266 replies to this topic

[Bryan_S]

I would think that as the yamanaka factors, or 4F, were discovered by looking at the chemical forces at play in the environment of reproductive cells such as embryos, that this would not be a problem. Whatever epigenetics you inherited would very likely be spared. There might be some small exceptions as a whole organism is much more complicated compared to an embryo, but I imagine that even if disrupted, whatever it was that lead to to those changes would restore them. Homeostasis being what it is, is this time, to our benefit.

 

YOLF, I think you might be right about inherited DNA methylation patterns being spared as can be seen from my last post. So far not much has been published to support this idea but I found a study supporting your statement.

 

As you point out the Yamanaka factors were born from reproductive studies but taking this approach with an adult organism has its risks. Studies like; "Repression of the Heat Shock Response Is a Programmed Event at the Onset of Reproduction" suggest once maturity is reached an over-arching epigenetic regulator is switched off, causing what we see as aging. A simple idea for a large cascade of epigenetic changes.

 

So as we look to what might be "lost" in the In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming process it "appears" some of our fears might be asswaged by this study as the original DNAm pattern survives in an immature version of the adult counterpart. This seems to be the only study to ask these questions.

 

"5. Impact of Reprogramming-Associated Alterations in the Study of Age-Related Diseases

 

The application of the analysis of DNAm pattern in iPSCs and their derivatives indicate that while reprogramming is associated with a reversion of DNAm patterns to embryonic-like state, the differentiation process does not lead to a full re-establishment of the cellular specific DNAm-profile. These results fit with what emerges from recent reports, indicating that tissues differentiated from iPSCs do not present the same physiological and functional features of the target cells rather than they are more similar to an immature version of their adult counterpart (Figure 2) [70,71]."

 

As always JMHO

Bryan

 

To the Group,

As I filter my search for studies trying to identify key epigenetic regulators I'm continuously struck with research on Extracellular Vesicles. Not long ago Extracellular Vesicles (EV's) were once thought to be just cellular debris, "junk," but no longer. It appears thru EV's certain epigenetic promotors are down-regulated and other pro-inflammatory regulators are up-regulated over time. In study after study, these epigenetic indicators can be tied to changes in the amount and kinds of Extracellular Vesicles released by cells. Coding efforts of these EV's specifically translates to up and down regulators of genes.

 

We would all like to see a master regulator (one target) at work and keep it simple. I'd like to believe it could be this easy, but the evidence is suggesting a large interrelated web of epigenetic feedback loops. So where to focus, which key genes need to stay active to save off cellular decline? I think this research is well underway by tracking Extracellular Vesicles and the cargo they carry. See: Aging affects extracellular RNA and extracellular vesicles. This is a 42-minute video showing ongoing NIH data collection on EV's and DNAm patterns.

 

"Nicole Noren Hooten from the National Institute on Aging at NIH contributes basic science research to the Healthy Aging in Neighborhoods of Diversity across the Life Span (HANDLS) project, a long-term study of health disparities and aging in Baltimore, MD.

 

Aging is the major risk factor for most chronic diseases. Dr. Noren Hooten discusses here how non-coding RNAs and extracellular vesicles (EVs) in the blood change with age, and future prospects for how knowledge about exRNA and EVs will impact our understanding of aging and its contribution to disease.

 

This web seminar was presented as part of the Extracellular RNA Communication Consortium (ERCC) seminar series on September 7th, 2017."

 

We've spoken about epigenetic targets, and in reality, we are searching for one or more needles in a haystack. Along this path, amazing insights are being drawn about disease states and changes in the EV's being delivered to the affected tissues. We've discussed vectors in general and EV's have been the conserved method our bodies developed to reach the most inaccessible places. Here is one such example; Extracellular vesicles: mediators and biomarkers of pathology along CNS barriers.

 

 

So in this effort, cell to cell communications thru EV's plays an important indicator as to whats going on. I think following the bouncing ball by profiling aging individuals thru time will lead to a manageable number of key genes that "need" to stay active but are later down regulated. To this, I believe custom Extracellular RNA's can be written to stroke and keep them active as aging treatments, key epigenetic regulators that will save off the changes to the genes that later become active with aging.

 

#1 So as we look for a practical way to roll back the clock, #2 and since we don't have an OSKM polycistronic expression cassette installed in each cell of our bodies, we need vast numbers of researchers to uncover the mechanisms of disease and from this the upstream promotors of those states. This is pointing us deeper into the epigenome and Extracellular Vesicles as the vehicle of change and how we might encourage DNA methylation stability of key targets.

 

I hope I'm keeping the concepts global with ubiquitous examples. As you look at the success of the "In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming" project, it looks simple enough but, I don't think a single one of us would take this precise path. Also for me, I don't want to have to make permanent changes to my DNA through CRISPR or a retrovirus. Nature already gives us many conserved delivery paths to take and EV's are already there filling that role. So I hope that we will learn how to "play the instrument," rather than re-engineer the machine by blunt force.

 

As always JMHO

 

Bryan

Edited by Bryan_S, 31 July 2018 - 06:45 PM.

[YOLF]

Good post Bryan! I'm wondering how the remodelling of extracellular vesicles or disruption of maintenance mechanisms, if that is the case, with Yamanaka factors (4F), might affect ECM remodelling. We might just discover an ECM remodelling response through this research. 

