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Geller S, Lieberman H, Kloss A, Ivanov AR. A systematic approach to development of analytical scale and microflow-based liquid chromatography coupled to mass spectrometry metabolomics methods to support drug discovery and development. J Chromatogr A 2021; 1642:462047. [PMID: 33744605 DOI: 10.1016/j.chroma.2021.462047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 12/21/2022]
Abstract
As the reliance on metabolic biomarkers within drug discovery and development increases, there is also an increased demand for global metabolomics methods to provide broad metabolome coverage and sensitivity towards differences in metabolite expression and reproducibility. A systematic approach is necessary for the development, and evaluation, of metabolomics methods using either conventional techniques or when establishing new methods that allow for additional gains in sensitivity and a reduction in requirements for amounts of a biological sample, such as those seen with methods based on microseparations. We developed a novel standard mixture and used a systematic approach for the development and optimization of optimal, ion-pair free, liquid chromatography-mass spectrometry (LC-MS) global profiling methods. These methods were scaled-down to microflow-based LC separations and compared with analytical flow ion-pairing reagent containing methods. Average peak volume improvements of 7- and 22-fold were observed in the positive and negative ionization mode microflow methods as compared to the ion-pairing reagent analytical flow methods, respectively. The linear range of the newly developed microflow methods showed up to a 10-fold increase in the lower limit of detection in the negative ionization mode. The developed microflow LC-MS methods were further evaluated using wild-type mouse plasma where up to a 9-fold increase in peak volume was observed.
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Affiliation(s)
| | | | - Alla Kloss
- Sanofi, Waltham, MA 02451, United States
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, United States.
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52
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Augustijn D, de Groot HJM, Alia A. HR-MAS NMR Applications in Plant Metabolomics. Molecules 2021; 26:molecules26040931. [PMID: 33578691 PMCID: PMC7916392 DOI: 10.3390/molecules26040931] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/24/2022] Open
Abstract
Metabolomics is used to reduce the complexity of plants and to understand the underlying pathways of the plant phenotype. The metabolic profile of plants can be obtained by mass spectrometry or liquid-state NMR. The extraction of metabolites from the sample is necessary for both techniques to obtain the metabolic profile. This extraction step can be eliminated by making use of high-resolution magic angle spinning (HR-MAS) NMR. In this review, an HR-MAS NMR-based workflow is described in more detail, including used pulse sequences in metabolomics. The pre-processing steps of one-dimensional HR-MAS NMR spectra are presented, including spectral alignment, baseline correction, bucketing, normalisation and scaling procedures. We also highlight some of the models which can be used to perform multivariate analysis on the HR-MAS NMR spectra. Finally, applications of HR-MAS NMR in plant metabolomics are described and show that HR-MAS NMR is a powerful tool for plant metabolomics studies.
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Affiliation(s)
- Dieuwertje Augustijn
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands;
- Correspondence: (D.A.); (A.A.)
| | - Huub J. M. de Groot
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands;
| | - A. Alia
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands;
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16–17, D-04107 Leipzig, Germany
- Correspondence: (D.A.); (A.A.)
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Solovyev PA, Fauhl-Hassek C, Riedl J, Esslinger S, Bontempo L, Camin F. NMR spectroscopy in wine authentication: An official control perspective. Compr Rev Food Sci Food Saf 2021; 20:2040-2062. [PMID: 33506593 DOI: 10.1111/1541-4337.12700] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 11/30/2020] [Accepted: 12/23/2020] [Indexed: 12/14/2022]
Abstract
Wine authentication is vital in identifying malpractice and fraud, and various physical and chemical analytical techniques have been employed for this purpose. Besides wet chemistry, these include chromatography, isotopic ratio mass spectrometry, optical spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy, which have been applied in recent years in combination with chemometric approaches. For many years, 2 H NMR spectroscopy was the method of choice and achieved official recognition in the detection of sugar addition to grape products. Recently, 1 H NMR spectroscopy, a simpler and faster method (in terms of sample preparation), has gathered more and more attention in wine analysis, even if it still lacks official recognition. This technique makes targeted quantitative determination of wine ingredients and nontargeted detection of the metabolomic fingerprint of a wine sample possible. This review summarizes the possibilities and limitations of 1 H NMR spectroscopy in analytical wine authentication, by reviewing its applications as reported in the literature. Examples of commercial and open-source solutions combining NMR spectroscopy and chemometrics are also examined herein, together with its opportunities of becoming an official method.
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Affiliation(s)
- Pavel A Solovyev
- Department of Food Quality and Nutrition, Research and Innovation Center, Fondazione Edmund Mach (FEM), via E. Mach 1, San Michele all'Adige, 38010, Italy
| | - Carsten Fauhl-Hassek
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, Unit Product Identity, Supply Chains and Traceability, Max-Dohrn Strasse, 8-10, Berlin, 10589, Germany
| | - Janet Riedl
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, Unit Product Identity, Supply Chains and Traceability, Max-Dohrn Strasse, 8-10, Berlin, 10589, Germany
| | - Susanne Esslinger
- German Federal Institute for Risk Assessment, Department Safety in the Food Chain, Unit Product Identity, Supply Chains and Traceability, Max-Dohrn Strasse, 8-10, Berlin, 10589, Germany
| | - Luana Bontempo
- Department of Food Quality and Nutrition, Research and Innovation Center, Fondazione Edmund Mach (FEM), via E. Mach 1, San Michele all'Adige, 38010, Italy
| | - Federica Camin
- Department of Food Quality and Nutrition, Research and Innovation Center, Fondazione Edmund Mach (FEM), via E. Mach 1, San Michele all'Adige, 38010, Italy.,Center Agriculture Food Environment (C3A), University of Trento, via Mach 1, San Michele all'Adige, Tennessee, 38010, Italy
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54
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Yang B, Zhang C, Cheng S, Li G, Griebel J, Neuhaus J. Novel Metabolic Signatures of Prostate Cancer Revealed by 1H-NMR Metabolomics of Urine. Diagnostics (Basel) 2021; 11:149. [PMID: 33498542 PMCID: PMC7909529 DOI: 10.3390/diagnostics11020149] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/13/2021] [Accepted: 01/16/2021] [Indexed: 12/16/2022] Open
Abstract
Prostate cancer (PC) is one of the most common male cancers worldwide. Until now, there is no consensus about using urinary metabolomic profiling as novel biomarkers to identify PC. In this study, urine samples from 50 PC patients and 50 non-cancerous individuals (control group) were collected. Based on 1H nuclear magnetic resonance (1H-NMR) analysis, 20 metabolites were identified. Subsequently, principal component analysis (PCA), partial least squares-differential analysis (PLS-DA) and ortho-PLS-DA (OPLS-DA) were applied to find metabolites to distinguish PC from the control group. Furthermore, Wilcoxon test was used to find significant differences between the two groups in metabolite urine levels. Guanidinoacetate, phenylacetylglycine, and glycine were significantly increased in PC, while L-lactate and L-alanine were significantly decreased. The receiver operating characteristics (ROC) analysis revealed that the combination of guanidinoacetate, phenylacetylglycine, and glycine was able to accurately differentiate 77% of the PC patients with sensitivity = 80% and a specificity = 64%. In addition, those three metabolites showed significant differences in patients stratified for Gleason score 6 and Gleason score ≥7, indicating potential use to detect significant prostate cancer. Pathway enrichment analysis using the KEGG (Kyoto Encyclopedia of Genes and Genomes) and the SMPDB (The Small Molecule Pathway Database) revealed potential involvement of KEGG "Glycine, Serine, and Threonine metabolism" in PC. The present study highlights that guanidinoacetate, phenylacetylglycine, and glycine are potential candidate biomarkers of PC. To the best knowledge of the authors, this is the first study identifying guanidinoacetate, and phenylacetylglycine as potential novel biomarkers in PC.
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Affiliation(s)
- Bo Yang
- Department of Urology, University of Leipzig, 04103 Leipzig, Germany; (B.Y.); (C.Z.)
- Department of Urology, Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - Chuan Zhang
- Department of Urology, University of Leipzig, 04103 Leipzig, Germany; (B.Y.); (C.Z.)
| | - Sheng Cheng
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China;
| | - Gonghui Li
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China;
| | - Jan Griebel
- Leibniz Institute of Surface Engineering (IOM), Permoserstraße 15, 04318 Leipzig, Germany;
| | - Jochen Neuhaus
- Department of Urology, University of Leipzig, 04103 Leipzig, Germany; (B.Y.); (C.Z.)
- Department of Urology, Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China;
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55
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Klare J, Rurik M, Rottmann E, Bollen A, Kohlbacher O, Fischer M, Hackl T. Determination of the Geographical Origin of Asparagus officinalis L. by 1H NMR Spectroscopy. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14353-14363. [PMID: 33103896 DOI: 10.1021/acs.jafc.0c05642] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Food authenticity concerning the geographical origin becomes increasingly important for consumers, food industries, and food authorities. In this study, nontargeted 1H NMR metabolomics combined with machine learning methodologies was applied to successfully distinguish the geographical origin of 237 samples of white asparagus from Germany, Poland, The Netherlands, Spain, Greece, and Peru. Support vector classification of the geographical origin achieved an accuracy of 91.5% for the entire sample set and 87.8% after undersampling the majority class. Important regions of the spectra could be identified and assigned to potential chemical markers. A subset of samples was compared to isotope-ratio mass spectrometry (IRMS), an established method for the determination of origin of white asparagus in Germany. Here, SVM classification led to accuracies of 79.4% for NMR and 70.9% for IRMS. Finally, the classification of asparagus from different German regions was evaluated, and the influence of year and variety was analyzed.
