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Correas AG, Olaso-Gonzalez G, Roca M, Blanco-Gandía MC, Nascimento C, Lahoz A, Rodriguez-Arias M, Miñarro J, Gomez-Cabrera MC, Viña J. Glucose 6 phosphate dehydrogenase overexpression rescues the loss of cognition in the double transgenic APP/PS1 mouse model of Alzheimer's disease. Redox Biol 2024; 75:103242. [PMID: 38908073 DOI: 10.1016/j.redox.2024.103242] [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: 04/02/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 06/24/2024] Open
Abstract
Mice models of Alzheimer's disease (APP/PS1) typically experience cognitive decline with age. G6PD overexpressing mice (G6PD-Tg) exhibit better protection from age-associated functional decline including improvements in metabolic and muscle functions as well as reduced frailty compared to their wild-type counterparts. Importantly G6PD-Tg mice show diminished accumulation of DNA oxidation in the brain at different ages in both males and females. To further explore the potential benefits of modulating the G6PD activity in neurodegenerative diseases, triple transgenic mice (3xTg G6PD) were generated, overexpressing APP, PSEN1, and G6PD genes. The cognitive decline characteristic of APP/PS1 mice was prevented in 3xTg G6PD mice, despite similar amyloid-β (Aβ) levels in the hippocampus. This challenges the dominant hypothesis in Alzheimer's disease (AD) etiology and the majority of therapeutic efforts in the field, based on the notion that Aβ is pivotal in cognitive preservation. Notably, the antioxidant properties of G6PD led to a decrease in oxidative stress parameters, such as improved GSH/GSSG and GSH/CysSSG ratios, without major changes in oxidative damage markers. Additionally, metabolic changes in 3xTg G6PD mice increased brain energy status, countering the hypometabolism observed in Alzheimer's models. Remarkably, a higher respiratory exchange ratio suggested increased carbohydrate utilization. The relative failures of Aβ-targeted clinical trials have raised significant skepticism on the amyloid cascade hypothesis and whether the development of Alzheimer's drugs has followed the correct path. Our findings highlight the significance of targeting glucose-metabolizing enzymes rather than solely focusing on Aβ in Alzheimer's research, advocating for a deeper exploration of glucose metabolism's role in cognitive preservation.
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Affiliation(s)
- Angela G Correas
- Freshage Research Group, Department of Physiology. Faculty of Medicine, University of Valencia, CIBERFES, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - Gloria Olaso-Gonzalez
- Freshage Research Group, Department of Physiology. Faculty of Medicine, University of Valencia, CIBERFES, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain.
| | - Marta Roca
- Analytical Unit, Instituto de Investigación Sanitaria Fundación Hospital La Fe, Valencia, Spain
| | - Mari Carmen Blanco-Gandía
- Departamento de Psicología y Sociología, Facultad de Ciencias Sociales y Humanas, Universidad de Zaragoza, Teruel, Spain
| | - Carla Nascimento
- Freshage Research Group, Department of Physiology. Faculty of Medicine, University of Valencia, CIBERFES, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - Agustin Lahoz
- Analytical Unit, Instituto de Investigación Sanitaria Fundación Hospital La Fe, Valencia, Spain; Biomarkers and Precision Medicine Unit, Instituto de Investigación Sanitaria Fundación Hospital La Fe, Valencia, Spain
| | - Marta Rodriguez-Arias
- Unidad de Investigacion Psicobiologia de las Drogodependencias, Departamento de Psicobiologia, Facultad de Psicologia, Universidad de Valencia, Valencia, Spain
| | - José Miñarro
- Unidad de Investigacion Psicobiologia de las Drogodependencias, Departamento de Psicobiologia, Facultad de Psicologia, Universidad de Valencia, Valencia, Spain
| | - Mari Carmen Gomez-Cabrera
- Freshage Research Group, Department of Physiology. Faculty of Medicine, University of Valencia, CIBERFES, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
| | - José Viña
- Freshage Research Group, Department of Physiology. Faculty of Medicine, University of Valencia, CIBERFES, Fundación Investigación Hospital Clínico Universitario/INCLIVA, Valencia, Spain
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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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Šofranko J, Gondáš E, Murín R. Application of the Hydrophilic Interaction Liquid Chromatography (HILIC-MS) Novel Protocol to Study the Metabolic Heterogeneity of Glioblastoma Cells. Metabolites 2024; 14:297. [PMID: 38921432 PMCID: PMC11205371 DOI: 10.3390/metabo14060297] [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: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Glioblastoma is a highly malignant brain tumor consisting of a heterogeneous cellular population. The transformed metabolism of glioblastoma cells supports their growth and division on the background of their milieu. One might hypothesize that the transformed metabolism of a primary glioblastoma could be well adapted to limitations in the variety and number of substrates imported into the brain parenchyma and present it their microenvironment. Additionally, the phenotypic heterogeneity of cancer cells could promote the variations among their metabolic capabilities regarding the utilization of available substrates and release of metabolic intermediates. With the aim to identify the putative metabolic footprint of different types of glioblastoma cells, we exploited the possibility for separation of polar and ionic molecules present in culture media or cell lysates by hydrophilic interaction liquid chromatography (HILIC). The mass spectrometry (MS) was then used to identify and quantify the eluted compounds. The introduced method allows the detection and quantification of more than 150 polar and ionic metabolites in a single run, which may be present either in culture media or cell lysates and provide data for polaromic studies within metabolomics. The method was applied to analyze the culture media and cell lysates derived from two types of glioblastoma cells, T98G and U118. The analysis revealed that even both types of glioblastoma cells share several common metabolic aspects, and they also exhibit differences in their metabolic capability. This finding agrees with the hypothesis about metabolic heterogeneity of glioblastoma cells. Furthermore, the combination of both analytical methods, HILIC-MS, provides a valuable tool for metabolomic studies based on the simultaneous identification and quantification of a wide range of polar and ionic metabolites-polaromics.
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Affiliation(s)
- Jakub Šofranko
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4D, 036 01 Martin, Slovakia
| | - Eduard Gondáš
- Department of Pharmacology, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4D, 036 01 Martin, Slovakia
| | - Radovan Murín
- Department of Medical Biochemistry, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4D, 036 01 Martin, Slovakia
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Fang L, Zhai Q, Zhang H, Ji P, Chen C, Zhang H. Comparisons of different extraction methods and solvents for saliva samples. Metabolomics 2024; 20:38. [PMID: 38460055 DOI: 10.1007/s11306-024-02105-2] [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: 02/27/2023] [Accepted: 02/19/2024] [Indexed: 03/11/2024]
Abstract
INTRODUCTION Changes in the categories and concentrations of salivary metabolites may be closely related to oral, intestinal or systemic diseases. To study salivary metabolites, the first analytical step is to extract them from saliva samples as much as possible, while reducing interferences to a minimum. Frequently used extraction methods are protein precipitation (PPT), liquid-liquid extraction (LLE) and solid-phase extraction (SPE), with various organic solvents. The types and quantities of metabolites extracted with different methods may vary greatly, but few studies have systematically evaluated them. OBJECTIVES This study aimed to select the most suitable methods and solvents for the extraction of saliva according to different analytical targets. METHODS An untargeted metabolomics approach based on liquid chromatography-mass spectrometry was applied to obtain the raw data. The numbers of metabolites, repeatability of the data and intensities of mass spectrometry signals were used as evaluation criteria. RESULTS PPT resulted in the highest coverage. Among the PPT solvents, acetonitrile displayed the best repeatability and the highest coverage, while acetone resulted in the best signal intensities for the extracted compounds. LLE with the mixture of chloroform and methanol was the most suitable for the extraction of small hydrophobic compounds. CONCLUSION PPT with acetonitrile or acetone was recommended for untargeted analysis, while LLE with the mixture of chloroform and methanol was recommended for small hydrophobic compounds.
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Affiliation(s)
- Lingli Fang
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Qiming Zhai
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Hua Zhang
- Department of Obstetrics, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Ping Ji
- Chongqing Key Laboratory of Oral Disease and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Chang Chen
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.
| | - Hongmei Zhang
- Department of Pediatric Dentistry, Stomatological Hospital of Chongqing Medical University, Chongqing, China.
