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Chen S, Zhou Z, Zhou Z, Liu Y, Sun S, Huang K, Yang Q, Guo Y. Non-targeted metabolomics revealed novel links between serum metabolites and primary ovarian insufficiency: a Mendelian randomization study. Front Endocrinol (Lausanne) 2024; 15:1307944. [PMID: 38737546 PMCID: PMC11082646 DOI: 10.3389/fendo.2024.1307944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/03/2024] [Indexed: 05/14/2024] Open
Abstract
Background Primary ovarian insufficiency (POI) is a common clinical endocrine disorder with a high heterogeneity in both endocrine hormones and etiological phenotypes. However, the etiology of POI remains unclear. Herein, we unraveled the causality of genetically determined metabolites (GDMs) on POI through Mendelian randomization (MR) study with the overarching goal of disclosing underlying mechanisms. Methods Genetic links with 486 metabolites were retrieved from GWAS data of 7824 European participants as exposures, while GWAS data concerning POI were utilized as the outcome. Via MR analysis, we selected inverse-variance weighted (IVW) method for primary analysis and several additional MR methods (MR-Egger, weighted median, and MR-PRESSO) for sensitivity analyses. MR-Egger intercept and Cochran's Q statistical analysis were conducted to assess potential heterogeneity and pleiotropy. In addition, genetic variations in the key target metabolite were scrutinized further. We conducted replication, meta-analysis, and linkage disequilibrium score regression (LDSC) to reinforce our findings. The MR Steiger test and reverse MR analysis were utilized to assess the robustness of genetic directionality. Furthermore, to deeply explore causality, we performed colocalization analysis and metabolic pathway analysis. Results Via IVW methods, our study identified 33 metabolites that might exert a causal effect on POI development. X-11437 showed a robustly significant relationship with POI in four MR analysis methods (P IVW=0.0119; P weighted-median =0.0145; PMR-Egger =0.0499; PMR-PRESSO =0.0248). Among the identified metabolites, N-acetylalanine emerged as the most significant in the primary MR analysis using IVW method, reinforcing its pivotal status as a serum biomarker indicative of an elevated POI risk with the most notable P-value (P IVW=0.0007; PMR-PRESSO =0.0022). Multiple analyses were implemented to further demonstrate the reliability and stability of our deduction of causality. Reverse MR analysis did not provide evidence for the causal effects of POI on 33 metabolites. Colocalization analysis revealed that some causal associations between metabolites and POI might be driven by shared genetic variants. Conclusion By incorporating genomics with metabolomics, this study sought to offer a comprehensive analysis in causal impact of serum metabolome phenotypes on risks of POI with implications for underlying mechanisms, disease screening and prevention.
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Affiliation(s)
- Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zhaokai Zhou
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Zihan Zhou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yu Liu
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shihao Sun
- Department of Breast Surgery, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Kai Huang
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qingling Yang
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yihong Guo
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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Almalki AH. Recent Analytical Advances for Decoding Metabolic Reprogramming in Lung Cancer. Metabolites 2023; 13:1037. [PMID: 37887362 PMCID: PMC10609104 DOI: 10.3390/metabo13101037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 10/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Metabolic reprogramming is a fundamental trait associated with lung cancer development that fuels tumor proliferation and survival. Monitoring such metabolic pathways and their intermediate metabolites can provide new avenues concerning treatment strategies, and the identification of prognostic biomarkers that could be utilized to monitor drug responses in clinical practice. In this review, recent trends in the analytical techniques used for metabolome mapping of lung cancer are capitalized. These techniques include nuclear magnetic resonance (NMR), gas chromatography-mass spectrometry (GC-MS), liquid chromatography-mass spectrometry (LC-MS), and imaging mass spectrometry (MSI). The advantages and limitations of the application of each technique for monitoring the metabolite class or type are also highlighted. Moreover, their potential applications in the analysis of many biological samples will be evaluated.
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Affiliation(s)
- Atiah H. Almalki
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
- Addiction and Neuroscience Research Unit, Health Science Campus, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
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Vignoli A, Risi E, McCartney A, Migliaccio I, Moretti E, Malorni L, Luchinat C, Biganzoli L, Tenori L. Precision Oncology via NMR-Based Metabolomics: A Review on Breast Cancer. Int J Mol Sci 2021; 22:ijms22094687. [PMID: 33925233 PMCID: PMC8124948 DOI: 10.3390/ijms22094687] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 04/23/2021] [Accepted: 04/27/2021] [Indexed: 12/22/2022] Open
Abstract
Precision oncology is an emerging approach in cancer care. It aims at selecting the optimal therapy for the right patient by considering each patient’s unique disease and individual health status. In the last years, it has become evident that breast cancer is an extremely heterogeneous disease, and therefore, patients need to be appropriately stratified to maximize survival and quality of life. Gene-expression tools have already positively assisted clinical decision making by estimating the risk of recurrence and the potential benefit from adjuvant chemotherapy. However, these approaches need refinement to further reduce the proportion of patients potentially exposed to unnecessary chemotherapy. Nuclear magnetic resonance (NMR) metabolomics has demonstrated to be an optimal approach for cancer research and has provided significant results in BC, in particular for prognostic and stratification purposes. In this review, we give an update on the status of NMR-based metabolomic studies for the biochemical characterization and stratification of breast cancer patients using different biospecimens (breast tissue, blood serum/plasma, and urine).
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Emanuela Risi
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Amelia McCartney
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
- School of Clinical Sciences, Monash University, Melbourne 3800, Australia
| | - Ilenia Migliaccio
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Erica Moretti
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Luca Malorni
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), 50019 Sesto Fiorentino, Italy
- Correspondence: ; Tel.: +39-055-457-4296
| | - Laura Biganzoli
- Department of Medical Oncology, New Hospital of Prato S. Stefano, 59100 Prato, Italy; (E.R.); (A.M.); (I.M.); (E.M.); (L.M.); (L.B.)
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, 50019 Sesto Fiorentino, Italy; (A.V.); (L.T.)
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (C.I.R.M.M.P.), 50019 Sesto Fiorentino, Italy
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LC–NMR for Natural Product Analysis: A Journey from an Academic Curiosity to a Robust Analytical Tool. SCI 2021. [DOI: 10.3390/sci3010006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Liquid chromatography (LC)–nuclear magnetic resonance (NMR) combines the advantage of the outstanding separation power of liquid chromatography (LC) and the superior structural elucidating capability of nuclear magnetic resonance (NMR). NMR has proved that it is a standout detector for LC by providing maximum structural information about plant originated extracts, particularly on the isolating ability of isomeric (same molecular formula) and/or isobaric (same molecular weight) compounds as compared to other detectors. The present review provides an overview of the developmental trends and application of LC–NMR in natural product analysis. The different LC–NMR operational modes are described, and how technical improvements assist in establishing this powerful technique as an important analytical tool in the analysis of complex plant-derived compounds is also highlighted. On-flow, stop-flow and loop-storage modes, as well as the new offline mode LC–solid phase extraction (SPE)–NMR and capillary LC (capLC)–NMR configurations which avoid the ingestion of expensive deuterated solvents throughout the experiment, are mentioned. Utilization of cryogenic probe and microprobe technologies, which are the other important promising approaches for guaranteeing sensitivity, are also described. Concluding remarks and future outlooks are also discussed.
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Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a major analytical method used in the growing field of metabolomics. Although NMR is relatively less sensitive than mass spectrometry, this analytical platform has numerous characteristics including its high reproducibility and quantitative abilities, its nonselective and noninvasive nature, and the ability to identify unknown metabolites in complex mixtures and trace the downstream products of isotope labeled substrates ex vivo, in vivo, or in vitro. Metabolomic analysis of highly complex biological mixtures has benefitted from the advances in both NMR data acquisition and analysis methods. Although metabolomics applications span a wide range of disciplines, a majority has focused on understanding, preventing, diagnosing, and managing human diseases. This chapter describes NMR-based methods relevant to the rapidly expanding metabolomics field.
