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Mahmod II, Ismail IS, Normi YM, Chong SG. Protective effect of Clinacanthus nutans in cisplatin-induced nephrotoxicity on human kidney cell (PCS-400-010) elucidated by an LCMS-based metabolomics approach. Biomed Chromatogr 2023; 37:e5750. [PMID: 37778127 DOI: 10.1002/bmc.5750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023]
Abstract
Cisplatin-induced nephrotoxicity has been widely reported in numerous studies. The objective of this study is to assess the potential nephroprotective effects of Clinacanthus nutans (Burm. f.) Lindau (Acanthaceae) leaf extracts on human kidney cells (PCS-400-010) in vitro using an LCMS-based metabolomics approach. Orthogonal partial least square-discriminant analysis identified 16 significantly altered metabolites when comparing the control and pre-treated C. nutans cisplatin-induced groups. These metabolites were found to be associated with glycerophospholipid, purine, and amino acid metabolism, as well as the glycolysis pathway. Pre-treatment with C. nutans aqueous extract (125 μg/mL) for 24 h, followed by 48 h of cisplatin induction in PCS-400-010 cells, demonstrated a nephroprotective effect, particularly involving the regulation of amino acid metabolism.
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Affiliation(s)
- Ilya Iryani Mahmod
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Intan Safinar Ismail
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Siok-Geok Chong
- Natural Medicines and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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2
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Domingo-Ortí I, Ferrer-Torres P, Armiñán A, Vicent MJ, Pineda-Lucena A, Palomino-Schätzlein M. NMR-Based Mitochondria Metabolomic Profiling: A New Approach To Reveal Cancer-Associated Alterations. Anal Chem 2023; 95:16539-16548. [PMID: 37906730 DOI: 10.1021/acs.analchem.3c02432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Studying metabolism may assist in understanding the relationship between normal and dysfunctional mitochondrial activity and various diseases, such as neurodegenerative, cardiovascular, autoimmune, psychiatric, and cancer. Nuclear magnetic resonance-based metabolomics represents a powerful method to characterize the chemical content of complex samples and has been successfully applied to studying a range of conditions. However, an optimized methodology is lacking for analyzing isolated organelles, such as mitochondria. In this study, we report the development of a protocol to metabolically profile mitochondria from healthy, tumoral, and metastatic tissues. Encouragingly, this approach provided quantitative information about up to 45 metabolites in one comprehensive and robust analysis. Our results revealed significant differences between whole-cell and mitochondrial metabolites, which supports a more refined approach to metabolic analysis. We applied our optimized methodology to investigate aggressive and metastatic breast cancer in mouse tissues, discovering that lung mitochondria exhibit an altered metabolic fingerprint. Specific amino acids, organic acids, and lipids showed significant increases in levels when compared with mitochondria from healthy tissues. Our optimized methodology could promote a better understanding of the molecular mechanisms underlying breast cancer aggressiveness and mitochondrial-related diseases and support the optimization of new advanced therapies.
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Affiliation(s)
- Inés Domingo-Ortí
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Laboratory and CIBERONC, Valencia 46012, Spain
- NMR Facility, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain
| | | | - Ana Armiñán
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Laboratory and CIBERONC, Valencia 46012, Spain
| | - María J Vicent
- Centro de Investigación Príncipe Felipe, Polymer Therapeutics Laboratory and CIBERONC, Valencia 46012, Spain
| | - Antonio Pineda-Lucena
- Drug Discovery Unit, Instituto de Investigación Sanitaria La Fe, Valencia 46026, Spain
- Molecular Therapeutics Program, CIMA Universidad de Navarra, Pamplona 31008, Spain
| | - Martina Palomino-Schätzlein
- NMR Facility, Centro de Investigación Príncipe Felipe, Valencia 46012, Spain
- ProtoQSAR, CEEI, Parque Tecnológico Valencia, Paterna 46980, Spain
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3
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Cheredath A, Uppangala S, Jijo A, Lakshmi RV, Gowda GAN, Kalthur G, Adiga SK. Use of sensitivity-enhanced nuclear magnetic resonance spectroscopy equipped with a 1.7-mm cryogenically cooled micro-coil probe in identifying human sperm intracellular metabolites. Reprod Fertil Dev 2023; 35:661-668. [PMID: 37643634 DOI: 10.1071/rd22246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
CONTEXT The clinical value of human sperm metabolites has not been established due to the technical complexity in detecting these metabolites when sperm numbers are low. AIMS To detect endogenous intracellular metabolites in fresh and post-thaw human spermatozoa using 800MHz nuclear magnetic resonance (NMR) spectroscopy equipped with a 1.7-mm cryo-probe. METHODS Processed spermatozoa from 25 normozoospermic ejaculates were subjected to extraction of intracellular metabolites and then profiled by sensitivity-enhanced NMR spectroscopy equipped with a 1.7-mm cryogenically cooled micro-coil probe. In parallel, some of the processed sperm fractions were subjected to freeze-thawing and were then analysed for intracellular metabolites. KEY RESULTS Twenty-three metabolites were profiled from only 1.25million sperm cells. Comparison of the metabolomic signature of pre-freeze and post-thaw sperm cells did not show significant changes in the levels of metabolites. CONCLUSIONS Sensitivity-enhanced NMR spectroscopy equipped with a 1.7-mm cryogenically cooled micro-coil probe is a potential tool for identifying intracellular metabolites when sperm number is low. IMPLICATIONS Use of sensitivity-enhanced NMR spectroscopy opens up the opportunity to test for endogenous metabolites in samples with a limited number of spermatozoa, to understand the patho-physiology of infertility.