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Ikeda K, Takahashi M, Bamba T, Izumi Y. Comparison of Amine-Modified Polymeric Stationary Phases for Polar Metabolomic Analysis Based on Unified-Hydrophilic Interaction/Anion Exchange Liquid Chromatography/High-Resolution Mass Spectrometry (Unified-HILIC/AEX/HRMS). Mass Spectrom (Tokyo) 2024; 13:A0143. [PMID: 38410254 PMCID: PMC10894851 DOI: 10.5702/massspectrometry.a0143] [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: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 02/28/2024] Open
Abstract
In metabolomic analysis, one of the most commonly used techniques to support the detection sensitivity and quantitation of mass spectrometry is combining it with liquid chromatography. Recently, we developed a method that enables comprehensive single-run measurement of hydrophilic metabolites using unified-hydrophilic interaction/anion exchange liquid chromatography/high-resolution mass spectrometry (unified-HILIC/AEX/HRMS) with a polymer-based mixed amines column (Gelpack GL-HilicAex). However, the importance of stationary phase functional groups and mobile phase conditions for the separation mechanisms and sensitive detection in unified-HILIC/AEX/HRMS is not yet fully understood. This study aimed to understand the importance of the mobile and stationary phases in unified-HILIC/AEX/HRMS. Two different alkali-resistant polymer-based amines-modified columns (Gelpack GL-HilicAex, primary, secondary, tertiary, and quaternary amine-modified polyglycerol dimethacrylate gel; Asahipak NH2P-50 2D, secondary amine-modified polyvinyl alcohol gel) and two eluents (acetonitrile and ammonium bicarbonate solution, pH 9.8) were used for comparative validation. A comparison of mobile phase conditions using both columns confirmed that the two-step separation from HILIC to AEX characteristic of unified-HILIC/AEX requires a linear gradient condition from acetonitrile to nearly 50% water and AEX with up to 40 mM bicarbonate ions. We found that when alkali-resistant hydrophilic polymer packing materials are modified with amines, unified-HILIC/AEX separation can be reproduced if at least one secondary amine associated with the amine series is present in the stationary phase. Furthermore, the difference in sensitivity in the HILIC and AEX modes owing to the different columns indicates the need for further improvements in the mobile phase composition and stationary phase.
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Affiliation(s)
- Kazuki Ikeda
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatomo Takahashi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Lewis IA. Boundary flux analysis: an emerging strategy for investigating metabolic pathway activity in large cohorts. Curr Opin Biotechnol 2024; 85:103027. [PMID: 38061263 DOI: 10.1016/j.copbio.2023.103027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 02/09/2024]
Abstract
Many biological phenotypes are rooted in metabolic pathway activity rather than the concentrations of individual metabolites. Despite this, most metabolomics studies only capture steady-state metabolism - not metabolic flux. Although sophisticated metabolic flux analysis strategies have been developed, these methods are technically challenging and difficult to implement in large-cohort studies. Recently, a new boundary flux analysis (BFA) approach has emerged that captures large-scale metabolic flux phenotypes by quantifying changes in metabolite levels in the media of cultured cells. This approach is advantageous because it is relatively easy to implement yet captures complex metabolic flux phenotypes. We describe the opportunities and challenges of BFA and illustrate how it can be harnessed to investigate a wide transect of biological phenomena.
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Affiliation(s)
- Ian A Lewis
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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Ma J, Li X, Yang Z, Liu Q, Liu Y, Liu A. Widely targeted metabolomics unveils baicalin-induced hippocampal metabolic alternations in a rat model of chronic unpredictable mild stress. J Pharm Biomed Anal 2024; 237:115766. [PMID: 37820491 DOI: 10.1016/j.jpba.2023.115766] [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: 04/07/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
Baicalin has various neuroprotective effects in models of nervous system disease. Our study has shown baicalin could alleviate depressive-like behaviors in a neuroendocrine mouse model. But the systematic metabolic characteristic and particular targets of baicalin in regulating depressive behaviors have never been investigated. Therefore, this study aims to reveal the hippocampal metabolic profiling of chronic unpredictable mild stress (CUMS) induced depressive rats and the potential metabolic variations after baicalin treatment. We first used the sucrose preference test and open field test to access the antidepressant effects of baicalin. Then, metabolites of the hippocampus after baicalin therapy were monitored by widely-targeted metabolomics based on ultra-performance liquid chromatography-tandem mass spectrometry technology. Finally, the potential mechanism associated with neurogenesis obtained from metabolomics was verified by immunohistochemistry. The results showed that baicalin(40,80 mg/kg) could significantly alleviate depressive behaviors induced by CUMS as demonstrated by an increase in sucrose preference and movement distance and stand-up times in open field test. In the metabolomic analysis, a total of 733 metabolites were identified after baicalin treatment including 15 differential metabolites such as organic acid and its derivatives, heterocyclic compounds, fatty acid, bile acids, amino acid and its metabolites, and so on. Enrichment for differential metabolites showed that the differential metabolites might be involved in the process of folate and cofactor biosynthesis, cholesterol metabolism, primary bile acid biosynthesis, tyrosine metabolism and dopaminergic synapse. Moreover, immunohistochemical analysis confirmed baicalin could facilitate hippocampal neurogenesis of depressive rats in CUMS model. These results suggested baicalin might exert antidepressant effects through regulating the differential metabolites which might play a crucial role in inhibiting oxidative stress and improving neurogenesis. Our findings wish to discover the potential mechanism of baicalin on depression from the metabolomics perspective and promote its clinical application.
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Affiliation(s)
- Jie Ma
- Department of Pharmacy, Qilu Hospital of Shandong University, 250012 Jinan, PR China
| | - Xiaoyu Li
- Shandong Academy of Chinese Medicine, 250014 Jinan, PR China
| | - Zongtong Yang
- Shandong Academy of Chinese Medicine, 250014 Jinan, PR China
| | - Qingming Liu
- Shandong Second Provincial General Hospital, 250021 Jinan, PR China.
| | - Yiming Liu
- Department of Neurology, Qilu Hospital of Shandong University, 250012 Jinan, PR China.
| | - Anchang Liu
- Department of Pharmacy, Qilu Hospital of Shandong University, 250012 Jinan, PR China.
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de Souza HMR, Pereira TTP, de Sá HC, Alves MA, Garrett R, Canuto GAB. Critical Factors in Sample Collection and Preparation for Clinical Metabolomics of Underexplored Biological Specimens. Metabolites 2024; 14:36. [PMID: 38248839 PMCID: PMC10819689 DOI: 10.3390/metabo14010036] [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: 11/24/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
This review article compiles critical pre-analytical factors for sample collection and extraction of eight uncommon or underexplored biological specimens (human breast milk, ocular fluids, sebum, seminal plasma, sweat, hair, saliva, and cerebrospinal fluid) under the perspective of clinical metabolomics. These samples are interesting for metabolomics studies as they reflect the status of living organisms and can be applied for diagnostic purposes and biomarker discovery. Pre-collection and collection procedures are critical, requiring protocols to be standardized to avoid contamination and bias. Such procedures must consider cleaning the collection area, sample stimulation, diet, and food and drug intake, among other factors that impact the lack of homogeneity of the sample group. Precipitation of proteins and removal of salts and cell debris are the most used sample preparation procedures. This review intends to provide a global view of the practical aspects that most impact results, serving as a starting point for the designing of metabolomic experiments.
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Affiliation(s)
- Hygor M. R. de Souza
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
| | - Tássia T. P. Pereira
- Departamento de Genética, Ecologia e Evolucao, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
- Departamento de Biodiversidade, Evolução e Meio Ambiente, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil
| | - Hanna C. de Sá
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
| | - Marina A. Alves
- Instituto de Pesquisa de Produtos Naturais Walter Mors, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil;
| | - Rafael Garrett
- Instituto de Química, Universidade Federal do Rio de Janeiro, LabMeta—LADETEC, Rio de Janeiro 21941-598, Brazil;
- Department of Laboratory Medicine, Boston Children’s Hospital—Harvard Medical School, Boston, MA 02115, USA
| | - Gisele A. B. Canuto
- Departamento de Química Analítica, Instituto de Química, Universidade Federal da Bahia, Salvador 40170-115, Brazil;
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Chen CJ, Lee DY, Yu J, Lin YN, Lin TM. Recent advances in LC-MS-based metabolomics for clinical biomarker discovery. MASS SPECTROMETRY REVIEWS 2023; 42:2349-2378. [PMID: 35645144 DOI: 10.1002/mas.21785] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/14/2021] [Accepted: 11/18/2021] [Indexed: 06/15/2023]
Abstract
The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.
