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Nikjoo H, Rahmanian S, Taleei R. Modelling DNA damage-repair and beyond. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 190:1-18. [PMID: 38754703 DOI: 10.1016/j.pbiomolbio.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/27/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024]
Abstract
The paper presents a review of mechanistic modelling studies of DNA damage and DNA repair, and consequences to follow in mammalian cell nucleus. We hypothesize DNA deletions are consequences of repair of double strand breaks leading to the modifications of genome that play crucial role in long term development of genetic inheritance and diseases. The aim of the paper is to review formation mechanisms underlying naturally occurring DNA deletions in the human genome and their potential relevance for bridging the gap between induced DNA double strand breaks and deletions in damaged human genome from endogenous and exogenous events. The model of the cell nucleus presented enables simulation of DNA damage at molecular level identifying the spectrum of damage induced in all chromosomal territories and loops. Our mechanistic modelling of DNA repair for double stand breaks (DSB), single strand breaks (SSB) and base damage (BD), shows the complexity of DNA damage is responsible for the longer repair times and the reason for the biphasic feature of mammalian cells repair curves. In the absence of experimentally determined data, the mechanistic model of repair predicts the in vivo rate constants for the proteins involved in the repair of DSB, SSB, and of BD.
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Affiliation(s)
- Hooshang Nikjoo
- Department of Physiology, Anatomy and Genetics (DPAG), Oxford University, Oxford, OX1 3PT, UK.
| | | | - Reza Taleei
- Medical Physics Division, Department of Radiation Oncology Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA, 19107, USA.
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Taleei R, Rahmanian S, Nikjoo H. Modelling Cellular Response to Ionizing Radiation: Mechanistic, Semi-Mechanistic, and Phenomenological Approaches - A Historical Perspective. Radiat Res 2024; 202:143-160. [PMID: 38916125 DOI: 10.1667/rade-24-00019.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/23/2024] [Indexed: 06/26/2024]
Abstract
Radiation research is a multidisciplinary field, and among its many branches, mathematical and computational modelers have played a significant role in advancing boundaries of knowledge. A fundamental contribution is modelling cellular response to ionizing radiation as that is the key to not only understanding how radiation can kill cancer cells, but also cause cancer and other health issues. The invention of microdosimetry in the 1950s by Harold Rossi paved the way for brilliant scientists to study the mechanism of radiation at cellular and sub-cellular scales. This paper reviews some snippets of ingenious mathematical and computational models published in microdosimetry symposium proceedings and publications of the radiation research community. Among these are simulations of radiation tracks at atomic and molecular levels using Monte Carlo methods, models of cell survival, quantification of the amount of energy required to create a single strand break, and models of DNA-damage-repair. These models can broadly be categorized into mechanistic, semi-mechanistic, and phenomenological approaches, and this review seeks to provide historical context of their development. We salute pioneers of the field and great teachers who supported and educated the younger members of the community and showed them how to build upon their work.
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Affiliation(s)
- Reza Taleei
- Medical Physics Division, Department of Radiation Oncology, Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, Pennsylvania, 19107
| | | | - Hooshang Nikjoo
- Department of Physiology, Anatomy and Genetics (DPAG) Oxford University, Oxford, OX1 3PT, United Kingdom
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Nikjoo H, Hoffmann G, Baverstock K. In Memoriam - Krishnaswami Sankaranarayanan (1933-2022). Mutat Res 2022; 825:111789. [PMID: 35763981 DOI: 10.1016/j.mrfmmm.2022.111789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 06/16/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Hooshang Nikjoo
- Department of Physiology, Anatomy and Genetics, Oxford University, Oxford OX1 3PT, UK.
