SNAPSHOT

Event: 1686: Direct Deposition of Energy

Short Name: Energy Deposition

AOPs Including This Key Event

Stressors

Biological Context

Energy can be deposited into any substrate, both living and non-living; it is independent of age, taxa, sex, or life-stage.

Event: 1635: Increase, DNA strand breaks

Short Name: Increase, DNA strand breaks

AOPs Including This Key Event

Stressors

Biological Context

DNA strand breaks can occur in any eukaryotic or prokaryotic cell.

Event: 155: N/A, Inadequate DNA repair

Short Name: N/A, Inadequate DNA repair

AOPs Including This Key Event

Stressors

Biological Context

The retention of adducts has been directly measured in many different types of eukaryotic somatic cells (in vitro and in vivo). In male germ cells, work has been done on hamsters, rats and mice. The accumulation of mutation and changes in mutation spectrum has been measured in mice and human cells in culture. Theoretically, saturation of DNA repair occurs in every species (prokaryotic and eukaryotic). The principles of this work were established in prokaryotic models. Nagel et al. (2014) have produced an assay that directly measures DNA repair in human cells in culture.

NHEJ is primarily used by vertebrate multicellular eukaryotes, but it also been observed in plants. Furthermore, it has recently been discovered that some bacteria (Matthews et al., 2014) and yeast (Emerson et al., 2016) also use NHEJ. In terms of invertebrates, most lack the core DNA-PK_cs and Artemis proteins; they accomplish end joining by using the RA50:MRE11:NBS1 complex (Chen et al., 2001).  HR occurs naturally in eukaryotes, bacteria, and some viruses (Bhatti et al., 2016).

Event: 185: Increase, Mutations

Short Name: Increase, Mutations

AOPs Including This Key Event

Stressors

Biological Context

Mutations can occur in any organism and in any cell type, and are the fundamental material of evolution. The test guidelines described above range from analysis from prokaryotes, to rodents, to human cells in vitro. Mutations have been measured in virtually every human tissue sampled in vivo.

Event: 1636: Increase, Chromosomal aberrations

Short Name: Increase, Chromosomal aberrations

AOPs Including This Key Event

Stressors

Biological Context

Chromosomal aberrations indicating clastogenicity can occur in any eukaryotic or prokaryotic cell. However, dose-response curves can differ depending on the cell cycle stage when the DSB agent was introduced (Obe et al., 2002).

Event: 870: Increase, Cell Proliferation

Short Name: Increase, Cell Proliferation

AOPs Including This Key Event

Stressors

Biological Context

Cell proliferation is a central process supporting development, tissue homeostasis and carcinogenesis, each of which occur in all vertebrates. This key event has been observed nasal tissues of rats exposed to the chemical initiator vinyl acetate. In general, cell proliferation is necessary in the biological development and reproduction of most organisms. This KE is thus relevant and applicable to all multicellular cell types, tissue types, and taxa.

Event: 1556: Increase, lung cancer

Short Name: Increase, lung cancer

AOPs Including This Key Event

Stressors

Biological Context

Lung cancer and subsequent metastasis occurs in multicellular eukaryotic vertebrate organisms that have lungs.

Relationship: 1977: Energy Deposition leads to Increase, DNA strand breaks

AOPs Referencing Relationship

Evidence Supporting Applicability of this Relationship

The domain of applicability relates to all eukaryotic species that contain genetic information in the form of a double strand helix of DNA (Parris et al., 2015; Cannan & Pederson, 2016).

Key Event Relationship Description

Direct deposition of ionizing energy refers to imparted energy interacting directly with the DNA double helix and producing randomized damage in the form of strand breaks. Among the different types of damage, the most detrimental type of DNA damage to a cell is the double-strand break (DSB). DSBs are caused by the breaking of the sugar-phosphate backbone on both strands of the DNA double helix molecule, either directly across from each other or several nucleotides apart (Ward, 1988; Iliakis et al., 2015). The number of DSBs produced and the complexity of the breaks is highly dependent on the amount of energy deposited on and absorbed by the cell. This can vary as a function of the dose-rate (Brooks et al., 2016) and the radiation quality which is a function of its linear energy transfer (LET) (Sutherland et al., 2000; Nikjoo et al., 2001; Jorge et al., 2012). LET describes the amount of energy that an ionizing particle transfers to media per unit distance (Smith et al., 2003; Okayasu, 2012a; Christensen et al., 2014).  High LET radiation, such as alpha particle radiation, can deposit larger quantities of energy within a single track than low LET radiation, such as gamma-ray radiation (Kadhim et al., 2006; Franken et al., 2012; Frankenberg et al., 1999; Rydberg et al., 2002; Belli et al., 2000; Antonelli et al., 2015). As such, radiation with higher LETs tends to produce more complex, dense structural damage, particularly in the form of clustered damage, in comparison to lower LET radiation (Nikjoo et al., 2001; Terato and Ide, 2005; Hada and Georgakilas, 2008; Okayasu, 2012a; Lorat et al., 2015; Nikitaki et al., 2016). Thus, the complexity and yield of clustered DNA damage increases with ionizing density (Ward, 1988; Goodhead, 2006).

However, clustered damage can also be induced even by a single radiation track through a cell.

Evidence Supporting this KER

The biological rationale linking the direct deposition of energy on DNA with an increase in DSB formation is strongly supported by numerous literature reviews that are available on this topic (J .F. Ward, 1988; Terato & Ide, 2005; Goodhead, 2006; Asaithamby et al., 2008; Hada & Georgakilas, 2008; Okayasu, 2012b; M. E. Lomax et al., 2013; Moore et al., 2014; Desouky et al., 2015; Sage & Shikazono, 2017; Jeggo, 2009). Ionizing radiation can be in the form of high energy particles (such as alpha particles, beta particles, or charged ions) or high energy waves (such as gamma-rays or X-rays). Ionizing radiation can break the DNA within chromosomes both directly and indirectly, as shown through using velocity sedimentation of DNA through neutral and alkaline sucrose gradients. The most direct path entails a collision between a high-energy particle or photon and a strand of DNA. The high-energy subatomic particles can interact with the orbital electrons of the DNA causing ionization (where electrons are ejected from atoms) and excitation (where electrons are raised to higher energy levels) (Joiner, 2009). These processes ultimately break the phosphodiester backbone.

Additionally, excitation of secondary electrons in the DNA allows for a cascade of ionization events to occur, which can lead to the formation of multiple damage sites (Joiner, 2009). As an example, high-speed electrons will traverse a DNA molecule in a mammalian cell within 10^-18 s and 10^-14 s, resulting in 100,000 ionizing events per 1 Gy dose in a 10 μm cell (Joiner, 2009). The amount of damage can be influenced by factors such as the cell cycle stage and chromatin structure. It has been shown that in more condensed, packed chromatin structures such as those present in intact cells and heterochromatin, it is more difficult for the DNA to be damaged (Radulescu et al., 2006; Agrawala et al., 2008; Falk et al., 2008; Venkatesh et al., 2016). In contrast, DNA damage is more easily induced in lightly-packed chromatin such as euchromatin, nucleoids, and naked genome DNA (Radulescu et al., 2006; Falk et al., 2008; Venkatesh et al., 2016).

DNA damage can be in the form of DSBs, single-strand breaks, base damage, or the crosslinking of DNA to other molecules  (Smith et al., 2003; Joiner, 2009; Christensen, 2014; Sage and Shikazono, 2017). Of the possible radiation-induced DNA damage types, DSB is considered to be the most harmful to the cell, as there may be severe consequences if this damage is not adequately repaired (Khanna & Jackson, 2001; Smith et al., 2003; Okayasu, 2012a; M. E. Lomax et al., 2013; Rothkamm et al., 2015).

A considerable fraction of DSBs can also be formed in cells through indirect mechanisms.  In this case, deposited energy can split water molecules near DNA, which can generate a significant quantity of reactive oxygen species in the form of hydroxyl free radicals (Ward, 1988; Desouky et al., 2015; Maier et al., 2016). Estimates using models and experimental results suggest that hydroxyl radicals may be present within nanoseconds of energy deposition by radiation (Yamaguchi et al., 2005). These short-lived but highly reactive hydroxyl radicals may react with nearby DNA. This will produce DNA damage, including single-strand breaks and DSBs (Ward, 1988; Desouky et al., 2015; Maier et al., 2016). DNA breaks are especially likely to be produced if the sugar moiety is damaged, and DSBs occur when two single-strand breaks are in close proximity to each other  (Ward, 1988).

Empirical data strongly supports this KER. The evidence presented below is summarized in table 1, here (click link). The types of DNA damage produced by ionizing radiation and the associated mechanisms, including the induction of DSBs, are reviewed by Lomax et al. (2013) and documents produced by international radiation governing frameworks (Valentin, 1998; UNSCEAR, 2000). Other reviews also highlight the relationship between DSB induction and the deposition of energy by radiation, and discuss the various methods available to detect these DSBs (Terato & Ide, 2005; Rothkamm et al., 2015; Sage & Shikazono, 2017). A visual respresentation of the time frames and dose ranges probed by the dedicated studies discussed here is shown in Figures 1 & 2 below.

Figure 1: Plot of example studies (y-axis) against equivalent dose (Sv) used to determine the empircal link between direct deposition of energy and DSBs. The z-axis denotes the equivalent dose rate used in each study. The y-axis is ordered from low LET to high LET from top to bottom.

Figure 2: Plot of example studies (y-axis) against time scales used to determine the empircal link between direct deposition of energy and DSBs. The z-axis denotes the equivalent dose rate used in each study. The y-axis is ordered from low LET to high LET from top to bottom.

