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Epigenetic clock and telomeres

horvath clock epigenetic clock telomeres

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#1 xEva

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Posted 25 March 2018 - 07:22 PM


Josh Mitteldorf's latest  post on telomerase and epigenetic clock is worth reading -- and discussing :) here is better coz in his blog it takes a while for him to post the comments.
 
The key study: GWAS of epigenetic aging rates in blood reveals a critical role for TERT, 2017 
 
Turns out, telomerase also regulates the epigenetic clock (as measured by DNA methylation patterns in a subset of SNPs, selected to strongly correlate with chronological age -- the so called Horvath clock).
 
The idea that Josh drives at is that telomerase accelerates the Horvath clock. ...though I'm not sure why he views these particular changes in methylation patterns as detrimental, considering that the advancing age, as shown by the clock, did not affect the vigor with which the cultured cells kept dividing. Here is quote from the study, broken up for easier reading, the underline mine:
 

While non-TERT cells senesced after ~150 days, TERT-expressing cells continued to proliferate unabated at a constant rate with time in culture. Single-time point analyses showed that TERT-expressing cells exhibited a linear relationship between time in culture and the Horvath estimate of DNAm age (equivalent to a DNAm age of 50 years at 150 days), whereas in non-TERT cells DNAm age plateaued (equivalent to a DNAm age of 13 years) in spite of continued proliferation to the point of replicative senescence.

 

Notably, DNAm age did not increase in TERT-expressing cells that received regular media change but were not passaged throughout the entire observation period of 170 days [== these cells did not proliferate but remained static, fig.3d]. These cells were not senescent, given that their subsequent passaging resulted in normal proliferation.

 

In multivariable regression analysis, the associations of DNAm age with cell passage number and cell population doubling number were highly modified by TERT-expression. In the absence of TERT-expression, DNAm age did not increase with cell passage number, cell population doubling number, or time in culture.

 
So, if the advancement in the Horvath clock has no effect on cells viability, why view it as detrimental? Until it is shown that, as the Horvath clock advances, the cell's machinery begins to falter, I'd rather view it as a sort of a memory of the cell, sort of its way of keeping time.
 
 
Regarding the correlation of short telomeres with cardiovascular disease -- it can be interpreted differently: If we take another strong correlation of CVD, which is with chronic infections (e.g. gum disease), then shorter telomeres in leukocytes could simply reflect the fact that the immune cells are proliferating rapidly trying to contain the infection -- and that's what, currently, makes their telomeres shorter. 
 
In this regard, NASA recently reported an interesting observation in their 'twin study'. Apparently, spending substantial time in space significantly increases telomere length, but the return to Earth shortens them, within just 2 days (!). So I was wondering why would leukocyte telomeres shorten so dramatically in such a short time -- and the only thing I could think of is the sudden change in the environment: i.e. after Scott spent many month in the space station in orbit, which must be an unusual yet stable environment, suddenly, his immune sys had to deal with a wide variety of microbes back on Earth (-?)
 
 
It stands to reason that, all things being equal (including the level of telomerase expression), shorter telomeres in a given tissue type (compared to the average for a this tissue type in a population) reflect the stress on this tissue in the given individual -- and this stress could be due to trauma, toxins (metabolic or xenobiotic) or, again, infection (which may cause apoptosis in infected cells and trigger the need to replace them).
 
So, we could view the telomere length as the reflection of the rate of living, so to speak -- the demands made on organism by various stressors. Then the difference between a faster and a slower aging person will boil down to two major factors: 1. how many stressors these people encountered in a given period; and 2. how resistant they are to stress (and resistance to stress is usually a measure of expression of certain genes, like HSR for example, and BTW, caloric restriction tends to upregulate them).
 
 
IOW, rather than seeing the advancement of the Horvath clock as 'aging', in detrimental sense, we could view it as memory of the number of divisions. I intend to keep this view -- until it will be shown that at certain point the Horvath clock starts to correlate with the decline in cell's viability. 
 
 
PS

Actually, the fact that the viability of the cells in culture does not seem to decline with ticking of the Horvath clock gives an important clue to what drives aging: it's the mileu, the immediate environment of the cell, that determines its behavior (e.g. research in heterochronic parabiosis and its variants where 'old' or 'young' cells are cultured in old on young serum).  Currently, the consensus seems to converge on the idea that some molecule(s) secreted in the brain --could be something in the hippocampus-- act as ever-growing in persistence signal directed at a cell faced with accumulating damage of all sorts; and the message of this signal is, don't bother fixing that!

