1
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Kato R, Miyazawa K, Imura T, Minamikawa T. Toward nanoscale structural and chemical analysis of microbial surfaces. Biosci Biotechnol Biochem 2025; 89:489-495. [PMID: 39577857 DOI: 10.1093/bbb/zbae176] [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: 09/14/2024] [Accepted: 11/18/2024] [Indexed: 11/24/2024]
Abstract
Microbial surfaces play a critical role in various biological processes, including cell adhesion and biofilm formation. Understanding these surfaces at the nanoscale is essential for both fundamental and applied microbiology. This review explores recent advancements in nanoscale structural and chemical analyses of microbial surfaces, with a focus on vibrational spectroscopy, such as Raman spectroscopy, infrared spectroscopy, and atomic force microscopy. The review also discusses current challenges of these techniques, including variability in sample preparation and the reproducibility of data, and highlights future directions in nanoscale analysis that could lead to new insights in microbial physiology, antimicrobial resistance, and biofilm research.
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Affiliation(s)
- Ryo Kato
- Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Keisuke Miyazawa
- Faculty of Frontier Engineering, Kanazawa University, Kanazawa, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Takumi Imura
- Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Takeo Minamikawa
- Department of Systems Innovation, Graduate School of Engineering Science, Osaka University, Osaka, Japan
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2
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Conca DV, Bano F, Graul M, von Wirén J, Scherrer L, Pace H, Sharma H, Svirelis J, Thorsteinsson K, Dahlin A, Bally M. Variant-Specific Interactions at the Plasma Membrane: Heparan Sulfate's Impact on SARS-CoV-2 Binding Kinetics. Anal Chem 2025; 97:4318-4328. [PMID: 39976108 PMCID: PMC11883730 DOI: 10.1021/acs.analchem.4c04283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 01/16/2025] [Accepted: 02/10/2025] [Indexed: 02/21/2025]
Abstract
The spread of SARS-CoV-2 led to the emergence of several variants of concern (VOCs). The spike glycoprotein, responsible for engaging the viral receptor, exhibits the highest density of mutations, suggesting an ongoing evolution to optimize viral entry. This study characterizes the bond formed by virion mimics carrying the SARS-CoV-2 spike protein and the plasma membrane of host cells in the early stages of virus entry. Contrary to the traditional analysis of isolated ligand-receptor pairs, we utilized well-defined biomimetic models and biochemical and biophysical techniques to characterize the multivalent interaction of VOCs with the complex cell membrane. We observed an overall increase in the binding affinity for newer VOCs. By progressively reducing the system complexity, we identify heparan sulfate (HS) as a main driver of this variation, with a 10-fold increase in affinity for Omicron BA.1 over that of the original strain. These results demonstrate the essential role of coreceptors, particularly HS, in the modulation of SARS-CoV-2 infection and highlight the importance of multiscale biophysical and biochemical assays that account for membrane complexity to fully characterize and understand the role of molecular components and their synergy in viral attachment and entry.
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Affiliation(s)
- Dario Valter Conca
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Fouzia Bano
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Małgorzata Graul
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Julius von Wirén
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Lauriane Scherrer
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Hudson Pace
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Himanshu Sharma
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
- Department
of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
- Laboratory
for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå 901 87, Sweden
| | - Justas Svirelis
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg 412 96, Sweden
| | - Konrad Thorsteinsson
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
| | - Andreas Dahlin
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology, Gothenburg 412 96, Sweden
| | - Marta Bally
- Department
of Clinical Microbiology, Umeå University, Umeå 901 87, Sweden
- Wallenberg
Centre for Molecular Medicine (WCMM), Umeå
University, Umeå 901 87, Sweden
- Umeå
Centre for Microbial Research (UCMR), Umeå
University, Umeå 901 87, Sweden
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3
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Yang D, Liu X, Ma J, Cui B, Wang Y, Xu J, Zhang Y, Ding H, Wang D, Liu Q, Zhang F. Probing Single-Cell Adhesion Kinetics and Nanomechanical Force with Surface Plasmon Resonance Imaging. ACS NANO 2025; 19:2651-2664. [PMID: 39788128 DOI: 10.1021/acsnano.4c14578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2025]
Abstract
Single cell adhesion plays a significant role in numerous physiological and pathological processes. Real-time imaging and quantification of single cell adhesion kinetics and corresponding cell-substrate mechanical interaction forces are crucial for elucidating the cellular mechanisms involved in tissue formation, immune responses, and cancer metastasis. Here, we present the development of a plasmonic-based nanomechanical sensing and imaging system (PNMSi) for the real-time measurement of single cell adhesion kinetics and associated nanomechanical forces with plasmonic tracking and monitoring of cell-substrate interactions and the accompanying nanoscale fluctuations. Both the slow binding and dynamic nanomechanical interaction processes were tracked and analyzed with a thermodynamic model to determine the adhesion kinetic parameters and quantity the mechanical forces. To demonstrate the capabilities of the PNMSi platform, we examined single cell binding interactions across four different surface modifications, and obvious alterations in binding kinetics and corresponding nanomechanical forces were observed, influenced by surface charges and interfacial hydrophilicity. Additionally, we investigated changes in mechanical interaction forces of single cells during cytoskeleton modification, revealing the cross-linking-induced cell adhesion changes. Furthermore, to demonstrate the application capability of the system, the adhesion profiling of primary tumor and metastatic tumor cells was explored, and obvious alterations were observed in the kinetic forces of single cell-substrate interaction. The PNMSi platform facilitates high-throughput single cell adhesion imaging and the quantification of adhesion interaction kinetics and nanomechanical forces with high sensitivity and serves as a promising platform for identifying biomarkers for tumor metastasis and for screening potential therapeutic agents.
