Genomic Instability

In this article, we explore DNA damage, its consequences, and how researchers are developing potential ways to repair it.

What is genomic instability?

Genomic instability is caused by DNA damage that isn’t repaired, as explained in the Hallmarks of Aging [1].

Our cells rely on a stable genome to transmit genetic information accurately. For our regular somatic cells, this means dividing to form new cells. This process involves copying genetic material without errors. It also fixes mistakes made during copying and repairs damaged DNA.

Our cells use DNA as a blueprint to make proteins and other materials for cell function and survival. However, a lot of information in the DNA is not used; this is junk DNA, a reminder of our evolutionary past.

DNA damage can affect genes and their transcription, resulting in dysfunctional cells that may jeopardize tissue integrity and function. This is especially important when this damage affects stem cells. Damaged stem cells have a reduced capacity to make replacement cells for tissue renewal.

When cells in the body become damaged, whether due to DNA mutations, oxidative stress, or exposure to harmful substances, they often lose their ability to function properly. In many cases, these compromised cells cannot repair themselves effectively. To prevent potential harm to the organism, these damaged cells initiate a process known as apoptosis.

Apoptosis, often referred to as programmed cell death, is a highly regulated process in which cells effectively “self-destruct.” This process is characterized by a series of biochemical events that lead to distinct morphological changes in the cell. During apoptosis, the cell shrinks, the chromatin condenses, and the nuclear envelope breaks down.

Eventually, the cell’s contents are packaged into small vesicles known as apoptotic bodies, which are then recognized and engulfed by neighboring cells or immune cells.

One of the critical aspects of apoptosis is that it is a clean process. Unlike necrosis, which is a form of uncontrolled cell death that can lead to inflammation and damage to surrounding tissues, apoptosis minimizes the risk of inflammation.

This is achieved because the apoptotic bodies are quickly removed by the immune system, particularly by specialized immune cells called macrophages. These cells recognize the signals emitted by dying cells and efficiently clear them away, thereby maintaining tissue health and preventing the spread of potentially harmful substances.

The signaling pathways that trigger apoptosis can be initiated by various factors, including internal signals, such as DNA damage or oxidative stress, and external signals, such as death ligands that bind to specific receptors on the cell surface. The balance between pro-apoptotic and anti-apoptotic signals determines whether a cell will undergo apoptosis or continue to survive. This balance is crucial for the proper functioning of multicellular organisms, as it helps regulate cell turnover, development, and responses to stress.

In summary, damaged cells that are unable to repair themselves generally resort to apoptosis, a controlled self-destruction process. This mechanism both protects the organism from potentially dangerous cells that could lead to diseases but also ensures that the immune system can efficiently clear away these cells without causing additional harm to the surrounding tissues.

Causes and consequences of genomic instability

A few dysfunctional cells are not a huge problem, but with aging, an increasing number of cells with DNA damage begin to accumulate. Eventually, the number of these damaged cells reaches a point where they can compromise organ and tissue function. The body usually removes these problem cells via apoptosis.

Unfortunately, as we age, some cells evade apoptosis. These rogue cells take up space in the tissue and send harmful signals that damage the local tissue. These are senescent cells, and they are another reason we age.

Another possible outcome of damaged DNA is cells that mutate but do not destroy themselves. Instead, they continue to replicate, becoming increasingly mutated with each division. Cancer results if a mutation damages the systems that regulate cell division or disables tumor suppression. The unchecked and rampant growth of cancer is probably the most well-known consequence of DNA damage.

There are many ways for DNA to become damaged. UV rays, X-ray radiation, chemicals, and tobacco can all damage the genome. Even chemotherapy agents designed to kill cancer can also potentially damage DNA. Such toxic agents can also create senescent cells, leading to later relapse [2].

Finally, even without all the external threats to DNA, the body still damages itself. Oxidative stress produced by normal metabolism can damage nuclear and mitochondrial DNA. Double-strand breaks are often the result of this metabolic damage and can be lethal to the cell.

How do we repair DNA damage?

Maintaining the integrity of genetic code is paramount for survival. Cells are equipped with sophisticated defense mechanisms to prevent and address myriad threats to DNA stability.

Antioxidant defense systems

Scientific efforts to improve antioxidant defense systems and DNA repair have been underway for several decades. Antioxidants gained popularity in the 1950s-60s when Dr. Denham Harman created the “free radical theory of aging” [4].

