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Relationship: 1909

Title

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

Increase, Oxidative DNA damage leads to Inadequate DNA repair

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
Oxidative DNA damage leading to chromosomal aberrations and mutations adjacent High Low Carole Yauk (send email) Open for comment. Do not cite EAGMST Approved

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
human Homo sapiens NCBI
mouse Mus musculus NCBI
rat Rattus norvegicus NCBI

Sex Applicability

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Sex Evidence
Unspecific

Life Stage Applicability

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

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

Oxidative DNA lesions are present in the cell at steady state due to low levels of reactive oxygen species (ROS) and other free radicals generated by endogenous processes involving redox reactions. The most prominent examples of oxidative DNA lesions include 7, 8-dihydro-8oxo-deoxyGuanine (8-oxo-dG), 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FaPydG), and thymidine glycol (Tg). Under homeostatic conditions, cells are able to regulate the level of free radicals and readily repair oxidized DNA bases using basal repair mechanisms to prevent irreversible damage (Swenberg et al., 2011). Oxidative DNA lesions are mainly repaired by base excision repair (BER) initiated by DNA glycosylases such as oxoguanine glycosylase 1 (OGG1), endonuclease III homologue 1 (NTH1), and Nei-like DNA glycosylases (NEIL 1/2), which detect and remove damaged bases. Abasic sites are then cleaved by endonucleases or lyases, resulting in transient single-strand breaks (SSB) that enter either short-patch or long-patch repair. Nucleotide excision repair (NER) is involved in repairing oxidized bases to a lesser extent (Shafirovich et al., 2016). Increase in free radicals or exposure to oxidizing agents can increase the level of oxidative DNA lesions and overwhelm the repair pathways, compromising the quality of repair. If the repair mechanisms are compromised, oxidative lesions may accumulate (insufficient repair) and cause incorrect base pairing during replication or incomplete repair (indicated by accumulation of repair intermediates) (Markkanen, 2017).

Evidence Collection Strategy

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Evidence Supporting this KER

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

Inadequate repair of oxidative lesions is indicated by an increase in oxidative lesions above background, activation of repair enzymes, increase in repair intermediates (abasic sites and single strand breaks), and incorrect base insertion opposite lesion during replication (lesion bypass by translesion DNA synthesis).

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

The mechanism of repair of oxidative DNA lesions in humans is well-established and numerous literature reviews are available on this topic (Berquist and Wilson III, 2012; Cadet and Wagner, 2013). As described above, oxidative DNA lesions are mostly repaired via BER and, to a lesser extent, NER. Previous studies have reported thresholded dose-response curves in oxidative DNA damage and attributed these observations to exceeded repair capacity at the inflection point on the curve (Gagne et al., 2012; Seager et al., 2012). In vivo, increase and accumulation of oxidative DNA lesions despite the activation of BER have been observed following chemical exposures, demonstrating insufficient repair of oxidative DNA lesions past a certain level (Ma et al., 2008).

OGG1 and NTH1, the glycosylases that initiate the BER of 8-oxo-dG and thymine glycol (Tg) lesions, respectively, are bifunctional, containing both glycosylase and lyase activities. The glycosylase removes the oxidized guanine by cleaving the glycosidic bond, giving rise to an apurinic site. The lyase then cleaves the phosphodiester bond 5’ to the AP site; a transient SSB is created for further processing in BER (Delaney et al., 2012). Abasic sites created by OGG1 and other glycosylases are also processed by apuric/apyrimidinic endonucleases (APE1) to create the 5’ nick (Allgayer et al., 2016).

Previous studies have demonstrated that an imbalance in any one of the multiple steps of BER can lead to an accumulation of repair intermediates and failed repair. Given that OGG1 is relatively slower in releasing its catalytic product than other glycosylases, it is highly likely that a disproportionate increase in oxidative DNA lesions compared to the level of available OGG1 would lead to an imbalance between lesions and the initiating step of BER (Brenerman et al., 2014). Accumulation of oxidative lesions would be observed as a result. Moreover, studies have reported accumulation of SSB due to OGG1 and NTH1 overexpression, demonstrating that the imbalanced lyase activity generates excessive SSB intermediates (Yang et al., 2004; Yoshikawa et al., 2015; Wang et al., 2018). 

