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Beyoğlu D, Popov YV, Idle JR. The Metabolomic Footprint of Liver Fibrosis. Cells 2024; 13:1333. [PMID: 39195223 DOI: 10.3390/cells13161333] [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: 07/06/2024] [Revised: 08/08/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024] Open
Abstract
Both experimental and clinical liver fibrosis leave a metabolic footprint that can be uncovered and defined using metabolomic approaches. Metabolomics combines pattern recognition algorithms with analytical chemistry, in particular, 1H and 13C nuclear magnetic resonance spectroscopy (NMR), gas chromatography-mass spectrometry (GC-MS) and various liquid chromatography-mass spectrometry (LC-MS) platforms. The analysis of liver fibrosis by each of these methodologies is reviewed separately. Surprisingly, there was little general agreement between studies within each of these three groups and also between groups. The metabolomic footprint determined by NMR (two or more hits between studies) comprised elevated lactate, acetate, choline, 3-hydroxybutyrate, glucose, histidine, methionine, glutamine, phenylalanine, tyrosine and citrate. For GC-MS, succinate, fumarate, malate, ascorbate, glutamate, glycine, serine and, in agreement with NMR, glutamine, phenylalanine, tyrosine and citrate were delineated. For LC-MS, only β-muricholic acid, tryptophan, acylcarnitine, p-cresol, valine and, in agreement with NMR, phosphocholine were identified. The metabolomic footprint of liver fibrosis was upregulated as regards glutamine, phenylalanine, tyrosine, citrate and phosphocholine. Several investigators employed traditional Chinese medicine (TCM) treatments to reverse experimental liver fibrosis, and a commentary is given on the chemical constituents that may possess fibrolytic activity. It is proposed that molecular docking procedures using these TCM constituents may lead to novel therapies for liver fibrosis affecting at least one-in-twenty persons globally, for which there is currently no pharmaceutical cure. This in-depth review summarizes the relevant literature on metabolomics and its implications in addressing the clinical problem of liver fibrosis, cirrhosis and its sequelae.
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Affiliation(s)
- Diren Beyoğlu
- Department of Pharmaceutical and Administrative Sciences, College of Pharmacy and Health Sciences, Western New England University, Springfield, MA 01119, USA
| | - Yury V Popov
- Division of Gastroenterology, Hepatology and Nutrition, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jeffrey R Idle
- Department of Pharmaceutical and Administrative Sciences, College of Pharmacy and Health Sciences, Western New England University, Springfield, MA 01119, USA
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2
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Tanaka Y. Metabolomics in liver diseases: A novel alternative for liver biopsy? World J Hepatol 2024; 16:12-16. [PMID: 38313246 PMCID: PMC10835480 DOI: 10.4254/wjh.v16.i1.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024] Open
Abstract
Hepatitis C virus (HCV) remains a significant public health problem as it can cause acute and chronic hepatitis. Chronic HCV infection is a major cause of liver fibrosis, and evaluation of liver fibrosis is essential because the prognosis of patients with chronic HCV infection is closely related to the stage of fibrosis. Liver fibrosis is traditionally evaluated based on pathological analysis of biopsy specimens, which is considered the gold standard. Nevertheless, liver biopsy is invasive and susceptible to sampling error and inter- and intraobserver variation in pathological interpretation; it is also costly. Therefore, noninvasive diagnostic investigations have been developed, including the use of fibrotic markers, scoring systems based on routine blood tests, and transient elastography with magnetic resonance imaging or ultrasonography. Recently, metabolomics, an emerging technology, has been used to detect the fibrosis stage. In this editorial, I comment on the article titled "Metabolomics in chronic hepatitis C: Decoding fibrosis grading and underlying pathways" by Ferrasi et al published in the recent issue of the World Journal of Hepatology. I discuss previous studies on the use of metabolome analysis for the diagnosis of HCV-related liver fibrosis and the potential development of biopsy-free diagnostic techniques.
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Affiliation(s)
- Yasuo Tanaka
- Department of Gastroenterology, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.
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3
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Yang J, Wang D, Li Y, Wang H, Hu Q, Wang Y. Metabolomics in viral hepatitis: advances and review. Front Cell Infect Microbiol 2023; 13:1189417. [PMID: 37265499 PMCID: PMC10229802 DOI: 10.3389/fcimb.2023.1189417] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Viral hepatitis is a major worldwide public health issue, affecting hundreds of millions of people and causing substantial morbidity and mortality. The majority of the worldwide burden of viral hepatitis is caused by five biologically unrelated hepatotropic viruses: hepatitis A virus (HAV), hepatitis B virus (HBV), hepatitis C virus (HCV), hepatitis D virus (HDV), and hepatitis E virus (HEV). Metabolomics is an emerging technology that uses qualitative and quantitative analysis of easily accessible samples to provide information of the metabolic levels of biological systems and changes in metabolic and related regulatory pathways. Alterations in glucose, lipid, and amino acid levels are involved in glycolysis, the tricarboxylic acid cycle, the pentose phosphate pathway, and amino acid metabolism. These changes in metabolites and metabolic pathways are associated with the pathogenesis and medication mechanism of viral hepatitis and related diseases. Additionally, differential metabolites can be utilized as biomarkers for diagnosis, prognosis, and therapeutic responses. In this review, we present a thorough overview of developments in metabolomics for viral hepatitis.