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Affiliation(s)
- Juliane Klare
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Marc Rurik
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Eric Rottmann
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Anke Bollen
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Sand 14, 72076 Tübingen, Germany
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
- Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Strasse 9, 72076 Tübingen, Germany
| | - Markus Fischer
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Thomas Hackl
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Hamburg School of Food Science-Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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56
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Sailwal M, Das AJ, Gazara RK, Dasgupta D, Bhaskar T, Hazra S, Ghosh D. Connecting the dots: Advances in modern metabolomics and its application in yeast system. Biotechnol Adv 2020; 44:107616. [DOI: 10.1016/j.biotechadv.2020.107616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
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Te Pas MFW, Jansman AJM, Kruijt L, van der Meer Y, Vervoort JJM, Schokker D. Sanitary Conditions Affect the Colonic Microbiome and the Colonic and Systemic Metabolome of Female Pigs. Front Vet Sci 2020; 7:585730. [PMID: 33195612 PMCID: PMC7649119 DOI: 10.3389/fvets.2020.585730] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 09/22/2020] [Indexed: 12/04/2022] Open
Abstract
Differences in sanitary conditions, as model to induce differences in subclinical immune stimulation, affect the growth performance and nutrient metabolism in pigs. The objective of the present study was to evaluate the colonic microbiota and the colonic and systemic metabolome of female pigs differing in health status induced by sanitary conditions. We analyzed blood and colon digesta metabolite profiles using Nuclear Magnetic Resonance (1H NMR) and Triple quadrupole mass spectrometry, as well as colonic microbiota profiles. 1H NMR is a quantitative metabolomics technique applicable to biological samples. Weaned piglets of 4 weeks of age were kept under high or low sanitary conditions for the first 9 weeks of life. The microbiota diversity in colon digesta was higher in pigs subjected to low sanitary conditions (n = 18 per treatment group). The abundance of 34 bacterial genera was higher in colon digesta of low sanitary condition pigs, while colon digesta of high sanitary status pigs showed a higher abundance for four bacterial groups including the Megasphaera genus (p < 0.003) involved in lactate fermentation. Metabolite profiles (n = 18 per treatment group) in blood were different between both groups of pigs. These different profiles suggested changes in general nutrient metabolism, and more specifically in amino acid metabolism. Moreover, differences in compounds related to the immune system and responses to stress were observed. Microbiome-specific metabolites in blood were also affected by sanitary status of the pigs. We conclude that the microbiome composition in colon and the systemic metabolite profiles are affected by sanitary conditions and related to suboptimal health. These data are useful for exploring further relationships between health, metabolic status and performance and for the identification of biomarkers related to health (indices) and performance.
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Affiliation(s)
- Marinus F W Te Pas
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Alfons J M Jansman
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Leo Kruijt
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Yvonne van der Meer
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Jacques J M Vervoort
- Department of Agrotechnology and Food Sciences, Biochemistry, Wageningen University, Wageningen, Netherlands
| | - Dirkjan Schokker
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
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Fraga-Corral M, Carpena M, Garcia-Oliveira P, Pereira AG, Prieto MA, Simal-Gandara J. Analytical Metabolomics and Applications in Health, Environmental and Food Science. Crit Rev Anal Chem 2020; 52:712-734. [DOI: 10.1080/10408347.2020.1823811] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- M. Fraga-Corral
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - M. Carpena
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
| | - P. Garcia-Oliveira
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - A. G. Pereira
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
| | - M. A. Prieto
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
| | - J. Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo, Ourense, Spain
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59
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Chen L, Zhong F, Zhu J. Bridging Targeted and Untargeted Mass Spectrometry-Based Metabolomics via Hybrid Approaches. Metabolites 2020; 10:E348. [PMID: 32867165 PMCID: PMC7570162 DOI: 10.3390/metabo10090348] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 08/19/2020] [Accepted: 08/23/2020] [Indexed: 01/11/2023] Open
Abstract
This mini-review aims to discuss the development and applications of mass spectrometry (MS)-based hybrid approaches in metabolomics. Several recently developed hybrid approaches are introduced. Then, the overall workflow, frequently used instruments, data handling strategies, and applications are compared and their pros and cons are summarized. Overall, the improved repeatability and quantitative capability in large-scale MS-based metabolomics studies are demonstrated, in comparison to either targeted or untargeted metabolomics approaches alone. In summary, we expect this review to serve as a first attempt to highlight the development and applications of emerging hybrid approaches in metabolomics, and we believe that hybrid metabolomics approaches could have great potential in many future studies.
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Affiliation(s)
- Li Chen
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA;
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
| | - Fanyi Zhong
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA;
| | - Jiangjiang Zhu
- Department of Human Sciences, The Ohio State University, Columbus, OH 43210, USA;
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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60
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Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs. Genes (Basel) 2020; 11:genes11080920. [PMID: 32796712 PMCID: PMC7464449 DOI: 10.3390/genes11080920] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/13/2022] Open
Abstract
Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.
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61
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Aliferis KA, Bernard-Perron D. Cannabinomics: Application of Metabolomics in Cannabis ( Cannabis sativa L.) Research and Development. FRONTIERS IN PLANT SCIENCE 2020; 11:554. [PMID: 32457786 PMCID: PMC7225349 DOI: 10.3389/fpls.2020.00554] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/14/2020] [Indexed: 05/18/2023]
Abstract
Cannabis (Cannabis sativa L.) is a complex, polymorphic plant species, which produces a vast array of bioactive metabolites, the two major chemical groups being cannabinoids and terpenoids. Nonetheless, the psychoactive cannabinoid tetrahydrocannabinol (Δ 9 -THC) and the non-psychoactive cannabidiol (CBD), are the two major cannabinoids that have monopolized the research interest. Currently, more than 600 Cannabis varieties are commercially available, providing access to a multitude of potent extracts with complex compositions, whose genetics are largely inconclusive. Recently introduced legislation on Cannabis cultivation in many countries represents a great opportunity, but at the same time, a great challenge for Cannabis research and development (R&D) toward applications in the pharmaceutical, food, cosmetics, and agrochemical industries. Based on its versatility and unique capabilities in the deconvolution of the metabolite composition of complex matrices, metabolomics represents an ideal bioanalytical tool that could greatly assist and accelerate Cannabis R&D. Among others, Cannabis metabolomics or cannabinomics can be applied in the taxonomy of Cannabis varieties in chemovars, the research on the discovery and assessment of new Cannabis-based sources of bioactivity in medicine, the development of new food products, and the optimization of its cultivation, aiming for improvements in yield and potency. Although Cannabis research is still in its infancy, it is highly foreseen that the employment of advanced metabolomics will provide insights that could assist the sector to face the aforementioned challenges. Within this context, here, the current state-of-the-art and conceptual aspects of cannabinomics are presented.
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Affiliation(s)
- Konstantinos A. Aliferis
- Laboratory of Pesticide Science, Agricultural University of Athens, Athens, Greece
- Department of Plant Science, McGill University, Montreal, QC, Canada
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62
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Castellanos L, Naranjo-Gaybor SJ, Forero AM, Morales G, Wilson EG, Ramos FA, Choi YH. Metabolic fingerprinting of banana passion fruits and its correlation with quorum quenching activity. PHYTOCHEMISTRY 2020; 172:112272. [PMID: 32032827 DOI: 10.1016/j.phytochem.2020.112272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 01/07/2020] [Accepted: 01/13/2020] [Indexed: 06/10/2023]
Abstract
Banana passion fruit of the Passiflora genus, are commercially cultivated on a small to medium scale, mainly as edible fruits or as components of traditional herbal medicines. This subgenus comprises several species and hybrid specimens that grow readily in the wild. Due to their taxonomical complexity, many of these species have recently been reclassified (Ocampo Pérez and Coppens d'Eeckenbrugge, 2017), and their chemical profile has still to be determined. In this study, an 1H NMR-based platform was applied to the chemical profiling of seven wild species of the Passiflora subgenus, and UHPLC-DAD-MS was additionally used for the identification of phenolic compounds. A total of 59 compounds were detected including 26 O- and C-glycosidated flavonoids and polyphenols, nine organic acids, seven amino acids, GABA, sucrose, glucose, myo-inositol, and five other non-identified compounds. Two of the identified compounds are the previously undescribed C-glycosyl flavonoids, apigenin-4'-O-β-glucopyranosyl, 8-C-β-(6″acetyl)-glucopyranoside and apigenin-4-O-β-glucopyranosyl-8-C-β-neohesperidoside. These C-glycosyl flavonoids were isolated to confirm their proposed structures by NMR and LCMS analysis. The PCA score plots obtained from the 1H NMR data of the studied Passiflora samples showed P. cumbalensis and P. uribei as the species with the most distinguishable chemical profile. In addition, a correlation analysis using OPLS-DA was conducted between 1H-NMR data and the quorum quenching activity (QQ) of Chromobacterium violaceum ATCC 31532. This analysis revealed P. lehmannii, and P. uribei extracts to be the most active, and apigenin-4'-O-β-glucopyranosyl, 8-C-β-(6″acetyl)-glucopyranoside and apigenin-4-O-β-glucopyranosyl-8-C-β-neohesperidoside were identified as possibly responsible for the QQ activity. To confirm this, QQ activity of both compounds was tested against C. violaceum ATCC 3153. An inhibition of violacein production of 0.135 mM (100 μg/mL) and 0.472 mM (300 μg/mL) was observed for apigenin-4'-O-β-glucopyranosyl,8-C-β-(6″acetyl)-glucopyranoside and apigenin-4-O-β-glucopyranosyl-8-C-β-neohesperidoside respectively, while bacterial growth was unaffected in both cases. Furthermore, both compounds showed the ability to inhibit the production of the toxoflavin of the phytopathogen Burkholderia glumae ATCC 33617.
