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Solov’yov AV, Verkhovtsev AV, Mason NJ, Amos RA, Bald I, Baldacchino G, Dromey B, Falk M, Fedor J, Gerhards L, Hausmann M, Hildenbrand G, Hrabovský M, Kadlec S, Kočišek J, Lépine F, Ming S, Nisbet A, Ricketts K, Sala L, Schlathölter T, Wheatley AEH, Solov’yov IA. Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment. Chem Rev 2024; 124:8014-8129. [PMID: 38842266 PMCID: PMC11240271 DOI: 10.1021/acs.chemrev.3c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
This roadmap reviews the new, highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The Review highlights several recent advances in the field and provides a roadmap for the development of the field over the next decade. Condensed matter systems exposed to radiation can be inorganic, organic, or biological, finite or infinite, composed of different molecular species or materials, exist in different phases, and operate under different thermodynamic conditions. Many of the key phenomena related to the behavior of irradiated systems are very similar and can be understood based on the same fundamental theoretical principles and computational approaches. The multiscale nature of such phenomena requires the quantitative description of the radiation-induced effects occurring at different spatial and temporal scales, ranging from the atomic to the macroscopic, and the interlinks between such descriptions. The multiscale nature of the effects and the similarity of their manifestation in systems of different origins necessarily bring together different disciplines, such as physics, chemistry, biology, materials science, nanoscience, and biomedical research, demonstrating the numerous interlinks and commonalities between them. This research field is highly relevant to many novel and emerging technologies and medical applications.
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Affiliation(s)
| | | | - Nigel J. Mason
- School
of Physics and Astronomy, University of
Kent, Canterbury CT2 7NH, United
Kingdom
| | - Richard A. Amos
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Ilko Bald
- Institute
of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Gérard Baldacchino
- Université
Paris-Saclay, CEA, LIDYL, 91191 Gif-sur-Yvette, France
- CY Cergy Paris Université,
CEA, LIDYL, 91191 Gif-sur-Yvette, France
| | - Brendan Dromey
- Centre
for Light Matter Interactions, School of Mathematics and Physics, Queen’s University Belfast, Belfast BT7 1NN, United Kingdom
| | - Martin Falk
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61200 Brno, Czech Republic
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Juraj Fedor
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Luca Gerhards
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
| | - Michael Hausmann
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff-Institute
for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
- Faculty
of Engineering, University of Applied Sciences
Aschaffenburg, Würzburger
Str. 45, 63743 Aschaffenburg, Germany
| | | | - Stanislav Kadlec
- Eaton European
Innovation Center, Bořivojova
2380, 25263 Roztoky, Czech Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Franck Lépine
- Université
Claude Bernard Lyon 1, CNRS, Institut Lumière
Matière, F-69622, Villeurbanne, France
| | - Siyi Ming
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Andrew Nisbet
- Department
of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, U.K.
| | - Kate Ricketts
- Department
of Targeted Intervention, University College
London, Gower Street, London WC1E 6BT, United Kingdom
| | - Leo Sala
- J.
Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czech Republic
| | - Thomas Schlathölter
- Zernike
Institute for Advanced Materials, University
of Groningen, Nijenborgh
4, 9747 AG Groningen, The Netherlands
- University
College Groningen, University of Groningen, Hoendiepskade 23/24, 9718 BG Groningen, The Netherlands
| | - Andrew E. H. Wheatley
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield
Road, Cambridge CB2 1EW, United Kingdom
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
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2
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Schneckenburger H. Laser Application in Life Sciences. Int J Mol Sci 2023; 24:ijms24108526. [PMID: 37239881 DOI: 10.3390/ijms24108526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/06/2023] [Indexed: 05/28/2023] Open
Abstract
Since their invention by Theodore Maiman in 1960, lasers represent a class of light sources based on the stimulated emission of radiation in the visible, ultraviolet or infrared spectral range [...].
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3
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Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
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Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
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Chapman KB, Filipsky F, Peschke N, Gelléri M, Weinhardt V, Braun A, Hausmann M, Cremer C. A comprehensive method to study the DNA's association with lamin and chromatin compaction in intact cell nuclei at super resolution. NANOSCALE 2023; 15:742-756. [PMID: 36524744 PMCID: PMC9813922 DOI: 10.1039/d2nr02684h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 10/14/2022] [Indexed: 06/17/2023]
Abstract
Super-resolution fluorescence microscopy has revolutionized multicolor imaging of nuclear structures due to the combination of high labeling specificity and high resolution. Here we expanded the recently developed fBALM (DNA structure fluctuation-assisted binding activated localization microscopy) method by developing a stable methodological sequence that enables dual-color imaging of high-resolution genomic DNA together with an immunofluorescently labeled intranuclear protein. Our measurements of the nuclear periphery, imaging DNA and LaminB1 in biologically relevant samples, show that this novel dual-color imaging method is feasible for further quantitative evaluations. We were able to study the relative spatial signal organization between DNA and LaminB1 by means of highly specific colocalization measurements at nanometer resolution. Measurements were performed with and without the antifade embedding medium ProLong Gold, which proved to be essential for imaging of LaminB1, but not for imaging of SytoxOrange labeled DNA. The localization precision was used to differentiate between localizations with higher and lower amounts of emitting photons. We interpret high intensity localizations to be renatured DNA sections in which a high amount of Sytox Orange molecules were bound. This could give insight into the denaturation kinetics of DNA during fBALM. These results were further complemented by measurements of γH2AX and H3K9me3 signal organization to demonstrate differences within the chromatin landscape, which were quantified with image processing methods such as Voronoi segmentation.
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Affiliation(s)
- Katarina B Chapman
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Filip Filipsky
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Nicolas Peschke
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
| | - Márton Gelléri
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
| | - Venera Weinhardt
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Andrejs Braun
- Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
| | - Christoph Cremer
- Kirchhoff-Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany.
