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Patterns of MicroRNA Expression as a Biomarker of Aging

As a complement to the DNA methylation based biomarkers of aging, researchers are also finding that patterns of microRNA levels can serve a similar purpose. These tools offer the potential for a rapid assessment of candidate rejuvenation therapies rather than having to run lengthy life span studies, something that is prohibitively expensive for most research groups even in mice, and entirely out of the question in humans. It is hoped that a generally agreed upon biomarker of aging, a low-cost test that fairly accurately reflects biological age, defined as the burden of cell and tissue damage that causes dysfunction and death, will speed up progress towards the development of rejuvenation treatments. The advent of senescent cell clearance as a viable rejuvenation therapy should greatly help the development and validation of such biomarkers: the two lines of development will support one another.

Human aging is a complex process that has been linked to dysregulation of numerous cellular and molecular processes. Recent studies have revealed that human aging can be characterized by changing patterns of DNA methylation and expression of protein-coding genes. A growing body of research suggests that aging is associated with changes in DNA methylation both genome-wide and at specific C-G dinucleotide (CpG) loci. At the messenger RNA (mRNA) level, a recent meta-analysis of whole-blood gene expression in ~15,000 individuals identified 1497 mRNAs that are differentially expressed in relation to age. An age predictor based on mRNA expression (i.e., mRNA age) highlighted genes involved in mitochondrial, metabolic, and immune function-related pathways as key components of aging processes. The difference between mRNA age and chronological age correlated with many metabolic risk factors including blood pressure, total cholesterol levels, fasting glucose, and body mass index (BMI).

MicroRNAs (miRNAs) are a class of small noncoding RNAs that downregulate protein-coding genes by either cleaving target mRNAs or suppressing translation of mRNAs into proteins. Research in a Caenorhabditis elegans model system revealed changes in miRNA expression in relation to lifespan and longevity. In humans, highly specific miRNA expression patterns are correlated with many age-related diseases including cardiovascular disease and cancer. Recent studies have examined differentially expressed miRNAs in relation to age in whole blood, peripheral blood mononuclear cells (PBMC), and serum. These studies, however, were based on small sample sizes, limiting the power to investigate age-related changes in miRNA expression. We hypothesized, a priori, that it would be possible to create a miRNA signature of age that is predictive of chronological age and that age prediction based on miRNA expression is biologically meaningful and can be used as a biomarker of risk for age-related outcomes including all-cause mortality.

In a previous study, we measured miRNA expression in whole blood from more than 5,000 Framingham Heart Study (FHS) participants. We investigated the heritability of miRNA expression and performed a genome-wide association study (GWAS) of miRNA expression. Our results showed that miRNAs are under strong genetic control. In the present study, we further investigated whole-blood miRNA expression in relation to chronological age in FHS participants. We identified 127 miRNAs that were differentially expressed in relation to chronological age, and performed internal validation by splitting the samples 1:1 into two independent sample sets. An integrative miRNA-mRNA coexpression analysis and miRNA target prediction revealed many age-related pathways underlying age-associated molecular changes. We also defined and evaluated an age predictor based on miRNA expression levels (i.e., miRNA age). Our results indicate that the difference between miRNA age and chronological age is associated with multiple age-related clinical traits including all-cause mortality, coronary heart disease (CHD), hypertension, blood pressure, and glucose levels.

Link: https://doi.org/10.1111/acel.12687

Comments

But are we confident that upcoming treatments, i.e. senolytics, will have any impact on the Horvath Clock, for example, given that this measure of aging has absolutely nothing to do with cellular senescence?

Posted by: Mark at October 25th, 2017 9:25 AM

@Mark: Epigenetic changes are a reaction to the damage of aging - they are not a program somehow completely independent of that. Or at least, it would be very surprising to find that something that reliably extends life and turns back all sorts of age-related disease doesn't have any effect on the epigenetic reaction to the causes of aging.

Posted by: Reason at October 25th, 2017 3:52 PM

But as Horvath has shown his clock is independent of cellular senescence. Whether that means his clock is not a good measure of the damage of aging as we currently experience it, or whether it means there are other causes of aging independent of cellular senescence, is yet to be determined. But my point is that senolytics will not turn the Horvath clock back, so you'll have to look elsewhere for a helpful biomarker, maybe miRNA levels will work, or blood plasma protein levels, I don't know.

