Genomic instability: a force behind aging and cancer

Highlights:

• Genomic instability is a phenomenon of the high frequency of mutations within the genome
• One of the main reasons behind genomic instability is replication stress that results from DNA damage
• Genomic instability is considered a primary hallmark of aging and one of the hallmarks of cancer

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Introduction

Each cell undergoes up to one million DNA changes per day, and though most of them are rapidly repaired, but the accumulation of the damage can lead to grave consequences. Genomic instability is a term used to describe a high frequency of mutations within the genome (all genetic information of an organism). Such mutations can occur through various mechanisms, including changes in nucleic acid sequences, chromosomal rearrangements, or aneuploidy (abnormal number of chromosomes in a cell). Though crucial for genetic diversity and evolution, genomic instability was linked to carcinogenesis in multicellular organisms. Genomic instability has also been connected to multiple pathologies in humans, including neurodegenerative and neuromuscular diseases. Genomic instability is considered a primary hallmark of aging due to its detrimental influence on cell and organism functionality.

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Why does genomic instability occur?

Cell cycle involves multiple fine-tuned processes that ensure genome integrity. The key to the proper flow of these processes is efficient and error-free DNA replication. The main reason behind genomic instability is DNA replication stress, which occurs to the cell undergoing replication and can stall this process. Replication stress can occur due to many factors, among them (1):

• Damaged or unusual DNA structure,
• Common fragile sites,
• Overexpression of oncogenes, 
• Conflicts between replication and transcription.

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Irreversible DNA damage is considered the main cause of genomic instability, which, in turn, encompasses multiple genetic alterations from point mutations to chromosome rearrangements. Depending on the consequences of replication stress event, genomic instability can be divided into two main classes (2):

• Chromosomal instability (CIN) that leads to chromosome gain or loss;
• Micro- and minisatellite instability (MIN) that increases the tendency to DNA mutations due to the errors in the mismatch repair mechanism (DNA repair mechanism that fixes erroneous insertion, deletion, and misincorporation of bases). MIN is linked to satellites - areas of DNA where certain motifs are repeated.

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Damaged DNA

DNA damage occurs from both endogenous and exogenous factors. On average, the human genome accumulates around 105 DNA lesions per day (3). Endogenous agents that cause DNA damage include mainly reactive oxygen species (ROS), reactive nitrogen species , and environmental sources are DNA damaging agents, such as radiation, chemical mutagens, and carcinogens. 

There are several main types of DNA damage (4): 

• Oxidative damage caused by ROS, an example being oxidation of guanine; 
• Alkylation of bases, the most common type being methylation;
• Base loss caused by hydrolysis of either purine or pyrimidine base that can happen eiether spontaneously or due to the errors in DNA repair;
• Bulky adduct formation happens when a big reactive molecule (such as the components of cigarette smoke) attaches itself to one of the DNA strands and branches out from it;
• DNA crosslinking, when chemical agents react with two nucleotides and form a link between them either within the same strand (intrastrand) or between two opposite strands (interstrand);
• DNA strand breaks when one or both DNA strands break entirely.

Despite the high DNA damage rate, most DNA lesions do not convert into DNA mutations due to a range of sophisticated DNA-damage sensing and repairing mechanisms. Most of them are rapidly corrected (5), but some – such as single-strand (SSB) and double-strand (DSB) DNA breaks – are extremely dangerous. Among the repair mechanisms, nucleotide excision repair (NER) is targeted mainly at bulky lesions. Small base damages and SSB are fixed by base excision repair (BER), which is critically important during embryogenesis. During replication, the mismatch repair pathways (MMR) are activated, which can correct nucleotide misincorporation. DSBs are repaired by two major mechanisms - homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is a highly accurate mechanism, which can use a sister chromatid (one half of a duplicated chromosome, an identical copy created during DNA replication of a chromosome) as a template. Unlike HR, NHEJ is a simpler mechanism that directly reconnects two broken DNA ends without a homologous template. NHEJ can result in small deletions or translocations, but it appears to be a major repair mechanism in non-dividing somatic cells (i.e., skin cells and neurons). Highly toxic DNA intra- or inter-strand crosslinks can be removed by HR pathways in symphony with other pathways such as NER (6). 

Irreversible DNA damage 

Even the highly efficient mechanism of repairment can malfunction, and then DNA damage can cause mutations in critical genes (such as tumor suppressor genes). In most cases, when a cell suffers DNA damage that is beyond repair, it is disposed of through apoptosis (a programmed cell death) or becomes senescent (7). Both apoptosis and senescence are heavily regulated through tumor protein p53, known as the guardian of the genome. Autophagy - a process of cellular self-degradation - can also be triggered by DNA damage (8). However, if these cellular response malfunctions, the mutated cells are accumulated and continue to proliferate, potentially leading to cancer. 