 

Alpha hydroxy acids are known to remodel ECMs, I'm wondering how those might interact with extracellular vesicles. Klotho, FGF, and tocotrienols could be advantageous towards what you're looking at, even if it just comes down to learning a few new words as klotho seems to upregulate cellular turnover which in my mind is the rolling over of cells across the scaffolding as the pressure of stem proliferation acts upon cells in their periphery eventually pushing so far as to 'squish' potentially malignant cells. Therefore, more FGF, in my estimation will generally decrease overall cancer risk rather than increase it and this very likely the reason why there are mixed results in FGF research. Even if I'm wrong about total rollover of cells on the ECM, the 'squishing' part will always be changing the extracellular interface of cells, and as donor organs from older donors are restored to healthier states, I would expect that extracellular vesicles are largely plastic and turnover of them is key to having healthy vesicles. So I'm thinking there's less cause for worry.

 

Further, older people will have more marginally pathogenic cells which could be 'squished' into further dysfunction. So old people will need to match their FGF dosing until cancer risk markers show a consistent pattern of decline. This is part of 'passive immunity' or perhaps some similar term.

[Bryan_S]

Good post Bryan! I'm wondering how the remodelling of extracellular vesicles or disruption of maintenance mechanisms, if that is the case, with Yamanaka factors (4F), might affect ECM remodelling. We might just discover an ECM remodelling response through this research. 

 

That's fair, The Extracellular matrix (ECM) I believe fits into the equation and is related to the previously posted Laterally confined growth of cells induces nuclear reprogramming in the absence of exogenous biochemical factors. I believe the physical framework a cell is attached offers remodeling and cell signaling potential. So it would be interesting to see a cell reverted back to a Pluripotent state and placed into an ECM environment devoid of other cells avoiding EV influence.

 

On that note, I'm actively looking for research similar to the Laterally confined growth of cells induces nuclear reprogramming in the absence of exogenous biochemical factors as a non-chemically induced means of producing the Pluripotent state. I'm wondering if cells in this state might be a means to produce EV's in mass, and what effect this might have on adult differentiated and undifferentiated cells. Hopefully this would reduce the risks of cancer and tumor growth displayed by the Yamanaka factors. This has already begun to be explored. https://biomedres.us...S.ID.000888.pdf

 

 

Alpha hydroxy acids are known to remodel ECMs, I'm wondering how those might interact with extracellular vesicles.

 

I've read several componds have been researched.

 

Chemical compound-based direct reprogramming for future clinical applications

 

"In addition, the effects of several new compounds such as AM580, EPZ004777, SGC0946, and 5-Aza-dC on the chemical reprogramming were investigated. The retinoic acid receptor agonist and epigenetic modulators in combination with VC6TF increased the efficiency up to 1000-fold greater than that described in their previous reports. Not only MEFs but also neonatal dermal fibroblasts and adult lung fibroblasts were chemically reprogrammed, suggesting a broad availability of the chemical cocktail for the reprogramming. Further studies are required to reveal in more detail the molecular mechanism by which each chemical compound facilitates the chemical reprogramming through regulation of targetted signaling pathways and epigenetic modifications."

 

There is a lot going on.

 

JMHO

 

Bryan 

 

 

[YOLF]

Perhaps you'll find just that with bioprinted organs research? Whole beating hearts have been grown for mice on ECMs that were chemically washed. They've printed whole kidneys and livers using this technology too, but the organs aren't always perfect. Still, there are ways of making cells more permeable which I image if cycled could lead to improvement. I'm wondering how well a bioprinted kidney would fair after being transplanted in the long term. Perhaps in patients who only have one.

 

Here's some good news on the research you're looking for:

https://molecularneu...3024-016-0108-1

 

This sounds like a clue:

 

 

Although distinct biogenesis pathways lead to different types of extracellular vesicles, EVs could be grouped in three main classes: exosomes, microvesicles and apoptotic bodies (Table 1) (Akers et al., 2013, EL Andaloussi et al., 2013, Katsuda et al., 2013).

https://www.scienced...014299916304277

 

Here's another one:

 

 

By using this system, we provided original evidence demonstrating that (i) the endosome can serve as a nucleation site for the formation of signaling complexes, (ii) endosomal EGFR signaling is sufficient to activate the major signaling pathways leading to cell proliferation and survival,

https://www.ncbi.nlm...pubmed/12242303

 

Perhaps things that promote the survival of proliferating cells such as pomegranate extracts could offer some leads? 

[Bryan_S]

Here's some good news on the research you're looking for:

https://molecularneu...3024-016-0108-1

 

This sounds like a clue:

https://www.scienced...014299916304277

 

Here's another one:

https://www.ncbi.nlm...pubmed/12242303

 

Perhaps things that promote the survival of proliferating cells such as pomegranate extracts could offer some leads? 

 

 

Thank's YOLF for the info on PRotein Organic Solvent PRecipitation (PROSPR). "PROSPR encompasses a rapid three-step protocol to remove soluble proteins from plasma via precipitation in cold acetone, leaving the lipid-encapsulated EVs behind in suspension. This generates higher purity EVs that can then be obtained from filtration or classical ultracentrifugation methods."

