Abstract
Cells encounter DNA damage induced by both endogenous and exogenous factors, and have evolved damage-specific repair pathways. DNA is an important of target radiation. The most significant types of DNA damage are base lesions, single-strand breaks, and double-strand breaks. Any of these types of damage acts as a substrate for the specific repair pathway. Cells that are not able to properly repair DNA damage undergo cell death or the unrepaired and imprecisely repaired DNA damage can cause of mutations and chromosomal aberrations. Proton beams (PBs) induce DNA damage and majorityof them are repaired without significant biological consequences. However, some DNA damage is more difficult to repair and leads to cell death. Understanding the cascading events in both normal and cancer cells after exposure to PBs is crucial for the development of efficient PB-based therapies and successful space missions. The focus of the current chapter is PB-induced DNA damage and related repair pathways.
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References
Vysin L, Pachnerova Brabcova K, Stepan V, Moretto-Capelle P, Bugler B, Legube G et al (2015) Proton-induced direct and indirect damage of plasmid DNA. Radiat Environ Biophys 54(3):343–352. https://doi.org/10.1007/s00411-015-0605-6
Zenkoh J, Gerelchuluun A, Wang Y, Miwa Y, Ohno T, Tsuboi K (2017) The abscopal effect induced by in situ -irradiated peripheral tumor cells in a murine GL261 brain tumor model. Transl Cancer Res 6(1):136–148
Edwards AA, Lloyd DC, Prosser JS, Finnon P, Moquet JE (1986) Chromosome aberrations induced in human lymphocytes by 8.7 MeV protons and 23.5 MeV helium-3 ions. Int J Radiat Biol Relat Stud Phys Chem Med 50(1):137–145
Mitteer RA, Wang YL, Shah J, Gordon S, Fager M, Butter PP et al (2015) Proton beam radiation induces DNA damage and cell apoptosis in glioma stem cells through reactive oxygen species. Sci Rep 5:13961. https://doi.org/10.1038/Srep13961
Hong Z, Kase Y, Moritake T, Gerelchuluun A, Sun L, Suzuki K et al (2013) Lineal energy-based evaluation of oxidative DNA damage induced by proton beams and X-rays. Int J Radiat Biol 89(1):36–43. https://doi.org/10.3109/09553002.2012.715791
Lindahl T (1993) Instability and decay of the primary structure of DNA. Nature 362(6422):709–715. https://doi.org/10.1038/362709a0
Dalhus B, Laerdahl JK, Backe PH, Bjoras M (2009) DNA base repair--recognition and initiation of catalysis. FEMS Microbiol Rev 33(6):1044–1078. https://doi.org/10.1111/j.1574-6976.2009.00188.x
Maki H, Sekiguchi M (1992) MutT protein specifically hydrolyses a potent mutagenic substrate for DNA synthesis. Nature 355(6357):273–275. https://doi.org/10.1038/355273a0
Tommasino F, Durante M (2015) Proton Radiobiology. Cancer 7(1):353
Chaudhary P, Marshall TI, Currell FJ, Kacperek A, Schettino G, Prise KM (2016) Variations in the processing of DNA double-strand breaks along 60-MeV therapeutic proton beams. Int J Radiat Oncol Biol Phys 95(1):86–94. https://doi.org/10.1016/j.ijrobp.2015.07.2279
Wouters BG, Skarsgard LD, Gerweck LE, Carabe-Fernandez A, Wong M, Durand RE et al (2015) Radiobiological intercomparison of the 160 MeV and 230 MeV proton therapy beams at the Harvard Cyclotron Laboratory and at Massachusetts General Hospital (vol 183, pg 174, 2015). Radiat Res 183(4):E51. https://doi.org/10.1667/RROL13.1
Gerelchuluun A, Hong Z, Sun L, Suzuki K, Terunuma T, Yasuoka K et al (2011) Induction of in situ DNA double-strand breaks and apoptosis by 200 MeV protons and 10 MV X-rays in human tumour cell lines. Int J Radiat Biol 87(1):57–70. https://doi.org/10.3109/09553002.2010.518201
George KA, Hada M, Chappell L, Cucinotta FA (2013) Biological effectiveness of accelerated particles for the induction of chromosome damage: track structure effects. Radiat Res 180(1):25–33. https://doi.org/10.1667/RR3291.1
Ibanez IL, Bracalente C, Molinari BL, Palmieri MA, Policastro L, Kreiner AJ et al (2009) Induction and rejoining of DNA double strand breaks assessed by H2AX phosphorylation in melanoma cells irradiated with proton and lithium beams. Int J Radiat Oncol Biol Phys 74(4):1226–1235. https://doi.org/10.1016/j.ijrobp.2009.02.070
Abraham RT (2001) Cell cycle checkpoint signaling through the ATM and ATR kinases. Genes Dev 15(17):2177–2196. https://doi.org/10.1101/gad.914401
Marechal A, Zou L (2013) DNA damage sensing by the ATM and ATR kinases. Cold Spring Harb Perspect Biol 5(9):a012716. https://doi.org/10.1101/cshperspect.a012716
College O. Control of the cell cycle.. OpneStax CNX. 2015.
