1
|
Pelicci S, Furia L, Pelicci PG, Faretta M. From Cell Populations to Molecular Complexes: Multiplexed Multimodal Microscopy to Explore p53-53BP1 Molecular Interaction. Int J Mol Sci 2024; 25:4672. [PMID: 38731890 PMCID: PMC11083188 DOI: 10.3390/ijms25094672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/17/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Surpassing the diffraction barrier revolutionized modern fluorescence microscopy. However, intrinsic limitations in statistical sampling, the number of simultaneously analyzable channels, hardware requirements, and sample preparation procedures still represent an obstacle to its widespread diffusion in applicative biomedical research. Here, we present a novel pipeline based on automated multimodal microscopy and super-resolution techniques employing easily available materials and instruments and completed with open-source image-analysis software developed in our laboratory. The results show the potential impact of single-molecule localization microscopy (SMLM) on the study of biomolecules' interactions and the localization of macromolecular complexes. As a demonstrative application, we explored the basis of p53-53BP1 interactions, showing the formation of a putative macromolecular complex between the two proteins and the basal transcription machinery in situ, thus providing visual proof of the direct role of 53BP1 in sustaining p53 transactivation function. Moreover, high-content SMLM provided evidence of the presence of a 53BP1 complex on the cell cytoskeleton and in the mitochondrial space, thus suggesting the existence of novel alternative 53BP1 functions to support p53 activity.
Collapse
Affiliation(s)
- Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (P.G.P.)
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (P.G.P.)
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (P.G.P.)
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Pelicci S, Furia L, Pelicci PG, Faretta M. Correlative Multi-Modal Microscopy: A Novel Pipeline for Optimizing Fluorescence Microscopy Resolutions in Biological Applications. Cells 2023; 12:cells12030354. [PMID: 36766696 PMCID: PMC9913119 DOI: 10.3390/cells12030354] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/05/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
The modern fluorescence microscope is the convergence point of technologies with different performances in terms of statistical sampling, number of simultaneously analyzed signals, and spatial resolution. However, the best results are usually obtained by maximizing only one of these parameters and finding a compromise for the others, a limitation that can become particularly significant when applied to cell biology and that can reduce the spreading of novel optical microscopy tools among research laboratories. Super resolution microscopy and, in particular, molecular localization-based approaches provide a spatial resolution and a molecular localization precision able to explore the scale of macromolecular complexes in situ. However, its use is limited to restricted regions, and consequently few cells, and frequently no more than one or two parameters. Correlative microscopy, obtained by the fusion of different optical technologies, can consequently surpass this barrier by merging results from different spatial scales. We discuss here the use of an acquisition and analysis correlative microscopy pipeline to obtain high statistical sampling, high content, and maximum spatial resolution by combining widefield, confocal, and molecular localization microscopy.
Collapse
Affiliation(s)
- Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, 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, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Correspondence:
| |
Collapse
|
4
|
Furia L, Pelicci S, Perillo F, Bolognesi MM, Pelicci PG, Facciotti F, Cattoretti G, Faretta M. Automated multimodal fluorescence microscopy for hyperplex spatial-proteomics: Coupling microfluidic-based immunofluorescence to high resolution, high sensitivity, three-dimensional analysis of histological slides. Front Oncol 2022; 12:960734. [PMCID: PMC9606676 DOI: 10.3389/fonc.2022.960734] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
In situ multiplexing analysis and in situ transcriptomics are now providing revolutionary tools to achieve the comprehension of the molecular basis of cancer and to progress towards personalized medicine to fight the disease. The complexity of these tasks requires a continuous interplay among different technologies during all the phases of the experimental procedures. New tools are thus needed and their characterization in terms of performances and limits is mandatory to reach the best resolution and sensitivity. We propose here a new experimental pipeline to obtain an optimized costs-to-benefits ratio thanks to the alternate employment of automated and manual procedures during all the phases of a multiplexing experiment from sample preparation to image collection and analysis. A comparison between ultra-fast and automated immunofluorescence staining and standard staining protocols has been carried out to compare the performances in terms of antigen saturation, background, signal-to-noise ratio and total duration. We then developed specific computational tools to collect data by automated analysis-driven fluorescence microscopy. Computer assisted selection of targeted areas with variable magnification and resolution allows employing confocal microscopy for a 3D high resolution analysis. Spatial resolution and sensitivity were thus maximized in a framework where the amount of stored data and the total requested time for the procedure were optimized and reduced with respect to a standard experimental approach.
