1
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Chan YJ, Dileep D, Rothstein SM, Cochran EW, Reuel NF. Single-Use, Metabolite Absorbing, Resonant Transducer (SMART) Culture Vessels for Label-Free, Continuous Cell Culture Progression Monitoring. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401260. [PMID: 38900081 DOI: 10.1002/advs.202401260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 05/16/2024] [Indexed: 06/21/2024]
Abstract
Secreted metabolites are an important class of bio-process analytical technology (PAT) targets that can correlate to cell conditions. However, current strategies for measuring metabolites are limited to discrete measurements, resulting in limited understanding and ability for feedback control strategies. Herein, a continuous metabolite monitoring strategy is demonstrated using a single-use metabolite absorbing resonant transducer (SMART) to correlate with cell growth. Polyacrylate is shown to absorb secreted metabolites from living cells containing hydroxyl and alkenyl groups such as terpenoids, that act as a plasticizer. Upon softening, the polyacrylate irreversibly conformed into engineered voids above a resonant sensor, changing the local permittivity which is interrogated, contact-free, with a vector network analyzer. Compared to sensing using the intrinsic permittivity of cells, the SMART approach yields a 20-fold improvement in sensitivity. Tracking growth of many cell types such as Chinese hamster ovary, HEK293, K562, HeLa, and E. coli cells as well as perturbations in cell proliferation during drug screening assays are demonstrated. The sensor is benchmarked to show continuous measurement over six days, ability to track different growth conditions, selectivity to transducing active cell growth metabolites against other components found in the media, and feasibility to scale out for high throughput campaigns.
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Affiliation(s)
- Yee Jher Chan
- Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Dhananjay Dileep
- Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | | | - Eric W Cochran
- Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Nigel F Reuel
- Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
- Skroot Laboratory Inc, Ames, IA, 50010, USA
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2
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Thorp EB, Karlstaedt A. Intersection of Immunology and Metabolism in Myocardial Disease. Circ Res 2024; 134:1824-1840. [PMID: 38843291 DOI: 10.1161/circresaha.124.323660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/15/2024] [Indexed: 06/12/2024]
Abstract
Immunometabolism is an emerging field at the intersection of immunology and metabolism. Immune cell activation plays a critical role in the pathogenesis of cardiovascular diseases and is integral for regeneration during cardiac injury. We currently possess a limited understanding of the processes governing metabolic interactions between immune cells and cardiomyocytes. The impact of this intercellular crosstalk can manifest as alterations to the steady state flux of metabolites and impact cardiac contractile function. Although much of our knowledge is derived from acute inflammatory response, recent work emphasizes heterogeneity and flexibility in metabolism between cardiomyocytes and immune cells during pathological states, including ischemic, cardiometabolic, and cancer-associated disease. Metabolic adaptation is crucial because it influences immune cell activation, cytokine release, and potential therapeutic vulnerabilities. This review describes current concepts about immunometabolic regulation in the heart, focusing on intercellular crosstalk and intrinsic factors driving cellular regulation. We discuss experimental approaches to measure the cardio-immunologic crosstalk, which are necessary to uncover unknown mechanisms underlying the immune and cardiac interface. Deeper insight into these axes holds promise for therapeutic strategies that optimize cardioimmunology crosstalk for cardiac health.
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Affiliation(s)
- Edward B Thorp
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL (E.B.T.)
| | - Anja Karlstaedt
- Department of Cardiology, Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA (A.K.)
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3
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Joseph A, Muhammad L F, S Vijayan A, Xavier J, K B M, Karthikeyan A, Gopinath N, P V M, Nair BG. 3D printed arrowroot starch-gellan scaffolds for wound healing applications. Int J Biol Macromol 2024; 264:130604. [PMID: 38447843 DOI: 10.1016/j.ijbiomac.2024.130604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/08/2024]
Abstract
Skin, the largest organ in the body, blocks the entry of environmental pollutants into the system. Any injury to this organ allows infections and other harmful substances into the body. 3D bioprinting, a state-of-the-art technique, is suitable for fabricating cell culture scaffolds to heal chronic wounds rapidly. This study uses starch extracted from Maranta arundinacea (Arrowroot plant) (AS) and gellan gum (GG) to develop a bioink for 3D printing a scaffold capable of hosting animal cells. Field emission scanning electron microscopy (FE-SEM) and X-ray diffraction analysis (XRD) prove that the isolated AS is analogous to commercial starch. The cell culture scaffolds developed are superior to the existing monolayer culture. Infrared microscopy shows the AS-GG interaction and elucidates the mechanism of hydrogel formation. The physicochemical properties of the 3D-printed scaffold are analyzed to check the cell adhesion and growth; SEM images have confirmed that the AS-GG printed scaffold can support cell growth and proliferation, and the MTT assay shows good cell viability. Cell behavioral and migration studies reveal that cells are healthy. Since the scaffold is biocompatible, it can be 3D printed to any shape and structure and will biodegrade in the requisite time.
