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Zhou Z, Sun Y, Yang J, Abliz Z. Mapping the Metabolic Characteristics and Perturbation of Adult Casper Zebrafish by Ambient Mass Spectrometry Imaging. Metabolites 2024; 14:204. [PMID: 38668332 PMCID: PMC11051737 DOI: 10.3390/metabo14040204] [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: 02/03/2024] [Revised: 03/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Casper, a type of transparent mutant-line zebrafish, was generated to overcome the opaque trunk of an adult zebrafish for tumor modeling to realize real-time visualization of transplanted cells in vivo. However, the molecular information at the metabolic level has not received much attention. Herein, a spatially resolved metabolomics method based on an airflow-assisted desorption electrospray ionization-mass spectrometry imaging (AFADESI-MSI) system for whole-body zebrafish was used to investigate small molecules and the distribution of adult casper (Mitfaw2/w2, roya9/a9) and the differences from wild-type zebrafish. Finally, the spatial distribution information of more than 1500 endogenous ions was obtained in positive and negative detection modes, and 186 metabolites belonging to a variety of structural categories were identified or annotated. Compared with wild-type samples, 85 variables, including 37 known metabolites, were screened out. In addition, the disordered metabolic pathways caused by the genetic mutation were excavated, involving downregulation of purine metabolism and arachidonic acid metabolism, upregulation of glycerophospholipid metabolism, and biosynthesis of unsaturated fatty acids. All these results were observed in the most intuitive way through MSI. This study revealed important metabolic characteristics of and perturbation in adult casper zebrafish, and provides indispensable fundamental knowledge for tumor research based on it.
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Affiliation(s)
- Zhi Zhou
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China;
- College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China; (Y.S.); (J.Y.)
| | - Yue Sun
- College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China; (Y.S.); (J.Y.)
| | - Ji Yang
- College of Life and Environmental Sciences, Minzu University of China, 27 Zhongguancun South Avenue, Beijing 100081, China; (Y.S.); (J.Y.)
| | - Zeper Abliz
- Key Laboratory of Mass Spectrometry Imaging and Metabolomics (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China;
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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2
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Chen X, Qiu TT, Wang Y, Xu LY, Sun J, Jiang ZH, Zhao W, Tao T, Zhou YW, Wei LS, Li YQ, Zheng YY, Zhou GH, Chen HQ, Zhang J, Feng XB, Wang FY, Li N, Zhang XN, Jiang J, Zhu MS. A Shigella species variant is causally linked to intractable functional constipation. J Clin Invest 2022; 132:e150097. [PMID: 35617029 PMCID: PMC9282927 DOI: 10.1172/jci150097] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/17/2022] [Indexed: 11/22/2022] Open
Abstract
Intractable functional constipation (IFC) is the most severe form of constipation, but its etiology has long been unknown. We hypothesized that IFC is caused by refractory infection by a pathogenic bacterium. Here, we isolated from patients with IFC a Shigella species - peristaltic contraction-inhibiting bacterium (PIB) - that significantly inhibited peristaltic contraction of the colon by production of docosapentenoic acid (DPA). PIB colonized mice for at least 6 months. Oral administration of PIB was sufficient to induce constipation, which was reversed by PIB-specific phages. A mutated PIB with reduced DPA was incapable of inhibiting colonic function and inducing constipation, suggesting that DPA produced by PIB was the key mediator of the genesis of constipation. PIBs were detected in stools of 56% (38 of 68) of the IFC patients, but not in those of non-IFC or healthy individuals (0 of 180). DPA levels in stools were elevated in 44.12% (30 of 68) of the IFC patients but none of the healthy volunteers (0 of 97). Our results suggest that Shigella sp. PIB may be the critical causative pathogen for IFC, and detection of fecal PIB plus DPA may be a reliable method for IFC diagnosis and classification.
