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Klobučar I, Habisch H, Klobučar L, Trbušić M, Pregartner G, Berghold A, Kostner GM, Scharnagl H, Madl T, Frank S, Degoricija V. Serum Levels of Adiponectin Are Strongly Associated with Lipoprotein Subclasses in Healthy Volunteers but Not in Patients with Metabolic Syndrome. Int J Mol Sci 2024; 25:5050. [PMID: 38732266 PMCID: PMC11084877 DOI: 10.3390/ijms25095050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024] Open
Abstract
Metabolic syndrome (MS) is a widespread disease in developed countries, accompanied, among others, by decreased adiponectin serum levels and perturbed lipoprotein metabolism. The associations between the serum levels of adiponectin and lipoproteins have been extensively studied in the past under healthy conditions, yet it remains unexplored whether the observed associations also exist in patients with MS. Therefore, in the present study, we analyzed the serum levels of lipoprotein subclasses using nuclear magnetic resonance spectroscopy and examined their associations with the serum levels of adiponectin in patients with MS in comparison with healthy volunteers (HVs). In the HVs, the serum levels of adiponectin were significantly negatively correlated with the serum levels of large buoyant-, very-low-density lipoprotein, and intermediate-density lipoprotein, as well as small dense low-density lipoprotein (LDL) and significantly positively correlated with large buoyant high-density lipoprotein (HDL). In patients with MS, however, adiponectin was only significantly correlated with the serum levels of phospholipids in total HDL and large buoyant LDL. As revealed through logistic regression and orthogonal partial least-squares discriminant analyses, high adiponectin serum levels were associated with low levels of small dense LDL and high levels of large buoyant HDL in the HVs as well as high levels of large buoyant LDL and total HDL in patients with MS. We conclude that the presence of MS weakens or abolishes the strong associations between adiponectin and the lipoprotein parameters observed in HVs and disturbs the complex interplay between adiponectin and lipoprotein metabolism.
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Affiliation(s)
- Iva Klobučar
- Department of Cardiology, Sisters of Charity University Hospital Centre, 10000 Zagreb, Croatia; (I.K.); (M.T.)
| | - Hansjörg Habisch
- Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria; (H.H.); (T.M.)
| | - Lucija Klobučar
- Department of Medicine, University Hospital Centre Osijek, 31000 Osijek, Croatia;
| | - Matias Trbušić
- Department of Cardiology, Sisters of Charity University Hospital Centre, 10000 Zagreb, Croatia; (I.K.); (M.T.)
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Gudrun Pregartner
- Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, 8036 Graz, Austria; (G.P.); (A.B.)
| | - Andrea Berghold
- Institute for Medical Informatics, Statistics, and Documentation, Medical University of Graz, 8036 Graz, Austria; (G.P.); (A.B.)
| | - Gerhard M. Kostner
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria;
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, 8036 Graz, Austria;
| | - Tobias Madl
- Otto Loewi Research Center, Medicinal Chemistry, Medical University of Graz, 8010 Graz, Austria; (H.H.); (T.M.)
- BioTechMed-Graz, 8010 Graz, Austria
| | - Saša Frank
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, 8010 Graz, Austria;
- BioTechMed-Graz, 8010 Graz, Austria
| | - Vesna Degoricija
- School of Medicine, University of Zagreb, 10000 Zagreb, Croatia;
- Department of Medicine, Sisters of Charity University Hospital Centre, 10000 Zagreb, Croatia
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2
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Kemsley EK. Graphical exploration of 600- and 60-MHz proton NMR spectral datasets from ground roast coffee extracts. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2024; 62:236-251. [PMID: 37311710 DOI: 10.1002/mrc.5373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/15/2023]
Abstract
This article uses a variety of graphical and mathematical approaches to analyse 600- and 60-MHz ('benchtop') proton NMR spectra acquired from lipophilic and hydrophilic extracts of roasted coffee beans. The collection of 40 authenticated samples comprised various coffee species, cultivars and hybrids. The spectral datasets were analysed by a combination of metabolomics approaches, cross-correlation and whole spectrum methods, assisted by visualisation and mathematical techniques not conventionally employed to treat NMR data. A large amount of information content was shared between the 600-MHz and benchtop datasets, including in its magnitude spectral form, suggesting the potential for a lower cost, lower tech route to conducting informative metabolomics studies.
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Affiliation(s)
- E Kate Kemsley
- Core Science Resources Group, Quadram Institute Bioscience, Norwich, UK
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3
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Stadler JT, Habisch H, Prüller F, Mangge H, Bärnthaler T, Kargl J, Pammer A, Holzer M, Meissl S, Rani A, Madl T, Marsche G. HDL-Related Parameters and COVID-19 Mortality: The Importance of HDL Function. Antioxidants (Basel) 2023; 12:2009. [PMID: 38001862 PMCID: PMC10669705 DOI: 10.3390/antiox12112009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/03/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
COVID-19, caused by the SARS-CoV-2 coronavirus, emerged as a global pandemic in late 2019, resulting in significant global public health challenges. The emerging evidence suggests that diminished high-density lipoprotein (HDL) cholesterol levels are associated with the severity of COVID-19, beyond inflammation and oxidative stress. Here, we used nuclear magnetic resonance spectroscopy to compare the lipoprotein and metabolic profiles of COVID-19-infected patients with non-COVID-19 pneumonia. We compared the control group and the COVID-19 group using inflammatory markers to ensure that the differences in lipoprotein levels were due to COVID-19 infection. Our analyses revealed supramolecular phospholipid composite (SPC), phenylalanine, and HDL-related parameters as key discriminators between COVID-19-positive and non-COVID-19 pneumonia patients. More specifically, the levels of HDL parameters, including apolipoprotein A-I (ApoA-I), ApoA-II, HDL cholesterol, and HDL phospholipids, were significantly different. These findings underscore the potential impact of HDL-related factors in patients with COVID-19. Significantly, among the HDL-related metrics, the cholesterol efflux capacity (CEC) displayed the strongest negative association with COVID-19 mortality. CEC is a measure of how well HDL removes cholesterol from cells, which may affect the way SARS-CoV-2 enters cells. In summary, this study validates previously established markers of COVID-19 infection and further highlights the potential significance of HDL functionality in the context of COVID-19 mortality.
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Affiliation(s)
- Julia T. Stadler
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
| | - Hansjörg Habisch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (H.H.); (T.M.)
| | - Florian Prüller
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
| | - Harald Mangge
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria;
| | - Thomas Bärnthaler
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
| | - Julia Kargl
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
- BioTechMed Graz, 8010 Graz, Austria
| | - Anja Pammer
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
| | - Michael Holzer
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
| | - Sabine Meissl
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
| | - Alankrita Rani
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (H.H.); (T.M.)
- BioTechMed Graz, 8010 Graz, Austria
| | - Gunther Marsche
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria; (J.T.S.); (T.B.); (J.K.); (A.P.); (M.H.); (S.M.); (A.R.)
- BioTechMed Graz, 8010 Graz, Austria
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Cannet C, Frauendienst-Egger G, Freisinger P, Götz H, Götz M, Himmelreich N, Kock V, Spraul M, Bus C, Biskup S, Trefz F. Ex vivo proton spectroscopy ( 1 H-NMR) analysis of inborn errors of metabolism: Automatic and computer-assisted analyses. NMR IN BIOMEDICINE 2023; 36:e4853. [PMID: 36264537 DOI: 10.1002/nbm.4853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/29/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
There are about 1500 genetic metabolic diseases. A small number of treatable diseases are diagnosed by newborn screening programs, which are continually being developed. However, most diseases can only be diagnosed based on clinical symptoms or metabolic findings. The main biological fluids used are urine, plasma and, in special situations, cerebrospinal fluid. In contrast to commonly used methods such as gas chromatography and high performance liquid chromatography mass spectrometry, ex vivo proton spectroscopy (1 H-NMR) is not yet used in routine clinical practice, although it has been recommended for more than 30 years. Automatic analysis and improved NMR technology have also expanded the applications used for the diagnosis of inborn errors of metabolism. We provide a mini-overview of typical applications, especially in urine but also in plasma, used to diagnose common but also rare genetic metabolic diseases with 1 H-NMR. The use of computer-assisted diagnostic suggestions can facilitate interpretation of the profiles. In a proof of principle, to date, 182 reports of 59 different diseases and 500 reports of healthy children are stored. The percentage of correct automatic diagnoses was 74%. Using the same 1 H-NMR profile-targeted analysis, it is possible to apply an untargeted approach that distinguishes profile differences from healthy individuals. Thus, additional conditions such as lysosomal storage diseases or drug interferences are detectable. Furthermore, because 1 H-NMR is highly reproducible and can detect a variety of different substance categories, the metabolomic approach is suitable for monitoring patient treatment and revealing additional factors such as nutrition and microbiome metabolism. Besides the progress in analytical techniques, a multiomics approach is most effective to combine metabolomics with, for example, whole exome sequencing, to also diagnose patients with nondetectable metabolic abnormalities in biological fluids. In this mini review we also provide our own data to demonstrate the role of NMR in a multiomics platform in the field of inborn errors of metabolism.
