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Sugawara K, Uno SN, Kamiya M, Sakamoto A, Urano Y, Funatsu T, Okabe K. Nanoscale dynamics and localization of single endogenous mRNAs in stress granules. Nucleic Acids Res 2024:gkae588. [PMID: 39069641 DOI: 10.1093/nar/gkae588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/30/2024] Open
Abstract
Stress granules (SGs) are cytoplasmic messenger ribonucleoprotein granules transiently formed in stressed mammalian cells. Although SG components have been well characterized, detailed insights into the molecular behavior inside SGs remain unresolved. We investigated nanoscale dynamics and localization of endogenous mRNAs in SGs combining single mRNA tracking and super-resolution localization microscopy. First, we developed a methodology for tracking single mRNAs within SGs, revealing that although mRNAs in SGs are mainly stationary (∼40%), they also move in a confined (∼25%) or freely diffusing (∼35%) manner. Second, the super-resolution localization microscopy showed that the mRNAs in SGs are heterogeneously distributed and partially form high-density clusters. Third, we simultaneously performed single mRNA tracking and super-resolution microscopy in SGs, demonstrating that single mRNA trajectories are mainly found around high-density clusters. Finally, a quantitative analysis of mRNA localization and dynamics during stress removal was conducted using live super-resolution imaging and single-molecule tracking. These results suggest that SGs have a highly organized structure that enables dynamic regulation of the mRNAs at the nanoscale, which is responsible for the ordered formation and the wide variety of functions of SGs.
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Affiliation(s)
- Ko Sugawara
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- RIKEN Center for Biosystems Dynamics Research, Hyogo 650-0047, Japan
| | - Shin-Nosuke Uno
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Mako Kamiya
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Akihiko Sakamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Department of Pharmacology, Yamaguchi University Graduate School of Medicine, Yamaguchi 755-8505, Japan
| | - Yasuteru Urano
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Kohki Okabe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
- JST, PRESTO, Saitama 332-0012, Japan
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2
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Yu X, Liu J, Bauer A, Wei X, Smith S, Ning S, Wang C. Enhancing tumor endothelial permeability using MUC18-targeted gold nanorods and mild hyperthermia. J Colloid Interface Sci 2024; 676:101-109. [PMID: 39018803 DOI: 10.1016/j.jcis.2024.07.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/13/2024] [Accepted: 07/05/2024] [Indexed: 07/19/2024]
Abstract
The Enhanced Permeability and Retention (EPR) effect, an elevated accumulation of drugs and nanoparticles in tumors versus in normal tissues, is a widely used concept in the field of cancer therapy. It assumes that the vasculature of solid tumors would possess abnormal, leaky endothelial cell barriers, allowing easy access of intravenous-delivered drugs and nanoparticles to tumor regions. However, the EPR effect is not always effective owing to the heterogeneity of tumor endothelium over time, location, and species. Herein, we introduce a unique nanoparticle-based approach, using MUC18-targeted gold nanorods coupled with mild hyperthermia, to specifically enhance tumor endothelial permeability. This improves the efficacy of traditional cancer therapy including photothermal therapy and anticancer drug delivery by increasing the transport of photo-absorbers and drugs across the tumor endothelium. Using single cell imaging tools and classic analytical approaches in molecular biology, we demonstrate that MUC18-targeted gold nanorods and mild hyperthermia enlarge the intercellular gaps of tumor endothelium by inducing circumferential actin remodeling, stress fiber formation, and cell contraction of adjacent endothelial cells. Considering MUC18 is overexpressed on a variety of tumor endothelium and cancer cells, this approach paves a new avenue to improve the efficacy of cancer therapy by actively enhancing the tumor endothelial permeability.
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Affiliation(s)
- Xiao Yu
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, USA
| | - Jinyuan Liu
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, USA
| | - Aaron Bauer
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, USA
| | - Xianqing Wei
- Department of Breast Surgery, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Steve Smith
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, USA
| | - Shipeng Ning
- Department of Breast Surgery, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China.
| | - Congzhou Wang
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, USA.
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Cichos F, Xia T, Yang H, Zijlstra P. The ever-expanding optics of single-molecules and nanoparticles. J Chem Phys 2024; 161:010401. [PMID: 38949895 DOI: 10.1063/5.0221680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Accepted: 06/10/2024] [Indexed: 07/03/2024] Open
Affiliation(s)
- F Cichos
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - T Xia
- Institute for Immunology, School of Medicine, Tsinghua University, Beijing, China
| | - H Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - P Zijlstra
- Department of Applied Physics and Science Education, Eindhoven University of Technology (TU/e), Eindhoven, The Netherlands
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Gunasekara H, Perera T, Chao CJ, Bruno J, Saed B, Anderson J, Zhao Z, Hu YS. Phalloidin-PAINT: Enhanced quantitative nanoscale imaging of F-actin. Biophys J 2024:S0006-3495(24)00442-9. [PMID: 38961624 DOI: 10.1016/j.bpj.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 07/05/2024] Open
Abstract
We present phalloidin-based points accumulation for imaging in nanoscale topography (phalloidin-PAINT), enabling quantitative superresolution imaging of filamentous actin (F-actin) in the cell body and delicate membrane protrusions. We demonstrate that the intrinsic phalloidin dissociation enables PAINT superresolution microscopy in an imaging buffer containing low concentrations of dye-conjugated phalloidin. We further show enhanced single-molecule labeling by chemically promoting phalloidin dissociation. Two benefits of phalloidin-PAINT are its ability to consistently quantify F-actin at the nanoscale throughout the entire cell and its enhanced preservation of fragile cellular structures. In a proof-of-concept study, we employed phalloidin-PAINT to superresolve F-actin structures in U2OS and dendritic cells (DCs). We demonstrate more consistent F-actin quantification in the cell body and structurally delicate membrane protrusions of DCs compared with direct stochastic optical reconstruction microscopy (dSTORM). Using DC2.4 mouse DCs as the model system, we show F-actin redistribution from podosomes to actin filaments and altered prevalence of F-actin-associated membrane protrusions on the culture glass surface after lipopolysaccharide exposure. The concept of our work opens new possibilities for quantitative protein-specific PAINT using commercially available reagents.
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Affiliation(s)
- Hirushi Gunasekara
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Chih-Jia Chao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois
| | - Joshua Bruno
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois
| | - Jesse Anderson
- Department of Chemical Engineering, College of Engineering, University of Illinois Chicago, Chicago, Illinois
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, Illinois
| | - Ying S Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, Illinois.
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Lai JZ, Lin CY, Chen SJ, Cheng YM, Abe M, Lin TC, Chien FC. Temporal-Focusing Multiphoton Excitation Single-Molecule Localization Microscopy Using Spontaneously Blinking Fluorophores. Angew Chem Int Ed Engl 2024; 63:e202404942. [PMID: 38641901 DOI: 10.1002/anie.202404942] [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: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Single-molecule localization microscopy (SMLM) based on temporal-focusing multiphoton excitation (TFMPE) and single-wavelength excitation is used to visualize the three-dimensional (3D) distribution of spontaneously blinking fluorophore-labeled subcellular structures in a thick specimen with a nanoscale-level spatial resolution. To eliminate the photobleaching effect of unlocalized molecules in out-of-focus regions for improving the utilization rate of the photon budget in 3D SMLM imaging, SMLM with single-wavelength TFMPE achieves wide-field and axially confined two-photon excitation (TPE) of spontaneously blinking fluorophores. TPE spectral measurement of blinking fluorophores is then conducted through TFMPE imaging at a tunable excitation wavelength, yielding the optimal TPE wavelength for increasing the number of detected photons from a single blinking event during SMLM. Subsequently, the TPE fluorescence of blinking fluorophores is recorded to obtain a two-dimensional TFMPE-SMLM image of the microtubules in cancer cells with a localization precision of 18±6 nm and an overall imaging resolution of approximately 51 nm, which is estimated based on the contribution of Nyquist resolution and localization precision. Combined with astigmatic imaging, the system is capable of 3D TFMPE-SMLM imaging of brain tissue section of a 5XFAD transgenic mouse with the pathological features of Alzheimer's disease, revealing the distribution of neurotoxic amyloid-beta peptide deposits.
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Affiliation(s)
- Jian-Zong Lai
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Yu-Min Cheng
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8526, Japan
| | - Tzu-Chau Lin
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
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Kochanowsky JA, Mira PM, Elikaee S, Muratore K, Rai AK, Riestra AM, Johnson PJ. Trichomonas vaginalis extracellular vesicles up-regulate and directly transfer adherence factors promoting host cell colonization. Proc Natl Acad Sci U S A 2024; 121:e2401159121. [PMID: 38865261 PMCID: PMC11194581 DOI: 10.1073/pnas.2401159121] [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: 01/31/2024] [Accepted: 05/16/2024] [Indexed: 06/14/2024] Open
Abstract
Trichomonas vaginalis, a common sexually transmitted parasite that colonizes the human urogenital tract, secretes extracellular vesicles (TvEVs) that are taken up by human cells and are speculated to be taken up by parasites as well. While the crosstalk between TvEVs and human cells has led to insight into host:parasite interactions, roles for TvEVs in infection have largely been one-sided, with little known about the effect of TvEV uptake by T. vaginalis. Approximately 11% of infections are found to be coinfections of multiple T. vaginalis strains. Clinical isolates often differ in their adherence to and cytolysis of host cells, underscoring the importance of understanding the effects of TvEV uptake within the parasite population. To address this question, our lab tested the ability of a less adherent strain of T. vaginalis, G3, to take up fluorescently labeled TvEVs derived from both itself (G3-EVs) and TvEVs from a more adherent strain of the parasite (B7RC2-EVs). Here, we showed that TvEVs generated from the more adherent strain are internalized more efficiently compared to the less adherent strain. Additionally, preincubation of G3 parasites with B7RC2-EVs increases parasite aggregation and adherence to host cells. Transcriptomics revealed that TvEVs up-regulate expression of predicted parasite membrane proteins and identified an adherence factor, heteropolysaccharide binding protein (HPB2). Finally, using comparative proteomics and superresolution microscopy, we demonstrated direct transfer of an adherence factor, cadherin-like protein, from TvEVs to the recipient parasite's surface. This work identifies TvEVs as a mediator of parasite:parasite communication that may impact pathogenesis during mixed infections.
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Affiliation(s)
- Joshua A. Kochanowsky
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Portia M. Mira
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Samira Elikaee
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Katherine Muratore
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Anand Kumar Rai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
| | - Angelica M. Riestra
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
- Department of Biology, San Diego State University, San Diego, CA92182
| | - Patricia J. Johnson
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA90095
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7
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Bíró P, Novák T, Czvik E, Mihály J, Szikora S, van de Linde S, Erdélyi M. Triggered cagedSTORM microscopy. BIOMEDICAL OPTICS EXPRESS 2024; 15:3715-3726. [PMID: 38867795 PMCID: PMC11166440 DOI: 10.1364/boe.517480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 06/14/2024]
Abstract
In standard SMLM methods, the photoswitching of single fluorescent molecules and the data acquisition processes are independent, which leads to the detection of single molecule blinking events on several consecutive frames. This mismatch results in several data points with reduced localization precision, and it also increases the possibilities of overlapping. Here we discuss how the synchronization of the fluorophores' ON state to the camera exposure time increases the average intensity of the captured point spread functions and hence improves the localization precision. Simulations and theoretical results show that such synchronization leads to fewer localizations with 15% higher sum signal on average, while reducing the probability of overlaps by 10%.
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Affiliation(s)
- Péter Bíró
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
| | - Tibor Novák
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
| | - Elvira Czvik
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
| | - József Mihály
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, Temesvári körút 62, Szeged 6726, Hungary
- Department of Genetics, University of Szeged, Közép fasor 52, Szeged 6726, Hungary
| | - Szilárd Szikora
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, Temesvári körút 62, Szeged 6726, Hungary
| | - Sebastian van de Linde
- Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, Scotland, United Kingdom
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
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Sun T, Zhao H, Hu L, Shao X, Lu Z, Wang Y, Ling P, Li Y, Zeng K, Chen Q. Enhanced optical imaging and fluorescent labeling for visualizing drug molecules within living organisms. Acta Pharm Sin B 2024; 14:2428-2446. [PMID: 38828150 PMCID: PMC11143489 DOI: 10.1016/j.apsb.2024.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 06/05/2024] Open
Abstract
The visualization of drugs in living systems has become key techniques in modern therapeutics. Recent advancements in optical imaging technologies and molecular design strategies have revolutionized drug visualization. At the subcellular level, super-resolution microscopy has allowed exploration of the molecular landscape within individual cells and the cellular response to drugs. Moving beyond subcellular imaging, researchers have integrated multiple modes, like optical near-infrared II imaging, to study the complex spatiotemporal interactions between drugs and their surroundings. By combining these visualization approaches, researchers gain supplementary information on physiological parameters, metabolic activity, and tissue composition, leading to a comprehensive understanding of drug behavior. This review focuses on cutting-edge technologies in drug visualization, particularly fluorescence imaging, and the main types of fluorescent molecules used. Additionally, we discuss current challenges and prospects in targeted drug research, emphasizing the importance of multidisciplinary cooperation in advancing drug visualization. With the integration of advanced imaging technology and molecular design, drug visualization has the potential to redefine our understanding of pharmacology, enabling the analysis of drug micro-dynamics in subcellular environments from new perspectives and deepening pharmacological research to the levels of the cell and organelles.
