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Sun J, Xia Y. Pretreating and normalizing metabolomics data for statistical analysis. Genes Dis 2024; 11:100979. [PMID: 38299197 PMCID: PMC10827599 DOI: 10.1016/j.gendis.2023.04.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/09/2023] [Indexed: 02/02/2024] Open
Abstract
Metabolomics as a research field and a set of techniques is to study the entire small molecules in biological samples. Metabolomics is emerging as a powerful tool generally for precision medicine. Particularly, integration of microbiome and metabolome has revealed the mechanism and functionality of microbiome in human health and disease. However, metabolomics data are very complicated. Preprocessing/pretreating and normalizing procedures on metabolomics data are usually required before statistical analysis. In this review article, we comprehensively review various methods that are used to preprocess and pretreat metabolomics data, including MS-based data and NMR -based data preprocessing, dealing with zero and/or missing values and detecting outliers, data normalization, data centering and scaling, data transformation. We discuss the advantages and limitations of each method. The choice for a suitable preprocessing method is determined by the biological hypothesis, the characteristics of the data set, and the selected statistical data analysis method. We then provide the perspective of their applications in the microbiome and metabolome research.
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Affiliation(s)
- Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, Department of Microbiology/Immunology, UIC Cancer Center, University of Illinois Chicago, Jesse Brown VA Medical Center Chicago (537), Chicago, IL 60612, USA
| | - Yinglin Xia
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois Chicago, Chicago, IL 60612, USA
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2
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Lorente JA, Nin N, Villa P, Vasco D, Miguel-Coello AB, Rodriguez I, Herrero R, Peñuelas O, Ruiz-Cabello J, Izquierdo-Garcia JL. Metabolomic diferences between COVID-19 and H1N1 influenza induced ARDS. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2021; 25:390. [PMID: 34781986 PMCID: PMC8591432 DOI: 10.1186/s13054-021-03810-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a type of respiratory failure characterized by lung inflammation and pulmonary edema. Coronavirus disease 2019 (COVID-19) is associated with ARDS in the more severe cases. This study aimed to compare the specificity of the metabolic alterations induced by COVID-19 or Influenza A pneumonia (IAP) in ARDS. METHODS Eighteen patients with ARDS due to COVID-19 and twenty patients with ARDS due to IAP, admitted to the intensive care unit. ARDS was defined as in the American-European Consensus Conference. As compared with patients with COVID-19, patients with IAP were younger and received more often noradrenaline to maintain a mean arterial pressure > 65 mm Hg. Serum samples were analyzed by Nuclear Magnetic Resonance Spectroscopy. Multivariate Statistical Analyses were used to identify metabolic differences between groups. Metabolic pathway analysis was performed to identify the most relevant pathways involved in ARDS development. RESULTS ARDS due to COVID-19 or to IAP induces a different regulation of amino acids metabolism, lipid metabolism, glycolysis, and anaplerotic metabolism. COVID-19 causes a significant energy supply deficit that induces supplementary energy-generating pathways. In contrast, IAP patients suffer more marked inflammatory and oxidative stress responses. The classificatory model discriminated against the cause of pneumonia with a success rate of 100%. CONCLUSIONS Our findings support the concept that ARDS is associated with a characteristic metabolomic profile that may discriminate patients with ARDS of different etiologies, being a potential biomarker for the diagnosis, prognosis, and management of this condition.
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Affiliation(s)
- Jose Angel Lorente
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain.,Universidad Europea de Madrid, Madrid, Spain
| | | | - Palmira Villa
- Centro de Asistencia a La Investigación Bioimagen Complutense, Universidad Complutense de Madrid, Madrid, Spain
| | - Dovami Vasco
- Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain
| | - Ana B Miguel-Coello
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain
| | - Ignacio Rodriguez
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Química en CC. Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Raquel Herrero
- Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain
| | - Oscar Peñuelas
- Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain
| | - Jesús Ruiz-Cabello
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain.,Departamento de Química en CC. Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose L Izquierdo-Garcia
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain. .,Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo Juan XXIII, 1, Madrid, Spain. .,Departamento de Química en CC. Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.
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3
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Changes in the Salivary Metabolic Profile of Generalized Periodontitis Patients after Non-surgical Periodontal Therapy: A Metabolomic Analysis Using Nuclear Magnetic Resonance Spectroscopy. J Clin Med 2020; 9:jcm9123977. [PMID: 33302593 PMCID: PMC7763572 DOI: 10.3390/jcm9123977] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022] Open
Abstract
Pattern analysis of the salivary metabolic profile has been proven accurate in discriminating between generalized periodontitis (GP) patients and healthy individuals (HI), as this disease modifies the salivary concentrations of specific metabolites. Due to the scarcity of data from previous studies, this study aimed to evaluate if non-surgical periodontal therapy (NST) could affect the metabolomic profile in GP patients’ saliva and if it compares to that of HI. Unstimulated salivary samples were collected from 11 HI and 12 GP patients before and 3 months after NST. Nuclear Magnetic Resonance (NMR) spectroscopy, followed by a supervised multivariate statistical approach on entire saliva spectra and partial least square (PLS) discriminant analysis, were performed to obtain metabolic profiles. In the GP group, periodontal treatment improved all clinical parameters, but not all the diseased sites were eradicated. PLS revealed an accuracy of 100% in distinguishing between metabolic profiles of GP patients before and after NST. Orthogonal projection to latent structure was able to discriminate between the three groups of subjects with an accuracy of 85.6%. However, the post-NST metabolic profile of GP patients could not be completely assimilated to that of HI. Although NST may produce significant changes in the metabolic profile, GP patients maintained a distinctive fingerprint compared to HI.
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Rodriguez-Martinez A, Ayala R, Posma JM, Harvey N, Jiménez B, Sonomura K, Sato TA, Matsuda F, Zalloua P, Gauguier D, Nicholson JK, Dumas ME. pJRES Binning Algorithm (JBA): a new method to facilitate the recovery of metabolic information from pJRES 1H NMR spectra. Bioinformatics 2020; 35:1916-1922. [PMID: 30351417 PMCID: PMC6546129 DOI: 10.1093/bioinformatics/bty837] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/24/2018] [Accepted: 10/22/2018] [Indexed: 01/21/2023] Open
Abstract
Motivation Data processing is a key bottleneck for 1H NMR-based metabolic profiling of complex biological mixtures, such as biofluids. These spectra typically contain several thousands of signals, corresponding to possibly few hundreds of metabolites. A number of binning-based methods have been proposed to reduce the dimensionality of 1 D 1H NMR datasets, including statistical recoupling of variables (SRV). Here, we introduce a new binning method, named JBA (“pJRES Binning Algorithm”), which aims to extend the applicability of SRV to pJRES spectra. Results The performance of JBA is comprehensively evaluated using 617 plasma 1H NMR spectra from the FGENTCARD cohort. The results presented here show that JBA exhibits higher sensitivity than SRV to detect peaks from low-abundance metabolites. In addition, JBA allows a more efficient removal of spectral variables corresponding to pure electronic noise, and this has a positive impact on multivariate model building Availability and implementation The algorithm is implemented using the MWASTools R/Bioconductor package. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrea Rodriguez-Martinez
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Epidemiology and Biostatistics School of Public Health, Imperial College London, London, UK
| | - Rafael Ayala
- Section of Structural Biology, Department of Medicine, Shimadzu Corporation, Kyoto, Japan
| | - Joram M Posma
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Epidemiology and Biostatistics School of Public Health, Imperial College London, London, UK
| | - Nikita Harvey
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Beatriz Jiménez
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Kazuhiro Sonomura
- Life Science Research Center, Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Taka-Aki Sato
- Life Science Research Center, Technology Research Laboratory, Shimadzu Corporation, Kyoto, Japan.,Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Pierre Zalloua
- School of Medicine, Lebanese American University, Beirut, Lebanon
| | - Dominique Gauguier
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan.,Cordeliers Research Centre, INSERM UMR_S, Paris, France
| | - Jeremy K Nicholson
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Marc-Emmanuel Dumas
- Division of Integrative Systems Medicine and Digestive Diseases, Department of Surgery and Cancer, Imperial College London, London, UK
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Basoglu A, Baspinar N, Tenori L, Licari C, Gulersoy E. Nuclear magnetic resonance (NMR)-based metabolome profile evaluation in dairy cows with and without displaced abomasum. Vet Q 2020; 40:1-15. [PMID: 31858882 PMCID: PMC6968509 DOI: 10.1080/01652176.2019.1707907] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background Displaced abomasum (DA) is a condition of dairy cows that severely impacts animal welfare and causes huge economic losses. Objective To assess the metabolic status of the disease using metabolomics in serum, urine and liver samples aimed at both water soluble and lipid soluble fractions. Methods Fifty Holstein multiparous cows with DA (42 left, 8 right) and 20 clinically healthy Holstein multiparous cows were used. Left DA was associated with concomitant ketosis in 19 animals and right in two. NMR-based metabolomics approach and hematological and biochemical analyses were performed. Statistical analysis was carried out on 1H-NMR data after they have been normalized using PQN method. Results Contrary to generated PCA score plots the OPLS-supervised method revealed differences between healthy animals and diseased ones based on serum water-soluble samples. While water and lipid soluble metabolites decreased in serum samples, fatty acid fractions and cholesterol were increased in liver samples in DA affected cows. The metabolomic and chemical profiles clearly revealed that cows with DA (especially with LDA) were at risk of ketosis and fatty liver. Serum hippuric acid concentration was significantly higher in healthy cows in comparison with LDA, whereas serum glycine concentration was reported higher for healthy when compared to RDA affected animals. Conclusion A biochemical network and pathway mapping revealed ‘valine, leucine and isoleucine biosynthesis’ and ‘phenylalanine, tyrosine and tryptophan biosynthesis’ as the most probable altered metabolic pathway in DA condition. Serum was advocated as the optimal biological matrix for the 1H-NMR analysis.
