Epigenetic aging clocks suggest an improvement to this article

Epigenetic clocks are predictors of biological age based on alterations in an individual's DNA methylation profile. Methylations – biochemical processes that modify the activity of a DNA segment without changing its sequence – occur naturally and regulate gene expression to control normal growth and development. With age, the methylation state of various genes may change. These changes are quantifiable and serve as a means to gauge epigenetic age, which is often different from chronological age.

The term "epigenetic clock" is also a collective designation referring to the natural biological mechanisms that drive DNA methylation. These innate mechanisms, which play critical roles in an organism's development and maintenance, leave a molecular "footprint" that reflects the biological life history of the organism. This overview will focus primarily on predictive epigenetic clocks, with a brief mention of the innate.

Overview of concepts underpinning epigenetic clocks

Epigenetics

Epigenetics is a biological mechanism that regulates gene expression (how and when certain genes are turned on or off). Diet, lifestyle, and environmental exposures can cause epigenetic changes throughout an individual's lifespan to influence health and disease. For example, epigenetic processes are dysregulated in diseases such as cancer and Alzheimer's disease.[1][2] Scientific evidence suggests that epigenetic changes can be passed from generation to generation.[3]

Three biochemical processes are thought to drive epigenetic change: DNA methylation, histone modification, and non-coding RNA-associated gene silencing. DNA methylation has relevance for predicting biological age via epigenetic clocks.

DNA methylation

DNA methylation occurs naturally when a methyl group – a chemical structure containing three carbon atoms and one hydrogen atom – attaches to one of DNA's four nucleotide bases (adenine [A], cytosine [C], guanine [G], or thymine [T]). Methylation creates a biological record of the varied molecular processes that participate in an individual's development, maintenance, and decline. A vast array of factors promote methylation, including dietary intake, exercise, stress, smoking, and even social factors, such as maternal-infant interaction, among others.[4]

The most common DNA methylation process involves the addition of a methyl group to one of the carbon atoms in the cytosine base, forming 5-methylcytosine. This addition alters the overall geometry of the DNA strand, ultimately influencing gene expression. Most 5-methylcytosine is found on areas of the DNA known as CpG islands – short stretches of DNA where the frequency of the cytosine-guanine (CG) sequence is higher than other regions. (The "p" in CpG simply reflects the presence of a phosphate group between the two nucleotides.) Methylation of a CpG island in the promoter region of a gene turns off, or "silences," the gene's expression. DNA methylation may promote age-related diseases such as cancer.[5]

Methylation is a dynamic process that is not only reversible, but appears to be under circadian control in some tissues.[5][6] It increases with age and the rate of change over the lifespan varies among CpGs, averaging 3.2 percent organism-wide and ranging from 7 to 91 percent for certain individual genes.[7][8]

Aging

Aging comprises the collective physiological, functional, and mental changes that accrue in a biological organism over time. It is the primary risk factor for many chronic diseases in humans, including cancer, Alzheimer's disease, and cardiovascular disease. Individuals age at different rates, however, a phenomenon observed across sexes, ethnic groups, and races. For example, women typically outlive men, despite having higher incidence of disease. Similarly, Hispanics living in the United States exhibit what is commonly referred to as the "Hispanic paradox," a phenomenon in which their life expectancy is similar to whites, despite having lower income and education levels and reduced access to health care.[9] Epigenetic clocks may provide a means of explaining these and other differential aging rates.

Aging in humans is measured according to three different standards: chronological age, epigenetic age, and biological (sometimes referred to as phenotypic) age.

Chronological age

An individual's chronological age simply reflects the number of months or years a person has been alive. Although certain developmental milestones and characteristics correlate with chronological age, it is an unreliable measure of the aging process.