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Affiliation(s)
- Aswathi Cheredath
- Centre of Excellence in Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576 104, India
| | - Shubhashree Uppangala
- Division of Reproductive Genetics, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576 104, India
| | - Ameya Jijo
- Centre of Excellence in Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576 104, India
| | - R Vani Lakshmi
- Department of Data Science, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal 576 104, India
| | - G A Nagana Gowda
- Northwest Metabolomics Research Centre, Anaesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Guruprasad Kalthur
- Division of Reproductive Biology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576 104, India
| | - Satish Kumar Adiga
- Centre of Excellence in Clinical Embryology, Department of Reproductive Science, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal 576 104, India
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Rademaker G, Boumahd Y, Peiffer R, Anania S, Wissocq T, Liégeois M, Luis G, Sounni NE, Agirman F, Maloujahmoum N, De Tullio P, Thiry M, Bellahcène A, Castronovo V, Peulen O. Myoferlin targeting triggers mitophagy and primes ferroptosis in pancreatic cancer cells. Redox Biol 2022; 53:102324. [PMID: 35533575 PMCID: PMC9096673 DOI: 10.1016/j.redox.2022.102324] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/26/2022] [Accepted: 04/25/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- Gilles Rademaker
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Yasmine Boumahd
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium; Center for Interdisciplinary Research on Medicines (CIRM), Mitochondria Adaptation in Cancer Group, University of Liège, B-4000, Liège, Belgium
| | - Raphaël Peiffer
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium; Center for Interdisciplinary Research on Medicines (CIRM), Mitochondria Adaptation in Cancer Group, University of Liège, B-4000, Liège, Belgium
| | - Sandy Anania
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium; Center for Interdisciplinary Research on Medicines (CIRM), Mitochondria Adaptation in Cancer Group, University of Liège, B-4000, Liège, Belgium
| | - Tom Wissocq
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Maude Liégeois
- Laboratory of Cellular and Molecular Immunology, GIGA Institute, University of Liège, B-4000, Liège, Belgium
| | - Géraldine Luis
- Laboratory of Tumor and Development Biology, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Nor Eddine Sounni
- Laboratory of Tumor and Development Biology, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Ferman Agirman
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Naïma Maloujahmoum
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Pascal De Tullio
- Center for Interdisciplinary Research on Medicines (CIRM), Metabolomics Group, University of Liège, B-4000, Liège, Belgium
| | - Marc Thiry
- Laboratory of Cellular and Tissular Biology, GIGA-Neurosciences, Cell Biology L3, University of Liège, B-4000, Liège, Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-cancer, University of Liège, Pathology Institute B23, B-4000, Liège, Belgium; Center for Interdisciplinary Research on Medicines (CIRM), Mitochondria Adaptation in Cancer Group, University of Liège, B-4000, Liège, Belgium.
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Letertre MPM, Giraudeau P, de Tullio P. Nuclear Magnetic Resonance Spectroscopy in Clinical Metabolomics and Personalized Medicine: Current Challenges and Perspectives. Front Mol Biosci 2021; 8:698337. [PMID: 34616770 PMCID: PMC8488110 DOI: 10.3389/fmolb.2021.698337] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 12/12/2022] Open
Abstract
Personalized medicine is probably the most promising area being developed in modern medicine. This approach attempts to optimize the therapies and the patient care based on the individual patient characteristics. Its success highly depends on the way the characterization of the disease and its evolution, the patient’s classification, its follow-up and the treatment could be optimized. Thus, personalized medicine must combine innovative tools to measure, integrate and model data. Towards this goal, clinical metabolomics appears as ideally suited to obtain relevant information. Indeed, the metabolomics signature brings crucial insight to stratify patients according to their responses to a pathology and/or a treatment, to provide prognostic and diagnostic biomarkers, and to improve therapeutic outcomes. However, the translation of metabolomics from laboratory studies to clinical practice remains a subsequent challenge. Nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) are the two key platforms for the measurement of the metabolome. NMR has several advantages and features that are essential in clinical metabolomics. Indeed, NMR spectroscopy is inherently very robust, reproducible, unbiased, quantitative, informative at the structural molecular level, requires little sample preparation and reduced data processing. NMR is also well adapted to the measurement of large cohorts, to multi-sites and to longitudinal studies. This review focus on the potential of NMR in the context of clinical metabolomics and personalized medicine. Starting with the current status of NMR-based metabolomics at the clinical level and highlighting its strengths, weaknesses and challenges, this article also explores how, far from the initial “opposition” or “competition”, NMR and MS have been integrated and have demonstrated a great complementarity, in terms of sample classification and biomarker identification. Finally, a perspective discussion provides insight into the current methodological developments that could significantly raise NMR as a more resolutive, sensitive and accessible tool for clinical applications and point-of-care diagnosis. Thanks to these advances, NMR has a strong potential to join the other analytical tools currently used in clinical settings.
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Affiliation(s)
| | | | - Pascal de Tullio
- Metabolomics Group, Center for Interdisciplinary Research of Medicine (CIRM), Department of Pharmacy, Université de Liège, Liège, Belgique
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6
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Gómez-Archila LG, Palomino-Schätzlein M, Zapata-Builes W, Galeano E. Development of an optimized method for processing peripheral blood mononuclear cells for 1H-nuclear magnetic resonance-based metabolomic profiling. PLoS One 2021; 16:e0247668. [PMID: 33630921 PMCID: PMC7906414 DOI: 10.1371/journal.pone.0247668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 02/11/2021] [Indexed: 01/04/2023] Open
Abstract
Human peripheral blood mononuclear cells (PBMCs) are part of the innate and adaptive immune system, and form a critical interface between both systems. Studying the metabolic profile of PBMC could provide valuable information about the response to pathogens, toxins or cancer, the detection of drug toxicity, in drug discovery and cell replacement therapy. The primary purpose of this study was to develop an improved processing method for PBMCs metabolomic profiling with nuclear magnetic resonance (NMR) spectroscopy. To this end, an experimental design was applied to develop an alternative method to process PBMCs at low concentrations. The design included the isolation of PBMCs from the whole blood of four different volunteers, of whom 27 cell samples were processed by two different techniques for quenching and extraction of metabolites: a traditional one using organic solvents and an alternative one employing a high-intensity ultrasound probe, the latter with a variation that includes the use of deproteinizing filters. Finally, all the samples were characterized by 1H-NMR and the metabolomic profiles were compared by the method. As a result, two new methods for PBMCs processing, called Ultrasound Method (UM) and Ultrasound and Ultrafiltration Method (UUM), are described and compared to the Folch Method (FM), which is the standard protocol for extracting metabolites from cell samples. We found that UM and UUM were superior to FM in terms of sensitivity, processing time, spectrum quality, amount of identifiable, quantifiable metabolites and reproducibility.
