MC modelling of initial radiation effects with PARTRAC Dr. Elke Schmitt
[email protected]
Helmholtz Zentrum München Department of Radiation Sciences Institute of Radiation Protection
DoReMi LD-RadStats workshop CREAL Barcelona, 27th October 2015
Outline •
Introduction Biophysical modelling of microdosimetric processes with track structure codes in radiation protection and medical physics How can they help for (low dose) radiation research questions and especially to estimate uncertainties?
• PARTRAC code Models for physics, chemistry and radiobiology Examples for (low dose) applications in radiation protection/medical physics and uncertainties
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Conclusion and further research topics PARTRAC future development and possible collaboration topics
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction
Radiation quality: quality: input and output parameters • Radiation quality (RQ): depends on {particle type, energy, dose rate, geometry, … } but usually simplification only by {particle type, energy} or by LET. is defined by the biological outcome (DNA damage as DSB cluster, repair products as dicentrics, cell survival, …) compared to a reference radiation (normally 60Co X-rays) in terms of RBE.
• Linear Energy Transfer (LET): amount of energy deposited ‚locally‘ per track length (as mean value or distribution = stochastic effect!) in unit keV/µm particle (and energy) related quantity
• Relative biological effectiveness (RBE): RBE(RQ) = doseRR /doseRQ where Bioeffect(RR, doseRR) = Bioeffect(RQ, doseRQ) with RR= reference radiation (usually photons as 60Co γ-rays) DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction
Biological radiation effects: effects: multi multi--scale issue Time Stage
Subject
Effect
Model
10-15 s physical
atom
ionization excitation reaction new species
track structure
biomolecule DNA
methylation strand break
initial damage
gene chromosome cell
regulation aberration apoptosis
damage response
physico-chemical
chemical 10-5 s biochemical
biological
radical
radiation chemistry
systems biology
105 s medical 1010 s
tissue organ organism
inflammation carcinogenesis death disease induction
epidemiological
population
life expectancy
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction
Biological radiation effects: effects: non non--linear in low low--dose region Biological effects after radiation are highly complex , related not only to physical quantity of dose but also depending on inter-individual variability.
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Low-dose radiation effects are highly stochastic because they occur by rare events (DNA damage by few tracks).
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For high-LET radiation the damage (DSB, cluster) caused by only one single track is crucial.
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MC simulation of radiation track structure and DNA damage & repair can contribute to solve open questions on the initial radiation response and thus provide input to more complex systems biology after.
Non-linear dose response is the main mechanism to be understood (especially in the low dose region). R(Dose, …)
•
? Low dose region
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction
Critical harm caused by DSB possible already at low doses
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
LET dependence of DNA repair (complexity of damage) damage) • Non repaired DNA Strand Breaks versus LET for different particles:
Overkill effect
Almost equal to RBE dependence for cell survival! Present DSB damage causes the lethal effects (including overkill) and some mutations.
With increasing LET the ionization density on relevant nm scale (DNA size) gets higher and therefore probability for DSB DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction
Why track structure based modelling of DNA damage? response ? • DNA damage response is of highest relevance for late effects (assuming that cells surviving with misrejoined DSB are critical) • Hypotheses on mechanisms of DNA damage response (e.g. processes leading to mis-rejoining of DNA ends) can be tested. UNSCEAR 2006
• Track structure based simulations of initial DNA damage provide very precise information on radiation damage at 1 µs after the passage of an ionizing particle. Experimental data (e.g. for model validation) are typically determined minutes or hours later even when ‘initial investigated. DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction to biophysical modelling:
Why track structure based simulation of biological effects?
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Allow the analysis of measurements (also for uncertainties) taking into account the influence of limiting boundary conditions and adopted algorithms.
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Include inherently the stochastic nature of radiation effects and may address the impact of rare events (as e.g. low dose effects).
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Offer extrapolations of radiation effects for irradiation conditions beyond limitations of experimental investigations (find methods for the prediction of radiation effects) .
Important for radiation protection (risk estimation for nuclear accidents, exposure at work or by medical radio diagnostics, space missions) and radio therapy (treatment planning).
