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Tedeschi G, Palomba F, Scipioni L, Digman MA. Multimodal Phasor Approach to study breast cancer cells invasion in 3D spheroid model. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598307. [PMID: 38915530 PMCID: PMC11195137 DOI: 10.1101/2024.06.10.598307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
We implemented a multimodal set of functional imaging techniques optimized for deep-tissue imaging to investigate how cancer cells invade surrounding tissues and how their physiological properties change in the process. As a model for cancer invasion of the extracellular matrix, we created 3D spheroids from triple-negative breast cancer cells (MDA-MB-231) and non-tumorigenic breast epithelial cells (MCF-10A). We analyzed multiple hallmarks of cancer within the same spheroid by combining a number of imaging techniques, such as metabolic imaging of NADH by Fluorescence Lifetime Imaging Microscopy (NADH-FLIM), hyperspectral imaging of a solvatochromic lipophilic dye (Nile Red) and extracellular matrix imaging by Second Harmonic Generation (SHG). We included phasor-based bioimage analysis of spheroids at three different time points, tracking both morphological and biological properties, including cellular metabolism, fatty acids storage, and collagen organization. Employing this multimodal deep-imaging framework, we observed and quantified cancer cell plasticity in response to changes in the environment composition.
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Affiliation(s)
- Giulia Tedeschi
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California, Irvine, Irvine, CA 92617 (USA)
| | - Francesco Palomba
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California, Irvine, Irvine, CA 92617 (USA)
| | - Lorenzo Scipioni
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California, Irvine, Irvine, CA 92617 (USA)
| | - Michelle A Digman
- Laboratory for Fluorescence Dynamics, Biomedical Engineering Department, University of California, Irvine, Irvine, CA 92617 (USA)
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2
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Coucke Q, Parveen N, Fernández GS, Qian C, Hofkens J, Debyser Z, Hendrix J. Particle-based phasor-FLIM-FRET resolves protein-protein interactions inside single viral particles. BIOPHYSICAL REPORTS 2023; 3:100122. [PMID: 37649577 PMCID: PMC10463199 DOI: 10.1016/j.bpr.2023.100122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) is a popular modality to create additional contrast in fluorescence images. By carefully analyzing pixel-based nanosecond lifetime patterns, FLIM allows studying complex molecular populations. At the single-molecule or single-particle level, however, image series often suffer from low signal intensities per pixel, rendering it difficult to quantitatively disentangle different lifetime species, such as during Förster resonance energy transfer (FRET) analysis in the presence of a significant donor-only fraction. In this article we investigate whether an object localization strategy and the phasor approach to FLIM have beneficial effects when carrying out FRET analyses of single particles. Using simulations, we first showed that an average of ∼300 photons, spread over the different pixels encompassing single fluorescing particles and without background, is enough to determine a correct phasor signature (SD < 5% for a 4-ns lifetime). For immobilized single- or double-labeled dsDNA molecules, we next validated that particle-based phasor-FLIM-FRET readily allows estimating fluorescence lifetimes and FRET from single molecules. Thirdly, we applied particle-based phasor-FLIM-FRET to investigate protein-protein interactions in subdiffraction HIV-1 viral particles. To do this, we first quantitatively compared the fluorescence brightness, lifetime, and photostability of different popular fluorescent protein-based FRET probes when genetically fused to the HIV-1 integrase enzyme in viral particles, and conclude that eGFP, mTurquoise2, and mScarlet perform best. Finally, for viral particles coexpressing FRET-donor/acceptor-labeled IN, we determined the absolute FRET efficiency of IN oligomers. Available in a convenient open-source graphical user interface, we believe that particle-based phasor-FLIM-FRET is a promising tool to provide detailed insights in samples suffering from low overall signal intensities.
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Affiliation(s)
- Quinten Coucke
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Nagma Parveen
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Guillermo Solís Fernández
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- UFIEC, National Institute of Health Carlos III, Madrid, Spain
| | - Chen Qian
- Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science Munich (CIPSM), and Nanosystems Initiative Munich (NIM), Ludwig Maximilians-Universität München, Munich, Germany
| | - Johan Hofkens
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Zeger Debyser
- Laboratory for Molecular Virology and Gene Therapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Molecular Imaging and Photonics Division, Department of Chemistry, KU Leuven, Leuven, Belgium
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre and Biomedical Research Institute, Hasselt University, Hasselt, Belgium
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3
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Pierzynska-Mach A, Cainero I, Oneto M, Ferrando-May E, Lanzanò L, Diaspro A. Imaging-based study demonstrates how the DEK nanoscale distribution differentially correlates with epigenetic marks in a breast cancer model. Sci Rep 2023; 13:12749. [PMID: 37550322 PMCID: PMC10406876 DOI: 10.1038/s41598-023-38685-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 07/12/2023] [Indexed: 08/09/2023] Open
Abstract
Epigenetic dysregulation of chromatin is one of the hallmarks of cancer development and progression, and it is continuously investigated as a potential general bio-marker of this complex disease. One of the nuclear factors involved in gene regulation is the unique DEK protein-a histone chaperon modulating chromatin topology. DEK expression levels increase significantly from normal to cancer cells, hence raising the possibility of using DEK as a tumor marker. Although DEK is known to be implicated in epigenetic and transcriptional regulation, the details of these interactions and their relevance in cancer development remain largely elusive. In this work, we investigated the spatial correlation between the nuclear distribution of DEK and chromatin patterns-alongside breast cancer progression-leveraging image cross-correlation spectroscopy (ICCS) coupled with Proximity Ligation Assay (PLA) analysis. We performed our study on the model based on three well-established human breast cell lines to consider this tumor's heterogeneity (MCF10A, MCF7, and MDA-MB-231 cells). Our results show that overexpression of DEK correlates with the overall higher level of spatial proximity between DEK and histone marks corresponding to gene promoters regions (H3K9ac, H3K4me3), although it does not correlate with spatial proximity between DEK and gene enhancers (H3K27ac). Additionally, we observed that colocalizing fractions of DEK and histone marks are lower for the non-invasive cell subtype than for the highly invasive cell line (MDA-MB-231). Thus, this study suggests that the role of DEK on transcriptionally active chromatin regions varies depending on the subtype of the breast cancer cell line.
