Pulsed Yamanaka Factors Set Back Epigenic Age

(without going all the way back to the womb, or causing cancer)

In a column last month, I posed the question whether the methylation clocks of Horvath are drivers of aging or responses to aging. If we intervene so as to set back the clock, are we signaling the body to be younger, or are we shutting down the repair mechanisms that the body has engaged in response to the damage of aging? 

There’s a preprint from David Sinclair’s Harvard laboratory, posted on BioRxiv but not yet published, with very encouraging news for those of us who think that resetting the epigenetic (methylation) clock is a path to anti-aging. They suggest that 3 of the 4 Yamanaka factors, administered in short pulses, can set back the Horvath methylation clock without turning functioning tissues back into stem cells. The same study offers evidence to support the hypothesis that the epigenetic clock is a lethal driver of aging, rather than an adaptive response to damage.

Cellular reprogramming slows aging in mice

Sinclair opens the paper with an un-footnoted statement that aging consists in accumulated damage, as if this is uncontested and incontrovertible. He refers to the straight-line methylation changes that happen predictably and consistently with age as “epigenetic drift”, as if these changes were random. He believes that they are ‘loss of information” when these changes show every sign of being predictable and directed.

In the standard evolutionary paradigm, the mouse is evolved to live as long as possible, all other things being equal. (To be explicit: I don’t believe this; I think the mouse is evolved for a lifespan optimized to its ecology, not longer or shorter.) If you believe this standard paradigm, then why doesn’t the old mouse reset its epigenetic clock without our having to do it for him? In Sinclair’s account, the mouse has lost information, and can’t do it. But the Yamanaka factors are all in the mouse genome, and if that is all the information the mouse needs, we have to ask why the mouse needs us to send the signals.

We wondered whether mammalian cells might retain a faithful copy of epigenetic information from earlier in life, analogous to Shannon’s “observer” system in Information Theory, essentially a back-up copy of the original signal to allow for its reconstitution at the receiving end if information is lost or noise is introduced during transmission17.

It’s cute that Sinclair invokes Claude Shannon’s foundational theory from the 1930s on transmission errors and signal correction. But is it relevant? The reason that Sinclair and many others assume the information (how to be a young mouse) is lost is that they believe that evolution has motivated the mouse to stay young and keep making babies if only it could. If the information isn’t lost, doesn’t that defeat the very premise of Sinclair’s “lost information” theory of aging?

The point is that Sinclair is a superb experimentalist. He is also realistic enough to accept the overwhelming evidence that aging is an epigenetic program, and that the best way to influence it is to reset our epigenetics. But he is still mired in the old theory that denies it is possible for an aging program to evolve, so his efforts to frame his work in the context of “lost information” and “random drift” are strained to say the least.

Now that I’ve got that off my chest, let’s get on to the substance of this new finding, and the carefully-designed experiments that support these findings. He and co-authors demonstrate that mice treated with OSK (the first 3 out of the 4 Yamanaka factors OSKM) have restored capacity to regenerate damaged nerve cells, a capacity which is normally lost early in life. They go on to show that OSK isn’t directly responsible for regenerative capacity. And they demonstrate that resetting the methylation pattern on the mouse DNA is necessary for the restoration.

Specifically, they engineer mice with a cellular switch that can turn on OSK in response to a applied antibiotics. They flip the switch in the eyes only, then crush the optic nerve to see if it grows back. Normally, a mouse is able to regenerate nerves only while it is in early stages of development.

Yes, the nerves grow back if the eyes are pre-treated with pulsed OSK. And the benefit is lost in the absence of methyl transferase enzymes. This last result was part of the experiment in order to demonstrate that the mechanism for restoration involves re-programming methylation patterns on the chromosomes.

rDNA methylation age of 12-month-old RGCs FACS isolated from retinas infected for 4 weeks with -OSK or +OSK AAV together with short-hairpin DNAs with a scrambled sequence (sh-Scr) or targeted to Tet1 or Tet2 (sh-Tet1/sh-Tet2).

Questions not addressed yet

I’m inclined to interpret this article as much for what it doesn’t report as for what it does.

In the main experiment, OSK was induced just in the eyes, so it was just the eyes that were rejuvenated. But they also report a “safety” test done, in which OSK was induced in the whole body at a low level for an entire year without toxic effects. Of course, it’s nice to know that the low-dose OSK was not toxic and that cancer risk did not increase. But did the mice benefit from the whole-body treatment? Did they show any signs of rejuvenation, or of enhanced stem cell function?

There is a Horvath methylation clock for mice. Did the mice get younger according to the Horvath clock? The authors report that damaging the retinal nerve made the nerve cells older according to the methylation clock, and that the application of OSK brought the cells back. But I don’t see anywhere in the paper a measurement of the eye’s methylation age before and after the OSK treatment, independent of injury. For that matter, there is no discussion of the methylation age of the mice treated with whole-body OSK for a year. These omissions are curious. Are they suspicious? Have they tried and failed to set back the methylation clock, and they don’t want to report it? Certainly it’s a question I would ask if I were reviewing this ms. Maybe we’ll know the answer when the paper is published.

Did mice live longer after treatment with OSK? Answering this one takes time, and perhaps the Sinclair lab has mice even now that are living longer, but it will be a few years before we know. Or perhaps the treatment has failed so far to extend lifespan, and Sinclair is reluctant to report a failure.

