Geant4-DNA simulation of human cancer cells irradiation with helium ion beams

Review of the geometrical developments in GEANT4-DNA: From a biological perspective

GEANT4-DNA is an expansion of the widely utilised GEANT4 Monte Carlo toolkit. This extension focuses on modelling the physical, chemical, and biological stages of ionising radiation for radiobiological applications at cellular and DNA level interactions. To date, review papers on GEANT4-DNA focus solely on evaluating a selection of the latest developments with a greater focus on mechanistic developments rather than progress in biologically specific geometries. In this work, an overview of biological analysis and biological geometries that have been developed are discussed, highlighting the latest developments and future possible development avenues for GEANT4-DNA for this application. An overview of the biological organisation levels, namely DNA, cellular, and population levels, and how GEANT4-DNA models the physical, chemical, and biological processes are also described. This review emphasises the need for persistent development of specific biological geometry accompanied by personalised DNA damage analysis parameters dependent on the biological processes considered within a specific model. It also provides an in-depth understanding of the advances at all the biological organisation levels (DNA, cellular, and population) and the use of co-operative platforms developed to model alongside GEANT4 to provide further detailed geometries and or biological damage analysis. The developments presented have been analytically discussed along with their key findings and prospects for GEANT4-DNA. Finally, a perspective on future necessary developments is portrayed since many of the advancements in the biological analysis and biological geometries discussed have not been exploited to their full potential. The development of GEANT4-DNA, using the advances discussed in this review, provides a favourable method for the evaluation of biological damage comparable to radiobiological studies.

In silico analysis of radiation-induced double-strand breaks by internal ex vivo irradiation of lymphocytes for 45 alpha- and beta/gamma-emitting radionuclides

BACKGROUND

The aim of this study is to evaluate the induction of DNA damage by 45 radionuclides, including those used in medical applications and others relevant to radiation protection. The research focuses on understanding the differential effects of irradiating lymphocytes with beta/gamma- and alpha-emitting radionuclides using Monte Carlo simulations. A validated Monte Carlo simulation model was used to assess radiation-induced DNA damage in lymphocytes. The model integrates GATE for macroscopic radiation transport and Geant4-DNA for microscopic simulations at the cellular level. For the study, 45 radionuclides were selected and their S-values and DNA double-strand break (DSB) induction were investigated. For beta- and gamma-emitting radionuclides, DSBs per cell per mGy were quantified, while for alpha-emitters, alpha tracks per cell per mGy, DSBs per cell per mGy, and DSBs per micrometer of alpha track were calculated.

RESULT

For beta/gamma emitters, the lowest number of DSBs was observed with 125I at 0.006 ± 0.003 DSBs·cell⁻¹·mGy⁻¹, while 99mTc had the highest at approximately 0.015 ± 0.005 DSBs·cell⁻¹·mGy⁻¹. The S-value for lymphocyte nuclei ranked from 0.91 ± 0.14 mGy∙h⁻¹∙MBq⁻¹ (63Ni) and 1.06 ± 0.15 mGy∙h⁻¹∙MBq⁻¹ (125I) to 61.83 ± 1.17 mGy∙h⁻¹∙MBq⁻¹ (90Sr). For alpha-emitting radionuclides, 213Bi produced 0.0677 ± 0.0005 DSB·cell⁻¹·mGy⁻¹ while 232Th yielded 0.0914 ± 0.0004 DSB·cell⁻¹·mGy⁻¹. The DSB linear density for alpha tracks ranged from 7.4 ± 0.1 DSBs/µm for 252Cf to 16.8 ± 0.1 DSBs/µm for 232Th. The S-values for lymphocyte nuclei for alpha emitters varied, from 232Th (0.29 ± 0.21 Gy∙h⁻¹∙MBq⁻¹) to 227Th having the highest at 2.22 ± 0.16 Gy∙h⁻¹∙MBq⁻¹, due to cumulative energy deposition.

CONCLUSIONS

Differences were observed in DNA damage induced by beta/gamma- and alpha-emitting radionuclides. High-energy beta emitters induced DSBs similarly to gamma emitters, but with greater fluctuations in low-energy beta and gamma emitters due to heterogeneous energy deposition and varying interaction probabilities at the cellular level. This study highlights that long half-life alpha-emitting radionuclides may cause more extensive DNA damage due to their higher LET. This work provides a comprehensive S-values database for future experimental studies on radiation-induced DNA damage in lymphocytes.

