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Loo RL, Chan Q, Nicholson JK, Holmes E. Balancing the Equation: A Natural History of Trimethylamine and Trimethylamine- N-oxide. J Proteome Res 2022; 21:560-589. [PMID: 35142516 DOI: 10.1021/acs.jproteome.1c00851] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Trimethylamine (TMA) and its N-oxide (TMAO) are ubiquitous in prokaryote and eukaryote organisms as well as in the environment, reflecting their fundamental importance in evolutionary biology, and their diverse biochemical functions. Both metabolites have multiple biological roles including cell-signaling. Much attention has focused on the significance of serum and urinary TMAO in cardiovascular disease risk, yet this is only one of the many facets of a deeper TMA-TMAO partnership that reflects the significance of these metabolites in multiple biological processes spanning animals, plants, bacteria, and fungi. We report on analytical methods for measuring TMA and TMAO and attempt to critically synthesize and map the global functions of TMA and TMAO in a systems biology framework.
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Affiliation(s)
- Ruey Leng Loo
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia
| | - Queenie Chan
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, United Kingdom.,MRC Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, United Kingdom
| | - Jeremy K Nicholson
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Institute of Global Health Innovation, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, United Kingdom
| | - Elaine Holmes
- Centre for Computational and Systems Medicine, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,The Australian National Phenome Centre, Health Futures Institute, Murdoch University, 5 Robin Warren Drive, Perth, Western Australia 6150, Australia.,Nutrition Research, Department of Metabolism, Nutrition and Reproduction, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, United Kingdom
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2
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Li S, Kararigas G. Role of Biological Sex in the Cardiovascular-Gut Microbiome Axis. Front Cardiovasc Med 2022; 8:759735. [PMID: 35083297 PMCID: PMC8785253 DOI: 10.3389/fcvm.2021.759735] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/16/2021] [Indexed: 12/28/2022] Open
Abstract
There has been a recent, unprecedented interest in the role of gut microbiota in host health and disease. Technological advances have dramatically expanded our knowledge of the gut microbiome. Increasing evidence has indicated a strong link between gut microbiota and the development of cardiovascular diseases (CVD). In the present article, we discuss the contribution of gut microbiota in the development and progression of CVD. We further discuss how the gut microbiome may differ between the sexes and how it may be influenced by sex hormones. We put forward that regulation of microbial composition and function by sex might lead to sex-biased disease susceptibility, thereby offering a mechanistic insight into sex differences in CVD. A better understanding of this could identify novel targets, ultimately contributing to the development of innovative preventive, diagnostic and therapeutic strategies for men and women.
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Affiliation(s)
- Shuangyue Li
- State Key Laboratory of Cardiovascular Diseases, National Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Georgios Kararigas
- Department of Physiology, Faculty of Medicine, University of Iceland, Reykjavík, Iceland
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3
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Pretorius L, Smith C. The trace aminergic system: a gender-sensitive therapeutic target for IBS? J Biomed Sci 2020; 27:95. [PMID: 32981524 PMCID: PMC7520957 DOI: 10.1186/s12929-020-00688-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/15/2020] [Indexed: 02/06/2023] Open
Abstract
Due to a lack of specific or sensitive biomarkers, drug discovery advances have been limited for individuals suffering from irritable bowel syndrome (IBS). While current therapies provide symptomatic relief, inflammation itself is relatively neglected, despite the presence of chronic immune activation and innate immune system dysfunction. Moreover, considering the microgenderome concept, gender is a significant aetiological risk factor. We believe that we have pinpointed a "missing link" that connects gender, dysbiosis, diet, and inflammation in the context of IBS, which may be manipulated as therapeutic target. The trace aminergic system is conveniently positioned at the interface of the gut microbiome, dietary nutrients and by-products, and mucosal immunity. Almost all leukocyte populations express trace amine associated receptors and significant amounts of trace amines originate from both food and the gut microbiota. Additionally, although IBS-specific data are sparse, existing data supports an interpretation in favour of a gender dependence in trace aminergic signalling. As such, trace aminergic signalling may be altered by fluctuations of especially female reproductive hormones. Utilizing a multidisciplinary approach, this review discusses potential mechanisms of actions, which include hyperreactivity of the immune system and aberrant serotonin signalling, and links outcomes to the symptomology clinically prevalent in IBS. Taken together, it is feasible that the additional level of regulation by the trace aminergic system in IBS has been overlooked, until now. As such, we suggest that components of the trace aminergic system be considered targets for future therapeutic action, with the specific focus of reducing oxidative stress and inflammation.
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Affiliation(s)
- Lesha Pretorius
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Stellenbosch, 7062, South Africa
| | - Carine Smith
- Department of Physiological Sciences, Stellenbosch University, Stellenbosch Private Bag X1, Stellenbosch, 7062, South Africa.
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4
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Long-term effects of western diet consumption in male and female mice. Sci Rep 2020; 10:14686. [PMID: 32895402 PMCID: PMC7477228 DOI: 10.1038/s41598-020-71592-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/12/2020] [Indexed: 02/08/2023] Open
Abstract
Long-term consumption of a diet with excessive fat and sucrose (Western diet, WD) leads to an elevated risk of obesity and metabolic syndrome in both males and females. However, there are sexual dimorphisms in metabolism which are apparent when considering the prevalence of complications of metabolic syndrome, such as non-alcoholic fatty liver disease. This study aimed to elucidate the impact of a WD on the metabolome and the gut microbiota of male and female mice at 5, 10, and 15 months to capture the dynamic and comprehensive changes brought about by diet at different stages of life. Here we show that there are important considerations of age and sex that should be considered when assessing the impact of diet on the gut microbiome and health.
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5
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Letertre M, Munjoma NC, Slade SE, Plumb RS, Swann J, Coen M, Nicholson JK, Wilson ID. Metabolic Phenotyping Using UPLC–MS and Rapid Microbore UPLC–IM–MS: Determination of the Effect of Different Dietary Regimes on the Urinary Metabolome of the Rat. Chromatographia 2020. [DOI: 10.1007/s10337-020-03900-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
AbstractA rapid reversed-phase gradient method employing a 50 mm × 1 mm i.d., C18 microbore column, combined with ion mobility and high-resolution mass spectrometry, was applied to the metabolic phenotyping of urine samples obtained from rats receiving different diets. This method was directly compared to a “conventional” method employing a 150 × 2.1 mm i.d. column packed with the same C18 bonded phase using the same samples. Multivariate statistical analysis of the resulting data showed similar class discrimination for both microbore and conventional methods, despite the detection of fewer mass/retention time features by the former. Multivariate statistical analysis highlighted a number of ions that represented diet-specific markers in the samples. Several of these were then identified using the combination of mass, ion-mobility-derived collision cross section and retention time including N-acetylglutamate, urocanic acid, and xanthurenic acid. Kynurenic acid was tentatively identified based on mass and ion mobility data.
