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Victor Oluwaloseyi A, Aduragbemi Noah O, Lydia Oluwatoyin A, Gaffar Y, Moses O, Oyedayo Phillips A, Comfort Onaolapo M, Sylvester Olateju B, Ademola Ayodele A, Mega Obukohwo O, Ayodeji Folorunsho A. Metabolomics of male infertility. Clin Chim Acta 2024; 556:117850. [PMID: 38431200 DOI: 10.1016/j.cca.2024.117850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
This review explores the use of metabolomics in male infertility. Metabolomics, an evolving omics technology that targets the products of cellular metabolism, is valuable for elucidating underlying pathophysiology of many disorders including male infertility. The identification of reliable biomarkers is essential for accurate diagnosis and for developing precision therapeutics for those afflicted by reproductive dysfunction. Unfortunately, despite significant progress to date, the intricate relationships between these metabolic pathways and male infertility remain elusive. It is clear, however, that additional research is required to more fully characterize the role of metabolomics in this disorder and in the potential development of targeted therapies for precision medicine.
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Affiliation(s)
- Amos Victor Oluwaloseyi
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria
| | - Odeyemi Aduragbemi Noah
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Ajayi Lydia Oluwatoyin
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Yusuff Gaffar
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | - Olotu Moses
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Moyinoluwa Comfort Onaolapo
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria
| | | | - Adelakun Ademola Ayodele
- Department of Medical Laboratory Sciences, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
| | | | - Ajayi Ayodeji Folorunsho
- Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria; Anchor Biomed Research Institute, Ogbomoso, Oyo State, Nigeria; Department of Physiology, Adeleke University, Ede, Osun State, Nigeria.
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Pourmand E, Zhang F, Sarparast M, Alan JK, Lee KSS. Quantitative Profiling Method for Oxylipins in Neurodegenerative Diseases by Liquid Chromatography Coupled with Tandem Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560544. [PMID: 37873260 PMCID: PMC10592938 DOI: 10.1101/2023.10.02.560544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Aging is one of the major risk factors for many chronic diseases, including diabetes, neuropathy, hypertension, cancer, and neurodegenerative diseases. However, the mechanism behind aging and how aging affects a variety of disease progression remains unknown. Recent research demonstrated the cytochrome P450 (CYP)-epoxide hydrolase (EH) metabolites of polyunsaturated fatty acids (PUFAs) play a critical role in the abovementioned age-associated diseases. Therefore, aging could affect the abovementioned chronic diseases by modulating CYP-EH PUFA metabolism. Unfortunately, investigating how aging affects CYP-EH metabolism in human and mammalian models poses significant challenges. In this regard, we will use C. elegans as a model organism to investigate the aging effects on CYP-EH metabolism of PUFA, owing to its long history of being used to study aging and its associated benefits of conducting aging research. This project will develop analytical tools to measure the endogenous levels of CYP-EH PUFA metabolites in C. elegans using state-of-the-art ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS). These metabolites are very potent but present in low abundance. The dramatic increase in sensitivity in UPLC-MS/MS allows us to monitor these metabolites over the lifespan of C. elegans with minimum samples. Our results show that C. elegans produces similar CYP PUFA metabolites to mammals and humans using our SPE-UPLC-MS/MS method. We will also show that our method successfully determined the CYP-EH PUFA metabolites profile changes induced by the inhibition of C. elegans EH. The method developed from this project will significantly improve our understanding of the role of dietary PUFAs and associated metabolism on aging and neurodegeneration and will uncover new mechanisms of how aging affects neurodegeneration through the modulation of PUFA metabolic pathways.
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Affiliation(s)
- Elham Pourmand
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Fan Zhang
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Morteza Sarparast
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Jamie K Alan
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
| | - Kin Sing Stephen Lee
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, USA
- Institute of Integrative Toxicology, Michigan State University, East Lansing, MI, USA
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Kocheril PA, Moore SC, Lenz KD, Mukundan H, Lilley LM. Progress Toward a Multiomic Understanding of Traumatic Brain Injury: A Review. Biomark Insights 2022; 17:11772719221105145. [PMID: 35719705 PMCID: PMC9201320 DOI: 10.1177/11772719221105145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Traumatic brain injury (TBI) is not a single disease state but describes an array
of conditions associated with insult or injury to the brain. While some
individuals with TBI recover within a few days or months, others present with
persistent symptoms that can cause disability, neuropsychological trauma, and
even death. Understanding, diagnosing, and treating TBI is extremely complex for
many reasons, including the variable biomechanics of head impact, differences in
severity and location of injury, and individual patient characteristics. Because
of these confounding factors, the development of reliable diagnostics and
targeted treatments for brain injury remains elusive. We argue that the
development of effective diagnostic and therapeutic strategies for TBI requires
a deep understanding of human neurophysiology at the molecular level and that
the framework of multiomics may provide some effective solutions for the
diagnosis and treatment of this challenging condition. To this end, we present
here a comprehensive review of TBI biomarker candidates from across the
multiomic disciplines and compare them with known signatures associated with
other neuropsychological conditions, including Alzheimer’s disease and
Parkinson’s disease. We believe that this integrated view will facilitate a
deeper understanding of the pathophysiology of TBI and its potential links to
other neurological diseases.