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction to biophysical modelling:
Track structure codes in radiation protection & medical physics
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MC transport codes (‘condensed history’): Geant4, FLUKA, PHITS & treatment planning codes (mm - cm scale) therapy
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MC track structure codes (‘event-by-event’, nuclear reactions are neglected as for dimensions of a single cell negligible): PARTRAC, Kurbuc_carbon, Geant4-DNA (nm - µm scale) micro-, nanodosimetry
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Basic assumptions in track structure codes: Based on cross sections for interaction of primary and secondary ionizing particles with the traversed matter: classical trajectory picture (no quantum effects), event-by-event. Damage to nuclear DNA is the main initiating event. (But recently other targets as e.g. mitochondria under investigation.) DSB in DNA are the crucial initial lesions. (But not sufficient, more criteria have to be investigated.)
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Introduction to biophysical modelling:
PARTRAC Code
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PARTRAC: Multi-scale model for initial effects and early damage response integrating physics, chemistry, DNA structure, DNA damage & repair but yet no cell survival. time scale days Test hypotheses on mechanisms of radiation response (correlation radiation quality RBE etc.), investigate relevant target structures (cell, DNA). Interpret experimental measurements and predict radiation effects beyond experimental limitations. Provide input data for higher-scale biological models (bystander effect etc.) Investigate current open research problems in micro-/nanodosimetry related to applications in radiation protection and therapy but not for larger scales of mm – cm.
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Modules
• •
MC based models describing biophysical effects of ionizing radiation. Developed at Institute of Radiation Protection Neuherberg since the 1980‘s.
Physical track structure simulation: cross sections in liquid water (photons, electrons, protons, alpha, ions Z≥3). Module 1 Physico-chemical and chemical stage: formation of radicals, diffusion and reactions. Module 2 Initial DNA damage: DSB/SSB yields and damage cluster on nano- and micro-scale, dose-dependent DNA fragment distribution. Module 3 DNA repair: mobility of DNA ends + action of repair enzymes, leading to repair or chromosome aberrations. Impact of nano- and micro-scale clustering! Module 4
Friedland et al. Mutat. Res. 711 (2011).
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Modules
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PARTRAC has no graphical user interface: All input given by parameter files or by steering files (partrac.input , partrac.csf, …) All output in dedicated files (nameofrun.dam4digitindex for direct DNA hits, …) and only some info displayed also on screen
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Physical track structure (module 1) Physical track structure is modelled event-by-event using cross sections
• •
Transport to next event determined by total cross section Characteristics of event determined by differential cross section regarding interaction processes (elastic scattering, ionisation, excitation, charge transfer), energy transfer and angular deviation for primary and secondary particles photons, electrons, protons, alpha, ions Z>2 in relevant target materials: photons all materials, ions + electrons only liquid water.
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Different models for
photons (photoeffect, Compton scattering, relaxation for element fractions of materials) electrons (elastic scattering, excitation, ionisation in liquid water) H and He (excitation and ionisation in liquid water) ions Z>2 (Barkas scaling of H data)
Paretzke et al „Kinetics of nonhomogenous processes“ Wiley (1987), Dingfelder et al Rad Phys Chem 53 (1998) DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Physical track structure of isotachic ions
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Isotachic ions are not equally effective. Ionization density (~ LET) depends on specific energy and particle type, nm and μm scale are important for relevant damage on DNA.
6.00 MeV/u Proton 1H
6.25 MeV/u 16O
6.25 MeV/u 4He DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Radiation chemistry (module 2) Determines OH radical attack to DNA resulting in indirect damage. • In the physico-chemical stage (10-12 – 10-6 s) Subexcitation electrons are thermalized and become hydrated. Excited and ionized water molecules lead to radicals and other reactive species
• Then modelling of the chemical stage at discrete time steps (10-12 – 10-6 s) for Diffusion, Chemical reactions and Scavenging.
