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Osik N, Lukzen NN, Yanshole VV, Tsentalovich YP. Loss of Volatile Metabolites during Concentration of Metabolomic Extracts. ACS OMEGA 2024; 9:24015-24024. [PMID: 38854568 PMCID: PMC11154959 DOI: 10.1021/acsomega.4c02439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/11/2024]
Abstract
Volatile metabolites can be lost during the preanalytical stage of metabolomic analysis. This work is aimed at the experimental and theoretical study of mechanisms of volatile substance evaporation and retention in the residues during the drying of extract solutions. We demonstrate that solvent evaporation leads to the unavoidable loss of nondissociating volatile metabolites with low boiling points and high vapor pressures (such as acetone and ethanol). The retention of dissociating volatile compounds (primarily organic acids RH) during the evaporation depends on the presence of buffer salts in solution, which are responsible for maintaining the neutral pH. An acid remains in the solution as long as it is present predominantly in the dissociated R- state. At the very last stage of solvent evaporation, buffer salts precipitate, forming a solid matrix for metabolite trapping in the residue. At the same time, buffer precipitation leads to a decrease of the solution pH, increase of the portion of RH in associated state, and acceleration of RH volatilization. The RH recovery is thus determined by the competition between the solute volatilization in the associated RH form and metabolite trapping in the solid matrix. The retention of volatile acids in the residue after extract drying can be improved either by adding buffer salts to maintain high pH or by incomplete sample drying.
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Affiliation(s)
- Nataliya
A. Osik
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
| | - Nikita N. Lukzen
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
- Novosibirsk
State University, Pirogova
str. 1, Novosibirsk 630090, Russia
| | - Vadim V. Yanshole
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
- Novosibirsk
State University, Pirogova
str. 1, Novosibirsk 630090, Russia
| | - Yuri P. Tsentalovich
- International
Tomography Center Siberian Branch of Russian Academy of Sciences, Institutskaya str. 3a, Novosibirsk 630090, Russia
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Zhang F, Shan S, Fu C, Guo S, Liu C, Wang S. Advanced Mass Spectrometry-Based Biomarker Identification for Metabolomics of Diabetes Mellitus and Its Complications. Molecules 2024; 29:2530. [PMID: 38893405 PMCID: PMC11173766 DOI: 10.3390/molecules29112530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 06/21/2024] Open
Abstract
Over the years, there has been notable progress in understanding the pathogenesis and treatment modalities of diabetes and its complications, including the application of metabolomics in the study of diabetes, capturing attention from researchers worldwide. Advanced mass spectrometry, including gas chromatography-tandem mass spectrometry (GC-MS/MS), liquid chromatography-tandem mass spectrometry (LC-MS/MS), and ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS), etc., has significantly broadened the spectrum of detectable metabolites, even at lower concentrations. Advanced mass spectrometry has emerged as a powerful tool in diabetes research, particularly in the context of metabolomics. By leveraging the precision and sensitivity of advanced mass spectrometry techniques, researchers have unlocked a wealth of information within the metabolome. This technology has enabled the identification and quantification of potential biomarkers associated with diabetes and its complications, providing new ideas and methods for clinical diagnostics and metabolic studies. Moreover, it offers a less invasive, or even non-invasive, means of tracking disease progression, evaluating treatment efficacy, and understanding the underlying metabolic alterations in diabetes. This paper summarizes advanced mass spectrometry for the application of metabolomics in diabetes mellitus, gestational diabetes mellitus, diabetic peripheral neuropathy, diabetic retinopathy, diabetic nephropathy, diabetic encephalopathy, diabetic cardiomyopathy, and diabetic foot ulcers and organizes some of the potential biomarkers of the different complications with the aim of providing ideas and methods for subsequent in-depth metabolic research and searching for new ways of treating the disease.
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Affiliation(s)
- Feixue Zhang
- Hubei Key Laboratory of Diabetes and Angiopathy, Medicine Research Institute, Medical College, Hubei University of Science and Technology, Xianning 437100, China; (F.Z.); (C.F.); (S.G.)
| | - Shan Shan
- College of Life Science, National R&D Center for Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China;
| | - Chenlu Fu
- Hubei Key Laboratory of Diabetes and Angiopathy, Medicine Research Institute, Medical College, Hubei University of Science and Technology, Xianning 437100, China; (F.Z.); (C.F.); (S.G.)
- School of Pharmacy, Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Shuang Guo
- Hubei Key Laboratory of Diabetes and Angiopathy, Medicine Research Institute, Medical College, Hubei University of Science and Technology, Xianning 437100, China; (F.Z.); (C.F.); (S.G.)
| | - Chao Liu
- Hubei Key Laboratory of Diabetes and Angiopathy, Medicine Research Institute, Medical College, Hubei University of Science and Technology, Xianning 437100, China; (F.Z.); (C.F.); (S.G.)
| | - Shuanglong Wang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China
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Trimigno A, Holderman NR, Dong C, Boardman KD, Zhao J, O’Day EM. NMR Precision Metabolomics: Dynamic Peak Sum Thresholding and Navigators for Highly Standardized and Reproducible Metabolite Profiling of Clinical Urine Samples. Metabolites 2024; 14:275. [PMID: 38786752 PMCID: PMC11122845 DOI: 10.3390/metabo14050275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Metabolomics, especially urine-based studies, offers incredible promise for the discovery and development of clinically impactful biomarkers. However, due to the unique challenges of urine, a highly precise and reproducible workflow for NMR-based urine metabolomics is lacking. Using 1D and 2D non-uniform sampled (NUS) 1H-13C NMR spectroscopy, we systematically explored how changes in hydration or specific gravity (SG) and pH can impact biomarker discovery. Further, we examined additional sources of error in metabolomics studies and identified Navigator molecules that could monitor for those biases. Adjustment of SG to 1.002-1.02 coupled with a dynamic sum-based peak thresholding eliminates false positives associated with urine hydration and reduces variation in chemical shift. We identified Navigator molecules that can effectively monitor for inconsistencies in sample processing, SG, protein contamination, and pH. The workflow described provides quality assurance and quality control tools to generate high-quality urine metabolomics data, which is the first step in biomarker discovery.
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Lösel H, Arndt M, Wenck S, Hansen L, Oberpottkamp M, Seifert S, Fischer M. Exploring the potential of high-resolution LC-MS in combination with ion mobility separation and surrogate minimal depth for enhanced almond origin authentication. Talanta 2024; 271:125598. [PMID: 38224656 DOI: 10.1016/j.talanta.2023.125598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/17/2024]
Abstract
Almonds (Prunus dulcisMill.) are consumed worldwide and their geographical origin plays a crucial role in determining their market value. In the present study, a total of 250 almond reference samples from six countries (Australia, Spain, Iran, Italy, Morocco, and the USA) were non-polar extracted and analyzed by UPLC-ESI-IM-qToF-MS. Four harvest periods, more than 30 different varieties, including both sweet and bitter almonds, were considered in the method development. Principal component analysis showed that there are three groups of samples with similarities: Australia/USA, Spain/Italy and Iran/Morocco. For origin determination, a random forest achieved an accuracy of 88.8 %. Misclassifications occurred mainly between almonds from the USA and Australia, due to similar varieties and similar external influences such as climate conditions. Metabolites relevant for classification were selected using Surrogate Minimal Depth, with triacylglycerides containing oxidized, odd chained or short chained fatty acids and some phospholipids proven to be the most suitable marker substances. Our results show that focusing on the identified lipids (e. g., using a QqQ-MS instrument) is a promising approach to transfer the origin determination of almonds to routine analysis.
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Affiliation(s)
- Henri Lösel
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Maike Arndt
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Soeren Wenck
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Lasse Hansen
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Marie Oberpottkamp
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Stephan Seifert
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science - Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146, Hamburg, Germany.
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Sun X, Yu Y, Qian K, Wang J, Huang L. Recent Progress in Mass Spectrometry-Based Single-Cell Metabolic Analysis. SMALL METHODS 2024; 8:e2301317. [PMID: 38032130 DOI: 10.1002/smtd.202301317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/10/2023] [Indexed: 12/01/2023]
Abstract
Single-cell analysis enables the measurement of biomolecules at the level of individual cells, facilitating in-depth investigations into cellular heterogeneity and precise interpretation of the related biological mechanisms. Among these biomolecules, cellular metabolites exhibit remarkable sensitivity to environmental and biochemical changes, unveiling a hidden world underlying cellular heterogeneity and allowing for the determination of cell physiological states. However, the metabolic analysis of single cells is challenging due to the extremely low concentrations, substantial content variations, and rapid turnover rates of cellular metabolites. Mass spectrometry (MS), characterized by its high sensitivity, wide dynamic range, and excellent selectivity, is employed in single-cell metabolic analysis. This review focuses on recent advances and applications of MS-based single-cell metabolic analysis, encompassing three key steps of single-cell isolation, detection, and application. It is anticipated that MS will bring profound implications in biomedical practices, serving as advanced tools to depict the single-cell metabolic landscape.
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Affiliation(s)
- Xuming Sun
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Yi Yu
- School of Medical Engineering, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Engineering Technology Research Center of Neurosense and Control of Henan Province, Xinxiang Medical University, Xinxiang, 453003, P. R. China
- Xinxiang Key Laboratory of Neurobiosensor, Xinxiang Medical University, Xinxiang, 453003, P. R. China
| | - Kun Qian
- School of Biomedical Engineering, Institute of Medical Robotics and Med X Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Jiayi Wang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
| | - Lin Huang
- Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200030, P. R. China
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Singh U, Al-Nemi R, Alahmari F, Emwas AH, Jaremko M. Improving quality of analysis by suppression of unwanted signals through band-selective excitation in NMR spectroscopy for metabolomics studies. Metabolomics 2023; 20:7. [PMID: 38114836 DOI: 10.1007/s11306-023-02069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/16/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Nuclear Magnetic Resonance (NMR) spectroscopy stands as a preeminent analytical tool in the field of metabolomics. Nevertheless, when it comes to identifying metabolites present in scant amounts within various types of complex mixtures such as plants, honey, milk, and biological fluids and tissues, NMR-based metabolomics presents a formidable challenge. This predicament arises primarily from the fact that the signals emanating from metabolites existing in low concentrations tend to be overshadowed by the signals of highly concentrated metabolites within NMR spectra. OBJECTIVES The aim of this study is to tackle the issue of intense sugar signals overshadowing the desired metabolite signals, an optimal pulse sequence with band-selective excitation has been proposed for the suppression of sugar's moiety signals (SSMS). This sequence serves the crucial purpose of suppressing unwanted signals, with a particular emphasis on mitigating the interference caused by sugar moieties' signals. METHODS We have implemented this comprehensive approach to various NMR techniques, including 1D 1H presaturation (presat), 2D J-resolved (RES), 2D 1H-1H Total Correlation Spectroscopy (TOCSY), and 2D 1H-13C Heteronuclear Single Quantum Coherence (HSQC) for the samples of dates-flesh, honey, a standard stock solution of glucose, and nine amino acids, and commercial fetal bovine serum (FBS). RESULTS The outcomes of this approach were significant. The suppression of the high-intensity sugar signals has considerably enhanced the visibility and sensitivity of the signals emanating from the desired metabolites. CONCLUSION This, in turn, enables the identification of a greater number of metabolites. Additionally, it streamlines the experimental process, reducing the time required for the comparative quantification of metabolites in statistical studies in the field of metabolomics.
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Affiliation(s)
- Upendra Singh
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Ruba Al-Nemi
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia
| | - Fatimah Alahmari
- Department of Nanomedicine Research, Institute for Research & Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam, 31441, Saudi Arabia
| | - Abdul-Hamid Emwas
- Core Lab of NMR, King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia.
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, 23955-6900, Saudi Arabia.