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Affiliation(s)
- Philip A Kocheril
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Shepard C Moore
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kiersten D Lenz
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Laura M Lilley
- Physical Chemistry and Applied Spectroscopy Group, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM, USA
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Nayak C, Chandra I, Singh P, Singh SK. Omics-Based Nanomedicine. Synth Biol (Oxf) 2018. [DOI: 10.1007/978-981-10-8693-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Pinna M, Manchia M. Preventing aggressive/violent behavior: a role for biomarkers? Biomark Med 2017; 11:701-704. [PMID: 30669857 DOI: 10.2217/bmm-2017-0135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Martina Pinna
- Unit of Psychiatry, Department of Mental Health & Addiction Services, Regional Health Agency, Oristano, Italy.,Section of Neurosciences & Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Mirko Manchia
- Department of Pharmacology, Dalhousie University, Halifax, Nova Scotia, Canada.,Section of Psychiatry, Department of Medical Sciences & Public Health, University of Cagliari, Cagliari, Italy
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Trivedi DK, Hollywood KA, Goodacre R. Metabolomics for the masses: The future of metabolomics in a personalized world. NEW HORIZONS IN TRANSLATIONAL MEDICINE 2017; 3:294-305. [PMID: 29094062 PMCID: PMC5653644 DOI: 10.1016/j.nhtm.2017.06.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/02/2017] [Accepted: 06/02/2017] [Indexed: 02/07/2023]
Abstract
Current clinical practices focus on a small number of biochemical directly related to the pathophysiology with patients and thus only describe a very limited metabolome of a patient and fail to consider the interations of these small molecules. This lack of extended information may prevent clinicians from making the best possible therapeutic interventions in sufficient time to improve patient care. Various post-genomics '('omic)' approaches have been used for therapeutic interventions previously. Metabolomics now a well-established'omics approach, has been widely adopted as a novel approach for biomarker discovery and in tandem with genomics (especially SNPs and GWAS) has the potential for providing systemic understanding of the underlying causes of pathology. In this review, we discuss the relevance of metabolomics approaches in clinical sciences and its potential for biomarker discovery which may help guide clinical interventions. Although a powerful and potentially high throughput approach for biomarker discovery at the molecular level, true translation of metabolomics into clinics is an extremely slow process. Quicker adaptation of biomarkers discovered using metabolomics can be possible with novel portable and wearable technologies aided by clever data mining, as well as deep learning and artificial intelligence; we shall also discuss this with an eye to the future of precision medicine where metabolomics can be delivered to the masses.
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Affiliation(s)
| | | | - Royston Goodacre
- Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Post-acquisition spectral stitching. An alternative approach for data processing in untargeted metabolomics by UHPLC-ESI(-)-HRMS. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1047:106-114. [PMID: 27825627 DOI: 10.1016/j.jchromb.2016.10.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/11/2016] [Accepted: 10/23/2016] [Indexed: 11/24/2022]
Abstract
INTRODUCTION In the case of the MS-based metabolomics, the large number of false positives remains a fundamental issue. OBJECTIVE The aim of this study was to develop a new strategy, which highlights the number of the reliable features i.e. the detected features that correspond to a consistent peak according to chromatographic and mass spectrometric criteria. METHOD For the analysis blood samples from 20 chickens, which were administrated with naringin and 9 samples from control, were analyzed by UHPLC-HRMS (Orbitrap Velos). Two methodologies have been compared for data processing. In the first one (classical approach), all data in the 100-900 m/z mass-to charge range were included for the data processing procedure whereas for the newly developed methodology, the data were shred in 100Da slices generating 8 datasets, which have been then subjected to the downstream MS data processing. Each dataset was treated separately and the m/z_tR features obtained by either VIP's or t-test values were merged and used as the input for the construction of the general model. RESULTS The new methodology resulted to a 4-fold increase of the peaks that could be considered chromatographically and mass spectrometrically valid. CONCLUSION A new strategy was reported on the detection of chromatographically reliable features during a metabolomic approach. The shredding of the LC-MS chromatograms into multiple m/z ranges increased the number of the identified chromatographically reliable features.
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Skirycz A, Kierszniowska S, Méret M, Willmitzer L, Tzotzos G. Medicinal Bioprospecting of the Amazon Rainforest: A Modern Eldorado? Trends Biotechnol 2016; 34:781-790. [PMID: 27113632 DOI: 10.1016/j.tibtech.2016.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/25/2022]
Abstract
Ignorant of the New World, Europeans believed in El Dorado, a hidden city of immense wealth in gold. Many consider the Amazonian forest to be a medicinal treasure chest and potentially the largest drug dispensary in the world. Yet, the quest to obtain drugs from indigenous tropical plants remains elusive. Here, we assess the potential of new technologies to tap into the metabolic diversity of tropical plants. We also consider how regulations affect access to plant resources. We conclude that, although the road to this medicinal El Dorado may be long and arduous, many other smaller but still valuable finds are hidden along the way.