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Affiliation(s)
- Abdullah Basoglu
- Department of Internal Medicine, Faculty of Veterinary Medicine, Selcuk University, Selcuklu, Konya, Turkey
| | - Nuri Baspinar
- Department of Biochemistry, Faculty of Veterinary Medicine, Selcuk University, Selcuklu, Konya, Turkey
| | - Leonardo Tenori
- Interuniversitary Consortium for Magnetic Resonance of Metalloproteins (C.I.R.M.M.P.), Sesto Fiorentino (Florence), Italy
| | - Cristina Licari
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino (FI), Italy
| | - Erdem Gulersoy
- Department of Internal Medicine, Faculty of Veterinary Medicine, Selcuk University, Selcuklu, Konya, Turkey
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Vignoli A, Santini G, Tenori L, Macis G, Mores N, Macagno F, Pagano F, Higenbottam T, Luchinat C, Montuschi P. NMR-Based Metabolomics for the Assessment of Inhaled Pharmacotherapy in Chronic Obstructive Pulmonary Disease Patients. J Proteome Res 2019; 19:64-74. [PMID: 31621329 DOI: 10.1021/acs.jproteome.9b00345] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The aim of this proof-of-concept, pilot study was the evaluation of the effects of steroid administration and suspension of an inhaled corticosteroid (ICS)-long-acting β2-agonist (LABA) extrafine fixed dose combination (FDC) on metabolomic fingerprints in subjects with chronic obstructive pulmonary disease (COPD). We hypothesized that a comprehensive metabolomics approach discriminates across inhaled pharmacotherapies and that their effects on metabolomic signatures depend on the biological fluids analyzed. We performed metabolomics via nuclear magnetic resonance (NMR) spectroscopy in exhaled breath condensate (EBC), sputum supernatants, serum, and urine. Fourteen patients suffering from COPD who were on regular inhaled fluticasone propionate/salmeterol therapy (visit 1) were consecutively treated with 2-week beclomethasone dipropionate/formoterol (visit 2), 4-week formoterol alone (visit 3), and 4-week beclomethasone/formoterol (visit 4). The comprehensive NMR-based metabolomics approach showed differences across all pharmacotherapies and that different biofluids provided orthogonal information. Serum formate was lower at visits 1 versus 3 (P = 0.03), EBC formate was higher at visit 1 versus 4 (P = 0.03), and urinary 1-methyl-nicotinamide was lower at 3 versus 4 visit (P = 0.002). NMR-based metabolomics of different biofluids distinguishes across inhaled pharmacotherapies, provides complementary information on the effects of an extrafine ICS/LABA FDC on metabolic fingerprints in COPD patients, and might be useful for elucidating the ICS mechanism of action.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM) , University of Florence , Via Luigi Sacconi 6 , Sesto Fiorentino , Italy 50019.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP) , Piazza San Marco 4 , Florence , Italy 50121
| | - Giuseppe Santini
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168,Pharmacology Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM) , University of Florence , Via Luigi Sacconi 6 , Sesto Fiorentino , Italy 50019.,Department of Experimental and Clinical Medicine , University of Florence , Largo Brambilla 3 , Florence , Italy 50100
| | - Giuseppe Macis
- Imaging Diagnostics,University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Nadia Mores
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168,Pharmacology Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Francesco Macagno
- Respiratory Medicine Unit,University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
| | - Francesco Pagano
- Ageing Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168,Department of Internal Medicine and Geriatrics, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168
| | - Tim Higenbottam
- Faculty of Pharmaceutical Medicine , Royal College of Physicians , London NW1 4LE , United Kingdom
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM) , University of Florence , Via Luigi Sacconi 6 , Sesto Fiorentino , Italy 50019.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP) , Piazza San Marco 4 , Florence , Italy 50121.,Department of Chemistry "Ugo Schiff" , University of Florence , Via della Lastruccia 3 , Sesto Fiorentino , Italy 50019
| | - Paolo Montuschi
- Department of Pharmacology, Faculty of Medicine, Catholic University of the Sacred Heart, Largo F. Vito, 1, Rome, Italy 00168,Pharmacology Unit, University Hospital Agostino Gemelli Foundation, IRCCS, Largo Agostino Gemelli, 8, Rome, Italy 00168
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McCartney A, Vignoli A, Tenori L, Fornier M, Rossi L, Risi E, Luchinat C, Biganzoli L, Di Leo A. Metabolomic analysis of serum may refine 21-gene expression assay risk recurrence stratification. NPJ Breast Cancer 2019; 5:26. [PMID: 31482106 PMCID: PMC6715716 DOI: 10.1038/s41523-019-0123-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 08/06/2019] [Indexed: 12/11/2022] Open
Abstract
Despite recent refinements to the 21-gene g score, allowing a better identification of patients who may derive no benefit from the addition of adjuvant chemotherapy to that of endocrine therapy, patients with early breast cancer still stand to be over-treated in the setting of clinical and/or genomic uncertainty or discordance. Here we describe and demonstrate a potential approach of further refining the OncotypeDX risk score by metabolomic analysis of serum. In a clinical dataset (N = 87), the risk of recurrence was further sub-stratified by metabolomic signature, with an effective splitting of each Oncotype risk classification. A total of seven recurrences were recorded, with metabolomic analysis accurately predicting six of these. Contrastingly, the genomic risk score of the seven recurrences ranged across all three Oncotype classifications (one recurrence occurred in the "low"-risk group, three in the "intermediate" group and three in the "high"-risk group).
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Affiliation(s)
- Amelia McCartney
- “Sandro Pitigliani” Department of Medical Oncology, Prato Hospital, Via Suor Niccolina 20, Prato, Italy
| | - Alessia Vignoli
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Centre for Magnetic Resonance (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Leonardo Tenori
- Centre for Magnetic Resonance (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla 3, Florence, 50100 Italy
| | - Monica Fornier
- Breast Medicine Service, Memorial Sloan-Kettering Cancer Center, Weill Cornell Medical College, New York, NY USA
| | - Lorenzo Rossi
- “Sandro Pitigliani” Department of Medical Oncology, Prato Hospital, Via Suor Niccolina 20, Prato, Italy
- Institute of Oncology of Southern Switzerland (IOSI), Bellinzona, Switzerland
- Breast Unit of Southern Switzerland (CSSI), Lugano, Switzerland
| | - Emanuela Risi
- “Sandro Pitigliani” Department of Medical Oncology, Prato Hospital, Via Suor Niccolina 20, Prato, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), Via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Centre for Magnetic Resonance (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Italy
| | - Laura Biganzoli
- “Sandro Pitigliani” Department of Medical Oncology, Prato Hospital, Via Suor Niccolina 20, Prato, Italy
| | - Angelo Di Leo
- “Sandro Pitigliani” Department of Medical Oncology, Prato Hospital, Via Suor Niccolina 20, Prato, Italy
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Meoni G, Lorini S, Monti M, Madia F, Corti G, Luchinat C, Zignego AL, Tenori L, Gragnani L. The metabolic fingerprints of HCV and HBV infections studied by Nuclear Magnetic Resonance Spectroscopy. Sci Rep 2019; 9:4128. [PMID: 30858406 PMCID: PMC6412048 DOI: 10.1038/s41598-019-40028-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/23/2019] [Indexed: 02/06/2023] Open
Abstract
Few studies are available on metabolic changes in liver injuries and this is the first metabolomic study evaluating a group of HCV-positive patients, before and after viral eradication via DAA IFN-free regimens, using 1H-NMR to characterize and compare their serum fingerprints to naïve HBV-patients and healthy donors. The investigation clearly shows differences in the metabolomic profile of HCV patients before and after effective DAA treatment. Significant changes in metabolites levels in patients undergoing therapy suggest alterations in several metabolic pathways. It has been shown that 1H-NMR fingerprinting approach is an optimal technique in predicting the specific infection and the healthy status of studied subjects (Monte-Carlo cross validated accuracies: 86% in the HCV vs HBV model, 98.7% in the HCV vs HC model). Metabolite data collected support the hypothesis that the HCV virus induces glycolysis over oxidative phosphorylation in a similar manner to the Warburg effect in cancer, moreover our results have demonstrated a different action of the two viruses on cellular metabolism, corroborating the hypothesis that the metabolic perturbation on patients could be attributed to a direct role in viral infection. This metabolomic study has revealed some alteration in metabolites for the first time (2-oxoglutarate and 3-hydroxybutrate) concerning the HCV-infection model that could explain several extrahepatic manifestations associated with such an infection.
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Affiliation(s)
- Gaia Meoni
- University of Florence, Magnetic Resonance Center (CERM), Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Serena Lorini
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Monica Monti
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Francesco Madia
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Giampaolo Corti
- Careggi University Hospital, Infectious and Tropical Diseases Unit, Florence, 50134, Italy
| | - Claudio Luchinat
- University of Florence, Magnetic Resonance Center (CERM), Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy.,University of Florence, Department of Chemistry "Ugo Schiff", Sesto Fiorentino, 50019, Italy
| | - Anna Linda Zignego
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Leonardo Tenori
- University of Florence, Magnetic Resonance Center (CERM), Sesto Fiorentino, 50019, Italy. .,University of Florence, Department of Experimental and Clinical Medicine, Florence, 50134, Italy.
| | - Laura Gragnani
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy.
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Taherkhani A, Kalantari S, Oskouie AA, Nafar M, Taghizadeh M, Tabar K. Network analysis of membranous glomerulonephritis based on metabolomics data. Mol Med Rep 2018; 18:4197-4212. [PMID: 30221719 PMCID: PMC6172390 DOI: 10.3892/mmr.2018.9477] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Membranous glomerulonephritis (MGN) is one of the most frequent causes of nephrotic syndrome in adults. It is characterized by the thickening of the glomerular basement membrane in the renal tissue. The current diagnosis of MGN is based on renal biopsy and the detection of antibodies to the few podocyte antigens. Due to the limitations of the current diagnostic methods, including invasiveness and the lack of sensitivity of the current biomarkers, there is a requirement to identify more applicable biomarkers. The present study aimed to identify diagnostic metabolites that are involved in the development of the disease using topological features in the component‑reaction‑enzyme‑gene (CREG) network for MGN. Significant differential metabolites in MGN compared with healthy controls were identified using proton nuclear magnetic resonance and gas chromatography‑mass spectrometry techniques, and multivariate analysis. The CREG network for MGN was constructed, and metabolites with a high centrality and a striking fold‑change in patients, compared with healthy controls, were introduced as putative diagnostic biomarkers. In addition, a protein‑protein interaction (PPI) network, which was based on proteins associated with MGN, was built and analyzed using PPI analysis methods, including molecular complex detection and ClueGene Ontology. A total of 26 metabolites were identified as hub nodes in the CREG network, 13 of which had salient centrality and fold‑changes: Dopamine, carnosine, fumarate, nicotinamide D‑ribonucleotide, adenosine monophosphate, pyridoxal, deoxyguanosine triphosphate, L‑citrulline, nicotinamide, phenylalanine, deoxyuridine, tryptamine and succinate. A total of 13 subnetworks were identified using PPI analysis. In total, two of the clusters contained seed proteins (phenylalanine‑4‑hydroxlylase and cystathionine γ‑lyase) that were associated with MGN based on the CREG network. The following biological processes associated with MGN were identified using gene ontology analysis: 'Pyrimidine‑containing compound biosynthetic process', 'purine ribonucleoside metabolic process', 'nucleoside catabolic process', 'ribonucleoside metabolic process' and 'aromatic amino acid family metabolic process'. The results of the present study may be helpful in the diagnostic and therapeutic procedures of MGN. However, validation is required in the future.