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Affiliation(s)
- Chao-Jung Chen
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Jiaxin Yu
- AI Innovation Center, China Medical University Hospital, Taichung, Taiwan
| | - Yu-Ning Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Tsung-Min Lin
- Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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Belloumi D, Calvet S, Roca MI, Ferrer P, Jiménez-Belenguer A, Cambra-López M, García-Rebollar P, Climent E, Martínez-Blanch J, Tortajada M, Chenoll E, Bermejo A, Cerisuelo A. Effect of providing citrus pulp-integrated diet on fecal microbiota and serum and fecal metabolome shifts in crossbred pigs. Sci Rep 2023; 13:17596. [PMID: 37845279 PMCID: PMC10579234 DOI: 10.1038/s41598-023-44741-z] [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: 01/30/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023] Open
Abstract
The study aimed to assess the impact of dehydrated citrus pulp (DCP) on growth performance, fecal characteristics, fecal bacterial composition (based on 16S rRNA analysis), and fecal and serum metabolomic profiles in crossbred pigs. 80 finishing pigs Duroc × (Landrace × Large White) were fed either a control diet (C) or a diet with 240 g/kg DCP (T) for six weeks. Including DCP in diets tended to decrease feed intake, increased (p < 0.05) the concentrations of acetic and heptanoic acids and decreased (p < 0.05) fecal butyric and branched-chain fatty acid concentrations in feces. Animals fed DCP exhibited a lower abundance of the genera Clostridium and Romboutsia, while Lachnospira significantly increased. Orthogonal partial least squares discriminant analysis plotted a clear separation of fecal and serum metabolites between groups. The main discriminant fecal metabolites were associated with bacterial protein fermentation and were downregulated in T-fed pigs. In serum, DCP supplementation upregulated metabolites related to protein and fatty acids metabolism. In conclusion, the addition of DCP as an environmentally friendly source of nutrients in pig diets, resulted in modifications of fecal bacterial composition, fermentation patterns, and overall pig metabolism, suggesting improvements in protein metabolism and gut health.
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Affiliation(s)
- Dhekra Belloumi
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, 12400, Segorbe, Spain
- Institute of Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Salvador Calvet
- Institute of Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Marta Isabel Roca
- Unidad Analítica, Instituto de Investigación Sanitaria La Fe, 46026, Valencia, Spain
| | - Pablo Ferrer
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, 12400, Segorbe, Spain
| | - Ana Jiménez-Belenguer
- Departamento de Biotecnología, Universitat Politècnica de València, 46022, Valencia, Spain
| | - María Cambra-López
- Institute of Animal Science and Technology, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Paloma García-Rebollar
- Departamento de Producción Agraria, ETSIAAB, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | | | | | | | | | - Almudena Bermejo
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, 46113, Moncada, Spain
| | - Alba Cerisuelo
- Centro de Investigación y Tecnología Animal, Instituto Valenciano de Investigaciones Agrarias, 12400, Segorbe, Spain.
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Guo R, Zhong Q, Liu J, Bai P, Wang Z, Kou J, Chen P, Zhang J, Zhang B. Polarity-extended liquid chromatography-triple quadrupole mass spectrometry for simultaneous hydrophilic and hydrophobic metabolite analysis. Anal Chim Acta 2023; 1277:341655. [PMID: 37604610 DOI: 10.1016/j.aca.2023.341655] [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: 04/10/2023] [Revised: 07/02/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023]
Abstract
Although various metabolomic methods have been reported in recent years, simultaneous detection of hydrophilic and hydrophobic metabolites in a single analysis remains a technical challenge. In this study, based on the combination of hydrophilic interaction liquid chromatography (HILIC) and reversed phase liquid chromatography (RPLC), an online two-dimensional liquid chromatography/triple quadrupole mass spectrometry method (2D-LC/TQMS) was developed for the simultaneous analysis of hydrophilic and hydrophobic metabolites of various biological samples. The method can measure 417 biologically important metabolites (e.g., amino acids and peptides, pyrimidines, purines, monosaccharides, fatty acids and conjugates, organic dicarboxylic acids, and others) with logP values ranging from -10.3 to 21.9. The metabolites are involved in a variety of metabolic pathways (e.g., purine metabolism, pyrimidine metabolism, tyrosine metabolism, galactose metabolism, gluconeogenesis, and TCA cycle). The developed method has good intra- and inter-day reproducibility (RSD of retention time <2%, RSD of peak area <30%), good linearity (R2 > 0.9) and wide linear range (from 0.0025 μg/mL to 5 μg/mL). The applicability of the method was tested using different biological samples (i.e., plasma, serum, urine, fecal, seminal plasma and liver) and it was found that 208 (out of 417) identical metabolites were detected in all biological samples. Furthermore, the metabolomic method was applied to a case/control study of urinary of bladder cancer. Thirty differential metabolites were identified that were involved in carbohydrate and amino acid metabolism.
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Affiliation(s)
- Rui Guo
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Qisheng Zhong
- Guangzhou Analytical Center Analytical & Measuring Instruments Division, Shimadzu (China) Co., LTD, Guangzhou, 510656, China
| | - Jiaqi Liu
- Guangzhou Analytical Center Analytical & Measuring Instruments Division, Shimadzu (China) Co., LTD, Guangzhou, 510656, China
| | - Peiming Bai
- Zhongshan Hospital Affiliated of Xiamen University, Xiamen, 361004, China
| | - Zongpeng Wang
- Jinjiang Jingchun Technology Ltd., Quanzhou, 362200, China
| | - Jieling Kou
- ScienceLife (Xiamen) Technology Co., Ltd., Xiamen, 361000, China
| | - Peijie Chen
- Zhongshan Hospital Affiliated of Xiamen University, Xiamen, 361004, China.
| | - Jie Zhang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen, 361102, China.
| | - Bo Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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12
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Narduzzi L, Delgado-Povedano MDM, Lara FJ, Le Bizec B, García-Campaña AM, Dervilly G, Hernández-Mesa M. A comparison of hydrophilic interaction liquid chromatography and capillary electrophoresis for the metabolomics analysis of human serum. J Chromatogr A 2023; 1706:464239. [PMID: 37541059 DOI: 10.1016/j.chroma.2023.464239] [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: 06/26/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/06/2023]
Abstract
Cationic, anionic, zwitterionic and, partially polar metabolites are very important constituents of blood serum. Several of these metabolites underpin the core metabolism of cells (e.g., Krebs cycle, urea cycle, proteins synthesis, etc.), while others might be considered ancillary but still important to grasp the status of any organism through blood serum analysis. Due to its wide chemical diversity, modern metabolomics analysis of serum is still struggling to provide a complete and comprehensive picture of the polar metabolome, due to the limitations of each specific analytical method. In this study, two metabolomics-based analytical methods using the most successful techniques for polar compounds separation in human serum samples, namely hydrophilic interaction liquid chromatography (HILIC) and capillary electrophoresis (CE), are evaluated, both coupled to a high-resolution time-of-flight mass spectrometer via electrospray ionization (ESI-Q-TOF-MS). The performance of the two methods have been compared using five terms of comparison, three of which are specific to metabolomics, such as (1) compounds' detectability (2) Pezzatti score (Pezzatti et al. 2018), (3) intra-day precision (repeatability), (4) ease of automatic analysis of the data (through a common deconvolution alignment and extrapolation software, MS-DIAL, and (5) time & cost analysis. From this study, HILIC-MS proved to be a better tool for polar metabolome analysis, while CE-MS helped identify some interesting variables that gave it interest in completing metabolome coverage in metabolomics studies. Finally, in this framework, MS-DIAL demonstrates for the first time its ability to process CE data for metabolomics, although it is not designed for it.
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Affiliation(s)
- Luca Narduzzi
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, Granada E-18071, Spain.
| | - María Del Mar Delgado-Povedano
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, Granada E-18071, Spain
| | - Francisco J Lara
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, Granada E-18071, Spain
| | | | - Ana María García-Campaña
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, Granada E-18071, Spain
| | | | - Maykel Hernández-Mesa
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Av. Fuentenueva s/n, Granada E-18071, Spain.
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13
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Hao JD, Chen YY, Wang YZ, An N, Bai PR, Zhu QF, Feng YQ. Novel Peak Shift Correction Method Based on the Retention Index for Peak Alignment in Untargeted Metabolomics. Anal Chem 2023; 95:13330-13337. [PMID: 37609864 DOI: 10.1021/acs.analchem.3c02583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Peak alignment is a crucial step in liquid chromatography-mass spectrometry (LC-MS)-based large-scale untargeted metabolomics workflows, as it enables the integration of metabolite peaks across multiple samples, which is essential for accurate data interpretation. Slight differences or fluctuations in chromatographic separation conditions, however, can cause the chromatographic retention time (RT) shift between consecutive analyses, ultimately affecting the accuracy of peak alignment between samples. Here, we introduce a novel RT shift correction method based on the retention index (RI) and apply it to peak alignment. We synthesized a series of N-acyl glycine (C2-C23) homologues via the amidation reaction between glycine with normal saturated fatty acids (C2-C23) as calibrants able to respond proficiently in both mass spectrometric positive- and negative-ion modes. Using these calibrants, we established an N-acyl glycine RI system. This RI system is capable of covering a broad chromatographic space and addressing chromatographic RT shift caused by variations in flow rate, gradient elution, instrument systems, and LC separation columns. Moreover, based on the RI system, we developed a peak shift correction model to enhance peak alignment accuracy. Applying the model resulted in a significant improvement in the accuracy of peak alignment from 15.5 to 80.9% across long-term data spanning a period of 157 days. To facilitate practical application, we developed a Python-based program, which is freely available at https://github.com/WHU-Fenglab/RI-based-CPSC.
