Vladimir A. Semenenko

A FAST MONTE CARLO ALGORITHM TO SIMULATE THE SPECTRUM OF DNA DAMAGES FORMED BY IONIZING RADIATION

Abstract Semenenko, V. A. and Stewart, R. D. A Fast Monte Carlo Algorithm to Simulate the Spectrum of DNA Damages Formed by Ionizing Radiation. Radiat. Res. 161, 451–457 (2004). Ionizing radiation produces both singly and multiply damaged DNA sites. Multiply damaged sites (MDS) have been implicated in radiation-induced cell killing and mutagenesis. The spatial distribution of elementary damages (strand breaks and base damages) that constitute MDS is of special interest, since the complexity of MDS has an impact on damage repair. A fast and easy-to-implement algorithm to simulate the local clustering of elementary damages produced by ionizing radiation is proposed. This algorithm captures the major trends in the DNA damage spectrum predicted using detailed track- structure simulations. An attractive feature of the proposed algorithm is that only four adjustable parameters need to be identified to simulate the formation of DNA damage. A convenient recipe to determine the parameters used in the fast Monte Carlo damage simulation algorithm is provided for selected low- and high-LET radiations. The good agreement among the damage yields predicted by the fast and detailed damage formation algorithms suggests that the small-scale spatial distribution of damage sites is determined primarily by independent and purely stochastic events and processes.

Fast Monte Carlo simulation of DNA damage formed by electrons and light ions.

The passage of ionizing radiation through living organisms initiates physical and chemical processes that create clusters of damaged nucleotides within one or two turns of the DNA. These clusters are widely considered an important initiating event for the induction of other biological endpoints, including cell killing and neoplastic transformation. Monte Carlo simulations of the DNA damage formation process are a useful adjunct to experiments because they provide additional information about the spatial configuration of damage within a cluster. In this paper, the fast Monte Carlo damage simulation (MCDS) algorithm is re-parameterized so that yields of double-strand breaks, single-strand breaks and sites of multiple base damage can be simulated for electrons, protons and alpha particles with kinetic energies on the order of GeV. The MCDS algorithm provides a useful, quasi-phenomenological scheme to interpolate damage yields from computationally expensive, but more detailed, track-structure simulations. The predicted characteristics of various classes of damage produced by electrons, protons and alpha particles, such as average number of lesions per DNA damage cluster and cluster length in base pairs, are presented. A study examining the effects on damage complexity of an extrinsic free radical scavenger, dimethyl sulfoxide, is also presented. The reported studies provide new information that will aid efforts to characterize the relative biological effectiveness of high-energy protons and other light ions, which are sometimes used in particle therapy for the treatment of cancer.

The use and QA of biologically related models for treatment planning: short report of the TG-166 of the therapy physics committee of the AAPM.

Treatment planning tools that use biologically related models for plan optimization and/or evaluation are being introduced for clinical use. A variety of dose-response models and quantities along with a series of organ-specific model parameters are included in these tools. However, due to various limitations, such as the limitations of models and available model parameters, the incomplete understanding of dose responses, and the inadequate clinical data, the use of biologically based treatment planning system (BBTPS) represents a paradigm shift and can be potentially dangerous. There will be a steep learning curve for most planners. The purpose of this task group is to address some of these relevant issues before the use of BBTPS becomes widely spread. In this report, the authors (1) discuss strategies, limitations, conditions, and cautions for using biologically based models and parameters in clinical treatment planning; (2) demonstrate the practical use of the three most commonly used commercially available BBTPS and potential dosimetric differences between biologically model based and dose-volume based treatment plan optimization and evaluation; (3) identify the desirable features and future directions in developing BBTPS; and (4) provide general guidelines and methodology for the acceptance testing, commissioning, and routine quality assurance (QA) of BBTPS.

