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Rejuvenation and the DNA Methylation Clock

by John G. Cramer

Alternate View Column AV-211
Keywords: rejuvenation, DNA methylation, Horvath Clock, epigenetic reprogramming, gene silencing
Published in the March-April-2021 issue of Analog Science Fiction & Fact Magazine;
This column was written and submitted 11/16/2020 and is copyrighted ©2020 by John G. Cramer.
All rights reserved. No part may be reproduced in any form without
the explicit permission of the author.

We are now familiar with the idea that our DNA determines our physical characteristics.  But consider the cells of a person at age 25 and the cells of that same person at age 85: except for a tiny fraction of cells with random mutations, the old and young cells must have exactly the same DNA.  What, then, tells the cells that they should function as those of an old person rather than a young person?  Further, for a particular person consider the cells of the brain, skin, bone marrow, muscles, liver, kidney, heart, etc.  Again, all of these cells have the same DNA, but they must act in very different ways in performing their essential functions.  So what is it that tells the cells what function they must perform and keeps them from doing something else?

The answer to both questions is that the cells differ in their epigenetic programming, which is related to the question of which of the protein-coding genes encoded in their DNA are switched on (expressed) and which are switched off (silenced).  As for aging, it has recently been discovered that there is a ticking epigenetic clock that progressively modifies the epigenetic programming of all the body cells as a person ages.  We will consider this clock and the possibility of resetting it.

Let's begin with a rough description of the mechanism behind epigenetic programming.  Your genome is the net DNA content of your cells, encoded using the ACGT sequences of nucleotides (adenine, cytosine, guanine, and thymine).  These encode instructions for producing proteins, the amino acid structures that are needed to sustain life.  The instructions are stored in the 23 chromosomes inherited from your father and the 23 from your mother, containing over three billion nucleotide base pairs forming about 49,000 genes.  Each DNA protein coding gene is preceded by a "promoter region", essentially an ID code used by the cell's transcription enzymes to find and identify the gene and its DNA code that needs to be transcribed.  One can think of this as if each gene is a book stored in the DNA library, with the title and call number on the book's spine represented by the gene's promoter region.   Some of these books are on locked away in inaccessible shelves and some are wide open on the library table.

Typically, each promoter region of a gene contains an "island" containing a repeating cluster of sequences of the nucleotide cytosine (C) followed by guanine (G).  These are called CpG islands, with "p" indicating pyrimidine, the 4 carbon and 2 nitrogen ring structure that is part of cytosine.  The significant feature of the CpG sequences is that one specific carbon atom in the pyrimidine ring can be methylated, i.e., a carbon-hydrogen CH3 methyl radical can be attached to it in place of a hydrogen atom.

When such methylation is present, it encourages that region of the DNA chain to be wrapped around spool-like histone structures for storage and made inactive, and it also discourages any wandering transcription factors from landing on the promoter region and transcribing the DNA coding into messenger RNA that will lead to protein production. When a sufficient number of methylations are present in a CpG island, it has the effect of silencing the gene.  In other words, while all body cells will have the same genes ready to express their proteins, only those genes with the promoter region relatively clear of methylation will actually express proteins.  This is a principle mechanism by which cells become specialized to perform a particular body function and by which cells are set to be young or old.

DNA methylation provides a very important analytic tool because it is reproduced in PCR amplification of DNA and because the Illumina company and others have developed CpG methylation microarrays that allow simultaneous identification of many thousands of methylation sites from a DNA sample.  In 2013, Prof. Steve Horvath (UCLA) used data from two sizes of Illumina microarrays that identify the methylation states of 27 thousand CpG sites.  Using advanced statistical techniques and machine learning, he discovered 353 CpG sites that were highly correlated with human calendar age, based on 7,844 tissue samples that spanned 51 different tissue types.  He found that methylation decreased with age in 55% of these sites and increased with age in the other 45%.  As the subjects aged, genes were being systematically switched, with some genes being brought to expression and others silenced.  This work became the Horvath DNAm Clock, and it has become the standard for aging research.  In 2018 Horvath improved the technique with a new clock algorithm with 513 CpG sites based on larger Illumina microarrays.  My own DNA methylation age has been measured from a blood sample by this technique, and it's a few years younger than my calendar age.

In the years since its creation, versions of the Horvath Clock have been used for a wide range of studies, including the differential aging of different tissue types, cell age acceleration due to cancer, accelerated aging in individuals with genetic diseases, demonstrating a poor correlation with telomere length, and analzing differential aging rates in animal species as compared to humans.  In particular, a modified Horvath clock established that a dog's human-equivalent age is not x7, but can be calculated as Aeq=16*ln(dog age)+31 ("ln" = natural-logarithm).  For example, my 7.25-year-old agility-champion Shetland Sheepdog MACH Taliesin has an equivalent human age of 70 years in terms of his epigenetic programming, (but he's still going strong), and my 1.4-year-old Shetland Sheepdog puppy Tristan is already the equivalent of 37.4 human years.

One central question raised by the discovery of this methylation clock is whether the epigenetic programming revealed is the result of aging or the cause of aging.  In other words, if one could provide a subject with treatment that would reset the Horvath Clock to a younger DNA methylation profile, would that rejuvenate the subject?  (Or would it be the equivalent of attempting time-travel by setting back your kitchen clock?)  The answer seems to be that resetting = rejuvenation.

