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Relationship: 164


A descriptive phrase which clearly defines the two KEs being considered and the sequential relationship between them (i.e., which is upstream, and which is downstream). More help

Inadequate DNA repair leads to Increase, Mutations

Upstream event
The causing Key Event (KE) in a Key Event Relationship (KER). More help
Downstream event
The responding Key Event (KE) in a Key Event Relationship (KER). More help

Key Event Relationship Overview

The utility of AOPs for regulatory application is defined, to a large extent, by the confidence and precision with which they facilitate extrapolation of data measured at low levels of biological organisation to predicted outcomes at higher levels of organisation and the extent to which they can link biological effect measurements to their specific causes.Within the AOP framework, the predictive relationships that facilitate extrapolation are represented by the KERs. Consequently, the overall WoE for an AOP is a reflection in part, of the level of confidence in the underlying series of KERs it encompasses. Therefore, describing the KERs in an AOP involves assembling and organising the types of information and evidence that defines the scientific basis for inferring the probable change in, or state of, a downstream KE from the known or measured state of an upstream KE. More help

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 Evgeniia Kazymova (send email) Open for citation & comment WPHA/WNT Endorsed
Alkylation of DNA leading to cancer 2 adjacent High Moderate Agnes Aggy (send email) Not under active development
Alkylation of DNA leading to cancer 1 non-adjacent High Moderate Arthur Author (send email) Open for adoption
Oxidative DNA damage leading to chromosomal aberrations and mutations adjacent High Low Brendan Ferreri-Hanberry (send email) Open for comment. Do not cite WPHA/WNT Endorsed
Deposition of energy leading to lung cancer adjacent Moderate Moderate Brendan Ferreri-Hanberry (send email) Open for citation & comment WPHA/WNT Endorsed
Bulky DNA adducts leading to mutations adjacent Evgeniia Kazymova (send email) Under development: Not open for comment. Do not cite Under Development
DNA damage and mutations leading to Metastatic Breast Cancer adjacent High High Agnes Aggy (send email) Under development: Not open for comment. Do not cite Under Development
Deposition of energy leading to occurrence of cataracts adjacent High Low Arthur Author (send email) Open for citation & comment

Taxonomic Applicability

Latin or common names of a species or broader taxonomic grouping (e.g., class, order, family) that help to define the biological applicability domain of the KER.In general, this will be dictated by the more restrictive of the two KEs being linked together by the KER.  More help
Term Scientific Term Evidence Link
mouse Mus musculus High NCBI
human Homo sapiens High NCBI
rat Rattus norvegicus High NCBI

Sex Applicability

An indication of the the relevant sex for this KER. More help
Sex Evidence
Unspecific High

Life Stage Applicability

An indication of the the relevant life stage(s) for this KER.  More help
Term Evidence
All life stages High

Key Event Relationship Description

Provides a concise overview of the information given below as well as addressing details that aren’t inherent in the description of the KEs themselves. More help

The described Key Event Relationship (KER) outlines a sequence of events related to DNA repair and its consequences. The upstream event is characterized by "Inadequate DNA repair," indicating that the cellular mechanisms responsible for repairing DNA damage are compromised or insufficient. This could result from various factors, such as genetic mutations, environmental exposures, or other cellular processes.

The downstream event in this KER is an "Increase in Mutations." As a consequence of inadequate DNA repair, the accumulation of unrepaired or incorrectly repaired DNA damage can lead to an elevated rate of mutations in the genome. These mutations can involve changes in the DNA sequence, structure, or arrangement, which may have various implications for cellular function, including potential disruptions to normal processes and pathways.

This KER highlights the critical role of DNA repair mechanisms in maintaining genomic stability and preventing the buildup of mutations that can contribute to various biological outcomes, including disease development and other adverse effects.

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.

Furthermore, other repair mechanisms such as a loss in the mismatch repair (MMR) system can lead to a buildup of errors such as base-base mismatches and insertion-deletion errors in repetitive DNA sequences which are known as microsatellites. This could occur if an MMR gene (e.g. MLH1, PMS2) is inactivated through mutations or epigenetic silencing (Wang et al., 2022). 

Evidence Collection Strategy

Include a description of the approach for identification and assembly of the evidence base for the KER. For evidence identification, include, for example, a description of the sources and dates of information consulted including expert knowledge, databases searched and associated search terms/strings.  Include also a description of study screening criteria and methodology, study quality assessment considerations, the data extraction strategy and links to any repositories/databases of relevant references.Tabular summaries and links to relevant supporting documentation are encouraged, wherever possible. More help

Adhering to OECD guidelines, a systematic and comprehensive evidence collection approach was executed to support the KER "Inadequate DNA repair leads to Increase, Mutations." To establish the first part of the relationship, the inadequacy of DNA repair processes, a range of molecular and cellular assays were employed. Comet assays provided direct quantification of unrepaired DNA lesions, while functional assays focusing on repair gene expression and protein activity offered mechanistic insights into repair deficiency. Crucial to establishing the link, genetic and biochemical studies delved into the interactions between the malfunctioning repair machinery and accumulating DNA lesions.