Epigenetic age

Epigenetic age is based on an individual's DNA methylation profile. An individual's epigenetic age is highly correlated with their chronological age. However, some exceptions to the rule exist. For example, the epigenetic ages of semi-supercentenarians (people who live to be 105 to 109 years old) are markedly younger than their chronological ages.[10]

Biological age

An individual's biological age, sometimes referred to as phenotypical age, provides a measure of their physiological and functional state. It is a calculation of an individual's risk of disease and death compared to individuals of the same chronological age, based on biochemical measures of inflammation and metabolic and immune function.[11]

Age acceleration

Age acceleration is a phenomenon that occurs when an individual's epigenetic age exceeds their chronological age and may be the result of either intrinsic or extrinsic factors. Intrinsic factors are largely driven by internal physiological factors such as normal metabolism and genetics. Extrinsic factors are those associated with lifestyle and environmental exposures, such as diet, tobacco use, ultraviolet radiation, and mental illness. Markers of accelerated extrinsic aging have been observed in the blood of suicide completers, for example.[12]

Epigenetic clock variants

Several variations of DNA methylation-based epigenetic clocks have been identified. They are generally categorized according to the type and number of tissues used to formulate the calculation, as well as the type of age measured (i.e., epigenetic versus phenotypic). Each is named for the scientist who created the clock. The most accurate and robust of these clocks are described here.

The Hannum clock

Created by Dr. Gregory Hannum, the Hannum clock is a single-tissue calculator of epigenetic age based on 71 CpGs present in DNA from human blood.[13] Although highly accurate in regard to lifespan prediction, the Hannum clock is based on adult blood biomarkers, so it is inappropriate for use in children or against other tissue types.

One study used the Hannum clock to investigate associations between DNAm age and chronological age in African Americans and whites and to identify links between race, poverty, sex, and epigenetic age acceleration. The study was based on methylation profiles present in DNA samples from 487 middle-aged African American and white men and women. The investigators found that African Americans had more age-associated DNAm changes in genes implicated in age-related diseases and cellular pathways involved in growth and development than whites. Interestingly, African Americans also demonstrated slower extrinsic aging than whites. These findings may have relevance for age- and race-related health disparities.[14]

Use of the Hannum clock also demonstrated that exposure to abuse, financial hardship, or neighborhood disadvantage around the age of 7.5 years alters methylation patterns, which may alter normal patterns of cellular aging.[15]

Another study investigated the effects of cigarette smoking on aging using the Hannum clock based on methylation data drawn from two large cohorts of adults living in the United States. The findings indicated that not only was smoking associated with accelerated biological aging, strong effects were observed even with low levels of exposure.[16]

The Horvath clock

The Horvath epigenetic clock, created by Dr. Steven Horvath, predicts age based on methylation patterns and rates on 353 CpG islands in the DNA of 51 different tissue and cell types.[7] This multi-tissue clock calculates epigenetic age by coupling a tissue's DNA methylation status on specific CpGs with a mathematical algorithm to provide an age estimate. The estimator's yield is referred to as DNAm (where "m" represents methylation) age. The Horvath clock can identify the epigenetic age of a donor with 96 percent accuracy within approximately four years.[7] Its accuracy extends across multiple tissue types and ages, including children.

Nonalcoholic steatohepatitis, or NASH, is a type of fatty liver disease characterized by liver inflammation and damage. In a study in which the Horvath clock was used to assess epigenetic age acceleration in people with NASH, the clock accurately predicted the chronological age of all the study subjects. Furthermore, the investigators found that NASH was associated with accelerated aging and closely correlated with hepatic collage content, a measure of liver fibrosis.[17]

Another study using the Horvath clock demonstrated that based on the DNA methylation patterns of 345 people with colorectal cancer tumors, epigenetic age acceleration was associated with certain molecular characteristics of the tumors. The study also demonstrated that epigenetic age predicted colorectal cancer survival rates and tumor stage.[18]

Stilbenoids are dietary compounds present in some plants. Examples include resveratrol, which is found in red grapes and peanuts, and pterostilbene, which is found in blueberries and almonds. The Horvath clock identified subtle alterations in the DNA methylation patterns of human immortalized mammary epithelial cells exposed to a noncytotoxic dose of resveratrol for nine days. The authors of the study suggested that these subtle changes reflected a kind of "remodeling" as opposed to turning off or on gene activity.[19]

Learn more about resveratrol in this overview article.