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Baranovicova E, Kalenska D, Kaplan P, Kovalska M, Tatarkova Z, Lehotsky J. Blood and Brain Metabolites after Cerebral Ischemia. Int J Mol Sci 2023; 24:17302. [PMID: 38139131 PMCID: PMC10743907 DOI: 10.3390/ijms242417302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
The study of an organism's response to cerebral ischemia at different levels is essential to understanding the mechanism of the injury and protection. A great interest is devoted to finding the links between quantitative metabolic changes and post-ischemic damage. This work aims to summarize the outcomes of the most studied metabolites in brain tissue-lactate, glutamine, GABA (4-aminobutyric acid), glutamate, and NAA (N-acetyl aspartate)-regarding their biological function in physiological conditions and their role after cerebral ischemia/reperfusion. We focused on ischemic damage and post-ischemic recovery in both experimental-including our results-as well as clinical studies. We discuss the role of blood glucose in view of the diverse impact of hyperglycemia, whether experimentally induced, caused by insulin resistance, or developed as a stress response to the cerebral ischemic event. Additionally, based on our and other studies, we analyze and critically discuss post-ischemic alterations in energy metabolites and the elevation of blood ketone bodies observed in the studies on rodents. To complete the schema, we discuss alterations in blood plasma circulating amino acids after cerebral ischemia. So far, no fundamental brain or blood metabolite(s) has been recognized as a relevant biological marker with the feasibility to determine the post-ischemic outcome or extent of ischemic damage. However, studies from our group on rats subjected to protective ischemic preconditioning showed that these animals did not develop post-ischemic hyperglycemia and manifested a decreased metabolic infringement and faster metabolomic recovery. The metabolomic approach is an additional tool for understanding damaging and/or restorative processes within the affected brain region reflected in the blood to uncover the response of the whole organism via interorgan metabolic communications to the stressful cerebral ischemic challenge.
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Affiliation(s)
- Eva Baranovicova
- Biomedical Center BioMed, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia;
| | - Dagmar Kalenska
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia
| | - Peter Kaplan
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia (Z.T.)
| | - Maria Kovalska
- Department of Histology and Embryology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia
| | - Zuzana Tatarkova
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia (Z.T.)
| | - Jan Lehotsky
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Mala Hora 4, 036 01 Martin, Slovakia (Z.T.)
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Takis PG, Aggelidou VA, Sands CJ, Louka A. Mapping of 1 H NMR chemical shifts relationship with chemical similarities for the acceleration of metabolic profiling: Application on blood products. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2023; 61:759-769. [PMID: 37666776 PMCID: PMC10946494 DOI: 10.1002/mrc.5392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
One-dimensional (1D) proton-nuclear magnetic resonance (1 H-NMR) spectroscopy is an established technique for the deconvolution of complex biological sample types via the identification/quantification of small molecules. It is highly reproducible and could be easily automated for small to large-scale bioanalytical, epidemiological, and in general metabolomics studies. However, chemical shift variability is a serious issue that must still be solved in order to fully automate metabolite identification. Herein, we demonstrate a strategy to increase the confidence in assignments and effectively predict the chemical shifts of various NMR signals based upon the simplest form of statistical models (i.e., linear regression). To build these models, we were guided by chemical homology in serum/plasma metabolites classes (i.e., amino acids and carboxylic acids) and similarity between chemical groups such as methyl protons. Our models, built on 940 serum samples and validated in an independent cohort of 1,052 plasma-EDTA spectra, were able to successfully predict the 1 H NMR chemical shifts of 15 metabolites within ~1.5 linewidths (Δv1/2 ) error range on average. This pilot study demonstrates the potential of developing an algorithm for the accurate assignment of 1 H NMR chemical shifts based solely on chemically defined constraints.
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Affiliation(s)
- Panteleimon G. Takis
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome Centre, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Varvara A. Aggelidou
- Department of Biological Applications and TechnologiesUniversity of IoanninaIoanninaGreece
| | - Caroline J. Sands
- Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
- National Phenome Centre, Department of Metabolism, Digestion and ReproductionImperial College LondonLondonUK
| | - Alexandra Louka
- Department of Clinical and Experimental Epilepsy, Queen Square Institute of NeurologyUniversity College LondonLondonUK
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Mix T, Janneschütz J, Ludwig R, Eichbaum J, Fischer M, Hackl T. From Nontargeted to Targeted Analysis: Feature Selection in the Differentiation of Truffle Species ( Tuber spp.) Using 1H NMR Spectroscopy and Support Vector Machine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18074-18084. [PMID: 37934755 DOI: 10.1021/acs.jafc.3c05786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
The price of different truffle types varies according to their culinary value, sometimes by more than a factor of 10. Nonprofessionals can hardly distinguish visually the species within the white or black truffles, making the possibility of food fraud very easy. Therefore, the identification of different truffle species (Tuber spp.) is an analytical task that could be solved in this study. The polar extract from a total of 80 truffle samples was analyzed by 1H NMR spectroscopy in combination with chemometric methods covering five commercially relevant species. All classification models were validated applying a repeated nested cross-validation. In direct comparison, the two very similar looking and closely related black representatives Tuber melanosporum and Tuber indicum could be classified 100% correctly. The most expensive truffle Tuber magnatum could be distinguished 100% from the other relevant white truffle Tuber borchii. In addition, signals for a potential Tuber borchii and a potential Tuber melanosporum marker for targeted approaches could be detected, and the corresponding molecules were identified as betaine and ribonate. A model covering all five truffle species Tuber aestivum, Tuber borchii, Tuber indicum, Tuber magnatum, and Tuber melanosporum was able to correctly discriminate between each of the species.
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Affiliation(s)
- Thorsten Mix
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Jasmin Janneschütz
- Department of Pharmaceutical Sciences, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Rami Ludwig
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Julia Eichbaum
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Thomas Hackl
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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10
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Wenck S, Mix T, Fischer M, Hackl T, Seifert S. Opening the Random Forest Black Box of 1H NMR Metabolomics Data by the Exploitation of Surrogate Variables. Metabolites 2023; 13:1075. [PMID: 37887402 PMCID: PMC10608983 DOI: 10.3390/metabo13101075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
The untargeted metabolomics analysis of biological samples with nuclear magnetic resonance (NMR) provides highly complex data containing various signals from different molecules. To use these data for classification, e.g., in the context of food authentication, machine learning methods are used. These methods are usually applied as a black box, which means that no information about the complex relationships between the variables and the outcome is obtained. In this study, we show that the random forest-based approach surrogate minimal depth (SMD) can be applied for a comprehensive analysis of class-specific differences by selecting relevant variables and analyzing their mutual impact on the classification model of different truffle species. SMD allows the assignment of variables from the same metabolites as well as the detection of interactions between different metabolites that can be attributed to known biological relationships.
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Affiliation(s)
- Soeren Wenck
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany (M.F.); (T.H.)
| | - Thorsten Mix
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany;
| | - Markus Fischer
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany (M.F.); (T.H.)
| | - Thomas Hackl
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany (M.F.); (T.H.)
- Institute of Organic Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany;
| | - Stephan Seifert
- Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany (M.F.); (T.H.)
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Dos Santos K, Bertho G, Caradeuc C, Baud V, Montagne A, Abergel D, Giraud N, Baudin M. A Toolbox for Glutamine Use in Dissolution Dynamic Nuclear Polarization: from Enzymatic Reaction Monitoring to the Study of Cellular Metabolic Pathways and Imaging. Chemphyschem 2023; 24:e202300151. [PMID: 36973178 DOI: 10.1002/cphc.202300151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023]
Abstract
Glutamine is under scrutiny regarding its metabolic deregulation linked to energetic reprogramming in cancer cells. Many analytical techniques have been used to better understand the impact of the metabolism of amino acids on biological processes, however only a few are suited to work with complex samples. Here, we report the use of a general dissolution dynamic nuclear polarization (D-DNP) formulation using an unexpensive radical as a multipurpose tool to study glutamine, with insights from enzymatic modelling to complex metabolic networks and fast imaging. First, hyperpolarized [5-13 C] glutamine is used as molecular probe to study the kinetic action of two enzymes: L-asparaginase that has been used as an anti-metabolic treatment for cancer, and glutaminase. These results are also compared with those acquired with another hyperpolarized amino acid, [1,4-13 C] asparagine. Second, we explored the use of hyperpolarized (HP) substrates to probe metabolic pathways by monitoring metabolic profiles arising from hyperpolarized glutamine in E. coli extracts. Finally, a highly concentrated sample formulation is proposed for the purpose of fast imaging applications. We think that this approach can be extended to formulate other amino acids as well as other metabolites and provide complementary insights into the analysis of metabolic networks.
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Affiliation(s)
- Karen Dos Santos
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Gildas Bertho
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Cédric Caradeuc
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Véronique Baud
- Laboratoire NF-κB, Différenciation et Cancer, Université Paris Cité, 24, Rue du faubourg Saint Jacques, 75014, Paris, France
| | - Aurélie Montagne
- Laboratoire NF-κB, Différenciation et Cancer, Université Paris Cité, 24, Rue du faubourg Saint Jacques, 75014, Paris, France
| | - Daniel Abergel
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université, 45 Rue d'Ulm, 75005, Paris, France
| | - Nicolas Giraud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
| | - Mathieu Baudin
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, Université Paris Cité, 45, Rue des Saints Pères, 75006, Paris, France
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université, 45 Rue d'Ulm, 75005, Paris, France
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van der Kemp WJM, Grinde MT, Malvik JO, van Laarhoven HWM, Prompers JJ, Klomp DWJ, Burgering B, Bathen TF, Moestue SA. Metabolic profiling of colorectal cancer organoids: A comparison between high-resolution magic angle spinning magnetic resonance spectroscopy and solution nuclear magnetic resonance spectroscopy of polar extracts. NMR IN BIOMEDICINE 2023; 36:e4882. [PMID: 36451530 DOI: 10.1002/nbm.4882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 11/18/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Patient-derived cancer cells cultured in vitro are a cornerstone of cancer metabolism research. More recently, the introduction of organoids has provided the research community with a more versatile model system. Physiological structure and organization of the cell source tissue are maintained in organoids, representing a closer link to in vivo tumor models. High-resolution magic angle spinning magnetic resonance spectroscopy (HR MAS MRS) is a commonly applied analytical approach for metabolic profiling of intact tissue, but its use has not been reported for organoids. The aim of the current work was to compare the performance of HR MAS MRS and extraction-based nuclear magnetic resonance (NMR) in metabolic profiling of wild-type and tumor progression organoids (TPOs) from human colon cancer, and further to investigate how the sequentially increased genetic alterations of the TPOs affect the metabolic profile. Sixteen metabolites were reliably identified and quantified both in spectra based on NMR of extracts and HR MAS MRS of intact organoids. The metabolite concentrations from the two approaches were highly correlated (r = 0.94), and both approaches were able to capture the systematic changes in metabolic features introduced by the genetic alterations characteristic of colorectal cancer progression (e.g., increased levels of lactate and decreased levels of myo-inositol and phosphocholine with an increasing number of mutations). The current work highlights that HR MAS MRS is a well-suited method for metabolic profiling of intact organoids, with the additional benefit that the nondestructive nature of HR MAS enables subsequent recovery of the organoids for further analyses based on nucleic acids or proteins.
