Investigation of Groove Damage Distribution in Proton-Induced Clustered B-DNA Damage.

To investigate the feasibility of using the high Zeff storage phosphor material BaFBrI:Eu2+ in conjunction with the low Zeff storage phosphor material KCl:Eu2+ for simultaneous proton dose and linear energy transfer (LET) measurements by (a) measuring the fundamental optical and dosimetric properties of BaFBrI:Eu2+ , (b) evaluating its compatibility in being readout simultaneously with KCl:Eu2+ dosimeters, and (c) modeling and validating its LET dependence under elevated proton LET irradiation. A commercial BaFBrI:Eu2+ storage phosphor detector (Model ST-VI, Fujifilm) was characterized with energy dispersive x-ray spectroscopy (EDS) analysis to obtain its elemental composition. The dosimeters were irradiated using both a Mevion S250 proton therapy unit (at the center of a spread-out Bragg peak, SOBP) and a Varian Clinac iX linear accelerator with the latter being a low LET irradiation. The photostimulated luminescence (PSL) emission spectra, excitation spectra, and luminescent lifetimes of the detector were measured after proton and photon irradiations. Dosimetric properties including dose linearity, dose rate dependence, radiation hardness, temporal, and readout stabilities were studied using a laboratory optical reader after proton irradiations. In addition, its proton energy dependence was analytically modeled and experimentally validated by irradiating the detectors at various depths within the SOBP (Range: 15.0g/cm2 , Modulation: 10.0g/cm2 ). The active detector composition for the high Zeff storage phosphor detector was found to be BaFBr0.85 I0.15 :Eu2+ . The BaFBr0.85 I0.15 :Eu2+ material's excitation and emission spectra were in agreement under proton and photon irradiations, with peaks of 586±1nm and 400±1nm, respectively, with a full width at half maximum (FWHM) of 119±3nm and 30±2nm, respectively. As dosimeter response under photon irradiation is generally believed to be free from LET effect, these results suggest LET independence of charge storage center types resulted from ionizing radiations. There is sufficient spectral overlaps with KCl:Eu2+ dosimeters allowing both dosimeters to be readout under equivalent readout conditions, that is, 594nm stimulation and 420nm detection wavelengths. Its PSL characteristic lifetime was found to be less than 5 microseconds which would make it suitable for fast 2D readout post irradiation. Its 420nm emission band intensity was found to be linear up to 10Gy absolute proton dose under the same irradiation conditions, dose rate independent, stable in time and under multiple readouts, and with high radiation hardness under cumulative proton dose histories up to 200Gy as tested in this study. BaFBr0.85 I0.15 :Eu2+ showed significant proton energy-dependent dose under-response in regions of high LET which could be modeled by stopping power ratio calculations with an accuracy of 3% in low LET regions and a distance-to-agreement (DTA) of 1mm in high LET regions (>5keV/μm). We have proven the feasibility of dual-storage phosphor proton dosimetry for simultaneous proton dose and LET measurements. BaFBr0.85 I0.15 :Eu2+ has shown equally excellent dosimetry performance as its low Zeff complement KCl:Eu2+ with distinctive LET dependence merely as a result of its higher Zeff . These promising results pave the way for future studies involving simultaneous proton dose and LET measurements using this novel approach.

The concept of radiation-induced clustered damage in DNA has grown over the past several decades to become a topic of considerable interest across the scientific disciplines involved in studies of the biological effects of ionizing radiation. This paper, prepared for the 70th anniversary issue of Radiation Research, traces historical development of the three main threads of physics, chemistry, and biochemical/cellular responses that led to the hypothesis and demonstration that a key component of the biological effectiveness of ionizing radiation is its characteristic of producing clustered DNA damage of varying complexities. The physics thread has roots that started as early as the 1920s, grew to identify critical nanometre-scale clusterings of ionizations relevant to biological effectiveness, and then, by the turn of the century, had produced an extensive array of quantitative predictions on the complexity of clustered DNA damage from different radiations. Monte Carlo track structure simulation techniques played a key role through these developments, and they are now incorporated into many recent and ongoing studies modelling the effects of radiation. The chemistry thread was seeded by water-radiolysis descriptions of events in water as radical-containing "spurs," demonstration of the important role of the hydroxyl radical in radiation-inactivation of cells and the difficulty of protection by radical scavengers. This led to the concept and description of locally multiply damaged sites (LMDS) for DNA double-strand breaks and other combinations of DNA base damage and strand breakage that could arise from a spur overlapping, or created in very close proximity to, the DNA. In these ways, both the physics and the chemistry threads, largely in parallel, put out the challenge to the experimental research community to verify these predictions of clustered DNA damage from ionizing radiations and to investigate their relevance to DNA repair and subsequent cellular effects. The third thread, biochemical and cell-based research, responded strongly to the challenge by demonstrating the existence and biological importance of clustered DNA damage. Investigations have included repair of a wide variety of defined constructs of clustered damage, evaluation of mutagenic consequences, identification of clustered base-damage within irradiated cells, and identification of co-localization of repair complexes indicative of complex clustered damage after high-LET irradiation, as well as extensive studies of the repair pathways involved in repair of simple double-strand breaks. There remains, however, a great deal more to be learned because of the diversity of clustered DNA damage and of the biological responses.