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Affiliation(s)
- Dehong Yang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Xiaoyin Liu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Jinbiao Ma
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Baiqi Cui
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Yunxiao Wang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Jiahao Xu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Yunrui Zhang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Haiying Ding
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Pharmacy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310005, China
| | - Di Wang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou 311100, China
| | - Qingjun Liu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
| | - Fenni Zhang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, PR China
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4
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Yu PS, Kim CU, Lee JB. Cryogenic single-molecule fluorescence imaging. BMB Rep 2025; 58:2-7. [PMID: 39701023 PMCID: PMC11788530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2024] [Revised: 12/01/2024] [Accepted: 12/09/2024] [Indexed: 12/21/2024] Open
Abstract
Cryo-fixation techniques, including cryo-electron and cryofluorescence microscopy, enable the preservation of biological samples in a near-native state by rapidly freezing them into an amorphous ice phase. These methods prevent the structural distortions often caused by chemical fixation, allowing for high-resolution imaging. At low temperatures, fluorophores exhibit improved properties, such as extended fluorescence lifetimes, reduced photobleaching, and enhanced signal-tonoise ratios, making single-molecule imaging more accurate and insightful. Despite these advantages, challenges remain, including limitations in numerical aperture of objectives and cryo-stage for single-molecule imaging, which can affect photon detection and spatial resolution. Recent advancements at low temperatures have mitigated these issues, achieving resolutions at the nanometer scale. Looking forward, innovations in super-resolution techniques, optimized fluorophores, and Artificial Intelligence (AI)-based data analysis promise to further advance the field, providing deeper insights into biomolecular dynamics and interactions. In this mini-review, we will introduce low-temperature single-molecule fluorescence imaging techniques and discuss future perspectives in this field. [BMB Reports 2025; 58(1): 2-7].
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Affiliation(s)
- Phil Sang Yu
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Chae Un Kim
- Department of Physics, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jong-Bong Lee
- Department of Physics, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
- Division of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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5
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Mizushima K, Kumamoto Y, Tamura S, Yamanaka M, Mochizuki K, Li M, Egoshi S, Dodo K, Harada Y, Smith NI, Sodeoka M, Tanaka H, Fujita K. Raman microscopy of cryofixed biological specimens for high-resolution and high-sensitivity chemical imaging. SCIENCE ADVANCES 2024; 10:eadn0110. [PMID: 39661690 PMCID: PMC11633761 DOI: 10.1126/sciadv.adn0110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/16/2024] [Indexed: 12/13/2024]
Abstract
Raman microscopy is an emerging molecular imaging technology, yet its signal-to-noise ratio (SNR) in measurements of biological specimens is severely limited because of the small cross section of Raman scattering. Here, we present Raman imaging techniques of cryofixed specimens to overcome SNR limitations by enabling long exposure of specimens under highly stabilized low-temperature conditions. The observation of frozen specimens in a cryostat at a constant low temperature immediately after rapid freezing enabled the improvement of SNR and enhanced the spatial and spectral resolution. We also confirmed that the cryofixation can preserve physicochemical states of specimens by observing alkyne-labeled coenzyme Q in cytosol and hemeproteins in acute ischemic myocardium, which cannot be done by fixation using chemical reagents. Last, we applied the technique for multiplex Raman imaging of label-free endogenous molecules and alkyne-tagged molecules in cryofixed HeLa cells, demonstrating its capability of high-content imaging of complex biological phenomena while maintaining physiological conditions.