Posted by: Mark at October 25th, 2017 4:08 PM

@Mark: Reference?

Posted by: Reason at October 25th, 2017 4:17 PM

Thanks. That doesn't show that cellular senescence has no effect on epigenetic age in the sense I mean. It is a study of senescent cells in culture, assessing the epigenetic clock in those senescent cells. That is completely different from the question of what senescent cells do to living tissues and the balance of signaling and cell behavior in a living organism. That is the question I am interested in - how the 1% of senescent cells changes the other 99%. Here is where I'd be surprised to see no change in an epigenetic clock.

Posted by: Reason at October 25th, 2017 6:34 PM

I watched a video where Horvath indicates cellular senescence is a different process from epigenetic age, and says the epigentic clock is not too accurate in older people. I think it was this video; sorry, I can't pinpoint where without watching the entire video again:

youtube.com/watch?v=dXRF-svtKOI

Posted by: NY2LA at October 25th, 2017 11:13 PM

Thanks Anonymoose, that's the ref.

Removing senescence cells in vivo would reduce inflammation, which might reduce MTOR somewhat, so you might see a slowing down in the pace of epigenetic change, but there is unlikely to be any reversing of the Horvath Clock.

No one really knows what the Horvath Clock is really showing, it's certainly correlated with mortality, but it's anyone's guess if it's causal.

Posted by: Mark at October 26th, 2017 3:12 AM

Hi all, (message a little long I apologize))

''The fact that maintenance
of telomere length by telomerase did not prevent cellular
ageing defines the singular role of telomeres as that of a
means by which cells restrict their proliferation to a certain
number; which was the function originally ascribed to it.
Cellular ageing on the other hand proceeds regardless of
telomere length. ''

''This is consistent with the fact that mice
with naturally long telomeres still age and eventually
die even though their telomere lengths are far longer
than the critical limit, and they age prematurely when
their telomeres are forcibly shortened, due to replicative
senescence.''

I think they are mixing their whole thing...
it's true from the study that epigenetic aging is independent from DNA damage response
by other means such as radiation, leading to spontaneous senescence. But their own
wording :

''Analyses of their DNA by the
previously described epigenetic clock [34], revealed
that the replicative senescent cells have indeed aged. "

and this :

''These cells
continue to proliferate in culture beyond passage 50 and
do not exhibit any signs of senescence, demonstrating
that the process of cellular ageing continues unabated
in cells whose telomeres were maintained''

This demonstrates that mice just don't have 'time' to reach their full life potential,
unlike a naked mole rat does much more. And, in humans, it's the inverse of mice; we have the
potential and we deplete it to its very maximum (because we no longer die below 50 years old
like in the past (disease, predators...etc. Now, we are safe, and with medical cares; thus
we are allowed live on, unabated, to the maximum of human lifespan)).

In a sense, humans (unlike mice) are constrained by this mechanism of replicative senescence.
They may call it whatever they want corcerning telomeres; but telomeres are still 'replicative
round counters'. And they themselves said it :

''...that the process of cellular ageing continues unabated
in cells whose ****telomeres were maintained****"

Sure the cell might age - but so what, it does not Senesce (Replicative Senescence) which
is the Crux of why we die in old age if we keep healthy and go on to live over a 100.
We might be epigenetically older (By cell epigenetic methylation changes/Horvath clock),
but the telomeres did not - Shrink (no loss of TTAGGG DNA repeats). This means :

''cellular ageing continues unabated in cells whose telomeres were maintained...''

and in humans, who keep homeostasis in most areas/organs; they continue to age 'healthily'
and live their decades, but their telomeres still are lost each replication round (in post-mitotic somatic cells such as undividing neurons or CNS cells who lack telomerase/or don't have enough).
Thus, less 'rounds' left; soon the cell will (replicatively) Senesce. Mice can't reach that, even if they have longer
telomeres because they lose genomic/metabolic/DNA repair homeostasis - Before reaching their full life potential, their long telomeres could allow them to beat NMRs (because once they do offspring reproduction, their body
no longer invests in DNA maintenance/the animal is disposable/did its contribution to the specie by reproducing thus die rapidly,
unlike humans relying on DNA longevity genes (DNA repair and Redox homeostasis genes for example, among many others) for that because of grand-mothering longevity DNA gene transfer in prehistory to counter low birthing in humans),

''cellular ageing continues unabated in cells whose telomeres were maintained...''