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Affiliation(s)
- Ting Sun
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Huanxin Zhao
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Luyao Hu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xintian Shao
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- School of Life Sciences, Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Zhiyuan Lu
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Yuli Wang
- Tianjin Pharmaceutical DA REN TANG Group Corporation Limited Traditional Chinese Pharmacy Research Institute, Tianjin 300457, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemistry Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Peixue Ling
- Institute of Biochemical and Biotechnological Drugs, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
- Key Laboratory of Biopharmaceuticals, Postdoctoral Scientific Research Workstation, Shandong Academy of Pharmaceutical Science, Jinan 250098, China
| | - Yubo Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Kewu Zeng
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qixin Chen
- School of Pharmaceutical Sciences, National Key Laboratory of Advanced Drug Delivery System, Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
- Departments of Diagnostic Radiology, Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore 119074, Singapore
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Gaire SK, Daneshkhah A, Flowerday E, Gong R, Frederick J, Backman V. Deep learning-based spectroscopic single-molecule localization microscopy. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:066501. [PMID: 38799979 PMCID: PMC11122423 DOI: 10.1117/1.jbo.29.6.066501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Significance Spectroscopic single-molecule localization microscopy (sSMLM) takes advantage of nanoscopy and spectroscopy, enabling sub-10 nm resolution as well as simultaneous multicolor imaging of multi-labeled samples. Reconstruction of raw sSMLM data using deep learning is a promising approach for visualizing the subcellular structures at the nanoscale. Aim Develop a novel computational approach leveraging deep learning to reconstruct both label-free and fluorescence-labeled sSMLM imaging data. Approach We developed a two-network-model based deep learning algorithm, termed DsSMLM, to reconstruct sSMLM data. The effectiveness of DsSMLM was assessed by conducting imaging experiments on diverse samples, including label-free single-stranded DNA (ssDNA) fiber, fluorescence-labeled histone markers on COS-7 and U2OS cells, and simultaneous multicolor imaging of synthetic DNA origami nanoruler. Results For label-free imaging, a spatial resolution of 6.22 nm was achieved on ssDNA fiber; for fluorescence-labeled imaging, DsSMLM revealed the distribution of chromatin-rich and chromatin-poor regions defined by histone markers on the cell nucleus and also offered simultaneous multicolor imaging of nanoruler samples, distinguishing two dyes labeled in three emitting points with a separation distance of 40 nm. With DsSMLM, we observed enhanced spectral profiles with 8.8% higher localization detection for single-color imaging and up to 5.05% higher localization detection for simultaneous two-color imaging. Conclusions We demonstrate the feasibility of deep learning-based reconstruction for sSMLM imaging applicable to label-free and fluorescence-labeled sSMLM imaging data. We anticipate our technique will be a valuable tool for high-quality super-resolution imaging for a deeper understanding of DNA molecules' photophysics and will facilitate the investigation of multiple nanoscopic cellular structures and their interactions.
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Affiliation(s)
- Sunil Kumar Gaire
- North Carolina Agricultural and Technical State University, Department of Electrical and Computer Engineering, Greensboro, North Carolina, United States
| | - Ali Daneshkhah
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Ethan Flowerday
- University of Tulsa, Department of Computer Science and Cyber Security, Tulsa, Oklahoma, United States
| | - Ruyi Gong
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Jane Frederick
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Vadim Backman
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
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Chen H, Yan G, Wen MH, Brooks KN, Zhang Y, Huang PS, Chen TY. Advancements and Practical Considerations for Biophysical Research: Navigating the Challenges and Future of Super-resolution Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:331-344. [PMID: 38817319 PMCID: PMC11134610 DOI: 10.1021/cbmi.4c00019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 06/01/2024]
Abstract
The introduction of super-resolution microscopy (SRM) has significantly advanced our understanding of cellular and molecular dynamics, offering a detailed view previously beyond our reach. Implementing SRM in biophysical research, however, presents numerous challenges. This review addresses the crucial aspects of utilizing SRM effectively, from selecting appropriate fluorophores and preparing samples to analyzing complex data sets. We explore recent technological advancements and methodological improvements that enhance the capabilities of SRM. Emphasizing the integration of SRM with other analytical methods, we aim to overcome inherent limitations and expand the scope of biological insights achievable. By providing a comprehensive guide for choosing the most suitable SRM methods based on specific research objectives, we aim to empower researchers to explore complex biological processes with enhanced precision and clarity, thereby advancing the frontiers of biophysical research.
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Affiliation(s)
- Huanhuan Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Guangjie Yan
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Meng-Hsuan Wen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Kameron N. Brooks
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Yuteng Zhang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Pei-San Huang
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| | - Tai-Yen Chen
- Department of Chemistry, University of Houston, Houston, Texas 77204, United States
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11
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Mussini A, Delcanale P, Berni M, Pongolini S, Jordà-Redondo M, Agut M, Steinbach PJ, Nonell S, Abbruzzetti S, Viappiani C. Concanavalin A Delivers a Photoactive Protein to the Bacterial Wall. Int J Mol Sci 2024; 25:5751. [PMID: 38891937 PMCID: PMC11172101 DOI: 10.3390/ijms25115751] [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: 04/17/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024] Open
Abstract
Modular supramolecular complexes, where different proteins are assembled to gather targeting capability and photofunctional properties within the same structures, are of special interest for bacterial photodynamic inactivation, given their inherent biocompatibility and flexibility. We have recently proposed one such structure, exploiting the tetrameric bacterial protein streptavidin as the main building block, to target S. aureus protein A. To expand the palette of targets, we have linked biotinylated Concanavalin A, a sugar-binding protein, to a methylene blue-labelled streptavidin. By applying a combination of spectroscopy and microscopy, we demonstrate the binding of Concanavalin A to the walls of Gram-positive S. aureus and Gram-negative E. coli. Photoinactivation is observed for both bacterial strains in the low micromolar range, although the moderate affinity for the molecular targets and the low singlet oxygen yields limit the overall efficiency. Finally, we apply a maximum entropy method to the analysis of autocorrelation traces, which proves particularly useful when interpreting signals measured for diffusing systems heterogeneous in size, such as fluorescent species bound to bacteria.
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Affiliation(s)
- Andrea Mussini
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Pietro Delcanale
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Melissa Berni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Strada dei Mercati, 13/A, 43126 Parma, Italy
| | - Stefano Pongolini
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia-Romagna, Strada dei Mercati, 13/A, 43126 Parma, Italy
| | - Mireia Jordà-Redondo
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Montserrat Agut
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Peter J. Steinbach
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Via Augusta 390, 08017 Barcelona, Spain
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
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12
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Bharadwaj A, Kumar A, Mitra R, Jaganathan BG, Boruah BR. Enhanced fluorescence blinking of AF647 fluorophores in Mowiol via violet and UV light induced recovery for superior localization microscopy. Methods Appl Fluoresc 2024; 12:035007. [PMID: 38740072 DOI: 10.1088/2050-6120/ad4ae6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/13/2024] [Indexed: 05/16/2024]
Abstract
Blinking of fluorophores is essential in the context of single molecule localization-based optical super-resolution microscopy methods. To make the fluorescence molecule undergo blinking specific complex chemical mounting buffer systems, combined with suitable oxygen scavengers, and reducing agents are required. For instance to realise blinking in widely used fluorescence tags, like Alexa Fluor 647 (AF647), they are to be mounted on anti-fading buffer such as Mowiol and reducing agent such as Beta (β) - ME. However, the quality of the super-resolved images is decided by the total number of blinking events or in other words net duration for which the fluorescence blinking persists. In this paper we investigate how a violet and UV light induced fluorescence recovery mechanism can enhance the duration of fluorescence blinking. Our study uses AF647 dye conjugated with Phalloidin antibody in U87MG cell line mounted on Mowiol andβ- ME. On the basis of the investigation we optimize the intensity, at the sample plane, of fluorescence excitation laser at 638 nm and fluorescence recovery beam at 405 nm or in the UV giving the maximum possible fluorescence blinking duration. We observe that the longer blinking duration, using the optimized illumination scheme, has brought down the resolution in the super-resolved image, as given by Fourier Ring Correlation method, from 168 nm to 112 nm, while the separation between two nearby resolvable filaments has been brought down to ≤ 60 nm.
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Affiliation(s)
- Anupam Bharadwaj
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Amalesh Kumar
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Rumela Mitra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bithiah Grace Jaganathan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bosanta R Boruah
- Department of Physics, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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13
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Qiu L, Xu H, Sui B, Jiang P, Wang J, Xu D, Liang F, Ma T, Wang H, Chen J. Elucidating the Functional Mechanism of PTK7 in Cancer Development through Spatial Assembly Analysis Using Super Resolution Imaging. Anal Chem 2024; 96:7669-7678. [PMID: 38708542 DOI: 10.1021/acs.analchem.4c00588] [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: 05/07/2024]
Abstract
Protein tyrosine kinase-7 (PTK7) has been reported as a vital participant in the Wnt signaling pathway, influencing tumorigenesis and metastasis. However, their specific roles in the mechanisms underlying cancer development and progression remain elusive. Here, using direct stochastic optical reconstruction microscopy (dSTORM) with aptamer-probe labeling, we first revealed that a weakening clustering distribution of PTK7 on the basal membranes happened as cellular migration increased during cancer progression. This correspondence was further supported by a diminished aggregated state of PTK7 caused by direct enhancement of cell migration. By comparing the alterations in PTK7 distribution with activation or inhibition of specific Wnt signaling pathway, we speculated that PTK7 could modulate cell migration by participating in the interplay between canonical Wnt (in MCF7 cells) and noncanonical Wnt signals (in MDA-MB-231 cells). Furthermore, we discovered that the spatial distribution morphology of PTK7 was also subject to the hydrolysis ability and activation state of the related hydrolase Matrix metallopeptidase14 (MMP14). This function-related specific assembly of PTK7 reveals a clear relationship between PTK7 and cancer. Meanwhile, potential molecular interactions predicted by the apparent assembly morphology can promote a deep understanding of the functional mechanism of PTK7 in cancer progress.
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Affiliation(s)
- Luqi Qiu
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Haijiao Xu
- Research Center of Biomembranomics, State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, Jilin 130022, China
| | - Binglin Sui
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Pengwei Jiang
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Jiaqi Wang
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Dandan Xu
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Feng Liang
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Tao Ma
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
| | - Hongda Wang
- Research Center of Biomembranomics, State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 5625 Renmin Street, Changchun, Jilin 130022, China
| | - Junling Chen
- School of Chemistry & Chemical Engineering, Wuhan University of Science and Technology, 947 Heping Street, Wuhan, Hubei 430081, China
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14
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Batey JE, Kim GW, Yang M, Heffer DC, Pott ED, Giang H, Dong B. High throughput spectrally resolved super-resolution fluorescence microscopy with improved photon usage. Analyst 2024; 149:2801-2805. [PMID: 38682955 DOI: 10.1039/d4an00343h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Single-molecule localization microscopy (SMLM), a type of super-resolution fluorescence microscopy, has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features at the nanoscopic level. It drastically improves the resolution of optical microscopes beyond the diffraction limit, with which previously unresolvable structures can now be studied. Spectrally resolved super-resolution fluorescence microscopy via multiplexing of different fluorophores is one of the greatest advancements among SMLM techniques. However, current spectrally resolved SMLM (SR-SMLM) methodologies present low spatial resolution due to loss of photons, low throughput due to spectral interferences, or require complex optical systems. Here, we overcome these drawbacks by developing a SR-SMLM methodology using a color glass filter. It enables high throughput and improved photon usage for hyperspectral imaging at the nanoscopic level. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5 nm spectral precisions.
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Affiliation(s)
- James Ethan Batey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Geun Wan Kim
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Meek Yang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Darby Claire Heffer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Elric Dion Pott
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Hannah Giang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Bin Dong
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
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15
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Liu Y, Cui S, Ma W, Wu Y, Xin R, Bai Y, Chen Z, Xu J, Ge J. Direct Imaging of Protein Clusters in Metal-Organic Frameworks. J Am Chem Soc 2024; 146:12565-12576. [PMID: 38661569 DOI: 10.1021/jacs.4c01483] [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: 04/26/2024]
Abstract
Protein@metal-organic frameworks (P@MOFs) prepared by coprecipitation of protein, metal ions, and organic ligands represent an effective method for protein stabilization with a wide spectrum of applications. However, the formation mechanism of P@MOFs via the coprecipitation process and the reason why proteins can retain their biological activity in the frameworks with highly concentrated metal ions remain unsettled. Here, by a combined methodology of single molecule localization microscopy and clustering analysis, we discovered that in this process enzyme molecules form clusters with metal ions and organic ligands, contributing to both the nucleation and subsequent crystal growth. We proposed that the clusters played an important role in the retention of overall enzymatic activity by sacrificing protein molecules on the cluster surface. This work offers fresh perspectives on protein behaviors in the formation of P@MOFs, inspiring future endeavors in the design and development of artificial bionanocomposites with high biological activities.