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Affiliation(s)
- Aleksandra Skirycz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany; Previous affiliation: ITV Institute, Vale. S.A., Belem, Brazil.
| | | | | | - Lothar Willmitzer
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - George Tzotzos
- Department of Agriculture, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy; Previous affiliation: ITV Institute, Vale. S.A., Belem, Brazil
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Ghazi N, Arjmand M, Akbari Z, Owsat Mellati A, Saheb-Kashaf H, Zamani Z. 1H NMR- based metabolomics approaches as non- invasive tools for diagnosis of endometriosis. Int J Reprod Biomed 2016. [DOI: 10.29252/ijrm.14.1.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Thomas MM, Sulek K, McKenzie EJ, Jones B, Han TL, Villas-Boas SG, Kenny LC, McCowan LME, Baker PN. Metabolite Profile of Cervicovaginal Fluids from Early Pregnancy Is Not Predictive of Spontaneous Preterm Birth. Int J Mol Sci 2015; 16:27741-8. [PMID: 26610472 PMCID: PMC4661910 DOI: 10.3390/ijms161126052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 10/23/2015] [Accepted: 11/06/2015] [Indexed: 11/24/2022] Open
Abstract
In our study, we used a mass spectrometry-based metabolomic approach to search for biomarkers that may act as early indicators of spontaneous preterm birth (sPTB). Samples were selected as a nested case-control study from the Screening for Pregnancy Endpoints (SCOPE) biobank in Auckland, New Zealand. Cervicovaginal swabs were collected at 20 weeks from women who were originally assessed as being at low risk of sPTB. Samples were analysed using gas chromatography-mass spectrometry (GC-MS). Despite the low amount of biomass (16–23 mg), 112 compounds were detected. Statistical analysis showed no significant correlations with sPTB. Comparison of reported infection and plasma inflammatory markers from early pregnancy showed two inflammatory markers were correlated with reported infection, but no correlation with any compounds in the metabolite profile was observed. We hypothesise that the lack of biomarkers of sPTB in the cervicovaginal fluid metabolome is simply because it lacks such markers in early pregnancy. We propose alternative biofluids be investigated for markers of sPTB. Our results lead us to call for greater scrutiny of previously published metabolomic data relating to biomarkers of sPTB in cervicovaginal fluids, as the use of small, high risk, or late pregnancy cohorts may identify metabolite biomarkers that are irrelevant for predicting risk in normal populations.
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Affiliation(s)
- Melinda M Thomas
- Liggins Institute, University of Auckland, 85 Park Road, Auckland 1023, New Zealand.
| | - Karolina Sulek
- Liggins Institute, University of Auckland, 85 Park Road, Auckland 1023, New Zealand.
| | - Elizabeth J McKenzie
- Liggins Institute, University of Auckland, 85 Park Road, Auckland 1023, New Zealand.
| | - Beatrix Jones
- Institute of Natural and Mathematical Sciences, Massey University, Albany Campus, Auckland 0632, New Zealand.
| | - Ting-Li Han
- Liggins Institute, University of Auckland, 85 Park Road, Auckland 1023, New Zealand.
| | - Silas G Villas-Boas
- School of Biological Sciences, University of Auckland, 3a Symonds Street, Auckland 1010, New Zealand.
| | - Louise C Kenny
- The Irish Centre for Fetal and Neonatal Translational Research, University College Cork, Wilton 06897, Cork, Ireland.
| | - Lesley M E McCowan
- Department of Obstetrics and Gynaecology, University of Auckland, 2 Park Road, Auckland 1023, New Zealand.
| | - Philip N Baker
- Liggins Institute, University of Auckland, 85 Park Road, Auckland 1023, New Zealand.
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Gromski PS, Muhamadali H, Ellis DI, Xu Y, Correa E, Turner ML, Goodacre R. A tutorial review: Metabolomics and partial least squares-discriminant analysis – a marriage of convenience or a shotgun wedding. Anal Chim Acta 2015; 879:10-23. [DOI: 10.1016/j.aca.2015.02.012] [Citation(s) in RCA: 509] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2014] [Revised: 02/03/2015] [Accepted: 02/06/2015] [Indexed: 01/14/2023]
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Gertsman I, Gangoiti JA, Barshop BA. Validation of a dual LC-HRMS platform for clinical metabolic diagnosis in serum, bridging quantitative analysis and untargeted metabolomics. Metabolomics 2014; 10:312-323. [PMID: 25411574 PMCID: PMC4234038 DOI: 10.1007/s11306-013-0582-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Mass spectrometry-based metabolomics is a rapidly growing field in both research and diagnosis. Generally, the methodologies and types of instruments used for clinical and other absolute quantification experiments are different from those used for biomarkers discovery and untargeted analysis, as the former requires optimal sensitivity and dynamic range, while the latter requires high resolution and high mass accuracy. We used a Q-TOF mass spectrometer with two different types of pentafluorophenyl (PFP) stationary phases, employing both positive and negative ionization, to develop and validate a hybrid quantification and discovery platform using LC-HRMS. This dual-PFP LC-MS platform quantifies over 50 clinically relevant metabolites in serum (using both MS and MS/MS acquisitions) while simultaneously collecting high resolution and high mass accuracy full scans to monitor all other co-eluting non-targeted analytes. We demonstrate that the linearity, accuracy, and precision results for the quantification of a number of metabolites, including amino acids, organic acids, acylcarnitines and purines/pyrimidines, meets or exceeds normal bioanalytical standards over their respective physiological ranges. The chromatography resolved highly polar as well as hydrophobic analytes under reverse-phase conditions, enabling analysis of a wide range of chemicals, necessary for untargeted metabolomics experiments. Though previous LC-HRMS methods have demonstrated quantification capabilities for various drug and small molecule compounds, the present study provides an HRMS quant/qual platform tailored to metabolic disease; and covers a multitude of different metabolites including compounds normally quantified by a combination of separate instrumentation.
