101
|
Jones OAH. Illuminating the dark metabolome to advance the molecular characterisation of biological systems. Metabolomics 2018; 14:101. [PMID: 30830382 DOI: 10.1007/s11306-018-1396-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/07/2018] [Indexed: 11/26/2022]
Abstract
BACKGROUND The latest version of the Human Metabolome Database (v4.0) lists 114,100 individual entries. Typically, however, metabolomics studies identify only around 100 compounds and many features identified in mass spectra are listed only as 'unknown compounds'. The lack of ability to detect all metabolites present, and fully identify all metabolites detected (the dark metabolome) means that, despite the great contribution of metabolomics to a range of areas in the last decade, a significant amount of useful information from publically funded studies is being lost or unused each year. This loss of data limits our potential gain in knowledge and understanding of important research areas such as cell biology, environmental pollution, plant science, food chemistry and health and biomedical research. Metabolomics therefore needs to develop new tools and methods for metabolite identification to advance as a field. AIM OF REVIEW In this critical review, some potential issues with metabolite identification are identified and discussed. New and novel emerging technologies and tools which may contribute to expanding the number of compounds identified in metabolomics studies (thus illuminating the dark metabolome) are reviewed. The aim is to stimulate debate and research in the molecular characterisation of biological systems to drive forward metabolomic research. KEY SCIENTIFIC CONCEPTS OF REVIEW The work specifically discusses dynamic nuclear polarisation nuclear magnetic resonance spectroscopy (DNP-NMR), non-proton NMR active nuclei, two-dimensional liquid chromatography (2DLC) and Raman spectroscopy (RS). It is suggested that developing new methods for metabolomics with these techniques could lead to advances in the field and better characterisation of biological systems.
Collapse
Affiliation(s)
- Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School Science, RMIT University, GPO Box 2476, Melbourne, VIC, 3001, Australia.
| |
Collapse
|
102
|
Yeo HC, Chen S, Ho YS, Lee DY. An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology. Metabolomics 2018; 14:98. [PMID: 30830409 DOI: 10.1007/s11306-018-1394-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/06/2018] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Given a raw LC-MS dataset, it is often required to rapidly generate initial hypotheses, in conjunction with other 'omics' datasets, without time-consuming lipid verifications. Furthermore, for meta-analysis of many datasets, it may be impractical to conduct exhaustive confirmatory analyses. In other cases, samples for validation may be difficult to obtain, replicate or maintain. Thus, it is critical that the computational identification of lipids is of appropriate accuracy, coverage, and unbiased by a researcher's experience and prior knowledge. OBJECTIVES We aim to prescribe a systematic framework for lipid identifications, without usage of their characteristic retention-time by fully exploiting their underlying mass features. RESULTS Initially, a hybrid technique, for deducing both common and distinctive daughter ions, is used to infer parent lipids from deconvoluted spectra. This is followed by parent confirmation using basic knowledge of their preferred product ions. Using the framework, we could achieve an accuracy of ~ 80% by correctly identified 101 species from 18 classes in Chinese hamster ovary (CHO) cells. The resulting inferences could explain the recombinant-producing capability of CHO-SH87 cells, compared to non-producing CHO-K1 cells. For comparison, a XCMS-based study of the same dataset, guided by a user's ad-hoc knowledge, identified less than 60 species of 12 classes from thousands of possibilities. CONCLUSION We describe a systematic LC-MS-based framework that identifies lipids for rapid hypothesis generation.
Collapse
Affiliation(s)
- Hock Chuan Yeo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore.
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
| |
Collapse
|
103
|
Zheng SJ, Liu SJ, Zhu QF, Guo N, Wang YL, Yuan BF, Feng YQ. Establishment of Liquid Chromatography Retention Index Based on Chemical Labeling for Metabolomic Analysis. Anal Chem 2018; 90:8412-8420. [DOI: 10.1021/acs.analchem.8b00901] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Shu-Jian Zheng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Shi-Jie Liu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Quan-Fei Zhu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Ning Guo
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Ya-Lan Wang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, Hubei 430072, P.R. China
| |
Collapse
|
104
|
Han S, Song Y, Guan H, Chen T, Chi Y, Deng H. A new selection principle for model compounds in quantitative structure-retention relationship by HPLC for the determination of n
-octanol/water partition coefficients of bisphenols. SEPARATION SCIENCE PLUS 2018. [DOI: 10.1002/sscp.201800041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shuying Han
- College of Pharmacy; Nanjing University of Chinese Medicine; Nanjing China
| | - Yilin Song
- College of Pharmacy; Nanjing University of Chinese Medicine; Nanjing China
| | - Hanyu Guan
- College of Pharmacy; Nanjing University of Chinese Medicine; Nanjing China
| | - Tao Chen
- College of Pharmacy; Nanjing University of Chinese Medicine; Nanjing China
| | - Yumei Chi
- College of Pharmacy; Nanjing University of Chinese Medicine; Nanjing China
| | - Haishan Deng
- College of Pharmacy; Nanjing University of Chinese Medicine; Nanjing China
| |
Collapse
|
105
|
Stoessel D, Stellmann JP, Willing A, Behrens B, Rosenkranz SC, Hodecker SC, Stürner KH, Reinhardt S, Fleischer S, Deuschle C, Maetzler W, Berg D, Heesen C, Walther D, Schauer N, Friese MA, Pless O. Metabolomic Profiles for Primary Progressive Multiple Sclerosis Stratification and Disease Course Monitoring. Front Hum Neurosci 2018; 12:226. [PMID: 29915533 PMCID: PMC5994544 DOI: 10.3389/fnhum.2018.00226] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/15/2018] [Indexed: 01/28/2023] Open
Abstract
Primary progressive multiple sclerosis (PPMS) shows a highly variable disease progression with poor prognosis and a characteristic accumulation of disabilities in patients. These hallmarks of PPMS make it difficult to diagnose and currently impossible to efficiently treat. This study aimed to identify plasma metabolite profiles that allow diagnosis of PPMS and its differentiation from the relapsing-remitting subtype (RRMS), primary neurodegenerative disease (Parkinson’s disease, PD), and healthy controls (HCs) and that significantly change during the disease course and could serve as surrogate markers of multiple sclerosis (MS)-associated neurodegeneration over time. We applied untargeted high-resolution metabolomics to plasma samples to identify PPMS-specific signatures, validated our findings in independent sex- and age-matched PPMS and HC cohorts and built discriminatory models by partial least square discriminant analysis (PLS-DA). This signature was compared to sex- and age-matched RRMS patients, to patients with PD and HC. Finally, we investigated these metabolites in a longitudinal cohort of PPMS patients over a 24-month period. PLS-DA yielded predictive models for classification along with a set of 20 PPMS-specific informative metabolite markers. These metabolites suggest disease-specific alterations in glycerophospholipid and linoleic acid pathways. Notably, the glycerophospholipid LysoPC(20:0) significantly decreased during the observation period. These findings show potential for diagnosis and disease course monitoring, and might serve as biomarkers to assess treatment efficacy in future clinical trials for neuroprotective MS therapies.
Collapse
Affiliation(s)
- Daniel Stoessel
- Metabolomic Discoveries GmbH, Potsdam, Germany.,Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany.,Bioinformatik, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Jan-Patrick Stellmann
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Klinik und Poliklinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Anne Willing
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Birte Behrens
- Neurodegenerative Erkrankungen, Hertie-Institut für klinische Hirnforschung, Eberhardt-Karls-Universität Tübingen, Tübingen, Germany
| | - Sina C Rosenkranz
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Klinik und Poliklinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Sibylle C Hodecker
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Klinik und Poliklinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Klarissa H Stürner
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Klinik und Poliklinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Stefanie Reinhardt
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Sabine Fleischer
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Deuschle
- Neurodegenerative Erkrankungen, Hertie-Institut für klinische Hirnforschung, Eberhardt-Karls-Universität Tübingen, Tübingen, Germany
| | - Walter Maetzler
- Neurodegenerative Erkrankungen, Hertie-Institut für klinische Hirnforschung, Eberhardt-Karls-Universität Tübingen, Tübingen, Germany.,Department of Neurology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Daniela Berg
- Neurodegenerative Erkrankungen, Hertie-Institut für klinische Hirnforschung, Eberhardt-Karls-Universität Tübingen, Tübingen, Germany.,Department of Neurology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Christoph Heesen
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany.,Klinik und Poliklinik für Neurologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Dirk Walther
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany.,Bioinformatik, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | | | - Manuel A Friese
- Zentrum für Molekulare Neurobiologie Hamburg, Institut für Neuroimmunologie und Multiple Sklerose, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Ole Pless
- Fraunhofer IME ScreeningPort, Hamburg, Germany
| |
Collapse
|
106
|
Zhang Q, Huo M, Zhang Y, Qiao Y, Gao X. A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case. J Chromatogr A 2018; 1552:17-28. [DOI: 10.1016/j.chroma.2018.03.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/23/2018] [Accepted: 03/27/2018] [Indexed: 11/27/2022]
|
107
|
Nizioł J, Bonifay V, Ossoliński K, Ossoliński T, Ossolińska A, Sunner J, Beech I, Arendowski A, Ruman T. Metabolomic study of human tissue and urine in clear cell renal carcinoma by LC-HRMS and PLS-DA. Anal Bioanal Chem 2018; 410:3859-3869. [PMID: 29658093 PMCID: PMC5956006 DOI: 10.1007/s00216-018-1059-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 03/01/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022]
Abstract
Renal cell carcinoma (RCC) is the most prevalent and lethal malignancy of the kidney. Despite all the efforts made, no tissue biomarker is currently used in the clinical management of patients with kidney cancer. A search for possible biomarkers in urine for clear cell renal cell carcinoma (ccRCC) has been conducted. Non-targeted metabolomic analyses were performed on paired samples of surgically removed renal cancer and normal tissue, as well as on urine samples. Extracts were analyzed by liquid chromatography/high-resolution mass spectrometry (LC-HRMS). Hydroxybutyrylcarnitine, decanoylcarnitine, propanoylcarnitine, carnitine, dodecanoylcarnitine, and norepinephrine sulfate were found in much higher concentrations in both cancer tissues (compared with the paired normal tissue) and in urine of cancer patients (compared with control urine). In contrast, riboflavin and acetylaspartylglutamate (NAAG) were present at significantly higher concentrations both in normal kidney tissue as well as in urine samples of healthy persons. This preliminary study resulted in the identification of several compounds that may be considered potential clear cell renal carcinoma biomarkers. Graphical abstract PLS-DA plot based on LC-MS data for normal and cancer human tissue samples. The aim of this work was the identification of up- and downregulated compounds that could potentially serve as renal cancer biomarkers.