Collapse
Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Federica Perillo
- Department of Experimental Oncology, 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, European Institute of Oncology IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Federica Facciotti
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, Milan, Italy
| | - Giorgio Cattoretti
- Department of Medicine and Surgery, Università di Milano-Bicocca, Monza, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology IRCCS, Milan, Italy
- *Correspondence: Mario Faretta,
| |
Collapse
|
5
|
Furia L, Pelicci S, Scanarini M, Pelicci PG, Faretta M. From Double-Strand Break Recognition to Cell-Cycle Checkpoint Activation: High Content and Resolution Image Cytometry Unmasks 53BP1 Multiple Roles in DNA Damage Response and p53 Action. Int J Mol Sci 2022; 23:ijms231710193. [PMID: 36077590 PMCID: PMC9456172 DOI: 10.3390/ijms231710193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/25/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
53BP1 protein has been isolated in-vitro as a putative p53 interactor. From the discovery of its engagement in the DNA-Damage Response (DDR), its role in sustaining the activity of the p53-regulated transcriptional program has been frequently under-evaluated, even in the case of a specific response to numerous DNA Double-Strand Breaks (DSBs), i.e., exposure to ionizing radiation. The localization of 53BP1 protein constitutes a key to decipher the network of activities exerted in response to stress. We present here an automated-microscopy for image cytometry protocol to analyze the evolution of the DDR, and to demonstrate how 53BP1 moved from damaged sites, where the well-known interaction with the DSB marker γH2A.X takes place, to nucleoplasm, interacting with p53, and enhancing the transcriptional regulation of the guardian of the genome protein. Molecular interactions have been quantitatively described and spatiotemporally localized at the highest spatial resolution by a simultaneous analysis of the impairment of the cell-cycle progression. Thanks to the high statistical sampling of the presented protocol, we provide a detailed quantitative description of the molecular events following the DSBs formation. Single-Molecule Localization Microscopy (SMLM) Analysis finally confirmed the p53–53BP1 interaction on the tens of nanometers scale during the distinct phases of the response.
Collapse
Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Simone Pelicci
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Mirco Scanarini
- Department of Experimental Oncology, European Institute of Oncology IRCCS, 20139 Milan, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, 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, European Institute of Oncology IRCCS, 20139 Milan, Italy
- Correspondence:
| |
Collapse
|
6
|
Pelicci S, Furia L, Scanarini M, Pelicci PG, Lanzanò L, Faretta M. Novel Tools to Measure Single Molecules Colocalization in Fluorescence Nanoscopy by Image Cross Correlation Spectroscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:686. [PMID: 35215014 PMCID: PMC8875509 DOI: 10.3390/nano12040686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [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.
Collapse
Affiliation(s)
- Simone Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (M.S.); (P.G.P.)
| | - Laura Furia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (M.S.); (P.G.P.)
| | - Mirco Scanarini
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (M.S.); (P.G.P.)
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (M.S.); (P.G.P.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy
| | - Luca Lanzanò
- Department of Physics and Astronomy “Ettore Majorana”, University of Catania, 95123 Catania, Italy;
- Nanoscopy and NIC@IIT, CHT Erzelli, Istituto Italiano di Tecnologia, 16152 Genoa, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan, Italy; (S.P.); (L.F.); (M.S.); (P.G.P.)