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Barbosa Breda J, Croitor Sava A, Himmelreich U, Somers A, Matthys C, Rocha Sousa A, Vandewalle E, Stalmans I. Metabolomic profiling of aqueous humor from glaucoma patients - The metabolomics in surgical ophthalmological patients (MISO) study. Exp Eye Res 2020; 201:108268. [PMID: 33011236 DOI: 10.1016/j.exer.2020.108268] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/06/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022]
Abstract
Glaucoma is still a poorly understood disease with a clear need for new biomarkers to help in diagnosis and potentially offer new therapeutic targets. We aimed to determine if the metabolic profile of aqueous humor (AH) as determined by nuclear magnetic resonance (NMR) spectroscopy allows the distinction between primary open-angle glaucoma patients and control subjects, and to distinguish between high-tension (POAG) and normal-tension glaucoma (NTG). We analysed the AH of patients with POAG, NTG and control subjects (n = 30/group). 1H NMR spectra were acquired using a 400 MHz spectrometer. Principle component analysis (PCA), machine learning algorithms and descriptive statistics were applied to analyse the metabolic variance between groups, identify the spectral regions, and hereby potential metabolites that can act as biomarkers for glaucoma. According to PCA, fourteen regions of the NMR spectra were significant in explaining the metabolic variance between the glaucoma and control groups, with no differences found between POAG and NTG groups. These regions were further used in building a classifier for separating glaucoma from control patients, which achieved an AUC of 0.93. Peak integration was performed on these regions and a statistical analysis, after false discovery rate correction and adjustment for the different perioperative topical drug regimen, revealed that five of them were significantly different between groups. The glaucoma group showed a higher content in regions typical for betaine and taurine, possibly linked to neuroprotective mechanisms, and also a higher content in regions that are typical for glutamate, which can indicate damaged neurons and oxidative stress. These results show how aqueous humor metabolomics based on NMR spectroscopy can distinguish glaucoma patients from controls with a high accuracy. Further studies are needed to validate these results in order to incorporate them in clinical practice.
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Affiliation(s)
- João Barbosa Breda
- Research Group Ophthalmology, Department of Neurosciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium; Cardiovascular R&D Center, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200-319, Portugal; Department of Ophthalmology, Centro Hospitalar e Universitário São João, Alameda Prof. Hernâni Monteiro, Porto, 4200-319, Portugal.
| | - Anca Croitor Sava
- Biomedical MRI Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Leuven, 3000, Belgium; Molecular Small Animal Imaging Center (MoSAIC), KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Uwe Himmelreich
- Biomedical MRI Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, Leuven, 3000, Belgium; Molecular Small Animal Imaging Center (MoSAIC), KU Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Alix Somers
- Department of Ophthalmology, University Hospitals Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Christophe Matthys
- Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism, and Aging, KU Leuven, Herestraat 49, Leuven, 3000, Belgium; Clinical Nutrition, Department of Endocrinology, University Hospitals Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Amândio Rocha Sousa
- Cardiovascular R&D Center, Faculty of Medicine of the University of Porto, Alameda Prof. Hernâni Monteiro, Porto, 4200-319, Portugal; Department of Ophthalmology, Centro Hospitalar e Universitário São João, Alameda Prof. Hernâni Monteiro, Porto, 4200-319, Portugal
| | - Evelien Vandewalle
- Research Group Ophthalmology, Department of Neurosciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium; Department of Ophthalmology, University Hospitals Leuven, Herestraat 49, Leuven, 3000, Belgium
| | - Ingeborg Stalmans
- Research Group Ophthalmology, Department of Neurosciences, KU Leuven, Herestraat 49, Leuven, 3000, Belgium; Department of Ophthalmology, University Hospitals Leuven, Herestraat 49, Leuven, 3000, Belgium
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He Z, Luo Q, Liu Z, Gong L. Extensive evaluation of sample preparation workflow for gas chromatography-mass spectrometry-based plasma metabolomics and its application in rheumatoid arthritis. Anal Chim Acta 2020; 1131:136-145. [DOI: 10.1016/j.aca.2020.06.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 12/16/2022]
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Hallingström M, Barman M, Savolainen O, Viklund F, Kacerovsky M, Brunius C, Jacobsson B. Metabolomic profiles of mid-trimester amniotic fluid are not associated with subsequent spontaneous preterm delivery or gestational duration at delivery. J Matern Fetal Neonatal Med 2020; 35:2054-2062. [PMID: 32543931 DOI: 10.1080/14767058.2020.1777271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Spontaneous preterm delivery (<37 gestational weeks) has a multifactorial etiology with still incompletely identified pathways. Amniotic fluid is a biofluid with great potential for insights into the feto-maternal milieu. It is rich in metabolites, and metabolic consequences of inflammation is yet researched only to a limited extent. Metabolomic profiling provides opportunities to identify potential biomarkers of inflammatory conditioned pregnancy complications such as spontaneous preterm delivery. OBJECTIVE The aim of this study was to perform metabolomic profiling of amniotic fluid from uncomplicated singleton pregnancies in the mid-trimester to identify potential biomarkers associated with spontaneous preterm delivery and gestational duration at delivery. A secondary aim was to replicate previously reported mid-trimester amniotic fluid metabolic biomarkers of spontaneous preterm delivery in asymptomatic women. METHOD A nested case-control study was performed within a larger cohort study of asymptomatic pregnant women undergoing mid-trimester genetic amniocentesis at 14-19 gestational weeks in Gothenburg, Sweden. Medical records were used to obtain clinical data and delivery outcome variables. Amniotic fluid samples from women with a subsequent spontaneous preterm delivery (n = 37) were matched with amniotic fluid samples from women with a subsequent spontaneous delivery at term (n = 37). Amniotic fluid samples underwent untargeted metabolomic analyses using liquid chromatography-mass spectrometry. Multivariate random forest analyses were used for data processing. A secondary targeted analysis was performed, aiming to replicate previously reported mid-trimester amniotic fluid metabolic biomarkers in women with a subsequent spontaneous preterm delivery. RESULTS Multivariate analysis did not distinguish the samples from women with a subsequent spontaneous preterm delivery from those with a subsequent term delivery. Neither was the metabolic profile associated with gestational duration at delivery. Potential metabolic biomarker candidates were identified from four publications by two different research groups relating mid-trimester amniotic fluid metabolomes to spontaneous PTD, of which fifteen markers were included in the secondary analysis. None of these were replicated. CONCLUSIONS Metabolomic profiles of early mid-trimester amniotic fluid were not associated with spontaneous preterm delivery or gestational duration at delivery in this cohort.
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Affiliation(s)
- Maria Hallingström
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital/Östra, Gothenburg, Sweden.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Malin Barman
- Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Otto Savolainen
- Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Felicia Viklund
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital/Östra, Gothenburg, Sweden.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Marian Kacerovsky
- Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic.,Department of Obstetrics and Gynecology, Faculty of Medicine in Hradec Kralove, University Hospital Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Carl Brunius
- Food and Nutrition Science, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital/Östra, Gothenburg, Sweden.,Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden.,Division of Health Data and Digitalisation, Department of Genetics and Bioinformatics, Institute of Public Health, Oslo, Norway
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Gathungu RM, Kautz R, Kristal BS, Bird SS, Vouros P. The integration of LC-MS and NMR for the analysis of low molecular weight trace analytes in complex matrices. MASS SPECTROMETRY REVIEWS 2020; 39:35-54. [PMID: 30024655 PMCID: PMC6339611 DOI: 10.1002/mas.21575] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/28/2018] [Indexed: 05/12/2023]
Abstract
This review discusses the integration of liquid chromatography (LC), mass spectrometry (MS), and nuclear magnetic resonance (NMR) in the comprehensive analysis of small molecules from complex matrices. We first discuss the steps taken toward making the three technologies compatible, so as to create an efficient analytical platform. The development of online LC-MS-NMR, highlighted by successful applications in the profiling of highly concentrated analytes (LODs 10 μg) is discussed next. This is followed by a detailed overview of the alternative approaches that have been developed to overcome the challenges associated with online LC-MS-NMR that primarily stem from the inherently low sensitivity of NMR. These alternative approaches include the use of stop-flow LC-MS-NMR, loop collection of LC peaks, LC-MS-SPE-NMR, and offline NMR. The potential and limitations of all these approaches is discussed in the context of applications in various fields, including metabolomics and natural product discovery.