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6
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Wang X, Li Y, Xie M, Deng L, Zhang M, Xie X. Urine metabolomics study of Bushen Huoxue Prescription on diabetic retinopathy rats by UPLC–Q‐exactive Orbitrap–MS. Biomed Chromatogr 2020; 34:e4792. [DOI: 10.1002/bmc.4792] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 12/22/2019] [Accepted: 12/30/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Xin Wang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest ChinaChengdu University of Traditional Chinese Medicine Chengdu China
| | - Yang Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest ChinaChengdu University of Traditional Chinese Medicine Chengdu China
| | - Mengjun Xie
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest ChinaChengdu University of Traditional Chinese Medicine Chengdu China
| | - Liping Deng
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest ChinaChengdu University of Traditional Chinese Medicine Chengdu China
| | - Mei Zhang
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest ChinaChengdu University of Traditional Chinese Medicine Chengdu China
| | - Xuejun Xie
- Hospital of Chengdu University of Traditional Chinese Medicine Chengdu China
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7
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Zhang R, Pan Y, Ahmed L, Block E, Zhang Y, Batista VS, Zhuang H. A Multispecific Investigation of the Metal Effect in Mammalian Odorant Receptors for Sulfur-Containing Compounds. Chem Senses 2019; 43:357-366. [PMID: 29659735 DOI: 10.1093/chemse/bjy022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metal-coordinating compounds are generally known to have strong smells, a phenomenon that can be attributed to the fact that odorant receptors for intense-smelling compounds, such as those containing sulfur, may be metalloproteins. We previously identified a mouse odorant receptor (OR), Olfr1509, that requires copper ions for sensitive detection of a series of metal-coordinating odorants, including (methylthio)methanethiol (MTMT), a strong-smelling component of male mouse urine that attracts female mice. By combining mutagenesis and quantum mechanics/molecular mechanics (QM/MM) modeling, we identified candidate binding sites in Olfr1509 that may bind to the copper-MTMT complex. However, whether there are other receptors utilizing metal ions for ligand-binding and other sites important for receptor activation is still unknown. In this study, we describe a second mouse OR for MTMT with a copper effect, namely Olfr1019. In an attempt to investigate the functional changes of metal-coordinating ORs in multiple species and to decipher additional sites involved in the metal effect, we cloned various mammalian orthologs of the 2 mouse MTMT receptors, and a third mouse MTMT receptor, Olfr15, that does not have a copper effect. We found that the function of all 3 MTMT receptors varies greatly among species and that the response to MTMT always co-occurred with the copper effect. Furthermore, using ancestral reconstruction and QM/MM modeling combined with receptor functional assay, we found that the amino acid residue R260 in Olfr1509 and the respective R261 site in Olfr1019 may be important for receptor activation.
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Affiliation(s)
- Ruina Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiaotong University School of Medicine, Huangpu District, Shanghai, P. R. China
| | - Yi Pan
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiaotong University School of Medicine, Huangpu District, Shanghai, P. R. China
| | - Lucky Ahmed
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Eric Block
- Department of Chemistry, University at Albany, State University of New York, NY, USA
| | - Yuetian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiaotong University School of Medicine, Huangpu District, Shanghai, P. R. China
| | | | - Hanyi Zhuang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiaotong University School of Medicine, Huangpu District, Shanghai, P. R. China
- Institute of Health Sciences, Shanghai Jiaotong University School of Medicine/Shanghai Institutes for Biological Sciences of Chinese Academy of Sciences, Xuhui District, Shanghai, P. R. China
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8
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Gika H, Virgiliou C, Theodoridis G, Plumb RS, Wilson ID. Untargeted LC/MS-based metabolic phenotyping (metabonomics/metabolomics): The state of the art. J Chromatogr B Analyt Technol Biomed Life Sci 2019; 1117:136-147. [PMID: 31009899 DOI: 10.1016/j.jchromb.2019.04.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/01/2019] [Accepted: 04/03/2019] [Indexed: 12/25/2022]
Abstract
Liquid chromatography (LC) hyphenated to mass spectrometry is currently the most widely used means of determining metabolic phenotypes via both untargeted and targeted analysis. At present a range of analytical separations, including reversed-phase, hydrophilic interaction and ion-pair LC are employed to maximise metabolome coverage with ultra (high) performance liquid chromatography (UHPLC) increasingly displacing conventional high performance liquid chromatography because of the need for short analysis times and high peak capacity in such applications. However, it is widely recognized that these methodologies do not entirely solve the problems facing researchers trying to perform comprehensive metabolic phenotyping and in addition to these "routine" approaches there are continuing investigations of alternative separation methods including 2-dimensional/multi column approaches. These involve either new stationary phases or multidimensional combinations of the more conventional materials currently used, as well as application of miniaturization or "new" approaches such as supercritical HP and UHP- chromatographic separations. There is also a considerable amount of interest in the combination of chromatographic and ion mobility separations, with the latter providing both an increase in resolution and the potential to provide additional structural information via the determination of molecular collision cross section data. However, key problems remain to be solved including ensuring quality, comparability across different laboratories and the ever present difficulty of identifying unknowns.
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Affiliation(s)
- Helen Gika
- Department of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece
| | - Christina Virgiliou
- Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Georgios Theodoridis
- Biomic AUTh, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; FoodOmicsGR Research Infrastructure, Center for Interdisciplinary Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, GR 57001 Thessaloniki, Greece; Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | | | - Ian D Wilson
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College, Exhibition Road, South Kensington, London SW7 2AZ, UK.
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9
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Abstract
Trace amines are endogenous compounds classically regarded as comprising β-phenylethyalmine, p-tyramine, tryptamine, p-octopamine, and some of their metabolites. They are also abundant in common foodstuffs and can be produced and degraded by the constitutive microbiota. The ability to use trace amines has arisen at least twice during evolution, with distinct receptor families present in invertebrates and vertebrates. The term "trace amine" was coined to reflect the low tissue levels in mammals; however, invertebrates have relatively high levels where they function like mammalian adrenergic systems, involved in "fight-or-flight" responses. Vertebrates express a family of receptors termed trace amine-associated receptors (TAARs). Humans possess six functional isoforms (TAAR1, TAAR2, TAAR5, TAAR6, TAAR8, and TAAR9), whereas some fish species express over 100. With the exception of TAAR1, TAARs are expressed in olfactory epithelium neurons, where they detect diverse ethological signals including predators, spoiled food, migratory cues, and pheromones. Outside the olfactory system, TAAR1 is the most thoroughly studied and has both central and peripheral roles. In the brain, TAAR1 acts as a rheostat of dopaminergic, glutamatergic, and serotonergic neurotransmission and has been identified as a novel therapeutic target for schizophrenia, depression, and addiction. In the periphery, TAAR1 regulates nutrient-induced hormone secretion, suggesting its potential as a novel therapeutic target for diabetes and obesity. TAAR1 may also regulate immune responses by regulating leukocyte differentiation and activation. This article provides a comprehensive review of the current state of knowledge of the evolution, physiologic functions, pharmacology, molecular mechanisms, and therapeutic potential of trace amines and their receptors in vertebrates and invertebrates.
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Affiliation(s)
- Raul R Gainetdinov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia (R.R.G.); Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia (R.R.G.); Neuroscience, Ophthalmology, and Rare Diseases Discovery and Translational Area, pRED, Roche Innovation Centre Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland (M.C.H.); and Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada (M.D.B.)
| | - Marius C Hoener
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia (R.R.G.); Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia (R.R.G.); Neuroscience, Ophthalmology, and Rare Diseases Discovery and Translational Area, pRED, Roche Innovation Centre Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland (M.C.H.); and Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada (M.D.B.)
| | - Mark D Berry
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia (R.R.G.); Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia (R.R.G.); Neuroscience, Ophthalmology, and Rare Diseases Discovery and Translational Area, pRED, Roche Innovation Centre Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland (M.C.H.); and Department of Biochemistry, Memorial University of Newfoundland, St. John's, Newfoundland and Labrador, Canada (M.D.B.)