Collapse
Affiliation(s)
- Joanna Nizioł
- Faculty of Chemistry, Rzeszow University of Technology, 35-959, Rzeszow, Poland.
| | - Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Krzysztof Ossoliński
- Department of General Surgery and Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Tadeusz Ossoliński
- Department of General Surgery and Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Anna Ossolińska
- Department of General Surgery and Urology, John Paul II Hospital, Grunwaldzka 4 St., 36-100, Kolbuszowa, Poland
| | - Jan Sunner
- Department of Chemistry, Montana State University, 103 Chemistry and Biochemistry Building, Bozeman, MT, 59717, USA
| | - Iwona Beech
- Center of Biofilm Engineering, Montana State University, 366 Barnard Hall, Bozeman, MT, 59717, USA
| | - Adrian Arendowski
- Faculty of Chemistry, Rzeszow University of Technology, 35-959, Rzeszow, Poland
| | - Tomasz Ruman
- Faculty of Chemistry, Rzeszow University of Technology, 35-959, Rzeszow, Poland
| |
Collapse
|
108
|
Alterations of Metabolic and Lipid Profiles in Polymyxin-Resistant Pseudomonas aeruginosa. Antimicrob Agents Chemother 2018; 62:AAC.02656-17. [PMID: 29632014 DOI: 10.1128/aac.02656-17] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 04/05/2018] [Indexed: 12/27/2022] Open
Abstract
Multidrug-resistant Pseudomonas aeruginosa presents a global medical challenge, and polymyxins are a key last-resort therapeutic option. Unfortunately, polymyxin resistance in P. aeruginosa has been increasingly reported. The present study was designed to define metabolic differences between paired polymyxin-susceptible and -resistant P. aeruginosa strains using untargeted metabolomics and lipidomics analyses. The metabolomes of wild-type P. aeruginosa strain K ([PAK] polymyxin B MIC, 1 mg/liter) and its paired pmrB mutant strains, PAKpmrB6 and PAKpmrB12 (polymyxin B MICs of 16 mg/liter and 64 mg/liter, respectively) were characterized using liquid chromatography-mass spectrometry, and metabolic differences were identified through multivariate and univariate statistics. PAKpmrB6 and PAKpmrB12, which displayed lipid A modifications with 4-amino-4-deoxy-l-arabinose, showed significant perturbations in amino acid and carbohydrate metabolism, particularly the intermediate metabolites from 4-amino-4-deoxy-l-arabinose synthesis and the methionine salvage cycle pathways. The genomics result showed a premature termination (Y275stop) in speE (encoding spermidine synthase) in PAKpmrB6, and metabolomics data revealed a decreased intracellular level of spermidine in PAKpmrB6 compared to that in PAKpmrB12 Our results indicate that spermidine may play an important role in high-level polymyxin resistance in P. aeruginosa Interestingly, both pmrB mutants had decreased levels of phospholipids, fatty acids, and acyl-coenzyme A compared to those in the wild-type PAK. Moreover, the more resistant PAKpmrB12 mutant exhibited much lower levels of phospholipids than the PAKpmrB6 mutant, suggesting that the decreased phospholipid level was associated with polymyxin resistance. In summary, this study provides novel mechanistic information on polymyxin resistance in P. aeruginosa and highlights its impacts on bacterial metabolism.
Collapse
|
109
|
Blaženović I, Kind T, Ji J, Fiehn O. Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. Metabolites 2018; 8:E31. [PMID: 29748461 PMCID: PMC6027441 DOI: 10.3390/metabo8020031] [Citation(s) in RCA: 389] [Impact Index Per Article: 64.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 04/26/2018] [Accepted: 05/06/2018] [Indexed: 01/17/2023] Open
Abstract
The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included.
Collapse
Affiliation(s)
- Ivana Blaženović
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
| | - Tobias Kind
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
| | - Jian Ji
- State Key Laboratory of Food Science and Technology, School of Food Science of Jiangnan University, School of Food Science Synergetic Innovation Center of Food Safety and Nutrition, Wuxi 214122, China.
| | - Oliver Fiehn
- NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis, CA 95616, USA.
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
| |
Collapse
|
110
|
Peters K, Worrich A, Weinhold A, Alka O, Balcke G, Birkemeyer C, Bruelheide H, Calf OW, Dietz S, Dührkop K, Gaquerel E, Heinig U, Kücklich M, Macel M, Müller C, Poeschl Y, Pohnert G, Ristok C, Rodríguez VM, Ruttkies C, Schuman M, Schweiger R, Shahaf N, Steinbeck C, Tortosa M, Treutler H, Ueberschaar N, Velasco P, Weiß BM, Widdig A, Neumann S, Dam NMV. Current Challenges in Plant Eco-Metabolomics. Int J Mol Sci 2018; 19:E1385. [PMID: 29734799 PMCID: PMC5983679 DOI: 10.3390/ijms19051385] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/24/2018] [Accepted: 04/25/2018] [Indexed: 12/22/2022] Open
Abstract
The relatively new research discipline of Eco-Metabolomics is the application of metabolomics techniques to ecology with the aim to characterise biochemical interactions of organisms across different spatial and temporal scales. Metabolomics is an untargeted biochemical approach to measure many thousands of metabolites in different species, including plants and animals. Changes in metabolite concentrations can provide mechanistic evidence for biochemical processes that are relevant at ecological scales. These include physiological, phenotypic and morphological responses of plants and communities to environmental changes and also interactions with other organisms. Traditionally, research in biochemistry and ecology comes from two different directions and is performed at distinct spatiotemporal scales. Biochemical studies most often focus on intrinsic processes in individuals at physiological and cellular scales. Generally, they take a bottom-up approach scaling up cellular processes from spatiotemporally fine to coarser scales. Ecological studies usually focus on extrinsic processes acting upon organisms at population and community scales and typically study top-down and bottom-up processes in combination. Eco-Metabolomics is a transdisciplinary research discipline that links biochemistry and ecology and connects the distinct spatiotemporal scales. In this review, we focus on approaches to study chemical and biochemical interactions of plants at various ecological levels, mainly plant⁻organismal interactions, and discuss related examples from other domains. We present recent developments and highlight advancements in Eco-Metabolomics over the last decade from various angles. We further address the five key challenges: (1) complex experimental designs and large variation of metabolite profiles; (2) feature extraction; (3) metabolite identification; (4) statistical analyses; and (5) bioinformatics software tools and workflows. The presented solutions to these challenges will advance connecting the distinct spatiotemporal scales and bridging biochemistry and ecology.
Collapse
Affiliation(s)
- Kristian Peters
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Anja Worrich
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
- UFZ-Helmholtz-Centre for Environmental Research, Department Environmental Microbiology, Permoserstraße 15, 04318 Leipzig, Germany.
| | - Alexander Weinhold
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
| | - Oliver Alka
- Applied Bioinformatics Group, Center for Bioinformatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany.
| | - Gerd Balcke
- Leibniz Institute of Plant Biochemistry, Cell and Metabolic Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Claudia Birkemeyer
- Institute of Analytical Chemistry, University of Leipzig, Linnéstr. 3, 04103 Leipzig, Germany.
| | - Helge Bruelheide
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle (Saale), Germany.
| | - Onno W Calf
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Sophie Dietz
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Kai Dührkop
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany.
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 360, 69120 Heidelberg, Germany.
| | - Uwe Heinig
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Marlen Kücklich
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Mirka Macel
- Molecular Interaction Ecology, Institute for Water and Wetland Research (IWWR), Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Caroline Müller
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Yvonne Poeschl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Informatics, Martin Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, 06120 Halle (Saale), Germany.
| | - Georg Pohnert
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Christian Ristok
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Victor Manuel Rodríguez
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Christoph Ruttkies
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Meredith Schuman
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745 Jena, Germany.
| | - Rabea Schweiger
- Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
| | - Nir Shahaf
- Weizmann Institute of Science, Faculty of Biochemistry, Department of Plant Sciences, 234 Herzl St., P.O. Box 26, Rehovot 7610001, Israel.
| | - Christoph Steinbeck
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Maria Tortosa
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Hendrik Treutler
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
| | - Nico Ueberschaar
- Institute of Inorganic and Analytical Chemistry, Friedrich Schiller University Jena, Lessingstr. 8, 07743 Jena, Germany.
| | - Pablo Velasco
- Group of Genetics, Breeding and Biochemistry of Brassica, Misión Biológica de Galicia (CSIC), Apartado 28, 36080 Pontevedra, Spain.
| | - Brigitte M Weiß
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
| | - Anja Widdig
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biology, University of Leipzig, Talstraße 33, 04109 Leipzig, Germany.
- Research Group of Primate Kin Selection, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Steffen Neumann
- Leibniz Institute of Plant Biochemistry, Stress and Developmental Biology, Weinberg 3, 06120 Halle (Saale), Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
| | - Nicole M van Dam
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany.
- Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger-Str. 159, 07743 Jena, Germany.
| |
Collapse
|
111
|
Schatschneider S, Abdelrazig S, Safo L, Henstra AM, Millat T, Kim DH, Winzer K, Minton NP, Barrett DA. Quantitative Isotope-Dilution High-Resolution-Mass-Spectrometry Analysis of Multiple Intracellular Metabolites in Clostridium autoethanogenum with Uniformly 13C-Labeled Standards Derived from Spirulina. Anal Chem 2018. [PMID: 29533656 DOI: 10.1021/acs.analchem.7b04758] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have investigated the applicability of commercially available lyophilized spirulina ( Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standards for the quantitative determination of intracellular bacterial metabolites. Metabolites of interest were analyzed by hydrophilic-interaction liquid chromatography coupled with high-resolution mass spectrometry. Multiple internal standards obtained from uniformly (U)-13C-labeled extracts from spirulina were used to enable isotope-dilution mass spectrometry (IDMS) in the identification and quantification of intracellular metabolites. Extraction of the intracellular metabolites of Clostridium autoethanogenum using 2:1:1 chloroform/methanol/water was found to be the optimal method in comparison with freeze-thaw, homogenization, and sonication methods. The limits of quantification were ≤1 μM with excellent linearity for all of the calibration curves ( R2 ≥ 0.99) for 74 metabolites. The precision and accuracy were found to be within relative standard deviations (RSDs) of 15% for 49 of the metabolites and within RSDs of 20% for all of the metabolites. The method was applied to study the effects of feeding different levels of carbon monoxide (as a carbon source) on the central metabolism and Wood-Ljungdahl pathway of C. autoethanogenum grown in continuous culture over 35 days. Using LC-IDMS with U-13C spirulina allowed the successful quantification of 52 metabolites in the samples, including amino acids, carboxylic acids, sugar phosphates, purines, and pyrimidines. The method provided absolute quantitative data on intracellular metabolites that was suitable for computational modeling to understand and optimize the C. autoethanogenum metabolic pathways active in gas fermentation.
