Epigenetic Clock
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An epigenetic clock is a biochemical test that can be used to measure age. The test is based on DNA methylation levels, measuring the accumulation of methyl groups to one's DNA molecules.


History

The strong effects of age on DNA methylation levels have been known since the late 1960s. A vast literature describes sets of CpGs whose DNA methylation levels correlate with age. The first robust demonstration that DNA methylation levels in saliva could generate age predictors with an average accuracy of 5.2 years was published by a
UCLA The University of California, Los Angeles (UCLA) is a public land-grant research university in Los Angeles, California. UCLA's academic roots were established in 1881 as a teachers college then known as the southern branch of the California ...
team including Sven Bocklandt, Steve Horvath, and
Eric Vilain Eric Vilain is a physician-scientist and professor in the fields of Disorders/Differences of Sex Development (DSDs) and precision medicine. He has been the director of the Center for Genetic Medicine Research at Children’s National Medical Cent ...
in 2011 (Bocklandt et al. 2011). The laboratories of Trey Ideker and Kang Zhang at the
University of California, San Diego The University of California, San Diego (UC San Diego or colloquially, UCSD) is a public land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is t ...
published the Hannum epigenetic clock (Hannum 2013), which consisted of 71 markers that accurately estimate age based on blood methylation levels. The first multi-tissue epigenetic clock, Horvath's epigenetic clock, was developed by Steve Horvath, a professor of
human genetics Human genetics is the study of inheritance as it occurs in human beings. Human genetics encompasses a variety of overlapping fields including: classical genetics, cytogenetics, molecular genetics, biochemical genetics, genomics, population gene ...
and biostatistics at
UCLA The University of California, Los Angeles (UCLA) is a public land-grant research university in Los Angeles, California. UCLA's academic roots were established in 1881 as a teachers college then known as the southern branch of the California ...
(Horvath 2013). Horvath spent over 4 years collecting publicly available Illumina DNA methylation data and identifying suitable statistical methods. The personal story behind the discovery was featured in ''Nature''. The age estimator was developed using 8,000 samples from 82 Illumina DNA methylation array datasets, encompassing 51 healthy tissues and cell types. The major innovation of Horvath's epigenetic clock lies in its wide applicability: the same set of 353 CpGs and the same prediction algorithm is used irrespective of the DNA source within the organism, i.e. it does not require any adjustments or offsets. This property allows one to compare the ages of different areas of the human body using the same aging clock. Shortly afterwards, a derivation of Horvath's clock, the IEAA (Intrinsic Epigenetic Age Acceleration), an estimator based on the cellular composition of the blood, was developed. A second generation of epigenetic clocks emerged a few years later and improved on the first in age estimation. This was thanks to the incorporation not only of epigenetic variants such as DNA methylation but also environmental variants such as smoking or chronological age. Among these clocks, the PhenoAge and GrimAge clocks stand out. PhenoAge is an epigenetic clock that takes chronological age into account, and GrimAge uses the mortality risks of age together with the smoking variant among others as a risk factor. Taking into account environmental variants allows GrimAge to outperform any other epigenetic clock in "predicting death". New age estimation tools have been developed continuously, which also facilitate the prognosis of certain diseases.


Relationship to a cause of biological aging

It is not yet known what exactly is measured by DNA methylation age. Horvath hypothesized that DNA methylation age measures the cumulative effect of an epigenetic maintenance system but details are unknown. The fact that DNA methylation age of blood predicts all-cause mortality in later life has been used to argue that it relates to a process that causes aging. However, if a particular CpG played a direct causal role in the aging process, the mortality it created would make it less likely to be observed in older individuals, making the site less likely to have been chosen as a predictor; the 353 clock CpGs therefore likely have no causal effect whatsoever. Rather, the epigenetic clock captures an
emergent property In philosophy, systems theory, science, and art, emergence occurs when an entity is observed to have properties its parts do not have on their own, properties or behaviors that emerge only when the parts interact in a wider whole. Emergence ...
of the epigenome.


Epigenetic clock theory of aging

In 2010, a new unifying model of aging and the development of complex diseases was proposed, incorporating classical aging theories and epigenetics. Horvath and Raj extended this theory, proposing an epigenetic clock theory of aging with the following tenets: * Biological aging results as an unintended consequence of both developmental programs and maintenance program, the molecular footprints of which give rise to DNA methylation age estimators. * The precise mechanisms linking the innate molecular processes (underlying DNAm age) to the decline in tissue function probably relate to both intracellular changes (leading to a loss of cellular identity) and subtle changes in cell composition, for example, fully functioning somatic stem cells. * At the molecular level, DNAm age is a proximal readout of a collection of innate aging processes that conspire with other, independent root causes of ageing to the detriment of tissue function.


