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Löffler J, Noom A, Ellinghaus A, Dienelt A, Kempa S, Duda GN. A comprehensive molecular profiling approach reveals metabolic alterations that steer bone tissue regeneration. Commun Biol 2023; 6:327. [PMID: 36973478 PMCID: PMC10042875 DOI: 10.1038/s42003-023-04652-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 03/01/2023] [Indexed: 03/29/2023] Open
Abstract
Bone regeneration after fracture is a complex process with high and dynamic energy demands. The impact of metabolism on bone healing progression and outcome, however, is so far understudied. Our comprehensive molecular profiling reveals that central metabolic pathways, such as glycolysis and the citric acid cycle, are differentially activated between rats with successful or compromised bone regeneration (young versus aged female Sprague-Dawley rats) early in the inflammatory phase of bone healing. We also found that the citric acid cycle intermediate succinate mediates individual cellular responses and plays a central role in successful bone healing. Succinate induces IL-1β in macrophages, enhances vessel formation, increases mesenchymal stromal cell migration, and potentiates osteogenic differentiation and matrix formation in vitro. Taken together, metabolites-here particularly succinate-are shown to play central roles as signaling molecules during the onset of healing and in steering bone tissue regeneration.
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Affiliation(s)
- Julia Löffler
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 10115, Berlin, Germany
| | - Anne Noom
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Agnes Ellinghaus
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Anke Dienelt
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany
| | - Stefan Kempa
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 10115, Berlin, Germany.
| | - Georg N Duda
- Julius Wolff Institute (JWI), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany.
- BIH Center for Regenerative Therapies (BCRT), Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353, Berlin, Germany.
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Opialla T, Gollasch B, Kuich PHJL, Klug L, Rahn G, Busjahn A, Spuler S, Boschmann M, Kirwan JA, Luft FC, Kempa S. Exercise blood-drop metabolic profiling links metabolism with perceived exertion. Front Mol Biosci 2022; 9:1042231. [PMID: 36619172 PMCID: PMC9822726 DOI: 10.3389/fmolb.2022.1042231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background: Assessing detailed metabolism in exercising persons minute-to-minute has not been possible. We developed a "drop-of-blood" platform to fulfill that need. Our study aimed not only to demonstrate the utility of our methodology, but also to give insights into unknown mechanisms and new directions. Methods: We developed a platform, based on gas chromatography and mass spectrometry, to assess metabolism from a blood-drop. We first observed a single volunteer who ran 13 km in 60 min. We particularly monitored relative perceived exertion (RPE). We observed that 2,3-bisphosphoglycerate peaked at RPE in this subject. We next expanded these findings to women and men volunteers who performed an RPE-based exercise protocol to RPE at Fi O 2 20.9% or Fi O 2 14.5% in random order. Results: At 6 km, our subject reached his maximum relative perceived exertion (RPE); however, he continued running, felt better, and finished his run. Lactate levels had stably increased by 2 km, ketoacids increased gradually until the run's end, while the hypoxia marker, 2,3 bisphosphoglycerate, peaked at maximum relative perceived exertion. In our normal volunteers, the changes in lactate, pyruvate, ß hydroxybutyrate and a hydroxybutyrate were not identical, but similar to our model proband runner. Conclusion: Glucose availability was not the limiting factor, as glucose availability increased towards exercise end in highly exerted subjects. Instead, the tricarboxylic acid→oxphos pathway, lactate clearance, and thus and the oxidative capacity appeared to be the defining elements in confronting maximal exertion. These ideas must be tested further in more definitive studies. Our preliminary work suggests that our single-drop methodology could be of great utility in studying exercise physiology.