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Affiliation(s)
- Jun-Di Hao
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yao-Yu Chen
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yan-Zhen Wang
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Na An
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Pei-Rong Bai
- Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Quan-Fei Zhu
- School of Public Health, Wuhan University, Wuhan 430071, China
| | - Yu-Qi Feng
- Department of Chemistry, Wuhan University, Wuhan 430072, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430071, China
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14
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Kaczmarek M, Zhang N, Buzhansky L, Gilead S, Gazit E. Optimization Strategies for Mass Spectrometry-Based Untargeted Metabolomics Analysis of Small Polar Molecules in Human Plasma. Metabolites 2023; 13:923. [PMID: 37623867 PMCID: PMC10456887 DOI: 10.3390/metabo13080923] [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: 06/25/2023] [Revised: 07/23/2023] [Accepted: 08/03/2023] [Indexed: 08/26/2023] Open
Abstract
The untargeted approach to mass spectrometry-based metabolomics has a wide potential to investigate health and disease states, identify new biomarkers for diseases, and elucidate metabolic pathways. All this holds great promise for many applications in biological and chemical research. However, the complexity of instrumental parameters on advanced hybrid mass spectrometers can make the optimization of the analytical method immensely challenging. Here, we report a strategy to optimize the selected settings of a hydrophilic interaction liquid chromatography-tandem mass spectrometry method for untargeted metabolomics studies of human plasma, as a sample matrix. Specifically, we evaluated the effects of the reconstitution solvent in the sample preparation procedure, the injection volume employed, and different mass spectrometry-related operating parameters including mass range, the number of data-dependent fragmentation scans, collision energy mode, duration of dynamic exclusion time, and mass resolution settings on the metabolomics data quality and output. This study highlights key instrumental variables influencing the detection of metabolites along with suggested settings for the IQ-X tribrid system and proposes a new methodological framework to ensure increased metabolome coverage.
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Affiliation(s)
- Michał Kaczmarek
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Nanyun Zhang
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Ludmila Buzhansky
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Sharon Gilead
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
| | - Ehud Gazit
- Division of Metabolite Medicine, Blavatnik Center for Drug Discovery, Tel Aviv University, Tel Aviv 69978, Israel; (N.Z.); (L.B.); (S.G.); (E.G.)
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 69978, Israel
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15
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Ong ES. Urine Metabolites and Bioactive Compounds from Functional Food: Applications of Liquid Chromatography Mass Spectrometry. Crit Rev Anal Chem 2023:1-16. [PMID: 37454386 DOI: 10.1080/10408347.2023.2235442] [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: 07/18/2023]
Abstract
Bioactive compounds in functional foods, medicinal plants and others are considered attractive value-added molecules based on their wide range of bioactivity. It is clear that an important role is occupied by polyphenol, phenolic compounds and others. Urine is an effective biofluid to evaluate and monitor alterations in homeostasis and other processes related to metabolism. The current review provides a detailed description of the formation of urine in human body, various aspects relevant to sampling and analysis of urinary metabolites before presenting recent developments leveraging on metabolite profiling of urine. For the profiling of small molecules in urine, advancement of liquid chromatography mass tandem spectrometry (LC/MS/MS), establishment of standardized chemical fragmentation libraries, computational resources, data-analysis approaches with pattern recognition tools have made it an attractive option. The profiling of urinary metabolites gives an overview of the biomarkers associated with the diet and evaluates its biological effects. Metabolic pathways such as glycolysis, tricarboxylic acid cycle, amino acid metabolism, energy metabolism, purine metabolism and others can be evaluated. Finally, a combination of metabolite profiling with chemical standardization and bioassay in functional food and medicinal plants will likely lead to the identification of new biomarkers and novel biochemical insights.
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Affiliation(s)
- Eng Shi Ong
- Singapore University of Technology and Design, Singapore, Republic of Singapore
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16
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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: 5] [Impact Index Per Article: 5.0] [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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17
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Jia Z, Qiu Q, He R, Zhou T, Chen L. Identification of Metabolite Interference Is Necessary for Accurate LC-MS Targeted Metabolomics Analysis. Anal Chem 2023; 95:7985-7992. [PMID: 37155916 DOI: 10.1021/acs.analchem.3c00804] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Targeted metabolomics has been broadly used for metabolite measurement due to its good quantitative linearity and simple metabolite annotation workflow. However, metabolite interference, the phenomenon where one metabolite generates a peak in another metabolite's MRM setting (Q1/Q3) with a close retention time (RT), may lead to inaccurate metabolite annotation and quantification. Besides isomeric metabolites having the same precursor and product ions that may interfere with each other, we found other metabolite interferences as the result of inadequate mass resolution of triple-quadruple mass spectrometry and in-source fragmentation of metabolite ions. Characterizing the targeted metabolomics data using 334 metabolite standards revealed that about 75% of the metabolites generated measurable signals in at least one other metabolite's MRM setting. Different chromatography techniques can resolve 65-85% of these interfering signals among standards. Metabolite interference analysis combined with the manual inspection of cell lysate and serum data suggested that about 10% out of ∼180 annotated metabolites were mis-annotated or mis-quantified. These results highlight that a thorough investigation of metabolite interference is necessary for accurate metabolite measurement in targeted metabolomics.
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Affiliation(s)
- Zhikun Jia
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Fudan University, Shanghai 200433, China
| | - Qiongju Qiu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Fudan University, Shanghai 200433, China
| | - Ruiping He
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Fudan University, Shanghai 200433, China
| | - Tianyu Zhou
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Fudan University, Shanghai 200433, China
- Shanghai Qi Zhi Institute, Shanghai 200030, China
| | - Li Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism & Integrative Biology, Fudan University, Shanghai 200433, China
- Shanghai Qi Zhi Institute, Shanghai 200030, China
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18
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Du TT, Liu XC, He Y, Gao X, Liu ZZ, Wang ZL, Li LQ. Changes of gut microbiota and tricarboxylic acid metabolites may be helpful in early diagnosis of necrotizing enterocolitis: A pilot study. Front Microbiol 2023; 14:1119981. [PMID: 37007499 PMCID: PMC10050441 DOI: 10.3389/fmicb.2023.1119981] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
PurposeWe aimed to explore the value of gut microbiota and tricarboxylic acid (TCA) metabolites in early diagnosis of necrotizing enterocolitis (NEC) among infants with abdominal manifestations.MethodsThirty-two preterm infants with abdominal manifestations at gestational age ≤ 34 weeks were included in the study and were divided into non-NEC (n = 16) and NEC (n = 16) groups. Faecal samples were collected when the infants were enrolled. The gut microbiota was analysed with high-throughput sequencing, and TCA metabolites were measured with multiple reaction monitoring (MRM) targeted metabolomics. Receiver operating characteristic (ROC) curves were generated to explore the predictive value of the obtained data.ResultsThere was no significant difference in alpha diversity or beta diversity between the two groups (p > 0.05). At the phylum level, Proteobacteria increased, and Actinomycetota decreased in the NEC group (p < 0.05). At the genus level, Bifidobacterium and Lactobacillaceae decreased significantly, and at the species level, unclassified Staphylococcus, Lactobacillaceae and Bifidobacterium animalis subsp. lactis decreased in the NEC group (p < 0.05). Further Linear discriminant analysis effect sizes (LEfSe) analysis showed that the change in Proteobacteria at the phylum level and Lactobacillaceae and Bifidobacterium at the genus level scored higher than 4. The concentrations of succinate, L-malic acid and oxaloacetate in the NEC group significantly increased (p < 0.05), and the areas under the ROC curve for these metabolites were 0.6641, 0.7617, and 0.7344, respectively.ConclusionDecreased unclassified Staphylococcus, Lactobacillaceae and Bifidobacterium animalis subsp. lactis at the species level as well as the increase in the contents of some TCA metabolites, including succinate, L-malic acid and oxaloacetate, have potential value for the early diagnosis of NEC.