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Affiliation(s)
- Kenta Mizushima
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, AIST, Suita, Osaka 565-0871, Japan
| | - Yasuaki Kumamoto
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shoko Tamura
- Department of Pathology and Cell Regulation, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Masahito Yamanaka
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kentaro Mochizuki
- Department of Pathology and Cell Regulation, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Menglu Li
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, AIST, Suita, Osaka 565-0871, Japan
| | - Syusuke Egoshi
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Kosuke Dodo
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Yoshinori Harada
- Department of Pathology and Cell Regulation, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Nicholas I. Smith
- Biophotonics Laboratory, Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
- Catalysis and Integrated Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Hideo Tanaka
- Department of Pathology and Cell Regulation, Kyoto Prefectural University of Medicine, Kamigyo-ku, Kyoto 602-8566, Japan
- Faculty of Health and Medical Science, Kyoto University of Advanced Science, Ukyo-ku, Kyoto 615-8577, Japan
| | - Katsumasa Fujita
- Department of Applied Physics, Osaka University, Suita, Osaka 565-0871, Japan
- Advanced Photonics and Biosensing Open Innovation Laboratory, AIST-Osaka University, AIST, Suita, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
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6
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Yang D, Fang Y, Liu X, Ma J, Xu J, Dong H, Ding H, Wang D, Liu Q, Zhang F. Lensless On-Chip Chemiluminescence Imaging for High-Throughput Single-Cell Heterogeneity Analysis. NANO LETTERS 2024; 24:14875-14883. [PMID: 39512117 DOI: 10.1021/acs.nanolett.4c04487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
Abstract
High-throughput single-cell heterogeneity imaging and analysis is essential for understanding complex biological systems and for advancing personalized precision disease diagnosis and treatment. Here, we present a miniaturized lensless chemiluminescence chip for high-throughput single-cell functional imaging with subcellular resolution. With the sensitive chemiluminescence sensing and wide field of view of contact lensless imaging, we demonstrated the chemiluminescent imaging of over 1000 single cells, and their membrane glycoprotein and the high-throughput single-cell heterogeneity of membrane protein imaging were examined for precision analysis. Furthermore, the functional adhesion and heterogeneity of single live cells were imaged and explored. This miniaturized lensless on-chip CL-CMOS imaging platform enables high-throughput single-cell imaging and analysis with high sensitivity and subcellular resolution, providing new techniques for the cellular study of biological heterogeneity and has potential application in precision disease diagnosis and treatment at the point-of-care settings.
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Affiliation(s)
- Dehong Yang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Ying Fang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xiaoyin Liu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jinbiao Ma
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiahao Xu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Hao Dong
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Haiying Ding
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- Department of Pharmacy, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310005, China
| | - Di Wang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Intelligent Perception Research Institute, Zhejiang Lab, Hangzhou, 311100, China
| | - Qingjun Liu
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Fenni Zhang
- Biosensor National Special Laboratory, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
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7
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Hwang SM, Awasthi D, Jeong J, Sandoval TA, Chae CS, Ramos Y, Tan C, Marin Falco M, Salvagno C, Emmanuelli A, McBain IT, Mishra B, Ivashkiv LB, Zamarin D, Cantillo E, Chapman-Davis E, Holcomb K, Morales DK, Yu X, Rodriguez PC, Conejo-Garcia JR, Kaczocha M, Vähärautio A, Song M, Cubillos-Ruiz JR. Transgelin 2 guards T cell lipid metabolism and antitumour function. Nature 2024; 635:1010-1018. [PMID: 39443795 PMCID: PMC11949091 DOI: 10.1038/s41586-024-08071-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 09/18/2024] [Indexed: 10/25/2024]
Abstract
Mounting effective immunity against pathogens and tumours relies on the successful metabolic programming of T cells by extracellular fatty acids1-3. Fatty-acid-binding protein 5 (FABP5) has a key role in this process by coordinating the efficient import and trafficking of lipids that fuel mitochondrial respiration to sustain the bioenergetic requirements of protective CD8+ T cells4,5. However, the mechanisms that govern this immunometabolic axis remain unexplored. Here we report that the cytoskeletal organizer transgelin 2 (TAGLN2) is necessary for optimal fatty acid uptake, mitochondrial respiration and anticancer function in CD8+ T cells. TAGLN2 interacts with FABP5 to facilitate its cell surface localization and function in activated CD8+ T cells. Analyses of ovarian cancer specimens revealed that endoplasmic reticulum (ER) stress responses induced by the tumour microenvironment repress TAGLN2 in infiltrating CD8+ T cells, thereby enforcing their dysfunctional state. Restoring TAGLN2 expression in ER-stressed CD8+ T cells increased their lipid uptake, mitochondrial respiration and cytotoxic capacity. Accordingly, chimeric antigen receptor T cells overexpressing TAGLN2 bypassed the detrimental effects of tumour-induced ER stress and demonstrated therapeutic efficacy in mice with metastatic ovarian cancer. Our study establishes the role of cytoskeletal TAGLN2 in T cell lipid metabolism and highlights the potential to enhance cellular immunotherapy in solid malignancies by preserving the TAGLN2-FABP5 axis.
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Affiliation(s)
- Sung-Min Hwang
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Deepika Awasthi
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Jieun Jeong
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tito A Sandoval
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Chang-Suk Chae
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Yusibeska Ramos
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
| | - Chen Tan
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Matías Marin Falco
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Camilla Salvagno
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Emmanuelli
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Ian T McBain
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Bikash Mishra
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Lionel B Ivashkiv
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, NY, USA
| | - Dmitriy Zamarin
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evelyn Cantillo
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Eloise Chapman-Davis
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Diana K Morales
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
| | - Xiaoqing Yu
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Paulo C Rodriguez
- Department of Immunology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Jose R Conejo-Garcia
- Department of Integrated Immunobiology, Duke School of Medicine, Durham, NC, USA
- Duke Cancer Institute, Duke School of Medicine, Durham, NC, USA
| | - Martin Kaczocha
- Department of Anesthesiology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
- Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA
- Stony Brook University Pain and Analgesia Research Center (SPARC), Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Anna Vähärautio
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Minkyung Song
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Departments of Integrative Biotechnology and of Biopharmaceutical Convergence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Juan R Cubillos-Ruiz
- Department of Obstetrics and Gynecology, Weill Cornell Medicine, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Graduate School of Medical Sciences, New York, NY, USA.