 

 

For the group; Rejuvenation by Partial Reprogramming of the Epigenome

Andrew R. Mendelsohn, James W. Larrick, and Jennifer L. Lei

 

Published Online:1 Apr 2017 https://doi.org/10.1089/rej.2017.1958

 

Has anyone else read this 11-page review? I did a search and could not find this paper mentioned on longecity. What I find interesting is one passage; "To answer these questions requires first answering the question: did transient induction of OSKM actually repair the epigenome? In one sense, yes, clearly DNA gammaH2AX damage- associated loci were reduced, as were the number of senescent cells, and H3K9me3 and H4K20me3 levels were normalized, as was nuclear staining of lamin A/C and morphology in cells from LAKI mice. However, in another sense, the results are disappointing, as the epigenetic effects were transient, they did not endure – a “reset” of the epigenome did not occur, since a new two-day induction of OSKM was necessary every 7 days to maintain the partially normalized phenotypes. If the ultimate goal of an epigenetic repair strategy is to actually repair and/or reset the epigenome of differentiated cells, it is possible that even induction of powerful sets of reprogramming factors for short amounts of time is insufficient and that other approaches will need to be developed."

 

 

So if this review is to be taken without question a "reset" of the epigenome did not take place in the In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming study and regular maintenance regiment was necessary.

 

I don't expect to find encouraging news with every paper, but this underlines the need for confirmation and alternate procedures to accomplish a "reset." As I suggested before in the Age-Related Epigenetic Derangement upon Reprogramming and Differentiation of Cells from the Elderly, it "appears" the original DNAm pattern survives in an immature version of the adult counterpart. If the missed Rejuvenation by Partial Reprogramming of the Epigenome review is correct, the "reset" might not be permanent, reverting to its original state.

 

 

Reading way too much, as always JMHO

 

Bryan

Edited by Bryan_S, 01 August 2018 - 07:21 PM.

[albedo]

...

 

What I find interesting as I move beyond that paper is this recently published study, Age-Related Epigenetic Derangement upon Reprogramming and Differentiation of Cells from the Elderly. They determined methylation aberrations between reprogrammed cells and hESCs and classified them into two main categories: de novo and inherited or memory (Figure 1). The former refers to DNA regions whose methylation levels are significantly different in iPSCs from both parental somatic cell line and hESCs and are specific for each newly-established-iPSC line

 

...

 

Thank you. I found it interesting too and helped to better clarify to my mind the uncoupling of the two dynamics of differentiation and epigenetic rejuvenation as expressed here. I liked in particular the modeling in Fig 2. The paper is from Claudio Franceschi's team, one of my heroes: inflammaging theory, centenarian characterization, centenarian microbiota changes etc... e.g. as posted on LC in the microbiome thread. Challenging to study as the centenarians population can be, this group is an incredibly useful model to study aging.

[albedo]

Bumping a bit for lack of lack of comments. I just finished reading an outstanding review article and might post later on when digested.

 

Here it is (on ResearchGate), outstanding! Check in particular, for the relevance in this thread, the section "Epigenetic clock in development and ageing". Even if I promised myself not to dig too much in the muddle of theories, I found also interesting their hinting to an "antagonist pleiotropy" effect we briefly touched earlier in this thread which also might lead to a satisfying convergence of the wear/tear and the programmed theories also touched earlier.

 

"...Although positive epigenetic age acceleration has been linked to a myriad of age-related conditions later in life (Table 1), it might be beneficial early in life, as
indicated by the following results: gestational week correlates with DNAm age..."

 

"...Wear-and-tear theories of ageing seem to be inconsistent with epigenetic ageing effects early in life but are consistent with epigenetic ageing effects later in life..."

 

Horvath S, Raj K. DNA methylation-based biomarkers and the epigenetic clock theory of ageing. Nat Rev Genet. 2018;19(6):371-384.

 

 

[albedo]

Well, definitely don't stop, some of us are reading diligently.  I'm very impressed with the knowledge and enthusiasm displayed here.

 

Here's something up for discussion, assuming it hasn't already been posted:

https://www.ncbi.nlm...les/PMC5831052/

 

This research shows that the NMR has cells that are resistant to reprogramming.  As we all know by now, the NMR is a negligibly senescent animal.

 

Of course, we are counting on being able to do the reprogramming on our own cells.  But the point is that this is more evidence that epigenetic mechanisms are the glue that holds the entire aging program together.

 

I tend to agree and I guess also in line with the thinking of Hovarth et al as in my last post. I think the paper you post brings an additional piece to the landscape puzzle profoundly linking senescence, cancer and epigenetic stability.

"...Our work provides evidence that epigenomic stability is associated with longevity and cancer resistance in a wild-type organism. The study of a naturally long-lived and cancer-resistant NMR may provide clues to engineering more stable epigenomes to prevent cancer and extend the human lifespan..."

 

[albedo]

...