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Affiliation(s)
- Ting-Ting Du
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Xiao-Chen Liu
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Yu He
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Xiong Gao
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Zhen-Zhen Liu
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Zheng-Li Wang
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
| | - Lu-Quan Li
- Neonatal Diagnosis and Treatment Centre of Children’s Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
- Jiangxi Hospital Affiliated Children’s Hospital of Chongqing Medical University, Nanchang, China
- *Correspondence: Lu-Quan Li,
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19
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Advances in Mass Spectrometry-Based Single Cell Analysis. BIOLOGY 2023; 12:biology12030395. [PMID: 36979087 PMCID: PMC10045136 DOI: 10.3390/biology12030395] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023]
Abstract
Technological developments and improvements in single-cell isolation and analytical platforms allow for advanced molecular profiling at the single-cell level, which reveals cell-to-cell variation within the admixture cells in complex biological or clinical systems. This helps to understand the cellular heterogeneity of normal or diseased tissues and organs. However, most studies focused on the analysis of nucleic acids (e.g., DNA and RNA) and mass spectrometry (MS)-based analysis for proteins and metabolites of a single cell lagged until recently. Undoubtedly, MS-based single-cell analysis will provide a deeper insight into cellular mechanisms related to health and disease. This review summarizes recent advances in MS-based single-cell analysis methods and their applications in biology and medicine.
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20
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Development of an Untargeted Metabolomics Strategy to Study the Metabolic Rewiring of Dendritic Cells upon Lipopolysaccharide Activation. Metabolites 2023; 13:metabo13030311. [PMID: 36984754 PMCID: PMC10058937 DOI: 10.3390/metabo13030311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023] Open
Abstract
Dendritic cells (DCs) are essential immune cells for defense against external pathogens. Upon activation, DCs undergo profound metabolic alterations whose precise nature remains poorly studied at a large scale and is thus far from being fully understood. The goal of the present work was to develop a reliable and accurate untargeted metabolomics workflow to get a deeper insight into the metabolism of DCs when exposed to an infectious agent (lipopolysaccharide, LPS, was used to mimic bacterial infection). As DCs transition rapidly from a non-adherent to an adherent state upon LPS exposure, one of the leading analytical challenges was to implement a single protocol suitable for getting comparable metabolomic snapshots of those two cellular states. Thus, a thoroughly optimized and robust sample preparation method consisting of a one-pot solvent-assisted method for the simultaneous cell lysis/metabolism quenching and metabolite extraction was first implemented to measure intracellular DC metabolites in an unbiased manner. We also placed special emphasis on metabolome coverage and annotation by using a combination of hydrophilic interaction liquid chromatography and reverse phase columns coupled to high-resolution mass spectrometry in conjunction with an in-house developed spectral database to identify metabolites at a high confidence level. Overall, we were able to characterize up to 171 unique meaningful metabolites in DCs. We then preliminarily compared the metabolic profiles of DCs derived from monocytes of 12 healthy donors upon in vitro LPS activation in a time-course experiment. Interestingly, the resulting data revealed differential and time-dependent activation of some particular metabolic pathways, the most impacted being nucleotides, nucleotide sugars, polyamines pathways, the TCA cycle, and to a lesser extent, the arginine pathway.
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21
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Sugimoto M, Aizawa Y, Tomita A. Data Processing and Analysis in Liquid Chromatography-Mass Spectrometry-Based Targeted Metabolomics. Methods Mol Biol 2023; 2571:241-255. [PMID: 36152165 DOI: 10.1007/978-1-0716-2699-3_21] [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
Mass spectrometry (MS)-based metabolomics provides high-dimensional datasets; that is, the data include various metabolite features. Data analysis begins by converting the raw data obtained from the MS to produce a data matrix (metabolite × concentrations). This is followed by several steps, such as peak integration, alignment of multiple data, metabolite identification, and calculation of metabolite concentrations. Each step yields the analytical results and the accompanying information used for the quality assessment of the anterior steps. Thus, the measurement quality can be analyzed through data processing. Here, we introduce a typical data processing procedure and describe a method to utilize the intermediate data as quality control. Subsequently, commonly used data analysis methods for metabolomics data, such as statistical analyses, are also introduced.
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Affiliation(s)
- Masahiro Sugimoto
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan.
- Institute for Advanced Biosciences, Yamagata, Japan.
| | - Yumi Aizawa
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Atsumi Tomita
- Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
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22
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Yan Y, Hemmler D, Schmitt-Kopplin P. HILIC-MS for Untargeted Profiling of the Free Glycation Product Diversity. Metabolites 2022; 12:metabo12121179. [PMID: 36557217 PMCID: PMC9783660 DOI: 10.3390/metabo12121179] [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: 11/03/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Glycation products produced by the non-enzymatic reaction between reducing carbohydrates and amino compounds have received increasing attention in both food- and health-related research. Although liquid chromatography mass spectrometry (LC-MS) methods for analyzing glycation products already exist, only a few common advanced glycation end products (AGEs) are usually covered by quantitative methods. Untargeted methods for comprehensively analyzing glycation products are still lacking. The aim of this study was to establish a method for simultaneously characterizing a wide range of free glycation products using the untargeted metabolomics approach. In this study, Maillard model systems consisting of a multitude of heterogeneous free glycation products were chosen for systematic method optimization, rather than using a limited number of standard compounds. Three types of hydrophilic interaction liquid chromatography (HILIC) columns (zwitterionic, bare silica, and amide) were tested due to their good retention for polar compounds. The zwitterionic columns showed better performance than the other two types of columns in terms of the detected feature numbers and detected free glycation products. Two zwitterionic columns were selected for further mobile phase optimization. For both columns, the neutral mobile phase provided better peak separation, whereas the acidic condition provided a higher quality of chromatographic peak shapes. The ZIC-cHILIC column operating under acidic conditions offered the best potential to discover glycation products in terms of providing good peak shapes and maintaining comparable compound coverage. Finally, the optimized HILIC-MS method can detect 70% of free glycation product features despite interference from the complex endogenous metabolites from biological matrices, which showed great application potential for glycation research and can help discover new biologically important glycation products.
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Affiliation(s)
- Yingfei Yan
- Research Unit Analytical BioGeoChemistry (BGC), Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Correspondence: (Y.Y.); (P.S.-K.)
| | - Daniel Hemmler
- Research Unit Analytical BioGeoChemistry (BGC), Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Comprehensive Foodomics Platform, Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry (BGC), Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
- Comprehensive Foodomics Platform, Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University Munich, Maximus-von-Imhof-Forum 2, 85354 Freising, Germany
- Correspondence: (Y.Y.); (P.S.-K.)
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23
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Broseta JJ, Roca M, Rodríguez-Espinosa D, López-Romero LC, Gómez-Bori A, Cuadrado-Payán E, Bea-Granell S, Devesa-Such R, Soldevila A, Sánchez-Pérez P, Hernández-Jaras J. The metabolomic differential plasma profile between dialysates. Pursuing to understand the mechanisms of citrate dialysate clinical benefits. Front Physiol 2022; 13:1013335. [PMID: 36467686 PMCID: PMC9709283 DOI: 10.3389/fphys.2022.1013335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 10/27/2022] [Indexed: 08/30/2023] Open
Abstract
Background: Currently, bicarbonate-based dialysate needs a buffer to prevent precipitation of bicarbonate salts with the bivalent cations, and acetate at 3-4 mmol/L is the most used. However, citrate is being postulated as a preferred option because of its association with better clinical results by poorly understood mechanisms. In that sense, this hypothesis-generating study aims to identify potential metabolites that could biologically explain these improvements found in patients using citrate dialysate. Methods: A unicentric, cross-over, prospective untargeted metabolomics study was designed to analyze the differences between two dialysates only differing in their buffer, one containing 4 mmol/L of acetate (AD) and the other 1 mmol/L of citrate (CD). Blood samples were collected in four moments (i.e., pre-, mid-, post-, and 30-min-post-dialysis) and analyzed in an untargeted metabolomics approach based on UPLC-Q-ToF mass spectrometry. Results: The 31 most discriminant metabolomic variables from the plasma samples of the 21 participants screened by their potential clinical implications show that, after dialysis with CD, some uremic toxins appear to be better cleared, the lysine degradation pathway is affected, and branched-chain amino acids post-dialysis levels are 9-10 times higher than with AD; and, on its part, dialysis with AD affects acylcarnitine clearance. Conclusion: Although most metabolic changes seen in this study could be attributable to the dialysis treatment itself, this study successfully identifies some metabolic variables that differ between CD and AD, which raise new hypotheses that may unveil the mechanisms involved in the clinical improvements observed with citrate in future research.
