1
|
Willency JA, Lin Y, Pirro V. Targeted metabolomics in human and animal biofluids and tissues using liquid chromatography coupled with tandem mass spectrometry. STAR Protoc 2024; 5:102884. [PMID: 38367229 PMCID: PMC10882138 DOI: 10.1016/j.xpro.2024.102884] [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: 01/15/2023] [Revised: 08/07/2023] [Accepted: 01/26/2024] [Indexed: 02/19/2024] Open
Abstract
Here, we present a targeted polar metabolomics protocol for the analysis of biofluids and frozen tissue biopsies using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). We describe steps for sample pretreatment, liquid-liquid extraction, and isolation of polar metabolites. We then detail procedures for target LC-MS/MS analysis. In this protocol, we focus on the analysis of plasma and serum samples. We also provide brief instructions on how to process other biological matrices as supplemental information. For complete details on the use and execution of this protocol, please refer to Coskun et al. (2022).1.
Collapse
Affiliation(s)
- Jill A Willency
- Technologies and Operations Group, Eli Lilly and Company, Indianapolis, IN 46225, USA
| | - Yanzhu Lin
- Discovery Statistics, Eli Lilly and Company, Indianapolis, IN 46225, USA
| | - Valentina Pirro
- Technologies and Operations Group, Eli Lilly and Company, Indianapolis, IN 46225, USA.
| |
Collapse
|
2
|
Wan C, Wu K, Lu X, Fang F, Li Y, Zhao Y, Li S, Gao J. Integrative Analysis of the Gut Microbiota and Metabolome for In Vitro Human Gut Fermentation Modeling. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:15414-15424. [PMID: 34889098 DOI: 10.1021/acs.jafc.1c04259] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
This study aimed to find the best in vitro fermentation method by integrative analysis of the gut microbiota and metabolome. We selected five different media: brain heart infusion broth, Luria-Bertani broth, Mueller-Hinton broth, anaerobe basal broth, and anaerobic medium base (AMB). After in vitro fermentation, the gut microbiota and metabolites were analyzed at different culture times. The results showed that different culture media have different effects on the bacterial community structure and metabolites. The integrative analysis of gut microbiota and metabolism also proved that AMB medium is effective in keeping a stable bacterial community structure and producing less metabolites and short-chain fatty acids by simulating the nutrient-poor microenvironment in the human gut during in vitro fermentation. Thus, culturing with AMB medium for 48 h is the most suitable in vitro model for human gut microbiota fermentation, which provides an alternative approach for diet and health research.
Collapse
Affiliation(s)
- Chu Wan
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Kaizhang Wu
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Xingyu Lu
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Fang Fang
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yaqian Li
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Yumin Zhao
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Shubo Li
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| | - Jie Gao
- School of Light Industry and Food Engineering, Guangxi University, Nanning 530004, China
| |
Collapse
|
3
|
Sakallioglu IT, Barletta RG, Dussault PH, Powers R. Deciphering the mechanism of action of antitubercular compounds with metabolomics. Comput Struct Biotechnol J 2021; 19:4284-4299. [PMID: 34429848 PMCID: PMC8358470 DOI: 10.1016/j.csbj.2021.07.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 07/28/2021] [Indexed: 01/08/2023] Open
Abstract
Tuberculosis (TB), one of the oldest and deadliest bacterial diseases, continues to cause serious global economic, health, and social problems. Current TB treatments are lengthy, expensive, and routinely ineffective against emerging drug resistant strains. Thus, there is an urgent need for the identification and development of novel TB drugs possessing comprehensive and specific mechanisms of action (MoAs). Metabolomics is a valuable approach to elucidating the MoA, toxicity, and potency of promising chemical leads, which is a critical step of the drug discovery process. Recent advances in metabolomics methodologies for deciphering MoAs include high-throughput screening techniques, the integration of multiple omics methods, mass spectrometry imaging, and software for automated analysis. This review describes recently introduced metabolomics methodologies and techniques for drug discovery, highlighting specific applications to the discovery of new antitubercular drugs and the elucidation of their MoAs.
