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Inadequate DNA repair leads to Increase, Mutations
Key Event Relationship Overview
AOPs Referencing Relationship
|AOP Name||Adjacency||Weight of Evidence||Quantitative Understanding||Point of Contact||Author Status||OECD Status|
|Alkylation of DNA in male pre-meiotic germ cells leading to heritable mutations||adjacent||High||Moderate||Carole Yauk (send email)||Open for citation & comment||WPHA/WNT Endorsed|
|Alkylation of DNA leading to cancer 2||adjacent||High||Moderate||Carole Yauk (send email)||Not under active development|
|Alkylation of DNA leading to cancer 1||non-adjacent||High||Moderate||Carole Yauk (send email)||Open for adoption|
|Oxidative DNA damage leading to chromosomal aberrations and mutations||adjacent||High||Low||Carole Yauk (send email)||Open for comment. Do not cite||EAGMST Under Review|
|Deposition of energy leading to lung cancer||adjacent||Moderate||Moderate||Vinita Chauhan (send email)||Under development: Not open for comment. Do not cite||EAGMST Approved|
|Bulky DNA adducts leading to mutations||adjacent||Carole Yauk (send email)||Under development: Not open for comment. Do not cite|
|DNA damage and mutations leading to Metastatic Breast Cancer||adjacent||High||High||Usha Adiga (send email)||Under development: Not open for comment. Do not cite|
Life Stage Applicability
|All life stages||High|
Key Event Relationship Description
Insufficient repair results in the retention of damaged DNA that is then used as a template during DNA replication. During replication of damaged DNA, incorrect nucleotides may be inserted, and upon replication these become ‘fixed’ in the cell. Further replication propagates the mutation to additional cells.
For example, it is well established that replication of alkylated DNA can cause insertion of an incorrect base in the DNA duplex (i.e., mutation). Replication of non-repaired O4 thymine alkylation leads primarily to A:T→G:C transitions. Retained O6 guanine alkylation causes primarily G:C→A:T transitions.
For repairing DNA double strand breaks (DSBs), non-homologous end joining (NHEJ) is one of the repair mechanisms used in human somatic cells (Petrini et al., 1997; Mao et al., 2008). However, this mechanism is error-prone and may create mutations during the process of DNA repair (Little, 2000). NHEJ is considered error-prone because it does not use a homologous template to repair the DSB. The NHEJ mechanism involves many proteins that work together to bridge the DSB gap by overlapping single-strand termini that are usually less than 10 nucleotides long (Anderson, 1993; Getts & Stamato, 1994; Rathmell & Chu, 1994). Inherent in this process is the introduction of errors that may result in mutations such as insertions, deletions, inversions, or translocations.
Evidence Supporting this KER
If DNA repair is able to correctly and efficiently repair DNA lesions introduced by a genotoxic stressor, then no increase in mutation frequency will occur.
For example, for alkylated DNA, efficient removal by AGT will result in no increases in mutation frequency. However, above a certain dose AGT becomes saturated and is no longer able to efficiently remove the alkyl adducts. Replication of O-alkyl adducts leads to mutation. The evidence demonstrating that replication of unrepaired O-alkylated DNA causes mutations is extensive in somatic cells and has been reviewed (Basu and Essigmann 1990; Shrivastav et al. 2010); specific examples are given below.
It is important to note that not all DNA lesions will cause mutations. It is well documented that many are bypassed error-free. For example, N-alkyl adducts can quite readily be bypassed error-free with no increase in mutations (Philippin et al., 2014).
Inadequate repair of DSB
Collective data from tumors and tumor cell lines has emerged that suggests that DNA repair mechanisms may be error-prone (reviewed in Sishc et al., 2017) (Sishc & Davis, 2017). NHEJ, the most common pathway used to repair DSBs, has been described as error-prone. The error-prone nature of NHEJ, however, is thought to be dependent on the structure of the DSB ends being repaired, and not necessarily dependent on the NHEJ mechanism itself (Bétermier et al., 2014). Usually when perfectly cohesive ends are formed as a result of a DSB event, ligase 4 (LIG4) will have limited end processing to perform, thereby keeping ligation errors to a minimum (Waters et al., 2014). When the ends are difficult to ligate, however, the resulting repair may not be completed properly; this often leads to point mutations and other chromosomal rearrangements. It has been shown that approximately 25 - 50% of DSBs are misrejoined after exposure to ionizing radiation (Löbrich et al., 1998; Kuhne et al., 2000; Lobrich et al., 2000). Defective repair mechanisms can increase sensitivity to agents that induce DSBs and lead eventually to genomic instability (reviewed in Sishc et al., (2017)).