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Radiochemical track structure ‚disappears‘ between 10 ns and 1 µs after the passage of the initiating particle
Kreipl et al, Rad. Env. Bioph. 48 (2008)
(10-12 s)
(10-7 s)
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
(10-8 s)
(10-6 s)
Microdosimetric modelling with PARTRAC code
Radiation chemistry details Parameters: Diffusion coefficients D Reaction rate constants k Scavenging constants
physical stage
10-15 – 10-12 s
Subexcitation el. (esub) States of water molecule: Ionisation (H2O+) ~90% Excitation (H2O*) ~10%
! A1B1:
Phys. processes: • relaxation • auto-ionisation • dissociation
physicochemical
Chem. Reactions: • diffusion • reaction Obtained reactive species: • scavenging eaq, •OH, H•, H2, H3O+, OH-, H2O2
Kreipl et al, Rad. Env. Bioph. 48 (2008)
esub
→ eaq
100%
Subexc. el
H2O+ + H2O
→ H3O+ + •OH
100%
Ionisation
35% 65% 30% 55% 15% 50% 50%
Excitation
H2O* H2O* H2O* B1A1: H2O* + H2O H2O* + H2O Ryd, db: H2O* H2O* + H2O
chemical stage
10-12 – 10-6 s
→ H2O + ∆E → H• + •OH → H2O + ∆E → H3O+ + •OH + eaq → H2 + 2•OH → H2O + ∆E → H3O+ + •OH + eaq
(from H2+ •O• + H2O)
eaq + eaq + 2H2O → H2 + 2OHeaq + •OH → OHeaq + H• + H2O → H2 + OHeaq + H3O+ → H• + H2O eaq + H2O2 → OH- + •OH •OH + •OH → H2O2 •OH + H• → H2O H• + H• → H2 + H3O + OH → 2H2O •OH + DNA (S,A,C,G,T) → •OH + histone → •OH + scavenger →
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
DNA model for biological damage • Coordinates of atoms in DNA and histones used to build nucleotides up to chromosome and whole nuclear DNA (6.62 Gbp) as target for the radiation. Atomic data: Bernhardt (2003). Chromosomes and integration: Friedland et al Rad Env Biophys 53 (2008)
• Options for modelling hetero- and euchromatin regions. Euchromatin less densely packed and higher gene concentration than heterochromatin.
Nucleotide
↕
0.34 nm
↕
Double helix
2 nm
Nucleosome
10 nm
↕
Chromatin fiber
30 nm
↕
Chromosome
3 µm
Cell nucleus
10 µm
Spherical chromatin domains with chromosome territories in interphase G0/G1 state: lymphocyte or fibroblast
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Biological damage (module 3) Calculation of radiation effects: DSB and SSB induction
by energy deposition to the sugar-phosphate backbone (direct effect) or
by interaction of •OH radicals with sugar (indirect effect).
Processes not known in detail many parameters adapted by matching published DSB and SSB yield data after 60Co γ irradiation: •Strand break induction parameterized by DNA target volume (van der Waals radii multiplied by 2, fills holes and accounts for hydration layer) energy necessary for strand break (probability increases linearly from 0 at 5 eV to 1 at 37.5 eV) fraction of OH – sugar interactions leading to strand break: 65 % (~13% OH-DNA interactions)
•DSB induction parameterized by 10 bp max. distance between breaks 1 % SSB to DSB conversion (DSB induction parallel to SSB and low DSB threshold) DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
DNA damage simulations compared to experimental data •
PARTRAC simulations for high-LET radiation predict large yields of short DNA fragments from DSB induction not detected in experiments!
All fragments
Fragments in detectable range
Calculations: Friedland et al (2006) Rad Protect Dosim 122 Experiments: Frankenberg (H, He), Rydberg (He), Höglund (B, N, He)
LET (keV/µm) DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
DNA repair as response to induced damage (module 4) How is repair kinetics linked to initial damage? Input for repair processes are the geometric/genomic position and complexity of DSB from the initial damage calculation.
Processes are complex and depend on many often still unknown biological parameters (also experimental data needed to tune the model parameters may vary under different conditions). Mechanistic modelling of DNA repair continues to be a challenge.
• DSB repair by NHEJ pathway (leading to correct repair, unrepaired ends and chromosomal aberrations as rings, dicentrics etc. by mis-rejoining) is modelled in PARTRAC accounting for enzyme kinetics (temporal development) of Ku70/80 & DNA-PKcs DNA end mobility (spatial development).