Collapse
Affiliation(s)
- Sarah Schatschneider
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Salah Abdelrazig
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Laudina Safo
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Anne M Henstra
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Thomas Millat
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Klaus Winzer
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Nigel P Minton
- Clostridia Research Group, SBRC-Nottingham, a BBSRC/EPSRC Synthetic Biology Research Centre, School of Life Sciences , University of Nottingham , Nottingham NG7 2RD , U.K
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy , University of Nottingham , Nottingham NG7 2RD , U.K
| |
Collapse
|
112
|
Deletion of transketolase triggers a stringent metabolic response in promastigotes and loss of virulence in amastigotes of Leishmania mexicana. PLoS Pathog 2018; 14:e1006953. [PMID: 29554142 PMCID: PMC5882173 DOI: 10.1371/journal.ppat.1006953] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/03/2018] [Accepted: 02/28/2018] [Indexed: 11/22/2022] Open
Abstract
Transketolase (TKT) is part of the non-oxidative branch of the pentose phosphate pathway (PPP). Here we describe the impact of removing this enzyme from the pathogenic protozoan Leishmania mexicana. Whereas the deletion had no obvious effect on cultured promastigote forms of the parasite, the Δtkt cells were not virulent in mice. Δtkt promastigotes were more susceptible to oxidative stress and various leishmanicidal drugs than wild-type, and metabolomics analysis revealed profound changes to metabolism in these cells. In addition to changes consistent with those directly related to the role of TKT in the PPP, central carbon metabolism was substantially decreased, the cells consumed significantly less glucose, flux through glycolysis diminished, and production of the main end products of metabolism was decreased. Only minor changes in RNA abundance from genes encoding enzymes in central carbon metabolism, however, were detected although fructose-1,6-bisphosphate aldolase activity was decreased two-fold in the knock-out cell line. We also showed that the dual localisation of TKT between cytosol and glycosomes is determined by the C-terminus of the enzyme and by engineering different variants of the enzyme we could alter its sub-cellular localisation. However, no effect on the overall flux of glucose was noted irrespective of whether the enzyme was found uniquely in either compartment, or in both. Leishmania parasites endanger over 1 billion people worldwide, infecting 300,000 people and causing 20,000 deaths annually. In this study, we scrutinized metabolism in Leishmania mexicana after deletion of the gene encoding transketolase (TKT), an enzyme involved in sugar metabolism via the pentose phosphate pathway which plays key roles in creating ribose 5-phosphate for nucleotide synthesis and also defence against oxidative stress. The insect stage of the parasite, grown in culture medium, did not suffer from any obvious growth defect after the gene was deleted. However, its metabolism changed dramatically, with metabolomics indicating profound changes to flux through the pentose phosphate pathway: decreased glucose consumption, and generally enhanced efficiency in using metabolic substrates with reduced secretion of partially oxidised end products of metabolism. This ‘stringent’ metabolism is reminiscent of the mammalian stage parasites. The cells were also more sensitive to oxidative stress inducing agents and leishmanicidal drugs. Crucially, mice inoculated with the TKT knock-out parasites did not develop an infection pointing to the enzyme playing a key role in allowing the parasites to remain viable in the host, indicating that TKT may be considered a useful target for development of new drugs against leishmaniasis.
Collapse
|
113
|
Stoessel D, Schulte C, Teixeira dos Santos MC, Scheller D, Rebollo-Mesa I, Deuschle C, Walther D, Schauer N, Berg D, Nogueira da Costa A, Maetzler W. Promising Metabolite Profiles in the Plasma and CSF of Early Clinical Parkinson's Disease. Front Aging Neurosci 2018; 10:51. [PMID: 29556190 PMCID: PMC5844983 DOI: 10.3389/fnagi.2018.00051] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/15/2018] [Indexed: 12/21/2022] Open
Abstract
Parkinson's disease (PD) shows high heterogeneity with regard to the underlying molecular pathogenesis involving multiple pathways and mechanisms. Diagnosis is still challenging and rests entirely on clinical features. Thus, there is an urgent need for robust diagnostic biofluid markers. Untargeted metabolomics allows establishing low-molecular compound biomarkers in a wide range of complex diseases by the measurement of various molecular classes in biofluids such as blood plasma, serum, and cerebrospinal fluid (CSF). Here, we applied untargeted high-resolution mass spectrometry to determine plasma and CSF metabolite profiles. We semiquantitatively determined small-molecule levels (≤1.5 kDa) in the plasma and CSF from early PD patients (disease duration 0-4 years; n = 80 and 40, respectively), and sex- and age-matched controls (n = 76 and 38, respectively). We performed statistical analyses utilizing partial least square and random forest analysis with a 70/30 training and testing split approach, leading to the identification of 20 promising plasma and 14 CSF metabolites. These metabolites differentiated the test set with an AUC of 0.8 (plasma) and 0.9 (CSF). Characteristics of the metabolites indicate perturbations in the glycerophospholipid, sphingolipid, and amino acid metabolism in PD, which underscores the high power of metabolomic approaches. Further studies will enable to develop a potential metabolite-based biomarker panel specific for PD.
Collapse
Affiliation(s)
- Daniel Stoessel
- Metabolomic Discoveries GmbH, Potsdam, Germany
- Department of Biochemistry and Biology, Universität Potsdam, Potsdam, Germany
- Max Planck Institute für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | - Claudia Schulte
- Department of Neurodegeneration, German Center for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
| | | | | | - Irene Rebollo-Mesa
- Exploratory Statistics, Global Exploratory Development, UCB Pharma SA, Slough, United Kingdom
| | - Christian Deuschle
- Department of Neurodegeneration, German Center for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
| | - Dirk Walther
- Department of Biochemistry and Biology, Universität Potsdam, Potsdam, Germany
- Max Planck Institute für Molekulare Pflanzenphysiologie, Potsdam, Germany
| | | | - Daniela Berg
- Department of Neurodegeneration, German Center for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- Department of Neurology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Andre Nogueira da Costa
- Experimental Medicine and Diagnostics, Global Exploratory Development, UCB Biopharma SPRL, Brussels, Belgium
| | - Walter Maetzler
- Department of Neurodegeneration, German Center for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany
- Department of Neurology, Christian-Albrechts-University Kiel, Kiel, Germany
| |
Collapse
|
114
|
Domingo-Almenara X, Montenegro-Burke JR, Benton HP, Siuzdak G. Annotation: A Computational Solution for Streamlining Metabolomics Analysis. Anal Chem 2018; 90:480-489. [PMID: 29039932 PMCID: PMC5750104 DOI: 10.1021/acs.analchem.7b03929] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolite identification is still considered an imposing bottleneck in liquid chromatography mass spectrometry (LC/MS) untargeted metabolomics. The identification workflow usually begins with detecting relevant LC/MS peaks via peak-picking algorithms and retrieving putative identities based on accurate mass searching. However, accurate mass search alone provides poor evidence for metabolite identification. For this reason, computational annotation is used to reveal the underlying metabolites monoisotopic masses, improving putative identification in addition to confirmation with tandem mass spectrometry. This review examines LC/MS data from a computational and analytical perspective, focusing on the occurrence of neutral losses and in-source fragments, to understand the challenges in computational annotation methodologies. Herein, we examine the state-of-the-art strategies for computational annotation including: (i) peak grouping or full scan (MS1) pseudo-spectra extraction, i.e., clustering all mass spectral signals stemming from each metabolite; (ii) annotation using ion adduction and mass distance among ion peaks; (iii) incorporation of biological knowledge such as biotransformations or pathways; (iv) tandem MS data; and (v) metabolite retention time calibration, usually achieved by prediction from molecular descriptors. Advantages and pitfalls of each of these strategies are discussed, as well as expected future trends in computational annotation.
Collapse
Affiliation(s)
- Xavier Domingo-Almenara
- Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - J Rafael Montenegro-Burke
- Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - H Paul Benton
- Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gary Siuzdak
- Scripps Center for Metabolomics, The Scripps Research Institute , 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| |
Collapse
|
115
|
Godzien J, Gil de la Fuente A, Otero A, Barbas C. Metabolite Annotation and Identification. COMPREHENSIVE ANALYTICAL CHEMISTRY 2018. [DOI: 10.1016/bs.coac.2018.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
116
|
Parr MK, Schmidt AH. Life cycle management of analytical methods. J Pharm Biomed Anal 2018; 147:506-517. [DOI: 10.1016/j.jpba.2017.06.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/10/2017] [Accepted: 06/12/2017] [Indexed: 11/30/2022]
|
117
|
Li Y, Liu C, Du J, Sheng X, Zhang Y. Plasma metabolic profiling analysis of Cortex Periplocae-induced cardiotoxicity based on UPLC/Q-TOF-MS. RSC Adv 2018; 8:4937-4945. [PMID: 35557996 PMCID: PMC9088751 DOI: 10.1039/c7ra12247k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/07/2018] [Indexed: 11/21/2022] Open
Abstract
Cortex Periplocae is a well-known form of traditional medicine with its unique cardiotonic action, anti-tumor activity and immune regulation effect. However, improper use of Cortex Periplocae often leads to cardiac toxicity, which in the most severe cases can even be life-threatening. Biochemical tests and histopathological examinations are primary methods for clinical trials. However, such approaches are time-consuming, lack specificity and have low sensitivity, which can easily lead to negative results in studies. Therefore, a more scientific and systematic evaluation of Cortex Periplocae cardiotoxicity is particularly important. In this study, we established a method that combines metabonomics with trend analysis of a gavage concentration series to find cardiac toxicity biomarkers of Cortex Periplocae. We created rat cardiotoxicity models, in which the toxicity was caused by Cortex Periplocae. We collected data from rat plasma samples based on metabonomics using ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC/Q-TOF-MS). Multiple statistical analyses, such as principal component analysis (PCA) and partial least squares-discriminant analysis (PLS-DA), were used to examine metabolite profile changes in plasma samples to screen potential cardiotoxicity biomarkers and metabolic pathways. Compared with the control group, after 7 days administration, the pathological sections showed cardiac toxicity. Moreover, some metabolites in the body changed significantly. Receiver operating characteristic curve (ROC) analysis showed that there are 11 metabolites related with cardiac toxicity, which play a role in “phenylalanine, tyrosine and tryptophan biosynthesis”; “phenylalanine metabolism”; “valine, leucine and isoleucine biosynthesis”; “glycerophospholipid metabolism” as well as “pantothenate and CoA biosynthesis”. These metabolites can better explain the cardiotoxicity mechanism of Cortex Periplocae and provide a scientific and systematic method to evaluate the cardiotoxicity of Cortex Periplocae. The experimental design flow for screening the cardiotoxicity biomarkers induced by Cortex Periplocae.![]()
Collapse
Affiliation(s)
- Yubo Li
- Tianjin State Key Laboratory of Modern Chinese Medicine
- School of Traditional Chinese Materia Medica
- Tianjin University of Traditional Chinese Medicine
- Tianjin 300193
- China
| | - Chuanxin Liu
- Tianjin State Key Laboratory of Modern Chinese Medicine
- School of Traditional Chinese Materia Medica
- Tianjin University of Traditional Chinese Medicine
- Tianjin 300193
- China
| | - Jun Du
- Tianjin State Key Laboratory of Modern Chinese Medicine
- School of Traditional Chinese Materia Medica
- Tianjin University of Traditional Chinese Medicine
- Tianjin 300193
- China
| | - Xue Sheng
- Tianjin State Key Laboratory of Modern Chinese Medicine
- School of Traditional Chinese Materia Medica
- Tianjin University of Traditional Chinese Medicine
- Tianjin 300193
- China
| | - Yanjun Zhang
- Tianjin State Key Laboratory of Modern Chinese Medicine
- Tianjin University of Traditional Chinese Medicine
- Tianjin 300193
- China
| |
Collapse
|
118
|
Adamiak J, Bonifay V, Otlewska A, Sunner JA, Beech IB, Stryszewska T, Kańka S, Oracz J, Żyżelewicz D, Gutarowska B. Untargeted Metabolomics Approach in Halophiles: Understanding the Biodeterioration Process of Building Materials. Front Microbiol 2017; 8:2448. [PMID: 29321766 PMCID: PMC5732225 DOI: 10.3389/fmicb.2017.02448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/24/2017] [Indexed: 11/13/2022] Open
Abstract
The aim of the study was to explore the halophile metabolome in building materials using untargeted metabolomics which allows for broad metabolome coverage. For this reason, we used high-performance liquid chromatography interfaced to high-resolution mass spectrometry (HPLC/HRMS). As an alternative to standard microscopy techniques, we introduced pioneering Coherent Anti-stokes Raman Scattering Microscopy (CARS) to non-invasively visualize microbial cells. Brick samples saturated with salt solution (KCl, NaCl (two salinity levels), MgSO4, Mg(NO3)2), were inoculated with the mixture of preselected halophilic microorganisms, i.e., bacteria: Halobacillus styriensis, Halobacillus naozhouensis, Halobacillus hunanensis, Staphylococcus succinus, Marinococcus halophilus, Virgibacillus halodenitryficans, and yeast: Sterigmatomyces halophilus and stored at 28°C and 80% relative humidity for a year. Metabolites were extracted directly from the brick samples and measured via HPLC/HRMS in both positive and negative ion modes. Overall, untargeted metabolomics allowed for discovering the interactions of halophilic microorganisms with buildings materials which together with CARS microscopy enabled us to elucidate the biodeterioration process caused by halophiles. We observed that halophile metabolome was differently affected by different salt solutions. Furthermore, we found indications for haloadaptive strategies and degradation of brick samples due to microbial pigment production as a salt stress response. Finally, we detected changes in lipid content related to changes in the structure of phospholipid bilayers and membrane fluidity.