 
 
As for those very rare cancers that correlate with longer telomeres -- first, they are too rare to worry about. Second, there has to be something else besides telomere length that triggers them. Is it possible that telomeres remain longer, because something prevents the stem cells from replicating -- perhaps because old, spent cells, which stem cells were meant to replace,  pathologically resist apoptosis (-? just a thought)

 


Edited by xEva, 25 March 2018 - 07:34 PM.

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#2 QuestforLife

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Posted 26 March 2018 - 02:33 PM

I agree with much of what you are saying. The Horvath clock correlates very closely with chronological age, as it was designed to do, so its connection with mortality should be viewed with that in mind - correlative rather than causative, until Horvath supplies more evidence. Given that his methylation markers do not affect gene expression as far as anyone is aware, and are so ubiquitous across tissues, I think the evidence so far is that it is just a clock.

 

Telomeres on the other hand are clearly very important in aging, either as a result of damage from infection and inflammation, as you point out, or causative through their replicative limit and effects on gene expression as the telomere shortens (primarily a slowing down of proliferation and internal molecular turnover). This I think is a clue to the higher telomerase - faster Horvath clock connection. Lots of telomerase / a long telomere is a growth factor. In the context of human telomeres of limited and reducing length it is clear that this would be good in the short run, offering more regenerative potential, but would run down the telomere in the long run. Hence why cells slow themselves down as they undergo more divisions. The story is the similar for those rare cancers that thrive on long telomeres. Higher proliferative capacity is always going to be a two edged sword, but that is far from saying we all want critically short telomeres. Ideally we all want telomeres maintained at a youthful length, without either constant telomerase expression or telomere attrition.

 

Researchers need to stop using the cancer word to halt all research on solving aging. We are not going to be able to remain indefinitely healthy without learning cancer's secrets and using some of the same tricks to our own ends.


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#3 xEva

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Posted 27 March 2018 - 03:03 AM

Yes, yours is a good  summary. I guess all I wanted to say was that it was misleading to say that higher telomerase by itself  accelerates the clock. Telomerase is necessary to make the Horvath clock tick, but it ticks only when a cell divides.  So, the Horvath clock does not reflect time per se -- it reflects the number of cell divisions.

 
This is clear in the part I quote where it says that TERT-expressing cells, that remained static, did not have their clock advance (their "DNAm age did not increase"), and they were senescent either, which was shown subsequently when their division was induced (they use word "passaged" for this). 
 
And so, speaking of slower or faster running Horvath clock, the key question is, what causes cell division? It should be triggered by the need to replace damaged cells. Or? Surely, we don't want those senescent cells to stick around (otherwise senolytics would not be so popular, no?)
 
Or we can look at it this way: There are two opposing forces that affect the clock: one is stress (which can kill a cell or make it senescent) and the other is ability to deal with this stress (which can repair the damage and keep the cell alive and functional). Stress is unavoidable, it is life itself -- so the only thing left is to make sure that the genes that define our stress response are up and running. Regarding this, they say in the paper, "offspring of centenarians exhibit a younger DNAm age" -- at the same time, it had been shown long ago that offspring of centenarians tend to have better variants in stress response genes. So, for them, the clock is ticking slower, because their cells are not knocked off quite as easily as in a person who ages faster. But if we could make the damaged cells replaced, just as when we were adolescent, who cares if with each division the clock keeps ticking -- unless! it starts triggering those nasty proaging programs, the ones that dampen the repairs... Ah! Maybe that's what Josh meant when he showed such aversion to the advancement of the clock-?

 

Re your thoughts on cancer, I used to have the same idea, but since then I learned that, paraphrasing Tolstoy, "healthy cells are all alike; every cancer cell is messed up in its own way" -- with an amendment, of course: "the only thing they have in common is that they learned to keep their telomeres long."  I'm still hopeful it could be easier to block the offending proaging signal.


Edited by xEva, 27 March 2018 - 03:13 AM.


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#4 QuestforLife

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Posted 27 March 2018 - 06:37 AM

Hi there. Actually cells don't need to divide to make the Horvath clock advance, just be metabolically active. Hence what I was saying about telomerase being like a growth hormone.

Re cancer, yes they all end up different - but that is a result of them maintaining short telomeres and the resulting genomic instability leading to great variation in DNA. They probably all start out similar, however.

#5 xEva

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Posted 27 March 2018 - 04:31 PM

Hi there. Actually cells don't need to divide to make the Horvath clock advance, just be metabolically active. Hence what I was saying about telomerase being like a growth hormone.