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Affiliation(s)
| | - Isotta Cainero
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genoa, Italy
| | - Michele Oneto
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
| | - Elisa Ferrando-May
- Department of Biology, University of Konstanz, Konstanz, Germany
- German Cancer Research Center, Heidelberg, Germany
| | - Luca Lanzanò
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy
- Department of Physics and Astronomy, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC @ IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83, 16152, Genoa, Italy.
- DIFILAB, Department of Physics, University of Genoa, Genoa, Italy.
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SPLIT-PIN software enabling confocal and super-resolution imaging with a virtually closed pinhole. Sci Rep 2023; 13:2741. [PMID: 36792719 PMCID: PMC9931717 DOI: 10.1038/s41598-023-29951-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
In point-scanning microscopy, optical sectioning is achieved using a small aperture placed in front of the detector, i.e. the detection pinhole, which rejects the out-of-focus background. The maximum level of optical sectioning is theoretically obtained for the minimum size of the pinhole aperture, but this is normally prevented by the dramatic reduction of the detected signal when the pinhole is closed, leading to a compromise between axial resolution and signal-to-noise ratio. We have recently demonstrated that, instead of closing the pinhole, one can reach a similar level of optical sectioning by tuning the pinhole size in a confocal microscope and by analyzing the resulting image series. The method, consisting in the application of the separation of photons by lifetime tuning (SPLIT) algorithm to series of images acquired with tunable pinhole size, is called SPLIT-pinhole (SPLIT-PIN). Here, we share and describe a SPLIT-PIN software for the processing of series of images acquired at tunable pinhole size, which generates images with reduced out-of-focus background. The software can be used on series of at least two images acquired on available commercial microscopes equipped with a tunable pinhole, including confocal and stimulated emission depletion (STED) microscopes. We demonstrate applicability on different types of imaging modalities: (1) confocal imaging of DNA in a non-adherent cell line; (2) removal of out-of-focus background in super-resolved STED microscopy; (3) imaging of live intestinal organoids stained with a membrane dye.
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Cerutti E, D'Amico M, Cainero I, Pelicci PG, Faretta M, Dellino GI, Diaspro A, Lanzanò L. Alterations induced by the PML-RARα oncogene revealed by image cross correlation spectroscopy. Biophys J 2022; 121:4358-4367. [PMID: 36196056 PMCID: PMC9703036 DOI: 10.1016/j.bpj.2022.10.003] [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: 05/20/2022] [Revised: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular mechanisms that underlie oncogene-induced genomic damage are still poorly understood. To understand how oncogenes affect chromatin architecture, it is important to visualize fundamental processes such as DNA replication and transcription in intact nuclei and quantify the alterations of their spatiotemporal organization induced by oncogenes. Here, we apply superresolution microscopy in combination with image cross correlation spectroscopy to the U937-PR9 cell line, an in vitro model of acute promyelocytic leukemia that allows us to activate the expression of the PML-RARα oncogene and analyze its effects on the spatiotemporal organization of functional nuclear processes. More specifically, we perform Tau-stimulated emission depletion imaging, a superresolution technique based on the concept of separation of photons by lifetime tuning. Tau-stimulated emission depletion imaging is combined with a robust image analysis protocol that quickly produces a value of colocalization fraction on several hundreds of single cells and allows observation of cell-to-cell variability. Upon activation of the oncogene, we detect a significant increase in the fraction of transcription sites colocalized with PML/PML-RARα. This increase of colocalization can be ascribed to oncogene-induced disruption of physiological PML bodies and the abnormal occurrence of a relatively large number of PML-RARα microspeckles. We also detect a significant cell-to-cell variability of this increase of colocalization, which can be ascribed, at least in part, to a heterogeneous response of the cells to the activation of the oncogene. These results prove that our method efficiently reveals oncogene-induced alterations in the spatial organization of nuclear processes and suggest that the abnormal localization of PML-RARα could interfere with the transcription machinery, potentially leading to DNA damage and genomic instability.
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Affiliation(s)
- Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy; Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy; DIFILAB, Department of Physics, University of Genoa, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy; Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy.
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6
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Measuring Molecular Diffusion in Dynamic Subcellular Nanostructures by Fast Raster Image Correlation Spectroscopy and 3D Orbital Tracking. Int J Mol Sci 2022; 23:ijms23147623. [PMID: 35886970 PMCID: PMC9323805 DOI: 10.3390/ijms23147623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 02/04/2023] Open
Abstract
Here we provide demonstration that fast fluorescence fluctuation spectroscopy is a fast and robust approach to extract information on the dynamics of molecules enclosed within subcellular nanostructures (e.g., organelles or vesicles) which are also moving in the complex cellular environment. In more detail, Raster Image Correlation Spectroscopy (RICS) performed at fast timescales (i.e., microseconds) reveals the fast motion of fluorescently labeled molecules within two exemplary dynamic subcellular nanostructures of biomedical interest, the lysosome and the insulin secretory granule (ISG). The measurement of molecular diffusion is then used to extract information on the average properties of subcellular nanostructures, such as macromolecular crowding or molecular aggregation. Concerning the lysosome, fast RICS on a fluorescent tracer allowed us to quantitatively assess the increase in organelle viscosity in the pathological condition of Krabbe disease. In the case of ISGs, fast RICS on two ISG-specific secreting peptides unveiled their differential aggregation propensity depending on intragranular concentration. Finally, a combination of fast RICS and feedback-based 3D orbital tracking was used to subtract the slow movement of subcellular nanostructures from the fast diffusion of molecules contained within them and independently validate the results. Results presented here not only demonstrate the acquired ability to address the dynamic behavior of molecules in moving, nanoscopic reference systems, but prove the relevance of this approach to advance our knowledge on cell function at the subcellular scale.