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10
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Christian SL, Berry MD. Trace Amine-Associated Receptors as Novel Therapeutic Targets for Immunomodulatory Disorders. Front Pharmacol 2018; 9:680. [PMID: 30013475 PMCID: PMC6036138 DOI: 10.3389/fphar.2018.00680] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/05/2018] [Indexed: 12/14/2022] Open
Abstract
Trace amines and their receptors (trace amine-associated receptors; TAARs) are an emerging pharmacological target for the treatment of human disorders. While most studies have focused on their therapeutic potential for neurologic and psychiatric disorders, TAARs are also expressed throughout the periphery, including prominent expression in human leukocytes. Furthermore, recent independent, unbiased metabolomic studies have consistently identified one or more TAAR ligands as potential etiologic factors in inflammatory bowel disease (IBD). The putative role of TAARs in diseases such as IBD that are associated with hyperactive immune responses has not, however, previously been systematically addressed. Here, we review the current state of the knowledge of the effects of TAARs on leukocyte function, in particular in the context of mucosal epithelial cells that interface with the environment; developing a model whereby TAARs may be considered as a novel therapeutic target for disorders associated with dysregulated immune responses to environmental factors. In this model, we hypothesize that altered trace amine homeostasis results in hyperactivity of the immune system. Such loss of homeostasis can occur through many different mechanisms including TAAR polymorphisms and altered trace amine load due to changes in host synthesis and/or degradative enzymes, diet, or microbial dysbiosis. The resulting alterations in TAAR functioning can then lead to a loss of homeostasis of leukocyte chemotaxis, differentiation, and activation, as well as an altered ability of members of the microbiota to adhere to and penetrate the epithelial cell layers. Such changes would generate a pro-inflammatory state at mucosal epithelial barrier layers that can manifest as clinical symptomatology such as that seen in IBD. These alterations may also have the potential to induce systemic effects, which could possibly contribute to immunomodulatory disorders in other systems, including neurological diseases.
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11
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Rodriguez-Martinez A, Posma JM, Ayala R, Harvey N, Jimenez B, Neves AL, Lindon JC, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME. J-Resolved 1H NMR 1D-Projections for Large-Scale Metabolic Phenotyping Studies: Application to Blood Plasma Analysis. Anal Chem 2017; 89:11405-11412. [DOI: 10.1021/acs.analchem.7b02374] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Andrea Rodriguez-Martinez
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Joram M. Posma
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Rafael Ayala
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Nikita Harvey
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Beatriz Jimenez
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Ana L. Neves
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - John C. Lindon
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Kazuhiro Sonomura
- Life
Science Research Center, Technology Research Laboratory, Shimadzu Corporation, Kyoto 604-8511, Japan
- Center
for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Taka-Aki Sato
- Life
Science Research Center, Technology Research Laboratory, Shimadzu Corporation, Kyoto 604-8511, Japan
- Center
for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Fumihiko Matsuda
- Center
for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan
| | - Pierre Zalloua
- School
of Medicine, Lebanese American University, Beirut 1102 2801, Lebanon
| | - Dominique Gauguier
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
- Cordeliers Research
Centre, INSERM UMR_S 1138, 75006 Paris, France
| | - Jeremy K. Nicholson
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
| | - Marc-Emmanuel Dumas
- Computational
and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London SW7 2AZ, U.K
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12
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Metabolomics analysis of Danggui Sini decoction on treatment of collagen-induced arthritis in rats. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1061-1062:282-291. [DOI: 10.1016/j.jchromb.2017.07.043] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/15/2017] [Accepted: 07/23/2017] [Indexed: 01/01/2023]
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13
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Abstract
AbstractMetabolic diversity leads to differences in nutrient requirements and responses to diet and medication between individuals. Using the concept of metabotyping – that is, grouping metabolically similar individuals – tailored and more efficient recommendations may be achieved. The aim of this study was to review the current literature on metabotyping and to explore its potential for better targeted dietary intervention in subjects with and without metabolic diseases. A comprehensive literature search was performed in PubMed, Google and Google Scholar to find relevant articles on metabotyping in humans including healthy individuals, population-based samples and patients with chronic metabolic diseases. A total of thirty-four research articles on human studies were identified, which established more homogeneous subgroups of individuals using statistical methods for analysing metabolic data. Differences between studies were found with respect to the samples/populations studied, the clustering variables used, the statistical methods applied and the metabotypes defined. According to the number and type of the selected clustering variables, the definitions of metabotypes differed substantially; they ranged between general fasting metabotypes, more specific fasting parameter subgroups like plasma lipoprotein or fatty acid clusters and response groups to defined meal challenges or dietary interventions. This demonstrates that the term ‘metabotype’ has a subjective usage, calling for a formalised definition. In conclusion, this literature review shows that metabotyping can help identify subgroups of individuals responding differently to defined nutritional interventions. Targeted recommendations may be given at such metabotype group levels. Future studies should develop and validate definitions of generally valid metabotypes by exploiting the increasingly available metabolomics data sets.
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14
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Abstract
INTRODUCTION The initial decades of the 21st century have witnessed striking technical advances that have made it possible to detect, identify and quantitatively measure large numbers of plasma or tissue metabolites. In parallel, similar advances have taken place in our ability to sequence DNA and RNA. Those advances have moved us beyond studies of single metabolites and single genetic polymorphisms to the study of hundreds or thousands of metabolites and millions of genomic variants in a single cell or subject. It is now possible to merge and integrate large data sets generated by the use of different "-omics" techniques to increase our understanding of the molecular basis for variation in disease risk and/or drug response phenotypes. OBJECTIVES This "Brief Review" will outline some of the challenges and opportunities associated with studies in which metabolomic data have been merged with genomics in an attempt to gain novel insight into mechanisms associated with variation in drug response phenotypes, with an emphasis on the application of a pharmacometabolomics-informed pharmacogenomic research strategy and with selected examples of the application of that strategy. METHODS Studies that used pharmacometabolomics to inform and guide pharmacogenomics were reviewed. Clinical studies that were used as the basis for pharmacometabolomics-informed pharmacogenomic studies, published in five independent manuscripts, are described briefly. RESULTS Within these five manuscripts, both pharmacokinetic and pharmacodynamic metabolomics approaches were used. Candidate gene and genome-wide approaches that were used in concert with these metabolomic data identified novel metabolite-gene relationships that were associated with drug response phenotypes in these pharmacometabolomics-informed pharmacogenomics studies. CONCLUSION This "Brief Review" outlines the emerging discipline of pharmacometabolomics-informed pharmacogenomics in which metabolic profiles are associated with both clinical phenotypes and genetic variants to identify novel genetic variants associated with drug response phenotypes based on metabolic profiles.