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8
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Mazalo JK, Tay SS, Kempe D, Biro M. Chemokine receptor distribution on the surface of repolarizing T cells. Biophys J 2024; 123:2328-2342. [PMID: 38327056 PMCID: PMC11331047 DOI: 10.1016/j.bpj.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/17/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024] Open
Abstract
T cells migrate constitutively with a polarized morphology, underpinned by signaling compartmentalization and discrete cytoskeletal organizations, giving rise to a dynamic and expansive leading edge, distinct from the stable and constricted uropod at the rear. In vivo, the motion and function of T cells at various stages of differentiation is highly directed by chemokine gradients. When cognate ligands bind chemokine receptors on their surface, T cells respond by reorientating their polarity axis and migrating toward the source of the chemokine signal. Despite the significance of such chemotactic repolarization to the accurate navigation and function of T cells, the precise signaling mechanisms that underlie it remain elusive. Notably, it remained unclear whether the distribution of chemokine receptors on the T cell surface is altered during repolarization. Here, we developed parallel cell-secreted and microfluidics-based chemokine gradient delivery methods and employed both fixed imaging and live lattice light-sheet microscopy to investigate the dynamics of chemokine receptor CCR5 on the surface of primary murine CD8+ T cells. Our findings show that, during constitutive migration, chemokine receptor distribution is largely isotropic on the T cell surface. However, upon exposure to a CCL3 gradient, surface chemokine receptor distributions exhibit a transient bias toward the uropod. The chemokine receptors then progressively redistribute from the uropod to cover the T cell surface uniformly. This study sheds new light on the dynamics of surface chemokine receptor distribution during T cell repolarization, advancing our understanding of the signaling of immune cells in the complex chemokine landscapes they navigate.
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Affiliation(s)
- Jessica K Mazalo
- EMBL Australia, Single Molecule Science Node, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Szun S Tay
- EMBL Australia, Single Molecule Science Node, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daryan Kempe
- EMBL Australia, Single Molecule Science Node, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia.
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Biomedical Sciences, University of New South Wales, Sydney, NSW, Australia.
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9
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Schwenzer N, Teiwes NK, Kohl T, Pohl C, Giller MJ, Lehnart SE, Steinem C. Ca V1.3 channel clusters characterized by live-cell and isolated plasma membrane nanoscopy. Commun Biol 2024; 7:620. [PMID: 38783117 PMCID: PMC11116533 DOI: 10.1038/s42003-024-06313-3] [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: 10/23/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
A key player of excitable cells in the heart and brain is the L-type calcium channel CaV1.3. In the heart, it is required for voltage-dependent Ca2+-signaling, i.e., for controlling and modulating atrial cardiomyocyte excitation-contraction coupling. The clustering of CaV1.3 in functionally relevant channel multimers has not been addressed due to a lack of stoichiometric labeling combined with high-resolution imaging. Here, we developed a HaloTag-labeling strategy to visualize and quantify CaV1.3 clusters using STED nanoscopy to address the questions of cluster size and intra-cluster channel density. Channel clusters were identified in the plasma membrane of transfected live HEK293 cells as well as in giant plasma membrane vesicles derived from these cells that were spread on modified glass support to obtain supported plasma membrane bilayers (SPMBs). A small fraction of the channel clusters was colocalized with early and recycling endosomes at the membranes. STED nanoscopy in conjunction with live-cell and SPMB imaging enabled us to quantify CaV1.3 cluster sizes and their molecular density revealing significantly lower channel densities than expected for dense channel packing. CaV1.3 channel cluster size and molecular density were increased in SPMBs after treatment of the cells with the sympathomimetic compound isoprenaline, suggesting a regulated channel cluster condensation mechanism.
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Affiliation(s)
- Niko Schwenzer
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany
| | - Nikolas K Teiwes
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Tobias Kohl
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany
| | - Celine Pohl
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Michelle J Giller
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Robert‑Koch‑Str. 42a, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany.
- DZHK (German Centre for Cardiovascular Research), partner site Göttingen, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Collaborative Research Center SFB 1190 "Compartmental Gates and Contact Sites in Cells", University of Göttingen, Humboldtallee 23, 37073, Göttingen, Germany.
| | - Claudia Steinem
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC 2067), University of Göttingen, 37073, Göttingen, Germany.
- Georg-August Universität, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077, Göttingen, Germany.
- Max-Planck-Institut für Dynamik und Selbstorganisation, Am Fassberg 17, 37077, Göttingen, Germany.