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Affiliation(s)
- Tobias Opialla
- Department of Proteomics and Metabolomics Max-Delbrück-Center for Molecular Medicine Berlin, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Muscle Research Unit, Experimental and Clinical Research Center, A Joint Collaboration Between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Benjamin Gollasch
- Experimental and Clinical Research Unit, Joint collaboration between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Peter H. J. L. Kuich
- Department of Proteomics and Metabolomics Max-Delbrück-Center for Molecular Medicine Berlin, Berlin Institute for Medical Systems Biology, Berlin, Germany
| | - Lars Klug
- Experimental and Clinical Research Unit, Joint collaboration between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriele Rahn
- Experimental and Clinical Research Unit, Joint collaboration between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Andreas Busjahn
- Experimental and Clinical Research Unit, Joint collaboration between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
- HealthTwiSt GmbH, Berlin, Germany
| | - Simone Spuler
- Muscle Research Unit, Experimental and Clinical Research Center, A Joint Collaboration Between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Boschmann
- Experimental and Clinical Research Unit, Joint collaboration between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jennifer A. Kirwan
- Berlin Institute of Health Metabolomics Platform, Charite Universitätsmedizin Berlin, Berlin, Germany
| | - Friedrich C. Luft
- Experimental and Clinical Research Unit, Joint collaboration between Max-Delbr ück-Center and Charité Universitätsmedizin Berlin, Berlin, Germany
- *Correspondence: Stefan Kempa, ; Friedrich C. Luft,
| | - Stefan Kempa
- Department of Proteomics and Metabolomics Max-Delbrück-Center for Molecular Medicine Berlin, Berlin Institute for Medical Systems Biology, Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, Charite Universitätsmedizin Berlin, Berlin, Germany
- *Correspondence: Stefan Kempa, ; Friedrich C. Luft,
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3
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Geisberger S, Bartolomaeus H, Neubert P, Willebrand R, Zasada C, Bartolomaeus T, McParland V, Swinnen D, Geuzens A, Maifeld A, Krampert L, Vogl M, Mähler A, Wilck N, Markó L, Tilic E, Forslund SK, Binger KJ, Stegbauer J, Dechend R, Kleinewietfeld M, Jantsch J, Kempa S, Müller DN. Salt Transiently Inhibits Mitochondrial Energetics in Mononuclear Phagocytes. Circulation 2021; 144:144-158. [PMID: 33906377 PMCID: PMC8270232 DOI: 10.1161/circulationaha.120.052788] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Supplemental Digital Content is available in the text. Background: Dietary high salt (HS) is a leading risk factor for mortality and morbidity. Serum sodium transiently increases postprandially but can also accumulate at sites of inflammation affecting differentiation and function of innate and adaptive immune cells. Here, we focus on how changes in extracellular sodium, mimicking alterations in the circulation and tissues, affect the early metabolic, transcriptional, and functional adaption of human and murine mononuclear phagocytes. Methods: Using Seahorse technology, pulsed stable isotope-resolved metabolomics, and enzyme activity assays, we characterize the central carbon metabolism and mitochondrial function of human and murine mononuclear phagocytes under HS in vitro. HS as well as pharmacological uncoupling of the electron transport chain under normal salt is used to analyze mitochondrial function on immune cell activation and function (as determined by Escherichiacoli killing and CD4+ T cell migration capacity). In 2 independent clinical studies, we analyze the effect of a HS diet during 2 weeks (URL: http://www.clinicaltrials.gov. Unique identifier: NCT02509962) and short-term salt challenge by a single meal (URL: http://www.clinicaltrials.gov. Unique identifier: NCT04175249) on mitochondrial function of human monocytes in vivo. Results: Extracellular sodium was taken up into the intracellular compartment, followed by the inhibition of mitochondrial respiration in murine and human macrophages. Mechanistically, HS reduces mitochondrial membrane potential, electron transport chain complex II activity, oxygen consumption, and ATP production independently of the polarization status of macrophages. Subsequently, cell activation is altered with improved bactericidal function in HS-treated M1-like macrophages and diminished CD4+ T cell migration in HS-treated M2-like macrophages. Pharmacological uncoupling of the electron transport chain under normal salt phenocopies HS-induced transcriptional changes and bactericidal function of human and murine mononuclear phagocytes. Clinically, also in vivo, rise in plasma sodium concentration within the physiological range reversibly reduces mitochondrial function in human monocytes. In both a 14-day and single meal HS challenge, healthy volunteers displayed a plasma sodium increase of and respectively, that correlated with decreased monocytic mitochondrial oxygen consumption. Conclusions: Our data identify the disturbance of mitochondrial respiration as the initial step by which HS mechanistically influences immune cell function. Although these functional changes might help to resolve bacterial infections, a shift toward proinflammation could accelerate inflammatory cardiovascular disease.
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Affiliation(s)
- Sabrina Geisberger
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Germany (S.G., C.Z., S.K.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Patrick Neubert
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, Germany (P.N., L.K., M.V., J.J.)
| | - Ralf Willebrand
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research, UHasselt, Campus Diepenbeek, Belgium (R.W., D.S., A.G., M.K.)
| | - Christin Zasada
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Germany (S.G., C.Z., S.K.)
| | | | - Victoria McParland
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Dries Swinnen
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research, UHasselt, Campus Diepenbeek, Belgium (R.W., D.S., A.G., M.K.)
| | - Anneleen Geuzens
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research, UHasselt, Campus Diepenbeek, Belgium (R.W., D.S., A.G., M.K.)
| | - András Maifeld
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Luka Krampert
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, Germany (P.N., L.K., M.V., J.J.)
| | - Marion Vogl
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, Germany (P.N., L.K., M.V., J.J.)
| | - Anja Mähler
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Nicola Wilck
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Germany (N.W.).,Department of Nephrology and Internal Intensive Care Medicine (N.W.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Lajos Markó
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Ekin Tilic
- Institute of Evolutionary Biology, University of Bonn, Germany (T.B., E.T.)
