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Redox Regulation and Metabolic Dependency of Zika Virus Replication: Inhibition by Nrf2-Antioxidant Response and NAD(H) Antimetabolites. J Virol 2023; 97:e0136322. [PMID: 36688653 PMCID: PMC9972919 DOI: 10.1128/jvi.01363-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Viral infections alter host cell metabolism and homeostasis; however, the mechanisms that regulate these processes have only begun to be elucidated. We report here that Zika virus (ZIKV) infection activates the antioxidant nuclear factor erythroid 2-related factor 2 (Nrf2), which precedes oxidative stress. Downregulation of Nrf2 or inhibition of glutathione (GSH) synthesis resulted in significantly increased viral replication. Interestingly, 6-amino-nicotinamide (6-AN), a nicotinamide analog commonly used as an inhibitor of the pentose phosphate pathway (PPP), decreased viral replication by over 1,000-fold. This inhibition was neither recapitulated by the knockdown of PPP enzymes, glucose 6-phosphate dehydrogenase (G6PD), or 6-phosphogluconate dehydrogenase (6PGD), nor prevented by supplementation with ribose 5-phosphate. Instead, our metabolomics and metabolic phenotype studies support a mechanism in which 6-AN depletes cells of NAD(H) and impairs NAD(H)-dependent glycolytic steps resulting in inhibition of viral replication. The inhibitory effect of 6-AN was rescued with precursors of the salvage pathway but not with those of other NAD+ biosynthesis pathways. Inhibition of glycolysis reduced viral protein levels, which were recovered transiently. This transient recovery in viral protein synthesis was prevented when oxidative metabolism was inhibited by blockage of the mitochondrial pyruvate carrier, fatty acid oxidation, or glutaminolysis, demonstrating a compensatory role of mitochondrial metabolism in ZIKV replication. These results establish an antagonistic role for the host cell Nrf2/GSH/NADPH-dependent antioxidant response against ZIKV and demonstrate the dependency of ZIKV replication on NAD(H). Importantly, our work suggests the potential use of NAD(H) antimetabolite therapy against the viral infection. IMPORTANCE Zika virus (ZIKV) is a major public health concern of international proportions. While the incidence of ZIKV infections has declined substantially in recent years, the potential for the reemergence or reintroduction remains high. Although viral infection alters host cell metabolism and homeostasis to promote its replication, deciphering the mechanism(s) involved in these processes is important for identifying therapeutic targets. The present work reveals the complexities of host cell redox regulation and metabolic dependency of ZIKV replication. An antagonistic effect of the Nrf2/GSH/NADP(H)-dependent antioxidant response against ZIKV infection and an essential role of NAD(H) metabolism and glycolysis for viral replication are established for the first time. These findings highlight the potential use of NAD(H) antimetabolites to counter ZIKV infection and pathogenesis.
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Saborano R, Shepherd E, Günther UL, Lalor PF. Tracer-Based Metabolic Analysis by NMR in Intact Perfused Human Liver Tissue. Methods Mol Biol 2023; 2675:167-180. [PMID: 37258763 DOI: 10.1007/978-1-0716-3247-5_13] [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] [Indexed: 06/02/2023]
Abstract
Human metabolic liver disease is dramatically increasing globally and presents an urgent clinical unmet need. Rodent models of non-alcoholic fatty liver disease (NAFLD) are available, but they fail to fully recreate the metabolic and cellular features of human disease. Thus, it is imperative to understand the metabolic interplay in human cells in the context of disease. We have applied nuclear magnetic resonance (NMR) spectroscopy approaches to enable the detection of numerous metabolites in human cells and within intact tissue in a single measurement. In this chapter, we describe the challenges of using isolated human hepatocytes vs perfused human liver tissue for metabolic tracer experiments and how experimental parameters can be refined to interrogate signals from intact tissue and cells.
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Affiliation(s)
- Raquel Saborano
- Centre for Liver and Gastroenterology Research, and NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK
| | - Emma Shepherd
- School of Biosciences, College of Health and Life Sciences, Aston University, Birmingham, UK
| | - Ulrich L Günther
- Institute for Chemistry and Metabolomics, University of Luebeck, Luebeck, Germany
| | - Patricia F Lalor
- Centre for Liver and Gastroenterology Research, and NIHR Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK.