- Institute of Molecular Biology, Ackermannweg 4, 55128 Mainz, Germany
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5
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Dobešová L, Gier T, Kopečná O, Pagáčová E, Vičar T, Bestvater F, Toufar J, Bačíková A, Kopel P, Fedr R, Hildenbrand G, Falková I, Falk M, Hausmann M. Incorporation of Low Concentrations of Gold Nanoparticles: Complex Effects on Radiation Response and Fate of Cancer Cells. Pharmaceutics 2022; 14:pharmaceutics14010166. [PMID: 35057061 PMCID: PMC8781406 DOI: 10.3390/pharmaceutics14010166] [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: 11/04/2021] [Revised: 12/28/2021] [Accepted: 01/04/2022] [Indexed: 01/27/2023] Open
Abstract
(1) Background: In oncology research, a long-standing discussion exists about pros and cons of metal nanoparticle-enhanced radiotherapy and real mechanisms behind the tumor cell response to irradiation (IR) in presence of gold nanoparticles (GNPs). A better understanding of this response is, however, necessary to develop more efficient and safety nanoparticle (NP) types designed to disturb specific processes in tumor cells. (2) Aims and Methods: We combined 3D confocal microscopy and super-resolution single molecule localization microscopy (SMLM) to analyze, at the multiscale, the early and late effects of 10 nm-GNPs on DNA double strand break (DSB) induction and repair in tumor cells exposed to different doses of photonic low-LET (linear energy transfer) radiation. The results were correlated to different aspects of short and long-term cell viability. SkBr3 breast cancer cells (selected for the highest incidence of this cancer type among all cancers in women, and because most breast tumors are treated with IR) were incubated with low concentrations of GNPs and irradiated with 60Co γ-rays or 6 MV X-rays. In numerous post-irradiation (PI) times, ranging from 0.5 to 24 h PI, the cells were spatially (3D) fixed and labeled with specific antibodies against γH2AX, 53BP1 and H3K9me3. The extent of DSB induction, multi-parametric micro- and nano-morphology of γH2AX and 53BP1 repair foci, DSB repair kinetics, persistence of unrepaired DSBs, nanoscale clustering of γH2AX and nanoscale (hetero)chromatin re-organization were measured by means of the mentioned microscopy techniques in dependence of radiation dose and GNP concentration. (3) Results: The number of γH2AX/53BP1 signals increased after IR and an additional increase was observed in GNP-treated (GNP(+)) cells compared to untreated controls. However, this phenomenon reflected slight expansion of the G2-phase cell subpopulation in irradiated GNP(+) specimens instead of enhanced DNA damage induction by GNPs. This statement is further supported by some micro- and nano-morphological parameters of γH2AX/53BP1 foci, which slightly differed for cells irradiated in absence or presence of GNPs. At the nanoscale, Ripley’s distance frequency analysis of SMLM signal coordinate matrices also revealed relaxation of heterochromatin (H3K9me3) clusters upon IR. These changes were more prominent in presence of GNPs. The slight expansion of radiosensitive G2 cells correlated with mostly insignificant but systematic decrease in post-irradiation survival of GNP(+) cells. Interestingly, low GNP concentrations accelerated DSB repair kinetics; however, the numbers of persistent γH2AX/53BP1 repair foci were slightly increased in GNP(+) cells. (4) Conclusions: Low concentrations of 10-nm GNPs enhanced the G2/M cell cycle arrest and the proportion of radiosensitive G2 cells, but not the extent of DNA damage induction. GNPs also accelerated DSB repair kinetics and slightly increased presence of unrepaired γH2AX/53BP1 foci at 24 h PI. GNP-mediated cell effects correlated with slight radiosensitization of GNP(+) specimens, significant only for the highest radiation dose tested (4 Gy).
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Affiliation(s)
- Lucie Dobešová
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
- Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Theresa Gier
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (T.G.); (G.H.)
| | - Olga Kopečná
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
| | - Eva Pagáčová
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
| | - Tomáš Vičar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00 Brno, Czech Republic;
| | - Felix Bestvater
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany;
| | - Jiří Toufar
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
- Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Alena Bačíková
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
| | - Pavel Kopel
- Department of Inorganic Chemistry, Faculty of Science, Palacky University Olomouc, 779 00 Olomouc, Czech Republic;
| | - Radek Fedr
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (T.G.); (G.H.)
| | - Iva Falková
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic; (L.D.); (O.K.); (E.P.); (J.T.); (A.B.); (R.F.); (I.F.)
- Correspondence: (M.F.); (M.H.); Tel.: +420-728-084-060 (M.F.); +49-6221-549-824 (M.H.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (T.G.); (G.H.)
- Correspondence: (M.F.); (M.H.); Tel.: +420-728-084-060 (M.F.); +49-6221-549-824 (M.H.)
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Hausmann M, Hildenbrand G, Pilarczyk G. Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology : (A Hypothesis and Experimental Verification Hints). Results Probl Cell Differ 2022; 70:3-34. [PMID: 36348103 DOI: 10.1007/978-3-031-06573-6_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The cell nucleus is a complex biological system in which simultaneous reactions and functions take place to keep the cell as an individualized, specialized system running well. The cell nucleus contains chromatin packed in various degrees of density and separated in volumes of chromosome territories and subchromosomal domains. Between the chromatin, however, there is enough "free" space for floating RNA, proteins, enzymes, ATPs, ions, water molecules, etc. which are trafficking by super- and supra-diffusion to the interaction points where they are required. It seems that this trafficking works somehow automatically and drives the system perfectly. After exposure to ionizing radiation causing DNA damage from single base damage up to chromatin double-strand breaks, the whole system "cell nucleus" responds, and repair processes are starting to recover the fully functional and intact system. In molecular biology, many individual epigenetic pathways of DNA damage response or repair of single and double-strand breaks are described. How these responses are embedded into the response of the system as a whole is often out of the focus of consideration. In this article, we want to follow the hypothesis of chromatin architecture's impact on epigenetic pathways and vice versa. Based on the assumption that chromatin acts like an "aperiodic solid state within a limited volume," functionally determined networks and local topologies ("islands") can be defined that drive the appropriate repair process at a given damage site. Experimental results of investigations of the chromatin nano-architecture and DNA repair clusters obtained by means of single-molecule localization microscopy offer hints and perspectives that may contribute to verifying the hypothesis.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
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Topological Analysis of γH2AX and MRE11 Clusters Detected by Localization Microscopy during X-ray-Induced DNA Double-Strand Break Repair. Cancers (Basel) 2021; 13:cancers13215561. [PMID: 34771723 PMCID: PMC8582740 DOI: 10.3390/cancers13215561] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 12/30/2022] Open
Abstract
DNA double-strand breaks (DSBs), known as the most severe damage in chromatin, were induced in breast cancer cells and normal skin fibroblasts by 2 Gy ionizing photon radiation. In response to DSB induction, phosphorylation of the histone variant H2AX to γH2AX was observed in the form of foci visualized by specific antibodies. By means of super-resolution single-molecule localization microscopy (SMLM), it has been recently shown in a first article about these data that these foci can be separated into clusters of about the same size (diameter ~400 nm). The number of clusters increased with the dose applied and decreased with the repair time. It has also been shown that during the repair period, antibody-labeled MRE11 clusters of about half of the γH2AX cluster diameter were formed inside several γH2AX clusters. MRE11 is part of the MRE11-RAD50-NBS1 (MRN) complex, which is known as a DNA strand resection and broken-end bridging component in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). This article is a follow-up of the former ones applying novel procedures of mathematics (topology) and similarity measurements on the data set: to obtain a measure for cluster shape and shape similarities, topological quantifications employing persistent homology were calculated and compared. In addition, based on our findings that γH2AX clusters associated with heterochromatin show a high degree of similarity independently of dose and repair time, these earlier published topological analyses and similarity calculations comparing repair foci within individual cells were extended by topological data averaging (2nd-generation heatmaps) over all cells analyzed at a given repair time point; thereby, the two dimensions (0 and 1) expressed by components and holes were studied separately. Finally, these mean value heatmaps were averaged, in addition. For γH2AX clusters, in both normal fibroblast and MCF-7 cancer cell lines, an increased similarity was found at early time points (up to 60 min) after irradiation for both components and holes of clusters. In contrast, for MRE11, the peak in similarity was found at later time points (2 h up to 48 h) after irradiation. In general, the normal fibroblasts showed quicker phosphorylation of H2AX and recruitment of MRE11 to γH2AX clusters compared to breast cancer cells and a shorter time interval of increased similarity for γH2AX clusters. γH2AX foci and randomly distributed MRE11 molecules naturally occurring in non-irradiated control cells did not show any significant topological similarity.