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Affiliation(s)
- Rose M. Gathungu
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Roger Kautz
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
| | - Bruce S. Kristal
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, Massachusetts
| | | | - Paul Vouros
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts
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LC-NMR for Natural Products Analysis: A Journey from an Academic Curiosity to a Robust Analytical Tool. SCI 2019. [DOI: 10.3390/sci1010031] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
LC–NMR combines the advantage of the outstanding separation power of liquid chromatography (LC) and the superior structural elucidating capability of nuclear magnetic resonance (NMR). NMR has proved that it is a standout detector for LC by providing maximum structural information about plant originated extracts particularly in its isolating ability of isomeric (same molecular formula) and/or isobaric (same molecular weight) compounds as compared to other detectors. The present review provides an overview of the LC–NMR developmental trends and its application in natural products analysis. The different LC–NMR operational modes are described, as well as how technical improvements assist in establishing this powerful technique as an important analytical tool in the analysis of complex plant-derived compounds. On-flow, stop-flow and loop-storage modes, as well as the new offline mode LC–SPE–NMR and capLC-NMR configurations that avoid the ingestion of expensive deuterated solvents throughout the experiment are mentioned. Utilization of cryogenic probe and microprobe technologies which are the other important promising approaches for guaranteeing the sensitivity issues are also described. Concluding remarks and future outlooks are also discussed.
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Souza RT, Mayrink J, Leite DF, Costa ML, Calderon IM, Rocha EA, Vettorazzi J, Feitosa FE, Cecatti JG. Metabolomics applied to maternal and perinatal health: a review of new frontiers with a translation potential. Clinics (Sao Paulo) 2019; 74:e894. [PMID: 30916173 PMCID: PMC6438130 DOI: 10.6061/clinics/2019/e894] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/27/2018] [Indexed: 12/31/2022] Open
Abstract
The prediction or early diagnosis of maternal complications is challenging mostly because the main conditions, such as preeclampsia, preterm birth, fetal growth restriction, and gestational diabetes mellitus, are complex syndromes with multiple underlying mechanisms related to their occurrence. Limited advances in maternal and perinatal health in recent decades with respect to preventing these disorders have led to new approaches, and "omics" sciences have emerged as a potential field to be explored. Metabolomics is the study of a set of metabolites in a given sample and can represent the metabolic functioning of a cell, tissue or organism. Metabolomics has some advantages over genomics, transcriptomics, and proteomics, as metabolites are the final result of the interactions of genes, RNAs and proteins. Considering the recent "boom" in metabolomic studies and their importance in the research agenda, we here review the topic, explaining the rationale and theory of the metabolomic approach in different areas of maternal and perinatal health research for clinical practitioners. We also demonstrate the main exploratory studies of these maternal complications, commenting on their promising findings. The potential translational application of metabolomic studies, especially for the identification of predictive biomarkers, is supported by the current findings, although they require external validation in larger datasets and with alternative methodologies.
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Affiliation(s)
- Renato Teixeira Souza
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
| | - Jussara Mayrink
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
| | - Débora Farias Leite
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
- Departamento Materno Infantil, Faculdade de Medicina, Universidade Federal de Pernambuco, Pernambuco, PE, BR
| | - Maria Laura Costa
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
| | - Iracema Mattos Calderon
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina de Botucatu, Universidade Estadual de Sao Paulo (UNESP), Botucatu, SP, BR
| | - Edilberto Alves Rocha
- Departamento Materno Infantil, Faculdade de Medicina, Universidade Federal de Pernambuco, Pernambuco, PE, BR
| | - Janete Vettorazzi
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Rio Grande do Sul, RS, BR
| | - Francisco Edson Feitosa
- Departamento de Ginecologia e Obstetricia, Faculdade de Medicina, Universidade Federal do Ceara, Ceara, CE, BR
| | - José Guilherme Cecatti
- Departamento de Ginecologia e Obstetricia, Faculdade de Ciencias Medicas, Universidade Estadual de Campinas, Campinas, SP, BR
- Corresponding author. E-mail:
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Carraro S, Baraldi E, Giordano G, Pirillo P, Stocchero M, Houben M, Bont L. Metabolomic Profile of Amniotic Fluid and Wheezing in the First Year of Life-A Healthy Birth Cohort Study. J Pediatr 2018; 196:264-269.e4. [PMID: 29548683 DOI: 10.1016/j.jpeds.2018.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/14/2017] [Accepted: 01/03/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVES To apply metabolomic analysis of amniotic fluid in a discovery cohort to see whether a specific biochemical-metabolic profile at birth is associated with the subsequent onset of wheezing over the first year of life. STUDY DESIGN This prospective exploratory study was conducted in a healthy term-born Dutch cohort recruited at 2 hospitals in Utrecht (UMCU, Utrecht, and Diakonessenhuis, Utrecht), The Netherlands. A metabolomic approach based on mass spectrometry was applied to analyze 142 amniotic fluid samples collected at birth. The infants were followed up during their first year of life with recording any respiratory symptoms daily, and they were classified according to the onset of wheezing. RESULTS Orthogonally constrained projection to latent structures discriminant analysis was used to investigate differences in the metabolic profiles of the infants with (n = 86) and without (n = 56) wheezing. A search of the available databases for amniotic fluid metabolites identified by stability selection, combined with pathway analysis, highlighted the possible metabolic perturbations involved in this condition. The model built using 16 relevant variables with plausible biological significance, showed an area under the curve of 0.82 (P < .001) and an area under the curve calculated by 7-fold full cross-validation of 0.72 (P = .003), with the steroid hormone biosynthesis and the 2-phenylalanine metabolism emerging as probably perturbed pathways. CONCLUSIONS Infants who will or will not experience wheezing in their first year of life have distinct amniotic fluid metabolomic profiles at birth. Changes occurring in biochemical-metabolic pathways in late intrauterine life may have a pathogenic role in early-onset wheezing.
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Affiliation(s)
- Silvia Carraro
- Department of Women's and Children's Health, University of Padova, Italy; The City of Hope Institute of Pediatric Research, Padova, Italy.
| | - Eugenio Baraldi
- Department of Women's and Children's Health, University of Padova, Italy; The City of Hope Institute of Pediatric Research, Padova, Italy
| | - Giuseppe Giordano
- Department of Women's and Children's Health, University of Padova, Italy; The City of Hope Institute of Pediatric Research, Padova, Italy
| | - Paola Pirillo
- Department of Women's and Children's Health, University of Padova, Italy; The City of Hope Institute of Pediatric Research, Padova, Italy
| | - Matteo Stocchero
- Department of Women's and Children's Health, University of Padova, Italy; The City of Hope Institute of Pediatric Research, Padova, Italy
| | - Michiel Houben
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Louis Bont
- Department of Pediatrics, University Medical Center Utrecht, Utrecht, The Netherlands
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13
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Fotiou M, Fotakis C, Tsakoumaki F, Athanasiadou E, Kyrkou C, Dimitropoulou A, Tsiaka T, Chatziioannou AC, Sarafidis K, Menexes G, Theodoridis G, Biliaderis CG, Zoumpoulakis P, Athanasiadis AP, Michaelidou AM. 1H NMR-based metabolomics reveals the effect of maternal habitual dietary patterns on human amniotic fluid profile. Sci Rep 2018; 8:4076. [PMID: 29511239 PMCID: PMC5840288 DOI: 10.1038/s41598-018-22230-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/13/2018] [Indexed: 12/25/2022] Open
Abstract
Maternal diet may influence offspring’s health, even within well-nourished populations. Amniotic fluid (AF) provides a rational compartment for studies on fetal metabolism. Evidence in animal models indicates that maternal diet affects AF metabolic profile; however, data from human studies are scarce. Therefore, we have explored whether AF content may be influenced by maternal diet, using a validated food-frequency questionnaire and implementing NMR-based metabolomics. Sixty-five AF specimens, from women undergoing second-trimester amniocentesis for prenatal diagnosis, were analysed. Complementary, maternal serum and urine samples were profiled. Hierarchical cluster analysis identified 2 dietary patterns, cluster 1 (C1, n = 33) and cluster 2 (C2, n = 32). C1 was characterized by significantly higher percentages of energy derived from refined cereals, yellow cheese, red meat, poultry, and “ready-to-eat” foods, while C2 by higher (P < 0.05) whole cereals, vegetables, fruits, legumes, and nuts. 1H NMR spectra allowed the identification of metabolites associated with these dietary patterns; glucose, alanine, tyrosine, valine, citrate, cis-acotinate, and formate were the key discriminatory metabolites elevated in C1 AF specimens. This is the first evidence to suggest that the composition of AF is influenced by maternal habitual dietary patterns. Our results highlight the need to broaden the knowledge on the importance of maternal nutrition during pregnancy.