Lim S, Kaldis P (2013) Cdks, cyclins and CKIs: roles beyond cell cycle regulation. Development 140(15):3079–3093. https://doi.org/10.1242/dev.091744
Falck J, Mailand N, Syljuasen RG, Bartek J, Lukas J (2001) The ATM-Chk2-Cdc25A checkpoint pathway guards against radioresistant DNA synthesis. Nature 410(6830):842–847. https://doi.org/10.1038/35071124
Khosravi R, Maya R, Gottlieb T, Oren M, Shiloh Y, Shkedy D (1999) Rapid ATM-dependent phosphorylation of MDM2 precedes p53 accumulation in response to DNA damage. Proc Natl Acad Sci U S A 96(26):14973–14977
Hirao A, Kong YY, Matsuoka S, Wakeham A, Ruland J, Yoshida H et al (2000) DNA damage-induced activation of p53 by the checkpoint kinase Chk2. Science 287(5459):1824–1827
Ferretti LP, Lafranchi L, Sartori AA (2013) Controlling DNA-end resection: a new task for CDKs. Front Genet 4:99. https://doi.org/10.3389/fgene.2013.00099
Tomimatsu N, Mukherjee B, Catherine Hardebeck M, Ilcheva M, Vanessa Camacho C, Louise Harris J et al (2014) Phosphorylation of EXO1 by CDKs 1 and 2 regulates DNA end resection and repair pathway choice. Nat Commun 5:3561. https://doi.org/10.1038/ncomms4561
Green LM, Murray DK, Bant AM, Kazarians G, Moyers MF, Nelson GA et al (2001) Response of thyroid follicular cells to gamma irradiation compared to proton irradiation. I. Initial characterization of DNA damage, micronucleus formation, apoptosis, cell survival, and cell cycle phase redistribution. Radiat Res 155(1 Pt 1):32–42
Yu S, Evans K, van Eijk P, Bennett M, Webster RM, Leadbitter M et al (2016) Global genome nucleotide excision repair is organized into domains that promote efficient DNA repair in chromatin. Genome Res 26(10):1376–1387. https://doi.org/10.1101/gr.209106.116
Nakanishi S, Prasad R, Wilson SH, Smerdon M (2007) Different structural states in oligonucleosomes are required for early versus late steps of base excision repair. Nucleic Acids Res 35(13):4313–4321. https://doi.org/10.1093/nar/gkm436
Carter RJ, Parsons JL (2016) Base excision repair, a pathway regulated by posttranslational modifications. Mol Cell Biol 36(10):1426–1437. https://doi.org/10.1128/MCB.00030-16
Xie Y, Yang H, Cunanan C, Okamoto K, Shibata D, Pan J et al (2004) Deficiencies in mouse Myh and Ogg1 result in tumor predisposition and G to T mutations in codon 12 of the K-ras oncogene in lung tumors. Cancer Res 64(9):3096–3102
Krokan HE, Bjoras M (2013) Base excision repair. Cold Spring Harb Perspect Biol 5(4):a012583. https://doi.org/10.1101/cshperspect.a012583
Jacobs AL, Schar P (2012) DNA glycosylases: in DNA repair and beyond. Chromosoma 121(1):1–20. https://doi.org/10.1007/s00412-011-0347-4
Tell G, Quadrifoglio F, Tiribelli C, Kelley MR (2009) The many functions of APE1/Ref-1: not only a DNA repair enzyme. Antioxid Redox Signal 11(3):601–620. https://doi.org/10.1089/ars.2008.2194
Doetsch PW, Cunningham RP (1990) The enzymology of apurinic/apyrimidinic endonucleases. Mutat Res 236(2-3):173–201
Svilar D, Goellner EM, Almeida KH, Sobol RW (2011) Base excision repair and lesion-dependent subpathways for repair of oxidative DNA damage. Antioxid Redox Signal 14(12):2491–2507. https://doi.org/10.1089/ars.2010.3466
Sobol RW, Wilson SH (2001) Mammalian DNA beta-polymerase in base excision repair of alkylation damage. Prog Nucleic Acid Res Mol Biol 68:57–74
Akbari M, Pena-Diaz J, Andersen S, Liabakk NB, Otterlei M, Krokan HE (2009) Extracts of proliferating and non-proliferating human cells display different base excision pathways and repair fidelity. DNA Repair 8(7):834–843. https://doi.org/10.1016/j.dnarep.2009.04.002