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8
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An Experimental Workflow for Studying Barrier Integrity, Permeability, and Tight Junction Composition and Localization in a Single Endothelial Cell Monolayer: Proof of Concept. Int J Mol Sci 2021; 22:ijms22158178. [PMID: 34360944 PMCID: PMC8347178 DOI: 10.3390/ijms22158178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/13/2022] Open
Abstract
Endothelial and epithelial barrier function is crucial for the maintenance of physiological processes. The barrier paracellular permeability depends on the composition and spatial distribution of the cell-to-cell tight junctions (TJ). Here, we provide an experimental workflow that yields several layers of physiological data in the setting of a single endothelial cell monolayer. Human umbilical vein endothelial cells were grown on Transwell filters. Transendothelial electrical resistance (TER) and 10 kDa FITC dextran flux were measured using Alanyl-Glutamine (AlaGln) as a paracellular barrier modulator. Single monolayers were immunolabelled for Zonula Occludens-1 (ZO-1) and Claudin-5 (CLDN5) and used for automated immunofluorescence imaging. Finally, the same monolayers were used for single molecule localization microscopy (SMLM) of ZO-1 and CLDN5 at the nanoscale for spatial clustering analysis. The TER increased and the paracellular dextran flux decreased after the application of AlaGln and these functional changes of the monolayer were mediated by an increase in the ZO-1 and CLDN5 abundance in the cell–cell interface. At the nanoscale level, the functional and protein abundance data were accompanied by non-random increased clustering of CLDN5. Our experimental workflow provides multiple data from a single monolayer and has wide applicability in the setting of paracellular studies in endothelia and epithelia.
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9
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Bartosova M, Zhang C, Schaefer B, Herzog R, Ridinger D, Damgov I, Levai E, Marinovic I, Eckert C, Romero P, Sallay P, Ujszaszi A, Unterwurzacher M, Wagner A, Hildenbrand G, Warady BA, Schaefer F, Zarogiannis SG, Kratochwill K, Schmitt CP. Glucose Derivative Induced Vasculopathy in Children on Chronic Peritoneal Dialysis. Circ Res 2021; 129:e102-e118. [PMID: 34233458 DOI: 10.1161/circresaha.121.319310] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Maria Bartosova
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
| | - Conghui Zhang
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
| | - Betti Schaefer
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
| | - Rebecca Herzog
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria (R.H., M.U., A.W., K.K.)
| | - David Ridinger
- Kirchhoff Institute for Physics (D.R., G.H.), University of Heidelberg, Heidelberg, Germany
| | - Ivan Damgov
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
| | - Eszter Levai
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
- ELKH-SE, Pediatrics and Nephrology Research Group, Budapest, Hungary (E.L.)
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary (E.L., P.S.)
| | - Iva Marinovic
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
| | - Christoph Eckert
- Institute of Pathology (C.E.), University of Heidelberg, Heidelberg, Germany
| | - Philipp Romero
- Division of Pediatric Surgery, Department of General, Visceral and Transplantation Surgery (P.R.), University of Heidelberg, Heidelberg, Germany
| | - Peter Sallay
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary (E.L., P.S.)
| | - Akos Ujszaszi
- Division of Nephrology, Heidelberg University Hospital, Heidelberg, Germany (A.U.)
| | - Markus Unterwurzacher
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria (R.H., M.U., A.W., K.K.)
| | - Anja Wagner
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria (R.H., M.U., A.W., K.K.)
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics (D.R., G.H.), University of Heidelberg, Heidelberg, Germany
| | | | - Franz Schaefer
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
| | - Sotirios G Zarogiannis
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
- Department of Physiology, Faculty of Medicine, University of Thessaly, Larissa, Greece (S.G.Z.)
| | - Klaus Kratochwill
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, Vienna, Austria (R.H., M.U., A.W., K.K.)
| | - Claus Peter Schmitt
- Center for Pediatric and Adolescent Medicine (M.B., C.Z., B.S., I.D., E.L., I.M., F.S., S.G.Z., C.P.S.), University of Heidelberg, Heidelberg, Germany
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10
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Erenpreisa J, Krigerts J, Salmina K, Gerashchenko BI, Freivalds T, Kurg R, Winter R, Krufczik M, Zayakin P, Hausmann M, Giuliani A. Heterochromatin Networks: Topology, Dynamics, and Function (a Working Hypothesis). Cells 2021; 10:1582. [PMID: 34201566 PMCID: PMC8304199 DOI: 10.3390/cells10071582] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
Open systems can only exist by self-organization as pulsing structures exchanging matter and energy with the outer world. This review is an attempt to reveal the organizational principles of the heterochromatin supra-intra-chromosomal network in terms of nonlinear thermodynamics. The accessibility of the linear information of the genetic code is regulated by constitutive heterochromatin (CHR) creating the positional information in a system of coordinates. These features include scale-free splitting-fusing of CHR with the boundary constraints of the nucleolus and nuclear envelope. The analysis of both the literature and our own data suggests a radial-concentric network as the main structural organization principle of CHR regulating transcriptional pulsing. The dynamic CHR network is likely created together with nucleolus-associated chromatin domains, while the alveoli of this network, including springy splicing speckles, are the pulsing transcription hubs. CHR contributes to this regulation due to the silencing position variegation effect, stickiness, and flexible rigidity determined by the positioning of nucleosomes. The whole system acts in concert with the elastic nuclear actomyosin network which also emerges by self-organization during the transcriptional pulsing process. We hypothesize that the the transcriptional pulsing, in turn, adjusts its frequency/amplitudes specified by topologically associating domains to the replication timing code that determines epigenetic differentiation memory.
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Affiliation(s)
- Jekaterina Erenpreisa
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Bogdan I. Gerashchenko
- R.E. Kavetsky Institute of Experimental Pathology, Oncology and Radiobiology, National Academy of Sciences of Ukraine, 03022 Kyiv, Ukraine;
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV-1004 Riga, Latvia;
| | - Reet Kurg
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia;
| | - Ruth Winter
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, LV-1067 Riga, Latvia; (J.K.); (K.S.); (P.Z.)
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (R.W.); (M.K.); (M.H.)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
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11
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Hausmann M, Falk M, Neitzel C, Hofmann A, Biswas A, Gier T, Falkova I, Heermann DW, Hildenbrand G. Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach. Int J Mol Sci 2021; 22:3636. [PMID: 33807337 PMCID: PMC8037797 DOI: 10.3390/ijms22073636] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/20/2021] [Accepted: 03/26/2021] [Indexed: 02/06/2023] Open
Abstract
In cancer therapy, the application of (fractionated) harsh radiation treatment is state of the art for many types of tumors. However, ionizing radiation is a "double-edged sword"-it can kill the tumor but can also promote the selection of radioresistant tumor cell clones or even initiate carcinogenesis in the normal irradiated tissue. Individualized radiotherapy would reduce these risks and boost the treatment, but its development requires a deep understanding of DNA damage and repair processes and the corresponding control mechanisms. DNA double strand breaks (DSBs) and their repair play a critical role in the cellular response to radiation. In previous years, it has become apparent that, beyond genetic and epigenetic determinants, the structural aspects of damaged chromatin (i.e., not only of DSBs themselves but also of the whole damage-surrounding chromatin domains) form another layer of complex DSB regulation. In the present article, we summarize the application of super-resolution single molecule localization microscopy (SMLM) for investigations of these structural aspects with emphasis on the relationship between the nano-architecture of radiation-induced repair foci (IRIFs), represented here by γH2AX foci, and their chromatin environment. Using irradiated HeLa cell cultures as an example, we show repair-dependent rearrangements of damaged chromatin and analyze the architecture of γH2AX repair clusters according to topological similarities. Although HeLa cells are known to have highly aberrant genomes, the topological similarity of γH2AX was high, indicating a functional, presumptively genome type-independent relevance of structural aspects in DSB repair. Remarkably, nano-scaled chromatin rearrangements during repair depended both on the chromatin domain type and the treatment. Based on these results, we demonstrate how the nano-architecture and topology of IRIFs and chromatin can be determined, point to the methodological relevance of SMLM, and discuss the consequences of the observed phenomena for the DSB repair network regulation or, for instance, radiation treatment outcomes.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Martin Falk
- Institute of Biophysics, Czech Academy of Sciences, 612 65 Brno, Czech Republic;
| | - Charlotte Neitzel
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Andreas Hofmann
- Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany; (A.H.); (D.W.H.)
| | - Abin Biswas
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Theresa Gier
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
| | - Iva Falkova
- Institute of Biophysics, Czech Academy of Sciences, 612 65 Brno, Czech Republic;
| | - Dieter W. Heermann
- Institute for Theoretical Physics, Heidelberg University, 69120 Heidelberg, Germany; (A.H.); (D.W.H.)