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7
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D'Amico M, Di Franco E, Cerutti E, Barresi V, Condorelli D, Diaspro A, Lanzanò L. A phasor-based approach to improve optical sectioning in any confocal microscope with a tunable pinhole. Microsc Res Tech 2022; 85:3207-3216. [PMID: 35686877 PMCID: PMC9542401 DOI: 10.1002/jemt.24178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/29/2022] [Indexed: 01/20/2023]
Abstract
Confocal fluorescence microscopy is a well‐established imaging technique capable of generating thin optical sections of biological specimens. Optical sectioning in confocal microscopy is mainly determined by the size of the pinhole, a small aperture placed in front of a point detector. In principle, imaging with a closed pinhole provides the highest degree of optical sectioning. In practice, the dramatic reduction of signal‐to‐noise ratio (SNR) at smaller pinhole sizes makes challenging the use of pinhole sizes significantly smaller than 1 Airy Unit (AU). Here, we introduce a simple method to “virtually” perform confocal imaging at smaller pinhole sizes without the dramatic reduction of SNR. The method is based on the sequential acquisition of multiple confocal images acquired at different pinhole aperture sizes and image processing based on a phasor analysis. The implementation is conceptually similar to separation of photons by lifetime tuning (SPLIT), a technique that exploits the phasor analysis to achieve super‐resolution, and for this reason we call this method SPLIT‐pinhole (SPLIT‐PIN). We show with simulated data that the SPLIT‐PIN image can provide improved optical sectioning (i.e., virtually smaller pinhole size) but better SNR with respect to an image obtained with closed pinhole. For instance, two images acquired at 2 and 1 AU can be combined to obtain a SPLIT‐PIN image with a virtual pinhole size of 0.2 AU but with better SNR. As an example of application to biological imaging, we show that SPLIT‐PIN improves confocal imaging of the apical membrane in an in vitro model of the intestinal epithelium.
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Affiliation(s)
- Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Elisabetta Di Franco
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Vincenza Barresi
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, Italy
| | - Daniele Condorelli
- Department of Biomedical and Biotechnological Sciences, Section of Medical Biochemistry, University of Catania, Catania, Italy
| | - Alberto Diaspro
- Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy.,DIFILAB, Department of Physics, University of Genoa, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy.,Nanoscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Genoa, Italy
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8
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Novel Tools to Measure Single Molecules Colocalization in Fluorescence Nanoscopy by Image Cross Correlation Spectroscopy. NANOMATERIALS 2022; 12:nano12040686. [PMID: 35215014 PMCID: PMC8875509 DOI: 10.3390/nano12040686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023]
Abstract
Super Resolution Microscopy revolutionized the approach to the study of molecular interactions by providing new quantitative tools to describe the scale below 100 nanometers. Single Molecule Localization Microscopy (SMLM) reaches a spatial resolution less than 50 nm with a precision in calculating molecule coordinates between 10 and 20 nanometers. However new procedures are required to analyze data from the list of molecular coordinates created by SMLM. We propose new tools based on Image Cross Correlation Spectroscopy (ICCS) to quantify the colocalization of fluorescent signals at single molecule level. These analysis procedures have been inserted into an experimental pipeline to optimize the produced results. We show that Fluorescent NanoDiamonds targeted to an intracellular compartment can be employed (i) to correct spatial drift to maximize the localization precision and (ii) to register confocal and SMLM images in correlative multiresolution, multimodal imaging. We validated the ICCS based approach on defined biological control samples and showed its ability to quantitatively map area of interactions inside the cell. The produced results show that the ICCS analysis is an efficient tool to measure relative spatial distribution of different molecular species at the nanoscale.
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9
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Cerutti E, D'Amico M, Cainero I, Dellino GI, Faretta M, Vicidomini G, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Evaluation of sted super-resolution image quality by image correlation spectroscopy (QuICS). Sci Rep 2021; 11:20782. [PMID: 34675304 PMCID: PMC8531054 DOI: 10.1038/s41598-021-00301-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/08/2021] [Indexed: 12/05/2022] Open
Abstract
Quantifying the imaging performances in an unbiased way is of outmost importance in super-resolution microscopy. Here, we describe an algorithm based on image correlation spectroscopy (ICS) that can be used to assess the quality of super-resolution images. The algorithm is based on the calculation of an autocorrelation function and provides three different parameters: the width of the autocorrelation function, related to the spatial resolution; the brightness, related to the image contrast; the relative noise variance, related to the signal-to-noise ratio of the image. We use this algorithm to evaluate the quality of stimulated emission depletion (STED) images of DNA replication foci in U937 cells acquired under different imaging conditions. Increasing the STED depletion power improves the resolution but may reduce the image contrast. Increasing the number of line averages improves the signal-to-noise ratio but facilitates the onset of photobleaching and subsequent reduction of the image contrast. Finally, we evaluate the performances of two different separation of photons by lifetime tuning (SPLIT) approaches: the method of tunable STED depletion power and the commercially available Leica Tau-STED. We find that SPLIT provides an efficient way to improve the resolution and contrast in STED microscopy.
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Affiliation(s)
- Elena Cerutti
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia 64, 95123, Catania, Italy.,Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Morgana D'Amico
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia 64, 95123, Catania, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.,DIFILAB, Department of Physics, University of Genoa, via Dodecaneso 33, 16143, Genoa, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy "Ettore Majorana", University of Catania, Via S. Sofia 64, 95123, Catania, Italy. .,Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152, Genoa, Italy.