Motivation for biological clocks

In general, biological aging clocks and
biomarkers of aging Biomarkers of aging are biomarkers that could predict functional capacity at some later age better than chronological age. Stated another way, biomarkers of aging would give the true "biological age", which may be different from the chronological ...
are expected to find many uses in biological research since age is a fundamental characteristic of most
organisms In biology, an organism () is any life, living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy (biology), taxonomy into groups such as Multicellular o ...
. Accurate measures of biological age (biological aging clocks) could be useful for * testing the validity of various theories of biological aging, * diagnosing various age related
disease A disease is a particular abnormal condition that negatively affects the structure or function of all or part of an organism, and that is not immediately due to any external injury. Diseases are often known to be medical conditions that a ...
s and for defining
cancer Cancer is a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body. These contrast with benign tumors, which do not spread. Possible signs and symptoms include a lump, abnormal b ...
subtypes, * predicting/prognosticating the onset of various diseases, * serving as surrogate markers for evaluating therapeutic interventions including
rejuvenation Rejuvenation is a medical discipline focused on the practical reversal of the aging process. Rejuvenation is distinct from life extension. Life extension strategies often study the causes of aging and try to oppose those causes in order to slow ...
approaches, * studying developmental biology and cell differentiation, *
forensic Forensic science, also known as criminalistics, is the application of science to criminal and civil laws, mainly—on the criminal side—during criminal investigation, as governed by the legal standards of admissible evidence and criminal p ...
applications, for example to estimate the age of a suspect based on blood left on a crime scene. Overall, biological clocks are expected to be useful for studying what causes aging and what can be done against it. However, they can only capture the effects of interventions that affect the rate of future aging, i.e. the slope of the
Gompertz curve The Gompertz curve or Gompertz function is a type of mathematical model for a time series, named after Benjamin Gompertz (1779–1865). It is a sigmoid function which describes growth as being slowest at the start and end of a given time period. Th ...
by which mortality increases with age, and not that of interventions that act at one moment in time, e.g. to lower mortality across all ages, i.e. the intercept of the Gompertz curve.


Properties of Horvath's clock

The clock is defined as an age estimation method based on 353 epigenetic markers on the DNA. The 353 markers measure DNA methylation of
CpG dinucleotide The CpG sites or CG sites are regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide in the linear sequence of bases along its 5' → 3' direction. CpG sites occur with high frequency in genomic regions called CpG isl ...
s. Estimated age ("predicted age" in mathematical usage), also referred to as DNA methylation age, has the following properties: first, it is close to zero for embryonic and
induced pluripotent stem cell Induced pluripotent stem cells (also known as iPS cells or iPSCs) are a type of pluripotent stem cell that can be generated directly from a somatic cell. The iPSC technology was pioneered by Shinya Yamanaka's lab in Kyoto, Japan, who showed in ...
s; second, it correlates with cell passage number; third, it gives rise to a highly heritable measure of age acceleration; and, fourth, it is applicable to chimpanzee tissues (which are used as human analogs for biological testing purposes). Organismal growth (and concomitant cell division) leads to a high ticking rate of the epigenetic clock that slows down to a constant ticking rate (linear dependence) after adulthood (age 20). The fact that DNA methylation age of blood predicts all-cause mortality in later life even after adjusting for known risk factors is compatible with a variety of causal relationships, e.g. a common cause for both. Similarly, markers of physical and mental fitness are associated with the epigenetic clock (lower abilities associated with age acceleration). It systematically underestimates age from older individuals. Salient features of Horvath's epigenetic clock include its applicability to a broad spectrum of tissues and cell types. Since it allows one to contrast the ages of different tissues from the same subject, it can be used to identify tissues that show evidence of accelerated age due to disease.