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Affiliation(s)
- Yu Liu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Shitong Cui
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Wenjun Ma
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yibo Wu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ruobing Xin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yunxiu Bai
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Zhuo Chen
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jianhong Xu
- The State Key Laboratory of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Jun Ge
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, China
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16
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Lebreton S, Paladino S, Lelek M, Tramier M, Zimmer C, Zurzolo C. Actin cytoskeleton differently regulates cell surface organization of GPI-anchored proteins in polarized epithelial cells and fibroblasts. Front Mol Biosci 2024; 11:1360142. [PMID: 38774234 PMCID: PMC11106487 DOI: 10.3389/fmolb.2024.1360142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/11/2024] [Indexed: 05/24/2024] Open
Abstract
The spatiotemporal compartmentalization of membrane-associated glycosylphosphatidylinositol-anchored proteins (GPI-APs) on the cell surface regulates their biological activities. These GPI-APs occupy distinct cellular functions such as enzymes, receptors, and adhesion molecules, and they are implicated in several vital cellular processes. Thus, unraveling the mechanisms and regulators of their membrane organization is essential. In polarized epithelial cells, GPI-APs are enriched at the apical surface, where they form small cholesterol-independent homoclusters and larger heteroclusters accommodating multiple GPI-AP species, all confined within areas of approximately 65-70 nm in diameter. Notably, GPI-AP homoclustering occurs in the Golgi apparatus through a cholesterol- and calcium-dependent mechanism that drives their apical sorting. Despite the critical role of Golgi GPI-AP clustering in their cell surface organization and the importance of cholesterol in heterocluster formation, the regulatory mechanisms governing GPI-AP surface organization, particularly in the context of epithelial polarity, remain elusive. Given that the actin cytoskeleton undergoes substantial remodeling during polarity establishment, this study explores whether the actin cytoskeleton regulates the spatiotemporal apical organization of GPI-APs in MDCK cells. Utilizing various imaging techniques (number and brightness, FRET/FLIM, and dSTORM coupled to pair correlation analysis), we demonstrate that the apical organization of GPI-APs, at different scales, does not rely on the actin cytoskeleton, unlike in fibroblastic cells. Interestingly, calcium chelation disrupts the organization of GPI-APs at the apical surface by impairing Golgi GPI-AP clustering, emphasizing the existence of an interplay among Golgi clustering, apical sorting, and surface organization in epithelial cells. In summary, our findings unveil distinct mechanisms regulating the organization of GPI-APs in cell types of different origins, plausibly allowing them to adapt to different external signals and different cellular environments in order to achieve specialized functions.
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Affiliation(s)
- Stéphanie Lebreton
- Institut Pasteur, Unité de Trafic Membranaire et Pathogenèse, Paris, France
| | - Simona Paladino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Marc Tramier
- Université Rennes, Centre National de la recherche scientifique, IGDR (Genetics and Development Institute of Rennes), Unité mixte de receherche 6290, Rennes, France
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational Biology, Institut Pasteur, Paris, France
- Rudolf Virchow Center, University of Würzburg, Würzburg, Germany
| | - Chiara Zurzolo
- Institut Pasteur, Unité de Trafic Membranaire et Pathogenèse, Paris, France
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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17
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Liu J, Yu X, Braucht A, Smith S, Wang C. N-Cadherin Targeted Melanin Nanoparticles Reverse the Endothelial-Mesenchymal Transition in Vascular Endothelial Cells to Potentially Slow the Progression of Atherosclerosis and Cancer. ACS NANO 2024; 18:8229-8247. [PMID: 38427686 DOI: 10.1021/acsnano.3c12281] [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: 03/03/2024]
Abstract
Endothelial-mesenchymal transition (EndoMT) of vascular endothelial cells has recently been considered as a key player in the early progression of a variety of vascular and nonvascular diseases, including atherosclerosis, cancer, and organ fibrosis. However, current strategies attempting to identify pharmacological inhibitors to block the regulatory pathways of EndoMT suffer from poor selectivity, unwanted side effects, and a heterogeneous response from endothelial cells with different origins. Furthermore, EndoMT inhibitors focus on preventing EndoMT, leaving the endothelial cells that have already undergone EndoMT unresolved. Here, we report the design of a simple but powerful nanoparticle system (i.e., N-cadherin targeted melanin nanoparticles) to convert cytokine-activated, mesenchymal-like endothelial cells back to their original endothelial phenotype. We term this process "Reversed EndoMT" (R-EndoMT). R-EndoMT allows the impaired endothelial barriers to recover their quiescence and intactness, with significantly reduced leukocyte and cancer cell adhesion and transmigration, which could potentially stop atheromatous plaque formation and cancer metastasis in the early stages. R-EndoMT is achieved on different endothelial cell types originating from arteries, veins, and capillaries, independent of activating cytokines. We reveal that N-cadherin targeted melanin nanoparticles reverse EndoMT by downregulating an N-cadherin dependent RhoA activation pathway. Overall, this approach offers a different prospect to treat multiple EndoMT-associated diseases by designing nanoparticles to reverse the phenotypical transition of endothelial cells.
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Affiliation(s)
- Jinyuan Liu
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
- BioSystems Networks & Translational Research (BioSNTR), 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
| | - Xiao Yu
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
- BioSystems Networks & Translational Research (BioSNTR), 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
| | - Annaliese Braucht
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
- BioSystems Networks & Translational Research (BioSNTR), 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
| | - Steve Smith
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
- BioSystems Networks & Translational Research (BioSNTR), 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
| | - Congzhou Wang
- Nanoscience and Biomedical Engineering, South Dakota School of Mines and Technology, 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
- BioSystems Networks & Translational Research (BioSNTR), 501 E St Joseph Street, Rapid City, South Dakota 57701, United States
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18
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Gunasekara H, Perera T, Chao CJ, Bruno J, Saed B, Anderson J, Zhao Z, Hu YS. Quantitative Superresolution Imaging of F-Actin in the Cell Body and Cytoskeletal Protrusions Using Phalloidin-Based Single-Molecule Labeling and Localization Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583337. [PMID: 38496456 PMCID: PMC10942307 DOI: 10.1101/2024.03.04.583337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We present single-molecule labeling and localization microscopy (SMLLM) using dye-conjugated phalloidin to achieve enhanced superresolution imaging of filamentous actin (F-actin). We demonstrate that the intrinsic phalloidin dissociation enables SMLLM in an imaging buffer containing low concentrations of dye-conjugated phalloidin. We further show enhanced single-molecule labeling by chemically promoting phalloidin dissociation. Two benefits of phalloidin-based SMLLM are better preservation of cellular structures sensitive to mechanical and shear forces during standard sample preparation and more consistent F-actin quantification at the nanoscale. In a proof-of-concept study, we employed SMLLM to super-resolve F-actin structures in U2OS and dendritic cells (DCs) and demonstrate more consistent F-actin quantification in the cell body and structurally delicate cytoskeletal proportions, which we termed membrane fibers, of DCs compared to direct stochastic optical reconstruction microscopy (dSTORM). Using DC2.4 mouse dendritic cells as the model system, we show F-actin redistribution from podosomes to actin filaments and altered prevalence of F-actin-associated membrane fibers on the culture glass surface after lipopolysaccharide exposure. While our work demonstrates SMLLM for F-actin, the concept opens new possibilities for protein-specific single-molecule labeling and localization in the same step using commercially available reagents.
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Affiliation(s)
- Hirushi Gunasekara
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Thilini Perera
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Chih-Jia Chao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Joshua Bruno
- Department of Biological Sciences, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Badeia Saed
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Jesse Anderson
- Department of Chemical Engineering, College of Engineering, University of Illinois Chicago, Chicago, IL, 60607, USA
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Ying S. Hu
- Department of Chemistry, College of Liberal Arts and Sciences, University of Illinois Chicago, Chicago, IL, 60607, USA
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19
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Singh MK, Kenney LJ. Visualizing the invisible: novel approaches to visualizing bacterial proteins and host-pathogen interactions. Front Bioeng Biotechnol 2024; 12:1334503. [PMID: 38415188 PMCID: PMC10898356 DOI: 10.3389/fbioe.2024.1334503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
Host-pathogen interactions play a critical role in infectious diseases, and understanding the underlying mechanisms is vital for developing effective therapeutic strategies. The visualization and characterization of bacterial proteins within host cells is key to unraveling the dynamics of these interactions. Various protein labeling strategies have emerged as powerful tools for studying host-pathogen interactions, enabling the tracking, localization, and functional analysis of bacterial proteins in real-time. However, the labeling and localization of Salmonella secreted type III secretion system (T3SS) effectors in host cells poses technical challenges. Conventional methods disrupt effector stoichiometry and often result in non-specific staining. Bulky fluorescent protein fusions interfere with effector secretion, while other tagging systems such as 4Cys-FLaSH/Split-GFP suffer from low labeling specificity and a poor signal-to-noise ratio. Recent advances in state-of-the-art techniques have augmented the existing toolkit for monitoring the translocation and dynamics of bacterial effectors. This comprehensive review delves into the bacterial protein labeling strategies and their application in imaging host-pathogen interactions. Lastly, we explore the obstacles faced and potential pathways forward in the realm of protein labeling strategies for visualizing interactions between hosts and pathogens.
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Affiliation(s)
- Moirangthem Kiran Singh
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
| | - Linda J. Kenney
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, United States
- Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, United States
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20
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Beckers CJ, Mrestani A, Komma F, Dannhäuser S. Versatile Endogenous Editing of GluRIIA in Drosophila melanogaster. Cells 2024; 13:323. [PMID: 38391936 PMCID: PMC10887371 DOI: 10.3390/cells13040323] [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: 01/15/2024] [Revised: 02/05/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Glutamate receptors at the postsynaptic side translate neurotransmitter release from presynapses into postsynaptic excitation. They play a role in many forms of synaptic plasticity, e.g., homeostatic scaling of the receptor field, activity-dependent synaptic plasticity and the induction of presynaptic homeostatic potentiation (PHP). The latter process has been extensively studied at Drosophila melanogaster neuromuscular junctions (NMJs). The genetic removal of the glutamate receptor subunit IIA (GluRIIA) leads to an induction of PHP at the synapse. So far, mostly imprecise knockouts of the GluRIIA gene have been utilized. Furthermore, mutated and tagged versions of GluRIIA have been examined in the past, but most of these constructs were not expressed under endogenous regulatory control or involved the mentioned imprecise GluRIIA knockouts. We performed CRISPR/Cas9-assisted gene editing at the endogenous locus of GluRIIA. This enabled the investigation of the endogenous expression pattern of GluRIIA using tagged constructs with an EGFP and an ALFA tag for super-resolution immunofluorescence imaging, including structured illumination microscopy (SIM) and direct stochastic optical reconstruction microscopy (dSTORM). All GluRIIA constructs exhibited full functionality and PHP could be induced by philanthotoxin at control levels. By applying hierarchical clustering algorithms to analyze the dSTORM data, we detected postsynaptic receptor cluster areas of ~0.15 µm2. Consequently, our constructs are suitable for ultrastructural analyses of GluRIIA.
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Affiliation(s)
- Constantin J. Beckers
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, D-97070 Würzburg, Germany
| | - Achmed Mrestani
- Department of Neurology, University of Leipzig Medical Center, D-04103 Leipzig, Germany;
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, D-04103 Leipzig, Germany
| | - Fabian Komma
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, D-97070 Würzburg, Germany
| | - Sven Dannhäuser
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, D-97070 Würzburg, Germany
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21
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Sisario D, Spindler M, Ermer KJ, Grütz N, Nicolai L, Gaertner F, Machesky LM, Bender M. Differential Role of the RAC1-Binding Proteins FAM49b (CYRI-B) and CYFIP1 in Platelets. Cells 2024; 13:299. [PMID: 38391912 PMCID: PMC10886774 DOI: 10.3390/cells13040299] [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: 12/15/2023] [Revised: 01/24/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Platelet function at vascular injury sites is tightly regulated through the actin cytoskeleton. The Wiskott-Aldrich syndrome protein-family verprolin-homologous protein (WAVE)-regulatory complex (WRC) activates lamellipodia formation via ARP2/3, initiated by GTP-bound RAC1 interacting with the WRC subunit CYFIP1. The protein FAM49b (Family of Unknown Function 49b), also known as CYRI-B (CYFIP-Related RAC Interactor B), has been found to interact with activated RAC1, leading to the negative regulation of the WRC in mammalian cells. To investigate the role of FAM49b in platelet function, we studied platelet-specific Fam49b-/--, Cyfip1-/--, and Cyfip1/Fam49b-/--mice. Platelet counts and activation of Fam49b-/- mice were comparable to those of control mice. On fully fibrinogen-coated surfaces, Fam49b-/--platelets spread faster with an increased mean projected cell area than control platelets, whereas Cyfip1/Fam49b-/--platelets did not form lamellipodia, phenocopying the Cyfip1-/--platelets. However, Fam49b-/--platelets often assumed a polarized shape and were more prone to migrate on fibrinogen-coated surfaces. On 2D structured micropatterns, however, Fam49b-/--platelets displayed reduced spreading, whereas spreading of Cyfip1-/-- and Cyfip1/Fam49b-/--platelets was enhanced. In summary, FAM49b contributes to the regulation of morphology and migration of spread platelets, but to exert its inhibitory effect on actin polymerization, the functional WAVE complex must be present.