Re cancer, yes they all end up different - but that is a result of them maintaining short telomeres and the resulting genomic instability leading to great variation in DNA. They probably all start out similar, however.

 

Re cancer as the result of genomic instability, totally agree. 

 

Re  metabolic activity leading to the advancement of the Horvath clock -- I must have missed this crucial part (!) this definitely throws a spanner the works. Gotta read more on this. Would appreciate if you could give a ref , thanks :)



#6 QuestforLife

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Posted 28 March 2018 - 08:52 PM

Any of the Horvath papers mentions how his method is applicable to many tissues, both proliferative and quiescent, so this isn't just about mitosis. Maybe methylation and demethylation is happening as a side effect of DNA repair, which in some ways is similar to mitosis, as presumably methylation has to be removed for the DNA to be checked. I'm just guessing about the mechanism, I don't think anyone knows.

#7 xEva

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Posted 29 March 2018 - 02:03 AM

Yes thanks I'm reading his key paper: DNA methylation age of human tissues and cell types 2013, -- very interesting!

 

And you're right, though the clock is highly correlated with cell divisions and  "passaging", it ticks at the same rate for the fast and slowly proliferating tissues. But I'm still not sold on telomerase as the prime driving force of the aging clock. BTW, the best known counterexample of cells with high telomerase and low epigenetic age is sperm.  How about it?

 

Have been reading a lot on Horvath's work. He is a mathematician and now proff. of biostatistics. So far the above paper (in the first post) is the only in vitro study that I've seen -- everything previously was just data mining.  Regarding this study, the cells that were not passaged were not necessarily metabolically inactive (they ate and pooped and required regular change of medium)  -- and yet their epigenetic clock stood still for 170 days -- while the same cells that were continuously "passaged" aged more than 50 years in 150 days.

 

But then, what if there is already a substance that can make the epigenetic clock tick slower or even reverse the age it shows? Would you jump on it? 

 

 

 


Edited by xEva, 29 March 2018 - 02:04 AM.


#8 Nate-2004

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Posted 29 March 2018 - 02:54 PM

This is just a comment on Josh's blog post and his theorizing about evolution:

 

I don't see how longer lifespan necessarily equates to lost resources and thus programmed aging was selected for. This is an argument that doesn't hold up for me, logically. Longer lifespan has always been associated with slower reproduction rates hasn't it? Also, isn't overpopulation a myth? We're talking hundreds of thousands of years ago, when our ape like ancestral populations were pretty low compared to the 7 billion humans today. How would environmental pressures like famine select for short lifespans? I guess maybe if shorter lifespans result in more reproduction then perhaps you end up with a larger population to help with the probability of going extinct in cases of disaster. I think the issue with longer lifespans in terms of selection is purely a problem of population size, the shorter the lifespan the larger the size of population which means greater probability of survival.

 

Regardless of the above, I really hope we can solve this epigenetic, methylation clock problem because I agree, it's likely that this, rather than telomeres alone, is at the very root of aging. As Eva suggests, it could be in the hypothalamus.


Edited by Nate-2004, 29 March 2018 - 03:06 PM.


#9 xEva

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Posted 29 March 2018 - 09:38 PM

 

This is just a comment on Josh's blog post and his theorizing about evolution:

 

I don't see how longer lifespan necessarily equates to lost resources and thus programmed aging was selected for. This is an argument that doesn't hold up for me, logically. Longer lifespan has always been associated with slower reproduction rates hasn't it? Also, isn't overpopulation a myth? We're talking hundreds of thousands of years ago, when our ape like ancestral populations were pretty low compared to the 7 billion humans today. How would environmental pressures like famine select for short lifespans? I guess maybe if shorter lifespans result in more reproduction then perhaps you end up with a larger population to help with the probability of going extinct in cases of disaster. I think the issue with longer lifespans in terms of selection is purely a problem of population size, the shorter the lifespan the larger the size of population which means greater probability of survival.

 

Regardless of the above, I really hope we can solve this epigenetic, methylation clock problem because I agree, it's likely that this, rather than telomeres alone, is at the very root of aging. As Eva suggests, it could be in the hypothalamus.

 

 

 

It's not just resources, though of course there are many examples of a population growth and subsequent collapse. In this regard, I find it telling that most (if not all) species with negl. senescence are not confined to a specific area but are free to move; the roam the whole planet (ocean, actually)

 

I think the popular models are lacking, because they assume a more or less stable environment -- and it's not just climate, though surely it affects everything else, from diet to pathogens. And the latter is one of the most  decisive factors, for, even in a climatically stable environment, microbes and parasites continue to evolve. Also new pathogens can be introduced at any time by migrating animals or brought in by the winds (e.g. african desert sand deposited on the skiing slopes in eastern europe, recently).   