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Affiliation(s)
- Maria Fotiou
- Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Charalambos Fotakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Foteini Tsakoumaki
- Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Elpiniki Athanasiadou
- 1st Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Charikleia Kyrkou
- Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Aristea Dimitropoulou
- Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Thalia Tsiaka
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | | | - Kosmas Sarafidis
- 1st Department of Neonatology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - George Menexes
- Department of Field Crops and Ecology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Costas G Biliaderis
- Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Panagiotis Zoumpoulakis
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece.
| | - Apostolos P Athanasiadis
- 3rd Department of Obstetrics and Gynecology, School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Alexandra-Maria Michaelidou
- Department of Food Science and Technology, School of Agriculture, Aristotle University of Thessaloniki, Thessaloniki, Greece.
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14
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Baraldi E, Giordano G, Stocchero M, Moschino L, Zaramella P, Tran MR, Carraro S, Romero R, Gervasi MT. Untargeted Metabolomic Analysis of Amniotic Fluid in the Prediction of Preterm Delivery and Bronchopulmonary Dysplasia. PLoS One 2016; 11:e0164211. [PMID: 27755564 PMCID: PMC5068788 DOI: 10.1371/journal.pone.0164211] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 09/21/2016] [Indexed: 11/18/2022] Open
Abstract
Objective Bronchopulmonary dysplasia (BPD) is a serious complication associated with preterm birth. A growing body of evidence suggests a role for prenatal factors in its pathogenesis. Metabolomics allows simultaneous characterization of low molecular weight compounds and may provide a picture of such a complex condition. The aim of this study was to evaluate whether an unbiased metabolomic analysis of amniotic fluid (AF) can be used to investigate the risk of spontaneous preterm delivery (PTD) and BPD development in the offspring. Study design We conducted an exploratory study on 32 infants born from mothers who had undergone an amniocentesis between 21 and 28 gestational weeks because of spontaneous preterm labor with intact membranes. The AF samples underwent untargeted metabolomic analysis using mass spectrometry combined with ultra-performance liquid chromatography. The data obtained were analyzed using multivariate and univariate statistical data analysis tools. Results Orthogonally Constrained Projection to Latent Structures-Discriminant Analysis (oCPLS2-DA) excluded effects on data modelling of crucial clinical variables. oCPLS2-DA was able to find unique differences in select metabolites between term (n = 11) and preterm (n = 13) deliveries (negative ionization data set: R2 = 0.47, mean AUC ROC in prediction = 0.65; positive ionization data set: R2 = 0.47, mean AUC ROC in prediction = 0.70), and between PTD followed by the development of BPD (n = 10), and PTD without BPD (n = 11) (negative data set: R2 = 0.48, mean AUC ROC in prediction = 0.73; positive data set: R2 = 0.55, mean AUC ROC in prediction = 0.71). Conclusions This study suggests that amniotic fluid metabolic profiling may be promising for identifying spontaneous preterm birth and fetuses at risk for developing BPD. These findings support the hypothesis that some prenatal metabolic dysregulations may play a key role in the pathogenesis of PTD and the development of BPD.
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Affiliation(s)
- Eugenio Baraldi
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Città della Speranza Institute of Pediatric Research (IRP), Padova, Italy
- * E-mail:
| | - Giuseppe Giordano
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Città della Speranza Institute of Pediatric Research (IRP), Padova, Italy
| | | | - Laura Moschino
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Città della Speranza Institute of Pediatric Research (IRP), Padova, Italy
| | - Patrizia Zaramella
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Maria Rosa Tran
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
| | - Silvia Carraro
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
- Città della Speranza Institute of Pediatric Research (IRP), Padova, Italy
| | - Roberto Romero
- Perinatology Research Branch, NICHD, NIH, DHHS, Wayne State University/Hutzel Women's Hospital, Detroit, United States of America
| | - Maria Teresa Gervasi
- Department of Women’s and Children’s Health, University of Padova, Padova, Italy
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15
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Planchart A, Mattingly CJ, Allen D, Ceger P, Casey W, Hinton D, Kanungo J, Kullman SW, Tal T, Bondesson M, Burgess SM, Sullivan C, Kim C, Behl M, Padilla S, Reif DM, Tanguay RL, Hamm J. Advancing toxicology research using in vivo high throughput toxicology with small fish models. ALTEX 2016; 33:435-452. [PMID: 27328013 PMCID: PMC5270630 DOI: 10.14573/altex.1601281] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/31/2016] [Indexed: 12/18/2022]
Abstract
Small freshwater fish models, especially zebrafish, offer advantages over traditional rodent models, including low maintenance and husbandry costs, high fecundity, genetic diversity, physiology similar to that of traditional biomedical models, and reduced animal welfare concerns. The Collaborative Workshop on Aquatic Models and 21st Century Toxicology was held at North Carolina State University on May 5-6, 2014, in Raleigh, North Carolina, USA. Participants discussed the ways in which small fish are being used as models to screen toxicants and understand mechanisms of toxicity. Workshop participants agreed that the lack of standardized protocols is an impediment to broader acceptance of these models, whereas development of standardized protocols, validation, and subsequent regulatory acceptance would facilitate greater usage. Given the advantages and increasing application of small fish models, there was widespread interest in follow-up workshops to review and discuss developments in their use. In this article, we summarize the recommendations formulated by workshop participants to enhance the utility of small fish species in toxicology studies, as well as many of the advances in the field of toxicology that resulted from using small fish species, including advances in developmental toxicology, cardiovascular toxicology, neurotoxicology, and immunotoxicology. We alsoreview many emerging issues that will benefit from using small fish species, especially zebrafish, and new technologies that will enable using these organisms to yield results unprecedented in their information content to better understand how toxicants affect development and health.
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Affiliation(s)
- Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Carolyn J. Mattingly
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - David Allen
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Patricia Ceger
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
| | - Warren Casey
- National Toxicology Program Interagency Center for the Evaluation of Alternative Toxicological Methods, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - David Hinton
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Jyotshna Kanungo
- National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Seth W. Kullman
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Tamara Tal
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - Maria Bondesson
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, USA
| | | | - Con Sullivan
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Carol Kim
- Department of Molecular & Biomedical Sciences, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono, ME, USA
| | - Mamta Behl
- Division of National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Stephanie Padilla
- Integrated Systems Toxicology Division, National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | - David M. Reif
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
- Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA
| | - Robert L. Tanguay
- Department of Environmental & Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Jon Hamm
- Integrated Laboratory Systems, Inc., Research Triangle Park, NC, USA
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16
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Orczyk-Pawilowicz M, Jawien E, Deja S, Hirnle L, Zabek A, Mlynarz P. Metabolomics of Human Amniotic Fluid and Maternal Plasma during Normal Pregnancy. PLoS One 2016; 11:e0152740. [PMID: 27070784 PMCID: PMC4829258 DOI: 10.1371/journal.pone.0152740] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 03/18/2016] [Indexed: 02/01/2023] Open
Abstract
Metabolic profiles of amniotic fluid and maternal blood are sources of valuable information about fetus development and can be potentially useful in diagnosis of pregnancy disorders. In this study, we applied 1H NMR-based metabolic profiling to track metabolic changes occurring in amniotic fluid (AF) and plasma (PL) of healthy mothers over the course of pregnancy. AF and PL samples were collected in the 2nd (T2) and 3rd (T3) trimester, prolonged pregnancy (PP) until time of delivery (TD). A multivariate data analysis of both biofluids reviled a metabolic switch-like transition between 2nd and 3rd trimester, which was followed by metabolic stabilization throughout the rest of pregnancy probably reflecting the stabilization of fetal maturation and development. The differences were further tested using univariate statistics at α = 0.001. In plasma the progression from T2 to T3 was related to increasing levels of glycerol, choline and ketone bodies (3-hydroxybutyrate and acetoacetate) while pyruvate concentration was significantly decreased. In amniotic fluid, T2 to T3 transition was associated with decreasing levels of glucose, carnitine, amino acids (valine, leucine, isoleucine, alanine, methionine, tyrosine, and phenylalanine) and increasing levels of creatinine, succinate, pyruvate, choline, N,N-dimethylglycine and urocanate. Lactate to pyruvate ratio was decreased in AF and conversely increased in PL. The results of our study, show that metabolomics profiling can be used to better understand physiological changes of the complex interdependencies of the mother, the placenta and the fetus during pregnancy. In the future, these results might be a useful reference point for analysis of complicated pregnancies.