101 thoughts on “Pulsed Yamanaka Factors Set Back Epigenic Age

  1. “But the Yamanaka factors are all in the mouse genome, and if that is all the information the mouse needs, we have to ask why the mouse needs us to send the signals.`”

    I also wonder if lengthening telomeres also restores epigenetic information. Perhaps mice telomerase activity is not sufficient to prevent telomere shortening? I’ve heard that human cells that have their telomeres lengthened show gene expression patterns of young cells. As I’d imagine gene expression reflects the epigenetic changes, that seems to suggest rejuvenation of epigenome, unless I’m mistaken.

    Inducing telomerase in human cells I’ve heard result in rejuvenation of gene expression(with the exception of about 100~ genes). It is said cells and tissues appear young after restoring telomeres.

  2. Yes the entire field of aging research is based on the false premise that aging is the result of random damages that thwart Nature’s desire for the immortality of the individual. It posits that this damage must occur (according to Hayflick through ‘entropy’), and yet offers no explanation for why some animals don’t age and spurious explanations for species-maximum lifespans, based on the quality of their repair and maintenance systems. Evidence that such systems change during post-adult development is never taken into account.

    • Harold,
      Are you able to comment further on what you’ve learned regarding youthful signalling, and any hints/advice on any interventions based on this?
      Thank you

    • Both paradigms need not be mutually exclusive. I gather planarians simply hit an evolutionary lottery as did immortal jellyfish.

    • the entire field of aging research is based on the false premise that aging is the result of random damages that thwart Nature’s desire for the immortality of the individual.

      Harold L. Katcher — Towards an Evidence-based Model of Aging

      The modern synthesis or evolutionary theory of aging assumes that aging results from the accumulation of errors or damages at the cellular level through the inadequacies of an organism’s repair and maintenance machinery. The demonstration of cellular and organic rejuvenation requires the hypothesis that aging is the result of irreparable damage to be rejected. I will propose basic principles of mammalian aging based only on experimental data, without imposing the constraints of evolutionary theory. Consideration of the results of experiment suggests that fundamental assumptions about cell and organ aging being autonomous process, and about the centrality of cellular aging in organismic aging are wrong. The derived principles indicate that exogenous control of age-phenotype at cellular and higher levels of biological organization is possible.

  3. It seems that many of the people that are emerging as aging research “superstars” from the perspective of the media and funding are all still mired in the entropy paradigm. This to me is very unfortunate as it probably holding back the field. In addition to your efforts Josh and the rest of us proponents of programmatic aging, I think it could help if we began promoting the work of those that have moved beyond this worn-out paradigm. I think it could be productive to focus on the work of Michael Levin at Tuffs, for example.

    • The work of Michael Levin is truly groundbreaking. I recommend everybody watch his latest talk at the MIT, available over on youtube at watch?v=4sFpJF0dp8Y.

      He begins asking the question of why is there anything other than cancer? Uncontrolled proliferation is the default state of single cells. His proving that voltage potentials across cell membranes drive cell behaviour is fascinating. The experiment in which a mouse embryo is injected with cancer cells and it goes on to develop normally tells us cancer may be enabled by mutations, but it is ultimately a cell behavioural disease.

      Cancer and aging are multicellar ‘diseases’. Or maybe we should relabel them as cell behaviours. In as much as single cell aging exists it is different than a multi-cellular organism aging. Although I take note of telomere shorting in single cells protists in non-sexual reproduction and its re-lengthening in the sexual one. A clue perhaps into how nature may have repurposed single cell programmed aging into multi-cellular one.

      • Michael levin works on organs regeneration and observations of METAMORPHOSIS in frogs has given experimental evidences that the DNA express itself as an electro-magnetic field of instructions (structure of the cell assembly, epigenetic for the functionnal aspect) to instruct any cells of the body.
        A cancer cell is in fact a malfunctioning stem cell and if injected at the right place like an embryo (unlike an adult mature tissue fully differentiated), may be reinstructed by the quite simple DNA E_M fœtal field.
        Electrical potential across cell membranes is a direct result of the electro-magnetic holographic field effects. To achieve an electrical potential the cell must displace charge carriers (electrons, and ions) and it do so because the electro-magnetic field instruct and supply the electric power for such.

          • Mark,
            With regards to your mention of Boswellia Serrata (Frankincense) and it’s inhibition of 5-lipoxygenase; it is one of the most remarkable nutraceuticals that I’ve ever seen.
            It seems to have powerful benefits for those with osteoarthritis and also very anti-cancer (more anti-proliferative than apoptotic).; very potent with respect to angiogensis.
            I’m sincerely wonder if this isn’t one of the most important supplements one could take wrt an anti-aging regimen.
            Aslan

          • Thanks Aslan, I’m glad I’m not the only one looking at this nutraceutical. There are some pretty awesome benefits to be had from 5-LOX inhibition; numerous lines of research have led me to this pathway and to top it off even the Conboys are using it via a TGF-B inhibitor! The fact it has proven effective at treating arthritis and also seems to have benefits for asthma, gives me hope that it’s bioavailability is not as bad as some have suggested.

          • To prevent joint problems due to my rigorous resistance training I take every day 1000 mg Boswellia resolved in a cup of home made Ginger/Tumeric tea along with a TSP of Ashwagandha root powder.

