effort to optimize and standardize these most essential steps when conducting a metabolomic study. While here we focus on liver tissue, these approaches will serve as a foundation for other tissues and biofluids as well as platforms including nuclear magnetic resonance spectroscopy and gas chromatography coupled with mass spectrometry. Based on the efforts of three independent laboratories with well-recognized expertise in metabolomics (Griffin Lab at the University of Cambridge and the UK Medical Research Council, Gonzalez Lab at the National Cancer Institute, and the Patterson Lab at Penn State University) we plan to systematically address and optimize each step (metabolite extraction, separation by liquid chromatography, and identification by mass spectrometry) across a range of metabolite classes, polarities and metabolic pathways, thus ensuring the delivery of high quality data to the vast array of already existing metabolomic data analysis platforms. Furthermore, in addition to publication in peer-reviewed journals, we will make our protocols and data freely available to the wider scientific community, including both academia and pharma, in an open format by making use of community-led open source facilities such as the European Bioinformatics Institute's MetaboLight (central repository for experimental metabolomics data) and the ISA-TAB initiative (a unified tool for meta data description of omic experiments).

Public Health Relevance

There remain significant gaps in our understanding of how extraction methodologies and separation approaches influence the data used in downstream chemometric analyses. Therefore, we have designed the four specific aims that address fundamentally essential aspects of any metabolomic study based on liquid chromatography coupled with mass spectrometry: extraction, separation, and identification with specific reference to the mammalian liver.

Agency
National Institute of Health (NIH)
Institute
National Institute of Environmental Health Sciences (NIEHS)
Type
Research Project (R01)
Project #
5R01ES022186-02
Application #
8545853
Study Section
Special Emphasis Panel (ZRG1-BST-P (50))
Program Officer
Balshaw, David M
Project Start
2012-09-15
Project End
2017-05-31
Budget Start
2013-07-01
Budget End
2014-05-31
Support Year
2
Fiscal Year
2013
Total Cost
$337,349
Indirect Cost
$82,945
Name
Pennsylvania State University
Department
Veterinary Sciences
Type
Schools of Earth Sciences/Natur
DUNS #
003403953
City
University Park
State
PA
Country
United States
Zip Code
16802
Kaushal, Naveen; Kudva, Avinash K; Patterson, Andrew D et al. (2014) Crucial role of macrophage selenoproteins in experimental colitis. J Immunol 193:3683-92
Mathé, Ewy A; Patterson, Andrew D; Haznadar, Majda et al. (2014) Noninvasive urinary metabolomic profiling identifies diagnostic and prognostic markers in lung cancer. Cancer Res 74:3259-70
Roberts, Lee D; Koulman, Albert; Griffin, Julian L (2014) Towards metabolic biomarkers of insulin resistance and type 2 diabetes: progress from the metabolome. Lancet Diabetes Endocrinol 2:65-75
Patterson, Andrew D; Turnbaugh, Peter J (2014) Microbial determinants of biochemical individuality and their impact on toxicology and pharmacology. Cell Metab 20:761-8
Fang, Zhong-Ze; Gonzalez, Frank J (2014) LC-MS-based metabolomics: an update. Arch Toxicol 88:1491-502
Ament, Zsuzsanna; Waterman, Claire L; West, James A et al. (2013) A metabolomics investigation of non-genotoxic carcinogenicity in the rat. J Proteome Res 12:5775-90
Li, Fei; Pang, Xiaoyan; Krausz, Kristopher W et al. (2013) Stable isotope- and mass spectrometry-based metabolomics as tools in drug metabolism: a study expanding tempol pharmacology. J Proteome Res 12:1369-76
Bi, Huichang; Krausz, Kristopher W; Manna, Soumen K et al. (2013) Optimization of harvesting, extraction, and analytical protocols for UPLC-ESI-MS-based metabolomic analysis of adherent mammalian cancer cells. Anal Bioanal Chem 405:5279-89
Montanez, Jessica E; Peters, Jeffrey M; Correll, Jared B et al. (2013) Metabolomics: an essential tool to understand the function of peroxisome proliferator-activated receptor alpha. Toxicol Pathol 41:410-8