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Affiliation(s)
- Leonardo Castellanos
- Universidad Nacional de Colombia - Sede Bogotá - Facultad de Ciencias - Departamento de Química, Carrera 30 # 45-03, Bogotá, D.C., 111321, Colombia; Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands.
| | - Sandra Judith Naranjo-Gaybor
- Universidad Nacional de Colombia - Sede Bogotá - Facultad de Ciencias - Departamento de Química, Carrera 30 # 45-03, Bogotá, D.C., 111321, Colombia; Universidad de las Fuerzas Armadas. ESPE Carrera de Ingeniería Agropecuaria Extensión Santo Domingo, Av. General Rumiñahui s/n, Sangolquí, Ecuador
| | - Abel M Forero
- Universidad Nacional de Colombia - Sede Bogotá - Facultad de Ciencias - Departamento de Química, Carrera 30 # 45-03, Bogotá, D.C., 111321, Colombia
| | - Gustavo Morales
- Universidad Nacional de Colombia - Sede Bogotá - Facultad de Ciencias - Departamento de Química, Carrera 30 # 45-03, Bogotá, D.C., 111321, Colombia
| | - Erica Georgina Wilson
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands
| | - Freddy A Ramos
- Universidad Nacional de Colombia - Sede Bogotá - Facultad de Ciencias - Departamento de Química, Carrera 30 # 45-03, Bogotá, D.C., 111321, Colombia
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, the Netherlands; College of Pharmacy, Kyung Hee University, 02447, Seoul, Republic of Korea
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63
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Viswan A, Singh C, Kayastha AM, Azim A, Sinha N. An NMR based panorama of the heterogeneous biology of acute respiratory distress syndrome (ARDS) from the standpoint of metabolic biomarkers. NMR IN BIOMEDICINE 2020; 33:e4192. [PMID: 31733128 DOI: 10.1002/nbm.4192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 08/16/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Acute respiratory distress syndrome (ARDS), manifested by intricate etiology and pathophysiology, demands careful clinical surveillance due to its high mortality and imminent life support measures. NMR based metabolomics provides an approach for ARDS which culminates from a wide spectrum of illness thereby confounding early manifestation and prognosis predictors. 1 H NMR with its manifold applications in critical disease settings can unravel the biomarker of ARDS thus holding potent implications by providing surrogate endpoints of clinical utility. NMR metabolomics which is the current apogee platform of omics trilogy is contributing towards the possible panacea of ARDS by subsequent validation of biomarker credential on larger datasets. In the present review, the physiological derangements that jeopardize the whole metabolic functioning in ARDS are exploited and the biomarkers involved in progression are addressed and substantiated. The following sections of the review also outline the clinical spectrum of ARDS from the standpoint of NMR based metabolomics which is an emerging element of systems biology. ARDS is the main premise of intensivists textbook, which has been thoroughly reviewed along with its incidence, progressive stages of severity, new proposed diagnostic definition, and the preventive measures and the current pitfalls of clinical management. The advent of new therapies, the need for biomarkers, the methodology and the contemporary promising approaches needed to improve survival and address heterogeneity have also been evaluated. The review has been stepwise illustrated with potent biometrics employed to selectively pool out differential metabolites as diagnostic markers and outcome predictors. The following sections have been drafted with an objective to better understand ARDS mechanisms with predictive and precise biomarkers detected so far on the basis of underlying physiological parameters having close proximity to diseased phenotype. The aim of this review is to stimulate interest in conducting more studies to help resolve the complex heterogeneity of ARDS with biomarkers of clinical utility and relevance.
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Affiliation(s)
- Akhila Viswan
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) - Campus, Lucknow, Uttar Pradesh, India
- Faculty of Engineering and Technology, Dr. A. P. J Abdul Kalam Technical University, Lucknow, India
| | - Chandan Singh
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) - Campus, Lucknow, Uttar Pradesh, India
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Arvind M Kayastha
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Afzal Azim
- Critical Care Medicine, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, India
| | - Neeraj Sinha
- Centre of Biomedical Research, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS) - Campus, Lucknow, Uttar Pradesh, India
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Dinges SS, Hohm A, Vandergrift LA, Nowak J, Habbel P, Kaltashov IA, Cheng LL. Cancer metabolomic markers in urine: evidence, techniques and recommendations. Nat Rev Urol 2020; 16:339-362. [PMID: 31092915 DOI: 10.1038/s41585-019-0185-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Urinary tests have been used as noninvasive, cost-effective tools for screening, diagnosis and monitoring of diseases since ancient times. As we progress through the 21st century, modern analytical platforms have enabled effective measurement of metabolites, with promising results for both a deeper understanding of cancer pathophysiology and, ultimately, clinical translation. The first study to measure metabolomic urinary cancer biomarkers using NMR and mass spectrometry (MS) was published in 2006 and, since then, these techniques have been used to detect cancers of the urological system (kidney, prostate and bladder) and nonurological tumours including those of the breast, ovary, lung, liver, gastrointestinal tract, pancreas, bone and blood. This growing field warrants an assessment of the current status of research developments and recommendations to help systematize future research.
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Affiliation(s)
- Sarah S Dinges
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Haematology and Oncology, CCM, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Hohm
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Diagnostic and Interventional Neuroradiology, University Hospital of Würzburg, Würzburg, Germany
| | - Lindsey A Vandergrift
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Johannes Nowak
- Department of Diagnostic and Interventional Radiology, University Hospital of Würzburg, Würzburg, Germany
| | - Piet Habbel
- Department of Haematology and Oncology, CCM, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
| | - Leo L Cheng
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Morozov SV, Tkacheva NI, Tkachev AV. On Problems of the Comprehensive Chemical Profiling of Medicinal Plants. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162019070070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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66
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Special Issue on "NMR-Based Metabolomics and Its Applications Volume 2". Metabolites 2020; 10:metabo10020045. [PMID: 31991891 PMCID: PMC7073525 DOI: 10.3390/metabo10020045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 01/21/2020] [Indexed: 11/24/2022] Open
Abstract
Over the last decade, the number of scientific publications in the metabolomics area has increased exponentially. The literature includes ~29,000 contributions (articles and reviews) during the period of 2009–2019, revealing metabolomics applications in a wide range of fields, including medical, plant, animal, and food sciences (this bibliographic data were retrieved from the SCOPUS database, searching “metabolomics” in keywords). The high applicability of this approach is due to its ability to qualitatively and quantitatively characterize the chemical profile of all the low molecular weight metabolites (metabolome) present in cells, tissues, organs, and biological fluids as end products of the cellular regulatory pathways. Thus, providing a snapshot of the phenotype of a biological system, metabolomics offers useful contributions to a comprehensive insight into the functional status of human, animal, plant, and microbe organisms. The contributions collected in this Special Issue (12 articles, one review and one technical report) report on the recent technical advances and practical applications of NMR spectroscopy to metabolomics analyses.
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Tian JS, Qin XM, Gao Y, Zhao YX, Xu T. Research progress on antidepressant therapeutic biomarkers of xiaoyaosan. WORLD JOURNAL OF TRADITIONAL CHINESE MEDICINE 2020. [DOI: 10.4103/wjtcm.wjtcm_16_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Yan JJ, Du GH, Qin XM, Gao L. Baicalein attenuates the neuroinflammation in LPS-activated BV-2 microglial cells through suppression of pro-inflammatory cytokines, COX2/NF-κB expressions and regulation of metabolic abnormality. Int Immunopharmacol 2019; 79:106092. [PMID: 31863920 DOI: 10.1016/j.intimp.2019.106092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/08/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022]
Abstract
Baicalein (5,6,7-trihydroxyflavone), isolated from the root of traditional Chinese herb Scutellaria baicalensis Georgi, has anti-inflammatory and anti-oxidative activities. This study explored the protective and modulatory mechanisms of baicalein on neuroinflammation, oxidative stress and metabolic abnormality in lipopolysaccharide (LPS)-activated BV-2 cells. Our results demonstrated that treatment with baicalein remarkably restrained the production of pro-inflammatory factors including nitric oxide (NO), interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) in LPS-activated BV-2 cells. Moreover, baicalein significantly inhibited reactive oxygen species (ROS) production, decreased cyclooxygenase-2 (COX-2) and nuclear factor-b (NF-κB)/p65 expression. 1H NMR metabolomics analysis revealed that 12 differential metabolites were regulated by baicalein, implicated in alanine, aspartate and glutamate metabolism, glutathione metabolism, arginine and proline metabolism, D-glutamine and D-glutamate metabolism. In conclusion, these results indicated that baicalein has protective and modulatory effects on neuroinflammation and oxidative stress in LPS-activated BV-2 cells.
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Affiliation(s)
- Jiao-Jiao Yan
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China; College of Chemistry and Chemical Engineering, Shanxi University, Taiyuan 030006, China
| | - Guan-Hua Du
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China; Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xue-Mei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.
| | - Li Gao
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan 030006, China.
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69
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Metabonomics study of fresh bruises on an apple using the gas chromatography–mass spectrometry (GC–MS) method. Eur Food Res Technol 2019. [DOI: 10.1007/s00217-019-03386-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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70
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Kopriva I, Jerić I, Hadžija MP, Hadžija M, Lovrenčić MV, Brkljačić L. Library-assisted nonlinear blind separation and annotation of pure components from a single 1H nuclear magnetic resonance mixture spectra. Anal Chim Acta 2019; 1080:55-65. [PMID: 31409475 DOI: 10.1016/j.aca.2019.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 01/07/2023]
Abstract
Due to its capability for high-throughput screening 1H nuclear magnetic resonance (NMR) spectroscopy is commonly used for metabolite research. The key problem in 1H NMR spectroscopy of multicomponent mixtures is overlapping of component signals and that is increasing with the number of components, their complexity and structural similarity. It makes metabolic profiling, that is carried out through matching acquired spectra with metabolites from the library, a hard problem. Here, we propose a method for nonlinear blind separation of highly correlated components spectra from a single 1H NMR mixture spectra. The method transforms a single nonlinear mixture into multiple high-dimensional reproducible kernel Hilbert Spaces (mRKHSs). Therein, highly correlated components are separated by sparseness constrained nonnegative matrix factorization in each induced RKHS. Afterwards, metabolites are identified through comparison of separated components with the library comprised of 160 pure components. Thereby, a significant number of them are expected to be related with diabetes type 2. Conceptually similar methodology for nonlinear blind separation of correlated components from two or more mixtures is presented in the Supplementary material. Single-mixture blind source separation is exemplified on: (i) annotation of five components spectra separated from one 1H NMR model mixture spectra; (ii) annotation of fifty five metabolites separated from one 1H NMR mixture spectra of urine of subjects with and without diabetes type 2. Arguably, it is for the first time a method for blind separation of a large number of components from a single nonlinear mixture has been proposed. Moreover, the proposed method pinpoints urinary creatine, glutamic acid and 5-hydroxyindoleacetic acid as the most prominent metabolites in samples from subjects with diabetes type 2, when compared to healthy controls.