Collapse
Affiliation(s)
- Isin T. Sakallioglu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Raúl G. Barletta
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska Lincoln, Lincoln, NE 68583-0905, USA
| | - Patrick H. Dussault
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
- Nebraska Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| |
Collapse
|
4
|
Rivera-Velez SM, Navas J, Villarino NF. Applying metabolomics to veterinary pharmacology and therapeutics. J Vet Pharmacol Ther 2021; 44:855-869. [PMID: 33719079 DOI: 10.1111/jvp.12961] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 02/08/2021] [Indexed: 02/06/2023]
Abstract
Metabolomics is the large-scale study of low-molecular-weight substances in a biological system in a given physiological state at a given time point. Metabolomics can be applied to identify predictors of inter-individual variability in drug response, provide clinicians with data useful for decision-making processes in drug selection, and inform about the pharmacokinetics and pharmacodynamics of a drug. It is, therefore, an exceptional approach for gaining new understanding effects in the field of comparative veterinary pharmacology. However, the incorporation of metabolomics into veterinary pharmacology and toxicology is not yet widespread, and this is probably, at least in part, a result of its highly multidisciplinary nature. This article reviews the potential applications of metabolomics in veterinary pharmacology and therapeutics. It integrates key concepts for designing metabolomics studies and analyzing and interpreting metabolomics data, providing solid foundations for applying metabolomics to the study of drugs in all veterinary species.
Collapse
Affiliation(s)
- Sol M Rivera-Velez
- Molecular Determinants Core, Johns Hopkins All Children's Hospital, Saint Petersburg, Florida, USA
| | - Jinna Navas
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| | - Nicolas F Villarino
- Program in Individualized Medicine, Department of Veterinary Clinical Sciences, College of Veterinary Medicine, Washington State University, Pullman, Washington, USA
| |
Collapse
|
5
|
Wang LM, Wang P, Teka T, Zhang YC, Yang WZ, Zhang Y, Wang T, Liu LX, Han LF, Liu CX. 1H NMR and UHPLC/Q-Orbitrap-MS-Based Metabolomics Combined with 16S rRNA Gut Microbiota Analysis Revealed the Potential Regulation Mechanism of Nuciferine in Hyperuricemia Rats. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14059-14070. [PMID: 33146009 DOI: 10.1021/acs.jafc.0c04985] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hyperuricemia seriously jeopardizes human health by increasing the risk of several diseases, such as gout and stroke. Nuciferine is able to alleviate hyperuricemia significantly. However, the underlying metabolic regulation mechanism remains unknown. To understand the metabolic effects of nuciferine on hyperuricemia by establishing a rat model of rapid hyperuricemia, 1H NMR and liquid chromatography-mass spectrometry were used to conduct nontargeted metabolomics studies. A total of 21 metabolites were authenticated in plasma and urine to be closely related with hyperuricemia, which were mainly correlated to the six metabolic pathways. Moreover, 16S rRNA analysis indicated that diversified intestinal microorganisms are closely related to changes in differential metabolites, especially bacteria from Firmicutes and Bacteroidetes. We propose that indoxyl sulfate and N-acetylglutamate in urine may be the potential biomarkers besides uric acid for early diagnosis and prevention of hyperuricemia. Gut microbiological analysis found that changes in the gut microbiota are closely related to these metabolites.