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10
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Le Gratiet A, Lanzano L, Bendandi A, Marongiu R, Bianchini P, Sheppard C, Diaspro A. Phasor approach of Mueller matrix optical scanning microscopy for biological tissue imaging. Biophys J 2021; 120:3112-3125. [PMID: 34224693 PMCID: PMC8390965 DOI: 10.1016/j.bpj.2021.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 05/05/2021] [Accepted: 06/04/2021] [Indexed: 11/06/2022] Open
Abstract
Mueller matrix microscopy is an advanced imaging technique providing a full characterization of the optical polarization fingerprint of a sample. The Lu-Chipman (LC) decomposition, a method based on the modeling of elementary polarimetric arrangements and matrix inversions, is the gold standard to extract each polarimetric component separately. However, this models the optical system as a small number of discrete optical elements and requires a priori knowledge of the order in which these elements occur. In stratified media or when the ordering is not known, the interpretation of the LC decomposition becomes difficult. In this work, we propose a new, to our knowledge, representation dedicated to the study of biological tissues that combines Mueller matrix microscopy with a phasor approach. We demonstrate that this method provides an easier and direct interpretation of the retardance images in any birefringent material without the use of mathematical assumptions regarding the structure of the sample and yields comparable contrast to the LC decomposition. By validating this approach through numerical simulations, we demonstrate that it is able to give access to localized structural information, resulting in a simple determination of the birefringent parameters at the microscopic level. We apply our novel, to our knowledge, method to typical biological tissues that are of interest in the field of biomedical diagnosis.
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Affiliation(s)
| | - Luca Lanzano
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genova, Italy; Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Artemi Bendandi
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genova, Italy; DIFILAB, Department of Physics, University of Genoa, Genova, Italy; CONCEPT Lab, Istituto Italiano di Tecnologia, Genova, Italy
| | - Riccardo Marongiu
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genova, Italy; DIFILAB, Department of Physics, University of Genoa, Genova, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genova, Italy
| | - Colin Sheppard
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genova, Italy; School of Chemistry, University of Wollongong, Wollongong, Australia
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genova, Italy; DIFILAB, Department of Physics, University of Genoa, Genova, Italy
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11
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Malacrida L, Ranjit S, Jameson DM, Gratton E. The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. Annu Rev Biophys 2021; 50:575-593. [PMID: 33957055 DOI: 10.1146/annurev-biophys-062920-063631] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.
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Affiliation(s)
- Leonel Malacrida
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, 11600 Montevideo, Uruguay.,Advanced Bioimaging Unit, Institut Pasteur Montevideo and Universidad de la República-Uruguay, 11400 Montevideo, Uruguay
| | - Suman Ranjit
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA; .,Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC 20057, USA
| | - David M Jameson
- Department of Cell and Molecular Biology, University of Hawaii at Manoa, Honolulu, Hawaii 96813, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California 92697, USA;
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12
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Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry. Sci Rep 2021; 11:10719. [PMID: 34021177 PMCID: PMC8140153 DOI: 10.1038/s41598-021-90002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 11/08/2022] Open
Abstract
Voltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.
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13
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Phasor S-FLIM: a new paradigm for fast and robust spectral fluorescence lifetime imaging. Nat Methods 2021; 18:542-550. [PMID: 33859440 PMCID: PMC10161785 DOI: 10.1038/s41592-021-01108-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 03/03/2021] [Indexed: 02/02/2023]
Abstract
Fluorescence lifetime imaging microscopy (FLIM) and spectral imaging are two broadly applied methods for increasing dimensionality in microscopy. However, their combination is typically inefficient and slow in terms of acquisition and processing. By integrating technological and computational advances, we developed a robust and unbiased spectral FLIM (S-FLIM) system. Our method, Phasor S-FLIM, combines true parallel multichannel digital frequency domain electronics with a multidimensional phasor approach to extract detailed and precise information about the photophysics of fluorescent specimens at optical resolution. To show the flexibility of the Phasor S-FLIM technology and its applications to the biological and biomedical field, we address four common, yet challenging, problems: the blind unmixing of spectral and lifetime signatures from multiple unknown species, the unbiased bleedthrough- and background-free Förster resonance energy transfer analysis of biosensors, the photophysical characterization of environment-sensitive probes in living cells and parallel four-color FLIM imaging in tumor spheroids.
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14
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Cainero I, Cerutti E, Faretta M, Dellino GI, Pelicci PG, Bianchini P, Vicidomini G, Diaspro A, Lanzanò L. Chromatin investigation in the nucleus using a phasor approach to structured illumination microscopy. Biophys J 2021; 120:2566-2576. [PMID: 33940021 PMCID: PMC8390874 DOI: 10.1016/j.bpj.2021.04.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 04/14/2021] [Accepted: 04/26/2021] [Indexed: 12/17/2022] Open
Abstract
Chromatin in the nucleus is organized in functional sites at variable level of compaction. Structured illumination microscopy (SIM) can be used to generate three-dimensional super-resolution (SR) imaging of chromatin by changing in phase and in orientation a periodic line illumination pattern. The spatial frequency domain is the natural choice to process SIM raw data and to reconstruct an SR image. Using an alternative approach, we demonstrate that the additional spatial information encoded in the knowledge of the position of the illumination pattern can be efficiently decoded using a generalized version of separation of photon by lifetime tuning (SPLIT) that does not require lifetime measurements. In the resulting SPLIT-SIM, the SR image is obtained by isolating a fraction of the intensity corresponding to the center of the diffraction-limited point spread function. This extends the use of the SPLIT approach from stimulated emission depletion microscopy to SIM. The SPLIT-SIM algorithm is based only on phasor analysis and does not require deconvolution. We show that SPLIT-SIM can be used to generate SR images of chromatin organizational motifs with tunable resolution and can be a valuable tool for the imaging of functional sites in the nucleus.