Genetic estimators in the Horvath clock

The Horvath clock, specifically the IEAA variant, is associated with several ageing-related genes:14 * TRIM59: of the
tripartite motif family The tripartite motif family (TRIM) is a protein family. Function Many TRIM proteins are induced by interferons, which are important component of resistance to pathogens and several TRIM proteins are known to be required for the restriction of infe ...
, strongly associated with chronological age and whose expression has been observed in multiple cancers *
SMC4 Structural maintenance of chromosomes protein 4 (SMC-4) also known as chromosome-associated polypeptide C (CAP-C) or XCAP-C homolog is a protein that in humans is encoded by the ''SMC4'' gene. SMC-4 is a core subunit of condensin Condensins are la ...
: inhibits cellular senescence, an established hallmark of ageing *
KPNA4 Importin subunit alpha-3, also known as karyopherin subunit alpha-4, is a protein that in humans is encoded by the ''KPNA4'' gene. Function The nuclear import of karyophilic proteins is directed by short amino acid sequences termed nuclear loca ...
: member of the importin family, nuclear transport receptors. Dysfunction of nuclear transport has been proposed as a marker of ageing *
CD46 CD46 complement regulatory protein also known as CD46 (cluster of differentiation 46) and Membrane Cofactor Protein is a protein which in humans is encoded by the ''CD46'' gene. CD46 is an inhibitory complement receptor. Gene This gene is fou ...
: encodes a regulator of T-cell function and the complement system, a key component of the innate immune system where it promotes inflammation * ATP8B4: encodes for a lipid transporter protein and contains variants that have been reported in association with Alzheimer's disease * CXXC4: encodes Idax, an inhibitor of Wnt signalling


Statistical approach

The basic approach is to form a weighted average of the 353 clock CpGs, which is then transformed to DNAm age using a calibration function. The calibration function reveals that the epigenetic clock has a high ticking rate until adulthood, after which it slows to a constant ticking rate. Using the training data sets, Horvath used a penalized regression model (
Elastic net regularization In statistics and, in particular, in the fitting of linear or logistic regression models, the elastic net is a regularized regression method that linearly combines the L1 and L2 penalties of the lasso and ridge methods. Specification The el ...
) to regress a calibrated version of chronological age on 21,369 CpG probes that were present both on the Illumina 450K and 27K platform and had fewer than 10 missing values. DNAm age is defined as estimated ("predicted") age. The elastic net predictor automatically selected 353 CpGs. 193 of the 353 CpGs correlate positively with age while the remaining 160 CpGs correlate negatively with age. R software and a freely available web-based tool can be found at the following webpage.


Accuracy

The median error of estimated age is 3.6 years across a wide spectrum of tissues and cell types, although this increases for older individuals The epigenetic clock performs well in heterogeneous tissues (for example, whole blood, peripheral blood mononuclear cells, cerebellar samples, occipital cortex, buccal epithelium, colon, adipose, kidney, liver, lung, saliva, uterine cervix, epidermis, muscle) as well as in individual cell types such as CD4 T cells, CD14 monocytes, glial cells, neurons, immortalized B cells, mesenchymal stromal cells. However, accuracy depends to some extent on the source of the DNA.


Comparison with other biological clocks

The epigenetic clock leads to a chronological age prediction that has a
Pearson correlation coefficient In statistics, the Pearson correlation coefficient (PCC, pronounced ) ― also known as Pearson's ''r'', the Pearson product-moment correlation coefficient (PPMCC), the bivariate correlation, or colloquially simply as the correlation coefficient ...
of r = 0.96 with chronological age (Figure 2 in). Thus the age correlation is close to its maximum possible correlation value of 1. Other biological clocks are based on a)
telomere A telomere (; ) is a region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes. Although there are different architectures, telomeres, in a broad sense, are a widespread genetic feature mos ...
length, b)
p16INK4a p16 (also known as p16INK4a, cyclin-dependent kinase inhibitor 2A, CDKN2A, multiple tumor suppressor 1 and numerous other synonyms), is a protein that slows cell division by slowing the progression of the cell cycle from the G1 phase to the S p ...
expression levels (also known as INK4a/ARF locus), and c) microsatellite mutations. The correlation between chronological age and
telomere A telomere (; ) is a region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes. Although there are different architectures, telomeres, in a broad sense, are a widespread genetic feature mos ...
length is r = −0.51 in women and r = −0.55 in men. The correlation between chronological age and expression levels of
p16INK4a p16 (also known as p16INK4a, cyclin-dependent kinase inhibitor 2A, CDKN2A, multiple tumor suppressor 1 and numerous other synonyms), is a protein that slows cell division by slowing the progression of the cell cycle from the G1 phase to the S p ...
in T cells is r = 0.56.


