Modelling and Measurement of Simple and Complex DNA Damage Induction by Ion Irradiation A thesis submitted to the University of Manchester for the degree of Doctor of Philosophy in the Faculty of Biology, Medicine and Health 2018 Nicholas T. Henthorn School of Medical Sciences Division of Cancer Sciences Contents 1. Introduction ...................................................................................17 1.1 Cancer ............................................................................................... 17 1.1.1 Incidence and Prevalence............................................................................. 17 1.1.2 Biology ............................................................................................................. 17 1.2 External Beam Radiotherapy .......................................................... 18 1.2.2 In Practice ........................................................................................................ 18 1.2.2 Photons ............................................................................................................ 19 1.2.3 Particles ........................................................................................................... 24 1.3 Proton Beam Therapy ..................................................................... 25 1.3.1 Delivery Techniques ...................................................................................... 27 1.3.2 Benefits ............................................................................................................ 30 1.3.3 Linear Energy Transfer .................................................................................. 31 1.3.4 Uncertainties and Areas of Research ......................................................... 34 1.4 Relative Biological Effectiveness .................................................. 36 1.4.1 Definition .......................................................................................................... 36 1.4.2 Experimental Data .......................................................................................... 39 1.4.3 RBE = 1.1 ........................................................................................................ 43 1.4.4 Clinical Implications ....................................................................................... 44 1.4.5 Phenomenological Models ............................................................................ 45 1.5 DNA Damage, Nanodosimetry, and DNA Repair .......................... 50 1.6 Modelling .......................................................................................... 54 1.6.1 Current Models ............................................................................................... 56 1.6.2 Mechanistic Models ....................................................................................... 61 1.6.3 Track Structure Codes................................................................................... 63 1.7 Geant4-DNA ...................................................................................... 66 1.7.1 Physics ............................................................................................................. 66 1.7.2 Chemistry......................................................................................................... 69 1.8 Summary and Aims ......................................................................... 70 2. Nanodosimetric Simulation of Direct Ion-Induced DNA Damage Using Different Chromatin Geometry Models ...............73 2.1 Introduction ...................................................................................... 76 2.2 Methods............................................................................................. 79 2.2.1 Model of DNA and Chromatin Geometries................................................. 79 2.2.2 Track Structure Simulation and Irradiation Details ................................... 81 2.2.3 Scoring of Clusters ......................................................................................... 82 2 2.2.4 Nanodosimetric Parameters ......................................................................... 83 2.3 Results .............................................................................................. 84 2.3.1 Damaged Backbone Cluster Size Distribution........................................... 84 2.3.2 Conditional Average Cluster Size (m1) ....................................................... 86 2.3.3 Relative Cumulative Distributions (F2 and F3) ........................................... 87 2.3.4 SSB to DSB Ratio .......................................................................................... 89 2.3.5 The Effect of Backbone Size ........................................................................ 90 2.4 Discussion ........................................................................................ 92 2.4.1 Chromatin Model Comparison ..................................................................... 92 2.4.2 Damage Complexity....................................................................................... 93 2.5 Summary and Conclusions ............................................................ 95 2.6 Acknowledgements ......................................................................... 96 3. Nanodosimetric Simulation of DNA Damage from Protons and Across a Clinically Relevant Proton Spread Out Bragg Peak with Direct and Indirect Effects ...............................................................97 3.1 Introduction ...................................................................................... 99 3.2 Methods........................................................................................... 101 3.2.1 Models of DNA Geometry ........................................................................... 101 3.2.2 Track Structure Simulation ......................................................................... 104 3.2.3 Direct and Indirect DNA Damage .............................................................. 105 3.2.4 Damage Classification ................................................................................. 106 3.2.5 Simulation of Plasmid Irradiation ............................................................... 108 3.2.6 Simulation of Chromatin Fibre Irradiation ................................................. 110 3.2.7 Total Damage Yields in a Cell Model ........................................................ 111 3.3 Results ............................................................................................ 112 3.3.1 Direct DNA Damage - Plasmid Irradiation ................................................ 112 3.3.2 Indirect DNA Damage – Chromatin Irradiation ........................................ 113 3.3.3 Damage Complexity..................................................................................... 114 3.3.4 Damage Complexity Distribution ............................................................... 116 3.3.5 Clinically Relevant Considerations ............................................................ 118 3.4 Discussion ...................................................................................... 119 3.5 Summary and Conclusions .......................................................... 122 3.6 Acknowledgements ....................................................................... 123 4. In Silico Non-Homologous End Joining Following Ion Induced DNA Double Strand Breaks Predicts That Repair Fidelity Depends on Break Density ........................................................... 124 3 4.1 Introduction .................................................................................... 126 4.2 Methods........................................................................................... 129 4.2.1 Simulation of DSBs ...................................................................................... 129 4.2.2 Non-Homologous End Joining Repair Model .......................................... 130 4.2.3 Data Availability ............................................................................................ 131 4.3 Results ............................................................................................ 131 4.3.1 Misrepair and LET ........................................................................................ 131 4.3.2 Cluster Density, Misrepair, and Residual DSBs ...................................... 134 4.3.3 Residual and Misrepaired DSB Yields ...................................................... 137 4.4 Discussion and Conclusions ....................................................... 139 4.5 Acknowledgements ....................................................................... 143 5. SDD: A Standardised Data Format to Record DNA Damage 144 5.1 Introduction .................................................................................... 145 5.2 The New Standard to Record DNA Damage ............................... 148 5.2.1 Website and Updates .................................................................................. 149 5.2.2 Header ........................................................................................................... 149 5.2.3 The Data Block ............................................................................................. 154 5.2.4 Dissemination and Repository ................................................................... 162 5.3 Discussion and Conclusions ......................................................