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Affiliation(s)
- Xin Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
- Shaanxi An-Ning-Yunsheng Biotechnology Limited Company, Xi’an, China
| | - Tian-Tian Qiu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Ye Wang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
- Shaanxi An-Ning-Yunsheng Biotechnology Limited Company, Xi’an, China
| | - Li-Yang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
- Shaanxi An-Ning-Yunsheng Biotechnology Limited Company, Xi’an, China
| | - Jie Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
- Shaanxi An-Ning-Yunsheng Biotechnology Limited Company, Xi’an, China
| | - Zhi-Hui Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Wei Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Tao Tao
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Yu-Wei Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Li-Sha Wei
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Ye-Qiong Li
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Yan-Yan Zheng
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Guo-Hua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Hua-Qun Chen
- School of Life Science, Nanjing Normal University, Nanjing, China
| | - Jian Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources, School of Life Sciences, Center for Life Sciences, Yunnan University, Kunming, China
| | - Xiao-Bo Feng
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Fang-Yu Wang
- Department of Gastroenterology and Hepatology, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Ning Li
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xue-Na Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
| | - Jun Jiang
- Research Institute of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Min-Sheng Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Key Laboratory of Molecular Medicine and
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3
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Liu Z, Wang P, Liu Z, Wei C, Li Y, Liu L. Evaluation of liver tissue extraction protocol for untargeted metabolomics analysis by ultra-high-performance liquid chromatography/tandem mass spectrometry. J Sep Sci 2021; 44:3450-3461. [PMID: 34129724 DOI: 10.1002/jssc.202100051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/06/2021] [Accepted: 06/12/2021] [Indexed: 12/29/2022]
Abstract
The aim of the untargeted metabolomics study is to obtain a global metabolome coverage from biological samples. Therefore, a comprehensive and systematic protocol for tissue metabolite extraction is highly desirable. In this study, we evaluated a comprehensive liver pretreatment strategy based on ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry to obtain more metabolites using four different protocols. These protocols included (A) methanol protein precipitation, (B) two-step extraction of dichloromethane-methanol followed by methanol-water, (C) two-step extraction of methyl tert-butyl ether-methanol followed by methanol-water, and (D) two-step extraction of isopropanol-methanol followed by methanol-water. Our results showed that protocol D was superior to the others due to more extracted features, annotated metabolites, and better reproducibility. And then, the stability and extraction sequence of protocol D were evaluated. The results showed that extraction with isopropanol-methanol followed by methanol-water was the optimum preparation sequence, which offered higher extraction efficiency, satisfactory repeatability, and acceptable stability. Furthermore, the optimal protocol was successfully applied by liver samples of rats after high-fat intervention. In summary, our protocol enabled a comprehensive and systematic evaluation of liver pretreatment to obtain more medium-polar and nonpolar metabolites and was suitable for high-throughput metabolomics analysis.
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Affiliation(s)
- Zhipeng Liu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, P. R. China
| | - Peng Wang
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, P. R. China
| | - Zengjiao Liu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, P. R. China
| | - Chunbo Wei
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, P. R. China
| | - Ying Li
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, P. R. China
| | - Liyan Liu
- National Key Discipline Laboratory, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, P. R. 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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5
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Zhang Q, Nong Y, Liu Z, Gong L. Proteinase K Combining Two-Step Liquid–Liquid Extraction for Plasma Untargeted Liquid Chromatography–Mass Spectrometry-Based Metabolomics To Discover the Potential Mechanism of Colorectal Adenoma. Anal Chem 2019; 91:14458-14466. [DOI: 10.1021/acs.analchem.9b03121] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Qisong Zhang
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Yanying Nong
- Guangdong Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, People’s Republic of China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Lingzhi Gong
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong 510006, People’s Republic of China
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Kim YH, Shim HS, Kim KH, Lee J, Chung BC, Kowall NW, Ryu H, Lee J. Metabolomic Analysis Identifies Alterations of Amino Acid Metabolome Signatures in the Postmortem Brain of Alzheimer's Disease. Exp Neurobiol 2019; 28:376-389. [PMID: 31308797 PMCID: PMC6614073 DOI: 10.5607/en.2019.28.3.376] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 05/19/2019] [Accepted: 05/21/2019] [Indexed: 02/06/2023] Open
Abstract
Despite significant advances in neuroscience research over the past several decades, the exact cause of AD has not yet fully understood. The metabolic hypothesis as well as the amyloid and tau hypotheses have been proposed to be associated with AD pathogenesis. In order to identify metabolome signatures from the postmortem brains of sporadic AD patients and control subjects, we performed ultra performance liquid chromatography coupled with linear ion trap-Orbitrap mass spectrometer (UPLC-LTQ-Orbitrap-MS). Not only our study identified new metabolome signatures but also verified previously known metabolome profiles in the brain. Statistical modeling of the analytical data and validation of the structural assignments discovered metabolic biomarkers associated with the AD pathogenesis. Interestingly, hypotaurin, myo-inositol and oxo-proline levels were markedly elevated in AD while lutamate and N-acetyl-aspartate were decreased in the postmortem brain tissue of AD patients. In addition, neurosteroid level such as cortisol was significantly increased in AD. Together, our data indicate that impaired amino acid metabolism is associated with AD pathogenesis and the altered amino acid signatures can be useful diagnostic biomarkers of AD. Thus, modulation of amino acid metabolism may be a possible therapeutic approach to treat AD.