Applications of Horvath's clock

By contrasting DNA methylation age (estimated age) with chronological age, one can define measures of age acceleration. Age acceleration can be defined as the difference between DNA methylation age and chronological age. Alternatively, it can be defined as the residual that results from regressing DNAm age on chronological age. The latter measure is attractive because it does not correlate with chronological age. A positive/negative value of epigenetic age acceleration suggests that the underlying tissue ages faster/slower than expected.


Genetic studies of epigenetic age acceleration

The broad sense heritability (defined via
Falconer's formula Heritability is the proportion of variance caused by genetic factors of a specific trait in a population. Falconer's formula is a mathematical formula that is used in twin studies to estimate the relative contribution of genetic vs. environmental ...
) of age acceleration of blood from older subjects is around 40% but it appears to be much higher in newborns. Similarly, the age acceleration of brain tissue (prefrontal cortex) was found to be 41% in older subjects. Genome-wide association studies (GWAS) of epigenetic age acceleration in postmortem brain samples have identified several
SNPs In genetics, a single-nucleotide polymorphism (SNP ; plural SNPs ) is a germline substitution of a single nucleotide at a specific position in the genome. Although certain definitions require the substitution to be present in a sufficiently larg ...
at a genomewide significance level. GWAS of age acceleration in blood have identified several genome-wide significant genetic loci including the telomerase reverse transcriptase gene (
TERT Telomerase reverse transcriptase (abbreviated to TERT, or hTERT in humans) is a catalytic subunit of the enzyme telomerase, which, together with the telomerase RNA component (TERC), comprises the most important unit of the telomerase complex. T ...
) locus. Genetic variants associated with longer leukocyte telomere length in TERT gene paradoxically confer higher epigenetic age acceleration in blood.


Lifestyle factors

In general, lifestyle factors have only weak associations with epigenetic age acceleration in blood. Cross sectional studies of extrinsic epigenetic aging rates in blood show reduced epigenetic aging correlates with higher education, eating a high plant diet with lean meats, moderate alcohol consumption, and physical activity and the risks associated with metabolic syndrome. However, studies suggest that high levels of alcohol consumption are associated with accelerated aging of certain epigenetic clocks.


Obesity and metabolic syndrome

The epigenetic clock was used to study the relationship between high body mass index (BMI) and the DNA methylation ages of human blood, liver, muscle and adipose tissue. A significant correlation (r = 0.42) between BMI and epigenetic age acceleration could be observed for the liver. A much larger sample size (n = 4200 blood samples) revealed a weak but statistically significant correlation (r = 0.09) between BMI and intrinsic age acceleration of blood. The same large study found that various biomarkers of metabolic syndrome (glucose-, insulin-, triglyceride levels, C-reactive protein, waist-to-hip ratio) were associated with epigenetic age acceleration in blood. Conversely, high levels of
HDL cholesterol High-density lipoprotein (HDL) is one of the five major groups of lipoproteins. Lipoproteins are complex particles composed of multiple proteins which transport all fat molecules (lipids) around the body within the water outside cells. They are t ...
were associated with a lower epigenetic aging rate of blood. Other research suggests very strong associations between higher body mass index, waist-to-hip ratio, and
waist circumference The waist is the part of the abdomen between the rib cage and hips. On people with slim bodies, the waist is the narrowest part of the torso. ''Waistline'' refers to the horizontal line where the waist is narrowest, or to the general appear ...
and accelerated epigenetic clocks, with evidence that
physical activity Physical activity is defined as any voluntary bodily movement produced by skeletal muscles that requires energy expenditure.Global Recommendations on Physical Activity for Health, 2009. World Health Organization. Geneva, Switzerland. Accessed 13/ ...
may lessen these effects.


Female breast tissue is older than expected

DNAm age is higher than chronological age in female breast tissue that is adjacent to breast cancer tissue. Since normal tissue which is adjacent to other cancer types does not exhibit a similar age acceleration effect, this finding suggests that normal female breast tissue ages faster than other parts of the body. Similarly, normal breast tissue samples from women without cancer have been found to be substantially older than blood samples collected from the same women at the same time.


Female breast cancer

In a study of three epigenetic clocks and breast cancer risk, DNAm age was found to be accelerated in blood samples of cancer-free women, years before diagnosis.


