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Daverio Z, Kolkman M, Perrier J, Brunet L, Bendridi N, Sanglar C, Berger MA, Panthu B, Rautureau GJP. Warburg-associated acidification represses lactic fermentation independently of lactate, contribution from real-time NMR on cell-free systems. Sci Rep 2023; 13:17733. [PMID: 37853114 PMCID: PMC10584866 DOI: 10.1038/s41598-023-44783-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023] Open
Abstract
Lactate accumulation and acidification in tumours are a cancer hallmark associated with the Warburg effect. Lactic acidosis correlates with cancer malignancy, and the benefit it offers to tumours has been the subject of numerous hypotheses. Strikingly, lactic acidosis enhances cancer cell survival to environmental glucose depletion by repressing high-rate glycolysis and lactic fermentation, and promoting an oxidative metabolism involving reactivated respiration. We used real-time NMR to evaluate how cytosolic lactate accumulation up to 40 mM and acidification up to pH 6.5 individually impact glucose consumption, lactate production and pyruvate evolution in isolated cytosols. We used a reductive cell-free system (CFS) to specifically study cytosolic metabolism independently of other Warburg-regulatory mechanisms found in the cell. We assessed the impact of lactate and acidification on the Warburg metabolism of cancer cytosols, and whether this effect extended to different cytosolic phenotypes of lactic fermentation and cancer. We observed that moderate acidification, independently of lactate concentration, drastically reduces the glucose consumption rate and halts lactate production in different lactic fermentation phenotypes. In parallel, for Warburg-type CFS lactate supplementation induces pyruvate accumulation at control pH, and can maintain a higher cytosolic pyruvate pool at low pH. Altogether, we demonstrate that intracellular acidification accounts for the direct repression of lactic fermentation by the Warburg-associated lactic acidosis.
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Affiliation(s)
- Zoé Daverio
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France
- Master de Biologie, École Normale Supérieure de Lyon, University of Lyon, Université Claude Bernard Lyon 1, 69342, Lyon Cedex 07, France
| | - Maxime Kolkman
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS UMR 5246, University of Lyon, Université Claude Bernard Lyon 1, 69622, Lyon, France
| | - Johan Perrier
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France
| | - Lexane Brunet
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France
| | - Nadia Bendridi
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France
| | - Corinne Sanglar
- Institut des Sciences Analytiques, UMR5280 CNRS, University of Lyon, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100, Villeurbanne, France
| | - Marie-Agnès Berger
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France
| | - Baptiste Panthu
- Laboratoire CarMeN, UMR INSERM U1060/INRAE U1397, University of Lyon, Université Claude Bernard Lyon 1, 69310, Pierre-Bénite, France.
| | - Gilles J P Rautureau
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, ICBMS UMR 5246, University of Lyon, Université Claude Bernard Lyon 1, 69622, Lyon, France.
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Zhang N, Kandalai S, Zhou X, Hossain F, Zheng Q. Applying multi-omics toward tumor microbiome research. IMETA 2023; 2:e73. [PMID: 38868335 PMCID: PMC10989946 DOI: 10.1002/imt2.73] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/30/2022] [Accepted: 11/28/2022] [Indexed: 06/14/2024]
Abstract
Rather than a "short-term tenant," the tumor microbiome has been shown to play a vital role as a "permanent resident," affecting carcinogenesis, cancer development, metastasis, and cancer therapies. As the tumor microbiome has great potential to become a target for the early diagnosis and treatment of cancer, recent research on the relevance of the tumor microbiota has attracted a wide range of attention from various scientific fields, resulting in remarkable progress that benefits from the development of interdisciplinary technologies. However, there are still a great variety of challenges in this emerging area, such as the low biomass of intratumoral bacteria and unculturable character of some microbial species. Due to the complexity of tumor microbiome research (e.g., the heterogeneity of tumor microenvironment), new methods with high spatial and temporal resolution are urgently needed. Among these developing methods, multi-omics technologies (combinations of genomics, transcriptomics, proteomics, and metabolomics) are powerful approaches that can facilitate the understanding of the tumor microbiome on different levels of the central dogma. Therefore, multi-omics (especially single-cell omics) will make enormous impacts on the future studies of the interplay between microbes and tumor microenvironment. In this review, we have systematically summarized the advances in multi-omics and their existing and potential applications in tumor microbiome research, thus providing an omics toolbox for investigators to reference in the future.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Shruthi Kandalai
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Xiaozhuang Zhou
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Farzana Hossain