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Affiliation(s)
- Dmitri Sisario
- Institute of Experimental Biomedicine–Chair I, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Markus Spindler
- Institute of Experimental Biomedicine–Chair I, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Katharina J. Ermer
- Institute of Experimental Biomedicine–Chair I, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Noah Grütz
- Institute of Experimental Biomedicine–Chair I, University Hospital Würzburg, 97080 Würzburg, Germany
| | - Leo Nicolai
- Medizinische Klinik und Poliklinik I, University Hospital Ludwig, Maximilian University, 81377 Munich, Germany (F.G.)
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, 81377 Munich, Germany
| | - Florian Gaertner
- Medizinische Klinik und Poliklinik I, University Hospital Ludwig, Maximilian University, 81377 Munich, Germany (F.G.)
- German Centre for Cardiovascular Research, Partner Site Munich Heart Alliance, 81377 Munich, Germany
| | - Laura M. Machesky
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Markus Bender
- Institute of Experimental Biomedicine–Chair I, University Hospital Würzburg, 97080 Würzburg, Germany
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22
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Carrara SC, Davila-Lezama A, Cabriel C, Berenschot EJ, Krol S, Gardeniers J, Izeddin I, Kolmar H, Susarrey-Arce A. 3D topographies promote macrophage M2d-Subset differentiation. Mater Today Bio 2024; 24:100897. [PMID: 38169974 PMCID: PMC10758855 DOI: 10.1016/j.mtbio.2023.100897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 11/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
In vitro cellular models denote a crucial part of drug discovery programs as they aid in identifying successful drug candidates based on their initial efficacy and potency. While tremendous headway has been achieved in improving 2D and 3D culture techniques, there is still a need for physiologically relevant systems that can mimic or alter cellular responses without the addition of external biochemical stimuli. A way forward to alter cellular responses is using physical cues, like 3D topographical inorganic substrates, to differentiate macrophage-like cells. Herein, protein secretion and gene expression markers for various macrophage subsets cultivated on a 3D topographical substrate are investigated. The results show that macrophages differentiate into anti-inflammatory M2-type macrophages, secreting increased IL-10 levels compared to the controls. Remarkably, these macrophage cells are differentiated into the M2d subset, making up the main component of tumour-associated macrophages (TAMs), as measured by upregulated Il-10 and Vegf mRNA. M2d subset differentiation is attributed to the topographical substrates with 3D fractal-like geometries arrayed over the surface, else primarily achieved by tumour-associated factors in vivo. From a broad perspective, this work paves the way for implementing 3D topographical inorganic surfaces for drug discovery programs, harnessing the advantages of in vitro assays without external stimulation and allowing the rapid characterisation of therapeutic modalities in physiologically relevant environments.
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Affiliation(s)
- Stefania C. Carrara
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Amanda Davila-Lezama
- Facultad de Ciencias de la Salud (FACISALUD), Universidad Autónoma de Baja California, Blvd. Universitario 1000, Valle de las Palmas, 22260 Tijuana, Mexico
- Mesoscale Chemical Systems, MESA+ Institute, University of Twente, P.O. Box 217, 7500AE Enschede, the Netherlands
| | - Clément Cabriel
- Institut Langevin, ESPCI Paris, CNRS, Université PSL, 75005 Paris, France
| | - Erwin J.W. Berenschot
- Mesoscale Chemical Systems, MESA+ Institute, University of Twente, P.O. Box 217, 7500AE Enschede, the Netherlands
| | - Silke Krol
- Mesoscale Chemical Systems, MESA+ Institute, University of Twente, P.O. Box 217, 7500AE Enschede, the Netherlands
- Encytos B.V., Piet Heinstraat 12, Enschede, the Netherlands
| | - J.G.E. Gardeniers
- Mesoscale Chemical Systems, MESA+ Institute, University of Twente, P.O. Box 217, 7500AE Enschede, the Netherlands
| | - Ignacio Izeddin
- Institut Langevin, ESPCI Paris, CNRS, Université PSL, 75005 Paris, France
| | - Harald Kolmar
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Alarich-Weiss-Strasse 4, D-64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Arturo Susarrey-Arce
- Mesoscale Chemical Systems, MESA+ Institute, University of Twente, P.O. Box 217, 7500AE Enschede, the Netherlands
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23
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Tolstik E, Lehnart SE, Soeller C, Lorenz K, Sacconi L. Cardiac multiscale bioimaging: from nano- through micro- to mesoscales. Trends Biotechnol 2024; 42:212-227. [PMID: 37806897 DOI: 10.1016/j.tibtech.2023.08.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 10/10/2023]
Abstract
Cardiac multiscale bioimaging is an emerging field that aims to provide a comprehensive understanding of the heart and its functions at various levels, from the molecular to the entire organ. It combines both physiologically and clinically relevant dimensions: from nano- and micrometer resolution imaging based on vibrational spectroscopy and high-resolution microscopy to assess molecular processes in cardiac cells and myocardial tissue, to mesoscale structural investigations to improve the understanding of cardiac (patho)physiology. Tailored super-resolution deep microscopy with advanced proteomic methods and hands-on experience are thus strategically combined to improve the quality of cardiovascular research and support future medical decision-making by gaining additional biomolecular information for translational and diagnostic applications.
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Affiliation(s)
- Elen Tolstik
- Department of Cardiovascular Pharmacology, Translational Research, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. Bunsen-Kirchhoff-Strasse 11, 44139 Dortmund, Germany.
| | - Stephan E Lehnart
- Department of Cardiology and Pneumology, Cellular Biophysics and Translational Cardiology Section, Heart Research Center Göttingen, University Medical Center Göttingen, Georg-August University Göttingen, Robert-Koch-Strasse 42a, 37075 Göttingen, Germany; Cluster of Excellence Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells (MBExC2067), University of Göttingen, 37073 Göttingen, Germany; Collaborative Research Center SFB1190 Compartmental Gates and Contact Sites in Cells, University of Göttingen, 37073 Göttingen, Germany
| | - Christian Soeller
- Department of Physiology, University of Bern, Bühlplatz 5, 3012 Bern, Switzerland
| | - Kristina Lorenz
- Department of Cardiovascular Pharmacology, Translational Research, Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V. Bunsen-Kirchhoff-Strasse 11, 44139 Dortmund, Germany; Institute of Pharmacology and Toxicology, University of Würzburg, Versbacher Strasse 9, 97078 Würzburg, Germany
| | - Leonardo Sacconi
- Institute of Clinical Physiology, National Research Council, Rome, Italy; Institute for Experimental Cardiovascular Medicine, University Freiburg, Elsässer Strasse 2q, 79110 Freiburg, Germany.
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24
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Seabury AG, Khodabocus AJ, Kogan IM, Hoy GR, DeSalvo GA, Wustholz KL. Blinking characteristics of organic fluorophores for blink-based multiplexing. Commun Chem 2024; 7:18. [PMID: 38280979 PMCID: PMC10821931 DOI: 10.1038/s42004-024-01106-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.
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Affiliation(s)
| | | | | | - Grayson R Hoy
- Chemistry Department, William & Mary, Williamsburg, VA, USA
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25
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Xu F, Zhang S, Ma L, Hou Y, Li J, Denisenko A, Li Z, Spatz J, Wrachtrup J, Lei H, Cao Y, Wei Q, Chu Z. Quantum-enhanced diamond molecular tension microscopy for quantifying cellular forces. SCIENCE ADVANCES 2024; 10:eadi5300. [PMID: 38266085 PMCID: PMC10807811 DOI: 10.1126/sciadv.adi5300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/22/2023] [Indexed: 01/26/2024]
Abstract
The constant interplay and information exchange between cells and the microenvironment are essential to their survival and ability to execute biological functions. To date, a few leading technologies such as traction force microscopy, optical/magnetic tweezers, and molecular tension-based fluorescence microscopy are broadly used in measuring cellular forces. However, the considerable limitations, regarding the sensitivity and ambiguities in data interpretation, are hindering our thorough understanding of mechanobiology. Here, we propose an innovative approach, namely, quantum-enhanced diamond molecular tension microscopy (QDMTM), to precisely quantify the integrin-based cell adhesive forces. Specifically, we construct a force-sensing platform by conjugating the magnetic nanotags labeled, force-responsive polymer to the surface of a diamond membrane containing nitrogen-vacancy centers. Notably, the cellular forces will be converted into detectable magnetic variations in QDMTM. After careful validation, we achieved the quantitative cellular force mapping by correlating measurement with the established theoretical model. We anticipate our method can be routinely used in studies like cell-cell or cell-material interactions and mechanotransduction.
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Affiliation(s)
- Feng Xu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials and Engineering, Sichuan University, Chengdu 610065, China
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Shuxiang Zhang
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials and Engineering, Sichuan University, Chengdu 610065, China
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Linjie Ma
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Yong Hou
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
| | - Jie Li
- College of Biomass Science and Engineering, Sichuan University, Chengdu 610065, China
| | - Andrej Denisenko
- 3rd Institute of Physics, Research Center SCoPE and IQST, University of Stuttgart, 70569 Stuttgart, Germany
| | - Zifu Li
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Joachim Spatz
- Department for Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials (IMSEAM), University of Heidelberg, Im Neuenheimer Feld 225, 69120 Heidelberg, Germany
| | - Jörg Wrachtrup
- 3rd Institute of Physics, Research Center SCoPE and IQST, University of Stuttgart, 70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, Stuttgart, Germany
| | - Hai Lei
- National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yi Cao
- National Laboratory of Solid State Microstructures, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Qiang Wei
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials and Engineering, Sichuan University, Chengdu 610065, China
| | - Zhiqin Chu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
- School of Biomedical Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong, China
- Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong, China
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26
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Farkas D, Szikora S, Jijumon AS, Polgár TF, Patai R, Tóth MÁ, Bugyi B, Gajdos T, Bíró P, Novák T, Erdélyi M, Mihály J. Peripheral thickening of the sarcomeres and pointed end elongation of the thin filaments are both promoted by SALS and its formin interaction partners. PLoS Genet 2024; 20:e1011117. [PMID: 38198522 PMCID: PMC10805286 DOI: 10.1371/journal.pgen.1011117] [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: 06/24/2023] [Revised: 01/23/2024] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
During striated muscle development the first periodically repeated units appear in the premyofibrils, consisting of immature sarcomeres that must undergo a substantial growth both in length and width, to reach their final size. Here we report that, beyond its well established role in sarcomere elongation, the Sarcomere length short (SALS) protein is involved in Z-disc formation and peripheral growth of the sarcomeres. Our protein localization data and loss-of-function studies in the Drosophila indirect flight muscle strongly suggest that radial growth of the sarcomeres is initiated at the Z-disc. As to thin filament elongation, we used a powerful nanoscopy approach to reveal that SALS is subject to a major conformational change during sarcomere development, which might be critical to stop pointed end elongation in the adult muscles. In addition, we demonstrate that the roles of SALS in sarcomere elongation and radial growth are both dependent on formin type of actin assembly factors. Unexpectedly, when SALS is present in excess amounts, it promotes the formation of actin aggregates highly resembling the ones described in nemaline myopathy patients. Collectively, these findings helped to shed light on the complex mechanisms of SALS during the coordinated elongation and thickening of the sarcomeres, and resulted in the discovery of a potential nemaline myopathy model, suitable for the identification of genetic and small molecule inhibitors.
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Affiliation(s)
- Dávid Farkas
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Szilárd Szikora
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - A S Jijumon
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Tamás F Polgár
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Mónika Ágnes Tóth
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Beáta Bugyi
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Tamás Gajdos
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Péter Bíró
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Tibor Novák
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - József Mihály
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
- University of Szeged, Department of Genetics, Szeged, Hungary
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27
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Ortiz-Perez A, Zhang M, Fitzpatrick LW, Izquierdo-Lozano C, Albertazzi L. Advanced optical imaging for the rational design of nanomedicines. Adv Drug Deliv Rev 2024; 204:115138. [PMID: 37980951 DOI: 10.1016/j.addr.2023.115138] [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: 06/09/2023] [Revised: 11/06/2023] [Accepted: 11/08/2023] [Indexed: 11/21/2023]
Abstract
Despite the enormous potential of nanomedicines to shape the future of medicine, their clinical translation remains suboptimal. Translational challenges are present in every step of the development pipeline, from a lack of understanding of patient heterogeneity to insufficient insights on nanoparticle properties and their impact on material-cell interactions. Here, we discuss how the adoption of advanced optical microscopy techniques, such as super-resolution optical microscopies, correlative techniques, and high-content modalities, could aid the rational design of nanocarriers, by characterizing the cell, the nanomaterial, and their interaction with unprecedented spatial and/or temporal detail. In this nanomedicine arena, we will discuss how the implementation of these techniques, with their versatility and specificity, can yield high volumes of multi-parametric data; and how machine learning can aid the rapid advances in microscopy: from image acquisition to data interpretation.
