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Marenda M, Lazarova E, van de Linde S, Gilbert N, Michieletto D. Parameter-free molecular super-structures quantification in single-molecule localization microscopy. J Cell Biol 2021. [PMID: 33734291 DOI: 10.1101/2020.08.19.254540] [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] [Indexed: 05/12/2023] Open
Abstract
Understanding biological function requires the identification and characterization of complex patterns of molecules. Single-molecule localization microscopy (SMLM) can quantitatively measure molecular components and interactions at resolutions far beyond the diffraction limit, but this information is only useful if these patterns can be quantified and interpreted. We provide a new approach for the analysis of SMLM data that develops the concept of structures and super-structures formed by interconnected elements, such as smaller protein clusters. Using a formal framework and a parameter-free algorithm, (super-)structures formed from smaller components are found to be abundant in classes of nuclear proteins, such as heterogeneous nuclear ribonucleoprotein particles (hnRNPs), but are absent from ceramides located in the plasma membrane. We suggest that mesoscopic structures formed by interconnected protein clusters are common within the nucleus and have an important role in the organization and function of the genome. Our algorithm, SuperStructure, can be used to analyze and explore complex SMLM data and extract functionally relevant information.
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Affiliation(s)
- Mattia Marenda
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
| | - Elena Lazarova
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sebastian van de Linde
- Scottish Universities Physics Alliance, Department of Physics, University of Strathclyde, Glasgow, UK
| | - Nick Gilbert
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Davide Michieletto
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Scottish Universities Physics Alliance, School of Physics and Astronomy, University of Edinburgh, Edinburgh, UK
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Danylchuk DI, Moon S, Xu K, Klymchenko AS. Switchable Solvatochromic Probes for Live-Cell Super-resolution Imaging of Plasma Membrane Organization. Angew Chem Int Ed Engl 2019; 58:14920-14924. [PMID: 31392763 DOI: 10.1002/anie.201907690] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/01/2019] [Indexed: 12/25/2022]
Abstract
Visualization of the nanoscale organization of cell membranes remains challenging because of the lack of appropriate fluorescent probes. Herein, we introduce a new design concept for super-resolution microscopy probes that combines specific membrane targeting, on/off switching, and environment sensing functions. A functionalization strategy for solvatochromic dye Nile Red that improves its photostability is presented. The dye is grafted to a newly developed membrane-targeting moiety composed of a sulfonate group and an alkyl chain of varied lengths. While the long-chain probe with strong membrane binding, NR12A, is suitable for conventional microscopy, the short-chain probe NR4A, owing to the reversible binding, enables first nanoscale cartography of the lipid order exclusively at the surface of live cells. The latter probe reveals the presence of nanoscopic protrusions and invaginations of lower lipid order in plasma membranes, suggesting a subtle connection between membrane morphology and lipid organization.
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Affiliation(s)
- Dmytro I Danylchuk
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
| | - Seonah Moon
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Andrey S Klymchenko
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 route du Rhin, 67401, Illkirch, France
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Switchable Solvatochromic Probes for Live‐Cell Super‐resolution Imaging of Plasma Membrane Organization. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907690] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Feiner-Gracia N, Olea RA, Fitzner R, El Boujnouni N, van Asbeck AH, Brock R, Albertazzi L. Super-resolution Imaging of Structure, Molecular Composition, and Stability of Single Oligonucleotide Polyplexes. NANO LETTERS 2019; 19:2784-2792. [PMID: 31001985 PMCID: PMC6509642 DOI: 10.1021/acs.nanolett.8b04407] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/11/2019] [Indexed: 05/20/2023]
Abstract
The successful application of gene therapy relies on the development of safe and efficient delivery vectors. Cationic polymers such as cell-penetrating peptides (CPPs) can condense genetic material into nanoscale particles, called polyplexes, and induce cellular uptake. With respect to this point, several aspects of the nanoscale structure of polyplexes have remained elusive because of the difficulty in visualizing the molecular arrangement of the two components with nanometer resolution. This limitation has hampered the rational design of polyplexes based on direct structural information. Here, we used super-resolution imaging to study the structure and molecular composition of individual CPP-mRNA polyplexes with nanometer accuracy. We use two-color direct stochastic optical reconstruction microscopy (dSTORM) to unveil the impact of peptide stoichiometry on polyplex structure and composition and to assess their destabilization in blood serum. Our method provides information about the size and composition of individual polyplexes, allowing the study of such properties on a single polyplex basis. Furthermore, the differences in stoichiometry readily explain the differences in cellular uptake behavior. Thus, quantitative dSTORM of polyplexes is complementary to the currently used characterization techniques for understanding the determinants of polyplex activity in vitro and inside cells.
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Affiliation(s)
- Natalia Feiner-Gracia
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - R. Alis Olea
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert Fitzner
- Department
of Mathematics and Computer Science, Eindhoven
University of Technology, Post Office
Box 513, 5600 MD Eindhoven, The Netherlands
| | - Najoua El Boujnouni
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander H. van Asbeck
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Roland Brock
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lorenzo Albertazzi
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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Staszowska AD, Fox-Roberts P, Hirvonen LM, Peddie CJ, Collinson LM, Jones GE, Cox S. The Rényi divergence enables accurate and precise cluster analysis for localization microscopy. Bioinformatics 2018; 34:4102-4111. [PMID: 29868717 PMCID: PMC6247934 DOI: 10.1093/bioinformatics/bty403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Abstract
Motivation Clustering analysis is a key technique for quantitatively characterizing structures in localization microscopy images. To build up accurate information about biological structures, it is critical that the quantification is both accurate (close to the ground truth) and precise (has small scatter and is reproducible). Results Here, we describe how the Rényi divergence can be used for cluster radius measurements in localization microscopy data. We demonstrate that the Rényi divergence can operate with high levels of background and provides results which are more accurate than Ripley’s functions, Voronoi tesselation or DBSCAN. Availability and implementation The data supporting this research and the software described are accessible at the following site: https://dx.doi.org/10.18742/RDM01-316. Correspondence and requests for materials should be addressed to the corresponding author. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Adela D Staszowska
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Patrick Fox-Roberts
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Liisa M Hirvonen
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, London, UK
| | - Gareth E Jones
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Susan Cox
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
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