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
| | - Katrina J Binger
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia (K.J.B.)
| | - Johannes Stegbauer
- Department of Nephrology, Medical Faculty, University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Germany (J.S.)
| | - Ralf Dechend
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Department of Cardiology and Nephrology, HELIOS-Klinikum, Berlin, Germany (R.D.)
| | - Markus Kleinewietfeld
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research, UHasselt, Campus Diepenbeek, Belgium (R.W., D.S., A.G., M.K.)
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, Germany (P.N., L.K., M.V., J.J.)
| | - Stefan Kempa
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Germany (S.G., C.Z., S.K.)
| | - Dominik N Müller
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück-Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,German Center for Cardiovascular Research, partner site Berlin (S.G., H.B., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Germany (H.B., V.M., A. Maifeld, A. Mähler, L.M., S.K.F., R.D., D.N.M.).,Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (S.G., H.B., V.M., A. Maifeld, A. Mähler, N.W., L.M., S.K.F., R.D., D.N.M.)
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Opialla T, Kempa S, Pietzke M. Towards a More Reliable Identification of Isomeric Metabolites Using Pattern Guided Retention Validation. Metabolites 2020; 10:metabo10110457. [PMID: 33198249 PMCID: PMC7696895 DOI: 10.3390/metabo10110457] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/04/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023] Open
Abstract
Reliable analyte identification is critical in metabolomics experiments to ensure proper interpretation of data. Due to chemical similarity of metabolites (as isobars and isomers) identification by mass spectrometry or chromatography alone can be difficult. Here we show that isomeric compounds are quite common in the metabolic space as given in common metabolite databases. Further, we show that retention information can shift dramatically between different experiments decreasing the value of external or even in-house compound databases. As a consequence the retention information in compound databases should be updated regularly, to allow a reliable identification. To do so we present a feasible and budget conscious method to guarantee updates of retention information on a regular basis using well designed compound mixtures. For this we combine compounds in "Ident-Mixes", showing a way to distinctly identify chemically similar compounds through combinatorics and principle of exclusion. We illustrate the feasibility of this approach by comparing Gas chromatography (GC)-columns with identical properties from three different vendors and by creating a compound database from measuring these mixtures by Liquid chromatography-mass spectrometry (LC-MS). The results show the high influence of used materials on retention behavior and the ability of our approach to generate high quality identifications in a short time.
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5
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Nerve damage induced skeletal muscle atrophy is associated with increased accumulation of intramuscular glucose and polyol pathway intermediates. Sci Rep 2020; 10:1908. [PMID: 32024865 PMCID: PMC7002415 DOI: 10.1038/s41598-020-58213-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 12/23/2019] [Indexed: 01/21/2023] Open
Abstract
Perturbations in skeletal muscle metabolism have been reported for a variety of neuromuscular diseases. However, the role of metabolism after constriction injury to a nerve and the associated muscle atrophy is unclear. We have analyzed rat tibialis anterior (TA) four weeks after unilateral constriction injury to the sciatic nerve (DMG) and in the contralateral control leg (CTRL) (n = 7) to investigate changes of the metabolome, immunohistochemistry and protein levels. Untargeted metabolomics identified 79 polar metabolites, 27 of which were significantly altered in DMG compared to CTRL. Glucose concentrations were increased 2.6-fold in DMG, while glucose 6-phosphate (G6-P) was unchanged. Intermediates of the polyol pathway were increased in DMG, particularly fructose (1.7-fold). GLUT4 localization was scattered as opposed to clearly at the sarcolemma. Despite the altered localization, we found GLUT4 protein levels to be increased 7.8-fold while GLUT1 was decreased 1.7-fold in nerve damaged TA. PFK1 and GS levels were both decreased 2.1-fold, indicating an inability of glycolysis and glycogen synthesis to process glucose at sufficient rates. In conclusion, chronic nerve constriction causes increased GLUT4 levels in conjunction with decreased glycolytic activity and glycogen storage in skeletal muscle, resulting in accumulation of intramuscular glucose and polyol pathway intermediates.
