DNA damage (naturally occurring)

Natural DNA damage is an alteration in the chemical structure of DNA, such as a break in a strand of DNA, a nucleobase missing from the backbone of DNA, or a chemically changed base such as 8-OHdG. DNA damage can occur naturally or via environmental factors, but is distinctly different from mutation, although both are types of error in DNA. DNA damage is an abnormal chemical structure in DNA, while a mutation is a change in the sequence of base pairs. DNA damages cause changes in the structure of the genetic material and prevents the replication mechanism from functioning and performing properly. The DNA damage response is a complex signal transduction pathway which recognizes when DNA is damaged and initiates the cellular response to the damage.
DNA damage and mutation have different biological consequences. While most DNA damages can undergo DNA repair, such repair is not 100% efficient. Un-repaired DNA damages accumulate in non-replicating cells, such as cells in the brains or muscles of adult mammals, and can cause aging. In replicating cells, such as cells lining the colon, errors occur upon replication of past damages in the template strand of DNA or during repair of DNA damages. These errors can give rise to mutations or epigenetic alterations. Both of these types of alteration can be replicated and passed on to subsequent cell generations. These alterations can change gene function or regulation of gene expression and possibly contribute to progression to cancer.
Throughout the cell cycle there are various checkpoints to ensure the cell is in good condition to progress to mitosis. The three main checkpoints are at G1/s, G2/m, and at the spindle assembly checkpoint regulating progression through anaphase. G1 and G2 checkpoints involve scanning for damaged DNA. During S phase the cell is more vulnerable to DNA damage than any other part of the cell cycle. G2 checkpoint checks for damaged DNA and DNA replication completeness.

Types

Damage to DNA that occurs naturally can result from metabolic or hydrolytic processes. Metabolism releases compounds that damage DNA including reactive oxygen species, reactive nitrogen species, reactive carbonyl species, lipid peroxidation products, and alkylating agents, among others, while hydrolysis cleaves chemical bonds in DNA. Naturally occurring oxidative DNA damages arise at least 10,000 times per cell per day in humans and as much as 100,000 per cell per day in rats as documented below.
Oxidative DNA damage can produce more than 20 types of altered bases as well as single strand breaks.
Other types of endogenous DNA damages, given below with their frequencies of occurrence, include depurinations, depyrimidinations, double-strand breaks, O6-methylguanines, and cytosine deamination.
DNA can be damaged via environmental factors as well. Environmental agents such as UV light, ionizing radiation, and genotoxic chemicals. Replication forks can be stalled due to damaged DNA and double strand breaks are also a form of DNA damage.

Frequencies

The list below shows some frequencies with which new naturally occurring DNA damages arise per day, due to endogenous cellular processes.

Oxidative damages
* Humans, per cell per day:
** 10,000
** 11,500
** 2,800 specific damages 8-oxoGua, 8-oxodG plus 5-HMUra
* Rats, per cell per day:
** 74,000
** 86,000
** 100,000
* Mice, per cell per day:
** 34,000 specific damages 8-oxoGua, 8-oxodG plus 5-HMUra
** 47,000 specific damages oxo8dG in mouse liver
** 28,000 specific damages 8-oxoGua, 8-oxodG, 5-HMUra
Depurinations
* Mammalian cells, per cell per day:
** 2,000 to 10,000
** 9,000
** 12,000
** 13,920
Depyrimidinations
* Mammalian cells, per cell per day:
** 600
** 696
Single-strand breaks
* Mammalian cells, per cell per day:
** 55,200
Double-strand breaks
* Human cells, per cell cycle
** 10
** 50
O6-methylguanines
* Mammalian cells, per cell per day:
** 3,120
Cytosine deamination
* Mammalian cells, per cell per day:
** 192

Another important endogenous DNA damage is M1dG, short for -pyrimido-purin-10. The excretion in urine of M1dG may be as much as 1,000-fold lower than that of 8-oxodG. However, a more important measure may be the steady-state level in DNA, reflecting both rate of occurrence and rate of DNA repair. The steady-state level of M1dG is higher than that of 8-oxodG. This points out that some DNA damages produced at a low rate may be difficult to repair and remain in DNA at a high steady-state level. Both M1dG and 8-oxodG are mutagenic.

Steady-state levels

Steady-state levels of DNA damages represent the balance between formation and repair. More than 100 types of oxidative DNA damage have been characterized, and 8-oxodG constitutes about 5% of the steady state oxidative damages in DNA. Helbock et al. estimated that there were 24,000 steady state oxidative DNA adducts per cell in young rats and 66,000 adducts per cell in old rats. This reflects the accumulation of DNA damage with age. DNA damage accumulation with age is further described in DNA damage theory of aging.
Swenberg et al. measured average amounts of selected steady state endogenous DNA damages in mammalian cells. The seven most common damages they evaluated are shown in Table 1.