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Affiliation(s)
- Amir Taherkhani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Shiva Kalantari
- Chronic Kidney Disease Research Center, Shahid Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran 1666663111, Iran
| | - Afsaneh Arefi Oskouie
- Department of Basic Science, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1971653313, Iran
| | - Mohsen Nafar
- Urology Nephrology Research Center, Shahid Labbafinejad Hospital, Shahid Beheshti University of Medical Sciences, Tehran 1666663111, Iran
| | - Mohammad Taghizadeh
- Bioinformatics Department, Institute of Biochemistry and Biophysics, Tehran University, Tehran 1417614411, Iran
| | - Koorosh Tabar
- Chemistry and Chemical Engineering Research Center of Iran, Tehran 1496813151, Iran
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Izquierdo-Garcia JL, Nin N, Cardinal-Fernandez P, Rojas Y, de Paula M, Granados R, Martínez-Caro L, Ruíz-Cabello J, Lorente JA. Identification of novel metabolomic biomarkers in an experimental model of septic acute kidney injury. Am J Physiol Renal Physiol 2018; 316:F54-F62. [PMID: 30379100 DOI: 10.1152/ajprenal.00315.2018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aim of this study is the identification of metabolomic biomarkers of sepsis and sepsis-induced acute kidney injury (AKI) in an experimental model. Pigs were anesthetized and monitored to measure mean arterial pressure (MAP), systemic blood flow (QT), mean pulmonary arterial pressure, renal artery blood flow (QRA), renal cortical blood flow (QRC), and urine output (UO). Sepsis was induced at t = 0 min by the administration of live Escherichia coli ( n = 6) or saline ( n = 8). At t = 300 min, animals were killed. Renal tissue, urine, and serum samples were analyzed by nuclear magnetic resonance (NMR) spectroscopy. Principal component analyses were performed on the processed NMR spectra to highlight kidney injury biomarkers. Sepsis was associated with decreased QT and MAP and decreased QRA, QRC, and UO. Creatinine serum concentration and neutrophil gelatinase-associated lipocalin (NGAL) serum and urine concentrations increased. NMR-based metabolomics analysis found metabolic differences between control and septic animals: 1) in kidney tissue, increased lactate and nicotinuric acid and decreased valine, aspartate, glucose, and threonine; 2) in urine, increased isovaleroglycine, aminoadipic acid, N-acetylglutamine, N-acetylaspartate, and ascorbic acid and decreased myoinositol and phenylacetylglycine; and 3) in serum, increased lactate, alanine, pyruvate, and glutamine and decreased valine, glucose, and betaine concentrations. The concentration of several metabolites altered in renal tissue and urine samples from septic animals showed a significant correlation with markers of AKI (i.e., creatinine and NGAL serum concentrations). NMR-based metabolomics is a potentially useful tool for biomarker identification of sepsis-induced AKI.
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Affiliation(s)
- Jose L Izquierdo-Garcia
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,CIC biomaGUNE, Donostia- San Sebastian , Spain
| | - Nicolás Nin
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,Hospital Español , Montevideo , Uruguay
| | - Pablo Cardinal-Fernandez
- Department of Emergency, Hospital Universitario HM Sanchinarro. Fundación de Investigación HM , Madrid , Spain
| | - Yenny Rojas
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,Department of Critical Care, Hospital Universitario de Getafe , Madrid , Spain
| | - Marta de Paula
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,Department of Critical Care, Hospital Universitario de Getafe , Madrid , Spain
| | - Rosario Granados
- Department of Critical Care, Hospital Universitario de Getafe , Madrid , Spain
| | - Leticia Martínez-Caro
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,Department of Critical Care, Hospital Universitario de Getafe , Madrid , Spain
| | - Jesús Ruíz-Cabello
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,CIC biomaGUNE, Donostia- San Sebastian , Spain.,Departamento de Química-Física II, Facultad de Farmacia, Universidad Complutense de Madrid , Madrid , Spain
| | - José A Lorente
- CIBER de Enfermedades Respiratorias, CIBERES, Madrid , Spain.,Department of Critical Care, Hospital Universitario de Getafe , Madrid , Spain.,Universidad Europea de Madrid , Madrid , Spain
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11
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Romano F, Meoni G, Manavella V, Baima G, Mariani GM, Cacciatore S, Tenori L, Aimetti M. Effect of non-surgical periodontal therapy on salivary metabolic fingerprint of generalized chronic periodontitis using nuclear magnetic resonance spectroscopy. Arch Oral Biol 2018; 97:208-214. [PMID: 30396039 DOI: 10.1016/j.archoralbio.2018.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/06/2018] [Accepted: 10/21/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Metabolomic analysis of saliva proved its accuracy in discriminating patients with generalized chronic periodontitis (GCP) from healthy subjects by identifying specific molecular signatures of the disease. There is lack of investigations concerning the effect of periodontal treatment on individual metabolic fingerprints. Therefore, the aim of this study was to determine whether non-surgical periodontal therapy could change salivary metabolomic profile in GCP to one more similar to periodontal health. DESIGN Unstimulated whole saliva of 32 controls and 19 GCP patients were obtained prior to and 3 months after conventional staged non-surgical periodontal therapy. Metabolic profiling was performed using Nuclear Magnetic Resonance (NMR) spectroscopy, followed by univariate and multivariate paired approaches to assess the changes introduced by the therapy. RESULTS In GCP group, periodontal treatment led to an improvement in all clinical parameters (p < 0.001). The accuracy of the multivariate model in discriminating the metabolomic profile of each GCP patient at two time points was 92.5%. Despite the almost perfect separation of the spectra in the metabolic space, the univariate analysis failed to identify significant variations in single metabolite content. The post-treatment metabolic profile of GCP patients could not be assimilated to that of healthy controls who exhibited different levels of lactate, pyruvate, valine, proline, tyrosine, and formate. CONCLUSIONS Based on these data, NMR-spectroscopic analysis revealed that, despite significant changes in the overall metabolomic fingerprint after non-surgical therapy, GCP patients maintained a distinctive metabolic profile compared to healthy individuals.
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Affiliation(s)
- Federica Romano
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
| | - Valeria Manavella
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giulia Maria Mariani
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Stefano Cacciatore
- Cancer Genomics Research Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Cape Town, South Africa
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Sesto Fiorentino, Italy
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy.
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12
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Romano F, Meoni G, Manavella V, Baima G, Tenori L, Cacciatore S, Aimetti M. Analysis of salivary phenotypes of generalized aggressive and chronic periodontitis through nuclear magnetic resonance-based metabolomics. J Periodontol 2018; 89:1452-1460. [PMID: 29877582 DOI: 10.1002/jper.18-0097] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Recent findings about the differential gene expression signature of periodontal lesions have raised the hypothesis of distinctive biological phenotypes expressed by generalized chronic periodontitis (GCP) and generalized aggressive periodontitis (GAgP) patients. Therefore, this cross-sectional investigation was planned, primarily, to determine the ability of nuclear magnetic resonance (NMR) spectroscopic analysis of unstimulated whole saliva to discriminate GCP and GAgP disease-specific metabolomic fingerprint and, secondarily, to assess potential metabolites discriminating periodontitis patients from periodontally healthy individuals (HI). METHODS NMR-metabolomics spectra were acquired from salivary samples of patients with a clinical diagnosis of GCP (n = 33) or GAgP (n = 28) and from HI (n = 39). The clustering of HI, GCP, and GAgP patients was achieved by using a combination of the Principal Component Analysis and Canonical Correlation Analysis on the NMR profiles. RESULTS These analyses revealed a significant predictive accuracy discriminating HI from GCP, and discriminating HI from GAgP patients (both 81%). In contrast, the GAgP and GCP saliva samples seem to belong to the same metabolic space (60% predictive accuracy). Significantly lower levels (P < 0.05) of pyruvate, N-acetyl groups and lactate and higher levels (P < 0.05) of proline, phenylalanine, and tyrosine were found in GCP and GAgP patients compared with HI. CONCLUSIONS Within the limitations of this study, CGP and GAgP metabolomic profiles were not unequivocally discriminated through a NMR-based spectroscopic analysis of saliva.
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Affiliation(s)
- Federica Romano
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Sesto Fiorentino, Italy
| | - Valeria Manavella
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Giacomo Baima
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Experimental and Clinical Medicine, University of Florence, Sesto Fiorentino, Italy
| | - Stefano Cacciatore
- Department of Surgery & Cancer, Imperial College, London, UK and International Centre for Genetic Engineering and Biotechnology, Cancer Genomics Group, Cape Town, South Africa
| | - Mario Aimetti
- Department of Surgical Sciences, C.I.R. Dental School, University of Turin, Turin, Italy
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13
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Chen J, Zhang C, Wu X, Ji H, Ma W, Wei S, Zhang L, Chen J. 1 H NMR-based nontargeted metabonomics study of plasma and urinary biochemical changes in Kudouzi treated rats. REVISTA BRASILEIRA DE FARMACOGNOSIA 2018. [DOI: 10.1016/j.bjp.2018.05.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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NMR-Based Plasma Metabolomics at Set Intervals in Newborn Dairy Calves with Severe Sepsis. Mediators Inflamm 2018; 2018:8016510. [PMID: 29743812 PMCID: PMC5883973 DOI: 10.1155/2018/8016510] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/09/2018] [Indexed: 12/13/2022] Open
Abstract
The aim of this first study was to reveal the new potential biomarkers by a metabolomics approach in severe septic calves. Sepsis is a common cause of morbidity and mortality in newborn dairy calves. The main challenges with the use of biomarkers of sepsis in domestic animals are their availability, cost, and time required to obtain a result. Metabolomics may offer the potential to identify biomarkers that define calf sepsis in terms of combined clinical, physiological, and pathobiological abnormalities. To our knowledge, this is the first study presenting an NMR- (nuclear magnetic resonance-) based plasma metabolomics at set intervals in neonatal septic calves. Twenty neonatal dairy calves with severe sepsis and ten healthy calves were used. Hematological and biochemical health profiles were gathered in plasma samples at set intervals. Similarly, NMR spectra were acquired. All diseased animals (except one) died after 72 hours. Clinical and laboratory results were in accordance with those of severe septic animals. Multivariate analysis on NMR plasma spectra proved to be an excellent tool for faster identification of calves with severe sepsis from healthy animals. The NMR-based metabolomic profile may contribute to the better understanding of severe sepsis in newborn calves.
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Costa Pereira J, Jarak I, Carvalho RA. Resolving NMR signals of short-chain fatty acid mixtures using unsupervised component analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2017; 55:936-943. [PMID: 28480544 DOI: 10.1002/mrc.4606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 04/28/2017] [Accepted: 05/03/2017] [Indexed: 06/07/2023]
Abstract
Nuclear magnetic resonance (NMR) is a very powerful instrumental technique suited to identify and characterize organic compounds. NMR has been successfully used in the analysis of complex biological and environmental samples; however, these applications are still rather limited. In this work, we describe unsupervised component analysis as a multivariate unsupervised method suited to identify the number of relevant NMR signal contributions and to deconvolve mixed signals into signal individual sources and respective contributions. Using this approach, we were able to advance further in the field of quantification of NMR spectra, and this methodology will help in the characterization of complex biological samples. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jorge Costa Pereira
- CQC, Department of Chemistry, University of Coimbra, P-3004 535, Coimbra, Portugal
| | - Ivana Jarak
- CICS-UBI, University of Beira Interior, 6201-506, Covilha, Portugal
- Centre for Functional Ecology, Faculty of Sciences and Technology, University of Coimbra, P-3000 456, Coimbra, Portugal
| | - Rui Albuquerque Carvalho
- Centre for Functional Ecology, Faculty of Sciences and Technology, University of Coimbra, P-3000 456, Coimbra, Portugal
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, P-3000 456, Coimbra, Portugal
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16
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Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD. Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Annu Rev Biochem 2017; 86:277-304. [PMID: 28654323 DOI: 10.1146/annurev-biochem-061516-044952] [Citation(s) in RCA: 261] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Metabolites are the small biological molecules involved in energy conversion and biosynthesis. Studying metabolism is inherently challenging due to metabolites' reactivity, structural diversity, and broad concentration range. Herein, we review the common pitfalls encountered in metabolomics and provide concrete guidelines for obtaining accurate metabolite measurements, focusing on water-soluble primary metabolites. We show how seemingly straightforward sample preparation methods can introduce systematic errors (e.g., owing to interconversion among metabolites) and how proper selection of quenching solvent (e.g., acidic acetonitrile:methanol:water) can mitigate such problems. We discuss the specific strengths, pitfalls, and best practices for each common analytical platform: liquid chromatography-mass spectrometry (LC-MS), gas chromatography-mass spectrometry (GC-MS), nuclear magnetic resonance (NMR), and enzyme assays. Together this information provides a pragmatic knowledge base for carrying out biologically informative metabolite measurements.