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Müthel S, Uyar B, He M, Krause A, Vitrinel B, Bulut S, Vasiljevic D, Marchal I, Kempa S, Akalin A, Tursun B. The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans. Aging Cell 2019; 18:e13012. [PMID: 31397537 PMCID: PMC6826145 DOI: 10.1111/acel.13012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/27/2022] Open
Abstract
Whether extension of lifespan provides an extended time without health deteriorations is an important issue for human aging. However, to which degree lifespan and aspects of healthspan regulation might be linked is not well understood. Chromatin factors could be involved in linking both aging aspects, as epigenetic mechanisms bridge regulation of different biological processes. The epigenetic factor LIN‐53 (RBBP4/7) associates with different chromatin‐regulating complexes to safeguard cell identities in Caenorhabditis elegans as well as mammals, and has a role in preventing memory loss and premature aging in humans. We show that LIN‐53 interacts with the nucleosome remodeling and deacetylase (NuRD) complex in C. elegans muscles to ensure functional muscles during postembryonic development and in adults. While mutants for other NuRD members show a normal lifespan, animals lacking LIN‐53 die early because LIN‐53 depletion affects also the histone deacetylase complex Sin3, which is required for a normal lifespan. To determine why lin‐53 and sin‐3 mutants die early, we performed transcriptome and metabolomic analysis revealing that levels of the disaccharide trehalose are significantly decreased in both mutants. As trehalose is required for normal lifespan in C. elegans, lin‐53 and sin‐3 mutants could be rescued by either feeding with trehalose or increasing trehalose levels via the insulin/IGF1 signaling pathway. Overall, our findings suggest that LIN‐53 is required for maintaining lifespan and muscle integrity through discrete chromatin regulatory mechanisms. Since both LIN‐53 and its mammalian homologs safeguard cell identities, it is conceivable that its implication in lifespan regulation is also evolutionarily conserved.
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Affiliation(s)
- Stefanie Müthel
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Bora Uyar
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Mei He
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Anne Krause
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Burcu Vitrinel
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Selman Bulut
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Djordje Vasiljevic
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Iris Marchal
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Stefan Kempa
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Altuna Akalin
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
| | - Baris Tursun
- Berlin Institute of Medical Systems Biology Berlin Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association Berlin Germany
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7
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Borgsmüller N, Gloaguen Y, Opialla T, Blanc E, Sicard E, Royer AL, Le Bizec B, Durand S, Migné C, Pétéra M, Pujos-Guillot E, Giacomoni F, Guitton Y, Beule D, Kirwan J. WiPP: Workflow for Improved Peak Picking for Gas Chromatography-Mass Spectrometry (GC-MS) Data. Metabolites 2019; 9:metabo9090171. [PMID: 31438611 PMCID: PMC6780109 DOI: 10.3390/metabo9090171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 02/02/2023] Open
Abstract
Lack of reliable peak detection impedes automated analysis of large-scale gas chromatography-mass spectrometry (GC-MS) metabolomics datasets. Performance and outcome of individual peak-picking algorithms can differ widely depending on both algorithmic approach and parameters, as well as data acquisition method. Therefore, comparing and contrasting between algorithms is difficult. Here we present a workflow for improved peak picking (WiPP), a parameter optimising, multi-algorithm peak detection for GC-MS metabolomics. WiPP evaluates the quality of detected peaks using a machine learning-based classification scheme based on seven peak classes. The quality information returned by the classifier for each individual peak is merged with results from different peak detection algorithms to create one final high-quality peak set for immediate down-stream analysis. Medium- and low-quality peaks are kept for further inspection. By applying WiPP to standard compound mixes and a complex biological dataset, we demonstrate that peak detection is improved through the novel way to assign peak quality, an automated parameter optimisation, and results in integration across different embedded peak picking algorithms. Furthermore, our approach can provide an impartial performance comparison of different peak picking algorithms. WiPP is freely available on GitHub (https://github.com/bihealth/WiPP) under MIT licence.
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Affiliation(s)
- Nico Borgsmüller
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Yoann Gloaguen
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Tobias Opialla
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Eric Blanc
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Charité - Universitätsmedizin Berlin, 10178 Berlin, Germany
| | - Emilie Sicard
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Anne-Lise Royer
- LABERCA, Oniris, INRA, Université Bretagne - Loire, 44307 Nantes, France
| | - Bruno Le Bizec
- LABERCA, Oniris, INRA, Université Bretagne - Loire, 44307 Nantes, France
| | - Stéphanie Durand
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Carole Migné
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Mélanie Pétéra
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Estelle Pujos-Guillot
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Franck Giacomoni
- Université Clermont Auvergne, INRA, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, 63000 Clermont - Ferrand, France
| | - Yann Guitton
- LABERCA, Oniris, INRA, Université Bretagne - Loire, 44307 Nantes, France
| | - Dieter Beule
- Core Unit Bioinformatics, Berlin Institute of Health, 10178 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Charité - Universitätsmedizin Berlin, 10178 Berlin, Germany
| | - Jennifer Kirwan
- Berlin Institute of Health Metabolomics Platform, 10178 Berlin, Germany.