Collapse
Affiliation(s)
- Li-Ming Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
| | - Piao Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
| | - Tekleab Teka
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
- Department of Pharmacy, College of Medicine and Health Sciences, Wollo University, P.O. Box 1145, Dessie +251-1145, Ethiopia
| | - You-Cai Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Wen-Zhi Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
| | - Yi Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
| | - Tao Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
| | - Lai-Xing Liu
- School of Management, Wuhan Institute of Technology, Wuhan 430205, China
| | - Li-Feng Han
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, P. R. China
| | - Cai-Xiang Liu
- CAS Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Centre for Magnetic Resonance in Wuhan, Innovation Academy for Precision Measurement Science and Technology, Wuhan Institute of Physics and Mathematics, The Chinese Academy of Sciences, Wuhan 430071, China
| |
Collapse
|
6
|
Azad RK, Shulaev V. Metabolomics technology and bioinformatics for precision medicine. Brief Bioinform 2019; 20:1957-1971. [PMID: 29304189 PMCID: PMC6954408 DOI: 10.1093/bib/bbx170] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 11/29/2017] [Indexed: 12/14/2022] Open
Abstract
Precision medicine is rapidly emerging as a strategy to tailor medical treatment to a small group or even individual patients based on their genetics, environment and lifestyle. Precision medicine relies heavily on developments in systems biology and omics disciplines, including metabolomics. Combination of metabolomics with sophisticated bioinformatics analysis and mathematical modeling has an extreme power to provide a metabolic snapshot of the patient over the course of disease and treatment or classifying patients into subpopulations and subgroups requiring individual medical treatment. Although a powerful approach, metabolomics have certain limitations in technology and bioinformatics. We will review various aspects of metabolomics technology and bioinformatics, from data generation, bioinformatics analysis, data fusion and mathematical modeling to data management, in the context of precision medicine.
Collapse
Affiliation(s)
| | - Vladimir Shulaev
- Corresponding author: Vladimir Shulaev, Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX 76210, USA. Tel.: 940-369-5368; Fax: 940-565-3821; E-mail:
| |
Collapse
|
7
|
Izumi Y, Matsuda F, Hirayama A, Ikeda K, Kita Y, Horie K, Saigusa D, Saito K, Sawada Y, Nakanishi H, Okahashi N, Takahashi M, Nakao M, Hata K, Hoshi Y, Morihara M, Tanabe K, Bamba T, Oda Y. Inter-Laboratory Comparison of Metabolite Measurements for Metabolomics Data Integration. Metabolites 2019; 9:E257. [PMID: 31683650 PMCID: PMC6918145 DOI: 10.3390/metabo9110257] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/26/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND One of the current problems in the field of metabolomics is the difficulty in integrating data collected using different equipment at different facilities, because many metabolomic methods have been developed independently and are unique to each laboratory. METHODS In this study, we examined whether different analytical methods among 12 different laboratories provided comparable relative quantification data for certain metabolites. Identical samples extracted from two cell lines (HT-29 and AsPc-1) were distributed to each facility, and hydrophilic and hydrophobic metabolite analyses were performed using the daily routine protocols of each laboratory. RESULTS The results indicate that there was no difference in the relative quantitative data (HT-29/AsPc-1) for about half of the measured metabolites among the laboratories and assay methods. Data review also revealed that errors in relative quantification were derived from issues such as erroneous peak identification, insufficient peak separation, a difference in detection sensitivity, derivatization reactions, and extraction solvent interference. CONCLUSION The results indicated that relative quantification data obtained at different facilities and at different times would be integrated and compared by using a reference materials shared for data normalization.
Collapse
Affiliation(s)
- Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata 997-0052, Japan.
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-Ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Yoshihiro Kita
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Kanta Horie
- Translational Science, Neurology Business Group, Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan.
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.
| | - Kosuke Saito
- Division of Medical Safety Science, National Institute of Health Science, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa 210-9501, Japan.
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
| | - Hiroki Nakanishi
- Research Center for Biosignal, Akita University, 1-1-1 Hondo, Akita-city, Akita 010-8543, Japan.
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Motonao Nakao
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Kosuke Hata
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Yutaro Hoshi
- Pharmacokinetic Research Laboratories, Ono Pharmaceutical Co., Ltd., 17-2 Wadai, Tsukuba, Ibaraki 300-4247, Japan.
| | - Motohiko Morihara
- Translational Research Laboratories, Ono Pharmaceutical Co., Ltd., 3-1-1 Sakurai Shimamoto-cho, Mishima-gun, Osaka 618-8585, Japan.
| | - Kazuhiro Tanabe
- Medical Solution Promotion Department, Medical Solution Segment, LSI Medience Corporation, 3-30-1, Shimura, Itabashi-ku, Tokyo 174-8555, Japan.