 

In humans, the largest variation is in genes of the immune response. Wide variation in immune response among individuals increases the chances of a population to survive, no matter what hits them.  (As an aside, this has a curious implication, and that is that most individuals in a population are not perfectly suited for the current conditions, which means that only a subset are 'perfectly healthy', while the rest must do their best -- while the nature waits for the conditions to change, and then a subset of the population that was not doing that well may suddenly thrive.)

 

This is easier to see on the example of unicellular eukaryotes, also mentioned by Josh. Most -- bacteria, fungi, infusoria, slime molds, etc. -- adopted the following strategy: while the conditions are good, they multiply by division, essentially cloning themselves; and when the conditions change, they congregate have sex, sporulate and rely on wind to spread their spores around -- all in hope that no matter in what conditions their spores land,  variations in the genome will allow some individuals to survive and maybe even thrive.

 

Josh mentions that while paramecia clone themselves, their telomerase is not expressed, which puts a cap on # of cell divisions. This ensures that no single clone will overtake the colony, because, while this clone will be perfectly suited for the given environment, the conditions will surely change and then the population will not collapse. 

 

IOW, the variation in population must be maintained, even if it comes at a cost of disadvantage to some (actually, most, if we seek perfection) individuals. Even though these individuals are not perfectly suited for the given environment, their 'imperfect' combo of SNPs must be preserved and maintained, as an insurance policy for the long-term survival of the population at large.

 

And so aging comes in because it forces the population to continuously reshuffle the genes and renew itself by influx of new individuals. This is a strategy for the population long-term survival in the conditions of ever-changing environment.

 

 

Don't ask for refs, this is my take on it, which boils down to the fact that popular evolutionary models tend to discount the importance of ever-changing environment, pathogens being one of the most important aspects of it.


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#10 QuestforLife

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Posted 30 March 2018 - 02:28 PM

Glad this thread is really taking off.

I believe the argument for aging being selected for (and group selection in general) is that traits like aging serve to help the species rather than the individual. One example of this is in out evolving a predator. If you breed faster you'll tend to die faster too, and the population will turnnover and evolve faster, so adapting more quickly to challenges such as a bigger animal trying to eat you. But once a species gets a really good defence, i.e. flight, living underground, intelligence, a shell, etc, it can then start evolving aging away.
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#11 QuestforLife

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Posted 30 March 2018 - 02:33 PM

I had an idea about why telomerase and epigenetic age are inversely correlated.

It could be that epigenetic age is measuring the time a somatic line of cells has existed since it was spawned from its stem cell progenitor. So a person with more telomerase and therefore longer telomeres will keep a somatic line longer because it takes longer to reach senescence, therefore an epigenetic age test would think their tissues are older. In actual fact their stem cells will have been used less so they are actually in better shape, I would expect.
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#12 Kentavr

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Posted 30 March 2018 - 09:25 PM

explanation here:

 

Hypothalamic stem cells control ageing speed partly through exosomal miRNAs

 

https://www.nature.c...es/nature23282 

 

and here:

 

https://nplus1.ru/ne...017/07/28/htnsk (news in Russian)  :)

 

The hypothalamus also influences the epigenetic clock. I'm trying to develop a method of cell rejuvenation that could rejuvenate the hypothalamus.
 
One method is the elongation of telomeres with the help of a preparation of various telomerase activators, which are applied sublingually.
 
The idea: telomerase activators more effectively rejuvenate the hypothalamus through the elongation of telomeres, thereby slowing down the degradation of the epigenetic clock.
 
The development of the technique is still at the very beginning.

Edited by Kentavr, 30 March 2018 - 09:39 PM.


#13 xEva

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Posted 30 March 2018 - 11:12 PM

I'm trying to develop a method of cell rejuvenation that could rejuvenate the hypothalamus.


there are already chemicals that, apparently, reverse the epigenetic clock of brain neurons (not necessarily of hypothalamus, but close)
 

 

:) but didn't you see this guys?

But then, what if there is already a substance that can make the epigenetic clock tick slower or even reverse the age it shows? Would you jump on it?


I've been trollying  for a couple of days already. Still waiting... I'm not posting the links, coz I'll be carpet-bombed with red buttons..

 

Can't resist bragging though.. I've had this idea for a long, long time and made a couple of feeble attempts at discussing it here... And just recently ran into two (already 2!) papers confirming it. Not an elixir of immortality, for sure, but these are well-known substances, not necessarily freely obtainable, but not that difficult or expensive either..  