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10
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Chen J, Stephan T, Gaedke F, Liu T, Li Y, Schauss A, Chen P, Wulff V, Jakobs S, Jüngst C, Chen Z. An aldehyde-crosslinking mitochondrial probe for STED imaging in fixed cells. Proc Natl Acad Sci U S A 2024; 121:e2317703121. [PMID: 38687792 PMCID: PMC11087744 DOI: 10.1073/pnas.2317703121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/22/2024] [Indexed: 05/02/2024] Open
Abstract
Fluorescence labeling of chemically fixed specimens, especially immunolabeling, plays a vital role in super-resolution imaging as it offers a convenient way to visualize cellular structures like mitochondria or the distribution of biomolecules with high detail. Despite the development of various distinct probes that enable super-resolved stimulated emission depletion (STED) imaging of mitochondria in live cells, most of these membrane-potential-dependent fluorophores cannot be retained well in mitochondria after chemical fixation. This lack of suitable mitochondrial probes has limited STED imaging of mitochondria to live cell samples. In this study, we introduce a mitochondria-specific probe, PK Mito Orange FX (PKMO FX), which features a fixation-driven cross-linking motif and accumulates in the mitochondrial inner membrane. It exhibits high fluorescence retention after chemical fixation and efficient depletion at 775 nm, enabling nanoscopic imaging both before and after aldehyde fixation. We demonstrate the compatibility of this probe with conventional immunolabeling and other strategies commonly used for fluorescence labeling of fixed samples. Moreover, we show that PKMO FX facilitates correlative super-resolution light and electron microscopy, enabling the correlation of multicolor fluorescence images and transmission EM images via the characteristic mitochondrial pattern. Our probe further expands the mitochondrial toolkit for multimodal microscopy at nanometer resolutions.
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Affiliation(s)
- Jingting Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
| | - Till Stephan
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
| | - Felix Gaedke
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Tianyan Liu
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Yiyan Li
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Astrid Schauss
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Peng Chen
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
| | - Veronika Wulff
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen37075, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology Translational, Neuroinflammation and Automated Microscopy, Göttingen37075, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Göttingen, Göttingen37099, Germany
| | - Christian Jüngst
- Faculty of Mathematics and Natural Sciences, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne50931, Germany
| | - Zhixing Chen
- College of Future Technology, Institute of Molecular Medicine, National Biomedical Imaging Center, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing100871, China
- Peking-Tsinghua Center for Life Science, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
- Peking University-Nanjing Institute of Translational Medicine, Nanjing211800, China
- Genvivo Biotech (PuHaiJingShan), Nanjing211800, China
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11
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Dong T, Wan S, Wang Y, Fu Y, Wang P. Effects of Chemical Fixatives on Kinetic Measurements of Biomolecular Interaction on Cell Membrane. J Membr Biol 2024; 257:131-142. [PMID: 38206377 DOI: 10.1007/s00232-024-00305-4] [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: 09/18/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
Understanding the interaction between ligands and membrane proteins is important for drug design and optimization. Although investigation using live cells is desirable, it is not feasible in some circumstances and cell fixation is performed to reduce cell motion and degradation. This study compared the effects of five fixatives, i.e., formaldehyde vapor (FV), paraformaldehyde (PFA), acetone, methanol, and ethanol, on kinetic measurements via the LigandTracer method. We found that all five fixatives exerted insignificant effects on lectin-glycan interaction. However, antibody-receptor interaction is markedly perturbed by coagulant fixatives. The acetone fixation changed the binding of the anti-human epidermal growth factor receptor 2 (HER2) antibody to HER2 on the cell membrane from a 1:2 to a 1:1 binding model, while methanol and ethanol abolished the antibody binding possibly by removal of the HER2 receptors on the cell membrane. The capability of binding was retained when methanol fixation was performed at lower temperatures, albeit with a binding model of 1:1 instead. Moreover, whereas cell morphology does not exert a substantial impact on lectin-glycan interaction, it can indeed modify the binding model of antibody-receptor interaction. Our results provided insights into the selection of fixatives for cell-based kinetic studies.
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Affiliation(s)
- Tianbao Dong
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Shengyang Wan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Yanhui Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Yaru Fu
- School of Biological Science and Technology, University of Jinan, Jinan, Shandong, 250022, P. R. China
| | - Pengcheng Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, P. R. China.
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12
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Jaiswal M, Tran TT, Guo J, Zhou M, Kundu S, Guo Z, Fanucci GE. Spin-labeling Insights into How Chemical Fixation Impacts Glycan Organization on Cells. APPLIED MAGNETIC RESONANCE 2024; 55:317-333. [PMID: 38469359 PMCID: PMC10927023 DOI: 10.1007/s00723-023-01624-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 03/13/2024]
Abstract
As new methods to interrogate glycan organization on cells develop, it is important to have a molecular level understanding of how chemical fixation can impact results and interpretations. Site-directed spin labeling technologies are well suited to study how the spin label mobility is impacted by local environmental conditions, such as those imposed by cross-linking effects of paraformaldehyde cell fixation methods. Here, we utilize three different azide-containing sugars for metabolic glycan engineering with HeLa cells to incorporate azido glycans that are modified with a DBCO-based nitroxide moiety via click reaction. Continuous wave X-band electron paramagnetic resonance spectroscopy is employed to characterize how the chronological sequence of chemical fixation and spin labeling impacts the local mobility and accessibility of the nitroxide-labeled glycans in the glycocalyx of HeLa cells. Results demonstrate that chemical fixation with paraformaldehyde can alter local glycan mobility and care should be taken in the analysis of data in any study where chemical fixation and cellular labeling occur.