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Affiliation(s)
- Jiajia Yang
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Dawei Wang
- Department of Infectious Disease, The Second People’s Hospital of Yancheng City, Yancheng, China
| | - Yuancheng Li
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and Sexually Transmitted Infections (STIs), Nanjing, China
| | - Hongmei Wang
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Qiang Hu
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- Department of Respiratory and Critical Care Medicine, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Ying Wang
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
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4
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Vignoli A, Meoni G, Ghini V, Di Cesare F, Tenori L, Luchinat C, Turano P. NMR-Based Metabolomics to Evaluate Individual Response to Treatments. Handb Exp Pharmacol 2023; 277:209-245. [PMID: 36318327 DOI: 10.1007/164_2022_618] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The aim of this chapter is to highlight the various aspects of metabolomics in relation to health and diseases, starting from the definition of metabolic space and of how individuals tend to maintain their own position in this space. Physio-pathological stimuli may cause individuals to lose their position and then regain it, or move irreversibly to other positions. By way of examples, mostly selected from our own work using 1H NMR on biological fluids, we describe the effects on the individual metabolomic fingerprint of mild external interventions, such as diet or probiotic administration. Then we move to pathologies (such as celiac disease, various types of cancer, viral infections, and other diseases), each characterized by a well-defined metabolomic fingerprint. We describe the effects of drugs on the disease fingerprint and on its reversal to a healthy metabolomic status. Drug toxicity can be also monitored by metabolomics. We also show how the individual metabolomic fingerprint at the onset of a disease may discriminate responders from non-responders to a given drug, or how it may be prognostic of e.g., cancer recurrence after many years. In parallel with fingerprinting, profiling (i.e., the identification and quantification of many metabolites and, in the case of selected biofluids, of the lipoprotein components that contribute to the 1H NMR spectral features) can provide hints on the metabolic pathways that are altered by a disease and assess their restoration after treatment.
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Affiliation(s)
- Alessia Vignoli
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Gaia Meoni
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Veronica Ghini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Francesca Di Cesare
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Tenori
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy.,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy
| | - Paola Turano
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino, Italy. .,Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy. .,Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine (CIRMMP), Sesto Fiorentino, Italy.
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5
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Lin C, Hu Q, Dong J, Wei Z, Li J, Chen Z. Serum metabolic signatures of schizophrenia patients complicated with hepatitis B virus infection: A 1H NMR-based metabolomics study. Front Psychiatry 2022; 13:998709. [PMID: 36620683 PMCID: PMC9810819 DOI: 10.3389/fpsyt.2022.998709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
INTRODUCTION Schizophrenia (SZ) is a severe chronic mental disorder with increased risk of hepatitis B virus (HBV) infection, which is incurable currently and induces various negative emotions and psychological pressures in patients to exacerbate mental disorders. To facilitate the therapeutic design for SZ patients complicated with HBV infection (SZ + HBV), it is helpful to first elucidate the metabolic perturbations in SZ + HBV patients. METHODS In this study, metabolic profiles of the serum samples from four groups of participants comprising healthy controls (HC, n = 72), HBV infection (n = 52), SZ patients (n = 37), and SZ + HBV (n = 41) patients were investigated using a high-resolution 1H NMR-based metabolomics approach. RESULTS AND DISCUSSION Distinguishable metabolic profiles were found in the four groups. In comparison with HC, HBV infection induced increased levels of citrate and succinate to perturbate the tricarboxylic acid cycle and succinate-related pathways. Similar to SZ cases, SZ + HBV patients exhibited decreased glucose but increased citrate, pyruvate, and lactate, suggesting the occurrence of disturbance in glucose metabolism. Moreover, in comparison with HC, several serum amino acid levels in SZ + HBV patients were significantly altered. Our findings suggest that Warburg effect, energy metabolism disorders, neurotransmitter metabolism abnormalities, mitochondrial dysfunction and several disturbed pathways in relation to tyrosine and choline appear to play specific and central roles in the pathophysiology of SZ + HBV. Apart from replicating metabolic alterations induced by SZ and HBV separately (e.g., in energy metabolism and Warburg effect), the specific metabolic abnormalities in the SZ + HBV group (e.g., several tyrosine- and choline-related pathways) highlighted the existence of a synergistic action between SZ and HBV pathologies. Current study revealed the metabolic alterations specific to the interaction between SZ and HBV pathologies, and may open important perspectives for designing precise therapies for SZ + HBV patients beyond the simple combination of two individual treatments.