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Affiliation(s)
- Isotta Cainero
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Elena Cerutti
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy.
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15
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Cainero I, Cerutti E, Faretta M, Dellino GI, Pelicci PG, Diaspro A, Lanzanò L. Measuring Nanoscale Distances by Structured Illumination Microscopy and Image Cross-Correlation Spectroscopy (SIM-ICCS). SENSORS (BASEL, SWITZERLAND) 2021; 21:2010. [PMID: 33809144 PMCID: PMC8001887 DOI: 10.3390/s21062010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/27/2022]
Abstract
Since the introduction of super-resolution microscopy, there has been growing interest in quantifying the nanoscale spatial distributions of fluorescent probes to better understand cellular processes and their interactions. One way to check if distributions are correlated or not is to perform colocalization analysis of multi-color acquisitions. Among all the possible methods available to study and quantify the colocalization between multicolor images, there is image cross-correlation spectroscopy (ICCS). The main advantage of ICCS, in comparison with other co-localization techniques, is that it does not require pre-segmentation of the sample into single objects. Here we show that the combination of structured illumination microscopy (SIM) with ICCS (SIM-ICCS) is a simple approach to quantify colocalization and measure nanoscale distances from multi-color SIM images. We validate the SIM-ICCS analysis on SIM images of optical nanorulers, DNA-origami-based model samples containing fluorophores of different colors at a distance of 80 nm. The SIM-ICCS analysis is compared with an object-based analysis performed on the same samples. Finally, we show that SIM-ICCS can be used to quantify the nanoscale spatial distribution of functional nuclear sites in fixed cells.
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Affiliation(s)
- Isotta Cainero
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16143 Genoa, Italy
| | - Elena Cerutti
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20100 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20100 Milan, Italy; (M.F.); (G.I.D.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20100 Milan, Italy
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16143 Genoa, Italy
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, Building B, 16152 Genoa, Italy; (I.C.); (E.C.)
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, Via S. Sofia 64, 95123 Catania, Italy
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16
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Mohebi A, Le Gratiet A, Marongiu R, Callegari F, Bianchini P, Diaspro A. Combined approach using circular intensity differential scattering microscopy under phasor map data analysis. APPLIED OPTICS 2021; 60:1558-1565. [PMID: 33690489 DOI: 10.1364/ao.417677] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Circular intensity differential scattering (CIDS) is based on the analysis of circular polarized light scattering and has been proven to be an interesting label-free microscopy technique sensitive to the chiral organization at the submicroscopic level. However, this approach averages the localized contrasts related to the sample polarimetric properties in the illumination volume. Additionally, the detection sensitivity suffers from the confinement of the mixture of structures, and it becomes an arduous task to discriminate the source of the signal. In this work, we show that a phasor map approach combined with CIDS microscopy has provided an intuitive view of the sample organization to recognize the presence of different molecular species in the illumination volume. The data represented in terms of polarization response mapped to a single point called a phasor also have the potential to pave the way for the analysis of large data sets. We validated this method by numerical simulations and compared the results with that of experimental data of optical devices of reference.
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17
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Wang W, Ma Y, Bonaccorsi S, Cong VT, Pandžić E, Yang Z, Goyette J, Lisi F, Tilley RD, Gaus K, Gooding JJ. Investigating Spatial Heterogeneity of Nanoparticles Movement in Live Cells with Pair-Correlation Microscopy and Phasor Analysis. Anal Chem 2021; 93:3803-3812. [PMID: 33590750 DOI: 10.1021/acs.analchem.0c04285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How nanoparticles distribute in living cells and overcome cellular barriers are important criteria in the design of drug carriers. Pair-correlation microscopy is a correlation analysis of fluctuation in the fluorescence intensity obtained by a confocal line scan that can quantify the dynamic properties of nanoparticle diffusion including the number of mobile nanoparticles, diffusion coefficient, and transit time across a spatial distance. Due to the potential heterogeneities in nanoparticle properties and the complexity within the cellular environment, quantification of averaged auto- and pair-correlation profiles may obscure important insights into the ability of nanoparticles to deliver drugs. To overcome this issue, we used phasor analysis to develop a data standardizing method, which can segment the scanned line into several subregions according to diffusion and address the spatial heterogeneity of nanoparticles moving inside cells. The phasor analysis is a fit-free method that represents autocorrelation profiles for each pixel relative to free diffusion on the so-called phasor plots. Phasor plots can then be used to select subpopulations for which the auto- and pair-correlation analysis can be performed separately. We demonstrate the phasor analysis for pair-correlation microscopy for investigating 16 nm, Cy5-labeled silica nanoparticles diffusing across the plasma membrane and green fluorescent proteins (GFP) diffusing across nuclear envelope in MCF-7 cells.
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Affiliation(s)
- Wenqian Wang
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Yuanqing Ma
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Simone Bonaccorsi
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Vu Thanh Cong
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Elvis Pandžić
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, Australia
| | - Zhengmin Yang
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Jesse Goyette
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Fabio Lisi
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Richard D Tilley
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
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18
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Tavakoli M, Jazani S, Sgouralis I, Heo W, Ishii K, Tahara T, Pressé S. Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics. CELL REPORTS. PHYSICAL SCIENCE 2020; 1:100234. [PMID: 34414380 PMCID: PMC8373049 DOI: 10.1016/j.xcrp.2020.100234] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.