Position in proton Bragg curve influences DNA damage complexity and survival in head and neck cancer cells

Background and purpose

Understanding the cellular and molecular effect of proton radiation, particularly the increased DNA damage complexity at the distal end of the Bragg curve, is current topic of investigation. This work aims to study in vitro clonogenic survival and DNA damage foci kinetics of a head and neck squamous cell carcinoma cell line at various positions along a double passively scattered Bragg curve. Complementary in silico studies are conducted to gain insights into the link between cell survival variations, experimentally yielded foci and the number and complexity of double strand breaks (DSBs).

Materials and methods

Proton irradiations are performed at the HollandPTC R&D proton beamline, using a double passively scattered setup. A custom water phantom setup is employed to accurately position the samples within the Bragg curve. FaDu cells are irradiated at the proximal 36 % point of the Bragg peak, (P36), proximal 80 % point of the Bragg peak (P80) and distal 20 % point of the Bragg peak (D20), with dose-averaged mean lineal energies (y D ¯ ) of 1.10 keV/μm, 1.80 keV/μm and 7.25 keV/μm, respectively.

Results

Clonogenic survival correlates strongly withy D ¯ , showing similar survival for P36 (D37%=3.0 Gy) and P80 (D37%=2.9 Gy), but decreased survival for D20 (D37% = 1.6 Gy). D20 irradiated samples exhibit increased 53BP1 foci shortly after irradiation, slower resolution of the foci, and larger residual 53BP1 foci after 24 h, indicating unrepaired complex breaks. These experimental observations are supported by the in silico study which demonstrates that irradiation at D20 leads to a 1.7-fold increase in complex DSBs with respect to the total number of strand breaks compared to P36 and P80.

Conclusions

This combined approach provides valuable insights into the cellular and molecular effect of proton radiation, emphasizing the increased DNA damage complexity at the distal end of the Bragg curve, and has the potential to enhance the efficacy of proton therapy.

Evaluating the biological impact of shelters on astronaut health during different solar particle events: a Geant4-DNA simulation study

Mechanistic Monte Carlo simulations have proven invaluable in tackling complex challenges in radiobiology, for example for protecting astronauts from solar particle events (SPEs) during deep space missions which remains an underexplored area. In this study, the Geant4-DNA Monte Carlo code was used to assess the DNA damage caused by SPEs and evaluate the protective effectiveness of a multilayer shelter. By examining the February 1956 and October 1989 SPEs-two extreme cases-the results showed that the proposed shelter reduced DNA damage by up to 57.9% for the October 1989 SPE and 36.7% for the February 1956 SPE. Cell repair and survival modeling further revealed enhanced cell survival with the shelter, reducing lethal DNA damage by up to 64.3% and 88.2% for February 1956 and October 1989 SPEs, respectively. The results presented here highlight the crucial importance of developing effective radiation shielding to protect astronauts during solar storms and emphasizes the need to improve predictions of solar particle events to optimize shelter design.

Simulation of cell cycle effects on DNA strand break induction due to α-particles

PURPOSE

Understanding cell cycle variations in radiosensitivity is important for α-particle therapies. Differences are due to both repair response mechanisms and the quantity of initial radiation-induced DNA strand breaks. Genome compaction within the nucleus has been shown to impact the yield of strand breaks. Compaction changes during the cell cycle are therefore likely to contribute to radiosensitivity differences. Simulation allows the strand break yield to be calculated independently of repair mechanisms which would be challenging experimentally.

METHODS

Using Geant4 the impact of genome compaction changes on strand break induction due to α-particles was simulated. Genome compaction is considered to be described by three metrics: global base pair density, chromatin fibre packing fraction and chromosome condensation. Nuclei in the G1, S, G2 and M phases from two cancer cell lines and one normal cell line are simulated. Repair mechanisms are not considered to study only the impact of genome compaction changes.

RESULTS

The three compaction metrics have differing effects on the strand break yield. For all cell lines the strand break yield is greatest in G2 cells and least in G1 cells. More strand breaks are induced in the two cancer cell lines than in the normal cell line.

CONCLUSIONS

Compaction of the genome affects the initial yield of strand breaks. Some radiosensitivity differences between cell lines can be attributed to genome compaction changes between the phases of the cell cycle. This study provides a basis for further analysis of how repair deficiencies impact radiation-induced lethality in normal and malignant cells.