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Affiliation(s)
- Ilya Gertsman
- Corresponding author. Contact info: Address: 9500 Gilman Dr. La Jolla CA, 92093-0830, Phone: 619-543-5260,
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Kell DB, Goodacre R. Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery. Drug Discov Today 2014; 19:171-82. [PMID: 23892182 PMCID: PMC3989035 DOI: 10.1016/j.drudis.2013.07.014] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 07/03/2013] [Accepted: 07/16/2013] [Indexed: 02/06/2023]
Abstract
Metabolism represents the 'sharp end' of systems biology, because changes in metabolite concentrations are necessarily amplified relative to changes in the transcriptome, proteome and enzyme activities, which can be modulated by drugs. To understand such behaviour, we therefore need (and increasingly have) reliable consensus (community) models of the human metabolic network that include the important transporters. Small molecule 'drug' transporters are in fact metabolite transporters, because drugs bear structural similarities to metabolites known from the network reconstructions and from measurements of the metabolome. Recon2 represents the present state-of-the-art human metabolic network reconstruction; it can predict inter alia: (i) the effects of inborn errors of metabolism; (ii) which metabolites are exometabolites, and (iii) how metabolism varies between tissues and cellular compartments. However, even these qualitative network models are not yet complete. As our understanding improves so do we recognise more clearly the need for a systems (poly)pharmacology.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Royston Goodacre
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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Cho JY, Sung HJ. Proteomic approaches in lung cancer biomarker development. Expert Rev Proteomics 2014; 6:27-42. [DOI: 10.1586/14789450.6.1.27] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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van der Kloet FM, Hendriks M, Hankemeier T, Reijmers T. A new approach to untargeted integration of high resolution liquid chromatography–mass spectrometry data. Anal Chim Acta 2013; 801:34-42. [DOI: 10.1016/j.aca.2013.09.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2013] [Revised: 09/12/2013] [Accepted: 09/14/2013] [Indexed: 11/16/2022]
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Wang B, Goodpaster AM, Kennedy MA. Coefficient of Variation, Signal-to-Noise Ratio, and Effects of Normalization in Validation of Biomarkers from NMR-based Metabonomics Studies. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS : AN INTERNATIONAL JOURNAL SPONSORED BY THE CHEMOMETRICS SOCIETY 2013; 128:9-16. [PMID: 24678137 PMCID: PMC3963315 DOI: 10.1016/j.chemolab.2013.07.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A primary goal of metabonomics research is biomarker discovery for human diseases based on differences in metabolic profiles between healthy and diseased patient populations. One of the most significant challenges in biomarker discovery is validation, which implicitly depends on the coefficient of variation (CV) associated with the measurement technique. This paper investigates how the CV of metabolite resonances measured by nuclear magnetic resonance spectroscopy (NMR) depends on signal-to-noise ratio (SNR) and normalization method. CVs were calculated for NMR resonance peaks in a series of NMR spectra of five synthetic urine samples collected over an eight-month period. An inverse correlation was detected between SNR and CV for all normalization methods. Small peaks with SNR<15 tended to have larger CVs (15-30%) compared to peaks with the highest SNR>150, which typically had smaller CVs (5-10%). The inverse relationship between CV and SNR roughly obeyed a log10 dependence. Quotient normalization (QN) tended to produce smaller CVs for smaller peaks, but larger CVs for the strongest peaks in the data, compared to no normalization, normalization to total intensity (NTI) or normalization to an internal standard (NIS). Consequently, quotient normalization appears optimal for validating low concentration metabolites. NTI or NIS appear superior to QN for samples that have very small variation in total signal intensity. While the inverse relationship between CV and log10(SNR) did not strictly hold for all metabolites, weaker concentration metabolites will likely require more rigorous validation as potential biomarkers since they tend to have poorer reproducibility.
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Affiliation(s)
| | | | - Michael A. Kennedy
- Contact Info: Michael A. Kennedy, Eminent Scholar and Professor, 106 Hughes Laboratory, Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, 513-529-8267,
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Collino S, Martin FPJ, Rezzi S. Clinical metabolomics paves the way towards future healthcare strategies. Br J Clin Pharmacol 2013; 75:619-29. [PMID: 22348240 DOI: 10.1111/j.1365-2125.2012.04216.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metabolomics is recognized as a powerful top-down system biological approach to understand genetic-environment-health paradigms paving new avenues to identify clinically relevant biomarkers. It is nowadays commonly used in clinical applications shedding new light on physiological regulatory processes of complex mammalian systems with regard to disease aetiology, diagnostic stratification and, potentially, mechanism of action of therapeutic solutions. A key feature of metabolomics lies in its ability to underpin the complex metabolic interactions of the host with its commensal microbial partners providing a new way to define individual and population phenotypes. This review aims at describing recent applications of metabolomics in clinical fields with insight into diseases, diagnostics/monitoring and improvement of homeostatic metabolic regulation.