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Affiliation(s)
- Ana Ortiz-Perez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Miao Zhang
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Laurence W Fitzpatrick
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Cristina Izquierdo-Lozano
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
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28
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McLaughlin MR, Weaver SA, Syed F, Evans-Molina C. Advanced Imaging Techniques for the Characterization of Subcellular Organelle Structure in Pancreatic Islet β Cells. Compr Physiol 2023; 14:5243-5267. [PMID: 38158370 DOI: 10.1002/cphy.c230002] [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: 01/03/2024]
Abstract
Type 2 diabetes (T2D) affects more than 32.3 million individuals in the United States, creating an economic burden of nearly $966 billion in 2021. T2D results from a combination of insulin resistance and inadequate insulin secretion from the pancreatic β cell. However, genetic and physiologic data indicate that defects in β cell function are the chief determinant of whether an individual with insulin resistance will progress to a diagnosis of T2D. The subcellular organelles of the insulin secretory pathway, including the endoplasmic reticulum, Golgi apparatus, and secretory granules, play a critical role in maintaining the heavy biosynthetic burden of insulin production, processing, and secretion. In addition, the mitochondria enable the process of insulin release by integrating the metabolism of nutrients into energy output. Advanced imaging techniques are needed to determine how changes in the structure and composition of these organelles contribute to the loss of insulin secretory capacity in the β cell during T2D. Several microscopy techniques, including electron microscopy, fluorescence microscopy, and soft X-ray tomography, have been utilized to investigate the structure-function relationship within the β cell. In this overview article, we will detail the methodology, strengths, and weaknesses of each approach. © 2024 American Physiological Society. Compr Physiol 14:5243-5267, 2024.
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Affiliation(s)
- Madeline R McLaughlin
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana, USA
| | - Staci A Weaver
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Farooq Syed
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Carmella Evans-Molina
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- The Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Roudebush VA Medical Center, Indianapolis, Indiana, USA
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29
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Munawar U, Zhou X, Prommersberger S, Nerreter S, Vogt C, Steinhardt MJ, Truger M, Mersi J, Teufel E, Han S, Haertle L, Banholzer N, Eiring P, Danhof S, Navarro-Aguadero MA, Fernandez-Martin A, Ortiz-Ruiz A, Barrio S, Gallardo M, Valeri A, Castellano E, Raab P, Rudert M, Haferlach C, Sauer M, Hudecek M, Martinez-Lopez J, Waldschmidt J, Einsele H, Rasche L, Kortüm KM. Impaired FADD/BID signaling mediates cross-resistance to immunotherapy in Multiple Myeloma. Commun Biol 2023; 6:1299. [PMID: 38129580 PMCID: PMC10739907 DOI: 10.1038/s42003-023-05683-4] [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: 07/03/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
The treatment landscape in multiple myeloma (MM) is shifting from genotoxic drugs to immunotherapies. Monoclonal antibodies, immunoconjugates, T-cell engaging antibodies and CART cells have been incorporated into routine treatment algorithms, resulting in improved response rates. Nevertheless, patients continue to relapse and the underlying mechanisms of resistance remain poorly understood. While Impaired death receptor signaling has been reported to mediate resistance to CART in acute lymphoblastic leukemia, this mechanism yet remains to be elucidated in context of novel immunotherapies for MM. Here, we describe impaired death receptor signaling as a novel mechanism of resistance to T-cell mediated immunotherapies in MM. This resistance seems exclusive to novel immunotherapies while sensitivity to conventional anti-tumor therapies being preserved in vitro. As a proof of concept, we present a confirmatory clinical case indicating that the FADD/BID axis is required for meaningful responses to novel immunotherapies thus we report impaired death receptor signaling as a novel resistance mechanism to T-cell mediated immunotherapy in MM.
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Affiliation(s)
- Umair Munawar
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Xiang Zhou
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | | | - Silvia Nerreter
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Cornelia Vogt
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | | | | | - Julia Mersi
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Eva Teufel
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Seungbin Han
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Larissa Haertle
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Nicole Banholzer
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Patrick Eiring
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
| | - Sophia Danhof
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | | | - Adrian Fernandez-Martin
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Alejandra Ortiz-Ruiz
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Santiago Barrio
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
- Altum Sequencing Co., Madrid, Spain
| | - Miguel Gallardo
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Antonio Valeri
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Eva Castellano
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Peter Raab
- Department of Orthopaedic Surgery, König Ludwig Haus, University of Würzburg, Würzburg, Germany
| | - Maximilian Rudert
- Department of Orthopaedic Surgery, König Ludwig Haus, University of Würzburg, Würzburg, Germany
| | | | - Markus Sauer
- Department of Hematology, Hospital Universitario 12 de Octubre, CNIO, Complutense University Madrid, Madrid, Spain
| | - Michael Hudecek
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - J Martinez-Lopez
- Department of Biotechnology and Biophysics, University of Würzburg, Würzburg, Germany
- Altum Sequencing Co., Madrid, Spain
| | - Johannes Waldschmidt
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Leo Rasche
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - K Martin Kortüm
- Department of Internal Medicine II, University Hospital of Würzburg, Würzburg, Germany.
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30
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Zhao W, Huang X, Yang J, Qu L, Qiu G, Zhao Y, Wang X, Su D, Ding X, Mao H, Jiu Y, Hu Y, Tan J, Zhao S, Pan L, Chen L, Li H. Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation. LIGHT, SCIENCE & APPLICATIONS 2023; 12:298. [PMID: 38097537 PMCID: PMC10721804 DOI: 10.1038/s41377-023-01321-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
In fluorescence microscopy, computational algorithms have been developed to suppress noise, enhance contrast, and even enable super-resolution (SR). However, the local quality of the images may vary on multiple scales, and these differences can lead to misconceptions. Current mapping methods fail to finely estimate the local quality, challenging to associate the SR scale content. Here, we develop a rolling Fourier ring correlation (rFRC) method to evaluate the reconstruction uncertainties down to SR scale. To visually pinpoint regions with low reliability, a filtered rFRC is combined with a modified resolution-scaled error map (RSM), offering a comprehensive and concise map for further examination. We demonstrate their performances on various SR imaging modalities, and the resulting quantitative maps enable better SR images integrated from different reconstructions. Overall, we expect that our framework can become a routinely used tool for biologists in assessing their image datasets in general and inspire further advances in the rapidly developing field of computational imaging.
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Affiliation(s)
- Weisong Zhao
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China
| | - Xiaoshuai Huang
- Biomedical Engineering Department, International Cancer Institute, Peking University Cancer Hospital and Institute, Health Science Center, Peking University, Beijing, China
| | - Jianyu Yang
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China
| | - Liying Qu
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Guohua Qiu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China
| | - Yue Zhao
- Department of Control Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Xinwei Wang
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Deer Su
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Xumin Ding
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Heng Mao
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Yaming Jiu
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Ying Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jiubin Tan
- Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China
| | - Shiqun Zhao
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China.
| | - Leiting Pan
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China.
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
- Beijing Academy of Artificial Intelligence, Beijing, China.
| | - Haoyu Li
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China.
- Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China.
- Frontiers Science Center for Matter Behave in Space Environment, Harbin Institute of Technology, Harbin, China.
- Key Laboratory of Micro-Systems and Micro-Structures Manufacturing of Ministry of Education, Harbin Institute of Technology, Harbin, China.
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31
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Delcanale P, Alampi MM, Mussini A, Fumarola C, Galetti M, Petronini PG, Viappiani C, Bruno S, Abbruzzetti S. A Photoactive Supramolecular Complex Targeting PD-L1 Reveals a Weak Correlation between Photoactivation Efficiency and Receptor Expression Levels in Non-Small-Cell Lung Cancer Tumor Models. Pharmaceutics 2023; 15:2776. [PMID: 38140116 PMCID: PMC10747218 DOI: 10.3390/pharmaceutics15122776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Photo-immunotherapy uses antibodies conjugated to photosensitizers to produce nanostructured constructs endowed with targeting properties and photo-inactivation capabilities towards tumor cells. The superficial receptor density on cancer cells is considered a determining factor for the efficacy of the photodynamic treatment. In this work, we propose the use of a photoactive conjugate that consists of the clinical grade PD-L1-binding monoclonal antibody Atezolizumab, covalently linked to either the well-known photosensitizer eosin or the fluorescent probe Alexa647. Using single-molecule localization microscopy (direct stochastic optical reconstruction microscopy, dSTORM), and an anti-PD-L1 monoclonal antibody labelled with Alexa647, we quantified the density of PD-L1 receptors exposed on the cell surface in two human non-small-cell lung cancer lines (H322 and A549) expressing PD-L1 to a different level. We then investigated if this value correlates with the effectiveness of the photodynamic treatment. The photodynamic treatment of H322 and A549 with the photo-immunoconjugate demonstrated its potential for PDT treatments, but the efficacy did not correlate with the PD-L1 expression levels. Our results provide additional evidence that receptor density does not determine a priori the level of photo-induced cell death.
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Affiliation(s)
- Pietro Delcanale
- Department of Mathematical, Physical and Computer Sciences, University of Parma, 43124 Parma, Italy; (P.D.); (M.M.A.); (A.M.); (C.V.)
| | - Manuela Maria Alampi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, 43124 Parma, Italy; (P.D.); (M.M.A.); (A.M.); (C.V.)
| | - Andrea Mussini
- Department of Mathematical, Physical and Computer Sciences, University of Parma, 43124 Parma, Italy; (P.D.); (M.M.A.); (A.M.); (C.V.)
| | - Claudia Fumarola
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (C.F.); (P.G.P.)
| | - Maricla Galetti
- Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, INAIL-Italian Workers’ Compensation Authority, 00078 Rome, Italy;
| | - Pier Giorgio Petronini
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (C.F.); (P.G.P.)
| | - Cristiano Viappiani
- Department of Mathematical, Physical and Computer Sciences, University of Parma, 43124 Parma, Italy; (P.D.); (M.M.A.); (A.M.); (C.V.)
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
| | - Stefania Abbruzzetti
- Department of Mathematical, Physical and Computer Sciences, University of Parma, 43124 Parma, Italy; (P.D.); (M.M.A.); (A.M.); (C.V.)
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32
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Mrestani A, Dannhäuser S, Pauli M, Kollmannsberger P, Hübsch M, Morris L, Langenhan T, Heckmann M, Paul MM. Nanoscaled RIM clustering at presynaptic active zones revealed by endogenous tagging. Life Sci Alliance 2023; 6:e202302021. [PMID: 37696575 PMCID: PMC10494931 DOI: 10.26508/lsa.202302021] [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: 03/02/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023] Open
Abstract
Chemical synaptic transmission involves neurotransmitter release from presynaptic active zones (AZs). The AZ protein Rab-3-interacting molecule (RIM) is important for normal Ca2+-triggered release. However, its precise localization within AZs of the glutamatergic neuromuscular junctions of Drosophila melanogaster remains elusive. We used CRISPR/Cas9-assisted genome engineering of the rim locus to incorporate small epitope tags for targeted super-resolution imaging. A V5-tag, derived from simian virus 5, and an HA-tag, derived from human influenza virus, were N-terminally fused to the RIM Zinc finger. Whereas both variants are expressed in co-localization with the core AZ scaffold Bruchpilot, electrophysiological characterization reveals that AP-evoked synaptic release is disturbed in rimV5-Znf but not in rimHA-Znf In addition, rimHA-Znf synapses show intact presynaptic homeostatic potentiation. Combining super-resolution localization microscopy and hierarchical clustering, we detect ∼10 RIMHA-Znf subclusters with ∼13 nm diameter per AZ that are compacted and increased in numbers in presynaptic homeostatic potentiation.