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Baker F, Polat IH, Abou-El-Ardat K, Alshamleh I, Thoelken M, Hymon D, Gubas A, Koschade SE, Vischedyk JB, Kaulich M, Schwalbe H, Shaid S, Brandts CH. Metabolic Rewiring Is Essential for AML Cell Survival to Overcome Autophagy Inhibition by Loss of ATG3. Cancers (Basel) 2021; 13:6142. [PMID: 34885250 PMCID: PMC8657081 DOI: 10.3390/cancers13236142] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/25/2021] [Accepted: 12/02/2021] [Indexed: 01/05/2023] Open
Abstract
Autophagy is an important survival mechanism that allows recycling of nutrients and removal of damaged organelles and has been shown to contribute to the proliferation of acute myeloid leukemia (AML) cells. However, little is known about the mechanism by which autophagy- dependent AML cells can overcome dysfunctional autophagy. In our study we identified autophagy related protein 3 (ATG3) as a crucial autophagy gene for AML cell proliferation by conducting a CRISPR/Cas9 dropout screen with a library targeting around 200 autophagy-related genes. shRNA-mediated loss of ATG3 impaired autophagy function in AML cells and increased their mitochondrial activity and energy metabolism, as shown by elevated mitochondrial ROS generation and mitochondrial respiration. Using tracer-based NMR metabolomics analysis we further demonstrate that the loss of ATG3 resulted in an upregulation of glycolysis, lactate production, and oxidative phosphorylation. Additionally, loss of ATG3 strongly sensitized AML cells to the inhibition of mitochondrial metabolism. These findings highlight the metabolic vulnerabilities that AML cells acquire from autophagy inhibition and support further exploration of combination therapies targeting autophagy and mitochondrial metabolism in AML.
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Affiliation(s)
- Fatima Baker
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
| | - Ibrahim H. Polat
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
| | - Khalil Abou-El-Ardat
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany;
| | - Islam Alshamleh
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Marlyn Thoelken
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
| | - Daniel Hymon
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Andrea Gubas
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, 60590 Frankfurt am Main, Germany;
| | - Sebastian E. Koschade
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany;
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, 60590 Frankfurt am Main, Germany;
| | - Jonas B. Vischedyk
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany;
| | - Manuel Kaulich
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany;
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, 60590 Frankfurt am Main, Germany;
- Cardio-Pulmonary Institute, 60590 Frankfurt am Main, Germany
| | - Harald Schwalbe
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
- Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Shabnam Shaid
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
| | - Christian H. Brandts
- Department of Medicine II, Hematology/Oncology, Goethe University, 60590 Frankfurt am Main, Germany; (F.B.); (I.H.P.); (K.A.-E.-A.); (M.T.); (S.E.K.); (J.B.V.)
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (D.H.); (H.S.)
- Frankfurt Cancer Institute, 60596 Frankfurt am Main, Germany;
- University Cancer Center Frankfurt (UCT), University Hospital, Goethe University, 60590 Frankfurt am Main, Germany
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Mostazo MGC, Kurrle N, Casado M, Fuhrmann D, Alshamleh I, Häupl B, Martín-Sanz P, Brüne B, Serve H, Schwalbe H, Schnütgen F, Marin S, Cascante M. Metabolic Plasticity Is an Essential Requirement of Acquired Tyrosine Kinase Inhibitor Resistance in Chronic Myeloid Leukemia. Cancers (Basel) 2020; 12:cancers12113443. [PMID: 33228196 PMCID: PMC7699488 DOI: 10.3390/cancers12113443] [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: 10/13/2020] [Revised: 11/06/2020] [Accepted: 11/17/2020] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Tyrosine kinase inhibitors (TKIs), such as imatinib, have become the standard initial treatment of choice for chronic myeloid leukemia (CML) patients. However, one obstacle to face is that a significant proportion of patients presents poor response to TKIs, or acquires resistance resulting in disease relapses. Mutations in BCR-ABL1 protein are a well described mechanism of resistance but other not well established mechanisms outside BCR-ABL1 mutations are emerging as important in the acquisition of resistance. Abnormal metabolism of CML cells that acquire