Development of a novel computational technique to create DNA and cell geometrical models for Geant4-DNA

BACKGROUND

This study aimed to develop a novel human cell geometry for the Geant4-DNA simulation toolkit that explicitly incorporates all 23 chromosome pairs of the human cell. This approach contrasts with the existing, default human cell, geometrical model, which utilizes a continuous Hilbert curve.

METHODS

A Python-based tool named "complexDNA" was developed to facilitate the design of both simple and complex DNA geometries. This tool was employed to construct a human cell geometry with individual pairs of chromosomes. Subsequently, the performance of this chromosomal model was compared to the standard human cell model provided in the "molecularDNA" Geant4-DNA example.

RESULTS

Simulations using the new chromosomal model revealed minimal discrepancies in DNA damage yield and fragment size distribution compared to the default human cell model. Notably, the chromosomal model demonstrated significant computational efficiency, requiring approximately three times less simulation time to achieve equivalent results.

CONCLUSIONS

This work highlights the importance of incorporating chromosomal structure into human cell models for radiation biology research. The "complexDNA" tool offers a valuable resource for creating intricate DNA structures for future studies. Further refinements, such as implementing smaller voxels for euchromatin regions, are proposed to enhance the model's accuracy.

Nanoscale gold nanoparticle (GNP)-laden tumor cell model and its use for estimation of intracellular dose from GNP-induced secondary electrons

BACKGROUND

Gold nanoparticles (GNPs) accumulated within tumor cells have been shown to sensitize tumors to radiotherapy. From a physics point of view, the observed GNP-mediated radiosensitization is due to various downstream effects of the secondary electron (SE) production from internalized GNPs such as GNP-mediated dose enhancement. Over the years, numerous computational investigations on GNP-mediated dose enhancement/radiosensitization have been conducted. However, such investigations have relied mostly on simple cellular geometry models and/or artificial GNP distributions. Thus, it is at least desirable, if not necessary, to conduct further investigations using cellular geometry models that properly reflect realistic cell morphology as well as internalized GNP distributions at the nanoscale.

PURPOSE

The primary aim of this study was to develop a nanometer-resolution geometry model of a GNP-laden tumor cell for computational investigations of GNP-mediated dose enhancement/radiosensitization. The secondary aim was to demonstrate the utility of this model by quantifying GNP-induced SE tracks/dose distribution at sub-cellular levels for further validation of a nanoscopic dose point kernel (nDPK) method against full-fledged Geant4 Monte Carlo (MC) simulation.

METHODS

A transmission electron microscopy (TEM) image of a single cell showing cytoplasm, cellular nucleus, and internalized GNPs in the cellular endosome was segmented into sub-cellular levels based on pixel value thresholding. A corresponding material density was allocated to each pixel, and, by adding a thickness, each pixel was transformed to a geometric voxel and imported as a Geant4-acceptable input geometry file. In Geant4-Penelope MC simulation, a clinical 6 MV photon beam was applied, vertically or horizontally to the cell surface, and energy deposition to the cellular nucleus and cytoplasm, due to SEs emitted by internalized GNPs, was scored. Next, nDPK calculations were performed by generating virtual electron tracks from each GNP voxel to all nucleus and cytoplasm voxels. Subsequently, another set of Geant4 simulation was performed with both Penelope and DNA physics models under the geometry closely mimicking in vitro cell irradiation with a clinical 6 MV photon beam, allowing for derivation of nDPK specific to this geometry and further comparison between Gean4 simulation and nDPK method.

RESULTS

The Geant4-calculated SE tracks and associated energy depositions showed significant dependence on photon incidence angle. For perpendicular incidence, nDPK results showed good agreement (average percentage pixel-to-pixel difference of 0.4% for cytoplasm and 0.5% for nucleus) with Geant4 results, while, for parallel incidence, the agreement became worse (-1.7%-0.7% for cytoplasm and -5.5%-0.8% for nucleus). Under the 6 MV cell irradiation geometry, nDPK results showed reasonable agreement (pixel-to-pixel Pearson's product moment correlation coefficient of 0.91 for cytoplasm and 0.98 for nucleus) with Geant4 results.