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Affiliation(s)
- Abey Joseph
- Department of Bioscience & Engineering, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Fathah Muhammad L
- Department of Bioscience & Engineering, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Athira S Vijayan
- School of Material Science and Engineering, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Joseph Xavier
- Toxicology division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojapura, Trivandrum, Kerala, India
| | - Megha K B
- Toxicology division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojapura, Trivandrum, Kerala, India
| | - Akash Karthikeyan
- Department of Bioscience & Engineering, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Nigina Gopinath
- Department of Bioscience & Engineering, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Mohanan P V
- Toxicology division, Biomedical Technology Wing, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Poojapura, Trivandrum, Kerala, India
| | - Baiju G Nair
- Department of Bioscience & Engineering, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India.
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4
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Liu B, Liu C, Chai X, Fan X, Huang T, Zhan J, Zhu Q, Zeng D, Gong Z, He L, Yang Y, Zhou X, Jiang B, Zhang X, Liu M. Real-Time NMR-Based Drug Discovery to Identify Inhibitors against Fatty Acid Synthesis in Living Cancer Cells. Anal Chem 2024. [PMID: 38334355 DOI: 10.1021/acs.analchem.3c04954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Abnormal fatty acid metabolism is recognized as a key driver of tumor development and progression. Although numerous inhibitors have been developed to target this pathway, finding drugs with high specificity that do not disrupt normal cellular metabolism remains a formidable challenge. In this paper, we introduced a novel real-time NMR-based drug screening technique that operates within living cells. This technique provides a direct way to putatively identify molecular targets involved in specific metabolic processes, making it a powerful tool for cell-based drug screening. Using 2-13C acetate as a tracer, combined with 3D cell clusters and a bioreactor system, our approach enables real-time detection of inhibitors that target fatty acid metabolism within living cells. As a result, we successfully demonstrated the initial application of this method in the discovery of traditional Chinese medicines that specifically target fatty acid metabolism. Elucidating the mechanisms behind herbal medicines remains challenging due to the complex nature of their compounds and the presence of multiple targets. Remarkably, our findings demonstrate the significant inhibitory effect of P. cocos on fatty acid synthesis within cells, illustrating the potential of this approach in analyzing fatty acid metabolism events and identifying drug candidates that selectively inhibit fatty acid synthesis at the cellular level. Moreover, this systematic approach represents a valuable strategy for discovering the intricate effects of herbal medicine.
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Affiliation(s)
- Biao Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Caixiang Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Chai
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xinyu Fan
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Tao Huang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Jianhua Zhan
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Qinjun Zhu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Danyun Zeng
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhou Gong
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun He
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunhuang Yang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Zhou
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Jiang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan 430074, China
| | - Xu Zhang
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan 430074, China
| | - Maili Liu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement of Science and Technology, Chinese Academy of Sciences, Wuhan 430071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Optics Valley Laboratory, Wuhan 430074, China
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5
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Urzì C, Meyer C, Nuoffer JM, Vermathen P. Methods for Oxygen Determination in an NMR Bioreactor as a Surrogate Marker for Metabolomic Studies in Living Cell Cultures. Anal Chem 2023; 95:17486-17493. [PMID: 37989262 DOI: 10.1021/acs.analchem.3c02314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Nuclear magnetic resonance (NMR) approaches have been described as a powerful method for measuring oxygen in tissue cultures and body fluids by using relaxation time dependencies of substances on pO2. The present NMR study describes methods to longitudinally monitor global, in situ intracellular, and spatially resolved oxygen tension in culture media and 3D cell cultures using relaxation times of water without the need to use external sensors. 1H NMR measurements of water using a modified inversion recovery pulse scheme were employed for global, i.e., intra- and extracellular oxygen estimation in an NMR-bioreactor. The combination of 1H relaxation time T1 and diffusion measurements of water was employed for in situ cellular oxygen content determination. Spatially selective water relaxation time estimations were used for spatially resolved oxygen quantification along the NMR tube length. The inclusion in a study protocol of the presented techniques for oxygen quantification, as a surrogate marker of oxidative phosphorylation (OXPHOS), provides the possibility to measure mitochondrial respiration and metabolic changes simultaneously.