Dose and Incidence Concordance

There is evidence in the literature suggesting a dose/incidence concordance between the direct deposition of energy by ionizing radiation and the incidence (Grudzenski et al., 2010) of DNA DSBs. Results from in vitro (Rogakou et al., 1999; Sutherland et al., 2000; Lara et al., 2001; Rothkamm and Lo, 2003; Kuhne et al., 2005; Sudprasert et al., 2006; Beels et al., 2009; Grudzenski et al., 2010; Shelke & Das, 2015; Antonelli et al., 2015; Franken et al., 2012; Frankenberg et al., 1999; Rydberg et al., 2002; Belli et al., 2000), in vivo (Sutherland et al., 2000; Rube et al., 2008; Beels et al., 2009; Grudzenski et al., 2010), ex vivo (Rube et al., 2008; Flegal et al., 2015)  and simulation studies (Charlton et al., 1989) suggest that there is a dose-dependent increase in DSBs with increasing deposition of energy across a wide range of radiation types (iron ions, X-rays, ultrasoft X-rays, gamma-rays, photons, and alpha particles) and radiation doses (1 mGy - 100 Gy). DSBs have been predicted to occur at energy deposition levels as low as 75 eV (Charlton et al., 1989). Although all the radiation types studied were able to induce DSBs, some types were found to be more damaging in terms of the number of DSBs induced per dose (Lara et al., 2001; Kuhne et al., 2005; Antonelli et al., 2015; Franken et al., 2012; Frankenberg et al., 1999).

Temporal Concordance

There is evidence suggesting a time concordance between the direct deposition of energy and the incidence of DSBs. A number of different models and experiments have provided evidence of DSBs seconds (Mosconi et al., 2011) or minutes after radiation exposure (Rogakou et al., 1999; Rothkamm and Lo, 2003; Rube et al., 2008; Beels et al., 2009; Kuefner et al., 2009; Grudzenski et al., 2010; Antonelli et al., 2015).  

Essentiality

Results from a number of antioxidant studies found that pre-treatment of in vitro and in vivo lymphocytes with various antioxidants resulted in reduced DNA damage in response to radiation exposure (results summarized in a review by (Kuefner et al., 2015)). Similar results were also found in numerous in vitro and in vivo studies using various cell types, rodents, and humans exposed to antioxidants prior to radiation (reviewed by (Smith et al., 2017)). This suggests that deposition of energy on DNA by ionizing radiation is required to produce DNA DSBs. 

Uncertainties and inconsistencies in this KER are as follows:

1. Studies have shown that dose-rates (Brooks et al., 2016) and radiation quality (Sutherland et al., 2000; Nikjoo et al., 2001; Jorge et al., 2012) are factors that can influence the dose-response relationship.  
2. Low-dose radiation has been observed to have beneficial effects and may even invoke protection against spontaneous genomic damage (Feinendegen, 2005; Day et al., 2007; Feinendegen et al., 2007; Shah et al., 2012; Nenoi et al., 2015). This protective effect has been documented in in vivo and in vitro, as reviewed by ICRP (2007) and UNSCEAR (2008) and can vary depending on the cell type, the tissue, the organ, or the entire organism (Brooks et al., 2016).
3. Depositing ionizing energy is a stochastic event; as such this can influence the location, degree and type of DNA damage imparted on a cell. As an example, studies have shown that mitochondrial DNA may also be an important target for genotoxic effects of ionizing radiation (Wu et al., 1999).

Quantitative Understanding of the Linkage

Quantitative understanding of this linkage suggests that DSBs can be predicted upon exposure to ionizing radiation. This is dependent on the biological model, the type of radiation and the radiation dose. In general, 1 Gy of radiation is thought to result in 3000 damaged bases (Maier et al., 2016), 1000 single-strand breaks, and 40 DSBs (Ward, 1988; Maier et al., 2016) . The table below provides representative examples of the calculated DNA damage rates across different model systems, most of which are examining DNA DSBs.

There is evidence of a response-response relationship between the deposition of energy and the frequency of DSBs. In studies encompassing a variety of biological models, radiation types and radiation doses, a positive, linear relationship was found between the radiation dose and the number of DSBs (Sutherland et al., 2000; de Lara et al., 2001; Rothkamm & Lo, 2003; Kuhne et al., 2005; Rube et al., 2008; Grudzenski et al., 2010; Shelke & Das, 2015; Antonelli et al., 2015; Frankenberg et al., 1999). There were, however, two exceptions reported. When human blood lymphocytes were irradiated with X-rays in vitro, a linear relationship was only found for doses ranging from 6 - 500 mGy; at low doses from 0 - 6 mGy, there was a quadratic relationship reported (Beels et al., 2009). Secondly, simulation studies predicted that there would be a non-linear increase in DSBs as energy deposition increased, with a saturation point at higher LETs (Charlton et al., 1989).

Data from temporal response studies suggests that DSBs likely occur within seconds to minutes of energy deposition by ionizing radiation. In a variety of biological models, the presence of DSBs has been well documented within 10 - 30 minutes of radiation exposure (Rogakou et al., 1999; Rube et al., 2008; Beels et al., 2009; Kuefner et al., 2009; Grudzenski et al., 2010; Antonelli et al., 2015); there is also evidence that DSBs may actually be present within 3 - 5 minutes of irradiation (Rogakou et al., 1999; Rothkamm & Lo, 2003; Rube et al., 2008; Grudzenski et al., 2010). Interestingly, one study that focussed on monitoring the cells before, during and after irradiation by taking photos every 5, 10 or 15 seconds found that foci indicative of DSBs were present 25 and 40 seconds after collision of the alpha particles and protons with the cell, respectively. The number of foci were found to increase over time until plateauing at approximately 200 seconds after alpha particle exposure and 800 seconds after proton exposure (Mosconi et al., 2011).

After the 30 minute mark, DSBs have been shown to rapidly decline in number. By 24 hours post-irradiation, DSB numbers had declined substantially in systems exposed to radiation doses between 40 mGy and 80 Gy (Rothkamm & Lo, 2003; Rube et al., 2008; Grudzenski et al., 2010; Russo et al., 2015; Antonelli et al., 2015), with the sharpest decrease documented within the first 5 hours (Rogakou et al., 1999; Rube et al., 2008; Kuefner et al., 2009; Grudzenski et al., 2010; Shelke and Das, 2015). Interestingly, DSBs were found to be more persistent when they were induced by higher LET radiation (Antonelli et al., 2015).

Some common clinical radiation modifiers include cisplatin, 5-fluorouracil, thiols, and nitroxides (reviewed in (Citrin and Mitchel, 2014)). Clinical approaches have identified many modulating radiation factors, which are often categorized as either sensitizers or protectors. Sensitizers enhance radiation-induced tumour cell killing, and protectors protect normal tissues from the deleterious effects of ionizing radiation (Citrin & Mitchel, 2014).

Not identified.

References

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Relationship: 1911: Increase, DNA strand breaks leads to N/A, Inadequate DNA repair

AOPs Referencing Relationship

Evidence Supporting Applicability of this Relationship

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).

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).

Temporal Concordance

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). 

Essentiality

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 in this KER are as follows:

1. 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).
2. 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).
3. 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.
4.  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).

Not identified.

Not identified.

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Zhu, C. et al. (2002), "Unrepaired DNA breaks in p53-deficient cells lead to oncogenic gene amplification subsequent to translocations.", Cell. 109(7):811–21. doi:10.1016/s0092-8674(02)00770-5.

Relationship: 164: N/A, Inadequate DNA repair leads to Increase, Mutations

AOPs Referencing Relationship

Evidence Supporting Applicability of this Relationship

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.

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).       

INSUFFICIENT REPAIR OF ALKYLATED DNA

Evidence in somatic cells

Empirical evidence to support this KER is primarily from studies in which synthetic oligonucleotides containing well-characterized DNA lesions were genetically engineered in viral or plasmid genomes and subsequently introduced into bacterial or mammalian cells. Mutagenicity of each lesion is ascertained by sequencing, confirming that replication of alkylated DNA (i.e., unrepaired DNA) causes mutations in addition to revealing the important DNA repair pathways and polymerases involved in the process. For example, plasmids containing O6-methyl or O6-ethylguanine were introduced into AGT deficient or normal Chinese hamster ovary cells (Ellison et al. 1989). Following replication, an increase in mutant fraction to 19% for O6-methylguanine and 11% for O6-ethylguanine adducts was observed in AGT deficient cells versus undetectable levels for control plasmids. The relationship between input of alkylated DNA versus recovered mutant fractions revealed that a large proportion of alkyl adducts were converted to mutations in the AGT deficient cells (relationship slightly sublinear, with more adducts than mutations). The primary mutation occurring was G:C-A:T transitions. The results indicate that replication of the adducted DNA caused mutations and that this was more prevalent with reduced repair capacity. The number of mutations measured is less than the unrepaired alkyl adducts transfected into cells, supporting that insufficient repair occurs prior to mutation. Moreover, the alkyl adducts occur prior to mutation formation, demonstrating temporal concordance.

Various studies in cultured cells and microorganisms have shown that the expression of AGT/MGMT (repair machinery – i.e., decrease in KE1) greatly reduces the incidence of mutations caused by exposure to methylating agents such as MNU and MNNG (reviewed in Kaina et al. 2007; Pegg 2011). Thomas et al. (2013) used O6-benzylguanine to specifically inhibit MGMT activity in AHH-1 cells. Inhibition was carried out for one hour prior to exposure to MNU, a potent alkylating agent. Inactivation of MGMT resulted in increased MNU-induced HPRT (hypoxanthine-guanine phosphoribosyltransferase) mutagenesis and shifted the concentrations at which induced mutations occurred to the left on the dose axis (10 fold reduction of the lowest observed genotoxic effect level from 0.01 to 0.001 µg/ml). The ratio of mutants recovered in DNA repair deficient cells was 3-5 fold higher than repair competent cells at concentrations below 0.01 µg/ml, but was approximately equal at higher concentrations, indicating that repair operated effectively to a certain concentration. Only at this concentration (above 0.01 µg/ml when repair machinery is overwhelmed and repair becomes deficient) do the induced mutations in the repair competent cells approach those of repair deficient. Thus, induced mutation frequencies in wild type cells are suppressed until repair is overwhelmed for this alkylating agent. The mutations prevented by MGMT are predominantly G:C-A:T transitions caused by O6-methylguanine.