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
| | - Qingfei Zheng
- Department of Radiation Oncology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
- Center for Cancer Metabolism, Ohio State University Comprehensive Cancer Center ‐ James Cancer Hospital and Solove Research InstituteThe Ohio State UniversityOhioColumbusUSA
- Department of Biological Chemistry and Pharmacology, College of MedicineThe Ohio State UniversityColumbusOhioUSA
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Nami F, Ferraz MJ, Bakkum T, Aerts JMFG, Pandit A. Real‐Time NMR Recording of Fermentation and Lipid Metabolism Processes in Live Microalgae Cells. Angew Chem Int Ed Engl 2022; 61:e202117521. [PMID: 35103372 PMCID: PMC9305762 DOI: 10.1002/anie.202117521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Indexed: 11/10/2022]
Abstract
Non‐invasive and real‐time recording of processes in living cells has been limited to detection of small cellular components such as soluble proteins and metabolites. Here we report a multiphase NMR approach using magic‐angle spinning NMR to synchronously follow microbial processes of fermentation, lipid metabolism and structural dynamic changes in live microalgae cells. Chlamydomonas reinhardtii green algae were highly concentrated, introducing dark fermentation and anoxia conditions. Single‐pulse NMR experiments were applied to obtain temperature‐dependent kinetic profiles of the formed fermentation products. Through dynamics‐based spectral editing NMR, simultaneous conversion of galactolipids into TAG and free fatty acids was observed and rapid loss of rigid lipid structures. This suggests that lipolysis under dark and anoxia conditions finally results in the breakdown of cell and organelle membranes, which could be beneficial for recovery of intracellular microbial useful products.
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Affiliation(s)
- Faezeh Nami
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Joao Ferraz
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Dept. of Bio Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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4
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Nami F, Ferraz MJ, Bakkum T, Aerts JMFG, Pandit A. Real‐Time NMR Recording of Fermentation and Lipid Metabolism Processes in Live Microalgae Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202117521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Faezeh Nami
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Maria Joao Ferraz
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Thomas Bakkum
- Dept. of Bio Organic Synthesis Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Dept. of Medicinal Biochemistry Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Anjali Pandit
- Dept. of Solid-State NMR Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
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Vilca-Melendez S, Uthaug MV, Griffin JL. 1H Nuclear Magnetic Resonance: A Future Approach to the Metabolic Profiling of Psychedelics in Human Biofluids? Front Psychiatry 2021; 12:742856. [PMID: 34966300 PMCID: PMC8710695 DOI: 10.3389/fpsyt.2021.742856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/18/2021] [Indexed: 11/25/2022] Open
Abstract
While psychedelics may have therapeutic potential for treating mental health disorders such as depression, further research is needed to better understand their biological effects and mechanisms of action when considering the development of future novel therapy approaches. Psychedelic research could potentially benefit from the integration of metabonomics by proton nuclear magnetic resonance (1H NMR) spectroscopy which is an analytical chemistry-based approach that can measure the breakdown of drugs into their metabolites and their metabolic consequences from various biofluids. We have performed a systematic review with the primary aim of exploring published literature where 1H NMR analysed psychedelic substances including psilocin, lysergic acid diethylamide (LSD), LSD derivatives, N,N-dimethyltryptamine (DMT), 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT) and bufotenin. The second aim was to assess the benefits and limitations of 1H NMR spectroscopy-based metabolomics as a tool in psychedelic research and the final aim was to explore potential future directions. We found that the most current use of 1H NMR in psychedelic research has been for the structural elucidation and analytical characterisation of psychedelic molecules and that no papers used 1H NMR in the metabolic profiling of biofluids, thus exposing a current research gap and the underuse of 1H NMR. The efficacy of 1H NMR spectroscopy was also compared to mass spectrometry, where both metabonomics techniques have previously shown to be appropriate for biofluid analysis in other applications. Additionally, potential future directions for psychedelic research were identified as real-time NMR, in vivo 1H nuclear magnetic resonance spectroscopy (MRS) and 1H NMR studies of the gut microbiome. Further psychedelic studies need to be conducted that incorporate the use of 1H NMR spectroscopy in the analysis of metabolites both in the peripheral biofluids and in vivo to determine whether it will be an effective future approach for clinical and naturalistic research.