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Affiliation(s)
- León Gabriel Gómez-Archila
- Grupo de Investigación en Sustancias Bioactivas, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia (UdeA), Medellín, Colombia
| | | | - Wildeman Zapata-Builes
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia (UdeA), Medellín, Colombia
- Grupo Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medelín, Colombia
| | - Elkin Galeano
- Grupo de Investigación en Sustancias Bioactivas, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia (UdeA), Medellín, Colombia
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7
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Mahmod II, Ismail IS, Alitheen NB, Normi YM, Abas F, Khatib A, Rudiyanto, Latip J. NMR and LCMS analytical platforms exhibited the nephroprotective effect of Clinacanthus nutans in cisplatin-induced nephrotoxicity in the in vitro condition. BMC Complement Med Ther 2020; 20:320. [PMID: 33092571 PMCID: PMC7579835 DOI: 10.1186/s12906-020-03067-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 09/01/2020] [Indexed: 12/29/2022] Open
Abstract
Background Clinacanthus nutans (C. nutans) Lind. locally known as Belalai Gajah or Sabah snake grass is a medicinal plant belonging to Acanthaceae family. In Asia, this plant is traditionally used for treating skin rashes, insects and snake bites, diabetes mellitus, fever and for diuretic effect. C. nutans has been reported to possess biological activities including anti-oxidant, anti-inflammation, anti-cancer, anti-diabetic and anti-viral activities. Methods Proton Nuclear Magnetic Resonance (1H NMR) and Liquid Chromatography Mass Spectroscopy (LCMS) coupled with multivariate data analysis were employed to characterize the metabolic variations of intracellular metabolites and the compositional changes of the corresponding culture media in rat renal proximal tubular cells (NRK-52E). Results NMR and LCMS analysis highlighted choline, creatine, phosphocholine, valine, acetic acid, phenylalanine, leucine, glutamic acid, threonine, uridine and proline as the main metabolites which differentiated the cisplatin-induced group of NRK-52E from control cells extract. The corresponding media exhibited lactic acid, glutamine, glutamic acid and glucose-1-phosphate as the varied metabolites. The altered pathways perturbed by cisplatin nephrotoxic on NRK-52E cells included changes in amino acid metabolism, lipid metabolism and glycolysis. Conclusion The C. nutans aqueous extract (1000 μg/mL) exhibited the most potential nephroprotective effect against cisplatin toxicity on NRK-52E cell lines at 89% of viability. The protective effect could be seen through the changes of the metabolites such as choline, alanine and valine in the C. nutans pre-treated samples with those of the cisplatin-induced group. Supplementary information Supplementary information accompanies this paper at 10.1186/s12906-020-03067-3.
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Affiliation(s)
- Ilya Iryani Mahmod
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Intan Safinar Ismail
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia. .,Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Noorjahan Banu Alitheen
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Faridah Abas
- Laboratory of Natural Products, Institute of Bioscience, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.,Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Alfi Khatib
- Faculty of Pharmacy, International Islamic University Malaysia, 25200, Kuantan, Pahang, Malaysia
| | - Rudiyanto
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Jalifah Latip
- School of Chemical Science and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bandar Baru Bangi, Selangor, Malaysia
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8
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The Budesonide-Hydroxypropyl-β-Cyclodextrin Complex Attenuates ROS Generation, IL-8 Release and Cell Death Induced by Oxidant and Inflammatory Stress. Study on A549 and A-THP-1 Cells. Molecules 2020; 25:molecules25214882. [PMID: 33105741 PMCID: PMC7660049 DOI: 10.3390/molecules25214882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/09/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
Synthetic glucocorticoids such as budesonide (BUD) are potent anti-inflammatory drugs commonly used to treat patients suffering from chronic inflammatory diseases. A previous animal study reported a higher anti-inflammatory activity with a 2-hydroxypropyl-β-cyclodextrin (HPβCD)-based formulation of BUD (BUD:HPβCD). This study investigated, on cellular models (A549 and A-THP-1), the effect of BUD:HPβD in comparison with BUD and HPβCD on the effects induced by oxidative and inflammatory stress as well as the role of cholesterol. We demonstrated the protective effect afforded by BUD:HPβCD against cytotoxicity and ROS generation induced by oxidative and inflammatory stress. The effect observed for BUD:HPβCD was comparable to that observed with HPβCD with no major effect of cholesterol content. We also demonstrated (i) the involvement of the canonical molecular pathway including ROS generation, a decrease in PI3K/Akt activation, and decrease in phosphorylated/unphosphorylated HDAC2 in the effect induced by BUD:HPβCD, (ii) the maintenance of IL-8 decrease with BUD:HPβCD, and (iii) the absence of improvement in glucocorticoid insensitivity with BUD:HPβCD in comparison with BUD, in conditions where HDAC2 was inhibited. Resulting from HPβCD antioxidant and anticytotoxic potential and protective capacity against ROS-induced PI3K/Akt signaling and HDAC2 inhibition, BUD:HPβCD might be more beneficial than BUD alone in a context of concomitant oxidative and inflammatory stress.