Other factors of replication stress

Fragile sites are specific loci in the human genome that are particularly difficult to replicate. They can be either common or rare. Common fragile sites are present in almost all individuals, whereas rare fragile sites are found in less than 5% of the population (9). These sites are characterized by trinucleotide repeats, most commonly CGG, CAG, GAA, and GCN (N standing for A or G), which can form into hairpin-like structures, leading to difficulty of replication (10). Common fragile sites are prone to replication stress-induced DNA DSBs. 

Another replication stress factor is overexpression of oncogenes such as cyclin E, which leads to normal replication perturbation, activation of the DNA damage response, and cellular arrest or senescence (11). c-Myc is another oncogene able to activate a DNA damage response and increase genomic instability (12).

Collisions between transcription and replication are an additional factor of genomic instability. In higher eukaryotes, replication and transcription are coordinated and occur within spatially and temporally separated domains. Nevertheless, if the transcription of a particularly large gene occurs during more than one cell cycle (13), it can lead to a collision and formation of DNA–RNA hybrids (R-loops).

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Genomic instability and aging

One common denominator of aging is the accumulation of genetic damage (14) linked to genomic instability, which is considered one of the primary hallmarks of aging (15).

Under normal conditions, cells recover effectively and rapidly after DNA damage. The repair capacity far exceeds the DNA damage rate at a young age. However, as organism ages, bursts of DNA damage (for example, from inflammation) give rise to an increasingly high rate of apoptosis, cellular senescence, or mutations. Age-related decline in genome maintenance mechanisms may intensify genomic instability. Studies show that multiple DNA damage repair functions become compromised and more error-prone with aging (16), among them BER and NHEJ. 

The frequency of genome rearrangements increases exponentially at old age, while cellular responses such as apoptosis become less efficient (17). Altogether, this increases the accumulation of damaged cells in tissues and organs. Moreover, even if DNA damage gets repaired at an older age, the frequency of errors made by DNA repair mechanisms also increases, leading to the accumulation of irreversible mutations.

Genomic instability and cancer

Aging and cancer are frequently regarded as two different manifestations of the same underlying process - the accumulation of cellular damage. In addition, several pathologies associated with aging, such as atherosclerosis and inflammation, involve uncontrolled cellular overgrowth or hyperactivity (18). Thus, genomic instability also presents one of the leading hallmarks of cancer.

Almost all human cancers are characterized by genomic instability. Most cancers are impacted by the CIN form of instability connected to the high rate by which chromosome structure and number change over time in cancer cells compared with normal cells. However, recent research shows that MIN also plays its role. Genomic instability is present in all stages, from precancerous lesions to advanced stages of the disease (19). The molecular basis is well understood only in hereditary cancers, in which it has been linked to mutations in DNA repair genes. However, the molecular basis of genomic instability in sporadic cancers is much less well defined. 

Can we stabilize the genome?

The stability of the genome can be estimated via the biomarkers of genome integrity, including telomere length. These biomarkers have been recently utilized to establish whether optimizing diet and nutrient intake can help to stabilize the genome (20). Though the research is ongoing, some promising results are already available. These findings also have prompted the development of nutrigenomics – a field that aims to determine how a particular genotype and expression profile are connected to nutrient metabolism and absorption (21).

There is limited evidence both from animal studies and human trials demonstrating the putative genome-stabilizing role of carotenoids and vitamin A (22–24), range of B vitamins (including niacin, folate, and vitamin B12) (25), vitamin D (26), and minerals such as iron (27), selenium (28), and zinc (29). Another positively influencing dietary factor is a diet high in plant-based food (30). ​​There is some, albeit limited evidence, that consumption of products, such as blueberry juice (31) and olive oil (32), can also counteract DNA damage.

A range of therapeutics targeted at various mechanisms of DNA repair and damage is being researched to decrease genomic instability (33). Among already known drugs, metformin, the diabetes drug, was shown to reduce DNA damage by a not yet completely understood mechanism (34).

While mitigating genomic instability is not a straightforward task, the factors that increase the risks are well-known – smoking, exposure to industrial chemicals, and extensive UV exposure. All these factors increase the risks of increasing DNA damage and, correspondingly, inducing genomic instability.

Conclusions

Genomic integrity is one of the crucial conditions for adequate cell proliferation and organism functioning. When this integrity is threatened, the organism becomes vulnerable to multiple diseases. Aging and cancer are strongly connected to genomic instability and the accumulation of harmful mutations in cells. Though the evidence is limited for effective prevention and treatment of genomic instability, the research is being actively carried out in this direction. Some data points towards the benefits of a healthy diet to maintain genomic integrity, and the benefits of avoiding harmful factors such as smoking are beyond doubt.

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