 

♫.. NA-na ^na-NA-na .. ♪

 


Edited by xEva, 30 March 2018 - 11:14 PM.

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#14 QuestforLife

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Posted 31 March 2018 - 10:08 AM

It depends what you mean by reduce epigenetic age. Because longer telomeres will mean somatic cells are replaced by stem cells less often, so your tissues will have an older epigenetic age (stem cells or cells that have just spawned from a stem cell will be epigenetically younger than cells that have been around for a while).

Conversely getting your tissues to turn over faster will give you a younger epigenetic age, as more of your cells will have recently been created from the stem cell pool, but this strategy will exhaust your stem cells faster. What you really need to do is give your stem cells nice long telomeres and get your somatic tissues turned over as fast as young person does. That basically makes you young.
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#15 Turnbuckle

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Posted 31 March 2018 - 11:20 AM

So, if the advancement in the Horvath clock has no effect on cells viability, why view it as detrimental? 

 

 

Methylation patterns determine which of the 200 cell types a particular cell is. Thus random changes in the patterns--the epigenome--degrade its functionality for a particular end use.


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#16 QuestforLife

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Posted 31 March 2018 - 12:51 PM

It stands to reason that replacing cells from a reliable template (i.e. a stem cell) would be better than keeping a somatic cell line going perpetually.

But the Horvath sites have no effect on protein expression Turnbuckle, so it's hard to see how changes in their methylation status could be behind loss of cell differentiation status. Similarly telomerase immortalised skin cells say, don't stop becoming skin cells in vitro, even after many doublings.
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#17 xEva

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Posted 31 March 2018 - 01:49 PM

 

So, if the advancement in the Horvath clock has no effect on cells viability, why view it as detrimental? 

 

 

Methylation patterns determine which of the 200 cell types a particular cell is. Thus random changes in the patterns--the epigenome--degrade its functionality for a particular end use.

 

 

 

That's the thing about the Horvath clock -- the methylation pattern is not random. To the contrary, he found 353 specific locations ("CpG sites", which is just a subset of SNPs, most of them hypermethylated and the rest undermethylated), whose methylation pattern correlates upto r=0.95-0.97 (!) with chronological age across various tissues (+/- 3.6 years)  -- though in some tissues the correlation is stronger than in others.   

 

 

It depends what you mean by reduce epigenetic age. Because longer telomeres will mean somatic cells are replaced by stem cells less often, so your tissues will have an older epigenetic age (stem cells or cells that have just spawned from a stem cell will be epigenetically younger than cells that have been around for a while).

Conversely getting your tissues to turn over faster will give you a younger epigenetic age, as more of your cells will have recently been created from the stem cell pool, but this strategy will exhaust your stem cells faster. What you really need to do is give your stem cells nice long telomeres and get your somatic tissues turned over as fast as young person does. That basically makes you young.

 

 

That was my initial assumption and you were the one who corrected me (thanks!). The mindboggling part is that it's the same SNPs, regardless of tissue type:

 

While DNAm age is correlated with cell passage number and the clock ticking rate is highest during organismal growth, it is clearly different from mitotic age since it tracks chronological age in non-proliferative tissue (for example, brain tissue) and assigns similar ages to both short and long lived blood cells

 

DNA methylation age of human tissues and cell types, 2013

 

 

Re "depends what you mean by reduce epigenetic age" -- well, true, so far it's not "reduce". So far it's only that the brain neurons of users of those substances show epigenetic age "significantly younger" than control, as measured by the Horvath clock (and there was no mention of telomeres -- at least I don't remember -- hardly relevant in this case anyway).

 

 

So, those who don't mind being bombed with that 'dangerous irresponsible' button (apparently, there are prudes here, and among moderators, too) can google Horvath clock, brain neurons and younger epigenetic age. Hey, I'm hoping the collective effort may turn up more than 2 papers   :)   


Edited by xEva, 31 March 2018 - 01:53 PM.


#18 Turnbuckle

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Posted 31 March 2018 - 01:56 PM

But the Horvath sites have no effect on protein expression Turnbuckle...

 

Not true. The clock measures the DNA methylation of specific CpG dinucleotides, and methylation of CpG sites turns off genes. Human DNA carries the genes to create all 200 cell types, and those genes unneeded for a specific type are turned off. In one cell organisms, almost no CpG sites are methylated as there is only one cell type, but in vertebrates, some 60-80% of genes are turned off in somatic cells.