Endogenous lesions	Number per cell
Abasic sites	30,000
N7-guanine	3,000
8-hydroxyguanine	2,400
7-guanine	1,500
Formaldehyde adducts	960
Acrolein-deoxyguanine	120
Malondialdehyde-deoxyguanine	60

Evaluating steady-state damages in specific tissues of the rat, Nakamura and Swenberg indicated that the number of abasic sites varied from about 50,000 per cell in liver, kidney and lung to about 200,000 per cell in the brain.

Biomolecular pathways

Proteins promoting endogenous DNA damage were identified in a 2019 paper as the DNA "damage-up" proteins. The DDP mechanisms fall into 3 clusters:

reactive oxygen increase by transmembrane transporters,
chromosome loss by replisome binding,
replication stalling by transcription factors.

The DDP human homologs are over-represented in known cancer drivers, and their RNAs in tumors predict heavy mutagenesis and a poor prognosis.

Repair of damaged DNA

In the presence of DNA damage, the cell can either repair the damage or induce cell death if the damage is beyond repair.

Types

The seven main types of DNA repair and one pathway of damage tolerance, the lesions they address, and the accuracy of the repair are shown in this table. For a brief description of the steps in repair see DNA repair mechanisms or see each individual pathway.

Repair pathway	Lesions	Accuracy	Ref.
Base excision repair	corrects DNA damage from oxidation, deamination and alkylation, also single-strand breaks	accurate
Nucleotide excision repair	oxidative endogenous lesions such as cyclopurine, sunlight-induced thymine dimers	accurate
Homology-directed repair	double-strand breaks in the mid-S phase or mid-G2 phase of the cell cycle	accurate
Non-homologous end joining	double-strand breaks if cells are in the G0 phase, the G1 phase, or the G2 phase of the cell cycle	somewhat inaccurate
Microhomology-mediated end joining or alt-End joining	double-strand breaks in the S phase of the cell cycle	always inaccurate
DNA mismatch repair	base substitution mismatches and insertion-deletion mismatches generated during DNA replication	accurate
Direct reversal	6-O-methylguanine is reversed to guanine by MGMT, some other methylated bases are demethylated by AlkB	accurate
Translesion synthesis	DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions	may be inaccurate

Aging and cancer

The schematic diagram indicates the roles of insufficient DNA repair in aging and cancer, and the role of apoptosis in cancer prevention. An excess of naturally occurring DNA damage, due to inherited deficiencies in particular DNA repair enzymes, can cause premature aging or increased risk for cancer. On the other hand, the ability to trigger apoptosis in the presence of excess un-repaired DNA damage is critical for prevention of cancer.

Apoptosis and cancer prevention

proteins are often activated or induced when DNA has sustained damage. However, excessive DNA damage can initiate apoptosis if the level of DNA damage exceeds the repair capacity. Apoptosis can prevent cells with excess DNA damage from undergoing mutagenesis and progression to cancer.
Inflammation is often caused by infection, such as with hepatitis B virus, hepatitis C virus or Helicobacter pylori. Chronic inflammation is also a central characteristic of obesity. Such inflammation causes oxidative DNA damage. This is due to the induction of reactive oxygen species by various intracellular inflammatory mediators. HBV and HCV infections, in particular, cause 10,000-fold and 100,000-fold increases in intracellular ROS production, respectively. Inflammation-induced ROS that cause DNA damage can trigger apoptosis, but may also cause cancer if repair and apoptotic processes are insufficiently protective.
Bile acids, stored in the gall bladder, are released into the small intestine in response to fat in the diet. Higher levels of fat cause greater release. Bile acids cause DNA damage, including oxidative DNA damage, double-strand DNA breaks, aneuploidy and chromosome breakage. High-normal levels of the bile acid deoxycholic acid cause apoptosis in human colon cells, but may also lead to colon cancer if repair and apoptotic defenses are insufficient.
Apoptosis serves as a safeguard mechanism against tumorigenesis. It prevents the increased mutagenesis that excess DNA damage could cause, upon replication.
At least 17 DNA repair proteins, distributed among five DNA repair pathways, have a "dual role" in response to DNA damage. With moderate levels of DNA damage, these proteins initiate or contribute to DNA repair. However, when excessive levels of DNA damage are present, they trigger apoptosis.