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9
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Lambert V, Hansen S, Schoumacher M, Lecomte J, Leenders J, Hubert P, Herfs M, Blacher S, Carnet O, Yip C, Blaise P, Duchateau E, Locht B, Thys M, Cavalier E, Gothot A, Govaerts B, Rakic JM, Noel A, de Tullio P. Pyruvate dehydrogenase kinase/lactate axis: a therapeutic target for neovascular age-related macular degeneration identified by metabolomics. J Mol Med (Berl) 2020; 98:1737-1751. [PMID: 33079232 DOI: 10.1007/s00109-020-01994-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 09/22/2020] [Accepted: 10/13/2020] [Indexed: 12/19/2022]
Abstract
Neovascular age-related macular degeneration (nAMD) is the leading cause of blindness in aging populations. Here, we applied metabolomics to human sera of patients with nAMD during an active (exudative) phase of the pathology and found higher lactate levels and a shift in the lipoprotein profile (increased VLDL-LDL/HDL ratio). Similar metabolomics changes were detected in the sera of mice subjected to laser-induced choroidal neovascularization (CNV). In this experimental model, we provide evidence for two sites of lactate production: first, a local one in the injured eye, and second a systemic site associated with the recruitment of bone marrow-derived inflammatory cells. Mechanistically, lactate promotes the angiogenic response and M2-like macrophage accumulation in the eyes. The therapeutic potential of our findings is demonstrated by the pharmacological control of lactate levels through pyruvate dehydrogenase kinase (PDK) inhibition by dichloroacetic acid (DCA). Mice treated with DCA exhibited normalized lactate levels and lipoprotein profiles, and inhibited CNV formation. Collectively, our findings implicate the key role of the PDK/lactate axis in AMD pathogenesis and reveal that the regulation of PDK activity has potential therapeutic value in this ocular disease. The results indicate that the lipoprotein profile is a traceable pattern that is worth considering for patient follow-up. KEY MESSAGES: Lactate and lipoprotein profile are associated with the active phase of AMD and CNV development. Lactate is a relevant and functional metabolite correlated with AMD progression. Modulating lactate through pyruvate dehydrogenase kinase led to a decrease of CNV progression. Pyruvate dehydrogenase kinase is a new therapeutic target for neovascular AMD.
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Affiliation(s)
- Vincent Lambert
- Department of Ophthalmology, University Hospital of Liège, Liège, Belgium.,Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Sylvain Hansen
- Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Matthieu Schoumacher
- Center for Interdisciplinary Research on Medicines, Metabolomics Group, Université de Liège, Liège, Belgium
| | - Julie Lecomte
- Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Justine Leenders
- Center for Interdisciplinary Research on Medicines, Metabolomics Group, Université de Liège, Liège, Belgium
| | - Pascale Hubert
- Laboratory of Experimental Pathology, GIGA, Université de Liège, avenue Hippocrate, Liège, Belgium
| | - Michael Herfs
- Laboratory of Experimental Pathology, GIGA, Université de Liège, avenue Hippocrate, Liège, Belgium
| | - Silvia Blacher
- Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Oriane Carnet
- Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Cassandre Yip
- Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Pierre Blaise
- Department of Ophthalmology, University Hospital of Liège, Liège, Belgium
| | - Edouard Duchateau
- Department of Ophthalmology, University Hospital of Liège, Liège, Belgium
| | - Bénédicte Locht
- Department of Ophthalmology, University Hospital of Liège, Liège, Belgium
| | - Michèle Thys
- Department of Ophthalmology, University Hospital of Liège, Liège, Belgium
| | - Etienne Cavalier
- Department of Medical Chemistry, University Hospital of Liège, Liège, Belgium
| | - André Gothot
- Department of Hematology and Immuno-Hematology, University Hospital of Liège, Liège, Belgium
| | - Bernadette Govaerts
- Institute of Statistics Biostatistics and Actuarial Sciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Jean-Marie Rakic
- Department of Ophthalmology, University Hospital of Liège, Liège, Belgium
| | - Agnès Noel
- Laboratory of Tumor and Development Biology, GIGA, Université de Liège, Liège, Belgium
| | - Pascal de Tullio
- Center for Interdisciplinary Research on Medicines, Metabolomics Group, Université de Liège, Liège, Belgium.
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10
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Mili M, Panthu B, Madec AM, Berger MA, Rautureau GJP, Elena-Herrmann B. Fast and ergonomic extraction of adherent mammalian cells for NMR-based metabolomics studies. Anal Bioanal Chem 2020; 412:5453-5463. [PMID: 32556564 DOI: 10.1007/s00216-020-02764-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/08/2020] [Accepted: 06/08/2020] [Indexed: 11/29/2022]
Abstract
Cellular metabolomics has become key to elucidate mechanistic aspects in various fields such as cancerology or pharmacology, and is rapidly becoming a standard phenotyping tool accessible to the broad biological community. Acquisition of reliable spectroscopic datasets, such as nuclear magnetic resonance (NMR) spectra, to characterize biological systems depends on the elaboration of robust methods for cellular metabolites extraction. Previous studies have addressed many issues raised by these protocols, however with little pondering on ergonomic and practical aspects of the methods that impact their scalability, reproducibility and hence their suitability to high-throughput studies or their use by non-metabolomics experts. Here, we optimize a fast and ergonomic protocol for extraction of metabolites from adherent mammalian cells for NMR metabolomics studies. The proposed extraction protocol, including cell washing, metabolism quenching and actual extraction of intracellular metabolites, was first optimized on HeLa cells. Efficiency of the protocol, in its globality and for the different individual steps, was assessed by NMR quantification of 27 metabolites from cellular extracts. We show that a single PBS wash provides a seemly compromise between contamination from growth medium and leakage of intracellular metabolites. In HeLa cells, extraction using pure methanol, without cell scraping, recovered a higher amount of intracellular metabolites than the reference methanol/water/chloroform method with cell scraping, with yields varying across metabolite classes. Optimized and reference protocols were further tested on eight cell lines of miscellaneous nature, and inter-operator reproducibility was demonstrated. Our results stress the need for tailored extraction protocols and show that fast protocols minimizing time-consuming steps, without compromising extraction yields, are suitable for high-throughput metabolomics studies. Graphical abstract.