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Affiliation(s)
| | - Ewa Jawien
- Department of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | | | - Lidia Hirnle
- 1 Department and Clinic of Gynaecology and Obstetrics, Wroclaw Medical University, Wrocław, Poland
| | - Adam Zabek
- Department of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
| | - Piotr Mlynarz
- Department of Chemistry, Wroclaw University of Technology, Wroclaw, Poland
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17
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Emwas AH, Roy R, McKay RT, Ryan D, Brennan L, Tenori L, Luchinat C, Gao X, Zeri AC, Gowda GAN, Raftery D, Steinbeck C, Salek RM, Wishart DS. Recommendations and Standardization of Biomarker Quantification Using NMR-Based Metabolomics with Particular Focus on Urinary Analysis. J Proteome Res 2016; 15:360-73. [PMID: 26745651 PMCID: PMC4865177 DOI: 10.1021/acs.jproteome.5b00885] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
NMR-based metabolomics has shown considerable promise in disease diagnosis and biomarker discovery because it allows one to nondestructively identify and quantify large numbers of novel metabolite biomarkers in both biofluids and tissues. Precise metabolite quantification is a prerequisite to move any chemical biomarker or biomarker panel from the lab to the clinic. Among the biofluids commonly used for disease diagnosis and prognosis, urine has several advantages. It is abundant, sterile, and easily obtained, needs little sample preparation, and does not require invasive medical procedures for collection. Furthermore, urine captures and concentrates many "unwanted" or "undesirable" compounds throughout the body, providing a rich source of potentially useful disease biomarkers; however, incredible variation in urine chemical concentrations makes analysis of urine and identification of useful urinary biomarkers by NMR challenging. We discuss a number of the most significant issues regarding NMR-based urinary metabolomics with specific emphasis on metabolite quantification for disease biomarker applications and propose data collection and instrumental recommendations regarding NMR pulse sequences, acceptable acquisition parameter ranges, relaxation effects on quantitation, proper handling of instrumental differences, sample preparation, and biomarker assessment.
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Affiliation(s)
- Abdul-Hamid Emwas
- Imaging and Characterization Core Lab, KAUST , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Raja Roy
- Centre of Biomedical Research, formerly, Centre of Biomedical Magnetic Resonance, Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus , Lucknow, Uttar Pradesh, India
| | - Ryan T McKay
- Department of Chemistry, University of Alberta , Edmonton, Alberta, Canada
| | - Danielle Ryan
- School of Agricultural and Wine Sciences, Charles Sturt University , Bathurst, New South Wales, Australia
| | - Lorraine Brennan
- UCD Insitute of Food and Health, UCD , Belfield, Dublin, Ireland
| | - Leonardo Tenori
- FiorGen Foundation , 50019 Sesto Fiorentino, Florence, Italy
| | - Claudio Luchinat
- Centro Risonanze Magnetiche - CERM, University of Florence , Florence, Italy
| | - Xin Gao
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ana Carolina Zeri
- Brazilian Biosciences National Laboratory, LNBio , Campinas, São Paulo, Brazil
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington , 850 Republican Street, Seattle, Washington 98109, United States.,Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue, Seattle, Washington 98109, United States
| | - Christoph Steinbeck
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - Reza M Salek
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI) , Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - David S Wishart
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta, Canada
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18
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Croitor-Sava A, Beck V, Sandaite I, Van Huffel S, Dresselaers T, Claus F, Himmelreich U, Deprest J. High-Resolution (1)H NMR Spectroscopy Discriminates Amniotic Fluid of Fetuses with Congenital Diaphragmatic Hernia from Healthy Controls. J Proteome Res 2015; 14:4502-10. [PMID: 26348471 DOI: 10.1021/acs.jproteome.5b00131] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lung hypoplasia in congenital diaphragmatic hernia (CDH) is a life-threatening birth defect. Severe cases can be offered tracheal occlusion to boost prenatal lung development, although defining those to benefit remains challenging. Metabonomics of (1)H NMR spectra collected from amniotic fluid (AF) can identify general changes in diseased versus healthy fetuses. AF embodies lung secretions and hence might contain pulmonary next to general markers of disease in CDH fetuses. AF from 81 healthy and 22 CDH fetuses was collected. NMR spectroscopy was performed at 400 MHz to compare AF from fetuses with CDH against controls. Several advanced feature extraction methods based on statistical tests that explore spectral variability, similarity, and dissimilarity were applied and compared. This resulted in the identification of 30 spectral regions, which accounted for 80% variability between CDH and controls. Combination with automated classification discriminates AF from CDH versus healthy fetuses with up to 92% accuracy. Within the identified spectral regions, isoleucine, leucine, valine, pyruvate, GABA, glutamate, glutamine, citrate, creatine, creatinine, taurine, and glucose were the most concentrated metabolites. As the metabolite pattern of AF changes with fetal development, we have excluded metabolites with a high age-related variability and repeated the analysis with 12 spectral regions, which has resulted in similar classification accuracy. From this analysis, it was possible to distinguish between AF from CDH fetuses versus healthy controls independent of gestational age.
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Affiliation(s)
- Anca Croitor-Sava
- Department of Electrical Engineering (ESAT) - STADIUS, University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium.,iMinds, Medical Information Technologies Department, University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Veronika Beck
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven , Herestraat 49, 3000 Leuven, Belgium.,Department of Obstetrics and Gynecology, University Hospital Gasthuisberg , Herestraat 49, 3000 Leuven, Belgium
| | - Inga Sandaite
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven , Herestraat 49, 3000 Leuven, Belgium.,Division of Medical Imaging, University Hospital Gasthuisberg , Herestraat 49, 3000 Leuven, Belgium
| | - Sabine Van Huffel
- Department of Electrical Engineering (ESAT) - STADIUS, University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium.,iMinds, Medical Information Technologies Department, University of Leuven , Kasteelpark Arenberg 10, 3001 Leuven, Belgium
| | - Tom Dresselaers
- Department of Imaging and Pathology, Biomedical MRI Unit, University of Leuven , Herestraat 49, 3000 Leuven, Belgium.,MoSAIC, University of Leuven , Herestraat 49, 3000 Leuven, Belgium
| | - Filip Claus
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven , Herestraat 49, 3000 Leuven, Belgium.,Division of Medical Imaging, University Hospital Gasthuisberg , Herestraat 49, 3000 Leuven, Belgium
| | - Uwe Himmelreich
- Department of Imaging and Pathology, Biomedical MRI Unit, University of Leuven , Herestraat 49, 3000 Leuven, Belgium.,MoSAIC, University of Leuven , Herestraat 49, 3000 Leuven, Belgium
| | - Jan Deprest
- Department of Development and Regeneration, Faculty of Medicine, University of Leuven , Herestraat 49, 3000 Leuven, Belgium.,Department of Obstetrics and Gynecology, University Hospital Gasthuisberg , Herestraat 49, 3000 Leuven, Belgium
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19
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Jain NS, Dürr UH, Ramamoorthy A. Bioanalytical methods for metabolomic profiling: Detection of head and neck cancer, including oral cancer. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.03.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Abu Bakar MH, Sarmidi MR, Cheng KK, Ali Khan A, Suan CL, Zaman Huri H, Yaakob H. Metabolomics – the complementary field in systems biology: a review on obesity and type 2 diabetes. MOLECULAR BIOSYSTEMS 2015; 11:1742-74. [DOI: 10.1039/c5mb00158g] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This paper highlights the metabolomic roles in systems biology towards the elucidation of metabolic mechanisms in obesity and type 2 diabetes.