Activation of mutagenic DNA repair pathways to withstand cellular or replication stress either from endogenous or exogenous sources can promote cellular viability, albeit at a cost of increased genome instability and mutagenesis (Fitzgerald et al., 2017). These salvage DNA repair pathways including, Break-induced Replication (BIR) and Microhomology-mediated Break-induced Replication (MMBIR). BIR repairs one-ended DSBs and has been extensively studied in yeast as well as in mammalian systems. BIR and MMBIR are linked with heightened levels of mutagenesis, chromosomal rearrangements and ensuing genome instability (Deem et al., 2011; Sakofsky et al., 2015; Saini et al., 2017; Kramara et al., 2018). In mammalian genomes BIR-like synthesis has been proposed to be involved in late stage Mitotic DNA Synthesis (MiDAS) that predominantly occurs at so-called Common Fragile Sites (CFSs) and maintains telomere length under s conditions of replication stress that serve to promote cell viability (Minocherhomji et al., 2015; Bhowmick et al., 2016; Dilley et al., 2016).
Uncertainties and Inconsistencies
Repair of alkylated DNA
There were no inconsistencies in the empirical data reviewed or in the literature relating to biological plausibility. Much of the support for this KER comes predominantly from data in somatic cells and in prokaryotic organisms. We note that all of the data in germ cells used in this KER are produced exclusively from ENU exposure. Data on other chemicals are required. We consider the overall weight of evidence of this KER to be strong because of the obvious biological plausibility of the KER, and documented temporal association and incidence concordance based on studies over-expressing and repressing DNA repair in somatic cells.
Repair of oxidative lesions
- Thresholded concentration-response curve of mutation frequency was observed in AHH-1 human lymphoblastoid cells after treatment with pro-oxidants (H2O2 and KBrO2) known to cause oxidative DNA damage (Seager et al., 2012), suggesting that cells are able to tolerate low levels of DNA damage using basal repair. However, increase in 8-oxo-dG lesions and up-regulation of DNA repair proteins were not observed under the same experimental condition.
- Mutagenicity of oxidative DNA lesions other than 8-oxo-dG, such as FaPydG and thymidine glycol, has not been as extensively studied and there are mixed results regarding the mutagenic outcome of these lesions.
- Mutation induction is stochastic, spontaneous, and dependent on the cell type as well as the individual’s capability to repair efficiently (NRC, 1990; Pouget & Mather, 2001).
Inadequate Repair of DSB
There is evidence of a response-response relationship between inadequate DNA repair and increased frequency of mutations. When exposed to a radiation stressor, there was a positive relationship between the radiation dose and the DSB misrepair rate, and between the mutation rate and the radiation dose (Mcmahon et al., 2016). Similarly, there was a negative correlation found between NER and the mutation densities at specific genomic regions in cancer patients. Specifically, inadequate NER resulted in more mutations in the promoter DHS and the TSS, but normal NER at DHS flanking regions resulted in fewer mutations (Perera et al., 2016).
Inadequate Repair of DSB
Two studies were used to provide data regarding the time scale of DNA repair and the appearance of mutations. In a study using plants, DNA damage was evident immediately following radiation with 30 Gy of radiation; 50% of repairs were complete by 51.7 minutes, 80% by 4 hours, and repair was completed by 24 hours post-irradiation. Although no mutational analysis was performed during the period of repair, irradiated plants were found to have increased mutations when they were examined 2 - 3 weeks later (Ptácek et al., 2001). Both DNA repair and mutation frequency were examined at the same time in a study comparing simple and complex ligation of linearized plasmids. In this study, repaired plasmids were first detected between 6 - 12 hours for simple ligation events and between 12 - 24 hours for more complex ligation events; this first period was when the most error-free rejoining occurred in both cases. After this initial period of repair until its completion at 48 hr, repair became increasingly more erroneous such that mutations were found in more than half of the repaired plasmids at 48 hr regardless of the type of required ligation (Smith et al., 2001).