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Affiliation(s)
- Achmed Mrestani
- https://ror.org/00fbnyb24 Department of Neurophysiology, Institute of Physiology, University of Würzburg, Würzburg, Germany
- Department of Neurology, Leipzig University Medical Center, Leipzig, Germany
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Sven Dannhäuser
- https://ror.org/00fbnyb24 Department of Neurophysiology, Institute of Physiology, University of Würzburg, Würzburg, Germany
| | - Martin Pauli
- https://ror.org/00fbnyb24 Department of Neurophysiology, Institute of Physiology, University of Würzburg, Würzburg, Germany
| | | | - Martha Hübsch
- https://ror.org/00fbnyb24 Department of Neurophysiology, Institute of Physiology, University of Würzburg, Würzburg, Germany
| | - Lydia Morris
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Tobias Langenhan
- Division of General Biochemistry, Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Manfred Heckmann
- https://ror.org/00fbnyb24 Department of Neurophysiology, Institute of Physiology, University of Würzburg, Würzburg, Germany
| | - Mila M Paul
- https://ror.org/00fbnyb24 Department of Neurophysiology, Institute of Physiology, University of Würzburg, Würzburg, Germany
- https://ror.org/03pvr2g57 Department of Orthopedic Trauma, Hand, Plastic and Reconstructive Surgery, University Hospital of Würzburg, Würzburg, Germany
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33
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Wei Y, Zhao M, He T, Chen N, Rao L, Chen L, Zhang Y, Yang Y, Yuan Q. Quantitatively Lighting up the Spatial Organization of CD47/SIRPα Immune Checkpoints on the Cellular Membrane with Single-Molecule Localization Microscopy. ACS NANO 2023; 17:21626-21638. [PMID: 37878521 DOI: 10.1021/acsnano.3c06709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Immunotherapy including immune checkpoint inhibition has reinvigorated the current cancer treatment field. The development of efficient cancer immunotherapies depends on a thorough understanding of the status of immune checkpoints and how they interact. However, the distribution and spatial organization changes of immune checkpoints during their interactions at the single-molecule level remain difficult to directly visualize due to the lack of in situ imaging techniques with appropriate spatial and stoichiometric resolution. Herein, we report the direct visualization and quantification of the spatial distribution and organization of CD47 on the bladder tumor cell membrane and SIRPα on the macrophage membrane by using a single-molecule localization imaging technique called quantitative direct stochastic optical reconstruction microscopy (QdSTORM). Results showed that a portion of CD47 and SIRPα was present on cell membranes as heterogeneous clusters of varying sizes and densities prior to activation. Quantitative analyses of the reconstructed super-resolution images and theoretical simulation revealed that CD47 and SIRPα were reorganized into larger clusters upon binding to each other. Furthermore, we found that blocking the immune checkpoint interaction with small-molecule inhibitors or antibodies significantly impacted the spatial clustering behavior of CD47 on bladder tumor cells, demonstrating the promise of our QdSTORM strategy in elucidating the molecular mechanisms underlying immunotherapy. This work offers a promising strategy to advance our understanding of immune checkpoint state and interactions while also contributing to the fields including signal regulation and cancer therapy.
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Affiliation(s)
- Yurong Wei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Molecular Medicine, Renmin Hospital of Wuhan University, School of Microelectronics, Wuhan University, Wuhan 430072, P. R. China
| | - Min Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Molecular Medicine, Renmin Hospital of Wuhan University, School of Microelectronics, Wuhan University, Wuhan 430072, P. R. China
| | - Tianpei He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Molecular Medicine, Renmin Hospital of Wuhan University, School of Microelectronics, Wuhan University, Wuhan 430072, P. R. China
| | - Na Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Molecular Medicine, Renmin Hospital of Wuhan University, School of Microelectronics, Wuhan University, Wuhan 430072, P. R. China
| | - Li Rao
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China
| | - Long Chen
- Department of Computer and Information Science, Faculty of Science and Technology, University of Macau, Macau 999078, P. R. China
| | - Yun Zhang
- CAS Key Laboratory of Design and Assembly of Functional Nanostructures, and Fujian Provincial Key Laboratory of Nanomaterials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350025, P. R. China
| | - Yanbing Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Molecular Medicine, Renmin Hospital of Wuhan University, School of Microelectronics, Wuhan University, Wuhan 430072, P. R. China
| | - Quan Yuan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Molecular Medicine, Renmin Hospital of Wuhan University, School of Microelectronics, Wuhan University, Wuhan 430072, P. R. China
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34
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Geiser A, Foylan S, Tinning PW, Bryant NJ, Gould GW. GLUT4 dispersal at the plasma membrane of adipocytes: a super-resolved journey. Biosci Rep 2023; 43:BSR20230946. [PMID: 37791639 PMCID: PMC10600063 DOI: 10.1042/bsr20230946] [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: 09/07/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/05/2023] Open
Abstract
In adipose tissue, insulin stimulates glucose uptake by mediating the translocation of GLUT4 from intracellular vesicles to the plasma membrane. In 2010, insulin was revealed to also have a fundamental impact on the spatial distribution of GLUT4 within the plasma membrane, with the existence of two GLUT4 populations at the plasma membrane being defined: (1) as stationary clusters and (2) as diffusible monomers. In this model, in the absence of insulin, plasma membrane-fused GLUT4 are found to behave as clusters. These clusters are thought to arise from exocytic events that retain GLUT4 at their fusion sites; this has been proposed to function as an intermediate hub between GLUT4 exocytosis and re-internalisation. By contrast, insulin stimulation induces the dispersal of GLUT4 clusters into monomers and favours a distinct type of GLUT4-vesicle fusion event, known as fusion-with-release exocytosis. Here, we review how super-resolution microscopy approaches have allowed investigation of the characteristics of plasma membrane-fused GLUT4 and further discuss regulatory step(s) involved in the GLUT4 dispersal machinery, introducing the scaffold protein EFR3 which facilitates localisation of phosphatidylinositol 4-kinase type IIIα (PI4KIIIα) to the cell surface. We consider how dispersal may be linked to the control of transporter activity, consider whether macro-organisation may be a widely used phenomenon to control proteins within the plasma membrane, and speculate on the origin of different forms of GLUT4-vesicle exocytosis.
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Affiliation(s)
- Angéline Geiser
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
| | - Shannan Foylan
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
| | - Peter W Tinning
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
| | - Nia J Bryant
- Department of Biology, University of York, Heslington, York, U.K
| | - Gwyn W Gould
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, U.K
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35
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Peeters W, Toyouchi S, Fujita Y, Wolf M, Fortuni B, Fron E, Inose T, Hofkens J, Endo T, Miyata Y, Uji-i H. Remote Excitation of Tip-Enhanced Photoluminescence with a Parallel AgNW Coupler. ACS OMEGA 2023; 8:38386-38393. [PMID: 37867716 PMCID: PMC10586305 DOI: 10.1021/acsomega.3c04952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/05/2023] [Indexed: 10/24/2023]
Abstract
Tip-enhanced photoluminescence (TEPL) microscopy allows for the correlation of scanning probe microscopic images and photoluminescent spectra at the nanoscale level in a similar way to tip-enhanced Raman scattering (TERS) microscopy. However, due to the higher cross-section of fluorescence compared to Raman scattering, the diffraction-limited background signal generated by far-field excitation is a limiting factor in the achievable spatial resolution of TEPL. Here, we demonstrate a way to overcome this drawback by using remote excitation TEPL (RE-TEPL). With this approach, the excitation and detection positions are spatially separated, minimizing the far-field contribution. Two probe designs are evaluated, both experimentally and via simulations. The first system consists of gold nanoparticles (AuNPs) through photoinduced deposition on a silver nanowire (AgNW), and the second system consists of two offset parallel AgNWs. This latter coupler system shows a higher coupling efficiency and is used to successfully demonstrate RE-TEPL spectral mapping on a MoSe2/WSe2 lateral heterostructure to reveal spatial heterogeneity at the heterojunction.
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Affiliation(s)
- Wannes Peeters
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Shuichi Toyouchi
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Yasuhiko Fujita
- Research
Institute for Sustainable Chemistry, National
Institute of Advanced Industrial Science and Technology (AIST Chugoku), Kagamiyama 3-11-32, Higashi-hiroshima, Hiroshima 739-0046, Japan
| | - Mathias Wolf
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Beatrice Fortuni
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Eduard Fron
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
| | - Tomoko Inose
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- The
HAKUBI Center for Advanced Research, Kyoto
University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Johan Hofkens
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
- Max
Planck Institute for Polymer Research, Mainz 55128, Germany
| | - Takahiko Endo
- Department
of Physics, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Yasumitsu Miyata
- Department
of Physics, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
| | - Hiroshi Uji-i
- Division
of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, Heverlee B-3001, Belgium
- Institute
for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
- RIES, Hokkaido University, N20 W10, Kita-Ward, Sapporo 001-0020, Japan
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36
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Galbraith JA, Galbraith CG. Using single molecule imaging to explore intracellular heterogeneity. Int J Biochem Cell Biol 2023; 163:106455. [PMID: 37586643 PMCID: PMC10528986 DOI: 10.1016/j.biocel.2023.106455] [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: 02/28/2023] [Revised: 08/14/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular condensates such as liquid-liquid phase separations (LLPSs) or non-liquid, functionally significant molecular aggregates, including synaptic densities, nucleoli, and Amyloid fibrils. Molecular condensates trigger intracellular signaling and drive processes ranging from gene expression to cell division. However, the descriptions of condensates tend to be qualitative and correlative. Here, we indicate how single-molecule imaging and analyses can be applied to quantify condensates. We discuss the pros and cons of different techniques for measuring differences between transient molecular behaviors inside and outside condensates. Finally, we offer suggestions for how imaging and analyses from different time and space regimes can be combined to identify molecular behaviors indicative of condensates within the dynamic high-density intracellular environment.
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Affiliation(s)
- James A Galbraith
- Oregon Health and Science University, Quantitative and Systems Biology Program in BME and The Knight Cancer Institute, Portland, OR 97239, USA.
| | - Catherine G Galbraith
- Oregon Health and Science University, Quantitative and Systems Biology Program in BME and The Knight Cancer Institute, Portland, OR 97239, USA.
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37
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Németh-Szatmári O, Nagy-Mikó B, Györkei Á, Varga D, Kovács BBH, Igaz N, Bognár B, Rázga Z, Nagy G, Zsindely N, Bodai L, Papp B, Erdélyi M, Kiricsi M, Blastyák A, Collart MA, Boros IM, Villányi Z. Phase-separated ribosome-nascent chain complexes in genotoxic stress response. RNA (NEW YORK, N.Y.) 2023; 29:1557-1574. [PMID: 37460154 PMCID: PMC10578487 DOI: 10.1261/rna.079755.123] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 06/26/2023] [Indexed: 09/20/2023]
Abstract
Assemblysomes are EDTA- and RNase-resistant ribonucleoprotein (RNP) complexes of paused ribosomes with protruding nascent polypeptide chains. They have been described in yeast and human cells for the proteasome subunit Rpt1, and the disordered amino-terminal part of the nascent chain was found to be indispensable for the accumulation of the Rpt1-RNP into assemblysomes. Motivated by this, to find other assemblysome-associated RNPs we used bioinformatics to rank subunits of Saccharomyces cerevisiae protein complexes according to their amino-terminal disorder propensity. The results revealed that gene products involved in DNA repair are enriched among the top candidates. The Sgs1 DNA helicase was chosen for experimental validation. We found that indeed nascent chains of Sgs1 form EDTA-resistant RNP condensates, assemblysomes by definition. Moreover, upon exposure to UV, SGS1 mRNA shifted from assemblysomes to polysomes, suggesting that external stimuli are regulators of assemblysome dynamics. We extended our studies to human cell lines. The BLM helicase, ortholog of yeast Sgs1, was identified upon sequencing assemblysome-associated RNAs from the MCF7 human breast cancer cell line, and mRNAs encoding DNA repair proteins were overall enriched. Using the radiation-resistant A549 cell line, we observed by transmission electron microscopy that 1,6-hexanediol, an agent known to disrupt phase-separated condensates, depletes ring ribosome structures compatible with assemblysomes from the cytoplasm of cells and makes the cells more sensitive to X-ray treatment. Taken together, these findings suggest that assemblysomes may be a component of the DNA damage response from yeast to human.
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Affiliation(s)
- Orsolya Németh-Szatmári
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Bence Nagy-Mikó
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Ádám Györkei
- Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
- Section for Physiology and Cell Biology, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Dániel Varga
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Bálint Barna H Kovács
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Nóra Igaz
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Bence Bognár
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Zsolt Rázga
- Department of Pathology, Faculty of Medicine, University of Szeged, 6720 Szeged, Hungary
| | - Gábor Nagy
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Nóra Zsindely
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - László Bodai
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Balázs Papp
- Institute of Biochemistry, Biological Research Centre, 6726 Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, 6720 Szeged, Hungary
| | - Mónika Kiricsi
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - András Blastyák
- Institute of Genetics, Biological Research Centre, 6726 Szeged, Hungary
| | - Martine A Collart
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva 4, Switzerland
| | - Imre M Boros
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
| | - Zoltán Villányi
- Department of Biochemistry and Molecular Biology, University of Szeged, 6726 Szeged, Hungary
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38
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Royer CA, Tyers M, Tollis S. Absolute quantification of protein number and dynamics in single cells. Curr Opin Struct Biol 2023; 82:102673. [PMID: 37595512 DOI: 10.1016/j.sbi.2023.102673] [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: 04/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/20/2023]
Abstract
Quantitative characterization of protein abundance and interactions in live cells is necessary to understand and predict cellular behavior. The accurate determination of copy number for individual proteins and heterologous complexes in individual cells is critical because small changes in protein dosage, often less than two-fold, can have strong phenotypic consequences. Here, we review the merits and pitfalls of different quantitative fluorescence imaging methods for single-cell determination of protein abundance, localization, interactions, and dynamics. In particular, we discuss how scanning number and brightness (sN&B) and its variation, Raster scanning image correlation spectroscopy (RICS), exploit stochastic noise in small measurement volumes to quantify protein abundance, stoichiometry, and dynamics with high accuracy.