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Affiliation(s)
- Manhal Mili
- Institut des Sciences Analytiques UMR 5280, CRMN FRE 2034, Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Baptiste Panthu
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Anne-Marie Madec
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Marie-Agnès Berger
- CarMeN laboratory, Univ Lyon, INSERM, INRA, INSA, Université Claude Bernard Lyon1, 69121, Oullins, France
| | - Gilles J P Rautureau
- Institut des Sciences Analytiques UMR 5280, CRMN FRE 2034, Univ Lyon, CNRS, Université Claude Bernard Lyon 1, ENS de Lyon, 5 rue de la Doua, 69100, Villeurbanne, France
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11
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Henglin M, Niiranen T, Watrous JD, Lagerborg KA, Antonelli J, Claggett BL, Demosthenes EJ, von Jeinsen B, Demler O, Vasan RS, Larson MG, Jain M, Cheng S. A Single Visualization Technique for Displaying Multiple Metabolite-Phenotype Associations. Metabolites 2019; 9:metabo9070128. [PMID: 31269707 PMCID: PMC6680673 DOI: 10.3390/metabo9070128] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/28/2019] [Accepted: 06/28/2019] [Indexed: 12/20/2022] Open
Abstract
To assist with management and interpretation of human metabolomics data, which are rapidly increasing in quantity and complexity, we need better visualization tools. Using a dataset of several hundred metabolite measures profiled in a cohort of ~1500 individuals sampled from a population-based community study, we performed association analyses with eight demographic and clinical traits and outcomes. We compared frequently used existing graphical approaches with a novel ‘rain plot’ approach to display the results of these analyses. The ‘rain plot’ combines features of a raindrop plot and a conventional heatmap to convey results of multiple association analyses. A rain plot can simultaneously indicate effect size, directionality, and statistical significance of associations between metabolites and several traits. This approach enables visual comparison features of all metabolites examined with a given trait. The rain plot extends prior approaches and offers complementary information for data interpretation. Additional work is needed in data visualizations for metabolomics to assist investigators in the process of understanding and convey large-scale analysis results effectively, feasibly, and practically.
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Affiliation(s)
- Mir Henglin
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Teemu Niiranen
- National Institute for Health and Welfare, FI 00271 Helsinki, Finland
- Department of Medicine, Turku University Hospital and University of Turku, FI 20521 Turku, Finland
| | - Jeramie D Watrous
- Departments of Medicine & Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Kim A Lagerborg
- Departments of Medicine & Pharmacology, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph Antonelli
- Department of Statistics, University of Florida, Gainesville, FL 32611, USA
| | - Brian L Claggett
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Emmanuella J Demosthenes
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | | | - Olga Demler
- Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, Framingham, MA 01701, USA
- Preventive Medicine, Department of Medicine, Boston University Medical Center, Boston, MA 02215, USA
| | - Martin G Larson
- Framingham Heart Study, Framingham, MA 01701, USA
- Preventive Medicine, Department of Medicine, Boston University Medical Center, Boston, MA 02215, USA
- Biostatistics Department, School of Public Health, Boston University, Boston, MA 02215, USA
| | - Mohit Jain
- Departments of Medicine & Pharmacology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Susan Cheng
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
- Framingham Heart Study, Framingham, MA 01701, USA.
- Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA.
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12
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Hvinden IC, Berg HE, Sachse D, Skaga E, Skottvoll FS, Lundanes E, Sandberg CJ, Vik-Mo EO, Rise F, Wilson SR. Nuclear Magnetic Resonance Spectroscopy to Identify Metabolite Biomarkers of Nonresponsiveness to Targeted Therapy in Glioblastoma Tumor Stem Cells. J Proteome Res 2019; 18:2012-2020. [PMID: 30964684 DOI: 10.1021/acs.jproteome.8b00801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Glioblastoma is the most common and malignant brain tumor, and current therapies confer only modest survival benefits. A major obstacle is our ability to monitor treatment effect on tumors. Current imaging modalities are ambiguous, and repeated biopsies are not encouraged. To scout for markers of treatment response, we used NMR spectroscopy to study the effects of a survivin inhibitor on the metabolome of primary glioblastoma cancer stem cells. Applying high resolution NMR spectroscopy (1H resonance frequency: 800.03 MHz) to just 3 million cells per sample, we achieved sensitive and high resolving determinations of, e.g., amino acids, nucleosides, and constituents of the citric acid cycle. For control samples that were cultured, prepared, and measured at varying dates, peak area relative standard deviations were 15-20%. Analyses of unfractionated lysates were performed for straightforward compound identification with COLMAR and HMDB databases. Principal component analysis revealed that citrate levels were clearly upregulated in nonresponsive cells, while lactate levels substantially decreased following treatment for both responsive and nonresponsive cells. Hence, lactate and citrate may be potential markers of successful drug uptake and poor response to survivin inhibitors, respectively. Our metabolomics approach provided alternative biomarker candidates compared to spectrometry-based proteomics, underlining benefits of complementary methodologies. These initial findings make a foundation for exploring in vivo MR spectroscopy (MRS) of brain tumors, as citrate and lactate are MRS-visible. In sum, NMR metabolomics is a tool for addressing glioblastoma.