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Affiliation(s)
- José Jesús Broseta
- Department of Nephrology and Renal Transplantation, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Marta Roca
- Analytcal Unit Platform, Medical Research Institute Hospital La Fe (IIS La Fe), Valencia, Spain
| | - Diana Rodríguez-Espinosa
- Department of Nephrology and Renal Transplantation, Hospital Clínic de Barcelona, Barcelona, Spain
| | | | - Aina Gómez-Bori
- Department of Nephrology, Hospital Universitari I Politècnic La Fe, Valencia, Spain
| | - Elena Cuadrado-Payán
- Department of Nephrology and Renal Transplantation, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Sergio Bea-Granell
- Department of Nephrology, Consorci Hospital General Universitari de València, Valencia, Spain
| | - Ramón Devesa-Such
- Department of Nephrology, Hospital Universitari I Politècnic La Fe, Valencia, Spain
| | - Amparo Soldevila
- Department of Nephrology, Hospital Universitari I Politècnic La Fe, Valencia, Spain
| | - Pilar Sánchez-Pérez
- Department of Nephrology, Hospital Universitari I Politècnic La Fe, Valencia, Spain
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24
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Marques C, Liu L, Duncan KD, Lanekoff I. A Direct Infusion Probe for Rapid Metabolomics of Low-Volume Samples. Anal Chem 2022; 94:12875-12883. [PMID: 36070505 PMCID: PMC9494293 DOI: 10.1021/acs.analchem.2c02918] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Targeted and nontargeted metabolomics has the potential
to evaluate
and detect global metabolite changes in biological systems. Direct
infusion mass spectrometric analysis enables detection of all ionizable
small molecules, thus simultaneously providing information on both
metabolites and lipids in chemically complex samples. However, to
unravel the heterogeneity of the metabolic status of cells in culture
and tissue a low number of cells per sample should be analyzed with
high sensitivity, which requires low sample volumes. Here, we present
the design and characterization of the direct infusion probe, DIP.
The DIP is simple to build and position directly in front of a mass
spectrometer for rapid metabolomics of chemically complex biological
samples using pneumatically assisted electrospray ionization at 1
μL/min flow rate. The resulting data is acquired in a square
wave profile with minimal carryover between samples that enhances
throughput and enables several minutes of uniform MS signal from 5
μL sample volumes. The DIP was applied to study the intracellular
metabolism of insulin secreting INS-1 cells and the results show that
exposure to 20 mM glucose for 15 min significantly alters the abundance
of several small metabolites, amino acids, and lipids.
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Affiliation(s)
- Cátia Marques
- Department of Chemistry─BMC, Uppsala University, 75123 Uppsala, Sweden
| | - Liangwen Liu
- Department of Medical Cell Biology, Uppsala University, 75123 Uppsala, Sweden
| | - Kyle D Duncan
- Department of Chemistry─BMC, Uppsala University, 75123 Uppsala, Sweden
| | - Ingela Lanekoff
- Department of Chemistry─BMC, Uppsala University, 75123 Uppsala, Sweden
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25
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Alcoriza-Balaguer MI, García-Cañaveras JC, Ripoll-Esteve FJ, Roca M, Lahoz A. LipidMS 3.0: an R-package and a web-based tool for LC-MS/MS data processing and lipid annotation. Bioinformatics 2022; 38:4826-4828. [PMID: 36005855 DOI: 10.1093/bioinformatics/btac581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 07/19/2022] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION LipidMS was initially envisioned to use fragmentation rules and data-independent acquisition (DIA) for lipid annotation. However, data-dependent acquisition (DDA) remains the most widespread acquisition mode for untargeted LC-MS/MS-based lipidomics. Here we present LipidMS 3.0, an R package that not only adds DDA and new lipid classes to its pipeline, but also the required functionalities to cover the whole data analysis workflow from pre-processing (i.e., peak-peaking, alignment and grouping) to lipid annotation. RESULTS We applied the new workflow in the data analysis of a commercial human serum pool spiked with 68 representative lipid standards acquired in full scan, DDA and DIA modes. When focusing on the detected lipid standard features and total identified lipids, LipidMS 3.0 data pre-processing performance is similar to XCMS, whereas it complements the annotations returned by MS-DIAL, providing a higher level of structural information and a lower number of incorrect annotations. To extend and facilitate LipidMS 3.0 usage among less experienced R-programming users, the workflow was also implemented as a web-based application. AVAILABILITY The LipidMS R-package is freely available at https://CRAN.R-project.org/package=LipidMS and as a website at http://www.lipidms.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- María Isabel Alcoriza-Balaguer
- Biomarkers and Precision Medicine Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Juan Carlos García-Cañaveras
- Biomarkers and Precision Medicine Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Francisco Javier Ripoll-Esteve
- Department of Informatics, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain
| | - Marta Roca
- Analytical Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026
| | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026, Spain.,Analytical Unit, Health Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, Valencia, 46026
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26
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Zhang T, Zhang G, Chen X, Chen Z, Tan AY, Lin A, Zhang C, Torres LK, Bajrami S, Zhang T, Zhang G, Xiang JZ, Hissong EM, Chen YT, Li Y, Du YCN. Low-dose carbon monoxide suppresses metastatic progression of disseminated cancer cells. Cancer Lett 2022; 546:215831. [PMID: 35868533 DOI: 10.1016/j.canlet.2022.215831] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/25/2022]
Abstract
Low-dose carbon monoxide (CO) is under investigation in clinical trials to treat non-cancerous diseases and has excellent safety profiles. Due to the early detection and cancer awareness, increasing cancer patients are diagnosed at early stages and potentially curative surgical resection can be done. However, many patients ultimately experience recurrence. Here, we evaluate the therapeutic effect of CO on cancer metastatic progression. We show that 250 ppm CO inhibits migration of multiple types of cancer cell lines including breast, pancreatic, colon, prostate, liver, and lung cancer and reduces the ability to adhere to fibronectin. We demonstrate that in mouse models, 250 ppm inhaled CO inhibits lung metastasis of breast cancer and liver metastasis of pancreatic cancer. Moreover, low-dose CO suppresses recurrence and increases survival after surgical removal of primary pancreatic cancer in mice. Mechanistically, low-dose CO blocks transcription of heme importers, leading to diminished intracellular heme levels and a heme-regulated enzyme, cytochrome P4501B1 (CYP1B1). Either supplementing heme or overexpressing CYP1B1 reverses the anti-migration effect of low-dose CO. Taken together, low-dose CO therapy inhibits cell migration, reduces adhesion to fibronectin, prevents disseminated cancer cells from expanding into gross metastases, and improves survival in pre-clinical mouse models of metastasis.
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Affiliation(s)
- Tiantian Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - George Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Xiang Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Zhengming Chen
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Adrian Y Tan
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Anthony Lin
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Cheryl Zhang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Lisa K Torres
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, NewYork-Presbyterian Hospital/Weill Cornell Medical Center, New York, NY, 10065, USA
| | - Sandi Bajrami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Tuo Zhang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Guoan Zhang
- Proteomics and Metabolomics Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jenny Z Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Erika M Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yao-Tseng Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Yi Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yi-Chieh Nancy Du
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
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27
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Groves RA, Mapar M, Aburashed R, Ponce LF, Bishop SL, Rydzak T, Drikic M, Bihan DG, Benediktsson H, Clement F, Gregson DB, Lewis IA. Methods for Quantifying the Metabolic Boundary Fluxes of Cell Cultures in Large Cohorts by High-Resolution Hydrophilic Liquid Chromatography Mass Spectrometry. Anal Chem 2022; 94:8874-8882. [PMID: 35700271 PMCID: PMC9244871 DOI: 10.1021/acs.analchem.2c00078] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Metabolomics is a
mainstream approach for investigating the metabolic
underpinnings of complex biological phenomena and is increasingly
being applied to large-scale studies involving hundreds or thousands
of samples. Although metabolomics methods are robust in smaller-scale
studies, they can be challenging to apply to larger cohorts due to
the inherent variability of liquid chromatography mass spectrometry
(LC-MS). Much of this difficulty results from the time-dependent changes
in the LC-MS system, which affects both the qualitative and quantitative
performances of the instrument. Herein, we introduce an analytical
strategy for addressing this problem in large-scale microbial studies.
Our approach quantifies microbial boundary fluxes using two zwitterionic
hydrophilic interaction liquid chromatography (ZIC-HILIC) columns
that are plumbed to enable offline column equilibration. Using this
strategy, we show that over 397 common metabolites can be resolved
in 4.5 min per sample and that metabolites can be quantified with
a median coefficient of variation of 0.127 across 1100 technical replicates.
We illustrate the utility of this strategy via an analysis of 960
strains of Staphylococcus aureus isolated
from bloodstream infections. These data capture the diversity of metabolic
phenotypes observed in clinical isolates and provide an example of
how large-scale investigations can leverage our novel analytical strategy.