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Affiliation(s)
| | - Georg Frauendienst-Egger
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | - Peter Freisinger
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | | | | | | | - Vanessa Kock
- Department of Pediatrics, Reutlingen, Klinikum Reutlingen, School of Medicine, University of Tuebingen, Reutlingen, Germany
| | | | - Christine Bus
- CEGAT, Tübingen, Germany and Human Genetics Institute, Tübingen, Germany
| | - Saskia Biskup
- CEGAT, Tübingen, Germany and Human Genetics Institute, Tübingen, Germany
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Dehghani F, Yousefinejad S, Walker DI, Omidi F. Metabolomics for exposure assessment and toxicity effects of occupational pollutants: current status and future perspectives. Metabolomics 2022; 18:73. [PMID: 36083566 DOI: 10.1007/s11306-022-01930-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Work-related exposures to harmful agents or factors are associated with an increase in incidence of occupational diseases. These exposures often represent a complex mixture of different stressors, challenging the ability to delineate the mechanisms and risk factors underlying exposure-disease relationships. The use of omics measurement approaches that enable characterization of biological marker patterns provide internal indicators of molecular alterations, which could be used to identify bioeffects following exposure to a toxicant. Metabolomics is the comprehensive analysis of small molecule present in biological samples, and allows identification of potential modes of action and altered pathways by systematic measurement of metabolites. OBJECTIVES The aim of this study is to review the application of metabolomics studies for use in occupational health, with a focus on applying metabolomics for exposure monitoring and its relationship to occupational diseases. METHODS PubMed, Web of Science, Embase and Scopus electronic databases were systematically searched for relevant studies published up to 2021. RESULTS Most of reviewed studies included worker populations exposed to heavy metals such as As, Cd, Pb, Cr, Ni, Mn and organic compounds such as tetrachlorodibenzo-p-dioxin, trichloroethylene, polyfluoroalkyl, acrylamide, polyvinyl chloride. Occupational exposures were associated with changes in metabolites and pathways, and provided novel insight into the relationship between exposure and disease outcomes. The reviewed studies demonstrate that metabolomics provides a powerful ability to identify metabolic phenotypes and bioeffect of occupational exposures. CONCLUSION Continued application to worker populations has the potential to enable characterization of thousands of chemical signals in biological samples, which could lead to discovery of new biomarkers of exposure for chemicals, identify possible toxicological mechanisms, and improved understanding of biological effects increasing disease risk associated with occupational exposure.
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Affiliation(s)
- Fatemeh Dehghani
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Research Center for Health Sciences, Research Institute for Health, Department of Occupational Health and Safety Engineering, School of Health Shiraz, University of Medical Sciences, Shiraz, Iran
| | - Saeed Yousefinejad
- Research Center for Health Sciences, Research Institute for Health, Department of Occupational Health and Safety Engineering, School of Health Shiraz, University of Medical Sciences, Shiraz, Iran.
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Fariborz Omidi
- Research Center for Environmental Determinants of Health (RCEDH), Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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6
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The PROVIT Study-Effects of Multispecies Probiotic Add-on Treatment on Metabolomics in Major Depressive Disorder-A Randomized, Placebo-Controlled Trial. Metabolites 2022; 12:metabo12080770. [PMID: 36005642 PMCID: PMC9414726 DOI: 10.3390/metabo12080770] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 12/15/2022] Open
Abstract
The gut–brain axis plays a role in major depressive disorder (MDD). Gut-bacterial metabolites are suspected to reduce low-grade inflammation and influence brain function. Nevertheless, randomized, placebo-controlled probiotic intervention studies investigating metabolomic changes in patients with MDD are scarce. The PROVIT study (registered at clinicaltrials.com NCT03300440) aims to close this scientific gap. PROVIT was conducted as a randomized, single-center, double-blind, placebo-controlled multispecies probiotic intervention study in individuals with MDD (n = 57). In addition to clinical assessments, metabolomics analyses (1H Nuclear Magnetic Resonance Spectroscopy) of stool and serum, and microbiome analyses (16S rRNA sequencing) were performed. After 4 weeks of probiotic add-on therapy, no significant changes in serum samples were observed, whereas the probiotic groups’ (n = 28) stool metabolome shifted towards significantly higher concentrations of butyrate, alanine, valine, isoleucine, sarcosine, methylamine, and lysine. Gallic acid was significantly decreased in the probiotic group. In contrast, and as expected, no significant changes resulted in the stool metabolome of the placebo group. Strong correlations between bacterial species and significantly altered stool metabolites were obtained. In summary, the treatment with multispecies probiotics affects the stool metabolomic profile in patients with MDD, which sets the foundation for further elucidation of the mechanistic impact of probiotics on depression.
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7
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Branched-Chain Amino Acids Can Predict Mortality in ICU Sepsis Patients. Nutrients 2021; 13:nu13093106. [PMID: 34578983 PMCID: PMC8469152 DOI: 10.3390/nu13093106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 01/08/2023] Open
Abstract
Sepsis biomarkers and potential therapeutic targets are urgently needed. With proton nuclear magnetic resonance (1H NMR) spectroscopy, several metabolites can be assessed simultaneously. Fifty-three adult medical ICU sepsis patients and 25 ICU controls without sepsis were prospectively enrolled. 1H NMR differences between groups and associations with 28-day and ICU mortality were investigated. In multivariate metabolomic analyses, we found separate clustering of ICU controls and sepsis patients, as well as septic shock survivors and non-survivors. Lipoproteins were significantly different between sepsis and control patients. Levels of the branched-chain amino acids (BCAA) valine (median 43.3 [29.0–53.7] vs. 64.3 [47.7–72.3] normalized signal intensity units; p = 0.005), leucine (57.0 [38.4–71.0] vs. 73.0 [54.3–86.3]; p = 0.034) and isoleucine (15.2 [10.9–21.6] vs. 17.9 [16.1–24.4]; p = 0.048) were lower in patients with septic shock compared to those without. Similarly, BCAA were lower in ICU non-survivors compared to survivors, and BCAA were good discriminators for ICU and 28-day mortality. In uni- and multivariable logistic regression analyses, higher BCAA levels were associated with decreased ICU- and 28-day mortality. In conclusion, metabolomics using 1H NMR spectroscopy showed encouraging potential for personalized medicine in sepsis. BCAA was significantly lower in sepsis non-survivors and may be used as early biomarkers for outcome prediction.
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8
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Raja G, Jung Y, Jung SH, Kim TJ. 1H-NMR-based metabolomics for cancer targeting and metabolic engineering –A review. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Kimhofer T, Lodge S, Whiley L, Gray N, Loo RL, Lawler NG, Nitschke P, Bong SH, Morrison DL, Begum S, Richards T, Yeap BB, Smith C, Smith KGC, Holmes E, Nicholson JK. Integrative Modeling of Quantitative Plasma Lipoprotein, Metabolic, and Amino Acid Data Reveals a Multiorgan Pathological Signature of SARS-CoV-2 Infection. J Proteome Res 2020; 19:4442-4454. [PMID: 32806897 PMCID: PMC7489050 DOI: 10.1021/acs.jproteome.0c00519] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 02/06/2023]
Abstract
The metabolic effects of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on human blood plasma were characterized using multiplatform metabolic phenotyping with nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS). Quantitative measurements of lipoprotein subfractions, α-1-acid glycoprotein, glucose, and biogenic amines were made on samples from symptomatic coronavirus disease 19 (COVID-19) patients who had tested positive for the SARS-CoV-2 virus (n = 17) and from age- and gender-matched controls (n = 25). Data were analyzed using an orthogonal-projections to latent structures (OPLS) method and used to construct an exceptionally strong (AUROC = 1) hybrid NMR-MS model that enabled detailed metabolic discrimination between the groups and their biochemical relationships. Key discriminant metabolites included markers of inflammation including elevated α-1-acid glycoprotein and an increased kynurenine/tryptophan ratio. There was also an abnormal lipoprotein, glucose, and amino acid signature consistent with diabetes and coronary artery disease (low total and HDL Apolipoprotein A1, low HDL triglycerides, high LDL and VLDL triglycerides), plus multiple highly significant amino acid markers of liver dysfunction (including the elevated glutamine/glutamate and Fischer's ratios) that present themselves as part of a distinct SARS-CoV-2 infection pattern. A multivariate training-test set model was validated using independent samples from additional SARS-CoV-2 positive patients and controls. The predictive model showed a sensitivity of 100% for SARS-CoV-2 positivity. The breadth of the disturbed pathways indicates a systemic signature of SARS-CoV-2 positivity that includes elements of liver dysfunction, dyslipidemia, diabetes, and coronary heart disease risk that are consistent with recent reports that COVID-19 is a systemic disease affecting multiple organs and systems. Metabolights study reference: MTBLS2014.
