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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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