title: Determining Omics spatiotemporal dimensions using exciting new nanoscopy techniques to assess complex cell responses to DNA damage: part A--radiomics.
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.
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Martin
authors: M
authors: Falk
authors: Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.
authors: Michael
authors: M
authors: Hausmann
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Emílie
authors: E
authors: Lukášová
authors: Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany; Department of Radiation Oncology, University Medical Center Mannheim, University of Heidelberg, Heidelberg, Germany.
authors: Abin
authors: A
authors: Biswas
authors: Department of Radiation Oncology, University Medical Center Mannheim, Kirchhoff Institute for Physics, University of Heidelberg, Heidelberg, Germany.
authors: Georg
authors: G
authors: Hildenbrand
authors: Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic.
authors: Marie
authors: M
authors: Davídková
authors: Joint Institute for Nuclear Research, Dubna, Moscow, Russia.
authors: Evgeny
authors: E
authors: Krasavin
authors: Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
authors: Zdeněk
authors: Z
authors: Kleibl
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Iva
authors: I
authors: Falková
authors: 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.
authors: Lucie
authors: L
authors: Ježková
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Lenka
authors: L
authors: Štefančíková
authors: Institute of Biochemistry and Experimental Oncology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
authors: Jan
authors: J
authors: Ševčík
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Michal
authors: M
authors: Hofer
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Alena
authors: A
authors: Bačíková
authors: 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.
authors: Pavel
authors: P
authors: Matula
authors: Joint Institute for Nuclear Research, Dubna, Moscow, Russia.
authors: Alla
authors: A
authors: Boreyko
authors: Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic.
authors: Jana
authors: J
authors: Vachelová
authors: Nuclear Physics Institute, Academy of Sciences of the Czech Republic, Rez, Czech Republic; Proton Therapy Center, Prague, Czech Republic.
authors: Anna
authors: A
authors: Michaelidesová
authors: Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
authors: Stanislav
authors: S
authors: Kozubek
mesh_terms: D045744:Cell Line, Tumor; D002467:Cell Nucleus / Q000235:genetics; D002843:Chromatin / Q000528:radiation effects; D004247:DNA / Q000528:radiation effects*; D004249:DNA Damage / Q000235:genetics / Q000528:radiation effects*; D004260:DNA Repair; D016678:Genome / Q000235:genetics / Q000528:radiation effects; D042822:Genomic Instability / Q000528:radiation effects*; D006801:Humans; D011839:Radiation, Ionizing; D011853:Radiobiology
chemical_list: D002843:Chromatin; D004247:DNA