 

For the group; Rejuvenation by Partial Reprogramming of the Epigenome

Andrew R. Mendelsohn, James W. Larrick, and Jennifer L. Lei

 

Published Online:1 Apr 2017 https://doi.org/10.1089/rej.2017.1958

 

Has anyone else read this 11-page review? I did a search and could not find this paper mentioned on longecity. What I find interesting is one passage; "To answer these questions requires first answering the question: did transient induction of OSKM actually repair the epigenome? In one sense, yes, clearly DNA gammaH2AX damage- associated loci were reduced, as were the number of senescent cells, and H3K9me3 and H4K20me3 levels were normalized, as was nuclear staining of lamin A/C and morphology in cells from LAKI mice. However, in another sense, the results are disappointing, as the epigenetic effects were transient, they did not endure – a “reset” of the epigenome did not occur, since a new two-day induction of OSKM was necessary every 7 days to maintain the partially normalized phenotypes. If the ultimate goal of an epigenetic repair strategy is to actually repair and/or reset the epigenome of differentiated cells, it is possible that even induction of powerful sets of reprogramming factors for short amounts of time is insufficient and that other approaches will need to be developed."

 

 

So if this review is to be taken without question a "reset" of the epigenome did not take place in the In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming study and regular maintenance regiment was necessary.

 

I don't expect to find encouraging news with every paper, but this underlines the need for confirmation and alternate procedures to accomplish a "reset." As I suggested before in the Age-Related Epigenetic Derangement upon Reprogramming and Differentiation of Cells from the Elderly, it "appears" the original DNAm pattern survives in an immature version of the adult counterpart. If the missed Rejuvenation by Partial Reprogramming of the Epigenome review is correct, the "reset" might not be permanent, reverting to its original state.

...

 

Another great finding Bryan! I did not go to the full (paywalled) paper yet (also never seen on LC on my side) and just reply on what you report, so I might be missing completely the point!

 

The quote of p. 11 you report reminds me a point the wear/tear objectors to programmed theory tenets often make, i.e. wear/tear never stops, there is no fundamental reset.

 

E.g. they say: "... I recently had the chance to chat with Yuri Deigin of Youthereum Genetics, and to ask some questions about his aims. As you can tell he is proceeding from a programmed aging point of view - something that I tend to present as standing in diametric opposition to the more mainstream view of aging as accumulated damage. Possibly oversimplifying, this is the question of whether in aging epigenetic change (a program) causes damage, or whether damage causes epigenetic change (a reaction). A programmed aging point of view leads one to intervene in processes that are, to the accumulated damage point of view, secondary consequences only, and attacking secondary consequences just won't be very effective. We are close to the years in which one side or the other will be definitively proven correct, due to the implementation of specific approaches to the treatment of aging as a medical condition.  Nothing is completely black and white, however, and it is interesting to see the development of areas where theorists from either side of this divide will meet in the middle at approaches to therapies that both will consider potentially useful enough to try, but for different reasons. Some classes of stem cell therapies and efforts to achieve similar effects through changes in signaling or reprogramming cells in situ rather than through delivery of cells are a good example of the type. From a programmed aging point of view, these are levers with which to change epigenetic signaling to more youthful levels, while from an accumulated damage point of view, they could be essentially compensatory in nature, like stem cell therapies, but picking the slack to some degree for native regenerative processes that are hampered by damage...." (bold mine)

https://www.fightagi...otency-factors/

 

"...For my part, I think that the best argument against programmed aging is that there are forms of metabolic waste that the body cannot effectively break down. Components of lipofuscin and glucosepane cross-links for example. You can change all the epigenetics you want, assuming a way can be found to force cells into a replica of their youthful state, but that won't enable them to clear out that harmful waste..."

https://www.fightagi...arch-community/

 

I am not sure but this objection seems not really standing up: (i) first we also have some evidence all the hallmarks of aging are regressed and (ii) even the SENS approach requires, to my understanding, regular interventions (sort of similarly to the time scheduled partial reprogramming in this thread), what I think they call LEV=longevity escape velocity, driven by the exponentially accelerated technology evolution.

[albedo]

Reading on mTOR1 inhibition by rapalogs, such as rapamycin, I pop into these two interesting studies by the team of Mannick et al at Novartis, one (1) which emphasizes the beneficial role in improving immune function in the elderly humans, decreasing infection rate, which is an increasing concern, and the other one (2) demonstrating the beneficial role in rats kidney function hopefully translatable to humans.

 

Kidneys function decrease is an interest of mine as one of the markers of aging (e.g. decrease in eGRF). Moreover, kidneys lacks the powerful regenerative power of organs such as liver so it was not a surprise to me reading in (2) the benefit was much more pronounced in kidney rather than liver (or skeletal muscle).

 

The link to the subject of this thread is that in (2) they indicate c-Myc (the “M” of OSKM) inhibition as a part of the mechanism by which mTORC1 is inhibited.