But, if the telomeres are maintained, the cell epigenetic age will continue - but the
phenotypic 'aging/damage' of the tissue will not - it Will Not Senesce; because it can
keep on replicative and as such, Replicative Senescence is thwarted.

Don't ask yourself why certain immortal cancer cells always keep 2kbs of teloemre 'frozen' there
and it never goes much below that - they never replicatively senesce when left to proliferate unabated. It just does not work, if you have 0kb telomere it's over.
Humans go to the max aroud 2k-3kb (2000-3000 basepair DNA nucleotides of telomeric TTAGGG),
there the DNA damage response (DDR) signal of p53 p21 p16 is much too strong; it is the 'replicative senescence signal'
that telomeres are 'encoded' with at the 2-5 kb region. I think we should not dismiss
telomeres so quickly in aging, they might be just a counter but that counter is our clock
and we are limited by it. Telomerase in Mrs.Parrish (Bioviva) did improve her telomere length (and from
this study her epigenetic age would not have changed); but who cares, if she could continue
'Aging' and age for a 1000 years (and thus her cell are 'epigenetically 1000 year old')
it does not matter; her replicatiev senescene is gone because her telomeres are maintained;
thus death would technially be cured because replicative senescence would not be a barrier
anymore into old age of humans who push their cells to the Very limit (the replicative senescence limit).

2 cents.

Posted by: CANanonymity at October 26th, 2017 6:41 PM

PS: and this, showing telomeres are crucial like the rest (in humans' longevity, at least) :

'' and they [mice] age prematurely when
their telomeres are forcibly shortened, due to replicative
senescence.''.

This is very important and shows that mice who show progeria or premature aging suyndrome (just like people with HGPS who lose 500 bp/year vs normal speed of 50bp/year) tells us that telomeres will just 'hasten' towards their 'conclusion' - replicative senescence - by low kbs region activation of inflammatory genes (p53..). TElling us that Telomeres, we are bound by them/this mechanism and as such, telomeres are far important than we think. Epigenetic aging is important too - but what's more important is stopping cell cycle arrest by multiple 'life-long' replication/replicative senescene - because that one kills you unlike a a cell that is 'epigenetically aged' - if it keeps on proliferating, it means things are working (lipofuscin is still low enough and ATP production also high enough to maintain all the requirement (DNA repair, Redox homeostasis, Stem cell renewal, etc..). The very fact that prematurely aging mice show telomere loss means that there is a 'pedal break' that is put on their cell replications (telomere becoming low/counting clock going to low in low-kb regions).
And thus they die. In humans, it just over decades instead of 2 years like a mice.

'' and they [mice] ***age prematurely*** when
their telomeres are forcibly shortened, due to ***replicative
senescence.***''

Posted by: CANanonymity at October 26th, 2017 7:00 PM

PPS: (a sort of farfetched) analogy to illustrate :

Cell epigenetic age : a 'tag', a 'number', a 50-day old cell, a 500-year old cell. It mostly just a measure of the age of the cell and not much else. Think of it like C-14, radiocarbon dating a cell; one cell by C-14 might 50 days and another might be 50,000 years old.
Your cells could technically be a 1000 year old 'epigenetically'. What's important is not this.

Replicative Senescence : The Aging as we know it (in humans). that is the **Intrinsic Limit** to humans life (manifest as a Maximum around 120-140 or so if they keep healthy and are genetically gifted) because they are linked to 'Telomeres' that are counters/breaks on 'cell replication'; if cells can't replicate anymore; they enter senescence (not Oncogene senscence nor Spontaneous senescence; but Replicative Senescence) and that Will happen in humans after 50-100 or so 'replication rounds' (over a lifetime) in most somatic cells ; becaus humans don'T maintain their telomere size - Thus, they will enter telomeric-dependent Replicative Senescence and thus die). How do we circumvent this problem beyong 'telomere lengthening/telomerase hTERT activation' is hard to say.