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Affiliation(s)
- Drew Neavin
- Department of Molecular Pharmacology and Experimental Therapeutics, 200 First Street SW, Mayo Clinic, Rochester, MN 55905
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Medicine, Duke Institute for Brain Sciences, 3552, Blue Zone, Duke South, Durham, NC 27710
| | - Richard Weinshilboum
- Department of Molecular Pharmacology and Experimental Therapeutics, 200 First Street SW, Mayo Clinic, Rochester, MN 55905
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15
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Kwak J, Jackson M, Faranda A, Osada K, Tashiro T, Mori K, Quan Y, Voznessenskaya VV, Preti G. On the persistence of mouse urine odour to human observers: a review. FLAVOUR FRAG J 2016. [DOI: 10.1002/ffj.3316] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jae Kwak
- Research Institute of Wildlife Ecology, Department of Integrative Biology and Evolution; University of Veterinary Medicine Vienna; Austria
- Monell Chemical Senses Center; 3500 Market Street Philadelphia PA 19104 USA
| | - Marcus Jackson
- Monell Chemical Senses Center; 3500 Market Street Philadelphia PA 19104 USA
| | - Adam Faranda
- Monell Chemical Senses Center; 3500 Market Street Philadelphia PA 19104 USA
| | - Kazumi Osada
- Department of Oral Biology, Division of Physiology, School of Dentistry; Health Sciences University of Hokkaido; Ishikari-Tobetsu Hokkaido 061-0293 Japan
| | - Takuya Tashiro
- Program for Drug Discovery and Medical Technology Platforms; RIKEN Research Cluster for Innovation; Hirosawa 2-1, Wako Saitama 351-0198 Japan
| | - Kenji Mori
- Program for Drug Discovery and Medical Technology Platforms; RIKEN Research Cluster for Innovation; Hirosawa 2-1, Wako Saitama 351-0198 Japan
| | - Ying Quan
- Suzhou Key Lab of Food Quality and Safety; Changshu Institute of Technology; 99 Nansanhuan Road Changshu 215500 Jiangsu Province P. R. China
| | - Vera V. Voznessenskaya
- A.N. Severtzov Institute of Ecology and Evolution RAS; 33 Leninski Prospect Moscow 119071 Russia
| | - George Preti
- Monell Chemical Senses Center; 3500 Market Street Philadelphia PA 19104 USA
- Department of Dermatology, School of Medicine; University of Pennsylvania; Philadelphia PA 19104 USA
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Using NMR-Based Metabolomics to Evaluate Postprandial Urinary Responses Following Consumption of Minimally Processed Wheat Bran or Wheat Aleurone by Men and Women. Nutrients 2016; 8:96. [PMID: 26901221 PMCID: PMC4772058 DOI: 10.3390/nu8020096] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 01/08/2016] [Accepted: 02/04/2016] [Indexed: 11/17/2022] Open
Abstract
Wheat bran, and especially wheat aleurone fraction, are concentrated sources of a wide range of components which may contribute to the health benefits associated with higher consumption of whole-grain foods. This study used NMR metabolomics to evaluate urine samples from baseline at one and two hours postprandially, following the consumption of minimally processed bran, aleurone or control by 14 participants (7 Females; 7 Males) in a randomized crossover trial. The methodology discriminated between the urinary responses of control, and bran and aleurone, but not between the two fractions. Compared to control, consumption of aleurone or bran led to significantly and substantially higher urinary concentrations of lactate, alanine, N-acetylaspartate acid and N-acetylaspartylglutamate and significantly and substantially lower urinary betaine concentrations at one and two hours postprandially. There were sex related differences in urinary metabolite profiles with generally higher hippurate and citrate and lower betaine in females compared to males. Overall, this postprandial study suggests that acute consumption of bran or aleurone is associated with a number of physiological effects that may impact on energy metabolism and which are consistent with longer term human and animal metabolomic studies that used whole-grain wheat diets or wheat fractions.
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Trezzi JP, Bulla A, Bellora C, Rose M, Lescuyer P, Kiehntopf M, Hiller K, Betsou F. LacaScore: a novel plasma sample quality control tool based on ascorbic acid and lactic acid levels. Metabolomics 2016; 12:96. [PMID: 27199628 PMCID: PMC4848344 DOI: 10.1007/s11306-016-1038-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/05/2016] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Metabolome analysis is complicated by the continuous dynamic changes of metabolites in vivo and ex vivo. One of the main challenges in metabolomics is the robustness and reproducibility of results, partially driven by pre-analytical variations. OBJECTIVES The objective of this study was to analyse the impact of pre-centrifugation time and temperature, and to determine a quality control marker in plasma samples. METHODS Plasma metabolites were measured by gas chromatography-mass spectrometry (GC-MS) and analysed with the MetaboliteDetector software. The metabolites, which were the most labile to pre-analytical variations, were further measured by enzymatic assays. A score was calculated for their use as quality control markers. RESULTS The pre-centrifugation temperature was shown to be critical in the stability of plasma samples and had a significant impact on metabolite concentration profiles. In contrast, pre-centrifugation delay had only a minor impact. Based on the results of this study, whole blood should be kept on wet ice and centrifuged within maximum 3 h as a prerequisite for preparing EDTA plasma samples fit for the purpose of metabolome analysis. CONCLUSIONS We have established a novel blood sample quality control marker, the LacaScore, based on the ascorbic acid to lactic acid ratio in plasma, which can be used as an indicator of the blood pre-centrifugation conditions, and hence the suitability of the sample for metabolome analyses. This method can be applied in research institutes and biobanks, enabling assessment of the quality of their plasma sample collections.
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Affiliation(s)
- Jean-Pierre Trezzi
- />Integrated Biobank of Luxembourg, 6 rue Ernest Barble, 1210 Luxembourg, Luxembourg
- />Luxembourg Centre for Systems Biomedicine, 7, Avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Alexandre Bulla
- />Sérothèque Centrale, Département de Médecine Génétique et de Laboratoire, Hôpitaux Universitaires de Geneve, 1211 Geneve 14, Switzerland
- />International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group, Vancouver, Canada
| | - Camille Bellora
- />Integrated Biobank of Luxembourg, 6 rue Ernest Barble, 1210 Luxembourg, Luxembourg
| | - Michael Rose
- />Institute of Clinical Chemistry and Laboratory Diagnostics and Integrierte BioBank Jena (IBBJ), Jena University Hospital, Erlanger Allee 101, 07740 Jena, Germany
| | - Pierre Lescuyer
- />Sérothèque Centrale, Département de Médecine Génétique et de Laboratoire, Hôpitaux Universitaires de Geneve, 1211 Geneve 14, Switzerland
| | - Michael Kiehntopf
- />Institute of Clinical Chemistry and Laboratory Diagnostics and Integrierte BioBank Jena (IBBJ), Jena University Hospital, Erlanger Allee 101, 07740 Jena, Germany
- />International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group, Vancouver, Canada
| | - Karsten Hiller
- />Luxembourg Centre for Systems Biomedicine, 7, Avenue des Hauts-Fourneaux, 4362 Esch-Belval, Luxembourg
| | - Fay Betsou
- />Integrated Biobank of Luxembourg, 6 rue Ernest Barble, 1210 Luxembourg, Luxembourg
- />International Society for Biological and Environmental Repositories (ISBER) Biospecimen Science Working Group, Vancouver, Canada
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18
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Griffin JL, Wang X, Stanley E. Does our gut microbiome predict cardiovascular risk? A review of the evidence from metabolomics. ACTA ACUST UNITED AC 2015; 8:187-91. [PMID: 25691688 DOI: 10.1161/circgenetics.114.000219] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Millions of microbes are found in the human gut, and are collectively referred as the gut microbiota. Recent studies have estimated that the microbiota genome contains 100-fold more genes than the host genome. These microbiota contribute to digestion by processing energy substrates unutilized by the host, with about half of the total genome of the gut microbiota being related to central carbon and amino acid metabolism as well as the biosynthesis of secondary metabolites. Therefore, the gut microbiome and its interaction with the host influences many aspects of health and disease, including the composition of biofluids such as urine and blood plasma. Metabolomics is uniquely suited to capture these functional host-microbe interactions. This review aims at providing an overview of recent metabolomics evidence of gut microbiota-host metabolic interactions with a specific focus on cardiovascular disease and related aspects of the metabolic syndrome. Furthermore, the emphasis is given on the complexities of translating these metabolite signatures as potential clinical biomarkers, as the composition and activity of gut microbiome change with many factors, particularly with diet, with special reference to trimethylamine-oxide.