Matsumoto Y, Kim K (1995) Excision of deoxyribose phosphate residues by DNA polymerase beta during DNA repair. Science 269(5224):699–702
Podlutsky AJ, Dianova II, Podust VN, Bohr VA, Dianov GL (2001) Human DNA polymerase beta initiates DNA synthesis during long-patch repair of reduced AP sites in DNA. EMBO J 20(6):1477–1482. https://doi.org/10.1093/emboj/20.6.1477
Craggs TD, Hutton RD, Brenlla A, White MF, Penedo JC (2014) Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates. Nucleic Acids Res 42(3):1857–1872. https://doi.org/10.1093/nar/gkt1116
Gao Y, Katyal S, Lee Y, Zhao J, Rehg JE, Russell HR et al (2011) DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair. Nature 471(7337):240–244. https://doi.org/10.1038/nature09773
Sugasawa K, Okamoto T, Shimizu Y, Masutani C, Iwai S, Hanaoka F (2001) A multistep damage recognition mechanism for global genomic nucleotide excision repair. Genes Dev 15(5):507–521. https://doi.org/10.1101/gad.866301
Scrima A, Konickova R, Czyzewski BK, Kawasaki Y, Jeffrey PD, Groisman R et al (2008) Structural basis of UV DNA-damage recognition by the DDB1-DDB2 complex. Cell 135(7):1213–1223. https://doi.org/10.1016/j.cell.2008.10.045
Yeh JI, Levine AS, Du S, Chinte U, Ghodke H, Wang H et al (2012) Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair. Proc Natl Acad Sci U S A 109(41):E2737–E2746. https://doi.org/10.1073/pnas.1110067109
Evans E, Moggs JG, Hwang JR, Egly JM, Wood RD (1997) Mechanism of open complex and dual incision formation by human nucleotide excision repair factors. EMBO J 16(21):6559–6573. https://doi.org/10.1093/emboj/16.21.6559
Tapias A, Auriol J, Forget D, Enzlin JH, Scharer OD, Coin F et al (2004) Ordered conformational changes in damaged DNA induced by nucleotide excision repair factors. J Biol Chem 279(18):19074–19083. https://doi.org/10.1074/jbc.M312611200
Saijo M, Takedachi A, Tanaka K (2011) Nucleotide excision repair by mutant xeroderma pigmentosum group A (XPA) proteins with deficiency in interaction with RPA. J Biol Chem 286(7):5476–5483. https://doi.org/10.1074/jbc.M110.172916
Saijo M, Matsuda T, Kuraoka I, Tanaka K (2004) Inhibition of nucleotide excision repair by anti-XPA monoclonal antibodies which interfere with binding to RPA, ERCC1, and TFIIH. Biochem Biophys Res Commun 321(4):815–822. https://doi.org/10.1016/j.bbrc.2004.07.030
Li L, Peterson CA, Lu X, Legerski RJ (1995) Mutations in XPA that prevent association with ERCC1 are defective in nucleotide excision repair. Mol Cell Biol 15(4):1993–1998
Fagbemi AF, Orelli B, Scharer OD (2011) Regulation of endonuclease activity in human nucleotide excision repair. DNA Repair 10(7):722–729. https://doi.org/10.1016/j.dnarep.2011.04.022
O’Donovan A, Davies AA, Moggs JG, West SC, Wood RD (1994) XPG endonuclease makes the 3′ incision in human DNA nucleotide excision repair. Nature 371(6496):432–435. https://doi.org/10.1038/371432a0
Sijbers AM, van der Spek PJ, Odijk H, van den Berg J, van Duin M, Westerveld A et al (1996) Mutational analysis of the human nucleotide excision repair gene ERCC1. Nucleic Acids Res 24(17):3370–3380
Gerelchuluun A, Manabe E, Ishikawa T, Sun L, Itoh K, Sakae T et al (2015) The major DNA repair pathway after both proton and carbon-ion radiation is NHEJ, but the HR pathway is more relevant in carbon ions. Radiat Res 183(3):345–356. https://doi.org/10.1667/RR13904.1