The central role of c-Myc in aging is clearly pointed out:

 

“…In the kidney, c-Myc mRNA itself was upregulated with age, and counter-regulated by 6-week treatment with the rapalog, as were genes that fall under the Myc-regulated pathway. This was of particular interest for a couple of reasons: first, it was recently shown that Myc haplo-insufficient mice had prolonged lifespans, and demonstrated a downregulation of several pathways, including mTORC1 signaling (17). A distinct study very recently demonstrated that transient upregulation of the Yamanaka factors, the four genes which are required to epigentically reprogram cells to their dedifferentiated form, inducing the formation of induced-pluripotent cells, could significantly increase life span (28). One of those genes is c-Myc (28). The combination of these studies and our current work point to a key role Myc may be playing in regulating the epigenetic changes associated with aging, and the potential therapeutic value of inhibiting those Myc-induced changes to treat age-related diseases, also highlighting mTORC1 inhibition as a strategy to intervene when Myc or Myc-induced genes are elevated. Of course, it is also of interest to note that part of the mechanism by which mTORC1 inhibition perturbs aging might be its ability to inhibit Myc, and this is a mechanism not previously implicated for rapalogs…” (bold mine)

 

(1) Mannick JB, Morris M, Hockey HP, et al. TORC1 inhibition enhances immune function and reduces infections in the elderly. Sci Transl Med. 2018;10(449)

 

(2) Shavlakadze T, Zhu J, Wang S, et al. Short-term Low-Dose mTORC1 Inhibition in Aged Rats Counter-Regulates Age-Related Gene Changes and Blocks Age-Related Kidney Pathology. J Gerontol A Biol Sci Med Sci. 2018;73(7):845-852.

[albedo]

Information on the recent crowdfunding campain launched by Youthereum Genetics and shared here with permission of Dr. Yuri Deigin:

 

"A few days ago we have launched a crowdfunding campaign for $15,000 dedicated to a proof-of-concept experiment designed to establish whether just one of the Yamanaka factors, Oct4, can be sufficient to lower epigenetic age while preserving cellular differentiation.

 

As you might know, the 4 Yamanaka factors (OSKM, where O stands for Oct4) were originally developed to force cells to lose their differentiation and become pluripotent. This is something we actually want to avoid if we want to be able to use partial reprogramming safely in vivo. That's why we have reason to believe that Oct4 just might be optimal for our purposes.

Please see the Experiments page on our website for more details, as well as our scientific whitepaper that can be found under the Science section of our site.

http://youthereum.io/experiments

And if you are able to help out with our crowdfunding, any donation (or just spreading the word) would be most appreciated!

Here are ways to donate:
 

BTC: 1JKgqMpHfo7iA2DwJo787U2GRuRkkzp8Vg
ETH: 0x56e0e27b16Ba5Bf2d64D9f1DD27b0023231F275F 
Paypal: ydeigin@gmail.com
Sberbank: 5469380067411503
Yandex.Money: 410014484258634 
WebMoney: Z377288589569 R616204925788
 

PS: In the few short days since the launch of our campaign we have raised almost $12,500.00 from 58 donations. The finish line is very close! If you are able to contribute even $1, we would greatly appreciate it, as the number of donations is in itself a very important indicator of whether what we are doing is received positively by all those who support the fight against aging.  

Eternally yours, 
Youthereum Genetics"

 

 

[albedo]

Maybe known already to most of you but if not I found interesting this general talk by Dr David Sinclair. He makes a quite clear case on:

 

1. epigenetic vs wear/tear hypothesis advantages
2. away from the mutation accumulation, mainly physicist lead theory of aging, to epigenetic (good news as epigenetics is reversible)
3. one leading cause of aging: the disturbed balance between (epigenetic) regulations of gene expression (e.g. by proteins such as sirtuins) focusing  on reproduction vs. the same proteins/mechanism being called by “genetic emergencies” (such as DNA breaks, occurring all the time, e.g. due to ionizing radiation) hence focusing on repair
4. item 3 proven (published) in yeast when being at MIT, with all hallmarks of agig (8-9) being reversed
5. gave some details of NMN restoring capillary density and blood flow in aging mice (see also the thread at LC, here)
6. gave some details on epigenetics (~33:30), epigenetic landscape (~36:00), NMN (~45:25), NMN/NR (~58:10)
7. on OSKM on ~57:05

at:

 

Incidentally: he is taking in the morning with his father: 1000mg Resveratrol, 800mg Metformin, 500-750mg NMN

 

(edit: adding point 5)

 

Edited by albedo, 09 August 2018 - 04:06 PM.

[albedo]

I have checked through the thread and could not find this nice review by Belmonte's team:

 

Beyret E, Martinez redondo P, Platero luengo A, Izpisua belmonte JC. Elixir of Life: Thwarting Aging With Regenerative Reprogramming. Circ Res. 2018;122(1):128-141.

 

I liked the complementarity of the two approaches to rejuvenation bringing huge therapeutic potential: the trans-differentiation (repopulating cells) and the transient Yamanaka factors induction (resetting the hallmarks of aging):

 

 transdifferentiation & reprogramming.PNG   386.21KB   0 downloads

 

There is a comment toward the end also on the approaches to safely delivering the factors to which we might possibly add the EV (Extracellular Vesicles) as brought by Bryan into this thread:

 

"...The technical barrier of delivering the inductive factors will eventually be overcome with the advancements in the fields of gene therapy^181,182 and nanoengineering.¹⁸³..."