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Affiliation(s)
- Mohamad Hafizi Abu Bakar
- Department of Bioprocess Engineering
- Faculty of Chemical Engineering
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
| | - Mohamad Roji Sarmidi
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
- Innovation Centre in Agritechnology for Advanced Bioprocessing (ICA)
| | - Kian-Kai Cheng
- Department of Bioprocess Engineering
- Faculty of Chemical Engineering
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
| | - Abid Ali Khan
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
- Department of Biosciences
| | - Chua Lee Suan
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
| | - Hasniza Zaman Huri
- Department of Pharmacy
- Faculty of Medicine
- University of Malaya
- 50603 Kuala Lumpur
- Malaysia
| | - Harisun Yaakob
- Institute of Bioproduct Development
- Universiti Teknologi Malaysia
- 81310 Johor Bahru
- Malaysia
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21
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Gérard N, Fahiminiya S, Grupen CG, Nadal-Desbarats L. Reproductive Physiology and Ovarian Folliculogenesis Examined via 1H-NMR Metabolomics Signatures: A Comparative Study of Large and Small Follicles in Three Mammalian Species (Bos taurus, Sus scrofa domesticus and Equus ferus caballus). OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:31-40. [DOI: 10.1089/omi.2014.0097] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Nadine Gérard
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Equipe Interactions Cellulaires et Fertilité, Nouzilly, France
| | - Somayyeh Fahiminiya
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, Equipe Interactions Cellulaires et Fertilité, Nouzilly, France
| | - Christopher G. Grupen
- Faculty of Veterinary Science, The University of Sydney, Camden, New South Wales, Australia
| | - Lydie Nadal-Desbarats
- INSERM U930, Equipe Neurogénetique et Neurométabolomique, Université François-Rabelais, Tours, France
- Département d'Analyses Chimique Biologique et Médicale, PPF Analyse des Systémes Biologiques, Université François-Rabelais, Tours, France
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22
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Geer LA, Pycke BFG, Sherer DM, Abulafia O, Halden RU. Use of amniotic fluid for determining pregnancies at risk of preterm birth and for studying diseases of potential environmental etiology. ENVIRONMENTAL RESEARCH 2015; 136:470-81. [PMID: 25460669 PMCID: PMC4279852 DOI: 10.1016/j.envres.2014.09.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 09/02/2014] [Accepted: 09/16/2014] [Indexed: 05/21/2023]
Abstract
Amniotic fluid (AF) is a biological medium uniquely suited for the study of early exposure of the human fetus to environmental contaminants acquired by the mother before and during pregnancy. Traditional diagnostic applications of AF have focused almost exclusively on the diagnosis of genetic aberrations such as Trisomy-21 and on heritable diseases in high-risk pregnancies. Since more than 50 anthropogenic compounds have been detected in AF, there is considerable potential in utilizing fetal protein biomarkers as indicators of health effects related to prenatal toxic exposure. Here, we focus on preterm birth (PTB) to illustrate opportunities and limitations of using AF as a diagnostic matrix. Representing a pervasive public health challenge worldwide, PTB cannot be managed simply by improving hygiene and broadening access to healthcare. This is illustrated by 15-year increases of PTB in the U.S. from 1989 to 2004. AF is uniquely suited as a matrix for early detection of the association between fetal exposures and PTB due to its fetal origin and the fact that it is sampled from women who are at higher risk of PTB. This critical review shows the occurrence in AF of a number of xenobiotics, including endocrine-disrupting compounds (EDCs), which are known or may reasonably be expected to shorten fetal gestation. It is not yet known whether EDCs, including bisphenol A, phytoestrogens, and polychlorinated biphenyls (PCBs), can affect the expression of proteins considered viable or potential biomarkers for the onset of PTB. As such, the diagnostic value of AF is broad and has not yet been fully explored for prenatal diagnosis of pregnancies at risk from toxic, environmental exposures and for the elucidation of mechanisms underlying important public health challenges including PTB.
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Affiliation(s)
- Laura A Geer
- Department of Environmental and Occupational Health Sciences, State University of New York, Downstate School of Public Health, Box 43, 450 Clarkson Avenue, Brooklyn, NY 11203-2533, USA.
| | - Benny F G Pycke
- Center for Environmental Security, The Biodesign Institute, Arizona State University, 781 E. Terrace Mall Tempe, AZ, USA.
| | - David M Sherer
- Department of Obstetrics and Gynecology, State University of New York Downstate Medical Center, 445 Lenox Road, Brooklyn, NY, USA.
| | - Ovadia Abulafia
- Department of Obstetrics and Gynecology, State University of New York Downstate Medical Center, 445 Lenox Road, Brooklyn, NY, USA.
| | - Rolf U Halden
- Center for Environmental Security, The Biodesign Institute, Arizona State University, 781 E. Terrace Mall Tempe, AZ, USA.
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23
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A metabolomic perspective on coeliac disease. Autoimmune Dis 2014; 2014:756138. [PMID: 24665364 PMCID: PMC3934717 DOI: 10.1155/2014/756138] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/30/2013] [Accepted: 10/20/2013] [Indexed: 12/16/2022] Open
Abstract
Metabolomics is an "omic" science that is now emerging with the purpose of elaborating a comprehensive analysis of the metabolome, which is the complete set of metabolites (i.e., small molecules intermediates) in an organism, tissue, cell, or biofluid. In the past decade, metabolomics has already proved to be useful for the characterization of several pathological conditions and offers promises as a clinical tool. A metabolomics investigation of coeliac disease (CD) revealed that a metabolic fingerprint for CD can be defined, which accounts for three different but complementary components: malabsorption, energy metabolism, and alterations in gut microflora and/or intestinal permeability. In this review, we will discuss the major advancements in metabolomics of CD, in particular with respect to the role of gut microbiome and energy metabolism.
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24
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Appiah-Amponsah E, Owusu-Sarfo K, Gowda GN, Ye T, Raftery D. Combining Hydrophilic Interaction Chromatography (HILIC) and Isotope Tagging for Off-Line LC-NMR Applications in Metabolite Analysis. Metabolites 2013; 3:575-591. [PMID: 24860727 PMCID: PMC3901292 DOI: 10.3390/metabo3030575] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/06/2013] [Accepted: 07/15/2013] [Indexed: 11/16/2022] Open
Abstract
The complementary use of liquid chromatography (LC) and nuclear magnetic resonance (NMR) has shown high utility in a variety of fields. While the significant benefit of spectral simplification can be achieved for the analysis of complex samples, other limitations remain. For example, (1)H LC-NMR suffers from pH dependent chemical shift variations, especially during urine analysis, owing to the high physiological variation of urine pH. Additionally, large solvent signals from the mobile phase in LC can obscure lower intensity signals and severely limit the number of metabolites detected. These limitations, along with sample dilution, hinder the ability to make reliable chemical shift assignments. Recently, stable isotopic labeling has been used to detect quantitatively specific classes of metabolites of interest in biofluids. Here we present a strategy that explores the combined use of two-dimensional hydrophilic interaction chromatography (HILIC) and isotope tagged NMR for the unambiguous identification of carboxyl containing metabolites present in human urine. The ability to separate structurally related compounds chromatographically, in off-line mode, followed by detection using (1)H-(15)N 2D HSQC (two-dimensional heteronuclear single quantum coherence) spectroscopy, resulted in the assignment of low concentration carboxyl-containing metabolites from a library of isotope labeled compounds. The quantitative nature of this strategy is also demonstrated.
