{"id":691,"date":"2018-02-14T20:27:01","date_gmt":"2018-02-14T20:27:01","guid":{"rendered":"http:\/\/joshmitteldorf.peachpuff-wolverine-566518.hostingersite.com\/?p=691"},"modified":"2018-02-17T14:51:42","modified_gmt":"2018-02-17T14:51:42","slug":"methylation-aging-clock-an-update","status":"publish","type":"post","link":"https:\/\/scienceblog.com\/joshmitteldorf\/2018\/02\/14\/methylation-aging-clock-an-update\/","title":{"rendered":"Methylation Aging Clock: An Update"},"content":{"rendered":"

Methylation of DNA is the best-known mode of epigenetic regulation (turning genes on and off). \u00a0Methylation patterns are stable unless they are actively changed, and can persist over decades, even\u00a0<\/span><\/i>across generations. \u00a0<\/span><\/i><\/p>\n

Four years ago, biostatistician Steve Horvath of UCLA identified a set of 353 methylation sites that are best-correlated with human (chronological) age. \u00a0These are sites where genes are turned on and off at particular stages of life. \u00a0A computer analysis of a gene sample (from blood or skin or even urine) can determine a person\u2019s age within about two years.<\/span><\/i><\/p>\n

Two reasons the Horvath Clock is important. \u00a0First, it is the best measure we have of a person\u2019s biological age, so it provides an objective measure of whether our anti-aging interventions are working. \u00a0Say you\u2019re excited about a new drug and you want to know whether it really makes people younger. \u00a0Before the Horvath clock, you had to give it to thousands of people and wait a long time to see if fewer of them were dying, compared to people who did not get the drug. \u00a0The Horvath clock is a huge shortcut. \u00a0You can give the drug to just a few people and measure their Horvath (methylation) age before and after. \u00a0With just a few dozen people over a two-year period, you can get a very good idea whether your drug is working.<\/span><\/i><\/p>\n

Second, there is evidence and theory to support the idea that the methylation sites that Horvath identified are not just markers of aging but causes of aging. \u00a0That means that if we can figure out how to get inside the cell nucleus and re-configure the methylation patterns on the chromosomes, we should be able to address a root cause of aging. (Before we get too excited: \u201cGene therapy\u201d has been around 20 years but is still in a developmental stage; \u201cepigenetic therapy\u201d is what we need, and it does not yet exist, but is technically feasible using genetically engineered viruses and CRISPR.)<\/span><\/i><\/p>\n

The write-up below is taken directly from two talks that Horvath gave, <\/span><\/i>2016 at NIH in Maryland<\/span><\/i><\/a> and just <\/span><\/i>last month in Los Angeles<\/span><\/i><\/a>.<\/span><\/i><\/p>\n

\n

In 2012-2013, three papers appeared proposing the idea that the deep cause of aging (in humans and many other higher animals) is an epigenetic program [<\/span>Johnson<\/span><\/a>, <\/span>Mitteldorf<\/span><\/a>, <\/span>Rando<\/span><\/a>]. \u00a0Genes are turned on and off at various stages of life, producing growth, development and aging in seamless sequence. \u00a0(A fourth <\/span>paper by Blagosklonny<\/span><\/a> proposed a similar idea, but focused on the role of a single transcription factor controlling gene expression (mTOR) and shied away from the conclusion that natural selection might have preferred aging affirmatively. \u00a0Here\u2019s an <\/span>earlier presentiment<\/span><\/a> by Blagosklonny.) <\/span><\/p>\n

It\u2019s a powerful hypothesis that proposes to resolve evolutionary and metabolic questions alike. \u00a0It contains a seed of a prescription for anti-aging research\u2014although epigenetics has proved to be so complicated that practical modification of the body\u2019s gene expression schedule may require a lot more groundwork.<\/span><\/p>\n

Unbeknownst to any of us working on these theoretical papers, Steve Horvath was already working on calibration and measurement of the epigenetic aging clock, and he <\/span>published<\/span><\/a> his basic result by the end of 2013.<\/span><\/p>\n

One remarkable property of the Horvath clock is that it is more accurate than chronological age for predicting who will contract aging diseases and who will die. \u00a0Even though the clock was derived with an algorithm that matched the output clock age as closely as possible to chronological age, the result proved to contain more information than chronological age. \u00a0\u201cIn deriving the clock, chronological age was used as a proxy for biological age.\u201d \u00a0People whose \u201cmethylation age\u201d is greater than their chronological age are likely to suffer health deterioration and to die sooner than people whose methylation age is less than their chronological age. \u00a0<\/span><\/p>\n