Collapse
Affiliation(s)
- Justyna Adamiak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Anna Otlewska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Jan A. Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Iwona B. Beech
- Center of Biofilm Engineering, Department of Chemical and Biochemical Engineering, Montana State University, Bozeman, MT, United States
| | - Teresa Stryszewska
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology, Cracow, Poland
| | - Stanisław Kańka
- Institute of Building Materials and Structures, Faculty of Civil Engineering, Cracow University of Technology, Cracow, Poland
| | - Joanna Oracz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Dorota Żyżelewicz
- Institute of Food Technology and Analysis, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Beata Gutarowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| |
Collapse
|
119
|
|
120
|
Bruderer T, Varesio E, Hopfgartner G. The use of LC predicted retention times to extend metabolites identification with SWATH data acquisition. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1071:3-10. [DOI: 10.1016/j.jchromb.2017.07.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2016] [Revised: 06/30/2017] [Accepted: 07/07/2017] [Indexed: 01/15/2023]
|
121
|
Fu Y, Zhao C, Lu X, Xu G. Nontargeted screening of chemical contaminants and illegal additives in food based on liquid chromatography–high resolution mass spectrometry. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.07.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
122
|
Taraji M, Haddad PR, Amos RI, Talebi M, Szucs R, Dolan JW, Pohl CA. Error measures in quantitative structure-retention relationships studies. J Chromatogr A 2017; 1524:298-302. [DOI: 10.1016/j.chroma.2017.09.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 01/31/2023]
|
123
|
Navarro-Reig M, Ortiz-Villanueva E, Tauler R, Jaumot J. Modelling of Hydrophilic Interaction Liquid Chromatography Stationary Phases Using Chemometric Approaches. Metabolites 2017; 7:E54. [PMID: 29064436 PMCID: PMC5746734 DOI: 10.3390/metabo7040054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 10/11/2017] [Accepted: 10/21/2017] [Indexed: 11/16/2022] Open
Abstract
Metabolomics is a powerful and widely used approach that aims to screen endogenous small molecules (metabolites) of different families present in biological samples. The large variety of compounds to be determined and their wide diversity of physical and chemical properties have promoted the development of different types of hydrophilic interaction liquid chromatography (HILIC) stationary phases. However, the selection of the most suitable HILIC stationary phase is not straightforward. In this work, four different HILIC stationary phases have been compared to evaluate their potential application for the analysis of a complex mixture of metabolites, a situation similar to that found in non-targeted metabolomics studies. The obtained chromatographic data were analyzed by different chemometric methods to explore the behavior of the considered stationary phases. ANOVA-simultaneous component analysis (ASCA), principal component analysis (PCA) and partial least squares regression (PLS) were used to explore the experimental factors affecting the stationary phase performance, the main similarities and differences among chromatographic conditions used (stationary phase and pH) and the molecular descriptors most useful to understand the behavior of each stationary phase.
Collapse
Affiliation(s)
- Meritxell Navarro-Reig
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Elena Ortiz-Villanueva
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Romà Tauler
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Joaquim Jaumot
- Department of Environmental Chemistry, IDAEA-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain.
| |
Collapse
|
124
|
Fenaille F, Barbier Saint-Hilaire P, Rousseau K, Junot C. Data acquisition workflows in liquid chromatography coupled to high resolution mass spectrometry-based metabolomics: Where do we stand? J Chromatogr A 2017; 1526:1-12. [PMID: 29074071 DOI: 10.1016/j.chroma.2017.10.043] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 10/15/2017] [Accepted: 10/16/2017] [Indexed: 01/08/2023]
Abstract
Typical mass spectrometry (MS) based untargeted metabolomics protocols are tedious as well as time- and sample-consuming. In particular, they often rely on "full-scan-only" analyses using liquid chromatography (LC) coupled to high resolution mass spectrometry (HRMS) from which metabolites of interest are first highlighted, and then tentatively identified by using targeted MS/MS experiments. However, this situation is evolving with the emergence of integrated HRMS based-data acquisition protocols able to perform multi-event acquisitions. Most of these protocols, referring to as data dependent and data independent acquisition (DDA and DIA, respectively), have been initially developed for proteomic applications and have recently demonstrated their applicability to biomedical studies. In this context, the aim of this article is to take stock of the progress made in the field of DDA- and DIA-based protocols, and evaluate their ability to change conventional metabolomic and lipidomic data acquisition workflows, through a review of HRMS instrumentation, DDA and DIA workflows, and also associated informatics tools.
Collapse
Affiliation(s)
- François Fenaille
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Pierre Barbier Saint-Hilaire
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Kathleen Rousseau
- Service de Pharmacologie et Immuno-Analyse (SPI), Laboratoire d'Etude du Métabolisme des Médicaments, CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France
| | - Christophe Junot
- Service de Pharmacologie et Immuno-Analyse (SPI), CEA, INRA, Université Paris Saclay, MetaboHUB, F-91191 Gif-sur-Yvette, France.
| |
Collapse
|
125
|
Taraji M, Haddad PR, Amos RIJ, Talebi M, Szucs R, Dolan JW, Pohl CA. Chemometric-assisted method development in hydrophilic interaction liquid chromatography: A review. Anal Chim Acta 2017; 1000:20-40. [PMID: 29289311 DOI: 10.1016/j.aca.2017.09.041] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/22/2017] [Accepted: 09/24/2017] [Indexed: 02/09/2023]
Abstract
With an enormous growth in the application of hydrophilic interaction liquid chromatography (HILIC), there has also been significant progress in HILIC method development. HILIC is a chromatographic method that utilises hydro-organic mobile phases with a high organic content, and a hydrophilic stationary phase. It has been applied predominantly in the determination of small polar compounds. Theoretical studies in computer-aided modelling tools, most importantly the predictive, quantitative structure retention relationship (QSRR) modelling methods, have attracted the attention of researchers and these approaches greatly assist the method development process. This review focuses on the application of computer-aided modelling tools in understanding the retention mechanism, the classification of HILIC stationary phases, prediction of retention times in HILIC systems, optimisation of chromatographic conditions, and description of the interaction effects of the chromatographic factors in HILIC separations. Additionally, what has been achieved in the potential application of QSRR methodology in combination with experimental design philosophy in the optimisation of chromatographic separation conditions in the HILIC method development process is communicated. Developing robust predictive QSRR models will undoubtedly facilitate more application of this chromatographic mode in a broader variety of research areas, significantly minimising cost and time of the experimental work.
Collapse
Affiliation(s)
- Maryam Taraji
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Paul R Haddad
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia.
| | - Ruth I J Amos
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Mohammad Talebi
- Australian Centre for Research on Separation Science (ACROSS), School of Physical Sciences-Chemistry, University of Tasmania, Private Bag 75, Hobart 7001, Australia
| | - Roman Szucs
- Pfizer Global Research and Development, CT13 9NJ, Sandwich, UK
| | - John W Dolan
- LC Resources, 1795 NW Wallace Rd., McMinnville, OR 97128, USA
| | | |
Collapse
|
126
|
“Thiol-ene” grafting of silica particles with three-dimensional branched copolymer for HILIC/cation-exchange chromatographic separation and N-glycopeptide enrichment. Anal Bioanal Chem 2017; 410:1019-1027. [DOI: 10.1007/s00216-017-0626-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/24/2017] [Accepted: 09/06/2017] [Indexed: 12/11/2022]
|
127
|
Burgess KEV, Borutzki Y, Rankin N, Daly R, Jourdan F. MetaNetter 2: A Cytoscape plugin for ab initio network analysis and metabolite feature classification. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1071:68-74. [PMID: 29030098 PMCID: PMC5726607 DOI: 10.1016/j.jchromb.2017.08.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 08/07/2017] [Accepted: 08/13/2017] [Indexed: 01/19/2023]
Abstract
An update to the ab-initio network construction tool MetaNetter has been produced. The tool creates networks of masses from high resolution mass spectrometry data. The new plugin provides both chemical transformation and adduct mapping. Tables mapping adduct and transform counts across samples can be generated. Retention time windows are supported for both adduct and transform network generation.