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Affiliation(s)
- Wenyun Lu
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Xiaoyang Su
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
| | - Matthias S Klein
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Science, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California, Davis, California 95616.,Department of Biochemistry, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Princeton, New Jersey 08544;
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17
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Le Moyec L, Triba MN, Nahon P, Bouchemal N, Hantz E, Goossens C, Amathieu R, Savarin P. Nuclear magnetic resonance metabolomics and human liver diseases: The principles and evidence associated with protein and carbohydrate metabolism. Biomed Rep 2017; 6:387-395. [PMID: 28413636 DOI: 10.3892/br.2017.868] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/16/2016] [Indexed: 12/12/2022] Open
Abstract
During the last decade, metabolomics has become widely used in the field of human diseases. Numerous studies have demonstrated that this is a powerful technique for improving the understanding, diagnosis and management of various types of liver disease, such as acute and chronic liver diseases, and liver transplantation. Nuclear magnetic resonance (NMR) spectroscopy is one of the two most commonly applied methods for metabolomics. The aim of the present review was to investigate the results from recent key publications focusing on aspects of protein and carbohydrate metabolism. The review includes existing procedures, which are currently used for NMR data acquisition and statistical analysis. In addition, notable results obtained by these studies on protein and carbohydrate metabolism concerning human liver diseases are presented.
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Affiliation(s)
- Laurence Le Moyec
- Unit of Integrative Biology for Exercise Adaptation (UBIAE), University of Evry Val d'Essonne, EA 7362, F-91025 Evry, France
| | - Mohamed N Triba
- University of Paris 13, Sorbonne Paris Cité, CSPBAT Laboratory, UMR 7244, CNRS, F-93000 Bobigny, France
| | - Pierre Nahon
- Department of Hepatology, AP-HP, Hôpital Jean Verdier, F-93140 Bondy, France.,University of Paris 13, Sorbonne Paris Cité, 'Team recognised by the League against Cancer', F-93206 Saint-Denis, France.,Inserm, UMR-1162, 'Functional Genomics of Solid Tumors', F-75000 Paris, France
| | - Nadia Bouchemal
- University of Paris 13, Sorbonne Paris Cité, CSPBAT Laboratory, UMR 7244, CNRS, F-93000 Bobigny, France
| | - Edith Hantz
- University of Paris 13, Sorbonne Paris Cité, CSPBAT Laboratory, UMR 7244, CNRS, F-93000 Bobigny, France
| | - Corentine Goossens
- University of Paris 13, Sorbonne Paris Cité, CSPBAT Laboratory, UMR 7244, CNRS, F-93000 Bobigny, France
| | - Roland Amathieu
- University of Paris 13, Sorbonne Paris Cité, CSPBAT Laboratory, UMR 7244, CNRS, F-93000 Bobigny, France.,Intensive Care Unit, AP-HP, Jean Verdier Hospital, AP-HP, Hôpital Jean Verdier, F-93140 Bondy, France
| | - Philippe Savarin
- University of Paris 13, Sorbonne Paris Cité, CSPBAT Laboratory, UMR 7244, CNRS, F-93000 Bobigny, France
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18
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Kanawaku Y, Hirakawa K, Koike K, Kanetake J, Ohno Y. Pattern recognition analysis of proton nuclear magnetic resonance spectra of postmortem cerebrospinal fluid from rats with drug-induced seizure or coma. Leg Med (Tokyo) 2017; 25:52-58. [PMID: 28457510 DOI: 10.1016/j.legalmed.2017.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/22/2016] [Accepted: 01/13/2017] [Indexed: 11/26/2022]
Abstract
Cerebrospinal fluid (CSF) is routinely subjected to gross evaluation in postmortem investigations; however, its use in chemical evaluations has not been fully realized. Analysis of nuclear magnetic resonance (NMR) spectra with pattern recognition methods was applied to CSF samples. Rats were treated with pentylenetetrazol (PTZ) to induce seizure or pentobarbital (PB) to induce coma, and postmortem CSF was collected after CO2 gas euthanization. Pattern recognition analysis of the NMR data was performed on individual postmortem CSF samples. The aim of this study was to determine if pattern recognition analysis of NMR data could be used to classify the rats according to their drug treatment. The applicability of NMR data with pattern recognition analysis using postmortem CSF was also assessed. Partial Least Squares-Discriminant Analysis (PLS-DA) score plots indicated that the PTZ, PB, and NS (control) groups were clustered and clearly separated. PLS-DA correlation loading plots showed respective spectral and category variances of 41% and 42% for factor 1, and 17% and 27% for factor 2. Thus, factors 1 and 2 together described 58% (41%+17%) and 69% (42%+27%) of the variation, respectively. NMR study of postmortem CSF has the potential to be utilized as both a novel forensic neurochemistry method and in the clinical setting.
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Affiliation(s)
- Yoshimasa Kanawaku
- Department of Legal Medicine, Nippon Medical School, 1-1-5 Sendagi Bunkyo-ku, Tokyo 113-8602, Japan.
| | - Keiko Hirakawa
- Department of Legal Medicine, Nippon Medical School, 1-1-5 Sendagi Bunkyo-ku, Tokyo 113-8602, Japan
| | - Kaoru Koike
- Department of Primary Care and Emergency Medicine, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Syogoin, Sakyo-ku, Kyoto City, Kyoto 606-8507, Japan
| | - Jun Kanetake
- Department of Forensic Medicine, National Defense Medical College, 3-2 Namiki, Tokorozawa, Saitama 359-8513, Japan
| | - Youkichi Ohno
- Department of Legal Medicine, Nippon Medical School, 1-1-5 Sendagi Bunkyo-ku, Tokyo 113-8602, Japan
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19
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Hart CD, Vignoli A, Tenori L, Uy GL, Van To T, Adebamowo C, Hossain SM, Biganzoli L, Risi E, Love RR, Luchinat C, Di Leo A. Serum Metabolomic Profiles Identify ER-Positive Early Breast Cancer Patients at Increased Risk of Disease Recurrence in a Multicenter Population. Clin Cancer Res 2017; 23:1422-1431. [PMID: 28082280 DOI: 10.1158/1078-0432.ccr-16-1153] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/24/2016] [Accepted: 08/28/2016] [Indexed: 11/16/2022]
Abstract
Purpose: Detecting signals of micrometastatic disease in patients with early breast cancer (EBC) could improve risk stratification and allow better tailoring of adjuvant therapies. We previously showed that postoperative serum metabolomic profiles were predictive of relapse in a single-center cohort of estrogen receptor (ER)-negative EBC patients. Here, we investigated this further using preoperative serum samples from ER-positive, premenopausal women with EBC who were enrolled in an international phase III trial.Experimental Design: Proton nuclear magnetic resonance (NMR) spectroscopy of 590 EBC samples (319 with relapse or ≥6 years clinical follow-up) and 109 metastatic breast cancer (MBC) samples was performed. A Random Forest (RF) classification model was built using a training set of 85 EBC and all MBC samples. The model was then applied to a test set of 234 EBC samples, and a risk of recurrence score was generated on the basis of the likelihood of the sample being misclassified as metastatic.Results: In the training set, the RF model separated EBC from MBC with a discrimination accuracy of 84.9%. In the test set, the RF recurrence risk score correlated with relapse, with an AUC of 0.747 in ROC analysis. Accuracy was maximized at 71.3% (sensitivity, 70.8%; specificity, 71.4%). The model performed independently of age, tumor size, grade, HER2 status and nodal status, and also of Adjuvant! Online risk of relapse score.Conclusions: In a multicenter group of EBC patients, we developed a model based on preoperative serum metabolomic profiles that was prognostic for disease recurrence, independent of traditional clinicopathologic risk factors. Clin Cancer Res; 23(6); 1422-31. ©2017 AACR.
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Affiliation(s)
- Christopher D Hart
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,FiorGen Foundation, Sesto Fiorentino, Italy
| | | | | | | | | | - Laura Biganzoli
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Emanuela Risi
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy
| | - Richard R Love
- The International Breast Cancer Research Foundation, Madison, Wisconsin
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Angelo Di Leo
- "Sandro Pitigliani" Medical Oncology Department, Hospital of Prato, Istituto Toscano Tumori, Prato, Italy.
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20
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Amberg A, Riefke B, Schlotterbeck G, Ross A, Senn H, Dieterle F, Keck M. NMR and MS Methods for Metabolomics. Methods Mol Biol 2017; 1641:229-258. [PMID: 28748468 DOI: 10.1007/978-1-4939-7172-5_13] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Metabolomics, also often referred as "metabolic profiling," is the systematic profiling of metabolites in biofluids or tissues of organisms and their temporal changes. In the last decade, metabolomics has become more and more popular in drug development, molecular medicine, and other biotechnology fields, since it profiles directly the phenotype and changes thereof in contrast to other "-omics" technologies. The increasing popularity of metabolomics has been possible only due to the enormous development in the technology and bioinformatics fields. In particular, the analytical technologies supporting metabolomics, i.e., NMR, UPLC-MS, and GC-MS, have evolved into sensitive and highly reproducible platforms allowing the determination of hundreds of metabolites in parallel. This chapter describes the best practices of metabolomics as seen today. All important steps of metabolic profiling in drug development and molecular medicine are described in great detail, starting from sample preparation to determining the measurement details of all analytical platforms, and finally to discussing the corresponding specific steps of data analysis.