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Affiliation(s)
- Sebastiano Collino
- Nestec Ltd, Nestlé Research Center, BioAnalytical Science, Metabolomics and Biomarkers, PO Box 44, CH-1000 Lausanne 26, Switzerland
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18
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Tao M, Xiu D. Metabonomic Analysis of Rats With Acute Heart Rejection. Transplant Proc 2013; 45:618-24. [DOI: 10.1016/j.transproceed.2012.06.085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 06/05/2012] [Accepted: 06/19/2012] [Indexed: 11/29/2022]
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Farshidfar F, Weljie AM, Kopciuk K, Buie WD, Maclean A, Dixon E, Sutherland FR, Molckovsky A, Vogel HJ, Bathe OF. Serum metabolomic profile as a means to distinguish stage of colorectal cancer. Genome Med 2012; 4:42. [PMID: 22583555 PMCID: PMC3506908 DOI: 10.1186/gm341] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 05/01/2012] [Accepted: 05/14/2012] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Presently, colorectal cancer (CRC) is staged preoperatively by radiographic tests, and postoperatively by pathological evaluation of available surgical specimens. However, present staging methods do not accurately identify occult metastases. This has a direct effect on clinical management. Early identification of metastases isolated to the liver may enable surgical resection, whereas more disseminated disease may be best treated with palliative chemotherapy. METHODS Sera from 103 patients with colorectal adenocarcinoma treated at the same tertiary cancer center were analyzed by proton nuclear magnetic resonance (1H NMR) spectroscopy and gas chromatography-mass spectroscopy (GC-MS). Metabolic profiling was done using both supervised pattern recognition and orthogonal partial least squares-discriminant analysis (O-PLS-DA) of the most significant metabolites, which enables comparison of the whole sample spectrum between groups. The metabolomic profiles generated from each platform were compared between the following groups: locoregional CRC (N = 42); liver-only metastases (N = 45); and extrahepatic metastases (N = 25). RESULTS The serum metabolomic profile associated with locoregional CRC was distinct from that associated with liver-only metastases, based on 1H NMR spectroscopy (P = 5.10 × 10-7) and GC-MS (P = 1.79 × 10-7). Similarly, the serum metabolomic profile differed significantly between patients with liver-only metastases and with extrahepatic metastases. The change in metabolomic profile was most markedly demonstrated on GC-MS (P = 4.75 × 10-5). CONCLUSIONS In CRC, the serum metabolomic profile changes markedly with metastasis, and site of disease also appears to affect the pattern of circulating metabolites. This novel observation may have clinical utility in enhancing staging accuracy and selecting patients for surgical or medical management. Additional studies are required to determine the sensitivity of this approach to detect subtle or occult metastatic disease.
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Affiliation(s)
- Farshad Farshidfar
- Department of Surgery, University of Calgary, 3330 Hospital Dr NW, Calgary, AB, Canada, T2N 4N1.
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Olszewski KL, Llinás M. Extraction of hydrophilic metabolites from Plasmodium falciparum-infected erythrocytes for metabolomic analysis. Methods Mol Biol 2012; 923:259-66. [PMID: 22990783 DOI: 10.1007/978-1-62703-026-7_17] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Metabolomics is an increasingly common analytical approach for investigating metabolic networks of pathogenic organisms. This may be of particular use in the study of parasitic infections due to the intrinsic metabolic connection between the parasite and its host. In vitro cultures of the malaria parasite Plasmodium falciparum present a valuable platform to elucidate the structure and dynamics of the parasite's metabolic network and to determine the mechanisms of action of antimalarial drugs and drug resistance mutations. Accurately measuring metabolite levels requires a reproducible method for quantifying intracellular metabolites. Here we present a simple protocol for extracting hydrophilic metabolites from P. falciparum-infected erythrocyte cultures.
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Affiliation(s)
- Kellen L Olszewski
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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Shao S, Zhou T, McGarvey BD. Comparative metabolomic analysis of Saccharomyces cerevisiae during the degradation of patulin using gas chromatography-mass spectrometry. Appl Microbiol Biotechnol 2011; 94:789-97. [PMID: 22159606 DOI: 10.1007/s00253-011-3739-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Revised: 11/01/2011] [Accepted: 11/15/2011] [Indexed: 11/29/2022]
Abstract
A comparative metabolomic analysis was conducted on Saccharomyces cerevisiae cells with and without patulin treatment using gas chromatography-mass spectrometry-based approach. A total of 72 metabolites were detected and compared, including 16 amino acids, 29 organic acids and alcohols, 19 sugars and sugar alcohols, 2 nucleotides, and 6 miscellaneous compounds. Principle component analysis showed a clear separation of metabolome between the cells with and without patulin treatment, and most of the identified metabolites contributed to the separation. A close examination of the identified metabolites showed an increased level of most of the free amino acids, an increased level of the intermediates in the tricarboxylic acid cycle, a higher amount of glycerol, a changed fatty acid composition, and a decreased level of cysteine and glutathione in the cells with patulin treatment. This finding indicated a slower protein synthesis rate and induced oxidative stress in the cells with patulin treatment, and provided new insights into the effect of toxic chemicals on the metabolism of organisms.