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Yoshiya Oda
- Department of Lipidomics, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
8
|
Shulaev V, Isaac G. Supercritical fluid chromatography coupled to mass spectrometry – A metabolomics perspective. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1092:499-505. [DOI: 10.1016/j.jchromb.2018.06.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/10/2018] [Accepted: 06/11/2018] [Indexed: 10/14/2022]
|
9
|
Abstract
Systemic sclerosis (SSc) is an autoimmune disease of unknown aetiology characterized by vascular lesions, immunological alterations and diffuse fibrosis of the skin and internal organs. Since recent evidence suggests that there is a link between metabolomics and immune mediated disease, serum metabolic profile of SSc patients and healthy controls was investigated by 1H-NMR and GC-MS techniques. The results indicated a lower level of aspartate, alanine, choline, glutamate, and glutarate in SSc patients compared with healthy controls. Moreover, comparing patients affected by limited SSc (lcSSc) and diffuse SSc (dcSSc), 6 discriminant metabolites were identified. The multivariate analysis performed using all the metabolites significantly different revealed glycolysis, gluconeogenesis, energetic pathways, glutamate metabolism, degradation of ketone bodies and pyruvate metabolism as the most important networks. Aspartate, alanine and citrate yielded a high area under receiver-operating characteristic (ROC) curves (AUC of 0.81; CI 0.726–0.93) for discriminating SSc patients from controls, whereas ROC curve generated with acetate, fructose, glutamate, glutamine, glycerol and glutarate (AUC of 0.84; CI 0.7–0.98) discriminated between lcSSc and dcSSc. These results indicated that serum NMR-based metabolomics profiling method is sensitive and specific enough to distinguish SSc from healthy controls and provided a feasible diagnostic tool for the diagnosis and classification of the disease.
Collapse
|
10
|
Zhao R, Chen D, Wu H. Effects of Pu-erh ripened tea on hyperuricemic mice studied by serum metabolomics. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1068-1069:149-156. [PMID: 29069630 DOI: 10.1016/j.jchromb.2017.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 09/27/2017] [Accepted: 10/01/2017] [Indexed: 11/30/2022]
Abstract
To evaluate effects of Pu-erh ripened tea in hyperuricemic mice, a mouse hyperuricemia model was developed by oral administration of potassium oxonate for 7 d. Serum metabolomics, based on gas chromatography-mass spectrometry, was used to generate metabolic profiles from normal control, hyperuricemic and allopurinol-treated hyperuricemic mice, as well as hyperuricemic mice given Pu-erh ripened tea at three doses. Pu-erh ripened tea significantly lowered serum uric acid levels. Twelve potential biomarkers associated with hyperuricemia were identified. Pu-erh ripened tea and allopurinol differed in their metabolic effects in the hyperuricemic mice. Levels of glutamic acid, indolelactate, L-allothreonine, nicotinoylglycine, isoleucine, l-cysteine and glycocyamine, all involved in amino acid metabolism, were significantly changed in hyperuricemic mice treated Pu-erh ripened tea. Thus, modulating amino acid metabolism might be the primary mechanism of anti-hyperuricemia by Pu-erh ripened tea.