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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8
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Beale DJ, Pinu FR, Kouremenos KA, Poojary MM, Narayana VK, Boughton BA, Kanojia K, Dayalan S, Jones OAH, Dias DA. Review of recent developments in GC-MS approaches to metabolomics-based research. Metabolomics 2018; 14:152. [PMID: 30830421 DOI: 10.1007/s11306-018-1449-2] [Citation(s) in RCA: 242] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 11/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND Metabolomics aims to identify the changes in endogenous metabolites of biological systems in response to intrinsic and extrinsic factors. This is accomplished through untargeted, semi-targeted and targeted based approaches. Untargeted and semi-targeted methods are typically applied in hypothesis-generating investigations (aimed at measuring as many metabolites as possible), while targeted approaches analyze a relatively smaller subset of biochemically important and relevant metabolites. Regardless of approach, it is well recognized amongst the metabolomics community that gas chromatography-mass spectrometry (GC-MS) is one of the most efficient, reproducible and well used analytical platforms for metabolomics research. This is due to the robust, reproducible and selective nature of the technique, as well as the large number of well-established libraries of both commercial and 'in house' metabolite databases available. AIM OF REVIEW This review provides an overview of developments in GC-MS based metabolomics applications, with a focus on sample preparation and preservation techniques. A number of chemical derivatization (in-time, in-liner, offline and microwave assisted) techniques are also discussed. Electron impact ionization and a summary of alternate mass analyzers are highlighted, along with a number of recently reported new GC columns suited for metabolomics. Lastly, multidimensional GC-MS and its application in environmental and biomedical research is presented, along with the importance of bioinformatics. KEY SCIENTIFIC CONCEPTS OF REVIEW The purpose of this review is to both highlight and provide an update on GC-MS analytical techniques that are common in metabolomics studies. Specific emphasis is given to the key steps within the GC-MS workflow that those new to this field need to be aware of and the common pitfalls that should be looked out for when starting in this area.
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Affiliation(s)
- David J Beale
- Land and Water, Commonwealth Scientific & Industrial Research Organization (CSIRO), P.O. Box 2583, Brisbane, QLD, 4001, Australia.
| | - Farhana R Pinu
- The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland, 1142, New Zealand
| | - Konstantinos A Kouremenos
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
- Trajan Scientific and Medical, 7 Argent Pl, Ringwood, 3134, Australia
| | - Mahesha M Poojary
- Chemistry Section, School of Science and Technology, University of Camerino, via S. Agostino 1, 62032, Camerino, Italy
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958, Frederiksberg C, Denmark
| | - Vinod K Narayana
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Berin A Boughton
- Metabolomics Australia, School of BioSciences, The University of Melbourne, Parkville, 3010, Australia
| | - Komal Kanojia
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Saravanan Dayalan
- Metabolomics Australia, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, 3010, Australia
| | - Oliver A H Jones
- Australian Centre for Research on Separation Science (ACROSS), School of Science, RMIT University, GPO Box 2476, Melbourne, 3001, Australia
| | - Daniel A Dias
- School of Health and Biomedical Sciences, Discipline of Laboratory Medicine, RMIT University, PO Box 71, Bundoora, 3083, Australia.
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9
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Fritsche-Guenther R, Zasada C, Mastrobuoni G, Royla N, Rainer R, Roßner F, Pietzke M, Klipp E, Sers C, Kempa S. Alterations of mTOR signaling impact metabolic stress resistance in colorectal carcinomas with BRAF and KRAS mutations. Sci Rep 2018; 8:9204. [PMID: 29907857 PMCID: PMC6003911 DOI: 10.1038/s41598-018-27394-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/23/2018] [Indexed: 11/18/2022] Open
Abstract
Metabolic reprogramming is as a hallmark of cancer, and several studies have reported that BRAF and KRAS tumors may be accompanied by a deregulation of cellular metabolism. We investigated how BRAFV600E and KRASG12V affect cell metabolism, stress resistance and signaling in colorectal carcinoma cells driven by these mutations. KRASG12V expressing cells are characterized by the induction of glycolysis, accumulation of lactic acid and sensitivity to glycolytic inhibition. Notably mathematical modelling confirmed the critical role of MCT1 designating the survival of KRASG12V cells. Carcinoma cells harboring BRAFV600E remain resistant towards alterations of glucose supply or application of signaling or metabolic inhibitors. Altogether these data demonstrate that an oncogene-specific decoupling of mTOR from AMPK or AKT signaling accounts for alterations of resistance mechanisms and metabolic phenotypes. Indeed the inhibition of mTOR in BRAFV600E cells counteracts the metabolic predisposition and demonstrates mTOR as a potential target in BRAFV600E-driven colorectal carcinomas.