Evidence in germ cells

That saturation of repair leads to mutation in spermatogonial cells is supported by work using the OECD TG488 rodent mutation reporter assay in sperm. A sub-linear dose-response was found using the lacZ MutaMouse assay in sperm exposed as spermatogonial stem cells, though the number of doses was limited (van Delft and Baan 1995). This is indirect evidence that repair occurs efficiently at low doses and that saturation of repair causes mutations at high doses. Lack of additional data motivated a dose-response study using the MutaMouse model following both acute and sub-chronic ENU exposure by oral gavage (O’Brien et al. 2015). The results indicate a linear dose-response for single acute exposures, but a sub-linear dose-response occurs for lower dose sub-chronic (28 day) exposures, during which mutation was only observed to occur at the highest dose. This is consistent with the expected pattern for dose-response based on the hypothesized AOP. Thus, this sub-linear curve for mutation at low doses following sub-chronic ENU exposure suggests that DNA repair in spermatogonia is effective in preventing mutations until the process becomes overwhelmed at higher doses.

Mutation spectrum: Following exposure to alkylating agents, the most mutagenic adducts to DNA in pre-meiotic male germ cells include O6-ethylguanine, O4-ethylthymine and O2-ethylthymine (Beranek 1990; Shelby and Tindall 1997). Studies on sperm samples collected post-ENU exposure in transgenic rodents have shown that 70% of the observed mutations are at A:T sites (Douglas et al. 1995). The mutations observed at G:C base pairs are almost exclusively G:C-A:T transitions, presumably resulting from O6-ethylguanine. It is proposed that the prevalence of mutations at A:T basepairs is the result of efficient removal of O6-alkylguanine by AGT in spermatogonia, which is consistent with observation in human somatic cells (Bronstein et al. 1991; Bronstein et al. 1992). This results in the majority of O6-ethylguanine adducts being removed, leaving O4- and O2-ethylthymine lesions to mispair during replication. Thus, lack of repair predominantly at thymines and guanines at increasing doses leads to mutations in these nucleotides, consistent with the concordance expected between diminished repair capabilities at these adducts and mutation induction (i.e., concordance relates to seeing these patterns across multiple studies, species and across the data in germ cells and offspring).

Inadequate repair of oxidative DNA lesions: In vitro studies

• AS52 Chinese hamster ovary cells (wild type and OGG1-overexpressing) were exposed to kJ/m² UVA radiation (Dahle et al., 2008).
  • Mutations in the gpt gene were quantified in both wild type and OGG1+ cells by sequencing after 13-15 days following 400 kJ/m² UVA irradiation
    • G:C-A:T mutations in UVA-irradiated OGG1+ cells were completely eliminated
    • G:C-A:T mutation frequency in wild type cells increased from 1.8 mutants/million cells to 3.8 mutants/million cells following irradiation – indicating incorrect repair or lack of repair of accumulated 8-oxo-dG
    • Elevated levels of OGG1 was able to prevent G:C-A:T mutations, while the OGG1 levels in wild type cells was insufficient, leading to an increase in mutants (demonstrates inadequate repair leading to mutations)
• Xeroderma pigmentosum complementation group A (XPA) knockout (KO) and wild type TSCER122 human lymphoblastoid cells were transfected with TK gene-containing vectors with no adduct, a single 8-oxo-dG, or two 8-oxo-dG adducts in tandem (Sassa et al., 2015).
  • XPA is a key protein in nucleotide excision repair (NER) that acts as a scaffold in the assembly the repair complex.
  • Mutation frequency was determined by the number of TK-revertant colonies
  • Control vector induced a mutation frequency of 1.3% in both WT and XPA KO
  • Two 8-oxo-dG in tandem on the transcribed strand were most mutagenic in XPA KO, inducing 12% mutant frequency compared to 7% in WT
  • For both XPA KO and WT, G:C-A:T transversion due to 8-oxo-dG was the most predominant point mutation in the mutants 
  • The lack of a key factor in NER leading to increased 8-oxo-dG-induced transversions demonstrates insufficient repair leading to increase in mutations 

Inadequate repair of oxidative DNA lesions: In vivo studies in mice

• Spontaneous mutation frequencies in the liver of Ogg1-deficient (-/-) Big Blue mice was measured at 10 weeks of age (Klungland et al., 1999).
  • Mutation frequencies were 2- to 3-fold higher in the Ogg1-/- mice than in wild type
  • Of the 16 base substitutions detected in Ogg1 -/- mutant plaques analyzed by sequencing, 10 indicated G:C-A:T transversions consistent with the known spectrum of mutation
  • The results support that insufficient repair of oxidized bases leads to mutation.
• Ogg1 knockout (Ogg1-/-) in C57BL/6J mice resulted in 4.2-fold and 12-fold increases in the amount of 8-oxo-dG in the liver compared to wild type at 9 and 14 weeks of age, respectively (Minowa et al., 2000).
  • In these mice, there was an average of 2.3-fold increase in mutation frequencies in the liver (measured between 16-20 weeks)
    • 57% of the observed base substitutions were G:C-A:T transversions, while 35% in wild type mice corresponded to this transversion.
    • Approximately 70% of the increase in mutation frequency was due to G to T transversions.
  • Concordantly, KBrO3 treatment resulted in a 2.9-fold increase in mutation frequency in the kidney of Ogg1 -/- mice compared to KBrO3-treated wild type (Arai et al., 2002).
    • G:C-A:T transversions made up 50% of the base substitutions in the Ogg1-/- mice.
  • Heterozygous Ogg1 mutants (Ogg1+/-) retained the original repair capacity, where no increase in 8-oxo-dG lesions was observed in the liver at 9 and 14 weeks (Minowa et al., 2000).
    • This observation was consistent even after KBrO3 treatment of the mice (Arai et al., 2002).
  • From these results, we can infer that OGG1 proteins are present in excess and that one functional copy of the gene is sufficient in addressing endogenous and, to a certain degree, chemical-induced oxidative DNA lesions.

Inadequate Repair of DSB

Empirical data obtained for this KER moderately supports the idea that inadequate DNA repair increases the frequency of mutations. The evidence presented below related to the inadequate repair of DSBs is summarized in table 5, here (click link). The review article by Sishc & Davis (2017) provides an overview of NHEJ mechanisms with a focus on the inherently error-prone nature of DSB repair mechanisms, particularly when core proteins of NHEJ are knocked-out. Another review also provides an overview of DSB induction, the repair process and how mutations may result, as well as the biological relevance of misrepaired or non-repaired DNA damage (Sage & Shikazono, 2017).

Dose and Incidence Concordance

There is evidence in the literature suggesting a dose/incidence concordance between inadequate DNA repair and increases in mutation frequencies. Evidence presented below related to the dose-response of mutation frequencies is summarized in table 2, here (click link). In response to increasing doses from a radiation stressor, dose-dependent increases in both measures of inadequate DNA repair and mutation frequency have been found. In an analysis that amalgamated results from several different studies conducted using in vitro cell-lines, the rate of DSB misrepair was revealed to increase in a dose-dependent fashion from 0 - 80 Gy, with the mutation rate also similarly increasing from 0 - 6 Gy (Mcmahon et al., 2016). Additionally, using a plant model, it was shown that increasing radiation dose from 0 - 10 Gy resulted in increased DNA damage as a consequence of inadequate repair.  Mutations were observed 2 - 3 weeks post-irradiation (Ptácek et al., 2001). Moreover, increases in mutation densities were found in specific genomic regions of cancer samples (namely promoter DNAse I-hypersensitive sites (DHS) and 100 bp upstream of transcription start sites (TSS)) that were also found to have decreased DNA repair rates attributable to inadequate nucleotide excision repair (NER) (Perera et al., 2016).
 

Interestingly, mutation rates have been shown to increase as the required DNA repair becomes more complex. Upon completion of DSB repair in response to radiation and treatment with restriction enzymes, more mutations were found in cases where the ends were non-complementary and thus required more complex DNA repair (1 - 4% error-free) relative to cases where ends were complementary (34 - 38% error-free) (Smith et al., 2001).

Temporal Concordance

There is evidence in the literature suggesting a time concordance between the initiation of DNA repair and the occurrence of mutations. For simple ligation events, mutations were not evident until 12 - 24 hours, whereas DSB repair was evident at 6 -12 hours. For complex ligation events, however, mutations and DSB repair were both evident at 12 - 24 hours. As the relative percent of DNA repair increased over time, the corresponding percent of error-free rejoining decreased over time in both ligation cases, suggesting that overall DNA repair fidelity decreases with time ((Smith et al., 2001).

Essentiality

There is evidence from knock-out/knock-down studies suggesting that there is a strong relationship between the adequacy of DNA repair and mutation frequency.  In all examined cases, deficiencies in proteins involved in DNA repair resulted in altered mutation frequencies relative to wild-type cases. There were significant decreases in the frequency and accuracy of DNA repair in cell lines deficient in LIG4 (Smith et al., 2003) and Ku80 (Feldmann et al., 2000); rescue experiments performed with these two cell lines further confirmed that inadequate DNA repair was the cause of the observed decreases in repair frequency  and accuracy (Feldmann et al., 2000; Smith et al., 2003). In primary Nibrin-deficient mouse fibroblasts, there was increased spontaneous DNA damage relative to wild-type controls, suggestive of inadequate DNA repair. Using the corresponding Nibrin-deficient and wild-type mice, in vivo mutation frequencies were also found to be elevated in the Nibrin-deficient animals (Wessendorf et al., 2014). Furthermore, mutation densities were differentially affected in specific genomic regions in cancer patients depending on their XPC status. Specifically, mutation frequencies were increased in XPC-wild-type patients at DHS promoters and 100 bp upstream of TSS relative to cancer patients lacking functional XPC (Perera et al., 2016) .  Lastly, in a study using WKT1 cells with less repair capacity, radiation exposure induced four times more mutations in these cells than in TK6 cell, which had a normal repair capacity (Amundson and Chen, 1996).