resistance to imatinib has been pointed out as a putative downstream key event, but deep studies aimed to unveil metabolic adaptations associated with acquired resistance are still lacking. Here, we perform an exhaustive study on metabolic reprogramming associated with acquired imatinib resistance and we identify metabolic vulnerabilities of CML imatinib resistant cells that could pave the way for new therapies targeting TKI failure. Abstract Tyrosine kinase inhibitors (TKIs) are currently the standard chemotherapeutic agents for the treatment of chronic myeloid leukemia (CML). However, due to TKI resistance acquisition in CML patients, identification of new vulnerabilities is urgently required for a sustained response to therapy. In this study, we have investigated metabolic reprogramming induced by TKIs independent of BCR-ABL1 alterations. Proteomics and metabolomics profiling of imatinib-resistant CML cells (ImaR) was performed. KU812 ImaR cells enhanced pentose phosphate pathway, glycogen synthesis, serine-glycine-one-carbon metabolism, proline synthesis and mitochondrial respiration compared with their respective syngeneic parental counterparts. Moreover, the fact that only 36% of the main carbon sources were utilized for mitochondrial respiration pointed to glycerol-phosphate shuttle as mainly contributors to mitochondrial respiration. In conclusion, CML cells that acquire TKIs resistance present a severe metabolic reprogramming associated with an increase in metabolic plasticity needed to overcome TKI-induced cell death. Moreover, this study unveils that KU812 Parental and ImaR cells viability can be targeted with metabolic inhibitors paving the way to propose novel and promising therapeutic opportunities to overcome TKI resistance in CML.
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Affiliation(s)
- Miriam G. Contreras Mostazo
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
- Institute of Biomedicine of University of Barcelona, 08028 Barcelona, Spain
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (N.K.); (B.H.); (H.S.); (F.S.)
| | - Nina Kurrle
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (N.K.); (B.H.); (H.S.); (F.S.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (H.S.)
- Frankfurt Cancer Institute (FCI), Goethe University, 60590 Frankfurt am Main, Germany;
| | - Marta Casado
- Biomedicine Institute of Valencia, IBV-CSIC, 46010 Valencia, Spain;
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain;
| | - Dominik Fuhrmann
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany;
| | - Islam Alshamleh
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (H.S.)
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Björn Häupl
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (N.K.); (B.H.); (H.S.); (F.S.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (H.S.)
- Frankfurt Cancer Institute (FCI), Goethe University, 60590 Frankfurt am Main, Germany;
| | - Paloma Martín-Sanz
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain;
- “Alberto Sols” Biomedical Research Institute, CSIC-UAM, 28029 Madrid, Spain
| | - Bernhard Brüne
- Frankfurt Cancer Institute (FCI), Goethe University, 60590 Frankfurt am Main, Germany;
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, 60590 Frankfurt am Main, Germany;
- Project Group Translational Medicine and Pharmacology TMP, Fraunhofer Institute for Molecular Biology and Applied Ecology, 60596 Frankfurt am Main, Germany
| | - Hubert Serve
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (N.K.); (B.H.); (H.S.); (F.S.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (H.S.)
- Frankfurt Cancer Institute (FCI), Goethe University, 60590 Frankfurt am Main, Germany;
| | - Harald Schwalbe
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (H.S.)
- Center for Biomolecular Magnetic Resonance, Institute of Organic Chemistry and Chemical Biology, Goethe-University, 60438 Frankfurt am Main, Germany
| | - Frank Schnütgen
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe-University, 60590 Frankfurt am Main, Germany; (N.K.); (B.H.); (H.S.); (F.S.)
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz, and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; (I.A.); (H.S.)
- Frankfurt Cancer Institute (FCI), Goethe University, 60590 Frankfurt am Main, Germany;
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
- Institute of Biomedicine of University of Barcelona, 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain;
- Metabolomics Node at Spanish National Bioinformatics Institute (INB-ISCIII-ES- ELIXIR), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Correspondence: (S.M.); (M.C.); Tel.: +34-934021217 (S.M.); +34-934021593 (M.C.)