Increases in oxidative lesions may produce more lesions and repair intermediates in close proximity to each other. Previous studies in mammalian cell extracts have reported reduction in repair efficiency when oxidative lesions are in tandem or opposite each other. For example, OGG1 showed reduced binding to 8-oxo-dG near an AP site incision. Furthermore, the OGG1-8-oxo-dG complex has been observed to hinder the repair of neighbouring AP site incision, delaying the completion of BER; this interaction between BER enzymes has been suggested to cause an accumulation of oxidative lesions and repair intermediates (Pearson et al., 2004; Budworth et al., 2005; Bellon et al., 2009; Yoshikawa et al., 2015; Sharma et al., 2016).

If oxidative lesions persist in the genome due to insufficient repair, incorrect base insertion opposite unrepaired oxidative DNA lesions may occur during replication. This is a well-established event. For example, 8-oxo-dG and FaPydG, the two most prominent oxidative DNA lesions, are able to form base pairs with dATP, giving rise to G:C→T:A transversions after subsequent DNA synthesis (Freudenthal et al., 2013; Gehrke et al., 2013; Markkanen, 2017). Replicative DNA polymerases such as DNA polymerase α, δ, and ε (pol α, δ, ε) have a poor ability to extend the DNA strand past 8-oxo-dG:dCTP base pairs and may cause replication to stall or incorrectly insert dATP opposite 8-oxo-dG (Hashimoto et al., 2004; Markkanen et al., 2012). In stalled replication forks, repair polymerases may be recruited to perform translesion DNA synthesis (TLS). Human Y-family DNA polymerases (Rev 1, pol κ, ι, and η) are DNA repair polymerases mainly involved in TLS in stalled replication forks. However, TLS is not free of error and its accuracy differs for each repair polymerase. For example, it is known that pol κ and η perform TLS across 8-oxo-dG and preferentially insert dATP opposite the lesion, generating G:C→T:A transversions. The error-prone nature of bypassing unrepaired oxidative lesions has been described in many previous studies and reviews (Greenberg, 2012; Maddukuri et al., 2014; Taggart et al., 2014; Shah et al., 2018).

Repair by OGG1 requires 8-oxo-dG:dC base pairing, thus, it is unable to repair 8-oxo-dG:dA mispairing in newly synthesized strands. The repair of 8-oxo-dG:dA base pairs post-replication is performed by MUT Y homologue, MYH, an adenine DNA glycosylase. However, the removal of dA instead of the damaged guanine may lead to futile cycles of BER because: 1) another dA is often inserted opposite the lesion, or 2) BER ligases have a poor ability of ligating the 3’end of dC opposite 8-oxo-dG (Hashimoto et al., 2004; Caglayan and Wilson, 2015). Accumulated 8-oxo-dG may be more resistant to repair post-replication due to this futile BER.         

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

Although the dual functionality of OGG1 as a glycosylase and lyase has been widely accepted and demonstrated experimentally, there are studies showing that the cleavage of phosphodiester bond 5’ to the lesion is mainly performed by apurinic endonuclease 1 (APE1) (Allgayer et al., 2016; R. Wang et al., 2018). In some cases, APE1 may be the main factor driving the accumulation of BER intermediates. Some studies suggest that OGG1 is involved in the repair of non-transcribed strands and is not required for transcription-coupled repair of 8-oxo-dG; Le Page et al. reported efficient repair of 8-oxo-dG in the transcribed sequence in Ogg1 knockout mouse cells (Le Page et al., 2000). Moreover, the repair of 8-oxo-dG is also affected by the neighbouring sequence; the position of the lesions may have a negative effect on repair efficiency (Pastoriza-Gallego et al., 2007). We note that the study by Allgayer et al. was investigating the fate and effect of 8-oxo-dG during transcription; repair mechanism may vary by situation and availability of repair enzymes at the time.