| |
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Dellino GI, Palluzzi F, Chiariello AM, Piccioni R, Bianco S, Furia L, De Conti G, Bouwman BAM, Melloni G, Guido D, Giacò L, Luzi L, Cittaro D, Faretta M, Nicodemi M, Crosetto N, Pelicci PG. Release of paused RNA polymerase II at specific loci favors DNA double-strand-break formation and promotes cancer translocations. Nat Genet 2019; 51:1011-1023. [PMID: 31110352 DOI: 10.1038/s41588-019-0421-z] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 04/12/2019] [Indexed: 01/05/2023]
Abstract
It is not clear how spontaneous DNA double-strand breaks (DSBs) form and are processed in normal cells, and whether they predispose to cancer-associated translocations. We show that DSBs in normal mammary cells form upon release of paused RNA polymerase II (Pol II) at promoters, 5' splice sites and active enhancers, and are processed by end-joining in the absence of a canonical DNA-damage response. Logistic and causal-association models showed that Pol II pausing at long genes is the main predictor and determinant of DSBs. Damaged introns with paused Pol II-pS5, TOP2B and XRCC4 are enriched in translocation breakpoints, and map at topologically associating domain boundary-flanking regions showing high interaction frequencies with distal loci. Thus, in unperturbed growth conditions, release of paused Pol II at specific loci and chromatin territories favors DSB formation, leading to chromosomal translocations.
Collapse
Affiliation(s)
- 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.
| | - Fernando Palluzzi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Brain and Behavioural Sciences, University of Pavia, Pavia, Italy
| | - Andrea Maria Chiariello
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant'Angelo, Naples, Italy
| | - Rossana Piccioni
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Simona Bianco
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant'Angelo, Naples, Italy
| | - Laura Furia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Giulia De Conti
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Britta A M Bouwman
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Giorgio Melloni
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Davide Guido
- Neurology, Public Health and Disability Unit, Foundation IRCCS Neurological Institute Carlo Besta, Milan, Italy
| | - Luciano Giacò
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lucilla Luzi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Davide Cittaro
- Center for Translational Genomics and Bioinformatics, IRCCS San Raffaele Hospital, Milan, Italy
| | - Mario Faretta
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Mario Nicodemi
- Department of Physics, University of Naples Federico II, and INFN Complesso di Monte Sant'Angelo, Naples, Italy.,Berlin Institute of Health, MDC-Berlin, Berlin, Germany
| | - Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - 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.
| |
Collapse
|
9
|
D'Alesio C, Punzi S, Cicalese A, Fornasari L, Furia L, Riva L, Carugo A, Curigliano G, Criscitiello C, Pruneri G, Pelicci PG, Faretta M, Bossi D, Lanfrancone L. RNAi screens identify CHD4 as an essential gene in breast cancer growth. Oncotarget 2018; 7:80901-80915. [PMID: 27779108 PMCID: PMC5348363 DOI: 10.18632/oncotarget.12646] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 09/29/2016] [Indexed: 12/15/2022] Open
Abstract
Epigenetic regulation plays an essential role in tumor development and epigenetic modifiers are considered optimal potential druggable candidates. In order to identify new breast cancer vulnerabilities and improve therapeutic chances for patients, we performed in vivo and in vitro shRNA screens in a human breast cancer cell model (MCF10DCIS.com cell line) using epigenetic libraries. Among the genes identified in our screening, we deeply investigated the role of Chromodomain Helicase DNA binding Protein 4 (CHD4) in breast cancer tumorigenesis. CHD4 silencing significantly reduced tumor growth in vivo and proliferation in vitro of MCF10DCIS.com cells. Similarly, in vivo breast cancer growth was decreased in a spontaneous mouse model of breast carcinoma (MMTV-NeuT system) and in metastatic patient-derived xenograft models. Conversely, no reduction in proliferative ability of non-transformed mammary epithelial cells (MCF10A) was detected. Moreover, we showed that CHD4 depletion arrests proliferation by inducing a G0/G1 block of cell cycle associated with up-regulation of CDKN1A (p21). These results highlight the relevance of genetic screens in the identification of tumor frailties and the role of CHD4 as a potential pharmacological target to inhibit breast cancer growth.