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Affiliation(s)
- Mohit Jaiswal
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Trang T Tran
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Jiatong Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Mingwei Zhou
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Sayan Kundu
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL 32611, USA
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13
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Nalezinková M, Loskot J, Myslivcová Fučíková A. The use of scanning electron microscopy and fixation methods to evaluate the interaction of blood with the surfaces of medical devices. Sci Rep 2024; 14:4622. [PMID: 38409219 PMCID: PMC10897226 DOI: 10.1038/s41598-024-55136-z] [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: 12/17/2023] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
Testing the hemocompatibility of medical devices after their interaction with blood entails the need to evaluate the activation of blood elements and the degree of their coagulation and adhesion to the device surface. One possible way to achieve this is to use scanning electron microscopy (SEM). The aim was to develop a novel SEM-based method to assess the thrombogenic potential of medical devices and their adhesiveness to blood cells. As a part of this task, also find a convenient procedure of efficient and non-destructive sample fixation for SEM while reducing the use of highly toxic substances and shortening the fixation time. A polymeric surgical mesh was exposed to blood so that blood elements adhered to its surface. Such prepared samples were then chemically fixed for a subsequent SEM measurement; a number of fixation procedures were tested to find the optimal one. The fixation results were evaluated from SEM images, and the degree of blood elements' adhesion was determined from the images using ImageJ software. The best fixation was achieved with the May-Grünwald solution, which is less toxic than chemicals traditionally used. Moreover, manipulation with highly toxic osmium tetroxide can be avoided in the proposed procedure. A convenient methodology for SEM image analysis has been developed too, enabling to quantitatively evaluate the interaction of blood with the surfaces of various medical devices. Our method replaces the subjective assessment of surface coverage with a better-defined procedure, thus offering more precise and reliable results.
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Affiliation(s)
- Martina Nalezinková
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic.
| | - Jan Loskot
- Department of Physics, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
| | - Alena Myslivcová Fučíková
- Department of Biology, Faculty of Science, University of Hradec Králové, Rokitanského 62, Hradec Králové, 500 03, Czech Republic
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14
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Liu Y, Liu X, Su A, Gong C, Chen S, Xia L, Zhang C, Tao X, Li Y, Li Y, Sun T, Bu M, Shao W, Zhao J, Li X, Peng Y, Guo P, Han Y, Zhu Y. Revolutionizing the structural design and determination of covalent-organic frameworks: principles, methods, and techniques. Chem Soc Rev 2024; 53:502-544. [PMID: 38099340 DOI: 10.1039/d3cs00287j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Covalent organic frameworks (COFs) represent an important class of crystalline porous materials with designable structures and functions. The interconnected organic monomers, featuring pre-designed symmetries and connectivities, dictate the structures of COFs, endowing them with high thermal and chemical stability, large surface area, and tunable micropores. Furthermore, by utilizing pre-functionalization or post-synthetic functionalization strategies, COFs can acquire multifunctionalities, leading to their versatile applications in gas separation/storage, catalysis, and optoelectronic devices. Our review provides a comprehensive account of the latest advancements in the principles, methods, and techniques for structural design and determination of COFs. These cutting-edge approaches enable the rational design and precise elucidation of COF structures, addressing fundamental physicochemical challenges associated with host-guest interactions, topological transformations, network interpenetration, and defect-mediated catalysis.
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Affiliation(s)
- Yikuan Liu
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Xiaona Liu
- National Engineering Research Center of Lower-Carbon Catalysis Technology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - An Su
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Chengtao Gong
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Shenwei Chen
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Liwei Xia
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Chengwei Zhang
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Xiaohuan Tao
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Yue Li
- Institute of Intelligent Computing, Zhejiang Lab, Hangzhou 311121, China
| | - Yonghe Li
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Tulai Sun
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Mengru Bu
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Wei Shao
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Jia Zhao
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Xiaonian Li
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Yongwu Peng
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
| | - Peng Guo
- National Engineering Research Center of Lower-Carbon Catalysis Technology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yu Han
- School of Emergent Soft Matter, South China University of Technology, Guangzhou, China.
- King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
| | - Yihan Zhu
- Center for Electron Microscopy, Institute for Frontier and Interdisciplinary Sciences, State Key Laboratory Breeding Base of Green Chemistry Synthesis Technology, College of Materials Science and Engineering and College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, Zhejiang, China.