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

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

Oxidative DNA damage can occur and overwhelm the repair mechanisms in any eukaryotic and prokaryotic cell. Observation of this KER has been described in mammalian cells, yeast, and bacteria.

References

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

Allgayer, J., Kitsera, N., Bartelt, S., Epe, B., Khobta, A. (2016), Widespread transcriptional gene inactivation initiated by a repair intermediate of 8-oxoguanine, Nucleic Acids Res, 44:7267-7280.

Bellon, S., Shikazono, N., Cunniffe, S., Lomax, M., O’Neill, P. (2009), Processing of thymine glycol in a clustered DNA damage site: mutagenic or cytotoxic, Nucleic Acids Res, 37:4430-4440.

Berquist, B., Wilson III, D. (2012), Pathways for Repairing and Tolerating the Spectrum of Oxidative DNA Lesions, Cancer Lett, 327:61-72.

Brenerman, B., Illuzzi, J., Wilson III, D. (2014), Base excision repair capacity in informing healthspan, Carcinogenesis, 35:2643-2652.

Budworth, H., Matthewman, G., O’Neill, P., Dianov, G. (2005), Repair of Tandem Base Lesions in DNA by Human Cell Extracts Generates Persisting Single-strand Breaks, J Mol Biol, 351:1020-1029.

Cadet, J., Wagner, J.R. (2013), DNA Base Damage by Reactive Oxygen Species, Oxidizing Agents, and UV Radiation, Cold Spring Harb Perspect Biol, 5:a012559.

Caglayan, M., Wilson, S. (2015), Oxidant and environmental toxicant-induced effects compromise DNA ligation during base excision DNA repair, DNA Repair, 35:85-89.

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.

Delaney, S., Jarem, D., Volle, C., Yennie, C. (2012), Chemical and Biological Consequences of Oxidatively Damaged Guanine in DNA, Free Radic Res, 46:420-441.

Freudenthal, B., Beard, W., Wilson, S. (2013), DNA polymerase minor groove interactions modulate mutagenic bypass of a templating 8-oxoguanine lesion., Nucleic Acids Res, 41:1848-1858.

Gagne, J., Rouleau, M., Poirier, G. (2012), PARP-1 Activation— Bringing the Pieces Together, Science, 336:678-279.

Gehrke, T., Lischke, U., Gasteiger, K., Schneider, S., Arnold, S., Muller, H., Stephenson, D., Zipse, H., Carell, T. (2013), Unexpected non-Hoogsteen–based mutagenicity mechanism of FaPy-DNA lesions, Nat Chem Biol, 9:455-461.

Greenberg, M. (2012), Purine Lesions Formed in Competition With 8-Oxopurines From Oxidative Stress, Acc Chem Res, 45:588-597.

Hashimoto, K., Tominaga, Y., Nakabeppu, Y., Moriya, M. (2004), Futile short-patch DNA base excision repair of adenine:8-oxoguanine mispair, Nucleic Acids Res, 32:5928-5934.

Le Page, F., Klunglund, A., Barnes, D., Sarasin, A., Boiteux, S. (2000), Transcription coupled repair of 8-oxoguanine in murine cells: The Ogg1 protein is required for repair in nontranscribed sequences but not in transcribed sequences, Proc Natl Acad Sci USA, 97:8397-8402.

Li, Y., Song, M., Kasai, H., Kawai, K. (2013), Generation and threshold level of 8-OHdG as oxidative DNA damage elicited by low dose ionizing radiation, Genes Environ, 35:88-92.

Ma, H., Wang, J., Abdel-Rahman, S., Boor, P., Firoze, M. (2008), Oxidative DNA damage and its repair in rat spleen following subchronic exposure to aniline, Toxicol Appl Pharmacol, 233:247-253.