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Affiliation(s)
- Sylvana Vilca-Melendez
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Malin V. Uthaug
- The Centre for Psychedelic Research, Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
- Department of Neuropsychology and Psychopharmacology, Faculty of Psychology and Neuroscience, Maastricht University, Maastricht, Netherlands
| | - Julian L. Griffin
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, United Kingdom
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Welte H, Sinn P, Kovermann M. Fluorine NMR Spectroscopy Enables to Quantify the Affinity Between DNA and Proteins in Cell Lysate. Chembiochem 2021; 22:2973-2980. [PMID: 34390111 PMCID: PMC8596521 DOI: 10.1002/cbic.202100304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/30/2021] [Indexed: 11/12/2022]
Abstract
The determination of the binding affinity quantifying the interaction between proteins and nucleic acids is of crucial interest in biological and chemical research. Here, we have made use of site-specific fluorine labeling of the cold shock protein from Bacillus subtilis, BsCspB, enabling to directly monitor the interaction with single stranded DNA molecules in cell lysate. High-resolution 19 F NMR spectroscopy has been applied to exclusively report on resonance signals arising from the protein under study. We have found that this experimental approach advances the reliable determination of the binding affinity between single stranded DNA molecules and its target protein in this complex biological environment by intertwining analyses based on NMR chemical shifts, signal heights, line shapes and simulations. We propose that the developed experimental platform offers a potent approach for the identification of binding affinities characterizing intermolecular interactions in native surroundings covering the nano-to-micromolar range that can be even expanded to in cell applications in future studies.
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Affiliation(s)
- Hannah Welte
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Pia Sinn
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
| | - Michael Kovermann
- Department of ChemistryUniversity of KonstanzUniversitätsstrasse 1078467KonstanzGermany
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Höfurthner T, Mateos B, Konrat R. On-Cell NMR Contributions to Membrane Receptor Binding Characterization. Chempluschem 2021; 86:938-945. [PMID: 34160899 DOI: 10.1002/cplu.202100134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/28/2021] [Indexed: 12/21/2022]
Abstract
NMR spectroscopy has matured into a powerful tool to characterize interactions between biological molecules at atomic resolution, most importantly even under near to native (physiological) conditions. The field of in-cell NMR aims to study proteins and nucleic acids inside living cells. However, cells interrogate their environment and are continuously modulated by external stimuli. Cell signaling processes are often initialized by membrane receptors on the cell surface; therefore, characterizing their interactions at atomic resolution by NMR, hereafter referred as on-cell NMR, can provide valuable mechanistic information. This review aims to summarize recent on-cell NMR tools that give information about the binding site and the affinity of membrane receptors to their ligands together with potential applications to in vivo drug screening systems.
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Affiliation(s)
- Theresa Höfurthner
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Borja Mateos
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030, Vienna, Austria
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Wapler MC, Testud F, Hucker P, Leupold J, von Elverfeldt D, Zaitsev M, Wallrabe U. MR-compatible optical microscope for in-situ dual-mode MR-optical microscopy. PLoS One 2021; 16:e0250903. [PMID: 33970948 PMCID: PMC8109821 DOI: 10.1371/journal.pone.0250903] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 04/15/2021] [Indexed: 11/18/2022] Open
Abstract
We present the development of a dual-mode imaging platform that combines optical microscopy with magnetic resonance microscopy. Our microscope is designed to operate inside a 9.4T small animal scanner with the option to use a 72mm bore animal RF coil or different integrated linear micro coils. With a design that minimizes the magnetic distortions near the sample, we achieved a field inhomogeneity of 19 ppb RMS. We further integrated a waveguide in the optical layout for the electromagnetic shielding of the camera, which minimizes the noise increase in the MR and optical images below practical relevance. The optical layout uses an adaptive lens for focusing, 2 × 2 modular combinations of objectives with 0.6mm to 2.3mm field of view and 4 configurable RGBW illumination channels and achieves a plano-apochromatic optical aberration correction with 0.6μm to 2.3μm resolution. We present the design, implementation and characterization of the prototype including the general optical and MR-compatible design strategies, a knife-edge optical characterization and different concurrent imaging demonstrations.
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Affiliation(s)
- Matthias C. Wapler
- Department of Microsystemes Engineering (IMTEK), Laborarory for Microactuators, University of Freiburg, Freiburg, Germany
| | - Frederik Testud
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Patrick Hucker
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jochen Leupold
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Dominik von Elverfeldt
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Maxim Zaitsev
- Center for Diagnostic and Therapeutic Radiology, Medical Physics, Medical Center—University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- Center for High-Field Magnetic Resonance, Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Vienna, Austria
| | - Ulrike Wallrabe
- Department of Microsystemes Engineering (IMTEK), Laborarory for Microactuators, University of Freiburg, Freiburg, Germany
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