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Affiliation(s)
- Ivica Kopriva
- Division of Electronics, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia.
| | - Ivanka Jerić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Marijana Popović Hadžija
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Mirko Hadžija
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
| | - Marijana Vučić Lovrenčić
- Department of Medical Biochemistry and Laboratory Medicine, University Hospital Merkur, Zajčeva 19, HR-10000, Zagreb, Croatia
| | - Lidija Brkljačić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000, Zagreb, Croatia
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Li C, Li Z, Zhang T, Wei P, Li N, Zhang W, Ding X, Li J. 1H NMR-Based Metabolomics Reveals the Antitumor Mechanisms of Triptolide in BALB/c Mice Bearing CT26 Tumors. Front Pharmacol 2019; 10:1175. [PMID: 31680959 PMCID: PMC6798008 DOI: 10.3389/fphar.2019.01175] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/12/2019] [Indexed: 11/13/2022] Open
Abstract
Triptolide, the main active ingredient in Tripterygium wilfordii Hook. f. (Celastraceae), has shown promising effects against a variety of tumors. However, the molecular pharmacological mechanisms explaining the action of triptolide remain unknown. In this study, the CT26 colon tumor cell line was inoculated subcutaneously into BALB/c mice, and plasma samples were subjected to 1H NMR metabolomics analysis. The metabolic signature identified five metabolites whose levels were lower and 15 whose levels were higher in CT26 tumor-bearing mice than in normal control mice. Triptolide treatment significantly reversed the levels of nine of these metabolites, including isoleucine, glutamine, methionine, proline, 3-hydroxybutyric acid, 2-hydroxyisovalerate, 2-hydroxyisobutyrate, and low-density lipoprotein/very low-density lipoprotein. Based on the identities of these potential biomarkers, we conclude that the antitumor mechanism of triptolide might rely on correcting perturbations in branched-chain amino acid metabolism, serine/glycine/methionine biosynthesis, and ketone bodies metabolism.
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Affiliation(s)
- Cheng Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Zhongfeng Li
- Department of Chemistry, Capital Normal University, Beijing, China
| | | | - Peihuang Wei
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Nuo Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Zhang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Xia Ding
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jian Li
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
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72
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Ranjan R, Sinha N. Nuclear magnetic resonance (NMR)-based metabolomics for cancer research. NMR IN BIOMEDICINE 2019; 32:e3916. [PMID: 29733484 DOI: 10.1002/nbm.3916] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/01/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
Nuclear magnetic resonance (NMR) has emerged as an effective tool in various spheres of biomedical research, amongst which metabolomics is an important method for the study of various types of disease. Metabolomics has proved its stronghold in cancer research by the development of different NMR methods over time for the study of metabolites, thus identifying key players in the aetiology of cancer. A plethora of one-dimensional and two-dimensional NMR experiments (in solids, semi-solids and solution phases) are utilized to obtain metabolic profiles of biofluids, cell extracts and tissue biopsy samples, which can further be subjected to statistical analysis. Any alteration in the assigned metabolite peaks gives an indication of changes in metabolic pathways. These defined changes demonstrate the utility of NMR in the early diagnosis of cancer and provide further measures to combat malignancy and its progression. This review provides a snapshot of the trending NMR techniques and the statistical analysis involved in the metabolomics of diseases, with emphasis on advances in NMR methodology developed for cancer research.
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Affiliation(s)
- Renuka Ranjan
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow, India
- School of Biotechnology, Institute of Science Banaras Hindu University, Varanasi, India
| | - Neeraj Sinha
- Centre of Biomedical Research, SGPGIMS Campus, Raebarelly Road, Lucknow, India
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Aliakbari A, Ehsani A, Vaez Torshizi R, Løvendahl P, Esfandyari H, Jensen J, Sarup P. Genetic variance of metabolomic features and their relationship with body weight and body weight gain in Holstein cattle1. J Anim Sci 2019; 97:3832-3844. [PMID: 31278866 DOI: 10.1093/jas/skz228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 07/04/2019] [Indexed: 11/14/2022] Open
Abstract
In recent years, metabolomics has been used to clarify the biology underlying biological samples. In the field of animal breeding, investigating the magnitude of genetic control on the metabolomic profiles of animals and their relationships with quantitative traits adds valuable information to animal improvement schemes. In this study, we analyzed metabolomic features (MFs) extracted from the metabolomic profiles of 843 male Holstein calves. The metabolomic profiles were obtained using nuclear magnetic resonance (NMR) spectroscopy. We investigated 2 alternative methods to control for peak shifts in the NMR spectra, binning and aligning, to determine which approach was the most efficient for assessing genetic variance. Series of univariate analyses were implemented to elucidate the heritability of each MF. Furthermore, records on BW and ADG from 154 to 294 d of age (ADG154-294), 294 to 336 d of age (ADG294-336), and 154 to 336 d of age (ADG154-336) were used in a series of bivariate analyses to establish the genetic and phenotypic correlations with MFs. Bivariate analyses were only performed for MFs that had a heritability significantly different from zero. The heritabilities obtained in the univariate analyses for the MFs in the binned data set were low (<0.2). In contrast, in the aligned data set, we obtained moderate heritability (0.2 to 0.5) for 3.5% of MFs and high heritability (more than 0.5) for 1% of MFs. The bivariate analyses showed that ~12%, ~3%, ~9%, and ~9% of MFs had significant additive genetic correlations with BW, ADG154-294, ADG294-336, and ADG154-336, respectively. In all of the bivariate analyses, the percentage of significant additive genetic correlations was higher than the percentage of significant phenotypic correlations of the corresponding trait. Our results provided insights into the influence of the underlying genetic mechanisms on MFs. Further investigations in this field are needed for better understanding of the genetic relationship among the MFs and quantitative traits.
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Affiliation(s)
- Amir Aliakbari
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Alireza Ehsani
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Rasoul Vaez Torshizi
- Department of Animal Science, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Peter Løvendahl
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Hadi Esfandyari
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Just Jensen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Pernille Sarup
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
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75
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Chronic kidney disease: Biomarker diagnosis to therapeutic targets. Clin Chim Acta 2019; 499:54-63. [PMID: 31476302 DOI: 10.1016/j.cca.2019.08.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 12/12/2022]
Abstract
Chronic kidney disease (CKD), characterized as renal dysfunction, is recognized as a major public health problem with high morbidity and mortality worldwide. Unfortunately, there are no obvious clinical symptoms in early stage disease until severe damage has occurred. Further complicating early diagnosis and treatment is the lack of sensitive and specific biomarkers. As such, novel biomarkers are urgently needed. Metabolomics has shown an increasing potential for identifying underlying disease mechanisms, facilitating clinical diagnosis and developing pharmaceutical treatments for CKD. Recent advances in metabolomics revealed that CKD was closely associated with the dysregulation of numerous metabolites, such as amino acids, lipids, nucleotides and glycoses, that might be exploited as potential biomarkers. In this review, we summarize recent metabolomic applications based on animal model studies and in patients with CKD and highlight several biomarkers that may play important roles in diagnosis, intervention and development of new therapeutic strategies.
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76
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Martinez-Farina CF, Driscoll S, Wicks C, Burton I, Wentzell PD, Berrué F. Chemical Barcoding: A Nuclear-Magnetic-Resonance-Based Approach To Ensure the Quality and Safety of Natural Ingredients. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7765-7774. [PMID: 31240917 DOI: 10.1021/acs.jafc.9b01066] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
One of the greatest challenges facing the functional food and natural health product (NHP) industries is sourcing high-quality, functional, natural ingredients for their finished products. Unfortunately, the lack of ingredient standards, modernized analytical methodologies, and industry oversight creates the potential for low quality and, in some cases, deliberate adulteration of ingredients. By exploring a diverse library of NHPs provided by the independent certification organization ISURA, we demonstrated that nuclear magnetic resonance (NMR) spectroscopy provides an innovative solution to authenticate botanicals and warrant the quality and safety of processed foods and manufactured functional ingredients. Two-dimensional NMR experiments were shown to be a robust and reproducible approach to capture the content of complex chemical mixtures, while a binary normalization step allows for emphasizing the chemical diversity in each sample, and unsupervised statistical methodologies provide key advantages to classify, authenticate, and highlight the potential presence of additives and adulterants.
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Affiliation(s)
- Camilo F Martinez-Farina
- Aquatic and Crop Resource Development , National Research Council of Canada , 1411 Oxford Street , Halifax , Nova Scotia B3H 3Z1 Canada
| | - Stephen Driscoll
- Trace Analysis Research Centre, Department of Chemistry , Dalhousie University , Post Office Box 15000, Halifax , Nova Scotia B3H 4R2 Canada
| | - Chelsi Wicks
- Trace Analysis Research Centre, Department of Chemistry , Dalhousie University , Post Office Box 15000, Halifax , Nova Scotia B3H 4R2 Canada
| | - Ian Burton
- Aquatic and Crop Resource Development , National Research Council of Canada , 1411 Oxford Street , Halifax , Nova Scotia B3H 3Z1 Canada
| | - Peter D Wentzell
- Trace Analysis Research Centre, Department of Chemistry , Dalhousie University , Post Office Box 15000, Halifax , Nova Scotia B3H 4R2 Canada
| | - Fabrice Berrué
- Aquatic and Crop Resource Development , National Research Council of Canada , 1411 Oxford Street , Halifax , Nova Scotia B3H 3Z1 Canada
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Emwas AH, Roy R, McKay RT, Tenori L, Saccenti E, Gowda GAN, Raftery D, Alahmari F, Jaremko L, Jaremko M, Wishart DS. NMR Spectroscopy for Metabolomics Research. Metabolites 2019; 9:E123. [PMID: 31252628 PMCID: PMC6680826 DOI: 10.3390/metabo9070123] [Citation(s) in RCA: 494] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/14/2019] [Accepted: 06/18/2019] [Indexed: 12/14/2022] Open
Abstract
Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of the three principal analytical techniques used in metabolomics (the other two being gas chromatography coupled to mass spectrometry (GC-MS) and liquid chromatography coupled with single-stage mass spectrometry (LC-MS)). The relative ease of sample preparation, the ability to quantify metabolite levels, the high level of experimental reproducibility, and the inherently nondestructive nature of NMR spectroscopy have made it the preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by the fact that most other analytical techniques, including both LC-MS and GC-MS, are inherently more sensitive than NMR, with lower limits of detection typically being 10 to 100 times better. This review is intended to introduce readers to the field of NMR-based metabolomics and to highlight both the advantages and disadvantages of NMR spectroscopy for metabolomic studies. It will also explore some of the unique strengths of NMR-based metabolomics, particularly with regard to isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, and the ability to noninvasively analyze native tissue specimens. Finally, this review will highlight a number of emerging NMR techniques and technologies that are being used to strengthen its utility and overcome its inherent limitations in metabolomic applications.