#19 QuestforLife

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Posted 31 March 2018 - 05:25 PM

Hi Turnbuckle, you'd think that wouldn't you? I did too. But Horvath mentioned in the Q&A of his recent video (22nd Jan) that he couldn't find any transcriptional changes; this kind of makes sense when you consider the same methylation changes occur across most cell types.

xEva, what i'm saying applies to fast turnover tissues as well as slowly or arrested tissues; the issue is how 'far' epigenetically a somatic cell is from its stem cell progenitor. This is what epigenetic age is, and it seems to tick across the body. So if my idea is correct, long telomeres would accelerate the epigenetic age of proliferating cell types more than those cells that don't copy much (it would still have some effect as telomerase can protect mitochondria). It's a falsifiable hypothesis. A consequence of this idea is that it proves some human tissues suffer from replicative senescence (it was never much of a question in my mind!)

#20 xEva

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Posted 31 March 2018 - 05:46 PM

In one cell organisms, almost no CpG sites are methylated as there is only one cell type,


Somehow this seems doubtful, coz unicellular eukaryotes have many tricks up their sleeve, and not just sporulation. Slime molds feed as unicellular, but then congregate, have sex and form a 'fruiting body' which consists of specialized cells (and genes of those who end up as 'stalk' get discarded). Or take dimorphic fungi, where unicellular 'yeast' are very different from mycelium cells. + most unicellulars have at least a few 'stages' (some many!), each looking and behaving very differently.  Seems logical to assume that each 'stage' has a different set of genes expressed, via methylation, though I have not checked it.


Edited by xEva, 31 March 2018 - 05:47 PM.

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#21 Turnbuckle

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Posted 31 March 2018 - 08:11 PM

 

In one cell organisms, almost no CpG sites are methylated as there is only one cell type,


Somehow this seems doubtful, coz unicellular eukaryotes have many tricks up their sleeve, and not just sporulation. Slime molds feed as unicellular, but then congregate, have sex and form a 'fruiting body' which consists of specialized cells (and genes of those who end up as 'stalk' get discarded). Or take dimorphic fungi, where unicellular 'yeast' are very different from mycelium cells. + most unicellulars have at least a few 'stages' (some many!), each looking and behaving very differently.  Seems logical to assume that each 'stage' has a different set of genes expressed, via methylation, though I have not checked it.

 

 

You are right. I was speaking generally, but it’s true that some single-celled organisms go through different growth stages and thus are actually multi-celled throughout their life cycle. Thus they have a need to turn off certain genes at certain times.



#22 Turnbuckle

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Posted 31 March 2018 - 08:25 PM

Hi Turnbuckle, you'd think that wouldn't you? I did too. But Horvath mentioned in the Q&A of his recent video (22nd Jan) that he couldn't find any transcriptional changes; this kind of makes sense when you consider the same methylation changes occur across most cell types.

 

 

 

I can't find your video, but I would expect most methylation changes with aging to be stochastic, and thus not the same across cell types, or even within the same cell types.



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#23 QuestforLife

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Posted 31 March 2018 - 08:52 PM



Here it is Turnbuckle.
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#24 Turnbuckle

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Posted 31 March 2018 - 09:42 PM

Hi Turnbuckle, you'd think that wouldn't you? I did too. But Horvath mentioned in the Q&A of his recent video (22nd Jan) that he couldn't find any transcriptional changes; this kind of makes sense when you consider the same methylation changes occur across most cell types.
 

 

 

Thanks for the video. I listened to Horvath's entire Q&A, but didn't hear anything about "transcriptional changes" in those words, though there is definitely some unknowns of how methylation affects gene expression. He gets into that briefly at 2:19, saying that in some cases it does, in some cases there's no clear association, and goes on to say that some think the methylated sites adjacent to the gene aren't actually the controlling factors, that maybe they are further away. There is research that backs that idea--

 

Here we show that most methylation alterations in colon cancer occur not in promoters, and also not in CpG islands but in sequences up to 2 kb distant which we term “CpG island shores.”...While both hypomethylation and hypermethylation in cancer involved CpG island shores, there were subtle differences in the precise regions that were altered. Thus, the hypermethylation often extended to include portions of the associated CpG islands in 11% of cases (Fig. 2), which could account for the island hypermethylation frequently reported in cancer, even though that is not the predominant site of modification. In contrast, the hypomethylation often extended away from the associated CpG islands in 34% of cases (Fig. 2).

https://www.ncbi.nlm...les/PMC2729128/

 


Edited by Turnbuckle, 31 March 2018 - 09:46 PM.


