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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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2
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Abstract
Metabolomics has long been used in a biomedical context. The most typical samples are body fluids in which small molecules can be detected and quantified using technologies such as Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). Many studies, in particular in the wider field of cancer research, are based on cellular models. Different cancer cells can have vastly different ways of regulating metabolism and responses to drug treatments depend on specific metabolic mechanisms which are often cell type specific. This has led to a series of publications using metabolomics to study metabolic mechanisms. Cell-based metabolomics has specific requirements and allows for interesting approaches where metabolism is followed in real-time. Here applications of metabolomics in cell biology have been reviewed, providing insight into specific technologies used and showing exemplary case studies with an emphasis towards applications which help to understand drug mechanisms.
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Affiliation(s)
- Zuhal Eraslan
- Department of Dermatology, Weill Cornell Medicine, New York, NY, USA
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, University of Barcelona, Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona, Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Ulrich L Günther
- Institute of Chemistry and Metabolomics, University of Lübeck, Lübeck, Germany.
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3
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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4
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Vilaplana-Lopera N, Cuminetti V, Almaghrabi R, Papatzikas G, Rout AK, Jeeves M, González E, Alyahyawi Y, Cunningham A, Erdem A, Schnütgen F, Raghavan M, Potluri S, Cazier JB, Schuringa JJ, Reed MAC, Arranz L, Günther UL, Garcia P. Crosstalk between AML and stromal cells triggers acetate secretion through the metabolic rewiring of stromal cells. eLife 2022; 11:e75908. [PMID: 36052997 PMCID: PMC9477493 DOI: 10.7554/elife.75908] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 09/01/2022] [Indexed: 11/18/2022] Open
Abstract
Acute myeloid leukaemia (AML) cells interact and modulate components of their surrounding microenvironment into their own benefit. Stromal cells have been shown to support AML survival and progression through various mechanisms. Nonetheless, whether AML cells could establish beneficial metabolic interactions with stromal cells is underexplored. By using a combination of human AML cell lines and AML patient samples together with mouse stromal cells and a MLL-AF9 mouse model, here we identify a novel metabolic crosstalk between AML and stromal cells where AML cells prompt stromal cells to secrete acetate for their own consumption to feed the tricarboxylic acid cycle (TCA) and lipid biosynthesis. By performing transcriptome analysis and tracer-based metabolic NMR analysis, we observe that stromal cells present a higher rate of glycolysis when co-cultured with AML cells. We also find that acetate in stromal cells is derived from pyruvate via chemical conversion under the influence of reactive oxygen species (ROS) following ROS transfer from AML to stromal cells via gap junctions. Overall, we present a unique metabolic communication between AML and stromal cells and propose two different molecular targets, ACSS2 and gap junctions, that could potentially be exploited for adjuvant therapy.
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Affiliation(s)
- Nuria Vilaplana-Lopera
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Vincent Cuminetti
- Stem Cells, Ageing and Cancer Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of NorwayTromsoNorway
| | - Ruba Almaghrabi
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Department of Laboratory Medicine (hematology), Faculty of Applied Medical Sciences. Albaha University, Kingdom of Saudi ArabiaAl BahahSaudi Arabia
| | - Grigorios Papatzikas
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Ashok Kumar Rout
- Institute of Chemistry and Metabolomics, University of LübeckLübeckGermany
| | - Mark Jeeves
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Elena González
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Yara Alyahyawi
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan UniversityJazanSaudi Arabia
| | - Alan Cunningham
- Department of Experimental Hematology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Ayşegül Erdem
- Department of Experimental Hematology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Frank Schnütgen
- Department of Medicine, Hematology/Oncology, University Hospital Frankfurt, Goethe University FrankfurtFrankfurtGermany
- Frankfurt Cancer Institute, Goethe University FrankfurtFrankfurtGermany
- German Cancer Consortium (DKTK), partner site Frankfurt/Mainz, and German Cancer Research Center (DKFZ)HeidelbergGermany
| | - Manoj Raghavan
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Clinical Haematology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Queen Elizabeth Medical CentreBirminghamUnited Kingdom
| | - Sandeep Potluri
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Clinical Haematology, University Hospitals Birmingham NHS Foundation Trust, Queen Elizabeth Hospital, Queen Elizabeth Medical CentreBirminghamUnited Kingdom
| | - Jean-Baptiste Cazier
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Centre for Computational Biology, University of BirminghamBirminghamUnited Kingdom
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, University Medical Center Groningen, University of GroningenGroningenNetherlands
| | - Michelle AC Reed
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
| | - Lorena Arranz
- Stem Cells, Ageing and Cancer Research Group, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of NorwayTromsoNorway
| | - Ulrich L Günther
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
- Institute of Chemistry and Metabolomics, University of LübeckLübeckGermany
| | - Paloma Garcia
- Institute of Cancer and Genomic Sciences, University of BirminghamBirminghamUnited Kingdom
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Abstract
During the past few decades, the direct analysis of metabolic intermediates in biological samples has greatly improved the understanding of metabolic processes. The most used technologies for these advances have been mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy. NMR is traditionally used to elucidate molecular structures and has now been extended to the analysis of complex mixtures, as biological samples: NMR-based metabolomics. There are however other areas of small molecule biochemistry for which NMR is equally powerful. These include the quantification of metabolites (qNMR); the use of stable isotope tracers to determine the metabolic fate of drugs or nutrients, unravelling of new metabolic pathways, and flux through pathways; and metabolite-protein interactions for understanding metabolic regulation and pharmacological effects. Computational tools and resources for automating analysis of spectra and extracting meaningful biochemical information has developed in tandem and contributes to a more detailed understanding of systems biochemistry. In this review, we highlight the contribution of NMR in small molecule biochemistry, specifically in metabolic studies by reviewing the state-of-the-art methodologies of NMR spectroscopy and future directions.
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Affiliation(s)
- Sofia Moco
- Division of Molecular and Computational Toxicology, Department of Chemistry and Pharmaceutical Sciences, Amsterdam Institute for Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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6
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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7
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Jeeves M, Roberts J, Ludwig C. Optimised collection of non-uniformly sampled 2D-HSQC NMR spectra for use in metabolic flux analysis. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2021; 59:287-299. [PMID: 32830359 DOI: 10.1002/mrc.5089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 08/06/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is integral to metabolic studies; yet, it can suffer from the long acquisition times required to collect data of sufficient signal strength and resolution. The use of non-uniform sampling (NUS) allows faster collection of NMR spectra without loss of spectral integrity. When planning experimental methodologies to perform metabolic flux analysis (MFA) of cell metabolism, a variety of options are available for the acquisition of NUS NMR data. Before beginning data collection, decisions have to be made regarding selection of pulse sequence, number of transients and NUS specific parameters such as the sampling level and sampling schedule. Poor choices will impact data quality, which may have a negative effect on the subsequent analysis and biological interpretation. Herein, we describe factors that should be considered when setting up non-uniformly sampled 2D-1 H,13 C HSQC NMR experiments for MFA and provide a standard protocol for users to follow.
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Affiliation(s)
- Mark Jeeves
- Henry Wellcome Building for Biomolecular NMR Spectroscopy, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Christian Ludwig
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
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8
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Edison AS, Colonna M, Gouveia GJ, Holderman NR, Judge MT, Shen X, Zhang S. NMR: Unique Strengths That Enhance Modern Metabolomics Research. Anal Chem 2020; 93:478-499. [DOI: 10.1021/acs.analchem.0c04414] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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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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10
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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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