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, 08028 Barcelona, Spain;
- Institute of Biomedicine of University of Barcelona, 08028 Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain;
- Metabolomics Node at Spanish National Bioinformatics Institute (INB-ISCIII-ES- ELIXIR), Institute of Health Carlos III (ISCIII), 28029 Madrid, Spain
- Correspondence: (S.M.); (M.C.); Tel.: +34-934021217 (S.M.); +34-934021593 (M.C.)
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Alshamleh I, Krause N, Richter C, Kurrle N, Serve H, Günther UL, Schwalbe H. Real-Time NMR Spectroscopy for Studying Metabolism. Angew Chem Int Ed Engl 2020; 59:2304-2308. [PMID: 31730253 PMCID: PMC7004128 DOI: 10.1002/anie.201912919] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/12/2019] [Indexed: 12/19/2022]
Abstract
Current metabolomics approaches utilize cellular metabolite extracts, are destructive, and require high cell numbers. We introduce here an approach that enables the monitoring of cellular metabolism at lower cell numbers by observing the consumption/production of different metabolites over several kinetic data points of up to 48 hours. Our approach does not influence cellular viability, as we optimized the cellular matrix in comparison to other materials used in a variety of in-cell NMR spectroscopy experiments. We are able to monitor real-time metabolism of primary patient cells, which are extremely sensitive to external stress. Measurements are set up in an interleaved manner with short acquisition times (approximately 7 minutes per sample), which allows the monitoring of up to 15 patient samples simultaneously. Further, we implemented our approach for performing tracer-based assays. Our approach will be important not only in the metabolomics fields, but also in individualized diagnostics.
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Affiliation(s)
- Islam Alshamleh
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Nina Krause
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Nina Kurrle
- German Cancer Consortium (DKTK) and DKFZ69120HeidelbergGermany
- Department of Medicine 2, Hematology/OncologyGoethe University60590Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)60590Frankfurt am MainGermany
| | - Hubert Serve
- German Cancer Consortium (DKTK) and DKFZ69120HeidelbergGermany
- Department of Medicine 2, Hematology/OncologyGoethe University60590Frankfurt am MainGermany
- Frankfurt Cancer Institute (FCI)60590Frankfurt am MainGermany
| | - Ulrich L. Günther
- Institute of Chemistry and MetabolomicsUniversity of LuebeckRatzeburger Allee 16023562LuebeckGermany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
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Alshamleh I, Krause N, Richter C, Kurrle N, Serve H, Günther UL, Schwalbe H. Real‐Time NMR Spectroscopy for Studying Metabolism. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912919] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Islam Alshamleh
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Nina Krause
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Christian Richter
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Nina Kurrle
- German Cancer Consortium (DKTK) and DKFZ 69120 Heidelberg Germany
- Department of Medicine 2, Hematology/OncologyGoethe University 60590 Frankfurt am Main Germany
- Frankfurt Cancer Institute (FCI) 60590 Frankfurt am Main Germany
| | - Hubert Serve
- German Cancer Consortium (DKTK) and DKFZ 69120 Heidelberg Germany
- Department of Medicine 2, Hematology/OncologyGoethe University 60590 Frankfurt am Main Germany
- Frankfurt Cancer Institute (FCI) 60590 Frankfurt am Main Germany
| | - Ulrich L. Günther
- Institute of Chemistry and MetabolomicsUniversity of Luebeck Ratzeburger Allee 160 23562 Luebeck Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical BiologyCenter for Biomolecular Magnetic Resonance (BMRZ)Johann Wolfgang Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
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Saborano R, Eraslan Z, Roberts J, Khanim FL, Lalor PF, Reed MAC, Günther UL. A framework for tracer-based metabolism in mammalian cells by NMR. Sci Rep 2019; 9:2520. [PMID: 30792403 PMCID: PMC6385278 DOI: 10.1038/s41598-018-37525-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022] Open
Abstract
Metabolism changes extensively during the normal proliferation and differentiation of mammalian cells, and in cancer and inflammatory diseases. Since changes in the metabolic network reflect interactions between genetic, epigenetic and environmental changes, it is helpful to study the flow of label from isotopically labelled precursors into other metabolites rather than static metabolite levels. For this Nuclear Magnetic Resonance (NMR) spectroscopy is an attractive technique as it can quantify site-specific label incorporation. However, for applications using human cells and cell lines, the challenge is to optimize the process to maximize sensitivity and reproducibility. Here we present a new framework to analyze metabolism in mammalian cell lines and primary cells, covering the workflow from the preparation of cells to the acquisition and analysis of NMR spectra. We have applied this new approach in hematological and liver cancer cell lines and confirm the feasibility of tracer-based metabolism in primary liver cells.
