Upstream eventIncrease, DNA strand breaks
N/A, Inadequate DNA repair
Key Event Relationship Overview
AOPs Referencing Relationship
|AOP Name||Adjacency||Weight of Evidence||Quantitative Understanding|
|Oxidative DNA damage leading to chromosomal aberrations and mutations||adjacent||High||Low|
|Direct deposition of ionizing energy onto DNA leading to lung cancer||adjacent||Moderate||Moderate|
Life Stage Applicability
|All life stages||High|
Key Event Relationship Description
The maintenance of DNA integrity is essential for genomic stability; for this reason cells have multiple response mechanisms that enable the repair of damaged DNA. Thus when DNA double strand breaks (DSBs) occur, the most detrimental type of lesion, the cell will initiate repair machinery. These mechanisms are not foolproof, and emerging evidence suggests that closely spaced lesions can compromise the repair machinery. The two most common DSB repair mechanisms are non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is initiated in G1 and early S phases of the cell cycle (Lieber et al., 2003) and is preferentially used to repair DSB damage (Godwint et al., 1994), as it is rapid and more efficient than HR (Lliakis, 1991; Jeggo, 1998; Mao et al., 2008). In higher-order eukaryotes such as humans, NHEJ is the favoured DNA repair mechanism because of the large non-coding regions within the genome. NHEJ can occur through one of two subtypes: canonical NHEJ (C‐NHEJ) or alternative non-homologous end joining (alt-NHEJ). C-NHEJ, as the name suggests, simply ligates the broken ends back together. In contrast, alt‐NHEJ occurs when one strand of the DNA on either side of the break is resected to repair the lesion (Bétermier et al., 2014). Both repair mechanisms are error‐prone, meaning insertions and deletions are sometimes formed due to the DSBs being repaired imperfectly (Thurtle-Schmidt and Lo, 2018). However, alt-NHEJ is considered more error-prone than C-NHEJ, as studies have shown that it more often leads to chromosomal aberrations (Zhu et al., 2002; Guirouilh-Barbat et al., 2007; Simsek & Jasin, 2010).
Evidence Supporting this KER
The biological rationale linking increased DNA DSB formation with inadequate DSB repair is supported strongly by literature. This is evident from the number of review articles that have been published on the subject. Of particular relevance is a recent review which focussed particularly on DSBs induced by ionizing radiation and extensively detailed the processes involved in repairing DSBs, including discussions of entire pathways and individual proteins involved in DNA repair (Thompson, 2012). Multiple other shorter reviews are also available on the subject, which cover such topics as: the mechanisms of DSB formation and repair, how to quantify these two events, and the biological consequences of unrepaired or misrepaired DNA damage (van Gent et al., 2001; Khanna & Jackson, 2001; Vignard et al., 2013; Moore et al., 2014; Rothkamm et al., 2015; Chang et al., 2017; Sage and Shikazono, 2017). A brief overview of the biological plausibility of this KER is given below; for more detail, please consult the above-cited reviews.
NHEJ is commonly used in repairing DSBs in multicellular eukaryotic organisms, especially in humans (Feldmann et al., 2000). Due to being inherently error-prone, this repair process is used to generate genetic variation within antigen receptor axons through VDJ recombination, a process that leads to the careful breakage and repair of DNA (Murakami & Keeney, 2008; Malu et al., 2012). Genetic variation is also often generated during the repair of highly toxic DSB lesions. Repair to these DSB sites normally triggers cell cycle delay. NHEJ is most active in the following order of the cell cycle: G1 > S > G2/M (Mao et al., 2008). Since most somatic mammalian cells are in the G1 pre-replicative phase, DSBs also usually appear in this phase and thus are often repaired using the error-prone NHEJ (Jeggo et al., 1995).
The two broken ends of DNA DSBs are bridged by overlapping single-strand microhomology termini (Anderson, 1993; Getts & Stamato, 1994; Rathmell & Chu, 1994; Jeggo et al., 1995; Miller et al., 1995; Kirchgessner et al., 1995). The microhomology termini are ligated only when complementary base pairs are overlapped and, depending on where this match is found on the termini, it can lead to deletions and other rearrangements. With increasing DSBs, the probability of insufficient or incorrect repair of these breaks increases proportionately. It has been suggested that clustered DNA damage is less easily repairable than any other form of DNA damage (United Nations, 2000). With multiple lesions in close proximity within a damaged cluster, the probability of misrepair is high. This leads to an increased number of misrepaired termini (Goodhead et al., 1994; Goodhead, 1980), as the presence of multiple damage sites interferes with the ability of the repair enzymes to recognize and bind to the DNA accurately (Harrison et al., 1999).