          • DNA is a long polymer chain which main matter fall in the dielectric category (insulator). However at each of the billions of base pairs of the DNA you will find and electric perfect ring conductor (that means were free electrons are able to create an electric current by displacing themselves) in the periphery of the hexagonal organic chemistry rings.
            When a pulsated magnetic field (generated in the first place by electrons displacements on those rings) point trough the area of such a conductive ring the induced current transmit coding informations as each ring may be informed (trough modulations of the signal) following the pair of bases encountered (reading, editing DNA with a four letter coding system)
            So the DNA (which is a very long coil around the histones, suitable for interaction with longitudinal magnetic wave only ) of each and every cell take part as an emitter-modulator and a receptor-modulator of this information magnetic field.. The longitudinal wave frequency there is in the GIGAHERTZ wave length band. This result for the structure part of the cell assembly into a standing holographic field (3D) blue-print of the assembly that a CCD camera sensitive to IR can DETECT BUT ONLY IN CASE OF METAMORPHOSIS.(trough the IR or UV bio-photons emitted by such field. When there is no morphogenetic changes for an adult assembly of cell, the holographic field is fully identic to the 3D material cells assembly and may only be detected on the edges of the matter as an AURA.field. (kirlian pictures)

  4. glass half empty>>>>
    “Did mice live longer after treatment with OSK? Answering this one takes time, and perhaps the Sinclair lab has mice even now that are living longer, but it will be a few years before we know. Or perhaps the treatment has failed so far to extend lifespan, and Sinclair is reluctant to report a failure.”

    Glass half full>>
    Or did Sinclair discover something amazing and is still trying to get some sort of patent???

    Now Josh we have to find out how to get those Yamanaka factors and get them into our cells…..any ideas? The hard way wold be to grab the gens for O S and K and transfer them into bacteria and crank out the proteins . I have friend with a company who does that stuff all day….But can we find herbal factors that do this as well? Harold? Or do we have hormones that will do it for us in our bodies already? Or do we have hormones in our bodies that shut down the yamanaka factors as we age?

    Oh and how about that crazy prediciton in some old 1998 paper that DNA methylation was a major driver of the aging process?? I guess it was a little ahead of its time…

    • Sinclair talks about this in his book, suggesting that like with the mice in his experiment that humans could/should be inoculated with OSK genes using AAV delivery vehicles in our 20s or 30s and then take an activator for as long as we want in order to “young” to the point we desire, and then stop taking the activator. The trick is of course to do this safely and in a manner that the whole body is uniformly younged.

        • Well, they’re genes not molecules, so they need to be delivered into the nucleus and incorporated. Which is why they’re delivered with an AAV. The trick apparently is to do this for the whole body in a way that achieves the same effect throughout the body.

          • I am not an expert, so forgive me if I write something stupid.
            If they are genes so they code for some proteins. Couldn’t we inject those proteins? Or it doesn’t work like that?

          • Patricio, you got it exactly right.
            Proteins are very large molecules, and there is no practical way to deliver them to cells. Even if we inject them into the bloodstream, they will be selectively excluded at cell membranes. The hardest part of this is that dosage is critical, and we have no way at present to control the dose of these proteins, cell by cell across the body.

    • The way the Sinclair Lab did it is clearly explained in the technical paper dude:

      OSK genes with inducible promoter
      Viral vector
      Inject

      Simple.

  5. It’s not really surprising that Yamanaka factors would make cells more plastic and able to repair damage. But yes, it would be nice to see a lifespan study on mice with pulsed OSK(M). Could we see a 10 year old mice from this? Maybe.

    In answer to Jeff’s question there are small molecules that can replace most of the Yamanaka factors. Not sure if they are safe in Vivo. I’m working on some ideas.

      • As an example alk5i, the tgf-b inhibitor used by the Conboys in their latest work rejuvenating mice (similar results to Harold and Akshay!) is one such small molecule, known to help with a particular stage of inducing pluripotent stem cells.

        Not having access to alk5i how might we substitute? Losartan perhaps, which has been shown to lower tgf-b.

        I’m also interested in ROCK inhibitors, which are used in conditional reprogramming. Again they cost the earth and are generally not available. Interestingly statins are known to exert their ‘pleitropic benefits’ through this pathway, likely by inducing cells to move backwards up the epigenetic valley to become progenitors again. Probably explains their side effects too.

        There may even be natural substances that can do everything we need.

        • How long lived are those proteins and how would you control their expression in the cell via this method- quantity of administration?

        • As an example alk5i, the tgf-b inhibitor used by the Conboys in their latest work rejuvenating mice (similar results to Harold and Akshay!) is one such small molecule, known to help with a particular stage of inducing pluripotent stem cells.

          Rejuvenation of brain, liver and muscle by simultaneous pharmacological modulation of two signaling determinants, that change in opposite directions with age

          The observed rejuvenating effects are at least as robust as, and act faster than, heterochronic parabiosis. Additionally, the effects of Alk5i+OT are more positive for neurogenesis and restore the functional behavior of old mice, as compared with heterochronic blood exchange.

          • I’m not an expert, but isn’t the paper referenced above an extremely big deal?

            In that it seems to answer the question of what constituents of blood plasma make the heterochronic parabiosis experiment work, and shows that even more effective results can be achieved with already-known biochemicals.

            Presumably, somebody will now try to replicate this experiment with large mammals, such as dogs or primates.