 

References are given also on how to boost or replace the Yamanaka factors even by chemicals (only in-vitro by now), shifting the focus from invasive treatment to self healing:

 

"...The next few years are bound to see the effect of 4F on the life span of wild-type models and on the injury settings that involve regeneration mechanisms mediated by stem cells or cell fate conversions. Given the recent progress in identifying chemicals that can boost195 or even replace196,197 4F in vitro, we envisage that findings related to 4F will also eventually lead to safe chemical-based therapeutic strategies in regenerative medicine that will shift the focus from invasive replacement therapies to regeneration-oriented self-healing..."

[albedo]

Wondering how much of rejuvenation and regeneration has or can be tested e.g. using mDNA, on organoids as already touched in this thread:

 

Tiny Organs Made From Stem Cells Are Accelerating Biology Research. Here’s How Organoids Work.

https://endpoints.el...rk-e6b1920560a4

 

[albedo]

Here the focus is on brain aging reversal:

 

"...Considering the ever-accelerating rate of cell reprogramming research, there is a clear promise that in the not-too-distant future reprogramming-based medical technologies will be developed not only to treat so far incurable age-related brain diseases like AD and PD but also to reverse the functional declines (like memory impairment) that occur in the human brain during normal aging..."

 

"...The excellent cell survival, function and scalability demonstrated by transplantation into parkinsonian monkeys, reveal a significant potential for implementation of cell therapies in PD patients..."

 

"...In an interesting study, human APP transgenic mice, which display progressive amyloid β deposition and at 8 weeks of age show significant deficits in spatial memory, were bilaterally transplanted in the hippocampus with neuronal precursors of cholinergic neuron phenotype that were derived from human iPSCs. After receiving the cell implants, the transgenic APP mice displayed a significant improvement in spatial memory performance as compared with untreated counterparts..." (APP=amyloid precursor protein )

 

López-león M, Outeiro TF, Goya RG. Cell reprogramming: Therapeutic potential and the promise of rejuvenation for the aging brain. Ageing Res Rev. 2017;40:168-181.

 

 

 

 

[Bryan_S]

Here the focus is on brain aging reversal:

 

"...Considering the ever-accelerating rate of cell reprogramming research, there is a clear promise that in the not-too-distant future reprogramming-based medical technologies will be developed not only to treat so far incurable age-related brain diseases like AD and PD but also to reverse the functional declines (like memory impairment) that occur in the human brain during normal aging..."

 

"...The excellent cell survival, function and scalability demonstrated by transplantation into parkinsonian monkeys, reveal a significant potential for implementation of cell therapies in PD patients..."

 

"...In an interesting study, human APP transgenic mice, which display progressive amyloid β deposition and at 8 weeks of age show significant deficits in spatial memory, were bilaterally transplanted in the hippocampus with neuronal precursors of cholinergic neuron phenotype that were derived from human iPSCs. After receiving the cell implants, the transgenic APP mice displayed a significant improvement in spatial memory performance as compared with untreated counterparts..." (APP=amyloid precursor protein )

 

López-león M, Outeiro TF, Goya RG. Cell reprogramming: Therapeutic potential and the promise of rejuvenation for the aging brain. Ageing Res Rev. 2017;40:168-181.

 

 

Here is a publication from 2017, the topic of exosomal microRNAs (miRNAs) Extracellular vesicles EV's is again mentioned.

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

 

https://www.scienced...70726132107.htm

[albedo]

Here is a publication from 2017, the topic of exosomal microRNAs (miRNAs) Extracellular vesicles EV's is again mentioned.

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

 

https://www.scienced...70726132107.htm

 

It is good you rediscovered this Bryan. I did see this study previously searching for something which can be thought as a master regulation of aging.

 

It might be too simplistic to think about about something mastering aging globally, such as here the hypothalamus activity, but even if the idea is wrong it will surely bring to new insight. Next to EV's notice also how Sox2 takes here a key role. Of the OSKM factors and in other situations, Oct4 seems to take the principal role and that looks one of the reasons Youthereum seems concentrating on it in the first phase of their tests. It might be also simpler, more controllable and safer.

 

The fascinating idea is that considering the vastly debilitating brain diseases related to aging such as AD and PD and the relation to aging overall possibly by a regulation in cascade of many other sub-processes, looking at the brain rejuvenation by stem cells regenerative medicine might turn to be a very fruitful path.

 

To All:

I might lack time to look at this thread in the coming couple of weeks (but will do so if I can). Please keep up the good work. Something I would like to research is on more endogenous driven reprogramming, EV's/miRNAs, facilitating chemicals and metabolism.

[albedo]

... Something I would like to research is on more endogenous driven reprogramming, EV's/miRNAs, facilitating chemicals and metabolism.

 

My apologizes to quote myself but looking at the chemical cocktails able, for some, to facilitate and even replace genetic manipulations, the following looks a good and recent (2018) review, focusing on direct-reprogramming (meaning chemically-induced) of various cells types (e.g. neurons):

 

Takeda Y, Harada Y, Yoshikawa T, Dai P. Chemical compound-based direct reprogramming for future clinical applications. Biosci Rep. 2018;38(3)

 

"...It has been reported that the reprogramming into iPS cells by forced expression of Yamanaka’s factors erases most of the age-associated cellular and epigenetic marks [36]. To study a relation between ageing and neurological disorders, neuronal cells differentiated from iPS cell lines might not be appropriate as a disease model. The advantage of direct reprogramming is bypassing a pluripotent state, so the induced neuronal cells might conserve the same ageing conditions as source cells..."