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany; (C.N.); (A.B.); (T.G.); (G.H.)
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12
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Krigerts J, Salmina K, Freivalds T, Zayakin P, Rumnieks F, Inashkina I, Giuliani A, Hausmann M, Erenpreisa J. Differentiating cancer cells reveal early large-scale genome regulation by pericentric domains. Biophys J 2021; 120:711-724. [PMID: 33453273 PMCID: PMC7896032 DOI: 10.1016/j.bpj.2021.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 02/07/2023] Open
Abstract
Finding out how cells prepare for fate change during differentiation commitment was our task. To address whether the constitutive pericentromere-associated domains (PADs) may be involved, we used a model system with known transcriptome data, MCF-7 breast cancer cells treated with the ErbB3 ligand heregulin (HRG), which induces differentiation and is used in the therapy of cancer. PAD-repressive heterochromatin (H3K9me3), centromere-associated-protein-specific, and active euchromatin (H3K4me3) antibodies, real-time PCR, acridine orange DNA structural test (AOT), and microscopic image analysis were applied. We found a two-step DNA unfolding after 15–20 and 60 min of HRG treatment, respectively. This behavior was consistent with biphasic activation of the early response genes (c-fos - fosL1/myc) and the timing of two transcriptome avalanches reported in the literature. In control, the average number of PADs negatively correlated with their size by scale-free distribution, and centromere clustering in turn correlated with PAD size, both indicating that PADs may create and modulate a suprachromosomal network by fusing and splitting a constant proportion of the constitutive heterochromatin. By 15 min of HRG treatment, the bursting unraveling of PADs from the nucleolus boundary occurred, coinciding with the first step of H3K4me3 chromatin unfolding, confirmed by AOT. The second step after 60 min of HRG treatment was associated with transcription of long noncoding RNA from PADs and peaking of fosL1/c-myc response. We hypothesize that the bursting of PAD clusters under a critical silencing threshold pushes the first transcription avalanche, whereas the destruction of the PAD network enables genome rewiring needed for differentiation repatterning, mediated by early response bivalent genes.
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Affiliation(s)
- Jekabs Krigerts
- Latvian Biomedicine Research and Study Centre, Riga, Latvia; University of Latvia, Riga, Latvia
| | | | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedicine Research and Study Centre, Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedicine Research and Study Centre, Riga, Latvia; University of Latvia, Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedicine Research and Study Centre, Riga, Latvia
| | - Alessandro Giuliani
- Environment and Health Department, Italian National Institute of Health, Rome, Italy
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, Heidelberg, Germany.
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Falk M, Hausmann M. A Paradigm Revolution or Just Better Resolution-Will Newly Emerging Superresolution Techniques Identify Chromatin Architecture as a Key Factor in Radiation-Induced DNA Damage and Repair Regulation? Cancers (Basel) 2020; 13:E18. [PMID: 33374540 PMCID: PMC7793109 DOI: 10.3390/cancers13010018] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 12/18/2020] [Indexed: 02/07/2023] Open
Abstract
DNA double-strand breaks (DSBs) have been recognized as the most serious lesions in irradiated cells. While several biochemical pathways capable of repairing these lesions have been identified, the mechanisms by which cells select a specific pathway for activation at a given DSB site remain poorly understood. Our knowledge of DSB induction and repair has increased dramatically since the discovery of ionizing radiation-induced foci (IRIFs), initiating the possibility of spatiotemporally monitoring the assembly and disassembly of repair complexes in single cells. IRIF exploration revealed that all post-irradiation processes-DSB formation, repair and misrepair-are strongly dependent on the characteristics of DSB damage and the microarchitecture of the whole affected chromatin domain in addition to the cell status. The microscale features of IRIFs, such as their morphology, mobility, spatiotemporal distribution, and persistence kinetics, have been linked to repair mechanisms. However, the influence of various biochemical and structural factors and their specific combinations on IRIF architecture remains unknown, as does the hierarchy of these factors in the decision-making process for a particular repair mechanism at each individual DSB site. New insights into the relationship between the physical properties of the incident radiation, chromatin architecture, IRIF architecture, and DSB repair mechanisms and repair efficiency are expected from recent developments in optical superresolution microscopy (nanoscopy) techniques that have shifted our ability to analyze chromatin and IRIF architectures towards the nanoscale. In the present review, we discuss this relationship, attempt to correlate still rather isolated nanoscale studies with already better-understood aspects of DSB repair at the microscale, and consider whether newly emerging "correlated multiscale structuromics" can revolutionarily enhance our knowledge in this field.
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Affiliation(s)
- Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany;
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14
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Alanyl-Glutamine Restores Tight Junction Organization after Disruption by a Conventional Peritoneal Dialysis Fluid. Biomolecules 2020; 10:biom10081178. [PMID: 32823646 PMCID: PMC7464725 DOI: 10.3390/biom10081178] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding and targeting the molecular basis of peritoneal solute and protein transport is essential to improve peritoneal dialysis (PD) efficacy and patient outcome. Supplementation of PD fluids (PDF) with alanyl-glutamine (AlaGln) increased small solute transport and reduced peritoneal protein loss in a recent clinical trial. Transepithelial resistance and 10 kDa and 70 kDa dextran transport were measured in primary human endothelial cells (HUVEC) exposed to conventional acidic, glucose degradation products (GDP) containing PDF (CPDF) and to low GDP containing PDF (LPDF) with and without AlaGln. Zonula occludens-1 (ZO-1) and claudin-5 were quantified by Western blot and immunofluorescence and in mice exposed to saline and CPDF for 7 weeks by digital imaging analyses. Spatial clustering of ZO-1 molecules was assessed by single molecule localization microscopy. AlaGln increased transepithelial resistance, and in CPDF exposed HUVEC decreased dextran transport rates and preserved claudin-5 and ZO-1 abundance. Endothelial clustering of membrane bound ZO-1 was higher in CPDF supplemented with AlaGln. In mice, arteriolar endothelial claudin-5 was reduced in CPDF, but restored with AlaGln, while mesothelial claudin-5 abundance was unchanged. AlaGln supplementation seals the peritoneal endothelial barrier, and when supplemented to conventional PD fluid increases claudin-5 and ZO-1 abundance and clustering of ZO-1 in the endothelial cell membrane.