| | - George Hoffmann
- Department of Biology, College of the Holy Cross, Worcester, MA 01610, USA
| | - Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland
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Satoh Y, Asakawa JI, Nishimura M, Kuo T, Shinkai N, Cullings HM, Minakuchi Y, Sese J, Toyoda A, Shimada Y, Nakamura N, Uchimura A. Characteristics of induced mutations in offspring derived from irradiated mouse spermatogonia and mature oocytes. Sci Rep 2020; 10:37. [PMID: 31913321 PMCID: PMC6949229 DOI: 10.1038/s41598-019-56881-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/18/2019] [Indexed: 01/07/2023] Open
Abstract
The exposure of germ cells to radiation introduces mutations in the genomes of offspring, and a previous whole-genome sequencing study indicated that the irradiation of mouse sperm induces insertions/deletions (indels) and multisite mutations (clustered single nucleotide variants and indels). However, the current knowledge on the mutation spectra is limited, and the effects of radiation exposure on germ cells at stages other than the sperm stage remain unknown. Here, we performed whole-genome sequencing experiments to investigate the exposure of spermatogonia and mature oocytes. We compared de novo mutations in a total of 24 F1 mice conceived before and after the irradiation of their parents. The results indicated that radiation exposure, 4 Gy of gamma rays, induced 9.6 indels and 2.5 multisite mutations in spermatogonia and 4.7 indels and 3.1 multisite mutations in mature oocytes in the autosomal regions of each F1 individual. Notably, we found two types of deletions, namely, small deletions (mainly 1~12 nucleotides) in non-repeat sequences, many of which showed microhomology at the breakpoint junction, and single-nucleotide deletions in mononucleotide repeat sequences. The results suggest that these deletions and multisite mutations could be a typical signature of mutations induced by parental irradiation in mammals.
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Affiliation(s)
- Yasunari Satoh
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan.
| | - Jun-Ichi Asakawa
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Mayumi Nishimura
- Department of Radiation Effects Research, National Institute of Radiological Sciences (NIRS), National Institutes for Quantum and Radiological Science and Technology (QST), Chiba, 263-8555, Japan
| | - Tony Kuo
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Real World Big-Data Computation Open Innovation Laboratory, AIST-Tokyo Tech, 2-12-1 Okayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Norio Shinkai
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Harry M Cullings
- Department of Statistics, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Yohei Minakuchi
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Jun Sese
- Artificial Intelligence Research Center, AIST, 2-3-26 Aomi, Koto-ku, Tokyo, 135-0064, Japan.,Real World Big-Data Computation Open Innovation Laboratory, AIST-Tokyo Tech, 2-12-1 Okayama, Meguro-ku, Tokyo, 152-8550, Japan.,Humanome Lab, Inc., L-HUB 3F, 1-4, Shumomiyabi-cho, Sinjuku-ku, Tokyo, 162-0822, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Yoshiya Shimada
- Department of Radiological Sciences, Graduate School of Human Health Sciences, Tokyo Metropolitan University, Tokyo, 116-8551, Japan.,Executive Director, QST, Chiba, 263-8555, Japan
| | - Nori Nakamura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan
| | - Arikuni Uchimura
- Department of Molecular Biosciences, Radiation Effects Research Foundation, 5-2 Hijiyama Park, Minami-ku, Hiroshima, 732-0815, Japan.
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Hoffmann GR. Twenty Years of Reflections in Mutation Research. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 780:106-120. [PMID: 31395355 DOI: 10.1016/j.mrrev.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/25/2019] [Indexed: 11/18/2022]
Abstract
Reflections is a component of Mutation Research Reviews devoted to historical and philosophical themes pertaining to the subject of mutation. Reflections was initiated in 1999 and has included a broad array of topics centered on mutation research, but overlapping other scientific fields and touching upon history, sociology, politics, philosophy and ethics. This commentary offers an editor's reflections on the 44 papers in the Reflections series, including the people who contributed to the series and the topics that they discussed.
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Affiliation(s)
- George R Hoffmann
- Department of Biology, College of the Holy Cross, One College Street, Worcester, MA 01610, USA.