Daley JM, Wilson TE (2005) Rejoining of DNA double-strand breaks as a function of overhang length. Mol Cell Biol 25(3):896–906. https://doi.org/10.1128/MCB.25.3.896-906.2005
Rothkamm K, Kruger I, Thompson LH, Lobrich M (2003) Pathways of DNA double-strand break repair during the mammalian cell cycle. Mol Cell Biol 23(16):5706–5715
Dibiase SJ, Zeng ZC, Chen R, Hyslop T, Curran WJ, Iliakis G (2000) DNA-dependent protein kinase stimulates an independently active, nonhomologous, end-joining apparatus. Cancer Res 60(5):1245–1253
Cheng Q, Barboule N, Frit P, Gomez D, Bombarde O, Couderc B et al (2011) Ku counteracts mobilization of PARP1 and MRN in chromatin damaged with DNA double-strand breaks. Nucleic Acids Res 39(22):9605–9619. https://doi.org/10.1093/nar/gkr656
Mimitou EP, Symington LS (2010) Ku prevents Exo1 and Sgs1-dependent resection of DNA ends in the absence of a functional MRX complex or Sae2. EMBO J 29(19):3358–3369. https://doi.org/10.1038/emboj.2010.193
Clerici M, Mantiero D, Guerini I, Lucchini G, Longhese MP (2008) The Yku70-Yku80 complex contributes to regulate double-strand break processing and checkpoint activation during the cell cycle. EMBO Rep 9(8):810–818. https://doi.org/10.1038/embor.2008.121
Ma Y, Pannicke U, Schwarz K, Lieber MR (2002) Hairpin opening and overhang processing by an Artemis/DNA-dependent protein kinase complex in nonhomologous end joining and V(D)J recombination. Cell 108(6):781–794
Niewolik D, Pannicke U, Lu H, Ma Y, Wang LC, Kulesza P et al (2006) DNA-PKcs dependence of Artemis endonucleolytic activity, differences between hairpins and 5′ or 3′ overhangs. J Biol Chem 281(45):33900–33909. https://doi.org/10.1074/jbc.M606023200
Mahajan KN, Nick McElhinny SA, Mitchell BS, Ramsden DA (2002) Association of DNA polymerase mu (pol mu) with Ku and ligase IV: role for pol mu in end-joining double-strand break repair. Mol Cell Biol 22(14):5194–5202
Lee JW, Blanco L, Zhou T, Garcia-Diaz M, Bebenek K, Kunkel TA et al (2004) Implication of DNA polymerase lambda in alignment-based gap filling for nonhomologous DNA end joining in human nuclear extracts. J Biol Chem 279(1):805–811. https://doi.org/10.1074/jbc.M307913200
Ma Y, Lu H, Tippin B, Goodman MF, Shimazaki N, Koiwai O et al (2004) A biochemically defined system for mammalian nonhomologous DNA end joining. Mol Cell 16(5):701–713. https://doi.org/10.1016/j.molcel.2004.11.017
Nick McElhinny SA, Snowden CM, McCarville J, Ramsden DA (2000) Ku recruits the XRCC4-ligase IV complex to DNA ends. Mol Cell Biol 20(9):2996–3003
Jeggo PA, Geuting V, Lobrich M (2011) The role of homologous recombination in radiation-induced double-strand break repair. Radiother Oncol 101(1):7–12. https://doi.org/10.1016/j.radonc.2011.06.019
Burma S, Chen BP, Murphy M, Kurimasa A, Chen DJ (2001) ATM phosphorylates histone H2AX in response to DNA double-strand breaks. J Biol Chem 276(45):42462–42467. https://doi.org/10.1074/jbc.C100466200
Shibata A, Moiani D, Arvai AS, Perry J, Harding SM, Genois MM et al (2014) DNA double-strand break repair pathway choice is directed by distinct MRE11 nuclease activities. Mol Cell 53(1):7–18. https://doi.org/10.1016/j.molcel.2013.11.003
Kakarougkas A, Ismail A, Katsuki Y, Freire R, Shibata A, Jeggo PA (2013) Co-operation of BRCA1 and POH1 relieves the barriers posed by 53BP1 and RAP80 to resection. Nucleic Acids Res 41(22):10298–10311. https://doi.org/10.1093/nar/gkt802