Known modulating factors
Known Feedforward/Feedback loops influencing this KER
Domain of Applicability
The domain of applicability is multicellular eukaryotes (Lieber, 2008; Hartlerode & Scully, 2009), plants (Gorbunova, 1997; Puchta, 2005), certain strains of bacteria such as Mycobacteria, Pseudomonas, Bacillus and Agrobacterium (Shuman & Glickman, 2007), and yeast (Wilson & Lieber, 1999).
All organisms, from prokaryotes to eukaryotes, have DNA repair systems. Indeed, much of the empirical evidence on the fundamental principles described in this KER are derived from prokaryotic models. DNA adducts can occur in any cell type, and may or may not be repaired, leading to mutation. While there are differences among DNA repair systems across eukaryotic taxa, all species develop mutations following excessive burdens of DNA lesions like DNA adducts. Theoretically, any sexually reproducing organism (i.e., producing gametes) can also acquire DNA lesions that may or may not be repaired, leading to mutations in gametes.
Albertini, R.J. et al. (1997), "Radiation Quality Affects the Efficiency of Induction and the Molecular Spectrum of HPRT Mutations in Human T Cells", 148(5 Suppl):S76-86.
Amundson, S.A. & D.J. Chen (1996), "Ionizing Radiation-Induced Mutation of Human Cells With Different DNA Repair Capacities.", Adv. Space Res. 18(1-2):119-126.
Anderson, C.W. 1993, "DNA damage and the DNA-activated protein kinase.", Trends Biochem. Sci. 18(11):433–437. doi:10.1016/0968-0004(93)90144-C.
Arai, T., Kelly, V.P., Minowa, O., Noda, T., Nishimura, S. (2002), High accumulation of oxidative DNA damage, 8-hydroxyguanine, in Mmh/Ogg1 deficient mice by chronic oxidative stress, Carcinogenesis, 23:2005-2010.
Basu, A.K. and J.M. Essigmann (1990), "Site-specific alkylated oligodeoxynucleotides: Probes for mutagenesis, DNA repair and the structure effects of DNA damage", Mutation Research, 233: 189-201.
Beranek, D.T. (1990), "Distribution of methyl and ethyl adducts following alkylation with monofunctional alkylating agents", Mutation Research, 231(1): 11-30.
Bétermier, M., P. Bertrand & B.S. Lopez (2014), "Is Non-Homologous End-Joining Really an Inherently Error-Prone Process?", PLoS Genet. 10(1). doi:10.1371/journal.pgen.1004086.
Bhowmick, R., S. Minocherhomji & I.D. Hickson (2016), "RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress", Mol. Cell., 64(6):1117-1126.
Dahle, J., Brunborg, G., Svendsrud, D., Stokke, T., Kvam, E. (2008), Overexpression of human OGG1 in mammalian cells decreases ultraviolet A induced mutagenesis, Cancer Lett, 267:18-25.
Deem, A. et al. (2011), "Break-Induced Replication Is Highly Inaccurate", PLoS Biol., 9(2):e1000594, doi: 10.1371/journal.pbio.1000594.
Dilley, R.L. et al. (2016), "Break-induced telomere synthesis underlies alternative telomere maintenance", Nature, 539:54-58.
Douglas, G.R., J. Jiao, J.D. Gingerich, J.A. Gossen and L.M. Soper (1995), "Temporal and molecular characteristics of mutations induced by ethylnitrosourea in germ cells isolated from seminiferous tubules and in spermatozoa of lacZ transgenic mice", Proc. Natl. Acad. Sci. USA, 92(16): 7485-7489.
Dubrova, Y.E. et al. (2002), "Elevated Minisatellite Mutation Rate in the Post-Chernobyl Families from Ukraine.", Am. J. Hum. Genet. 71(4): 801-809.