Empirical data obtained for this KER strongly supports the idea that an increase in DNA DSBs will increase the frequency of inadequate DSB repair. The evidence presented below is summarized in table 4, here (click link). Much of the evidence comes from work with radiation stressors, which directly cause DNA DSBs in the genome (Pinto & Prise, 2005; Dong et al., 2017) in a dose-dependent fashion (Dikomey & Brammer, 2000; Kuhne et al., 2000; Lobrich et al., 2000; Rothkamm & Lo, 2003; Kuhne et al., 2005; Asaithamby & Chen, 2009; Bracalente et al., 2013).
The formation of DSBs by ionizing radiation, the repair process, the various methods used to analyze this repair process, and the biological consequences of unrepaired or misrepaired DNA damage are reviewed in Sage & Shikazono (2017).
Dose and Incidence Concordance
There is evidence in the literature suggesting a dose/incidence concordance between the occurrence of DSBs and the incidence of inadequate DNA repair upon exposure to radiation. Inadequate DNA repair appears to occur at the same radiation dose as DSBs. Visually, immunofluorescence has demonstrated a colocalization of DNA repair proteins with DSB foci in response to a radiation stressor (Paull et al., 2000; Asaithamby & Chen, 2009; Dong et al., 2017). In studies examining cellular responses to increasing doses of radiation, which is known to evoke a dose-dependent increase in DNA DSBs (Dikomey & Brammer, 2000; Kuhne et al., 2000; Lobrich et al., 2000; Rothkamm & Lo, 2003; Kuhne et al., 2005; Asaithamby & Chen, 2009; Bracalente et al., 2013), there were resulting dose-dependent increases in non-repaired DSBs (Dikomey & Brammer, 2000), DSB misrepair rates (Mcmahon et al., 2016), and misrejoined DSBs (Kuhne et al., 2000; Kuhne et al., 2005; Rydberg et al., 2005), as well as a dose-dependent decrease in the total DSB rejoining (Lobrich et al., 2000). Furthermore, only 50% of the rejoined DSBs were found to be correctly repaired (Kuhne et al., 2000; Lobrich et al., 2000); 24 hours after being irradiated with an 80 Gy dose of alpha particles, this frequency of misrejoining increased to and remained constant at 80% (Kuhne et al., 2000). Furthermore, delivering radiation doses in fractionated increments also showed a dose-dependent change in the percentage of misrejoinings, such that larger fractionated doses (for example, 2 x 40 Gy) had a higher rate of DSB misrejoining than smaller fractionated doses (for example, 4 x 10 Gy) (Kuhne et al., 2000).
There is evidence suggesting a time concordance between DSBs and DNA repair. DSBs and DNA repair have both been observed within minutes to hours of radiation exposure (Paull et al., 2000; Rothkamm & Lo, 2003; Pinto & Prise, 2005; Asaithamby & Chen, 2009).
There is evidence from inhibition studies and knock-out/knock down studies suggesting that there is a strong relationship between DSBs and DNA repair. When an inhibitor of a DNA repair protein was added to cells prior to exposure to a radiation stressor, DNA repair foci were not formed post-irradiation (Paull et al., 2000), and there were significant increases in DSBs at 6 hours and 12 hours after the radiation treatment (Dong et al., 2017). Similarly, there have been several knock-out/knock-down studies in which cells lacking a DNA repair protein have been exposed to a radiation stressor. As a result, DSBs were found to persist in these cells longer than in the wild-type cells (Rothkamm and Lo, 2003; Bracalente et al., 2013; Mcmahon et al., 2016; Dong et al., 2017), and there was an increase in incorrectly rejoined DSBs (Lobrich et al., 2000). In one striking example, a human cell line lacking DNA ligase IV had DSBs that were still present approximately 240 - 340 hours post-irradiation (Mcmahon et al., 2016). Interestingly, there were also increased levels of DSBs in these cells prior to being exposed to a radiation stressor (Paull et al., 2000) . Similarly, a study examining DSB repair kinetics after irradiation found that DSBs persisted for a longer time period in two repair-deficient mouse strains relative to a repair-proficient mouse strain; this pattern was found in lymphocytes, as well as tissues from the brains, lungs, hearts and intestines of these mice (Rube et al., 2008). The roles of various DNA repair proteins in the context of DSBs are highlighted in reviews by Chang et al. (2001) and Van Gent et al. (2001) with discussions focussing on the consequences of losing some of these proteins in cells, mice and humans (Van Gent et al., 2001)
Uncertainties and Inconsistencies
Uncertainties and inconsistencies in this KER are as follows:
- There is controversy surrounding how error-prone NHEJ truly is. Recent studies suggest that the process may be quite accurate (reviewed in (Bétermier et al. 2014)). The accuracy of NHEJ may actually be dependent on the structure of the termini. Thus, the termini processing rather than the NHEJ mechanism itself is argued to be the error-prone process (Bétermier et al. 2014).