Maddukuri, L., Ketkar, A., Eddy, S., Zafar, M., Eoff, R. (2014), The Werner syndrome protein limits the error-prone 8-oxo-dG lesion bypass activity of human DNA polymerase kappa, Nucleic Acids Res, 42:12027-12040.

Markkanen, E. (2017), Not breathing is not an option: How to deal with oxidative DNA damage, DNA Repair, 59:82-105.

Markkanen, E., Castrec, B., Vilani, G., Hubscher, U. (2012), A switch between DNA polymerases δ and λ promotes error-free bypass of 8-oxo-G lesions, Proc Natl Acad Sci USA, 27:931-940.

Pastoriza-Gallego, M., Armier, J., Sarasin, A. (2007), Transcription through 8-oxoguanine in DNA repair-proficient and Csb−/Ogg1− DNA repair-deficient mouse embryonic fibroblasts is dependent upon promoter strength and sequence context, Mutagenesis, 22:343-351.

Pearson, C., Shikazono, N., Thacker, J., O’Neill, P. (2004), Enhanced mutagenic potential of 8-oxo-7,8-dihydroguanine when present within a clustered DNA damage site, Nucleic Acids Res, 32:263-270.

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.

Shafirovich, V., Kropachev, K., Anderson, T., Li, Z., Kolbanovskiy, M., Martin, B., Sugden, K., Shim, Y., Min, J., Ceacintov, N. (2016), Base and Nucleotide Excision Repair of Oxidatively Generated Guanine Lesions in DNA, J Biol Chem, 291:5309-5319.

Shah, A., Gray, K., Figg, N., Finigan, A., Starks, L., Bennett, M. (2018), . Defective Base Excision Repair of Oxidative DNA Damage in Vascular Smooth Muscle Cells Promotes Atherosclerosis, Circulation, 138:1446-1462.

Sharma, V., Collins, L., Chen, T., Herr, N., Takeda, S., Sun, W., Swenberg, J., Nakamura, J. (2016), Oxidative stress at low levels can induce clustered DNA lesions leading to NHEJ mediated mutations, Oncotarget, 7:25377-25390.

Sokhansanj, B., Wilson III, D. (2004), Oxidative DNA damage background estimated by a system model of base excision repair, Free Rad Biol Med, 37:433-427.

Swenberg, J., Lu, K., Moeller, B., Gao, L., Upton, P., Nakamura, J., Starr, T. (2011), Endogenous versus Exogenous DNA Adducts: Their Role in Carcinogenesis, Epidemiology, and Risk Assessment, Toxicol Sci, 120:S130-S145.

Taggart, D., Fredrickson, S., Gadkari, V., Suo, Z. (2014), Mutagenic Potential of 8-Oxo-7,8-dihydro-2′-deoxyguanosine Bypass Catalyzed by Human Y-Family DNA Polymerases, Chem Res Toxicol, 27:931-940.

Wang, C., Yang, J., Lu, D., Fan, Y., Zhao, M., Li, Z. (2016), Oxidative stress-related DNA damage and homologous recombination repairing induced by N,N-dimethylformamide , J Appl Toxicol, 36:936-945.

Wang, R., Li, C., Qiao, P., Xue, Y., Zheng, X., Chen, H., Zeng, X., Liu, W., Boldogh, I., Ba, X. (2018), OGG1-initiated base excision repair exacerbates oxidative stress-induced parthanatos, Cell Death and Disease, 9:628.

Yang, N., Galick, H., Wallace, S. (2004), Attempted base excision repair of ionizing radiation damage in human lymphoblastoid cells produces lethal and mutagenic double strand breaks, DNA Repair, 3:1323-1334.

Yoshikawa, Y., Yamasaki, A., Takatori., K., Suzuki, M., Kobayashi, J., Takao, M., Zhang-Akiyama, Q. (2015), Excess processing of oxidative damaged bases causes hypersensitivity to oxidative stress and low dose rate irradiation, Free Radic Res, 49:1239-1248.