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Affiliation(s)
- Suqin Shao
- Guelph Food Research Centre, Agriculture & Agri-Food Canada, 93 Stone Road West, Guelph, Ontario, Canada N1G 5C9
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Wedge DC, Allwood JW, Dunn W, Vaughan AA, Simpson K, Brown M, Priest L, Blackhall FH, Whetton AD, Dive C, Goodacre R. Is Serum or Plasma More Appropriate for Intersubject Comparisons in Metabolomic Studies? An Assessment in Patients with Small-Cell Lung Cancer. Anal Chem 2011; 83:6689-97. [DOI: 10.1021/ac2012224] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Warwick Dunn
- Centre for Advanced Discovery & Experimental Therapeutics (CADET), Central Manchester NHS Foundation Trust and School of Biomedicine, University of Manchester, Manchester Academic Health Science Centre (MAHSC), York Place, Oxford Road, Manchester, M13 9WL, U.K
| | | | - Kathryn Simpson
- Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research and Manchester Cancer Research Centre (MCRC), Manchester Academic Health Science Centre, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, U.K
| | - Marie Brown
- Centre for Advanced Discovery & Experimental Therapeutics (CADET), Central Manchester NHS Foundation Trust and School of Biomedicine, University of Manchester, Manchester Academic Health Science Centre (MAHSC), York Place, Oxford Road, Manchester, M13 9WL, U.K
| | - Lynsey Priest
- Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research and Manchester Cancer Research Centre (MCRC), Manchester Academic Health Science Centre, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, U.K
| | - Fiona H. Blackhall
- Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research and Manchester Cancer Research Centre (MCRC), Manchester Academic Health Science Centre, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, U.K
| | - Anthony D. Whetton
- School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, University of Manchester, Manchester, M20 3LJ, U.K
| | - Caroline Dive
- Clinical and Experimental Pharmacology Group, Paterson Institute for Cancer Research and Manchester Cancer Research Centre (MCRC), Manchester Academic Health Science Centre, University of Manchester, Wilmslow Road, Withington, Manchester, M20 4BX, U.K
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Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 2011; 6:1060-83. [PMID: 21720319 DOI: 10.1038/nprot.2011.335] [Citation(s) in RCA: 1847] [Impact Index Per Article: 142.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metabolism has an essential role in biological systems. Identification and quantitation of the compounds in the metabolome is defined as metabolic profiling, and it is applied to define metabolic changes related to genetic differences, environmental influences and disease or drug perturbations. Chromatography-mass spectrometry (MS) platforms are frequently used to provide the sensitive and reproducible detection of hundreds to thousands of metabolites in a single biofluid or tissue sample. Here we describe the experimental workflow for long-term and large-scale metabolomic studies involving thousands of human samples with data acquired for multiple analytical batches over many months and years. Protocols for serum- and plasma-based metabolic profiling applying gas chromatography-MS (GC-MS) and ultraperformance liquid chromatography-MS (UPLC-MS) are described. These include biofluid collection, sample preparation, data acquisition, data pre-processing and quality assurance. Methods for quality control-based robust LOESS signal correction to provide signal correction and integration of data from multiple analytical batches are also described.
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Wang H, Tso VK, Slupsky CM, Fedorak RN. Metabolomics and detection of colorectal cancer in humans: a systematic review. Future Oncol 2011; 6:1395-406. [PMID: 20919825 DOI: 10.2217/fon.10.107] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Metabolomics represents one of the new omics sciences and capitalizes on the unique presence and concentration of small molecules in tissues and body fluids to construct a 'fingerprint' that can be unique to the individual and, within that individual, unique to environmental influences, including health and disease states. As such, metabolomics has the potential to serve an important role in diagnosis and management of human conditions. Colorectal cancer is a major public health concern. Current population-based screening methods are suboptimal and whether metabolomics could represent a new tool of screening is under investigation. The purpose of this systematic review is to summarize existing literature on metabolomics and colorectal cancer, in terms of diagnostic accuracies and distinguishing metabolites. Eight studies are included. A total of 12 metabolites (taurine, lactate, choline, inositol, glycine, phosphocholine, proline, phenylalanine, alanine, threonine, valine and leucine) were found to be more prevalent in colorectal cancer and glucose was found to be in higher proportion in control specimens using tissue metabolomics. Serum and urine metabolomics identified several other differential metabolites between controls and colorectal cancer patients. This article highlights the novelty of the field of metabolomics in colorectal oncology.
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Affiliation(s)
- Haili Wang
- University of Alberta, 130 University Campus, 112th St & 85th Avenue, Edmonton, AB, Canada
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The role of metabolites and metabolomics in clinically applicable biomarkers of disease. Arch Toxicol 2010; 85:5-17. [PMID: 20953584 DOI: 10.1007/s00204-010-0609-6] [Citation(s) in RCA: 233] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 09/30/2010] [Indexed: 01/20/2023]
Abstract
Metabolomics allows the simultaneous and relative quantification of thousands of different metabolites within a given sample using sensitive and specific methodologies such as gas or liquid chromatography coupled to mass spectrometry, typically in discovery phases of studies. Biomarkers are biological characteristics that are objectively measured and evaluated as indicators of normal biological processes, pathological processes or pharmacologic responses to a therapeutic intervention. Biomarkers are widely used in clinical practice for the diagnosis, assessment of severity and response to therapy in a number of clinical disease states. In human studies, metabolomics has been applied to define biomarkers related to prognosis or diagnosis of a disease or drug toxicity/efficacy and in doing so hopes to provide greater pathophysiological understanding of disease or therapeutic toxicity/efficacy. This review discusses the application of metabolomics in the discovery and subsequent application of biomarkers in the diagnosis and management of inborn errors of metabolism, cardiovascular disease and cancer. We critically appraise how novel biomarkers discovered through metabolomic analysis may be utilized in future clinical practice by addressing the following three fundamental questions: (1) Can the clinician measure them? (2) Do they add new information? (3) Do they help the clinician to manage patients? Although a number of novel biomarkers have been discovered through metabolomic studies of human diseases in the last decade, none have currently made the transition to routine use in clinical practice. Metabolites identified from these early studies will need to form the basis of larger, prospective, externally validated studies in clinical cohorts for their future use as biomarkers. At this stage, the absolute quantification of these biomarkers will need to be assessed epidemiologically, as will the ultimate deployment in the clinic via routine biochemistry, dip stick or similar rapid at- or near-patient care technologies.