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Affiliation(s)
- Wybe J M van der Kemp
- Division of Imaging and Oncology, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Maria T Grinde
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Radiology and Nuclear Medicine, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Jon O Malvik
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Hanneke W M van Laarhoven
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanine J Prompers
- Division of Imaging and Oncology, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Dennis W J Klomp
- Division of Imaging and Oncology, University Medical Centre (UMC) Utrecht, Utrecht, The Netherlands
| | - Boudewijn Burgering
- Center for Molecular Medicine, Molecular Cancer Research, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Tone Frost Bathen
- Department of Circulation and Medical Imaging, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Siver Andreas Moestue
- Department of Clinical and Molecular Medicine, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- Department of Pharmacy, Nord University, Bodø, Norway
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Alfaifi A, Refai MY, Alsaadi M, Bahashwan S, Malhan H, Al-Kahiry W, Dammag E, Ageel A, Mahzary A, Albiheyri R, Almehdar H, Qadri I. Metabolomics: A New Era in the Diagnosis or Prognosis of B-Cell Non-Hodgkin's Lymphoma. Diagnostics (Basel) 2023; 13:diagnostics13050861. [PMID: 36900005 PMCID: PMC10000528 DOI: 10.3390/diagnostics13050861] [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: 01/20/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
A wide range of histological as well as clinical properties are exhibited by B-cell non-Hodgkin's lymphomas. These properties could make the diagnostics process complicated. The diagnosis of lymphomas at an initial stage is essential because early remedial actions taken against destructive subtypes are commonly deliberated as successful and restorative. Therefore, better protective action is needed to improve the condition of those patients who are extensively affected by cancer when diagnosed for the first time. The development of new and efficient methods for early detection of cancer has become crucial nowadays. Biomarkers are urgently needed for diagnosing B-cell non-Hodgkin's lymphoma and assessing the severity of the disease and its prognosis. New possibilities are now open for diagnosing cancer with the help of metabolomics. The study of all the metabolites synthesised in the human body is called "metabolomics." A patient's phenotype is directly linked with metabolomics, which can help in providing some clinically beneficial biomarkers and is applied in the diagnostics of B-cell non-Hodgkin's lymphoma. In cancer research, it can analyse the cancerous metabolome to identify the metabolic biomarkers. This review provides an understanding of B-cell non-Hodgkin's lymphoma metabolism and its applications in medical diagnostics. A description of the workflow based on metabolomics is also provided, along with the benefits and drawbacks of various techniques. The use of predictive metabolic biomarkers for the diagnosis and prognosis of B-cell non-Hodgkin's lymphoma is also explored. Thus, we can say that abnormalities related to metabolic processes can occur in a vast range of B-cell non-Hodgkin's lymphomas. The metabolic biomarkers could only be discovered and identified as innovative therapeutic objects if we explored and researched them. In the near future, the innovations involving metabolomics could prove fruitful for predicting outcomes and bringing out novel remedial approaches.
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Affiliation(s)
- Abdullah Alfaifi
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Fayfa General Hospital, Ministry of Health, Jazan 83581, Saudi Arabia
| | - Mohammed Y. Refai
- Department of Biochemistry, College of Science, University of Jeddah, Jeddah 21493, Saudi Arabia
| | - Mohammed Alsaadi
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Hematology Research Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salem Bahashwan
- Hematology Research Unit, King Fahad Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Department of Hematology, Faculty of Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- King Abdulaziz University Hospital, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hafiz Malhan
- Prince Mohammed Bin Nasser Hospital, Ministry of Health, Jazan 82943, Saudi Arabia
| | - Waiel Al-Kahiry
- Prince Mohammed Bin Nasser Hospital, Ministry of Health, Jazan 82943, Saudi Arabia
| | - Enas Dammag
- Prince Mohammed Bin Nasser Hospital, Ministry of Health, Jazan 82943, Saudi Arabia
| | - Ageel Ageel
- Prince Mohammed Bin Nasser Hospital, Ministry of Health, Jazan 82943, Saudi Arabia
| | - Amjed Mahzary
- Eradah Hospital, Ministry of Health, Jazan 82943, Saudi Arabia
| | - Raed Albiheyri
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hussein Almehdar
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Ishtiaq Qadri
- Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence:
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Saraiva A, Carrascosa C, Ramos F, Raheem D, Lopes M, Raposo A. Coconut Sugar: Chemical Analysis and Nutritional Profile; Health Impacts; Safety and Quality Control; Food Industry Applications. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3671. [PMID: 36834366 PMCID: PMC9964017 DOI: 10.3390/ijerph20043671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Consumers often wish to substitute refined sugar with alternative sweeteners, such as coconut sugar, given growing interest in healthy eating and the public's negative perception of excess sugar intake. Coconut sugar is a healthier, sweetener option than the majority of other sugars that are commercially available. Sap is collected from trees to be transported, stored, and evaporated during processing, which are labor- and resource-intensive operations. Consequently, the cost of production is higher than it is for cane sugar. Given its high nutritional value and low glycemic index, people are willing to pay higher prices for it. However, one barrier is ignorance of its health benefits. This review examines and deals in-depth with the most significant features of coconut sugar chemical analyses to focus on several analytical methodologies given the increasing demand for naturally derived sweeteners in the last 10 years. A deeper understanding of the quality control, safety, health effects, nutritional profile, and sustainability issues corresponding to coconut sugar is necessary to effectively implement them in the food industry.
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Affiliation(s)
- Ariana Saraiva
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - Conrado Carrascosa
- Department of Animal Pathology and Production, Bromatology and Food Technology, Faculty of Veterinary, Universidad de Las Palmas de Gran Canaria, Trasmontaña s/n, 35413 Arucas, Spain
| | - Fernando Ramos
- Faculty of Pharmacy, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
| | - Dele Raheem
- Northern Institute for Environmental and Minority Law (NIEM), Arctic Centre, University of Lapland, 96101 Rovaniemi, Finland
| | - Maria Lopes
- Faculty of Pharmacy, University of Coimbra, Azinhaga de Santa Comba, 3000-548 Coimbra, Portugal
- Associated Laboratory for Green Chemistry (LAQV) of the Network of Chemistry and Technology (REQUIMTE), Rua D. Manuel II, Apartado 55142, 4051-401 Porto, Portugal
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades e Tecnologias, Campo Grande 376, 1749-024 Lisboa, Portugal
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Qiu Y, Xu Z, Xie Q, Zhang R, Wang L, Zhao L, Liu H. Association of plasma lipid metabolism profiles with overall survival for patients with gastric cancer undergoing gastrectomy based on 1H-NMR spectroscopy. Nutr Metab (Lond) 2023; 20:7. [PMID: 36750880 PMCID: PMC9903497 DOI: 10.1186/s12986-023-00728-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Lipid metabolism dysregulation is a prominent metabolic alteration in various cancers. The study aimed to explore the association of plasma lipid metabolism profiles with overall survival (OS) for gastric cancer (GC) patients who received gastrectomy. METHODS GC patients who were treated with gastrectomy and measured with plasma lipid metabolism profiles using proton nuclear magnetic resonance (1H-NMR) spectroscopy in Nanfang Hospital between January 1, 2017, and October 31, 2018, were recruited. The Least Absolute Shrinkage and Selection Operator (LASSO) regression model was used to analyze variables selected by univariate analysis for OS. An index of plasma lipid metabolism profiles, named plasma lipid metabolism index (PLMI), was constructed by variables' coefficients in LASSO regression to explore its association with OS and its role in the prediction model. RESULTS A total of 158 GC patients were included in this study. Four of the 110 lipid profiles, including LDL-5 Apo-B, LDL-4 Cholesterol, HDL-4 Apo-A2, and HDL-4 Free Cholesterol, were selected to construct the PLMI. The optimal cut-off value of PLMI for OS was used to classify the population into two subgroups, the high PLMI group (≥ - 0.163) and the low PLMI group (< - 0.163). The high PLMI group had a shorter OS (p = 0.0034) and was the independent risk factor for OS (Hazard Ratio = 2.13, 95% Confidence Interval (CI): 1.07-4.22, p = 0.031) after adjusting for perineural invasion and tumor stage. In subsets of the I-III stage and treating postoperative chemotherapy, high PLMI also had an unfavorable correlation with OS (p = 0.016 and p = 0.0086, respectively). The nomogram prediction models of both the training cohort and validation cohort showed good calibration and discrimination with the concordance indexes of 0.806 (95% CI, 0.732-0.880) in the training cohort and 0.794 (95% CI, 0.725-0.862) in the validation cohort. CONCLUSIONS This study found that the index derived from the LDL-5 Apo-B, LDL-4 Cholesterol, HDL-4 Apo-A2, and HDL-4 Free Cholesterol, was significantly associated with overall survival, suggesting that regulating lipid metabolisms might improve the prognosis for GC patients.
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Affiliation(s)
- Yaopeng Qiu
- grid.284723.80000 0000 8877 7471Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou, 510515 China
| | - Zhou Xu
- grid.284723.80000 0000 8877 7471Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou, 510515 China
| | - Qingfeng Xie
- grid.284723.80000 0000 8877 7471Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou, 510515 China
| | - Renyi Zhang
- grid.284723.80000 0000 8877 7471Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou, 510515 China
| | - Luyao Wang
- Guangdong IFV Biomedical Technology Co., Ltd, Foshan, China
| | - Liying Zhao
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou, 510515, China.
| | - Hao Liu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, 1838 North Guangzhou Ave, Guangzhou, 510515, China.
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Targeting mitochondrial impairment for the treatment of cardiovascular diseases: From hypertension to ischemia-reperfusion injury, searching for new pharmacological targets. Biochem Pharmacol 2023; 208:115405. [PMID: 36603686 DOI: 10.1016/j.bcp.2022.115405] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023]
Abstract
Mitochondria and mitochondrial proteins represent a group of promising pharmacological target candidates in the search of new molecular targets and drugs to counteract the onset of hypertension and more in general cardiovascular diseases (CVDs). Indeed, several mitochondrial pathways result impaired in CVDs, showing ATP depletion and ROS production as common traits of cardiac tissue degeneration. Thus, targeting mitochondrial dysfunction in cardiomyocytes can represent a successful strategy to prevent heart failure. In this context, the identification of new pharmacological targets among mitochondrial proteins paves the way for the design of new selective drugs. Thanks to the advances in omics approaches, to a greater availability of mitochondrial crystallized protein structures and to the development of new computational approaches for protein 3D-modelling and drug design, it is now possible to investigate in detail impaired mitochondrial pathways in CVDs. Furthermore, it is possible to design new powerful drugs able to hit the selected pharmacological targets in a highly selective way to rescue mitochondrial dysfunction and prevent cardiac tissue degeneration. The role of mitochondrial dysfunction in the onset of CVDs appears increasingly evident, as reflected by the impairment of proteins involved in lipid peroxidation, mitochondrial dynamics, respiratory chain complexes, and membrane polarization maintenance in CVD patients. Conversely, little is known about proteins responsible for the cross-talk between mitochondria and cytoplasm in cardiomyocytes. Mitochondrial transporters of the SLC25A family, in particular, are responsible for the translocation of nucleotides (e.g., ATP), amino acids (e.g., aspartate, glutamate, ornithine), organic acids (e.g. malate and 2-oxoglutarate), and other cofactors (e.g., inorganic phosphate, NAD+, FAD, carnitine, CoA derivatives) between the mitochondrial and cytosolic compartments. Thus, mitochondrial transporters play a key role in the mitochondria-cytosol cross-talk by leading metabolic pathways such as the malate/aspartate shuttle, the carnitine shuttle, the ATP export from mitochondria, and the regulation of permeability transition pore opening. Since all these pathways are crucial for maintaining healthy cardiomyocytes, mitochondrial carriers emerge as an interesting class of new possible pharmacological targets for CVD treatments.