This theory proposed that aging results from free radical damage over time. Free radicals, including reactive oxygen species, are unstable molecules that can damage DNA. Antioxidants can stop these molecules’ effects, possibly slowing aging and lowering the chance of chronic diseases.

By the 1980s, the idea that antioxidants might extend life and prevent diseases had gained traction with the public. There was a surge in the sale of antioxidant supplements, including vitamins E and C, beta-carotene, and selenium. Antioxidants became even more popular in the 1990s due to studies and public interest in anti-aging products.

However, the simplistic idea that antioxidants are always good and oxidants are always bad has been challenged. Further studies revealed that antioxidant supplements could have varying or negative effects. These effects were more pronounced when the supplements were taken in high doses or outside their natural food context [5-7].

This led to a more nuanced understanding of how and when antioxidants can be beneficial. The focus shifted towards consuming antioxidants through a balanced diet rather than supplements.

Unfortunately, dietary antioxidant supplements can sometimes interfere with critical cellular processes. They also may not target the specific types of oxidative damage that contribute most significantly to aging.

Developing more focused antioxidants

Scientists are developing targeted antioxidants to address the most damaging types of reactive oxygen species (ROS) within cells. If successful, this could prevent the potential off-target effects that come from antioxidant supplementation.

Focusing on particular cellular compartments may help with mitochondrial dysfunction. In this condition, ROS cause damage to mitochondrial DNA (mtDNA). This then leads to increasingly poor energy production and inflammation.

mtDNA is located very close to the electron transport chain within the mitochondria. The electron transport chain produces lots of reactive oxygen species, primarily due to the leakage of electrons. These reactive oxygen species can potentially damage nearby molecules, including the mtDNA.

Mitochondria-targeted antioxidants like MitoQ [8] and SkQ1 [9, 10] target the mitochondria and may potentially reduce oxidative stress. These compounds act like coenzyme Q10 and plastoquinone, which neutralize ROS in animals and plants, respectively.

A 2018 meta-analysis found that taking MitoQ supplements may help reduce oxidative stress in mitochondria. However, the effects of MitoQ on other markers of oxidative stress and aging were unclear. Larger human studies are needed to fully understand the benefits of MitoQ in reducing oxidative stress and slowing aging.

Boosting antioxidant defenses

Researchers are also looking at boosting the body’s antioxidant systems to prevent genomic instability instead of just adding external antioxidants.

This approach aims to support the natural regulatory mechanisms that cells use to maintain oxidative balance. For example, one approach aims to increase activity in the Nrf2 pathway. This pathway can boost the body’s antioxidant defense mechanisms to improve genomic stability [11].

Another approach to bolstering endogenous antioxidants is to introduce genes that encode powerful antioxidant enzymes directly into cells. This could potentially offer a more sustained and effective defense against oxidative damage.

For example, Tang used a modified virus containing the manganese superoxide dismutase (SOD2) gene. This was delivered into eye cells in order to prevent retinal ischemia/reperfusion (I/R) injury. The treatment significantly reduced oxidative stress and protected the eyes from increased oxidative DNA damage [12].

Finally, indirect antioxidant approaches aim to reduce the production of ROS. This category includes caloric restriction mimetics and uncoupling proteins (UCPs).

Caloric restriction mimetics, such as resveratrol and rapamycin, directly improve mitochondrial function, modulate energy metabolism, induce autophagy, and enhance antioxidant defense.

UCPs act like a safety valve and stop too many electrons from building up in the electron transport chain. This chain is the energy-making part of the mitochondrion [13, 14]. This protects the cell from oxidative damage and helps regulate energy efficiency within the mitochondria.

The DNA damage response

The DNA damage response (DDR) is a multilevel signaling pathway. It contains sensors that detect DNA damage, transducing proteins that pass the message of DNA damage along, and effectors. These proteins initiate the proper response based on what kind of molecular damage has occurred to the DNA.

That response can include cell cycle transitions, including temporary and permanent arrest (senescence). It can also trigger transcription, DNA repair, or even apoptosis if the damage is too severe [15].

The system is complex, which allows for precise control. However, it can be damaged if the DNA code is harmed. This code is important for making proteins for the DDR system.

Therefore, the integrity of this system is central to the maintenance of genomic stability. Understanding it is central in research efforts that aim to improve its fidelity even further.

To solve this problem, scientists have focused on five basic DNA repair mechanisms: nitrogenous base excision repair, nucleotide excision repair, mismatch-mediated repair, homologous recombination, and non-homologous end-joining [3].