        • In this study:
          http://ejbio.imedpub.com/natural-compounds-targeting-transforming-growth-factorin-silico-and-in-vitro-study.php?aid=17673
          they showed that Myricetin and EGCG are inhibitors of TGF-b

          Maybe they are not as effective as alk5i.

          However, the Conboys have shown that a substantially lower dose of alk5i was required for rejuvenation, if oxytocin was administered at the same time.

          So, is it possible that by combining Myricetin, EGCG, and oxytocin, all of which are available and cheap, we could have some rejuvenation?

          • My top pick for tgf-b inhibition via a nutraceutical is Boswellia extract. Some of the proprietary extracts like apres Flex have shown in small double blinded trials to be effective for arthritis. The mechanism is believed to be via inhibition of LOX-5.

            So i’d combine this with a rho kinase inhibitor (got some ideas on a nutraceutical for that too, tongkat ali) daily, and then do a subQ injection of oxytocin now and again.

            It’s just an idea at this stage – untested, so be warned!

  6. One question I have is why should nerve damage cause epigenetic aging? This is something we also see in sun ‘damage’, lung ‘damage’ due to smoking, joint injury, etc.

    I put damage in quotations because it is worth thinking about what damage means in this context. Individual cell damage should not result in loss of fitness in a multi-cellular organism if it is allowed (time and resources) to proliferate to replace the missing cells.

    Michael Fossel posits that damage leading to aging is caused by increased cellular proliferation. Cells do get damaged/killed, tissues need healing by cell proliferation, telomeres shorten and gene expression changes (this last stage is key according to his model). Gene expression change ultimately leads to tissue disruption because as telomeres shorten its associated gene expression profile is damaging to multi-celleluar tissue (most likely due to an evolutionary conversed process, i.e., programming ageing, although he does not stress this point). Therefore, this is the path connecting cell damage to tissue aging and apparent organismal ‘damage’.

    But here is where we run into a contradiction with both the conventional wisdom re. aging and the DNAm clock studies so far. At least in most of them there is no correlation between cell proliferation and DNAm age. Nor is there a positive one with telomere length and DNAm age.

    Following this line of thinking, if DNAm is *THE* main driver of aging then what makes it tick cannot be cell doublings. It should be some kind of constant metabolic process. But if this is the case, why does cellular damage result in an increased DNAm age? How do we square this circle?

    • “Nor is there a positive one with telomere length and DNAm age.”

      Were the telomeres and DNAm age measured in the same cells? Because it is possible different cells may have different telomere lengths.

    • The cells he damaged cannot divide (optic nerve) and as far as I’m aware have no progenitors to replace them, so it is not a matter of telomere length.

      Presumably in this case the methylation changes are an attempted adaptation to the cells being crushed. Maybe apoptosis (for example) is turned off to preserve some residual function (as no replacements available).

      • Mark, even without cell divisions telomere attrition has a strong effect on gene expression b/c the shorter the telomeres get the more they harm preferred gene expression (it’s not fully understood why but it’s widely accepted that this is the case), so it seems that it could indeed be telomere re-lengthening that is the mechanism behind the optical nerve regeneration in this experiment.

    • I guess there is some observation bias in the general aging research community. When your most useful tool is a monolayer 2D cell culture everything looks like a cell internal problem. Because in monolayer dish you cannot model real life extracellular signalling (endocrine, paracrine, ECM binding).
      I think the extracellular state of the cell is just as important as the intracellular state. That is probably why manipulations with the intracellular state has not yet brought about a real breakthrough (like a 5 year old youthful mice with negligible mortality).
      There are papers that young cells transplanted into old environment cease to proliferate. There are papers that old cell differs from young mostly in ECM related expression profile. We know that cells in culture age like hell. Maybe because the environment in a dish is anything but similar to a young living tissue.
      There should be more focus on extracellular signalling in research.

      • David Sinclair takes Resveratrol, NMN, and Metformin every day for anti-aging and overall health.

        This is also discussed in his recent book, *Lifespan*, where he reports that he takes one gram of each, daily.

        http://www.amazon.com/Lifespan-Why-Age_and-Dont-Have/dp/1501191977

        commenter Jeff Bowles suggests the company Vitaspace as a cheap and reliable source of nutritional supplements.

        vitaspace.com/antioxidants.htm

        resveratrol and “nicotinamide” are both mentioned, although there is no price listed for the latter.

        Does anybody else have experience dealing with this company, and would you recommend it?

        • Sinclair has financial interests in NMN. IIRC there are only four trials recruiting for NMN… while if you go to clinicaltrials.gov, there are 44 trials listed for nicotinamide riboside.Tens of thousands of people have used NR for years now.

          Chromadex is the company that makes nicotinamide riboside in the US. Their brand is “Tru Niagen”… they’ve been selling in the US, China, Japan, Hong Kong, Singapore, New Zealand etc. for years. And just today, the EU approved nicotinamide riboside, so it is available there on Amazon and soon through Watsons drug store chain.

          • “nicotinamide” is what was listed on the page I referenced. I emailed them a few days ago to find out exactly what it was, but haven’t received any reply yet.

