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ISSN Druckformat: 1045-4403
ISSN Online: 2162-6502
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Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part B− Structuromics
ABSTRAKT
Recent groundbreaking developments in Omics and bioinformatics have generated new hope for overcoming the complexity and variability of (radio)biological systems while simultaneously shedding more light on fundamental radiobiological questions that have remained unanswered for decades. In the era of Omics, our knowledge of how genes and dozens of proteins interact in the frame of complex signaling and repair pathways (or, rather, networks) to preserve the integrity of the genome has been rapidly expanding. Nevertheless, these functional networks must be observed with strong correspondence to the cell nucleus, which is the main target of ionizing radiation. Information regarding these intricate processes cannot be achieved using high-throughput Omics approaches alone; it requires sophisticated structural probing and imaging. In the first part of this review, the article "Giving Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part A−Radiomics," we showed the development of different Omics solutions and how they are contributing to a better understanding of cellular radiation response. In this Part B we show how high-resolution confocal microscopy as well as novel approaches of molecular localization nanoscopy fill the gaps to successfully place Omics data in the context of space and time. The dynamics of double-strand breaks during repair processes and chromosomal rearrangements at the microscale correlated to aberration induction are explained. For the first time we visualize pan-nuclear nucleosomal rearrangements and clustering at the nanoscale during repair processes. Finally, we introduce a novel method of specific chromatin nanotargeting based on a computer database search of uniquely binding oligonucleotide combinations (COMBO-FISH). With these challenging techniques on hand, we speculate future perspectives that may combine specific COMBO-FISH nanoprobing and structural nanoscopy to observe structure-function correlations in living cells in real-time. Thus, the Omics networks obtained from function analyses may be enriched by real-time visualization of Structuromics.
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Müller Patrick, Lemmermann Niels A., Kaufmann Rainer, Gunkel Manuel, Paech Daniel, Hildenbrand Georg, Holtappels Rafaela, Cremer Christoph, Hausmann Michael, Spatial distribution and structural arrangement of a murine cytomegalovirus glycoprotein detected by SPDM localization microscopy, Histochemistry and Cell Biology, 142, 1, 2014. Crossref
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Hausmann Michael, Ilić Nataša, Pilarczyk Götz, Lee Jin-Ho, Logeswaran Abiramy, Borroni Aurora, Krufczik Matthias, Theda Franziska, Waltrich Nadine, Bestvater Felix, Hildenbrand Georg, Cremer Christoph, Blank Michael, Challenges for Super-Resolution Localization Microscopy and Biomolecular Fluorescent Nano-Probing in Cancer Research, International Journal of Molecular Sciences, 18, 10, 2017. Crossref
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Eberle Jan Philipp, Rapp Alexander, Krufczik Matthias, Eryilmaz Marion, Gunkel Manuel, Erfle Holger, Hausmann Michael, Super-Resolution Microscopy Techniques and Their Potential for Applications in Radiation Biophysics, in Super-Resolution Microscopy, 1663, 2017. Crossref
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Jezkova Lucie, Zadneprianetc Mariia, Kulikova Elena, Smirnova Elena, Bulanova Tatiana, Depes Daniel, Falkova Iva, Boreyko Alla, Krasavin Evgeny, Davidkova Marie, Kozubek Stanislav, Valentova Olga, Falk Martin, Particles with similar LET values generate DNA breaks of different complexity and reparability: a high-resolution microscopy analysis of γH2AX/53BP1 foci, Nanoscale, 10, 3, 2018. Crossref
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Krufczik Matthias, Sievers Aaron, Hausmann Annkathrin, Lee Jin-Ho, Hildenbrand Georg, Schaufler Wladimir, Hausmann Michael, Combining Low Temperature Fluorescence DNA-Hybridization, Immunostaining, and Super-Resolution Localization Microscopy for Nano-Structure Analysis of ALU Elements and Their Influence on Chromatin Structure, International Journal of Molecular Sciences, 18, 5, 2017. Crossref
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Eryilmaz Marion, Schmitt Eberhard, Krufczik Matthias, Theda Franziska, Lee Jin-Ho, Cremer Christoph, Bestvater Felix, Schaufler Wladimir, Hausmann Michael, Hildenbrand Georg, Localization Microscopy Analyses of MRE11 Clusters in 3D-Conserved Cell Nuclei of Different Cell Lines, Cancers, 10, 1, 2018. Crossref
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Hofmann Andreas, Krufczik Matthias, Heermann Dieter, Hausmann Michael, Using Persistent Homology as a New Approach for Super-Resolution Localization Microscopy Data Analysis and Classification of γH2AX Foci/Clusters, International Journal of Molecular Sciences, 19, 8, 2018. Crossref
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Bobkova Elizaveta, Depes Daniel, Lee Jin-Ho, Jezkova Lucie, Falkova Iva, Pagacova Eva, Kopecna Olga, Zadneprianetc Mariia, Bacikova Alena, Kulikova Elena, Smirnova Elena, Bulanova Tatiana, Boreyko Alla, Krasavin Evgeny, Wenz Frederik, Bestvater Felix, Hildenbrand Georg, Hausmann Michael, Falk Martin, Recruitment of 53BP1 Proteins for DNA Repair and Persistence of Repair Clusters Differ for Cell Types as Detected by Single Molecule Localization Microscopy, International Journal of Molecular Sciences, 19, 12, 2018. Crossref