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Ma L, Kazama Y, Hirano T, Morita R, Tanaka S, Abe T, Hatakeyama S. LET dependence on killing effect and mutagenicity in the model filamentous fungus Neurospora crassa. Int J Radiat Biol 2018; 94:1125-1133. [PMID: 30307372 DOI: 10.1080/09553002.2019.1524940] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
PURPOSE To assess the unique biological effects of different forms of ionizing radiation causing DNA double-strand breaks (DSBs), we compared the killing effect, mutagenesis frequency, and mutation type spectrum using the model filamentous fungus Neurospora. MATERIALS AND METHODS Asexual spores of wild-type Neurospora and two DSB repair-deficient strains [one homologous recombination- and the other non-homologous end-joining (NHEJ) pathway-deficient] were irradiated with argon (Ar)-ion beams, ferrous (Fe)-ion beams, or X-rays. Relative biological effectiveness (RBE), forward mutation frequencies at the ad-3 loci, and mutation spectra at the ad-3B gene were determined. RESULTS The canonical NHEJ (cNHEJ)-deficient strain showed resistance to higher X-ray doses, while other strains showed dose-dependent sensitivity. In contrast, the killing effects of Ar-ion and Fe-ion beam irradiation were dose-dependent in all strains tested. The rank order of RBE was Ar-ion > Fe-ion > C-ion. Deletion mutations were the most common, but deletion size incremented with the increasing value of linear energy transfer (LET). CONCLUSIONS We found marked differences in killing effect of a cNHEJ-deficient mutant between X-ray and high-LET ion beam irradiations (Ar and Fe). The mutation spectra also differed between irradiation types. These differences may be due to the physical properties of each radiation and the repair mechanism of induced damage in Neurospora crassa. These results may guide the choice of irradiation beam to kill or mutagenize fungi for agricultural applications or further research.
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Affiliation(s)
- Liqiu Ma
- a Laboratory of Genetics, Department of Regulatory Biology, Faculty of Science , Saitama University , Saitama , Japan.,b RIKEN Nishina Center , Saitama , Japan.,c Gunma University Heavy Ion Medical Center , Maebashi , Japan
| | | | - Tomonari Hirano
- b RIKEN Nishina Center , Saitama , Japan.,d Faculty of Agriculture , University of Miyazaki , Miyazaki , Japan
| | | | - Shuuitsu Tanaka
- a Laboratory of Genetics, Department of Regulatory Biology, Faculty of Science , Saitama University , Saitama , Japan
| | - Tomoko Abe
- b RIKEN Nishina Center , Saitama , Japan
| | - Shin Hatakeyama
- a Laboratory of Genetics, Department of Regulatory Biology, Faculty of Science , Saitama University , Saitama , Japan
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Martin RF, Feinendegen LE. The quest to exploit the Auger effect in cancer radiotherapy - a reflective review. Int J Radiat Biol 2016; 92:617-632. [PMID: 26926313 DOI: 10.3109/09553002.2015.1136854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
To identify the emergence of the recognition of the potential of the Auger effect for clinical application, and after tracing the salient milestones towards that goal, to evaluate the status quo and future prospects. It was not until 40 years after the discovery of Auger electrons, that the availability of radioactive DNA precursors enabled the biological power, and the clinical potential, of the Auger effect to be appreciated. Important milestones on the path to clinical translation have been identified and reached, but hurdles remain. Nevertheless the potential is still evident, and there is reasonable optimism that the goal of clinical translation is achievable.
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Affiliation(s)
- Roger F Martin
- a Molecular Radiation Biology Laboratory , Peter MacCallum Cancer Centre.,b The Sir Peter MacCallum Department of Oncology , The University of Melbourne.,c School of Chemistry and Bio-21 Molecular Science and Biotechnology Institute , University of Melbourne , Melbourne , Australia
| | - Ludwig E Feinendegen
- d Heinrich-Heine-University Düsseldorf , Germany.,e Brookhaven National Laboratory , Upton , NY , USA
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