Cancer tissue

Cancer tissues show both positive and negative age acceleration effects. For most tumor types, no significant relationship can be observed between age acceleration and tumor morphology (grade/stage). On average, cancer tissues with mutated
TP53 p53, also known as Tumor protein P53, cellular tumor antigen p53 (UniProt name), or transformation-related protein 53 (TRP53) is a regulatory protein that is often mutated in human cancers. The p53 proteins (originally thought to be, and often ...
have a lower age acceleration than those without it. Further, cancer tissues with high age acceleration tend to have fewer somatic mutations than those with low age acceleration. Age acceleration is highly related to various genomic aberrations in cancer tissues. Somatic mutations in
estrogen receptor Estrogen receptors (ERs) are a group of proteins found inside cells. They are receptors that are activated by the hormone estrogen (17β-estradiol). Two classes of ER exist: nuclear estrogen receptors ( ERα and ERβ), which are members of the ...
s or progesterone receptors are associated with accelerated DNAm age in breast cancer. Colorectal cancer samples with a BRAF (V600E) mutation or promoter hypermethylation of the mismatch repair gene MLH1 are associated with an increased age acceleration. Age acceleration in
glioblastoma multiforme Glioblastoma, previously known as glioblastoma multiforme (GBM), is one of the most aggressive types of cancer that begin within the brain. Initially, signs and symptoms of glioblastoma are nonspecific. They may include headaches, personality cha ...
samples is highly significantly associated with certain mutations in
H3F3A Histone H3.3 is a protein that in humans is encoded by the ''H3F3A'' and ''H3F3B'' genes. It plays an essential role in maintaining genome integrity during mammalian development. Histones are basic nuclear proteins that are responsible for the n ...
. One study suggests that the epigenetic age of blood tissue may be prognostic of lung cancer incidence.


Trisomy 21 (Down syndrome)

Down syndrome Down syndrome or Down's syndrome, also known as trisomy 21, is a genetic disorder caused by the presence of all or part of a third copy of chromosome 21. It is usually associated with physical growth delays, mild to moderate intellectual dis ...
entails an increased risk of many chronic diseases that are typically associated with older age. The clinical manifestations of accelerated aging suggest that trisomy 21 increases the biological age of tissues, but molecular evidence for this hypothesis has been sparse. According to the epigenetic clock, trisomy 21 significantly increases the age of blood and brain tissue (on average by 6.6 years).


Alzheimer's disease related neuropathology

Epigenetic age acceleration of the human prefrontal cortex was found to be correlated with several neuropathological measurements that play a role in Alzheimer's disease Further, it was found to be associated with a decline in global cognitive functioning, and memory functioning among individuals with Alzheimer's disease. The epigenetic age of blood relates to cognitive functioning in the elderly. Overall, these results strongly suggest that the epigenetic clock lends itself for measuring the biological age of the brain.


Cerebellum ages slowly

It has been difficult to identify tissues that seem to evade aging due to the lack of biomarkers of tissue age that allow one to contrast compare the ages of different tissues. An application of epigenetic clock to 30 anatomic sites from six centenarians and younger subjects revealed that the cerebellum ages slowly: it is about 15 years younger than expected in a centenarian. This finding might explain why the cerebellum exhibits fewer neuropathological hallmarks of age related dementias compared to other brain regions. In younger subjects (e.g. younger than 70), brain regions and brain cells appear to have roughly the same age. Several SNPs and genes have been identified that relate to the epigenetic age of the cerebellum.


Huntington's disease

Huntington's disease Huntington's disease (HD), also known as Huntington's chorea, is a neurodegenerative disease that is mostly inherited. The earliest symptoms are often subtle problems with mood or mental abilities. A general lack of coordination and an uns ...
has been found to increase the epigenetic aging rates of several human brain regions.


Centenarians age slowly

The offspring of semi-supercentenarians (subjects who reached an age of 105–109 years) have a lower epigenetic age than age-matched controls (age difference = 5.1 years in blood) and centenarians are younger (8.6 years) than expected based on their chronological age.


HIV infection

Infection with the Human Immunodeficiency Virus-1 (
HIV The human immunodeficiency viruses (HIV) are two species of ''Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immune ...
) is associated with clinical symptoms of accelerated aging, as evidenced by increased incidence and diversity of age-related illnesses at relatively young ages. But it has been difficult to detect an accelerated aging effect on a molecular level. An epigenetic clock analysis of human DNA from HIV+ subjects and controls detected a significant age acceleration effect in brain (7.4 years) and blood (5.2 years) tissue due to HIV-1 infection. These results are consistent with an independent study that also found an age advancement of 5 years in blood of HIV patients and a strong effect of the HLA locus.


Parkinson's disease

A large-scale study suggests that the blood of Parkinson's disease subjects, in particular, their granulocyte ratio, exhibits (relatively weak) accelerated aging effects.