Metabolomics frequently relies on the use of high resolution mass spectrometry data. Classification and filtering of this data remain a challenging task due to the plethora of complex mass spectral artefacts, chemical noise, adducts and fragmentation that occur during ionisation and analysis. Additionally, the relationships between detected compounds can provide a wealth of information about the nature of the samples and the biochemistry that gave rise to them. We present a biochemical networking tool: MetaNetter 2 that is based on the original MetaNetter, a Cytoscape plugin that creates ab initio networks. The new version supports two major improvements: the generation of adduct networks and the creation of tables that map adduct or transformation patterns across multiple samples, providing a readout of compound relationships. We have applied this tool to the analysis of adduct patterns in the same sample separated under two different chromatographies, allowing inferences to be made about the effect of different buffer conditions on adduct detection, and the application of the chemical transformation analysis to both a single fragmentation analysis and an all-ions fragmentation dataset. Finally, we present an analysis of a dataset derived from anaerobic and aerobic growth of the organism Staphylococcus aureus demonstrating the utility of the tool for biological analysis.
Collapse
Affiliation(s)
- K E V Burgess
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.
| | - Y Borutzki
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom; Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - N Rankin
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom; Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, United Kingdom
| | - R Daly
- Glasgow Polyomics, University of Glasgow, Glasgow, United Kingdom
| | - F Jourdan
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, Toulouse, France
| |
Collapse
|
128
|
Stimulation of 3D osteogenesis by mesenchymal stem cells using a nanovibrational bioreactor. Nat Biomed Eng 2017; 1:758-770. [DOI: 10.1038/s41551-017-0127-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 07/31/2017] [Indexed: 12/18/2022]
|
129
|
Siddiqui G, Srivastava A, Russell AS, Creek DJ. Multi-omics Based Identification of Specific Biochemical Changes Associated With PfKelch13-Mutant Artemisinin-Resistant Plasmodium falciparum. J Infect Dis 2017; 215:1435-1444. [PMID: 28368494 DOI: 10.1093/infdis/jix156] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 03/25/2017] [Indexed: 01/10/2023] Open
Abstract
Background The emergence of artemisinin resistance in the malaria parasite Plasmodium falciparum poses a major threat to the control and elimination of malaria. Certain point mutations in the propeller domain of PfKelch13 are associated with resistance, but PfKelch13 mutations do not always result in clinical resistance. The underlying mechanisms associated with artemisinin resistance are poorly understood, and the impact of PfKelch13 mutations on cellular biochemistry is not defined. Methods This study aimed to identify global biochemical differences between PfKelch13-mutant artemisinin-resistant and -sensitive strains of P. falciparum by combining liquid chromatography-mass spectrometry (LC-MS)-based proteomics, peptidomics, and metabolomics. Results Proteomics analysis found both PfKelch13 mutations examined to be specifically associated with decreased abundance of PfKelch13 protein. Metabolomics analysis demonstrated accumulation of glutathione and its precursor, gamma-glutamylcysteine, and significant depletion of 1 other putative metabolite in resistant strains. Peptidomics analysis revealed lower abundance of several endogenous peptides derived from hemoglobin (HBα and HBβ) in the artemisinin-resistant strains. Conclusion PfKelch13 mutations associated with artemisinin resistance lead to decreased abundance of PfKelch13 protein, decreased hemoglobin digestion, and enhanced glutathione production.
Collapse
Affiliation(s)
- Ghizal Siddiqui
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University,Parkville, Victoria, Australia
| | - Anubhav Srivastava
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University,Parkville, Victoria, Australia
| | - Adrian S Russell
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University,Parkville, Victoria, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University,Parkville, Victoria, Australia
| |
Collapse
|
130
|
Improving cartilage phenotype from differentiated pericytes in tunable peptide hydrogels. Sci Rep 2017; 7:6895. [PMID: 28761049 PMCID: PMC5537289 DOI: 10.1038/s41598-017-07255-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 06/26/2017] [Indexed: 01/03/2023] Open
Abstract
Differentiation of stem cells to chondrocytes in vitro usually results in a heterogeneous phenotype. This is evident in the often detected over expression of type X collagen which, in hyaline cartilage structure is not characteristic of the mid-zone but of the deep-zone ossifying tissue. Methods to better match cartilage developed in vitro to characteristic in vivo features are therefore highly desirable in regenerative medicine. This study compares phenotype characteristics between pericytes, obtained from human adipose tissue, differentiated using diphenylalanine/serine (F2/S) peptide hydrogels with the more widely used chemical induced method for chondrogenesis. Significantly higher levels of type II collagen were noted when pericytes undergo chondrogenesis in the hydrogel in the absence of induction media. There is also a balanced expression of collagen relative to aggrecan production, a feature which was biased toward collagen production when cells were cultured with induction media. Lastly, metabolic profiles of each system show considerable overlap between both differentiation methods but subtle differences which potentially give rise to their resultant phenotype can be ascertained. The study highlights how material and chemical alterations in the cellular microenvironment have wide ranging effects on resultant tissue type.
Collapse
|
131
|
Alakpa EV, Burgess KEV, Chung P, Riehle MO, Gadegaard N, Dalby MJ, Cusack M. Nacre Topography Produces Higher Crystallinity in Bone than Chemically Induced Osteogenesis. ACS NANO 2017; 11:6717-6727. [PMID: 28665112 DOI: 10.1021/acsnano.7b01044] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
It is counterintuitive that invertebrate shells can induce bone formation, yet nacre, or mother of pearl, from marine shells is both osteoinductive and osteointegrative. Nacre is composed of aragonite (calcium carbonate) and induces production of vertebrate bone (calcium phosphate). Exploited by the Mayans for dental implants, this remarkable phenomenon has been confirmed in vitro and in vivo, yet the characteristic of nacre that induces bone formation remains unknown. By isolating nacre topography from its inherent chemistry in the production of polycaprolactone (PCL) nacre replica, we show that, for mesenchymal stem cells, nacre topography is osteoinductive. Gene expression of specific bone marker proteins, osteopontin, osteocalcin, osteonectin, and osterix, is increased 10-, 2-, 1.7-, and 1.8-fold, respectively, when compared to planar PCL. Furthermore, we demonstrate that bone tissue that forms in response to the physical topographical features of nacre has a higher crystallinity than bone formed in response to chemical cues with a full width half-maximum for PO43- Raman shift of 7.6 ± 0.7 for mineral produced in response to nacre replica compared to a much broader 34.6 ± 10.1 in response to standard osteoinductive medium. These differences in mineral product are underpinned by differences in cellular metabolism. This observation can be exploited in the design of bone therapies; a matter that is most pressing in light of a rapidly aging human population.
Collapse
Affiliation(s)
- Enateri V Alakpa
- School of Geographical and Earth Sciences, College of Science and Engineering, University of Glasgow , Gregory Building, Glasgow G12 8QQ, United Kingdom
| | - Karl E V Burgess
- Scottish Polyomics Facility, Wolfson Wohl Cancer Research Centre, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Garscube Estate, Glasgow G61 1QH, United Kingdom
| | - Peter Chung
- School of Geographical and Earth Sciences, College of Science and Engineering, University of Glasgow , Gregory Building, Glasgow G12 8QQ, United Kingdom
| | - Mathis O Riehle
- Centre for Cell Engineering, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Joseph Black Building, Glasgow G12 8QQ, United Kingdom
| | - Nikolaj Gadegaard
- Division of Biomedical Engineering, School of Engineering, University of Glasgow , Glasgow G12 8LT, United Kingdom
| | - Matthew John Dalby
- Centre for Cell Engineering, Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow , Joseph Black Building, Glasgow G12 8QQ, United Kingdom
| | - Maggie Cusack
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling , Cottrell Building, Stirling FK9 4LA, United Kingdom
| |
Collapse
|
132
|
van der Hooft JJJ, Wandy J, Young F, Padmanabhan S, Gerasimidis K, Burgess KEV, Barrett MP, Rogers S. Unsupervised Discovery and Comparison of Structural Families Across Multiple Samples in Untargeted Metabolomics. Anal Chem 2017. [PMID: 28621528 PMCID: PMC5524435 DOI: 10.1021/acs.analchem.7b01391] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
In
untargeted metabolomics
approaches, the inability to structurally
annotate relevant features and map them to biochemical pathways is
hampering the full exploitation of many metabolomics experiments.
Furthermore, variable metabolic content across samples result in sparse
feature matrices that are statistically hard to handle. Here, we introduce
MS2LDA+ that tackles both above-mentioned problems. Previously, we
presented MS2LDA, which extracts biochemically relevant molecular
substructures (“Mass2Motifs”) from a collection of fragmentation
spectra as sets of co-occurring molecular fragments and neutral losses,
thereby recognizing building blocks of metabolomics. Here, we extend
MS2LDA to handle multiple metabolomics experiments in one analysis,
resulting in MS2LDA+. By linking Mass2Motifs across samples, we expose
the variability in prevalence of structurally related metabolite families.
We validate the differential prevalence of substructures between two
distinct samples groups and apply it to fecal samples. Subsequently,
within one sample group of urines, we rank the Mass2Motifs based on
their variance to assess whether xenobiotic-derived substructures
are among the most-variant Mass2Motifs. Indeed, we could ascribe 22
out of the 30 most-variant Mass2Motifs to xenobiotic-derived substructures
including paracetamol/acetaminophen mercapturate and dimethylpyrogallol.
In total, we structurally characterized 101 Mass2Motifs with biochemically
or chemically relevant substructures. Finally, we combined the discovered
metabolite families with full scan feature intensity information to
obtain insight into core metabolites present in most samples and rare
metabolites present in small subsets now linked through their common
substructures. We conclude that by biochemical grouping of metabolites
across samples MS2LDA+ aids in structural annotation of metabolites
and guides prioritization of analysis by using Mass2Motif prevalence.