Lyman–Kutcher–Burman NTCP model parameters for radiation pneumonitis and xerostomia based on combined analysis of published clinical data

Knowledge of accurate parameter estimates is essential for incorporating normal tissue complication probability (NTCP) models into biologically based treatment planning. The purpose of this work is to derive parameter estimates for the Lyman-Kutcher-Burman (LKB) NTCP model using a combined analysis of multi-institutional toxicity data for the lung (radiation pneumonitis) and parotid gland (xerostomia). A series of published clinical datasets describing dose response for radiation pneumonitis (RP) and xerostomia were identified for this analysis. The data support the notion of large volume effect for the lung and parotid gland with the estimates of the n parameter being close to unity. Assuming that n = 1, the m and TD(50) parameters of the LKB model were estimated by the maximum likelihood method from plots of complication rate as a function of mean organ dose. Ninety five percent confidence intervals for parameter estimates were obtained by the profile likelihood method. If daily fractions other than 2 Gy had been used in a published report, mean organ doses were converted to 2 Gy/fraction-equivalent doses using the linear-quadratic (LQ) formula with alpha/beta = 3 Gy. The following parameter estimates were obtained for the endpoint of symptomatic RP when the lung is considered a paired organ: m = 0.41 (95% CI 0.38, 0.45) and TD(50) = 29.9 Gy (95% CI 28.2, 31.8). When RP incidence was evaluated as a function of dose to the ipsilateral lung rather than total lung, estimates were m = 0.35 (95% CI 0.29, 0.43) and TD(50) = 37.6 Gy (95% CI 34.6, 41.4). For xerostomia expressed as reduction in stimulated salivary flow below 25% within six months after radiotherapy, the following values were obtained: m = 0.53 (95% CI 0.45, 0.65) and TD(50) = 31.4 Gy (95% CI 29.1, 34.0). Although a large number of parameter estimates for different NTCP models and critical structures exist and continue to appear in the literature, it is hard to justify the use of any single parameter set obtained at a selected institution for the purposes of biologically based treatment planning. Our expectation is that the proposed model parameters based on cumulative experience at various institutions are more representative of the overall practice of radiation therapy than any single-institution data, and could be more readily incorporated into clinical use.

Renin-Angiotensin System Suppression Mitigates Experimental Radiation Pneumonitis

PURPOSE To find the mitigators of pneumonitis induced by moderate doses of thoracic radiation (10-15 Gy). METHODS AND MATERIALS Unanesthetized WAG/RijCmcr female rats received a single dose of X-irradiation (10, 12, or 15 Gy at 1.615 Gy/min) to the thorax. Captopril (an angiotensin-converting enzyme inhibitor) or losartan (an angiotensin receptor blocker) was administered in the drinking water after irradiation. Pulmonary structure and function were assessed after 8 weeks in randomly selected rats by evaluating the breathing rate, ex vivo vascular reactivity, and histopathologic findings. Survival analysis was undertaken on all animals, except those scheduled for death. RESULTS Survival after a dose of 10 Gy to the thorax was not different from that of unirradiated rats for <or=1 year. Survival decreased to <50% by 45 weeks after 12 Gy and by 8-9 weeks after 15 Gy. Captopril (17-56 mg/kg/d) improved survival and reduced radiation-induced increases in breathing rate, changes in vascular reactivity, and histopathologic evidence of injury. Radiation-induced increases in the breathing rate were prevented even if captopril was started 1 week after irradiation or if it was discontinued after 5 weeks. Losartan, although effective in reducing mortality, was not as efficacious as captopril in mitigating radiation-induced increases in the breathing rate or altered vasoreactivity. CONCLUSION In rats, a moderate thoracic radiation dose induced pneumonitis and morbidity. These injuries were mitigated by captopril even when it was begun 1 week after radiation or if discontinued 5 weeks after exposure. Losartan was less effective in protecting against radiation-induced changes in vascular reactivity or tachypnea.

