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Naas J, Nies G, Li H, Stoldt S, Schmitzer B, Jakobs S, Munk A. MultiMatch: geometry-informed colocalization in multi-color super-resolution microscopy. Commun Biol 2024; 7:1139. [PMID: 39271907 PMCID: PMC11399439 DOI: 10.1038/s42003-024-06772-8] [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: 02/28/2024] [Accepted: 08/22/2024] [Indexed: 09/15/2024] Open
Abstract
With recent advances in multi-color super-resolution light microscopy, it is possible to simultaneously visualize multiple subunits within biological structures at nanometer resolution. To optimally evaluate and interpret spatial proximity of stainings on such an image, colocalization analysis tools have to be able to integrate prior knowledge on the local geometry of the recorded biological complex. We present MultiMatch to analyze the abundance and location of chain-like particle arrangements in multi-color microscopy based on multi-marginal optimal unbalanced transport methodology. Our object-based colocalization model statistically addresses the effect of incomplete labeling efficiencies enabling inference on existent, but not fully observable particle chains. We showcase that MultiMatch is able to consistently recover existing chain structures in three-color STED images of DNA origami nanorulers and outperforms geometry-uninformed triplet colocalization methods in this task. MultiMatch generalizes to an arbitrary number of color channels and is provided as a user-friendly Python package comprising colocalization visualizations.
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Affiliation(s)
- Julia Naas
- Center for Integrative Bioinformatics Vienna (CIBIV), Max Perutz Labs, University of Vienna and Medical University of Vienna, Vienna, Austria
- Vienna Biocenter PhD Program, a Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Giacomo Nies
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Housen Li
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
| | - Stefan Stoldt
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - Bernhard Schmitzer
- Institute for Computer Science, University of Göttingen, Göttingen, Germany
| | - Stefan Jakobs
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Clinic of Neurology, University Medical Center Göttingen, Göttingen, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Translational Neuroinflammation and Automated Microscopy TNM, Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen, Göttingen, Germany.
- Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells' (MBExC), University of Göttingen, Göttingen, Germany.
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Xu R, Wu Y, Liu Z, Liu J, Liu X. Lysosomal Targeted Cyclometallic Iridium(Ⅲ) Salicylaldehyde-Coumarin Schiff Base Complexes and Anticancer Application. Front Chem 2022; 10:906954. [PMID: 35620650 PMCID: PMC9127163 DOI: 10.3389/fchem.2022.906954] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/20/2022] [Indexed: 12/30/2022] Open
Abstract
Natural coumarin derivatives and cyclometallic iridium (Ⅲ) (IrⅢ) complexes have attracted much attention in the field of anticancer. In this study, six coumarin-modified cyclometallic IrⅢ salicylaldehyde Schiff base complexes ([(ppy)2Ir(O^N)]/[(ppy-CHO)2Ir(O^N)]) were designed and synthesized. Compared with coumarin and IrⅢ complex monomers, target complexes exhibited favorable cytotoxic activity toward A549 and BEAS-2B cells. These complexes could induce extensive apoptosis of A549 cell (late apoptosis), which was represented by the disturbance of cell cycle (G1-phase) and the accumulation of intracellular reactive oxygen species, exhibiting an anticancer mechanism of oxidation. With the help of suitable fluorescence of these complexes, no conflict with the probes, confocal detection confirmed that complexes showed an energy-dependent cellular uptake mechanism and triggered lysosome-mediated apoptosis in A549 cell line. Above all, our findings reveal the design of a lysosomal targeting cyclometallic IrⅢ Schiff base complexes and provide a new idea for the design of integrated drugs for diagnosis and treatment.
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Affiliation(s)
- Ruixi Xu
- Institute of Anticancer Agents Development and Theranostic Application, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, China
| | - Yuting Wu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Zhe Liu
- Institute of Anticancer Agents Development and Theranostic Application, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, China
- *Correspondence: Xicheng Liu, ; Zhe Liu,
| | - Jinfeng Liu
- College of Life Sciences, Qufu Normal University, Qufu, China
| | - Xicheng Liu
- Institute of Anticancer Agents Development and Theranostic Application, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, China
- *Correspondence: Xicheng Liu, ; Zhe Liu,
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Pike JA, Styles IB, Rappoport JZ, Heath JK. Quantifying receptor trafficking and colocalization with confocal microscopy. Methods 2017; 115:42-54. [PMID: 28131869 DOI: 10.1016/j.ymeth.2017.01.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 01/20/2017] [Accepted: 01/23/2017] [Indexed: 01/08/2023] Open
Abstract
Confocal microscopy is a powerful tool for the study of cellular receptor trafficking and endocytosis. Unbiased and robust image analysis workflows are required for the identification, and study, of aberrant trafficking. After a brief review of related strategies, identifying both good and bad practice, custom workflows for the analysis of live cell 3D time-lapse data are presented. Strategies for data pre-processing, including denoising and background subtraction are considered. We use a 3D level set protocol to accurately segment cells using only the signal from fluorescently labelled receptor. A protocol for the quantification of changes to subcellular receptor distribution over time is then presented. As an example, ligand stimulated trafficking of epidermal growth factor receptor (EGFR) is shown to be significantly reduced in both AG1478 and Dynasore treated cells. Protocols for the quantitative analysis of colocalization between receptor and endosomes are also introduced, including strategies for signal isolation and statistical testing. By calculating the Manders and Pearson coefficients, both co-occurrence and correlation can be assessed. A statistically significant decrease in the level of ligand induced co-occurrence between EGFR and rab5 positive endosomes is demonstrated for both the AG1478 and Dynasore treated cells relative to a control. Finally, a strategy for the visualisation of co-occurrence is presented, which provides an unbiased alternative to colour overlays.