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Affiliation(s)
| | - Björn Riefke
- Investigational Toxicology, Metabolic Profiling and Clinical Pathology, Bayer Pharma AG, Muellerstr. 178, Berlin, 13353, Germany.
| | - Götz Schlotterbeck
- School of Life Sciences, Institute for Chemistry and Bioanalytics, University of Applied Sciences, Northwestern Switzerland, Muttenz, Switzerland
| | - Alfred Ross
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Hans Senn
- Heythrop College UCL, Kensington Square, London W85HN, UK
| | - Frank Dieterle
- New Products and Medical, Near Patient Testing, Novartis, Basel, Switzerland
| | - Matthias Keck
- Analytical Development 1, Bayer Pharma AG, Wupperal, 42096, Germany
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Habchi B, Alves S, Paris A, Rutledge DN, Rathahao-Paris E. How to really perform high throughput metabolomic analyses efficiently? Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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22
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Dona AC, Kyriakides M, Scott F, Shephard EA, Varshavi D, Veselkov K, Everett JR. A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments. Comput Struct Biotechnol J 2016; 14:135-53. [PMID: 27087910 PMCID: PMC4821453 DOI: 10.1016/j.csbj.2016.02.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/16/2016] [Accepted: 02/23/2016] [Indexed: 01/14/2023] Open
Abstract
Metabonomics/metabolomics is an important science for the understanding of biological systems and the prediction of their behaviour, through the profiling of metabolites. Two technologies are routinely used in order to analyse metabolite profiles in biological fluids: nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS), the latter typically with hyphenation to a chromatography system such as liquid chromatography (LC), in a configuration known as LC-MS. With both NMR and MS-based detection technologies, the identification of the metabolites in the biological sample remains a significant obstacle and bottleneck. This article provides guidance on methods for metabolite identification in biological fluids using NMR spectroscopy, and is illustrated with examples from recent studies on mice.
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Affiliation(s)
- Anthony C Dona
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Michael Kyriakides
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Flora Scott
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Elizabeth A Shephard
- Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, United Kingdom
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent ME4 4TB, United Kingdom
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ, United Kingdom
| | - Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent ME4 4TB, United Kingdom
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Pechlivanis A, Papaioannou KG, Tsalis G, Saraslanidis P, Mougios V, Theodoridis GA. Monitoring the Response of the Human Urinary Metabolome to Brief Maximal Exercise by a Combination of RP-UPLC-MS and (1)H NMR Spectroscopy. J Proteome Res 2015; 14:4610-22. [PMID: 26419189 DOI: 10.1021/acs.jproteome.5b00470] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The delineation of exercise biochemistry by utilizing metabolic fingerprinting has become an established strategy. We present a combined RP-UPLC-MS and (1)H NMR strategy, supplemented by photometric assays, to monitor the response of the human urinary metabolome to short maximal exercise. Seventeen male volunteers performed two identical sprint sessions on separate days, consisting of three 80 m maximal runs. Using univariate and multivariate analyses, we followed the fluctuation of 37 metabolites at 1, 1.5, and 2 h postexercise. 2-Hydroxyisovalerate, 2-hydroxybutyrate, 2-oxoisocaproate, 3-methyl-2-oxovalerate, 3-hydroxyisobutyrate, 2-oxoisovalerate, 3-hydroxybutyrate, 2-hydroxyisobutyrate, alanine, pyruvate, and fumarate increased 1 h postexercise and then returned toward baseline. Lactate and acetate were higher than baseline at 1 and 1.5 h. Hypoxanthine and inosine remained above baseline throughout the postexercise period. Urate decreased at 1 h and increased at 1.5 h before returning to baseline. Valine, isoleucine, succinate, citrate, trimethylamine, trimethylamine N-oxide, tyrosine, and formate decreased at 1 h and/or 1.5 h postexercise and then returned to baseline. Creatinine gradually decreased over the sampling period. Glycine, 4-aminohippurate, and hippurate remained below baseline throughout the postexercise period. Our findings show that even one-half minute of maximal exercise elicited major perturbations in human metabolism, several of which persisted for at least 2 h.
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Affiliation(s)
- Alexandros Pechlivanis
- Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London , SW7 2AZ London, United Kingdom.,School of Chemistry, Aristotle University of Thessaloniki , 54124 Thessaloniki, Greece
| | - Konstantinos G Papaioannou
- School of Physical Education and Sport Science at Thessaloniki, Aristotle University of Thessaloniki , 54124 Thessaloniki, Greece
| | - George Tsalis
- School of Physical Education and Sport Science at Thessaloniki, Aristotle University of Thessaloniki , 54124 Thessaloniki, Greece
| | - Ploutarchos Saraslanidis
- School of Physical Education and Sport Science at Thessaloniki, Aristotle University of Thessaloniki , 54124 Thessaloniki, Greece
| | - Vassilis Mougios
- School of Physical Education and Sport Science at Thessaloniki, Aristotle University of Thessaloniki , 54124 Thessaloniki, Greece
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1H nuclear magnetic resonance-based extracellular metabolomic analysis of multidrug resistant Tca8113 oral squamous carcinoma cells. Oncol Lett 2015; 9:2551-2559. [PMID: 26137105 DOI: 10.3892/ol.2015.3128] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 03/19/2015] [Indexed: 01/13/2023] Open
Abstract
A major obstacle of successful chemotherapy is the development of multidrug resistance (MDR) in the cancer cells, which is difficult to reverse. Metabolomic analysis, an emerging approach that has been increasingly applied in various fields, is able to reflect the unique chemical fingerprints of specific cellular processes in an organism. The assessment of such metabolite changes can be used to identify novel therapeutic biomarkers. In the present study, 1H nuclear magnetic resonance (NMR) spectroscopy was used to analyze the extracellular metabolomic spectrum of the Tca8113 oral squamous carcinoma cell line, in which MDR was induced using the carboplatin (CBP) and pingyangmycin (PYM) chemotherapy drugs in vitro. The data were analyzed using the principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) methods. The results demonstrated that the extracellular metabolomic spectrum of metabolites such as glutamate, glycerophosphoethanol amine, α-Glucose and β-Glucose for the drug-induced Tca8113 cells was significantly different from the parental Tca8113 cell line. A number of biochemicals were also significantly different between the groups based on their NMR spectra, with drug-resistant cells presenting relatively higher levels of acetate and lower levels of lactate. In addition, a significantly higher peak was observed at δ 3.35 ppm in the spectrum of the PYM-induced Tca8113 cells. Therefore, 1H NMR-based metabolomic analysis has a high potential for monitoring the formation of MDR during clinical tumor chemotherapy in the future.
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Martin-Lorenzo M, Zubiri I, Maroto AS, Gonzalez-Calero L, Posada-Ayala M, de la Cuesta F, Mourino-Alvarez L, Lopez-Almodovar LF, Calvo-Bonacho E, Ruilope LM, Padial LR, Barderas MG, Vivanco F, Alvarez-Llamas G. KLK1 and ZG16B proteins and arginine-proline metabolism identified as novel targets to monitor atherosclerosis, acute coronary syndrome and recovery. Metabolomics 2015; 11:1056-1067. [PMID: 26413039 PMCID: PMC4573654 DOI: 10.1007/s11306-014-0761-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 12/03/2014] [Indexed: 01/03/2023]
Abstract
We pursued here the identification of specific signatures of proteins and metabolites in urine which respond to atherosclerosis development, acute event and/or recovery. An animal model (rabbit) of atherosclerosis was developed and molecules responding to atherosclerosis silent development were identified. Those molecules were investigated in human urine from patients suffering an acute coronary syndrome (ACS), at onset and discharge. Kallikrein1 (KLK1) and zymogen granule protein16B (ZG16B) proteins, and l-alanine, l-arabitol, scyllo-inositol, 2-hydroxyphenilacetic acid, 3-hydroxybutyric acid and N-acetylneuraminic acid metabolites were found altered in response to atherosclerosis progression and the acute event, composing a molecular panel related to cardiovascular risk. KLK1 and ZG16B together with 3-hydroxybutyric acid, putrescine and 1-methylhydantoin responded at onset but also showed normalized levels at discharge, constituting a molecular panel to monitor recovery. The observed decreased of KLK1 is in alignment with the protective mechanism of the kallikrein-kinin system. The connection between KLK1 and ZG16B shown by pathway analysis explains reduced levels of toll-like receptor 2 described in atherosclerosis. Metabolomic analysis revealed arginine and proline metabolism, glutathione metabolism and degradation of ketone bodies as the three main pathways altered. In conclusion, two novel urinary panels of proteins and metabolites are here for the first time shown related to atherosclerosis, ACS and patient's recovery.
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Affiliation(s)
- Marta Martin-Lorenzo
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
| | - Irene Zubiri
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
| | - Aroa S. Maroto
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
| | - Laura Gonzalez-Calero
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
| | - Maria Posada-Ayala
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
| | - Fernando de la Cuesta
- Department of Vascular Physiopathology, Hospital Nacional de Parapléjicos, SESCAM, Toledo, Spain
| | - Laura Mourino-Alvarez
- Department of Vascular Physiopathology, Hospital Nacional de Parapléjicos, SESCAM, Toledo, Spain
| | | | | | - Luis M. Ruilope
- Cardiovascular Risk and Hypertension, Instituto de Investigacion Hospital 12 de Octubre, Madrid, Spain
| | - Luis R. Padial
- Department of Cardiology, Hospital Virgen de la Salud, SESCAM, Toledo, Spain
| | - Maria G. Barderas
- Department of Vascular Physiopathology, Hospital Nacional de Parapléjicos, SESCAM, Toledo, Spain
| | - Fernando Vivanco
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
- Department of Biochemistry and Molecular Biology I, UCM, Madrid, Spain
| | - Gloria Alvarez-Llamas
- Department of Immunology, IIS-Fundacion Jimenez Diaz, UAM, REDinREN, Avenida Reyes Católicos 2, 28040 Madrid, Spain
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Dickens AM, Larkin JR, Griffin JL, Cavey A, Matthews L, Turner MR, Wilcock GK, Davis BG, Claridge TDW, Palace J, Anthony DC, Sibson NR. A type 2 biomarker separates relapsing-remitting from secondary progressive multiple sclerosis. Neurology 2014; 83:1492-9. [PMID: 25253748 PMCID: PMC4222850 DOI: 10.1212/wnl.0000000000000905] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 06/04/2014] [Indexed: 01/06/2023] Open
Abstract
OBJECTIVE We tested whether it is possible to differentiate relapsing-remitting (RR) from secondary progressive (SP) disease stages in patients with multiple sclerosis (MS) using a combination of nuclear magnetic resonance (NMR) metabolomics and partial least squares discriminant analysis (PLS-DA) of biofluids, which makes no assumptions on the underlying mechanisms of disease. METHODS Serum samples were obtained from patients with primary progressive MS (PPMS), SPMS, and RRMS; patients with other neurodegenerative conditions; and age-matched controls. Samples were analyzed by NMR and PLS-DA models were derived to separate disease groups. RESULTS The PLS-DA models for serum samples from patients with MS enabled reliable differentiation between RRMS and SPMS. This approach also identified significant differences between the metabolite profiles of each of the MS groups (PP, SP, and RR) and the healthy controls, as well as predicting disease group membership with high specificity and sensitivity. CONCLUSIONS NMR metabolomics analysis of serum is a sensitive and robust method for differentiating between different stages of MS, yielding diagnostic markers without a priori knowledge of disease pathogenesis. Critically, this study identified and validated a type II biomarker for the RR to SP transition in patients with MS. This approach may be of considerable benefit in categorizing patients for treatment and as an outcome measure in future clinical trials. CLASSIFICATION OF EVIDENCE This study provides Class II evidence that serum metabolite profiles accurately distinguish patients with different subtypes and stages of MS.
