Biological effects of radiation on the epigenome

The single-target single-hit model

In this model a single hit on a target is sufficient to kill a cell^[7] The equation used for this model is as follows:

${\displaystyle p(k)={\frac {m^{k}}{k!}}e^{-m}}$

Where k represents a hit on the cell and m represents the mass of the cell.

The three lambda model

This model showed the accuracy of survival description for higher or repeated doses.^[7]

The equation used for this model is as follows:

${\displaystyle S(D)=e^{-\lambda _{3}(1-e^{\lambda _{1}D}(1-(1-e^{-(\lambda _{2}-\lambda _{1})D})^{2}))}}$

The linear-quadratic-cubic model

The equation used for this model is as follows:^[7]

${\displaystyle S(D)=e^{-\alpha D-\beta D^{2}+\gamma D^{3}}}$

The repair-misrepair model

This model shows the mean number of lesions before any repair activations in a cell.^[7]

The equation used for this model is as follows:

${\displaystyle S_{\psi }=e^{-U_{0}}(1+{\frac {U_{0}(1-e^{-\lambda T})}{\epsilon }})^{\psi \epsilon }}$

where Uo represents the yield of initially induced lesions, with λ being the linear self-repair coefficient, and T equaling time

The lethal-potentially lethal model

This equation explores the hypothesis of a lesion becoming fatal within a given of time if it is not repair by repair enzymes.^[7]

The equation used for this model is as follows:

${\displaystyle S=e^{-n_{tot}(T+t_{r})}=e^{-N_{tot}}[{\frac {1+N_{PL}}{\epsilon (1-e^{-\epsilon _{PL}t_{r}})}}]^{\epsilon }}$

T is the radiation duration and tr is the available repair time.

The saturable repair model

This model illustrates the efficiency of the repair system decreasing as the dosage of radiation increases. This is due to the repair kinetics becoming increasingly saturated with the increase in radiation dosage.^[7]

The equation used for this model is as follows:

${\displaystyle S(D)=e^{-{\frac {n_{0}-c_{0}}{1-{\frac {c_{0}}{n_{0}}}e^{kT(c_{0}-n_{0})}}}}}$

n(t) is the number of unrepaired lesions, c(t) is the number of repair molecules or enzymes, k is the proportionality coefficient, and T is the time available for repair.

ROS-mediated protein adduct formation

ROS generated by ionizing radiation chemically modify histones which can cause a change in transcription. Oxidation of cellular lipid components result in an electrophilic molecule formation. The electrophilic molecule binds to the lysine residues of histones causing a ketoamide adduct formation. The ketoamide adduct formation blocks the lysine residues of histones from binding to acetylation proteins thus decreasing gene transcription.^[11]

ROS-mediated DNA methylation changes

DNA hypermethylation is seen in the genome with DNA breaks at a gene-specific basis, such as promoters of regulatory genes, but the global methylation of the genome shows a hypomethylation pattern during the period of reactive oxygen species stress.^[12]

DNA damage induced by reactive oxygen species results in increased gene methylation and ultimately gene silencing. Reactive oxygen species modify the mechanism of epigenetic methylation by inducing DNA breaks which are later repaired and then methylated by DNMTs. DNA damage response genes, such as GADD45A, recruit nuclear proteins Np95 to direct histone methyltransferase's towards the damaged DNA site. The breaks in DNA caused by the ionizing radiation then recruit the DNMTs in order to repair and further methylate the repair site.

Genome wide hypomethylation occurs due to reactive oxygen species hydroxylating methylcytosines to 5-hydroxymethylcytosine (5hmC).^[13] The production of 5hmC serves as an epigenetic marker for DNA damage which is recognizable by DNA repair enzymes. The DNA repair enzymes attracted by the marker convert 5hmC to an unmethylated cytosine base resulting in the hypomethylation of the genome.^[14]

Another mechanism that induces hypomethylation is the depletion of S-adenosyl methionine synthetase (SAM). The prevalence of super oxide species causes the oxidization of reduced glutathione (GSH) to GSSG. Due to this, synthesis of the cosubstrate SAM is stopped. SAM is an essential cosubtrate for the normal functioning of DNMTs and histone methyltrasnferase proteins.