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Affiliation(s)
- Caigui Lin
- Fujian Provincial Key Laboratory for Plasma and Magnetic Resonance, Department of Electronic Science, Xiamen University, Xiamen, Fujian, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qing Hu
- Xiamen Xianyue Hospital, Xiamen, Fujian, China
| | - Jiyang Dong
- Fujian Provincial Key Laboratory for Plasma and Magnetic Resonance, Department of Electronic Science, Xiamen University, Xiamen, Fujian, China
| | - Zhiliang Wei
- Department of Radiology, Johns Hopkins University, Baltimore, MD, United States
| | - Jie Li
- Department of Hepatobiliary Surgery, Zhongshan Hospital of Xiamen University, Xiamen, Fujian, China
| | - Zhong Chen
- Fujian Provincial Key Laboratory for Plasma and Magnetic Resonance, Department of Electronic Science, Xiamen University, Xiamen, Fujian, China
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Robinson EJ, Taddeo MC, Chu X, Shi W, Wood C, Still C, Rovnyak VG, Rovnyak D. Aqueous Metabolite Trends for the Progression of Nonalcoholic Fatty Liver Disease in Female Bariatric Surgery Patients by Targeted 1H-NMR Metabolomics. Metabolites 2021; 11:metabo11110737. [PMID: 34822395 PMCID: PMC8619318 DOI: 10.3390/metabo11110737] [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: 09/12/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 01/14/2023] Open
Abstract
Determining biomarkers and better characterizing the biochemical progression of nonalcoholic fatty liver disease (NAFLD) remains a clinical challenge. A targeted 1H-NMR study of serum, combined with clinical variables, detected and localized biomarkers to stages of NAFLD in morbidly obese females. Pre-surgery serum samples from 100 middle-aged, morbidly obese female subjects, grouped on gold-standard liver wedge biopsies (non-NAFLD; steatosis; and fibrosis) were collected, extracted, and analyzed in aqueous (D2O) buffer (1H, 600 MHz). Profiled concentrations were subjected to exploratory statistical analysis. Metabolites varying significantly between the non-NAFLD and steatosis groups included the ketone bodies 3-hydroxybutyrate (↓; p = 0.035) and acetone (↓; p = 0.012), and also alanine (↑; p = 0.004) and a putative pyruvate signal (↑; p = 0.003). In contrast, the steatosis and fibrosis groups were characterized by 2-hydroxyisovalerate (↑; p = 0.023), betaine (↓; p = 0.008), hypoxanthine (↓; p = 0.003), taurine (↓; p = 0.001), 2-hydroxybutyrate (↑; p = 0.045), 3-hydroxyisobutyrate (↑; p = 0.046), and increasing medium chain fatty acids. Exploratory classification models with and without clinical variables exhibited overall success rates ca. 75–85%. In the study conditions, inhibition of fatty acid oxidation and disruption of the hepatic urea cycle are supported as early features of NAFLD that continue in fibrosis. In fibrosis, markers support inflammation, hepatocyte damage, and decreased liver function. Complementarity of NMR concentrations and clinical information in classification models is shown. A broader hypothesis that standard-of-care sera can yield metabolomic information is supported.
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Affiliation(s)
- Emma J. Robinson
- Department of Chemistry, Bucknell University, 1 Dent Drive, Lewisburg, PA 17837, USA; (E.J.R.); (M.C.T.)
| | - Matthew C. Taddeo
- Department of Chemistry, Bucknell University, 1 Dent Drive, Lewisburg, PA 17837, USA; (E.J.R.); (M.C.T.)
| | - Xin Chu
- The Obesity Institute, Geisinger, Danville, PA 17822, USA; (X.C.); (W.S.); (C.W.); (C.S.)
| | - Weixing Shi
- The Obesity Institute, Geisinger, Danville, PA 17822, USA; (X.C.); (W.S.); (C.W.); (C.S.)
| | - Craig Wood
- The Obesity Institute, Geisinger, Danville, PA 17822, USA; (X.C.); (W.S.); (C.W.); (C.S.)
| | - Christopher Still
- The Obesity Institute, Geisinger, Danville, PA 17822, USA; (X.C.); (W.S.); (C.W.); (C.S.)
| | | | - David Rovnyak
- Department of Chemistry, Bucknell University, 1 Dent Drive, Lewisburg, PA 17837, USA; (E.J.R.); (M.C.T.)
