An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation
Complex DNA double-strand break (DSB), which is defined as a DSB coupled with additional strand breaks within 10 bp in this study, induced after ionizing radiation or X-rays, is recognized as fatal damage which can induce cell death with a certain probability. In general, a DSB site inside the nucle...
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MDPI AG
2023-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/2/1386 |
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| author | Yoshie Yachi Yusuke Matsuya Yuji Yoshii Hisanori Fukunaga Hiroyuki Date Takeshi Kai |
| author_facet | Yoshie Yachi Yusuke Matsuya Yuji Yoshii Hisanori Fukunaga Hiroyuki Date Takeshi Kai |
| author_sort | Yoshie Yachi |
| collection | DOAJ |
| description | Complex DNA double-strand break (DSB), which is defined as a DSB coupled with additional strand breaks within 10 bp in this study, induced after ionizing radiation or X-rays, is recognized as fatal damage which can induce cell death with a certain probability. In general, a DSB site inside the nucleus of live cells can be experimentally detected using the γ-H2AX focus formation assay. DSB complexity is believed to be detected by analyzing the focus size using such an assay. However, the relationship between focus size and DSB complexity remains uncertain. In this study, using Monte Carlo (MC) track-structure simulation codes, i.e., an in-house WLTrack code and a Particle and Heavy Ion Transport code System (PHITS), we developed an analytical method for qualifying the DSB complexity induced by photon irradiation from the microscopic image of γ-H2AX foci. First, assuming that events (i.e., ionization and excitation) potentially induce DNA strand breaks, we scored the number of events in a water cube (5.03 × 5.03 × 5.03 nm<sup>3</sup>) along electron tracks. Second, we obtained the relationship between the number of events and the foci size experimentally measured by the γ-H2AX focus formation assay. Third, using this relationship, we evaluated the degree of DSB complexity induced after photon irradiation for various X-ray spectra using the foci size, and the experimental DSB complexity was compared to the results estimated by the well-verified DNA damage estimation model in the PHITS code. The number of events in a water cube was found to be proportional to foci size, suggesting that the number of events intrinsically related to DSB complexity at the DNA scale. The developed method was applicable to focus data measured for various X-ray spectral situations (i.e., diagnostic kV X-rays and therapeutic MV X-rays). This method would contribute to a precise understanding of the early biological impacts of photon irradiation by means of the γ-H2AX focus formation assay. |
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| language | English |
| last_indexed | 2024-03-09T12:21:35Z |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-2a298784034c48d8be2003699efe46eb2023-11-30T22:39:38ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-01242138610.3390/ijms24021386An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure SimulationYoshie Yachi0Yusuke Matsuya1Yuji Yoshii2Hisanori Fukunaga3Hiroyuki Date4Takeshi Kai5Graduate School of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo 060-0812, JapanFaculty of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo 060-0812, JapanCentral Institute of Isotope Science, Hokkaido University, Kita-15 Nishi-7, Kita-ku, Sapporo 060-0815, JapanFaculty of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo 060-0812, JapanFaculty of Health Sciences, Hokkaido University, Kita-12 Nishi-5, Kita-ku, Sapporo 060-0812, JapanJapan Atomic Energy Agency (JAEA), Nuclear Science and Engineering Centre, Research Group for Radiation Transport Analysis, 2-4 Shirakata, Tokai, Naka-gun 319-1195, JapanComplex DNA double-strand break (DSB), which is defined as a DSB coupled with additional strand breaks within 10 bp in this study, induced after ionizing radiation or X-rays, is recognized as fatal damage which can induce cell death with a certain probability. In general, a DSB site inside the nucleus of live cells can be experimentally detected using the γ-H2AX focus formation assay. DSB complexity is believed to be detected by analyzing the focus size using such an assay. However, the relationship between focus size and DSB complexity remains uncertain. In this study, using Monte Carlo (MC) track-structure simulation codes, i.e., an in-house WLTrack code and a Particle and Heavy Ion Transport code System (PHITS), we developed an analytical method for qualifying the DSB complexity induced by photon irradiation from the microscopic image of γ-H2AX foci. First, assuming that events (i.e., ionization and excitation) potentially induce DNA strand breaks, we scored the number of events in a water cube (5.03 × 5.03 × 5.03 nm<sup>3</sup>) along electron tracks. Second, we obtained the relationship between the number of events and the foci size experimentally measured by the γ-H2AX focus formation assay. Third, using this relationship, we evaluated the degree of DSB complexity induced after photon irradiation for various X-ray spectra using the foci size, and the experimental DSB complexity was compared to the results estimated by the well-verified DNA damage estimation model in the PHITS code. The number of events in a water cube was found to be proportional to foci size, suggesting that the number of events intrinsically related to DSB complexity at the DNA scale. The developed method was applicable to focus data measured for various X-ray spectral situations (i.e., diagnostic kV X-rays and therapeutic MV X-rays). This method would contribute to a precise understanding of the early biological impacts of photon irradiation by means of the γ-H2AX focus formation assay.https://www.mdpi.com/1422-0067/24/2/1386Monte Carlo track-structure simulationcomplex DSBγ-H2AX focus formation assayphoton irradiation |
| spellingShingle | Yoshie Yachi Yusuke Matsuya Yuji Yoshii Hisanori Fukunaga Hiroyuki Date Takeshi Kai An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation International Journal of Molecular Sciences Monte Carlo track-structure simulation complex DSB γ-H2AX focus formation assay photon irradiation |
| title | An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation |
| title_full | An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation |
| title_fullStr | An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation |
| title_full_unstemmed | An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation |
| title_short | An Analytical Method for Quantifying the Yields of DNA Double-Strand Breaks Coupled with Strand Breaks by γ-H2AX Focus Formation Assay Based on Track-Structure Simulation |
| title_sort | analytical method for quantifying the yields of dna double strand breaks coupled with strand breaks by γ h2ax focus formation assay based on track structure simulation |
| topic | Monte Carlo track-structure simulation complex DSB γ-H2AX focus formation assay photon irradiation |
| url | https://www.mdpi.com/1422-0067/24/2/1386 |
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