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Critical Reviews™ in Eukaryotic Gene Expression
IF: 1.734 5-Year IF: 1.848 SJR: 0.627 SNIP: 0.516 CiteScore™: 1.96

ISSN Print: 1045-4403
ISSN Online: 2162-6502

Critical Reviews™ in Eukaryotic Gene Expression

DOI: 10.1615/CritRevEukaryotGeneExpr.2014010313
pages 205-223

Determining Omics Spatiotemporal Dimensions Using Exciting New Nanoscopy Techniques to Assess Complex Cell Responses to DNA Damage: PART A−Radiomics

Martin Falk
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Michael Hausmann
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Emilie Lukasova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Abin Biswas
Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Radiation Oncology, University Medical Center Mannheim, University of Heidelberg, Heidelberg, Germany
Georg Hildenbrand
Department of Radiation Oncology, University Medical Center Mannheim, Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany
Marie Davidkova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Evgeny Krasavin
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Zdenek Kleibl
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Iva Falkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Lucie Jezkova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Joint Institute for Nuclear Research, Dubna, Moscow, Russia; Institute of Chemical Technology Prague, Prague, Czech Republic
Lenka Stefancikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Jan Sevcik
Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic
Michal Hofer
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Alena Bacikova
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
Pavel Matula
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Centre for Biomedical Image Analysis, Faculty of Informatics, Masaryk University, Brno, Czech Republic
Alla Boreyko
Joint Institute for Nuclear Research, Dubna, Moscow, Russia
Jana Vachelova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic
Anna Michaelidesova
Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic; Proton Therapy Center, Prague, Czech Republic
Stanislav Kozubek
Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic

ABSTRACT

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.