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Affiliation(s)
- Ryan A Groves
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Maryam Mapar
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Raied Aburashed
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Luis F Ponce
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Stephanie L Bishop
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Thomas Rydzak
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Marija Drikic
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Dominique G Bihan
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Hallgrimur Benediktsson
- Cumming School of Medicine, Department of Pathology and Laboratory Medicine, University of Calgary, Calgary T2N 1N4, Canada.,Alberta Precision Laboratories, Calgary T2L 2K8, Canada
| | - Fiona Clement
- Cumming School of Medicine, Department of Community Health Sciences, University of Calgary, Calgary T2N 1N4, Canada
| | - Daniel B Gregson
- Cumming School of Medicine, Department of Pathology and Laboratory Medicine, University of Calgary, Calgary T2N 1N4, Canada.,Alberta Precision Laboratories, Calgary T2L 2K8, Canada.,Cumming School of Medicine, Department of Medicine, University of Calgary, Calgary T2N 1N4, Canada
| | - Ian A Lewis
- Department of Biological Sciences, University of Calgary, Calgary T2N 1N4, Canada
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28
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Wang T, Zhang C, Li H, Zhou R, Ye X, Yang Y, He K. The underlying rationality of Chinese medicine herb pair Coptis chinensis and Dolomiaea souliei: From the perspective of metabolomics and intestinal function. JOURNAL OF ETHNOPHARMACOLOGY 2022; 289:115065. [PMID: 35122977 DOI: 10.1016/j.jep.2022.115065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/14/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The combination of Coptis chinensis (RC) and Dolomiaea souliei (VR) has long been used as a classic herb pair for the treatment of gastrointestinal diseases, but the underlying mechanisms remain unknown. MATERIALS AND METHODS In this study, the rationality of evidence-based RC and VR combination was explored from the perspective of metabolism, gut microbiota and gastrointestinal function. RESULTS After 5 weeks treatment, VR extracts (700 mg/kg) and RC alkaloids (800 mg/kg) showed no toxic effect on mice. However, RC administration significantly decreased the body weight of mice. Gastric emptying, gastrointestinal motility function and the absorption of FITC dextran were retarded in the mice of RC group, taking RC along with low dose VR (RC-VRL) and high dose VR (RC-VRH) reversed the impaired gastrointestinal function caused by RC. RC administration significantly increased villus height/crypt depth value. Notably, VR administration increased the number of crypts in mice ileum and reduced villus height/crypt depth value in VR and RC combination group. RC treatment significantly increased the expression of occludin compared to NC group; RC-VRL treatment reversed this tendency. While, VR administration increased ZO1 expression by 99.4% compared to NC mice. As for gut microbiota, RC gavage decreased the gut microbiota diversity, but gut microbiota in VR group was similar to NC group, and VR and RC combination increased gut microbiota diversity. RC administration obviously increased the proportion of Akkermansia muciniphila, Bacteroides thetaiotaomicron, Parabacteroides distasonis, and Escherichia coli, compared to NC mice. VR treatment increased the richness of Bacteroides thetaiotaomicron, Parabacteroides distasonis. RC-VRL and RC-VRH treatment dose-dependently increased the richness of Rikenellaceae RC9, Lactobacillus, and decreased the abundance of Psychrobacter, Bacteroides and Ruminococcus in mice. Serum metabolomic analysis revealed that RC gavage significantly down regulated 76 metabolites and up regulated 31 metabolites. VR treatment significantly down regulated 30 metabolites and up regulated 12 metabolites. Weight loss caused by RC may attribute to the elevated methylxanthine level in mice. The potential adverse effects caused by high dose RC intake may partially alleviate by high serum contents of adenosine, inosine and urolithin A resulted from VR coadministration. CONCLUSION VR may alleviate RC caused "fluid retention" via normalizing gastrointestinal function, gut microbiota and modulating the perturbed metabolism.
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Affiliation(s)
- Ting Wang
- Hunan Provincial Key Laboratory of Dong Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Science, Hunan University of Medicine, Huaihua, 418000, Hunan, China
| | - Chongyang Zhang
- Hunan Provincial Key Laboratory of Dong Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Science, Hunan University of Medicine, Huaihua, 418000, Hunan, China
| | - Hui Li
- Hunan Provincial Key Laboratory of Dong Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Science, Hunan University of Medicine, Huaihua, 418000, Hunan, China
| | - Rui Zhou
- Hunan Provincial Key Laboratory of Dong Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Science, Hunan University of Medicine, Huaihua, 418000, Hunan, China
| | - Xiaoli Ye
- Engineering Research Center of Coptis Development and Utilization (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, 400715, China.
| | - Yong Yang
- School of Pharmacy, Hunan University of Traditional Chinese Medicine, Changsha, 410208, Hunan, China
| | - Kai He
- Hunan Provincial Key Laboratory of Dong Medicine, Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Science, Hunan University of Medicine, Huaihua, 418000, Hunan, China.
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29
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Zhang F, Zhao Y, Wang Y, Wang H, Guo Y, Xiong B. Effects of calcium propionate on milk performance and serum metabolome of dairy cows in early lactation. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2021.115185] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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da Silva Zandonadi F, dos Santos EAF, Marques MS, Sussulini A. Metabolomics: A Powerful Tool to Understand the Schizophrenia Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1400:105-119. [DOI: 10.1007/978-3-030-97182-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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31
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Feng J, Zhong Q, Kuang J, Liu J, Huang T, Zhou T. Simultaneous Analysis of the Metabolome and Lipidome Using Polarity Partition Two-Dimensional Liquid Chromatography-Mass Spectrometry. Anal Chem 2021; 93:15192-15199. [PMID: 34739231 DOI: 10.1021/acs.analchem.1c03905] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Comprehensive metabolic profiling is a considerable challenge for systems biology since the metabolites in biological samples have significant polarity differences. A heart-cutting two-dimensional liquid chromatography-mass spectrometry (2D-LC-MS) method-based polarity partition was established to analyze both the metabolome and lipidome in a single run. Based on the polarity partition strategy, metabolites with high polarity were retained and separated by one-dimensional hydrophilic chromatography, while low- and medium-polarity lipids were collected into a sample loop and injected into two-dimensional reversed-phase chromatography for separation. A simple online dilution strategy realized the online coupling of the 2D-LC-MS, which effectively solved band broadening and peak distortion caused by solvent incompatibility. Moreover, a dual gradient elution procedure was introduced to further broaden the coverage of low-polarity lipids. The metabolites' log P values, which this 2D-LC-MS method could analyze, ranged from -8.79 to 26.86. The feasibility of the 2D-LC-MS system was demonstrated by simultaneous analysis of the metabolome and lipidome in rat plasma related to depression. A total of 319 metabolites were determined within 40 min, including organic acids, nucleosides, carbohydrate derivatives, amino acids, lipids, and other organic compounds. Finally, 44 depression-related differential metabolites were screened. Compared with conventional LC-MS-based methods, the 2D-LC method covered over 99% of features obtained by two conventional methods. In addition, the selectivity and resolution of the hydrophilic metabolites were improved, and the matrix effects of the hydrophobic metabolites were reduced in the developed method. The results indicated that the established 2D-LC system is a powerful tool for comprehensive metabolomics studies.
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Affiliation(s)
- Jieqing Feng
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Qisheng Zhong
- Guangzhou Analytical Applications Center, Shimadzu (China) Co., LTD, Guangzhou 510010, China
| | - Jiangmeng Kuang
- Guangzhou Analytical Applications Center, Shimadzu (China) Co., LTD, Guangzhou 510010, China
| | - Jiaqi Liu
- Guangzhou Analytical Applications Center, Shimadzu (China) Co., LTD, Guangzhou 510010, China
| | - Taohong Huang
- Shanghai Analytical Applications Center, Shimadzu (China) Co., LTD, Shanghai 200233, China
| | - Ting Zhou
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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32
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Scolari F, Khamis FM, Pérez-Staples D. Beyond Sperm and Male Accessory Gland Proteins: Exploring Insect Reproductive Metabolomes. Front Physiol 2021; 12:729440. [PMID: 34690804 PMCID: PMC8529219 DOI: 10.3389/fphys.2021.729440] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/14/2021] [Indexed: 01/13/2023] Open
Abstract
Insect seminal fluid, the non-sperm component of the ejaculate, comprises a variegated set of molecules, including, but not limited to, lipids, proteins, carbohydrates, salts, hormones, nucleic acids, and vitamins. The identity and functional role of seminal fluid proteins (SFPs) have been widely investigated, in multiple species. However, most of the other small molecules in insect ejaculates remain uncharacterized. Metabolomics is currently adopted to deepen our understanding of complex biological processes and in the last 15years has been applied to answer different physiological questions. Technological advances in high-throughput methods for metabolite identification such as mass spectrometry and nuclear magnetic resonance (NMR) are now coupled to an expanded bioinformatics toolbox for large-scale data analysis. These improvements allow for the processing of smaller-sized samples and for the identification of hundreds to thousands of metabolites, not only in Drosophila melanogaster but also in disease vectors, animal, and agricultural pests. In this review, we provide an overview of the studies that adopted metabolomics-based approaches in insects, with a particular focus on the reproductive tract (RT) of both sexes and the ejaculate. Progress in the field of metabolomics will contribute not only to achieve a deeper understanding of the composition of insect ejaculates and how they are affected by endogenous and exogenous factors, but also to provide increasingly powerful tools to decipher the identity and molecular interactions between males and females during and after mating.