Patterns of Failure After Proton Therapy in Medulloblastoma; Linear Energy Transfer Distributions and Relative Biological Effectiveness Associations for Relapses

Previous study proposed a method to measure linear energy transfer (LET) at specific points using the quenching magnitude of thin film solar cells. This study was conducted to propose a more advanced method for measuring the LET distribution. This study focuses on evaluating the feasibility of estimating the proton LET distribution in proton therapy. The feasibility of measuring the proton LET and dose distribution simultaneously using a single-channel configuration comprising two solar cells with distinct quenching constants is investigated with the objective of paving the way for enhanced proton therapy dosimetry. Two solar cells with different quenching constants were used to estimate the proton LET distribution. Detector characteristics (e.g., dose linearity and dose-rate dependency) of the solar cells were evaluated to assess their suitability for dosimetry applications. First, using a reference beam condition, the quenching constants of the two solar cells were determined according to the modified Birks equation. The signal ratios of the two solar cells were then evaluated according to proton LET in relation to the estimated quenching constants. The proton LET distributions of six test beams were obtained by measuring the signal ratios of the two solar cells at each depth, and the ratios were evaluated by comparing them with those calculated by Monte Carlo simulation. The detector characterization of the two solar cells including dose linearity and dose-rate dependence affirmed their suitability for use in dosimetry applications. The maximum difference between the LET measured using the two solar cells and that calculated by Monte Carlo simulation was 2.34keV/µm. In the case of the dose distribution measured using the method proposed in this study, the maximum difference between range measured using the proposed method and that measured using a multilayered ionization chamber was 0.7mm. The expected accuracy of simultaneous LET and dose distribution measurement using the method proposed in this study were estimated to be 3.82%. The signal ratios of the two solar cells, which are related to quenching constants, demonstrated the feasibility of measuring LET and dose distribution simultaneously. The feasibility of measuring proton LET and dose distribution simultaneously using two solar cells with different quenching constants was demonstrated. Although the method proposed in this study was evaluated using a single channel by varying the measuring depth, the results suggest that the proton LET and dose distribution can be simultaneously measured if the detector is configured in a multichannel form. We believe that the results presented in this study provide the envisioned transition to a multichannel configuration, with the promise of substantially advancing proton therapy's accuracy and efficacy in cancer treatment.

Poly ADP Ribose Polymerase Inhibitors Potentiate Proton Therapy End-of-Range Effects by Accelerating Replication Forks and Promoting Transcription Conflict.

Thermus aquaticus MutS protein is a DNA mismatch repair protein that recognizes and binds to heteroduplex DNAs containing mispaired or unpaired bases. Using enzymatic and chemical probe methods, we have examined the binding of Taq MutS protein to a heteroduplex DNA having a single unpaired thymidine residue. DNase I footprinting identifies a symmetrical region of protection 24-28 nucleotides long centered on the unpaired base. Methylation protection and interference studies establish that Taq MutS protein makes contacts with the major groove of the heteroduplex in the immediate vicinity of the unpaired base. Hydroxyl radical and 1, 10-phenanthroline-copper footprinting experiments indicate that MutS also interacts with the minor groove near the unpaired base. Together with the identification of key phosphate groups detected by ethylation interference, these data reveal critical contact points residing in the major and minor grooves of the heteroduplex DNA.

The deoxyribonucleic acid (DNA) molecule damage simulations with an atom level geometric model use the traversal algorithm that has the disadvantages of quite time-consuming, slow convergence and high-performance computer requirement. Therefore, this work presents a density-based spatial clustering of applications with noise (DBSCAN) clustering algorithm based on the spatial distributions of energy depositions and hydroxyl radicals (·OH). The algorithm with probability and statistics can quickly get the DNA strand break yields and help to study the variation pattern of the clustered DNA damage. Firstly, we simulated the transportation of protons and secondary particles through the nucleus, as well as the ionization and excitation of water molecules by using Geant4-DNA that is the Monte Carlo simulation toolkit for radiobiology, and got the distributions of energy depositions and hydroxyl radicals. Then we used the damage probability functions to get the spatial distribution dataset of DNA damage points in a simplified geometric model. The DBSCAN clustering algorithm based on damage points density was used to determine the single-strand break (SSB) yield and double-strand break (DSB) yield. Finally, we analyzed the DNA strand break yield variation trend with particle linear energy transfer (LET) and summarized the variation pattern of damage clusters. The simulation results show that the new algorithm has a faster simulation speed than the traversal algorithm and a good precision result. The simulation results have consistency when compared to other experiments and simulations. This work achieves more precise information on clustered DNA damage induced by proton radiation at the molecular level with high speed, so that it provides an essential and powerful research method for the study of radiation biological damage mechanism.