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Affiliation(s)
- Raquel Saborano
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Zuhal Eraslan
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Jennie Roberts
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Farhat L Khanim
- University of Birmingham, School of Biosciences, Birmingham, B15 2TT, England
| | - Patricia F Lalor
- University of Birmingham, Institute of Immunology and Immunotherapy, Birmingham, B15 2TT, England
| | - Michelle A C Reed
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England
| | - Ulrich L Günther
- University of Birmingham, Institute of Cancer and Genomic Sciences, Birmingham, B15 2TT, England.
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. High-Throughput Metabolomics by 1D NMR. Angew Chem Int Ed Engl 2019; 58:968-994. [PMID: 29999221 PMCID: PMC6391965 DOI: 10.1002/anie.201804736] [Citation(s) in RCA: 204] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 12/12/2022]
Abstract
Metabolomics deals with the whole ensemble of metabolites (the metabolome). As one of the -omic sciences, it relates to biology, physiology, pathology and medicine; but metabolites are chemical entities, small organic molecules or inorganic ions. Therefore, their proper identification and quantitation in complex biological matrices requires a solid chemical ground. With respect to for example, DNA, metabolites are much more prone to oxidation or enzymatic degradation: we can reconstruct large parts of a mammoth's genome from a small specimen, but we are unable to do the same with its metabolome, which was probably largely degraded a few hours after the animal's death. Thus, we need standard operating procedures, good chemical skills in sample preparation for storage and subsequent analysis, accurate analytical procedures, a broad knowledge of chemometrics and advanced statistical tools, and a good knowledge of at least one of the two metabolomic techniques, MS or NMR. All these skills are traditionally cultivated by chemists. Here we focus on metabolomics from the chemical standpoint and restrict ourselves to NMR. From the analytical point of view, NMR has pros and cons but does provide a peculiar holistic perspective that may speak for its future adoption as a population-wide health screening technique.
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Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P.Via Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Veronica Ghini
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Gaia Meoni
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | - Cristina Licari
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of FlorenceLargo Brambilla 3FlorenceItaly
| | - Paola Turano
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
| | - Claudio Luchinat
- CERMUniversity of FlorenceVia Luigi Sacconi 650019 Sesto FiorentinoFlorenceItaly
- Department of Chemistry “Ugo Schiff”University of FlorenceVia della Lastruccia 3–1350019 Sesto FiorentinoFlorenceItaly
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9
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Vignoli A, Ghini V, Meoni G, Licari C, Takis PG, Tenori L, Turano P, Luchinat C. Hochdurchsatz‐Metabolomik mit 1D‐NMR. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Alessia Vignoli
- C.I.R.M.M.P. Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Veronica Ghini
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Gaia Meoni
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | - Cristina Licari
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
| | | | - Leonardo Tenori
- Department of Experimental and Clinical MedicineUniversity of Florence Largo Brambilla 3 Florence Italien
| | - Paola Turano
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
| | - Claudio Luchinat
- CERMUniversity of Florence Via Luigi Sacconi 6 50019 Sesto Fiorentino Florence Italien
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 3–13 50019 Sesto Fiorentino Florence Italien
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10
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Vinaixa M, Rodríguez MA, Aivio S, Capellades J, Gómez J, Canyellas N, Stracker TH, Yanes O. Positional Enrichment by Proton Analysis (PEPA): A One-Dimensional 1 H-NMR Approach for 13 C Stable Isotope Tracer Studies in Metabolomics. Angew Chem Int Ed Engl 2017; 56:3531-3535. [PMID: 28220994 PMCID: PMC5363230 DOI: 10.1002/anie.201611347] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/11/2017] [Indexed: 11/12/2022]
Abstract
A novel metabolomics approach for NMR-based stable isotope tracer studies called PEPA is presented, and its performance validated using human cancer cells. PEPA detects the position of carbon label in isotopically enriched metabolites and quantifies fractional enrichment by indirect determination of 13 C-satellite peaks using 1D-1 H-NMR spectra. In comparison with 13 C-NMR, TOCSY and HSQC, PEPA improves sensitivity, accelerates the elucidation of 13 C positions in labeled metabolites and the quantification of the percentage of stable isotope enrichment. Altogether, PEPA provides a novel framework for extending the high-throughput of 1 H-NMR metabolic profiling to stable isotope tracing in metabolomics, facilitating and complementing the information derived from 2D-NMR experiments and expanding the range of isotopically enriched metabolites detected in cellular extracts.