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Affiliation(s)
- Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy NY 12180, USA.
| | - Mike Tyers
- Program in Molecular Medicine, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Sylvain Tollis
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210 Finland
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39
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Chi W, Tan D, Qiao Q, Xu Z, Liu X. Spontaneously Blinking Rhodamine Dyes for Single-Molecule Localization Microscopy. Angew Chem Int Ed Engl 2023; 62:e202306061. [PMID: 37246144 DOI: 10.1002/anie.202306061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 05/30/2023]
Abstract
Single-molecule localization microscopy (SMLM) has found extensive applications in various fields of biology and chemistry. As a vital component of SMLM, fluorophores play an essential role in obtaining super-resolution fluorescence images. Recent research on spontaneously blinking fluorophores has greatly simplified the experimental setups and extended the imaging duration of SMLM. To support this crucial development, this review provides a comprehensive overview of the development of spontaneously blinking rhodamines from 2014 to 2023, as well as the key mechanistic aspects of intramolecular spirocyclization reactions. We hope that by offering insightful design guidelines, this review will contribute to accelerating the advancement of super-resolution imaging technologies.
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Affiliation(s)
- Weijie Chi
- Collaborative Innovation Center of One Health, School of Science, Hainan University, Renmin Road 58, Haikou, 570228, P. R. China
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Singapore
| | - Davin Tan
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Singapore
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, China
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, 487372, Singapore, Singapore
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40
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Sajman J, Yakovian O, Unger Deshet N, Almog S, Horn G, Waks T, Globerson Levin A, Sherman E. Nanoscale CAR Organization at the Immune Synapse Correlates with CAR-T Effector Functions. Cells 2023; 12:2261. [PMID: 37759484 PMCID: PMC10527520 DOI: 10.3390/cells12182261] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/03/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
T cells expressing chimeric antigen receptors (CARs) are at the forefront of clinical treatment of cancers. Still, the nanoscale organization of CARs at the interface of CAR-Ts with target cells, which is essential for TCR-mediated T cell activation, remains poorly understood. Here, we studied the nanoscale organization of CARs targeting CD138 proteoglycans in such fixed and live interfaces, generated optimally for single-molecule localization microscopy. CARs showed significant self-association in nanoclusters that was enhanced in interfaces with on-target cells (SKOV-3, CAG, FaDu) relative to negative cells (OVCAR-3). CARs also segregated more efficiently from the abundant membrane phosphatase CD45 in CAR-T cells forming such interfaces. CAR clustering and segregation from CD45 correlated with the effector functions of Ca++ influx and target cell killing. Our results shed new light on the nanoscale organization of CARs on the surfaces of CAR-Ts engaging on- and off-target cells, and its potential significance for CAR-Ts' efficacy and safety.
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Affiliation(s)
- Julia Sajman
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
- Jerusalem College of Technology, Jerusalem 91160, Israel
| | - Oren Yakovian
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
| | - Naamit Unger Deshet
- Immunology and Advanced CAR-T Cell Therapy Laboratory, Research & Development Department, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Shaked Almog
- Immunology and Advanced CAR-T Cell Therapy Laboratory, Research & Development Department, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Galit Horn
- Immunology and Advanced CAR-T Cell Therapy Laboratory, Research & Development Department, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Tova Waks
- Immunology and Advanced CAR-T Cell Therapy Laboratory, Research & Development Department, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Anat Globerson Levin
- Immunology and Advanced CAR-T Cell Therapy Laboratory, Research & Development Department, Tel-Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
- Dotan Center for Advanced Therapies, Tel-Aviv Sourasky Medical Center and Tel Aviv University, Tel Aviv 6423906, Israel
| | - Eilon Sherman
- Racah Institute of Physics, The Hebrew University, Jerusalem 91904, Israel
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Morgan STB, Whelan DR, Rozario AM. Visualizing DNA damage and repair using single molecule super resolution microscopy. Methods Cell Biol 2023; 182:237-245. [PMID: 38359980 DOI: 10.1016/bs.mcb.2023.02.004] [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] [Indexed: 02/17/2024]
Abstract
Single molecule super resolution microscopy overcomes the diffraction limit by separating individual fluorophore emissions over time, resulting in spatial resolutions that are far superior to epifluorescence microscopy. This allows for DNA damage response (DDR) events to be investigated in greater detail. A variety of DNA damaging drugs can be used on S-phase synchronized immortalized cell lines alongside 5-ethynyl-2'-deoxyuridine (EdU) pulse labelling to ultimately visualize DNA repair pathways at distinct time points and quantify colocalizations between nascent DNA and immunolabeled DDR proteins. This chapter will outline super resolution microscopy assays to interrogate the spatiotemporal organization of DNA repair proteins at damaged foci during DDR events within immortalized cell lines.
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Affiliation(s)
- Sophie T B Morgan
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Donna R Whelan
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia
| | - Ashley M Rozario
- La Trobe Institute for Molecular Science, La Trobe Rural Health School, La Trobe University, Bendigo, VIC, Australia.
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42
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Rinaldi DA, Kanagy WK, Kaye HC, Grattan RM, Lucero SR, Pérez MP, Wester MJ, Lidke KA, Wilson BS, Lidke DS. Antigen Geometry Tunes Mast Cell Signaling Through Distinct FcεRI Aggregation and Structural Changes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552060. [PMID: 37609336 PMCID: PMC10441289 DOI: 10.1101/2023.08.04.552060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Immunoreceptor tyrosine-based activation motif (ITAM)-containing Fc receptors are critical components of the innate and adaptive immune systems. FcεRI mediates the allergic response via crosslinking of IgE-bound receptors by multivalent antigens. Yet, the underlying molecular mechanisms that govern the response of FcεRI to specific antigens remain poorly understood. We compared responses induced by two antigens with distinct geometries, high valency DNP-BSA and trivalent DF3, and found unique secretion and receptor phosphorylation profiles that are due to differential recruitment of Lyn and SHIP1. To understand how these two antigens can cause such markedly different outcomes, we used direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging combined with Bayesian Grouping of Localizations (BaGoL) analysis to compare the nanoscale characteristics of FcεRI aggregates. DF3 aggregates were found to be smaller and more densely packed than DNP-BSA aggregates. Using lifetime-based Förster resonance energy transfer (FRET) measurements, we discovered that FcεRI subunits undergo structural rearrangements upon crosslinking with either antigen, and in response to interaction with monovalent antigen presented on a supported lipid bilayer. The extent of conformational change is positively correlated with signaling efficiency. Finally, we provide evidence for forces in optimizing FcεRI signaling, such that immobilizing DF3 on a rigid surface promoted degranulation while increasing DNP-BSA flexibility lowered degranulation. These results provide a link between the physical attributes of allergens, including size, shape, valency, and flexibility, and FcεRI signaling strength. Thus, the antigen modulates mast cell outcomes by creating unique aggregate geometries that tune FcεRI conformation, phosphorylation and signaling partner recruitment.
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Affiliation(s)
- Derek A. Rinaldi
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - William K. Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Present address: Department of Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Hannah C. Kaye
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Rachel M. Grattan
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Shayna R. Lucero
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | | | - Michael J. Wester
- Department Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Keith A. Lidke
- Department Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Bridget S. Wilson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
| | - Diane S. Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87131
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131
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43
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Basumatary J, Baro N, Zanacchi FC, Mondal PP. Temporally resolved SMLM (with large PAR shift) enabled visualization of dynamic HA cluster formation and migration in a live cell. Sci Rep 2023; 13:12561. [PMID: 37532749 PMCID: PMC10397235 DOI: 10.1038/s41598-023-39096-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/20/2023] [Indexed: 08/04/2023] Open
Abstract
The blinking properties of a single molecule are critical for single-molecule localization microscopy (SMLM). Typically, SMLM techniques involve recording several frames of diffraction-limited bright spots of single-molecules with a detector exposure time close to the blinking period. This sets a limit on the temporal resolution of SMLM to a few tens of milliseconds. Realizing that a substantial fraction of single molecules emit photons for time scales much shorter than the average blinking period, we propose accelerating data collection to capture these fast emitters. Here, we put forward a short exposure-based SMLM (shortSMLM) method powered by sCMOS detector for understanding dynamical events (both at single molecule and ensemble level). The technique is demonstrated on an Influenza-A disease model, where NIH3T3 cells (both fixed and live cells) were transfected by Dendra2-HA plasmid DNA. Analysis shows a 2.76-fold improvement in the temporal resolution that comes with a sacrifice in spatial resolution, and a particle resolution shift PAR-shift (in terms of localization precision) of [Formula: see text] 11.82 nm compared to standard SMLM. We visualized dynamic HA cluster formation in transfected cells post 24 h of DNA transfection. It is noted that a reduction in spatial resolution does not substantially alter cluster characteristics (cluster density, [Formula: see text] molecules/cluster, cluster spread, etc.) and, indeed, preserves critical features. Moreover, the time-lapse imaging reveals the dynamic formation and migration of Hemagglutinin (HA) clusters in a live cell. This suggests that [Formula: see text] using a synchronized high QE sCMOS detector (operated at short exposure times) is excellent for studying temporal dynamics in cellular system.
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Affiliation(s)
- Jigmi Basumatary
- Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, India
| | - Neptune Baro
- Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, India
| | | | - Partha Pratim Mondal
- Instrumentation and Applied Physics, Indian Institute of Science, Bangalore, India.
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Gardini L, Vignolini T, Curcio V, Pavone FS, Capitanio M. Optimization of highly inclined illumination for diffraction-limited and super-resolution microscopy. OPTICS EXPRESS 2023; 31:26208-26225. [PMID: 37710487 DOI: 10.1364/oe.492152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 09/16/2023]
Abstract
In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and of how this impacts on the image quality complicates the setting of HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy. We model the beam propagation through Gaussian optics and validate the model through far- and near-field experiments, thus characterizing the main geometrical features of the beam. Further, we fully quantify the effects of a progressive reduction of the inclined beam thickness on the image quality of both diffraction-limited and super-resolution images and we show that the most relevant impact is obtained by reducing the beam thickness to sub-cellular dimensions (< 3 µm). Based on this, we present a simple optical solution that exploits a rectangular slit to reduce the inclined beam thickness down to 2.6 µm while keeping a field-of-view dimension suited for cell imaging and allowing an increase in the number of localizations in super-resolution imaging of up to 2.6 folds.
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45
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Dimou E, Katsinelos T, Meisl G, Tuck BJ, Keeling S, Smith AE, Hidari E, Lam JYL, Burke M, Lövestam S, Ranasinghe RT, McEwan WA, Klenerman D. Super-resolution imaging unveils the self-replication of tau aggregates upon seeding. Cell Rep 2023; 42:112725. [PMID: 37393617 PMCID: PMC7614924 DOI: 10.1016/j.celrep.2023.112725] [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: 10/31/2022] [Revised: 04/03/2023] [Accepted: 06/14/2023] [Indexed: 07/04/2023] Open
Abstract
Tau is a soluble protein interacting with tubulin to stabilize microtubules. However, under pathological conditions, it becomes hyperphosphorylated and aggregates, a process that can be induced by treating cells with exogenously added tau fibrils. Here, we employ single-molecule localization microscopy to resolve the aggregate species formed in early stages of seeded tau aggregation. We report that entry of sufficient tau assemblies into the cytosol induces the self-replication of small tau aggregates, with a doubling time of 5 h inside HEK cells and 1 day in murine primary neurons, which then grow into fibrils. Seeding occurs in the vicinity of the microtubule cytoskeleton, is accelerated by the proteasome, and results in release of small assemblies into the media. In the absence of seeding, cells still spontaneously form small aggregates at lower levels. Overall, our work provides a quantitative picture of the early stages of templated seeded tau aggregation in cells.
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Affiliation(s)
- Eleni Dimou
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK.
| | - Taxiarchis Katsinelos
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Benjamin J Tuck
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Sophie Keeling
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Annabel E Smith
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Eric Hidari
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Jeff Y L Lam
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Melanie Burke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - Sofia Lövestam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Rohan T Ranasinghe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - William A McEwan
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK; UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, Hills Road, Cambridge CB2 0AH, UK.
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46
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Haake M, Haack B, Schäfer T, Harter PN, Mattavelli G, Eiring P, Vashist N, Wedekink F, Genssler S, Fischer B, Dahlhoff J, Mokhtari F, Kuzkina A, Welters MJP, Benz TM, Sorger L, Thiemann V, Almanzar G, Selle M, Thein K, Späth J, Gonzalez MC, Reitinger C, Ipsen-Escobedo A, Wistuba-Hamprecht K, Eichler K, Filipski K, Zeiner PS, Beschorner R, Goedemans R, Gogolla FH, Hackl H, Rooswinkel RW, Thiem A, Roche PR, Joshi H, Pühringer D, Wöckel A, Diessner JE, Rüdiger M, Leo E, Cheng PF, Levesque MP, Goebeler M, Sauer M, Nimmerjahn F, Schuberth-Wagner C, von Felten S, Mittelbronn M, Mehling M, Beilhack A, van der Burg SH, Riedel A, Weide B, Dummer R, Wischhusen J. Tumor-derived GDF-15 blocks LFA-1 dependent T cell recruitment and suppresses responses to anti-PD-1 treatment. Nat Commun 2023; 14:4253. [PMID: 37474523 PMCID: PMC10359308 DOI: 10.1038/s41467-023-39817-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 06/09/2023] [Indexed: 07/22/2023] Open
Abstract
Immune checkpoint blockade therapy is beneficial and even curative for some cancer patients. However, the majority don't respond to immune therapy. Across different tumor types, pre-existing T cell infiltrates predict response to checkpoint-based immunotherapy. Based on in vitro pharmacological studies, mouse models and analyses of human melanoma patients, we show that the cytokine GDF-15 impairs LFA-1/β2-integrin-mediated adhesion of T cells to activated endothelial cells, which is a pre-requisite of T cell extravasation. In melanoma patients, GDF-15 serum levels strongly correlate with failure of PD-1-based immune checkpoint blockade therapy. Neutralization of GDF-15 improves both T cell trafficking and therapy efficiency in murine tumor models. Thus GDF-15, beside its known role in cancer-related anorexia and cachexia, emerges as a regulator of T cell extravasation into the tumor microenvironment, which provides an even stronger rationale for therapeutic anti-GDF-15 antibody development.