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Shekher A, Puneet, Awasthee N, Kumar U, Raj R, Kumar D, Gupta SC. Association of altered metabolic profiles and long non-coding RNAs expression with disease severity in breast cancer patients: analysis by 1H NMR spectroscopy and RT-q-PCR. Metabolomics 2023; 19:8. [PMID: 36710275 DOI: 10.1007/s11306-023-01972-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Globally, one of the major causes of cancer related deaths in women is breast cancer. Although metabolic pattern is altered in cancer patients, robust metabolic biomarkers with a potential to improve the screening and disease monitoring are lacking. A complete metabolome profiling of breast cancer patients may lead to the identification of diagnostic/prognostic markers and potential targets. OBJECTIVES The aim of this study was to analyze the metabolic profile in the serum from 43 breast cancer patients and 13 healthy individuals. MATERIALS & METHODS We used 1H NMR spectroscopy for the identification and quantification of metabolites. q-RT-PCR was used to examine the relative expression of lncRNAs. RESULTS Metabolites such as amino acids, lipids, membrane metabolites, lipoproteins, and energy metabolites were observed in the serum from both patients and healthy individuals. Using unsupervised PCA, supervised PLS-DA, supervised OPLS-DA, and random forest classification, we observed that more than 25 metabolites were altered in the breast cancer patients. Metabolites with AUC value > 0.9 were selected for further analysis that revealed significant elevation of lactate, LPR and glycerol, while the level of glucose, succinate, and isobutyrate was reduced in breast cancer patients in comparison to healthy control. The level of these metabolites (except LPR) was altered in advanced-stage breast cancer patients in comparison to early-stage breast cancer patients. The altered metabolites were also associated with over 25 signaling pathways related to metabolism. Further, lncRNAs such as H19, MEG3 and GAS5 were dysregulated in the breast tumor tissue in comparison to normal adjacent tissue. CONCLUSION The study provides insights into metabolic alteration in breast cancer patients. It also provides an avenue to examine the association of lncRNAs with metabolic patterns in patients.
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Affiliation(s)
- Anusmita Shekher
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221 005, India
- Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221 005, India
| | - Puneet
- Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, 221 005, India
| | - Nikee Awasthee
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221 005, India
- Department of Anatomy and Cell Biology, College of Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Umesh Kumar
- Centre of Biomedical Research (CBMR), SGPGIMS, Lucknow, Uttar Pradesh, 226 014, India
| | - Ritu Raj
- Centre of Biomedical Research (CBMR), SGPGIMS, Lucknow, Uttar Pradesh, 226 014, India
| | - Dinesh Kumar
- Centre of Biomedical Research (CBMR), SGPGIMS, Lucknow, Uttar Pradesh, 226 014, India.
| | - Subash Chandra Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, 221 005, India.
- Department of Biochemistry, All India Institute of Medical Sciences, Guwahati, Assam, 781101, India.
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Ahmad F, Nadeem H. Mass Spectroscopy as an Analytical Tool to Harness the Production of Secondary Plant Metabolites: The Way Forward for Drug Discovery. Methods Mol Biol 2023; 2575:77-103. [PMID: 36301472 DOI: 10.1007/978-1-0716-2716-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The molecular map of diverse biological molecules linked with structure, function, signaling, and regulation within a cell can be elucidated using an analytically demanding omic approach. The latest trend of using "metabolomics" technologies has explained the natural phenomenon of opening a new avenue to understand and enhance bioactive compounds' production. Examination of sequenced plant genomes has revealed that a considerable portion of these encodes genes of secondary metabolism. In addition to genetic and molecular tools developed in the current era, the ever-increasing knowledge about plant metabolism's biochemistry has initiated an approach for wisely designed, more productive genetic engineering of plant secondary metabolism for improved defense systems and enhanced biosynthesis of beneficial metabolites. Secondary plant metabolites are natural products synthesized by plants that are not directly involved with their average growth and development but play a vital role in plant defense mechanisms. Plant secondary metabolites are classified into four major classes: terpenoids, phenolic compounds, alkaloids, and sulfur-containing compounds. More than 200,000 secondary metabolites are synthesized by plants having a unique and complex structure. Secondary plant metabolites are well characterized and quantified by omics approaches and therefore used by humans in different sectors such as agriculture, pharmaceuticals, chemical industries, and biofuel. The aim is to establish metabolomics as a comprehensive and dynamic model of diverse biological molecules for biomarkers and drug discovery. In this chapter, we aim to illustrate the role of metabolomic technology, precisely liquid chromatography-mass spectrometry, capillary electrophoresis mass spectrometry, gas chromatography-mass spectrometry, and nuclear magnetic resonance spectroscopy, specifically as a research tool in the production and identification of novel bioactive compounds for drug discovery and to obtain a unified insight of secondary metabolism in plants.
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Affiliation(s)
- Faheem Ahmad
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India.
| | - Hera Nadeem
- Department of Botany, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Abstract
Nuclear Magnetic Resonance (NMR) spectroscopy is one of the two major analytical platforms in the field of metabolomics, the other being mass spectrometry (MS). NMR is less sensitive than MS and hence it detects a relatively small number of metabolites. However, NMR exhibits numerous unique characteristics including its high reproducibility and non-destructive nature, its ability to identify unknown metabolites definitively, and its capabilities to obtain absolute concentrations of all detected metabolites, sometimes even without an internal standard. These characteristics outweigh the relatively low sensitivity and resolution of NMR in metabolomics applications. Since biological mixtures are highly complex, increased demand for new methods to improve detection, better identify unknown metabolites, and provide more accurate quantitation continues unabated. Technological and methodological advances to date have helped to improve the resolution and sensitivity and detection of a larger number of metabolite signals. Efforts focused on measuring unknown metabolite signals have resulted in the identification and quantitation of an expanded pool of metabolites including labile metabolites such as cellular redox coenzymes, energy coenzymes, and antioxidants. This chapter describes quantitative NMR methods in metabolomics with an emphasis on recent methodological developments, while highlighting the benefits and challenges of NMR-based metabolomics.
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Affiliation(s)
- G A Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, WA, USA.
- Mitochondria and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA.
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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Hu R, Li Y, Yang Y, Liu M. Mass spectrometry-based strategies for single-cell metabolomics. MASS SPECTROMETRY REVIEWS 2023; 42:67-94. [PMID: 34028064 DOI: 10.1002/mas.21704] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 06/12/2023]
Abstract
Single cell analysis has drawn increasing interest from the research community due to its capability to interrogate cellular heterogeneity, allowing refined tissue classification and facilitating novel biomarker discovery. With the advancement of relevant instruments and techniques, it is now possible to perform multiple omics including genomics, transcriptomics, metabolomics or even proteomics at single cell level. In comparison with other omics studies, single-cell metabolomics (SCM) represents a significant challenge since it involves many types of dynamically changing compounds with a wide range of concentrations. In addition, metabolites cannot be amplified. Although difficult, considerable progress has been made over the past decade in mass spectrometry (MS)-based SCM in terms of processing technologies and biochemical applications. In this review, we will summarize recent progress in the development of promising MS platforms, sample preparation methods and SCM analysis of various cell types (including plant cell, cancer cell, neuron, embryo cell, and yeast cell). Current limitations and future research directions in the field of SCM will also be discussed.
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Affiliation(s)
- Rui Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
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Quantitative Methods for Metabolite Analysis in Metabolic Engineering. BIOTECHNOL BIOPROC E 2022. [DOI: 10.1007/s12257-022-0200-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Bushell SM, Wright BA, Knue J, Tomco PL. 1H NMR-based metabolomics investigation on the biological effects of paralytic shellfish toxin in mussel Mytilus trossulus. MARINE POLLUTION BULLETIN 2022; 185:114326. [PMID: 36395714 DOI: 10.1016/j.marpolbul.2022.114326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Abstract
Paralytic shellfish poisoning is a global issue that would benefit from additional screening methods and rapid testing capacities. In this study, we applied 1H NMR spectroscopy-based metabolomics to identify biomarkers of Paralytic Shellfish Toxin (PST) exposure. We characterized the metabolic phenotypes of field-collected Alaskan mussels Mytilus trossulus across a wide range of bioaccumulated PST levels, from 0 to 1590 μg/100 g. A between-level grouping emerged for high (740-1590 μg/100 g) compared to low/non-detect (0-3.91 μg/100 g) PST levels. High levels of PST contamination in mussels were consistent with alterations to energy and amino acid metabolism, and disturbances in osmoregulation. This research demonstrates the effectiveness of 1H NMR-based metabolomics in elucidating the biological effects of paralytic shellfish toxin on the health of wild mussel populations, spatial variation, and identifies a metabolic signature indicative of PST contamination in Mytilus trossulus for potential use in a PSP biomarker panel.
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Affiliation(s)
- Solomia M Bushell
- Department of Biology, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, United States of America.
| | - Bruce A Wright
- Knik Tribe of Alaska, 1744 Prospect Dr., Palmer, AK 99645, United States of America
| | - Jacqueline Knue
- Department of Environmental Conservation, Alaska State Environmental Health Laboratory, Department of Environmental Conservation, 5251 Dr. MLK Jr. Ave, Anchorage, AK 99507, United States of America
| | - Patrick L Tomco
- Department of Biology, University of Alaska Anchorage, 3211 Providence Dr., Anchorage, AK 99508, United States of America
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23
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Bhinderwala F, E Roth H, Noel H, Feng D, Powers R. Chemical shift variations in common metabolites. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 345:107335. [PMID: 36410060 PMCID: PMC9742302 DOI: 10.1016/j.jmr.2022.107335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/31/2022] [Accepted: 11/09/2022] [Indexed: 05/12/2023]
Abstract
The reliability and robustness of metabolite assignments in 1H NMR is complicated by numerous factors including variations in temperature, pH, buffer choice, ionic strength, and mixture composition that led to peak overlap and spectral crowding. As sample conditions fluctuate, peak drift and line broadening further complicate peak deconvolution and subsequent chemical assignment. We present a collection of 1D 1H NMR spectra of 54 common metabolites at varied pH (6.0 to 8.0 in 0.5 step increments) and temperature (290 K to 308 K) to quantify chemical shift variability to facilitate automated metabolite assignments. Our results illustrate the fundamental challenges with accurately assigning NMR peaks under varied environmental conditions prevalent in complex mixtures. Phosphorylated metabolites showed a larger variation in chemical shifts due to pH, whereas; amino acids showed a higher variation due to temperature. Mixtures of phosphorous compounds showed a consistently poor reliability in achieving an accurate assignment. Phosphorylated cholines, amino acids, and glycerols yielded a 40 % false negative rate for 7 out of 9 mixture conditions. Amino acids had a false negative rate of 57 % at 298 K and pH 8. Our results demonstrate that the automated assignments of complex biofluid mixtures require an expert to intervene to confirm the accuracy of metabolite assignments. Our analysis also indicates the need for reference databases to include spectra under a variety of conditions that includes mixtures and a range of pH and temperature to improve the accuracy and reproducibility of metabolite assignments.
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Affiliation(s)
- Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States; University of Pittsburgh School of Medicine, Department of Structural Biology, Pittsburgh, PA 15260, United States(2)
| | - Heidi E Roth
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Hannah Noel
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Dennis Feng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States; Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, United States.