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.

Overall

• 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).

Quantitative Understanding of the Linkage

Thresholds for mutagenicity indicate that the response at low doses is modulated by the DNA repair machinery, which is effectively able to remove alkylated DNA at low doses [Gocke and Muller 2009; Lutz and Lutz 2009; Pozniak et al. 2009]. Kinetics of DNA repair saturation in somatic cells is described in Muller et al. [Muller et al. 2009].

For O-methyl adducts, once the primary repair process is saturated, in vitro data suggest that misreplication occurs almost every time a polymerase encounters a methylated guanine [Ellison et al. 1989; Singer et al. 1989]; however, it should be noted that this process can be modulated by flanking sequence. This conversion of adducts to mutations also appears to be reduced substantially in vivo [Ellison et al. 1989]. The probability of mutation will also depend on the type of adduct (e.g., O-alkyl adducts are more mutagenic than N-alkyl adducts; larger alkyl groups are generally more mutagenic, etc.). Overall, a substantive number of factors must be considered in developing a quantitative model.

Inadequate repair of oxidative lesions

The relationship between the quantity/activity of repair enzymes such as OGG1 in the cell and the quantity of oxidative lesions need to be better understood to define a threshold on the quantity of oxidative lesions exceeding basal repair capacity. Moreover, the proportion of oxidative lesions formed that lead to mutation versus strand breaks is not clearly understood.

Mutations resulting from oxidative DNA damage can occur via replicative polymerases and translesion synthesis (TLS) polymerases during replication, and during attempted repair. However, an in vitro study on TLS in yeast has shown that bypass of 8-oxo-dG by TLS polymerases during replication is approximately 94-95% accurate. Therefore, the mutagenicity of 8-oxo-dG and other oxidative lesions may depend on their abundance, not on a single lesion (Rodriguez et al., 2013). Applicability of this observation in mammalian cells needs further investigation. Information on the accuracy of 8-oxo-dG bypass in mammalian cells is limited.      

The most notable example of mutation arising from inadequate repair of DNA oxidation is G to T transversion due to 8-oxo-dG lesions. Previous studies have demonstrated higher mutation frequency of this lesion compared to other oxidative lesions; for example, Tan et al. (1999) compared the mutation rate of 8-oxo-dG and 8-oxo-dA in COS-7 monkey kidney cells and reported that under similar conditions, 8-oxo-dG was observed to be four times more likely to cause base substitution (Tan et al., 1999). 

Inadequate Repair of DSB

Quantitative understanding of this linkage is derived from the studies that examined DSB misrepair rates or mutation rates in response to a radiation stressor.  In general, combining results from these studies suggests that increased mutations can be predicted when DNA repair is inadequate. At a radiation dose of 10 Gy, the rate of DSB misrepair was found to be approximately 10 - 15% (Lobrich et al., 2000); this rate increased to 50 - 60% at a radiation exposure of 80 Gy (Kuhne et al., 2000; Lobrich et al., 2000; McMahon et al., 2016). For mutation rates in response to radiation across a variety of models and radiation doses, please refer to the example table below.

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).

Not identified.

Not identified.

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Relationship: 1912: N/A, Inadequate DNA repair leads to Increase, Chromosomal aberrations

AOPs Referencing Relationship

Evidence Supporting Applicability of this Relationship

The domain of applicability for this KER is multicellular eukaryotes at any stage of development, including plants (Varga & Aplan 2005; Schipler & Iliakis 2013; Manova & Gruszka 2015).

Key Event Relationship Description

Cells are exposed to many insults, both endogenous and exogenous, that may cause damage to their DNA. In response to this constant threat, cells have accordingly evolved many different pathways for repairing DNA damage (Pfeiffer & Goedecke, 2000; Hoeijmakers, 2001; Jeggo & Markus, 2015; Rode et al., 2016). When confronted with double strand breaks (DSBs), there are two common repair pathways employed by the cell: homologous recombination (HR) and non-homologous end-joining (NHEJ). In HR, a homologous sequence on a sister chromatid is used as a template, ensuring that no sequence information is lost over the course of repair (Ferguson & Alt, 2001; van Gent et al., 2001; Hoeijmakers, 2001; Jeggo & Markus, 2015; Schipler & Iliakis, 2013; Venkitaraman, 2002). However, this method of DNA repair may result in a loss of an allele leading to heterozygosity. This may occur if a non-homologous chromosome with a erronous sequence is used as the template instead of the homologous chromosome, thus leading to a loss of genetic information (Ferguson & Alt, 2001). Despite this possible error, HR is generally considered to be one of the more accurate methods of DNA repair because it does make use of a template (van Gent et al., 2001; Schipler & Iliakis, 2013; Venkitaraman, 2002) .  NHEJ, however, does not use a template and is generally described as being error-prone. This repair process allows for the direct religation of broken DNA ends without using template DNA as a guide (van Gent et al., 2001; Ferguson & Alt, 2001; Hoeijmakers, 2001; Venkitaraman, 2002; Schipler & Iliakis, 2013; Jeggo & Markus, 2015; Rode et al., 2016). In lieu of a template, NHEJ utilizes rapid repair kinetics to religate the broken ends before they have time to diffuse away from each other (Schipler & Iliakis, 2013), thus fitting two ‘sticky’ DNA ends back together (Danford, 2012). There is not, however, an inherent quality control check; as such, sections of DNA may be gained or lost, or the wrong ends may be rejoined (Schipler & Iliakis, 2013). There are two versions of this error-prone DNA repair: classical or canonical NHEJ (c-NHEJ), and alternative NHEJ (alt-NHEJ) (Schipler & Iliakis, 2013). It is not well understood when or why one pathway is selected over another (Venkitaraman, 2002; Schipler & Iliakis, 2013). It has been proposed that the phase of the cell cycle may influence repair pathway choice (Ferguson & Alt, 2001; Vodicka et al., 2018); for instance, HR is generally more common than NHEJ when sister chromatids are available in S and G2 phases of the cell cycle (Hoeijmakers, 2001; Venkitaraman, 2002). If both HR and c-NHEJ are compromised, alt-NHEJ, which is slower and more error-prone than c-NHEJ, is thought to be the stand-by repair mechanism (Schipler & Iliakis, 2013). 

If these repair processes are not able to properly and adequately repair the DNA, this may lead to the formation of chromosomal aberrations (CAs). CAs are defined as abnormalities in the chromosome structure, often due to losses or gains of chromosome sections or the entire chromosomes itself (van Gent et al., 2001). These abnormalities can take many different forms and can be classified according to several different schemes. CAs can be defined as breaks, which occur when DSBs are not rejoined, or as exchanges, where the presence of multiple DSBs results in misrejoining of the DNA ends (Danford, 2012; Registre et al., 2016). CA classes can be further subdivided into chromosome-type aberrations (CTAs) that affect both sister chromatids, and chromatid-type aberrations (CSAs), affecting only one chromatid (Danford, 2012) . Examples of CTAs include chromosome-type breaks, centric ring chromosomes, and dicentric chromosomes (which have two centromeres), while CSAs refer to chromatid-type breaks and chromatid exchanges (Hagmar et al., 2004; Bonassi et al., 2008). Other types of CAs that may occur include micronuclei (MN; small nucleus-like structures containing chromosome fragments enclosed by a nuclear membrane (Fenech & Natarajan, 2011; Doherty et al., 2016)), nucleoplasmic bridges (NPBs; a stretch of chromatin enclosed by a nuclear membrane that is attached to two centromeres (Fenech & Natarajan, 2011; Russo et al., 2015)), nuclear buds (NBUDs; a MN that is still connected to the nucleus by nucleoplasmic material (Fenech & Natarajan, 2011)), and copy number variants (CNVs;  base pair to megabase pair deletions or duplications of chromosomal segments (Russo et al., 2015)). CAs may also be classified as stable aberrations (translocations, inversions, insertions and deletions) and unstable aberrations (dicentric chromosomes, acentric fragments, centric rings and MN) (Hunter & Muirhead, 2009; Qian et al., 2016). 

Evidence Supporting this KER

There is strong biological plausibility for a relationship between inadequate repair of DNA damage and a corresponding increase in CAs. This is evident in a variety of reviews on the topic (van Gent et al., 2001; Hoeijmakers, 2001; Povirk, 2006; Weinstock et al., 2006; Lieber et al., 2010; Rode et al., 2016).

The two most common methods used to repair DSBs, which are one of the most dangerous types of DNA lesions, are HR and NHEJ. Mechanisms for these two methods of DNA repair are well-established and have been thoroughly reviewed (Van Gent et al. 2001; Hoeijmakers 2001; Lieber et al. 2010; Jeggo and Markus 2015; Sishc and Davis 2017). Briefly, HR requires a template DNA strand to repair damage and thus facilitates the invasion of the damaged strand with matching sequences on homologous chromosomes or sister chromatids (Ferguson and Alt 2001; van Gent et al. 2001; Hoeijmakers 2001; Jeggo and Markus 2015; Schipler and Iliakis 2013; Venkitaraman 2002). Proteins involved in the HR pathway include the RAD50 proteins, MRE11, BRCA1, and BRCA2 (Ferguson and Alt 2001; van Gent et al. 2001; Hoeijmakers 2001; Jeggo and Markus 2015; Venkitaraman 2002). In contrast to this relatively accurate form of DNA repair ( van Gent et al. 2001; Schipler and Iliakis 2013; Venkitaraman 2002), NHEJ is more error-prone. It does not require a template to guide repair, but simply re-ligates broken DNA ends back together (Van Gent et al. 2001; Ferguson and Alt 2001; Hoeijmakers 2001; Lieber et al. 2010; Schipler and Iliakis 2013; Jeggo and Markus 2015; Rode et al. 2016; Sishc and Davis 2017) Proteins used during NHEJ include the DNA-PK complex (encompassing Ku70, Ku80 and DNA-PK_cs), and the XRCC4-DNA ligase IV complex (Ferguson & Alt, 2001; van Gent et al., 2001; Hoeijmakers, 2001; Jeggo & Markus, 2015; Sishc & Davis, 2017).Interestingly, NHEJ is used in the biological V(D)J recombination process because its error-prone mechanism allows immune cells to develop a wide range of unique receptors for antigen detection (Ferguson & Alt, 2001; van Gent et al., 2001; Lieber, 2010).     