CONCLUSIONS

The currently developed TEM-based model of a GNP-laden cell offers unprecedented details of realistic intracellular GNP distributions for nanoscopic computational investigations of GNP-mediated dose enhancement/radiosensitization. A benchmarking study performed with this model showed reasonable agreement between Geant4- and nDPK-calculated intracellular dose deposition by SEs emitted from internalized GNPs, especially under perpendicular incidence - a popular cell irradiation geometry and when the Geant4-Penelope physics model was used.

A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study

Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.

"dsbandrepair" - An updated Geant4-DNA simulation tool for evaluating the radiation-induced DNA damage and its repair

PURPOSE

Interdisciplinary scientific communities have shown large interest to achieve a mechanistic description of radiation-induced biological damage, aiming to predict biological results produced by different radiation quality exposures. Monte Carlo track-structure simulations are suitable and reliable for the study of early DNA damage induction used as input for assessing DNA damage. This study presents the most recent improvements of a Geant4-DNA simulation tool named "dsbandrepair".

METHODS

"dsbandrepair" is a Monte Carlo simulation tool based on a previous code (FullSim) that estimates the induction of early DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). It uses DNA geometries generated by the DNAFabric computational tool for simulating the induction of early single-strand breaks (SSBs) and double-strand breaks (DSBs). Moreover, the new tool includes some published radiobiological models for survival fraction and un-rejoined DSB. Its application for a human fibroblast cell and human umbilical vein endothelial cell containing both heterochromatin and euchromatin was conducted. In addition, this new version offers the possibility of using the new IRT-syn method for computing the chemical stage.

RESULTS

The direct and indirect strand breaks, SSBs, DSBs, and damage complexity obtained in this work are equivalent to those obtained with the previously published simulation tool when using the same configuration in the physical and chemical stages. Simulation results on survival fraction and un-rejoined DSB are in reasonable agreement with experimental data.

CONCLUSIONS

"dsbandrepair" is a tool for simulating DNA damage and repair, benchmarked against experimental data. It has been released as an advanced example in Geant4.11.2.

Manipulating Radiation-Sensitive Z-DNA Conformation for Enhanced Radiotherapy

DNA double-strand breaks (DSBs) yield highly determines radiotherapy efficacy. However, improving the inherent radiosensitivity of tumor DNA to promote radiation-induced DSBs remains a challenge. Using theoretical and experimental models, the underexplored impact of Z-DNA conformations on radiosensitivity, yielding higher DSBs than other DNA conformations, is discovered. Thereout, a radiosensitization strategy focused on inducing Z-DNA conformation, utilizing CBL@HfO2 nanocapsules loaded with a Z-DNA inducer CBL0137, is proposed. A hollow mesoporous HfO2 (HM-HfO2) acts as a delivery and an energy depositor to promote Z-DNA breakage. The nanocapsule permits the smart DSBs accelerator that triggers its radiosensitization with irradiation stimulation. Impressively, the CBL@HfO2 facilitates the B-Z DNA conformational transition, augmenting DSBs about threefold stronger than irradiation alone, generating significant tumor suppression with a 30% cure rate. The approach enables DSBs augmentation by improving the inherent radiosensitivity of DNA. As such, it opens up an era of Z-DNA conformation manipulation in radiotherapy.

Ion-Type Dependence of DNA Electronic Excitation in Water under Proton, α-Particle, and Carbon Ion Irradiation: A First-Principles Simulation Study

Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy and other related approaches, such as boron neutron capture therapy. While protons have been the predominant ions of choice in ion beam cancer therapy, heavier ions, particularly carbon ions, have drawn significant attention over the past decade. Carbon ions are expected to transfer larger amounts of energy according to linear response theory. However, molecular-level details of the electronic excitation under heavier ion irradiation remain unknown. In this work, we use real-time time-dependent density functional theory simulations to examine the quantum-mechanical details of DNA electronic excitations in water under proton, α-particle, and carbon ion irradiation. Our results show that the energy transfer does indeed increase for the heavier ions, while the excitation remains highly conformal. However, the increase in the energy transfer rate, measured by electronic stopping power, does not match the prediction by the linear response model, even when accounting for the velocity dependence of the irradiating ion's charge. The simulations also reveal that while the number of holes generated on DNA increases for heavier ions, the increase is only partially responsible for the larger stopping power. Larger numbers of highly energetic holes formed from the heavier ions also contribute significantly to the increased electronic stopping power.