  7. Josh, how do we know that OSK’s effect on epigenetic markers is the causal mechanism here? I posed the same question to Sinclair and he said it very likely wasn’t changes in telomere length (another effect of OSK) b/c optical nerves don’t replicate and thus wouldn’t be impacted by telomere re-lengthening, revealing it seems a misunderstanding of the effects of telomere attrition on genetic expression independent of any cell replication effects that result from extreme telomere attrition in non-nerve cells. Thoughts?

      • Fossel has argued for years now that it is basically everything b/c it’s upstream of all other aging mechanisms. Sinclair argues in his book that sirtuin and other epigenetic dysregulation is most upstream, apparently a conflict with Fossel. Amano et al. 2019 with Sinclair as a coauthor also states that telomere dynamics are upstream of sirtuin dysregulation so I’m not clear on what Sinclair’s “official” position is on this. If aging is programmed, then it would actually make sense that nature had crafted a kind of master switch for controlling aging and planned death.

    • Well do optic nerve cells get short telomeres? My guess is they don’t because they last a lifetime (ideally) and only divide early in life. If their aging is driven by short telomeres then it must be the short telomeres of another cell type that supports them. In this particular experiment by Sinclair, OSK was targeted to the nerve cells, rather than more systemically, so it probably didn’t operate via telomerase elongation.
      Put another way, if you had a crushed optic nerve would a telomerase therapy (that is generally effective on aging) cure it? I would think no, not without supplying the required progenitor cells to rebuild the fibre.

      • I get your point and it definitely makes some sense but doesn’t the same logic weigh equallly strongly against epigenetic changes resulting from the crushed nerve and, when reprogrammed, achieving the regeneration? Why would crushing the nerve result in epigenetic aging?

        • Epigenetic changes could be an attempted adaption to impairment by crushing. Reverting the cell to a progenitor via OKM restores plasticity and ability to heal, perhaps. All speculation on my part.

          If you read Fossel’s first book from the 1990s, he discusses how longer telomeres can do nothing to help when the cell type is completely gone.

          I am a big fan of Fossel by the way, not arguing against telomeres being causal in aging.

          • Amano et al. and Fossel argue that telomeres are upstream of epigenetic rejuvenation, so wouldn’t the same logic weigh in favor of evolution rejuvenating telomeres for this purpose? I don’t have a dog in this fight but it seems that the weight of expert opinion lies more with telomeres being upstream. Sinclair suggests that it’s perhaps a dialectic between telomeres and sirtuins but as far as I can tell he seems to think sirtuins are upstream of telomeres even though he’s a coauthor on Amano et al. I have an interview with Sinclair coming out this week at LEAF with more info.

          • It’s all gene expression.

            If you have the gene expression of a 20 year old in all your cells, then as far as I’m concerned you are 20 years old (biologically).
            Telomere length appears to control gene expression within each cell type.

            But there are other genes that control cell type.

  8. Hi Josh – Can you expand on your comment: “But he is still mired in the old theory that denies it is possible for an aging program to evolve, so his efforts to frame his work in the context of “lost information” and “random drift” are strained to say the least.” How are you thinking about the aging program evolving to be reflected in changes to the epigenetic clock? It’s something you obviously feel strongly about and I want to be sure I understand where you are going with this. GREAT BLOG!

    • Yeah, I feel strongly about it because I’ve discovered in 1996 that aging is programmed, despite the fact that evolutionary biologists were telling the gerontologists that programmed aging is impossible–and I’ve been flogging the idea ever since. Here’s an introduction to my book on programmed aging.

      Specifically, why is Sinclair’s argument strained? (1) because aging clock is the most predictable and directed change with age that has yet to be discovered, yet Sinclair has to argue that it is just “random drift”. (2) because gene expression is so important that evolution has devoted a huge amount of machinery to assuring that the right gene is expressed at the right time, and yet Sinclair has to argue that this highly-evolved system fails in consistent and predictable ways, and (3) if you look at what genes are turned on with age, they’re not random at all, they’re self-destructive. E.g. over-expression of NFkB which drives inflammation and over-expression of P53, which increases levels of apoptosis so high that we lose healthy nerve and muscle cells.

        • Very interesting research from Andrei Gudkov. His hypothesis that line 1 DNA retrovirus are the clock and the cause of aging as usual are derived from experiments with diseased radiated mice .Mice are unlike man as they experience a huge telomere shortening rate which means a fast rate of disorganization in the instructions given to the cells as per the hypothesis of the electro-magnetic DNA bio-field model.
          This Andrei hypothesis should be challenged by observing if these same line 1 DNA retrovirus negative postulated effects are also found in species (like the LOBSTER, hyppocampus…. ) where the telomeres are not shortening when time passes and the tissues and organs remain astonishingly young as reported so far.
          The electro-magnetic DNA expression model point to other reasons why these retrovirus like portions are active in the whole DNA. Like for the dogs species where Andrei mention they are useful for ( survival and ) evolution of species. Did he investigate by which mechanism the memory of the picture of a life-threatening environnement (electric shocks in a certain ground configuration) is transmitted genetically to the off-springs (and consequently was TRANSCRIBED ANALOGICALY in the genome of the parents mice upon occurence) as was proved recently?
          With for Andrei mices, an environnement with life-threatening radiations, I am convinced this survival linked aspect of transcription should be exploding.