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Affiliation(s)
- Alex M Dickens
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - James R Larkin
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Julian L Griffin
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Ana Cavey
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Lucy Matthews
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Martin R Turner
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Gordon K Wilcock
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Benjamin G Davis
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Timothy D W Claridge
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Jacqueline Palace
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
| | - Daniel C Anthony
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK.
| | - Nicola R Sibson
- From the CR-UK/MRC Gray Institute for Radiation Oncology and Biology (A.M.D., J.R.L., N.R.S.), Department of Pharmacology (A.M.D., D.C.A.), Department of Chemistry (A.M.D., B.G.D., T.D.W.C.), Nuffield Department of Clinical Neurosciences (A.C., L.M., M.R.T.), and Nuffield Department of Medicine (G.K.W.), University of Oxford; and the Department of Biochemistry (J.L.G., J.P.), University of Cambridge, UK
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Tenori L, Oakman C, Morris PG, Gralka E, Turner N, Cappadona S, Fornier M, Hudis C, Norton L, Luchinat C, Di Leo A. Serum metabolomic profiles evaluated after surgery may identify patients with oestrogen receptor negative early breast cancer at increased risk of disease recurrence. Results from a retrospective study. Mol Oncol 2014; 9:128-39. [PMID: 25151299 DOI: 10.1016/j.molonc.2014.07.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/14/2014] [Accepted: 07/15/2014] [Indexed: 11/15/2022] Open
Abstract
PURPOSE Metabolomics is a global study of metabolites in biological samples. In this study we explored whether serum metabolomic spectra could distinguish between early and metastatic breast cancer patients and predict disease relapse. METHODS Serum samples were analysed from women with metastatic (n = 95) and predominantly oestrogen receptor (ER) negative early stage (n = 80) breast cancer using high resolution nuclear magnetic resonance spectroscopy. Multivariate statistics and a Random Forest classifier were used to create a prognostic model for disease relapse in early patients. RESULTS In the early breast cancer training set (n = 40), metabolomics correctly distinguished between early and metastatic disease in 83.7% of cases. A prognostic risk model predicted relapse with 90% sensitivity (95% CI 74.9-94.8%), 67% specificity (95% CI 63.0-73.4%) and 73% predictive accuracy (95% CI 70.6-74.8%). These results were reproduced in an independent early breast cancer set (n = 40), with 82% sensitivity, 72% specificity and 75% predictive accuracy. Disease relapse was associated with significantly lower levels of histidine (p = 0.0003) and higher levels of glucose (p = 0.01), and lipids (p = 0.0003), compared with patients with no relapse. CONCLUSIONS The performance of a serum metabolomic prognostic model for disease relapse in individuals with ER-negative early stage breast cancer is promising. A confirmation study is ongoing to better define the potential of metabolomics as a host and tumour-derived prognostic tool.
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Affiliation(s)
- Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; FiorGen Foundation, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Catherine Oakman
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| | - Patrick G Morris
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Ewa Gralka
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; FiorGen Foundation, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Natalie Turner
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| | - Silvia Cappadona
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
| | - Monica Fornier
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Cliff Hudis
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Larry Norton
- Breast Cancer Medicine Service, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
| | - Angelo Di Leo
- 'Sandro Pitigliani' Medical Oncology Department, Hospital of Prato, Via Suor Niccolina 20, Istituto Toscano Tumori, 59100 Prato, Italy.
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Hao J, Liebeke M, Astle W, De Iorio M, Bundy JG, Ebbels TMD. Bayesian deconvolution and quantification of metabolites in complex 1D NMR spectra using BATMAN. Nat Protoc 2014; 9:1416-27. [PMID: 24853927 DOI: 10.1038/nprot.2014.090] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Data processing for 1D NMR spectra is a key bottleneck for metabolomic and other complex-mixture studies, particularly where quantitative data on individual metabolites are required. We present a protocol for automated metabolite deconvolution and quantification from complex NMR spectra by using the Bayesian automated metabolite analyzer for NMR (BATMAN) R package. BATMAN models resonances on the basis of a user-controllable set of templates, each of which specifies the chemical shifts, J-couplings and relative peak intensities for a single metabolite. Peaks are allowed to shift position slightly between spectra, and peak widths are allowed to vary by user-specified amounts. NMR signals not captured by the templates are modeled non-parametrically by using wavelets. The protocol covers setting up user template libraries, optimizing algorithmic input parameters, improving prior information on peak positions, quality control and evaluation of outputs. The outputs include relative concentration estimates for named metabolites together with associated Bayesian uncertainty estimates, as well as the fit of the remainder of the spectrum using wavelets. Graphical diagnostics allow the user to examine the quality of the fit for multiple spectra simultaneously. This approach offers a workflow to analyze large numbers of spectra and is expected to be useful in a wide range of metabolomics studies.
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Affiliation(s)
- Jie Hao
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Manuel Liebeke
- 1] Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK. [2] Present address: Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - William Astle
- Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Maria De Iorio
- Department of Statistical Science, University College London, London, UK
| | - Jacob G Bundy
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Timothy M D Ebbels
- Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, UK
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Tang B, Ding J, Yang Y, Wu F, Song F. Systems biochemical responses of rats to Kansui and vinegar-processed Kansui exposure by integrated metabonomics. JOURNAL OF ETHNOPHARMACOLOGY 2014; 153:511-520. [PMID: 24631960 DOI: 10.1016/j.jep.2014.03.022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 01/15/2014] [Accepted: 03/09/2014] [Indexed: 06/03/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The dried root of Kansui (Euphorbia kansui L.) is an effective and commonly used traditional Chinese medicine. Even so, Kansui cannot be satisfactorily applied clinically because of toxic side effects. In China, the most common Kansui-processing method uses vinegar to reduce its toxicity. The present study was designed to investigate the toxic effects caused by Kansui and evaluate detoxification of Kansui by vinegar processing of Kansui. MATERIALS AND METHOD Thirty male Sprague Dawley (SD) rats were randomly assigned to five groups of six rats. Two experimental groups were oral gavaged with 7.875 and 15.75 g Kansui/kg body weight, two treated with 7.875 and 15.75 g VP-Kansui/kg body weight for 14 d, and the control group concurrently subjected to oral gavage with only distilled water. On day 14, plasma, liver and kidney tissues were collected from all rats for biochemistry assessments, histopathological examination, and NMR analyses. RESULTS The metabonome of rats treated with Kansui and vinegar-processed (VP-) Kansui was found to differ from that of controls. In liver extracts, the variational metabolites included elevated concentrations of isoleucine, leucine, valine, glutamate, and phenylalanine, with decreased taurine, glucose, and glycogen. However, changes in lysine, methionine, choline, phosphorylcholine, and tyrosine were only observed in Kansui-treated rats. In kidney extracts, prominent changes included elevations in isoleucine, leucine, valine, methionine, creatine/creatinine, and phenylalanine as well as decreased glutamine. Only Kansui treatment induced variations in alanine, lysine, acetate, choline, and phosphorylcholine. CONCLUSION Perturbations in endogenous metabolites induced by Kansui correlated with disturbances in glycolysis and amino acid and lipid metabolism, while biochemical pathway disorders caused by VP-Kansui only involved glycolysis and amino acid metabolism. All results were confirmed by histopathological examination of liver and kidney tissues and clinical biochemistry analyses.
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Affiliation(s)
- Bingwen Tang
- Department of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Jiajia Ding
- Department of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Yongxia Yang
- Department of Basic Course, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
| | - Fuhai Wu
- School of Public Health, Guangdong Key Laboratory of Molecular Epidemiology, Guangdong Pharmaceutical University, Guangzhou 510310, PR China.
| | - Fenyun Song
- Department of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China.
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Orr DJ, Barding GA, Tolley CE, Hicks GR, Raikhel NV, Larive CK. 1H NMR-based metabolomics methods for chemical genomics experiments. Methods Mol Biol 2014; 1056:225-39. [PMID: 24306877 DOI: 10.1007/978-1-62703-592-7_21] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Metabolomics and chemical genomics studies can each provide unique insights into plant biology. Although a variety of analytical techniques can be used for the interrogation of plant systems, nuclear magnetic resonance (NMR) provides unbiased characterization of abundant metabolites. An example methodology is provided for probing the metabolism of Arabidopsis thaliana in a chemical genomics experiment including methods for tissue treatment, tissue collection, metabolite extraction, and methods to minimize variance in biological and technical sample replicates. Additionally, considerations and methods for data analysis, including multivariate statistics, univariate statistics, and data interpretation are included. The process is illustrated by examining the metabolic effects of chemical treatment of Arabidopsis with Sortin 1, also known as vacuolar protein sorting inhibitor 1. Sortin 1 was applied to Arabidopsis seedlings to examine metabolic effects in a chemical genomics experiment and to demonstrate the utility of metabolomics in conjunction with other "omics" techniques.
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Affiliation(s)
- Daniel J Orr
- Department of Chemistry, University of California, Riverside, Riverside, CA, USA
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A machine-learned predictor of colonic polyps based on urinary metabolomics. BIOMED RESEARCH INTERNATIONAL 2013; 2013:303982. [PMID: 24307992 PMCID: PMC3838851 DOI: 10.1155/2013/303982] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Revised: 08/29/2013] [Accepted: 09/08/2013] [Indexed: 12/15/2022]
Abstract
We report an automated diagnostic test that uses the NMR spectrum of a single spot urine sample to accurately distinguish patients who require a colonoscopy from those who do not. Moreover, our approach can be adjusted to tradeoff between sensitivity and specificity. We developed our system using a group of 988 patients (633 normal and 355 who required colonoscopy) who were all at average or above-average risk for developing colorectal cancer. We obtained a metabolic profile of each subject, based on the urine samples collected from these subjects, analyzed via 1H-NMR and quantified using targeted profiling. Each subject then underwent a colonoscopy, the gold standard to determine whether he/she actually had an adenomatous polyp, a precursor to colorectal cancer. The metabolic profiles, colonoscopy outcomes, and medical histories were then analysed using machine learning to create a classifier that could predict whether a future patient requires a colonoscopy. Our empirical studies show that this classifier has a sensitivity of 64% and a specificity of 65% and, unlike the current fecal tests, allows the administrators of the test to adjust the tradeoff between the two.
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Savorani F, Rasmussen MA, Mikkelsen MS, Engelsen SB. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics. Food Res Int 2013. [DOI: 10.1016/j.foodres.2012.12.025] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xie G, Li X, Li H, Jia W. Toward personalized nutrition: comprehensive phytoprofiling and metabotyping. J Proteome Res 2013; 12:1547-59. [PMID: 23421653 DOI: 10.1021/pr301222b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nutrition research is increasingly concerned with the complex interactions between multicomponent dietary ingredients and the human metabolic regulatory system. The substantiation of nutritional health benefits is challenged by the intrinsic complexity of macro- and micronutrients and individualized human metabolic responses. Metabonomics, uniquely suited to assess metabolic responses to deficiencies or excesses of nutrients, is used to characterize the metabolic phenotype of individuals integrating genetic polymorphisms, metabolic interactions with commensal and symbiotic partners such as gut microbiota, as well as environmental and behavioral factors including dietary preferences. The two profiling strategies, metabolic phenotyping (metabotyping) and phytochemical profiling (phytoprofiling), greatly facilitate the measurement of these important health determinants and the discovery of new biomarkers associated with nutritional requirements and specific phytochemical interventions. This paper presents an overview of the applications of these two profiling approaches for personalized nutrition research, with a focus on recent advances in the study of the role of phytochemicals in regulating the human or animal metabolic regulatory system.