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Affiliation(s)
- Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, Formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Uttar Pradesh 226014, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta, Edmonton, AB T6G 2W2, Canada
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, 50134 Florence, Italy
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology Wageningen University & Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican St., Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA
| | - Fatimah Alahmari
- Department of NanoMedicine Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman bin Faisal University, Dammam 31441, Saudi Arabia
| | - Lukasz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - David S Wishart
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E8, Canada
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Decq L, Abatih E, Van Keulen H, Leyman V, Cattersel V, Steyaert D, Van Binnebeke E, Fremout W, Saverwyns S, Lynen F. Nontargeted Pattern Recognition in the Search for Pyrolysis Gas Chromatography/Mass Spectrometry Resin Markers in Historic Lacquered Objects. Anal Chem 2019; 91:7131-7138. [PMID: 31071264 DOI: 10.1021/acs.analchem.9b00240] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A differential expression analysis technology developed for linear modeling of gene expression data was used in combination with thermally assisted hydrolysis and methylation gas chromatography/mass spectrometry (THM-GC/MS) to support the analysis of lacquers and varnishes on historical objects. Exudates from tropical trees, such as Manila copal, sandarac, South American copal, and Congo copal, which were frequently used in finishing layers on decorative objects up to the early 20th century, were compared through this approach. Highly discriminating features indicate biomarkers that can help to identify copals in resinous lacquers. The approach allows new, more systematic ways for finding biomarkers in the analysis of lacquered objects of art and varnishes.
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Affiliation(s)
- Louise Decq
- Department Laboratories , Royal Institute for Cultural Heritage (KIK-IRPA) , Jubelpark 1 , 1000 Brussels , Belgium.,Separation Science Group, Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 , 9000 Ghent , Belgium
| | - Emmanuel Abatih
- Fostering Innovative Research Based on Evidence (FIRE) , Ghent University , Krijgslaan 281 , 9000 Ghent , Belgium
| | - Henk Van Keulen
- Cultural Heritage Agency of The Netherlands , Hobbemastraat 22 1071 ZC Amsterdam , The Netherlands
| | - Viviane Leyman
- Meise Botanic Garden , Nieuwelaan 38 , 1860 Meise , Belgium
| | - Vincent Cattersel
- Conservation Studies-Heritage & Sustainability , University of Antwerp , Blindestraat 9 , 2000 Antwerp , Belgium
| | - Delphine Steyaert
- Royal Museums of Art and History (RMAH) , Jubelpark 10 , 1000 Brussels , Belgium
| | - Emile Van Binnebeke
- Royal Museums of Art and History (RMAH) , Jubelpark 10 , 1000 Brussels , Belgium
| | - Wim Fremout
- Department Laboratories , Royal Institute for Cultural Heritage (KIK-IRPA) , Jubelpark 1 , 1000 Brussels , Belgium
| | - Steven Saverwyns
- Department Laboratories , Royal Institute for Cultural Heritage (KIK-IRPA) , Jubelpark 1 , 1000 Brussels , Belgium
| | - Frédéric Lynen
- Separation Science Group, Department of Organic and Macromolecular Chemistry , Ghent University , Krijgslaan 281 , 9000 Ghent , Belgium
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79
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Ultra-Clean Pure Shift 1H-NMR applied to metabolomics profiling. Sci Rep 2019; 9:6900. [PMID: 31053763 PMCID: PMC6499883 DOI: 10.1038/s41598-019-43374-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022] Open
Abstract
Even though Pure Shift NMR methods have conveniently been used in the assessment of crowded spectra, they are not commonly applied to the analysis of metabolomics data. This paper exploits the recently published SAPPHIRE-PSYCHE methodology in the context of plant metabolome. We compare single pulse, PSYCHE, and SAPPHIRE-PSYCHE spectra obtained from aqueous extracts of Physalis peruviana fruits. STOCSY analysis with simplified SAPPHIRE-PSYCHE spectra of six types of Cape gooseberry was carried out and the results attained compared with classical STOCSY data. PLS coefficients analysis combined with 1D-STOCSY was performed in an effort to simplify biomarker identification. Several of the most compromised proton NMR signals associated with critical constituents of the plant mixture, such as amino acids, organic acids, and sugars, were more cleanly depicted and their inter and intra correlation better reveled by the Pure Shift methods. The simplified data allowed the identification of glutamic acid, a metabolite not observed in previous studies of Cape gooseberry due to heavy overlap of its NMR signals. Overall, the results attained indicated that Ultra-Clean Pure Shift spectra increase the performance of metabolomics data analysis such as STOCSY and multivariate coefficients analysis, and therefore represent a feasible and convenient additional tool available to metabolomics.
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80
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Zheng J, Zheng SJ, Cai WJ, Yu L, Yuan BF, Feng YQ. Stable isotope labeling combined with liquid chromatography-tandem mass spectrometry for comprehensive analysis of short-chain fatty acids. Anal Chim Acta 2019; 1070:51-59. [PMID: 31103167 DOI: 10.1016/j.aca.2019.04.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/06/2019] [Accepted: 04/09/2019] [Indexed: 12/13/2022]
Abstract
Short-chain fatty acids (SCFAs) are one class of bacterial metabolites mainly formed by gut microbiota from undigested fibers and proteins. These molecules are able to mediate signal conduction processes of cells, acting as G protein-coupled receptors (GPR) activators and histone deacetylases (HDAC) inhibitors. It was reported that SCFAs were closely associated with various human diseases. However, it is still challenging to analyze SCFAs because of their diverse structures and broad range of concentrations. In this study, we developed a highly sensitive method for simultaneous detection of 34 SCFAs by stable isotope labeling coupled with ultra-high performance liquid chromatography-electrospray ionization-mass spectrometry (UHPLC-ESI-MS/MS) analysis. In this respect, a pair of isotope labeling reagents, N-(4-(aminomethyl)benzyl)aniline (4-AMBA) and N-(4-(aminomethyl)benzyl)aniline-d5 (4-AMBA-d5), were synthesized to label SCFAs from the feces of mice and SCFA standards, respectively. The 4-AMBA-d5 labeled SCFAs were used as internal standards to compensate the ionization variances resulting from matrix effect and thus minimize quantitation deviation in MS detection. After 4-AMBA labeling, the retention of SCFAs on the reversed-phase column increased and the separation resolution of isomers were improved. In addition, the MS responses of most SCFAs were enhanced by up to three orders of magnitude compared to unlabeled SCFAs. The limits of detection (LODs) of SCFAs were as low as 0.005 ng/mL. Moreover, good linearity for 34 SCFAs was obtained with the coefficient of determination (R2) ranging from 0.9846 to 0.9999 and the intra- and inter-day relative standard deviations (RSDs) were <17.8% and 15.4%, respectively, indicating the acceptable reproducibility of the developed method. Using the developed method, we successfully quantified 21 SCFAs from the feces of mice. Partial least squares discriminant analysis (PLS-DA) and t-test analysis showed that the contents of 9 SCFAs were significantly different between Alzheimer's disease (AD) and wide type (WT) mice fecal samples. Compared to WT mice, the contents of propionic acid, isobutyric acid, 3-hydroxybutyric acid, and 3-hydroxyisocaleric acid were decreased in AD mice, while lactic acid, 2-hydroxybutyric acid, 2-hydroxyisobutyric acid, levulinic acid, and valpronic acid were increased in AD mice. These significantly changed SCFAs in the feces of AD mice may afford to a better understanding of the pathogenesis of AD. Taken together, the developed UHPLC-ESI-MS/MS method could be applied for the sensitive and comprehensive determination of SCFAs from complex biological samples.
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Affiliation(s)
- Jie Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Shu-Jian Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Wen-Jing Cai
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Lei Yu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, PR China.