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Affiliation(s)
- Julian L Griffin
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom.
| | - Xinzhu Wang
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom
| | - Elizabeth Stanley
- From the Department of Lipid Profiling and Signalling, MRC Human Nutrition Research, Elsie Widdowson Laboratory (J.L.G., X.W., E.S.); and Department of Biochemistry, Cambridge Systems Biology Centre (J.L.G., X.W.), University of Cambridge, Cambridge, United Kingdom
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19
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Emwas AH, Luchinat C, Turano P, Tenori L, Roy R, Salek RM, Ryan D, Merzaban JS, Kaddurah-Daouk R, Zeri AC, Nagana Gowda GA, Raftery D, Wang Y, Brennan L, Wishart DS. Standardizing the experimental conditions for using urine in NMR-based metabolomic studies with a particular focus on diagnostic studies: a review. Metabolomics 2015; 11:872-894. [PMID: 26109927 PMCID: PMC4475544 DOI: 10.1007/s11306-014-0746-7] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/27/2014] [Indexed: 02/08/2023]
Abstract
The metabolic composition of human biofluids can provide important diagnostic and prognostic information. Among the biofluids most commonly analyzed in metabolomic studies, urine appears to be particularly useful. It is abundant, readily available, easily stored and can be collected by simple, noninvasive techniques. Moreover, given its chemical complexity, urine is particularly rich in potential disease biomarkers. This makes it an ideal biofluid for detecting or monitoring disease processes. Among the metabolomic tools available for urine analysis, NMR spectroscopy has proven to be particularly well-suited, because the technique is highly reproducible and requires minimal sample handling. As it permits the identification and quantification of a wide range of compounds, independent of their chemical properties, NMR spectroscopy has been frequently used to detect or discover disease fingerprints and biomarkers in urine. Although protocols for NMR data acquisition and processing have been standardized, no consensus on protocols for urine sample selection, collection, storage and preparation in NMR-based metabolomic studies have been developed. This lack of consensus may be leading to spurious biomarkers being reported and may account for a general lack of reproducibility between laboratories. Here, we review a large number of published studies on NMR-based urine metabolic profiling with the aim of identifying key variables that may affect the results of metabolomics studies. From this survey, we identify a number of issues that require either standardization or careful accounting in experimental design and provide some recommendations for urine collection, sample preparation and data acquisition.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia
| | - Claudio Luchinat
- Centro Risonanze Magnetiche – CERM, University of Florence, Florence, Italy
| | - Paola Turano
- Centro Risonanze Magnetiche – CERM, University of Florence, Florence, Italy
| | | | - Raja Roy
- Centre of Biomedical Research, Formerly known as Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Lucknow, India
| | - Reza M. Salek
- Department of Biochemistry & Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, CB10 1SD UK
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, Australia
| | - Jasmeen S. Merzaban
- Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, KSA, Thuwal, Saudi Arabia
| | - Rima Kaddurah-Daouk
- Pharmacometabolomics Center, School of Medicine, Duke University, Durham, USA
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio, Campinas, SP Brazil
| | - G. A. Nagana Gowda
- Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA
| | - Daniel Raftery
- Department of Anethesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, 850 Republican St., Seattle, WA 98109 USA
| | - Yulan Wang
- Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Beijing, China
| | - Lorraine Brennan
- Institute of Food and Health and Conway Institute, School of Agriculture & Food Science, Dublin 4, Ireland
| | - David S. Wishart
- Department of Computing Science, University of Alberta, Edmonton, Alberta Canada
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20
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Kosmides AK, Kamisoglu K, Calvano SE, Corbett SA, Androulakis IP. Metabolomic fingerprinting: challenges and opportunities. Crit Rev Biomed Eng 2014; 41:205-21. [PMID: 24579644 DOI: 10.1615/critrevbiomedeng.2013007736] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Systems biology has primarily focused on studying genomics, transcriptomics, and proteomics and their dynamic interactions. These, however, represent only the potential for a biological outcome since the ultimate phenotype at the level of the eventually produced metabolites is not taken into consideration. The emerging field of metabolomics provides complementary guidance toward an integrated approach to this problem: It allows global profiling of the metabolites of a cell, tissue, or host and presents information on the actual end points of a response. A wide range of data collection methods are currently used and allow the extraction of global or tissue-specific metabolic profiles. The great amount and complexity of data that are collected require multivariate analysis techniques, but the increasing amount of work in this field has made easy-to-use analysis programs readily available. Metabolomics has already shown great potential in drug toxicity studies, disease modeling, and diagnostics and may be integrated with genomic and proteomic data in the future to provide in-depth understanding of systems, pathways, and their functionally dynamic interactions. In this review we discuss the current state of the art of metabolomics, its applications, and future potential.
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Affiliation(s)
- Alyssa K Kosmides
- Department of Biomedical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Kubra Kamisoglu
- Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Steve E Calvano
- Department of Surgery, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Siobhan A Corbett
- Department of Surgery, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ
| | - Ioannis P Androulakis
- Department of Surgery, Robert Wood Johnson Medical School, Department of Biomedical Engineering, Department of Chemical and Biochemical Engineering, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
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21
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Lees HJ, Swann JR, Wilson ID, Nicholson JK, Holmes E. Hippurate: The Natural History of a Mammalian–Microbial Cometabolite. J Proteome Res 2013; 12:1527-46. [DOI: 10.1021/pr300900b] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Hannah J. Lees
- Biomolecular
Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7
2AZ, United Kingdom
| | - Jonathan R. Swann
- Department
of Food and Nutritional Sciences, School of Chemistry, Food and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AP,
United Kingdom
| | - Ian D. Wilson
- Biomolecular
Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7
2AZ, United Kingdom
| | - Jeremy K. Nicholson
- Biomolecular
Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7
2AZ, United Kingdom
| | - Elaine Holmes
- Biomolecular
Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, South Kensington, London SW7
2AZ, United Kingdom
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22
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Wallrabenstein I, Kuklan J, Weber L, Zborala S, Werner M, Altmüller J, Becker C, Schmidt A, Hatt H, Hummel T, Gisselmann G. Human trace amine-associated receptor TAAR5 can be activated by trimethylamine. PLoS One 2013; 8:e54950. [PMID: 23393561 PMCID: PMC3564852 DOI: 10.1371/journal.pone.0054950] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/17/2012] [Indexed: 11/19/2022] Open
Abstract
In addition to the canonical olfactory receptors, TAARs were currently suggested to be a second class of chemosensory receptors in the olfactory epithelium of vertebrates. In contrast to several deorphanized murine TAARs, agonists for the intact human TAAR genes 2, 5, 6, 8 and 9 that are potentially expressed in the human olfactory epithelium have not been determined so far. Moreover, the physiological relevance of TAARs still remains elusive. We present the first successful functional expression of a human TAAR and agonists of human TAAR5. We performed a ligand screening using recombinantly expressed human TAAR5 in HANA3A cells and Xenopus laevis oocytes. In order to measure receptor activity, we used a cAMP-dependent reporter gene assay and two-electrode voltage clamp technique. As a result, human TAAR5 can be activated in a concentration-dependent manner by trimethylamine and with less efficacy by dimethylethylamine. It could neither be activated by any other of the tested single amines with a related chemical structure (42 in total), nor by any of the tested odorant mixtures. The hypothesis that Single Nucleotide Polymorphisms (SNP) within the reading frame of an olfactory receptor gene can cause a specific anosmia, formed the basis for clarifying the question, if anosmia for trimethylamine is caused by a SNP in a TAAR coding sequence. All functional human TAAR gene reading frames of subjects with specific anosmia for trimethylamine were amplified and products analyzed regarding SNP distribution. We demonstrated that the observed specific anosmia for trimethylamine is not correlated with a SNP in the coding sequence of one of the putatively functional human TAAR genes.