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Affiliation(s)
- Guoxiang Xie
- Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital , Shanghai 200233, China
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Fedele TA, Galdos-Riveros AC, Jose de Farias e Melo H, Magalhães A, Maria DA. Prognostic relationship of metabolic profile obtained of melanoma B16F10. Biomed Pharmacother 2013; 67:146-56. [DOI: 10.1016/j.biopha.2012.10.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 10/23/2012] [Indexed: 12/20/2022] Open
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Abd Rahman S, Schirra HJ, Lichanska AM, Huynh T, Leong GM. Urine metabonomic profiling of a female adolescent with PIT-1 mutation before and during growth hormone therapy: insights into the metabolic effects of growth hormone. Growth Horm IGF Res 2013; 23:29-36. [PMID: 23380306 DOI: 10.1016/j.ghir.2012.12.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 12/02/2012] [Accepted: 12/08/2012] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Growth hormone (GH) is a protein hormone with important roles in growth and metabolism. The objective of this study was to investigate the metabolism of a human subject with severe GH deficiency (GHD) due to a PIT-1 gene mutation and the metabolic effects of GH therapy using Nuclear Magnetic Resonance (NMR)-based metabonomics. NMR-based metabonomics is a platform that allows the metabolic profile of biological fluids such as urine to be recorded, and any alterations in the profile modulated by GH can potentially be detected. DESIGN Urine samples were collected from a female subject with severe GHD before, during and after GH therapy, and from healthy age- and sex-matched controls and analysed with NMR-based metabonomics. SETTING The samples were collected at a hospital and the study was performed at a research facility. PARTICIPANTS We studied a 17 year old female adolescent with severe GHD secondary to PIT-1 gene mutation who had reached final adult height and who had ceased GH therapy for over 3 years. The subject was subsequently followed for 5 years with and without GH therapy. Twelve healthy age-matched female subjects acted as control subjects. INTERVENTION The GH-deficient subject re-commenced GH therapy at a dose of 1 mg/day to normalise serum IGF-1 levels. MAIN OUTCOME MEASURES Urine metabolic profiles were recorded using NMR spectroscopy and analysed with multivariate statistics to distinguish the profiles at different time points and identify significant metabolites affected by GH therapy. RESULTS NMR-based metabonomics revealed that the metabolic profile of the GH-deficient subject altered with GH therapy and that her profile was different from healthy controls before, and during withdrawal of GH therapy. CONCLUSION This study illustrates the potential use of NMR-based metabonomics for monitoring the effects of GH therapy on metabolism by profiling the urine of GH-deficient subjects. Further controlled studies in larger numbers of GH-deficient subjects are required to determine the clinical benefits of NMR-based metabonomics in subjects receiving GH therapy.
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Affiliation(s)
- Shaffinaz Abd Rahman
- The University of Queensland, Obesity Research Centre, Institute for Molecular Bioscience, St. Lucia, Queensland 4072, Australia
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Hu JZ, Rommereim DN, Minard KR, Woodstock A, Harrer BJ, Wind RA, Phipps RP, Sime PJ. Metabolomics in lung inflammation:a high-resolution (1)h NMR study of mice exposedto silica dust. Toxicol Mech Methods 2012; 18:385-98. [PMID: 20020862 DOI: 10.1080/15376510701611032] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
ABSTRACT Here we report the first (1)H NMR metabolomics studies on excised lungs and bronchoalveolar lavage fluid (BALF) from mice exposed to crystalline silica. High-resolution (1)H NMR metabolic profiling on intact excised lungs was performed using slow magic angle sample spinning (slow-MAS) (1)H PASS (phase-altered spinning sidebands) at a sample spinning rate of 80 Hz. Metabolic profiling on BALF was completed using fast magic angle spinning at 2 kHz. Major findings are that the relative concentrations of choline, phosphocholine (PC), and glycerophosphocholine (GPC) were statistically significantly increased in silica-exposed mice compared to sham controls, indicating an altered membrane choline phospholipids metabolism (MCPM). The relative concentrations of glycogen/glucose, lactate, and creatine were also statistically significantly increased in mice exposed to silica dust, suggesting that cellular energy pathways were affected by silica dust. Elevated levels of glycine, lysine, glutamate, proline, and 4-hydroxyproline were also increased in exposed mice, suggesting the activation of a collagen pathway. Furthermore, metabolic profiles in mice exposed to silica dust were found to be spatially heterogeneous, consistent with regional inflammation revealed by in vivo magnetic resonance imaging (MRI).
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Affiliation(s)
- Jian Zhi Hu
- Pacific Northwest National Laboratory, Richland, WA
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NMR and pattern recognition methods in metabolomics: From data acquisition to biomarker discovery: A review. Anal Chim Acta 2012; 750:82-97. [DOI: 10.1016/j.aca.2012.05.049] [Citation(s) in RCA: 303] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/25/2012] [Accepted: 05/26/2012] [Indexed: 01/09/2023]
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Zhou XM, He CC, Liu YM, Zhao Y, Zhao D, Du Y, Zheng WY, Li JX. Metabonomic classification and detection of small molecule biomarkers of malignant pleural effusions. Anal Bioanal Chem 2012; 404:3123-33. [PMID: 23052876 DOI: 10.1007/s00216-012-6432-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/01/2012] [Accepted: 09/18/2012] [Indexed: 02/03/2023]
Abstract
To date, most research has been focused on the benign molecules in pleural effusions, and diagnosis of malignant ones still remains challenging. In the present study, targeting the small molecules as potential biomarkers to predict the malignancy of the effusions, the metabolic profiles of 81 clinical pleural effusions (41 malignant effusions from lung cancer and 40 benign ones) were investigated through a NMR-based metabonomic approach. In (1)H NMR analysis, a total of ten small molecules in the effusions were simultaneously determined. Significantly higher mean values of valine, lactate, and alanine and markedly lower signal intensities of acetoacetate, trimethylamine-N-oxide, and α- and β-glucose were observed in malignant pleural effusions compared with those in benign ones. DFA modeling of NMR spectra subjected to a validation allowed the malignant effusions to be discriminated from benign ones in both training and validation groups. Currently, the conventional clinical analyses on chemical constituents in effusions could not provide a reliable prediction of malignancy of the effusions; the present results revealed that the small molecules might serve as useful biomarkers for diagnosis of the effusions, and the present NMR-based metabonomic approach provided a valuable potential to rapidly and sensitively predict the malignancy of the pleural effusions.
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Affiliation(s)
- Xian-Mei Zhou
- Department of Respiratory Medicine, Affiliated Jiangsu Province Hospital of Traditional Chinese Medicine, Nanjing University of Traditional Chinese Medicine, Nanjing 210029, China.
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Roux A, Xu Y, Heilier JF, Olivier MF, Ezan E, Tabet JC, Junot C. Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer. Anal Chem 2012; 84:6429-37. [PMID: 22770225 DOI: 10.1021/ac300829f] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Metabolic profiles of biofluids obtained by atmospheric pressure ionization mass spectrometry-based technologies contain hundreds to thousands of features, most of them remaining unknown or at least not characterized in analytical systems. We report here on the annotation of the human adult urinary metabolome and metabolite identification from electrospray ionization mass spectrometry (ESI-MS)-based metabolomics data sets. Features of biological interest were first of all annotated using the ESI-MS database of the laboratory. They were also grouped, thanks to software tools, and annotated using public databases. Metabolite identification was achieved using two complementary approaches: (i) formal identification by matching chromatographic retention times, mass spectra, and also product ion spectra (if required) of metabolites to be characterized in biological data sets to those of reference compounds and (ii) putative identification from biological data thanks to MS/MS experiments for metabolites not available in our chemical library. By these means, 384 metabolites corresponding to 1484 annotated features (659 in negative ion mode and 825 in positive ion mode) were characterized in human urine samples. Of these metabolites, 192 and 66 were formally and putatively identified, respectively, and 54 are reported in human urine for the first time. These lists of features could be used by other laboratories to annotate their ESI-MS metabolomics data sets.
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Affiliation(s)
- Aurelie Roux
- CEA-Centre d'Etude de Saclay, Gif-sur-Yvette, France
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Sample preparation method to minimize chemical shift variability for NMR-based urinary metabonomics of genetically hypertensive rats. J Pharm Biomed Anal 2012; 66:339-44. [DOI: 10.1016/j.jpba.2012.02.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/21/2012] [Accepted: 02/24/2012] [Indexed: 11/21/2022]
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Kim JH, Park JD, Park SS, Hwang GS. Correlation analysis of human urinary metabolites related to gender and obesity using NMR-based metabolic profiling. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2012. [DOI: 10.6564/jkmrs.2012.16.1.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Astle W, De Iorio M, Richardson S, Stephens D, Ebbels T. A Bayesian Model of NMR Spectra for the Deconvolution and Quantification of Metabolites in Complex Biological Mixtures. J Am Stat Assoc 2012. [DOI: 10.1080/01621459.2012.695661] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Abstract
Infectious diseases can be difficult to cure, especially if the pathogen forms a biofilm. After decades of extensive research into the morphology, physiology and genomics of biofilm formation, attention has recently been directed toward the analysis of the cellular metabolome in order to understand the transformation of a planktonic cell to a biofilm. Metabolomics can play an invaluable role in enhancing our understanding of the underlying biological processes related to the structure, formation and antibiotic resistance of biofilms. A systematic view of metabolic pathways or processes responsible for regulating this 'social structure' of microorganisms may provide critical insights into biofilm-related drug resistance and lead to novel treatments. This review will discuss the development of NMR-based metabolomics as a technology to study medically relevant biofilms. Recent advancements from case studies reviewed in this manuscript have shown the potential of metabolomics to shed light on numerous biological problems related to biofilms.
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Affiliation(s)
- Bo Zhang
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, 722 Hamilton Hall, Lincoln, NE 68588-0304, USA
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Tang B, Ding J, Wu F, Chen L, Yang Y, Song F. 1H NMR-based metabonomics study of the urinary biochemical changes in Kansui treated rat. JOURNAL OF ETHNOPHARMACOLOGY 2012; 141:134-142. [PMID: 22406398 DOI: 10.1016/j.jep.2012.02.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 01/09/2012] [Accepted: 02/07/2012] [Indexed: 05/31/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The dried root of Kansui (Euphorbia kansui L.) is a commonly used and effective traditional Chinese medicine (TCM). AIM OF THE STUDY We combined the urinary metabolites alteration and traditional assays of Kansui-induced rats to discuss the mechanism of toxicity of Kansui. MATERIALS AND METHODS The Sprague-Dawley rats were dosed with 7.875g Kansui/kg weight and 15.75g Kansui/kg weight. Urine samples were collected at day -1 (before treatment), and days 7, 14 and 21 for NMR analysis. Plasma and liver and kidney tissues were collected at day 14 for biochemical assays and histopathological examination, respectively. RESULTS The metabonome of rats treated with Kansui differed markedly from that of the controls. This was confirmed by the histopathology of liver and kidney tissue and clinical biochemistry analysis. The toxicity of Kansui accumulated with dosing time, and persisted even when treatment was stopped. The corresponding biochemical pathways alterations included inhibited TCA cycle, increased anaerobic glycolysis, and perturbed amino acids metabolism. CONCLUSION The biochemical pathways disorder conjunction with histopathology changes provides new clues to evaluate the toxicity of Kansui from a systematic and holistic view.