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Affiliation(s)
- Torben Kimhofer
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Samantha Lodge
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Luke Whiley
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
- Perron Institute for Neurological and
Translational Science, Nedlands, Western Australia 6009,
Australia
| | - Nicola Gray
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Ruey Leng Loo
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Nathan G. Lawler
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Philipp Nitschke
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Sze-How Bong
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - David L. Morrison
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
| | - Sofina Begum
- Section for Nutrition Research, Imperial
College London, Sir Alexander Fleming Building, South Kensington, London
SW7 2AZ, U.K.
| | - Toby Richards
- Medical School, Faculty of Health and Medical
Sciences, University of Western Australia, and Department of Endocrinology and Diabetes,
Fiona Stanley Hospital, Harry Perkins Building, Murdoch,
Perth, Western Australia 6150, Australia
| | - Bu B. Yeap
- Medical School, Faculty of Health and Medical
Sciences, University of Western Australia, and Department of Endocrinology and Diabetes,
Fiona Stanley Hospital, Harry Perkins Building, Murdoch,
Perth, Western Australia 6150, Australia
| | - Chris Smith
- The Cambridge Institute of Therapeutic Immunology and
Infectious Disease, Department of Medicine, University of Cambridge,
Addenbrooke’s Hospital, Cambridge CB2 0QQ,
U.K.
| | - Kenneth G. C. Smith
- The Cambridge Institute of Therapeutic Immunology and
Infectious Disease, Department of Medicine, University of Cambridge,
Addenbrooke’s Hospital, Cambridge CB2 0QQ,
U.K.
| | - Elaine Holmes
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
- Section for Nutrition Research, Imperial
College London, Sir Alexander Fleming Building, South Kensington, London
SW7 2AZ, U.K.
| | - Jeremy K. Nicholson
- Australian National Phenome Centre, Computational and
Systems Medicine, Health Futures Institute, Murdoch University,
Harry Perkins Building, Perth, Western Australia 6150, Australia
- Medical School, Faculty of Health and Medical
Sciences, University of Western Australia, and Department of Endocrinology and Diabetes,
Fiona Stanley Hospital, Harry Perkins Building, Murdoch,
Perth, Western Australia 6150, Australia
- Institute of Global Health Innovation, Imperial
College London, Level 1, Faculty Building South Kensington Campus, London
SW7 2AZ, U.K.
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10
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Loo RL, Lodge S, Kimhofer T, Bong SH, Begum S, Whiley L, Gray N, Lindon JC, Nitschke P, Lawler NG, Schäfer H, Spraul M, Richards T, Nicholson JK, Holmes E. Quantitative In-Vitro Diagnostic NMR Spectroscopy for Lipoprotein and Metabolite Measurements in Plasma and Serum: Recommendations for Analytical Artifact Minimization with Special Reference to COVID-19/SARS-CoV-2 Samples. J Proteome Res 2020; 19:4428-4441. [PMID: 32852212 PMCID: PMC7640974 DOI: 10.1021/acs.jproteome.0c00537] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 12/14/2022]
Abstract
Quantitative nuclear magnetic resonance (NMR) spectroscopy of blood plasma is widely used to investigate perturbed metabolic processes in human diseases. The reliability of biochemical data derived from these measurements is dependent on the quality of the sample collection and exact preparation and analysis protocols. Here, we describe systematically, the impact of variations in sample collection and preparation on information recovery from quantitative proton (1H) NMR spectroscopy of human blood plasma and serum. The effects of variation of blood collection tube sizes and preservatives, successive freeze-thaw cycles, sample storage at -80 °C, and short-term storage at 4 and 20 °C on the quantitative lipoprotein and metabolite patterns were investigated. Storage of plasma samples at 4 °C for up to 48 h, freezing at -80 °C and blood sample collection tube choice have few and minor effects on quantitative lipoprotein profiles, and even storage at 4 °C for up to 168 h caused little information loss. In contrast, the impact of heat-treatment (56 °C for 30 min), which has been used for inactivation of SARS-CoV-2 and other viruses, that may be required prior to analytical measurements in low level biosecurity facilities induced marked changes in both lipoprotein and low molecular weight metabolite profiles. It was conclusively demonstrated that this heat inactivation procedure degrades lipoproteins and changes metabolic information in complex ways. Plasma from control individuals and SARS-CoV-2 infected patients are differentially altered resulting in the creation of artifactual pseudo-biomarkers and destruction of real biomarkers to the extent that data from heat-treated samples are largely uninterpretable. We also present several simple blood sample handling recommendations for optimal NMR-based biomarker discovery investigations in SARS CoV-2 studies and general clinical biomarker research.
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Affiliation(s)
- Ruey Leng Loo
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
| | - Samantha Lodge
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
| | - Torben Kimhofer
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
| | - Sze-How Bong
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
| | - Sofina Begum
- Section
for Nutrition Research, Imperial College
London, Sir Alexander Fleming Building, South Kensington, London SW72AZ, U.K.
| | - Luke Whiley
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Perron
Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Nicola Gray
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
| | - John C. Lindon
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Department
of Metabolism, Nutrition and Reproduction, Imperial College London, Sir Alexander Fleming Building, London SW72AZ, U.K.
| | - Philipp Nitschke
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
| | - Nathan G. Lawler
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
| | | | - Manfred Spraul
- Biospin
GmbH, Silberstreifen, 76287 Rheinstetten, Germany
| | - Toby Richards
- Division
of Surgery, Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Harry Perkins Building, Robert Warren Drive, Murdoch, Perth, WA 6150, Australia
- Department
of Endocrinology and Diabetes, Fiona Stanley
Hospital, Harry Perkins
Building, Murdoch, Perth, WA 6150, Australia
| | - Jeremy K. Nicholson
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Division
of Surgery, Medical School, Faculty of Health and Medical Sciences, University of Western Australia, Harry Perkins Building, Robert Warren Drive, Murdoch, Perth, WA 6150, Australia
- Institute
of Global Health Innovation, Imperial College
London, Level 1, Faculty Building, South Kensington Campus, London SW72NA, U.K.
| | - Elaine Holmes
- Australian
National Phenome Centre, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, Australia
- Center
for Computational and Systems Medicine, Health Futures Institute, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Section
for Nutrition Research, Imperial College
London, Sir Alexander Fleming Building, South Kensington, London SW72AZ, U.K.
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11
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Linking 24-h urines to clinical phenotypes: what alternatives does the future bring? Curr Opin Urol 2019; 30:177-182. [PMID: 31834081 DOI: 10.1097/mou.0000000000000702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW The 24-h urine test is recommended as part of the metabolic evaluation for patients with nephrolithiasis to guide preventive interventions. However, this test may be challenging to interpret and has limits in its predictive ability. In this review, we summarize and discuss the most recent research on the opportunities and challenges for utilizing urinary biomarkers for kidney stone prevention. RECENT FINDINGS Contemporary studies utilizing the 24-h urine test have improved our understanding of how to better administer testing and interpret test results. Beyond the standard panel of 24-h urine parameters, recent applications of proteomics and metabolomics have identified protein and metabolic profiles of stone formers. These profiles can be assayed in future studies as potential biomarkers for risk stratification and prediction. Broad collaborative efforts to create large datasets and biobanks from kidney stone formers will be invaluable for kidney stone research. SUMMARY Recent advances in our understanding of kidney stone risk have opened opportunities to improve metabolic testing for kidney stone formers. These strategies do not appear to be mutually exclusive of 24-h urine testing but instead complementary in their approach. Finally, large clinical datasets hold promise to be leveraged to identify new avenues for stone prevention.
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12
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Advanced understanding of genetic risk and metabolite signatures in construction workers via cytogenetics and metabolomics analysis. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Serum Concentrations of Citrate, Tyrosine, 2- and 3- Hydroxybutyrate are Associated with Increased 3-Month Mortality in Acute Heart Failure Patients. Sci Rep 2019; 9:6743. [PMID: 31043697 PMCID: PMC6494857 DOI: 10.1038/s41598-019-42937-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 04/12/2019] [Indexed: 12/21/2022] Open
Abstract
Considering the already established relationship between the extent of the metabolic dysfunction and the severity of heart failure (HF), it is conceivable that the metabolomic profile of the serum may have a prognostic capacity for 3-month mortality in acute heart failure (AHF). Out of 152 recruited patients, 130 serum samples were subjected to the metabolomic analyses. The 3-month mortality rate was 24.6% (32 patients). Metabolomic profiling by nuclear magnetic resonance spectroscopy found that the serum levels of 2-hydroxybutyrate (2-HB), 3-hydoxybutyrate (3-HB), lactate, citrate, and tyrosine, were higher in patients who died within 3 months compared to those who were alive 3 months after onset of AHF, which was confirmed by univariable logistic regression analyses (p = 0.009, p = 0.005, p = 0.008, p<0.001, and p<0.001, respectively). These associations still remained significant for all tested metabolites except for lactate after adjusting for established prognostic parameters in HF. In conclusion, serum levels of 2-HB, 3-HB, tyrosine, and citrate measured at admission are associated with an increased 3-month mortality rate in AHF patients and might thus be of prognostic value in AHF.