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23
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Li Q, Korzan WJ, Ferrero DM, Chang RB, Roy DS, Buchi M, Lemon JK, Kaur AW, Stowers L, Fendt M, Liberles SD. Synchronous evolution of an odor biosynthesis pathway and behavioral response. Curr Biol 2012. [PMID: 23177478 DOI: 10.1016/j.cub.2012.10.047] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Rodents use olfactory cues for species-specific behaviors. For example, mice emit odors to attract mates of the same species, but not competitors of closely related species. This implies rapid evolution of olfactory signaling, although odors and chemosensory receptors involved are unknown. RESULTS Here, we identify a mouse chemosignal, trimethylamine, and its olfactory receptor, trace amine-associated receptor 5 (TAAR5), to be involved in species-specific social communication. Abundant (>1,000-fold increased) and sex-dependent trimethylamine production arose de novo along the Mus lineage after divergence from Mus caroli. The two-step trimethylamine biosynthesis pathway involves synergy between commensal microflora and a sex-dependent liver enzyme, flavin-containing monooxygenase 3 (FMO3), which oxidizes trimethylamine. One key evolutionary alteration in this pathway is the recent acquisition in Mus of male-specific Fmo3 gene repression. Coincident with its evolving biosynthesis, trimethylamine evokes species-specific behaviors, attracting mice, but repelling rats. Attraction to trimethylamine is abolished in TAAR5 knockout mice, and furthermore, attraction to mouse scent is impaired by enzymatic depletion of trimethylamine or TAAR5 knockout. CONCLUSIONS TAAR5 is an evolutionarily conserved olfactory receptor required for a species-specific behavior. Synchronized changes in odor biosynthesis pathways and odor-evoked behaviors could ensure species-appropriate social interactions.
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Affiliation(s)
- Qian Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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24
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Kuang H, Li Z, Peng C, Liu L, Xu L, Zhu Y, Wang L, Xu C. Metabonomics Approaches and the Potential Application in Foodsafety Evaluation. Crit Rev Food Sci Nutr 2012; 52:761-74. [DOI: 10.1080/10408398.2010.508345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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25
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Garcia-Perez I, Villaseñor A, Wijeyesekera A, Posma JM, Jiang Z, Stamler J, Aronson P, Unwin R, Barbas C, Elliott P, Nicholson J, Holmes E. Urinary metabolic phenotyping the slc26a6 (chloride-oxalate exchanger) null mouse model. J Proteome Res 2012; 11:4425-35. [PMID: 22594923 DOI: 10.1021/pr2012544] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The prevalence of renal stone disease is increasing, although it remains higher in men than in women when matched for age. While still somewhat controversial, several studies have reported an association between renal stone disease and hypertension, but this may be confounded by a shared link with obesity. However, independent of obesity, hyperoxaluria has been shown to be associated with hypertension in stone-formers, and the most common type of renal stone is composed of calcium oxalate. The chloride-oxalate exchanger slc26a6 (also known as CFEX or PAT-1), located in the renal proximal tubule, was originally thought to have an important role in sodium homeostasis and thereby blood pressure control, but it has recently been shown to have a key function in oxalate balance by mediating oxalate secretion in the gut. We have applied two orthogonal analytical platforms (NMR spectroscopy and capillary electrophoresis with UV detection) in parallel to characterize the urinary metabolic signatures related to the loss of the renal chloride-oxalate exchanger in slc26a6 null mice. Clear metabolic differentiation between the urinary profiles of the slc26a6 null and the wild type mice were observed using both methods, with the combination of NMR and CE-UV providing extensive coverage of the urinary metabolome. Key discriminating metabolites included oxalate, m-hydroxyphenylpropionylsulfate (m-HPPS), trimethylamine-N-oxide, glycolate and scyllo-inositol (higher in slc26a6 null mice) and hippurate, taurine, trimethylamine, and citrate (lower in slc26a6 null mice). In addition to the reduced efficiency of anion transport, several of these metabolites (hippurate, m-HPPS, methylamines) reflect alteration in gut microbial cometabolic activities. Gender-related metabotypes were also observed in both wild type and slc26a6 null groups. Urinary metabolites that showed a sex-specific pattern included trimethylamine, trimethylamine-N-oxide, citrate, spermidine, guanidinoacetate, and 2-oxoisocaproate. The gender-dependent metabolic expression of the consequences of slc26a6 deletion might have relevance to the difference in prevalence of renal stone formation in men and women. The different composition of microbial metabolites in the slc26a6 null mice is consistent with the fact that the slc26a6 transporter is found in a range of tissues, including the kidney and intestine, and provides further evidence for the "long reach" of the microbiota in physiological and pathological processes.
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Affiliation(s)
- Isabel Garcia-Perez
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
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26
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Lee SH, An JH, Park HM, Jung BH. Investigation of endogenous metabolic changes in the urine of pseudo germ-free rats using a metabolomic approach. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 887-888:8-18. [PMID: 22300547 DOI: 10.1016/j.jchromb.2011.12.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 11/28/2011] [Accepted: 12/29/2011] [Indexed: 02/08/2023]
Abstract
Gut microflora are recognized as an active metabolic compartment in whole body systems. Understanding their impact on host physiology is an ongoing process, although many studies demonstrate that they play significant roles in host life. To assess the impact of gut microflora on host physiology in normal or close to normal conditions of the intestine, we prepared pseudo germ-free rats by antibiotic treatment, and we investigated urinary metabolite profiles of pseudo germ-free rats using UPLC-QTOF-MS based on metabolomics. The repeatability and stability of the analysis were evaluated using QC samples and testmixes in both positive and negative ionization modes. When data sets were analyzed with OPLS-DA, 25 metabolites related to the activities of gut microflora were identified. The changes of amino acid metabolism, especially aromatic or sulfur amino acids, and alternations of bioactive nutrients, such as isoflavonoid and riboflavin were observed in the pseudo germ-free rats. Among the sulfur amino acid metabolites, the metabolites reflecting oxidative stress increased in the urine of pseudo germ-free animals, which imply that the activities of intestinal microorganisms can affect the host redox homeostasis. Altered isoflavonoid metabolism due to lack of gut bacteria may impact on steroid hormone metabolism in the body, especially estrogen metabolism. These results indicate that the some essential metabolic pathways are sensitive to the activities of gut microorganism and directly or indirectly affected by the state of intestinal bacteria, thus gut microflora plays an important role in whole body physiology.
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Affiliation(s)
- Soo Hyun Lee
- Biomolecules Function Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
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27
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Martin FPJ, Collino S, Rezzi S. 1H NMR-based metabonomic applications to decipher gut microbial metabolic influence on mammalian health. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2011; 49 Suppl 1:S47-S54. [PMID: 22290709 DOI: 10.1002/mrc.2810] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Recent advances in molecular biology and microbiology have increased awareness on the importance of the gut microbiota to the overall mammalian host's health status. There is therefore increasing interest in nutrition research to characterise the molecular foundations of the gut microbial mammalian crosstalk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology strategies based on the measurement of metabolites to assess the highly complex metabolic exchanges between diverse biological compartments, including organs, biofluids and microbial symbionts. By opening a direct biochemical window into the metabolome, metabonomics is uniquely suited for the identification of biomarkers providing better understanding of these complex metabolic processes. Recent applications of top-down system biology based on (1)H NMR spectroscopy coupled to advanced chemometric modelling approaches provided compelling evidence that system-wide and organ-specific changes in biochemical processes may be finely tuned by gut microbial activities. This review aims at describing current advances in NMR-based metabonomics where the main objective is to discern the molecular pathways and biochemical mechanisms under the influence of the gut microbiota. Furthermore, emphasis is given on nutritional approaches, where the quest for homeostatic balance is dependent not only on the host but also on the nutritional modulation of the gut microbiota-host metabolic interactions, using, for instance, probiotics and prebiotics.
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Affiliation(s)
- François-Pierre J Martin
- BioAnalytical Science, Metabonomics & Biomarkers, Nestlé Research Center, Lausanne, Switzerland.