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Affiliation(s)
- Bingwen Tang
- Department of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, PR China
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Investigating the effect of antioxidant treatment on the protective effect of preconditioning in anesthetized rabbits. J Cardiovasc Pharmacol 2012; 58:609-16. [PMID: 21822143 DOI: 10.1097/fjc.0b013e31822fc783] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Reactive oxygen and nitrogen species are critical in preconditioning (PC). We sought to determine the effect of N-2-mercaptopropionyl glycine (MPG) on infarct size and on the oxidative status. Rabbits were exposed to 30-minute regional ischemia of the heart, which was followed by 3-hour reperfusion: (1) a control group without further intervention, (2) a PC1 group that was subjected to one cycle of PC, (3) a PC4 group that was subjected to 4 cycles of PC, (4) an MPG group that was treated with MPG for 60 minutes, starting 10 minutes before reperfusion, (5) MPG-PC1, and (6) the MPG-PC4 groups that were treated with the same dose of MPG and with 1 or 4 cycles of PC, respectively. Blood samples were drawn and collected for metabonomic analysis. In another series of experiments, 6 groups respective to the described ones were subjected to 30-minute regional ischemia of the heart and 20 minutes of reperfusion, after which pieces of heart tissue were quickly excised for malondialdehyde, nitrotyrosine, and glutathione content assessment. All PC and MPG groups developed smaller infarct size compared with control (16.5% ± 3.9%, 13.7% ± 3.1%, 18.6% ± 5.0%, 9.7% ± 2.0%, 15.0% ± 2.8% vs. 48.05% ± 7.2%; P < 0.05). MPG did not prevent lipid peroxidation and nitrotyrosine formation but enhanced the glutathione content. PC and MPG induced similar nuclear magnetic resonance changes. Long MPG infusion reduces the infarct size without abolishing the effect of PC, providing novel insights into the activity of MPG in PC.
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Stretch C, Eastman T, Mandal R, Eisner R, Wishart DS, Mourtzakis M, Prado CMM, Damaraju S, Ball RO, Greiner R, Baracos VE. Prediction of skeletal muscle and fat mass in patients with advanced cancer using a metabolomic approach. J Nutr 2012; 142:14-21. [PMID: 22157537 DOI: 10.3945/jn.111.147751] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Urine and plasma metabolites originate from endogenous metabolic pathways in different organs and exogenous sources (diet). Urine and plasma were obtained from advanced cancer patients and investigated to determine if variations in lean and fat mass, dietary intake, and energy metabolism relate to variation in metabolite profiles. Patients (n = 55) recorded their diets for 3 d and after an overnight fast they were evaluated by DXA and indirect calorimetry. Metabolites were measured by NMR and direct injection MS. Three algorithms were used [partial least squares discriminant-analysis, support vector machines (SVM), and least absolute shrinkage and selection operator] to relate patients' plasma/urine metabolic profile with their dietary/physiological assessments. Leave-one-out cross-validation and permutation testing were conducted to determine statistical validity. None of the algorithms, using 63 urine metabolites, could learn to predict variations in individual's resting energy expenditure, respiratory quotient, or their intake of total energy, fat, sugar, or carbohydrate. Urine metabolites predicted appendicular lean tissue (skeletal muscle) with excellent cross-validation accuracy (98% using SVM). Total lean tissue correlated highly with appendicular muscle (Pearson r = 0.98; P < 0.0001) and gave similar cross-validation accuracies. Fat mass was effectively predicted using the 63 urine metabolites or the 143 plasma metabolites, exclusively. In conclusion, in this population, lean and fat mass variation could be effectively predicted using urinary metabolites, suggesting a potential role for metabolomics in body composition research. Furthermore, variation in lean and fat mass potentially confounds metabolomic studies attempting to characterize diet or disease conditions. Future studies should account or correct for such variation.
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Affiliation(s)
- Cynthia Stretch
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
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McKenzie JS, Donarski JA, Wilson JC, Charlton AJ. Analysis of complex mixtures using high-resolution nuclear magnetic resonance spectroscopy and chemometrics. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 59:336-59. [PMID: 22027342 DOI: 10.1016/j.pnmrs.2011.04.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 04/27/2011] [Indexed: 05/16/2023]
Affiliation(s)
- James S McKenzie
- The Food and Environment Research Agency, Sand Hutton, York YO41 1LZ, United Kingdom
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A metabolomic approach for diagnosis of experimental sepsis. Intensive Care Med 2011; 37:2023-32. [PMID: 21976186 DOI: 10.1007/s00134-011-2359-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 08/16/2011] [Indexed: 10/17/2022]
Abstract
BACKGROUND The search for reliable diagnostic biomarkers of sepsis remains necessary. Assessment of global metabolic profiling using quantitative nuclear magnetic resonance (NMR)-based metabolomics offers an attractive modern methodology for fast and comprehensive determination of multiple circulating metabolites and for defining the metabolic phenotype of sepsis. OBJECTIVE To develop a novel NMR-based metabolomic approach for diagnostic evaluation of sepsis. METHODS Male Sprague-Dawley rats (weight 325-375 g) underwent cecal ligation and puncture (n = 14, septic group) or sham procedure (n = 14, control group) and 24 h later were euthanized. Lung tissue, bronchoalveolar lavage (BAL) fluid, and serum samples were obtained for (1)H NMR and high-resolution magic-angle spinning analysis. Unsupervised principal components analysis was performed on the processed spectra, and a predictive model for diagnosis of sepsis was constructed using partial least-squares discriminant analysis. RESULTS NMR-based metabolic profiling discriminated characteristics between control and septic rats. Characteristic metabolites changed markedly in septic rats as compared with control rats: alanine, creatine, phosphoethanolamine, and myoinositol concentrations increased in lung tissue; creatine increased and myoinositol decreased in BAL fluid; and alanine, creatine, phosphoethanolamine, and acetoacetate increased whereas formate decreased in serum. A predictive model for diagnosis of sepsis using these metabolites classified cases with sensitivity and specificity of 100%. CONCLUSIONS NMR metabolomic analysis is a potentially useful technique for diagnosis of sepsis. The concentrations of metabolites involved in energy metabolism and in the inflammatory response change in this model of sepsis.
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Zhang H, Ding L, Fang X, Shi Z, Zhang Y, Chen H, Yan X, Dai J. Biological responses to perfluorododecanoic acid exposure in rat kidneys as determined by integrated proteomic and metabonomic studies. PLoS One 2011; 6:e20862. [PMID: 21677784 PMCID: PMC3108999 DOI: 10.1371/journal.pone.0020862] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 05/15/2011] [Indexed: 11/19/2022] Open
Abstract
Background Perfluorododecanoic acid (PFDoA) is a perfluorinated carboxylic chemical (PFC) that has broad applications and distribution in the environment. While many studies have focused on hepatotoxicity, immunotoxicity, and reproductive toxicity of PFCAs, few have investigated renal toxicity. Methodology/Principal Findings Here, we used comparative proteomic and metabonomic technologies to provide a global perspective on renal response to PFDoA. Male rats were exposed to 0, 0.05, 0.2, and 0.5 mg/kg/day of PFDoA for 110 days. After 2-D DIGE and MALDI TOF/TOF analysis, 79 differentially expressed proteins between the control and the PFDoA treated rats (0.2 and 0.5 mg-dosed groups) were successfully identified. These proteins were mainly involved in amino acid metabolism, the tricarboxylic acid cycle, gluconeogenesis, glycolysis, electron transport, and stress response. Nuclear magnetic resonance-based metabonomic analysis showed an increase in pyruvate, lactate, acetate, choline, and a variety of amino acids in the highest dose group. Furthermore, the profiles of free amino acids in the PFDoA treated groups were investigated quantitatively by high-coverage quantitative iTRAQ-LC MS/MS, which showed levels of sarcosine, asparagine, histidine, 1-methylhistidine, Ile, Leu, Val, Trp, Tyr, Phe, Cys, and Met increased markedly in the 0.5 mg dosed group, while homocitrulline, α-aminoadipic acid, β-alanine, and cystathionine decreased. Conclusion/Significance These observations provide evidence that disorders in glucose and amino acid metabolism may contribute to PFDoA nephrotoxicity. Additionally, α2u globulin may play an important role in protecting the kidneys from PFDoA toxicity.
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Affiliation(s)
- Hongxia Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lina Ding
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xuemei Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhimin Shi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yating Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hebing Chen
- National Center of Biomedical Analysis, Beijing, People's Republic of China
| | - Xianzhong Yan
- National Center of Biomedical Analysis, Beijing, People's Republic of China
- * E-mail: (XY); (JD)
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (XY); (JD)
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Rahmioglu N, Le Gall G, Heaton J, Kay KL, Smith NW, Colquhoun IJ, Ahmadi KR, Kemsley EK. Prediction of variability in CYP3A4 induction using a combined 1H NMR metabonomics and targeted UPLC-MS approach. J Proteome Res 2011; 10:2807-16. [PMID: 21491888 DOI: 10.1021/pr200077n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The activity of Cytochrome P450 3A4 (CYP3A4) enzyme is associated with many adverse or poor therapeutic responses to drugs. We used (1)H NMR-based metabonomics to identify a metabolic signature associated with variation in induced CYP3A4 activity. A total of 301 female twins, aged 45--84, participated in this study. Each volunteer was administered a potent inducer of CYP3A4 (St. John's Wort) for 14 days and the activity of CYP3A4 was quantified through the metabolism of the exogenously administered probe drug quinine sulfate (300 mg). Pre- and postintervention fasting urine samples were used to obtain metabolite profiles, using (1)H NMR spectroscopy, and were analyzed using UPLC--MS to obtain a marker for CYP3A4 induction, via the ratio of 3-hydroxyquinine to quinine (3OH-Q:Q). Multiple linear regression was used to build a predictive model for 3OH-Q:Q values based on the preintervention metabolite profiles. A combination of seven metabolites and seven covariates showed a strong (r = 0.62) relationship with log(3OH-Q:Q). This regression model demonstrated significant (p < 0.00001) predictive ability when applied to an independent validation set. Our results highlight the promise of metabonomics for predicting CYP3A4-mediated drug response.
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Affiliation(s)
- Nilufer Rahmioglu
- Department of Twin Research & Genetic Epidemiology, King's College London, London, United Kingdom
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