Developmental disorder: syndrome X

Children with a very rare disorder known as syndrome X maintain the façade of persistent toddler-like features while aging from birth to adulthood. Since the physical development of these children is dramatically delayed, these children appear to be a toddler or at best a preschooler. According to an epigenetic clock analysis, blood tissue from syndrome X cases is not younger than expected.


Menopause accelerates epigenetic aging

The following results strongly suggest that the loss of female hormones resulting from menopause accelerates the epigenetic aging rate of blood and possibly that of other tissues. First, early
menopause Menopause, also known as the climacteric, is the time in women's lives when menstrual periods stop permanently, and they are no longer able to bear children. Menopause usually occurs between the age of 47 and 54. Medical professionals often ...
has been found to be associated with an increased epigenetic age acceleration of blood. Second, surgical menopause (due to bilateral
oophorectomy Oophorectomy (; from Greek , , 'egg-bearing' and , , 'a cutting out of'), historically also called ''ovariotomy'' is the surgical removal of an ovary or ovaries. The surgery is also called ovariectomy, but this term is mostly used in reference ...
) is associated with epigenetic age acceleration in blood and saliva. Third,
menopausal hormone therapy Hormone replacement therapy (HRT), also known as menopausal hormone therapy or postmenopausal hormone therapy, is a form of hormone therapy used to treat symptoms associated with female menopause. These symptoms can include hot flashes, vaginal ...
, which mitigates hormonal loss, is associated with a negative age acceleration of buccal cells (but not of blood cells). Fourth, genetic markers that are associated with early menopause are also associated with increased epigenetic age acceleration in blood.


Cellular senescence versus epigenetic aging

A confounding aspect of biological aging is the nature and role of senescent cells. It is unclear whether the three major types of cellular senescence, namely replicative senescence, oncogene-induced senescence and DNA damage-induced senescence are descriptions of the same phenomenon instigated by different sources, or if each of these is distinct, and how they are associated with epigenetic aging. Induction of replicative senescence (RS) and oncogene-induced senescence (OIS) were found to be accompanied by epigenetic aging of primary cells but senescence induced by DNA damage was not, even though RS and OIS activate the cellular DNA damage response pathway. These results highlight the independence of cellular senescence from epigenetic aging. Consistent with this, telomerase-immortalised cells continued to age (according to the epigenetic clock) without having been treated with any senescence inducers or DNA-damaging agents, re-affirming the independence of the process of epigenetic ageing from telomeres, cellular senescence, and the DNA damage response pathway. Although the uncoupling of senescence from cellular aging appears at first sight to be inconsistent with the fact that senescent cells contribute to the physical manifestation of organism ageing, as demonstrated by Baker et al., where removal of senescent cells slowed down aging. The epigenetic clock analysis of senescence, however, suggests that cellular senescence is a state that cells are forced into as a result of external pressures such as DNA damage, ectopic oncogene expression and exhaustive proliferation of cells to replenish those eliminated by external/environmental factors. These senescent cells, in sufficient numbers, will probably cause the deterioration of tissues, which is interpreted as organism ageing. However, at the cellular level, aging, as measured by the epigenetic clock, is distinct from senescence. It is an intrinsic mechanism that exists from the birth of the cell and continues. This implies that if cells are not shunted into senescence by the external pressures described above, they would still continue to age. This is consistent with the fact that mice with naturally long telomeres still age and eventually die even though their telomere lengths are far longer than the critical limit, and they age prematurely when their telomeres are forcibly shortened, due to replicative senescence. Therefore, cellular senescence is a route by which cells exit prematurely from the natural course of cellular aging.


Effect of sex and race/ethnicity

Men age faster than women according to epigenetic age acceleration in blood, brain, saliva, but it depends on the structure being researched and the lifestyle. The epigenetic clock method applies to all examined racial/ethnic groups in the sense that DNAm age is highly correlated with chronological age. But ethnicity can be associated with epigenetic age acceleration. For example, the blood of Hispanics and the
Tsimané The Tsimané, also known as the Tsimane' or Chimane, are an indigenous people of lowland Bolivia, living chiefly in the Beni Department municipalities of San Borja, San Ignacio de Moxos, Rurrenabaque, and Santa Ana del Yacuma. The Tsimané are th ...
ages more slowly than that of other populations which might explain the Hispanic mortality paradox.