Horvath has openly shared his methodology and his computer program. \u00a0Based on the Horvath clock, a California company began last year to offer a commercial test for methylation age. \u00a0You can send a blood or urine sample to <\/span>Zymo Research<\/span><\/a>.<\/span><\/p>\n

 <\/p>\n

Candidate aging clocks<\/b><\/p>\n

Horvath describes how he came up with the idea of a methylation clock by a process of elimination, beginning with four candidate clocks:<\/span><\/p>\n

    \n
  1. Telomere length<\/span><\/li>\n
  2. Gene expression profile<\/span><\/li>\n
  3. Proteomic data<\/span><\/li>\n
  4. DNA Methylation<\/span><\/li>\n<\/ol>\n

    In detail:<\/span><\/p>\n

      \n
    1. Telomere length – This had been measured easily and cheaply for more than a decade, but its correlation with chronological age (and with mortality) is not strong enough to be useful as a biological clock.<\/span>
      \n<\/span>
      \n<\/span>\"\"<\/li>\n
    2. Gene expression profile: Which genes are being transcribed into RNA at a given time? \u00a0This can be measured by extracting RNA, and turns out to be highly tissue-specific. \u00a0In other words, it varies according to which part of the body you\u2019re looking at.<\/span><\/li>\n
    3. Proteomic data: \u00a0Genes, once transcribed, are translated into proteins. \u00a0Some of these proteins stay in the cell while others circulate through the body. \u00a0Gene CHIP technology measures levels of different proteins reliably and inexpensively.<\/span><\/li>\n
    4. DNA Methylation: Easier to measure than (2) or (3). Methylation is only one of many mechanisms controlling gene expression, but it is one of the most persistent. \u00a0Horvath found that a subset of DNA methylation sites seems to be characteristic of age no matter where in the body they are measured.<\/span><\/li>\n<\/ol>\n

      What is DNA methylation?<\/b><\/p>\n

      Adjacent to many genes is a <\/span>promoter site<\/span><\/a>, a location on the same chromosome which stores temporary information about whether the gene is turned on or off. \u00a0Promoter sites contain the base sequence C-G-C-G-C-G-C repeated. \u00a0This is called a <\/span>CpG island<\/span><\/a> (where the \u201cp\u201d just tells you that the C is linked to G on the same strand, rather than being linked across strands, in which C is paired with G.)<\/span><\/p>\n

      C stands for \u201cCytosine\u201d, and the Cytosine molecule can be modified by adding an extra methyl group (CH<\/span>3<\/span>) to form 5-methyl Cytosine.<\/span><\/p>\n

      <\/p>\n

      The cell has molecular workers that are deployed to go around specifically adding methyl groups in some parts of the DNA or removing them in others. \u00a0The bottom line is that methylated Cytosine is a sign that says \u201cdon\u2019t transcribe the adjacent gene.\u201d \u00a0When the methyl groups are removed, it is a signal that the gene are to be transcribed once more.<\/span><\/p>\n

      Enzymes called methyl transferases are deployed to precise regions of the genome to turn genes on and off. \u00a0Methylation can be transient. \u00a0There is <\/span>evidence<\/span><\/a> for circadian cycles of methylation. \u00a0Or it can be quite long-lasting. \u00a0Methylation patterns can persist for decades, and are copied when cells replicate, so that methylation patterns can be passed to offspring as part of one\u2019s epigenetic legacy. \u00a0Inherited methylation sites are the exception however; most of the genome is programmed fresh with age-zero, pluripotent methylation patterns when egg and sperm cells are generated.<\/span><\/p>\n

       <\/p>\n

      How the methylation clock works<\/b><\/p>\n

      Using a standard statistical algorithm, Horvath identified 353 CpG sites that were most strongly correlated with chronological age, no matter where in the body he looked. \u00a0The same algorithm provided 353 numbers to be multiplied by methylation levels at each site, then added up to produce a number. \u00a0The number is not directly a measure of age, but in the last step a table is used (an empirically-derived curve) to associate the number with an age.<\/span><\/p>\n

      \"\"<\/p>\n

      This is the raw output of the function before it is transformed into an age. \u00a0Notice that methylation changes very rapidly during the first 5 years of life, gradually slowing during the growth phase and straightening out to constant slope after about age 18.<\/span><\/p>\n