- There may be different cellular responses associated with low-dose radiation exposure and high-dose radiation exposure; these differences may also be dependent on a DSB threshold being exceeded prior to initiation repair. It has been suggested that DNA repair may not be activated at low doses of radiation exposure in order to prevent the risk of mutations from error-prone repair mechanisms (Marples 2004).
- DSB repair fidelity varies in terms of confounding factors and the genetic characteristics of individuals (Scott 2006). For example, individuals who smoke have a 50% reduction in the mean level of DSB repair capacity relative to the non-smokers; this is due to an increased methylation index in smokers. A higher methylation index indicates more inactivation of gene expression. It is thus possible that expression of DNA repair proteins in smokers is decreased due to increased methylation of the genes encoding for repair proteins. In terms of individual genetics, single nucleotide polymorphisms (SNPs) within the MRE11A, CHEK2, XRCC3, DNA-PKcs, and NBN repair genes have been highly associated with the methylation index (Leng et al. 2008). SNPs can critically affect the function of these core proteins, varying the fidelity of DNA repair from person to person.
- Cells containing DNA damaged may be eliminated by apoptotic pathways, therefore not undergo repair, alternatively evidence has also shown that damaged cells can propagate due to lack of detection by repair machinery (Valentin 2005).
Quantitative Understanding of the Linkage
Quantitative understanding of this linkage suggests that DSB repair can be predicted from the presence of DSBs. In terms of DNA repair in response to radiation-induced DSBs, one study suggests that complete DNA DSB repair occurs starting at a threshold dose of 5 mGy (0.005 Gy), as measured by phosphorylation of gamma-H2AX (Lobrich et al., 2005) and presence of 53BPI foci (Asaithamby & Chen, 2009). After a 10 Gy dose of radiation, approximately 10 - 15% of DSBs were found to be misrepaired (Mcmahon et al., 2016); at a dose of 80 Gy, the relative percentage of DSBs incorrectly repaired was estimated at 50 - 60% (Kuhne et al., 2000; Lobrich et al., 2000; Mcmahon et al., 2016). Twenty-four hours post-irradiation, this rate increased to approximately 80% for alpha particle irradiation at 80 Gy, and remained constant until the end of the assay (10 days) (Kuhne et al., 2000).
There is evidence of a response-response relationship for DNA repair of radiation-induced DSBs. The frequency of DSBs has been shown to increase linearly with radiation dose (Lobrich et al., 2000; Rothkamm & Lo, 2003; Kuhne et al., 2005; Asaithamby & Chen, 2009). For DNA repair, increasing doses of a radiation stressor were found to cause a linear-quadratic relationship between the radiation dose and the number of misrejoined DSBs per cell (Kuhne et al., 2005). Interestingly, the relationships between radiation and DNA repair were found to vary depending on the type of radiation. There was a more linear response between radiation dose and the number of misrejoined DSBs for high LET particles relative to a more curvilinear relationship for lower LET particles (Rydberg et al., 2005). Additionally, a linear relationship was defined for low dose-rate radiation and the number of non-repaired DNA DSBs, but a linear-quadratic equation was described for high dose-rate radiation (Dikomey & Brammer, 2000).
Data from temporal response studies suggests that DSB repair may occur within 15 - 30 minutes of a DSB-inducing radiation stressor (Paull et al., 2000; Rothkamm & Lo, 2003; Pinto & Prise, 2005; Dong et al., 2017), with foci documented as early as 3-5 minutes post-irradiation (Asaithamby & Chen, 2009). The majority of DSB repair has been reported to occur within the first 3 - 6 hours following DSB induction (Rothkamm & Lo, 2003; Pinto & Prise, 2005; Asaithamby & Chen, 2009; Dong et al., 2017), with complete or near-complete DSB repair within 24 hours of the radiation stressor (Dikomey & Brammer, 2000; Lobrich et al., 2000; Rothkamm & Lo, 2003; Asaithamby & Chen, 2009; Mcmahon et al., 2016). In one 48-hour time-course experiment for DSB repair using two different types of radiation, the following repair progression was found at 30 minutes, 1 hour, 3 hours, 24 hours and 48 hours, respectively: 40 - 55%, 55 - 70%, 85%, 97 - 98% and 98% repair for X-rays and 30%, 45 - 50%, 65 - 70%, 85 - 90% and 90 - 96% repair for alpha particles (Pinto & Prise, 2005). Twenty-four hours post-irradiation, the frequency of DSB misrejoining was found to remain constant at approximately 80% for the 10 days that the DSB repair was monitored (Kuhne et al., 2000).
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).
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