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14
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1H NMR-based metabolomic study of metabolic profiling for the urine of kidney stone patients. Urolithiasis 2019; 48:27-35. [DOI: 10.1007/s00240-019-01132-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/28/2019] [Indexed: 01/22/2023]
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15
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Huber K, Hofer DC, Trefely S, Pelzmann HJ, Madreiter-Sokolowski C, Duta-Mare M, Schlager S, Trausinger G, Stryeck S, Graier WF, Kolb D, Magnes C, Snyder NW, Prokesch A, Kratky D, Madl T, Wellen KE, Bogner-Strauss JG. N-acetylaspartate pathway is nutrient responsive and coordinates lipid and energy metabolism in brown adipocytes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:337-348. [PMID: 30595160 PMCID: PMC6390944 DOI: 10.1016/j.bbamcr.2018.08.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/27/2018] [Indexed: 12/22/2022]
Abstract
The discovery of significant amounts of metabolically active brown adipose tissue (BAT) in adult humans renders it a promising target for anti-obesity therapies by inducing weight loss through increased energy expenditure. The components of the N-acetylaspartate (NAA) pathway are highly abundant in BAT. Aspartate N-acetyltransferase (Asp-NAT, encoded by Nat8l) synthesizes NAA from acetyl-CoA and aspartate and increases energy expenditure in brown adipocytes. However, the exact mechanism how the NAA pathway contributes to accelerated mobilization and oxidation of lipids and the physiological regulation of the NAA pathway remained elusive. Here, we demonstrate that the expression of NAA pathway genes corresponds to nutrient availability and specifically responds to changes in exogenous glucose. NAA is preferentially produced from glucose-derived acetyl-CoA and aspartate and its concentration increases during adipogenesis. Overexpression of Nat8l drains glucose-derived acetyl-CoA into the NAA pool at the expense of cellular lipids and certain amino acids. Mechanistically, we elucidated that a combined activation of neutral and lysosomal (acid) lipolysis is responsible for the increased lipid degradation. Specifically, translocation of the transcription factor EB to the nucleus activates the biosynthesis of autophagosomes and lysosomes. Lipid degradation within lysosomes accompanied by adipose triglyceride lipase-mediated lipolysis delivers fatty acids for the support of elevated mitochondrial respiration. Together, our data suggest a crucial role of the NAA pathway in energy metabolism and metabolic adaptation in BAT.
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Affiliation(s)
- Katharina Huber
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Dina C Hofer
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Sophie Trefely
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA; AJ Drexel Autism Institute, Drexel University, Philadelphia, USA
| | - Helmut J Pelzmann
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Corina Madreiter-Sokolowski
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Madalina Duta-Mare
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Stefanie Schlager
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Gert Trausinger
- HEALTH Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | - Sarah Stryeck
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Wolfgang F Graier
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kolb
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria
| | - Christoph Magnes
- HEALTH Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | | | - Andreas Prokesch
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Histology and Embryology, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Dagmar Kratky
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Cell Biology, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed-Graz, Graz, Austria
| | - Kathryn E Wellen
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, USA; Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, USA
| | - Juliane G Bogner-Strauss
- Institute of Biochemistry, Graz University of Technology, Graz, Austria; BioTechMed-Graz, Graz, Austria.
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16
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Sethi S, Pedrini M, Rizzo LB, Zeni-Graiff M, Mas CD, Cassinelli AC, Noto MN, Asevedo E, Cordeiro Q, Pontes JGM, Brasil AJM, Lacerda A, Hayashi MAF, Poppi R, Tasic L, Brietzke E. 1H-NMR, 1H-NMR T 2-edited, and 2D-NMR in bipolar disorder metabolic profiling. Int J Bipolar Disord 2017; 5:23. [PMID: 28447334 PMCID: PMC5457743 DOI: 10.1186/s40345-017-0088-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/15/2017] [Indexed: 12/24/2022] Open
Abstract
Background The objective of this study was to identify molecular alterations in the human blood serum related to bipolar disorder, using nuclear magnetic resonance (NMR) spectroscopy and chemometrics. Methods Metabolomic profiling, employing 1H-NMR, 1H-NMR T2-edited, and 2D-NMR spectroscopy and chemometrics of human blood serum samples from patients with bipolar disorder (n = 26) compared with healthy volunteers (n = 50) was performed. Results The investigated groups presented distinct metabolic profiles, in which the main differential metabolites found in the serum sample of bipolar disorder patients compared with those from controls were lipids, lipid metabolism-related molecules (choline, myo-inositol), and some amino acids (N-acetyl-l-phenyl alanine, N-acetyl-l-aspartyl-l-glutamic acid, l-glutamine). In addition, amygdalin, α-ketoglutaric acid, and lipoamide, among other compounds, were also present or were significantly altered in the serum of bipolar disorder patients. The data presented herein suggest that some of these metabolites differentially distributed between the groups studied may be directly related to the bipolar disorder pathophysiology. Conclusions The strategy employed here showed significant potential for exploring pathophysiological features and molecular pathways involved in bipolar disorder. Thus, our findings may contribute to pave the way for future studies aiming at identifying important potential biomarkers for bipolar disorder diagnosis or progression follow-up. Electronic supplementary material The online version of this article (doi:10.1186/s40345-017-0088-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sumit Sethi
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil
| | - Mariana Pedrini
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil
| | - Lucas B Rizzo
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil
| | - Maiara Zeni-Graiff
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil
| | - Caroline Dal Mas
- Department of Pharmacology, Universidade Federal de São Paulo-UNIFESP, Rua Três de Maio, 100. Vila Clementino, São Paulo, CEP 04044-020, Brazil
| | - Ana Cláudia Cassinelli
- Department of Psychiatry, Irmandade da Santa Casa de Misericórdia de São Paulo (ISCMSP), Rua Major Maragliano, 287. Vila Mariana, São Paulo, CEP 04017-030, Brazil
| | - Mariane N Noto
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil.,Department of Psychiatry, Irmandade da Santa Casa de Misericórdia de São Paulo (ISCMSP), Rua Major Maragliano, 287. Vila Mariana, São Paulo, CEP 04017-030, Brazil
| | - Elson Asevedo
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil
| | - Quirino Cordeiro
- Department of Psychiatry, Irmandade da Santa Casa de Misericórdia de São Paulo (ISCMSP), Rua Major Maragliano, 287. Vila Mariana, São Paulo, CEP 04017-030, Brazil
| | - João G M Pontes
- Laboratório de Química Biológica, Department of Organic Chemistry, Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Caixa Postal 6154, Campinas, São Paulo, CEP 13083-970, Brazil
| | - Antonio J M Brasil
- Laboratório de Química Biológica, Department of Organic Chemistry, Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Caixa Postal 6154, Campinas, São Paulo, CEP 13083-970, Brazil
| | - Acioly Lacerda
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil
| | - Mirian A F Hayashi
- Department of Pharmacology, Universidade Federal de São Paulo-UNIFESP, Rua Três de Maio, 100. Vila Clementino, São Paulo, CEP 04044-020, Brazil
| | - Ronei Poppi
- Department of Analytical Chemistry, Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Caixa Postal 6154, Campinas, São Paulo, CEP 13083-970, Brazil
| | - Ljubica Tasic
- Laboratório de Química Biológica, Department of Organic Chemistry, Institute of Chemistry, Universidade Estadual de Campinas-UNICAMP, Caixa Postal 6154, Campinas, São Paulo, CEP 13083-970, Brazil.
| | - Elisa Brietzke
- Department of Psychiatry, Universidade Federal de São Paulo-UNIFESP, Rua Borges Lagoa, 570. Vila Clementino, São Paulo, CEP 04038-020, Brazil.
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17
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Liu PF, Du Y, Meng L, Li X, Liu Y. Metabolic profiling in kidneys of Atlantic salmon infected with Aeromonas salmonicida based on 1H NMR. FISH & SHELLFISH IMMUNOLOGY 2016; 58:292-301. [PMID: 27577538 DOI: 10.1016/j.fsi.2016.08.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 08/19/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
Aeromonas salmonicida, an important pathogenic bacterium which induces furunculosis, is globally causing increased risks in Atlantic salmon (Salmo salar) farming. Although the kidney is the main target organ of A. salmonicida, the metabolic profiling of kidney in response to A. salmonicida in vivo remains unknown. Here, we used 1H nuclear magnetic resonance (NMR) to comprehensively analyze the metabolic changes in the kidney of Atlantic salmon. Through the NOESYPR1D spectrum combined with multi-variate pattern recognition analysis, including principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) models, significant metabolic changes were observed seven and 14 days post-infection and in a control group. Hence, the main objective of this study was to estimate the significant metabolites with resistance to furunculosis and further understand the mechanism of A. salmonicida in Atlantic salmon. Notably, substantial alterations of kidney metabolites were observed, such as with fumarate, alanine, valine, glycine, aspartate, choline, glycerophosphocholine and betaine, and summarized by metabolic pathways including the citrate cycle, glycolysis/gluconeogenesis, tryptophan metabolism, and urea cycle, respectively. Changes were also observed in 3-hydroxybutyrate and phosphocholine which were not involved in these four metabolic pathways. After analyzing the alteration trend of these metabolites, we inferred that A. salmonicida caused absorption inhibition of amino acids and disturbed protein metabolism as well as cell metabolism in favor of its replication. These observations offered novel insights into the mechanisms of infection at a functional level and facilitated further assessment and clarification of fish disease from A. salmonicida exposure.