Collapse
Affiliation(s)
- Carolina D'Alesio
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Simona Punzi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Angelo Cicalese
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Lorenzo Fornasari
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Laura Riva
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia, Milan 20139, Italy
| | - Alessandro Carugo
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy.,Department of Molecular and Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Giuseppe Curigliano
- Division of Experimental Therapeutics, European Institute of Oncology, Milan 20141, Italy
| | - Carmen Criscitiello
- Division of Experimental Therapeutics, European Institute of Oncology, Milan 20141, Italy
| | - Giancarlo Pruneri
- School of Medicine, University of Milan, Milan 20122, Italy.,Biobank for Translational Medicine Unit, Department of Pathology, European Institute of Oncology, Milan 20141, Italy
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy.,Department of Oncology, University of Milan, Milan 20139, Italy
| | - Mario Faretta
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Daniela Bossi
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, European Institute of Oncology, Milan 20141, Italy
| |
Collapse
|
10
|
Arifulin EA, Bragina EE, Kurilo LF, Sheval EV. High-throughput analysis of TUNEL-stained sperm using image cytometry. Cytometry A 2017; 91:854-858. [PMID: 28678382 DOI: 10.1002/cyto.a.23164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/06/2017] [Accepted: 06/11/2017] [Indexed: 01/06/2023]
Affiliation(s)
- E. A. Arifulin
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University; Moscow 119992 Russian Federation
- Рeoples' Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St; Moscow 117198 Russian Federation
| | - E. E. Bragina
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University; Moscow 119992 Russian Federation
- Federal State Budgetary Institution “Research Centre for Medical Genetics”; Moscow Russian Federation
| | - L. F. Kurilo
- Federal State Budgetary Institution “Research Centre for Medical Genetics”; Moscow Russian Federation
| | - E. V. Sheval
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University; Moscow 119992 Russian Federation
- LIA 1066 LFR2O French-Russian Joint Cancer Research Laboratory, 94805 Villejuif; Paris France
| |
Collapse
|
11
|
PML is required for telomere stability in non-neoplastic human cells. Oncogene 2015; 35:1811-21. [PMID: 26119943 PMCID: PMC4830905 DOI: 10.1038/onc.2015.246] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 04/13/2015] [Accepted: 05/10/2015] [Indexed: 12/16/2022]
Abstract
Telomeres interact with numerous proteins, including components of the shelterin complex, whose alteration, similarly to proliferation-induced telomere shortening, initiates cellular senescence. In tumors, telomere length is maintained by Telomerase activity or by the Alternative Lengthening of Telomeres mechanism, whose hallmark is the telomeric localization of the promyelocytic leukemia (PML) protein. Whether PML contributes to telomeres maintenance in normal cells is unknown. We show that in normal human fibroblasts the PML protein associates with few telomeres, preferentially when they are damaged. Proliferation-induced telomere attrition or their damage due to alteration of the shelterin complex enhances the telomeric localization of PML, which is increased in human T-lymphocytes derived from patients genetically deficient in telomerase. In normal fibroblasts, PML depletion induces telomere damage, nuclear and chromosomal abnormalities, and senescence. Expression of the leukemia protein PML/RARα in hematopoietic progenitors displaces PML from telomeres and induces telomere shortening in the bone marrow of pre-leukemic mice. Our work provides a novel view of the physiologic function of PML, which participates in telomeres surveillance in normal cells. Our data further imply that a diminished PML function may contribute to cell senescence, genomic instability, and tumorigenesis.