Collapse
Affiliation(s)
- Justin J J van der Hooft
- Glasgow Polyomics, University of Glasgow , Glasgow G61 1HQ, United Kingdom.,Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Joe Wandy
- Glasgow Polyomics, University of Glasgow , Glasgow G61 1HQ, United Kingdom
| | - Francesca Young
- Glasgow Polyomics, University of Glasgow , Glasgow G61 1HQ, United Kingdom
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, College of Medical, Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Konstantinos Gerasimidis
- Human Nutrition, School of Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow , New Lister Building, Glasgow Royal Infirmary, Glasgow G31 2ER, United Kingdom
| | - Karl E V Burgess
- Glasgow Polyomics, University of Glasgow , Glasgow G61 1HQ, United Kingdom
| | - Michael P Barrett
- Glasgow Polyomics, University of Glasgow , Glasgow G61 1HQ, United Kingdom.,Wellcome Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow , Glasgow G12 8TA, United Kingdom
| | - Simon Rogers
- Glasgow Polyomics, University of Glasgow , Glasgow G61 1HQ, United Kingdom.,School of Computing Science, University of Glasgow , Glasgow G12 8RZ, United Kingdom
| |
Collapse
|
133
|
Use of dual-filtering to create training sets leading to improved accuracy in quantitative structure-retention relationships modelling for hydrophilic interaction liquid chromatographic systems. J Chromatogr A 2017; 1507:53-62. [DOI: 10.1016/j.chroma.2017.05.044] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/17/2017] [Accepted: 05/18/2017] [Indexed: 01/31/2023]
|
134
|
Mwenechanya R, Kovářová J, Dickens NJ, Mudaliar M, Herzyk P, Vincent IM, Weidt SK, Burgess KE, Burchmore RJS, Pountain AW, Smith TK, Creek DJ, Kim DH, Lepesheva GI, Barrett MP. Sterol 14α-demethylase mutation leads to amphotericin B resistance in Leishmania mexicana. PLoS Negl Trop Dis 2017. [PMID: 28622334 PMCID: PMC5498063 DOI: 10.1371/journal.pntd.0005649] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Amphotericin B has emerged as the therapy of choice for use against the leishmaniases. Administration of the drug in its liposomal formulation as a single injection is being promoted in a campaign to bring the leishmaniases under control. Understanding the risks and mechanisms of resistance is therefore of great importance. Here we select amphotericin B-resistant Leishmania mexicana parasites with relative ease. Metabolomic analysis demonstrated that ergosterol, the sterol known to bind the drug, is prevalent in wild-type cells, but diminished in the resistant line, where alternative sterols become prevalent. This indicates that the resistance phenotype is related to loss of drug binding. Comparing sequences of the parasites' genomes revealed a plethora of single nucleotide polymorphisms that distinguish wild-type and resistant cells, but only one of these was found to be homozygous and associated with a gene encoding an enzyme in the sterol biosynthetic pathway, sterol 14α-demethylase (CYP51). The mutation, N176I, is found outside of the enzyme's active site, consistent with the fact that the resistant line continues to produce the enzyme's product. Expression of wild-type sterol 14α-demethylase in the resistant cells caused reversion to drug sensitivity and a restoration of ergosterol synthesis, showing that the mutation is indeed responsible for resistance. The amphotericin B resistant parasites become hypersensitive to pentamidine and also agents that induce oxidative stress. This work reveals the power of combining polyomics approaches, to discover the mechanism underlying drug resistance as well as offering novel insights into the selection of resistance to amphotericin B itself.
Collapse
Affiliation(s)
- Roy Mwenechanya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
| | - Julie Kovářová
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
| | - Nicholas J. Dickens
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
| | - Manikhandan Mudaliar
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Pawel Herzyk
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Isabel M. Vincent
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
| | - Stefan K. Weidt
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Karl E. Burgess
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Richard J. S. Burchmore
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
| | - Andrew W. Pountain
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
| | - Terry K. Smith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St. Andrews, Fife, United Kingdom
| | - Darren J. Creek
- Drug Delivery, Disposition & Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Dong-Hyun Kim
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, University Park, Nottingham, United Kingdom
| | - Galina I. Lepesheva
- Vanderbilt University School of Medicine, Nashville, TN, United States of America
| | - Michael P. Barrett
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place, Glasgow, United Kingdom
- Glasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Garscube Estate, Bearsden, Glasgow, United Kingdom
- * E-mail:
| |
Collapse
|
135
|
Chervin J, Stierhof M, Tong MH, Peace D, Hansen KØ, Urgast DS, Andersen JH, Yu Y, Ebel R, Kyeremeh K, Paget V, Cimpan G, Wyk AV, Deng H, Jaspars M, Tabudravu JN. Targeted Dereplication of Microbial Natural Products by High-Resolution MS and Predicted LC Retention Time. JOURNAL OF NATURAL PRODUCTS 2017; 80:1370-1377. [PMID: 28445069 DOI: 10.1021/acs.jnatprod.6b01035] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
A new strategy for the identification of known compounds in Streptomyces extracts that can be applied in the discovery of natural products is presented. The strategy incorporates screening a database of 5555 natural products including 5098 structures from Streptomyces sp., using a high-throughput LCMS data processing algorithm that utilizes HRMS data and predicted LC retention times (tR) as filters for rapid identification of known compounds in the natural product extract. The database, named StrepDB, contains for each compound the structure, molecular formula, molecular mass, and predicted LC retention time. All identified compounds are annotated and color coded for easier visualization. It is an indirect approach to quickly assess masses (which are not annotated) that may potentially lead to the discovery of new or novel structures. In addition, a spectral database named MbcDB was generated using the ACD/Spectrus DB Platform. MbcDB contains 665 natural products, each with structure, experimental HRESIMS, MS/MS, UV, and NMR spectra. StrepDB was used to screen a mutant Streptomyces albus extract, which led to the identification and isolation of two new compounds, legonmaleimides A and B, the structures of which were elucidated with the aid of MbcDB and spectroscopic techniques. The structures were confirmed by computer-assisted structure elucidation (CASE) methods using ACD/Structure Elucidator Suite. The developed methodology suggests a pipeline approach to the dereplication of extracts and discovery of novel natural products.
Collapse
Affiliation(s)
- Justine Chervin
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Marc Stierhof
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Ming Him Tong
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Doe Peace
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Kine Østnes Hansen
- Marbio, UiT The Arctic University of Norway, Breivika , N-9037, Tromsø, Norway
| | - Dagmar Solveig Urgast
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | | | - Yi Yu
- Key Laboratory of Combinatory Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University , 185 East Lake Road, Wuhan 430071, People's Repupblic of China
| | - Rainer Ebel
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Kwaku Kyeremeh
- Marine and Plant Research Laboratory of Ghana, Department of Chemistry, University of Ghana , P.O. Box LG 56, Accra, Ghana
| | - Veronica Paget
- Advanced Chemistry Development, UK Ltd. , Venture House, Arlington Square, Downshire Way, Bracknell, Berkshire RG12 1WA, U.K
| | - Gabriela Cimpan
- Advanced Chemistry Development, UK Ltd. , Venture House, Arlington Square, Downshire Way, Bracknell, Berkshire RG12 1WA, U.K
| | - Albert Van Wyk
- Advanced Chemistry Development, UK Ltd. , Venture House, Arlington Square, Downshire Way, Bracknell, Berkshire RG12 1WA, U.K
| | - Hai Deng
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Marcel Jaspars
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| | - Jioji N Tabudravu
- The Marine Biodiscovery Centre, Department of Chemistry, University of Aberdeen , Aberdeen AB24 3UE, Scotland, U.K
| |
Collapse
|
136
|
Hamilton JS, Aguilar R, Petros RA, Verbeck GF. DAPNe with micro-capillary separatory chemistry-coupled to MALDI-MS for the analysis of polar and non-polar lipid metabolism in one cell. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:918-928. [PMID: 28251574 DOI: 10.1007/s13361-017-1623-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 01/27/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
The cellular metabolome is considered to be a representation of cellular phenotype and cellular response to changes to internal or external events. Methods to expand the coverage of the expansive physiochemical properties that makeup the metabolome currently utilize multi-step extractions and chromatographic separations prior to chemical detection, leading to lengthy analysis times. In this study, a single-step procedure for the extraction and separation of a sample using a micro-capillary as a separatory funnel to achieve analyte partitioning within an organic/aqueous immiscible solvent system is described. The separated analytes are then spotted for MALDI-MS imaging and distribution ratios are calculated. Initially, the method is applied to standard mixtures for proof of partitioning. The extraction of an individual cell is non-reproducible; therefore, a broad chemical analysis of metabolites is necessary and will be illustrated with the one-cell analysis of a single Snu-5 gastric cancer cell taken from a cellular suspension. The method presented here shows a broad partitioning dynamic range as a single-step method for lipid analysis demonstrating a decrease in ion suppression often present in MALDI analysis of lipids. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Jason S Hamilton
- Department of Chemistry, University of North Texas, Denton, TX, USA
| | - Roberto Aguilar
- Department of Chemistry, University of North Texas, Denton, TX, USA
| | - Robby A Petros
- Department of Chemistry, Texas Women's Univeristy, Denton, TX, USA
| | - Guido F Verbeck
- Department of Chemistry, University of North Texas, Denton, TX, USA.
| |
Collapse
|
137
|
Abstract
Metabolomics incorporates the study of metabolites that are produced and released through physiological processes at both the systemic and cellular levels. Biological compounds at the metabolite level are of paramount interest in the sport and exercise sciences, although research in this field has rarely been referred to with the global 'omics terminology. Commonly studied metabolites in exercise science are notably within cellular pathways for adenosine triphosphate production such as glycolysis (e.g., pyruvate and lactate), β-oxidation of free fatty acids (e.g., palmitate) and ketone bodies (e.g., β-hydroxybutyrate). Non-targeted metabolomic technologies are able to simultaneously analyse the large numbers of metabolites present in human biological samples such as plasma, urine and saliva. These analytical technologies predominately employ nuclear magnetic resonance spectroscopy and chromatography coupled to mass spectrometry. Performing experiments based on non-targeted methods allows for systemic metabolite changes to be analysed and compared to a particular physiological state (e.g., pre-/post-exercise) and provides an opportunity to prospect for metabolite signatures that offer beneficial information for translation into an exercise science context, for both elite performance and public health monitoring. This narrative review provides an introduction to non-targeted metabolomic technologies and discusses current and potential applications in sport and exercise science.
Collapse
Affiliation(s)
- Liam M Heaney
- a Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit , University of Leicester, Glenfield Hospital , Leicester , UK
| | - Kevin Deighton
- b Institute for Sport, Physical Activity and Leisure , Leeds Beckett University , Leeds, UK
| | - Toru Suzuki
- a Department of Cardiovascular Sciences and NIHR Leicester Cardiovascular Biomedical Research Unit , University of Leicester, Glenfield Hospital , Leicester , UK
| |
Collapse
|
138
|
Counihan NA, Chisholm SA, Bullen HE, Srivastava A, Sanders PR, Jonsdottir TK, Weiss GE, Ghosh S, Crabb BS, Creek DJ, Gilson PR, de Koning-Ward TF. Plasmodium falciparum parasites deploy RhopH2 into the host erythrocyte to obtain nutrients, grow and replicate. eLife 2017; 6. [PMID: 28252383 PMCID: PMC5365316 DOI: 10.7554/elife.23217] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 02/26/2017] [Indexed: 11/13/2022] Open
Abstract
Plasmodium falciparum parasites, the causative agents of malaria, modify their host erythrocyte to render them permeable to supplementary nutrient uptake from the plasma and for removal of toxic waste. Here we investigate the contribution of the rhoptry protein RhopH2, in the formation of new permeability pathways (NPPs) in Plasmodium-infected erythrocytes. We show RhopH2 interacts with RhopH1, RhopH3, the erythrocyte cytoskeleton and exported proteins involved in host cell remodeling. Knockdown of RhopH2 expression in cycle one leads to a depletion of essential vitamins and cofactors and decreased de novo synthesis of pyrimidines in cycle two. There is also a significant impact on parasite growth, replication and transition into cycle three. The uptake of solutes that use NPPs to enter erythrocytes is also reduced upon RhopH2 knockdown. These findings provide direct genetic support for the contribution of the RhopH complex in NPP activity and highlight the importance of NPPs to parasite survival.