DNA damage that distorts the shape of DNA, such as adducts, is repaired by nucleotide excision repair. DNA glycosylase removes damaged bases in base excision repair. The phosphodiester bond is cleaved by endonucleases, and the correct base is added by DNA polymerase.

DNA ligase then seals the phosphodiester backbone. DNA double-strand breaks (DSBs) are the most cytotoxic and mutagenic DNA lesions. DSBs are repaired by homologous repair (HR) or nonhomologous end joining (NHEJ) repair.

NHEJ is more common but is error-prone [3]. HR displays more fidelity, employing a homologous sequence as a template for repair.

Mismatch-mediated repair (MMR) replaces mispaired bases that are damaged and, if not replaced, would result in heritable mutations. MMR is usually needed for errors in DNA replication and recombination.

Aging itself is not considered a disease, so most research is focused on diseases linked to abnormal DNA repair. DNA repair system defects are caused by mutations in repair protein code. Scientists are trying to fix this by replacing damaged DNA codes with corrected ones.

The most popular techniques for doing this are traditional gene transfer and editing technologies. These enable the deletion and insertion of the DNA that codes for the various DNA repair pathways [16].

Genes are transferred into the body using vectors like viruses and liposomes. These vectors can naturally enter specific cells and deliver genetic material efficiently. The genetic material can be delivered permanently or temporarily.

Traditional gene transfer methods can struggle to target the right spot in DNA. This can then lead to an unwanted knockout of a functional gene [16].

Gene editing tools

Gene editing tools include CRISPR-Cas9, TALENs, ZFNs, and base and prime editors. CRISPR-Cas9 is the most famous and widely used gene editing technique. The CRISPR-Cas9 system was created by re-engineering a natural defense mechanism in bacteria. This system normally protects these organisms from invading viruses and plasmids.

It allows for very precise editing of DNA at specific locations [16]. Base editors are a more recent innovation derived from CRISPR technology. Base editors allow users to change one base in DNA without causing or repairing a double-strand break in the DNA [17].

Prime editing is another recent development derived from CRISPR technology. It is superior to CRISPR-Cas9 editing because it doesn’t require the creation of potentially hazardous double-strand breaks. It is also more precise, reducing any possibility of off-target effects [18].

More than two dozen enzymes are involved in the five DNA repair processes. It is theoretically possible to create permanent or temporary changes in these enzymes to repair mutations in them. Beyond that, they could potentially be improved to emulate the mechanisms found in longer-lived species.

Vera Gorbunova and her team have studied the DNA repair systems in mice, naked mole rats, and humans. This study offered invaluable information that could be used to improve the DNA repair efficiency of people.

They identified 12 DNA genes involved in repair that were upregulated in the naked mole rat. The greater expression of these genes in these animals suggests that they have more effective DNA repair. This more robust system likely contributes to their extreme longevity and resistance to cancer [19].

Fanconi anemia

This condition is caused by mutations in genes that help fix DNA, especially the ones that repair DNA crosslinks. CRISPR has been used to correct mutations in FANCA and FANCC genes in patient-derived cells, restoring normal function [20].

Xeroderma pigmentosum

Patients with this condition are very vulnerable to UV-induced DNA damage due to genetic mutations in the nucleotide excision repair pathway. CRISPR has been used to fix mutations in genes like XPC. This gene is important for starting the repair of DNA damage caused by UV light [21, 22].

Cancer research

CRISPR has been used to study and potentially reverse gene mutations such as BRCA1 and BRCA2. These genes are involved in the homologous recombination pathway, a key mechanism for repairing double-strand DNA breaks. Correcting these mutations may restore normal DNA repair and reduce the likelihood of cancer [23-25].

These studies serve as proof of principle and a beacon of hope that aging DNA damage repair systems can be fixed. There is also the potential for them to be upgraded to significantly extend health and lifespan.

The future of DNA repair research

Even with the many repair systems that humans have developed, the body faces constant attacks. These come from environmental stressors and its own metabolic processes.

The body’s repair systems also decline in effectiveness over time, meaning that DNA damage and mutations are inevitable. Some evidence suggests that caloric restriction may help combat this, but as of yet, no drugs or therapies can prevent or repair DNA damage.

One thing is certain: rejuvenation biotechnology needs to find a way to repair the genome. This could help to lower cancer risk as we age and may also lead to longer lifespans.

For now, the best we can do is avoid risks such as excessive sun exposure, industrial chemicals, and smoking; of course. We should also avoid radioactive waste, as these mutations do not give us comic book superpowers!

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