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15
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Hausmann M, Lee JH, Sievers A, Krufczik M, Hildenbrand G. COMBinatorial Oligonucleotide FISH (COMBO-FISH) with Uniquely Binding Repetitive DNA Probes. Methods Mol Biol 2020; 2175:65-77. [PMID: 32681484 DOI: 10.1007/978-1-0716-0763-3_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
During the last decade, genome sequence databases of many species have been more and more completed so that it has become possible to further develop a recently established technique of FISH (Fluorescence In Situ Hybridization) called COMBO-FISH (COMBinatorial Oligo FISH). In contrast to standard FISH techniques, COMBO-FISH makes use of a bioinformatic search in sequence databases for probe design, so that it can be done for any species so far sequenced. In the original approach, oligonucleotide stretches of typical lengths of 15-30 nucleotides were selected in such a way that they only co-localize at the given genome target. Typical probe sets of about 20-40 stretches were used to label about 50-250 kb specifically. The probes of different lengths can be composed of purines and pyrimidines, but were often restricted to homo-purine or homo-pyrimidine probe sets because of the experimental advantage of using a protocol omitting denaturation of the target strand and triple strand binding of the probes. This allows for a better conservation of the 3D folding and arrangement of the genome. With an improved, rigorous genome sequence database analysis and sequence search according to statistical frequency and uniqueness, a novel family of probes repetitively binding to characteristic genome features like SINEs (Short Interspersed Nuclear Elements, e.g., ALU elements), LINEs (Long Interspersed Nuclear Elements, e.g., L1), or centromeres has been developed. These probes can be synthesized commercially as DNA or PNA probes with high purity and labeled by fluorescent dye molecules. Here, new protocols are described for purine-pyrimidine probes omitting heat treatment for denaturation of the target so that oligonucleotide labeling can also be combined with immune-staining by specific antibodies. If the dyes linked to the oligonucleotide stretches undergo reversible photo-bleaching (laser-induced slow blinking), the labeled cell nuclei can be further subjected to super-resolution localization microscopy for complex chromatin architecture research.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.
| | - Jin-Ho Lee
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Matthias Krufczik
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
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16
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Scherthan H, Lee JH, Maus E, Schumann S, Muhtadi R, Chojowski R, Port M, Lassmann M, Bestvater F, Hausmann M. Nanostructure of Clustered DNA Damage in Leukocytes after In-Solution Irradiation with the Alpha Emitter Ra-223. Cancers (Basel) 2019; 11:cancers11121877. [PMID: 31779276 PMCID: PMC6966434 DOI: 10.3390/cancers11121877] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/22/2019] [Accepted: 11/23/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Cancer patients are increasingly treated with alpha-particle-emitting radiopharmaceuticals. At the subcellular level, alpha particles induce densely spaced ionizations and molecular damage. Induction of DNA lesions, especially clustered DNA double-strand breaks (DSBs), threatens a cell's survival. Currently, it is under debate to what extent the spatial topology of the damaged chromatin regions and the repair protein arrangements are contributing. METHODS Super-resolution light microscopy (SMLM) in combination with cluster analysis of single molecule signal-point density regions of DSB repair markers was applied to investigate the nano-structure of DNA damage foci tracks of Ra-223 in-solution irradiated leukocytes. RESULTS Alpha-damaged chromatin tracks were efficiently outlined by γ-H2AX that formed large (super) foci composed of numerous 60-80 nm-sized nano-foci. Alpha damage tracks contained 60-70% of all γ-H2AX point signals in a nucleus, while less than 30% of 53BP1, MRE11 or p-ATM signals were located inside γ-H2AX damage tracks. MRE11 and p-ATM protein fluorescent tags formed focal nano-clusters of about 20 nm peak size. There were, on average, 12 (± 9) MRE11 nanoclusters in a typical γ-H2AX-marked alpha track, suggesting a minimal number of MRE11-processed DSBs per track. Our SMLM data suggest regularly arranged nano-structures during DNA repair in the damaged chromatin domain.
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Affiliation(s)
- Harry Scherthan
- Bundeswehr Institute of Radiobiology, University of Ulm, Neuherbergstraße 11, 80937 München, Germany; (J.-H.L.); (E.M.); (R.M.); (M.P.)
- Correspondence: (H.S.); (M.H.); Tel.: +49-89-992692-2272 (H.S.); +49-6221-549824 (M.H.)
| | - Jin-Ho Lee
- Bundeswehr Institute of Radiobiology, University of Ulm, Neuherbergstraße 11, 80937 München, Germany; (J.-H.L.); (E.M.); (R.M.); (M.P.)
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany;
| | - Emanuel Maus
- Bundeswehr Institute of Radiobiology, University of Ulm, Neuherbergstraße 11, 80937 München, Germany; (J.-H.L.); (E.M.); (R.M.); (M.P.)
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany;
| | - Sarah Schumann
- Department of Nuclear Medicine, University of Würzburg, Oberdürrbacher Str. 6, 97080 Würzburg, Germany; (S.S.); (M.L.)
| | - Razan Muhtadi
- Bundeswehr Institute of Radiobiology, University of Ulm, Neuherbergstraße 11, 80937 München, Germany; (J.-H.L.); (E.M.); (R.M.); (M.P.)
| | - Robert Chojowski
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany;
| | - Matthias Port
- Bundeswehr Institute of Radiobiology, University of Ulm, Neuherbergstraße 11, 80937 München, Germany; (J.-H.L.); (E.M.); (R.M.); (M.P.)
| | - Michael Lassmann
- Department of Nuclear Medicine, University of Würzburg, Oberdürrbacher Str. 6, 97080 Würzburg, Germany; (S.S.); (M.L.)
| | - Felix Bestvater
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany;
- Correspondence: (H.S.); (M.H.); Tel.: +49-89-992692-2272 (H.S.); +49-6221-549824 (M.H.)
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17
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Pilarczyk G, Papenfuß F, Bestvater F, Hausmann M. Spatial Arrangements of Connexin43 in Cancer Related Cells and Re-Arrangements under Treatment Conditions: Investigations on the Nano-Scale by Super-Resolution Localization Light Microscopy. Cancers (Basel) 2019; 11:cancers11030301. [PMID: 30836676 PMCID: PMC6468626 DOI: 10.3390/cancers11030301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 12/14/2022] Open
Abstract
Cancer studies suggest that the spatial localization of connexin43 (Cx43) could play an important role during tumor genesis and the formation of metastasis. Cx43 has been shown to be upregulated in cancer cells; thereby a shift from Cx43 normal localization in gap junctions in the cell membrane towards a primarily cytoplasmic localization was observed in many studies. So far neither the spatial arrangements of Cx43 in breast cancer cells nor the effects of treatment outcome (ionizing radiation and antibody therapy) on the spatial arrangements of Cx43, have been microscopically studied on the nanoscale. This has brought up the idea to study the micro- and nanoscaled spatial Cx43 arrangements in a model of breast cancer-related cell types, i.e., SkBr3 breast cancer cells, BJ fibroblasts, and primary human internal mammary artery endothelial cells (HIMAECs). The cells were treated with neuregulin1 (NRG1), trastuzumab (Herceptin), or 6MeV-photon irradiation at a dose of 4 Gy. NRG1 stimulates further NRG1 release in the tumor endothelium that may lead to an enhanced tumor protective effect whereas Herceptin, used in antibody treatment, works in an antagonistic fashion to NRG1. After fluorescent labelling with specific antibodies, the molecular positions of Cx43 in the perinuclear cytosol and in the cell periphery at the membrane were determined for the three treatment related applications (NRG1, trastuzumab, 4 Gy irradiation) using confocal laser scanning microscopy (CLSM) and single molecule localization microscopy (SMLM). These techniques enable investigations of Cx43 enrichment and topological arrangements of Cx43 molecules from the micro-scale of a whole cell to the nano-scale of single molecules. In SkBr3 cells with and without radiation treatment high density accumulations were detected which seem to be diluted after NRG1 and trastuzumab treatment although the SMLM distance frequency distributions did not significantly vary. In BJ fibroblasts and HIMAECs differences between periphery and perinuclear cytosol were observed after the different treatment processes. HIMAECs showed significant Cx43 accumulation after NRG1, trastuzumab, and radiation treatment in the perinuclear region whereas in the periphery radiation has less influence as compared to the control. BJ cells were reacting to the treatments by Cx43 accumulations in the perinuclear region but also in the periphery. In conclusion, it was shown that by using CLSM and super-resolution SMLM, treatment effects on the spatial and thus functional arrangements of Cx43 became detectable for investigations of tumor response mechanisms.