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Affiliation(s)
- Yoon Hwan Kim
- MolecularRecognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea
- Department of Biotechnology, Graduate School, Korea University, Seoul 02792, Korea
| | - Hyun Soo Shim
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul 02792, Korea
| | - Junghee Lee
- Veteran's Affairs Boston Healthcare System, Boston, MA 02130, USA
- Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Bong Chul Chung
- MolecularRecognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Neil W. Kowall
- Veteran's Affairs Boston Healthcare System, Boston, MA 02130, USA
- Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Hoon Ryu
- Center for Neuroscience, Brain Science Institute, Korea Institute of Science and Technology, Seoul 02792, Korea
- Veteran's Affairs Boston Healthcare System, Boston, MA 02130, USA
- Boston University Alzheimer's Disease Center and Department of Neurology, Boston University School of Medicine, Boston, MA 02118, USA
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Jeongae Lee
- MolecularRecognition Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea
- Convergence Research Center for Diagnosis, Treatment and Care System of Dementia, Korea Institute of Science and Technology, Seoul 02792, Korea
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7
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Rombouts C, De Spiegeleer M, Van Meulebroek L, De Vos WH, Vanhaecke L. Validated comprehensive metabolomics and lipidomics analysis of colon tissue and cell lines. Anal Chim Acta 2019; 1066:79-92. [PMID: 31027537 DOI: 10.1016/j.aca.2019.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
Current untargeted approaches for metabolic fingerprinting of colon tissue and cell lines lack validation of reproducibility and/or focus on a selection of metabolites as opposed to the entire metabolome. Yet, both are critical to ensure reliable results and pursue a fully holistic analysis. Therefore, we have optimized and validated a platform for analyzing the polar metabolome and lipidome of colon-derived cell and tissue samples based on a consecutive extraction of polar and apolar components. Peak areas of selected targeted analytes and the number of untargeted components were assessed. Analysis was performed using ultra-high performance liquid-chromatography (UHPLC) coupled to hybrid quadrupole-Orbitrap high-resolution mass spectrometry (HRMS). This resulted in an optimized extraction protocol using 50% methanol/ultrapure water to obtain the polar fraction followed by a dichloromethane-based lipid extraction. Using this comprehensive approach, we have detected more than 15,000 components with CV < 30% in internal quality control (IQC) samples and were able to discriminate the non-transformed (NT) and transformed (T) state in human colon tissue and cell lines based on validated OPLS-DA models (R2Y > 0.719 and Q2 > 0.674). To conclude, our validated polar metabolomics and lipidomics fingerprinting approach could be of great value to reveal gastrointestinal disease-associated biomarkers and mechanisms.