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24
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Bhinderwala F, Vu T, Smith TG, Kosacki J, Marshall DD, Xu Y, Morton M, Powers R. Leveraging the HMBC to Facilitate Metabolite Identification. Anal Chem 2022; 94:16308-16318. [PMID: 36374521 PMCID: PMC10948112 DOI: 10.1021/acs.analchem.2c02902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The accuracy and ease of metabolite assignments from a complex mixture are expected to be facilitated by employing a multispectral approach. The two-dimensional (2D) 1H-13C heteronuclear single quantum coherence (HSQC) and 2D 1H-1H-total correlation spectroscopy (TOCSY) are the experiments commonly used for metabolite assignments. The 2D 1H-13C HSQC-TOCSY and 2D 1H-13C heteronuclear multiple-bond correlation (HMBC) are routinely used by natural products chemists but have seen minimal usage in metabolomics despite the unique information, the nearly complete 1H-1H and 1H-13C and spin systems provided by these experiments that may improve the accuracy and reliability of metabolite assignments. The use of a 13C-labeled feedstock such as glucose is a routine practice in metabolomics to improve sensitivity and to emphasize the detection of specific metabolites but causes severe artifacts and an increase in spectral complexity in the HMBC experiment. To address this issue, the standard HMBC pulse sequence was modified to include carbon decoupling. Nonuniform sampling was also employed for rapid data collection. A dataset of reference 2D 1H-13C HMBC spectra was collected for 94 common metabolites. 13C-13C spin connectivity was then obtained by generating a covariance pseudo-spectrum from the carbon-decoupled HMBC and the 1H-13C HSQC-TOCSY spectra. The resulting 13C-13C pseudo-spectrum provides a connectivity map of the entire carbon backbone that uniquely describes each metabolite and would enable automated metabolite identification.
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Affiliation(s)
- Fatema Bhinderwala
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, United States
| | - Thao Vu
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0963, United States
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045-2609
| | - Thomas G. Smith
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
| | - Julian Kosacki
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
| | - Darrell D. Marshall
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
| | - Yuhang Xu
- Department of Statistics, University of Nebraska-Lincoln, Lincoln, Nebraska 68583-0963, United States
- Department of Applied Statistics and Operations Research, Bowling Green State University, Bowling Green, Ohio 43403-0001
| | - Martha Morton
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln Nebraska 68588-0304
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25
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Pillai MS, Paritala ST, Shah RP, Sharma N, Sengupta P. Cutting-edge strategies and critical advancements in characterization and quantification of metabolites concerning translational metabolomics. Drug Metab Rev 2022; 54:401-426. [PMID: 36351878 DOI: 10.1080/03602532.2022.2125987] [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: 11/11/2022]
Abstract
Despite remarkable progress in drug discovery strategies, significant challenges are still remaining in translating new insights into clinical applications. Scientists are devising creative approaches to bridge the gap between scientific and translational research. Metabolomics is a unique field among other omics techniques for identifying novel metabolites and biomarkers. Fortunately, characterization and quantification of metabolites are becoming faster due to the progress in the field of orthogonal analytical techniques. This review detailed the advancement in the progress of sample preparation, and data processing techniques including data mining tools, database, and their quality control (QC). Advances in data processing tools make it easier to acquire unbiased data that includes a diverse set of metabolites. In addition, novel breakthroughs including, miniaturization as well as their integration with other devices, metabolite array technology, and crystalline sponge-based method have led to faster, more efficient, cost-effective, and holistic metabolomic analysis. The use of cutting-edge techniques to identify the human metabolite, including biomarkers has proven to be advantageous in terms of early disease identification, tracking the progression of illness, and possibility of personalized treatments. This review addressed the constraints of current metabolomics research, which are impeding the facilitation of translation of research from bench to bedside. Nevertheless, the possible way out from such constraints and future direction of translational metabolomics has been conferred.
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Affiliation(s)
- Megha Sajakumar Pillai
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, India
| | - Sree Teja Paritala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, India
| | - Ravi P Shah
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, India
| | - Nitish Sharma
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, India
| | - Pinaki Sengupta
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research (NIPER), Ahmedabad, India
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26
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Abdelzaher H, Tawfik SM, Nour A, Abdelkader S, Elbalkiny ST, Abdelkader M, Abbas WA, Abdelnaser A. Climate change, human health, and the exposome: Utilizing OMIC technologies to navigate an era of uncertainty. Front Public Health 2022; 10:973000. [PMID: 36211706 PMCID: PMC9533016 DOI: 10.3389/fpubh.2022.973000] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/17/2022] [Indexed: 01/25/2023] Open
Abstract
Climate change is an anthropogenic phenomenon that is alarming scientists and non-scientists alike. The emission of greenhouse gases is causing the temperature of the earth to rise and this increase is accompanied by a multitude of climate change-induced environmental exposures with potential health impacts. Tracking human exposure has been a major research interest of scientists worldwide. This has led to the development of exposome studies that examine internal and external individual exposures over their lifetime and correlate them to health. The monitoring of health has also benefited from significant technological advances in the field of "omics" technologies that analyze physiological changes on the nucleic acid, protein, and metabolism levels, among others. In this review, we discuss various climate change-induced environmental exposures and their potential health implications. We also highlight the potential integration of the technological advancements in the fields of exposome tracking, climate monitoring, and omics technologies shedding light on important questions that need to be answered.
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Affiliation(s)
| | | | | | | | | | | | | | - Anwar Abdelnaser
- Institute of Global Health and Human Ecology, The American University in Cairo, New Cairo, Egypt
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27
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Plant Metabolomics as a Tool for Detecting Adulterants in Edible Plant: A Case Study of Allium ursinum. Metabolites 2022; 12:metabo12090849. [PMID: 36144253 PMCID: PMC9501555 DOI: 10.3390/metabo12090849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022] Open
Abstract
Allium ursinum and poisonous adulterants Convallaria majalis and Arum maculatum were used as a model for detection of adulterants in edible plant. A. ursinum samples were spiked with C. majalis and A. maculatum to mimic adulteration. Metabolomic fingerprinting of all samples was performed using 1H NMR spectroscopy, and the resulting data sets were subjected to multivariate data analysis. As a result of this analysis, signals of adulterants were extracted from the data, and the structures of biomarkers of adulteration from partially purified samples were elucidated using 2D NMR and LC-MS techniques. Thus, isovitexin and vicenin II, azetidine-2-carboxylic acid, and trigonelline indicated adulteration of A. ursinum samples with C. majalis. Isovitexin was also recognized to be an indicator of adulteration of A. ursinum with A. maculatum. In conclusion, the case study of A. ursinum suggested that plant metabolomics approach could be utilized for identification of low molecular weight biomarkers of adulteration in edible plants.
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28
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Stability of Metabolomic Content during Sample Preparation: Blood and Brain Tissues. Metabolites 2022; 12:metabo12090811. [PMID: 36144215 PMCID: PMC9505456 DOI: 10.3390/metabo12090811] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Thermal and enzymatic reactions can significantly change the tissue metabolomic content during the sample preparation. In this work, we evaluated the stability of metabolites in human whole blood, serum, and rat brain, as well as in metabolomic extracts from these tissues. We measured the concentrations of 63 metabolites in brain and 52 metabolites in blood. We have shown that metabolites in the extracts from biological tissues are stable within 24 h at 4 °C. Serum and whole blood metabolomes are also rather stable, changes in metabolomic content of the whole blood homogenate become apparent only after 1–2 h of incubation at 4 °C, and become strong after 24 h. The most significant changes correspond to energy metabolites: the concentrations of ATP and ADP decrease fivefold, and the concentrations of NAD, NADH, and NADPH decrease below the detectable level. A statistically significant increase was observed for AMP, IMP, hypoxanthine, and nicotinamide. The brain tissue is much more metabolically active than human blood, and significant metabolomic changes occur already within the first several minutes during the brain harvest and sample homogenization. At a longer timescale (hours), noticeable changes were observed for all classes of compounds, including amino acids, organic acids, alcohols, amines, sugars, nitrogenous bases, nucleotides, and nucleosides.
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29
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NMR Metabolomics in Serum Fingerprinting of Schizophrenia Patients in a Serbian Cohort. Metabolites 2022; 12:metabo12080707. [PMID: 36005580 PMCID: PMC9416612 DOI: 10.3390/metabo12080707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/19/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
Schizophrenia is a widespread mental disorder that leads to significant functional impairments and premature death. The state of the art indicates gaps in the understanding and diagnosis of this disease, but also the need for personalized and precise approaches to patients through customized medical treatment and reliable monitoring of treatment response. In order to fulfill existing gaps, the establishment of a universal set of disorder biomarkers is a necessary step. Metabolomic investigations of serum samples of Serbian patients with schizophrenia (51) and healthy controls (39), based on NMR analyses associated with chemometrics, led to the identification of 26 metabolites/biomarkers for this disorder. Principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) models with prediction accuracies of 0.9718 and higher were accomplished during chemometric analysis. The established biomarker set includes aspartate/aspartic acid, lysine, 2-hydroxybutyric acid, and acylglycerols, which are identified for the first time in schizophrenia serum samples by NMR experiments. The other 22 identified metabolites in the Serbian samples are in accordance with the previously established NMR-based serum biomarker sets of Brazilian and/or Chinese patient samples. Thirteen metabolites (lactate/lactic acid, threonine, leucine, isoleucine, valine, glutamine, asparagine, alanine, gamma-aminobutyric acid, choline, glucose, glycine and tyrosine) that are common for three different ethnic and geographic origins (Serbia, Brazil and China) could be a good start point for the setup of a universal NMR serum biomarker set for schizophrenia.
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30
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Sharon I, Quijada NM, Pasolli E, Fabbrini M, Vitali F, Agamennone V, Dötsch A, Selberherr E, Grau JH, Meixner M, Liere K, Ercolini D, de Filippo C, Caderni G, Brigidi P, Turroni S. The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept. Nutrients 2022; 14:nu14142872. [PMID: 35889831 PMCID: PMC9323970 DOI: 10.3390/nu14142872] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.
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Affiliation(s)
- Itai Sharon
- Migal-Galilee Research Institute, P.O. Box 831, Kiryat Shmona 11016, Israel
- Faculty of Sciences and Technology, Tel-Hai Academic College, Upper Galilee 1220800, Israel
- Correspondence:
| | - Narciso Martín Quijada
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, A-3430 Tulln an der Donau, Austria
| | - Edoardo Pasolli
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Francesco Vitali
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Valeria Agamennone
- Microbiology and Systems Biology, Netherlands Organization for Applied Scientific Research (TNO), Utrechtseweg 48, 3704 HE Zeist, The Netherlands;
| | - Andreas Dötsch
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut (MRI)-Federal Research Institute of Nutrition and Food, 76131 Karlsruhe, Germany;
| | - Evelyne Selberherr
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, A-1210 Vienna, Austria; (N.M.Q.); (E.S.)
| | - José Horacio Grau
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
- Center for Species Survival, Smithsonian Conservation Biology Institute, Washington, DC 20008, USA
| | - Martin Meixner
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Karsten Liere
- Amedes Genetics, Amedes Medizinische Dienstleistungen GmbH, 10117 Berlin, Germany; (J.H.G.); (M.M.); (K.L.)
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, 80055 Portici, Italy; (E.P.); (D.E.)
- Task Force on Microbiome Studies, University of Naples Federico II, 80055 Portici, Italy
| | - Carlotta de Filippo
- Institute of Agricultural Biology and Biotechnology (IBBA), National Research Council (CNR), Via Moruzzi 1, 56124 Pisa, Italy; (F.V.); (C.d.F.)
| | - Giovanna Caderni
- NEUROFARBA Department, Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini 6, 50139 Florence, Italy;
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy;
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy; (M.F.); (S.T.)