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15
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Diogenes L, Dellavance A, Baldo DC, Gozzi-Silva SC, Gomes K, Prado MS, Andrade LEC, Keppeke GD. Detection of Autoantibodies Against the Acetylcholine Receptor, Evaluation of Commercially Available Methodologies: Fixed Cell-Based Assay, Radioimmunoprecipitation Assay and Enzyme-Linked Immunosorbent Assay1. J Neuromuscul Dis 2024; 11:613-623. [PMID: 38578899 PMCID: PMC11091553 DOI: 10.3233/jnd-230210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND/OBJECTIVE Myasthenia Gravis (MG) is an autoimmune disorder characterized by pathogenic autoantibodies (AAbs) targeting nicotinic acetylcholine receptors (AChR), disrupting neuromuscular communication. RadioImmunoPrecipitation Assay (RIPA) is recommended to detect AChR AAbs, but its complexity and radioactive requirements limit widespread use. We compare non-RIPA anti-AChR immunoassays, including Cell-Based Assay (CBA) and two ELISA kits, against the gold standard RIPA. METHODS/RESULTS 145 samples were included with medical indication for anti-AChR testing. By the RIPA method, 63 were negative (RIPA-Neg < 0.02 nmol/L), 18 were classified as Borderline (≥0.02 -1 nmol/L), and 64 were positive (RIPA-Pos > 1 nmol/L). The competitive ELISA showed poor agreement with RIPA (Kappa = 0.216). The indirect ELISA demonstrated substantial agreement with RIPA (Kappa = 0.652), with ∼76% sensitivity and ∼94% specificity for MG diagnostic. The CBA, where fixed cells expressing clustered AChR were used as substrate, exhibited almost perfect agreement with RIPA (Kappa = 0.984), yielding ∼98% sensitivity and 96% specificity for MG. In addition, a semiquantitative analysis showed a strong correlation between CBA titration, indirect ELISA, and RIPA levels (r = 0.793 and r = 0.789, respectively). CONCLUSIONS The CBA displayed excellent analytical performance for MG diagnostic when compared to RIPA, making it a potential replacement for RIPA in clinical laboratories. Some solid-phase assays (such as the indirect ELISA applied here), as well as CBA titration, offer reliable options to estimate anti-AChR AAb levels after confirming positivity by the CBA.∥.
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Affiliation(s)
- Larissa Diogenes
- Disciplina de Reumatologia, Departamento de Medicina, Universidade Federal de São Paulo, Brasil
| | - Alessandra Dellavance
- Divisão de Imunologia, Departamento de Pesquisa e Desenvolvimento, Laboratório Fleury, São Paulo, Brasil
| | - Danielle Cristiane Baldo
- Divisão de Imunologia, Departamento de Pesquisa e Desenvolvimento, Laboratório Fleury, São Paulo, Brasil
| | - Sarah Cristina Gozzi-Silva
- Divisão de Imunologia, Departamento de Pesquisa e Desenvolvimento, Laboratório Fleury, São Paulo, Brasil
| | - Kethellen Gomes
- Disciplina de Reumatologia, Departamento de Medicina, Universidade Federal de São Paulo, Brasil
| | - Monica Simon Prado
- Disciplina de Reumatologia, Departamento de Medicina, Universidade Federal de São Paulo, Brasil
| | - Luis Eduardo C. Andrade
- Disciplina de Reumatologia, Departamento de Medicina, Universidade Federal de São Paulo, Brasil
- Divisão de Imunologia, Departamento de Pesquisa e Desenvolvimento, Laboratório Fleury, São Paulo, Brasil
| | - Gerson Dierley Keppeke
- Disciplina de Reumatologia, Departamento de Medicina, Universidade Federal de São Paulo, Brasil
- Departamento de Ciencias Biom dicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
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16
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Mastrangelo R, Okada T, Ogura T, Ogura T, Baglioni P. Direct observation of the effects of chemical fixation in MNT-1 cells: A SE-ADM and Raman study. Proc Natl Acad Sci U S A 2023; 120:e2308088120. [PMID: 38091295 PMCID: PMC10743460 DOI: 10.1073/pnas.2308088120] [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: 05/15/2023] [Accepted: 10/16/2023] [Indexed: 12/18/2023] Open
Abstract
Aldehydes fixation was accidentally discovered in the early 20th century and soon became a widely adopted practice in the histological field, due to an excellent staining enhancement in tissues imaging. However, the fixation process itself entails cell proteins denaturation and crosslinking. The possible presence of artifacts, that depends on the specific system under observation, must therefore be considered to avoid data misinterpretation. This contribution takes advantage of scanning electron assisted-dielectric microscopy (SE-ADM) and Raman 2D imaging to reveal the possible presence and the nature of artifacts in unstained, and paraformldehyde, PFA, fixed MNT-1 cells. The high resolution of the innovative SE-ADM technique allowed the identification of globular protein clusters in the cell cytoplasm, formed after protein denaturation and crosslinking. Concurrently, SE-ADM images showed a preferential melanosome adsorption on the cluster's outer surface. The micron-sized aggregates were discernible in Raman 2D images, as the melanosomes signal, extracted through 2D principal component analysis, unequivocally mapped their location and distribution within the cells, appearing randomly distributed in the cytoplasm. Protein clusters were not observed in living MNT-1 cells. In this case, mature melanosomes accumulate preferentially at the cell periphery and are more closely packed than in fixed cells. Our results show that, although PFA does not affect the melanin structure, it disrupts melanosome distribution within the cells. Proteins secondary structure, conversely, is partially lost, as shown by the Raman signals related to α-helix, β-sheets, and specific amino acids that significantly decrease after the PFA treatment.