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Affiliation(s)
- Maria Vinaixa
- Department of Electronic Engineering-Universitat Rovira i VirgiliSpanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM)43204ReusSpain
| | - Miguel A. Rodríguez
- Universitat Rovira i VirgiliSpanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM)43204ReusSpain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology08028BarcelonaSpain
| | - Jordi Capellades
- Universitat Rovira i VirgiliSpanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM)43204ReusSpain
| | - Josep Gómez
- Department of Electronic Engineering-Universitat Rovira i Virgili43007TarragonaSpain
| | - Nicolau Canyellas
- Department of Electronic Engineering-Universitat Rovira i Virgili43007TarragonaSpain
| | - Travis H. Stracker
- Institute for Research in Biomedicine (IRB Barcelona)The Barcelona Institute of Science and Technology08028BarcelonaSpain
| | - Oscar Yanes
- Department of Electronic Engineering-Universitat Rovira i VirgiliSpanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM)43204ReusSpain
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11
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Chong M, Jayaraman A, Marin S, Selivanov V, de Atauri Carulla PR, Tennant DA, Cascante M, Günther UL, Ludwig C. Combined Analysis of NMR and MS Spectra (CANMS). Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611634] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mei Chong
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Anusha Jayaraman
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | | | - Daniel A. Tennant
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham UK B15 2TT
| | - Marta Cascante
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Ulrich L. Günther
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham UK B15 2TT
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12
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Chong M, Jayaraman A, Marin S, Selivanov V, de Atauri Carulla PR, Tennant DA, Cascante M, Günther UL, Ludwig C. Combined Analysis of NMR and MS Spectra (CANMS). Angew Chem Int Ed Engl 2017; 56:4140-4144. [DOI: 10.1002/anie.201611634] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 12/23/2022]
Affiliation(s)
- Mei Chong
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Anusha Jayaraman
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Vitaly Selivanov
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | | | - Daniel A. Tennant
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham, B15 2TT UK
| | - Marta Cascante
- Department of Biochemistry and Molecular Biology; Faculty of Biology; Universitat de Barcelona; Spain
| | - Ulrich L. Günther
- Institute of Cancer and Genome Sciences; University of Birmingham; UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research; University of Birmingham; IBR West Tower Birmingham, B15 2TT UK
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13
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Vinaixa M, Rodríguez MA, Aivio S, Capellades J, Gómez J, Canyellas N, Stracker TH, Yanes O. Positional Enrichment by Proton Analysis (PEPA): A One‐Dimensional
1
H‐NMR Approach for
13
C Stable Isotope Tracer Studies in Metabolomics. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Maria Vinaixa
- Department of Electronic Engineering-Universitat Rovira i Virgili Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) 43204 Reus Spain
| | - Miguel A. Rodríguez
- Universitat Rovira i Virgili Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) 43204 Reus Spain
| | - Suvi Aivio
- Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology 08028 Barcelona Spain
| | - Jordi Capellades
- Universitat Rovira i Virgili Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) 43204 Reus Spain
| | - Josep Gómez
- Department of Electronic Engineering- Universitat Rovira i Virgili 43007 Tarragona Spain
| | - Nicolau Canyellas
- Department of Electronic Engineering- Universitat Rovira i Virgili 43007 Tarragona Spain
| | - Travis H. Stracker
- Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology 08028 Barcelona Spain
| | - Oscar Yanes
- Department of Electronic Engineering-Universitat Rovira i Virgili Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM) 43204 Reus Spain
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14