Effects of oxygen on intrinsic radiation sensitivity: A test of the relationship between aerobic and hypoxic linear-quadratic (LQ) model parametersa)

The poor treatment prognosis for tumors with high levels of hypoxia is usually attributed to the decreased sensitivity of hypoxic cells to ionizing radiation. Mechanistic considerations suggest that linear quadratic (LQ) survival model radiosensitivity parameters for hypoxic (H) and aerobic (A) cells are related by αH=αA∕oxygen enhancement ratio (OER) and (α∕β)H=OER(α∕β)A. The OER parameter may be interpreted as the ratio of the dose to the hypoxic cells to the dose to the aerobic cells required to produce the same number of DSBs per cell. The validity of these expressions is tested against survival data for mammalian cells irradiated in vitro with low- and high-LET radiation. Estimates of hypoxic and aerobic radiosensitivity parameters are derived from independent and simultaneous least-squares fits to the survival data. An external bootstrap procedure is used to test whether independent fits to the survival data give significantly better predictions than simultaneous fits to the aerobic and hypoxic data. For low-LET radiation, estimates of the OER derived from the in vitro data are between 2.3 and 3.3 for extreme levels of hypoxia. The estimated range for the OER is similar to the oxygen enhancement ratios reported in the literature for the initial yield of DSBs. The half-time for sublethal damage repair was found to be independent of oxygen concentration. Analysis of patient survival data for cervix cancer suggests an average OER less than or equal to 1.5, which corresponds to a pO2 of 5mmHg (0.66%) in the in vitro experiments. Because the OER derived from the cervix cancer data is averaged over cells at all oxygen levels, cells irradiated in vivo under extreme levels of hypoxia (<0.5mmHg) may have an OER substantially higher than 1.5. The reported analyses of in vitro data, as well as mechanistic considerations, provide strong support for the expressions relating hypoxic and aerobic radiosensitivity parameters. The formulas are also useful for the analysis of clinical data because the number of radiosensitivity parameters that need to be determined is reduced from four to three without a substantial decrease in the ability of the LQ to accurately predict the surviving faction. The relationships among radiosensitivity parameters imply that the dose to the hypoxic subvolume of the tumor needs to be escalated by a factor of the OER to achieve the same level of tumor control as in well oxygenated tumor regions.

Combined Use of Monte Carlo DNA Damage Simulations and Deterministic Repair Models to Examine Putative Mechanisms of Cell Killing

Abstract Carlson, D. J., Stewart, R. D., Semenenko, V. A. and Sandison, G. A. Combined Use of Monte Carlo DNA Damage Simulations and Deterministic Repair Models to Examine Putative Mechanisms of Cell Killing. Radiat. Res. 169, 447–459 (2008). A kinetic repair-misrepair-fixation (RMF) model is developed to better link double-strand break (DSB) induction to reproductive cell death. Formulas linking linear-quadratic (LQ) model radiosensitivity parameters to DSB induction and repair explicitly account for the contribution to cell killing of unrejoinable DSBs, misrepaired and fixed DSBs, and exchanges formed through intra- and intertrack DSB interactions. Information from Monte Carlo simulations is used to determine the initial yields and complexity of DSBs formed by low- and high-LET radiations. Our analysis of published survival data for human kidney cells suggests that intratrack DSB interactions are negligible for low-LET radiations but increase rapidly with increasing LET. The analysis suggests that no class of DSB is intrinsically unrejoinable or that DSB reparability is not strictly determined by the number of lesions forming the DSB. For radiations with LET >110 keV/μm, the model predicts that the relative cell killing efficiency, per unit absorbed dose, should continue to increase, whereas data from published experiments indicate a reduced cell killing efficiency. This observation suggests that the Monte Carlo simulation overestimates the DSB yield beyond 110 keV/μm or that other biological phenomena not included in the model, such as proximity effects, are important. For 200–250 kVp X rays (∼1.9 keV/μm), only about 1% of the one-track killing is attributed to intratrack binary misrepair interactions. The analysis indicates that the remaining 99% of the lethal damage is due to other types of one-track damage, including possible unrepairable, misrepaired and fixed damage. Compared to the analysis of the X-ray results, 48% of the one-track lethal damage caused by 5.1 MeV α particles (∼88 keV/μm) is due to intratrack DSB interactions while the remainder is due to other forms of one-track damage.