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31
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Li DW, Leggett A, Bruschweiler-Li L, Brüschweiler R. COLMARq: A Web Server for 2D NMR Peak Picking and Quantitative Comparative Analysis of Cohorts of Metabolomics Samples. Anal Chem 2022; 94:8674-8682. [PMID: 35672005 PMCID: PMC9218957 DOI: 10.1021/acs.analchem.2c00891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Highly quantitative metabolomics studies of complex biological mixtures are facilitated by the resolution enhancement afforded by 2D NMR spectra such as 2D 13C-1H HSQC spectra. Here, we describe a new public web server, COLMARq, for the semi-automated analysis of sets of 2D HSQC spectra of cohorts of samples. The workflow of COLMARq includes automated peak picking using the deep neural network DEEP Picker, quantitative cross-peak volume extraction by numerical fitting using Voigt Fitter, the matching of corresponding cross-peaks across cohorts of spectra, peak volume normalization between different spectra, database query for metabolite identification, and basic univariate and multivariate statistical analyses of the results. COLMARq allows the analysis of cross-peaks that belong to both known and unknown metabolites. After a user has uploaded cohorts of 2D 13C-1H HSQC and optionally 2D 1H-1H TOCSY spectra in their preferred format, all subsequent steps on the web server can be performed fully automatically, allowing manual editing if needed and the sessions can be saved for later use. The accuracy, versatility, and interactive nature of COLMARq enables quantitative metabolomics analysis, including biomarker identification, of a broad range of complex biological mixtures as is illustrated for cohorts of samples from bacterial cultures of Pseudomonas aeruginosa in both its biofilm and planktonic states.
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Affiliation(s)
- Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Abigail Leggett
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rafael Brüschweiler
- Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, United States
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32
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Fraser R, Rutjes FPJT, Feiters MC, Tessari M. Analysis of Complex Mixtures by Chemosensing NMR Using para-Hydrogen-Induced Hyperpolarization. Acc Chem Res 2022; 55:1832-1844. [PMID: 35709417 PMCID: PMC9260963 DOI: 10.1021/acs.accounts.1c00796] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Nuclear magnetic resonance (NMR) is a powerful technique for chemical
analysis. The use of NMR to investigate dilute analytes in complex
systems is, however, hampered by its relatively low sensitivity. An
additional obstacle is represented by the NMR signal overlap. Because
solutes in a complex mixture are usually not isotopically labeled,
NMR studies are often limited to 1H measurements, which,
because of the modest dispersion of the 1H resonances (typically
∼10 ppm), can result in challenging signal crowding. The low
NMR sensitivity issue can be alleviated by nuclear spin hyperpolarization
(i.e., transiently increasing the differences in nuclear spin populations),
which determines large NMR signal enhancements. This has been demonstrated
for hyperpolarization methods such as dynamic nuclear polarization,
spin-exchange optical pumping and para-hydrogen-induced
polarization (PHIP). In particular, PHIP has grown into a fast, efficient,
and versatile technique since the recent discovery of non-hydrogenative
routes to achieve nuclear spin hyperpolarization. For instance,
signal amplification by reversible exchange (SABRE)
can generate proton as well as heteronuclear spin hyperpolarization
in a few seconds in compounds that are able to transiently bind to
an iridium catalyst in the presence of para-hydrogen
in solution. The hyperpolarization transfer catalyst acts as a chemosensor
in the sense that it is selective for analytes that can coordinate
to the metal center, such as nitrogen-containing aromatic heterocycles,
sulfur heteroaromatic compounds, nitriles, Schiff bases, diaziridines,
carboxylic acids, and amines. We have demonstrated that the signal
enhancement achieved by SABRE allows rapid NMR detection and quantification
of a mixture of substrates down to low-micromolar concentration. Furthermore,
in the transient complex, the spin configuration of p-H2 can be easily converted to spin hyperpolarization
to produce up to 1000-fold enhanced NMR hydride signals. Because the
hydrides’ chemical shifts are highly sensitive to the structure
of the analyte associating with the iridium complex, they can be employed
as hyperpolarized “probes” to signal the presence of
specific compounds in the mixture. This indirect detection of the
analytes in solution provides important benefits in the case of complex
systems, as hydrides resonate in a region of the 1H spectrum
(at ca. −20 ppm) that is generally signal-free. The enhanced
sensitivity provided by non-hydrogenative PHIP (nhPHIP), together
with the absence of interference from the complex matrix (usually
resonating between 0 and 10 ppm), set the detection limit for this
NMR chemosensor down to sub-μM concentrations, approximately
3 orders of magnitude lower than for conventional NMR. This nhPHIP
approach represents, therefore, a powerful tool for NMR analysis of
dilute substrates in complex mixtures as it addresses at once the
issues of signal crowding and NMR sensitivity. Importantly, being
performed at high field inside the NMR spectrometer, the method allows
for rapid acquisition of multiple scans, multidimensional hyperpolarized
NMR spectra, in a fashion comparable to that of standard NMR measurements. In this Account, we focus on our chemosensing NMR technology, detailing
its principles, advantages, and limitations and presenting a number
of applications to real systems such as biofluids, beverages, and
natural extracts.
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Affiliation(s)
- Roan Fraser
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Floris P J T Rutjes
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Martin C Feiters
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Marco Tessari
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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33
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Resurreccion EP, Fong KW. The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer. Metabolites 2022; 12:metabo12060488. [PMID: 35736421 PMCID: PMC9230859 DOI: 10.3390/metabo12060488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 02/06/2023] Open
Abstract
Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.
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Affiliation(s)
- Eleazer P. Resurreccion
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
| | - Ka-wing Fong
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40506, USA;
- Markey Cancer Center, University of Kentucky, Lexington, KY 40506, USA
- Correspondence: ; Tel.: +1-859-562-3455
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Brinca AT, Ramalhinho AC, Sousa Â, Oliani AH, Breitenfeld L, Passarinha LA, Gallardo E. Follicular Fluid: A Powerful Tool for the Understanding and Diagnosis of Polycystic Ovary Syndrome. Biomedicines 2022; 10:1254. [PMID: 35740276 PMCID: PMC9219683 DOI: 10.3390/biomedicines10061254] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 02/04/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) represents one of the leading causes of anovulatory infertility and affects 5% to 20% of women worldwide. Until today, both the subsequent etiology and pathophysiology of PCOS remain unclear, and patients with PCOS that undergo assisted reproductive techniques (ART) might present a poor to exaggerated response, low oocyte quality, ovarian hyperstimulation syndrome, as well as changes in the follicular fluid metabolites pattern. These abnormalities originate a decrease of Metaphase II (MII) oocytes and decreased rates for fertilization, cleavage, implantation, blastocyst conversion, poor egg to follicle ratio, and increased miscarriages. Focus on obtaining high-quality embryos has been taken into more consideration over the years. Nowadays, the use of metabolomic analysis in the quantification of proteins and peptides in biological matrices might predict, with more accuracy, the success in assisted reproductive technology. In this article, we review the use of human follicular fluid as the matrix in metabolomic analysis for diagnostic and ART predictor of success for PCOS patients.
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Affiliation(s)
- Ana Teresa Brinca
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
| | - Ana Cristina Ramalhinho
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira, 6200-251 Covilhã, Portugal;
- C4-Cloud Computing Competence Centre, University of Beira Interior, 6201-001 Covilhã, Portugal
| | - Ângela Sousa
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
| | - António Hélio Oliani
- Assisted Reproduction Laboratory of Academic Hospital of Cova da Beira, 6200-251 Covilhã, Portugal;
- São José do Rio Preto School of Medicine, Gynaecology and Obstetrics, São José do Rio Preto 15090-000, Brazil
| | - Luiza Breitenfeld
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- C4-Cloud Computing Competence Centre, University of Beira Interior, 6201-001 Covilhã, Portugal
| | - Luís A. Passarinha
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- UCIBIO–Applied Molecular Biosciences Unit, Departament of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- Laboratório de Fármaco-Toxicologia, UBIMedical, University of Beira Interior, 6200-284 Covilhã, Portugal
| | - Eugenia Gallardo
- Health Sciences Research Centre, Faculty of Health Sciences, University of Beira Interior, 6200-506 Covilhã, Portugal; (A.T.B.); (Â.S.); (L.B.)
- Laboratório de Fármaco-Toxicologia, UBIMedical, University of Beira Interior, 6200-284 Covilhã, Portugal
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Bachmann R, Horns AL, Paasch N, Schrieck R, Weidner M, Fransson I, Schrör JP. Minor metabolites as chemical marker for the differentiation of cane, beet and coconut blossom sugar. From profiling towards identification of adulterations. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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36
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Bica R, Palarea-Albaladejo J, Lima J, Uhrin D, Miller GA, Bowen JM, Pacheco D, Macrae A, Dewhurst RJ. Methane emissions and rumen metabolite concentrations in cattle fed two different silages. Sci Rep 2022; 12:5441. [PMID: 35361825 PMCID: PMC8971404 DOI: 10.1038/s41598-022-09108-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, 18 animals were fed two forage-based diets: red clover (RC) and grass silage (GS), in a crossover-design experiment in which methane (CH4) emissions were recorded in respiration chambers. Rumen samples obtained through naso-gastric sampling tubes were analysed by NMR. Methane yield (g/kg DM) was significantly lower from animals fed RC (17.8 ± 3.17) compared to GS (21.2 ± 4.61) p = 0.008. In total 42 metabolites were identified, 6 showing significant differences between diets (acetate, propionate, butyrate, valerate, 3-phenylopropionate, and 2-hydroxyvalerate). Partial least squares discriminant analysis (PLS-DA) was used to assess which metabolites were more important to distinguish between diets and partial least squares (PLS) regressions were used to assess which metabolites were more strongly associated with the variation in CH4 emissions. Acetate, butyrate and propionate along with dimethylamine were important for the distinction between diets according to the PLS-DA results. PLS regression revealed that diet and dry matter intake are key factors to explain CH4 variation when included in the model. Additionally, PLS was conducted within diet, revealing that the association between metabolites and CH4 emissions can be conditioned by diet. These results provide new insights into the methylotrophic methanogenic pathway, confirming that metabolite profiles change according to diet composition, with consequences for CH4 emissions.
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Affiliation(s)
- R Bica
- Scotland's Rural College, SRUC, West Mains Rd, Edinburgh, EH9 3JG, UK. .,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. .,Institute National de La Recherche Agronomique (INRAE), 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France.
| | - J Palarea-Albaladejo
- Biomathematics and Statistics Scotland, JCMB, Peter Guthrie Tait Road, The King's Buildings, Edinburgh, EH9 3FD, UK.,Department of Computer Science, Applied Mathematics and Statistics, University of Girona, 17003, Girona, Spain
| | - J Lima
- Scotland's Rural College, SRUC, West Mains Rd, Edinburgh, EH9 3JG, UK.,Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - D Uhrin
- The University of Edinburgh, EaStCHEM School of Chemistry, The King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - G A Miller
- Scotland's Rural College, SRUC, West Mains Rd, Edinburgh, EH9 3JG, UK
| | - J M Bowen
- Scotland's Rural College, SRUC, West Mains Rd, Edinburgh, EH9 3JG, UK
| | - D Pacheco
- AgResearch Grasslands Research Centre, Tennent Drive, 11 Dairy Farm Road, Palmerston North, 4442, New Zealand
| | - A Macrae
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - R J Dewhurst
- Scotland's Rural College, SRUC, West Mains Rd, Edinburgh, EH9 3JG, UK
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Alarcon-Barrera JC, Kostidis S, Ondo-Mendez A, Giera M. Recent advances in metabolomics analysis for early drug development. Drug Discov Today 2022; 27:1763-1773. [PMID: 35218927 DOI: 10.1016/j.drudis.2022.02.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/25/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022]
Abstract
The pharmaceutical industry adapted proteomics and other 'omics technologies for drug research early following their initial introduction. Although metabolomics lacked behind in this development, it has now become an accepted and widely applied approach in early drug development. Over the past few decades, metabolomics has evolved from a pure exploratory tool to a more mature and quantitative biochemical technology. Several metabolomics-based platforms are now applied during the early phases of drug discovery. Metabolomics analysis assists in the definition of the physiological response and target engagement (TE) markers as well as elucidation of the mode of action (MoA) of drug candidates under investigation. In this review, we highlight recent examples and novel developments of metabolomics analyses applied during early drug development.