Objective: A constant relative biological effectiveness of 1.1 in current clinical practice of proton radiotherapy (RT) is a crude approximation and may severely underestimate the biological dose from proton RT to normal tissues, especially near the treatment target at the end of Bragg peaks that exhibits high linear energy transfer (LET). LET optimization can account for biological effectiveness of protons during treatment planning, for minimizing biological proton dose and hot spots to normal tissues. However, the LET optimization is usually nonlinear and nonconvex to solve, for which this work will develop an effective optimization method based on iterative convex relaxation (ICR). Approach: In contrast to the generic nonlinear optimization method, such as Quasi-Newton (QN) method, that does not account for specific characteristics of LET optimization, ICR is tailored to LET modeling and optimization in order to effectively and efficiently solve the LET problem. Specifically, nonlinear dose-averaged LET term is iteratively linearized and becomes convex during ICR, while nonconvex dose-volume constraint and minimum-monitor-unit constraint are also handled by ICR, so that the solution for LET optimization is obtained by solving a sequence of convex and linearized convex subproblems. Since the high LET mostly occurs near the target, a 1 cm normal-tissue expansion of clinical target volume (CTV) (excluding CTV), i.e. CTV1cm, is defined to as an auxiliary structure during treatment planning, where LET is minimized. Main results: ICR was validated in comparison with QN for abdomen, lung, and head-and-neck cases. ICR was effective for LET optimization, as ICR substantially reduced the LET and biological dose in CTV1cm the ring, with preserved dose conformality to CTV. Compared to QN, ICR had smaller LET, physical and biological dose in CTV1cm, and higher conformity index values; ICR was also computationally more efficient, which was about 3 times faster than QN. Significance: A LET-specific optimization method based on ICR has been developed for solving proton LET optimization, which has been shown to be more computationally efficient than generic nonlinear optimizer via QN, with better plan quality in terms of LET, biological and physical dose conformality.

PurposeThe dose response of Gafchromic EBT3 films exposed to proton beams depends on the dose, and additionally on the beam quality, which is often quantified with the linear energy transfer (LET) and, hence, also referred to as LET quenching. Fundamentally different methods to determine correction factors for this LET quenching effect have been reported in literature and a new method using the local proton fluence distribution differential in LET is presented. This method was exploited to investigate whether a more practical correction based on the dose‐ or fluence‐averaged LET is feasible in a variety of clinically possible beam arrangements.MethodsThe relative effectiveness (RE) was characterized within a high LET spread‐out Bragg peak (SOBP) in water made up by the six lowest available energies (62.4–67.5 MeV, configuration “b1”) resulting in one of the highest clinically feasible dose‐averaged LET distributions. Additionally, two beams were measured where a low LET proton beam (252.7 MeV) was superimposed on “b1”, which contributed either 50% of the initial particle fluence or 50% of the dose in the SOBP, referred to as configuration “b2” and “b3,” respectively. The proton LET spectrum was simulated with GATE/Geant4 at all measurement positions. The net optical density change differential in LET was integrated over the local proton spectrum to calculate the net optical density and therefrom the beam quality correction factor. The LET dependence of the film response was accounted for by an LET dependence of one of the three parameters in the calibration function and was determined from inverse optimization using measurement “b1.” This method was then validated on the measurements of “b2” and “b3” and subsequently used to calculate the RE at 900 positions in nine clinically relevant beams. The extrapolated RE set was used to derive a simple linear correction function based on dose‐averaged LET (Ld) and verify the validity in all points of the comprehensive RE set.ResultsThe uncorrected film dose deviated up to 26% from the reference dose, whereas the corrected film dose agreed within 3% in all three beams in water (“b1”, “b2” and “b3”). The LET dependence of the calibration function started to strongly increase around 5 keV/μm and flatten out around 30 keV/μm. All REs calculated from the proton fluence in the nine simulated beams could be approximated with a linear function of dose‐averaged LET (RE = 1.0258−0.0211 μm/keV Ld). However, no functional relationship of RE‐ and fluence‐averaged LET could be found encompassing all beam energies and modulations.ConclusionsThe film quenching was found to be nonlinear as a function of proton LET as well as of the dose‐averaged LET. However, the linear relation of RE on dose‐averaged LET was a good approximation in all cases. In contrast to dose‐averaged LET, fluence‐averaged LET could not describe the RE when multiple beams were applied.