Collapse
Affiliation(s)
| | | | | | - Anubhav Srivastava
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | | | - Thorey K Jonsdottir
- Burnet Institute, Melbourne, Australia.,Department of Medicine, University of Melbourne, Parkville, Australia
| | | | - Sreejoyee Ghosh
- School of Medicine, Deakin University, Waurn Ponds, Australia
| | - Brendan S Crabb
- Burnet Institute, Melbourne, Australia.,Department of Medicine, University of Melbourne, Parkville, Australia.,Monash University, Melbourne, Australia
| | - Darren J Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Paul R Gilson
- Burnet Institute, Melbourne, Australia.,Monash University, Melbourne, Australia
| | | |
Collapse
|
139
|
Zisi C, Sampsonidis I, Fasoula S, Papachristos K, Witting M, Gika HG, Nikitas P, Pappa-Louisi A. QSRR Modeling for Metabolite Standards Analyzed by Two Different Chromatographic Columns Using Multiple Linear Regression. Metabolites 2017; 7:metabo7010007. [PMID: 28208794 PMCID: PMC5372210 DOI: 10.3390/metabo7010007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/05/2017] [Indexed: 01/07/2023] Open
Abstract
Modified quantitative structure retention relationships (QSRRs) are proposed and applied to describe two retention data sets: A set of 94 metabolites studied by a hydrophilic interaction chromatography system under organic content gradient conditions and a set of tryptophan and its major metabolites analyzed by a reversed-phase chromatographic system under isocratic as well as pH and/or simultaneous pH and organic content gradient conditions. According to the proposed modification, an additional descriptor is added to a conventional QSRR expression, which is the analyte retention time, tR(R), measured under the same elution conditions, but in a second chromatographic column considered as a reference one. The 94 metabolites were studied on an Amide column using a Bare Silica column as a reference. For the second dataset, a Kinetex EVO C18 and a Gemini-NX column were used, where each of them was served as a reference column of the other. We found in all cases a significant improvement of the performance of the QSRR models when the descriptor tR(R) was considered.
Collapse
Affiliation(s)
- Chrysostomi Zisi
- Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.F.); (K.P.); (P.N.); (A.P.-L.)
- Correspondence: ; Tel.: +30-231-099-7765
| | - Ioannis Sampsonidis
- Infrastructure and Environment Research Division, School of Engineering, University of Glasgow, Rankine Building, Oakfield Avenue, Glasgow G12 8LT, UK;
| | - Stella Fasoula
- Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.F.); (K.P.); (P.N.); (A.P.-L.)
| | - Konstantinos Papachristos
- Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.F.); (K.P.); (P.N.); (A.P.-L.)
| | - Michael Witting
- Helmholtz Zentrum München, Research Unit Analytical BioGeoChemistry, Ingolstaedter Landstrasse 1, D-85764 Neuherberg, Germany;
| | - Helen G. Gika
- Department of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Panagiotis Nikitas
- Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.F.); (K.P.); (P.N.); (A.P.-L.)
| | - Adriani Pappa-Louisi
- Department of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (S.F.); (K.P.); (P.N.); (A.P.-L.)
| |
Collapse
|
140
|
Prediction of retention in hydrophilic interaction liquid chromatography using solute molecular descriptors based on chemical structures. J Chromatogr A 2017; 1486:59-67. [DOI: 10.1016/j.chroma.2016.12.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 12/07/2016] [Accepted: 12/11/2016] [Indexed: 11/23/2022]
|
141
|
Böcker S. Searching molecular structure databases using tandem MS data: are we there yet? Curr Opin Chem Biol 2017; 36:1-6. [DOI: 10.1016/j.cbpa.2016.12.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
|
142
|
Bonifay V, Wawrik B, Sunner J, Snodgrass EC, Aydin E, Duncan KE, Callaghan AV, Oldham A, Liengen T, Beech I. Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion. Front Microbiol 2017; 8:99. [PMID: 28197141 PMCID: PMC5281625 DOI: 10.3389/fmicb.2017.00099] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/13/2017] [Indexed: 01/06/2023] Open
Abstract
Corrosion processes in two North Sea oil production pipelines were studied by analyzing pig envelope samples via metagenomic and metabolomic techniques. Both production systems have similar physico-chemical properties and injection waters are treated with nitrate, but one pipeline experiences severe corrosion and the other does not. Early and late pigging material was collected to gain insight into the potential causes for differential corrosion rates. Metabolites were extracted and analyzed via ultra-high performance liquid chromatography/high-resolution mass spectrometry with electrospray ionization (ESI) in both positive and negative ion modes. Metabolites were analyzed by comparison with standards indicative of aerobic and anaerobic hydrocarbon metabolism and by comparison to predicted masses for KEGG metabolites. Microbial community structure was analyzed via 16S rRNA gene qPCR, sequencing of 16S PCR products, and MySeq Illumina shotgun sequencing of community DNA. Metagenomic data were used to reconstruct the full length 16S rRNA genes and genomes of dominant microorganisms. Sequence data were also interrogated via KEGG annotation and for the presence of genes related to terminal electron accepting (TEA) processes as well as aerobic and anaerobic hydrocarbon degradation. Significant and distinct differences were observed when comparing the ‘high corrosion’ (HC) and the ‘low corrosion’ (LC) pipeline systems, especially with respect to the TEA utilization potential. The HC samples were dominated by sulfate-reducing bacteria (SRB) and archaea known for their ability to utilize simple carbon substrates, whereas LC samples were dominated by pseudomonads with the genetic potential for denitrification and aerobic hydrocarbon degradation. The frequency of aerobic hydrocarbon degradation genes was low in the HC system, and anaerobic hydrocarbon degradation genes were not detected in either pipeline. This is in contrast with metabolite analysis, which demonstrated the presence of several succinic acids in HC samples that are diagnostic of anaerobic hydrocarbon metabolism. Identifiable aerobic metabolites were confined to the LC samples, consistent with the metagenomic data. Overall, these data suggest that corrosion management might benefit from a more refined understanding of microbial community resilience in the face of disturbances such as nitrate treatment or pigging, which frequently prove insufficient to alter community structure toward a stable, less-corrosive assemblage.
Collapse
Affiliation(s)
- Vincent Bonifay
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Boris Wawrik
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Jan Sunner
- Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Institute for Energy and the Environment, University of Oklahoma, NormanOK, USA
| | - Emily C Snodgrass
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Egemen Aydin
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Kathleen E Duncan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Amy V Callaghan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman OK, USA
| | - Athenia Oldham
- Department of Biology, University of Texas of the Permian Basin, Odessa TX, USA
| | - Turid Liengen
- Research Centre Porsgrunn, Statoil ASA, Herøya Industripark Porsgrunn, Norway
| | - Iwona Beech
- Department of Microbiology and Plant Biology, University of Oklahoma, NormanOK, USA; Institute for Energy and the Environment, University of Oklahoma, NormanOK, USA
| |
Collapse
|
143
|
Guder JC, Schramm T, Sander T, Link H. Time-Optimized Isotope Ratio LC–MS/MS for High-Throughput Quantification of Primary Metabolites. Anal Chem 2017; 89:1624-1631. [DOI: 10.1021/acs.analchem.6b03731] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jan Christopher Guder
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Thorben Schramm
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Timur Sander
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 16, 35043 Marburg, Germany
| |
Collapse
|
144
|
Akram MI, Vincent IM, Siddiqui AJ, Musharraf SG. Polymeric hydrophilic interaction liquid chromatography coupled with Orbitrap mass spectrometry and chemometric analysis for untargeted metabolite profiling of natural rice variants. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2017.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
145
|
Vincent IM, Daly R, Courtioux B, Cattanach AM, Biéler S, Ndung’u JM, Bisser S, Barrett MP. Metabolomics Identifies Multiple Candidate Biomarkers to Diagnose and Stage Human African Trypanosomiasis. PLoS Negl Trop Dis 2016; 10:e0005140. [PMID: 27941966 PMCID: PMC5152828 DOI: 10.1371/journal.pntd.0005140] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 10/26/2016] [Indexed: 12/01/2022] Open
Abstract
Treatment for human African trypanosomiasis is dependent on the species of trypanosome causing the disease and the stage of the disease (stage 1 defined by parasites being present in blood and lymphatics whilst for stage 2, parasites are found beyond the blood-brain barrier in the cerebrospinal fluid (CSF)). Currently, staging relies upon detecting the very low number of parasites or elevated white blood cell numbers in CSF. Improved staging is desirable, as is the elimination of the need for lumbar puncture. Here we use metabolomics to probe samples of CSF, plasma and urine from 40 Angolan patients infected with Trypanosoma brucei gambiense, at different disease stages. Urine samples provided no robust markers indicative of infection or stage of infection due to inherent variability in urine concentrations. Biomarkers in CSF were able to distinguish patients at stage 1 or advanced stage 2 with absolute specificity. Eleven metabolites clearly distinguished the stage in most patients and two of these (neopterin and 5-hydroxytryptophan) showed 100% specificity and sensitivity between our stage 1 and advanced stage 2 samples. Neopterin is an inflammatory biomarker previously shown in CSF of stage 2 but not stage 1 patients. 5-hydroxytryptophan is an important metabolite in the serotonin synthetic pathway, the key pathway in determining somnolence, thus offering a possible link to the eponymous symptoms of “sleeping sickness”. Plasma also yielded several biomarkers clearly indicative of the presence (87% sensitivity and 95% specificity) and stage of disease (92% sensitivity and 81% specificity). A logistic regression model including these metabolites showed clear separation of patients being either at stage 1 or advanced stage 2 or indeed diseased (both stages) versus control. Human African trypanosomiasis, also known as sleeping sickness, is a parasitic disease that affects people in sub-Saharan Africa. There are two stages of the infection. The first stage involves parasites proliferating in the bloodstream following introduction via the bite of an infected tsetse fly. The second, more serious stage, involves parasite invasion and proliferation within the central nervous system causing characteristic disturbances to the patients’ sleep wake patterns and progressive appearance of other neurological signs, including walking disabilities behaviour changes, abnormal movements, incontinence, then ultimately coma and death. Drugs are available to treat both stages of the disease, but the drugs for stage 2 disease have serious side effects and must be administered in hospital settings. Stage determination is thus a key element for disease management. Currently staging involves microscopic evaluation of CSF following a lumbar puncture. Here, we have analysed the metabolome of CSF, blood and urine of patients to seek biomarkers to stage the disease based on these biofluids. CSF and blood fluids were found to have distinctive metabolic biomarkers and when several of these metabolites are combined, a sensitive and robust discriminatory staging test can be developed. Some CSF metabolic markers relate to brain inflammation, whilst others may be related to somnolence associated with the disease in stage 2 patients, which may also help in understanding disease progression. Interestingly, distinctive biomarkers were also found in plasma, potentially abrogating the need for diagnostic lumbar punctures in the future.