Ellison, K.S., E. Dogliotti, T.D. Connors, A.K. Basu and J.M. Essigmann (1989), "Site-specific mutagenesis by O6-alkyguanines located in the chromosomes of mammalian cells: Influence of the mammalian O6-alkylguanine-DNA alkyltransferase", Proc. Natl. Acad. Sci. USA, 86: 8620-8624.
Feldmann, E. et al. (2000), "DNA double-strand break repair in cell-free extracts from Ku80-deficient cells : implications for Ku serving as an alignment factor in non-homologous DNA end joining.", Nucleic Acids Res. 28(13):2585–2596.
Fitzgerald, D.M., P.J. Hastings, and S.M. Rosenberg (2017), "Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance", Ann. Rev. Cancer Biol., 1:119-140, doi: 10.1146/annurev-cancerbio-050216-121919.
Getts, R.C. & T.D. Stamato (1994), "Absence of a Ku-like DNA end binding activity in the xrs double-strand DNA repair-deficient mutant.", J. Biol. Chem. 269(23):15981–15984.
Gocke, E. and L. Muller (2009), "In vivo studies in the mouse to define a threhold for the genotoxicity of EMS and ENU", Mutat. Res., 678, 101-107.
Gorbunova, V. (1997), "Non-homologous DNA end joining in plant cells is associated with deletions and filler DNA insertions.", Nucleic Acids Res. 25(22):4650–4657. doi:10.1093/nar/25.22.4650.
Hartlerode, A.J. & R. Scully (2009), "Mechanisms of double-strand break in somatic mammalian cells.", Biochem J. 423(2):157–168. doi:10.1042/BJ20090942.Mechanisms.
Kaina, B., M. Christmann, S. Naumann and W.P. Roos (2007), "MGMT: Key node in the battle against genotoxicity, carcinogenicity and apoptosis induced by alkylating agents", DNA Repair, 6: 1079–1099.
Klungland, A., Rosewell, I., Hollenbach, S., Larsen, E., Daly, G., Epe, B., Seeberg, E., Lindahl, T., Barnes, D. (1999), Accumulation of premutagenic DNA lesions in mice defective in removal of oxidative base damage, Proc Natl Acad Sci USA, 96:13300-13305.
Kramara, J., B. Osia & A. Malkova (2018), "Break-Induced Replication: The Where, The Why, and The How", Trends Genet. 34(7):518-531, doi: 10.1016/j.tig.2018.04.002.
Kuhne, M., K. Rothkamm & M. Lobrich (2000), "No dose-dependence of DNA double-strand break misrejoining following a -particle irradiation.", Int. J. Radiat. Biol. 76(7):891-900
Lieber, M.R. (2008), "The mechanism of human nonhomologous DNA End joining.", J Biol Chem. 283(1):1–5. doi:10.1074/jbc.R700039200.
Little, J.B. (2000), "Radiation carcinogenesis.", Carcinogenesis 21(3):397-404 doi:10.1093/carcin/21.3.397.
Lobrich, M. et al. (2000), "Joining of Correct and Incorrect DNA Double-Strand Break Ends in Normal Human and Ataxia Telangiectasia Fibroblasts.", 68(July 1999):59–68. doi:DOI: 10.1002/(SICI)1098-2264(200001)27:1<59::AID-GCC8>3.0.CO;2-9.
Mao Z, Bozzella M, Seluanov A, Gorbunova V. 2008. DNA repair by nonhomologous end joining and homologous recombination during cell cycle in human cells. Cell Cycle. 7(18):2902–2906. doi:10.4161/cc.7.18.6679.
Matuo Y, Izumi Y, Furusawa Y, Shimizu K. 2018. Mutat Res Fund Mol Mech Mutagen Biological e ff ects of carbon ion beams with various LETs on budding yeast Saccharomyces cerevisiae. Mutat Res Fund Mol Mech Mutagen. 810(November 2017):45–51. doi:10.1016/j.mrfmmm.2017.10.003.
Mcmahon SJ, Schuemann J, Paganetti H, Prise KM. 2016. Mechanistic Modelling of DNA Repair and Cellular Survival Following Radiation-Induced DNA Damage. Nat Publ Gr.(April):1–14. doi:10.1038/srep33290.
Minocherhomji, S. et al. (2015), "Replication stress activates DNA repair synthesis in mitosis", Nature, 528(7581):286-290.