Clinical Impact of Spatial Variations in Proton Relative Biological Effectiveness (RBE) Among Patients Receiving Radiation to the Head and Neck

Nonhomologous End Joining Is More Important Than Proton Linear Energy Transfer in Dictating Cell Death

Objectives. (1) To examine to what extent the cell- and exposure- specific information neglected in the phenomenological proton relative biological effectiveness (RBE) models could influence the computed RBE in proton therapy. (2) To explore similarities and differences in the formalism and the results between the linear energy transfer (LET)-based phenomenological proton RBE models and the microdosimetry-based Mayo Clinic Florida microdosimetric kinetic model (MCF MKM). (3) To investigate how the relationship between the RBE and the dose-mean proton LET is affected by the proton energy spectrum and the secondary fragments. Approach. We systematically compared six selected phenomenological proton RBE models with the MCF MKM in track-segment simulations, monoenergetic proton beams in a water phantom, and two spread-out Bragg peaks. A representative comparison with in vitro data for human glioblastoma cells (U87 cell line) is also included. Main results. Marked differences were observed between the results of the phenomenological proton RBE models, as reported in previous studies. The dispersion of these models’ results was found to be comparable to the spread in the MCF MKM results obtained by varying the cell-specific parameters neglected in the phenomenological models. Furthermore, while single cell-specific correlation between RBE and the dose-mean proton LET seems reasonable above 2 keV μm−1, caution is necessary at lower LET values due to the relevant contribution of secondary fragments. The comparison with in vitro data demonstrates comparable agreement between the MCF MKM predictions and the results of the phenomenological models. Significance. The study highlights the importance of considering cell-specific characteristics and detailed radiation quality information for accurate RBE calculations in proton therapy. Furthermore, these results provide confidence in the use of the MCF MKM for clonogenic survival RBE calculations in proton therapy, offering a more mechanistic approach compared to phenomenological models.

Objective.Given the increased interest in incorporating linear energy transfer (LET) as an optimization parameter in intensity-modulated proton therapy (IMPT), a solution for experimental validation of simulations and patient-specific quality assurance (PSQA) in terms of proton LET is needed. Here, we present the methodology and results of LET spectra measurements for spread-out Bragg peak (SOBP) and IMPT plans using a miniaturized pixel detector Timepix3.Approach.We used a MiniPIX Timepix3 detector that provides single-particle tracking, type-resolving power, and spectral information while allowing measurement in quasi-continuous mode. We performed measurements for SOBP and IMPT plans in homogeneous RW3 and heterogeneous CIRS head phantoms with reduced beam current. An artificial intelligence-based model was applied for proton identification and a GPU-accelerated FRED Monte Carlo (MC) code was applied for corresponding MC simulations.Main results.We compared the deposited energy and LET spectra obtained in mixed radiation fields from measurements and MC simulations. The peak positions of deposited energy and LET spectra for the SOBP and IMPT plans agree within the error bars. Discrepancies exceeding the error bars are only visible in the logarithmic scale in high-energy deposition and high-LET tails of the distributions. The mean relative difference of dose-averaged LET values between measurements and MC simulations for individual energy layers is about 5.1%.Significance.This study presents a methodology for assessing radiation quality in proton therapy through energy deposition and LET spectra measurements in uniform and clinical IMPT fields. Findings show an agreement between experimental data and MC simulations, validating our approach. The presented results demonstrate the feasibility of a commercially available Timepix3 detector to validate LET computations in IMPT fields and perform PSQA in terms of LET. This will support the implementation of LET in treatment planning, which will ultimately increase the effectiveness of the treatment.

DNA damage induced by the direct effect of radiation

Although DNA DSBs are known to be important in producing the damaging effects of ionizing radiation in cells, bistranded clustered DNA damages-two or more oxidized bases, abasic sites or strand breaks on opposing DNA strands within a few helical turns-are postulated to be difficult to repair and thus to be critical radiation-induced lesions. Gamma rays can induce clustered damages in DNA in solution, and high-energy iron ions produce DSBs and oxidized pyrimidine clusters in human cells, but it was not known whether sparsely ionizing radiation can produce clustered damages in mammalian cells. We show here that X rays induce abasic clusters, oxidized pyrimidine clusters, and oxidized purine clusters in DNA in human cells. Non-DSB clustered damages comprise about 70% of the complex lesions produced in cells. The relative levels of specific cluster classes depend on the environment of the DNA.