      Even though the Horvath clock was designed to be independent of what part of the body DNA was drawn from, some variations appear. \u00a0Most noticeable is female breast tissue, which ages faster than the rest of the body, and brain tissue, which ages more slowly. \u00a0Blood and bone tissue tend to age a little faster. \u00a0(Sperm and egg cells are \u201cage zero\u201d no matter the age of the person from whom the germ cells were drawn. \u00a0Placentas from women of all ages are age zero.) Similarly, induced stem cells (using the 4 Yamanaka factors) have zero age. \u00a0In contrast, a similar treatment can change one differentiated cell type into another, for example, turning a skin cell into a neuron. \u00a0This does not affect epigentic age.<\/span><\/p>\n

      Liver cells tend to be older than the rest of the body in people who are overweight, and younger than the rest of the body in people who are underweight. \u00a0Other tissues don\u2019t seem to show this relationship. \u00a0For example, fat cells do not have older methylation ages in people who are obese. \u00a0And, perhaps surprisingly, weight loss does not reverse the accelerated methylation age of the liver (at least, not within the 9-month time frame of the <\/span>one study<\/span><\/a> looking at this).<\/span>
      \n\"\uf61e\"<\/p>\n

      Studies have been done correlating methylation age with various diseases and, of course, mortality. \u00a0Corrections are made for every kind of environmental factor, including smoking, obesity, exercise, workplace hazards, etc, called collectively the \u201cextrinsic factors\u201d. \u00a0The result is that methylation age rises with extrinsic factors, and independently methylation age is also correlated with intrinsic (genetic) factors that affect lifespan. \u00a0Horvath estimates that genetics controls 40% of the variation in methylation age (as it differs from chronological age).<\/span><\/p>\n

      \"\"<\/p>\n

      Men are slightly older than women in methylation age. \u00a0This is already evident by age 2. Delayed menopause is associated with lower epigenetic age. Cognitive function correlates inversely with methylation age of the brain. <\/span><\/p>\n

      Speaking before Horvath at the same conference, Jim Watson claims there are many supplements and medications that can slow the Horvath clock. \u00a0The one he focuses on is metformin, which, he says, has epigenetic effects<\/a> via an entirely different pathway from lowering blood sugar (the purpose for which it has been prescribed to tens of millions of diabetics). <\/span><\/p>\n

       <\/p>\n

      Here\u2019s a curious clue: \u00a0There is a tiny number of <\/span>children who never develop or grow<\/span><\/a>, and continue to look like babies through age 20 and perhaps beyond. \u00a0These children have <\/span>normal methylation age<\/span><\/a>. \u00a0Whatever it is that blocks their growth, it is not the methylation changes in their DNA. \u00a0Does this mean that there are other epigenetic controls, more powerful than methylation, that control growth and development? \u00a0Or does it mean that children with this syndrome have normal epigenetic development, but something downstream from gene expression is blocking their growth? \u00a0Conversely, Hutchinson-Gilford progeria is caused by a defect in the LMNA gene which causes children to age and die before they even grow up. \u00a0Hutchinson-Gilford children have normal methylation ages by the Horvath clock.<\/span>
      \n<\/p>\n

      Radiation, like smoking and exposure to environmental oxidation, tends to age the body faster. \u00a0This is independent of methylation age\u2014which is unaffected by radiation. \u00a0Neither smoking nor radiation exposure affect epigenetic age. \u00a0HIV also accelerates aging, and HIV <\/span>does<\/i><\/b> affect methylation age.<\/span><\/p>\n

      Methylation age and telomere age are both correlated with chronological age, and they both predict mortality and morbidity independent of chronological age. \u00a0But the two measures are not correlated with each other. \u00a0In other words, the information contained in the methylation clock and in measures of telomere length complement one another to offer a better predictor of future aging decline than either of them separately.<\/span><\/p>\n

      Diet has a weak effect on methylation age. \u00a0Very high carbohydrate, very low protein diets are noticeably terrible. \u00a0Beyond this, there seem to be two sweet spots: one for the Ornish-style protein-restricted diet and one for the Zone\/Atkins style diet. \u00a0Weak evidence to be sure, but suggestive that they both work.<\/span><\/p>\n

      \u201cThe epigenetic clock is broken in cancer tissue.\u201d [<\/span>ref<\/span><\/a>]<\/span><\/p>\n

       <\/p>\n

      Building on the original clock<\/b><\/p>\n

      The original clock was optimized to track chronological age, and yet it fortuitously provided more information than chronological age. \u00a0In a second iteration, Horvath set out explicitly to track biological age. \u00a0He used historic blood samples from the 1990s, and paired them with hospital records and death certificates to search for methylation sites that correlate best with aging-related health outcomes. \u00a0The result was the phenotypic clock, DNAm phenoAge. \u00a0This uses 513 methylation sites to predict <\/span><\/p>\n