Damaged DNA in the form of DSBs can follow  three possible outcomes: the DSB is rejoined accurately, with no changes made to the genome; the DSB is left unrepaired and the ends diffuse away from each other; or the DSB is repaired incorrectly such that the repaired version is different from the original version (Danford, 2012). These latter two errors in repair (the complete absence of repair or inaccurate repair) could arise due to interruptions to the repair process that allow time for the broken ends to move away from each other before they can be rejoined, mis-rejoining of the wrong DNA ends, or post-repair alterations that modify the junction point and lead to nucleotide losses (Schipler and Iliakis 2013). Errors occurring during repair may be particularly detrimental if they interrupt or modify key genes, or if chromosome structures are created that cannot undergo proper mitosis (Schipler and Iliakis 2013).

The classic model of CA formation has centred around misrepair of DSBs. Exposing DNA to an endogenous or exogenous DSB-inducing agent directly results in DSBs, which may either persist or be misrepaired by inadequate repair mechanisms; in the event of this erroneous repair, CAs often eventually result (Bignold, 2009; Danford, 2012; Schipler & Iliakis, 2013) . Another model has been proposed that suggests CAs may actually be due to failure of enzymes that tether the DNA strands during the repair of enzyme-induced breaks in the DNA; the various pathways in the cell would likely employ assorted tethering enzymes. The numerous types of CAs would thus result from different kinds of tethering errors (Bignold 2009).

The type of CA that results may be dependent on the timing of inadequate repair. For example, DSBs may result in CSAs or CTAs depending on when during the cell cycle the DSB was incurred. DSBs that are not repaired before DNA duplication in the S-phase will be replicated and result in CTAs. If DSBs are incurred after the S-phase and are improperly repaired, CSAs  will result (Danford, 2012; Registre et al., 2016; Vodicka et al., 2018). Similarly, CNVs are thought to be induced during the DNA replication phase. Although the mechanism is not well studied, it has been suggested that stress during replication, in particular stalling replication forks, prompt microhomology-mediated mechanisms to overcome the replication stall, which often results in duplications or deletions. Two models that have been proposed to explain this mechanism include the Fork Stalling and Template Switching (FoSTeS) model, and the Microhomology-Mediated Break-Induced Replication (MMBIR) model (Lee et al. 2007; Hastings et al. 2009; Arlt et al. 2012; Arlt et al. 2014; Wilson et al. 2015).

The type of CA may also be dependent on the type of erroneous repair that occurs. Deletions or chromosome breaks may occur when DSBs are left unrepaired (Danford 2012). Deletions may also occur when nucleotides are removed at the junctions (Schipler and Iliakis 2013) or when the wrong DNA ends are religated (Venkitaraman 2002). Ligation of the incorrect ends of DNA DSBs may also lead to translocations (Ferguson & Alt, 2001;  Lieber, 2010; Povirk, 2006; Venkitaraman, 2002). This type of error may occur when there are two or more DSBs in close proximity to each other that are misrejoined, thus resulting in the exchange of genetic material and a translocated chromosome (Ferguson and Alt 2001; Povirk 2006). NHEJ has been shown to play a significant role in the generation of translocations ( Lieber 2010; Povirk 2006; Weinstock et al. 2006). Evidence for this comes from analysis of breakpoint junctions, which typically have little to no chromosomal homology when NHEJ repair is used (Povirk 2006; Weinstock et al. 2006); this was demonstrated in studies using translocation reporters (reviewed in Weinstock et al., 2006). There are, however, two types of NHEJ. c-NHEJ has been shown to suppress translocations (Simsek and Jasin 2010) , which may be due to its relatively rapid repair kinetics (Schipler and Iliakis 2013). Translocations are thus suggested to originate more often from alt-NHEJ (Simsek and Jasin 2010; Zhang and Jasin 2011; Schipler and Iliakis 2013) .

NHEJ is also thought to mediate the formation of other types of CAs. Based on analysis of breakpoint junctions in lung adenocarcinoma samples where reciprocal inversions were found between genes RET and KIF5B/CCDC6, the majority of the inversions were thought to be induced by NHEJ (Mizukami et al. 2014). Chromothripsis, which refers to a single event that results in a massive number of CAs localized to a single or very few chromosomes (Russo et al. 2015; Leibowitz et al. 2015; Rode et al. 2016), may also be linked to NHEJ. The single catastrophic event sparking chromothripsis likely induces a large quantity of DSBs, essentially shattering the chromosome(s). These DSBs are then processed mainly by the error-prone NHEJ, which results in a large number of CAs, including chromosomal rearrangements, CNVs, and loss of heterozygosity (Leibowitz et al. 2015; Rode et al. 2016).

Fusing two broken chromosomes may lead to the formation of dicentric chromosomes, which are characterized by the presence of two centromeres. Dicentrics may also be formed by telomere-to-telomere end fusions (Fenech and Natarajan 2011; Rode et al. 2016). Telomeres, composed of TTAGGG repeats, are important structures that protect the ends of chromosomes and ensure accurate replication (Ferguson and Alt 2001; Hoeijmakers 2001; Vodicka et al. 2018); these nucleoprotein structures are shortened (Vodicka et al. 2018) by approximately 100 base pairs after each division, and are only replenished in cell types expressing the enzyme telomerase (Hoeijmakers 2001). If the telomeres become critically short, they can be mistaken for broken DNA ends by DNA repair machinery, and thus may be ‘repaired’ by fusing the ends of two chromosomes together (Ferguson and Alt 2001; Vodicka et al. 2018). 

Dicentrics can also contribute to other types of CAs. During mitosis, dicentric chromosomes may be pulled to opposite ends of the cell by mitotic spindle (Ferguson and Alt 2001; Fenech and Natarajan 2011; Leibowitz et al. 2015; Rode et al. 2016). Because the ends of the chromosomes are fused, this can lead to the formation of an anaphase chromatin bridge between the daughter cells (Russo et al. 2015; Leibowitz et al. 2015; Rode et al. 2016). If this bridge persists beyond anaphase, it may become enclosed in a nucleoplasmic membrane along with the nucleus, thus generating a NPB (Fenech and Natarajan 2011). Eventually, however, these bridges do break (Ferguson and Alt 2001; Fenech and Natarajan 2011; Russo et al. 2015; Leibowitz et al. 2015; Rode et al. 2016); the break is nearly always uneven, meaning that one daughter cell will be missing genetic material and one will have extra genetic material (Fenech and Natarajan 2011). These fragments, with their ‘sticky’ ends from the break, may further propagate the formation of CAs by being ligated inappropriately to another chromosome. Thus the cycle, known as the breakage-fusion-bridge (BFB) cycle, is propagated and further contributes to chromosomal instability (Ferguson and Alt 2001; Fenech and Natarajan 2011; Russo et al. 2015; Leibowitz et al. 2015; Rode et al. 2016) . 

MN may also be formed during this BFB cycle. When the anaphase bridges break, the remaining chromosome fragments may be packaged by a nuclear membrane into its own mini nucleus, thus forming an MN. MN may also enclose acentric chromosome fragments, chromatid fragments, or even entire chromosomes that were not properly segregated during mitosis (Fenech and Natarajan 2011; Doherty et al. 2016). Similar to MN in structure are NBUDs; the only difference between these two structures is that NBUDs are still attached to the nucleus by nucleoplasmic material. A NBUD is formed if there is amplified DNA that needs to be removed; this amplified material is often segregated from the other DNA at the periphery of the nuclear membrane and excluded from the nucleus by budding, resulting in a NBUD. Additionally, NBUDs may also result from NPB breakages (Fenech and Natarajan 2011).

There is moderate empirical evidence supporting the relationship between inadequate DNA repair and the frequency of CAs. The evidence presented below is summarized in table 6, here (click link). Several reviews discuss evidence that associates these two events (Ferguson and Alt 2001; van Gent et al. 2001; Sishc and Davis 2017; Venkitaraman 2002). Overall, however, there is weak empirical evidence available supporting a dose and incidence concordance, little empirical evidence supporting a temporal concordance, and strong empirical evidence supporting essentiality for this KER. 

Dose and Incidence Concordance

There is weak empirical evidence available that directly examines the dose and incidence concordance between DNA repair and CAs within the same study. There are, however, studies that use an ionizing radiation stressor to examine dose concordance of either inadequate DNA repair in response to radiation exposure, or CA frequencies in response to irradiation. In an analysis that amalgamated results from several different studies conducted using in vitro experiments, the rate of DSB misrepair was revealed to increase in a dose-dependent fashion from 0 - 80 Gy (Mcmahon et al. 2016). Similarly, there was a clear correlation between radiation dose (i.e., increasing amounts of energy deposition) between 0 - 10 Gy and different clastogenic endpoints (Thomas et al. 2003; Tucker et al. 2005A; George et al. 2009; Arlt et al. 2014; Balajee et al. 2014; Lin et al. 2014; Suto et al. 2015; Mcmahon et al. 2016) . Overall, this suggests that exposure to radiation may increase both inadequate repair of DNA damage and the frequency of CAs in a dose-dependent fashion. More studies, however, are required to better assess the dose and incidence concordance of this KER.