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Affiliation(s)
- Jeremy A Pike
- PSIBS Doctoral Training Centre, School of Chemistry, University of Birmingham, Birmingham B15 2TT, UK; School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK.
| | - Iain B Styles
- School of Computer Science, University of Birmingham, Birmingham B15 2TT, UK
| | - Joshua Z Rappoport
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK; Center for Advanced Microscopy and the Nikon Imaging Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John K Heath
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Moser B, Hochreiter B, Herbst R, Schmid JA. Fluorescence colocalization microscopy analysis can be improved by combining object-recognition with pixel-intensity-correlation. Biotechnol J 2017; 12:1600332. [PMID: 27420480 PMCID: PMC5244660 DOI: 10.1002/biot.201600332] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/15/2016] [Accepted: 07/05/2016] [Indexed: 12/15/2022]
Abstract
The question whether two proteins interact with each other or whether a protein localizes to a certain region of the cell is often addressed with fluorescence microscopy and analysis of a potential colocalization of fluorescence markers. Since a mere visual estimation does not allow quantification of the degree of colocalization, different statistical methods of pixel-intensity correlation are commonly used to score it. We observed that these correlation coefficients are prone to false positive results and tend to show high values even for molecules that reside in different organelles. Our aim was to improve this type of analysis and we developed a novel method combining object-recognition based colocalization analysis with pixel-intensity correlation to calculate an object-corrected Pearson coefficient. We designed a macro for the Fiji-version of the software ImageJ and tested the performance systematically with various organelle markers revealing an improved robustness of our approach over classical methods. In order to prove that colocalization does not necessarily mean a physical interaction, we performed FRET (fluorescence resonance energy transfer) microscopy. This confirmed that non-interacting molecules can exhibit a nearly complete colocalization, but that they do not show any significant FRET signal in contrast to proteins that are bound to each other.
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Affiliation(s)
- Bernhard Moser
- Dept. of Vascular Biology and Thrombosis Research, Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Bernhard Hochreiter
- Dept. of Vascular Biology and Thrombosis Research, Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Ruth Herbst
- Inst. of Immunology, Center for Pathophysiology, Infectiology and ImmunologyMedical University of ViennaViennaAustria
| | - Johannes A. Schmid
- Dept. of Vascular Biology and Thrombosis Research, Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
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Li KC, Huang LLH, Liang JH, Chan MC. Simple approach to three-color two-photon microscopy by a fiber-optic wavelength convertor. BIOMEDICAL OPTICS EXPRESS 2016; 7:4803-4815. [PMID: 27896017 PMCID: PMC5119617 DOI: 10.1364/boe.7.004803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/13/2016] [Accepted: 10/25/2016] [Indexed: 05/26/2023]
Abstract
A simple approach to multi-color two-photon microscopy of the red, green, and blue fluorescent indicators was reported based on an ultra-compact 1.03-μm femtosecond laser and a nonlinear fiber. Inside the nonlinear fiber, the 1.03-μm laser pulses were simultaneously blue-shifted to 0.6~0.8 μm and red-shifted to 1.2~1.4 μm region by the Cherenkov radiation and fiber Raman gain effects. The wavelength-shifted 0.6~0.8 μm and 1.2~1.4 μm radiations were co-propagated with the residual non-converted 1.03-μm pulses inside the same nonlinear fiber to form a fiber-output three-color femtosecond source. The application of the multi-wavelength sources on multi-color two-photon fluorescence microscopy were also demonstrated. Overall, due to simple system configuration, convenient wavelength conversion, easy wavelength tunability within the entire 0.7~1.35 μm bio-penetration window and less requirement for high power and bulky light sources, the simple approach to multi-color two-photon microscopy could be widely applicable as an easily implemented and excellent research tool for future biomedical and possibly even clinical applications.
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Affiliation(s)
- Kuen-Che Li
- College of Photonics, National Chiao-Tung University, Taiwan
- Equal contribution
| | - Lynn L. H. Huang
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Taiwan
- Institute of Biotechnology, National Cheng Kung University, Taiwan
- Research Center of Excellence in Regenerative Medicine, National Cheng Kung University, Taiwan
- Equal contribution
| | - Jhih-Hao Liang
- Institute of Biotechnology, National Cheng Kung University, Taiwan
| | - Ming-Che Chan
- College of Photonics, National Chiao-Tung University, Taiwan
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