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Affiliation(s)
- Rosangela Mastrangelo
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8566, Japan
- NIKKOL GROUP Nikko Chemicals Co., Ltd., Tokyo174-0046, Japan
- Department of Chemistry and Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (Center for Colloid and Surface Science), University of Florence, FlorenceI-50019, Italy
| | - Tomoko Okada
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8566, Japan
| | - Taku Ogura
- NIKKOL GROUP Nikko Chemicals Co., Ltd., Tokyo174-0046, Japan
| | - Toshihiko Ogura
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba305-8566, Japan
| | - Piero Baglioni
- Department of Chemistry and Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (Center for Colloid and Surface Science), University of Florence, FlorenceI-50019, Italy
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Zimmermann L, Zhao X, Makroczyova J, Wachsmuth-Melm M, Prasad V, Hensel Z, Bartenschlager R, Chlanda P. SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle. Nat Commun 2023; 14:7894. [PMID: 38036567 PMCID: PMC10689437 DOI: 10.1038/s41467-023-43666-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus replication is associated with the remodeling of cellular membranes, resulting in the formation of double-membrane vesicles (DMVs). A DMV-spanning pore was identified as a putative portal for viral RNA. However, the exact components and the structure of the SARS-CoV-2 DMV pore remain to be determined. Here, we investigate the structure of the DMV pore by in situ cryo-electron tomography combined with subtomogram averaging. We identify non-structural protein (nsp) 3 and 4 as minimal components required for the formation of a DMV-spanning pore, which is dependent on nsp3-4 proteolytic cleavage. In addition, we show that Mac2-Mac3-DPUP-Ubl2 domains are critical for nsp3 oligomerization and crown integrity which influences membrane curvature required for biogenesis of DMVs. Altogether, SARS-CoV-2 nsp3-4 have a dual role by driving the biogenesis of replication organelles and assembly of DMV-spanning pores which we propose here to term replicopores.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Xiaohan Zhao
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, 69120, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany.
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Idziak A, Inavalli VVGK, Bancelin S, Arizono M, Nägerl UV. The Impact of Chemical Fixation on the Microanatomy of Mouse Organotypic Hippocampal Slices. eNeuro 2023; 10:ENEURO.0104-23.2023. [PMID: 37709524 PMCID: PMC10521345 DOI: 10.1523/eneuro.0104-23.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023] Open
Abstract
Chemical fixation using paraformaldehyde (PFA) is a standard step for preserving cells and tissues for subsequent microscopic analyses such as immunofluorescence or electron microscopy (EM). However, chemical fixation may introduce physical alterations in the spatial arrangement of cellular proteins, organelles, and membranes. With the increasing use of super-resolution microscopy to visualize cellular structures with nanometric precision, assessing potential artifacts, and knowing how to avoid them, takes on special urgency. We addressed this issue by taking advantage of live-cell super-resolution microscopy that makes it possible to directly observe the acute effects of PFA on organotypic hippocampal brain slices, allowing us to compare tissue integrity in a "before-and-after" experiment. We applied super-resolution shadow imaging (SUSHI) to assess the structure of the extracellular space (ECS) and regular super-resolution microscopy of fluorescently labeled neurons and astrocytes to quantify key neuroanatomical parameters. While the ECS volume fraction (VF) and microanatomic organization of astrocytes remained largely unaffected by the PFA treatment, we detected subtle changes in dendritic spine morphology and observed substantial damage to cell membranes. Our experiments show that PFA application via immersion does not cause a noticeable shrinkage of the ECS in hippocampal brain slices maintained in culture, unlike the situation in transcardially perfused animals in vivo where the ECS typically becomes nearly depleted. Our study outlines an experimental strategy to evaluate the quality and pitfalls of various fixation protocols for the molecular and morphologic preservation of cells and tissues.
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Affiliation(s)
- Agata Idziak
- Unité Mixte de Recherche 5297, Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux F-33000, France
| | - V V G Krishna Inavalli
- Unité Mixte de Recherche 5297, Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux F-33000, France
| | - Stéphane Bancelin
- Unité Mixte de Recherche 5297, Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux F-33000, France
| | - Misa Arizono
- Unité Mixte de Recherche 5297, Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux F-33000, France
- Department of Pharmacology, Kyoto University Graduate School of Medicine/The Hakubi Center for Advanced Research, Kyoto University, Kyoto 606-8501, Japan
| | - U Valentin Nägerl
- Unité Mixte de Recherche 5297, Interdisciplinary Institute for Neuroscience, Centre National de la Recherche Scientifique, University of Bordeaux, Bordeaux F-33000, France
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Jaiswal M, Tran TT, Guo J, Zhou M, Kunda S, Guo Z, Fanucci G. Spin-labeling Insights into How Chemical Fixation Impacts Glycan Organization on Cells. RESEARCH SQUARE 2023:rs.3.rs-3039983. [PMID: 37398188 PMCID: PMC10312935 DOI: 10.21203/rs.3.rs-3039983/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
As new methods to interrogate glycan organization on cells develop, it is important to have a molecular level understanding of how chemical fixation can impact results and interpretations. Site-directed spin labeling technologies are well suited to study how the spin label mobility is impacted by local environmental conditions, such as those imposed by cross-linking effects of paraformaldehyde cell fixation methods. Here, we utilize three different azide-containing sugars for metabolic glycan engineering with HeLa cells to incorporate azido glycans that are modified with a DBCO-based nitroxide moiety via click reaction. Continuous wave X-band electron paramagnetic resonance spectroscopy is employed to characterize how the chronological sequence of chemical fixation and spin labeling impacts the local mobility and accessibility of the nitroxide-labeled glycans in the glycocalyx of HeLa cells. Results demonstrate that chemical fixation with paraformaldehyde can alter local glycan mobility and care should be taken in the analysis of data in any study where chemical fixation and cellular labeling occur.
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