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Reed MAC, Ludwig C, Bunce CM, Khanim FL, Günther UL. Malonate as a ROS product is associated with pyruvate carboxylase activity in acute myeloid leukaemia cells. Cancer Metab 2016; 4:15. [PMID: 27493727 PMCID: PMC4972992 DOI: 10.1186/s40170-016-0155-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 07/01/2016] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND The role of anaplerotic nutrient entry into the Krebs cycle via pyruvate carboxylase has been the subject of increased scrutiny and in particular whether this is dysregulated in cancer. Here, we use a tracer-based NMR analysis involving high-resolution (1)H-(13)C-HSQC spectra to assess site-specific label incorporation into a range of metabolite pools, including malate, aspartate and glutamate in the acute myeloid leukaemia cell line K562. We also determine how this is affected following treatment with the redeployed drug combination of the lipid-regulating drug bezafibrate and medroxyprogesterone (BaP). RESULTS Using the tracer-based approach, we assessed the contribution of pyruvate carboxylase (PC) vs. pyruvate dehydrogenase (PDH) activity in the derivation of Krebs cycle intermediates. Our data show that PC activity is indeed high in K562 cells. We also demonstrate a branched entry to the Krebs cycle of K562 cells with one branch running counterclockwise using PC-derived oxaloacetate and the other clockwise from the PDH activity. Finally, we show that the PC activity of K562 cells exclusively fuels the ROS-induced decarboxylation of oxaloacetate to malonate in response to BaP treatment; resulting in further Krebs cycle disruption via depletion of oxaloacetate and malonate-mediated inhibition of succinate dehydrogenase (SDH) resulting in a twofold reduction of fumarate. CONCLUSIONS This study extends the interest in the PC activity in solid cancers to include leukaemias and further demonstrates the value of tracer-based NMR approaches in generating a more accurate picture of the flow of carbons and metabolites within the increasingly inappropriately named Krebs cycle. Moreover, our studies indicate that the PC activity in cancer cells can be exploited as an Achilles heel by using treatments, such as BaP, that elevate ROS production.
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Affiliation(s)
- Michelle A. C. Reed
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Christian Ludwig
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT UK
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, B15 2TT UK
| | | | - Farhat L. Khanim
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT UK
| | - Ulrich L. Günther
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT UK
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15
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Carrigan JB, Reed MAC, Ludwig C, Khanim FL, Bunce CM, Günther UL. Tracer-Based Metabolic NMR-Based Flux Analysis in a Leukaemia Cell Line. Chempluschem 2016; 81:453-459. [PMID: 27347458 PMCID: PMC4916734 DOI: 10.1002/cplu.201500549] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/24/2016] [Indexed: 11/08/2022]
Abstract
High levels of reactive oxygen species (ROS) have a profound impact on acute myeloid leukaemia cells and can be used to specifically target these cells with novel therapies. We have previously shown how the combination of two redeployed drugs, the contraceptive steroid medroxyprogesterone and the lipid-regulating drug bezafibrate exert anti-leukaemic effects by producing ROS. Here we report a 13C-tracer-based NMR metabolic study to understand how these drugs work in K562 leukaemia cells. Our study shows that [1,2-13C]glucose is incorporated into ribose sugars, indicating activity in oxidative and non-oxidative pentose phosphate pathways alongside lactate production. There is little label incorporation into the tricarboxylic acid cycle from glucose, but much greater incorporation arises from the use of [3-13C]glutamine. The combined medroxyprogesterone and bezafibrate treatment decreases label incorporation from both glucose and glutamine into α-ketoglutarate and increased that for succinate, which is consistent with ROS-mediated conversion of α-ketoglutarate to succinate. Most interestingly, this combined treatment drastically reduced the production of several pyrimidine synthesis intermediates.
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Affiliation(s)
- John B. Carrigan
- Institute of Cancer and Genomics SciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Michelle A. C. Reed
- Institute of Cancer and Genomics SciencesUniversity of BirminghamBirminghamB15 2TTUK
| | - Christian Ludwig
- Institute of Metabolism and Systems BiologyUniversity of BirminghamBirminghamB15 2TTUK
| | - Farhat L. Khanim
- School of BiosciencesUniversity of BirminghamBirminghamB15 2TTUK
| | | | - Ulrich L. Günther
- Institute of Cancer and Genomics SciencesUniversity of BirminghamBirminghamB15 2TTUK
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