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History
The strong effects of age on DNA methylation levels have been known since the late 1960s.
[6] A vast literature describes sets of
CpGs whose DNA methylation levels correlate with age, e.g.
[7][8][9][10][11] The first robust demonstration that DNA methylation levels in saliva could generate accurate age predictors was published by a
UCLA team including
Steve Horvath in 2011 (Bocklandt et al 2011).
[12]
The labs of Trey Ideker and Kang Zhang at the University of California
San Diego published the Hannum epigenetic clock (Hannum 2013),
[5]
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 and of
biostatistics at
UCLA (Horvath 2013).
[1][3]
Horvath spent over 4 years collecting publicly available Illumina DNA
methylation data and identifying suitable statistical methods.
[13] The personal story behind the discovery was featured in Nature.
[14]
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.
[1] This property allows one to compare the ages of different areas of the human body using the same aging clock.
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
[15][16][17][18] strongly suggests that it relates to a process that causes aging.
[19] However, it is unlikely that the 353 clock CpGs are special or play a direct causal role in the aging process.
[1] Rather, the epigenetic clock captures an
emergent property of the epigenome.
Epigenetic clock theory of aging
Horvath and Raj
[20] proposed 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 ageing 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 are expected to find many uses in biological research since age is a fundamental characteristic of most
organisms. Accurate measures of biological age (
biological aging clocks) could be useful for
Overall, biological clocks are expected to be useful for studying what causes aging and what can be done against it.
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 dinucleotides.
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 cells; 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).
[1]
The fact that DNA methylation age of blood predicts all-cause mortality
in later life even after adjusting for known risk factors
[15][16]
suggests that it relates to a process that causes aging. Similarly,
markers of physical and mental fitness are associated with the
epigenetic clock (lower abilities associated with age acceleration).
[21]
Salient features of Horvath's epigenetic clock include its high
accuracy and 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.
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)
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.
[22]
Accuracy
The median error of estimated age is 3.6 years across a wide spectrum of tissues and cell types .
[1]
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.
[1] 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 of r=0.96 with chronological age (Figure 2 in
[1]). Thus the age correlation is close to its maximum possible correlation value of 1. Other biological clocks are based on a)
telomere length, b)
p16INK4a expression levels (also known as INK4a/ARF locus),
[23] and c)
microsatellite mutations.
[24] The correlation between chronological age and
telomere length is r=−0.51 in women and r=−0.55 in men.
[25] The correlation between chronological age and expression levels of
p16INK4a in T cells is r=0.56.
[26] p16INK4a expression levels only relate to age in T cells, a type of white blood cells.[citation needed] The microsatellite clock measures not chronological age but age in terms of elapsed cell divisions within a tissue.[citation needed]
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) of age acceleration of blood from older subjects is around 40% but it appears to be much higher in newborns.
[1] Similarly, the age acceleration of brain tissue (prefrontal cortex) was found to be 41% in older subjects.
[27] Genome-wide association studies (GWAS) of epigenetic age acceleration in postmortem brain samples have identified several
SNPs at a genomewide significance level.
[28][29]
GWAS of age acceleration in blood have identified several genome-wide
significant genetic loci including the telomerase reverse transcriptase
gene (
TERT) locus .
[30]
Genetic variants associated with longer leukocyte telomere length in
TERT gene paradoxically confer higher epigenetic age acceleration in
blood.
[30]
Lifestyle factors
In general, lifestyle factors have only weak effects on epigenetic age acceleration in blood.
[31]
However, cross sectional studies of extrinsic epigenetic aging rates in
blood confirm the conventional wisdom regarding the benefits of
education, eating a high plant diet with lean meats, moderate alcohol
consumption, physical activity and the risks associated with
metabolic syndrome.
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.
[32]
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.
[31] 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.
[31] Conversely, high levels of the good cholesterol
HDL were associated with a lower epigenetic aging rate of blood.
[31]
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.
[1]
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.
[1]
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
PMID 28364215.
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).
[1][2] On average, cancer tissues with mutated
TP53 have a lower age acceleration than those without it.
[1] Further, cancer tissues with high age acceleration tend to have fewer somatic mutations than those with low age acceleration.