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Affiliation(s)
- Ingvild Comfort Hvinden
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway.,Department of Chemistry , Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Henriette Engen Berg
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway
| | - Daniel Sachse
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway
| | - Erlend Skaga
- Vilhelm Magnus Laboratory of Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery , Oslo University Hospital , 4950 Nydalen NO-0424 , Oslo , Norway.,Institute of Clinical Medicine, Faculty of Medicine , University of Oslo , Post Box 1171, Blindern NO-0318 , Oslo , Norway
| | - Frøydis Sved Skottvoll
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway.,Hybrid Technology Hub, Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , PO Box 1112, Blindern NO-0317 , Oslo , Norway
| | - Elsa Lundanes
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway
| | - Cecilie J Sandberg
- Vilhelm Magnus Laboratory of Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery , Oslo University Hospital , 4950 Nydalen NO-0424 , Oslo , Norway
| | - Einar O Vik-Mo
- Vilhelm Magnus Laboratory of Neurosurgical Research, Institute for Surgical Research and Department of Neurosurgery , Oslo University Hospital , 4950 Nydalen NO-0424 , Oslo , Norway
| | - Frode Rise
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway
| | - Steven Ray Wilson
- Department of Chemistry , University of Oslo , Post Box 1033, Blindern NO-0315 , Oslo , Norway.,Hybrid Technology Hub, Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine , University of Oslo , PO Box 1112, Blindern NO-0317 , Oslo , Norway
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13
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Hayton S, Maker GL, Mullaney I, Trengove RD. Experimental design and reporting standards for metabolomics studies of mammalian cell lines. Cell Mol Life Sci 2017; 74:4421-4441. [PMID: 28669031 PMCID: PMC11107723 DOI: 10.1007/s00018-017-2582-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/21/2017] [Accepted: 06/26/2017] [Indexed: 02/07/2023]
Abstract
Metabolomics is an analytical technique that investigates the small biochemical molecules present within a biological sample isolated from a plant, animal, or cultured cells. It can be an extremely powerful tool in elucidating the specific metabolic changes within a biological system in response to an environmental challenge such as disease, infection, drugs, or toxins. A historically difficult step in the metabolomics pipeline is in data interpretation to a meaningful biological context, for such high-variability biological samples and in untargeted metabolomics studies that are hypothesis-generating by design. One way to achieve stronger biological context of metabolomic data is via the use of cultured cell models, particularly for mammalian biological systems. The benefits of in vitro metabolomics include a much greater control of external variables and no ethical concerns. The current concerns are with inconsistencies in experimental procedures and level of reporting standards between different studies. This review discusses some of these discrepancies between recent studies, such as metabolite extraction and data normalisation. The aim of this review is to highlight the importance of a standardised experimental approach to any cultured cell metabolomics study and suggests an example procedure fully inclusive of information that should be disclosed in regard to the cell type/s used and their culture conditions. Metabolomics of cultured cells has the potential to uncover previously unknown information about cell biology, functions and response mechanisms, and so the accurate biological interpretation of the data produced and its ability to be compared to other studies should be considered vitally important.
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Affiliation(s)
- Sarah Hayton
- Separation Sciences and Metabolomics Laboratories, Murdoch University, Perth, WA, Australia
- School of Veterinary and Life Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Garth L Maker
- Separation Sciences and Metabolomics Laboratories, Murdoch University, Perth, WA, Australia.
- School of Veterinary and Life Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia.
| | - Ian Mullaney
- School of Veterinary and Life Sciences, Murdoch University, 90 South St, Murdoch, WA, 6150, Australia
| | - Robert D Trengove
- Separation Sciences and Metabolomics Laboratories, Murdoch University, Perth, WA, Australia
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14
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Gehrke S, Reisz JA, Nemkov T, Hansen KC, D’Alessandro A. Characterization of rapid extraction protocols for high-throughput metabolomics. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:1445-1452. [PMID: 28586533 PMCID: PMC5547002 DOI: 10.1002/rcm.7916] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 05/29/2017] [Accepted: 06/01/2017] [Indexed: 06/07/2023]
Abstract
RATIONALE In the last five years, high-throughput metabolomics has significantly advanced scientific research and holds the potential to promote strides in the fields of clinical metabolomics and personalized medicine. While innovations in the field of flow-injection mass spectrometry and three-minute metabolomics methods now allow investigators to process hundreds to thousands of samples per day, time-sensitive clinical applications, particularly in the emergency department, are limited by a lack of rapid extraction methods. METHODS Here we characterized the efficacy of fast liquid-liquid extractions for characterization of hydrophilic compounds through ultra-high-pressure liquid chromatography/mass spectrometry. Internal stable-isotope-labeled standards were used to quantitatively characterize markers of energy and oxidative metabolism in human whole blood, plasma and red blood cells - three common matrices of clinical relevance. RESULTS For all the tested matrices, vortexing time (4-60 min) did not significantly affect extraction yields for the tested hydrophilic metabolites. Coefficients of variations <<20% for all tested compounds, except for the redox-sensitive metabolite cystine (accumulating over time). Internal standards and second extractions confirmed recoveries >80% for all tested metabolites, except for basic amino acids and polyamines, which showed reproducible yields ranging from 50 to 75%. Global profiling and absolute quantitation of 24 metabolites revealed similarities between the plasma and red blood cell metabolomes. CONCLUSIONS Rapid extraction (~4 min) of hydrophilic compounds is a viable and potentially automatable strategy to perform quantitative analysis of whole blood, plasma and red blood cells for research or clinical applications.
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Affiliation(s)
- Sarah Gehrke
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Julie A. Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
| | - Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver – Anschutz Medical Campus, 12801 East 17 Ave, Aurora, CO, 80045 USA
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15
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Ennis K, Lusczek E, Rao R. Characterization of the concurrent metabolic changes in brain and plasma during insulin-induced moderate hypoglycemia using 1H NMR spectroscopy in juvenile rats. Neurosci Lett 2017. [PMID: 28627374 DOI: 10.1016/j.neulet.2017.06.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Treatment of hypoglycemia in children is currently based on plasma glucose measurements. This approach may not ensure neuroprotection since plasma glucose does not reflect the dynamic state of cerebral energy metabolism. To determine whether cerebral metabolic changes during hypoglycemia could be better characterized using plasma metabolomic analysis, insulin-induced acute hypoglycemia was induced in 4-week-old rats. Brain tissue and concurrent plasma samples were collected from hypoglycemic (N=7) and control (N=7) rats after focused microwave fixation to prevent post-mortem metabolic changes. The concentration of 29 metabolites in brain and 34 metabolites in plasma were determined using 1H NMR spectroscopy at 700MHz and examined using partial least squares-discriminant analysis. The sensitivity of plasma glucose for detecting cerebral energy failure was assessed by determining its relationship to brain phosphocreatine. The brain and plasma metabolite profiles of the hypoglycemia group were distinct from the control group (brain: R2=0.92, Q2=0.31; plasma: R2=0.95, Q2=0.74). Concentration differences in glucose, ketone bodies and amino acids were responsible for the intergroup separation. There was 45% concordance between the brain and plasma metabolite profiles. Brain phosphocreatine correlated with brain glucose (control group: R2=0.86; hypoglycemia group: R2=0.59; p<0.05), but not with plasma glucose. The results confirm that plasma glucose is an insensitive biomarker of cerebral energy changes during hypoglycemia and suggest that a plasma metabolite profile is superior for monitoring cerebral metabolism.