Collapse
|
12
|
Darzynkiewicz Z, Zhao H, Zhang S, Marietta YL, Ernest YL, Zhang Z. Initiation and termination of DNA replication during S phase in relation to cyclins D1, E and A, p21WAF1, Cdt1 and the p12 subunit of DNA polymerase δ revealed in individual cells by cytometry. Oncotarget 2015; 6:11735-50. [PMID: 26059433 PMCID: PMC4494901 DOI: 10.18632/oncotarget.4149] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 05/03/2015] [Indexed: 12/18/2022] Open
Abstract
During our recent studies on mechanism of the regulation of human DNA polymerase δ in preparation for DNA replication or repair, multiparameter imaging cytometry as exemplified by laser scanning cytometry (LSC) has been used to assess changes in expression of the following nuclear proteins associated with initiation of DNA replication: cyclin A, PCNA, Ki-67, p21(WAF1), DNA replication factor Cdt1 and the smallest subunit of DNA polymerase δ, p12. In the present review, rather than focusing on Pol δ, we emphasize the application of LSC in these studies and outline possibilities offered by the concurrent differential analysis of DNA replication in conjunction with expression of the nuclear proteins. A more extensive analysis of the data on a correlation between rates of EdU incorporation, likely reporting DNA replication, and expression of these proteins, is presently provided. New data, specifically on the expression of cyclin D1 and cyclin E with respect to EdU incorporation as well as on a relationship between expression of cyclin A vs. p21(WAF1) and Ki-67 vs. Cdt1, are also reported. Of particular interest is the observation that this approach makes it possible to assess the temporal sequence of degradation of cyclin D1, p21(WAF1), Cdt1 and p12, each with respect to initiation of DNA replication and with respect to each other. Also the sequence or reappearance of these proteins in G2 after termination of DNA replication is assessed. The reviewed data provide a more comprehensive presentation of potential markers, whose presence or absence marks the DNA replicating cells. Discussed is also usefulness of these markers as indicators of proliferative activity in cancer tissues that may bear information on tumor progression and have a prognostic value.
Collapse
Affiliation(s)
- Zbigniew Darzynkiewicz
- Brander Cancer Research Institute, Department of Pathology, New York Medical College, Valhalla, NY
| | - Hong Zhao
- Brander Cancer Research Institute, Department of Pathology, New York Medical College, Valhalla, NY
| | - Sufang Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY
| | - Y.W.T. Lee Marietta
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY
| | - Y.C. Lee Ernest
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY
| | - Zhongtao Zhang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY
| |
Collapse
|
13
|
Leifert WR, Siddiqui SM. γH2AX is a biomarker of modulated cytostatic drug resistance. Cytometry A 2015; 87:692-5. [PMID: 25902732 DOI: 10.1002/cyto.a.22672] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/06/2015] [Indexed: 12/11/2022]
Affiliation(s)
- Wayne R Leifert
- CSIRO Food and Nutrition Flagship, Genome Health and Healthy Ageing, Adelaide, South Australia, 5000, Australia
| | - Sabbir Mohammad Siddiqui
- CSIRO Food and Nutrition Flagship, Genome Health and Healthy Ageing, Adelaide, South Australia, 5000, Australia.,School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, 5064, Australia
| |
Collapse
|
14
|
Jett JH. How long does it take a cell to divide? Cytometry A 2015; 87:383-4. [PMID: 25821133 DOI: 10.1002/cyto.a.22665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Accepted: 03/06/2015] [Indexed: 11/06/2022]
Affiliation(s)
- James H Jett
- Department of Cell Biology and Physiology, University of New Mexico Albuquerque, New Mexico
| |
Collapse
|
15
|
Furia L, Pelicci P, Faretta M. Confocal microscopy for high-resolution and high-content analysis of the cell cycle. ACTA ACUST UNITED AC 2014; 70:7.42.1-14. [PMID: 25271962 DOI: 10.1002/0471142956.cy0742s70] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Optical fluorescence microscopy offers a wide range of technological solutions to address many questions in biomedical research. Spatial resolution has been greatly improved by the use of confocal microscopes, providing a 3-D analysis of the intracellular space. Automation has contributed to make confocal analysis available for high-content image cytometry studies. However, the storage, browsing, and analysis of the amount of data generated can challenge the feasibility of such studies. Presented in this chapter is a multistep acquisition and analysis protocol that can bypass such difficulties by an analysis-driven data collection. Cell-cycle analysis of low-resolution data can be employed to select cell populations of interest that can then be imaged at extremely high resolution and subjected to high-content analysis.