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Affiliation(s)
- Markus Haake
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Beatrice Haack
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Tina Schäfer
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Patrick N Harter
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Neurological Institute (Edinger Institute), University Hospital, Goethe University, Frankfurt/Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt/Main, Germany
- Center for Neuropathology and Prion Research, Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Greta Mattavelli
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | - Patrick Eiring
- Department of Biotechnology and Biophysics, Julius Maximilians University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Neha Vashist
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Florian Wedekink
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | | | - Birgitt Fischer
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Julia Dahlhoff
- Department of Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Fatemeh Mokhtari
- Department of Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Anastasia Kuzkina
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Marij J P Welters
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Tamara M Benz
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Lena Sorger
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Vincent Thiemann
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Giovanni Almanzar
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- Department of Pediatrics, University Hospital Würzburg, Würzburg, Germany
| | - Martina Selle
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Klara Thein
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Jacob Späth
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | | | - Carmen Reitinger
- Division of Genetics, Department of Biology, University of Erlangen, 91058, Erlangen, Germany
| | - Andrea Ipsen-Escobedo
- Division of Genetics, Department of Biology, University of Erlangen, 91058, Erlangen, Germany
| | - Kilian Wistuba-Hamprecht
- Department of Dermatology, University Medical Center Tübingen, Tübingen, Germany
- Department of Immunology, University of Tübingen, Tübingen, Germany
- Section for Clinical Bioinformatics, Department of Internal Medicine I, University Medical Center Tübingen, Tübingen, Germany
| | - Kristin Eichler
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Katharina Filipski
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Neurological Institute (Edinger Institute), University Hospital, Goethe University, Frankfurt/Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt/Main, Germany
| | - Pia S Zeiner
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Neurological Institute (Edinger Institute), University Hospital, Goethe University, Frankfurt/Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt/Main, Germany
- Dr. Senckenberg Institute of Neurooncology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Rudi Beschorner
- Department of Neuropathology, University of Tübingen, Tübingen, Germany
| | - Renske Goedemans
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Falk Hagen Gogolla
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | - Hubert Hackl
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 80, 6020, Innsbruck, Austria
| | | | - Alexander Thiem
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
- Clinic for Dermatology and Venereology, Rostock University Medical Center, Rostock, Germany
| | - Paula Romer Roche
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Hemant Joshi
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
- Division of Infectious Diseases, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63130, USA
| | - Dirk Pühringer
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Achim Wöckel
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Joachim E Diessner
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | | | - Eugen Leo
- CatalYm GmbH, Am Klopferspitz 19, 82152, Munich, Germany
| | - Phil F Cheng
- Department of Dermatology, University of Zurich, University of Zurich Hospital, Wagistrasse 18, 8952, Zürich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University of Zurich, University of Zurich Hospital, Wagistrasse 18, 8952, Zürich, Switzerland
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius Maximilians University Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Falk Nimmerjahn
- Division of Genetics, Department of Biology, University of Erlangen, 91058, Erlangen, Germany
| | | | - Stefanie von Felten
- oikostat GmbH, Statistical Analyses and Consulting, Lucerne, Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute, University of Zurich, Hirschengraben 84, 8001, Zürich, Switzerland
| | - Michel Mittelbronn
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
- Luxembourg Centre of Neuropathology (LCNP), Luxembourg, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Luxembourg, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Matthias Mehling
- Department of Biomedicine and Neurology Department, University Hospital Basel, 4031, Basel, Switzerland
| | - Andreas Beilhack
- Department of Medicine II, University Hospital of Würzburg, Würzburg, Germany
| | - Sjoerd H van der Burg
- Department of Medical Oncology, Oncode Institute, Leiden University Medical Center, Albinusdreef 2, Leiden, 2333 ZA, The Netherlands
| | - Angela Riedel
- Mildred Scheel Early Career Center, University Hospital of Würzburg, Würzburg, Germany
| | - Benjamin Weide
- Department of Dermatology, University Medical Center Tübingen, Tübingen, Germany
| | | | - Jörg Wischhusen
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany.
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47
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Paupiah AL, Marques X, Merlaud Z, Russeau M, Levi S, Renner M. Introducing Diinamic, a flexible and robust method for clustering analysis in single-molecule localization microscopy. BIOLOGICAL IMAGING 2023; 3:e14. [PMID: 38487695 PMCID: PMC10936397 DOI: 10.1017/s2633903x23000156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 05/26/2023] [Accepted: 06/22/2023] [Indexed: 03/17/2024]
Abstract
Super-resolution microscopy allowed major improvements in our capacity to describe and explain biological organization at the nanoscale. Single-molecule localization microscopy (SMLM) uses the positions of molecules to create super-resolved images, but it can also provide new insights into the organization of molecules through appropriate pointillistic analyses that fully exploit the sparse nature of SMLM data. However, the main drawback of SMLM is the lack of analytical tools easily applicable to the diverse types of data that can arise from biological samples. Typically, a cloud of detections may be a cluster of molecules or not depending on the local density of detections, but also on the size of molecules themselves, the labeling technique, the photo-physics of the fluorophore, and the imaging conditions. We aimed to set an easy-to-use clustering analysis protocol adaptable to different types of data. Here, we introduce Diinamic, which combines different density-based analyses and optional thresholding to facilitate the detection of clusters. On simulated or real SMLM data, Diinamic correctly identified clusters of different sizes and densities, being performant even in noisy datasets with multiple detections per fluorophore. It also detected subdomains ("nanodomains") in clusters with non-homogeneous distribution of detections.
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Affiliation(s)
- Anne-Lise Paupiah
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Xavier Marques
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
- Museum National d’Histoire Naturelle, CNRS UMR 7196-INSERM U1154, Paris, France
| | - Zaha Merlaud
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Marion Russeau
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Sabine Levi
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
| | - Marianne Renner
- Inserm UMR-S 1270, Paris, France
- Sorbonne Université, Paris, France
- Institut du Fer à Moulin, INSERM-Sorbonne Université, Paris, France
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Hoboth P, Sztacho M, Quaas A, Akgül B, Hozák P. Quantitative super-resolution microscopy reveals the differences in the nanoscale distribution of nuclear phosphatidylinositol 4,5-bisphosphate in human healthy skin and skin warts. Front Cell Dev Biol 2023; 11:1217637. [PMID: 37484912 PMCID: PMC10361526 DOI: 10.3389/fcell.2023.1217637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/22/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction: Imaging of human clinical formalin-fixed paraffin-embedded (FFPE) tissue sections provides insights into healthy and diseased states and therefore represents a valuable resource for basic research, as well as for diagnostic and clinical purposes. However, conventional light microscopy does not allow to observe the molecular details of tissue and cell architecture due to the diffraction limit of light. Super-resolution microscopy overcomes this limitation and provides access to the nanoscale details of tissue and cell organization. Methods: Here, we used quantitative multicolor stimulated emission depletion (STED) nanoscopy to study the nanoscale distribution of the nuclear phosphatidylinositol 4,5-bisphosphate (nPI(4,5)P2) with respect to the nuclear speckles (NS) marker SON. Results: Increased nPI(4,5)P2 signals were previously linked to human papillomavirus (HPV)-mediated carcinogenesis, while NS-associated PI(4,5)P2 represents the largest pool of nPI(4,5)P2 visualized by staining and microscopy. The implementation of multicolor STED nanoscopy in human clinical FFPE skin and wart sections allowed us to provide here the quantitative evidence for higher levels of NS-associated PI(4,5)P2 in HPV-induced warts compared to control skin. Discussion: These data expand the previous reports of HPV-induced increase of nPI(4,5)P2 levels and reveal for the first time the functional, tissue-specific localization of nPI(4,5)P2 within NS in clinically relevant samples. Moreover, our approach is widely applicable to other human clinical FFPE tissues as an informative addition to the classical histochemistry.
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Affiliation(s)
- Peter Hoboth
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Martin Sztacho
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Alexander Quaas
- Institute of Pathology, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Baki Akgül
- Institute of Virology, University of Cologne, Medical Faculty and University Hospital Cologne, Cologne, Germany
| | - Pavel Hozák
- Department of Biology of the Cell Nucleus, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
- Microscopy Centre, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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González Morales N, Marescal O, Szikora S, Katzemich A, Correia-Mesquita T, Bíró P, Erdelyi M, Mihály J, Schöck F. The oxoglutarate dehydrogenase complex is involved in myofibril growth and Z-disc assembly in Drosophila. J Cell Sci 2023; 136:jcs260717. [PMID: 37272588 PMCID: PMC10323237 DOI: 10.1242/jcs.260717] [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: 10/17/2022] [Accepted: 05/24/2023] [Indexed: 06/06/2023] Open
Abstract
Myofibrils are long intracellular cables specific to muscles, composed mainly of actin and myosin filaments. The actin and myosin filaments are organized into repeated units called sarcomeres, which form the myofibrils. Muscle contraction is achieved by the simultaneous shortening of sarcomeres, which requires all sarcomeres to be the same size. Muscles have a variety of ways to ensure sarcomere homogeneity. We have previously shown that the controlled oligomerization of Zasp proteins sets the diameter of the myofibril. Here, we looked for Zasp-binding proteins at the Z-disc to identify additional proteins coordinating myofibril growth and assembly. We found that the E1 subunit of the oxoglutarate dehydrogenase complex localizes to both the Z-disc and the mitochondria, and is recruited to the Z-disc by Zasp52. The three subunits of the oxoglutarate dehydrogenase complex are required for myofibril formation. Using super-resolution microscopy, we revealed the overall organization of the complex at the Z-disc. Metabolomics identified an amino acid imbalance affecting protein synthesis as a possible cause of myofibril defects, which is supported by OGDH-dependent localization of ribosomes at the Z-disc.
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Affiliation(s)
- Nicanor González Morales
- Department of Biology, McGill University, Quebec H3A 1B1, Canada
- Department of Biology, Dalhousie University, Nova Scotia B3H 4R2, Canada
| | - Océane Marescal
- Department of Biology, McGill University, Quebec H3A 1B1, Canada
| | - Szilárd Szikora
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Anja Katzemich
- Department of Biology, McGill University, Quebec H3A 1B1, Canada
| | | | - Péter Bíró
- Department of Optics and Quantum Electronics, University of Szeged, Szeged 6720, Hungary
| | - Miklos Erdelyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged 6720, Hungary
| | - József Mihály
- Institute of Genetics, Biological Research Centre, Hungarian Academy of Sciences, Szeged 6726, Hungary
- Department of Genetics, University of Szeged, Szeged 6726, Hungary
| | - Frieder Schöck
- Department of Biology, McGill University, Quebec H3A 1B1, Canada
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50
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Martin‐Fernandez ML. A perspective of fluorescence microscopy for cellular structural biology with EGFR as witness. J Microsc 2023; 291:73-91. [PMID: 36282005 PMCID: PMC10952613 DOI: 10.1111/jmi.13151] [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: 09/20/2022] [Revised: 09/20/2022] [Accepted: 10/11/2022] [Indexed: 10/31/2022]
Abstract
The epidermal growth factor receptor (EGFR) is a poster child for the understanding of receptor behaviour, and of paramount importance to cell function and human health. Cloned almost forty years ago, the interest in EGFR's structure/function relationships remains unabated, not least because changes in oncogenic EGFR mutants are key drivers of the formation of lung and brain tumours. The structure of the assemblies formed by EGFR have been comprehensibly investigated by techniques such as high-resolution X-ray crystallography, NMR and all-atom molecular dynamics (MD) simulations. However, the complexity embedded in the portfolio of EGFR states that are only possible in the physiological environment of cells has often proved refractory to cell-free structural methods. Conversely, some key inroads made by quantitative fluorescence microscopy and super-resolution have depended on exploiting the wealth of structures available. Here, a brief personal perspective is provided on how quantitative fluorescence microscopy and super-resolution methods have cross-fertilised with cell-free-derived EGFR structural information. I primarily discuss areas in which my research group has made a contribution to fill gaps in EGFR's cellular structural biology and towards developing new tools to investigate macromolecular assemblies in cells.
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Affiliation(s)
- M. L. Martin‐Fernandez
- Central Laser FacilityScience and Technology Facilities Council, Rutherford Appleton LaboratoryDidcotUK
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