- Correspondence:
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7
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Shanmuganathan M, Sarfaraz MO, Kroezen Z, Philbrick H, Poon R, Don-Wauchope A, Puglia M, Wishart D, Britz-McKibbin P. A Cross-Platform Metabolomics Comparison Identifies Serum Metabolite Signatures of Liver Fibrosis Progression in Chronic Hepatitis C Patients. Front Mol Biosci 2021; 8:676349. [PMID: 34414211 PMCID: PMC8370474 DOI: 10.3389/fmolb.2021.676349] [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: 03/05/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
Metabolomics offers new insights into disease mechanisms that is enhanced when adopting orthogonal instrumental platforms to expand metabolome coverage, while also reducing false discoveries by independent replication. Herein, we report the first inter-method comparison when using multisegment injection-capillary electrophoresis-mass spectrometry (MSI-CE-MS) and nuclear magnetic resonance (NMR) spectroscopy for characterizing the serum metabolome of patients with liver fibrosis in chronic hepatitis C virus (HCV) infection (n = 20) and non-HCV controls (n = 14). In this study, 60 and 30 serum metabolites were detected frequently (>75%) with good technical precision (median CV < 10%) from serum filtrate samples (n = 34) when using standardized protocols for MSI-CE-MS and NMR, respectively. Also, 20 serum metabolite concentrations were consistently measured by both methods over a 500-fold concentration range with an overall mean bias of 9.5% (n = 660). Multivariate and univariate statistical analyses independently confirmed that serum choline and histidine were consistently elevated (p < 0.05) in HCV patients with late-stage (F2-F4) as compared to early-stage (F0-F1) liver fibrosis. Overall, the ratio of serum choline to uric acid provided optimal differentiation of liver disease severity (AUC = 0.848, p = 0.00766) using a receiver operating characteristic curve, which was positively correlated with liver stiffness measurements by ultrasound imaging (r = 0.606, p = 0.0047). Moreover, serum 5-oxo-proline concentrations were higher in HCV patients as compared to non-HCV controls (F = 4.29, p = 0.0240) after adjustment for covariates (age, sex, BMI), indicative of elevated oxidative stress from glutathione depletion with the onset and progression of liver fibrosis. Both instrumental techniques enable rapid yet reliable quantification of serum metabolites in large-scale metabolomic studies with good overlap for biomarker replication. Advantages of MSI-CE-MS include greater metabolome coverage, lower operating costs, and smaller sample volume requirements, whereas NMR offers a robust platform supported by automated spectral and data processing software.
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Affiliation(s)
- Meera Shanmuganathan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | | | - Zachary Kroezen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Holly Philbrick
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Richel Poon
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Andrew Don-Wauchope
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
| | - Marco Puglia
- Department of Medicine, Division of Gastroenterology, McMaster University, Hamilton, ON, Canada
| | - David Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, AB, Canada
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
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8
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Tounta V, Liu Y, Cheyne A, Larrouy-Maumus G. Metabolomics in infectious diseases and drug discovery. Mol Omics 2021; 17:376-393. [PMID: 34125125 PMCID: PMC8202295 DOI: 10.1039/d1mo00017a] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022]
Abstract
Metabolomics has emerged as an invaluable tool that can be used along with genomics, transcriptomics and proteomics to understand host-pathogen interactions at small-molecule levels. Metabolomics has been used to study a variety of infectious diseases and applications. The most common application of metabolomics is for prognostic and diagnostic purposes, specifically the screening of disease-specific biomarkers by either NMR-based or mass spectrometry-based metabolomics. In addition, metabolomics is of great significance for the discovery of druggable metabolic enzymes and/or metabolic regulators through the use of state-of-the-art flux analysis, for example, via the elucidation of metabolic mechanisms. This review discusses the application of metabolomics technologies to biomarker screening, the discovery of drug targets in infectious diseases such as viral, bacterial and parasite infections and immunometabolomics, highlights the challenges associated with accessing metabolite compartmentalization and discusses the available tools for determining local metabolite concentrations.
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Affiliation(s)
- Vivian Tounta
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College LondonLondonUK
| | - Yi Liu
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College LondonLondonUK
| | - Ashleigh Cheyne
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College LondonLondonUK
| | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College LondonLondonUK
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Song Z, Wang H, Yin X, Deng P, Jiang W. Application of NMR metabolomics to search for human disease biomarkers in blood. Clin Chem Lab Med 2019; 57:417-441. [PMID: 30169327 DOI: 10.1515/cclm-2018-0380] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/16/2018] [Indexed: 02/05/2023]
Abstract
Recently, nuclear magnetic resonance spectroscopy (NMR)-based metabolomics analysis and multivariate statistical techniques have been incorporated into a multidisciplinary approach to profile changes in small molecules associated with the onset and progression of human diseases. The purpose of these efforts is to identify unique metabolite biomarkers in a specific human disease so as to (1) accurately predict and diagnose diseases, including separating distinct disease stages; (2) provide insights into underlying pathways in the pathogenesis and progression of the malady and (3) aid in disease treatment and evaluate the efficacy of drugs. In this review we discuss recent developments in the application of NMR-based metabolomics in searching disease biomarkers in human blood samples in the last 5 years.