Minowa, O., Arai, T., Hirano, M., Monden, Y., Nakai, S., Fukuda, M., Itoh, M., Takano, H., Hippou, Y., Aburatani, H., Masumura, K., Nohmi, T., Nishimura, S., Noda, T. (2000), Mmh/Ogg1 gene inactivation results in accumulation of 8-hydroxyguanine in mice, Proc Natl Acad Sci USA, 97:4156-4161.
Muller, L., E. Gocke, T. Lave and T. Pfister (2009), "Ethyl methanesulfonate toxicity in Viracept – A comprehensive human risk assessment based on threshold data for genotoxicity", Toxicology Letters, 190: 317-329.
Nagashima, H. et al. (2018), "Induction of somatic mutations by low-dose X-rays : the challenge in recognizing radiation-induced events.", J. Radiat. Res., Na 59(October 2017):11–17. doi:10.1093/jrr/rrx053.
NRC (1990), "Health Effects of Exposure to Low Levels of Ionizing Radiation", (BEIR V).
O'Brien, J.M., A. Williams, J. Gingerich, G.R. Douglas, F. Marchetti and C.L. Yauk CL. (2013), "No evidence for transgenerational genomic instability in the F1 or F2 descendants of Muta™Mouse males exposed to N-ethyl-N-nitrosourea", Mutat. Res., 741-742:11-7
O’Brien, J.M., M. Walker, A. Sivathayalan, G.R. Douglas, C.L. Yauk and F. Marchetti (2015), "Sublinear response in lacZ mutant frequency of Muta™ Mouse spermatogonial stem cells after low dose subchronic exposure to N-ethyl-N-nitrosourea", Environ. Mol. Mutagen., 56(4): 347-55.
Pegg, A.E., (2011), "Multifaceted roles of alkyltransferase and related proteins in DNA repair, DNA damage, resistance to chemotherapy, and research tools", Chem. Res. Toxicol., 24(5): 618-639.
Perera, D. et al. (2016), "Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes.", Nature 532, 259-263.
Petrini, J.H.J., D.A. Bressan & M.S. Yao (1997), "The RAD52 epistasis group in mammalian double strand break repair.", Semin Immunol. 9(3):181–188. doi:10.1006/smim.1997.0067
Philippin, G., J. Cadet, D. Gasparutto, G. Mazon, R.P. Fuchs (2014), "Ethylene oxide and propylene oxide derived N7-alkylguanine adducts are bypassed accurately in vivo", DNA Repair (Amst), 22:133-6.
Pouget, J.P. & S.J. Mather (2001), "General aspects of the cellular response to low- and high-LET radiation.", Eur. J. Nucl. Med. 28(4):541–561. doi:10.1007/s002590100484
Ptácek, O. et al. (2001), "Induction and repair of DNA damage as measured by the Comet assay and the yield of somatic mutations in gamma-irradiated tobacco seedlings.", Mutat Res. 491(1-2):17–23
Puchta, H. (2005), "The repair of double-strand breaks in plants: Mechanisms and consequences for genome evolution.", J. Exp. Bot. 56(409):1–14. doi:10.1093/jxb/eri025
Pzoniak, A., L. Muller, M. Salgo, J.K. Jone, P. Larson and D. Tweats (2009), "Elevated ethyl methansulfonate in nelfinavir mesylate (Viracept, Roche): overview", Aids Research and Therapy, 6: 18.
Rathmell, W.K. & G. Chu (1994), "Involvement of the Ku autoantigen in the cellular response to DNA double-strand breaks.", Proc. Natl. Acad. Sci. 91(16):7623–7627. doi:10.1073/pnas.91.16.7623
Rodriguez, G.P., Song, J.B., Crouse, G.F. (2013), In Vivo Bypass of 8-oxodG, PLoS Genetics, 9:e1003682.
Sage, E. & N. Shikazono (2017), "Free Radical Biology and Medicine Radiation-induced clustered DNA lesions : Repair and mutagenesis ☆.", Free Radic. Biol. Med. 107(December 2016):125–135. doi:10.1016/j.freeradbiomed.2016.12.008
Saini, N. et al. (2017), "Migrating bubble during break-induced replication drives conservative DNA synthesis", Nature, 502:389-392.