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Affiliation(s)
- Raphaela Fritsche-Guenther
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health (BIH), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Christin Zasada
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Guido Mastrobuoni
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Nadine Royla
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Robert-Roessle-Str. 10, 13125, Berlin, Germany
| | - Roman Rainer
- Humboldt University Berlin, Theoretical Biophysics, Invalidenstraße 42, 10115, Berlin, Germany
| | - Florian Roßner
- Charité Universitätsmedizin, Institute of Pathology, Chariteplatz 1, 10117, Berlin, Germany
| | - Matthias Pietzke
- Beatson Institute, Switchback Road, Bearsden, Glasgow, G61 1BD, United Kingdom
| | - Edda Klipp
- Charité Universitätsmedizin, Institute of Pathology, Chariteplatz 1, 10117, Berlin, Germany
| | - Christine Sers
- Charité Universitätsmedizin, Institute of Pathology, Chariteplatz 1, 10117, Berlin, Germany
| | - Stefan Kempa
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute of Health (BIH), Robert-Roessle-Str. 10, 13125, Berlin, Germany. .,Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Robert-Roessle-Str. 10, 13125, Berlin, Germany.
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10
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Mhlongo MI, Piater LA, Madala NE, Labuschagne N, Dubery IA. The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:112. [PMID: 29479360 PMCID: PMC5811519 DOI: 10.3389/fpls.2018.00112] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/22/2018] [Indexed: 05/21/2023]
Abstract
Plant roots communicate with microbes in a sophisticated manner through chemical communication within the rhizosphere, thereby leading to biofilm formation of beneficial microbes and, in the case of plant growth-promoting rhizomicrobes/-bacteria (PGPR), resulting in priming of defense, or induced resistance in the plant host. The knowledge of plant-plant and plant-microbe interactions have been greatly extended over recent years; however, the chemical communication leading to priming is far from being well understood. Furthermore, linkage between below- and above-ground plant physiological processes adds to the complexity. In metabolomics studies, the main aim is to profile and annotate all exo- and endo-metabolites in a biological system that drive and participate in physiological processes. Recent advances in this field has enabled researchers to analyze 100s of compounds in one sample over a short time period. Here, from a metabolomics viewpoint, we review the interactions within the rhizosphere and subsequent above-ground 'signalomics', and emphasize the contributions that mass spectrometric-based metabolomic approaches can bring to the study of plant-beneficial - and priming events.
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Affiliation(s)
- Msizi I. Mhlongo
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Ntakadzeni E. Madala
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
| | - Nico Labuschagne
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Johannesburg, South Africa
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11
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Wilck N, Matus MG, Kearney SM, Olesen SW, Forslund K, Bartolomaeus H, Haase S, Mähler A, Balogh A, Markó L, Vvedenskaya O, Kleiner FH, Tsvetkov D, Klug L, Costea PI, Sunagawa S, Maier L, Rakova N, Schatz V, Neubert P, Frätzer C, Krannich A, Gollasch M, Grohme DA, Côrte-Real BF, Gerlach RG, Basic M, Typas A, Wu C, Titze JM, Jantsch J, Boschmann M, Dechend R, Kleinewietfeld M, Kempa S, Bork P, Linker RA, Alm EJ, Müller DN. Salt-responsive gut commensal modulates T H17 axis and disease. Nature 2017; 551:585-589. [PMID: 29143823 PMCID: PMC6070150 DOI: 10.1038/nature24628] [Citation(s) in RCA: 797] [Impact Index Per Article: 113.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 10/10/2017] [Indexed: 12/12/2022]
Abstract
A Western lifestyle with high salt consumption can lead to hypertension and cardiovascular disease. High salt may additionally drive autoimmunity by inducing T helper 17 (TH17) cells, which can also contribute to hypertension. Induction of TH17 cells depends on gut microbiota; however, the effect of salt on the gut microbiome is unknown. Here we show that high salt intake affects the gut microbiome in mice, particularly by depleting Lactobacillus murinus. Consequently, treatment of mice with L. murinus prevented salt-induced aggravation of actively induced experimental autoimmune encephalomyelitis and salt-sensitive hypertension by modulating TH17 cells. In line with these findings, a moderate high-salt challenge in a pilot study in humans reduced intestinal survival of Lactobacillus spp., increased TH17 cells and increased blood pressure. Our results connect high salt intake to the gut-immune axis and highlight the gut microbiome as a potential therapeutic target to counteract salt-sensitive conditions.
