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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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4
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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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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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Ashraf MW, Le Gratiet A, Diaspro A. Computational Modeling of Chromatin Fiber to Characterize Its Organization Using Angle-Resolved Scattering of Circularly Polarized Light. Polymers (Basel) 2021; 13:polym13193422. [PMID: 34641237 PMCID: PMC8512730 DOI: 10.3390/polym13193422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 12/19/2022] Open
Abstract
Understanding the structural organization of chromatin is essential to comprehend the gene functions. The chromatin organization changes in the cell cycle, and it conforms to various compaction levels. We investigated a chromatin solenoid model with nucleosomes shaped as cylindrical units arranged in a helical array. The solenoid with spherical-shaped nucleosomes was also modeled. The changes in chiral structural parameters of solenoid induced different compaction levels of chromatin fiber. We calculated the angle-resolved scattering of circularly polarized light to probe the changes in the organization of chromatin fiber in response to the changes in its chiral parameters. The electromagnetic scattering calculations were performed using discrete dipole approximation (DDA). In the chromatin structure, nucleosomes have internal interactions that affect chromatin compaction. The merit of performing computations with DDA is that it takes into account the internal interactions. We demonstrated sensitivity of the scattering signal’s angular behavior to the changes in these chiral parameters: pitch, radius, the handedness of solenoid, number of solenoid turns, the orientation of solenoid, the orientation of nucleosomes, number of nucleosomes, and shape of nucleosomes. These scattering calculations can potentially benefit applying a label-free polarized-light-based approach to characterize chromatin DNA and chiral polymers at the nanoscale level.
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Affiliation(s)
- Muhammad Waseem Ashraf
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy;
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
- Correspondence: (M.W.A.); (A.D.)
| | - Aymeric Le Gratiet
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy;
- Institut FOTON-UMR 6082, Université de Rennes, CNRS, F-22305 Rennes, France
| | - Alberto Diaspro
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, Via Enrico Melen 83, 16152 Genoa, Italy;
- DIFILAB, Department of Physics, University of Genoa, Via Dodecaneso 33, 16146 Genoa, Italy
- Correspondence: (M.W.A.); (A.D.)
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