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Affiliation(s)
- Caroline Rombouts
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium; Ghent University, Faculty of Bioscience Engineering, Department of Molecular Biotechnology, Cell Systems & Imaging, Coupure Links 653, 9000, Ghent, Belgium; Antwerp University, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Laboratory of Cell Biology & Histology, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Margot De Spiegeleer
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Lieven Van Meulebroek
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium
| | - Winnok H De Vos
- Ghent University, Faculty of Bioscience Engineering, Department of Molecular Biotechnology, Cell Systems & Imaging, Coupure Links 653, 9000, Ghent, Belgium; Antwerp University, Faculty of Veterinary Medicine, Department of Veterinary Sciences, Laboratory of Cell Biology & Histology, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Lynn Vanhaecke
- Ghent University, Faculty of Veterinary Medicine, Department of Veterinary Public Health and Food Safety, Laboratory of Chemical Analysis, Salisburylaan 133, B-9820, Merelbeke, Belgium; Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, Northern Ireland, United Kingdom.
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8
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Zheng H, Ni Z, Cai A, Zhang X, Chen J, Shu Q, Gao H. Balancing metabolome coverage and reproducibility for untargeted NMR-based metabolic profiling in tissue samples through mixture design methods. Anal Bioanal Chem 2018; 410:7783-7792. [PMID: 30298192 DOI: 10.1007/s00216-018-1396-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 01/15/2023]
Abstract
Untargeted metabolomics attempts to acquire a comprehensive and reproducible set of small-molecule metabolites in biological systems. However, metabolite extraction method significantly affects the quality of metabolomics data. In the present study, we calculated the number of peaks (NP) and coefficient of variation (CV) to reflect metabolome coverage and reproducibility in untargeted NMR-based metabolic profiling of tissue samples in rats under different methanol/chloroform/water (MCW) extraction conditions. Different MCW extractions expectedly generated diverse characteristics of metabolome. Moreover, the classic MCW method revealed tissue-specific differences in the NP and CV values. To obtain high-quality metabolomics data, therefore, we used mixture design methods to optimize the MCW extraction strategy by maximizing the NP value and minimizing the CV value in each tissue sample. Results show that the optimal formulations of MCW extraction were 2:2:8 (ml/mg tissue) for brain sample, 2:4:6 (ml/mg tissue) for heart sample, 1.3:2:8.7 (ml/mg tissue) for liver sample, 4:2:6 (ml/mg tissue) for kidney sample, 2:3:7 (ml/mg tissue) for muscle sample, and 2:4:6 (ml/mg tissue) for pancreas sample. Therefore, these findings demonstrate that different tissue samples need a specific optimal extraction condition for balancing metabolome coverage and reproducibility in the untargeted metabolomics study. Mixture design method is an effective tool to optimize metabolite extraction strategy for tissue samples. Graphical abstract ᅟ.
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Affiliation(s)
- Hong Zheng
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Zhitao Ni
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Aimin Cai
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Xi Zhang
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jiuxia Chen
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Qi Shu
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China
| | - Hongchang Gao
- Institute of Metabonomics & Medical NMR, School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, 325035, China.
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9
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Gong ZG, Hu J, Wu X, Xu YJ. The Recent Developments in Sample Preparation for Mass Spectrometry-Based Metabolomics. Crit Rev Anal Chem 2017. [PMID: 28631936 DOI: 10.1080/10408347.2017.1289836] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Metabolomics is a critical member in systems biology. Although great progress has been achieved in metabolomics, there are still some problems in sample preparation, data processing and data interpretation. In this review, we intend to explore the roles, challenges and trends in sample preparation for mass spectrometry- (MS-) based metabolomics. The newly emerged sample preparation methods were also critically examined, including laser microdissection, in vivo sampling, dried blood spot, microwave, ultrasound and enzyme-assisted extraction, as well as microextraction techniques. Finally, we provide some conclusions and perspectives for sample preparation in MS-based metabolomics.