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Affiliation(s)
- Juan Carlos Alarcon-Barrera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands; Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands
| | - Alejandro Ondo-Mendez
- Clinical Research Group, School of Medicine and Health Sciences, Universidad del Rosario, Carrera 24 # 63C-69, Bogotá, Colombia
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, the Netherlands.
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38
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Leggett A, Li DW, Sindeldecker D, Staats A, Rigel N, Bruschweiler-Li L, Brüschweiler R, Stoodley P. Cadaverine Is a Switch in the Lysine Degradation Pathway in Pseudomonas aeruginosa Biofilm Identified by Untargeted Metabolomics. Front Cell Infect Microbiol 2022; 12:833269. [PMID: 35237533 PMCID: PMC8884266 DOI: 10.3389/fcimb.2022.833269] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 01/18/2022] [Indexed: 12/16/2022] Open
Abstract
There is a critical need to accurately diagnose, prevent, and treat biofilms in humans. The biofilm forming P. aeruginosa bacteria can cause acute and chronic infections, which are difficult to treat due to their ability to evade host defenses along with an inherent antibiotic-tolerance. Using an untargeted NMR-based metabolomics approach, we identified statistically significant differences in 52 metabolites between P. aeruginosa grown in the planktonic and lawn biofilm states. Among them, the metabolites of the cadaverine branch of the lysine degradation pathway were systematically decreased in biofilm. Exogenous supplementation of cadaverine caused significantly increased planktonic growth, decreased biofilm accumulation by 49% and led to altered biofilm morphology, converting to a pellicle biofilm at the air-liquid interface. Our findings show how metabolic pathway differences directly affect the growth mode in P. aeruginosa and could support interventional strategies to control biofilm formation.
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Affiliation(s)
- Abigail Leggett
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
| | - Da-Wei Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, United States
| | - Devin Sindeldecker
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, United States
| | - Amelia Staats
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
| | - Nicholas Rigel
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
| | - Lei Bruschweiler-Li
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, United States
| | - Rafael Brüschweiler
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, United States
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH, United States
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH, United States
- *Correspondence: Rafael Brüschweiler, ; Paul Stoodley,
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, United States
- Department of Microbiology, The Ohio State University, Columbus, OH, United States
- Department of Orthopaedics, The Ohio State University, Columbus, OH, United States
- National Biofilm Innovation Centre (NBIC) and National Centre for Advanced Tribology at Southampton (nCATS), Mechanical Engineering, University of Southampton, Southampton, United Kingdom
- *Correspondence: Rafael Brüschweiler, ; Paul Stoodley,
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Bertho G, Lordello L, Chen X, Lucas-Torres C, Oumezziane IE, Caradeuc C, Baudin M, Nuan-Aliman S, Thieblemont C, Baud V, Giraud N. Ultrahigh-Resolution NMR with Water Signal Suppression for a Deeper Understanding of the Action of Antimetabolic Drugs on Diffuse Large B-Cell Lymphoma. J Proteome Res 2022; 21:1041-1051. [PMID: 35119866 DOI: 10.1021/acs.jproteome.1c00914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ultrahigh-resolution NMR has recently attracted considerable attention in the field of complex samples analysis. Indeed, the implementation of broadband homonuclear decoupling techniques has allowed us to greatly simplify crowded 1H spectra, yielding singlets for almost every proton site from the analyzed molecules. Pure shift methods have notably shown to be particularly suitable for deciphering mixtures of metabolites in biological samples. Here, we have successfully implemented a new pure shift pulse sequence based on the PSYCHE method, which incorporates a block for solvent suppression that is suitable for metabolomics analysis. The resulting experiment allows us to record ultrahigh-resolution 1D NOESY 1H spectra of biofluids with suppression of the water signal, which is a crucial step for highlighting metabolite mixtures in an aqueous phase. We have successfully recorded pure shift spectra on extracellular media of diffuse large B-cell lymphoma (DLBCL) cells. Despite a lower sensitivity, the resolution of pure shift data was found to be better than that of the standard approach, which provides a more detailed vision of the exo-metabolome. The statistical analyses carried out on the resulting metabolic profiles allow us to successfully highlight several metabolic pathways affected by these drugs. Notably, we show that Kidrolase plays a major role in the metabolic pathways of this DLBCL cell line.
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Affiliation(s)
- Gildas Bertho
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France
| | - Leonardo Lordello
- NF-κB, Différenciation et Cancer, Université de Paris, F-75006 Paris, France
| | - Xi Chen
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France
| | - Covadonga Lucas-Torres
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France
| | - Imed Eddine Oumezziane
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France
| | - Cédric Caradeuc
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France
| | - Mathieu Baudin
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France.,Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Catherine Thieblemont
- NF-κB, Différenciation et Cancer, Université de Paris, F-75006 Paris, France.,AP-HP, Hôpital Saint-Louis, Service Hémato-Oncologie, F-75010 Paris, France
| | - Véronique Baud
- NF-κB, Différenciation et Cancer, Université de Paris, F-75006 Paris, France
| | - Nicolas Giraud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université de Paris, CNRS, F-75006 Paris, France
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Giera M, Yanes O, Siuzdak G. Metabolite discovery: Biochemistry's scientific driver. Cell Metab 2022; 34:21-34. [PMID: 34986335 PMCID: PMC10131248 DOI: 10.1016/j.cmet.2021.11.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/26/2021] [Accepted: 11/09/2021] [Indexed: 01/19/2023]
Abstract
Metabolite identification represents a major challenge, and opportunity, for biochemistry. The collective characterization and quantification of metabolites in living organisms, with its many successes, represents a major biochemical knowledgebase and the foundation of metabolism's rebirth in the 21st century; yet, characterizing newly observed metabolites has been an enduring obstacle. Crystallography and NMR spectroscopy have been of extraordinary importance, although their applicability in resolving metabolism's fine structure has been restricted by their intrinsic requirement of sufficient and sufficiently pure materials. Mass spectrometry has been a key technology, especially when coupled with high-performance separation technologies and emerging informatic and database solutions. Even more so, the collective of artificial intelligence technologies are rapidly evolving to help solve the metabolite characterization conundrum. This perspective describes this challenge, how it was historically addressed, and how metabolomics is evolving to address it today and in the future.
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Affiliation(s)
- Martin Giera
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Albinusdreef 2, Leiden 2333 ZA, the Netherlands
| | - Oscar Yanes
- Universitat Rovira i Virgili, Department of Electronic Engineering, IISPV, Tarragona, Spain; CIBER on Diabetes and Associated Metabolic Diseases (CIBERDEM), Instituto de Salud Carlos III, Madrid, Spain.
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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41
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Jagannathan N, Reddy RR. Potential of nuclear magnetic resonance metabolomics in the study of prostate cancer. Indian J Urol 2022; 38:99-109. [PMID: 35400867 PMCID: PMC8992727 DOI: 10.4103/iju.iju_416_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/16/2021] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Nuclear magnetic resonance (NMR) metabolomics is a powerful analytical technique and a tool which has unique characteristics and capabilities for the evaluation of a number of biochemicals/metabolites of cancer and other disease processes that are present in biofluids (urine and blood) and tissues. The potential of NMR metabolomics in prostate cancer (PCa) has been explored by researchers and its usefulness has been documented. A large number of metabolites such as citrate, choline, and sarcosine were detected by NMR metabolomics from biofluids and tissues related to PCa and their levels were compared with controls and benign prostatic hyperplasia. The changes in the levels of these metabolites aid in the diagnosis and help to understand the dysregulated metabolic pathways in PCa. We review recent studies on in vitro and ex vivo NMR spectroscopy-based PCa metabolomics and its possible role as a diagnostic tool.
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42
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Nagarajan K, Ibrahim B, Ahmad Bawadikji A, Lim JW, Tong WY, Leong CR, Khaw KY, Tan WN. Recent Developments in Metabolomics Studies of Endophytic Fungi. J Fungi (Basel) 2021; 8:28. [PMID: 35049968 PMCID: PMC8781825 DOI: 10.3390/jof8010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/24/2021] [Accepted: 12/24/2021] [Indexed: 01/19/2023] Open
Abstract
Endophytic fungi are microorganisms that colonize living plants' tissues without causing any harm. They are known as a natural source of bioactive metabolites with diverse pharmacological functions. Many structurally different chemical metabolites were isolated from endophytic fungi. Recently, the increasing trends in human health problems and diseases have escalated the search for bioactive metabolites from endophytic fungi. The conventional bioassay-guided study is known as laborious due to chemical complexity. Thus, metabolomics studies have attracted extensive research interest owing to their potential in dealing with a vast number of metabolites. Metabolomics coupled with advanced analytical tools provides a comprehensive insight into systems biology. Despite its wide scientific attention, endophytic fungi metabolomics are relatively unexploited. This review highlights the recent developments in metabolomics studies of endophytic fungi in obtaining the global metabolites picture.
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Affiliation(s)
- Kashvintha Nagarajan
- Chemistry Section, School of Distance Education, Universiti Sains Malaysia, Penang 11800, Malaysia;
| | - Baharudin Ibrahim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia; (B.I.); (A.A.B.)
- Department of Clinical Pharmacy & Pharmacy Practice, Faculty of Pharmacy, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | | | - Jun-Wei Lim
- Department of Fundamental and Applied Sciences, HICoE-Centre for Biofuel and Biochemical Research, Institute of Self-Sustainable Building, Universiti Teknologi PETRONAS, Seri Iskandar 32610, Perak Darul Ridzuan, Malaysia;
| | - Woei-Yenn Tong
- Drug Discovery and Delivery Research Laboratory, Malaysian Institute of Chemical and Bioengineering Technology, Universiti Kuala Lumpur, Alor Gajah, Melaka 78000, Malaysia; (W.-Y.T.); (C.-R.L.)
| | - Chean-Ring Leong
- Drug Discovery and Delivery Research Laboratory, Malaysian Institute of Chemical and Bioengineering Technology, Universiti Kuala Lumpur, Alor Gajah, Melaka 78000, Malaysia; (W.-Y.T.); (C.-R.L.)
| | - Kooi Yeong Khaw
- School of Pharmacy, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway 47500, Malaysia;
| | - Wen-Nee Tan
- Chemistry Section, School of Distance Education, Universiti Sains Malaysia, Penang 11800, Malaysia;
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43
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Defining Blood Plasma and Serum Metabolome by GC-MS. Metabolites 2021; 12:metabo12010015. [PMID: 35050137 PMCID: PMC8779220 DOI: 10.3390/metabo12010015] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 01/04/2023] Open
Abstract
Metabolomics uses advanced analytical chemistry methods to analyze metabolites in biological samples. The most intensively studied samples are blood and its liquid components: plasma and serum. Armed with advanced equipment and progressive software solutions, the scientific community has shown that small molecules’ roles in living systems are not limited to traditional “building blocks” or “just fuel” for cellular energy. As a result, the conclusions based on studying the metabolome are finding practical reflection in molecular medicine and a better understanding of fundamental biochemical processes in living systems. This review is not a detailed protocol of metabolomic analysis. However, it should support the reader with information about the achievements in the whole process of metabolic exploration of human plasma and serum using mass spectrometry combined with gas chromatography.
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44
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Ausmees K, Reimets N, Reile I. Parahydrogen hyperpolarization of minimally altered urine samples for sensitivity enhanced NMR metabolomics. Chem Commun (Camb) 2021; 58:463-466. [PMID: 34908034 DOI: 10.1039/d1cc05665d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Parahydrogen hyperpolarization has been shown to enhance NMR sensitivity in urine analysis by several orders of magnitude if urine samples are prepared by solid phase extraction (SPE). We present a different approach, developed for minimal sample alteration before analysis. Removing SPE from the workflow allows to retain a wider range of metabolites and paves the way towards more universal hyperpolarized NMR metabolomics of low abundance metabolites.