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Affiliation(s)
- Götz Pilarczyk
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
- Department of High Content Analysis of the Cell "HiCell", BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
| | - Franziska Papenfuß
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Felix Bestvater
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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18
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Pagáčová E, Štefančíková L, Schmidt-Kaler F, Hildenbrand G, Vičar T, Depeš D, Lee JH, Bestvater F, Lacombe S, Porcel E, Roux S, Wenz F, Kopečná O, Falková I, Hausmann M, Falk M. Challenges and Contradictions of Metal Nano-Particle Applications for Radio-Sensitivity Enhancement in Cancer Therapy. Int J Mol Sci 2019; 20:ijms20030588. [PMID: 30704035 PMCID: PMC6387067 DOI: 10.3390/ijms20030588] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 01/24/2019] [Indexed: 12/12/2022] Open
Abstract
From the very beginnings of radiotherapy, a crucial question persists with how to target the radiation effectiveness into the tumor while preserving surrounding tissues as undamaged as possible. One promising approach is to selectively pre-sensitize tumor cells by metallic nanoparticles. However, though the "physics" behind nanoparticle-mediated radio-interaction has been well elaborated, practical applications in medicine remain challenging and often disappointing because of limited knowledge on biological mechanisms leading to cell damage enhancement and eventually cell death. In the present study, we analyzed the influence of different nanoparticle materials (platinum (Pt), and gold (Au)), cancer cell types (HeLa, U87, and SKBr3), and doses (up to 4 Gy) of low-Linear Energy Transfer (LET) ionizing radiation (γ- and X-rays) on the extent, complexity and reparability of radiation-induced γH2AX + 53BP1 foci, the markers of double stand breaks (DSBs). Firstly, we sensitively compared the focus presence in nuclei during a long period of time post-irradiation (24 h) in spatially (three-dimensionally, 3D) fixed cells incubated and non-incubated with Pt nanoparticles by means of high-resolution immunofluorescence confocal microscopy. The data were compared with our preliminary results obtained for Au nanoparticles and recently published results for gadolinium (Gd) nanoparticles of approximately the same size (2⁻3 nm). Next, we introduced a novel super-resolution approach-single molecule localization microscopy (SMLM)-to study the internal structure of the repair foci. In these experiments, 10 nm Au nanoparticles were used that could be also visualized by SMLM. Altogether, the data show that different nanoparticles may or may not enhance radiation damage to DNA, so multi-parameter effects have to be considered to better interpret the radiosensitization. Based on these findings, we discussed on conclusions and contradictions related to the effectiveness and presumptive mechanisms of the cell radiosensitization by nanoparticles. We also demonstrate that SMLM offers new perspectives to study internal structures of repair foci with the goal to better evaluate potential differences in DNA damage patterns.
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Affiliation(s)
- Eva Pagáčová
- Czech Academy of Sciences, Institute of Biophysics, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
| | - Lenka Štefančíková
- Czech Academy of Sciences, Institute of Biophysics, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
- Institute des Sciences Moléculaires d'Orsay (ISMO), Université Paris Saclay, Université Paris Sud, CNRS, 91405 Orsay Cedex, France.
| | - Franz Schmidt-Kaler
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Georg Hildenbrand
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
- Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany.
| | - Tomáš Vičar
- Brno University of Technology, Department of Biomedical Engineering, Technická 3082/12, 61600 Brno, Czech Republic.
| | - Daniel Depeš
- Czech Academy of Sciences, Institute of Biophysics, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
| | - Jin-Ho Lee
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Felix Bestvater
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany.
| | - Sandrine Lacombe
- Institute des Sciences Moléculaires d'Orsay (ISMO), Université Paris Saclay, Université Paris Sud, CNRS, 91405 Orsay Cedex, France.
| | - Erika Porcel
- Institute des Sciences Moléculaires d'Orsay (ISMO), Université Paris Saclay, Université Paris Sud, CNRS, 91405 Orsay Cedex, France.
| | - Stéphane Roux
- Institute UTINAM, UMR CNRS 6213-Université de Bourgogne Franche-Comté, 25020 Besançon Cedex, France.
| | - Frederik Wenz
- Department of Radiation Oncology, Universitätsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, 68159 Mannheim, Germany.
| | - Olga Kopečná
- Czech Academy of Sciences, Institute of Biophysics, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
| | - Iva Falková
- Czech Academy of Sciences, Institute of Biophysics, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Martin Falk
- Czech Academy of Sciences, Institute of Biophysics, v.v.i., Kralovopolska 135, 612 65 Brno, Czech Republic.
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19
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van Wijk SJ, Fulda S, Dikic I, Heilemann M. Visualizing ubiquitination in mammalian cells. EMBO Rep 2019; 20:embr.201846520. [PMID: 30665942 DOI: 10.15252/embr.201846520] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 12/17/2018] [Accepted: 12/21/2018] [Indexed: 12/19/2022] Open
Abstract
Covalent modification of proteins with ubiquitin is essential for the majority of biological processes in mammalian cells. Numerous proteins are conjugated with single or multiple ubiquitin molecules or chains in a dynamic fashion, often determining protein half-lives, localization or function. Experimental approaches to study ubiquitination have been dominated by genetic and biochemical analysis of enzyme structure-function relationships, reaction mechanisms and physiological relevance. Here, we provide an overview of recent developments in microscopy-based imaging of ubiquitination, available reagents and technologies. We discuss the progress in direct and indirect imaging of differentially linked ubiquitin chains in fixed and living cells using confocal fluorescence microscopy and super-resolution microscopy, illustrated by the role of ubiquitin in antibacterial autophagy and pro-inflammatory signalling. Finally, we speculate on future developments and forecast a transition from qualitative to quantitative super-resolution approaches to understand fundamental aspects of ubiquitination and the formation and distribution of functional E3 ligase protein complexes in their native environment.
