51
|
Vasilopoulou CG, Margarity M, Klapa MI. Metabolomic Analysis in Brain Research: Opportunities and Challenges. Front Physiol 2016; 7:183. [PMID: 27252656 PMCID: PMC4878281 DOI: 10.3389/fphys.2016.00183] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/09/2016] [Indexed: 12/11/2022] Open
Abstract
Metabolism being a fundamental part of molecular physiology, elucidating the structure and regulation of metabolic pathways is crucial for obtaining a comprehensive perspective of cellular function and understanding the underlying mechanisms of its dysfunction(s). Therefore, quantifying an accurate metabolic network activity map under various physiological conditions is among the major objectives of systems biology in the context of many biological applications. Especially for CNS, metabolic network activity analysis can substantially enhance our knowledge about the complex structure of the mammalian brain and the mechanisms of neurological disorders, leading to the design of effective therapeutic treatments. Metabolomics has emerged as the high-throughput quantitative analysis of the concentration profile of small molecular weight metabolites, which act as reactants and products in metabolic reactions and as regulatory molecules of proteins participating in many biological processes. Thus, the metabolic profile provides a metabolic activity fingerprint, through the simultaneous analysis of tens to hundreds of molecules of pathophysiological and pharmacological interest. The application of metabolomics is at its standardization phase in general, and the challenges for paving a standardized procedure are even more pronounced in brain studies. In this review, we support the value of metabolomics in brain research. Moreover, we demonstrate the challenges of designing and setting up a reliable brain metabolomic study, which, among other parameters, has to take into consideration the sex differentiation and the complexity of brain physiology manifested in its regional variation. We finally propose ways to overcome these challenges and design a study that produces reproducible and consistent results.
Collapse
Affiliation(s)
- Catherine G Vasilopoulou
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT)Patras, Greece; Human and Animal Physiology Laboratory, Department of Biology, University of PatrasPatras, Greece
| | - Marigoula Margarity
- Human and Animal Physiology Laboratory, Department of Biology, University of Patras Patras, Greece
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research and Technology-Hellas (FORTH/ICE-HT)Patras, Greece; Departments of Chemical and Biomolecular Engineering and Bioengineering, University of MarylandCollege Park, MD, USA
| |
Collapse
|
53
|
Johnson CH, Patti GJ, Courade JP, Shriver LP, Hoang LT, Manchester M, Siuzdak G. Alterations in Spinal Cord Metabolism during Treatment of Neuropathic Pain. J Neuroimmune Pharmacol 2015; 10:396-401. [PMID: 26232265 PMCID: PMC4548716 DOI: 10.1007/s11481-015-9624-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022]
Abstract
Therapeutic options for neuropathic pain have improved over the last 20 years yet still only provide partial relief with numerous side effects. Recently, metabolomics revealed that the concentration of the endogenous metabolite N,N-dimethylsphingosine (DMS) is increased in the spinal cord in a model of neuropathic pain. Additionally, it was shown that introduction of DMS to the central nervous system (CNS) resulted in mechanical allodynia. Here, we have examined two compounds; pregabalin (Lyrica®), a drug used to treat neuropathic pain, and N-oleoylethanolamine (NOE), an endogenous endocannabinoid-like compound that is known to affect multiple lipid pathways. We found that the concentration of DMS in the spinal cord was not significantly altered upon pregabalin treatment of rats suffering from neuropathic pain. We further explored whether modulating lipid metabolism may impact neuropathic pain by testing NOE as a potential novel therapeutic.
Collapse
Affiliation(s)
- Caroline H. Johnson
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Gary J. Patti
- Departments of Chemistry, Genetics and Medicine, Washington University, St. Louis, MO 63130, USA
| | | | - Leah P. Shriver
- Departments of Chemistry and Biology, University of Akron, Akron, OH 44325, USA
| | - Linh T. Hoang
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Marianne Manchester
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gary Siuzdak
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
- Departments of Chemistry, Molecular, and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| |
Collapse
|
54
|
Benton PH, Ivanisevic J, Rinehart D, Epstein A, Kurczy ME, Boska MD, Gendelman HE, Siuzdak G. An Interactive Cluster Heat Map to Visualize and Explore Multidimensional Metabolomic Data. Metabolomics 2015; 11. [PMID: 26195918 PMCID: PMC4505375 DOI: 10.1007/s11306-014-0759-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Heat maps are a commonly used visualization tool for metabolomic data where the relative abundance of ions detected in each sample is represented with color intensity. A limitation of applying heat maps to global metabolomic data, however, is the large number of ions that have to be displayed and the lack of information provided about important metabolomic parameters such as m/z and retention time. Here we address these challenges by introducing the interactive cluster heat map in the data-processing software XCMS Online. XCMS Online (xcmsonline.scripps.edu) is a cloud-based informatic platform designed to process, statistically evaluate, and visualize mass-spectrometry based metabolomic data. An interactive heat map is provided for all data processed by XCMS Online. The heat map is clickable, allowing users to zoom and explore specific metabolite metadata (EICs, Box-and-whisker plots, mass spectra) that are linked to the METLIN metabolite database. The utility of the XCMS interactive heat map is demonstrated on metabolomic data set generated from different anatomical regions of the mouse brain.