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Affiliation(s)
- Peng-Fei Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Yishuai Du
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Lingjie Meng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xian Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Ying Liu
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Dalian Ocean University, Dalian, China.
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18
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Holmes E, Wijeyesekera A, Taylor-Robinson SD, Nicholson JK. The promise of metabolic phenotyping in gastroenterology and hepatology. Nat Rev Gastroenterol Hepatol 2015. [PMID: 26194948 DOI: 10.1038/nrgastro.2015.114] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Disease risk and treatment response are determined, at the individual level, by a complex history of genetic and environmental interactions, including those with our endogenous microbiomes. Personalized health care requires a deep understanding of patient biology that can now be measured using a range of '-omics' technologies. Patient stratification involves the identification of genetic and/or phenotypic disease subclasses that require different therapeutic strategies. Stratified medicine approaches to disease diagnosis, prognosis and therapeutic response monitoring herald a new dimension in patient care. Here, we explore the potential value of metabolic profiling as applied to unmet clinical needs in gastroenterology and hepatology. We describe potential applications in a number of diseases, with emphasis on large-scale population studies as well as metabolic profiling on the individual level, using spectrometric and imaging technologies that will leverage the discovery of mechanistic information and deliver novel health care solutions to improve clinical pathway management.
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Affiliation(s)
- Elaine Holmes
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Anisha Wijeyesekera
- Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | | | - Jeremy K Nicholson
- MRC-NIHR National Phenome Centre, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
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19
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Probert F, Rice P, Scudamore CL, Wells S, Williams R, Hough TA, Cox IJ. 1H NMR Metabolic Profiling of Plasma Reveals Additional Phenotypes in Knockout Mouse Models. J Proteome Res 2015; 14:2036-45. [DOI: 10.1021/pr501039k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fay Probert
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
- Institute of Hepatology, Foundation for Liver Research, 69-75 Chenies Mews, London WC1E 6HX, United Kingdom
| | - Paul Rice
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
| | | | - Sara Wells
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
| | - Roger Williams
- Institute of Hepatology, Foundation for Liver Research, 69-75 Chenies Mews, London WC1E 6HX, United Kingdom
| | - Tertius A. Hough
- Mary
Lyon Centre, MRC Harwell, Oxfordshire OX11 0RD, United Kingdom
| | - I. Jane Cox
- Institute of Hepatology, Foundation for Liver Research, 69-75 Chenies Mews, London WC1E 6HX, United Kingdom
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20
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Stec DF, Wang S, Stothers C, Avance J, Denson D, Harris R, Voziyan P. Alterations of urinary metabolite profile in model diabetic nephropathy. Biochem Biophys Res Commun 2015; 456:610-4. [PMID: 25499815 PMCID: PMC4287263 DOI: 10.1016/j.bbrc.2014.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
Countering the diabetes pandemic and consequent complications, such as nephropathy, will require better understanding of disease mechanisms and development of new diagnostic methods. Animal models can be versatile tools in studies of diabetic renal disease when model pathology is relevant to human diabetic nephropathy (DN). Diabetic models using endothelial nitric oxide synthase (eNOS) knock-out mice develop major renal lesions characteristic of human disease. However, it is unknown whether they can also reproduce changes in urinary metabolites found in human DN. We employed Type 1 and Type 2 diabetic mouse models of DN, i.e. STZ-eNOS(-/-) C57BLKS and eNOS(-/-) C57BLKS db/db, with the goal of determining changes in urinary metabolite profile using proton nuclear magnetic resonance (NMR). Six urinary metabolites with significantly lower levels in diabetic compared to control mice have been identified. Specifically, major changes were found in metabolites from tricarboxylic acid (TCA) cycle and aromatic amino acid catabolism including 3-indoxyl sulfate, cis-aconitate, 2-oxoisocaproate, N-phenyl-acetylglycine, 4-hydroxyphenyl acetate, and hippurate. Levels of 4-hydroxyphenyl acetic acid and hippuric acid showed the strongest reverse correlation to albumin-to-creatinine ratio (ACR), which is an indicator of renal damage. Importantly, similar changes in urinary hydroxyphenyl acetate and hippurate were previously reported in human renal disease. We demonstrated that STZ-eNOS(-/-) C57BLKS and eNOS(-/-) C57BLKS db/db mouse models can recapitulate changes in urinary metabolome found in human DN and therefore can be useful new tools in metabolomic studies relevant to human pathology.
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Affiliation(s)
- Donald F Stec
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Suwan Wang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Cody Stothers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Josh Avance
- Berea College, 1916 CPO, Berea, KY 40404, United States
| | - Deon Denson
- Choctaw Central High School, Philadelphia, MS 39350, United States
| | - Raymond Harris
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States
| | - Paul Voziyan
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, United States.
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21
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Liu PF, Liu QH, Wu Y, Jie H. A pilot metabolic profiling study in hepatopancreas of Litopenaeus vannamei with white spot syndrome virus based on 1H NMR spectroscopy. J Invertebr Pathol 2015; 124:51-6. [DOI: 10.1016/j.jip.2014.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/19/2014] [Accepted: 09/26/2014] [Indexed: 11/26/2022]
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22
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Zhou A, Ni J, Xu Z, Wang Y, Lu S, Sha W, Karakousis PC, Yao YF. Application of (1)h NMR spectroscopy-based metabolomics to sera of tuberculosis patients. J Proteome Res 2013; 12:4642-9. [PMID: 23980697 DOI: 10.1021/pr4007359] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is an ideal platform for the metabolic analysis of biofluids due to its high reproducibility, nondestructiveness, nonselectivity in metabolite detection, and the ability to simultaneously quantify multiple classes of metabolites. Tuberculosis (TB) is a chronic wasting inflammatory disease characterized by multisystem involvement, which can cause metabolic derangements in afflicted patients. In this study, we combined multivariate pattern recognition (PR) analytical techniques with (1)H NMR spectroscopy to explore the metabolic profile of sera from TB patients. A total of 77 serum samples obtained from patients with TB (n = 38) and healthy controls (n = 39) were investigated. Orthogonal partial least-squares discriminant analysis (OPLS-DA) was capable of distinguishing TB patients from controls and establishing a TB-specific metabolite profile. A total of 17 metabolites differed significantly in concentration between the two groups. Serum samples from TB patients were characterized by increased concentrations of 1-methylhistidine, acetoacetate, acetone, glutamate, glutamine, isoleucine, lactate, lysine, nicotinate, phenylalanine, pyruvate, and tyrosine, accompanied by reduced concentrations of alanine, formate, glycine, glycerolphosphocholine, and low-density lipoproteins relative to control subjects. Our study reveals the metabolic profile of sera from TB patients and indicates that NMR-based methods can distinguish TB patients from healthy controls. NMR-based metabolomics has the potential to be developed into a novel clinical tool for TB diagnosis or therapeutic monitoring and could contribute to an improved understanding of disease mechanisms.
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Affiliation(s)
- Aiping Zhou
- Laboratory of Bacterial Pathogenesis, Department of Microbiology and Immunology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine , 280 South Chongqing Road, Shanghai 200025, China
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23
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Kutyshenko VP, Beskaravayny PM, Molchanov MV, Paskevich SI, Prokhorov DA, Uversky VN. Looking at microbial metabolism by high-resolution (2)H-NMR spectroscopy. PeerJ 2013; 1:e101. [PMID: 23862103 PMCID: PMC3709107 DOI: 10.7717/peerj.101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 06/21/2013] [Indexed: 12/18/2022] Open
Abstract
We analyzed the applicability of high-resolution 2H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D2O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics.
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Affiliation(s)
- Victor P Kutyshenko
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences , Pushchino , Russia
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24
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Li M, Wang X, Aa J, Qin W, Zha W, Ge Y, Liu L, Zheng T, Cao B, Shi J, Zhao C, Wang X, Yu X, Wang G, Liu Z. GC/TOFMS analysis of metabolites in serum and urine reveals metabolic perturbation of TCA cycle in db/db mice involved in diabetic nephropathy. Am J Physiol Renal Physiol 2013; 304:F1317-24. [DOI: 10.1152/ajprenal.00536.2012] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Early diagnosis of diabetic nephropathy (DN) is difficult although it is of crucial importance to prevent its development. To probe potential markers and the underlying mechanism of DN, an animal model of DN, the db/db mice, was used and serum and urine metabolites were profiled using gas chromatography/time-of-flight mass spectrometry. Metabolic patterns were evaluated based on serum and urine data. Principal component analysis of the data revealed an obvious metabonomic difference between db/db mice and controls, and db/db mice showed distinctly different metabolic patterns during the progression from diabetes to early, medium, and later DN. The identified metabolites discriminating between db/db mice and controls suggested that db/db mice have perturbations in the tricarboxylic acid cycle (TCA, citrate, malate, succinate, and aconitate), lipid metabolism, glycolysis, and amino acid turnover. The db/db mice were characterized by acidic urine, high TCA intermediates in serum at week 6 and a sharp decline thereafter, and gradual elevation of free fatty acids in the serum. The sharp drop of serum TCA intermediates from week 6 to 8 indicated the downregulated glycolysis and insulin resistance. However, urinary TCA intermediates did not decrease in parallel with those in the serum from week 6 to 10, and an increased portion of TCA intermediates in the serum was excreted into the urine at 8, 10, and 12 wk than at 6 wk, indicating kidney dysfunction occurred. The relative abundances of TCA intermediates in urine relative to those in serum were suggested as an index of renal damage.