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Affiliation(s)
- Zikuan Song
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Haoyu Wang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Xiaotong Yin
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China.,West China School of Basic Medical Science and Forensic Medicine, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Pengchi Deng
- Analytical and Testing Center, Sichuan University, Chengdu, Sichuan, P.R. China
| | - Wei Jiang
- Molecular Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, P.R. China
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10
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Meoni G, Lorini S, Monti M, Madia F, Corti G, Luchinat C, Zignego AL, Tenori L, Gragnani L. The metabolic fingerprints of HCV and HBV infections studied by Nuclear Magnetic Resonance Spectroscopy. Sci Rep 2019; 9:4128. [PMID: 30858406 PMCID: PMC6412048 DOI: 10.1038/s41598-019-40028-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 01/23/2019] [Indexed: 02/06/2023] Open
Abstract
Few studies are available on metabolic changes in liver injuries and this is the first metabolomic study evaluating a group of HCV-positive patients, before and after viral eradication via DAA IFN-free regimens, using 1H-NMR to characterize and compare their serum fingerprints to naïve HBV-patients and healthy donors. The investigation clearly shows differences in the metabolomic profile of HCV patients before and after effective DAA treatment. Significant changes in metabolites levels in patients undergoing therapy suggest alterations in several metabolic pathways. It has been shown that 1H-NMR fingerprinting approach is an optimal technique in predicting the specific infection and the healthy status of studied subjects (Monte-Carlo cross validated accuracies: 86% in the HCV vs HBV model, 98.7% in the HCV vs HC model). Metabolite data collected support the hypothesis that the HCV virus induces glycolysis over oxidative phosphorylation in a similar manner to the Warburg effect in cancer, moreover our results have demonstrated a different action of the two viruses on cellular metabolism, corroborating the hypothesis that the metabolic perturbation on patients could be attributed to a direct role in viral infection. This metabolomic study has revealed some alteration in metabolites for the first time (2-oxoglutarate and 3-hydroxybutrate) concerning the HCV-infection model that could explain several extrahepatic manifestations associated with such an infection.
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Affiliation(s)
- Gaia Meoni
- University of Florence, Magnetic Resonance Center (CERM), Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Serena Lorini
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Monica Monti
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Francesco Madia
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Giampaolo Corti
- Careggi University Hospital, Infectious and Tropical Diseases Unit, Florence, 50134, Italy
| | - Claudio Luchinat
- University of Florence, Magnetic Resonance Center (CERM), Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy.,University of Florence, Department of Chemistry "Ugo Schiff", Sesto Fiorentino, 50019, Italy
| | - Anna Linda Zignego
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy
| | - Leonardo Tenori
- University of Florence, Magnetic Resonance Center (CERM), Sesto Fiorentino, 50019, Italy. .,University of Florence, Department of Experimental and Clinical Medicine, Florence, 50134, Italy.
| | - Laura Gragnani
- Careggi University Hospital, Department of Experimental and Clinical Medicine, Interdepartmental Center for Systemic Manifestations of Hepatitis Viruses (MaSVE), Florence, 50134, Italy.
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11
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Quantitative analysis, pharmacokinetics and metabolomics study for the comprehensive characterization of the salt-processing mechanism of Psoraleae Fructus. Sci Rep 2019; 9:661. [PMID: 30679561 PMCID: PMC6345873 DOI: 10.1038/s41598-018-36908-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 11/27/2018] [Indexed: 01/11/2023] Open
Abstract
Research based on quantitative analysis, pharmacokinetics and metabolomics was conducted to explore the effects of salt-processing on Psoraleae Fructus (PF). Quantitative analysis showed that the contents of bioactive components were higher in salt-processed Psoraleae Fructus (SPF) extract than in PF extract. Pharmacokinetics indicated that the overall AUC and tmax levels was higher, while Cmax was lower in the SPF group. In the metabolomics study, the differential influences of PF and SPF on 22 common biomarkers and associated metabolic pathways showed that salt-processing could enhance the effect of PF and reduce toxicity in the cardiovascular and renal systems. The internal correlations among these results, together with the influence of salt-processing, suggested that the effects of heating and newly generated surfactants during the salt-processing procedure were the primary causes of the changes in chemical composition and absorption characteristics, as well as the subsequent enhanced efficacy and minor toxicity.
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Kirwan JA, Brennan L, Broadhurst D, Fiehn O, Cascante M, Dunn WB, Schmidt MA, Velagapudi V. Preanalytical Processing and Biobanking Procedures of Biological Samples for Metabolomics Research: A White Paper, Community Perspective (for "Precision Medicine and Pharmacometabolomics Task Group"-The Metabolomics Society Initiative). Clin Chem 2018; 64:1158-1182. [PMID: 29921725 DOI: 10.1373/clinchem.2018.287045] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022]
Abstract
BACKGROUND The metabolome of any given biological system contains a diverse range of low molecular weight molecules (metabolites), whose abundances can be affected by the timing and method of sample collection, storage, and handling. Thus, it is necessary to consider the requirements for preanalytical processes and biobanking in metabolomics research. Poor practice can create bias and have deleterious effects on the robustness and reproducibility of acquired data. CONTENT This review presents both current practice and latest evidence on preanalytical processes and biobanking of samples intended for metabolomics measurement of common biofluids and tissues. It highlights areas requiring more validation and research and provides some evidence-based guidelines on best practices. SUMMARY Although many researchers and biobanking personnel are familiar with the necessity of standardizing sample collection procedures at the axiomatic level (e.g., fasting status, time of day, "time to freezer," sample volume), other less obvious factors can also negatively affect the validity of a study, such as vial size, material and batch, centrifuge speeds, storage temperature, time and conditions, and even environmental changes in the collection room. Any biobank or research study should establish and follow a well-defined and validated protocol for the collection of samples for metabolomics research. This protocol should be fully documented in any resulting study and should involve all stakeholders in its design. The use of samples that have been collected using standardized and validated protocols is a prerequisite to enable robust biological interpretation unhindered by unnecessary preanalytical factors that may complicate data analysis and interpretation.
