**2. The molecular mechanisms of aging**

The molecular mechanisms of aging include genome instability as a consequence of the accumulation of gene mutations, telomere attrition, and epigenetic alterations. Interestingly, instability occurs more frequently in some genome regions than in others. The association and interactions between the above mechanisms lead to the functional decline of aging organisms.

### **2.1. Aging due to DNA damage**

Alzheimer's disease (AD) patients. Moreover, a decrease in the levels of dopaminergic neurons of up to 40–50% may be observed in the *substantia nigra* and of dopamine in the striatum at the end of the sixth decade of life, which are typical changes seen in patients with

**Figure 1.** Molecular factors associated with aging and age-related neurological diseases. The pathological changes starting at the molecular level induce oxidative stress and disturb cell cycle that affects cells of the aging organism and lead to systemic deterioration. The genetic variation may give rise to age-related neurological diseases. ROS reactive oxygen species, HHcy—hyperhomocysteinemia, AEDs—antiepileptic drugs, AD—Alzheimer's disease, and

Increased longevity in much of the developed world appears to have lead to higher stroke incidence. Apart from an aging population, there is a significant impact of the growing prevalence of hypertension, diabetes, obesity, and disorders of the cardiovascular system on the increase in the incidence of stroke. The prevalence of these diseases increases with age.

Parkinson's disease (PD).

PD—Parkinson's disease.

64 Senescence - Physiology or Pathology

The theory of aging establishes that somatic mutations happen randomly during an organism's lifetime and their accumulation eventually affects key functions such as DNA synthesis, degradation, and repair, consequently causing the "error catastrophe." Genetic damage occurs both in nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) [1, 2]. However, mitochondria have an oxidative environment, due to multiple redox reactions in the electron transport chain, and a less efficient DNA repair system, which results in the accumulation of more damaged mDNA than nDNA [3, 4]. The decreased activity of autophagy and mitophagy may also be responsible for the accumulation of mtDNA mutations and mitochondrial dysfunction during aging [5].

The integrity and stability of DNA may be disrupted both by exogenous factors, such as physical, chemical or biological agents, as well as endogenous factors, including DNA replication errors and reactive oxygen species (ROS) [6]. Most of the damage to DNA occurs during the replication process, and the majority of this damage is corrected by a complex network of DNA repair mechanisms. The mismatch repair (MMR) system provides the fidelity of replication. The checkpoint response is activated by damage that is unrepaired and leads to cell senescence or death, which may also alter tissue and the homeostasis of the body. The loss of key MMR proteins has been observed during aging. The question becomes: is such deterioration a cause or an effect of senescence [7, 8]?

The cell cycle and repair processes are controlled by tumor protein 53 (p53, encoded by *TP53* gene), which is a pivotal regulator of multiple cellular processes, such as reversible and irreversible cell cycle arrest and senescence. The protein is activated by various stress factors to induce apoptosis or autophagic cell death, depending on the cell category [9]. The initiation of cellular aging is designed to prevent proliferation of damaged cells and tumorigenesis. Two main groups of signals activate p53: DNA damage and oncogenic stress. It has been demonstrated that loss of p53 function occurs in senescent cells, as 50% of human neoplasms possesses a mutated copy of the *TP53* gene [10]. Moreover, the mutations in *TP53* were observed also in age-related dementias, such as AD in both humans and its murine model [11, 12] (**Figure 1**).

#### **2.2. The role of telomeres**

Telomere attrition is another molecular mechanism responsible for senescence. Telomeres are a structural component of chromosomes localized at the end of each chromatid. They consist of DNA and telomere binding proteins. Telomere DNA is made up of the sequence 5′-TTAGGG-3′ repeated 150–2000 times [13]. The main functions of telomeres are protection against loss of genetic information during replication and prevention of abnormal recombination, chromosome fusion, or chromosomal degradation by exonucleases [14]. During each cell division, the telomere sequence is shortened by a length of 50–200 base pairs (bp) and the structure of telomeres changes. This biological clock is considered to be one of the main mechanisms determining the number of possible cell divisions. Hayflick's observations [15] on somatic cells specified the maximum number of divisions after which cells stop dividing but remain metabolically active. This maximum number is called the Hayflick limit and varies by tissue type and organism. It is known that a reduction in the number of divisions prevents the accumulation of mutations [16].