 

A previous (2016) paper from Belmonte's team also refers to the chemically induced reprogramming strategy:

 

"...Remarkably, Hongkui Deng’s group showed in a series of papers that a core set of small molecules (i.e., valproic acid, CHIR99021, E-616542, tranylcypromine, forskolin and DZNep) are sufficient to reprogram multiple cell types of all three germ layers to pluripotency, thus circumventing the need for genetic manipulation47,48..."

Li M, Izpisua belmonte JC. Looking to the future following 10 years of induced pluripotent stem cell technologies. Nat Protoc. 2016;11(9):1579-85.

[Harkijn]

I have nothing of substance to add to this learned thread and am just trying to follow it, but I understand more of the subject matter after scrutinizing Vincent Guliano's latest post:

http://www.anti-agin...n-and-the-sasp/

[albedo]

I have nothing of substance to add to this learned thread and am just trying to follow it, but I understand more of the subject matter after scrutinizing Vincent Guliano's latest post:

http://www.anti-agin...n-and-the-sasp/

 

Good read Harkijn. Thank you for sharing. Vince Giuliano approaches 90 and is very knowledgeable.

 

Quoting from his blog entry and references therein on sentences that catch my attention.

 

“…In this context, transient and/or partial reprogramming of adult somatic cells towards pluripotency can be a promising tool for neuroregeneration. Temporary and controlled in vivo overexpression of Yamanaka reprogramming factors (Oct3/4, Sox2, Klf4, and c-Myc (OSKM)) has been proven feasible …”

 

Notice Oct4 alone has been proposed to be tested first and potentially safer (e.g. here and here). Sox2 also takes the leading role in other situations (e.g. see here).  Also, next to possibly using only Oct4 or Sox2, others tend to avoid c-Myc (oncogenic?):

 

“…Swapping to AAV8 permitted to efficiently reprogram somatic cells in adult mice by intravenous vector delivery, evidenced by hepatic or extra-hepatic teratomas and iPSC in the blood. Notably, we accomplished full in vivo reprogramming without c-Myc…”

 

Tend to agree with the following also in the spirit of what Bryan brought to the thread on self-healing:

 

“…While this publication is about introduction of OSKM into the body to trigger reprogramming, I think the more subtle, natural and interesting approach is that used in the body, such as the local triggering of OSKM by cell senescence and the inflammatory cytokine IL-6 …”

 

“…Reparative reprogramming therapeutics: enhancing the body’s self-cell therapy for resistance to damage and disease. A cellular reprogramming-centered view of epigenetic plasticity as a fundamental dimension of a tissue’s capacity to undergo successful repair may provide new therapeutic approaches for aging and cancer. (1) Epigenetic modifiers: small molecules capable of mimicking the transient amelioration of tissue functions occurring upon short-term induction of OSKM-induced nuclear reprogramming (Mahmoudi and Brunet, 2016; Ocampo et al., 2016) might increase epigenetic plasticity and to enhance regeneration in aging tissues; (2) anti-inflammatory drugs: NFκB-targeting drugs and commonly employed NSAIDs might help reduce some aging- and cancer-promoting inflammatory feedback loops to reestablish the functioning of reparative reprogramming; (3) IL-6-targeting and senolytic agents: IL-6 blockade and senescent cell ablation might help unlock the chronic epigenetic plasticity of SASP-damaged tissues to successfully achieve tissue rejuvenation if accompanied by reparative differentiation phenomena…”

 

Again, as follow on Bryan's EV (extracellular vesicles, sort of natural nanotech devices ensuring intercellular communication) particular focus:

 

“…That is some have to be injured or senescent or dying and releasing noxious cytokines in order for other cells in the neighborhood to be undergoing epigenetic regression and regeneration using the OSKM factors. Paracrine (in the neighborhood) Intercellular communication is required for this to take place…”

 

Interesting perspective on IL-6, inflammasome, SASP (senescence-associated secretory phenotype) and SAIS (Senescence-associated inflammatory signalling):

 

“…We have recently reported that cellular senescence, through the paracrine release of interleukin-6 (IL6) and other soluble factors, strongly favors cellular reprogramming by Oct4, Sox2, Klf4, and c-Myc (OSKM) in nonsenescent cells. Indeed, activation of OSKM in mouse tissues triggers senescence in some cells and reprogramming in other cells, both processes occurring concomitantly and in close proximity…”

 

“…Senescence-associated inflammatory signaling (SAIS)-regulated in vivo reprogramming: a threshold model of epigenetic plasticity in aging and cancer. The degree of senescence/inflammation deviation from the homeostatic state delineates a thresholding algorithm distinguishing beneficial vs. deleterious effects of in vivo reprogramming…”

 

Wow!!:

 

“…An interesting angle is that it may be possible to treat some cancers by in vivo reprogramming of cancer cells back to their original cell types. What a coup this could be if it worked!  For example, glioblastoma …”

 

[Harkijn]

Yes, and perhaps on a more personal note: he will put up for sale a new supplement related to these findings. So I am very curious.