#25 QuestforLife

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Posted 01 April 2018 - 03:16 PM

They are saying they can't find any effects of the methylation changes - but they're speculating it must have some effects on distant genes. Until they find them - and bear in mind telomerase immortalised cells have been studied quite extensively and found to be unimpeded by the Horvath clock continuing to tick - I'm going to remain skeptical this is anything more than a clock. Still useful, but just a clock. We'll see if they do anything to prove my current position wrong over the next few years.

Edited by QuestforLife, 01 April 2018 - 03:18 PM.


#26 xEva

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Posted 02 April 2018 - 12:46 AM

They are saying they can't find any effects of the methylation changes - but they're speculating it must have some effects on distant genes. Until they find them - and bear in mind telomerase immortalised cells have been studied quite extensively and found to be unimpeded by the Horvath clock continuing to tick - I'm going to remain skeptical this is anything more than a clock. Still useful, but just a clock. We'll see if they do anything to prove my current position wrong over the next few years.

 

 

Agree. In the comments section of Josh's blog Bill Walker says he "immortalized cells using telomerase back in 2001 that are still in culture."  I'd be curious to know what age the Horvath clock would assign to them. What if they are well past 100 and yet still doing fine?

 

 

xEva, what i'm saying applies to fast turnover tissues as well as slowly or arrested tissues; the issue is how 'far' epigenetically a somatic cell is from its stem cell progenitor. This is what epigenetic age is, and it seems to tick across the body. So if my idea is correct, long telomeres would accelerate the epigenetic age of proliferating cell types more than those cells that don't copy much (it would still have some effect as telomerase can protect mitochondria). It's a falsifiable hypothesis. A consequence of this idea is that it proves some human tissues suffer from replicative senescence (it was never much of a question in my mind!)

 

Maybe I don't understand what you mean. I agree that an older cell is not bad in itself -- it simply lived longer, without a need to replace it -- why is it a bad thing? Horvath mentions this too in his talk, as one of the suggested explanations.

 

But I don't understand how telomerase affects epigenetic age in cells that don't proliferate. Horvath suggests it may be due to epigenome maintenance (as in response to DNA damage -?) In this 2017 review Epigenome maintenance in response to DNA damage there is no mention of telomerase and only one mention of telomeres.

 

Also, I don't understand how, by protecting mitochondria, telomerase would affect the epigenetic age of a non-proliferating cell. 

 

Also, regarding methylation and gene expression, which I tried to look into after Turnbuckle comments, apparently, not that much is known in this regard. And my question was, how many CpG sites must be methylated to turn off an active gene. Intuitively is seems that just one-two randomly methylated CpG sites should not be enough -? unless they happen in some key loci-? Well, the answer is, nobody knows at the moment.

 

As Horvath says in his talk, there is no lack of interesting ideas and theories, what is needed is more data at this point.

 

 

So, guys, I'm sure you found the papers. What's your take on judicial use of the substances associated with "significantly younger" epigenetic age in brain neurons? Or, considering the latest developments on reddit, must we go underground to discuss this? Where?


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#27 QuestforLife

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Posted 02 April 2018 - 07:07 AM

Hi xEva, longer telomeres mean somatic cells need replacement from the stem cell pool less often, hence an average older epigenetic age (as measured by the drift on methylation sites). But this shouldn't be the case in quiecent cells - I agree - except telomerase can leave the nucleus and protect mitchondria from oxidative stress. So even quiescent cell tissues will live a little longer with long telomeres. Plus most tissues do renew to some extent, and this should correlate the effect of telomere length on epigenetic age: the quicker the tissues renew, the bigger the effect. That's why I said this is testable; the answer to whether this is right or wrong should be in Horvath's data. He probably makes various adjustments for tissue type so it might be hidden in there.

I don't know the answer to methylation and gene switching. It's probably also more to do with histones being in an open or closed configuration.

I must admit I don't know what papers on reducing epigenetic age you are talking about. Grateful if you could point me in the right direction. Thing to be careful of is that you're not just using up your stem cells.

#28 Turnbuckle

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Posted 02 April 2018 - 01:02 PM

 

 

. And my question was, how many CpG sites must be methylated to turn off an active gene. Intuitively is seems that just one-two randomly methylated CpG sites should not be enough -? unless they happen in some key loci-? Well, the answer is, nobody knows at the moment.

As Horvath says in his talk, there is no lack of interesting ideas and theories, what is needed is more data at this point.

 

 

 

Logically, the large size of the CpG islands--300 to 3,000 base pairs--indicates it's more than one, and likely more than two. Likely genes are turned off with a dimmer switch rather than an on-off switch, which would give evolution far more possibilities to work with. And thus the random hyper and hypomethylation of aging would be like throwing sand in the gears rather than wrenches.