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Affiliation(s)
- Emmanuel Appiah-Amponsah
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; E-Mails: (E.A.-A.); (K.O.-S.); (G.A.N.G.); (T.Y.)
| | - Kwadwo Owusu-Sarfo
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; E-Mails: (E.A.-A.); (K.O.-S.); (G.A.N.G.); (T.Y.)
| | - G.A. Nagana Gowda
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; E-Mails: (E.A.-A.); (K.O.-S.); (G.A.N.G.); (T.Y.)
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
| | - Tao Ye
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; E-Mails: (E.A.-A.); (K.O.-S.); (G.A.N.G.); (T.Y.)
| | - Daniel Raftery
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; E-Mails: (E.A.-A.); (K.O.-S.); (G.A.N.G.); (T.Y.)
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98109, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Author to whom correspondence should be addressed; E-Mail: ; Tel: +206-543-9709; Fax: +206-616-4819
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25
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Metabolomics application in maternal-fetal medicine. BIOMED RESEARCH INTERNATIONAL 2013; 2013:720514. [PMID: 23841090 PMCID: PMC3690726 DOI: 10.1155/2013/720514] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/10/2013] [Accepted: 05/13/2013] [Indexed: 12/24/2022]
Abstract
Metabolomics in maternal-fetal medicine is still an “embryonic” science. However, there is already an increasing interest in metabolome of normal and complicated pregnancies, and neonatal outcomes. Tissues used for metabolomics interrogations of pregnant women, fetuses and newborns are amniotic fluid, blood, plasma, cord blood, placenta, urine, and vaginal secretions. All published papers highlight the strong correlation between biomarkers found in these tissues and fetal malformations, preterm delivery, premature rupture of membranes, gestational diabetes mellitus, preeclampsia, neonatal asphyxia, and hypoxic-ischemic encephalopathy. The aim of this review is to summarize and comment on original data available in relevant published works in order to emphasize the clinical potential of metabolomics in obstetrics in the immediate future.
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26
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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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27
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Current trends and challenges in sample preparation for global metabolomics using liquid chromatography-mass spectrometry. Anal Bioanal Chem 2012; 403:1523-48. [PMID: 22576654 DOI: 10.1007/s00216-012-6039-y] [Citation(s) in RCA: 317] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2012] [Revised: 03/13/2012] [Accepted: 04/10/2012] [Indexed: 01/26/2023]
Abstract
The choice of sample-preparation method is extremely important in metabolomic studies because it affects both the observed metabolite content and biological interpretation of the data. An ideal sample-preparation method for global metabolomics should (i) be as non-selective as possible to ensure adequate depth of metabolite coverage; (ii) be simple and fast to prevent metabolite loss and/or degradation during the preparation procedure and enable high-throughput; (iii) be reproducible; and (iv) incorporate a metabolism-quenching step to represent true metabolome composition at the time of sampling. Despite its importance, sample preparation is often an overlooked aspect of metabolomics, so the focus of this review is to explore the role, challenges, and trends in sample preparation specifically within the context of global metabolomics by liquid chromatography-mass spectrometry (LC-MS). This review will cover the most common methods including solvent precipitation and extraction, solid-phase extraction and ultrafiltration, and discuss how to improve analytical quality and metabolite coverage in metabolomic studies of biofluids, tissues, and mammalian cells. Recent developments in this field will also be critically examined, including in vivo methods, turbulent-flow chromatography, and dried blood spot sampling.
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28
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Graça G, Goodfellow BJ, Barros AS, Diaz S, Duarte IF, Spagou K, Veselkov K, Want EJ, Lindon JC, Carreira IM, Galhano E, Pita C, Gil AM. UPLC-MS metabolic profiling of second trimester amniotic fluid and maternal urine and comparison with NMR spectral profiling for the identification of pregnancy disorder biomarkers. MOLECULAR BIOSYSTEMS 2012; 8:1243-54. [PMID: 22294348 DOI: 10.1039/c2mb05424h] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We report on the first untargeted UPLC-MS study of 2nd trimester maternal urine and amniotic fluid (AF), to investigate the possible metabolic effects of fetal malformations (FM), gestational diabetes mellitus (GDM) and preterm delivery (PTD). For fetal malformations, considerable metabolite variations were identified in AF and, to a lesser extent, in urine. Using validated PLS-DA models and statistical correlations between UPLC-MS data and previously acquired NMR data, a metabolic picture of fetal hypoxia, enhanced gluconeogenesis, TCA activity and hindered kidney development affecting FM pregnancies was reinforced. Moreover, changes in carnitine, pyroglutamate and polyols were newly noted, respectively, reflecting lipid oxidation, altered placental amino acid transfer and alterations in polyol pathways. Higher excretion of conjugated products in maternal urine was seen suggesting alterations in conjugation reactions. For the pre-diagnostic GDM group, no significant changes were observed, either considering amniotic fluid or maternal urine, whereas, for the pre-PTD group, some newly observed changes were noted, namely, the decrease of particular amino acids and the increase of an hexose (possibly glucose), suggesting alteration in placental amino acid fluxes and a possible tendency for hyperglycemia. This work shows the potential of UPLC-MS for the study of fetal and maternal biofluids, particularly when used in tandem with comparable NMR data. The important roles played by sampling characteristics (e.g. group dimensions) and the specific experimental conditions chosen for MS methods are discussed.
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Affiliation(s)
- Gonçalo Graça
- CICECO-Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
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29
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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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30
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Amorini AM, Giorlandino C, Longo S, D’Urso S, Mesoraca A, Santoro ML, Picardi M, Gullotta S, Cignini P, Lazzarino D, Lazzarino G, Tavazzi B. Metabolic profile of amniotic fluid as a biochemical tool to screen for inborn errors of metabolism and fetal anomalies. Mol Cell Biochem 2011; 359:205-16. [DOI: 10.1007/s11010-011-1015-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 07/27/2011] [Indexed: 01/28/2023]
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31
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Serriere S, Barantin L, Seguin F, Tranquart F, Nadal-Desbarats L. Impact of prenatal stress on 1H NMR-based metabolic profiling of rat amniotic fluid. MAGNETIC RESONANCE MATERIALS IN PHYSICS BIOLOGY AND MEDICINE 2011; 24:267-75. [DOI: 10.1007/s10334-011-0260-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 04/15/2011] [Accepted: 05/06/2011] [Indexed: 01/05/2023]
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32
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Chen X, Jiang ZH, Chen S, Qin W. Microbial and bioconversion production of D-xylitol and its detection and application. Int J Biol Sci 2010; 6:834-44. [PMID: 21179590 PMCID: PMC3005349 DOI: 10.7150/ijbs.6.834] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 12/06/2010] [Indexed: 11/22/2022] Open
Abstract
D-Xylitol is found in low content as a natural constituent of many fruits and vegetables. It is a five-carbon sugar polyol and has been used as a food additive and sweetening agent to replace sucrose, especially for non-insulin dependent diabetics. It has multiple beneficial health effects, such as the prevention of dental caries, and acute otitis media. In industry, it has been produced by chemical reduction of D-xylose mainly from photosynthetic biomass hydrolysates. As an alternative method of chemical reduction, biosynthesis of D-xylitol has been focused on the metabolically engineered Saccharomyces cerevisiae and Candida strains. In order to detect D-xylitol in the production processes, several detection methods have been established, such as gas chromatography (GC)-based methods, high performance liquid chromatography (HPLC)-based methods, LC-MS methods, and capillary electrophoresis methods (CE). The advantages and disadvantages of these methods are compared in this review.