Information on how to calculate DNAm age using Horvath's method is freely available.

The Levine clock

Dr. Morgan Levine created a multi-tissue clock that calculates an individual's phenotypical age, called PhenoAge.[11] It is distinct from other clocks in that it predicts time to death based on DNA methylation at 513 CpG islands as well as biochemical markers of age-related disease, including albumin, creatinine, glucose, C-reactive protein, alkaline phosphatase, and several blood components. Several physiological responses are associated with accelerated phenotypical aging, including increased activation of proinflammatory pathways and decreased DNA repair activities.[11]

One study used the Levine clock to investigate the effects of heavy, chronic alcohol intake on epigenetic age acceleration using clinical biomarkers such as liver function enzymes. The study, which estimated DNA methylation age in 331 people with alcohol use disorder, found that the disorder accelerated aging by an average of 2.2 years. A genome-wide meta-analysis of accelerated epigenetic aging among the study subjects indicated that the presence of a single nucleotide polymorphism in the APOL2 gene (a member of the apolipoprotein-L family) further accelerated aging.[20]

The Levine clock was also employed as a means to assess breast cancer risk. The study gauged the DNA methylation age of more than 1,500 women with breast cancer and determined that for every 5-year acceleration in a woman's epigenetic aging, her risk of developing breast cancer increased by 15 percent.[21]

Exposure to air pollutants is associated with poor health outcomes and increased risk of disease. A study using the Levine clock to gauge epigenetic age of more than 2,700 white women living in the United States who were exposed to particulate air pollutants found that the women's epigenetic aging was accelerated by as much as six years.[22]

Altering the native epigenetic clock's rate of ticking

In general, the native epigenetic clock's ticking rate across multiple types of tissue from a single individual is fairly consistent. However, the cerebellum tends to age more slowly, while female breast tissue tends to age more quickly.[7] In addition, certain types of cancer may be considerably older or younger than predicted.[7] Interestingly, some evidence suggests that the epigenetic age of adult cells can be reset. Dr. Shinya Yamanaka discovered a group of proteins that can reprogram differentiated (mature) cells into pluripotent stem cells. These proteins, now called Yamanaka factors, are highly expressed in embryonic stem cells in mice and humans. Their short-term expression can ameliorate cellular and physiological hallmarks of aging and prolong lifespan by resetting the innate epigenetic clock.[23]

Some individuals may be genetically predisposed to a slower overall clock rate. For example, one study analyzed the DNA methylation levels of peripheral blood mononuclear cells (a type of white blood cell) from semi-supercentenarians and their offspring. The investigators found that the average epigenetic age of the semi-supercentenarians was nearly nine years younger than their chronological age. The epigenetic age of their offspring was approximately five years younger than that of their age-matched controls.[10]

Lifestyle factors and exposures can influence the native ticking rate, as well. For example, an obesogenic diet can increase methylation and the clock's subsequent ticking rate.[24] And, as described above, smoking cigarettes and exposure to particulate air pollutants increases the tick rate.[16][22] Some interventions have been identified that may slow the ticking rate, however. These measures have been studied for their longevity-enhancing effects and include caloric restriction and administration of rapamycin, an immunosuppressant drug.[25]

Conclusion

Epigenetic clocks predict biological age based on molecular markers on an individual's DNA. Several variants of clocks have been identified, and they vary based on the type and number of tissues in which the markers are measured as well as the final output. In general, the epigenetic ticking rate across multiple types of tissue from a single individual is fairly consistent, but some exceptions do exist. The use of epigenetic clocks may have widespread applications in health and society, including forensic science and early prevention and treatment of disease to promote healthy aging. Rather than asking whether a person's biomarkers look better, soon clinical trials may ask whether the person is simply aging better.

A COMPREHENSIVE OVERVIEW OF EPIGENETIC AGING CLOCKS

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