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Affiliation(s)
- Meysam Tavakoli
- Department of Physics, Indiana University-Purdue University, Indianapolis, IN 46202, USA
| | - Sina Jazani
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ioannis Sgouralis
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wooseok Heo
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kunihiko Ishii
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287, USA
- Lead Contact
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19
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Shi W, Koo DES, Kitano M, Chiang HJ, Trinh LA, Turcatel G, Steventon B, Arnesano C, Warburton D, Fraser SE, Cutrale F. Pre-processing visualization of hyperspectral fluorescent data with Spectrally Encoded Enhanced Representations. Nat Commun 2020; 11:726. [PMID: 32024828 PMCID: PMC7002680 DOI: 10.1038/s41467-020-14486-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 01/12/2020] [Indexed: 11/09/2022] Open
Abstract
Hyperspectral fluorescence imaging is gaining popularity for it enables multiplexing of spatio-temporal dynamics across scales for molecules, cells and tissues with multiple fluorescent labels. This is made possible by adding the dimension of wavelength to the dataset. The resulting datasets are high in information density and often require lengthy analyses to separate the overlapping fluorescent spectra. Understanding and visualizing these large multi-dimensional datasets during acquisition and pre-processing can be challenging. Here we present Spectrally Encoded Enhanced Representations (SEER), an approach for improved and computationally efficient simultaneous color visualization of multiple spectral components of hyperspectral fluorescence images. Exploiting the mathematical properties of the phasor method, we transform the wavelength space into information-rich color maps for RGB display visualization. We present multiple biological fluorescent samples and highlight SEER’s enhancement of specific and subtle spectral differences, providing a fast, intuitive and mathematical way to interpret hyperspectral images during collection, pre-processing and analysis. Spectral phasor analysis allows unmixing fluorescence microscopy images, but it requires user involvement and has a limited number of labels that can be analyzed and displayed. Here the authors present a semi-automated solution to visualise multiple spectral components of hyperspectral fluorescence images, simultaneously.
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Affiliation(s)
- Wen Shi
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Daniel E S Koo
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Masahiro Kitano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Hsiao J Chiang
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Le A Trinh
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Department of Biological Sciences, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Gianluca Turcatel
- Developmental Biology and Regenerative Medicine Program, Saban Research Institute, Children's Hospital, 4661 Sunset Blvd, Los Angeles, CA, 90089, USA.,Keck School of Medicine and Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Benjamin Steventon
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Cosimo Arnesano
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - David Warburton
- Developmental Biology and Regenerative Medicine Program, Saban Research Institute, Children's Hospital, 4661 Sunset Blvd, Los Angeles, CA, 90089, USA.,Keck School of Medicine and Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Scott E Fraser
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA
| | - Francesco Cutrale
- Translational Imaging Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA. .,Biomedical Engineering, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA. .,Molecular and Computational Biology, University of Southern California, 1002 West Childs Way, Los Angeles, CA, 90089, USA.
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20
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Petazzi RA, Aji AK, Chiantia S. Fluorescence microscopy methods for the study of protein oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 169:1-41. [DOI: 10.1016/bs.pmbts.2019.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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21
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Oneto M, Scipioni L, Sarmento MJ, Cainero I, Pelicci S, Furia L, Pelicci PG, Dellino GI, Bianchini P, Faretta M, Gratton E, Diaspro A, Lanzanò L. Nanoscale Distribution of Nuclear Sites by Super-Resolved Image Cross-Correlation Spectroscopy. Biophys J 2019; 117:2054-2065. [PMID: 31732142 PMCID: PMC6895719 DOI: 10.1016/j.bpj.2019.10.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 02/07/2023] Open
Abstract
Deciphering the spatiotemporal coordination between nuclear functions is important to understand its role in the maintenance of human genome. In this context, super-resolution microscopy has gained considerable interest because it can be used to probe the spatial organization of functional sites in intact single-cell nuclei in the 20-250 nm range. Among the methods that quantify colocalization from multicolor images, image cross-correlation spectroscopy (ICCS) offers several advantages, namely it does not require a presegmentation of the image into objects and can be used to detect dynamic interactions. However, the combination of ICCS with super-resolution microscopy has not been explored yet. Here, we combine dual-color stimulated emission depletion (STED) nanoscopy with ICCS (STED-ICCS) to quantify the nanoscale distribution of functional nuclear sites. We show that super-resolved ICCS provides not only a value of the colocalized fraction but also the characteristic distances associated to correlated nuclear sites. As a validation, we quantify the nanoscale spatial distribution of three different pairs of functional nuclear sites in MCF10A cells. As expected, transcription foci and a transcriptionally repressive histone marker (H3K9me3) are not correlated. Conversely, nascent DNA replication foci and the proliferating cell nuclear antigen(PCNA) protein have a high level of proximity and are correlated at a nanometer distance scale that is close to the limit of our experimental approach. Finally, transcription foci are found at a distance of 130 nm from replication foci, indicating a spatial segregation at the nanoscale. Overall, our data demonstrate that STED-ICCS can be a powerful tool for the analysis of the nanoscale distribution of functional sites in the nucleus.
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Affiliation(s)
- Michele Oneto
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Maria J Sarmento
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Isotta Cainero
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy
| | - Laura Furia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Pier G Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Gaetano I Dellino
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy; Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, California
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy; Department of Physics, University of Genoa, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.
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22
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Phasor histone FLIM-FRET microscopy quantifies spatiotemporal rearrangement of chromatin architecture during the DNA damage response. Proc Natl Acad Sci U S A 2019; 116:7323-7332. [PMID: 30918123 PMCID: PMC6462080 DOI: 10.1073/pnas.1814965116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
To investigate how chromatin architecture is spatiotemporally organized at a double-strand break (DSB) repair locus, we established a biophysical method to quantify chromatin compaction at the nucleosome level during the DNA damage response (DDR). The method is based on phasor image-correlation spectroscopy of histone fluorescence lifetime imaging microscopy (FLIM)-Förster resonance energy transfer (FRET) microscopy data acquired in live cells coexpressing H2B-eGFP and H2B-mCherry. This multiplexed approach generates spatiotemporal maps of nuclear-wide chromatin compaction that, when coupled with laser microirradiation-induced DSBs, quantify the size, stability, and spacing between compact chromatin foci throughout the DDR. Using this technology, we identify that ataxia-telangiectasia mutated (ATM) and RNF8 regulate rapid chromatin decompaction at DSBs and formation of compact chromatin foci surrounding the repair locus. This chromatin architecture serves to demarcate the repair locus from the surrounding nuclear environment and modulate 53BP1 mobility.