Collapse
Affiliation(s)
- Ran Zhao
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China; Key Laboratory of Ministry of Education for Tea Science, Hunan Agriculture University, Changsha, Hunan 410128, China; Guangdong Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, Guangdong 510640, China.
| | - Dong Chen
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China; Guangdong Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, Guangdong 510640, China.
| | - Hualing Wu
- Tea Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510640, China; Guangdong Key Laboratory of Tea Plant Resources Innovation and Utilization, Guangzhou, Guangdong 510640, China.
| |
Collapse
|
11
|
Turi CE, Finley J, Shipley PR, Murch SJ, Brown PN. Metabolomics for phytochemical discovery: development of statistical approaches using a cranberry model system. JOURNAL OF NATURAL PRODUCTS 2015; 78:953-966. [PMID: 25751407 DOI: 10.1021/np500667z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Metabolomics is the qualitative and quantitative analysis of all of the small molecules in a biological sample at a specific time and influence. Technologies for metabolomics analysis have developed rapidly as new analytical tools for chemical separations, mass spectrometry, and NMR spectroscopy have emerged. Plants have one of the largest metabolomes, and it is estimated that the average plant leaf can contain upward of 30 000 phytochemicals. In the past decade, over 1200 papers on plant metabolomics have been published. A standard metabolomics data set contains vast amounts of information and can either investigate or generate hypotheses. The key factors in using plant metabolomics data most effectively are the experimental design, authentic standard availability, extract standardization, and statistical analysis. Using cranberry (Vaccinium macrocarpon) as a model system, this review will discuss and demonstrate strategies and tools for analysis and interpretation of metabolomics data sets including eliminating false discoveries and determining significance, metabolite clustering, and logical algorithms for discovery of new metabolites and pathways. Together these metabolomics tools represent an entirely new pipeline for phytochemical discovery.
Collapse
Affiliation(s)
- Christina E Turi
- †Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Jamie Finley
- ‡Natural Health Products and Food Research Group, British Columbia Institute of Technology, 4355 Mathissi Place, Burnaby, British Columbia, Canada, V5G 3H2
| | - Paul R Shipley
- †Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Susan J Murch
- †Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada, V1V 1V7
| | - Paula N Brown
- ‡Natural Health Products and Food Research Group, British Columbia Institute of Technology, 4355 Mathissi Place, Burnaby, British Columbia, Canada, V5G 3H2
| |
Collapse
|
12
|
Cao H, Zhang A, Zhang H, Sun H, Wang X. The application of metabolomics in traditional Chinese medicine opens up a dialogue between Chinese and Western medicine. Phytother Res 2014; 29:159-66. [PMID: 25331169 DOI: 10.1002/ptr.5240] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 06/09/2014] [Accepted: 08/04/2014] [Indexed: 12/16/2022]
Abstract
Metabolomics provides an opportunity to develop the systematic analysis of the metabolites and has been applied to discovering biomarkers and perturbed pathways which can clarify the action mechanism of traditional Chinese medicines (TCM). TCM is a comprehensive system of medical practice that has been used to diagnose, treat and prevent illnesses more than 3000 years. Metabolomics represents a powerful approach that provides a dynamic picture of the phenotype of biosystems through the study of endogenous metabolites, and its methods resemble those of TCM. Recently, metabolomics tools have been used for facilitating interactional effects of both Western medicine and TCM. We describe a protocol for investigating how metabolomics can be used to open up 'dialogue' between Chinese and Western medicine, and facilitate lead compound discovery and development from TCM. Metabolomics will bridge the cultural gap between TCM and Western medicine and improve development of integrative medicine, and maximally benefiting the human.