Temporal Concordance

Temporal concordance between inadequate DNA repair and CA frequency is not well established. One study using cells pretreated with a DNA-PK inhibitor and irradiated with gamma rays found that DNA repair and MN were evident when they were assessed at 3 hours post-irradiation and 24 hours post-irradiation, respectively (Chernikova et al. 1999). This study does therefore suggest that there may be temporal concordance between these two events.  Other radiation-based studies examining these two events separately, however, do not provide clear evidence of temporal concordance between DNA repair and CA frequency. 

Essentiality

There is strong evidence for essentiality. Numerous studies demonstrate that simply knocking-out one gene involved in DNA repair, without any other added stressor, is enough to increase the frequency of CAs in several types of cells (Karanjawala et al. 1999; Patel et al. 1998; Wilhelm et al. 2014). Further fortifying this relationship, addition of a DSB-inducing stressor to these DNA repair knock-out cells also significantly increases CA levels relative to wild-type cells receiving the same treatment (Cornforth and Bedford 1985; Simsek and Jasin 2010; Lin et al. 2014; Mcmahon et al. 2016) .

Inhibitor studies have also found similar results. Two strains of wild-type cells that were treated with hydroxyurea, which is known to inhibit DNA repair, both had increased CAs relative to untreated wild-type cells (Wilhelm et al. 2014). Similarly, immortalized myeloid cell lines, cells from patients with myeloid leukemia, and cells from healthy donors were all found to have dose-dependent decreases in ligation efficiency after being treated with increasing doses of antibodies against various NHEJ proteins (Heterodimer et al. 2002). Lastly, cells that were pretreated with DNA-PK inhibitor wortmannin prior to being irradiated were found to have not only increased levels of MN, but also decreased rates of DNA rejoining (Chernikova et al. 1999). 

A rescue experiment provided further evidence of the essential role DNA repair plays in relation to CA frequencies. Inhibition of NHEJ through knocking out either Ku70 or Xrcc4 resulted in higher CA frequencies in the form of translocations; when Xrcc4 was transiently expressed in Xrcc4-/- cells, translocations were significantly decreased by 5-fold(Simsek and Jasin 2010) . This provides strong evidence that the NHEJ repair pathway plays an important role in the formation of CAs, specifically translocations.

Uncertainties in this KER are as follows:

1. In an experiment using both wild-type and Ku70-/- cells, knock-down of alt-NHEJ protein CtIP resulted in significantly decreased translocations in both cell types. When CtIP expression was rescued, translocation frequencies in these cells also returned to normal levels. This however, is opposite to results obtained in a similar study, where knock-out of Ku70 or Xrcc4 led to increased translocation frequency, and Xrcc4 rescue experiments resulted in decreased translocations (Simsek and Jasin 2010). It should be noted that alt-NHEJ is thought to be the major repair pathway responsible for generating translocations (Simsek and Jasin 2010; Zhang and Jasin 2011; Schipler and Iliakis 2013).  
2. There is currently discussion regarding the accuracy of HR relative to NHEJ. Traditionally HR has been considered the more accurate type of DNA repair, while NHEJ is classically described as error-prone. There is emerging evidence, however, suggesting that HR may in fact be a mutagenic process. Evidence supporting HR as an error-prone repair pathway has been reviewed (Guirouilh-barbat et al. 2014).

Quantitative Understanding of the Linkage

Quantitative understanding of this linkage is lacking. Most data is derived from the studies that examined DSB misrepair rates or CA rates in response to a radiation stressor.  In terms of inadequate DNA repair, the rate of DSB misrepair was found to be approximately 10 - 15% at 10 Gy of radiation (Lobrich et al. 2000); this rate increased to 50 - 60% at a radiation exposure of 80 Gy (Kuhne et al. 2000; Lobrich et al. 2000; Mcmahon et al. 2016). It is not known, however, how this rate of inadequate repair directly relates to CA frequency. Overall, more studies are required that directly assess this relationship.

Studies directly examining the response-response relationship between inadequate repair and CA frequency are lacking. One study examined both DNA repair and CA frequency in cells exposed to DNA-PK inhibitor wortmannin. There was a negative, approximately linear relationship between DNA repair and increasing wortmannin dose, and a positive, approximately linear relationship between MN frequency and increasing wortmannin dose; this suggests that as adequate DNA repair declines, CA frequency increases (Chernikova et al. 1999). More studies are required, however, that directly assess the quantitative response-response relationship between inadequate DNA repair and CAs. 

The time scale between inadequate DNA repair and the increased frequency of CAs has not been well-established. Most data comes from studies that assess only one of these events in relation to a radiation stressor rather than assessing the timing of the events relative to each other. More studies are thus required that directly assess this relationship.

Not identified.

Not identified.

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Relationship: 1978: Increase, Mutations leads to Increase, Cell Proliferation

AOPs Referencing Relationship

Evidence Supporting Applicability of this Relationship

The domain of applicability pertains to all multicellular organisms, as cell proliferation and death regulate tissue homeostasis (Pucci et al. 2000).

Key Event Relationship Description

Mutations are defined as changes in the DNA sequence, which could occur in the form of deletions, insertions, missense mutations, nonsense mutations or frameshift mutations (Bertram, 2001; Danesi et al., 2003; Lodish, 2000). Elevated mutation frequencies may impact cellular activities by activating or inhibiting essential processes that control the natural course of cell proliferation (Bertram, 2001; Vogelstein and Kinzler, 2004; Lodish, 2000). Increased rates of cellular proliferation may arise due to mutations that activate proto-oncogenes, which results in sustained signaling for cell growth (Bertram, 2001; Vogelstein and Kinzler, 2004; Larsen and Minna, 2011; Lodish, 2000) and due to mutations that inactivate tumour suppressor genes (TSGs), resulting in the removal of cell cycle inhibition and/or decreased cell death signaling (Bertram, 2001; Vogelstein and Kinzler, 2004; Lodish, 2000). Mutations altering gene expression or protein activity can enable cells to escape growth inhibition by increasing resistance to apoptosis, or other inhibitory signals, or by escape of cell cycle checkpoints. Alternatively, mutations can stimulate growth by activating proliferative pathways such as EGFR.

Evidence Supporting this KER

There is a strong biological plausibility for a relationship between increasing mutation frequencies and increasing cellular proliferation.  This relationship is especially evident when examining the molecular biology of carcinogenesis. It is well-known that exposure of cells to a DNA-damaging agent, such as ionizing radiation, may result in damage to the DNA that manifests as genomic instability, including mutations. If enough mutations accumulate in critical genes, cells may begin to proliferate uncontrollably. This, alongside other events, may eventually result in tumourigenesis and cancer (reviewed in Bertram, 2001; Vogelstein and Kinzler, 2004; Panov, 2005; Lodish, 2000). In fact, one of the hallmarks of cancer is sustained proliferative signalling, and one of the enabling characteristics of this increased proliferation is genomic instability/mutations (Hanahan and Weinberg, 2011).

For a mutation to occur, damaged DNA must be passed on to the next generation (Bertram, 2001).  To prevent the propagation of erroneous DNA, there are specific cell cycle checkpoints that must be passed before DNA replication and mitosis can proceed. One of the most important checkpoints for committing to cell proliferation occurs during late G1 (Bertram, 2001; Lodish, 2000). This checkpoint is managed by retinoblastoma protein (RB), transcription factor E2F, and transcription factor p53. In a resting cell, RB is tightly bound to E2F; when growth factor signals are present, proteins are activated that phosphorylate RB, resulting in a conformation change and the release of E2F. This transcription factor then initiates transcription of genes required for DNA synthesis and thus cell proliferation. If there is damage to the DNA, p53 is upregulated and binds to unphosphorylated RB, thereby preventing the dissociation of RB and E2F (Bertram, 2001). This gives the cell enough time to repair the damaged DNA prior to DNA replication, and thus minimizes the propagation of the DNA errors. Existing mutations in the checkpoint genes, however, may compromise this process. For example, if mutations in p53 render it non-functional, damaged DNA will not be stopped at the checkpoint and will continue to be synthesized, despite the damage. Accumulation of mutations in this manner may affect genes that impact cell proliferation rates (Bertram, 2001; Lodish, 2000). There are three categories of genes that, if mutated, may allow for uncontrolled cell proliferation: proto-oncogenes, TSGs, and caretaker/stability genes. 

Proto-oncogenes are defined as genes that, when activated, promote cellular proliferation (Bertram, 2001; Lodish, 2000); they have been likened to the gas pedal of the car (Vogelstein and Kinzler, 2004). These genes are particularly dangerous if they are rendered abnormally active by gain-of-function (GOF) mutations; this may result in cellular proliferation being aberrantly activated (Bertram, 2001; Vogelstein and Kinzler,, 2004; Larsen and Minna 2011; Lodish, 2000).  Two common examples of mutated proto-oncogenes that contribute to increased cell proliferation rates are EGFR and KRAS. The EGFR gene encodes the epidermal growth factor receptor (EGFR), a trans-membrane protein with tyrosine kinase activity. Binding of growth factors to EGFRs results in receptor dimerization, autophosphorylation, and propagation of pro-proliferative signals to the nucleus (Danesi et al., 2003; Santos et al., 2010; Larsen and Minna, 2011; NIH, 2018 EGFR). KRAS is responsible for making the KRAS protein, which is a G-protein with GTPase activity that is used in the RAS/MAPK signalling pathway. When a signal that promotes cellular growth is detected, KRAS binds to GTP and activates downstream signalling molecules, thus facilitating signal propagation to the nucleus (Adjei, 2001; Panov, 2005; Jancik et al., 2010; NIH, 2018 KRAS). Mutations that render these receptors constitutively active would thus result in increased rates of cellular proliferation (Sanders and Albitar, 2010).