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Affiliation(s)
- Jennifer A Kirwan
- Berlin Institute of Health, Berlin, Germany; .,Max Delbrück Center for Molecular Medicine, Berlin-Buch, Germany
| | - Lorraine Brennan
- UCD School of Agriculture and Food Science, Institute of Food and Health, UCD, Dublin, Ireland
| | | | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis, Davis, CA
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine and IBUB, Universitat de Barcelona, Barcelona and Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBER-EHD), Madrid, Spain
| | - Warwick B Dunn
- School of Biosciences and Phenome Centre Birmingham, University of Birmingham, Birmingham, UK
| | - Michael A Schmidt
- Advanced Pattern Analysis and Countermeasures Group, Research Innovation Center, Colorado State University, Fort Collins, CO.,Sovaris Aerospace, LLC, Boulder, CO
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki, Finland.
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Faitot F, Besch C, Battini S, Ruhland E, Onea M, Addeo P, Woehl-Jaeglé ML, Ellero B, Bachellier P, Namer IJ. Impact of real-time metabolomics in liver transplantation: Graft evaluation and donor-recipient matching. J Hepatol 2018; 68:699-706. [PMID: 29191459 DOI: 10.1016/j.jhep.2017.11.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 11/09/2017] [Accepted: 11/15/2017] [Indexed: 12/29/2022]
Abstract
BACKGROUND & AIMS There is an emerging need to assess the metabolic state of liver allografts especially in the novel setting of machine perfusion preservation and donor in cardiac death (DCD) grafts. High-resolution magic-angle-spinning nuclear magnetic resonance (HR-MAS-NMR) could be a useful tool in this setting as it can extemporaneously provide untargeted metabolic profiling. The purpose of this study was to evaluate the potential value of HR-MAS-NMR metabolomic analysis of back-table biopsies for the prediction of early allograft dysfunction (EAD) and donor-recipient matching. METHOD The metabolic profiles of back-table biopsies obtained by HR-MAS-NMR, were compared according to the presence of EAD using partial least squares discriminant analysis. Network analysis was used to identify metabolites which changed significantly. The profiles were compared to native livers to identify metabolites for donor-recipient matching. RESULTS The metabolic profiles were significantly different in grafts that caused EAD compared to those that did not. The constructed model can be used to predict the graft outcome with excellent accuracy. The metabolites showing the most significant differences were lactate level >8.3 mmol/g and phosphocholine content >0.646 mmol/g, which were significantly associated with graft dysfunction with an excellent accuracy (AUROClactates = 0.906; AUROCphosphocholine = 0.816). Native livers from patients with sarcopenia had low lactate and glycerophosphocholine content. In patients with sarcopenia, the risk of EAD was significantly higher when transplanting a graft with a high-risk graft metabolic score. CONCLUSION This study underlines the cost of metabolic adaptation, identifying lactate and choline-derived metabolites as predictors of poor graft function in both native livers and liver grafts. HR-MAS-NMR seems a valid technique to evaluate graft quality and the consequences of cold ischemia on the graft. It could be used to assess the efficiency of graft resuscitation on machine perfusion in future studies. LAY SUMMARY Real-time metabolomic profiles of human grafts during back-table can accurately predict graft dysfunction. High lactate and phosphocholine content are highly predictive of graft dysfunction whereas low lactate and phosphocholine content characterize patients with sarcopenia. In these patients, the cost of metabolic adaptation may explain the poor outcomes.
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Affiliation(s)
- Francois Faitot
- Hepatobiliopancreatic Surgery and Transplantation Department, Hopital de Hautepierre, CHU de Strasbourg, France; Laboratoire ICube, UMR7357, University of Strasbourg, France
| | - Camille Besch
- Hepatobiliopancreatic Surgery and Transplantation Department, Hopital de Hautepierre, CHU de Strasbourg, France
| | | | - Elisa Ruhland
- Laboratoire ICube, UMR7357, University of Strasbourg, France
| | - Mihaela Onea
- Pathology Department, Hopital de Hautepierre, CHU de Strasbourg, France
| | - Pietro Addeo
- Hepatobiliopancreatic Surgery and Transplantation Department, Hopital de Hautepierre, CHU de Strasbourg, France
| | - Marie-Lorraine Woehl-Jaeglé
- Hepatobiliopancreatic Surgery and Transplantation Department, Hopital de Hautepierre, CHU de Strasbourg, France
| | - Bernard Ellero
- Hepatobiliopancreatic Surgery and Transplantation Department, Hopital de Hautepierre, CHU de Strasbourg, France
| | - Philippe Bachellier
- Hepatobiliopancreatic Surgery and Transplantation Department, Hopital de Hautepierre, CHU de Strasbourg, France
| | - Izzie-Jacques Namer
- Laboratoire ICube, UMR7357, University of Strasbourg, France; Nuclear Medicine Department, Hôpital de Hautepierre, CHU de Strasbourg, France.