Sakofsky, C.J. et al. (2015), "Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements", Mol. Cell, 60:860-872.
Sassa, A., Kamoshita, N., Kanemaru, Y., Honma, M., Yasui, M. (2015), Xeroderma Pigmentosum Group A Suppresses Mutagenesis Caused by Clustered Oxidative DNA Adducts in the Human Genome, PLoS One, 10:e0142218.
Seager, A., Shah, U., Mikhail, J., Nelson, B., Marquis, B., Doak, S., Johnson, G., Griffiths, S., Carmichael, P., Scott, S., Scott, A., Jenkins, G. (2012), Pro-oxidant Induced DNA Damage in Human Lymphoblastoid Cells: Homeostatic Mechanisms of Genotoxic Tolerance, Toxicol Sci, 128:387-397.
Shelby, M.D. and K.R. Tindall (1997), "Mammalian germ cell mutagenicity of ENU, IPMS and MMS, chemicals selected for a transgenic mouse collaborative study. Mutation Research 388(2-3):99-109.
Shrivastav, N., D. Li and J.M. Essignmann (2010), "Chemical biology of mutagenesis and DNA repair: cellular response to DNA alkylation", Carcinogenesis, 31(1): 59-70.
Shuman, S. & M.S. Glickman (2007), "Bacterial DNA repair by non-homologous end joining.", Nat. Rev. Microbiol. 5(11):852–861. doi:10.1038/nrmicro1768.
Singer, B., F. Chavez, M.F. Goodman, J.M. Essigman and M.K. Dosanjh (1989), "Effect of 3' flanking neighbors on kinetics of pairing of dCTP or dTTP opposite O6-methylguanine in a defined primed oligonucleotide when Escherichia coli DNA polymerase I is used", Proc. Natl. Acad. Sci. USA, 86(21): 8271-8274.
Sishc-Brock J. & A.J. Davis (2017), "The role of the core non-homologous end joining factors in carcinogenesis and cancer.", Cancers (Basel). 9(7). doi:10.3390/cancers9070081.
Smith, J. et al. (2001), "The influence of DNA double-strand break structure on end-joining in human cells.", Nucleic Acids Res. 29(23):4783–4792
Smith, J. et al. (2003), "Impact of DNA ligase IV on the ® delity of end joining in human cells.", Nucleic Acids Res., 31(8):2157-67. doi:10.1093/nar/gkg317
Tan, X., Grollman, A., Shibutani, S. (1999), Comparison of the mutagenic properties of 8-oxo-7,8-dihydro-2'-deoxyadenosine and 8-oxo-7,8-dihydro-2'-deoxyguanosine DNA lesions in mammalian cells, Carcinogenesis, 20:2287-2292.
Thomas, A.D., G.J. Jenkins, B. Kaina, O.G. Bodger, K.H. Tomaszowski, P.D. Lewis, S.H. Doak and G.E. Johnson (2013), "Influence of DNA repair on nonlinear dose-responses for mutation", Toxicol. Sci., 132(1): 87-95.
van Delft, J.H. and R.A. Baan (1995), "Germ cell mutagenesis in lambda lacZ transgenic mice treated with ethylnitrosourea; comparison with specific-locus test", Mutagenesis, 10(3): 209-214.
Waters, C.A. et al. (2014), "The fidelity of the ligation step determines how ends are resolved during nonhomologous end joining.", Nat Commun. 5:1–11. doi:10.1038/ncomms5286.
Wessendorf P. et al. (2014), "Mutation Research / Fundamental and Molecular Mechanisms of Mutagenesis Deficiency of the DNA repair protein nibrin increases the basal but not the radiation induced mutation frequency in vivo.", Mutat. Res. - Fundam. Mol. Mech. Mutagen. 769:11–16. doi:10.1016/j.mrfmmm.2014.07.001.
Wilson, T.E. & M.R. Lieber (1999), "Efficient Processing of DNA Ends during Yeast Nonhomologous End Joining.", J. Biol. Chem. 274(33):23599–23609. doi:10.1074/jbc.274.33.23599.