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81
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Non-invasive prediction of blood glucose trends during hypoglycemia. Anal Chim Acta 2019; 1052:37-48. [DOI: 10.1016/j.aca.2018.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 11/30/2018] [Accepted: 12/07/2018] [Indexed: 12/16/2022]
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82
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Misra BB, Ruiz-Hernández IM, Hernández-Bolio GI, Hernández-Núñez E, Díaz-Gamboa R, Colli-Dula RC. 1H NMR metabolomic analysis of skin and blubber of bottlenose dolphins reveals a functional metabolic dichotomy. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 30:25-32. [PMID: 30771562 DOI: 10.1016/j.cbd.2019.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 11/27/2022]
Abstract
The common bottlenose dolphin (Tursiops truncatus) is a carnivorous cetacean that thrives in marine environments, one of the apex predators of the marine food web. They are found in coastal and estuarine ecosystems, which are known to be sensitive to environmental impacts. Dolphins are considered sentinel organisms for monitoring the health of coastal marine ecosystems due to their role as predators that can bioaccumulate contaminants. Although recent studies have focused on capturing the circulating metabolomes of these mammals, and in the context of pollutants and exposures in the marine environment, skin and blubber are important surface and protective tissues that have not been adequately probed for metabolism. Using a proton nuclear magnetic resonance spectroscopy (1H NMR) based metabolomics approach, we quantified 51 metabolites belonging to 74 different metabolic pathways in the skin and blubber of stranded bottlenose dolphin (n = 4) samples collected at different localities in the Southern Zone coast of Yucatan Peninsula of Mexico. Results indicate that metabolism of skin and blubber are quantitatively very different. These metabolite abundances could help discriminate the tissue-types using supervised partial least square regression discriminant analysis (PLSDA). Further, using hierarchical clustering analysis and random forest analysis of the metabolite abundances, the results pointed to unique metabolites that are important classifiers of the tissue-type. On one hand, the differential metabolic patterns, mainly linking fatty acid metabolism and ketogenic amino acids, seem to constitute a characteristic of blubber, thus pointing to fat synthesis and deposition. On the other hand, the skin showed several metabolites involved in gluconeogenic pathways, pointing towards an active anabolic energy-generating metabolism. The most notable pathways found in both tissues included: urea cycle, nucleotide metabolism, amino acid metabolism, glutathione metabolism among others. Our 1H NMR metabolomics analysis allowed the quantification of metabolites associated with these two organs, i.e., pyruvic acid, arginine, ornithine, 2-hydroxybutyric acid, 3-hydroxyisobutyric acid, and acetic acid, as discriminatory and classifying metabolites. These results would lead to further understanding of the functional and physiological roles of dolphin skin and blubber metabolism for better efforts in their conservation, as well as useful target biopsy tissues for monitoring of dolphin health conditions in marine pollution and ecotoxicology studies.
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Affiliation(s)
- Biswapriya B Misra
- Center for Precision Medicine, Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem 27157, NC, USA
| | | | | | - Emanuel Hernández-Núñez
- Departamento de Recursos del Mar, Cinvestav Unidad Mérida, Mérida, Yucatán 97310, Mexico; Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico
| | - Raúl Díaz-Gamboa
- Universidad Autónoma de Yucatán, Campus de Ciencias Biológicas y Agropecuarias, 97100 Mérida, Yucatán, Mexico
| | - Reyna Cristina Colli-Dula
- Departamento de Recursos del Mar, Cinvestav Unidad Mérida, Mérida, Yucatán 97310, Mexico; Consejo Nacional de Ciencia y Tecnología (CONACYT), Mexico.
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83
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. High-Throughput Metabolomics by 1D NMR. Angew Chem Int Ed Engl 2019; 58:968-994. [PMID: 29999221 PMCID: PMC6391965 DOI: 10.1002/anie.201804736] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.
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Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P.Via Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Veronica Ghini
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Gaia Meoni
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Cristina Licari
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of FlorenceLargo Brambilla 3FlorenceItaly
| | - Paola Turano
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| | - Claudio Luchinat
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
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84
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Osteoarthritic Synovial Fluid Modulates Cell Phenotype and Metabolic Behavior In Vitro. Stem Cells Int 2019; 2019:8169172. [PMID: 30766606 PMCID: PMC6350599 DOI: 10.1155/2019/8169172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/10/2018] [Accepted: 10/21/2018] [Indexed: 12/11/2022] Open
Abstract
Synovial fluid holds a population of mesenchymal stem cells (MSC) that could be used for clinical treatment. Our goal was to characterize the inflammatory and metabolomic profile of the synovial fluid from osteoarthritic patients and to identify its modulatory effect on synovial fluid cells. Synovial fluid was collected from non-OA and OA patients, which was centrifuged to isolate cells. Cells were cultured for 21 days, characterized with specific markers for MSC, and exposed to a specific cocktail to induce chondrogenic, osteogenic, and adipogenic differentiation. Then, we performed a MTT assay exposing SF cells from non-OA and OA patients to a medium containing non-OA and OA synovial fluid. Synovial fluid from non-OA and OA patients was submitted to ELISA to evaluate BMP-2, BMP-4, IL-6, IL-10, TNF-α, and TGF-β1 concentrations and to a metabolomic evaluation using 1H-NMR. Synovial fluid cells presented spindle-shaped morphology in vitro. Samples from OA patients formed a higher number of colonies than the ones from non-OA patients. After 21 days, the colony-forming cells from OA patients differentiated into the three mesenchymal cell lineages, under the appropriated induction protocols. Synovial fluid cells increased its metabolic activity after being exposed to the OA synovial fluid. ELISA assay showed that OA synovial fluid samples presented higher concentration of IL-10 and TGF-β1 than the non-OA, while the NMR showed that OA synovial fluid presents higher concentrations of glucose and glycerol. In conclusion, SFC activity is modulated by OA synovial fluid, which presents higher concentration of IL-10, TGF-β, glycerol, and glucose.
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85
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Abstract
NMR spectroscopy is one of the major analytical techniques used in the metabolomics studies of food. There are many applications of metabolomics on food-related topics and on the food itself. Here, we describe protocols for performing NMR-based metabolomics of foods ranging from simple beverages to solid foods and semisolid foods. Beverages can be analyzed either directly or after sample preprocessing to remove interfering macromolecules, muscle-based foods can be analyzed after extraction, and semisolid foods can be analyzed directly using high-resolution magic-angle spinning (HR-MAS) NMR. Finally, we discuss metabolomic data analysis as well as different procedures and strategies for targeted and untargeted approaches.
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Affiliation(s)
| | - Nina Eggers
- Department of Food Science, Aarhus University, Årslev, Denmark
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86
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Quintero M, Stanisic D, Cruz G, Pontes JGM, Costa TBBC, Tasic L. Metabolomic Biomarkers in Mental Disorders: Bipolar Disorder and Schizophrenia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1118:271-293. [PMID: 30747428 DOI: 10.1007/978-3-030-05542-4_14] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Psychiatric disorders are some of the most impairing human diseases. Among them, bipolar disorder and schizophrenia are the most common. Both have complicated diagnostics due to their phenotypic, biological, and genetic heterogeneity, unknown etiology, and the underlying biological pathways, and molecular mechanisms are still not completely understood. Given the multifactorial complexity of these disorders, identification and implementation of metabolic biomarkers would assist in their early detection and diagnosis and facilitate disease monitoring and treatment responses. To date, numerous studies have utilized metabolomics to better understand psychiatric disorders, and findings from these studies have begun to converge. In this chapter, we briefly describe some of the metabolomic biomarkers found in these two disorders.
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Affiliation(s)
- Melissa Quintero
- Laboratory of Chemical Biology, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Danijela Stanisic
- Laboratory of Chemical Biology, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Guilherme Cruz
- Laboratory of Chemical Biology, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - João G M Pontes
- Laboratory of Microbial Chemical Biology, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Tássia Brena Barroso Carneiro Costa
- Laboratory of Chemical Biology, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Ljubica Tasic
- Laboratory of Chemical Biology, Department of Organic Chemistry, Institute of Chemistry, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil.
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87
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Abstract
Metabolomics is a comprehensive characterization of the small polar molecules (metabolites) in different biological systems. One of the analytical platforms commonly used to study metabolic alterations in biofluid samples is proton nuclear magnetic resonance (1H NMR) spectroscopy. NMR spectroscopy is very specific, quantitative, and highly reproducible. Moreover, sample preparation for NMR experiments is very simple and straightforward, and this gives NMR spectroscopy a distinct advantage over other metabolic profiling methods. It has already been shown that 1H NMR-based profiling of biological fluids can be effective in differentiating benign from malignant lesions and in investigating the efficacy of specific cancer treatments. Therefore, 1H NMR spectroscopy may become a promising tool for early noninvasive diagnosis and rapid assessment of treatment effects in cancer patients. Here, we describe a detailed protocol for 1H NMR metabolite profiling in serum, plasma, and urine samples, including sample collection procedures, sample preparation for 1H NMR experiments, spectral acquisition and processing, and quantitative profiling of 1H NMR spectra. We also discuss several aspects of appropriate study design and some multivariate statistical methods that are commonly used to analyze metabolomics datasets.
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88
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French CD, Willoughby RE, Pan A, Wong SJ, Foley JF, Wheat LJ, Fernandez J, Encarnacion R, Ondrush JM, Fatteh N, Paez A, David D, Javaid W, Amzuta IG, Neilan AM, Robbins GK, Brunner AM, Hu WT, Mishchuk DO, Slupsky CM. NMR metabolomics of cerebrospinal fluid differentiates inflammatory diseases of the central nervous system. PLoS Negl Trop Dis 2018; 12:e0007045. [PMID: 30557317 PMCID: PMC6312347 DOI: 10.1371/journal.pntd.0007045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 12/31/2018] [Accepted: 12/02/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Myriad infectious and noninfectious causes of encephalomyelitis (EM) have similar clinical manifestations, presenting serious challenges to diagnosis and treatment. Metabolomics of cerebrospinal fluid (CSF) was explored as a method of differentiating among neurological diseases causing EM using a single CSF sample. METHODOLOGY/PRINCIPAL FINDINGS 1H NMR metabolomics was applied to CSF samples from 27 patients with a laboratory-confirmed disease, including Lyme disease or West Nile Virus meningoencephalitis, multiple sclerosis, rabies, or Histoplasma meningitis, and 25 controls. Cluster analyses distinguished samples by infection status and moderately by pathogen, with shared and differentiating metabolite patterns observed among diseases. CART analysis predicted infection status with 100% sensitivity and 93% specificity. CONCLUSIONS/SIGNIFICANCE These preliminary results suggest the potential utility of CSF metabolomics as a rapid screening test to enhance diagnostic accuracies and improve patient outcomes.