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Batista AD, Barros CJP, Costa TBBC, Godoy MMGD, Silva RD, Santos JC, de Melo Lira MM, Jucá NT, Lopes EPDA, Silva RO. Proton nuclear magnetic resonance-based metabonomic models for non-invasive diagnosis of liver fibrosis in chronic hepatitis C: Optimizing the classification of intermediate fibrosis. World J Hepatol 2018; 10:105-115. [PMID: 29399284 PMCID: PMC5787674 DOI: 10.4254/wjh.v10.i1.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/16/2017] [Accepted: 01/16/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To develop metabonomic models (MMs), using 1H nuclear magnetic resonance (NMR) spectra of serum, to predict significant liver fibrosis (SF: Metavir ≥ F2), advanced liver fibrosis (AF: METAVIR ≥ F3) and cirrhosis (C: METAVIR = F4 or clinical cirrhosis) in chronic hepatitis C (CHC) patients. Additionally, to compare the accuracy of the MMs with the aspartate aminotransferase to platelet ratio index (APRI) and fibrosis index based on four factors (FIB-4).
METHODS Sixty-nine patients who had undergone biopsy in the previous 12 mo or had clinical cirrhosis were included. The presence of any other liver disease was a criterion for exclusion. The MMs, constructed using partial least squares discriminant analysis and linear discriminant analysis formalisms, were tested by cross-validation, considering SF, AF and C.
RESULTS Results showed that forty-two patients (61%) presented SF, 28 (40%) AF and 18 (26%) C. The MMs showed sensitivity and specificity of 97.6% and 92.6% to predict SF; 96.4% and 95.1% to predict AF; and 100% and 98.0% to predict C. Besides that, the MMs correctly classified all 27 (39.7%) and 25 (38.8%) patients with intermediate values of APRI and FIB-4, respectively.
CONCLUSION The metabonomic strategy performed excellently in predicting significant and advanced liver fibrosis in CHC patients, including those in the gray zone of APRI and FIB-4, which may contribute to reducing the need for these patients to undergo liver biopsy.
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Affiliation(s)
- Andrea Dória Batista
- Postgraduate Program in Tropical Medicine, Center for Health Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
- Department of Gastroenterology and Hepatology, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Carlos Jonnatan Pimentel Barros
- Department of Fundamental Chemistry, Center for Exact and Nature Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Tássia Brena Barroso Carneiro Costa
- Department of Fundamental Chemistry, Center for Exact and Nature Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | | | - Ronaldo Dionísio Silva
- Department of Fundamental Chemistry, Center for Exact and Nature Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Joelma Carvalho Santos
- Postgraduate Program in Tropical Medicine, Center for Health Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | | | - Norma Thomé Jucá
- Department of Pathology, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Edmundo Pessoa de Almeida Lopes
- Postgraduate Program in Tropical Medicine, Center for Health Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
- Department of Gastroenterology and Hepatology, Hospital das Clínicas, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
| | - Ricardo Oliveira Silva
- Department of Fundamental Chemistry, Center for Exact and Nature Sciences, Universidade Federal de Pernambuco, Recife, Pernambuco 50670-901, Brazil
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Bruno C, Patin F, Bocca C, Nadal-Desbarats L, Bonnier F, Reynier P, Emond P, Vourc'h P, Joseph-Delafont K, Corcia P, Andres CR, Blasco H. The combination of four analytical methods to explore skeletal muscle metabolomics: Better coverage of metabolic pathways or a marketing argument? J Pharm Biomed Anal 2017; 148:273-279. [PMID: 29059617 DOI: 10.1016/j.jpba.2017.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 10/12/2017] [Accepted: 10/13/2017] [Indexed: 01/11/2023]
Abstract
OBJECTIVES Metabolomics is an emerging science based on diverse high throughput methods that are rapidly evolving to improve metabolic coverage of biological fluids and tissues. Technical progress has led researchers to combine several analytical methods without reporting the impact on metabolic coverage of such a strategy. The objective of our study was to develop and validate several analytical techniques (mass spectrometry coupled to gas or liquid chromatography and nuclear magnetic resonance) for the metabolomic analysis of small muscle samples and evaluate the impact of combining methods for more exhaustive metabolite covering. DESIGN AND METHODS We evaluated the muscle metabolome from the same pool of mouse muscle samples after 2 metabolite extraction protocols. Four analytical methods were used: targeted flow injection analysis coupled with mass spectrometry (FIA-MS/MS), gas chromatography coupled with mass spectrometry (GC-MS), liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS), and nuclear magnetic resonance (NMR) analysis. We evaluated the global variability of each compound i.e., analytical (from quality controls) and extraction variability (from muscle extracts). We determined the best extraction method and we reported the common and distinct metabolites identified based on the number and identity of the compounds detected with low analytical variability (variation coefficient<30%) for each method. Finally, we assessed the coverage of muscle metabolic pathways obtained. RESULTS Methanol/chloroform/water and water/methanol were the best extraction solvent for muscle metabolome analysis by NMR and MS, respectively. We identified 38 metabolites by nuclear magnetic resonance, 37 by FIA-MS/MS, 18 by GC-MS, and 80 by LC-HRMS. The combination led us to identify a total of 132 metabolites with low variability partitioned into 58 metabolic pathways, such as amino acid, nitrogen, purine, and pyrimidine metabolism, and the citric acid cycle. This combination also showed that the contribution of GC-MS was low when used in combination with other mass spectrometry methods and nuclear magnetic resonance to explore muscle samples. CONCLUSION This study reports the validation of several analytical methods, based on nuclear magnetic resonance and several mass spectrometry methods, to explore the muscle metabolome from a small amount of tissue, comparable to that obtained during a clinical trial. The combination of several techniques may be relevant for the exploration of muscle metabolism, with acceptable analytical variability and overlap between methods However, the difficult and time-consuming data pre-processing, processing, and statistical analysis steps do not justify systematically combining analytical methods.