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Affiliation(s)
- Nicola Wilck
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Mariana G Matus
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Sean M Kearney
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Scott W Olesen
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Kristoffer Forslund
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
| | - Stefanie Haase
- Department of Neurology, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Anja Mähler
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - András Balogh
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Lajos Markó
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Olga Vvedenskaya
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Integrative Proteomics and Metabolomics Platform, Berlin Institute for Medical Systems Biology BIMSB, 13125 Berlin, Germany
- Berlin School of Integrative Oncology, Charité University Medicine Berlin, Berlin, Germany
| | - Friedrich H Kleiner
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
| | - Dmitry Tsvetkov
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Lars Klug
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Paul I Costea
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Institute of Microbiology, ETH Zurich, 8092 Zurich, Switzerland
| | - Lisa Maier
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Natalia Rakova
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Department of Neurology, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Valentin Schatz
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Patrick Neubert
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | | | | | - Maik Gollasch
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Diana A Grohme
- Translational Immunology, Department of Clinical Pathobiochemistry, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Beatriz F Côrte-Real
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Campus Diepenbeek, 3590 Diepenbeek, Belgium
| | - Roman G Gerlach
- Project Group 5, Robert Koch Institute, 38855 Wernigerode, Germany
| | - Marijana Basic
- Hannover Medical School, Institute for Laboratory Animal Science and Central Animal Facility, 30625 Hannover, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA
| | - Jens M Titze
- Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Jonathan Jantsch
- Institute of Clinical Microbiology and Hygiene, University Hospital of Regensburg, University of Regensburg, 93053 Regensburg, Germany
| | - Michael Boschmann
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Ralf Dechend
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Markus Kleinewietfeld
- Translational Immunology, Department of Clinical Pathobiochemistry, Medical Faculty Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
- VIB Laboratory of Translational Immunomodulation, VIB Center for Inflammation Research (IRC), Hasselt University, Campus Diepenbeek, 3590 Diepenbeek, Belgium
- Center for Regenerative Therapies Dresden (CRTD), 01307 Dresden, Germany
| | - Stefan Kempa
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- Integrative Proteomics and Metabolomics Platform, Berlin Institute for Medical Systems Biology BIMSB, 13125 Berlin, Germany
| | - Peer Bork
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, 69120 Heidelberg, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Ralf A Linker
- Department of Neurology, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Eric J Alm
- Center for Microbiome Informatics and Therapeutics, and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Dominik N Müller
- Experimental and Clinical Research Center, a joint cooperation of Max-Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, 13125 Berlin, Germany
- Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
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12
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Perez de Souza L, Naake T, Tohge T, Fernie AR. From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. Gigascience 2017; 6:1-20. [PMID: 28520864 PMCID: PMC5499862 DOI: 10.1093/gigascience/gix037] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/08/2017] [Accepted: 05/12/2017] [Indexed: 01/19/2023] Open
Abstract
The grand challenge currently facing metabolomics is the expansion of the coverage of the metabolome from a minor percentage of the metabolic complement of the cell toward the level of coverage afforded by other post-genomic technologies such as transcriptomics and proteomics. In plants, this problem is exacerbated by the sheer diversity of chemicals that constitute the metabolome, with the number of metabolites in the plant kingdom generally considered to be in excess of 200 000. In this review, we focus on web resources that can be exploited in order to improve analyte and ultimately metabolite identification and quantification. There is a wide range of available software that not only aids in this but also in the related area of peak alignment; however, for the uninitiated, choosing which program to use is a daunting task. For this reason, we provide an overview of the pros and cons of the software as well as comments regarding the level of programing skills required to effectively exploit their basic functions. In addition, the torrent of available genome and transcriptome sequences that followed the advent of next-generation sequencing has opened up further valuable resources for metabolite identification. All things considered, we posit that only via a continued communal sharing of information such as that deposited in the databases described within the article are we likely to be able to make significant headway toward improving our coverage of the plant metabolome.