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Dunn WB, Broadhurst DI, Atherton HJ, Goodacre R, Griffin JL. Systems level studies of mammalian metabolomes: the roles of mass spectrometry and nuclear magnetic resonance spectroscopy. Chem Soc Rev 2010; 40:387-426. [PMID: 20717559 DOI: 10.1039/b906712b] [Citation(s) in RCA: 543] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The study of biological systems in a holistic manner (systems biology) is increasingly being viewed as a necessity to provide qualitative and quantitative descriptions of the emergent properties of the complete system. Systems biology performs studies focussed on the complex interactions of system components; emphasising the whole system rather than the individual parts. Many perturbations to mammalian systems (diet, disease, drugs) are multi-factorial and the study of small parts of the system is insufficient to understand the complete phenotypic changes induced. Metabolomics is one functional level tool being employed to investigate the complex interactions of metabolites with other metabolites (metabolism) but also the regulatory role metabolites provide through interaction with genes, transcripts and proteins (e.g. allosteric regulation). Technological developments are the driving force behind advances in scientific knowledge. Recent advances in the two analytical platforms of mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy have driven forward the discipline of metabolomics. In this critical review, an introduction to metabolites, metabolomes, metabolomics and the role of MS and NMR spectroscopy will be provided. The applications of metabolomics in mammalian systems biology for the study of the health-disease continuum, drug efficacy and toxicity and dietary effects on mammalian health will be reviewed. The current limitations and future goals of metabolomics in systems biology will also be discussed (374 references).
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Affiliation(s)
- Warwick B Dunn
- Manchester Centre for Integrative Systems Biology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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Baumgartner C, Lewis GD, Netzer M, Pfeifer B, Gerszten RE. A new data mining approach for profiling and categorizing kinetic patterns of metabolic biomarkers after myocardial injury. ACTA ACUST UNITED AC 2010; 26:1745-51. [PMID: 20483816 DOI: 10.1093/bioinformatics/btq254] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION The discovery of new and unexpected biomarkers in cardiovascular disease is a highly data-driven process that requires the complementary power of modern metabolite profiling technologies, bioinformatics and biostatistics. Clinical biomarkers of early myocardial injury are lacking. A prospective biomarker cohort study was carried out to identify, categorize and profile kinetic patterns of early metabolic biomarkers of planned myocardial infarction (PMI) and spontaneous (SMI) myocardial infarction. We applied a targeted mass spectrometry (MS)-based metabolite profiling platform to serial blood samples drawn from carefully phenotyped patients undergoing alcohol septal ablation for hypertrophic obstructive cardiomyopathy serving as a human model of PMI. Patients with SMI and patients undergoing catheterization without induction of myocardial infarction served as positive and negative controls to assess generalizability of markers identified in PMI. RESULTS To identify metabolites of high predictive value in tandem mass spectrometry data, we introduced a new feature selection method for the categorization of metabolic signatures into three classes of weak, moderate and strong predictors, which can be easily applied to both paired and unpaired samples. Our paradigm outperformed standard null-hypothesis significance testing and other popular methods for feature selection in terms of the area under the receiver operating curve and the product of sensitivity and specificity. Our results emphasize that this new method was able to identify, classify and validate alterations of levels in multiple metabolites participating in pathways associated with myocardial injury as early as 10 min after PMI. AVAILABILITY The algorithm as well as supplementary material is available for download at: www.umit.at/page.cfm?vpath=departments/technik/iebe/tools/bi
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Affiliation(s)
- Christian Baumgartner
- Research Group for Clinical Bioinformatics, Institute of Electrical, Electronic and Bioengineering, University for Health Sciences, Medical Informatics and Technology (UMIT), A-6060 Hall in Tirol, Austria.
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Yang J, Schmelzer K, Georgi K, Hammock BD. Quantitative profiling method for oxylipin metabolome by liquid chromatography electrospray ionization tandem mass spectrometry. Anal Chem 2009; 81:8085-93. [PMID: 19715299 PMCID: PMC3290520 DOI: 10.1021/ac901282n] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclooxygenase, lipoxygenase, and epoxygenase derived oxylipins, especially eicosanoids, play important roles in many physiological processes. Assessment of oxidized fatty acid levels is important for understanding their homeostatic and pathophysiological roles. Most reported methods examine these pathways in isolation. The work described here employed a solid phase extraction-liquid chromatography-electrospray ionization MS/MS (SPE-LC-ESI MS/MS) method to monitor these metabolites. In 21 min, 39 oxylipins were quantified along with eight corresponding internal standards. The limits of quantification were between 0.07 and 32 pg (20 pM-10 nM). Finally, the validated method was used to evaluate oxylipin profiles in lipopolysaccharide-exposed mice, an established septic inflammatory model. The method described here offers a useful tool for the evaluation of complex regulatory oxylipin responses in in vitro or in vivo studies.