This brings us to the question of what aging actually is.  There has been a decades-long debate in the biomedical community on whether (a) aging is accumulated cell damage, simply the wear and tear of living in an environment full of radiation, germs, and toxins, or (b) it is the result of natural programming, perhaps with enzymes in the bloodstream that inform all cells as to what their age profile should be.  Although hypothesis (a) has been widely accepted for many years, there is a growing body of evidence supporting hypothesis (b).  For example, there are decades of "parabiosis" experiments in which, for some period of time, an old and a young mouse or rat are lashed together and share the same blood.  Result: the old animal seems younger and the young animal seems older.  There have also been experiments in which blood plasma from a young donor seems to rejuvenate an older recipient.  Now, with the development of the Horvath Clock, we have an analytic tool that can tell us whether such rejuvenation has actually happened.

There are at least three recently-reported techniques that have been applied to mice and rats that actually reset the measured DNA methylation age and show evidence of restoring physical and behavioral performance to an old animal at levels comparable to those of a younger animal.

The first of these studies starts with the Yamanaka Factors, four proteins (Oct4, Sox2, Klf4, and cMyc, summarized as "OSKM") discovered in embryos in 2006.  When applied to cultures of various cell types, they were found to convert them the equivalent of embryonic stem cells.  (See my AV column in the September-October-2019 Analog.)   Following this, researchers genetically modified a mouse strain, splicing in a DNA "cassette" which, when triggered by the antibiotic tetracycline, expresses the four Yamanaka Factor proteins.  In such trans-genetic mice, with ages near the end of their 3-year lifespans, it was found that brief triggering of OSKM expression dramatically reduced Horvath Clock age readings and also increased physical fitness and alertness of the mice.

A second study, performed by Nugenics Research ( Mumbai , India ), identified in young rats special rejuvenating components in the blood plasma (which they have called "Elixir").  When this Elixir was administered to old rats, the results were spectacular.  They found the Horvath DNAm age was reduced in the liver cells by 75%, blood by 66%, heart by 57%, and hypothalamus by19% (average overall reduction 54.2%).  Biomarkers including fitness and memory showed similar improvements.   The company plans to complement this work with tests of Elixir on dogs and humans.  Dr. Harold Katcher, leader of the work, commented that ultimately the trade-secret active ingredients in Elixir will be produced by chemical synthesis, so that it will not need to be extracted from the blood plasma of young donors.  It appears that Katcher has found the enzymes circulating in the bloodstream that command cells to be young.

A third study was done by the Conboy Group (UC Berkeley).  They posed the following question:  Does young-plasma rejuvenation come from something positive in the young plasma or something negative in the old plasma?  Are there enzymes that command cells to be old?  To test the latter possibility, they replaced about 50% of the blood plasma of old mice with normal saline solution to which blood-normal level of albumin had been added.  Unfortunately, the Horvath Clock was not used in their study, but fitness and alertness improved, and a blood-protein assay showed a significantly more youthful profile.  The results strongly suggest that the old mice were indeed rejuvenated.  Apparently, just diluting the "get old" enzymes present in old blood plasma has a rejuvenating effect.  I am told that the group is now in the process of confirming these results using the Horvath Clock. 

So the bottom line is that Mother Nature seems to have programmed our bodies to grow progressively more frail and nonfunctional as we age by placing enzymes in our bloodstream that inform all of our cells as to just how old they are supposed to be and setting the methylation to enforce that.  But now we have identified some of the switches used by this epigenetic programming and have found ways of measuring and resetting them to a younger profile.  We are on the threshold of being able to wrest the aging controls away from Mother Nature and to dial back our biological ages.

How soon will this happen?  The problem is that our Federal health and safety bureaucracy has erected many barriers impeding the movement of revolutionary biochemical discoveries from the laboratory to the drugstore.  Further, aging itself is not considered by the US Food & Drug Administration to be a disease for which cures should be developed.  For example, the FDA halted human young plasma anti-aging treatments in the USA , citing a lack of proven safety.  Essentially all Federal funds related to aging go to treating the consequences of aging like cancer, heart disease, diabetes, …, with nothing to deal with aging itself.

Human rejuvenation with Yamanaka factors or Elixir must successfully surmount many regulatory hurdles, requiring years of testing.  Plasma dilution, in  principle, can be done now at existing blood-treatment facilities, if the procedure can be demonstrated to be safe.  Two Russian "bio-hackers" have already tried it with no ill effects.  In any case, it may take a while.  Dogs will probably be rejuvenated before humans.

John G. Cramer's 2016 nonfiction book (Amazon gives it 5 stars) describing his transactional interpretation of quantum mechanics, The Quantum Handshake - Entanglement, Nonlocality, and Transactions, (Springer, January-2016) is available online as a hardcover or eBook at: or

SF Novels by John Cramer:  Printed editions of John's hard SF novels Twistor and Einstein's Bridge are available from Amazon at and .  His new novel, Fermi's Question is coming soon from Baen Books.

Alternate View Columns Online: Electronic reprints of 212 or more "The Alternate View" columns by John G. Cramer published in Analog between 1984 and the present are currently available online at: .


The Horvath Methylation Clock:
Steve Horvath, "DNA methylation age of human tissues and cell types", Genome Biology 14 (10), R115 (2013);

Elixir Rejuvenation:
Steve Horvath, et al, "Reversing age: dual species measurement of epigenetic age with a single clock", bioRxiv preprint (not yet published); (2020).

Plasma Dilution Rejuvenation:
Melod Mehdipour, et al, "Rejuvenation of three germ layers tissues by exchanging old blood plasma with saline-albumin", Aging ( Albany NY ) 12:8790-8819 (2020);

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 This page was created by John G. Cramer on 01/27/2021.