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#29 xEva

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Posted 04 April 2018 - 01:05 AM

Turnbuckle, that's what I thought too: some critical mass is reached and bam! the gene is off. But then I remembered that genes are methylated daily, according to diurnal and circadian cycles. And so I checked -- and sure enough, there is infinitely more to DNA methylation than just keeping certain genes permanently off:  

 

 

In this study, we examined levels of DNA methylation at>400,000 sites across the genome in the brains of 738 human subjects and showed significant 24-hour rhythms of DNA methylation. Moreover, we showed that for specific locations of DNA methylation site, these rhythms of methylation were linked to rhythms of gene expression. This is important because it suggests that circadian rhythms of DNA methylation may be an important mechanism underlying circadian rhythms of gene expression in the human brain, and hence circadian rhythms of normal and abnormal brain function.

 

 Circadian rhythms are maintained by a near 24-hour feedback loop mediated by a series of “clock” genes that are similar across species, including humans.

_______________________

 

Epigenetic mechanisms in diurnal cycles of metabolism and neurodevelopment, 2015

 

The circadian cycle is a genetically encoded clock that drives cellular rhythms of transcription, translation and metabolism. The circadian clock interacts with the diurnal environment that also drives transcription and metabolism during light/dark, sleep/wake, hot/cold and feast/fast daily and seasonal cycles. Epigenetic regulation provides a mechanism for cells to integrate genetic programs with environmental signals in order produce an adaptive and consistent output. Recent studies have revealed that DNA methylation is one epigenetic mechanism that entrains the circadian clock to a diurnal environment. 

 

All organisms have evolved to exist in a rhythmically cycling environment driven by the 24-h day and seasonal variations. As a result, they have adapted their physiological rhythms to mirror their environment. Physiological rhythms are driven by both ongoing environmental influences (light/dark cycling, food availability, wake/sleep) and an intrinsic, genetically encoded clock mechanism.
 
In mammals, the genetically encoded clock resides in the suprachiasmatic nucleus (SCN) located within the hypothalamus to regulate cyclical metabolism in peripheral tissues. This mammalian clock is called the ‘circadian’ cycle because it continues to cycle in the absence of environmental inputs. The circadian cycle orchestrates a complex rhythm of transcription, post-transcription, translation and post-translational regulation with the circadian factors 
 
In contrast, the environmentally driven cycle is called the ‘diurnal’ cycle. In most instances, the two cycles are in synchrony, with the diurnal cycle acting to entrain the circadian cycle. However, the two can become unsynchronized 
 
In this review, we will focus on recent work highlighting the role of epigenetic mechanisms, in particular, DNA methylation, at the interface of circadian and diurnal cycles, and give examples of epigenetic neurodevelopmental disorders with circadian and diurnal rhythm disruptions.

 

 

It could be that the proaging signal is a product of the clock that resides in the suprachiasmatic nucleus (located within the hypothalamus). And it looks like it counts not just hours in a day but seasons, and, most likely, years too. 

 

And surely, if DNA methylation patterns are rearranged daily (and in response to external stimuli), there are plenty of opportunities for something to go awry.

 

Also, these fluctuations in DNA methylation patterns are reflected in when the samples were taken -- and, if the time of day and season were not recorded, most of it is meaningless. But since Horvath found a subset of CpGs which strongly correlate with chronological age, they could be the ones engaged in keeping track of years.

 

 

Still don't see what telomerase has to do with it. They should have stressed the TERT-expressing cells that were not passaged. Say, gave them a small dose of radiation to see if the epigenome maintenance program that will run as DNA damage response will affect the clock (I hear, in another study, a large dose of radiation did not advance the clock). Or they could put the static culture through cycles of light/dark, warm/cold -- this could turn on the genes engaged in diurnal rhythms and that in turn could engaged the circadian genes. In the end, this may, or may not, advance the clock in non-proliferating cells.   

 

 

 


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#30 HighDesertWizard

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Posted 20 May 2018 - 05:38 PM

 

But then, what if there is already a substance that can make the epigenetic clock tick slower or even reverse the age it shows? Would you jump on it? 

 

xEva... Great thread... I'm bewildered by the huge set of puzzle pieces missing from the discussion so far... I can easily add it... It's the set of puzzle pieces I always add, right?  :)

 

An answer to your question... Yes. Of course. I'm likely to be doing some of the ones you have in mind already. It would be useful to compare notes. Is there a detailed discussion going on somewhere?







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