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Affiliation(s)
- Mengjie Li
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Xufang Wang
- Research Institute of Nephrology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Jiye Aa
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Weisong Qin
- Research Institute of Nephrology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Weibin Zha
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Yongchun Ge
- Research Institute of Nephrology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Linsheng Liu
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Tian Zheng
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Bei Cao
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Jian Shi
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Chunyan Zhao
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Xinwen Wang
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Xiaoyi Yu
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Guangji Wang
- Laboratory of Metabolomics, Key Laboratory of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China; and
| | - Zhihong Liu
- Research Institute of Nephrology, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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Clos LJ, Jofre MF, Ellinger JJ, Westler WM, Markley JL. NMRbot: Python scripts enable high-throughput data collection on current Bruker BioSpin NMR spectrometers. Metabolomics 2013; 9:558-563. [PMID: 23678341 PMCID: PMC3651530 DOI: 10.1007/s11306-012-0490-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 12/11/2012] [Indexed: 11/21/2022]
Abstract
To facilitate the high-throughput acquisition of nuclear magnetic resonance (NMR) experimental data on large sets of samples, we have developed a simple and straightforward automated methodology that capitalizes on recent advances in Bruker BioSpin NMR spectrometer hardware and software. Given the daunting challenge for non-NMR experts to collect quality spectra, our goal was to increase user accessibility, provide customized functionality, and improve the consistency and reliability of resultant data. This methodology, NMRbot, is encoded in a set of scripts written in the Python programming language accessible within the Bruker BioSpin TopSpin™ software. NMRbot improves automated data acquisition and offers novel tools for use in optimizing experimental parameters on the fly. This automated procedure has been successfully implemented for investigations in metabolomics, small-molecule library profiling, and protein-ligand titrations on four Bruker BioSpin NMR spectrometers at the National Magnetic Resonance Facility at Madison. The investigators reported benefits from ease of setup, improved spectral quality, convenient customizations, and overall time savings.
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Affiliation(s)
- Lawrence J Clos
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706 USA
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26
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Li L, Sui W, Che W, Li W, Chen J, Li H, Tang D, Li M, Dai Y. 1H NMR-Based Metabolic Profiling of Human Serum Before and After Renal Transplantation. ASAIO J 2013; 59:286-93. [DOI: 10.1097/mat.0b013e31828e2d9f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Qi S, Ouyang X, Wang L, Peng W, Wen J, Dai Y. A pilot metabolic profiling study in serum of patients with chronic kidney disease based on (1) H-NMR-spectroscopy. Clin Transl Sci 2012; 5:379-85. [PMID: 23067349 DOI: 10.1111/j.1752-8062.2012.00437.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is the end point of a number of renal and systemic diseases. The metabolomics with a highly multiplexed and efficient manner is a challenging goal in nephrology. METHODS A (1) H-NMR based metabolomics approach was applied to establish a human CKD serum metabolic profile. Serum samples were obtained from CKD patients with four stages (N= 80) and healthy controls (N= 28). The data acquired by CMPG spectrum were further processed by pattern recognition (PR) analysis. Principal components analysis (PCA) and partial least-squares-discriminant analysis (PLS-DA) was capable of clustering the disease groups and establishing disease-specific metabolites profile. RESULTS The classification models could grade CKD patients with considerably high value of Q(2) and R(2) . The significant endogenous metabolites that contributed to distinguish CKD in different stages included the products of glycolysis (glucose, lactate), amino acids (valine, alanine, glutamate, glycine), organic osmolytes (betaine, myo-inositol, taurine, glycerophosphcholine), and so on. Based on these metabolites, the model for diagnosing patients with CKD achieved the sensitivity and specificity of 100%. CONCLUSION The study illustrated that serum metabolic profile was altered in response to renal dysfunction and the progression of CKD. The identified metabolic biomarkers may provide useful information for the diagnosis of CKD, especially in early stages.
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Affiliation(s)
- Suwen Qi
- The Department of Biomedical Engineering, Medical school, Shenzhen University, Guangdong, P.R. China
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Abstract
Chemometrics in Medicine and PharmacyThis minireview summarizes the basic ways of application of chemometrics in medicine and pharmacy. It brings a collection of applications of chemometric used for the solution of diverse practical problems, e.g. exploitation of biologically active species, effective use of biomarkers, advancement of clinical diagnosis, monitoring of the patient's state and prediction of its perspectives, drug design or classification of toxic chemical substances. The aim of this contribution is a brief presentation of versatile potentialities of contemporary chemometrical techniques and relevant software. They are exemplified by typical cases from literature as well as by own research results of the Chemometrics group at Department of Chemistry, the University of Ss. Cyril & Methodius in Trnava.
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29
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Sui W, Li L, Che W, Guimai Z, Chen J, Li W, Dai Y. A proton nuclear magnetic resonance-based metabonomics study of metabolic profiling in immunoglobulin a nephropathy. Clinics (Sao Paulo) 2012; 67:363-73. [PMID: 22522762 PMCID: PMC3317244 DOI: 10.6061/clinics/2012(04)10] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 11/28/2011] [Accepted: 12/26/2011] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES Immunoglobulin A nephropathy is the most common cause of chronic renal failure among primary glomerulonephritis patients. The ability to diagnose immunoglobulin A nephropathy remains poor. However, renal biopsy is an inconvenient, invasive, and painful examination, and no reliable biomarkers have been developed for use in routine patient evaluations. The aims of the present study were to identify immunoglobulin A nephropathy patients, to identify useful biomarkers of immunoglobulin A nephropathy and to establish a human immunoglobulin A nephropathy metabolic profile. METHODS Serum samples were collected from immunoglobulin A nephropathy patients who were not using immunosuppressants. A pilot study was undertaken to determine disease-specific metabolite biomarker profiles in three groups: healthy controls (N = 23), low-risk patients in whom immunoglobulin A nephropathy was confirmed as grades I-II by renal biopsy (N = 23), and high-risk patients with nephropathies of grades IV-V (N = 12). Serum samples were analyzed using proton nuclear magnetic resonance spectroscopy and by applying multivariate pattern recognition analysis for disease classification. RESULTS Compared with the healthy controls, both the low-risk and high-risk patients had higher levels of phenylalanine, myo-Inositol, lactate, L6 lipids ( = CH-CH2-CH = O), L5 lipids (-CH2-C = O), and L3 lipids (-CH2-CH2-C = O) as well as lower levels of β -glucose, α-glucose, valine, tyrosine, phosphocholine, lysine, isoleucine, glycerolphosphocholine, glycine, glutamine, glutamate, alanine, acetate, 3-hydroxybutyrate, and 1-methylhistidine. CONCLUSIONS These metabolites investigated in this study may serve as potential biomarkers of immunoglobulin A nephropathy. Point scoring of pattern recognition analysis was able to distinguish immunoglobulin A nephropathy patients from healthy controls. However, there were no obvious differences between the low-risk and high-risk groups in our research. These results offer new, sensitive and specific, noninvasive approaches that may be of great benefit to immunoglobulin A nephropathy patients by enabling earlier diagnosis.
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Affiliation(s)
- Weiguo Sui
- Laboratory of Metabolic Diseases Research, Central Laboratory, 181st Hospital Guangxi, Guangxi Province, China.