Collapse
Affiliation(s)
- Paul H Benton
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Julijana Ivanisevic
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Duane Rinehart
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Adrian Epstein
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, United States
| | - Michael E Kurczy
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Michael D Boska
- Department of Radiology, University of Nebraska Medical Center, Omaha, NE 68198-5880, United States
| | - Howard E Gendelman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198-5880, United States
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| |
Collapse
|
55
|
Abstract
This special edition of the Journal of Neuroimmune Pharmacology focuses on the leading edge of metabolomics in brain metabolism research. The topics covered include a metabolomic field overview and the challenges in neuroscience metabolomics. The workflow and utility of different analytical platforms to profile complex biological matrices that include biofluids, brain tissue and cells, are shown in several case studies. These studies demonstrate how global and targeted metabolite profiling can be applied to distinguish disease stages and to understand the effects of drug action on the central nervous system (CNS). Finally, we discuss the importance of metabolomics to advance the understanding of brain function that includes ligand-receptor interactions and new insights into the mechanisms of CNS disorders.
Collapse
Affiliation(s)
- Julijana Ivanisevic
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | | |
Collapse
|
56
|
Kurczy ME, Zhu ZJ, Ivanisevic J, Schuyler AM, Lalwani K, Santidrian AF, David JM, Giddabasappa A, Roberts AJ, Olivos HJ, O'Brien PJ, Franco L, Fields MW, Paris LP, Friedlander M, Johnson CH, Epstein AA, Gendelman HE, Wood MR, Felding BH, Patti GJ, Spilker ME, Siuzdak G. Comprehensive bioimaging with fluorinated nanoparticles using breathable liquids. Nat Commun 2015; 6:5998. [PMID: 25601659 DOI: 10.1038/ncomms6998] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 11/28/2014] [Indexed: 01/19/2023] Open
Abstract
Fluorocarbons are lipophobic and non-polar molecules that exhibit remarkable biocompatibility, with applications in liquid ventilation and synthetic blood. The unique properties of these compounds have also enabled mass spectrometry imaging of tissues where the fluorocarbons act as a Teflon-like coating for nanostructured surfaces to assist in desorption/ionization. Here we report fluorinated gold nanoparticles (f-AuNPs) designed to facilitate nanostructure imaging mass spectrometry. Irradiation of f-AuNPs results in the release of the fluorocarbon ligands providing a driving force for analyte desorption. The f-AuNPs allow for the mass spectrometry analysis of both lipophilic and polar (central carbon) metabolites. An important property of AuNPs is that they also act as contrast agents for X-ray microtomography and electron microscopy, a feature we have exploited by infusing f-AuNPs into tissue via fluorocarbon liquids to facilitate multimodal (molecular and anatomical) imaging.
Collapse
Affiliation(s)
- Michael E Kurczy
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Zheng-Jiang Zhu
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Julijana Ivanisevic
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Adam M Schuyler
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Kush Lalwani
- Pfizer Worldwide Research and Development, 10724 Science Center Dr, San Diego, CA 92121, USA
| | - Antonio F Santidrian
- Departments of Chemical Physiology and Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - John M David
- Pfizer Worldwide Research and Development, 10724 Science Center Dr, San Diego, CA 92121, USA
| | - Anand Giddabasappa
- Pfizer Worldwide Research and Development, 10724 Science Center Dr, San Diego, CA 92121, USA
| | - Amanda J Roberts
- Department of Molecular and Cellular Neuroscience, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Hernando J Olivos
- Waters Corporation, 100 Cummings Center, Beverly, Massachusetts 01915, USA
| | - Peter J O'Brien
- Pfizer Worldwide Research and Development, 10724 Science Center Dr, San Diego, CA 92121, USA
| | - Lauren Franco
- Department of Microbiology and Immunology and Center for Biofilm Engineering, Montana State University, 109 Lewis Hall, Montana State University, Bozeman, Montana 59717, USA
| | - Matthew W Fields
- Department of Microbiology and Immunology and Center for Biofilm Engineering, Montana State University, 109 Lewis Hall, Montana State University, Bozeman, Montana 59717, USA
| | - Liliana P Paris
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Martin Friedlander
- Department of Cell and Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Caroline H Johnson
- Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Adrian A Epstein
- The Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68198-5880, USA
| | - Howard E Gendelman
- The Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68198-5880, USA
| | - Malcolm R Wood
- The Core Microscopy Facility, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Brunhilde H Felding
- Departments of Chemical Physiology and Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Gary J Patti
- 1] Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, USA [2] Departments Genetics and Medicine, Washington University School of Medicine, 660 South Euclid Ave., St Louis, Missouri 63110, USA
| | - Mary E Spilker
- Pfizer Worldwide Research and Development, 10724 Science Center Dr, San Diego, CA 92121, USA
| | - Gary Siuzdak
- 1] Scripps Center for Metabolomics and Mass Spectrometry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA [2] Departments of Chemistry, Molecular and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| |
Collapse
|