The subsequent increase in mutations was substantiated by genetic analysis techniques such as whole-genome sequencing and polymerase chain reaction (PCR)-based assays. These methods not only quantified mutations but also pinpointed their specific locations, aiding in understanding their origins and patterns. Parallel assessments across different experimental conditions, strains, and species enhanced the robustness of the evidence. Additionally, case-control studies involving populations exposed to DNA damaging agents supported the real-world relevance of the KER, revealing a notable association between inadequate DNA repair and elevated mutation rates.

The integration of results from diverse experimental models, mechanistic studies, and epidemiological data in line with OECD principles established a compelling and well-substantiated evidence base for the KER "Inadequate DNA repair leads to Increase, Mutations."

Evidence Supporting this KER

Addresses the scientific evidence supporting KERs in an AOP setting the stage for overall assessment of the AOP. More help

Overall Weight of Evidence: High 

Biological Plausibility
Addresses the biological rationale for a connection between KEupstream and KEdownstream.  This field can also incorporate additional mechanistic details that help inform the relationship between KEs, this is useful when it is not practical/pragmatic to represent these details as separate KEs due to the difficulty or relative infrequency with which it is likely to be measured.   More help

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 O6-alkylguanine DNA alkyltransferase 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
Addresses inconsistencies or uncertainties in the relationship including the identification of experimental details that may explain apparent deviations from the expected patterns of concordance. More help

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.

Repair of double strand breaks 

  • One review paper found that DNA DSBs are repaired more efficiently at low dose (≤0.1 Gy) compared to high dose (>1 Gy) X-rays, but delayed mutation induction and genomic instability have also been demonstrated to occur at low doses (<1 cGy) of ionizing radiation (Preston et al., 2013).  


  • 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).

Known modulating factors

This table captures specific information on the MF, its properties, how it affects the KER and respective references.1.) What is the modulating factor? Name the factor for which solid evidence exists that it influences this KER. Examples: age, sex, genotype, diet 2.) Details of this modulating factor. Specify which features of this MF are relevant for this KER. Examples: a specific age range or a specific biological age (defined by...); a specific gene mutation or variant, a specific nutrient (deficit or surplus); a sex-specific homone; a certain threshold value (e.g. serum levels of a chemical above...) 3.) Description of how this modulating factor affects this KER. Describe the provable modification of the KER (also quantitatively, if known). Examples: increase or decrease of the magnitude of effect (by a factor of...); change of the time-course of the effect (onset delay by...); alteration of the probability of the effect; increase or decrease of the sensitivity of the downstream effect (by a factor of...) 4.) Provision of supporting scientific evidence for an effect of this MF on this KER. Give a list of references.  More help

Not identified.

Response-response Relationship
Provides sources of data that define the response-response relationships between the KEs.  More help

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).

Information regarding the approximate time-scale of the changes in KEdownstream relative to changes in KEupstream (i.e., do effects on KEdownstream lag those on KEupstream by seconds, minutes, hours, or days?). More help

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 Feedforward/Feedback loops influencing this KER
Define whether there are known positive or negative feedback mechanisms involved and what is understood about their time-course and homeostatic limits. More help

Not identified.

Domain of Applicability

A free-text section of the KER description that the developers can use to explain their rationale for the taxonomic, life stage, or sex applicability structured terms. More help

This KER is plausible in all life stages, sexes, and organisms with DNA. The majority of the evidence is from in vivo adult mice and male human, and mice in vitro models. 

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 with DNA, 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.


List of the literature that was cited for this KER description. More help

Ainsbury, E. A. et al. (2016), “Ionizing radiation induced cataracts: recent biological and mechanistic developments and perspectives for future research”, Mutation research. Reviews in mutation research, Vol. 770, Elsevier B.V.,    

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.

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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.

Ceccaldi, R. et al. (2016), “Repair Pathway Choices and Consequences at the Double-Strand Break.” Trends in cell biology, Vol. 26/1, Elsevier, Amsterdam, 

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.

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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.

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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.

Garrett, J et al. (2020), “The protective effect of estrogen against radiation cataractogenesis is dependent upon the type of radiation”, Radiation Research, Vol. 194/5, Radiation Research Society, United States, 

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Kuhne, M., K. Rothkamm & M. Löbrich (2000), "No dose-dependence of DNA double-strand break misrejoining following a -particle irradiation.", Int. J. Radiat. Biol. 76(7):891-900

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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.

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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.

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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.

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Preston, R. et al. (2013), “Uncertainties in estimating health risks associated with exposure to ionising radiation”, Journal of Radiological Protection, Vol.33/3, IOP Publishing, Bristol, 

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

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Sakofsky, C.J. et al. (2015), "Translesion Polymerases Drive Microhomology-Mediated Break-Induced Replication Leading to Complex Chromosomal Rearrangements", Mol. Cell, 60:860-872.

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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.

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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.

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