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Affiliation(s)
- Jun Yang
- University of California, Department of Entomology, One Shields Avenue, Davis, CA 95616, United States University of California, Cancer Center, One Shields Avenue, Davis, CA 95616, United States
| | - Kara Schmelzer
- University of California, Department of Entomology, One Shields Avenue, Davis, CA 95616, United States University of California, Cancer Center, One Shields Avenue, Davis, CA 95616, United States
| | - Katrin Georgi
- University of California, Department of Entomology, One Shields Avenue, Davis, CA 95616, United States University of California, Cancer Center, One Shields Avenue, Davis, CA 95616, United States
| | - Bruce D Hammock
- University of California, Department of Entomology, One Shields Avenue, Davis, CA 95616, United States University of California, Cancer Center, One Shields Avenue, Davis, CA 95616, United States
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Kell DB. Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Med Genomics 2009; 2:2. [PMID: 19133145 PMCID: PMC2672098 DOI: 10.1186/1755-8794-2-2] [Citation(s) in RCA: 364] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 01/08/2009] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The production of peroxide and superoxide is an inevitable consequence of aerobic metabolism, and while these particular 'reactive oxygen species' (ROSs) can exhibit a number of biological effects, they are not of themselves excessively reactive and thus they are not especially damaging at physiological concentrations. However, their reactions with poorly liganded iron species can lead to the catalytic production of the very reactive and dangerous hydroxyl radical, which is exceptionally damaging, and a major cause of chronic inflammation. REVIEW We review the considerable and wide-ranging evidence for the involvement of this combination of (su)peroxide and poorly liganded iron in a large number of physiological and indeed pathological processes and inflammatory disorders, especially those involving the progressive degradation of cellular and organismal performance. These diseases share a great many similarities and thus might be considered to have a common cause (i.e. iron-catalysed free radical and especially hydroxyl radical generation).The studies reviewed include those focused on a series of cardiovascular, metabolic and neurological diseases, where iron can be found at the sites of plaques and lesions, as well as studies showing the significance of iron to aging and longevity. The effective chelation of iron by natural or synthetic ligands is thus of major physiological (and potentially therapeutic) importance. As systems properties, we need to recognise that physiological observables have multiple molecular causes, and studying them in isolation leads to inconsistent patterns of apparent causality when it is the simultaneous combination of multiple factors that is responsible.This explains, for instance, the decidedly mixed effects of antioxidants that have been observed, since in some circumstances (especially the presence of poorly liganded iron) molecules that are nominally antioxidants can actually act as pro-oxidants. The reduction of redox stress thus requires suitable levels of both antioxidants and effective iron chelators. Some polyphenolic antioxidants may serve both roles.Understanding the exact speciation and liganding of iron in all its states is thus crucial to separating its various pro- and anti-inflammatory activities. Redox stress, innate immunity and pro- (and some anti-)inflammatory cytokines are linked in particular via signalling pathways involving NF-kappaB and p38, with the oxidative roles of iron here seemingly involved upstream of the IkappaB kinase (IKK) reaction. In a number of cases it is possible to identify mechanisms by which ROSs and poorly liganded iron act synergistically and autocatalytically, leading to 'runaway' reactions that are hard to control unless one tackles multiple sites of action simultaneously. Some molecules such as statins and erythropoietin, not traditionally associated with anti-inflammatory activity, do indeed have 'pleiotropic' anti-inflammatory effects that may be of benefit here. CONCLUSION Overall we argue, by synthesising a widely dispersed literature, that the role of poorly liganded iron has been rather underappreciated in the past, and that in combination with peroxide and superoxide its activity underpins the behaviour of a great many physiological processes that degrade over time. Understanding these requires an integrative, systems-level approach that may lead to novel therapeutic targets.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess St, Manchester, M1 7DN, UK.
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Shlomi T. Metabolic Network-Based Interpretation of Gene Expression Data Elucidates Human Cellular Metabolism. Biotechnol Genet Eng Rev 2009; 26:281-96. [DOI: 10.5661/bger-26-281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Shlomi T, Cabili MN, Herrgård MJ, Palsson BØ, Ruppin E. Network-based prediction of human tissue-specific metabolism. Nat Biotechnol 2008; 26:1003-10. [PMID: 18711341 DOI: 10.1038/nbt.1487] [Citation(s) in RCA: 446] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Direct in vivo investigation of mammalian metabolism is complicated by the distinct metabolic functions of different tissues. We present a computational method that successfully describes the tissue specificity of human metabolism on a large scale. By integrating tissue-specific gene- and protein-expression data with an existing comprehensive reconstruction of the global human metabolic network, we predict tissue-specific metabolic activity in ten human tissues. This reveals a central role for post-transcriptional regulation in shaping tissue-specific metabolic activity profiles. The predicted tissue specificity of genes responsible for metabolic diseases and tissue-specific differences in metabolite exchange with biofluids extend markedly beyond tissue-specific differences manifest in enzyme-expression data, and are validated by large-scale mining of tissue-specificity data. Our results establish a computational basis for the genome-wide study of normal and abnormal human metabolism in a tissue-specific manner.
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Affiliation(s)
- Tomer Shlomi
- School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel.
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Heazell A, Brown M, Dunn W, Worton S, Crocker I, Baker P, Kell D. Analysis of the Metabolic Footprint and Tissue Metabolome of Placental Villous Explants Cultured at Different Oxygen Tensions Reveals Novel Redox Biomarkers. Placenta 2008; 29:691-8. [DOI: 10.1016/j.placenta.2008.05.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Revised: 05/01/2008] [Accepted: 05/02/2008] [Indexed: 11/25/2022]
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