Posted by: CANanonymity at October 26th, 2017 7:32 PM

PPPS: it was suggested that the way to beat that was recreating completey the organs or the cells (All the Cells, and 'reinputting' them in the bodies, as like a complete removal of what is dead/dying - with new fresh 'organoids/organs/cells....Everything Totally Replaced'...it (just might) work. Or we even close to that though, organoids are dawing on us though so we closing in; I guess we will have to totally 'replace' ourselve with time/become sort of continously self mutating/self replacing-cyborgs (I think there the AdG's car analogy could work replacing the parts - but only if Alll the parts (in Totality and become a brand new 'You' each rejuvenation) are replaced totally and continuously, this could twarth replicative senescence; that is tall order)..

Posted by: CANanonymity at October 26th, 2017 7:39 PM

With the immune system, there are some things we can do to slow down replicative senescence and telomere shortening and loss of function. We can try to prevent inflammaging whenever it raises its ugly aging head. For example, Centenarians have very low expression of CD39 and CD73 in the peripheral blood system, whereas older control adults have much higher levels that grow exponentially higher with age (Crooke, 2017). What causes this difference, do the Centenarians avoid getting the CMV virus that ruins the immune system of most people at older ages? Or is there some other protective reason the Centenarians have? Perhaps it is little known that a couple genes in the immune system express telomerase when the telomeres of LEUKOCYTES get too short, including OBFC1 rs9420907 AA, rs9419958 CC, and rs2487999 CC, and ADA rs73598374 CC. I happen to be homozygous for all of the above alleles, so my immune system should continue to function much longer than people who don't have the longevity alleles. Possibly in the future, you could have the longevity alleles transplanted to your genome by CRISPR technology.

Posted by: Biotechy at October 29th, 2017 1:28 PM

@Biotechy

Hi Biotechy ! Thanks for that.

It's a very good question, I am not sure really; just my 2 cents... I guess it's a combination of things (so far, it pretty much always has been, aging is multifactorial and a combination of things, clearly, evidently and thus most obviously (so many studies have shown the complex intertwining nature of it like a huge messy untangleable & untangible Tangle or unending labrat Maze where rats die in them of being lost/never finding the exit).

But some points like that,
- Thymic involution (thymus) and BMD (bone mineral density) loss; and thus bone marrow loss; and thus bone marrow stem cell production loss/loss of nascent/immature T CD8+ cells (immune cells) that go on to be 'activated' in the thymus (the thymus shrinking) and thus immunity loss = cancer, diseases, short life. Immunity equals MLSP (maximum lifespan potential). As you said telomeres protection and mtaintenance in Leukocytes are crucial for they are immune components. And as you said, telomerase does increase their telomeres there - not in many other cells though (or not sufficiently enough to compensate telomere loss; one study had showed that ecessive telomerase activation creates chromosomal aberattions and SCEs (sister chromatid exchanges); basically, telomerase does help to solidify telomeres and increases their size - but only to a certain 'activity' level - if too much, it becomes detrimal Too. And as we know telomerase contributes to cancers, for they highjack it for themselves (to become immortal))) Not all of them though, some use ALT instead, they found other ways to trick the immune system and avoid eraction by immmune cells (like passing as 'impostor' 'normal' cells, thus the immune cells can't detect them (Camouflage) and thus, void being phaged by NK-cells/T-Cells/macrophages and other white blood cells).

That is I worry about the SENS therapy of 'cutting telomerase' completely; it should only be 'pinpointed'in the cancer tumors that's it- the rest you don'T touch it - if other cells, such as leukocytes, lose telomerase during this therarpy this exposes us to cancer formation while doing SENS - despite the therapy Itself - About stopping the Cancer (through blocking telomerase enzyme highjacking in tumors) - thus, it is self-defeating. If they can mitigate this, not removing the telomerase in the cells that need it, then it could work.

Centenarians live long becauise they keep their immunity intact, and yes not getting CMV is one reason for sure - it means they have sufficient immunity left. On study showed that,
A woman of 115 years old had leukocytes telomeres in teh 2-3 kb region...the fact that she reached all the way down to that, means that her telomeres were 'kept long/telomerase was 'maintaining 'enough lenghtening'' to counter loss and keep the immune system active - to allow to live to a supercentenarian of 115 years old.