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Affiliation(s)
- Caitlin D. French
- Department of Nutrition, University of California, Davis, California, United States of America
| | - Rodney E. Willoughby
- Department of Pediatrics, Division of Infectious Disease, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
- * E-mail: (REW); (CMS)
| | - Amy Pan
- Department of Pediatrics, Division of Infectious Disease, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Susan J. Wong
- Wadsworth Center Diagnostic Immunology Laboratory, New York State Department of Health, Albany, New York, United States of America
| | - John F. Foley
- Intermountain Healthcare, Salt Lake City, Utah, United States of America
| | - L. Joseph Wheat
- Department of Medicine, Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Josefina Fernandez
- Hospital Infantil Robert Reid Cabral, Santo Domingo, Distrito Nacional, República Dominicana
| | - Rafael Encarnacion
- Hospital Infantil Robert Reid Cabral, Santo Domingo, Distrito Nacional, República Dominicana
| | | | - Naaz Fatteh
- Inova Fairfax Hospital, Fairfax, Virginia, United States of America
| | - Andres Paez
- Departamento de Ciencias Basicas, Universidad de la Salle, Bogotá, Colombia
| | - Dan David
- Rabies Lab, Kimron Veterinary Institute, Beit Dagan, Israel
| | - Waleed Javaid
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Ioana G. Amzuta
- Department of Medicine, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Anne M. Neilan
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Gregory K. Robbins
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Andrew M. Brunner
- Department of Medicine, Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - William T. Hu
- Mayo Clinic, Rochester, Minnesota, United States of America
| | - Darya O. Mishchuk
- Department of Food Science and Technology, University of California, Davis, California, United States of America
| | - Carolyn M. Slupsky
- Department of Nutrition, University of California, Davis, California, United States of America
- Department of Food Science and Technology, University of California, Davis, California, United States of America
- * E-mail: (REW); (CMS)
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89
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Duan L, Guo L, Wang L, Yin Q, Zhang CM, Zheng YG, Liu EH. Application of metabolomics in toxicity evaluation of traditional Chinese medicines. Chin Med 2018; 13:60. [PMID: 30524499 PMCID: PMC6278008 DOI: 10.1186/s13020-018-0218-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 11/29/2018] [Indexed: 01/14/2023] Open
Abstract
Traditional Chinese medicines (TCM) have a long history of use because of its potential complementary therapy and fewer adverse effects. However, the toxicity and safety issues of TCM have drawn considerable attention in the past two decades. Metabolomics is an “omics” approach that aims to comprehensively analyze all metabolites in biological samples. In agreement with the holistic concept of TCM, metabolomics has shown great potential in efficacy and toxicity evaluation of TCM. Recently, a large amount of metabolomic researches have been devoted to exploring the mechanism of toxicity induced by TCM, such as hepatotoxicity, nephrotoxicity, and cardiotoxicity. In this paper, the application of metabolomics in toxicity evaluation of bioactive compounds, TCM extracts and TCM prescriptions are reviewed, and the potential problems and further perspectives for application of metabolomics in toxicological studies are also discussed.
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Affiliation(s)
- Li Duan
- 1College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China
| | - Long Guo
- 2School of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China.,4Hebei Key Laboratory of Chinese Medicine Research on Cardio-cerebrovascular Disease, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
| | - Lei Wang
- 2School of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
| | - Qiang Yin
- Department of Management, Xinjiang Uygur Pharmaceutical Co., Ltd., Wulumuqi, 830001 China
| | - Chen-Meng Zhang
- 1College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024 China
| | - Yu-Guang Zheng
- 2School of Pharmacy, Hebei University of Chinese Medicine, Shijiazhuang, 050200 China
| | - E-Hu Liu
- 3State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009 China
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90
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Hatzakis E. Nuclear Magnetic Resonance (NMR) Spectroscopy in Food Science: A Comprehensive Review. Compr Rev Food Sci Food Saf 2018; 18:189-220. [PMID: 33337022 DOI: 10.1111/1541-4337.12408] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/28/2018] [Accepted: 10/18/2018] [Indexed: 12/15/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a robust method, which can rapidly analyze mixtures at the molecular level without requiring separation and/or purification steps, making it ideal for applications in food science. Despite its increasing popularity among food scientists, NMR is still an underutilized methodology in this area, mainly due to its high cost, relatively low sensitivity, and the lack of NMR expertise by many food scientists. The aim of this review is to help bridge the knowledge gap that may exist when attempting to apply NMR methodologies to the field of food science. We begin by covering the basic principles required to apply NMR to the study of foods and nutrients. A description of the discipline of chemometrics is provided, as the combination of NMR with multivariate statistical analysis is a powerful approach for addressing modern challenges in food science. Furthermore, a comprehensive overview of recent and key applications in the areas of compositional analysis, food authentication, quality control, and human nutrition is provided. In addition to standard NMR techniques, more sophisticated NMR applications are also presented, although limitations, gaps, and potentials are discussed. We hope this review will help scientists gain some of the knowledge required to apply the powerful methodology of NMR to the rich and diverse field of food science.
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Affiliation(s)
- Emmanuel Hatzakis
- Dept. of Food Science and Technology, The Ohio State Univ., Parker Building, 2015 Fyffe Rd., Columbus, OH, U.S.A.,Foods for Health Discovery Theme, The Ohio State Univ., Parker Building, 2015 Fyffe Rd., Columbus, OH, U.S.A
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91
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Influence of Metabolite Extraction Methods on 1H-NMR-Based Metabolomic Profiling of Enteropathogenic Yersinia. Methods Protoc 2018. [PMCID: PMC6481057 DOI: 10.3390/mps1040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Metabolite extraction is one of the critical steps in microbial metabolome analysis. It affects both the observed metabolite content and biological interpretation of the data. Several methods exist for metabolite extraction of microbes, but the literature is not consistent regarding the sample model, adequacy, and performance of each method. In this study, an optimal extraction protocol for Yersinia intracellular metabolites was investigated. The effect of five extraction protocols consisting of different extraction solvent systems (60% methanol, 100% methanol, acetonitrile/methanol/water (2:2:1), chloroform/methanol/water (2:1:1), and 60% ethanol) on Yersinia metabolic profiles were compared. The number of detected peaks, sample-to-sample variation, and metabolite yield were used as criteria. Extracted metabolites were analyzed by 1H-NMR and principal component analysis (PCA), as well as partial least squares discriminant analysis (PLS-DA) multivariate statistics. The extraction protocol using 100% methanol as the extraction solvent provided the highest number of detected peaks for both Yersinia species analyzed, yielding more spectral information. Together with the reproducibility and spectrum quality, 100% methanol extraction was suitable for intracellular metabolite extraction from both species. However, depending on the metabolites of interest, other solvents might be more suitable for future studies, as distinct profiles were observed amongst the extraction methods.
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92
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Abstract
The aim of this study was to analyze the metabolome of several Klebsiella pneumoniae strains characterized by different resistance patterns. A total of 59 bacterial strains (27 carbapenemase-negative and 32 carbapenemase-positive) were included and their metabolic features were assessed in basal conditions. Moreover, 8 isolates (4 wild-type and 4 KPC-producers) were randomly selected to evaluate the impact of sub-lethal concentrations of meropenem on bacterial metabolism. The metabolomic analysis was performed by 1H-NMR spectroscopy both on filtered supernatants and cell lysates. A total of 40 and 20 molecules were quantified in the intracellular and the extracellular metabolome, respectively. While in basal conditions only five metabolites showed significant differences between carbapenemase-positive and negative strains, the use of meropenem had a profound impact on the whole bacterial metabolism. In the intracellular compartment, a reduction of different overflow metabolites and organic acids (e.g. formate, acetate, isobutyrate) was noticed, whereas, in the extracellular metabolome, the levels of several organic acids (e.g. succinate, acetate, formate, lactate) and amino acids (aspartate, threonine, lysine, alanine) were modified by meropenem stimulation. Interestingly, carbapenemase-positive and negative strains reacted differently to meropenem in terms of number and type of perturbed metabolites. In wild-type strains, meropenem had great impact on the metabolic pathways related to methane metabolism and alanine, aspartate and glutamate metabolism, whereas in KPC-producers the effect was predominant on pyruvate metabolism. The knowledge about the bacterial metabolic profiles could help to set up innovative diagnostic methods and new antimicrobial strategies to fight the global crisis against carbapenemase-positive K. pneumoniae.
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93
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. Hochdurchsatz‐Metabolomik mit 1D‐NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P. Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Veronica Ghini
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Gaia Meoni
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Cristina Licari
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of Florence Largo Brambilla 3 Florence Italien
| | - Paola Turano
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| | - Claudio Luchinat
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
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94
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Wirsching J, Graßmann S, Eichelmann F, Harms LM, Schenk M, Barth E, Berndzen A, Olalekan M, Sarmini L, Zuberer H, Aleksandrova K. Development and reliability assessment of a new quality appraisal tool for cross-sectional studies using biomarker data (BIOCROSS). BMC Med Res Methodol 2018; 18:122. [PMID: 30400827 PMCID: PMC6219097 DOI: 10.1186/s12874-018-0583-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 10/19/2018] [Indexed: 12/12/2022] Open
Abstract
Background Biomarker-based analyses are commonly reported in observational epidemiological studies; however currently there are no specific study quality assessment tools to assist evaluation of conducted research. Accounting for study design and biomarker measurement would be important for deriving valid conclusions when conducting systematic data evaluation. Methods We developed a study quality assessment tool designed specifically to assess biomarker-based cross-sectional studies (BIOCROSS) and evaluated its inter-rater reliability. The tool includes 10-items covering 5 domains: ‘Study rational’, ‘Design/Methods’, ‘Data analysis’, ‘Data interpretation’ and ‘Biomarker measurement’, aiming to assess different quality features of biomarker cross-sectional studies. To evaluate the inter-rater reliability, 30 studies were distributed among 5 raters and intraclass correlation coefficients (ICC-s) were derived from respective ratings. Results The estimated overall ICC between the 5 raters was 0.57 (95% Confidence Interval (CI): 0.38–0.74) indicating a good inter-rater reliability. The ICC-s ranged from 0.11 (95% CI: 0.01–0.27) for the domain ‘Study rational’ to 0.56 (95% CI: 0.40–0.72) for the domain ‘Data interpretation’. Conclusion BIOCROSS is a new study quality assessment tool suitable for evaluation of reporting quality from cross-sectional epidemiological studies employing biomarker data. The tool proved to be reliable for use by biomedical scientists with diverse backgrounds and could facilitate comprehensive review of biomarker studies in human research. Electronic supplementary material The online version of this article (10.1186/s12874-018-0583-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jan Wirsching
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Sophie Graßmann
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Fabian Eichelmann
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Laura Malin Harms
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Matthew Schenk
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Eva Barth
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Alide Berndzen
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Moses Olalekan
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Leen Sarmini
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Hedwig Zuberer
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany
| | - Krasimira Aleksandrova
- Nutrition, Immunity and Metabolism Senior Scientist Group, Department of Nutrition and Gerontology, German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany. .,University of Potsdam, Institute of Nutritional Science, Potsdam, Germany.