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Affiliation(s)
- Francesca Scolari
- Institute of Molecular Genetics (IGM)-CNR "Luigi Luca Cavalli-Sforza", Pavia, Italy
| | - Fathiya M Khamis
- International Centre of Insect Physiology and Ecology (icipe), Nairobi, Kenya
| | - Diana Pérez-Staples
- Instituto de Biotecnología y Ecología Aplicada (INBIOTECA), Universidad Veracruzana, Xalapa, Mexico
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33
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Yu S, Fan J, Zhang L, Qin X, Li Z. Assessment of Biphasic Extraction Methods of Mouse Fecal Metabolites for Liquid Chromatography-Mass Spectrometry-Based Metabolomic Studies. J Proteome Res 2021; 20:4487-4494. [PMID: 34435490 DOI: 10.1021/acs.jproteome.1c00450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
With the increasing knowledge about the important roles of gut microbiota on the biological system, a systematic strategy to profile the fecal metabolome is urgently needed. Thus, an unbiased, efficient, and reproducible fecal metabolite extraction protocol needs to be established; however, the effect of biphasic extraction methods for the fecal samples remains unclear. In this study, five different methods were assessed in the extraction of polar and non-polar metabolites for the liquid chromatography-mass spectrometry (LC-MS)-based mouse fecal metabolomic study. First, the detection coverage of two extraction systems, the Bligh and Dyer extraction method (M1, chloroform/methanol/water, 2/2/1.8) and Matyash method (M2, methyl tert-butyl ether (MTBE)/methanol/water, 10/3/2.5), was compared; then, MTBE/methanol/water system with different solvent ratios (M3, 2.6/2.0/2.4; M4, 4.5/1/2.5; and M5, 3/2.5/2.5) were further evaluated. The results showed that M2 showed higher detection coverage than M1. For the MTBE/methanol/water system with different solvent ratios, M3 showed the largest detection coverage based on peak numbers and numbers of putatively annotated metabolites, while M4 presented the least overlap between two phases, higher peak intensities of metabolites, and superior reproducibility. Based on the above evidence, M4 was recommended for the biphasic extraction of fecal metabolites in the LC-MS-based mouse fecal metabolomic study.
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Affiliation(s)
- Shuting Yu
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, People's Republic of China
| | - Jianxin Fan
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, People's Republic of China
| | - Lin Zhang
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, People's Republic of China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, People's Republic of China
| | - Zhenyu Li
- Modern Research Center for Traditional Chinese Medicine, the Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, No. 92, Wucheng Road, Taiyuan, Shanxi 030006, People's Republic of China
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Macioszek S, Dudzik D, Jacyna J, Wozniak A, Schöffski P, Markuszewski MJ. A Robust Method for Sample Preparation of Gastrointestinal Stromal Tumour for LC/MS Untargeted Metabolomics. Metabolites 2021; 11:metabo11080554. [PMID: 34436495 PMCID: PMC8400919 DOI: 10.3390/metabo11080554] [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: 07/23/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 12/31/2022] Open
Abstract
Gastrointestinal stromal tumour has already been well explored at the genome level; however, little is known about metabolic processes occurring in the sarcoma. Sample preparation is a crucial step in untargeted metabolomics workflow, highly affecting the metabolome coverage and the quality of the results. In this study, four liquid-liquid extraction methods for the isolation of endogenous compounds from gastrointestinal stromal tumours were compared and evaluated. The protocols covered two-step or stepwise extraction with methyl-tert-butyl ether (MTBE) or dichloromethane. The extracts were subjected to LC-MS analysis by the application of reversed-phase and hydrophilic interaction liquid chromatography to enable the separation and detection of both polar and nonpolar analytes. The extraction methods were compared in terms of efficiency (total number of detected metabolites) and reproducibility. The method was based on the stepwise extraction with MTBE, methanol, and water proved to be the most reproducible, and thus, its robustness to fluctuations in experimental conditions was assessed employing Plackett–Burman design and hierarchical modelling. While most studied factors had no effect on the metabolite abundance, the highest coefficient value was observed for the volume of MTBE added during extraction. Herein, we demonstrate the application and the feasibility of the selected protocol for the analysis of gastrointestinal stromal tumour samples. The method selected could be considered as a reference for the best characterization of underlying molecular changes associated with complex tissue extracts of GIST.
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Affiliation(s)
- Szymon Macioszek
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
| | - Danuta Dudzik
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
| | - Julia Jacyna
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
| | - Agnieszka Wozniak
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (A.W.); (P.S.)
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Patrick Schöffski
- Department of General Medical Oncology, Leuven Cancer Institute, University Hospitals Leuven, 3000 Leuven, Belgium; (A.W.); (P.S.)
- Laboratory of Experimental Oncology, Department of Oncology, KU Leuven, 3000 Leuven, Belgium
| | - Michał J. Markuszewski
- Department of Biopharmaceutics and Pharmacodynamics, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland; (S.M.); (D.D.); (J.J.)
- Correspondence: ; Tel.: +48-58-349-1493
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García-Cañaveras JC, Lahoz A. Tumor Microenvironment-Derived Metabolites: A Guide to Find New Metabolic Therapeutic Targets and Biomarkers. Cancers (Basel) 2021; 13:3230. [PMID: 34203535 PMCID: PMC8268968 DOI: 10.3390/cancers13133230] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 12/11/2022] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that enables cancer cells to grow, proliferate and survive. This metabolic rewiring is intrinsically regulated by mutations in oncogenes and tumor suppressors, but also extrinsically by tumor microenvironment factors (nutrient and oxygen availability, cell-to-cell interactions, cytokines, hormones, etc.). Intriguingly, only a few cancers are driven by mutations in metabolic genes, which lead metabolites with oncogenic properties (i.e., oncometabolites) to accumulate. In the last decade, there has been rekindled interest in understanding how dysregulated metabolism and its crosstalk with various cell types in the tumor microenvironment not only sustains biosynthesis and energy production for cancer cells, but also contributes to immune escape. An assessment of dysregulated intratumor metabolism has long since been exploited for cancer diagnosis, monitoring and therapy, as exemplified by 18F-2-deoxyglucose positron emission tomography imaging. However, the efficient delivery of precision medicine demands less invasive, cheaper and faster technologies to precisely predict and monitor therapy response. The metabolomic analysis of tumor and/or microenvironment-derived metabolites in readily accessible biological samples is likely to play an important role in this sense. Here, we review altered cancer metabolism and its crosstalk with the tumor microenvironment to focus on energy and biomass sources, oncometabolites and the production of immunosuppressive metabolites. We provide an overview of current pharmacological approaches targeting such dysregulated metabolic landscapes and noninvasive approaches to characterize cancer metabolism for diagnosis, therapy and efficacy assessment.
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Affiliation(s)
- Juan C. García-Cañaveras
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
| | - Agustín Lahoz
- Biomarkers and Precision Medicine Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
- Analytical Unit, Medical Research Institute-Hospital La Fe, Av. Fernando Abril Martorell 106, 46026 Valencia, Spain
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Pure Ion Chromatograms Combined with Advanced Machine Learning Methods Improve Accuracy of Discriminant Models in LC-MS-Based Untargeted Metabolomics. Molecules 2021; 26:molecules26092715. [PMID: 34063107 PMCID: PMC8125400 DOI: 10.3390/molecules26092715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 11/17/2022] Open
Abstract
Untargeted metabolomics based on liquid chromatography coupled with mass spectrometry (LC-MS) can detect thousands of features in samples and produce highly complex datasets. The accurate extraction of meaningful features and the building of discriminant models are two crucial steps in the data analysis pipeline of untargeted metabolomics. In this study, pure ion chromatograms were extracted from a liquor dataset and left-sided colon cancer (LCC) dataset by K-means-clustering-based Pure Ion Chromatogram extraction method version 2.0 (KPIC2). Then, the nonlinear low-dimensional embedding by uniform manifold approximation and projection (UMAP) showed the separation of samples from different groups in reduced dimensions. The discriminant models were established by extreme gradient boosting (XGBoost) based on the features extracted by KPIC2. Results showed that features extracted by KPIC2 achieved 100% classification accuracy on the test sets of the liquor dataset and the LCC dataset, which demonstrated the rationality of the XGBoost model based on KPIC2 compared with the results of XCMS (92% and 96% for liquor and LCC datasets respectively). Finally, XGBoost can achieve better performance than the linear method and traditional nonlinear modeling methods on these datasets. UMAP and XGBoost are integrated into KPIC2 package to extend its performance in complex situations, which are not only able to effectively process nonlinear dataset but also can greatly improve the accuracy of data analysis in non-target metabolomics.
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