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Affiliation(s)
- Kathleen Ennis
- Division of Neonatology, Department of Pediatrics, University of Minnesota, Mayo Mail Code 39, 420 Delaware Street, SE, Minneapolis, MN 55455, USA.
| | - Elizabeth Lusczek
- Department of Surgery, University of Minnesota, Mayo Mail Code 195, 420 Delaware Street, SE, Minneapolis, MN 55455, USA.
| | - Raghavendra Rao
- Division of Neonatology, Department of Pediatrics, University of Minnesota, Mayo Mail Code 39, 420 Delaware Street, SE, Minneapolis, MN 55455, USA; Center for Neurobehavioral Development, University of Minnesota, Mayo Mail Code 39, 420 Delaware Street, SE, Minneapolis, MN 55455, USA.
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16
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Blomme A, Costanza B, de Tullio P, Thiry M, Van Simaeys G, Boutry S, Doumont G, Di Valentin E, Hirano T, Yokobori T, Gofflot S, Peulen O, Bellahcène A, Sherer F, Le Goff C, Cavalier E, Mouithys-Mickalad A, Jouret F, Cusumano PG, Lifrange E, Muller RN, Goldman S, Delvenne P, De Pauw E, Nishiyama M, Castronovo V, Turtoi A. Myoferlin regulates cellular lipid metabolism and promotes metastases in triple-negative breast cancer. Oncogene 2016; 36:2116-2130. [DOI: 10.1038/onc.2016.369] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/30/2016] [Accepted: 08/28/2016] [Indexed: 02/07/2023]
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17
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Dowood RK, Adusumalli R, Tykesson E, Johnsen E, Lundanes E, Prydz K, Wilson SR. Determination of 3'-phosphoadenosine-5'-phosphosulfate in cells and Golgi fractions using hydrophilic interaction liquid chromatography-mass spectrometry. J Chromatogr A 2016; 1470:70-75. [PMID: 27720175 DOI: 10.1016/j.chroma.2016.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/29/2016] [Accepted: 10/02/2016] [Indexed: 11/28/2022]
Abstract
3'-Phosphoadenosine-5'-phosphosulfate (PAPS) is a key player in the sulfation of biomolecules, but methods for selective measurements are lacking. A liquid chromatography-mass spectrometry (LC-MS) approach for measuring PAPS was developed. A central feature of the method was employing hydrophilic interaction liquid chromatography (HILIC), which is highly suited for separating very polar/charged compounds, and is compatible with electrospray MS. Using simple instrumentation, the analysis time per sample was below 10min and the method was characterized by easy sample preparation. The method was used to monitor decreasing levels of PAPS as function of sodium chlorate treatment (an inhibitor of PAPS synthesis) in whole-cell lysates as well as Golgi-fractions. The method allowed PAPS to be chromatographically separated from ADP and ATP, which can interfere with measurements if a less resolving LC-MS method is used.
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Affiliation(s)
- Rua Kareem Dowood
- Department of Chemistry, University of Oslo, Post Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Ravi Adusumalli
- Department of Biosciences, University of Oslo, Post Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Emil Tykesson
- Department of Experimental Medical Science, Lund University, Box 117, 221 00, Lund, Sweden
| | - Elin Johnsen
- Department of Chemistry, University of Oslo, Post Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Post Box 1033, Blindern, NO-0315 Oslo, Norway
| | - Kristian Prydz
- Department of Biosciences, University of Oslo, Post Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Steven Ray Wilson
- Department of Chemistry, University of Oslo, Post Box 1033, Blindern, NO-0315 Oslo, Norway.
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18
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Fontana F, Ge X, Su X, Hathi D, Xiang J, Cenci S, Civitelli R, Shoghi KI, Akers WJ, D'avignon A, Weilbaecher KN, Shokeen M. Evaluating Acetate Metabolism for Imaging and Targeting in Multiple Myeloma. Clin Cancer Res 2016; 23:416-429. [PMID: 27486177 DOI: 10.1158/1078-0432.ccr-15-2134] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 11/16/2022]
Abstract
PURPOSE We hypothesized that in multiple myeloma cells (MMC), high membrane biosynthesis will induce acetate uptake in vitro and in vivo Here, we studied acetate metabolism and targeting in MMC in vitro and tested the efficacy of 11C-acetate-positron emission tomography (PET) to detect and quantitatively image myeloma treatment response in vivo EXPERIMENTAL DESIGN: Acetate fate tracking using 13C-edited-1H NMR (nuclear magnetic resonance) was performed to study in vitro acetate uptake and metabolism in MMC. Effects of pharmacological modulation of acetate transport or acetate incorporation into lipids on MMC cell survival and viability were assessed. Preclinical mouse MM models of subcutaneous and bone tumors were evaluated using 11C-acetate-PET/CT imaging and tissue biodistribution. RESULTS In vitro, NMR showed significant uptake of acetate by MMC and acetate incorporation into intracellular metabolites and membrane lipids. Inhibition of lipid synthesis and acetate transport was toxic to MMC, while sparing resident bone cells or normal B cells. In vivo, 11C-acetate uptake by PET imaging was significantly enhanced in subcutaneous and bone MMC tumors compared with unaffected bone or muscle tissue. Likewise, 11C-acetate uptake was significantly reduced in MM tumors after treatment. CONCLUSIONS Uptake of acetate from the extracellular environment was enhanced in MMC and was critical to cellular viability. 11C-Acetate-PET detected the presence of myeloma cells in vivo, including uptake in intramedullary bone disease. 11C-Acetate-PET also detected response to therapy in vivo Our data suggested that acetate metabolism and incorporation into lipids was crucial to MM cell biology and that 11C-acetate-PET is a promising imaging modality for MM. Clin Cancer Res; 23(2); 416-29. ©2016 AACR.