'Centenarians and their offspring were able to maintain long telomeres, but telomere length was not a predictor of successful ageing in centenarians and semi-supercentenarians. We conclude that inflammation is an important malleable driver of ageing up to extreme old age in humans.'

In this study what is important is this* :
''Centenarians and their offspring were able to maintain long telomeres,...''

When you accumulate many short uncapped-demethylated-unstable-inflammatory telomeres, it is catastrophic and premature aging happens. Short telomeres in leukocytes will be catastrophic to the immune system because telomerase could not stop the 'dwindling down' to the 2-3kb region; and that is Immuno-Replicative Senescence that will follow (the immune system will be dysfunctional, harmful bacterial load will increase (infection, microbial diseases, virus - CMV...) and cancers will proliferate (no immune system = cancer; cancer = epigenetic premature aging and accelerated telomere shortening (by just enough ROS inflammation to surrounding cells, thanks to suractivation (in compensation) of Tumor Suppressor P53, P21 and P16 oncogenes...) until a 2kb frozen or ALT 'sweet spot' for cancer cells viability))).

One more thing that centenarians is higher HDL and better composition of it(HDL has more antioxidative capability in vessels, and LDL (it seems) needs more TAC FRAP ORAC because LDL oxidative lag is equal to what happens in atherosclerosis. The senescent macrophages and LDL filled atherosclerotic lesions create an uneding ROS fest that creates necrotic lesions of arteries. AT a certain point blood TAC can't quench this anymore (dried out), that's when lesions appear. HDL and certain APOlipoportein variant in humans is capable of better quenching this; and does not end up in a vicious circle of macrophage trying to clear the LDL pockets.
One study demonstrated that the longest lived people have the highest HDL and the lowest LDL, in a very specific ration, along with a better foam cell composition.

And naother thing, is they keep their redox and ATP levels (their mitos become hyperfused to maintain ATP (avoid cell senescence by energy depletion), and they maintenance of antioxidative powers (that falls in the TAC)), such as activation of NRF2/ARE/EpRE (nuclear respone factor 2"antioxidant response element/electrophile response element), this in turns increases NAD+ levels; and this increases the redox power (the 'reduced' power (quenched)), but keeping the cell in a lower mV (GSH/GST/GSPx/y-glumatate cysteine ligase/TRX/PRX/...).

IN sum, they maintain many things longer and often have a 'foot ahead' in terms of youth (they were born with longer chuncks of telomeres; all this contributes to keep healthy for longer and staving off the damage/diseases the longest possible)

Just a 2 cents.

Inflammation, But Not Telomere Length, Predicts Successful Ageing at Extreme Old Age: A Longitudinal Study of Semi-supercentenarians

1.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4634197/

Posted by: CANanonymity at October 30th, 2017 8:33 PM

CANanonymity, Thanks for your excellent comments above on the main causes of aging and mortality among Centenarians, and the important Japanese Study on Centenarian longevity. After reviewing your comments, I came up with another major reason why Centenarians live so long, they stay physically active often well beyond 100. What that physical activity does, I think, is to maintain BMD (bone mineral density and reduce bone marrow and IMMUNITY loss, as you pointed out. Immunity equals MLSP (maximum life span potential. Now the main gene that determines human physical activity is DRD4 with the longevity SNP being rs1800955 CC alleles. In 2013, Grady published a paper on the longevity aspects of this gene in mice and humans, and found that among the oldest humans with the CC alleles or CT alleles, lived 66% longer than younger controls. Those homozygous for TT lived about 8-9% less long than normal. This is an amazing finding in my opinion in why Centenarians live so long. Of course, muscle longevity is very important as well, as the muscles move the bones. The gene UPC3 rs180949 AA is very protective of muscle wasting and in maintaining good hand grip strength in the very elderly. I am homozygous for the longevity alleles of both of these genes, which should help me in my goal of living to 120.

Posted by: Biotechy at November 1st, 2017 8:36 AM

Error correction for my above comment, 66% of the oldest cohort had the CC or CT longevity alleles, rather than lived 66% longer.

Posted by: Biotechy at November 1st, 2017 11:45 AM

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