Friedland et al (2012) Int J Radiat Biol 88, Friedland et al (2013) Mutat Res 756 DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Biological DNA repair model schematic view •Model for DSB repair via NHEJ pathway: temporal development Friedland et al (2012) Int J Radiat Biol 88, Italic numbers are time constants in seconds Friedland et al (2013) Mutat Res 756 (1) Chromatin remodeling (2) (3) (4) (5) (6) (7) (8) (9) (10) (11)
Weterings & Chen 2008 Cell Res 18
(12) (13) (14) (15) (a) (b) (c) (d)
DSB formation from labile sites Processing of DSB from labile sites before synapsis Inhibition of Ku70/Ku80 attachment Release from Ku70/Ku80 attachment inhibition Ku70/Ku80 attachment to DNA Ku70/Ku80-DNA dissociation DNA-PKcs attachment to DNA DNA-PK – DNA dissociation Synapsis Phosphorylation, recruitment and action of nucleases, polymerases, ligases Cleaning of single-strand breaks and base lesions Final ligation and removal of repair enzymes Inhibition of final ligation Release form inhibition of final ligation Correct rejoining Ring formation Chromosomal exchange aberration Incorrect joining other than (b) and (c)
DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Repair kinetics compared to experiments • By case adapted repair model as temporary solution:
repair outcome over time (for a certain radiation type and dose)
Increased fraction of slow rejoining DSB with increasing LET of N ions (Stenerlöw et al 2000) is well reproduced by the calculation. But too many free parameters and high uncertainty regarding data from experiments! Need to reduce parameters and uncertainties by better data (if possible) and testing hypotheses. Ongoing DSB generation from labile sites Relevant nearby lesions Limited availability of repair enzymes
Calculation of DSB repair after N ion and 60Co γ irradiation Friedland et al. (2011) Mutat Res 711
Yield of DNA fragments in detectable range Friedland et al. (2012) Int J Radiat Biol 88 DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Microdosimetric modelling with PARTRAC code
Dose dependence of DNA repair at low low--LET • DNA repair result depends on dose (for low-LET radiation):
repair outcome over dose (for a certain radiation type and time endpoint)
Possibility of sub-lethal damage repair Model for X-rays at high doses was extrapolated to low doses (with good results).
Testing different repair hypotheses
Dose-dependent DSB mis-rejoining Exp. (X-rays): Rydberg et al., Radiat Res 163 (2005)
Dose-dependent yield of chromosomal aberrations Exp.: Nasonova et al 2004 Int J Radiat Biol 80 DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Application examples of PARTRAC in radiation protection and medical physics
DoReMi Initium low dose (with A. Ottolenghi, Ottolenghi, Univ. Pavia & M. Dingfelder,, Univ. East Carolina) Dingfelder • Investigation of low-dose effects (DoReMi): Simulating biological damage of low-energy ions at distal Bragg peak region in hadron therapy and neutron irradiation [1, 2].
Development of new Barkas scaling method (including charge transfer) for ions heavier than He at low energies ≤ 1 MeV/u and scoring of range, stopping power, SSB & DSB yields for varying parameters such as initial energy, mean LET and dose. Still uncertainties for range, SP, dose, DSB yields in codes and measured data.
[1] Schmitt, Friedland, Kundrát, Dingfelder, Ottolenghi: “Cross section scaling for track structure simulations of low-energy ions in liquid water” (2015, Rad Prot Dosim 166, 15-18) [2] Schmitt, Friedland, Kundrát, Li: “PARTRAC – Recent developments towards medical applications” (2015, Poster Annual GBS workshop Dresden Germany) DoReMi LD-RadStats workshop CREAL, Barcelona, 27th October 2015
Application examples of PARTRAC in radiation protection and medical physics
DoReMi Initium low dose (with A. Ottolenghi, Ottolenghi, Univ. Pavia & S. Tapio, Tapio, HMGU München) München) •
Investigation of low-dose effects (DoReMi): Simulating side effects on heart mitochondria and especially their mtDNA as possible new sub-cellular target when exposed to low-dose during breast cancer therapy [3].
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Damage to mitochondria can lead to bystander effects or cause severe diseases including carcinogenesis and cardiovascular effects. Barjaktarovic et al (2011) reported deregulation of genes even at 0.2 Gy. But calculated mtDNA damage of 0.015% per Gy is seen not to be critical.
Development of mtDNA model with set-up for 1000 mitochondria (each with 10 mtDNA copies) in cytoplasm of coronar cell model and DNA damage scoring for simulation of 60Co photons and 5 MeV α-irradiation. 1000 mitochondria distributed in cytoplasm with 10 mtDNA copies each (= 0.167 Gbp) to mimic heart cells.
Circular mtDNA molecule of 16.6 kbp (CG 44 %). 180° U-turns every 20 bp, size