      • Hi Josh – I totally get it – thank you – and for what its worth – completely agree with you! I think you are dead on…. Here is some news from the front: GSA Annual Conference this past week, there was lot’s of talk about the aging as a disease, there was lot’s of great work presented, thoughts on a network systems, etc. The best part was that some of the young up & coming researchers remarked that they noted a ground shift in the discussion and unified approach to aging – as if it had happened overnight. This was my second GSA annual conference and even I noted a difference from last year. I think a lot as to be attributed to the Horvath Clock and Sinclair’s book (although no one dared to mention his name) – so I wouldn’t be surprised if we start to see further shift towards your theory of aging – which seems right to me. Keep up the great work!

          • I don’t know that they were reticent… there was just not mention… it seemed odd given the conversation among researchers and the relevance to the book…. this is the world of researchers though… they don’t like to give credit to others… and are fighting for credit for ideas and discoveries themselves….

          • That makes sense but is unfortunate. I really wish academia wasn’t so much like high school in feeling like a zero sum popularity contest

    • Very promising research. I think they should also test the SKM cells as MLL-AF4 induced hematopoietec progenitors. Here traditional iPSC fail spectacularly compared to ESCs because leukemic transformation is very likely with iPSC but not with ESCs.

  9. epigenetic manipulations (rejuvanating the methylation pattern and so on) or elongating abnormaly the lenght of telomeres only show that researchers completely ignore the reasons why we age.
    We age basically because our telomeres shorten from an ideal lenght pattern. year after years the total double helix DNA lenght (forget the chromosones here) wrapped around the histones shorten and must after each division rearrange itself with another shape and lenght. That fact impede the DNA to transmit by torsion fields correct (youthfull epigenetic) informations from cells to cells. When informations are incorrectly transmitted diseases and cancers occurs because amongst other stem cells divide the wrong way.
    The telomere shortening and the consequent change in the hologram of magnetic field generated by the cells DNA cause a decayed state of cells functions (for the worse). The telomere shortening rate is one way for the cell assembly (the body) to measure the time elapsing. The speed of attrition is an indication of the speed of aging. Of course everybody speak of cells communication, vibrations, scalar waves, magnetic torsion field, you name it.
    Pseudoscience?
    First take a look at the unified field theory based on electric and magnetic fields which do not contradict these cells communications trough DNA.
    .
    But what do you think now if these cells communication fields could be indirectly observed in a labo experimentation? So far that is possible but only in case of METAMORPHOSIS.
    TUFT university made in 2012 amongst other a strange observation they did not understand. A CCD camera was filming a FROG larvae. The larvae eventually transformed itself into a tadpole. The epigenetic pattern in the DNA of a larvae and the one of a tadpole are of course very different altough the cells remain the same initial material to turn one body into the other.So the genetic material had to wrap itself differently in order to express other genes.
    They saw that the CCD camera altough the object fimed was still a larvae showed a kind of visual holiogram (visible for a CCD camera in the IR range but not to the researchers eyes) representing already the tasdpole boundaries (including mouth and eyes) This hologram superposed itself to the material larvae.
    What did happen? The magnetic hologram (made of magnetic vortices emitted by the DNA) decayed locally by emitting bio-photon (it must be a very sensible camera however) in the IR range that the camera was able to make a picture of . So this magnetic hologram normally invisible gave these astonishing picture of the epigenetic generated tadpole at a time when this tadpole did not yet exist by cellular topological moves. This magnetic hologram was of course the 3D blue-print and the energy source in order for the cells to migrate and divide further in order to create the new life form.

    • That sounds like an interesting hypothesis, but then how to address it? You say this process is driven by telomere shortening, but this doesn’t seem like a clear enough driver, nor does it explain why short lived species like mice have longer telomeres than other long lived ones. While short telomeres are important, they certainly don’t seem to be what is DRIVING the pathology of aging. Besides, stem cells seem to be quite capable of producing telomerase when needed, and to begin proliferating and replacing senescent cells when provided the right signaling via plasma. Certainly the electrical field aspect needs to be investigated further. As Josh has mentioned on occasion, the role of electric fields has been a neglected area in the study of longevity and tissue growth and homeostasis.

    • The reviewers’ position on your 2005 paper that was incorporated into Figure 2 was:
      “In our view, recent evidence that senescence is based on an unterminated developmental growth program and the finding that the concept of post-mitotic senescence requires the activation of expansion, or ‘growth’ factors as a second hit, favor the assumption that aging underlies a grating of genetic determination similarly to what is summarized above under the pseudo-programmed causative approach.”

  10. Josh. I posted a 7 minute excerpt from my July Sinclair video interview on your post last month. In the 90 minute interview, I returned to the question of “Is aging programmed” at least 5 times, kind of pestering him with it. He responded at one point that we are speaking about word definitions. I think, importantly, you two actually agree on the process, the differences may not actually matter in terms of the remedy. I will post another excerpt where I ask him this.

    • Surprising result. Berberine stripped the weight off me like nothing else I’ve tried. I wouldn’t go near it again for that reason. Lab mice just seem like a mess metabolically.

      • Hi Mark – weight loss could be good. any idea what % yours was for fat and muscle. how did you dose? did you have any benefits with exercise parameters. maybe best to take intermittently. in above mentioned study was very benefical for mice – “The oral administration of BBR in mice resulted in significantly improved health span, fur density, and behavioral activity.” Thanks

      • Has this type of problem reported by others?
        I actually take berberine for a few years but did not see any substantial weight reduction.

