每年出版 6 期
ISSN 打印: 1045-4403
ISSN 在线: 2162-6502
Indexed in
Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: PART A−Radiomics
摘要
Recent ground-breaking developments in Omics have generated new hope for overcoming the complexity and variability of 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 proteins interact in the frame of complex networks to preserve genome integrity 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. Nuclear architecture and nuclear processes, including DNA damage responses, are precisely organized in space and time. Information regarding these intricate processes cannot be achieved using high-throughput Omics approaches alone, but requires sophisticated structural probing and imaging. Based on the results obtained from studying the relationship between higher-order chromatin structure, DNA double-strand break induction and repair, and the formation of chromosomal translocations, we show the development of Omics solutions especially for radiation research (radiomics) (discussed in this article) and how confocal microscopy as well as novel approaches of molecular localization nanoscopy fill the gaps to successfully place the Omics data in the context of space and time (discussed in our other article in this issue, "Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: Part B−Structuromics"). Finally, we introduce a novel method of specific chromatin nanotargeting and speculate future perspectives, which may combine 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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Bach Margund, Savini Claudia, Krufczik Matthias, Cremer Christoph, Rösl Frank, Hausmann Michael, Super-Resolution Localization Microscopy of γ-H2AX and Heterochromatin after Folate Deficiency, International Journal of Molecular Sciences, 18, 8, 2017. 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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Avanzo Michele, Stancanello Joseph, El Naqa Issam, Beyond imaging: The promise of radiomics, Physica Medica, 38, 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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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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Hausmann Michael, Wagner Emma, Lee Jin-Ho, Schrock Gerrit, Schaufler Wladimir, Krufczik Matthias, Papenfuß Franziska, Port Matthias, Bestvater Felix, Scherthan Harry, Super-resolution localization microscopy of radiation-induced histone H2AX-phosphorylation in relation to H3K9-trimethylation in HeLa cells, Nanoscale, 10, 9, 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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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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Varga Dániel, Majoros Hajnalka, Ujfaludi Zsuzsanna, Erdélyi Miklós, Pankotai Tibor, Quantification of DNA damage induced repair focus formation via super-resolution dSTORM localization microscopy, Nanoscale, 11, 30, 2019. 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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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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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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Michaelidesová Anna, Vachelová Jana, Klementová Jana, Urban Tomáš, Pachnerová Brabcová Kateřina, Kaczor Stanislav, Falk Martin, Falková Iva, Depeš Daniel, Vondráček Vladimír, Davídková Marie, In Vitro Comparison of Passive and Active Clinical Proton Beams, International Journal of Molecular Sciences, 21, 16, 2020. 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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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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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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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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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