Collapse
Affiliation(s)
- Isabel M. Vincent
- Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rónán Daly
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Bertrand Courtioux
- INSERM U1094, Tropical Neuroepidemiology, Limoges, France; Université de Limoges, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France
| | - Amy M. Cattanach
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Sylvain Biéler
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | | | - Sylvie Bisser
- INSERM U1094, Tropical Neuroepidemiology, Limoges, France; Université de Limoges, Institute of Neuroepidemiology and Tropical Neurology, Limoges, France
- * E-mail: (MPB); (SBis)
| | - Michael P. Barrett
- Wellcome Trust Centre of Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- Glasgow Polyomics, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
- * E-mail: (MPB); (SBis)
| |
Collapse
|
146
|
Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA. Untargeted Metabolomics Strategies-Challenges and Emerging Directions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1897-1905. [PMID: 27624161 PMCID: PMC5110944 DOI: 10.1007/s13361-016-1469-y] [Citation(s) in RCA: 678] [Impact Index Per Article: 84.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 05/05/2023]
Abstract
Metabolites are building blocks of cellular function. These species are involved in enzyme-catalyzed chemical reactions and are essential for cellular function. Upstream biological disruptions result in a series of metabolomic changes and, as such, the metabolome holds a wealth of information that is thought to be most predictive of phenotype. Uncovering this knowledge is a work in progress. The field of metabolomics is still maturing; the community has leveraged proteomics experience when applicable and developed a range of sample preparation and instrument methodology along with myriad data processing and analysis approaches. Research focuses have now shifted toward a fundamental understanding of the biology responsible for metabolomic changes. There are several types of metabolomics experiments including both targeted and untargeted analyses. While untargeted, hypothesis generating workflows exhibit many valuable attributes, challenges inherent to the approach remain. This Critical Insight comments on these challenges, focusing on the identification process of LC-MS-based untargeted metabolomics studies-specifically in mammalian systems. Biological interpretation of metabolomics data hinges on the ability to accurately identify metabolites. The range of confidence associated with identifications that is often overlooked is reviewed, and opportunities for advancing the metabolomics field are described. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Alexandra C Schrimpe-Rutledge
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - Simona G Codreanu
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - Stacy D Sherrod
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA
| | - John A McLean
- Department of Chemistry, Vanderbilt University, Nashville, TN, 37235, USA.
- Center for Innovative Technology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, 37235, USA.
- Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, Nashville, TN, 37235, USA.
| |
Collapse
|
147
|
Singh C, Glaab E, Linster CL. Molecular Identification of d-Ribulokinase in Budding Yeast and Mammals. J Biol Chem 2016; 292:1005-1028. [PMID: 27909055 DOI: 10.1074/jbc.m116.760744] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/29/2016] [Indexed: 12/13/2022] Open
Abstract
Proteomes of even well characterized organisms still contain a high percentage of proteins with unknown or uncertain molecular and/or biological function. A significant fraction of those proteins is predicted to have catalytic properties. Here we aimed at identifying the function of the Saccharomyces cerevisiae Ydr109c protein and its human homolog FGGY, both of which belong to the broadly conserved FGGY family of carbohydrate kinases. Functionally identified members of this family phosphorylate 3- to 7-carbon sugars or sugar derivatives, but the endogenous substrate of S. cerevisiae Ydr109c and human FGGY has remained unknown. Untargeted metabolomics analysis of an S. cerevisiae deletion mutant of YDR109C revealed ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared with a wild-type strain. In human HEK293 cells, ribulose could only be detected when ribitol was added to the cultivation medium, and under this condition, FGGY silencing led to ribulose accumulation. Biochemical characterization of the recombinant purified Ydr109c and FGGY proteins showed a clear substrate preference of both kinases for d-ribulose over a range of other sugars and sugar derivatives tested, including l-ribulose. Detailed sequence and structural analyses of Ydr109c and FGGY as well as homologs thereof furthermore allowed the definition of a 5-residue d-ribulokinase signature motif (TCSLV). The physiological role of the herein identified eukaryotic d-ribulokinase remains unclear, but we speculate that S. cerevisiae Ydr109c and human FGGY could act as metabolite repair enzymes, serving to re-phosphorylate free d-ribulose generated by promiscuous phosphatases from d-ribulose 5-phosphate. In human cells, FGGY can additionally participate in ribitol metabolism.
Collapse
Affiliation(s)
- Charandeep Singh
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Enrico Glaab
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Carole L Linster
- From the Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| |
Collapse
|
148
|
van der Hooft JJJ, Wandy J, Barrett MP, Burgess KEV, Rogers S. Topic modeling for untargeted substructure exploration in metabolomics. Proc Natl Acad Sci U S A 2016; 113:13738-13743. [PMID: 27856765 PMCID: PMC5137707 DOI: 10.1073/pnas.1608041113] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The potential of untargeted metabolomics to answer important questions across the life sciences is hindered because of a paucity of computational tools that enable extraction of key biochemically relevant information. Available tools focus on using mass spectrometry fragmentation spectra to identify molecules whose behavior suggests they are relevant to the system under study. Unfortunately, fragmentation spectra cannot identify molecules in isolation but require authentic standards or databases of known fragmented molecules. Fragmentation spectra are, however, replete with information pertaining to the biochemical processes present, much of which is currently neglected. Here, we present an analytical workflow that exploits all fragmentation data from a given experiment to extract biochemically relevant features in an unsupervised manner. We demonstrate that an algorithm originally used for text mining, latent Dirichlet allocation, can be adapted to handle metabolomics datasets. Our approach extracts biochemically relevant molecular substructures ("Mass2Motifs") from spectra as sets of co-occurring molecular fragments and neutral losses. The analysis allows us to isolate molecular substructures, whose presence allows molecules to be grouped based on shared substructures regardless of classical spectral similarity. These substructures, in turn, support putative de novo structural annotation of molecules. Combining this spectral connectivity to orthogonal correlations (e.g., common abundance changes under system perturbation) significantly enhances our ability to provide mechanistic explanations for biological behavior.
Collapse
Affiliation(s)
- Justin Johan Jozias van der Hooft
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, United Kingdom
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Joe Wandy
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, United Kingdom
- School of Computing Science, University of Glasgow, Glasgow G12 8RZ, United Kingdom
| | - Michael P Barrett
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, United Kingdom
- Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, United Kingdom
| | - Karl E V Burgess
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, United Kingdom
| | - Simon Rogers
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, United Kingdom;
- School of Computing Science, University of Glasgow, Glasgow G12 8RZ, United Kingdom
| |
Collapse
|
149
|
Weidt S, Haggarty J, Kean R, Cojocariu CI, Silcock PJ, Rajendran R, Ramage G, Burgess KEV. A novel targeted/untargeted GC-Orbitrap metabolomics methodology applied to Candida albicans and Staphylococcus aureus biofilms. Metabolomics 2016; 12:189. [PMID: 28003796 PMCID: PMC5097782 DOI: 10.1007/s11306-016-1134-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 10/18/2016] [Indexed: 10/26/2022]
Abstract
INTRODUCTION Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus-hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality. Due to this tight association we hypothesised that metabolic effects were also in evidence. OBJECTIVES To explore the interaction, we used a novel GC-Orbitrap-based mass spectrometer, the Q Exactive GC, which combines the high peak capacity and chromatographic resolution of gas chromatography with the sub-ppm mass accuracy of an Orbitrap system. This allows the capability to leverage the widely available electron ionisation libraries for untargeted applications, along with expanding accurate mass libraries and targeted matches based around authentic standards. METHODS Optimised C. albicans and S. aureus mono- and co-cultured biofilms were analysed using the new instrument in addition to the fresh and spent bacterial growth media. RESULTS The targeted analysis experiment was based around 36 sugars and sugar phosphates, 22 amino acids and five organic acids. Untargeted analysis resulted in the detection of 465 features from fresh and spent medium and 405 from biofilm samples. Three significantly changing compounds that matched to high scoring library fragment patterns were chosen for validation. CONCLUSION Evaluation of the results demonstrates that the Q Exactive GC is suitable for metabolomics analysis using a targeted/untargeted methodology. Many of the results were as expected: e.g. rapid consumption of glucose and fructose from the medium regardless of the cell type. Modulation of sugar-phosphate levels also suggest that the pentose phosphate pathway could be enhanced in the cells from co-cultured biofilms. Untargeted metabolomics results suggested significant production of cell-wall biosynthesis components and the consumption of non-proteinaceous amino-acids.
Collapse
Affiliation(s)
- Stefan Weidt
- Polyomics, University of Glasgow, 211 Wolfson Wohl Translational Cancer Research Centre, Garscube Campus, Glasgow, G61 1QH UK
| | - Jennifer Haggarty
- Polyomics, University of Glasgow, 211 Wolfson Wohl Translational Cancer Research Centre, Garscube Campus, Glasgow, G61 1QH UK
| | - Ryan Kean
- Oral Sciences Research Group, Glasgow Dental School, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ranjith Rajendran
- Oral Sciences Research Group, Glasgow Dental School, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Gordon Ramage
- Oral Sciences Research Group, Glasgow Dental School, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Karl E. V. Burgess
- Polyomics, University of Glasgow, 211 Wolfson Wohl Translational Cancer Research Centre, Garscube Campus, Glasgow, G61 1QH UK
| |
Collapse
|
150
|
Metabolomics-Based Screening of the Malaria Box Reveals both Novel and Established Mechanisms of Action. Antimicrob Agents Chemother 2016; 60:6650-6663. [PMID: 27572396 DOI: 10.1128/aac.01226-16] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/16/2016] [Indexed: 12/22/2022] Open
Abstract
High-throughput phenotypic screening of chemical libraries has resulted in the identification of thousands of compounds with potent antimalarial activity, although in most cases, the mechanism(s) of action of these compounds remains unknown. Here we have investigated the mode of action of 90 antimalarial compounds derived from the Malaria Box collection using high-coverage, untargeted metabolomics analysis. Approximately half of the tested compounds induced significant metabolic perturbations in in vitro cultures of Plasmodium falciparum In most cases, the metabolic profiles were highly correlated with known antimalarials, in particular artemisinin, the 4-aminoquinolines, or atovaquone. Select Malaria Box compounds also induced changes in intermediates in essential metabolic pathways, such as isoprenoid biosynthesis (i.e., 2-C-methyl-d-erythritol 2,4-cyclodiphosphate) and linolenic acid metabolism (i.e., traumatic acid). This study provides a comprehensive database of the metabolic perturbations induced by chemically diverse inhibitors and highlights the utility of metabolomics for triaging new lead compounds and defining specific modes of action, which will assist with the development and optimization of new antimalarial drugs.
Collapse
|