Rejuvenation effect due to stem cell transplantation in blood

Hematopoietic stem cell transplantation Hematopoietic stem-cell transplantation (HSCT) is the transplantation of multipotent hematopoietic stem cells, usually derived from bone marrow, peripheral blood, or umbilical cord blood in order to replicate inside of a patient and to produce ...
, which transplants these cells from a young donor to an older recipient, rejuvenates the epigenetic age of blood to that of the donor. However, graft-versus-host disease is associated with increased DNA methylation age.


Progeria

Adult progeria also known as
Werner syndrome Werner syndrome (WS) or Werner's syndrome, also known as "adult progeria",James, William; Berger, Timothy; Elston, Dirk (2005). ''Andrews' Diseases of the Skin: Clinical Dermatology''. (10th ed.). Saunders. . is a rare, autosomal recessive disorder ...
is associated with epigenetic age acceleration in blood. Fibroblast samples from children with Hutchinson-Gilford
Progeria Progeria is a specific type of progeroid syndrome, also known as Hutchinson–Gilford syndrome. A single gene mutation is responsible for progeria. The gene, known as lamin A (LMNA), makes a protein necessary for holding the Nucleus of the cell ...
exhibit accelerated epigenetic aging effects according to the "skin & blood" epigenetic clock but not according to the original pan tissue clock from Horvath.


Biological mechanism behind the epigenetic clock

Despite the fact that biomarkers of ageing based on DNA methylation data have enabled accurate age estimates for any tissue across the entire life course, the precise biological mechanism behind the epigenetic clock is currently unknown. However, epigenetic biomarkers may help to address long-standing questions in many fields, including the central question: why do we age? To understand the essence of mechanisms behind the epigenetic clock, it would be advisable to make a comparison and find the relationship between the readings of the epigenetic clock and the
transcriptome The transcriptome is the set of all RNA transcripts, including coding and non-coding, in an individual or a population of cells. The term can also sometimes be used to refer to all RNAs, or just mRNA, depending on the particular experiment. The t ...
aging clock. The following explanations have been proposed for now in the literature.


Possible explanation 1: Epigenomic maintenance system

Horvath hypothesized that his clock arises from a methylation footprint left by an epigenomic maintenance system.


Possible explanation 2: Unrepaired DNA damages

Endogenous DNA damages occur frequently including about 50 double-strand DNA breaks per cell cycle and about 10,000 oxidative damages per day (see
DNA damage (naturally occurring) 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 fac ...
). During repair of double-strand breaks many epigenetic alterations are introduced, and in a percentage of cases epigenetic alterations remain after repair is completed, including increased methylation of CpG island promoters. Similar, but usually transient epigenetic alterations were recently found during repair of oxidative damages caused by H2O2, and it was suggested that occasionally these epigenetic alterations may also remain after repair. These accumulated epigenetic alterations may contribute to the epigenetic clock. Accumulation of epigenetic alterations may parallel the accumulation of un-repaired DNA damages that are proposed to cause aging (see
DNA damage theory of aging The DNA damage theory of aging proposes that aging is a consequence of unrepaired accumulation of naturally occurring DNA damage. Damage in this context is a DNA alteration that has an abnormal structure. Although both mitochondrial and nuclear D ...
).