TSGs, which are analogous to the brakes in a car (Vogelstein and Kinzler, 2004; Lodish, 2000), are genes that negatively regulate cellular growth by preventing proliferation and in some cases, promoting apoptosis (Bertram, 2001; Vogelstein and Kinzler, 2004; Panov, 2005; Sanders and Albitar, 2010; Lodish, 2000). Many of the cell cycle checkpoint proteins and proteins controlling cell death are TSGs (Bertram, 2001; Lodish, 2000). Loss-of function (LOF) mutations that result in the inactivation of these TSGs may thus promote cellular proliferation (Bertram, 2001; Vogelstein and Kinzler, 2004; Lodish, 2000). A common example of a mutated TSG is TP53, which encodes the p53 protein. As mentioned above, p53 is a cell checkpoint protein that delays replication when damaged DNA is present; if damage is severe enough, p53 may also activate an apoptotic pathway (Bertram, 2001; Danesi et al., 2003; Panov, 2005; Larsen and Minna, 2011; Lodish, 2000, NIH 2018c). Inactivating mutations in p53 thus allow for unhindered progression through the cell cycle, resulting in higher cell proliferation rates (Danesi et al., 2003).

Finally, caretaker/stability genes encode for proteins involved in the detection, repair and prevention of DNA damage (Vogelstein and Kinzler 2004; Hanahan and Weinberg 2011).  Genes involved in mismatch repair (MMR), nucleotide excision repair (NER) and base-excision repair (BER) pathways are examples of caretaker/stability genes (Vogelstein and Kinzler, 2004). Mutations in these genes may compromise aspects of DNA repair—the detection of damage, the initiation of repair, the repair process itself, or the removal of mutagens that could possibly damage DNA—thus allowing for more mutations to accumulate in the genome than usual (Hanahan and Weinberg, 2011). Although all genes may suffer from increased mutation rates when caretaker/stability genes are improperly functioning, mutations in TSGs and proto-oncogenes are the main contributors to increased cellular proliferation (Vogelstein and Kinzler, 2004). Caretaker/stability genes are similar to TSGs in that disruption of both alleles must occur for the gene function to be compromised (Vogelstein and Kinzler, 2004; Hanahan and Weinberg, 2011).

There is moderate empirical evidence supporting the relationship between mutations and the cellular proliferation. The evidence presented below is summarized in table 7, here (click link). There are some available reviews that provide evidence for this relationship in the context of carcinogenesis (Welcker 2008, Kim 2018, Iwakuma 2007, Muller 2011), as one of the hallmarks of this disease is high levels of cellular proliferation (Hanahan and Weinberg 2011). Another review article explores the relationship between mutation accumulation and cellular proliferation through discussion of the stem cell division theory of cancer, and how it compares to the somatic mutation theory of cancer (López-lázaro 2018).  Overall, however, there is little empirical evidence available supporting dose and incidence concordance, little empirical evidence supporting temporal concordance, and strong empirical evidence supporting essentiality for this KER.  Some evidence from human epidemiology association and genetic studies also provides support for this KER.

Dose and Incidence Concordance

There are few studies available that assess the dose and incidence concordance between mutations and cell proliferation. One study providing dose information on this particular relationship analyzed the effect of sequentially adding mutations to mouse lung epithelial cells. Addition of mutations in the form of LT (suppression of p53 and pRB) or Kras(G12V) (an activated oncogene) on their own to lung epithelial cells did not increase tumour volume, but a combination of these genetic manipulations resulted in increasing tumour volume (suggestive of increased cell proliferation) over 40 days. The same results for LT and EGFR(ex19del) genetic manipulations were also achieved. This suggests that addition of multiple mutations increases cell proliferation (Sato et al. 2017). More studies, however, are required to directly assess this particular aspect of the relationship between mutations and cellular proliferation.

Time Concordance

Few studies are available that study the time concordance between mutations and cell proliferation. The timing between these two events is explored in a review that discusses theories of carcinogenesis. The somatic mutation theory of cancer states that accumulation of mutations results in higher rates of cellular proliferation, which eventually leads to cancer. A component of the stem cell division theory of cancer also states that an increased mutation burden may elevate rates of stem cell divisions in late carcinogenesis; however, a high frequency of stem cell division in the initial stages of cancer development is thought to be a key factor that contributes to mutation accumulation (López-lázaro 2018). More research is thus required to definitively determine whether mutations occur prior to increased rates of cellular proliferation.

Essentiality

There is strong evidence for the essentiality component of this KER. Numerous studies indicate that cellular proliferation is increased in biological systems with genetically manipulated TSGs and/or proto-oncogenes. It is important to note that uncontrolled cellular proliferation is a hallmark of human cancers (Hanahan and Weinberg 2011); the Catalogue of Somatic Mutations in Cancer (COSMIC) includes over 136,000 coding mutations in over 500,000 tumour samples (83 major cancer genes and 49 fusion gene pairs) and this number is continually increasing (Forbes et al. 2011). The managers of COSMIC note that key amongst all of these genes is TP53. Several review articles that focussed on genetic manipulations of TP53 demonstrated that mutant or knocked-out p53 increased carcinogenesis across a variety of biological systems (Iwakuma and Lozano 2007; Muller et al. 2011; Kim and Lozano 2018). Furthermore, a number of studies that measured cellular proliferation directly found that both cells and mice lacking p53 had increased rates of cell proliferation (Hundley et al. 1997; Lang et al. 2004; Ventura et al. 2007; Duan et al. 2008; Li and Xiong 2017), in addition to modifications to the cell cycle such that more cells were found in the S- and G2/M phases and less in the G1 phase (Hundley et al. 1997).  Some p53 mutations, including 515A, may also result in increased cellular proliferation (Lang et al. 2004). Further underlining the importance of p53 in controlling cellular proliferation, restoration of p53 in a p53-/- mouse model resulted in a significant size reduction in 7 out of 10 tumours, with some tumours disappearing altogether (Ventura et al. 2007).  

Manipulations to other genes have also been shown to affect cellular proliferation. A review article centred on the tumour suppressor FBW7, which is a ubiquitin ligase that plays a role in degrading proto-oncogene products and thus controlling cellular proliferation, demonstrated that mutations to FBW7 may contribute to carcinogenesis (Welcker and Clurman 2008). Knock-out of prostate SPOP (an E3 ubiquitin ligase adaptor commonly mutated in primary prostate adenocarcinoma) in Spop^fl/fl;PBCre(+) mice resulted in prostates with significantly higher masses, significantly more cellular proliferation, and increased expression of c-MYC protein relative to prostates from Spop^fl/fl;PBCre(-) controls with normal prostate SPOP expression. Furthermore, there was a strong inverse correlation between c-MYC activity and SPOP mRNA levels in two independent prostate cancer patient cohorts, suggesting that c-MYC upregulation in the absence of SPOP may be responsible for the increased cellular proliferation (Geng et al. 2017). Similarly, mouse embryonic fibroblasts lacking Cul9, a scaffold protein for assembly of E3 ubiquitin ligases, had an increased cellular proliferation rate and an increased number of cells in the S-phase of the cell cycle relative to wild-type controls. Cul9 mutant cells also showed similar cellular proliferation rates to Cul9-/- cells. In contrast, Arf-/- cells, p53-/- cells, and Cul9-/-p53-/- double knock-out cells had significantly higher cellular proliferation rates relative to the Cul9-/- and Cul9 mutant cells; all of these mutant cells, however, showed increased proliferation relative to wild-type cells (Li and Xiong 2017).

Inhibitor studies further highlight the role of mutations in increasing cellular proliferation. Mouse lung epithelial cells transformed with both Large T-antigen (LT; suppresses TSGs p53 and pRB) and activated oncogene Kras(G12V) or EGFR(ex19del) resulted in increased tumour volumes, which is suggestive of cell proliferation. Increasing concentrations of MEK inhibitor, which blocks the signalling pathway downstream of both Kras and EGFR, caused declines in cell number in the two transformed cell lines and in the parental lung epithelial cells. An EGFR inhibitor, which blocks signalling downstream of EGFR but upstream of Kras, had no effect on the transformed cells with activated Kras, but caused rapid declines in cell proliferation of transformed cells with activated EGFR. Altogether, these inhibitor studies suggest that the activated oncogene has an important role in promoting high rates of cell proliferation (Sato et al. 2017).

Human epidemiology association and genetic studies

Association studies in humans clearly show the correlation between mutations in specific genes and the proliferative status of human tumours. Human lung adenocarcinoma tumours were assessed for mutational status of KRAS, TP53 and STK11, and cellular proliferation levels were measured in the mutant tumours relative to the wild-type tumours. Overall, mutations in TP53 were associated with significantly increased proliferation levels regardless of the mutational status of KRAS. In contrast, mutations in STK11, either alone or in combination with KRAS mutations, were not associated with increased proliferation (Schabath et al. 2016). Assessment of breast cancer tumours demonstrated that those with low BRCA1 expression displayed increased cellular proliferation relative to those with high BRCA1 expression, as measured by nuclear Ki-67 levels (Jarvis et al. 1998).

Uncertainties in this KER are as follows:

1. The location of the mutation will be critical in determining the downstream effects. This can also be modulated by an individual’s susceptibility (Loewe and Hill 2010).
2. Although activating mutations in oncogenes such as RAS and MYC may induce abnormally high rates of cellular proliferation, extremely high levels of these proteins may actually lead to the opposite—cells may enter into a state of senescence and cease proliferation (Hanahan and Weinberg 2011).\
3. Cellular proliferation may be impacted by circadian cycles, such that disruptions to this natural circadian rhythm may also affect the cell cycle (Shostak 2017).

Quantitative Understanding of the Linkage

Data establishing a quantitative understanding between mutation frequency and cellular proliferation was not identified. More research is required to establish the quantitative relationship between these two events.

Data establishing a response-response relationship between mutation frequency and cellular proliferation was not identified. More research is required to establish the response-response relationship between these two events.