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23
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Scipioni L, Lanzanó L, Diaspro A, Gratton E. Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the Zeiss Airyscan detector. Nat Commun 2018; 9:5120. [PMID: 30504919 PMCID: PMC6269422 DOI: 10.1038/s41467-018-07513-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/29/2018] [Indexed: 11/08/2022] Open
Abstract
The availability of the Airyscan detector in the Zeiss LSM 880 has made possible the development of a new concept in fluctuation correlation spectroscopy using super-resolution. The Airyscan unit acquires data simultaneously on 32 detectors arranged in a hexagonal array. This detector opens up the possibility to use fluctuation methods based on time correlation at single points or at a number of points simultaneously, as well as methods based on spatial correlation in the area covered by the detector. Given the frame rate of this detector, millions of frames can be acquired in seconds, providing a robust statistical basis for fluctuation data. We apply the comprehensive analysis to the molecular fluctuations of free GFP diffusing in live cells at different subcellular compartments to show that at the nanoscale different cell environments can be distinguished by the comprehensive fluctuation analysis.
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Affiliation(s)
- L Scipioni
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, 92697, CA, USA
| | - L Lanzanó
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - A Diaspro
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
- Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - E Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, 92697, CA, USA.
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24
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Ferri G, Digiacomo L, D'Autilia F, Durso W, Caracciolo G, Cardarelli F. Time-lapse confocal imaging datasets to assess structural and dynamic properties of subcellular nanostructures. Sci Data 2018; 5:180191. [PMID: 30226484 PMCID: PMC6142892 DOI: 10.1038/sdata.2018.191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/23/2018] [Indexed: 01/14/2023] Open
Abstract
Time-lapse optical microscopy datasets from living cells can potentially afford an enormous amount of quantitative information on the relevant structural and dynamic properties of sub-cellular organelles/structures, provided that both the spatial and temporal dimensions are properly sampled during the experiment. Here we provide exemplary live-cell, time-lapse confocal imaging datasets corresponding to three sub-cellular structures of the endo-lysosomal pathway, i.e. early endosomes, late endosomes and lysosomes, along with detailed guidelines to produce analogous experiments. Validation of the datasets is conducted by means of established analytical tools to extract the structural and dynamic properties at the sub-cellular scale, such as Single Particle Tracking (SPT) and imaging derived Mean Square Displacement (iMSD) analyses. In our aim, the present work would help other researchers in the field to reuse the provided datasets for their own scopes, and to combine their creative approaches/analyses to similar acquisitions.
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Affiliation(s)
- Gianmarco Ferri
- NEST-Scuola Normale Superiore, Istituto Nanoscienze-CNR (CNR-NANO), 56127 Pisa, Italy.,Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
| | - Luca Digiacomo
- Department of Molecular Medicine, "La Sapienza" University of Rome, 00161 Rome, Italy
| | - Francesca D'Autilia
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, 56127 Pisa, Italy
| | - William Durso
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, 56127 Pisa, Italy
| | - Giulio Caracciolo
- Department of Molecular Medicine, "La Sapienza" University of Rome, 00161 Rome, Italy
| | - Francesco Cardarelli
- NEST-Scuola Normale Superiore, Istituto Nanoscienze-CNR (CNR-NANO), 56127 Pisa, Italy
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25
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Sarmento MJ, Oneto M, Pelicci S, Pesce L, Scipioni L, Faretta M, Furia L, Dellino GI, Pelicci PG, Bianchini P, Diaspro A, Lanzanò L. Exploiting the tunability of stimulated emission depletion microscopy for super-resolution imaging of nuclear structures. Nat Commun 2018; 9:3415. [PMID: 30143630 PMCID: PMC6109149 DOI: 10.1038/s41467-018-05963-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/27/2018] [Indexed: 11/23/2022] Open
Abstract
Imaging of nuclear structures within intact eukaryotic nuclei is imperative to understand the effect of chromatin folding on genome function. Recent developments of super-resolution fluorescence microscopy techniques combine high specificity, sensitivity, and less-invasive sample preparation procedures with the sub-diffraction spatial resolution required to image chromatin at the nanoscale. Here, we present a method to enhance the spatial resolution of a stimulated-emission depletion (STED) microscope based only on the modulation of the STED intensity during the acquisition of a STED image. This modulation induces spatially encoded variations of the fluorescence emission that can be visualized in the phasor plot and used to improve and quantify the effective spatial resolution of the STED image. We show that the method can be used to remove direct excitation by the STED beam and perform dual color imaging. We apply this method to the visualization of transcription and replication foci within intact nuclei of eukaryotic cells.
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Affiliation(s)
- Maria J Sarmento
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Biophysical Chemistry, J. Heyrovský Institute of Physical Chemistry of the A.S.C.R. v.v.i., Prague, Czech Republic
| | - Michele Oneto
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Simone Pelicci
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Luca Pesce
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Gaetano Ivan Dellino
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Via Santa Sofia 9, 20142, Milan, Italy
| | - Paolo Bianchini
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy.