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Affiliation(s)
- Christian Urzì
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Christoph Meyer
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Jean-Marc Nuoffer
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland
- Department of Pediatric Endocrinology, Diabetology and Metabolism, University Children's Hospital of Bern, Freiburgstrasse, 3010 Bern, Switzerland
| | - Peter Vermathen
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland
- Translational Imaging Center (TIC), Swiss Institute for Translational and Entrepreneurial Medicine, 3010 Bern, Switzerland
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6
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de Janon A, Mantalaris A, Panoskaltsis N. Three-Dimensional Human Bone Marrow Organoids for the Study and Application of Normal and Abnormal Hematoimmunopoiesis. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:895-904. [PMID: 36947817 PMCID: PMC7614371 DOI: 10.4049/jimmunol.2200836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 01/18/2023] [Indexed: 03/24/2023]
Abstract
Hematoimmunopoiesis takes place in the adult human bone marrow (BM), which is composed of heterogeneous niches with complex architecture that enables tight regulation of homeostatic and stress responses. There is a paucity of representative culture systems that recapitulate the heterogeneous three-dimensional (3D) human BM microenvironment and that can endogenously produce soluble factors and extracellular matrix that deliver culture fidelity for the study of both normal and abnormal hematopoiesis. Native BM lymphoid populations are also poorly represented in current in vitro and in vivo models, creating challenges for the study and treatment of BM immunopathology. BM organoid models leverage normal 3D organ structure to recreate functional niche microenvironments. Our focus herein is to review the current state of the art in the use of 3D BM organoids, focusing on their capacities to recreate critical quality attributes of the in vivo BM microenvironment for the study of human normal and abnormal hematopoiesis.
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Affiliation(s)
- Alejandro de Janon
- BioMedical Systems Engineering Laboratory, Wallace H. Coulter Department of Biomedical Engineering, The Georgia Institute of Technology, Atlanta, GA, USA
| | - Athanasios Mantalaris
- BioMedical Systems Engineering Laboratory, Wallace H. Coulter Department of Biomedical Engineering, The Georgia Institute of Technology, Atlanta, GA, USA
- School of Pharmacy & Pharmaceutical Sciences, Trinity College Dublin, Ireland
- National Institute for Bioprocessing Research and Training, Ireland
| | - Nicki Panoskaltsis
- BioMedical Systems Engineering Laboratory, Wallace H. Coulter Department of Biomedical Engineering, The Georgia Institute of Technology, Atlanta, GA, USA
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
- School of Pharmacy & Pharmaceutical Sciences, Trinity College Dublin, Ireland
- Department of Haematology, St. James’s Hospital Dublin, Ireland
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7
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington
| | - Daniel Raftery
- Northwest Metabolomics Research Center, Department of Anesthesiology and Pain Medicine, University of Washington
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109
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8
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Sciolino N, Reverdatto S, Premo A, Breindel L, Yu J, Theophall G, Burz DS, Liu A, Sulchek T, Schmidt AM, Ramasamy R, Shekhtman A. Messenger RNA in lipid nanoparticles rescues HEK 293 cells from lipid-induced mitochondrial dysfunction as studied by real time pulse chase NMR, RTPC-NMR, spectroscopy. Sci Rep 2022; 12:22293. [PMID: 36566335 PMCID: PMC9789524 DOI: 10.1038/s41598-022-26444-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/14/2022] [Indexed: 12/25/2022] Open
Abstract
Analytical tools to study cell physiology are critical for optimizing drug-host interactions. Real time pulse chase NMR spectroscopy, RTPC-NMR, was introduced to monitor the kinetics of metabolite production in HEK 293T cells treated with COVID-19 vaccine-like lipid nanoparticles, LNPs, with and without mRNA. Kinetic flux parameters were resolved for the incorporation of isotopic label into metabolites and clearance of labeled metabolites from the cells. Changes in the characteristic times for alanine production implicated mitochondrial dysfunction as a consequence of treating the cells with lipid nanoparticles, LNPs. Mitochondrial dysfunction was largely abated by inclusion of mRNA in the LNPs, the presence of which increased the size and uniformity of the LNPs. The methodology is applicable to all cultured cells.
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Affiliation(s)
- Nicholas Sciolino
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - Sergey Reverdatto
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - Aaron Premo
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - Leonard Breindel
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - Jianchao Yu
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - Gregory Theophall
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - David S Burz
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA
| | - Anna Liu
- Georgia Tech, School of Mechanical Engineering, Atlanta, GA, 30332, USA
| | - Todd Sulchek
- Georgia Tech, School of Mechanical Engineering, Atlanta, GA, 30332, USA
| | - Ann Marie Schmidt
- New York University, Grossman School of Medicine, New York, NY, 10016, USA
| | | | - Alexander Shekhtman
- Department of Chemistry, State University of New York, Albany, NY, 12222, USA.