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95
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Pečnik K, Todorović V, Bošnjak M, Čemažar M, Kononenko I, Serša G, Plavec J. The General Explanation Method with NMR Spectroscopy Enables the Identification of Metabolite Profiles Specific for Normal and Tumor Cell Lines. Chembiochem 2018; 19:2066-2071. [PMID: 30067305 PMCID: PMC6220813 DOI: 10.1002/cbic.201800392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Indexed: 12/11/2022]
Abstract
Machine learning models in metabolomics, despite their great prediction accuracy, are still not widely adopted owing to the lack of an efficient explanation for their predictions. In this study, we propose the use of the general explanation method to explain the predictions of a machine learning model to gain detailed insight into metabolic differences between biological systems. The method was tested on a dataset of 1 H NMR spectra acquired on normal lung and mesothelial cell lines and their tumor counterparts. Initially, the random forests and artificial neural network models were applied to the dataset, and excellent prediction accuracy was achieved. The predictions of the models were explained with the general explanation method, which enabled identification of discriminating metabolic concentration differences between individual cell lines and enabled the construction of their specific metabolic concentration profiles. This intuitive and robust method holds great promise for in-depth understanding of the mechanisms that underline phenotypes as well as for biomarker discovery in complex diseases.
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Affiliation(s)
- Klemen Pečnik
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
| | | | - Maša Bošnjak
- Institute of OncologyZaloška cesta 21000LjubljanaSlovenia
| | - Maja Čemažar
- Institute of OncologyZaloška cesta 21000LjubljanaSlovenia
| | - Igor Kononenko
- Faculty of Computer and Information ScienceUniversity of LjubljanaVečna pot 1131001LjubljanaSlovenia
| | - Gregor Serša
- Institute of OncologyZaloška cesta 21000LjubljanaSlovenia
| | - Janez Plavec
- Slovenian NMR CentreNational Institute of ChemistryHajdrihova 19SI-1000LjubljanaSlovenia
- EN-FIST Centre of ExcellenceTrg OF 131000LjubljanaSlovenia
- Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaVečna pot 1131000LjubljanaSlovenia
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96
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Yang B, Liao GQ, Wen XF, Chen WH, Cheng S, Stolzenburg JU, Ganzer R, Neuhaus J. Nuclear magnetic resonance spectroscopy as a new approach for improvement of early diagnosis and risk stratification of prostate cancer. J Zhejiang Univ Sci B 2018; 18:921-933. [PMID: 29119730 DOI: 10.1631/jzus.b1600441] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Prostate cancer (PCa) is the second most common male cancer worldwide and the fifth leading cause of death from cancer in men. Early detection and risk stratification is the most effective way to improve the survival of PCa patients. Current PCa biomarkers lack sufficient sensitivity and specificity to cancer. Metabolite biomarkers are evolving as a new diagnostic tool. This review is aimed to evaluate the potential of metabolite biomarkers for early detection, risk assessment, and monitoring of PCa. Of the 154 identified publications, 27 and 38 were original papers on urine and serum metabolomics, respectively. Nuclear magnetic resonance (NMR) is a promising method for measuring concentrations of metabolites in complex samples with good reproducibility, high sensitivity, and simple sample processing. Especially urine-based NMR metabolomics has the potential to be a cost-efficient method for the early detection of PCa, risk stratification, and monitoring treatment efficacy.
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Affiliation(s)
- Bo Yang
- Department of Urology, Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - Guo-Qiang Liao
- Department of Urology, Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - Xiao-Fei Wen
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Wei-Hua Chen
- Department of Urology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Sheng Cheng
- Department of Urology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
| | - Jens-Uwe Stolzenburg
- Department of Urology, University Hospital of Leipzig, Liebigstraße 20, 04103 Leipzig, Germany
| | - Roman Ganzer
- Department of Urology, University Hospital of Leipzig, Liebigstraße 20, 04103 Leipzig, Germany
| | - Jochen Neuhaus
- Department of Urology, Zhoupu Hospital, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China.,Division of Urology, Research Laboratory, University of Leipzig, Liebigstraße 19, 04103 Leipzig, Germany
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97
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Martin M, Legat B, Leenders J, Vanwinsberghe J, Rousseau R, Boulanger B, Eilers PH, De Tullio P, Govaerts B. PepsNMR for 1H NMR metabolomic data pre-processing. Anal Chim Acta 2018; 1019:1-13. [DOI: 10.1016/j.aca.2018.02.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/15/2018] [Accepted: 02/27/2018] [Indexed: 11/29/2022]
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98
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Chihanga T, Ruby HN, Ma Q, Bashir S, Devarajan P, Kennedy MA. NMR-based urine metabolic profiling and immunohistochemistry analysis of nephron changes in a mouse model of hypoxia-induced acute kidney injury. Am J Physiol Renal Physiol 2018; 315:F1159-F1173. [PMID: 29993280 DOI: 10.1152/ajprenal.00500.2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Acute kidney injury can be caused by multiple factors, including sepsis, respiratory failure, heart failure, trauma, or nephrotoxic medications, among others. Here, a mouse model was used to investigate potential urinary metabolic biomarkers of hypoxia-induced AKI. Urine metabolic profiles of 48 Swiss Webster mice were assessed using nuclear magnetic resonance spectroscopy (NMR) for 7 days following 72 h exposure to a hypoxic 6.5% oxygen environment. Histological analyses indicated a lack of gross nephron structural changes in the aftermath of hypoxia. Immunohistochemical (IHC) analyses, however, indicated elevated expression of protein injury biomarkers in distal and proximal tubules but not glomeruli. Kidney injury molecule-1 levels peaked in distal tubules at 72 h and were still increasing in proximal tubules at 7 days posthypoxia, whereas cystatin C levels were elevated at 24 h but decreased thereafter, and were elevated and still increasing in proximal tubules at 7 days posthypoxia. Neutrophil gelatinase-associated lipocalin levels were modestly elevated from 24 h to 7 days posthypoxia. NMR-based metabolic profiling revealed that urine metabolites involved in energy metabolism and associated biosynthetic pathways were initially decreased at 24 h posthypoxia, consistent with metabolic suppression as a mechanism for cell survival, but were significantly elevated at 48 and 72 h posthypoxia, indicating a burst in organism metabolism associated with reactivation of cellular energetics during recovery after cessation of hypoxia and return to a normoxic environment. The IHC results indicated that kidney injury persists long after plasma and urine biomarkers of hypoxia return to normal values.
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Affiliation(s)
- Tafadzwa Chihanga
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio
| | - Hannah N Ruby
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio
| | - Qing Ma
- Department of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, University of Cincinnati , Cincinnati, Ohio
| | - Sabina Bashir
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio
| | - Prasad Devarajan
- Department of Nephrology and Hypertension, Cincinnati Children's Hospital Medical Center, University of Cincinnati , Cincinnati, Ohio
| | - Michael A Kennedy
- Department of Chemistry and Biochemistry, Miami University , Oxford, Ohio
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99
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Vuckovic D. Improving metabolome coverage and data quality: advancing metabolomics and lipidomics for biomarker discovery. Chem Commun (Camb) 2018; 54:6728-6749. [PMID: 29888773 DOI: 10.1039/c8cc02592d] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This Feature Article highlights some of the key challenges within the field of metabolomics and examines what role separation and analytical sciences can play to improve the use of metabolomics in biomarker discovery and personalized medicine. Recent progress in four key areas is highlighted: (i) improving metabolite coverage, (ii) developing accurate methods for unstable metabolites including in vivo global metabolomics methods, (iii) advancing inter-laboratory studies and reference materials and (iv) improving data quality, standardization and quality control of metabolomics studies.
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Affiliation(s)
- Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec H4B 1R6, Canada.
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100
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Pietzner M, Kacprowski T, Friedrich N. Empowering thyroid hormone research in human subjects using OMICs technologies. J Endocrinol 2018; 238:R13-R29. [PMID: 29724864 DOI: 10.1530/joe-18-0117] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 12/16/2022]
Abstract
OMICs subsume different physiological layers including the genome, transcriptome, proteome and metabolome. Recent advances in analytical techniques allow for the exhaustive determination of biomolecules in all OMICs levels from less invasive human specimens such as blood and urine. Investigating OMICs in deeply characterized population-based or experimental studies has led to seminal improvement of our understanding of genetic determinants of thyroid function, identified putative thyroid hormone target genes and thyroid hormone-induced shifts in the plasma protein and metabolite content. Consequently, plasma biomolecules have been suggested as surrogates of tissue-specific action of thyroid hormones. This review provides a brief introduction to OMICs in thyroid research with a particular focus on metabolomics studies in humans elucidating the important role of thyroid hormones for whole body metabolism in adults.
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Affiliation(s)
- Maik Pietzner
- Institute of Clinical Chemistry and Laboratory MedicineUniversity Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research)Partner Site Greifswald, Greifswald, Germany
| | - Tim Kacprowski
- Chair of Experimental BioinformaticsTUM School of Life Sciences Weihenstephan Technical University of Munich, Freising-Weihenstephan, Germany
| | - Nele Friedrich
- Institute of Clinical Chemistry and Laboratory MedicineUniversity Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research)Partner Site Greifswald, Greifswald, Germany
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