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Affiliation(s)
- Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Thomas Naake
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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13
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Varano G, Raffel S, Sormani M, Zanardi F, Lonardi S, Zasada C, Perucho L, Petrocelli V, Haake A, Lee AK, Bugatti M, Paul U, Van Anken E, Pasqualucci L, Rabadan R, Siebert R, Kempa S, Ponzoni M, Facchetti F, Rajewsky K, Casola S. The B-cell receptor controls fitness of MYC-driven lymphoma cells via GSK3β inhibition. Nature 2017; 546:302-306. [PMID: 28562582 DOI: 10.1038/nature22353] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 04/10/2017] [Indexed: 12/11/2022]
Abstract
Similar to resting mature B cells, where the B-cell antigen receptor (BCR) controls cellular survival, surface BCR expression is conserved in most mature B-cell lymphomas. The identification of activating BCR mutations and the growth disadvantage upon BCR knockdown of cells of certain lymphoma entities has led to the view that BCR signalling is required for tumour cell survival. Consequently, the BCR signalling machinery has become an established target in the therapy of B-cell malignancies. Here we study the effects of BCR ablation on MYC-driven mouse B-cell lymphomas and compare them with observations in human Burkitt lymphoma. Whereas BCR ablation does not, per se, significantly affect lymphoma growth, BCR-negative (BCR-) tumour cells rapidly disappear in the presence of their BCR-expressing (BCR+) counterparts in vitro and in vivo. This requires neither cellular contact nor factors released by BCR+ tumour cells. Instead, BCR loss induces the rewiring of central carbon metabolism, increasing the sensitivity of receptor-less lymphoma cells to nutrient restriction. The BCR attenuates glycogen synthase kinase 3 beta (GSK3β) activity to support MYC-controlled gene expression. BCR- tumour cells exhibit increased GSK3β activity and are rescued from their competitive growth disadvantage by GSK3β inhibition. BCR- lymphoma variants that restore competitive fitness normalize GSK3β activity after constitutive activation of the MAPK pathway, commonly through Ras mutations. Similarly, in Burkitt lymphoma, activating RAS mutations may propagate immunoglobulin-crippled tumour cells, which usually represent a minority of the tumour bulk. Thus, while BCR expression enhances lymphoma cell fitness, BCR-targeted therapies may profit from combinations with drugs targeting BCR- tumour cells.
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Affiliation(s)
- Gabriele Varano
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Simon Raffel
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, 69120 Heidelberg, Germany
| | - Martina Sormani
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Federica Zanardi
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | - Silvia Lonardi
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, Spedali Civili, 25123 Brescia, Italy
| | - Christin Zasada
- Max-Delbrück-Center of Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Laura Perucho
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
| | | | - Andrea Haake
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Albert K Lee
- Department of Systems Biology and Department of Biomedical Informatics, Columbia University, New York, New York 10027, USA
| | - Mattia Bugatti
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, Spedali Civili, 25123 Brescia, Italy
| | - Ulrike Paul
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105 Kiel, Germany
| | - Eelco Van Anken
- Division of Genetics and Cell Biology, San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Laura Pasqualucci
- Institute for Cancer Genetics and the Department of Pathology and Cell Biology, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| | - Raul Rabadan
- Department of Systems Biology and Department of Biomedical Informatics, Columbia University, New York, New York 10027, USA
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel, 24105 Kiel, Germany.,Institute of Human Genetics, University Hospital of Ulm, 89081 Ulm, Germany
| | - Stefan Kempa
- Max-Delbrück-Center of Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Maurilio Ponzoni
- Ateneo Vita Salute and San Raffaele Scientific Institute, Pathology and Lymphoid Malignancies Units, 20132 Milan, Italy
| | - Fabio Facchetti
- Department of Molecular and Translational Medicine, Section of Pathology, University of Brescia, Spedali Civili, 25123 Brescia, Italy
| | - Klaus Rajewsky
- Max-Delbrück-Center of Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Stefano Casola
- IFOM, the FIRC Institute of Molecular Oncology, 20139 Milan, Italy
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14
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Park TJ, Reznick J, Peterson BL, Blass G, Omerbašić D, Bennett NC, Kuich PHJL, Zasada C, Browe BM, Hamann W, Applegate DT, Radke MH, Kosten T, Lutermann H, Gavaghan V, Eigenbrod O, Bégay V, Amoroso VG, Govind V, Minshall RD, Smith ESJ, Larson J, Gotthardt M, Kempa S, Lewin GR. Fructose-driven glycolysis supports anoxia resistance in the naked mole-rat. Science 2017; 356:307-311. [DOI: 10.1126/science.aab3896] [Citation(s) in RCA: 404] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022]
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15
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Misra BB, van der Hooft JJJ. Updates in metabolomics tools and resources: 2014-2015. Electrophoresis 2015; 37:86-110. [DOI: 10.1002/elps.201500417] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Revised: 10/04/2015] [Accepted: 10/05/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Biswapriya B. Misra
- Department of Biology, Genetics Institute; University of Florida; Gainesville FL USA
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