Although the time scale is not well-established for this KER, there are a few studies that have examined how cellular proliferation changes overtime in the presence of mutations. In Cul9-/- mouse embryonic fibroblasts, a higher proliferation rate relative to Cul9+/+ cells was evident by 3 days in culture (Li and Xiong 2017). A similar relationship was observed in mouse embryonic fibroblasts with p53 manipulations. Increased proliferation in p53-/-, p53 515A/+ and p53 515A/515A relative to p53+/- and p53+/+ cells was present by the fourth day in culture (Lang et al. 2004).  Examination of population doublings in various cell lines found that Cul9-/- and Cul9 mutant cells had higher population doublings than wild-type cells by approximately passage 7; Arf-/-, p53-/-, and Cul9-/-p53-/- cells, however, displayed even higher rates of population doublings by passage 6  (Li and Xiong 2017). Additionally, tumour growth in mice inoculated with lung epithelial cells engineered with LT (suppresses p53 and pRB) and an activated oncogene (either EGFR or KRAS) was monitored over 40 days post-injection. Relative to mice inoculated with either LT-lung epithelial cells or activated oncogene-lung epithelial cells, mice inoculated cells containing both mutations had detectable tumours by approximately day 10 - 12 post-injection; the volumes of these tumours continued increasing until the end of the experiment (Sato et al. 2017).

There were also differences in the rate of DNA synthesis over time, which could possibly indicate higher rates of cell division. In all cell types examined (p53-/-, p53+/- and p53+/+, p53 515A/+, and p53 515A/515A), DNA synthesis declined over the first 6 days in culture, though the mutant p53 lines always had higher synthesis rates than p53-/-, p53+/- and p53+/+ cells. During culture days 6 - 10, DNA synthesis in the mutant p53 lines drastically increased, while the other p53 lines remained at the same relatively low level of synthesis (Lang et al. 2004).  

Proliferation increases the likelihood that existing DNA damage will result in mutation and creates new mutations through errors in replication.

It is generally accepted that proliferation increases the risk of mutation and cancer (Preston-Martin, Pike et al. 1990). DNA damage that has not been completely or correctly repaired when a cell undergoes mitosis can be fixed in the genome permanently as a mutation, to be propagated to future daughter cells. Incomplete DNA repair can also cause additional DNA damage when encountered by replicative forks. Therefore, in the presence of any DNA damage (and there is a background rate of damage in addition to any other genotoxic stimuli) mutations will increase with cell division (Kiraly, Gong et al. 2015). Mutation-prone double strand breaks can also arise from replicative stress in hyperplastic cells including hyperplasia arising from excess growth factor stimulation (Gorgoulis, Vassiliou et al. 2005). This relationship between proliferation and mutation is thought to drive a significant portion of the risk of cancer from estrogen exposure since breast cells proliferate in response to estrogen or estrogen plus progesterone and risk increases with cumulative estrogen exposure (Preston-Martin, Pike et al. 1990).

Not all proliferating tissue shows replicative stress and DSBs - tissue with a naturally high proliferative index like colon cells don’t show any sign of damage (Halazonetis, Gorgoulis et al. 2008). Additional factors are therefore required beyond replication for damage and mutation from replicative stress, but replication is essential for the expression of these factors.

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Relationship: 1979: Increase, Chromosomal aberrations leads to Increase, Cell Proliferation

AOPs Referencing Relationship

Evidence Supporting Applicability of this Relationship

The domain of applicability pertains to all multicellular organisms, as cell proliferation and death regulate tissue homeostasis (Pucci et al., 2000).

Key Event Relationship Description

CAs are defined as abnormalities in the chromosome structure, often due to losses or gains of chromosome sections or the entire chromosomes itself, or chromosomal rearrangements (van Gent et al., 2001). These aberrant structures can come in a multitude of different forms. Types of CAs include: inversions, insertions, deletions, translocations, dicentric chromosomes (chromosomes that contain two centromeres, often resulting from telomere end fusions (Fenech & Natarajan 2011; Rode et al., 2016), centric ring chromosomes, acentric chromosome fragments, micronuclei (MN; small nucleus-like structures containing entire chromosomes or chromosome fragments (Fenech & Natarajan, 2011; Doherty et al., 2016), nucleoplasmic bridges (NBPs; a corridor of nucleoplasmic material containing chromatin that is attached to both daughter cell nuclei), nuclear buds (NBUDs; small MN-type structures that are still connected to the main nucleus (Fenech & Natarajan, 2011), and copy number variants (CNVs; deletions or duplications of chromosome segments (Russo et al., 2015).

If these CAs affect genes involved in controlling the cell cycle, this may result in increased cellular proliferation. There are three types of genes that, if modified, may result in high rates of proliferation: proto-oncogenes, tumour suppressor genes (TSGs), and caretaker/stability genes (Vogelstein & Kinzler, 2004; Hanahan & Weinberg, 2011). Furthermore, gene fusions that result from CAs have also been implicated in augmenting cellular proliferation (Sanders & Albitar, 2010; Ghazavi et al., 2015; Kang et al., 2016).

Evidence Supporting this KER

There is a strong biological plausibility for a relationship between CAs and rates of cellular proliferation. This is particularly emphasized in the context of carcinogenesis, as high cellular proliferation is a known hallmark of cancer, and an enabling characteristic of increased proliferation is genomic instability (Hanahan & Weinberg, 2011).Topical reviews are available documenting the contribution of CAs to cellular proliferation and/or cancer development  (Mes-Masson & Witte, 1987; Bertram, 2001; Vogelstein & Kinzler, 2004; Ghazavi et al. ,2015; Kang et al., 2016). The link between chromosomal instability (CIN), which describes the rate of chromosome gains and losses, and cancer development has also been well documented (Thompson et al., 2017; Gronroos, 2018; Targa & Rancati, 2018; Lepage et al., 2019).

Many CAs are thought to be formed through two main mechanisms: inadequate repair of DNA damage, and errors in mitosis. If there is damage to the DNA that the cell is unable to properly repair, the unrepaired lesion may translate into a CAs (Bignold, 2009; Danford, 2012; Schipler & Iliakis, 2013); the type of resulting CA is often influenced by the cell cycle stage when the damage occurred (Danford, 2012; Registre et al., 2016; Vodicka et al., 2018), and the type of erroneous repair (Ferguson & Alt, 2001; Povirk, 2006; Bignold, 2009; Danford, 2012; Schipler & Iliakis, 2013). Errors made during repair may be particularly detrimental if they interrupt or modify critical genes, or if chromosome structures are created that cannot undergo mitosis (Schipler & Iliakis, 2013). Similarly, errors in mitosis that prevent chromosomes from being properly segregated may also lead to CAs. These errors could be due to by improper timing of centrosome separation, the presence of extra centrosomes, inappropriate mitotic spindle assembly and attachment to kinetochores (found on the centromeres), and incorrect sister-chromatid cohesion (Levine & Holland, 2018).

The presence of CAs in cells may be particularly detrimental if they alter the rate of cellular proliferation by affecting  genes that control the cell cycle, namely proto-oncogenes, TSGs (Bertram, 2001; Vogelstein & Kinzler, 2004) or caretaker/stability genes (Vogelstein & Kinzler, 2004). Proto-oncogenes are genes that, when activated, promote cellular proliferation. CAs that increase activation of these genes may aberrantly boost cell cycling and therefore increase proliferation (Bertram, 2001; Vogelstein & Kinzler, 2004). Activation of proto-oncogenes have also been implicated in the cancer stem cell theory of carcinogenesis (Vicente-duen et al., 2013). Examples or proto-oncogenes include EGFR and KRAS (Sanders & Albitar, 2010). TSGs refer to genes that actively suppress cell proliferation and, in some cases, promote apoptosis (Bertram, 2001; Vogelstein & Kinzler, 2004; Sanders & Albitar, 2010). If these genes are silenced by CAs, this may remove cell cycle checkpoints, thus allowing for unhindered cellular proliferation and decreased apoptosis (Bertram, 2001; Vogelstein & Kinzler, 2004). Common TSGs are TP53 and RB (Hanahan & Weinberg, 2011). Lastly, caretaker/stability genes are those involved in the prevention and detection of DNA damage, and the instigation and completion of the required DNA repair (Vogelstein & Kinzler, 2004; Hanahan & Weinberg, 2011). If the function of these caretaker/stability genes is affected by CAs, this may result in genome-wide inadequate DNA repair, which in turn may result in genetic damage to TSGs or proto-oncogenes (Vogelstein & Kinzler, 2004). Genes involved in mismatch repair (MMR), nucleotide-excision repair (NER) and base-excision repair (BER) are all examples of caretaker/stability genes (Vogelstein & Kinzler, 2004). 

There are also other CAs commonly associated with cancer. In prostate cancer, truncated TSGs such as TP53, PTEN, BRCA1, and BRCA2 are a result of chromosomal rearrangements (Mao et al., 2011). Similarly, chromosomal inversions were found to be responsible for just over half of the RET gene fusions associated with lung adenocarcinoma samples (Mizukami et al., 2014).

There is moderate empirical evidence supporting the relationship between CAs and the cellular proliferation. The evidence presented below is summarized in table 8, here (click link). There are some available reviews that provide evidence for this relationship in the context of carcinogenesis, as high levels of cellular proliferation is one of the hallmarks of cancer (Hanahan & Weinberg, 2011). Many of these reviews focus especially on the structure and function of specific cancer-associated CAs (Mes-Masson & Witte, 1987; Ghazavi et al., 2015; Kang et al., 2016). Another interesting review discusses transgenic mouse models that have contributed to our understanding of how oncogenes and TSGs promote carcinogenesis in a variety of tissues (Fowlis & Balmain, 1992). Overall, however, there is a lack of empirical evidence available supporting dose and incidence concordance, little empirical evidence supporting temporal concordance, but strong empirical evidence supporting essentiality for this KER. 

Dose and Incidence Concordance

Not identified.

Temporal Concordance