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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26
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Scipioni L, Di Bona M, Vicidomini G, Diaspro A, Lanzanò L. Local raster image correlation spectroscopy generates high-resolution intracellular diffusion maps. Commun Biol 2018; 1:10. [PMID: 30271897 PMCID: PMC6053083 DOI: 10.1038/s42003-017-0010-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/15/2017] [Indexed: 01/01/2023] Open
Abstract
Raster image correlation spectroscopy (RICS) is a powerful method for measuring molecular diffusion in live cells directly from images acquired on a laser scanning microscope. However, RICS only provides single average diffusion coefficients from regions with a lateral size on the order of few micrometers, which means that its spatial resolution is mainly limited to the cellular level. Here we introduce the local RICS (L-RICS), an easy-to-use tool that generates high resolution maps of diffusion coefficients from images acquired on a laser scanning microscope. As an application we show diffusion maps of a green fluorescent protein (GFP) within the nucleus and within the nucleolus of live cells at an effective spatial resolution of 500 nm. We find not only that diffusion in the nucleolus is slowed down compared to diffusion in the nucleoplasm, but also that diffusion in the nucleolus is highly heterogeneous. Lorenzo Scipioni et al. present Local Raster Image Correlation Spectroscopy (L-RICS), a method for generating sub-micrometer diffusion maps. They apply L-RICS to GFP in live cells and find that diffusion coefficients differ between the nucleus and nucleolus and are highly heterogeneous within compartments.
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Affiliation(s)
- Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Informatics, Bioengineering, Robotics and Systems Engineering, University of Genoa, Via All'Opera Pia, 13, 16145, Genoa, Italy
| | - Melody Di Bona
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.,Department of Physics, University of Genoa, via Dodecaneso 33, 16146, Genoa, Italy.,Nikon Imaging Center, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy
| | - Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, 16163, Genoa, Italy.
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27
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Dynamic fingerprinting of sub-cellular nanostructures by image mean square displacement analysis. Sci Rep 2017; 7:14836. [PMID: 29093485 PMCID: PMC5665924 DOI: 10.1038/s41598-017-13865-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/27/2017] [Indexed: 11/08/2022] Open
Abstract
Here we provide demonstration that image mean square displacement (iMSD) analysis is a fast and robust platform to address living matter dynamic organization at the level of sub-cellular nanostructures (e.g. endocytic vesicles, early/late endosomes, lysosomes), with no a-priori knowledge of the system, and no need to extract single trajectories. From each iMSD, a unique triplet of average parameters (namely: diffusivity, anomalous coefficient, size) are extracted and represented in a 3D parametric space, where clustering of single-cell points readily defines the structure "dynamic fingerprint", at the whole-cell-population level. We demonstrate that different sub-cellular structures segregate into separate regions of the parametric space. The potency of this approach is further proved through application to two exemplary, still controversial, cases: i) the intracellular trafficking of lysosomes, comprising both free diffusion and directed motion along cytoskeletal components, and ii) the evolving dynamic properties of macropinosomes, passing from early to late stages of intracellular trafficking. We strongly believe this strategy may represent a flexible, multiplexed platform to address the dynamic properties of living matter at the sub-cellular level, both in the physiological and pathological state.
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28
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Lanzanò L, Scipioni L, Di Bona M, Bianchini P, Bizzarri R, Cardarelli F, Diaspro A, Vicidomini G. Measurement of nanoscale three-dimensional diffusion in the interior of living cells by STED-FCS. Nat Commun 2017; 8:65. [PMID: 28684735 PMCID: PMC5500520 DOI: 10.1038/s41467-017-00117-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 06/01/2017] [Indexed: 01/12/2023] Open
Abstract
The observation of molecular diffusion at different spatial scales, and in particular below the optical diffraction limit (<200 nm), can reveal details of the subcellular topology and its functional organization. Stimulated-emission depletion microscopy (STED) has been previously combined with fluorescence correlation spectroscopy (FCS) to investigate nanoscale diffusion (STED-FCS). However, stimulated-emission depletion fluorescence correlation spectroscopy has only been used successfully to reveal functional organization in two-dimensional space, such as the plasma membrane, while, an efficient implementation for measurements in three-dimensional space, such as the cellular interior, is still lacking. Here we integrate the STED-FCS method with two analytical approaches, the recent separation of photons by lifetime tuning and the fluorescence lifetime correlation spectroscopy, to simultaneously probe diffusion in three dimensions at different sub-diffraction scales. We demonstrate that this method efficiently provides measurement of the diffusion of EGFP at spatial scales tunable from the diffraction size down to ∼80 nm in the cytoplasm of living cells. The measurement of molecular diffusion at sub-diffraction scales has been achieved in 2D space using STED-FCS, but an implementation for 3D diffusion is lacking. Here the authors present an analytical approach to probe diffusion in 3D space using STED-FCS and measure the diffusion of EGFP at different spatial scales.
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Affiliation(s)
- Luca Lanzanò
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.
| | - Lorenzo Scipioni
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,Department of Computer Science, Bioengineering, Robotics and Systems Engineering, University of Genoa, Genoa, 16145, Italy
| | - Melody Di Bona
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,Department of Physics, University of Genoa, via Dodecaneso 33, Genoa, 16146, Italy
| | - Paolo Bianchini
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,Nikon Imaging Center, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy
| | - Ranieri Bizzarri
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.,NEST, Scuola Normale Superiore and Istituto Nanoscienze, CNR (NANO-CNR) piazza San Silvestro 12, Pisa, 56127, Italy
| | - Francesco Cardarelli
- Center for Nanotechnology Innovation @NEST, Istituto Italiano di Tecnologia, piazza San Silvestro 12, Pisa, 56127, Italy.,NEST, Scuola Normale Superiore and Istituto Nanoscienze-CNR, Piazza San Silvestro 12, Pisa, 56127, Italy
| | - Alberto Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy. .,Department of Physics, University of Genoa, via Dodecaneso 33, Genoa, 16146, Italy. .,Nikon Imaging Center, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, via Morego 30, Genoa, 16163, Italy.
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