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Affiliation(s)
- Sjoerd Jl van Wijk
- Institute for Experimental Cancer Research in Paediatrics, Goethe University, Frankfurt am Main, Germany
| | - Simone Fulda
- Institute for Experimental Cancer Research in Paediatrics, Goethe University, Frankfurt am Main, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Goethe University - Medical Faculty, University Hospital Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Frankfurt am Main, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe University, Frankfurt am Main, Germany
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20
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Recruitment of 53BP1 Proteins for DNA Repair and Persistence of Repair Clusters Differ for Cell Types as Detected by Single Molecule Localization Microscopy. Int J Mol Sci 2018; 19:ijms19123713. [PMID: 30469529 PMCID: PMC6321197 DOI: 10.3390/ijms19123713] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 01/30/2023] Open
Abstract
DNA double stranded breaks (DSBs) are the most serious type of lesions introduced into chromatin by ionizing radiation. During DSB repair, cells recruit different proteins to the damaged sites in a manner dependent on local chromatin structure, DSB location in the nucleus, and the repair pathway entered. 53BP1 is one of the important players participating in repair pathway decision of the cell. Although many molecular biology details have been investigated, the architecture of 53BP1 repair foci and its development during the post-irradiation time, especially the period of protein recruitment, remains to be elucidated. Super-resolution light microscopy is a powerful new tool to approach such studies in 3D-conserved cell nuclei. Recently, we demonstrated the applicability of single molecule localization microscopy (SMLM) as one of these highly resolving methods for analyses of dynamic repair protein distribution and repair focus internal nano-architecture in intact cell nuclei. In the present study, we focused our investigation on 53BP1 foci in differently radio-resistant cell types, moderately radio-resistant neonatal human dermal fibroblasts (NHDF) and highly radio-resistant U87 glioblastoma cells, exposed to high-LET 15N-ion radiation. At given time points up to 24 h post irradiation with doses of 1.3 Gy and 4.0 Gy, the coordinates and spatial distribution of fluorescently tagged 53BP1 molecules was quantitatively evaluated at the resolution of 10⁻20 nm. Clusters of these tags were determined as sub-units of repair foci according to SMLM parameters. The formation and relaxation of such clusters was studied. The higher dose generated sufficient numbers of DNA breaks to compare the post-irradiation dynamics of 53BP1 during DSB processing for the cell types studied. A perpendicular (90°) irradiation scheme was used with the 4.0 Gy dose to achieve better separation of a relatively high number of particle tracks typically crossing each nucleus. For analyses along ion-tracks, the dose was reduced to 1.3 Gy and applied in combination with a sharp angle irradiation (10° relative to the cell plane). The results reveal a higher ratio of 53BP1 proteins recruited into SMLM defined clusters in fibroblasts as compared to U87 cells. Moreover, the speed of foci and thus cluster formation and relaxation also differed for the cell types. In both NHDF and U87 cells, a certain number of the detected and functionally relevant clusters remained persistent even 24 h post irradiation; however, the number of these clusters again varied for the cell types. Altogether, our findings indicate that repair cluster formation as determined by SMLM and the relaxation (i.e., the remaining 53BP1 tags no longer fulfill the cluster definition) is cell type dependent and may be functionally explained and correlated to cell specific radio-sensitivity. The present study demonstrates that SMLM is a highly appropriate method for investigations of spatiotemporal protein organization in cell nuclei and how it influences the cell decision for a particular repair pathway at a given DSB site.
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21
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Exploring Protein⁻Protein Interaction in the Study of Hormone-Dependent Cancers. Int J Mol Sci 2018; 19:ijms19103173. [PMID: 30326622 PMCID: PMC6213999 DOI: 10.3390/ijms19103173] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/09/2018] [Accepted: 10/10/2018] [Indexed: 12/20/2022] Open
Abstract
Estrogen receptors promote target gene transcription when they form a dimer, in which two identical (homodimer) or different (heterodimer) proteins are bound to each other. In hormone-dependent cancers, hormone receptor dimerization plays pivotal roles, not only in the pathogenesis or development of the tumors, but also in the development of therapeutic resistance. Protein–protein interactions (PPIs), including dimerization and complex formation, have been also well-known to be required for proteins to exert their functions. The methods which could detect PPIs are genetic engineering (i.e., resonance energy transfer) and/or antibody technology (i.e., co-immunoprecipitation) using cultured cells. In addition, visualization of the target proteins in tissues can be performed using antigen–antibody reactions, as in immunohistochemistry. Furthermore, development of microscopic techniques (i.e., electron microscopy and confocal laser microscopy) has made it possible to visualize intracellular and/or intranuclear organelles. We have recently reported the visualization of estrogen receptor dimers in breast cancer tissues by using the in situ proximity ligation assay (PLA). PLA was developed along the lines of antibody technology development, and this assay has made it possible to visualize PPIs in archival tissue specimens. Localization of PPI in organelles has also become possible using super-resolution microscopes exceeding the resolution limit of conventional microscopes. Therefore, in this review, we summarize the methodologies used for studying PPIs in both cells and tissues, and review the recently reported studies on PPIs of hormones.
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Hofmann A, Krufczik M, Heermann DW, Hausmann M. Using Persistent Homology as a New Approach for Super-Resolution Localization Microscopy Data Analysis and Classification of γH2AX Foci/Clusters. Int J Mol Sci 2018; 19:E2263. [PMID: 30072594 PMCID: PMC6121565 DOI: 10.3390/ijms19082263] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/27/2018] [Accepted: 08/01/2018] [Indexed: 12/18/2022] Open
Abstract
DNA double strand breaks (DSB) are the most severe damages in chromatin induced by ionizing radiation. In response to such environmentally determined stress situations, cells have developed repair mechanisms. Although many investigations have contributed to a detailed understanding of repair processes, e.g., homologous recombination repair or non-homologous end-joining, the question is not sufficiently answered, how a cell decides to apply a certain repair process at a certain damage site, since all different repair pathways could simultaneously occur in the same cell nucleus. One of the first processes after DSB induction is phosphorylation of the histone variant H2AX to γH2AX in the given surroundings of the damaged locus. Since the spatial organization of chromatin is not random, it may be conclusive that the spatial organization of γH2AX foci is also not random, and rather, contributes to accessibility of special repair proteins to the damaged site, and thus, to the following repair pathway at this given site. The aim of this article is to demonstrate a new approach to analyze repair foci by their topology in order to obtain a cell independent method of categorization. During the last decade, novel super-resolution fluorescence light microscopic techniques have enabled new insights into genome structure and spatial organization on the nano-scale in the order of 10 nm. One of these techniques is single molecule localization microscopy (SMLM) with which the spatial coordinates of single fluorescence molecules can precisely be determined and density and distance distributions can be calculated. This method is an appropriate tool to quantify complex changes of chromatin and to describe repair foci on the single molecule level. Based on the pointillist information obtained by SMLM from specifically labeled heterochromatin and γH2AX foci reflecting the chromatin morphology and repair foci topology, we have developed a new analytical methodology of foci or foci cluster characterization, respectively, by means of persistence homology. This method allows, for the first time, a cell independent comparison of two point distributions (here the point distributions of two γH2AX clusters) with each other of a selected ensample and to give a mathematical measure of their similarity. In order to demonstrate the feasibility of this approach, cells were irradiated by low LET (linear energy transfer) radiation with different doses and the heterochromatin and γH2AX foci were fluorescently labeled by antibodies for SMLM. By means of our new analysis method, we were able to show that the topology of clusters of γH2AX foci can be categorized depending on the distance to heterochromatin. This method opens up new possibilities to categorize spatial organization of point patterns by parameterization of topological similarity.
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Affiliation(s)
- Andreas Hofmann
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany.
| | - Matthias Krufczik
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
| | - Dieter W Heermann
- Institute for Theoretical Physics, Heidelberg University, Philosophenweg 19, 69120 Heidelberg, Germany.
| | - Michael Hausmann
- Kirchhoff-Institute for Physics, Heidelberg University, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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23
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Koganti P, Levy-Cohen G, Blank M. Smurfs in Protein Homeostasis, Signaling, and Cancer. Front Oncol 2018; 8:295. [PMID: 30116722 PMCID: PMC6082930 DOI: 10.3389/fonc.2018.00295] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitination is an evolutionary conserved highly-orchestrated enzymatic cascade essential for normal cellular functions and homeostasis maintenance. This pathway relies on a defined set of cellular enzymes, among them, substrate-specific E3 ubiquitin ligases (E3s). These ligases are the most critical players, as they define the spatiotemporal nature of ubiquitination and confer specificity to this cascade. Smurf1 and Smurf2 (Smurfs) are the C2-WW-HECT-domain E3 ubiquitin ligases, which recently emerged as important determinants of pivotal cellular processes. These processes include cell proliferation and differentiation, chromatin organization and dynamics, DNA damage response and genomic integrity maintenance, gene expression, cell stemness, migration, and invasion. All these processes are intimately connected and profoundly altered in cancer. Initially, Smurf proteins were identified as negative regulators of the bone morphogenetic protein (BMP) and the transforming growth factor beta (TGF-β) signaling pathways. However, recent studies have extended the scope of Smurfs' biological functions beyond the BMP/TGF-β signaling regulation. Here, we provide a critical literature overview and updates on the regulatory roles of Smurfs in molecular and cell biology, with an emphasis on cancer. We also highlight the studies demonstrating the impact of Smurf proteins on tumor cell sensitivity to anticancer therapies. Further in-depth analyses of Smurfs' biological functions and influences on molecular pathways could provide novel therapeutic targets and paradigms for cancer diagnosis and treatment.