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9
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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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10
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Wu ST, Chen PC, Tseng YH, Chen TH, Wang YJ, Tsai ZL, Lin EC. Assessment of cellular responses in three-dimensional cell cultures through chemical exchange saturation transfer and 1 H MRS. NMR IN BIOMEDICINE 2022; 35:e4757. [PMID: 35510307 DOI: 10.1002/nbm.4757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Metabolic responses to physiological changes have been detected using chemical exchange saturation transfer (CEST) imaging in clinical settings. Similarly to other MRI techniques, the CEST technique was based originally on phantoms from buffer solutions and was then further developed through animal experiments. However, CEST imaging can capture certain dynamics of metabolism that solution phantoms cannot model. Cell culture phantoms can fill the gap between buffer phantoms and animal models. In this study, we used 1 H NMR and CEST in a B0 field of 9.4 T to investigate HEK293T cells from two-dimensional (2D) cultures, three-dimensional (3D) cultures, and 3D cultures seeded with cell spheroids. Two CEST dips were observed: the magnitude of the amine dip at 2.8 ppm increased during the incubation period, whereas the hydroxyl dip at 1.2 ppm remained approximately the same or modestly increased. We also observed a CEST dip at 2.8 ppm from the 2D culture responding dramatically to doxorubicin treatment. By cross-validating with pH values and the concentrations of amine and hydroxyl protons extracted through 1 H NMR, we observed that they did not correspond to an increase in the amine pool. We believe that the denaturation or degradation of proteins from the fetal bovine serum increased the size of the amine pool. Although 3D culture conditions can be further improved, our study suggests that 3D cultures have the potential to bridge studies of solution phantoms and those on animals.
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Affiliation(s)
- Ssu-Ting Wu
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Pin-Chen Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Yu-Hsien Tseng
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Ting-Hao Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Yi-Jiun Wang
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Zong-Lin Tsai
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Eugene C Lin
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
- Center for Nano Bio-detection, National Chung Cheng University, Chiayi, Taiwan
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11
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Urzì C, Hertig D, Meyer C, Maddah S, Nuoffer JM, Vermathen P. Determination of Intra- and Extracellular Metabolic Adaptations of 3D Cell Cultures upon Challenges in Real-Time by NMR. Int J Mol Sci 2022; 23:ijms23126555. [PMID: 35743000 PMCID: PMC9223855 DOI: 10.3390/ijms23126555] [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: 04/06/2022] [Revised: 06/08/2022] [Accepted: 06/10/2022] [Indexed: 02/04/2023] Open
Abstract
NMR flow devices provide longitudinal real-time quantitative metabolome characterisation of living cells. However, discrimination of intra- and extracellular contributions to the spectra represents a major challenge in metabolomic NMR studies. The present NMR study demonstrates the possibility to quantitatively measure both metabolic intracellular fingerprints and extracellular footprints on human control fibroblasts by using a commercially available flow tube system with a standard 5 mm NMR probe. We performed a comprehensive 3D cell culture system characterisation. Diffusion NMR was employed for intra- and extracellular metabolites separation. In addition, complementary extracellular footprints were determined. The implemented perfused NMR bioreactor system allowed the determination of 35 metabolites and intra- and extracellular separation of 19 metabolites based on diffusion rate differences. We show the reliability and sensitivity of NMR diffusion measurements to detect metabolite concentration changes in both intra- and extracellular compartments during perfusion with different selective culture media, and upon complex I inhibition with rotenone. We also demonstrate the sensitivity of extracellular footprints to determine metabolic variations at different flow rates. The current method is of potential use for the metabolomic characterisation of defect fibroblasts and for improving physiological comprehension.
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Affiliation(s)
- Christian Urzì
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland; (C.U.); (D.H.); (C.M.); (S.M.)
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Damian Hertig
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland; (C.U.); (D.H.); (C.M.); (S.M.)
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Christoph Meyer
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland; (C.U.); (D.H.); (C.M.); (S.M.)
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland;
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Mittelstrasse 43, 3012 Bern, Switzerland
| | - Sally Maddah
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland; (C.U.); (D.H.); (C.M.); (S.M.)
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland;
| | - Jean-Marc Nuoffer
- Department of Clinical Chemistry, University Hospital Bern, Freiburgstrasse, 3010 Bern, Switzerland;
- Department of Pediatric Endocrinology, Diabetology and Metabolism, University Children’s Hospital of Bern, Freiburgstrasse, 3010 Bern, Switzerland
| | - Peter Vermathen
- Departments of Biomedical Research and Neuroradiology, University of Bern, Hochschulstrasse 6, 3012 Bern, Switzerland; (C.U.); (D.H.); (C.M.); (S.M.)
- Translational Imaging Center (TIC), Swiss Institute for Translational and Entrepreneurial Medicine, 3010 Bern, Switzerland
- Correspondence:
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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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
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