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Affiliation(s)
- Zhi-Gang Gong
- a Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , P. R. China.,b Key Lab of Training , Monitoring and Intervention of Aquatic Sports of General Administration of Sport of P. R. China, Faculty of Physical Education, Jiangxi Normal University , Nanchang , P. R. China
| | - Jing Hu
- a Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , P. R. China.,c College of Life Science and Technology , Minnan Normal University , Fujian , P. R. China
| | - Xi Wu
- a Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , P. R. China
| | - Yong-Jiang Xu
- a Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai , P. R. China.,d Department of Medicine , University of California San Diego , La Jolla , California , USA
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10
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Wu ZY, Zeng ZD, Xiao ZD, Mok DKW, Liang YZ, Chau FT, Chan HY. Semiautomated Alignment of High-Throughput Metabolite Profiles with Chemometric Tools. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2017; 2017:9402045. [PMID: 28168083 PMCID: PMC5267077 DOI: 10.1155/2017/9402045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 11/12/2016] [Accepted: 12/04/2016] [Indexed: 06/06/2023]
Abstract
The rapid increase in the use of metabolite profiling/fingerprinting techniques to resolve complicated issues in metabolomics has stimulated demand for data processing techniques, such as alignment, to extract detailed information. In this study, a new and automated method was developed to correct the retention time shift of high-dimensional and high-throughput data sets. Information from the target chromatographic profiles was used to determine the standard profile as a reference for alignment. A novel, piecewise data partition strategy was applied for the determination of the target components in the standard profile as markers for alignment. An automated target search (ATS) method was proposed to find the exact retention times of the selected targets in other profiles for alignment. The linear interpolation technique (LIT) was employed to align the profiles prior to pattern recognition, comprehensive comparison analysis, and other data processing steps. In total, 94 metabolite profiles of ginseng were studied, including the most volatile secondary metabolites. The method used in this article could be an essential step in the extraction of information from high-throughput data acquired in the study of systems biology, metabolomics, and biomarker discovery.
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Affiliation(s)
- Ze-ying Wu
- School of Mathematics, Physics and Chemical Engineering, Changzhou Institute of Technology, Changzhou 213002, China
- State Key Testing Laboratory of Food Contact Materials, Changzhou Entry-Exit Inspection and Quarantine Bureau, Changzhou 213002, China
| | - Zhong-da Zeng
- Chemometrics and Herbal Medicine Laboratory, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- Dalian ChemDataSolution Technology Co. Ltd., High-Tech Zone, Dalian, Liaoning 116023, China
| | - Zi-dan Xiao
- School of Chemical and Biological Engineering, Changsha University of Science & Technology, Changsha 410114, China
| | - Daniel Kam-Wah Mok
- Chemometrics and Herbal Medicine Laboratory, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology, Shenzhen 518057, China
| | - Yi-zeng Liang
- Research Center of Modernization of Chinese Medicines, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, China
| | - Foo-tim Chau
- Chemometrics and Herbal Medicine Laboratory, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
- State Key Laboratory of Chinese Medicine and Molecular Pharmacology, Shenzhen 518057, China
| | - Hoi-yan Chan
- School of Chemical and Biological Engineering, Changsha University of Science & Technology, Changsha 410114, China
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Song Q, Zhao Y, Chen X, Li J, Li P, Jiang Y, Wang Y, Song Y, Tu P. New instrumentation for large-scale quantitative analysis of components spanning a wide polarity range by column-switching hydrophilic interaction chromatography-turbulent flow chromatography-reversed phase liquid chromatography-tandem mass spectrometry. RSC Adv 2017. [DOI: 10.1039/c7ra03788k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
New instrumentation, namely column-switching HILIC-TFC-RPLC-MS/MS, was configured for large-scale quantitative analysis of components spanning a wide polarity range in a mimic complicated sample.
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Affiliation(s)
- Qingqing Song
- Modern Research Center for Traditional Chinese Medicine
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Yunfang Zhao
- Modern Research Center for Traditional Chinese Medicine
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Xiaojia Chen
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Taipa 999078
- Macao
| | - Jun Li
- Modern Research Center for Traditional Chinese Medicine
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Peng Li
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Taipa 999078
- Macao
| | - Yong Jiang
- State Key Laboratory of Natural and Biomimetic Drugs
- School of Pharmaceutical Sciences
- Peking University
- Beijing 100191
- China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine
- Institute of Chinese Medical Sciences
- University of Macau
- Taipa 999078
- Macao
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100029
- China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine
- School of Chinese Materia Medica
- Beijing University of Chinese Medicine
- Beijing 100029
- China
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