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30
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Maher AD, Fonville JM, Coen M, Lindon JC, Rae CD, Nicholson JK. Statistical Total Correlation Spectroscopy Scaling for Enhancement of Metabolic Information Recovery in Biological NMR Spectra. Anal Chem 2011; 84:1083-91. [DOI: 10.1021/ac202720f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anthony D. Maher
- Neuroscience Research Australia, Barker Street, Randwick 2031, Australia
- School of Medical Sciences, University of New South Wales, New South Wales 2052,
Australia
- Biomolecular Medicine,
Department
of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
| | - Judith M. Fonville
- Biomolecular Medicine,
Department
of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
| | - Muireann Coen
- Biomolecular Medicine,
Department
of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
| | - John C. Lindon
- Biomolecular Medicine,
Department
of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
| | - Caroline D. Rae
- Neuroscience Research Australia, Barker Street, Randwick 2031, Australia
| | - Jeremy K. Nicholson
- Biomolecular Medicine,
Department
of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, United Kingdom
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31
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1H NMR based metabolomics of CSF and blood serum: A metabolic profile for a transgenic rat model of Huntington disease. Biochim Biophys Acta Mol Basis Dis 2011; 1812:1371-9. [DOI: 10.1016/j.bbadis.2011.08.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Revised: 07/19/2011] [Accepted: 08/08/2011] [Indexed: 11/20/2022]
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32
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Ouyang X, Dai Y, Wen JL, Wang LX. 1H NMR-based metabolomic study of metabolic profiling for systemic lupus erythematosus. Lupus 2011; 20:1411-20. [PMID: 21976403 DOI: 10.1177/0961203311418707] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Systemic lupus erythematosus (SLE) is a chronic inflammatory disease characterized by multi-system involvement, diverse clinical presentation, and alterations in circulating metabolites. In this study, a 1H NMR spectroscopy-based metabolomics approach was applied to establish a human SLE serum metabolic profile. Serum samples were obtained from patients with SLE ( n = 64), patients with rheumatoid arthritis (RA) ( n = 30) and healthy controls ( n = 35). The NOESYPR1D spectrum combined with multi-variate pattern recognition analysis was used to cluster the groups and establish a disease-specific metabolites phenotype. Principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) models were capable of distinguishing SLE or RA patients from healthy subjects. The OPLS-DA model was able to predict diagnosis of SLE with a sensitivity rate of 60.9% and a specificity rate of 97.1%. For diagnosing RA, the model has much higher sensitivity (96.7%) and specificity (91.4%). The SLE serum samples were characterized by reduced concentrations of valine, tyrosine, phenylalanine, lysine, isoleucine, histidine, glutamine, alanine, citrate, creatinine, creatine, pyruvate, high-density lipoprotein, cholesterol, glycerol, formate and increased concentrations of N-acetyl glycoprotein, very low-density lipoprotein and low-density lipoprotein in comparison with the control population. Theresults not only indicated that serum NMR-based metabolomic methods had sufficient sensitivity and specificity to distinguish SLE and RA from healthy controls, but also have the potential to be developed into a clinically useful diagnostic tool, and could also contribute to a further understanding of disease mechanisms.
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Affiliation(s)
- X Ouyang
- The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong Province PR China
| | - Y Dai
- The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong Province PR China
| | - JL Wen
- The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong Province PR China
| | - LX Wang
- The Second Clinical Medical College, Jinan University, Shenzhen People's Hospital, Shenzhen, Guangdong Province PR China
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33
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Chen J, Zhang X, Cao R, Lu X, Zhao S, Fekete A, Huang Q, Schmitt-Kopplin P, Wang Y, Xu Z, Wan X, Wu X, Zhao N, Xu C, Xu G. Serum 27-nor-5β-Cholestane-3,7,12,24,25 Pentol Glucuronide Discovered by Metabolomics as Potential Diagnostic Biomarker for Epithelium Ovarian Cancer. J Proteome Res 2011; 10:2625-32. [DOI: 10.1021/pr200173q] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jing Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China
| | - Xiaoyan Zhang
- Obstetrics & Gynecology Hospital, Shanghai Medical School, Institute of Biomedical Science, Fudan University, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Rui Cao
- Department of the Obstetrics and Gynecology Hospital, Dalian Medical University, 116033 Dalian, China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China
| | - Sumin Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China
| | - Agnes Fekete
- Department of BioGeoChemistry and Analytics, Institute of Ecological Chemistry, Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Ingoldstaedter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Qiang Huang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China
| | - Philippe Schmitt-Kopplin
- Department of BioGeoChemistry and Analytics, Institute of Ecological Chemistry, Helmholtz-Zentrum Muenchen-German Research Center for Environmental Health, Ingoldstaedter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Yisheng Wang
- Obstetrics & Gynecology Hospital, Shanghai Medical School, Institute of Biomedical Science, Fudan University, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Zhiliang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China
| | - Xiaoping Wan
- The International Peace Maternity and Child Health Hospital, Shanghai Jiaotong University School of Medicine, 200030 Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Cancer Hospital, Fudan University, 200032 Shanghai, China
| | - Naiqing Zhao
- Department of Biostatistics and Social Medicine, School of Public Health, Fudan University, 200032 Shanghai, China
| | - Congjian Xu
- Obstetrics & Gynecology Hospital, Shanghai Medical School, Institute of Biomedical Science, Fudan University, Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai 200011, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 116023 Dalian, China
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Schattka B, Alexander M, Ying SL, Man A, Shaw RA. Metabolic Fingerprinting of Biofluids by Infrared Spectroscopy: Modeling and Optimization of Flow Rates for Laminar Fluid Diffusion Interface Sample Preconditioning. Anal Chem 2010; 83:555-62. [DOI: 10.1021/ac102338n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bernhard Schattka
- National Research Council of Canada, Institute for Biodiagnostics, 435 Ellice Avenue, Winnipeg, Manitoba, Canada. R3B 1Y6
| | - Murray Alexander
- National Research Council of Canada, Institute for Biodiagnostics, 435 Ellice Avenue, Winnipeg, Manitoba, Canada. R3B 1Y6
| | - Sarah Low Ying
- National Research Council of Canada, Institute for Biodiagnostics, 435 Ellice Avenue, Winnipeg, Manitoba, Canada. R3B 1Y6
| | - Angela Man
- National Research Council of Canada, Institute for Biodiagnostics, 435 Ellice Avenue, Winnipeg, Manitoba, Canada. R3B 1Y6
| | - R. Anthony Shaw
- National Research Council of Canada, Institute for Biodiagnostics, 435 Ellice Avenue, Winnipeg, Manitoba, Canada. R3B 1Y6
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Forseth RR, Schroeder FC. NMR-spectroscopic analysis of mixtures: from structure to function. Curr Opin Chem Biol 2010; 15:38-47. [PMID: 21071261 DOI: 10.1016/j.cbpa.2010.10.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Accepted: 10/08/2010] [Indexed: 12/22/2022]
Abstract
NMR spectroscopy as a particularly information-rich method offers unique opportunities for improving the structural and functional characterization of metabolomes, which will be essential for advancing the understanding of many biological processes. Whereas traditionally NMR spectroscopy was mostly relegated to the characterization of pure compounds, the past few years have seen a surge of interest in using NMR-spectroscopic techniques for characterizing complex metabolite mixtures. Development of new methods was motivated partly by the realization that using NMR for the analysis of metabolite mixtures can help identify otherwise inaccessible small molecules, for example compounds that are prone to chemical decomposition and thus cannot be isolated. Furthermore, comparative metabolomics and statistical analyses of NMR spectra have proven highly effective at identifying novel and known metabolites that correlate with changes in genotype or phenotype. In this review, we provide an overview of the range of NMR-spectroscopic techniques recently developed for characterizing metabolite mixtures, including methods used in discovery-oriented natural product chemistry, in the study of metabolite biosynthesis and function, or for comparative analyses of entire metabolomes.
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Affiliation(s)
- Ry R Forseth
- Boyce Thompson Institute and Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
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36
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Novoa-Carballal R, Fernandez-Megia E, Jimenez C, Riguera R. NMR methods for unravelling the spectra of complex mixtures. Nat Prod Rep 2010; 28:78-98. [PMID: 20936238 DOI: 10.1039/c005320c] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The main methods for the simplification of the NMR of complex mixtures by selective attenuation/suppression of the signals of certain components are presented. The application of relaxation, diffusion and PSR filters and other techniques to biological samples, pharmaceuticals, foods, living organisms and natural products are illustrated with examples.
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Affiliation(s)
- Ramon Novoa-Carballal
- Department of Organic Chemistry and Centre for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, Santiago de Compostela, Spain
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37
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Zhang S, Nagana Gowda GA, Ye T, Raftery D. Advances in NMR-based biofluid analysis and metabolite profiling. Analyst 2010; 135:1490-8. [PMID: 20379603 PMCID: PMC4720135 DOI: 10.1039/c000091d] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significant improvements in NMR technology and methods have propelled NMR studies to play an important role in a rapidly expanding number of applications involving the profiling of metabolites in biofluids. This review discusses recent technical advances in NMR spectroscopy based metabolite profiling methods, data processing and analysis over the last three years.
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Affiliation(s)
- Shucha Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - G. A. Nagana Gowda
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Tao Ye
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Daniel Raftery
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
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38
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39
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Fonville JM, Maher AD, Coen M, Holmes E, Lindon JC, Nicholson JK. Evaluation of Full-Resolution J-Resolved 1H NMR Projections of Biofluids for Metabonomics Information Retrieval and Biomarker Identification. Anal Chem 2010; 82:1811-21. [DOI: 10.1021/ac902443k] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Judith M. Fonville
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Anthony D. Maher
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Muireann Coen
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Elaine Holmes
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - John C. Lindon
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
| | - Jeremy K. Nicholson
- Biomolecular Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, Sir Alexander Fleming Building, South Kensington, London SW7 2AZ, United Kingdom
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40
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Sukumaran DK, Garcia E, Hua J, Tabaczynski W, Odunsi K, Andrews C, Szyperski T. Standard operating procedure for metabonomics studies of blood serum and plasma samples using a 1H-NMR micro-flow probe. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2009; 47 Suppl 1:S81-S85. [PMID: 19688872 DOI: 10.1002/mrc.2469] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A standard operating procedure (SOP) is presented for high-throughput metabonomics studies using a 600 MHz NMR spectrometer equipped with a micro-flow probe that is connected to an auto-sampler. The procedure is designed to minimize random and systematic variation of NMR data collection. In addition, a protocol is described to assess the quality of the data acquired by a given NMR spectroscopist to ensure that (i) all researchers involved in the NMR data acquisition of a metabonomics research program perform equally and (ii) operator-associated variation of NMR data collection is statistically not relevant for the interpretation of results obtained from multivariate data analyses.