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Affiliation(s)
- C Bruno
- CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France; UMR INSERM U930, Université François Rabelais de Tours, France
| | - F Patin
- CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France; UMR INSERM U930, Université François Rabelais de Tours, France
| | - C Bocca
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, Angers, France
| | | | - F Bonnier
- Université François-Rabelais de Tours, Faculté de Pharmacie, EA 6295 Nanomédicaments et Nanosondes, Tours, France
| | - P Reynier
- Institut MITOVASC, CNRS 6015, INSERM U1083, Université d'Angers, Angers, France
| | - P Emond
- UMR INSERM U930, Université François Rabelais de Tours, France
| | - P Vourc'h
- CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France; UMR INSERM U930, Université François Rabelais de Tours, France
| | - K Joseph-Delafont
- CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France
| | - P Corcia
- UMR INSERM U930, Université François Rabelais de Tours, France; Centre de Ressources et de Compétences SLA, CHU Tours, France; Fédération des Centres de Ressources et de Compétences de Tours et Limoges, Litorals, France
| | - C R Andres
- CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France; UMR INSERM U930, Université François Rabelais de Tours, France
| | - H Blasco
- CHRU de Tours, Laboratoire de Biochimie et Biologie Moléculaire, Tours, France; UMR INSERM U930, Université François Rabelais de Tours, France.
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Simillion C, Semmo N, Idle JR, Beyoğlu D. Robust Regression Analysis of GCMS Data Reveals Differential Rewiring of Metabolic Networks in Hepatitis B and C Patients. Metabolites 2017; 7:metabo7040051. [PMID: 28991180 PMCID: PMC5746731 DOI: 10.3390/metabo7040051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 09/30/2017] [Accepted: 10/05/2017] [Indexed: 12/17/2022] Open
Abstract
About one in 15 of the world’s population is chronically infected with either hepatitis virus B (HBV) or C (HCV), with enormous public health consequences. The metabolic alterations caused by these infections have never been directly compared and contrasted. We investigated groups of HBV-positive, HCV-positive, and uninfected healthy controls using gas chromatography-mass spectrometry analyses of their plasma and urine. A robust regression analysis of the metabolite data was conducted to reveal correlations between metabolite pairs. Ten metabolite correlations appeared for HBV plasma and urine, with 18 for HCV plasma and urine, none of which were present in the controls. Metabolic perturbation networks were constructed, which permitted a differential view of the HBV- and HCV-infected liver. HBV hepatitis was consistent with enhanced glucose uptake, glycolysis, and pentose phosphate pathway metabolism, the latter using xylitol and producing threonic acid, which may also be imported by glucose transporters. HCV hepatitis was consistent with impaired glucose uptake, glycolysis, and pentose phosphate pathway metabolism, with the tricarboxylic acid pathway fueled by branched-chain amino acids feeding gluconeogenesis and the hepatocellular loss of glucose, which most probably contributed to hyperglycemia. It is concluded that robust regression analyses can uncover metabolic rewiring in disease states.
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Affiliation(s)
- Cedric Simillion
- Interfaculty Bioinformatics Unit and SIB Swiss Institute of Bioinformatics, University of Bern, Baltzerstrasse 6, 3012 Bern, Switzerland.
- Department of BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland.
| | - Nasser Semmo
- Department of BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland.
- Department of Visceral Surgery and Medicine, Department of Hepatology, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland.
| | - Jeffrey R Idle
- Department of BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland.
- Department of Visceral Surgery and Medicine, Department of Hepatology, Inselspital, University Hospital of Bern, 3010 Bern, Switzerland.
- Division of Systems Pharmacology and Pharmacogenomics, Samuel J. and Joan B. Williamson Institute, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, 11201 New York, NY, USA.
| | - Diren Beyoğlu
- Department of BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland.
- Division of Systems Pharmacology and Pharmacogenomics, Samuel J. and Joan B. Williamson Institute, Arnold & Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, 11201 New York, NY, USA.
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