ROS-mediated post-translation modification

Double stranded DNA breaks caused by exposure to ionizing radiation are known to alter chromatin structure. Double stranded breaks are primarily repaired by poly ADP (PAR) polymerases which accumulate at the site of the break leading to activation of the chromatin remodeling protein ALC1. ALC1 causes the nucleosome to relax resulting in the epigenetic up-regulation of genes. A similar mechanism involves the ataxia telangiectasia mutated (ATM) serine/threonine kinase which is an enzyme involved in the repair of double stranded breaks caused by ionizing radiation. ATM phosphorylates KAP1 which causes the heterochromatin to relax, allowing increased transcription to occur.

The DNA mismatch repair gene (MSH2) promoter has shown a hypermethylation pattern when exposed to ionizing radiation. Reactive oxygen species induce the oxidization of deoxyguanosine into 8-hydroxydeoxyguanosine (8-OHdG) causing a change in chromatin structure. Gene promoters that contain 8-OHdG deactivate the chromatin by inducing trimethyl-H3K27 in the genome. Other enzymes such as transglutaminases (TGs) control chromatin remodeling through proteins such as sirtuin1 (SIRT1). TGs cause transcriptional repression during reactive oxygen species stress by binding to the chromatin and inhibiting the sirtuin 1 histone deacetylase from performing its function.^[11]

ROS-mediated loss of epigenetic imprinting

Epigenetic imprinting is lost during reactive oxygen species stress. This type of oxidative stress causes a loss of NF- κB signaling. Enhancer blocking element CCCTC-binding factor (CTCF) binds to the imprint control region of insulin-like growth factor 2 (IGF2) preventing the enhancers from allowing the transcription of the gene. The NF- κB proteins interact with IκB inhibitory proteins, but during oxidative stress IκB proteins are degraded in the cell. The loss of IκB proteins for NF- κB proteins to bind to results in NF- κB proteins entering the nucleus to bind to specific response elements to counter the oxidative stress. The binding of NF- κB and corepressor HDAC1 to response elements such as the CCCTC-binding factor causes a decrease in expression of the enhancer blocking element. This decrease in expression hinders the binding to the IGF2 imprint control region therefore causing the loss of imprinting and biallelic IGF2 expression.^[11]

Genomic instability via hypomethylation of LINE1

Ionizing radiation exposure affects patterns of DNA methylation. Breast cancer cells treated with fractionated doses of ionizing radiation showed DNA hypomethylation at the various gene loci; dose fractionation refers to breaking down one dose of radiation into separate, smaller doses.^[15] Hypomethylation of these genes correlated with decreased expression of various DNMTs and methyl CpG binding proteins. LINE1 transposable elements have been identified as targets for ionizing radiation. The hypomethylation of LINE1 elements results in activation of the elements and thus an increase in LINE1 protein levels. Increased transcription of LINE1 transposable elements results in greater mobilization of the LINE1 loci and therefore increases genomic instability.^[11]

Ionizing radiation and histone modification

Irradiated cells can be linked to a variety of histone modifications. Ionizing radiation in breast cancer cell inhibits H4 lysine tri-methylation. Mouse models exposed to high levels of X-ray irradiation exhibited a decrease in both the tri-methylation of H4-Lys20 and the compaction of the chromatin. With the loss of tri-methylation of H4-Lys20, DNA hypomethylation increased resulting in DNA damage and increased genomic instability.^[11]

Loss of methylation via repair mechanisms

Breaks in DNA due to ionizing radiation can be repaired. New DNA synthesis by DNA polymerases is one of the ways radiation induced DNA damage can be repaired. However, DNA polymerases do not insert methylated bases which leads to a decrease in methylation of the newly synthesized strand. Reactive oxygen species also inhibit DNMT activity which would normally add the missing methyl groups. This increases the chance that the demethylated state of DNA will eventually become permanent.^[16]