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Affiliation(s)
- Xi Chen
- Biorefining Research Initiative and Department of Biology, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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33
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Graça G, Duarte IF, Barros AS, Goodfellow BJ, Diaz SO, Pinto J, Carreira IM, Galhano E, Pita C, Gil AM. Impact of Prenatal Disorders on the Metabolic Profile of Second Trimester Amniotic Fluid: A Nuclear Magnetic Resonance Metabonomic Study. J Proteome Res 2010; 9:6016-24. [DOI: 10.1021/pr100815q] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Gonçalo Graça
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Iola F. Duarte
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - António S. Barros
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Brian J. Goodfellow
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Sílvia O. Diaz
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Joana Pinto
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Isabel M. Carreira
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Eulália Galhano
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Cristina Pita
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Ana M. Gil
- CICECO−Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, QOPNA Research Unit, Department of Chemistry, Campus Universitário de Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, Pólo III, University of Coimbra, 3000-354 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
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Zhang S, Nagana Gowda GA, Ye T, Raftery D. Advances in NMR-based biofluid analysis and metabolite profiling. Analyst 2010; 135:1490-8. [PMID: 20379603 PMCID: PMC4720135 DOI: 10.1039/c000091d] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Significant improvements in NMR technology and methods have propelled NMR studies to play an important role in a rapidly expanding number of applications involving the profiling of metabolites in biofluids. This review discusses recent technical advances in NMR spectroscopy based metabolite profiling methods, data processing and analysis over the last three years.
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Affiliation(s)
- Shucha Zhang
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - G. A. Nagana Gowda
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Tao Ye
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - Daniel Raftery
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
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Romero R, Mazaki-Tovi S, Vaisbuch E, Kusanovic JP, Chaiworapongsa T, Gomez R, Nien JK, Yoon BH, Mazor M, Luo J, Banks D, Ryals J, Beecher C. Metabolomics in premature labor: a novel approach to identify patients at risk for preterm delivery. J Matern Fetal Neonatal Med 2010; 23:1344-59. [PMID: 20504069 DOI: 10.3109/14767058.2010.482618] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Biomarkers for preterm labor (PTL) and delivery can be discovered through the analysis of the transcriptome (transcriptomics) and protein composition (proteomics). Characterization of the global changes in low-molecular weight compounds which constitute the 'metabolic network' of cells (metabolome) is now possible by using a 'metabolomics' approach. Metabolomic profiling has special advantages over transcriptomics and proteomics since the metabolic network is downstream from gene expression and protein synthesis, and thus more closely reflects cell activity at a functional level. This study was conducted to determine if metabolomic profiling of the amniotic fluid can identify women with spontaneous PTL at risk for preterm delivery, regardless of the presence or absence of intraamniotic infection/inflammation (IAI). STUDY DESIGN Two retrospective cross-sectional studies were conducted, including three groups of pregnant women with spontaneous PTL and intact membranes: (1) PTL who delivered at term; (2) PTL without IAI who delivered preterm; and (3) PTL with IAI who delivered preterm. The first was an exploratory study that included 16, 19, and 20 patients in groups 1, 2, and 3, respectively. The second study included 40, 33, and 40 patients in groups 1, 2, and 3, respectively. Amniotic fluid metabolic profiling was performed by combining chemical separation (with gas and liquid chromatography) and mass spectrometry. Compounds were identified using authentic standards. The data were analyzed using discriminant analysis for the first study and Random Forest for the second. RESULTS (1) In the first study, metabolomic profiling of the amniotic fluid was able to identify patients as belonging to the correct clinical group with an overall 96.3% (53/55) accuracy; 15 of 16 patients with PTL who delivered at term were correctly classified; all patients with PTL without IAI who delivered preterm neonates were correctly identified as such (19/19), while 19/20 patients with PTL and IAI were correctly classified. (2) In the second study, metabolomic profiling was able to identify patients as belonging to the correct clinical group with an accuracy of 88.5% (100/113); 39 of 40 patients with PTL who delivered at term were correctly classified; 29 of 33 patients with PTL without IAI who delivered preterm neonates were correctly classified. Among patients with PTL and IAI, 32/40 were correctly classified. The metabolites responsible for the classification of patients in different clinical groups were identified. A preliminary draft of the human amniotic fluid metabolome was generated and found to contain products of the intermediate metabolism of mammalian cells and xenobiotic compounds (e.g. bacterial products and Salicylamide). CONCLUSION Among patients with spontaneous PTL with intact membranes, metabolic profiling of the amniotic fluid can be used to assess the risk of preterm delivery in the presence or absence of infection/inflammation.
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Affiliation(s)
- Roberto Romero
- Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, Maryland, USA.
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Mazumder A, Kumar A, Purohit AK, Dubey DK. Application of high performance liquid chromatography coupled to on-line solid-phase extraction-nuclear magnetic resonance spectroscopy for the analysis of degradation products of V-class nerve agents and nitrogen mustard. J Chromatogr A 2010; 1217:2887-94. [DOI: 10.1016/j.chroma.2010.02.071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 10/19/2022]
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Álvarez-Sánchez B, Priego-Capote F, Luque de Castro M. Metabolomics analysis I. Selection of biological samples and practical aspects preceding sample preparation. Trends Analyt Chem 2010. [DOI: 10.1016/j.trac.2009.12.003] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Appiah-Amponsah E, Shanaiah N, Nagana Gowda GA, Owusu-Sarfo K, Ye T, Raftery D. Identification of 4-deoxythreonic acid present in human urine using HPLC and NMR techniques. J Pharm Biomed Anal 2009; 50:878-85. [PMID: 19615840 DOI: 10.1016/j.jpba.2009.06.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Revised: 06/02/2009] [Accepted: 06/03/2009] [Indexed: 01/09/2023]
Abstract
The 1H NMR spectrum of urine exhibits a large number of detectable and quantifiable metabolites and hence urine metabolite profiling is potentially useful for the study of systems biology and the discovery of biomarkers for drug development or clinical applications. While a number of metabolites (50-100) are readily detectable in urine by NMR, a much larger number is potentially available if lower concentration species can be detected unambiguously. Lower concentration metabolites are thought to be more specific to certain disease states and thus it is important to detect these metabolites with certainty. We report the identification of 4-deoxythreonic acid, a relatively low concentration endogenous metabolite that has not been previously identified in the 1H NMR spectrum of human urine. The use of HPLC and NMR spectroscopy facilitated the unequivocal and non-invasive identification of the molecule in urine which is complicated by extensive peak overlap and multiple, similar resonances from other metabolites such as 3-hydroxybutanoic acid. High-resolution detection and good sensitivity were achieved by the combination of multiple chromatographic fraction collection, sample pre-concentration, and the use of a cryogenically cooled NMR probe.
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39
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Graça G, Duarte IF, Barros AS, Goodfellow BJ, Diaz S, Carreira IM, Couceiro AB, Galhano E, Gil AM. 1H NMR Based Metabonomics of Human Amniotic Fluid for the Metabolic Characterization of Fetus Malformations. J Proteome Res 2009; 8:4144-50. [DOI: 10.1021/pr900386f] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Gonçalo Graça
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Iola F. Duarte
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - António S. Barros
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Brian J. Goodfellow
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Sílvia Diaz
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Isabel M. Carreira
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Ana Bela Couceiro
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Eulália Galhano
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
| | - Ana M. Gil
- CICECO, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, QOPNAA, Department of Chemistry, Campus Universitário de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal, Cytogenetics Laboratory and Center of Neurosciences and Cellular Biology, Faculty of Medicine, University of Coimbra, 3001-401 Coimbra, Portugal, and Maternidade Bissaya Barreto, Centro Hospitalar de Coimbra, 3000 Coimbra, Portugal
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Metabolomics: moving to the clinic. J Neuroimmune Pharmacol 2009; 5:4-17. [PMID: 19399626 DOI: 10.1007/s11481-009-9156-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 04/06/2009] [Indexed: 12/12/2022]
Abstract
Assessment of a biological system by means of global and non-targeted metabolite profiling--metabolomics or metabonomics--provides the investigator with molecular information that is close to the phenotype in question in the sense that metabolites are an ultimate product of gene, mRNA, and protein activity. Over the last few years, there has been a rapidly growing number of metabolomics applications aimed at finding biomarkers which could assist diagnosis, provide therapy guidance, and evaluate response to therapy for particular diseases. Also, within the fields of drug discovery, drug toxicology, and personalized pharmacology, metabolomics is emerging as a powerful tool. This review seeks to update the reader on analytical strategies, biomarker findings, and implications of metabolomics for the clinic. Particular attention is paid to recent biomarkers found related to neurological, cardiovascular, and cancer diseases. Moreover, the impact of metabolomics in the drug discovery and development process is examined.
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