        • I started off relatively lean and it made me substantially more so, even to the extent of neighbours not immediately recognising me because of the thinness of my face. I’ve no doubt it made me look older.

          On the bright side, I didnt lose any strength (I didn’t gain any either) at the gym during this period (a year or so of one capsule a day).

          For me it was an effective weight loss supplement, which would be helpful for those who need to lose weight. I did also exercise fairly intensely (as I always do), but the berberine was the decisive factor in my weight loss.

  11. On the subject of what makes the epigenetic clock tick upstream, I think we haven’t discussed here a very recent pre-print in which David Sinclair participated and that found a link between DNA double strand breaks and epigenetic alterations.

    Steve Hill did a very good summary over at https://www.leafscience.org/dna-damage-leads-to-epigenetic-alterations/.

    I wonder if both studies were connected in linking damage to epigenetic ageing, with one leading to the other.

    Myself, I suppose I am still reluctant to view eAge a result of a metabolic process because this rate must be rather close in most species or even cells types, but the rates of ageing are very different even between species of the same class. That’s why I always harp about telomeres and cell proliferation, because I view them as a more likely candidate to the rate of ageing.

    But if DBS are one, or the main driver, of DNAm age it would fit the observations so far in non-proliferating tissues and as a result of different types of damage.

    • I’m in the process of reading Sinclair’s book. Whilst it is interesting, and he and I agree on many things, he has yet to completely convince me of his ‘information theory of aging’. It is obvious that gene expression changes are occuring with age, and that this is driving pathology. But he is fuzzy on how random DNA damage leads to epigenetic dysregulation, beyond using up NAD+ and distracting sirtuins. He also has not (as far as I’ve read) explained how what should be a random process of demethylation could lead to such a non random downregulation of various cellular defenses. He also assumes such epigenetic changes are upstream of things like telomere attrition, when it is clear the reverse is certainly true (as well). Finally, making a mouse with lots of DSB and seeing it ages faster doesn’t to my mind prove the point he is trying to make. There are many models of aging. We need more before we can say this is the ‘true’ one.

      Sinclair is primarily coming from a yeast aging point of view. Yeast are weird. They can extend telomeres – but at the cost of genomic instability. Or allow telomeres to erode and suffer from cellular senescence. Not the same situation in humans at all.

      • After 7 years of trying to understand the aging process I have come to the conclusion that it is the result of several intracellular and extracellular processes that are not evolutionary economical to repair. Just because we know that a few hundred cells out of 1e14 or 1e15 cells of the organism get the chance to completely rejuvenate – under very specific circumstances – it very likely does not mean that there exists a built in cellular process to rejuvenate a whole body.
        As there are publications that extracellular signalling from surrounding aging tissue retards stem cell function, there might be some limited scope in finding a pharmaceutical solution to slow down aging and get 80 or 90 in healthy aging.
        But eventually a solution must be found to create a large number of safe, healthy autologous young cells probably ex vivo – this is almost done – and get them to replace old crappy cells in the living tissue. The latter is a far shot at the moment I think.

    • I think the simplest explanation to DNA methylation changes is that it is damage which is evolutionary uneconomical to repair.
      It may result from intracellular or extracellular stress but must likely it is just the result of competing DNA methylases and histone methylases of the large methyltransferase complexes like PRC2. When a PRC2 complex builds up near promoter it wants to methylate the histones but sometimes a DNMT molecule binds to the complex and the DNA is methylated instead, which is harder to reverse. So the only thing that drives these changes is the number of PRC bindings which may be roughly linear with time.
      Thats why DNA methylation is such a good proxy for aging.
      Sinclair can speed this process up by breaking the DNA which in turn dissociates and reassociates PRC2 and the likes to DNA – more opportunities to drive the clock.
      Also intracellular or extracellular stress may make the DNMT more active and pushing the process in the direction of more DNA methylation.

      • Characterization of Skin Aging–Associated Secreted Proteins (SAASP)
        Produced by Dermal Fibroblasts Isolated from Intrinsically Aged Human Skin

        According to the publication above there is NO telomere shortening in primary dermal fibroblast cells from age 20-70

        • Thanks for your insights GaborB. I agree with many of them.

          Regarding the telomere paper, I will read it with interest. Clearly though, fibroblasts will shorten their telomeres between the fetus and an adult. I can believe that they remain largely static in an adult, however. Nevertheless we cannot rule out their ageing being a consequence of telomere shortening in other cell types they are dependent on. On the other hand skin ageing has alot to with oxidative stress induced senescence, which then causes arrest of undamaged cells through SASP. This probably involved telomere damage but not necessarily shortening.

          • Regarding the paper, which I have now read, there is nothing too surprising there. They took fibroblasts from under womens’ breasts, so it’s not surprising they didn’t need to turnover much during a normal lifetime (little to no sun exposure). But they did adapt to the wider systemic influences of the ageing body (I surmise) and change their own secretory phenotype to become more inflammatory.

            It is just SO hard, and takes so much energy to battle entropy. Just look at my kids’ bedrooms! I’d have to be on it constantly to keep them well ordered. You can see why ageing is the norm and not the exception in nature.