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28
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Qiao Q, Li T, Sun J, Liu X, Ren J, Fei J. Metabolomic analysis of normal (C57BL/6J, 129S1/SvImJ) mice by gas chromatography-mass spectrometry: detection of strain and gender differences. Talanta 2011; 85:718-24. [PMID: 21645764 DOI: 10.1016/j.talanta.2011.04.060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Revised: 04/20/2011] [Accepted: 04/21/2011] [Indexed: 11/25/2022]
Abstract
Previous studies have shown that the C57 and 129 strains of mice display marked differences in behavioural performance, neuroanatomy, neurochemistry and synaptic plasticity. However, few metabolomic studies of their biofluids have been performed. As part of a series of metabolic phenotyping, the effects of gender and strain upon serum metabolite composition and variation are examined in this study using gas chromatography-mass spectrometry (GC-MS) in normal C57BL/6J and 129S1/SvImJ strains of mice. The 129S1/SvImJ strain is phenotypically distinct from the C57BL/6J strain and characteristic metabotypes are produced for both male and female mice of each strain. These data demonstrate that the C57BL/6J and 129S1/SvImJ strains of mice show a wide range of metabolic differences across glycine, serine and threonine metabolism; valine, leucine and isoleucine biosynthesis; and tricarboxylic acid cycle pathways. Remarkably, the concentration of glyceric acid in the 129S1/SvImJ strain is significantly increased compared to the C57BL/6J mouse strain, reflecting important considerations for studies that use the 129S1/SvImJ mouse as the human d-glycericaciduria model. We infer that a deficiency of d-glycerate kinase would explain such a glyceric acid accumulation in the 129S1/SvImJ strain. More importantly, this differential metabolite level data provide insight into specific metabolic pathways and lay the groundwork for integrated studies of the mouse models.
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Affiliation(s)
- Qian Qiao
- Department of Chemistry, Tongji University, Shanghai, China
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29
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Ferrero DM, Liberles SD. The secret codes of mammalian scents. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2010; 2:23-33. [DOI: 10.1002/wsbm.39] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- David M. Ferrero
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
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Bictash M, Ebbels TM, Chan Q, Loo RL, Yap IKS, Brown IJ, de Iorio M, Daviglus ML, Holmes E, Stamler J, Nicholson JK, Elliott P. Opening up the "Black Box": metabolic phenotyping and metabolome-wide association studies in epidemiology. J Clin Epidemiol 2010; 63:970-9. [PMID: 20056386 DOI: 10.1016/j.jclinepi.2009.10.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 10/02/2009] [Indexed: 12/20/2022]
Abstract
BACKGROUND Metabolic phenotyping of humans allows information to be captured on the interactions between dietary, xenobiotic, other lifestyle and environmental exposures, and genetic variation, which together influence the balance between health and disease risks at both individual and population levels. OBJECTIVES We describe here the main procedures in large-scale metabolic phenotyping and their application to metabolome-wide association (MWA) studies. METHODS By use of high-throughput technologies and advanced spectroscopic methods, application of metabolic profiling to large-scale epidemiologic sample collections, including metabolome-wide association (MWA) studies for biomarker discovery and identification. DISCUSSION Metabolic profiling at epidemiologic scale requires optimization of experimental protocol to maximize reproducibility, sensitivity, and quantitative reliability, and to reduce analytical drift. Customized multivariate statistical modeling approaches are needed for effective data visualization and biomarker discovery with control for false-positive associations since 100s or 1,000s of complex metabolic spectra are being processed. CONCLUSION Metabolic profiling is an exciting addition to the armamentarium of the epidemiologist for the discovery of new disease-risk biomarkers and diagnostics, and to provide novel insights into etiology, biological mechanisms, and pathways.
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Affiliation(s)
- Magda Bictash
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
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Bertram HC, Jeppesen PB, Hermansen K. An NMR-based metabonomic investigation on effects of supplementation with isosteviol or soy protein to diabetic KKAy mice. Diabetes Obes Metab 2009; 11:992-5. [PMID: 19558611 DOI: 10.1111/j.1463-1326.2009.01077.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Liberles SD. Trace Amine-associated Receptors Are Olfactory Receptors in Vertebrates. Ann N Y Acad Sci 2009; 1170:168-72. [DOI: 10.1111/j.1749-6632.2009.04014.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
In recent years, considerable progress has been achieved in the comprehension of the profound effects of pheromones on reproductive physiology and behavior. Pheromones have been classified as molecules released by individuals and responsible for the elicitation of specific behavioral expressions in members of the same species. These signaling molecules, often chemically unrelated, are contained in body fluids like urine, sweat, specialized exocrine glands, and mucous secretions of genitals. The standard view of pheromone sensing was based on the assumption that most mammals have two separated olfactory systems with different functional roles: the main olfactory system for recognizing conventional odorant molecules and the vomeronasal system specifically dedicated to the detection of pheromones. However, recent studies have reexamined this traditional interpretation showing that both the main olfactory and the vomeronasal systems are actively involved in pheromonal communication. The current knowledge on the behavioral, physiological, and molecular aspects of pheromone detection in mammals is discussed in this review.
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Gao XX, Ge HM, Zheng WF, Tan RX. NMR-based metabonomics for detection of Helicobacter pylori infection in gerbils: which is more descriptive. Helicobacter 2008; 13:103-11. [PMID: 18321300 DOI: 10.1111/j.1523-5378.2008.00590.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Helicobacter pylori, the human pathogenic gram-negative microaerophilic bacterium, causes chronic gastric infection in more than half of the human population regardless of race. The infection of microbe is not yet controllable to pose a substantial public health impact and a growing social burden. The management of H. pylori infection primarily necessitates accurate and timely diagnosis at case level, on-demand supervision of pathologic progression, and reliable evaluation of the impact of pharmacologic interventions on the patients' population. METHODS The characterization of H. pylori infection on gerbils model was performed by metabolic profiling, employing 1H NMR spectroscopy compounding multivariate pattern recognition strategies. In the same manner, urine samples were individually collected from 10 gerbils infected with H. pylori GS13, and from 10 uninfected control animals equally accessible to feed and water. RESULTS The resultant metabolic profiles indicate that H. pylori infection disturbs carbohydrate metabolism to elevate the levels of alpha- and beta-glucose, and cis-aconitate (a TCA cycle intermediate). In addition to the energy metabolism alteration, the colonization of H. pylori in gerbil stomach generates a remarkable deviation of amino acid metabolism as indicated by depletion of taurine and arginine, and elevation of proline and glutamine in the animal urine. Moreover, the H. pylori infection modifies the gut microbiota as highlighted by a range of microbial-related metabolites such as indoxyl sulfate and hippurate. CONCLUSIONS These findings demonstrate that the (1)H NMR-based urine metabolic profiling is a promising technique capable of providing an accurate, noninvasive, and rapid diagnosis of H. pylori infection.
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Affiliation(s)
- Xing X Gao
- Institute of Functional Biomolecules, State Key Laboratory of Pharmaceutical Biotechnology, Medical School, Nanjing University, Nanjing 210093, China
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Martin FPJ, Wang Y, Sprenger N, Yap IKS, Lundstedt T, Lek P, Rezzi S, Ramadan Z, van Bladeren P, Fay LB, Kochhar S, Lindon JC, Holmes E, Nicholson JK. Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol 2008; 4:157. [PMID: 18197175 PMCID: PMC2238715 DOI: 10.1038/msb4100190] [Citation(s) in RCA: 315] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 10/17/2007] [Indexed: 01/12/2023] Open
Abstract
The transgenomic metabolic effects of exposure to either Lactobacillus paracasei or Lactobacillus rhamnosus probiotics have been measured and mapped in humanized extended genome mice (germ-free mice colonized with human baby flora). Statistical analysis of the compartmental fluctuations in diverse metabolic compartments, including biofluids, tissue and cecal short-chain fatty acids (SCFAs) in relation to microbial population modulation generated a novel top-down systems biology view of the host response to probiotic intervention. Probiotic exposure exerted microbiome modification and resulted in altered hepatic lipid metabolism coupled with lowered plasma lipoprotein levels and apparent stimulated glycolysis. Probiotic treatments also altered a diverse range of pathways outcomes, including amino-acid metabolism, methylamines and SCFAs. The novel application of hierarchical-principal component analysis allowed visualization of multicompartmental transgenomic metabolic interactions that could also be resolved at the compartment and pathway level. These integrated system investigations demonstrate the potential of metabolic profiling as a top-down systems biology driver for investigating the mechanistic basis of probiotic action and the therapeutic surveillance of the gut microbial activity related to dietary supplementation of probiotics.