[1][2] Age acceleration is highly related to various genomic aberrations in cancer tissues. Somatic mutations in
estrogen receptors or
progesterone receptors are associated with accelerated DNAm age in breast cancer.
[1] Colorectal cancer samples with a
BRAF (V600E) mutation or promoter hypermethylation of the mismatch repair gene
MLH1 are associated with an increased age acceleration.
[1] Age acceleration in
glioblastoma multiforme samples is highly significantly associated with certain mutations in
H3F3A.
[1] One study suggests that the epigenetic age of blood tissue may be prognostic of lung cancer incidence.
[33]
Trisomy 21 (Down syndrome)
Down Syndrome (DS)
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).
[34]
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
[27]
Further, it was found to be associated with a decline in global
cognitive functioning, and memory functioning among individuals with
Alzheimer's disease.
[27] The epigenetic age of
blood relates to cognitive functioning in the elderly.
[21] 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.
[35]
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.
[1][35] Several SNPs and genes have been identified that relate to the epigenetic age of the cerebellum
[28]
Huntington's disease
Huntington's disease has been found to increase the epigenetic aging rates of several human brain regions.
[36]
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.
[18]
HIV infection
Infection with the Human Immunodeficiency Virus-1 (
HIV)
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.
[37]
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.
[38]
Parkinson's disease
A
large-scale study suggests that the blood of Parkinson's disease
subjects exhibits (relatively weak) accelerated aging effects.
[39]
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.
[40]
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.
[41] First, early
menopause has been found to be associated with an increased epigenetic age acceleration of blood.
[41] Second, surgical menopause (due to bilateral
oophorectomy) is associated with epigenetic age acceleration in blood and saliva. Third,
menopausal hormone therapy, which mitigates hormonal loss, is associated with a negative age acceleration of buccal cells (but not of blood cells).
[41]
Fourth, genetic markers that are associated with early menopause are
also associated with increased epigenetic age acceleration in blood.
[41]
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.
[42] 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.
[43]
However, the epigenetic clock analysis of senescence 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.
[42]
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.
[42]
Effect of sex and race/ethnicity
Men age faster than women according to epigenetic age acceleration in blood, brain, saliva, and many other tissues.
[44]
The epignetic 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.
[44] For example, the blood of Hispanics and the
Tsimané ages more slowly than that of other populations which might explain the
Hispanic mortality paradox.
[44]
Rejuvenation effect due to stem cell transplantation in blood
Hematopoietic stem cell transplantation,
which transplants these cells from a young donor to an older recipient,
rejuvenates the epigenetic age of blood to that of the donor
PMID 28550187. However,
graft-versus-host disease is associated with increased DNA methyhlation age
PMID 28550187.
Progeria
Adult progeria also known as
Werner syndrome is associated with epigenetic age acceleration in blood.
[45]
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.
[20]
However, epigenetic biomarkers may help to address long-standing
questions in many fields, including the central question: why do we age?
The following explanations have been proposed 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.
[1]
Possible explanation 2: Unrepaired DNA damages
Endogenous DNA damages occur frequently including about 50 double-strand DNA breaks per cell cycle
[46] and about 10,000 oxidative damages per day (see
DNA damage (naturally occurring)). 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.
[47][48][49] Similar, but usually transient epigenetic alterations were recently found during repair of oxidative damages caused by H
2O
2, and it was suggested that occasionally these epigenetic alterations may also remain after repair.
[50]
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).
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)).
[51]
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.
[52] But the sparse estimator was developed for pyrosequencing data and is highly cost effective.
[53]
2) Hannum et al. (2013)
[5]
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:
[1]
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
[2][54]
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.
[57] They wish to apply this method also to historical and relatively ancient human teeth.
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.
[58]
Other species
Wang et al., (in mice livers)
[59] and Petkovich et al.,(based on mice blood DNA methylation profiles)
[60]
examined whether mice and humans experience similar patterns of change
in the methylome with age. They found that mice treated with
lifespan-extending interventions (surch 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 4 weeks
(~5% of lifespan). An attempt to use the human clock sites in mouse for
age predictions showed that human clock is not fully conserved in mouse.
[61] Differences between human and mouse clocks suggests that epigenetic
clocks need to be trained specifically for different species.
[62]
Changes to DNA methylation patterns have great potential for age estimation and biomarker search in domestic and wild animals.
[63]