Chapman JR, Sossick AJ, Boulton SJ, Jackson SP (2012) BRCA1-associated exclusion of 53BP1 from DNA damage sites underlies temporal control of DNA repair. J Cell Sci 125(Pt 15):3529–3534. https://doi.org/10.1242/jcs.105353
McVey M, Lee SE (2008) MMEJ repair of double-strand breaks (director’s cut): deleted sequences and alternative endings. Trends Genet 24(11):529–538. https://doi.org/10.1016/j.tig.2008.08.007
Nussenzweig A, Nussenzweig MC (2007) A backup DNA repair pathway moves to the forefront. Cell 131(2):223–225. https://doi.org/10.1016/j.cell.2007.10.005
Truong LN, Li Y, Shi LZ, Hwang PY, He J, Wang H et al (2013) Microhomology-mediated End Joining and Homologous Recombination share the initial end resection step to repair DNA double-strand breaks in mammalian cells. Proc Natl Acad Sci U S A 110(19):7720–7725. https://doi.org/10.1073/pnas.1213431110
Tartier L, Spenlehauer C, Newman HC, Folkard M, Prise KM, Michael BD et al (2003) Local DNA damage by proton microbeam irradiation induces poly(ADP-ribose) synthesis in mammalian cells. Mutagenesis 18(5):411–416
Zhang Y, Jasin M (2011) An essential role for CtIP in chromosomal translocation formation through an alternative end-joining pathway. Nat Struct Mol Biol 18(1):80–84. https://doi.org/10.1038/nsmb.1940
Kent T, Chandramouly G, McDevitt SM, Ozdemir AY, Pomerantz RT (2015) Mechanism of microhomology-mediated end-joining promoted by human DNA polymerase theta. Nat Struct Mol Biol 22(3):230–237. https://doi.org/10.1038/nsmb.2961
Wang M, Wu W, Wu W, Rosidi B, Zhang L, Wang H et al (2006) PARP-1 and Ku compete for repair of DNA double strand breaks by distinct NHEJ pathways. Nucleic Acids Res 34(21):6170–6182. https://doi.org/10.1093/nar/gkl840
Aylon Y, Liefshitz B, Kupiec M (2004) The CDK regulates repair of double-strand breaks by homologous recombination during the cell cycle. EMBO J 23(24):4868–4875. https://doi.org/10.1038/sj.emboj.7600469
Ira G, Pellicioli A, Balijja A, Wang X, Fiorani S, Carotenuto W et al (2004) DNA end resection, homologous recombination and DNA damage checkpoint activation require CDK1. Nature 431(7011):1011–1017. https://doi.org/10.1038/nature02964
Shibata A, Conrad S, Birraux J, Geuting V, Barton O, Ismail A et al (2011) Factors determining DNA double-strand break repair pathway choice in G2 phase. EMBO J 30(6):1079–1092. https://doi.org/10.1038/emboj.2011.27
Sartori AA, Lukas C, Coates J, Mistrik M, Fu S, Bartek J et al (2007) Human CtIP promotes DNA end resection. Nature 450(7169):509–514. https://doi.org/10.1038/nature06337
Nimonkar AV, Genschel J, Kinoshita E, Polaczek P, Campbell JL, Wyman C et al (2011) BLM-DNA2-RPA-MRN and EXO1-BLM-RPA-MRN constitute two DNA end resection machineries for human DNA break repair. Genes Dev 25(4):350–362. https://doi.org/10.1101/gad.2003811
Bizard AH, Hickson ID (2014) The dissolution of double Holliday junctions. Cold Spring Harb Perspect Biol 6(7):a016477. https://doi.org/10.1101/cshperspect.a016477
George KA, Hada M, Cucinotta FA (2015) Biological effectiveness of accelerated protons for chromosome exchanges. Front Oncol 5:226. https://doi.org/10.3389/fonc.2015.00226
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Gerelchuluun, A. (2020). DNA Damage, Repair Mechanisms, and Chromosomal Aberrations. In: Tsuboi, K., Sakae, T., Gerelchuluun, A. (eds) Proton Beam Radiotherapy. Springer, Singapore. https://doi.org/10.1007/978-981-13-7454-8_15
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