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Affiliation(s)
- Kerti Ausmees
- The National Institute of Chemical Physics and Biophysics (NICPB), Tallinn, Estonia.
| | - Nele Reimets
- The National Institute of Chemical Physics and Biophysics (NICPB), Tallinn, Estonia.
| | - Indrek Reile
- The National Institute of Chemical Physics and Biophysics (NICPB), Tallinn, Estonia.
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45
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Lorente JA, Nin N, Villa P, Vasco D, Miguel-Coello AB, Rodriguez I, Herrero R, Peñuelas O, Ruiz-Cabello J, Izquierdo-Garcia JL. Metabolomic diferences between COVID-19 and H1N1 influenza induced ARDS. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2021; 25:390. [PMID: 34781986 PMCID: PMC8591432 DOI: 10.1186/s13054-021-03810-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/03/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Acute respiratory distress syndrome (ARDS) is a type of respiratory failure characterized by lung inflammation and pulmonary edema. Coronavirus disease 2019 (COVID-19) is associated with ARDS in the more severe cases. This study aimed to compare the specificity of the metabolic alterations induced by COVID-19 or Influenza A pneumonia (IAP) in ARDS. METHODS Eighteen patients with ARDS due to COVID-19 and twenty patients with ARDS due to IAP, admitted to the intensive care unit. ARDS was defined as in the American-European Consensus Conference. As compared with patients with COVID-19, patients with IAP were younger and received more often noradrenaline to maintain a mean arterial pressure > 65 mm Hg. Serum samples were analyzed by Nuclear Magnetic Resonance Spectroscopy. Multivariate Statistical Analyses were used to identify metabolic differences between groups. Metabolic pathway analysis was performed to identify the most relevant pathways involved in ARDS development. RESULTS ARDS due to COVID-19 or to IAP induces a different regulation of amino acids metabolism, lipid metabolism, glycolysis, and anaplerotic metabolism. COVID-19 causes a significant energy supply deficit that induces supplementary energy-generating pathways. In contrast, IAP patients suffer more marked inflammatory and oxidative stress responses. The classificatory model discriminated against the cause of pneumonia with a success rate of 100%. CONCLUSIONS Our findings support the concept that ARDS is associated with a characteristic metabolomic profile that may discriminate patients with ARDS of different etiologies, being a potential biomarker for the diagnosis, prognosis, and management of this condition.
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Affiliation(s)
- Jose Angel Lorente
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain.,Universidad Europea de Madrid, Madrid, Spain
| | | | - Palmira Villa
- Centro de Asistencia a La Investigación Bioimagen Complutense, Universidad Complutense de Madrid, Madrid, Spain
| | - Dovami Vasco
- Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain
| | - Ana B Miguel-Coello
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain
| | - Ignacio Rodriguez
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Departamento de Química en CC. Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Raquel Herrero
- Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain
| | - Oscar Peñuelas
- Department of Critical Care, Hospital Universitario de Getafe, Madrid, Spain
| | - Jesús Ruiz-Cabello
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain.,Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastián, Spain.,Departamento de Química en CC. Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | - Jose L Izquierdo-Garcia
- CIBER de Enfermedades Respiratorias, CIBERES, Instituto de Salud Carlos III, Madrid, Spain. .,Instituto Pluridisciplinar, Universidad Complutense de Madrid, Paseo Juan XXIII, 1, Madrid, Spain. .,Departamento de Química en CC. Farmacéuticas, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain.
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46
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Nagana Gowda GA, Pascua V, Raftery D. Extending the Scope of 1H NMR-Based Blood Metabolomics for the Analysis of Labile Antioxidants: Reduced and Oxidized Glutathione. Anal Chem 2021; 93:14844-14850. [PMID: 34704738 DOI: 10.1021/acs.analchem.1c03763] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Glutathione is a ubiquitous cellular antioxidant, which is critically required to protect cells from oxidative damage and free radical injury. It is practically impossible to analyze glutathione in its native form after isolation from biological mixtures since the active form (reduced glutathione, GSH) spontaneously gets converted to the oxidized form (oxidized glutathione, GSSG). To address this challenge, numerous highly sensitive detection methods, including mass spectrometry, have been used in conjunction with derivatization to block the oxidation of GSH. Efforts so far to quantitate GSH and GSSG using the nuclear magnetic resonance (NMR) spectroscopy method have remained unsuccessful. With a focus on addressing this challenge, in this study, we describe an extension to our recent whole blood analysis method [ Anal. Chem. 2017, 89, 4620-4627] that includes the important antioxidants GSH and GSSG. Fresh and frozen human whole blood specimens as well as standard GSH and GSSG were comprehensively investigated using NMR without and with derivatization using N-ethylmaleimide (NEM). NMR experiments detect two diastereomers, distinctly, for the derivatized GSH and enable the analysis of both GSH and GSSG in human whole blood with an accuracy of >99%. Interestingly, the excess (unreacted) NEM used for blocking the GSH can be removed from the samples during a drying step after extraction, with no need for additional processing. This is an important characteristic that offers an added advantage for simultaneous analysis of the antioxidants (GSH and GSSG), redox coenzymes (oxidized nicotinamide adenine dinucleotide (NAD+), reduced nicotinamide adenine dinucleotide (NADH), oxidized nicotinamide adenine dinucleotide phosphate (NADP+), reduced nicotinamide adenine dinucleotide phosphate (NADPH)), energy coenzymes (adenosine 5'-triphosphate (ATP), adenosine 5'-diphosphate (ADP), adenosine 5'-monophosphate (AMP)), and a large number of other blood metabolites using the same one-dimensional (1D) NMR spectrum. The presented method broadens the scope of global metabolite profiling and adds a new dimension to NMR-based blood metabolomics. Further, the method demonstrated here for human blood can be extended to virtually any biological specimen.
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Affiliation(s)
| | | | - Daniel Raftery
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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47
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Mohammad S, Bhattacharjee J, Vasanthan T, Harris CS, Bainbridge SA, Adamo KB. Metabolomics to understand placental biology: Where are we now? Tissue Cell 2021; 73:101663. [PMID: 34653888 DOI: 10.1016/j.tice.2021.101663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/16/2022]
Abstract
Metabolomics, the application of analytical chemistry methodologies to survey the chemical composition of a biological system, is used to globally profile and compare metabolites in one or more groups of samples. Given that metabolites are the terminal end-products of cellular metabolic processes, or 'phenotype' of a cell, tissue, or organism, metabolomics is valuable to the study of the maternal-fetal interface as it has the potential to reveal nuanced complexities of a biological system as well as differences over time or between individuals. The placenta acts as the primary site of maternal-fetal exchange, the success of which is paramount to growth and development of offspring during pregnancy and beyond. Although the study of metabolomics has proven moderately useful for the screening, diagnosis, and understanding of the pathophysiology of pregnancy complications, the placental metabolome in the context of a healthy pregnancy remains poorly characterized and understood. Herein, we discuss the technical aspects of metabolomics and review the current literature describing the placental metabolome in human and animal models, in the context of health and disease. Finally, we highlight areas for future opportunities in the emerging field of placental metabolomics.
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Affiliation(s)
- S Mohammad
- School of Human Kinetics, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - J Bhattacharjee
- School of Human Kinetics, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - T Vasanthan
- School of Human Kinetics, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada
| | - C S Harris
- Department of Biology & Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - S A Bainbridge
- Interdisciplinary School of Health Sciences, Faculty of Health Sciences, University of Ottawa, ON, Canada; Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, ON, Canada
| | - K B Adamo
- School of Human Kinetics, Faculty of Health Sciences, University of Ottawa, Ottawa, ON, Canada.
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48
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Araújo AM, Carvalho F, Guedes de Pinho P, Carvalho M. Toxicometabolomics: Small Molecules to Answer Big Toxicological Questions. Metabolites 2021; 11:692. [PMID: 34677407 PMCID: PMC8539642 DOI: 10.3390/metabo11100692] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/05/2021] [Accepted: 10/05/2021] [Indexed: 12/17/2022] Open
Abstract
Given the high biological impact of classical and emerging toxicants, a sensitive and comprehensive assessment of the hazards and risks of these substances to organisms is urgently needed. In this sense, toxicometabolomics emerged as a new and growing field in life sciences, which use metabolomics to provide new sets of susceptibility, exposure, and/or effects biomarkers; and to characterize in detail the metabolic responses and altered biological pathways that various stressful stimuli cause in many organisms. The present review focuses on the analytical platforms and the typical workflow employed in toxicometabolomic studies, and gives an overview of recent exploratory research that applied metabolomics in various areas of toxicology.
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Affiliation(s)
- Ana Margarida Araújo
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Félix Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Paula Guedes de Pinho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
| | - Márcia Carvalho
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (F.C.); (P.G.d.P.)
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira nº228, 4050-313 Porto, Portugal
- FP-I3ID, FP-ENAS, University Fernando Pessoa, Praça 9 de Abril, 349, 4249-004 Porto, Portugal
- Faculty of Health Sciences, University Fernando Pessoa, Rua Carlos da Maia, 296, 4200-150 Porto, Portugal
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49
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Metabolomic Studies for Metabolic Alterations Induced by Non-Steroidal Anti-Inflammatory Drugs: Mini Review. Biomolecules 2021; 11:biom11101456. [PMID: 34680089 PMCID: PMC8533408 DOI: 10.3390/biom11101456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/01/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022] Open
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are Food and Drug Administration (FDA) approved antipyretic, anti-inflammatory, and analgesic drugs to mitigate pain, however it is associated with gastrointestinal injury and cardiovascular disease in some individuals. Metabolomics has the potential to understand the interaction of host and the drugs, such as NSAIDs administration. This discipline has been used by many researchers to understand the serious side effects of NSAIDs. We highlighted (1) the potential of metabolomics in understanding the pathogenesis of adverse events due to NSAIDs administration; (2) choice of metabolomics techniques, bio sample handling; (3) review of metabolomics studies in the front of NSAIDs in different biofluids and tissues; (4) pathway analysis of the data presented in the published literature. In our analysis we find tricarboxylic acid cycle (TCA), "glycine serine and threonine metabolism," "alanine, aspartate, and glutamate metabolism," and fatty acid metabolism to be altered by the NSAIDs like ibuprofen, indomethacin, naproxen, aspirin, and celecoxib. In conclusion, metabolomics allows the use of biological samples to identify useful pathways involved in disease progression, and subsequently inform a greater understanding of the disease pathogenesis. A further in-depth investigation of the associated pathways mentioned above holds the potential for drug targets for side effects mitigation.
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50
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Mason S, Solomons R. CSF Metabolomics of Tuberculous Meningitis: A Review. Metabolites 2021; 11:661. [PMID: 34677376 PMCID: PMC8541251 DOI: 10.3390/metabo11100661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 02/07/2023] Open
Abstract
From the World Health Organization's global TB report for 2020, it is estimated that in 2019 at least 80,000 children (a particularly vulnerable population) developed tuberculous meningitis (TBM)-an invariably fatal disease if untreated-although this is likely an underestimate. As our latest technologies have evolved-with the unprecedented development of the various "omics" disciplines-a mountain of new data on infectious diseases have been created. However, our knowledge and understanding of infectious diseases are still trying to keep pace. Metabolites offer much biological information, but the insights they permit can be difficult to derive. This review summarizes current metabolomics studies on cerebrospinal fluid (CSF) from TBM cases and collates the metabolic data reported. Collectively, CSF metabolomics studies have identified five classes of metabolites that characterize TBM: amino acids, organic acids, nucleotides, carbohydrates, and "other". Taken holistically, the information given in this review serves to promote the mechanistic action of hypothesis generation that will drive and direct future studies on TBM.
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Affiliation(s)
- Shayne Mason
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2531, South Africa
| | - Regan Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa;
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