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Affiliation(s)
- Francesca Fontana
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Xia Ge
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Xinming Su
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Deep Hathi
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Jingyu Xiang
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Simone Cenci
- San Raffaele Scientific Institute (SRSI), Division of Genetics and Cell Biology, and Università Vita-Salute San Raffaele, Milano, Italy
| | - Roberto Civitelli
- Department of Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, Missouri
| | - Kooresh I Shoghi
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Walter J Akers
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Andre D'avignon
- Department of Chemistry, Washington University, St. Louis, Missouri
| | - Katherine N Weilbaecher
- Department of Medicine, Division of Molecular Oncology, Washington University School of Medicine, St. Louis, Missouri.
| | - Monica Shokeen
- Department of Radiology, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri.
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19
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Frédérich M, Pirotte B, Fillet M, de Tullio P. Metabolomics as a Challenging Approach for Medicinal Chemistry and Personalized Medicine. J Med Chem 2016; 59:8649-8666. [PMID: 27295417 DOI: 10.1021/acs.jmedchem.5b01335] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
"Omics" sciences have been developed to provide a holistic point of view of biology and to better understand the complexity of an organism as a whole. These systems biology approaches can be examined at different levels, starting from the most fundamental, i.e., the genome, and finishing with the most functional, i.e., the metabolome. Similar to how genomics is applied to the exploration of DNA, metabolomics is the qualitative and quantitative study of metabolites. This emerging field is clearly linked to genomics, transcriptomics, and proteomics. In addition, metabolomics provides a unique and direct vision of the functional outcome of an organism's activities that are required for it to survive, grow, and respond to internal and external stimuli or stress, e.g., pathologies and drugs. The links between metabolic changes, patient phenotype, physiological and/or pathological status, and treatment are now well established and have opened a new area for the application of metabolomics in the drug discovery process and in personalized medicine.
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Affiliation(s)
- Michel Frédérich
- Laboratory of Pharmacognosy, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Bernard Pirotte
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Marianne Fillet
- Laboratory for the Analysis of Medicines, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
| | - Pascal de Tullio
- Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege , Quartier Hôpital, Avenue Hippocrate 15, B-4000 Liege, Belgium
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20
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Wang H, Xu J, Chen Y, Zhang R, He J, Wang Z, Zang Q, Wei J, Song X, Abliz Z. Optimization and Evaluation Strategy of Esophageal Tissue Preparation Protocols for Metabolomics by LC–MS. Anal Chem 2016; 88:3459-64. [DOI: 10.1021/acs.analchem.5b04709] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Huiqing Wang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jing Xu
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Yanhua Chen
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Ruiping Zhang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jiuming He
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Zhonghua Wang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Qingce Zang
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Jinfeng Wei
- New
Drug Safety Evaluation Center, Institute of Materia Medica, Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Xiaowei Song
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
| | - Zeper Abliz
- State
Key Laboratory of Bioactive Substance and Function of Natural Medicines,
Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, People’s Republic of China
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21
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Nuclear magnetic resonance: a key metabolomics platform in the drug discovery process. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 13:39-46. [PMID: 26190682 DOI: 10.1016/j.ddtec.2015.06.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 06/02/2015] [Accepted: 06/17/2015] [Indexed: 12/11/2022]
Abstract
Metabolomics is an innovative tool that is now emerging in the drug discovery process. Indeed, its ability to follow the dynamic perturbations in the metabolome resulting from pathologies but also from drug treatment and or/toxicity is of value for the development of new therapeutic approaches. Nuclear magnetic resonance (NMR) spectroscopy, which is an important analytical technique for several steps of the lead discovery, validation and optimization processes, has been described, together with mass spectrometry (MS) as one of the major platform that could be used for metabolomics studies. This review highlights why NMR could be considered a key tool for the application of metabolomics in drug discovery.
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Ulmer CZ, Yost RA, Chen J, Mathews CE, Garrett TJ. Liquid Chromatography-Mass Spectrometry Metabolic and Lipidomic Sample Preparation Workflow for Suspension-Cultured Mammalian Cells using Jurkat T lymphocyte Cells. ACTA ACUST UNITED AC 2015; 8:126-132. [PMID: 26401069 DOI: 10.4172/jpb.1000360] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Metabolomics is the comprehensive study of metabolism as it pertains to an organism or biological system. Lipidomics, a subset discipline of metabolomics, encompasses the study of cellular lipid functions: including pathways, networks, and interactions. The abundance of metabolites and lipids, along with their contribution to health and disease, makes metabolomics a valuable tool for biomarker research. Disease biomarker identification requires a reproducible, sensitive, and accurate analytical platform. Although transcriptomic and proteomic areas have well-established protocols for sample preparation and data processing, the metabolomics field is still developing comparable standardized conventions. Furthermore, of the few comparative LC-MS metabolomic studies that have been applied to mammalian cell cultures, most are targeted to adherent cell lines. The purpose of this work was to optimize a sample preparation workflow for the cellular metabolomic analysis of suspension-cultured mammalian cells using commercially available Jurkat T lymphocytes as a model system. The current investigation evaluated commonly used sample preparation techniques for reproducibility, accuracy, and applicability to untargeted biomarker discovery. Results show ammoniated cell rinsing solutions to be an effective means to remove extracellular components present in the media without causing ion suppression or affecting the integrity of the cellular membrane. Additionally, a novel workflow was designed to allow for the combined analysis of metabolites and lipids from mammalian suspension cells from a single cell pellet. The Folch lipid extraction protocol was coupled to an 80% MeOH metabolite isolation to ensure high extraction efficiency for phospholipids and triacylglycerides. While the workflow was tailored to cells in suspension, it could also be applied to adherent cell lines.
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Affiliation(s)
- Candice Z Ulmer
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | - Richard A Yost
- Department of Chemistry, University of Florida, Gainesville, FL, USA ; Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL, USA
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Larive CK, Barding GA, Dinges MM. NMR spectroscopy for metabolomics and metabolic profiling. Anal Chem 2014; 87:133-46. [PMID: 25375201 DOI: 10.1021/ac504075g] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Cynthia K Larive
- Department of Chemistry, University of California-Riverside , Riverside, California 92521, United States
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