Evaluation of a commercial biologically based IMRT treatment planning system

A new inverse treatment planning system (TPS) for external beam radiation therapy with high energy photons is commercially available that utilizes both dose-volume-based cost functions and a selection of cost functions which are based on biological models. The purpose of this work is to evaluate quality of intensity-modulated radiation therapy (IMRT) plans resulting from the use of biological cost functions in comparison to plans designed using a traditional TPS employing dose-volume-based optimization. Treatment planning was performed independently at two institutions. For six cancer patients, including head and neck (one case from each institution), prostate, brain, liver, and rectal cases, segmental multileaf collimator IMRT plans were designed using biological cost functions and compared with clinically used dose-based plans for the same patients. Dose-volume histograms and dosimetric indices, such as minimum, maximum, and mean dose, were extracted and compared between the two types of treatment plans. Comparisons of the generalized equivalent uniform dose (EUD), a previously proposed plan quality index (fEUD), target conformity and heterogeneity indices, and the number of segments and monitor units were also performed. The most prominent feature of the biologically based plans was better sparing of organs at risk (OARs). When all plans from both institutions were combined, the biologically based plans resulted in smaller EUD values for 26 out of 33 OARs by an average of 5.6 Gy (range 0.24 to 15 Gy). Owing to more efficient beam segmentation and leaf sequencing tools implemented in the biologically based TPS compared to the dose-based TPS, an estimated treatment delivery time was shorter in most (five out of six) cases with some plans showing up to 50% reduction. The biologically based plans were generally characterized by a smaller conformity index, but greater heterogeneity index compared to the dose-based plans. Overall, compared to plans based on dose-volume optimization, plans with equivalent target coverage obtained using the biologically based TPS demonstrate improved dose distributions for the majority of normal structures.

Monte Carlo simulation of base and nucleotide excision repair of clustered DNA damage sites. I. Model properties and predicted trends.

Abstract Semenenko, V. A., Stewart, R. D. and Ackerman, E. J. Monte Carlo Simulation of Base and Nucleotide Excision Repair of Clustered DNA Damage Sites. I. Model Properties and Predicted Trends. Radiat. Res. 164, 180–193 (2005). DNA is constantly damaged through endogenous processes and by exogenous agents, such as ionizing radiation. Base excision repair (BER) and nucleotide excision repair (NER) help maintain the stability of the genome by removing many different types of DNA damage. We present a Monte Carlo excision repair (MCER) model that simulates key steps in the short-patch and long-patch BER pathways and the NER pathway. The repair of both single and clustered damages, except double-strand breaks (DSBs), is simulated in the MCER model. Output from the model includes estimates of the probability that a cluster is repaired correctly, the fraction of the clusters converted into DSBs through the action of excision repair enzymes, the fraction of the clusters repaired with mutations, and the expected number of repair cycles needed to completely remove a clustered damage site. The quantitative implications of alternative hypotheses regarding the postulated repair mechanisms are investigated through a series of parameter sensitivity studies. These sensitivity studies are also used to help define the putative repair characteristics of clustered damage sites other than DSBs.

Improved critical structure sparing with biologically based IMRT optimization

The impact of using biological models in treatment planning on plan quality is studied by comparing IMRT plans generated using selected commercially available treatment planning systems (TPSs) employing biological models/quantities in IMRT optimization (bIMRT) and the conventional physically (dose-volume) based optimization (pIMRT). A total of 25 IMRT plans, generated for five cases of different anatomic sites (brain, head and neck, lung, pancreas, and prostate) using five TPSs, two bIMRT (CMS Monaco and Phillips Pinnacle3 P3IMRT) and three pIMRT (CMS Xio, Phillips Pinnacle3, and Tomotherapy) systems, were compared. Dose-volume histograms, maximum, minimum, and mean doses, target heterogeneity and conformity indices, equivalent uniform dose (EUD), and an overall plan-ranking index (fEUD) were used in the comparison. It is clear from the comparison that the use of biological models in treatment planning optimization can generate IMRT plans with significantly improved normal tissue sparing with similar or slightly increased dose heterogeneity in the target, as compared to the conventional dose-volume based optimization for the same beam arrangement. For example, the bIMRT plans lead to smaller EUDs in 32 out of 37 normal structures in all five cases combined, as compared to the pIMRT plans. Caution should be exercised in choosing appropriate models and/or model parameters and in evaluating the plan obtained when using the biologically based treatment planning system.