Collapse
Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | | | | |
Collapse
|
16
|
Furia L, Pelicci P, Faretta M. High-resolution cytometry for high-content cell cycle analysis. ACTA ACUST UNITED AC 2014; 70:7.41.1-15. [PMID: 25271961 DOI: 10.1002/0471142956.cy0741s70] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
One of the major limitations of flow cytometry (FCM) is the absence of an intracellular view. Automated microscopy and image analysis, together with technological developments, led to new approaches in cytometry that bypass the above limitation, introducing high resolution, high content, and large statistical sampling. However, few attempts have been made, until now, to translate the wide repertoire of FCM assays into high-content image screening. This unit describes the implementation of an acquisition and analysis protocol for evaluation of the cell cycle by automated microscopy. The approach grants the possibility to perform simultaneous analysis of a high number of different parameters. A large part of this unit is devoted to the description of hardware features that can optimize the recorded information together with the acquisition and analysis procedures employed to produce good-quality data.
Collapse
Affiliation(s)
- Laura Furia
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | | | | |
Collapse
|
17
|
Willitzki A, Lorenz S, Hiemann R, Guttek K, Goihl A, Hartig R, Conrad K, Feist E, Sack U, Schierack P, Heiserich L, Eberle C, Peters V, Roggenbuck D, Reinhold D. Fully automated analysis of chemically induced γH2AX foci in human peripheral blood mononuclear cells by indirect immunofluorescence. Cytometry A 2013; 83:1017-26. [DOI: 10.1002/cyto.a.22350] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 07/26/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Annika Willitzki
- Institute of Molecular and Clinical Immunology; Otto-von-Guericke-University; Magdeburg Germany
| | | | - Rico Hiemann
- Faculty of Sciences; Brandenburg Technical University Cottbus-Senftenberg; Senftenberg Germany
| | - Karina Guttek
- Institute of Molecular and Clinical Immunology; Otto-von-Guericke-University; Magdeburg Germany
| | - Alexander Goihl
- Institute of Molecular and Clinical Immunology; Otto-von-Guericke-University; Magdeburg Germany
| | - Roland Hartig
- Institute of Molecular and Clinical Immunology; Otto-von-Guericke-University; Magdeburg Germany
| | - Karsten Conrad
- Institute of Immunology; Technical University Dresden; Dresden Germany
| | - Eugen Feist
- Department of Rheumatology and Clinical Immunology; Charité-Universitätsmedizin; Berlin Germany
| | - Ulrich Sack
- Institute of Clinical Immunology, Medical Faculty; University of Leipzig; Germany
| | - Peter Schierack
- Faculty of Sciences; Brandenburg Technical University Cottbus-Senftenberg; Senftenberg Germany
| | | | | | | | - Dirk Roggenbuck
- Medipan GmbH; Dahlewitz/Berlin Germany
- Faculty of Sciences; Brandenburg Technical University Cottbus-Senftenberg; Senftenberg Germany
| | - Dirk Reinhold
- Institute of Molecular and Clinical Immunology; Otto-von-Guericke-University; Magdeburg Germany
| |
Collapse
|
18
|
Tarnok A, Darzynkiewicz Z. New insights into cell cycle and DNA damage response machineries through high-resolution AMICO quantitative imaging cytometry. Cell Prolif 2013; 46:497-500. [PMID: 23952744 DOI: 10.1111/cpr.12050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/28/2013] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE Progress in biology and medicine research is being driven by development of new instrumentation and associated methodologies which open analytical capabilities that expand understanding of complexity of biological systems. Application of cytometry, which is now widely used in so many disciplines of biology, is the best example of such a progress. METHODOLOGY Recent publications push the envelope in expanding capabilities of cytometry by introducing a high resolution imaging cytometry defined as Automated Microscopy for Image CytOmetry (AMICO). This instrumentation is utilized to further elucidate mechanisms of the cell cycle progression and also the DNA damage response. This approach is going beyond the presently possible analytical technologies regarding throughput and depth of information. CONCLUSIONS The possibility of multiparametric analysis combined with the high resolution mapping of individual constituents of cell cycle and DNA damage response machineries provides new tools to probe molecular mechanism of these processes. The capability of analysis of proximity of these constituents to each other offered by AMICO is a novel and potentially important approach that can be used to elucidate mechanisms of other biological processes.