Collapse
Affiliation(s)
- Hongxin Cao
- National TCM Key Laboratory of Serum Pharmacochemistry, Key Laboratory of Metabolomics and Chinmedomics, Department of Pharmaceutical Analysis, Heilongjiang University of Chinese Medicine, Heping Road 24, Harbin, 150040, China; China Academy of Chinese Medical Science, Southern Street of Dongzhimen No. 16, Beijing, 100700, China
| | | | | | | | | |
Collapse
|
13
|
Sato Y, Bernier F, Suzuki I, Kotani S, Nakagawa M, Oda Y. Comparative lipidomics of mouse brain exposed to enriched environment. J Lipid Res 2013; 54:2687-96. [PMID: 23833247 DOI: 10.1194/jlr.m038075] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Several studies have shown that housing conditions and environmental exposure to a series of stimuli lead to behavior improvement in several species. While more works have been focused on illustrating changes of the proteome and transcriptome following enriched environment exposure in mice, little has been done to understand changes in the brain metabolome in this paradigm due to the complexity of this type of analysis. In this paper, lipidomics focused on phospholipids and gangliosides were conducted for brain tissues of mice exposed to enriched or impoverished conditions. We optimized previously reported method and established a reliable relative comparison method for phospholipids and gangliosides in brain tissue using prefractionation with weak anion exchange cartridge. We used liquid chromatography mass spectrometry to explore metabolic signatures of the cerebral cortex and hippocampus after confirming the animals had significant memory differences using the fear conditioning paradigm and brain immunohistochemistry. Although both cerebral cortex and hippocampus regions did not show major alterations in ganglioside composition, we found significant differences in a series of phospholipids containing 22:6 fatty acid in the prefrontal cortex, indicating that environmental enrichment and impoverished housing conditions might be a relevant paradigm to study aberrant lipid metabolism of docosahexaenoic acid consumption. Our study highlights the hypothesis-generating potential of lipidomics and identifies novel region-specific lipid changes possibly linked not only to change of memory function in these models, but also to help us better understand how lipid changes may contribute to memory disorders.
Collapse
Affiliation(s)
- Yoshiaki Sato
- Eisai Company, Limited, Ibaraki 300-2635, Japan; and
| | | | | | | | | | | |
Collapse
|
14
|
Wang W, Zhang W, Liu J, Sun Y, Li Y, Li H, Xiao S, Shen X. Metabolomic changes in follicular fluid induced by soy isoflavones administered to rats from weaning until sexual maturity. Toxicol Appl Pharmacol 2013; 269:280-9. [PMID: 23454585 DOI: 10.1016/j.taap.2013.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Revised: 01/06/2013] [Accepted: 02/11/2013] [Indexed: 01/29/2023]
Abstract
Female Wistar rats at 21 days of age were treated with one of three concentrations of soy isoflavones (SIF) (50, 100 or 200mg/kg body weight, orally, once per day) from weaning until sexual maturity (3 months) in order to evaluate the influence of SIF on ovarian follicle development. After treatment, the serum sex hormone levels and enumeration of ovarian follicles of the ovary were measured. The metabolic profile of follicular fluid was determined using HPLC-MS. Principal component analysis (PCA) and partial least-squares-discriminant analysis (PLS-DA) was used to identify differences in metabolites and reveal useful toxic biomarkers. The results indicated that modest doses of SIF affect ovarian follicle development, as demonstrated by decreased serum estradiol levels and increases in both ovarian follicle atresia and corpora lutea number in the ovary. SIF treatment-related metabolic alterations in follicular fluid were also found in the PCA and PLS-DA models. The 24 most significantly altered metabolites were identified, including primary sex hormones, amino acids, fatty acids and metabolites involved in energy metabolism. These findings may indicate that soy isoflavones affect ovarian follicle development by inducing metabolomic variations in the follicular fluid.
Collapse
Affiliation(s)
- Wenxiang Wang
- Department of Nutrition and Health Care, School of Public Health, Fujian Medical University, Fuzhou, Fujian, PR China
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Abstract
Metabolomics aims to provide a global snapshot of all small-molecule metabolites in cells and biological fluids, free of observational biases inherent to more focused studies of metabolism. However, the staggeringly high information content of such global analyses introduces a challenge of its own; efficiently forming biologically relevant conclusions from any given metabolomics dataset indeed requires specialized forms of data analysis. One approach to finding meaning in metabolomics datasets involves multivariate analysis (MVA) methods such as principal component analysis (PCA) and partial least squares projection to latent structures (PLS), where spectral features contributing most to variation or separation are identified for further analysis. However, as with any mathematical treatment, these methods are not a panacea; this review discusses the use of multivariate analysis for metabolomics, as well as common pitfalls and misconceptions.