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Affiliation(s)
- Francois-Pierre J Martin
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
- Nestlé Research Center, Lausanne, Switzerland
| | - Yulan Wang
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
| | | | - Ivan K S Yap
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
| | - Torbjörn Lundstedt
- AcurePharmaAB, Uppsala, Sweden
- Department of Medicinal Chemistry, BMC, Uppsala University, Uppsala, Sweden
| | - Per Lek
- AcurePharmaAB, Uppsala, Sweden
| | - Serge Rezzi
- Nestlé Research Center, Lausanne, Switzerland
| | | | | | | | | | - John C Lindon
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
| | - Elaine Holmes
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
| | - Jeremy K Nicholson
- Department of Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics, Faculty of Medicine, Imperial College London, London, UK
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Hines A, Yeung WH, Craft J, Brown M, Kennedy J, Bignell J, Stentiford GD, Viant MR. Comparison of histological, genetic, metabolomics, and lipid-based methods for sex determination in marine mussels. Anal Biochem 2007; 369:175-86. [PMID: 17655819 DOI: 10.1016/j.ab.2007.06.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 06/04/2007] [Accepted: 06/07/2007] [Indexed: 11/18/2022]
Abstract
Omics technologies are increasingly being used to monitor organismal responses to environmental stressors. Previous studies have shown that species identification, an appreciation of life history traits, and organism phenotype (e.g., gender) are essential for the accurate interpretation of omics data from field samples. As marine mussels are increasingly being used in ecotoxicogenomics and monitoring, a technique to determine mussel gender throughout their annual reproductive cycle is urgently needed. This study examines four methods for sex determination in the two mussel species found in the United Kingdom, Mytilus edulis and Mytilus galloprovincialis, and their hybrid. Each of these methods-histology, a lipid-based assay, a new reverse transcriptase polymerase chain reaction (RT-PCR) assay, and nuclear magnetic resonance (NMR)-based metabolomics-initially was evaluated using sexually mature ("ripe") mussels whose gender was clearly distinguishable using histology. The methods subsequently were tested on spawned ("spent") mussels. For ripe animals, all techniques yielded high classification accuracies: histology, 100%; RT-PCR, 94.6%; lipid analysis, 90.6%; and metabolomics, 89.5%. The gender of spent animals, however, could not be determined by histology (0%) or lipid analysis (55.6%), but RT-PCR (100%) and metabolomics (88.9%) both proved to be successful. In addition, the RT-PCR, metabolomics, and lipid-based methods identified animals of mixed sex. Our findings highlight the application of a novel RT-PCR method as a robust technique for gender determination of ripe and spent mussels.
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Affiliation(s)
- Adam Hines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Holmes E, Loo RL, Cloarec O, Coen M, Tang H, Maibaum E, Bruce S, Chan Q, Elliott P, Stamler J, Wilson ID, Lindon JC, Nicholson JK. Detection of urinary drug metabolite (xenometabolome) signatures in molecular epidemiology studies via statistical total correlation (NMR) spectroscopy. Anal Chem 2007; 79:2629-40. [PMID: 17323917 PMCID: PMC6688492 DOI: 10.1021/ac062305n] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Western populations use prescription and nonprescription drugs extensively, but large-scale population usage is rarely assessed objectively in epidemiological studies. Here we apply statistical methods to characterize structural pathway connectivities of metabolites of commonly used drugs detected routinely in 1H NMR spectra of urine in a human population study. 1H NMR spectra were measured for two groups of urine samples obtained from U.S. participants in a known population study. The novel application of a statistical total correlation spectroscopy (STOCSY) approach enabled rapid identification of the major and certain minor drug metabolites in common use in the population, in particular, from acetaminophen and ibuprofen metabolites. This work shows that statistical connectivities between drug metabolites can be established in routine "high-throughput" NMR screening of human samples from participants who have randomly self-administered drugs. This approach should be of value in considering interpopulation patterns of drug metabolism in epidemiological and pharmacogenetic studies.
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Affiliation(s)
- Elaine Holmes
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Ruey Leng Loo
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Olivier Cloarec
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Muireann Coen
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Huiru Tang
- State Key Laboratory of Magnetic Resonance and Molecular and Atomic Physics, Wuhan Magnetic Resonance Centre, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan, 430071, PR China
| | - Elaine Maibaum
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Stephen Bruce
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Queenie Chan
- Department of Epidemiology and Public Health, Imperial College London, St Mary’s Campus, London, UK
| | - Paul Elliott
- Department of Epidemiology and Public Health, Imperial College London, St Mary’s Campus, London, UK
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ian D. Wilson
- Department of Drug Metabolism and Pharmacokinetics, Astra Zeneca, Macclesfield, UK
| | - John C. Lindon
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Jeremy K. Nicholson
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
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Athersuch TJ, Nicholson JK, Wilson ID. Isotopic enrichment enhancement in metabonomic analysis of UPLC–MS data sets. J Labelled Comp Radiopharm 2007. [DOI: 10.1002/jlcr.1217] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Griffin JL, Nicholls AW. Metabolomics as a functional genomic tool for understanding lipid dysfunction in diabetes, obesity and related disorders. Pharmacogenomics 2006; 7:1095-107. [PMID: 17054419 DOI: 10.2217/14622416.7.7.1095] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
With the rise of systems biology, a number of approaches have been developed to globally profile a tier of organization in a cell, tissue or organism. Metabolomics is an approach that attempts to profile all the metabolites in a biological matrix. One of the major challenges of this approach, as with other 'omic' technologies, is that the metabolome is context-dependent and will vary with pathology, developmental stage and environmental factors. Thus, the possibility of globally profiling the metabolome of an organism is a genuine analytical challenge, as by definition this must also take into consideration all relevant factors that influence metabolism. Despite these challenges, the approach has already been applied to understand the metabolism in a range of animal models, and has more recently started to be projected into the clinical situation. In this review, the technologies currently being used in metabolomics will be assessed prior to examining their use to study diseases related to the metabolic syndrome, including Type II diabetes, obesity, cardiovascular disease and fatty liver disease.
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Affiliation(s)
- Julian L Griffin
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
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Liberles SD, Buck LB. A second class of chemosensory receptors in the olfactory epithelium. Nature 2006; 442:645-50. [PMID: 16878137 DOI: 10.1038/nature05066] [Citation(s) in RCA: 489] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 07/11/2006] [Indexed: 11/09/2022]
Abstract
The mammalian olfactory system detects chemicals sensed as odours as well as social cues that stimulate innate responses. Odorants are detected in the nasal olfactory epithelium by the odorant receptor family, whose approximately 1,000 members allow the discrimination of a myriad of odorants. Here we report the discovery of a second family of receptors in the mouse olfactory epithelium. Genes encoding these receptors, called 'trace amine-associated receptors' (TAARs), are present in human, mouse and fish. Like odorant receptors, individual mouse TAARs are expressed in unique subsets of neurons dispersed in the epithelium. Notably, at least three mouse TAARs recognize volatile amines found in urine: one detects a compound linked to stress, whereas the other two detect compounds enriched in male versus female urine-one of which is reportedly a pheromone. The evolutionary conservation of the TAAR family suggests a chemosensory function distinct from odorant receptors. Ligands identified for TAARs thus far suggest a function associated with the detection of social cues.
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Affiliation(s)
- Stephen D Liberles
- Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, Washington 98109, USA
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