#### **2.3. Epigenetics of aging**

Epigenetic alterations are another molecular mechanism involved in aging and include DNA methylation and histone modifications [17]. The epigenome becomes deregulated with age. Global levels of DNA methylation decrease with age, and changes in the methylation profile may lead to age-associated immune deficiency [18]. The chemical modification of histones include s acetylation, methylation, phosphorylation, ubiquitination, deamination, citrullination, sumoylation, ADP (adenosine diphosphate) ribosylation, and proline isomerization and lead to changes in histone-DNA or histone-histone interactions [19]. Both changes in the DNA methylation pattern and histone modifications can directly alter chromatin packaging, resulting in different parts of the DNA being exposed to transcriptional factors and results in the expression of different genes. Epigenetic studies have demonstrated progressive changes at the transcriptomic level associated with aging. The age range of 49–56 years in humans seems to be critical in transcriptional senescence. Changes in gene expression, either their increase or decrease, are a longitudinal and dynamic process [20] (**Figure 1**).

### **2.4. Aging of the brain**

of replication. The checkpoint response is activated by damage that is unrepaired and leads to cell senescence or death, which may also alter tissue and the homeostasis of the body. The loss of key MMR proteins has been observed during aging. The question becomes: is such

The cell cycle and repair processes are controlled by tumor protein 53 (p53, encoded by *TP53* gene), which is a pivotal regulator of multiple cellular processes, such as reversible and irreversible cell cycle arrest and senescence. The protein is activated by various stress factors to induce apoptosis or autophagic cell death, depending on the cell category [9]. The initiation of cellular aging is designed to prevent proliferation of damaged cells and tumorigenesis. Two main groups of signals activate p53: DNA damage and oncogenic stress. It has been demonstrated that loss of p53 function occurs in senescent cells, as 50% of human neoplasms possesses a mutated copy of the *TP53* gene [10]. Moreover, the mutations in *TP53* were observed also in age-related dementias, such as AD in both humans and its murine model

Telomere attrition is another molecular mechanism responsible for senescence. Telomeres are a structural component of chromosomes localized at the end of each chromatid. They consist of DNA and telomere binding proteins. Telomere DNA is made up of the sequence 5′-TTAGGG-3′ repeated 150–2000 times [13]. The main functions of telomeres are protection against loss of genetic information during replication and prevention of abnormal recombination, chromosome fusion, or chromosomal degradation by exonucleases [14]. During each cell division, the telomere sequence is shortened by a length of 50–200 base pairs (bp) and the structure of telomeres changes. This biological clock is considered to be one of the main mechanisms determining the number of possible cell divisions. Hayflick's observations [15] on somatic cells specified the maximum number of divisions after which cells stop dividing but remain metabolically active. This maximum number is called the Hayflick limit and varies by tissue type and organism. It is known that a reduction in the number of divisions prevents

Epigenetic alterations are another molecular mechanism involved in aging and include DNA methylation and histone modifications [17]. The epigenome becomes deregulated with age. Global levels of DNA methylation decrease with age, and changes in the methylation profile may lead to age-associated immune deficiency [18]. The chemical modification of histones include s acetylation, methylation, phosphorylation, ubiquitination, deamination, citrullination, sumoylation, ADP (adenosine diphosphate) ribosylation, and proline isomerization and lead to changes in histone-DNA or histone-histone interactions [19]. Both changes in the DNA methylation pattern and histone modifications can directly alter chromatin packaging, resulting in different parts of the DNA being exposed to transcriptional factors and results in the expression of different genes. Epigenetic studies have demonstrated progressive changes at the

deterioration a cause or an effect of senescence [7, 8]?

[11, 12] (**Figure 1**).

**2.2. The role of telomeres**

66 Senescence - Physiology or Pathology

the accumulation of mutations [16].

**2.3. Epigenetics of aging**

Furthermore, senescence comprises aging of the cerebral white matter (WM) and gray matter (GM), including progressive neuronal loss, decreased levels of neurotransmitters, increased inflammation, disrupted integrity, lesions, infarction, and microbleeds [21]. Aging affects not only neurons but also glial cells (astrocytes, oligodendrocytes, microglia), vascular cells, and the basal lamina matrix and interferes with their functions such as maintaining metabolic and ion homeostasis in the CNS, regulating the cerebral blood flow, impulse conduction, and phagocytosis [22]. During aging, the reduction of WM volume is almost threefold higher (loss of 28% of neurons) than the reduction of GM volume (10% of neurons). Thus, changes in WM may result in behavioral and cognitive decline in the elderly. Additionally, the ability for WM repair has been found to be decreased in older individuals. Changes in WM are observed in diseases, such as stroke, PD, and AD [21].

Multiple molecular changes take place during aging, and these form a vast network of interactions. This makes it nearly impossible to determine if age-related diseases are caused by a snowball effect of senescence, or if the converse is true: that these diseases are the result of individual variability. It seems that both hypotheses may be true, as aging is an important risk factor for diseases such as stroke, epilepsy, PD, AD, and brain tumors, but not a certain causative factor (**Figure 1**).