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Affiliation(s)
- Dinesh K Sukumaran
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, NY, USA
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Sussulini A, Prando A, Maretto DA, Poppi RJ, Tasic L, Banzato CEM, Arruda MAZ. Metabolic Profiling of Human Blood Serum from Treated Patients with Bipolar Disorder Employing 1H NMR Spectroscopy and Chemometrics. Anal Chem 2009; 81:9755-63. [DOI: 10.1021/ac901502j] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Alessandra Sussulini
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
| | - Alessandra Prando
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
| | - Danilo Althmann Maretto
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
| | - Ronei Jesus Poppi
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
| | - Ljubica Tasic
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
| | - Cláudio Eduardo Muller Banzato
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
| | - Marco Aurélio Zezzi Arruda
- Group of Spectrometry, Sample Preparation and Mechanization (GEPAM), National Institute of Science and Technology for Bioanalytics, Organic Chemistry Department, Chemometrics Laboratory in Analytical Chemistry, and National Institute of Science and Technology for Structural Biology and Bioimaging, Institute of Chemistry, University of Campinas (Unicamp), P.O. Box 6154, 13083-970 Campinas, and Department of Psychiatry, Faculty of Medical Sciences, Unicamp, P.O. Box 6111, 13081-970 Campinas, SP, Brazil
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Abstract
PURPOSE OF REVIEW Recent advances in metabolomic tools now permit to characterize dysregulated metabolic pathways in various diseases associated with the identification of sensitive and specific early responding biomarkers that are critical both for the diagnosis of the type of insult as well as for the selection and evaluation of therapy. RECENT FINDINGS This short review describes progresses made in analytical science and their applications in the field of glucose disorders. Recent studies focused mainly on type 2 diabetes both in human and animal models in order to validate early biomarkers and effects of drugs on disease progression. The potential of using the metabolomic approach was also demonstrated for diagnosing diabetic complications such as diabetic nephropathy. SUMMARY In addition to its application in the discovery of disease biomarkers, metabolomics can contribute to the elucidation of pathophysiological mechanisms.
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Affiliation(s)
- Jean-Louis Sébédio
- Plate-Forme Exploration du Métabolisme, INRA UMR 1019 Nutrition Humaine, Saint Genes Champanelle, France.
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Loo RL, Coen M, Ebbels T, Cloarec O, Maibaum E, Bictash M, Yap I, Elliott P, Stamler J, Nicholson JK, Holmes E. Metabolic profiling and population screening of analgesic usage in nuclear magnetic resonance spectroscopy-based large-scale epidemiologic studies. Anal Chem 2009; 81:5119-29. [PMID: 19489597 PMCID: PMC2726443 DOI: 10.1021/ac900567e] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The application of a (1)H nuclear magnetic resonance (NMR) spectroscopy-based screening method for determining the use of two widely available analgesics (acetaminophen and ibuprofen) in epidemiologic studies has been investigated. We used samples and data from the cross-sectional INTERMAP Study involving participants from Japan (n = 1145), China (n = 839), U.K. (n = 501), and the U.S. (n = 2195). An orthogonal projection to latent structures discriminant analysis (OPLS-DA) algorithm with an incorporated Monte Carlo resampling function was applied to the NMR data set to determine which spectra contained analgesic metabolites. OPLS-DA preprocessing parameters (normalization, bin width, scaling, and input parameters) were assessed systematically to identify an optimal acetaminophen prediction model. Subsets of INTERMAP spectra were examined to verify and validate the presence/absence of acetaminophen/ibuprofen based on known chemical shift and coupling patterns. The optimized and validated acetaminophen model correctly predicted 98.2%, and the ibuprofen model correctly predicted 99.0% of the urine specimens containing these drug metabolites. The acetaminophen and ibuprofen models were subsequently used to predict the presence/absence of these drug metabolites for the remaining INTERMAP specimens. The acetaminophen model identified 415 out of 8436 spectra as containing acetaminophen metabolite signals while the ibuprofen model identified 245 out of 8604 spectra as containing ibuprofen metabolite signals from the global data set after excluding samples used to construct the prediction models. The NMR-based metabolic screening strategy provides a new objective approach for evaluation of self-reported medication data and is extendable to other aspects of population xenometabolome profiling.
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Affiliation(s)
- Ruey Leng Loo
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Muireann Coen
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Timothy Ebbels
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Olivier Cloarec
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Elaine Maibaum
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Magda Bictash
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
- Department of Epidemiology and Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Ivan Yap
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
- Department of Epidemiology and Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Paul Elliott
- Department of Epidemiology and Public Health, Imperial College London, St Mary's Campus, London, UK
| | - Jeremiah Stamler
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jeremy K. Nicholson
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
| | - Elaine Holmes
- Biomolecular Medicine, Division of Surgery, Oncology, Reproductive Biology and Anaesthetics (SORA), Faculty of Medicine, Imperial College London, SW7 2AZ, UK
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Abstract
Diabetes is characterized by hyperglycemia due to dysfunction of insulin secretion or action. The two most common forms are Type 1 diabetes, in which pancreatic β-cells are destroyed, and Type 2 diabetes, in which a combination of disordered insulin action and secretion results in abnormal carbohydrate, lipid and protein metabolism. Metabonomics employs analytical technologies to measure ‘global’ metabolic responses to a disease state. With the aid of statistical pattern recognition, this can reveal novel insights into the biochemical consequences of diabetes. The metabonomic method can be divided into four stages: sample collection; preparation; data acquisition and processing; and statistical analyses. In this review, we describe the most recent developments at each experimental stage in detail, and comment on specific precautions or improvements that should be taken into account when studying diabetes. Finally, we end with speculations as to where and how the field will develop in the future. Metabonomics provides a logical framework for understanding the global metabolic effects of diabetes. Continuing technological improvements will expand our knowledge of the causes and progression of this disease, and enhance treatment options for individuals.
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Righi V, Durante C, Cocchi M, Calabrese C, Di Febo G, Lecce F, Pisi A, Tugnoli V, Mucci A, Schenetti L. Discrimination of Healthy and Neoplastic Human Colon Tissues by ex Vivo HR-MAS NMR Spectroscopy and Chemometric Analyses. J Proteome Res 2009; 8:1859-69. [DOI: 10.1021/pr801094b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Valeria Righi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Caterina Durante
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Marina Cocchi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Carlo Calabrese
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Giulio Di Febo
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Ferdinando Lecce
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Annamaria Pisi
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Vitaliano Tugnoli
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Adele Mucci
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
| | - Luisa Schenetti
- Dipartimento di Biochimica “G. Moruzzi”, Università di Bologna, Via Belmeloro 8/2, 40126 Bologna, Italy, Dipartimento di Chimica, Università di Modena e Reggio Emilia, Via G. Campi 183, 41100 Modena, Italy, Dipartimento di Medicina Interna e Gastroenterologia, Università di Bologna, Via G. Massarenti 9, 40138, Bologna, Italy, Dipartimento Emergenza/Urgenza, Chirurgia Generale e dei Trapianti, Università di Bologna, Via G. Massarenti 9, 40138 Bologna, Italy, and DiSTA, Università di Bologna, Viale Fanin
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Balayssac S, Delsuc MA, Gilard V, Prigent Y, Malet-Martino M. Two-dimensional DOSY experiment with Excitation Sculpting water suppression for the analysis of natural and biological media. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2009; 196:78-83. [PMID: 18926751 DOI: 10.1016/j.jmr.2008.09.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2008] [Revised: 09/17/2008] [Accepted: 09/19/2008] [Indexed: 05/26/2023]
Abstract
The Bipolar Pulse Pair Stimulated Echo NMR pulse sequence was modified to blend the original Excitation Sculpting water signal suppression. The sequence is a powerful tool to generate rapidly, with a good spectrum quality, bidimensional DOSY experiments without solvent signal, thus allowing the analysis of complex mixtures such as plant extracts or biofluids. The sequence has also been successfully implemented for a protein at very-low concentration in interaction with a small ligand, namely the salivary IB5 protein binding the polyphenol epigallocatechine gallate. The artifacts created by this sequence can be observed, checked and removed thanks to NPK and NMRnotebook softwares to give a perfect bidimensional DOSY spectrum.
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Affiliation(s)
- Stéphane Balayssac
- Groupe de RMN Biomédicale, Laboratoire SPCMIB (UMR CNRS 5068), Université Paul Sabatier, Toulouse, France
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