          • there is an even better article I recently found:

            Senescent human melanocytes drive skin ageing via paracrine telomere dysfunction

            its available on researchgate.

            this is about the epidermis. the epidermis consists of a few (10%) melanocytes, the rest are keratinocytes. the melanocytes are long living, the keratinocytes are quickly turning over.
            what they found was that telomere shortening was not characteristic of either cell populations. however the long lived melanocytes exhibited internal stress signalling (p16) and also exhibited “dysfnuctional telomeres” in an age dependent manner. the senescent melanocytes also secreted molecules that caused damage in the fast dividing keratinocytes. the researchers were able to rescue keratinocytes with senolytic treatment against the melanocytes.

            this is a new paradigm for me. cell division makes the cell younger. because all the DNA scaffolding is reorganized and replenished and so do the cellular organnelles. structural damage cannot accumulate in fast dividing cells. however the opposite is true for the long living cells.
            nevertheless it may happen that fast dividing cells also degrade in quality with time, they just dont sit idle for a long time so that the rot becomes visible.

          • Yes it is like bacteria, so long as they can divide they can overcome a build up of damage. Potentially animals that continue to grow may benefit from some of this mechanism. With dividing cells, their ageing is not so dissimilar – as telomeres shorten division slows and some of the same problems ensue, even without reaching replicative arrest.

            I’ve read that paper before, very interesting that melanocytes are the culprit (at least in their skin model). Skin is an interesting case. Here the ageing is driven via UV on melanocytes. Suppressing oxidative stress should also work, which is probably why people have positive things to say about methylene blue and mitoQ skin creams.

    • Scientists from Institut Pasteur and CNRS demonstrated that progressive depletion of a protein drives proliferating cells into irreversible ageing. Moreover, such a depletion is a very early trigger, and therefore a determinant of cellular ageing, or senescence.

      This factor, called CSB is involved in Cockayne syndrome, a disease affecting about one in every 200,000 people in European countries. The absence of CSB protein or its dysfunction causes early ageing, photosensitivity, progressive neurological disorders and intellectual deficit in patients with Cockayne syndrome. “We had previously shown that the absence or impairment of CSB is also responsible for dysfunction of mitochondria, the power plant of cells” says Dr. Miria Ricchetti, head of the team Stability of Nuclear and Mitochondrial DNA within the Stem Cells and Development Unit at the Institut Pasteur. “This new study reveals the very same alterations in replicative senescence, a process strictly linked to physiological ageing” say Dr. Ricchetti.

      The importance of the present discovery is that it shows that a factor that was considered to be stable in normal cells is instead progressively depleted when they proliferate. When this happens, the cell is irreparably committed to the dead end of senescence.

      The exhaustion of CSB is driven by epigenetic modifications (reversible and regulated modifications of gene expression, without altering the DNA) that block its expression at the DNA level. Moreover, a molecule previously identified by these researchers as being able to reverse the defects of Cockayne syndrome patient cells, is also able to attenuate the commitment of normal cells to senescence.

      “These studies demonstrate an important link between the [pathological] accelerated ageing process and normal aging, and also expose the CSB protein as a key factor against cellular ageing” concludes Dr. Ricchetti.

      Story Source:

      Materials provided by Institut Pasteur. Note: Content may be edited for style and length.

      Journal Reference:

      Clément Crochemore, Cristina Fernández-Molina, Benjamin Montagne, Audrey Salles, Miria Ricchetti. CSB promoter downregulation via histone H3 hypoacetylation is an early determinant of replicative senescence. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-13314-y

      • Late Life Metformin Shortens Lifespan
        That means hormesis doesnt work in old age – can be lethal.
        https://www.biorxiv.org/content/10.1101/863357v1

        Highlights

        Late life metformin treatment limits cell survival and shortens lifespan.

        Metformin exacerbates aging-associated mitochondrial dysfunction causing fatal ATP exhaustion.

        Old cells fail to upregulate glycolysis as a compensatory response to metformin.

        The dietary restriction (DR) mimetic response to metformin is abrogated in old animals.

        PKA and not AMPK pathway instigates the early life DR response to metformin.

        Stabilization of cellular ATP levels alleviates late life metformin toxicity in vitro and in vivo.

        • That does makes sense. You also wouldn’t but an older person suffering from sarcopenia on a reduced calorie diet or intermittent fasting.

          • CR is likely beneficial because of freeing amino acids from the muscle for oxidative defenses (not just organelle recycling). In the case of an old, wasted person I think you’d actually want to use cysteine+glycine to control oxidative stress and inflammation, and cautiously use more anabolic aminos and resistance exercise to build muscle and an amino acid reserve.

            There’s only so much blood you can ring out of a stone.

      • An interesting study Akshay, and one that supports yours and Sinclair’s position that ageing is caused by epigenetic changes, in what might otherwise be healthy cells. Something does spring to mind however. They stipulate the senescence effect of CSB downregulation is telomere independent, and given its location near a centromere on a long arm of chromosome 10, I may be inclined to believe it. But why then do immortalised cells not senesce via this mechanism? Or even conditionally immortalised cells using ROCK inhibitors? In these circumstances there must be an overriding epigenetic signal from the (long enough) telomere that inhibits p21. Could you overcome this with enough oxidative stress? Of course. But then that’s not relevant to human ageing. So we have the problem of too many variables in a dynamic system to know what is causal.

        Noticing that CSB downregulation is caused by acetylation removal, and your reference also to Metformin/hormesis not being beneficial at old ages, are you suggesting that sirtuins might be harmful if they accidentally deacetylate an active gene?

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