Other age estimators based on DNA methylation levels

Several other age estimators have been described in the literature. 1) Weidner et al. (2014) describe an age estimator for DNA from blood that uses only three CpG sites of genes hardly affected by aging (cg25809905 in integrin, alpha 2b (ITGA2B); cg02228185 in aspartoacylase (ASPA) and cg17861230 in phosphodiesterase 4C, cAMP specific (PDE4C)). The age estimator by Weidener et al. (2014) applies only to blood. Even in blood this sparse estimator is far less accurate than Horvath's epigenetic clock (Horvath 2014) when applied to data generated by the Illumina 27K or 450K platforms. But the sparse estimator was developed for pyrosequencing data and is highly cost effective. 2) Hannum et al. (2013) report several age estimators: one for each tissue type. Each of these estimators requires covariate information (e.g. gender, body mass index, batch). The authors mention that each tissue led to a clear linear offset (intercept and slope). Therefore, the authors had to adjust the blood-based age estimator for each tissue type using a linear model. When the Hannum estimator is applied to other tissues, it leads to a high error (due to poor calibration) as can be seen from Figure 4A in Hannum et al. (2013). Hannum et al. adjusted their blood-based age estimator (by adjusting the slope and the intercept term) in order to apply it to other tissue types. Since this adjustment step removes differences between tissue, the blood-based estimator from Hannum et al. cannot be used to compare the ages of different tissues/organs. In contrast, a salient characteristic of the epigenetic clock is that one does not have to carry out such a calibration step: it always uses the same CpGs and the same coefficient values. Therefore, Horvath's epigenetic clock can be used to compare the ages of different tissues/cells/organs from the same individual. While the age estimators from Hannum et al. cannot be used to compare the ages of different normal tissues, they can be used to compare the age of a cancerous tissue with that of a corresponding normal (non-cancerous) tissue. Hannum et al. reported pronounced age acceleration effects in all cancers. In contrast, Horvath's epigenetic clock reveals that some cancer types (e.g. triple negative breast cancers or uterine corpus endometrial carcinoma) exhibit negative age acceleration, i.e. cancer tissue can be much younger than expected. An important difference relates to additional covariates. Hannum's age estimators make use of covariates such as gender, body mass index, diabetes status, ethnicity, and batch. Since new data involve different batches, one cannot apply it directly to new data. However, the authors present coefficient values for their CpGs in Supplementary Tables which can be used to define an aggregate measure that tends to be strongly correlated with chronological age but may be poorly calibrated (i.e. lead to high errors). 3) Giuliani et al. identify genomic regions whose DNA methylation level correlates with age in human teeth. They propose the evaluation of DNA methylation at ELOVL2, FHL2, and PENK genes in DNA recovered from both cementum and pulp of the same modern teeth. They wish to apply this method also to historical and relatively ancient human teeth. 4) Galkin et al. used deep neural networks to train an epigenetic aging clock of unprecedented accuracy using >6,000 blood samples. The clock uses information from 1000 CpG sites and predicts people with certain conditions older than healthy controls: IBD, frontotemporal dementia, ovarian cancer, obesity. The aging clock is planned to be released for public use in 2021 by an Insilico Medicine spinoff company Deep Longevity. In a multicenter benchmarking study 18 research groups from three continents compared all promising methods for analyzing DNA methylation in the clinic and identified the most accurate methods, having concluded that epigenetic tests based on DNA methylation are a mature technology ready for broad clinical use. 5) McCartney et al. Plasminogen activator inhibitor 1 ( PAI1) can also be used as an age estimator related to DNA methylation levels, as it has been shown to exhibit stronger associations with cardiometabolic disease than some epigenetic clocks. 6) de Lima Camillo et al. (2022) used an optimized deep neural network to create a highly accurate, robust pan-tissue epigenetic clock. The predictor, dubbed AltumAge, was trained on 142 datasets and uses 20,318 CpG sites to achieve one of the lowest reported median absolute errors for human epigenetic age prediction of 2.153 years. Partly, that increase in performance of Horvath's linear method is due to AltumAge's ability to detect CpG-CpG interactions. AltumAge predicts higher age for people with autism, HIV, multiple sclerosis, non-alcoholic fatty liver disease, type 2 diabetes, and atherosclerosis. In contrast to Horvath's clock, AltumAge predicts cancer to be older than normal tissues. The code for the clock is publicly available.


Other species

Wang et al., (in mice livers) and Petkovich et al. (based on mice blood DNA methylation profiles) examined whether mice and humans experience similar patterns of change in the methylome with age. They found that mice treated with lifespan-extending interventions (such as calorie restriction or dietary rapamycin) were significantly younger in epigenetic age than their untreated, wild-type age-matched controls. Mice age predictors also detects the longevity effects of gene knockouts, and rejuvenation of fibroblast-derived iPSCs. Mice multi-tissue age predictor based on DNA methylation at 329 unique CpG sites reached a median absolute error of less than four weeks (~5 percent of lifespan). An attempt to use the human clock sites in mice for age predictions showed that the human clock is not fully conserved in mice. Differences between human and mouse clocks suggests that epigenetic clocks need to be trained specifically for different species. A novel method of ageing lobsters was published in 2021 that used a ribosomal DNA methylation-based clock which may allow non-invasive sampling and ageing of wild European lobster populations (Homarus gammarus) Changes to DNA methylation patterns have great potential for age estimation and biomarker search in domestic and wild animals.


References


Further reading

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External links

* {{Cite web , last=Wickelgren , first=Ingrid , date=2022-08-17 , title=Epigenetic ‘Clocks’ Predict Animals’ True Biological Age , url=https://www.quantamagazine.org/epigenetic-clocks-predict-animals-true-biological-age-20220817/, website= Quanta Magazine , language=en Ageing Cancer Biogerontology Epigenetics Life extension