Collapse
Affiliation(s)
- Bradley Worley
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304
| |
Collapse
|
16
|
Sato Y, Suzuki I, Nakamura T, Bernier F, Aoshima K, Oda Y. Identification of a new plasma biomarker of Alzheimer's disease using metabolomics technology. J Lipid Res 2011; 53:567-576. [PMID: 22203775 DOI: 10.1194/jlr.m022376] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We performed unbiased analysis of steroid-related compounds to identify novel Alzheimer's disease (AD) plasma biomarkers using liquid chromatography-atmospheric pressure chemical ionization-mass spectroscopy. The analysis revealed that desmosterol was found to be decreased in AD plasma versus controls. To precisely quantify variations in desmosterol, we established an analytical method to measure desmosterol and cholesterol. Using this LC-based method, we discovered that desmosterol and the desmosterol/cholesterol ratio are significantly decreased in AD. Finally, the validation of this assay using 109 clinical samples confirmed the decrease of desmosterol in AD as well as a change in the desmosterol/cholesterol ratio in AD. Interestingly, we could also observe a difference between mild cognitive impairment and control. In addition, the decrease of desmosterol was somewhat more significant in females. Receiver operating characteristic (ROC) analysis between controls and AD, using plasma desmosterol shows a score of 0.80, indicating a good discrimination power for this marker in the two reference populations and confirms the potential usefulness of measuring plasma desmosterol levels for diagnosing AD. Further analysis showed a significant correlation of plasma desmosterol with Mini-Mental State Examination scores. Although larger sample populations will be needed to confirm this diagnostic marker sensitivity, our studies demonstrate a sensitive and accurate method of detecting plasma desmosterol concentration and suggest that plasma desmosterol could become a powerful new specific biomarker for early and easy AD diagnosis.
Collapse
Affiliation(s)
- Yoshiaki Sato
- Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Ikumi Suzuki
- Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Tatsuji Nakamura
- Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Francois Bernier
- Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | - Ken Aoshima
- Eisai Co., Ltd., 5-1-3 Tokodai, Tsukuba, Ibaraki 300-2635, Japan
| | | |
Collapse
|
17
|
Li S, Liu H, Jin Y, Lin S, Cai Z, Jiang Y. Metabolomics study of alcohol-induced liver injury and hepatocellular carcinoma xenografts in mice. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:2369-75. [PMID: 21763219 DOI: 10.1016/j.jchromb.2011.06.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Revised: 06/03/2011] [Accepted: 06/08/2011] [Indexed: 12/16/2022]
Abstract
Alcohol abuse is one of the major causes of liver injury and a promoter for hepatocellular carcinoma (HCC). To understand the disease-associated metabolic changes, we investigated and compared the profiles of metabolites in nude mice with alcohol-induced liver injury or bearing a HCC xenograft (HCCX). Alcohol-induced liver injury was achieved by daily administration of grain liquor, and HCC xenografts were generated by subcutaneous inoculation of HepG2 cells in nude mice. Metabolites in serum samples were profiled by ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF MS). The acquired data was analyzed by principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) to identify potential disease-specific biomarkers. Results showed that the phosphatidylcholine (PC) levels were significantly higher in both liver injury and HCCX mice compared with the control. Interestingly, lysophosphatidylcholines (LPCs) that contain saturated or monounsaturated fatty acids were reduced in both liver injury and HCCX mice, but polyunsaturated fatty acids LPCs were elevated in liver injury mice only. These data delineated the disease-related metabolic alterations of LPCs in liver injury and HCC, suggesting that the LPC profile in serum may be biomarkers for these two common liver diseases.
Collapse
Affiliation(s)
- Shangfu Li
- Department of Chemistry, Tsinghua University, Beijing 100084, PR China
| | | | | | | | | | | |
Collapse
|
18
|
Strategy of using microsome-based metabolite production to facilitate the identification of endogenous metabolites by liquid chromatography mass spectrometry. Anal Chim Acta 2011; 685:36-44. [DOI: 10.1016/j.aca.2010.11.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2010] [Revised: 11/04/2010] [Accepted: 11/07/2010] [Indexed: 11/22/2022]
|