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Depes Daniel, Lee Jin-Ho, Bobkova Elizaveta, Jezkova Lucie, Falkova Iva, Bestvater Felix, Pagacova Eva, Kopecna Olga, Zadneprianetc Mariia, Bacikova Alena, Kulikova Elena, Smirnova Elena, Bulanova Tatiana, Boreyko Alla, Krasavin Evgeny, Hausmann Michael, Falk Martin, Single-molecule localization microscopy as a promising tool for γH2AX/53BP1 foci exploration, The European Physical Journal D, 72, 9, 2018. Crossref
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Falk Martin, Horakova Zuzana, Svobodova Marketa, Masarik Michal, Kopecna Olga, Gumulec Jaromir, Raudenska Martina, Depes Daniel, Bacikova Alena, Falkova Iva, Binkova Hana, γH2AX/53BP1 foci as a potential pre-treatment marker of HNSCC tumors radiosensitivity – preliminary methodological study and discussion, The European Physical Journal D, 71, 9, 2017. Crossref
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Pagáčová Eva, Štefančíková Lenka, Schmidt-Kaler Franz, Hildenbrand Georg, Vičar Tomáš, Depeš Daniel, Lee Jin-Ho, Bestvater Felix, Lacombe Sandrine, Porcel Erika, Roux Stéphane, Wenz Frederik, Kopečná Olga, Falková Iva, Hausmann Michael, Falk Martin, Challenges and Contradictions of Metal Nano-Particle Applications for Radio-Sensitivity Enhancement in Cancer Therapy, International Journal of Molecular Sciences, 20, 3, 2019. Crossref
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Falk Martin, Hausmann Michael, 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, 13, 1, 2020. Crossref
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Hausmann Michael, Neitzel Charlotte, Bobkova Elizaveta, Nagel David, Hofmann Andreas, Chramko Tatyana, Smirnova Elena, Kopečná Olga, Pagáčová Eva, Boreyko Alla, Krasavin Evgeny, Falkova Iva, Heermann Dieter W., Pilarczyk Götz, Hildenbrand Georg, Bestvater Felix, Falk Martin, Single Molecule Localization Microscopy Analyses of DNA-Repair Foci and Clusters Detected Along Particle Damage Tracks, Frontiers in Physics, 8, 2020. Crossref
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Lee Jin-Ho, Hausmann Michael, Super-Resolution Radiation Biology: From Bio-Dosimetry towards Nano-Studies of DNA Repair Mechanisms, in DNA - Damages and Repair Mechanisms, 2021. Crossref
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Hahn Hannes, Neitzel Charlotte, Kopečná Olga, Heermann Dieter W., Falk Martin, Hausmann Michael, Topological Analysis of γH2AX and MRE11 Clusters Detected by Localization Microscopy during X-ray-Induced DNA Double-Strand Break Repair, Cancers, 13, 21, 2021. Crossref
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Hausmann Michael, Falk Martin, Neitzel Charlotte, Hofmann Andreas, Biswas Abin, Gier Theresa, Falkova Iva, Heermann Dieter W., Hildenbrand Georg, Elucidation of the Clustered Nano-Architecture of Radiation-Induced DNA Damage Sites and Surrounding Chromatin in Cancer Cells: A Single Molecule Localization Microscopy Approach, International Journal of Molecular Sciences, 22, 7, 2021. Crossref
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Hofer Michal, Falk Martin, Komůrková Denisa, Falková Iva, Bačíková Alena, Klejdus Bořivoj, Pagáčová Eva, Štefančíková Lenka, Weiterová Lenka, Angelis Karel J., Kozubek Stanislav, Dušek Ladislav, Galbavý Štefan, Two New Faces of Amifostine: Protector from DNA Damage in Normal Cells and Inhibitor of DNA Repair in Cancer Cells, Journal of Medicinal Chemistry, 59, 7, 2016. Crossref
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Hausmann Michael, Neitzel Charlotte, Hahn Hannes, Winter Ruth, Falkova Iva, Heermann Dieter W., Pilarczyk Götz, Hildenbrand Georg, Scherthan Harry, Falk Martin, Space and Time in the Universe of the Cell Nucleus after Ionizing Radiation Attacks: A Comparison of Cancer and Non-Cancer Cell Response, The 1st International Electronic Conference on Cancers: Exploiting Cancer Vulnerability by Targeting the DNA Damage Response, 2021. Crossref
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Dobešová Lucie, Gier Theresa, Kopečná Olga, Pagáčová Eva, Vičar Tomáš, Bestvater Felix, Toufar Jiří, Bačíková Alena, Kopel Pavel, Fedr Radek, Hildenbrand Georg, Falková Iva, Falk Martin, Hausmann Michael, Incorporation of Low Concentrations of Gold Nanoparticles: Complex Effects on Radiation Response and Fate of Cancer Cells, Pharmaceutics, 14, 1, 2022. Crossref
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Müller Patrick, Rößler Jens, Schwarz-Finsterle Jutta, Schmitt Eberhard, Hausmann Michael, PNA-COMBO-FISH: From combinatorial probe design in silico to vitality compatible, specific labelling of gene targets in cell nuclei, Experimental Cell Research, 345, 1, 2016. Crossref
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Vicar Tomas, Gumulec Jaromir, Kolar Radim, Kopecna Olga, Pagacova Eva, Falkova Iva, Falk Martin, DeepFoci: Deep learning-based algorithm for fast automatic analysis of DNA double-strand break ionizing radiation-induced foci, Computational and Structural Biotechnology Journal, 19, 2021. Crossref
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Hausmann Michael, Hildenbrand Georg, Pilarczyk Götz, Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology, in Nuclear, Chromosomal, and Genomic Architecture in Biology and Medicine, 70, 2022. Crossref