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Affiliation(s)
- Praveen Koganti
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Gal Levy-Cohen
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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24
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Hausmann M, Wagner E, Lee JH, Schrock G, Schaufler W, Krufczik M, Papenfuß F, Port M, Bestvater F, Scherthan H. Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells. NANOSCALE 2018; 10:4320-4331. [PMID: 29443341 DOI: 10.1039/c7nr08145f] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Ionizing radiation (IR)-induced damage confers functional and conformational changes to nuclear chromatin associated with DNA single and double strand breaks. This leads to the activation of complex DNA repair machineries that aim to preserve the integrity of the DNA molecule. Since hetero- and euchromatin are differentially accessible to DNA repair pathways, local chromatin re-arrangements and structural changes are among the consequences of an activated DNA damage response. Using super-resolution localization microscopy (SRLM), we investigated the X-ray-induced repositioning of γ-H2AX and histone H3K9me3 heterochromatin marks in the nuclei of HeLa cells. Aliquots of cells exposed to different IR doses (0.5, 1 and 2 Gy) were fixed at certain repair times for SRLM imaging. The number and size of nano-scale γ-H2AX molecule signal clusters detected increased with rising irradiation doses, with the number and size being the highest 0.5 h after irradiation. With growing repair time both the number and size of γ-H2AX nano-clusters decreased. Eight hours after irradiation, the number of clusters reached control levels, in agreement with the disappearance of most IR-induced foci seen by conventional microscopy. SRLM investigation of heterochromatin marks in spatial relation to γ-H2AX clusters showed that on average the heterochromatin density was high in the vicinity of γ-H2AX, which is in agreement with the observation that DSBs seem to relocate to the surface of heterochromatin clusters for DNA repair. The data demonstrate the potential of pointillist images obtained by SRLM for quantitative investigations of chromatin conformation changes and repair-protein recruitment on the nanoscale as measures for a radiation response.
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Affiliation(s)
- Michael Hausmann
- Kirchhoff-Instit ute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany.
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25
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Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines. Cancers (Basel) 2018; 10:cancers10010025. [PMID: 29361783 PMCID: PMC5789375 DOI: 10.3390/cancers10010025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/12/2018] [Accepted: 01/17/2018] [Indexed: 01/01/2023] Open
Abstract
In radiation biophysics, it is a subject of nowadays research to investigate DNA strand break repair in detail after damage induction by ionizing radiation. It is a subject of debate as to what makes up the cell’s decision to use a certain repair pathway and how the repair machinery recruited in repair foci is spatially and temporarily organized. Single-molecule localization microscopy (SMLM) allows super-resolution analysis by precise localization of single fluorescent molecule tags, resulting in nuclear structure analysis with a spatial resolution in the 10 nm regime. Here, we used SMLM to study MRE11 foci. MRE11 is one of three proteins involved in the MRN-complex (MRE11-RAD50-NBS1 complex), a prominent DNA strand resection and broken end bridging component involved in homologous recombination repair (HRR) and alternative non-homologous end joining (a-NHEJ). We analyzed the spatial arrangements of antibody-labelled MRE11 proteins in the nuclei of a breast cancer and a skin fibroblast cell line along a time-course of repair (up to 48 h) after irradiation with a dose of 2 Gy. Different kinetics for cluster formation and relaxation were determined. Changes in the internal nano-scaled structure of the clusters were quantified and compared between the two cell types. The results indicate a cell type-dependent DNA damage response concerning MRE11 recruitment and cluster formation. The MRE11 data were compared to H2AX phosphorylation detected by γH2AX molecule distribution. These data suggested modulations of MRE11 signal frequencies that were not directly correlated to DNA damage induction. The application of SMLM in radiation biophysics offers new possibilities to investigate spatial foci organization after DNA damaging and during subsequent repair.
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26
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Jezkova L, Zadneprianetc M, Kulikova E, Smirnova E, Bulanova T, Depes D, Falkova I, Boreyko A, Krasavin E, Davidkova M, Kozubek S, Valentova O, Falk M. Particles with similar LET values generate DNA breaks of different complexity and reparability: a high-resolution microscopy analysis of γH2AX/53BP1 foci. NANOSCALE 2018; 10:1162-1179. [PMID: 29271466 DOI: 10.1039/c7nr06829h] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Biological effects of high-LET (linear energy transfer) radiation have received increasing attention, particularly in the context of more efficient radiotherapy and space exploration. Efficient cell killing by high-LET radiation depends on the physical ability of accelerated particles to generate complex DNA damage, which is largely mediated by LET. However, the characteristics of DNA damage and repair upon exposure to different particles with similar LET parameters remain unexplored. We employed high-resolution confocal microscopy to examine phosphorylated histone H2AX (γH2AX)/p53-binding protein 1 (53BP1) focus streaks at the microscale level, focusing on the complexity, spatiotemporal behaviour and repair of DNA double-strand breaks generated by boron and neon ions accelerated at similar LET values (∼135 keV μm-1) and low energies (8 and 47 MeV per n, respectively). Cells were irradiated using sharp-angle geometry and were spatially (3D) fixed to maximize the resolution of these analyses. Both high-LET radiation types generated highly complex γH2AX/53BP1 focus clusters with a larger size, increased irregularity and slower elimination than low-LET γ-rays. Surprisingly, neon ions produced even more complex γH2AX/53BP1 focus clusters than boron ions, consistent with DSB repair kinetics. Although the exposure of cells to γ-rays and boron ions eliminated a vast majority of foci (94% and 74%, respectively) within 24 h, 45% of the foci persisted in cells irradiated with neon. Our calculations suggest that the complexity of DSB damage critically depends on (increases with) the particle track core diameter. Thus, different particles with similar LET and energy may generate different types of DNA damage, which should be considered in future research.
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Affiliation(s)
- Lucie Jezkova
- Joint Institute for Nuclear Research, Dubna, Russia and University of Chemistry and Technology Prague, Prague, Czech Republic
- University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Mariia Zadneprianetc
- Joint Institute for Nuclear Research, Dubna, Russia and Dubna State University, Dubna, Russia
- Dubna State University, Dubna, Russia
| | - Elena Kulikova
- Joint Institute for Nuclear Research, Dubna, Russia and Dubna State University, Dubna, Russia
- Dubna State University, Dubna, Russia
| | | | - Tatiana Bulanova
- Joint Institute for Nuclear Research, Dubna, Russia and Dubna State University, Dubna, Russia
- Dubna State University, Dubna, Russia
| | - Daniel Depes
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
| | - Iva Falkova
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
| | - Alla Boreyko
- Joint Institute for Nuclear Research, Dubna, Russia and Dubna State University, Dubna, Russia
- Dubna State University, Dubna, Russia
| | - Evgeny Krasavin
- Joint Institute for Nuclear Research, Dubna, Russia and Dubna State University, Dubna, Russia
- Dubna State University, Dubna, Russia
| | - Marie Davidkova
- Czech Academy of Sciences, Nuclear Physics Institute, Prague, Czech Republic
| | - Stanislav Kozubek
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
| | - Olga Valentova
- University of Chemistry and Technology Prague, Prague, Czech Republic
| | - Martin Falk
- Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
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