Collapse
Affiliation(s)
- A Tarnok
- Department of Paediatric Cardiology, Cardiac Centre, and Translational Centre for Regenerative Medicine (TRM), Universität Leipzig, 04289, Leipzig, Germany
| | | |
Collapse
|
19
|
Bernas T, Berniak K, Rybak P, Zarębski M, Zhao H, Darzynkiewicz Z, Dobrucki JW. Analysis of spatial correlations between patterns of DNA damage response and DNA replication in nuclei of cells subjected to replication stress or oxidative damage. Cytometry A 2013; 83:925-32. [PMID: 23900967 DOI: 10.1002/cyto.a.22325] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/29/2013] [Accepted: 06/06/2013] [Indexed: 12/30/2022]
Abstract
Sites of DNA replication (EdU incorporation) and DNA damage signaling (γH2AX) induced by camptothecin (Cpt) or hydrogen peroxide (H2O2) form characteristic patterns of foci in cell nuclei. The overlap between these patterns is a function of the number of DNA double strand breaks (DSBs) formed in replication sites. The goal of this study was to optimize a method of quantitative assessment of a degree of correlation between these two patterns. Such a correlation can be used to estimate a probability of inducing damage in sections of replicating DNA. The damage and replication foci are imaged in 3D with confocal microscopy and their respective positions within nuclei are determined with adaptive image segmentation. Using correlation functions spatial proximity of the resultant point patterns is quantified over the range of distances in cells in early-, mid- and late S-phase. As the numbers (and nuclear densities) of γH2AX and replication foci differ significantly in the subsequent substages of S phase, the detected association values were corrected for the expected random overlap between both classes of foci. Thus, the probability of their nonrandom association was estimated. Moreover, self association (clustering) of DNA replication sites in different stages of S-phase of the cell cycle was detected and accounted for. While the analysis revealed a strong correlation between the γH2AX foci and the sites of DNA replication in cells treated with Cpt, only a low correlation was apparent in cells exposed to H2O2. © 2013 International Society for Advancement of Cytometry.
Collapse
Affiliation(s)
- Tytus Bernas
- Division of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland; Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | | | | | | | | | | | | |
Collapse
|
20
|
Berniak K, Rybak P, Bernas T, Zarębski M, Biela E, Zhao H, Darzynkiewicz Z, Dobrucki JW. Relationship between DNA damage response, initiated by camptothecin or oxidative stress, and DNA replication, analyzed by quantitative 3D image analysis. Cytometry A 2013; 83:913-24. [PMID: 23846844 DOI: 10.1002/cyto.a.22327] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/29/2013] [Accepted: 06/06/2013] [Indexed: 01/03/2023]
Abstract
A method of quantitative analysis of spatial (3D) relationship between discrete nuclear events detected by confocal microscopy is described and applied in analysis of a dependence between sites of DNA damage signaling (γH2AX foci) and DNA replication (EdU incorporation) in cells subjected to treatments with camptothecin (Cpt) or hydrogen peroxide (H2O2). Cpt induces γH2AX foci, likely reporting formation of DNA double-strand breaks (DSBs), almost exclusively at sites of DNA replication. This finding is consistent with the known mechanism of induction of DSBs by DNA topoisomerase I (topo1) inhibitors at the sites of collisions of the moving replication forks with topo1-DNA "cleavable complexes" stabilized by Cpt. Whereas an increased level of H2AX histone phosphorylation is seen in S-phase of cells subjected to H2O2, only a minor proportion of γH2AX foci coincide with DNA replication sites. Thus, the increased level of H2AX phosphorylation induced by H2O2 is not a direct consequence of formation of DNA lesions at the sites of moving DNA replication forks. These data suggest that oxidative stress induced by H2O2 and formation of the primary H2O2-induced lesions (8-oxo-7,8-dihydroguanosine) inhibits replication globally and triggers formation of γH2AX at various distances from replication forks. Quantitative analysis of a frequency of DNA replication sites and γH2AX foci suggests also that stalling of replicating forks by Cpt leads to activation of new DNA replication origins. © 2013 International Society for Advancement of Cytometry.
Collapse
Affiliation(s)
- K Berniak
- Division of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | | | | | | | | | | | | | | |
Collapse
|