Also he says he takes NR though he does not say since when and at what dosage. IIRC  he was much more reserved about NR some years ago. (BTW mailing to his website is no use, he is probably too busy reading studies or taking cold showers. So am I actually )

[Phoebus]

Reading on mTOR1 inhibition by rapalogs, such as rapamycin, I pop into these two interesting studies by the team of Mannick et al at Novartis, one (1) which emphasizes the beneficial role in improving immune function in the elderly humans, decreasing infection rate, which is an increasing concern, and the other one (2) demonstrating the beneficial role in rats kidney function hopefully translatable to humans.

.

 

 

 

Anthocyanins ability to inhibit mTOR on par with rapamycin in this study. Especially interesting in light of anthocyanins many other health benefits. Also rapa depresses the immune system which may or may not be of benefits to anti aging goals. 

 

 

 

 

Anthocyanins target AMPK/mTOR and AMPK/Wnt pathways in exerting anti-tumor effects in colon cancer or hepatocarcinoma cells

 

Published Online:1 Apr 2010

AMP-activated kinase, a sensor of cellular energy status, has emerged as a potent target for cancer prevention and/or treatment. Thus, the application of dietary origin AMPK activators could link to an effective strategy of cancer control. We have found that the activation of AMPK with anthocyanin extracted from Meoru exerted growth inhibitory effects through regulation of mTOR or GSK3β/β-catenin pathway in HT-29 colon and Hep3B cells respectively. In both types of cancer cells, the growth signal IGF-1 stimulated mTOR or Wnt pathway components. AMPK appeared to inhibit phosphorylation of mTOR possibly through interacting with one of the subunit, raptor.

 

The effect of anthocyanins on cancer cell survival and AMPK/mTOR pathway was compared with a classical mTOR inhibitor rapamycin, and anthocyanins were found to inhibit growth through mTOR comparable to rapamycin.

 

Moreover, anthocyanins stimulated β-catenin degradation through GSK3β activation, and it seemed to be regulated by AMPK. This work has shown that the cell energy controller AMPK can control two important cell growth regulators mTOR and Wnt, and the modulation of AMPK/mTOR or AMPK/Wnt pathways by phytochemicals such as anthocyanins can further strengthen the use of phytochemicals for cancer control.

https://www.fasebj.o...upplement.lb259

 

anthocyanins also inhibite NF-κB, which is mentioned in this thread as an anti aging strategy 

 

https://www.ncbi.nlm...pubmed/24565673

Edited by Phoebus, 10 September 2018 - 01:04 AM.

[albedo]

....

 

Interesting perspective on IL-6, inflammasome, SASP (senescence-associated secretory phenotype) and SAIS (Senescence-associated inflammatory signalling):

 

“…We have recently reported that cellular senescence, through the paracrine release of interleukin-6 (IL6) and other soluble factors, strongly favors cellular reprogramming by Oct4, Sox2, Klf4, and c-Myc (OSKM) in nonsenescent cells. Indeed, activation of OSKM in mouse tissues triggers senescence in some cells and reprogramming in other cells, both processes occurring concomitantly and in close proximity…”

 

“…Senescence-associated inflammatory signaling (SAIS)-regulated in vivo reprogramming: a threshold model of epigenetic plasticity in aging and cancer. The degree of senescence/inflammation deviation from the homeostatic state delineates a thresholding algorithm distinguishing beneficial vs. deleterious effects of in vivo reprogramming…”

 

....

 

Dissecting the Italian review pointed to by Giuliano (thanks again Harkijn), very interesting question:

 

"...An interesting question about the relationship between aging and reprogramming is posed by a comparison of the Mosteiro et al. [10] and Ocampo et al. [11] studies: Ocampo et al.’s study showed that short cyclic induction (2 days) of reprogramming factors reversed the senescence/aging phenotype, whereas Mosteiro et al.’s study demonstrated that longterm induction (7 days) caused senescence to enhance cellular reprogramming via IL-6 secretion by SASP. These findings might depend on the different properties of individual reprogramming stages and their different relationship with senescence..."

 

Tamanini S, Comi GP, Corti S. In Vivo Transient and Partial Cell Reprogramming to Pluripotency as a Therapeutic Tool for Neurodegenerative Diseases. Mol Neurobiol. 2018;55(8):6850-6862.

 

edit: spelling

 

 

 

 

Edited by albedo, 10 September 2018 - 03:06 PM.

[albedo]

A good example of application of the technology (again from Belmonte's team):

 

In vivo reprogramming of wound-resident cells generates skin epithelial tissue

https://www.nature.c...1586-018-0477-4

"Large cutaneous ulcers are, in severe cases, life threatening^1,2. As the global population ages, non-healing ulcers are becoming increasingly common^1,2. Treatment currently requires the transplantation of pre-existing epithelial components, such as skin grafts, or therapy using cultured cells². Here we develop alternative supplies of epidermal coverage for the treatment of these kinds of wounds. We generated expandable epithelial tissues using in vivo reprogramming of wound-resident mesenchymal cells. Transduction of four transcription factors that specify the skin-cell lineage enabled efficient and rapid de novo epithelialization from the surface of cutaneous ulcers in mice. Our findings may provide a new therapeutic avenue for treating skin wounds and could be extended to other disease situations in which tissue homeostasis and repair are impaired"

 

[HaplogroupW]

Sinclair made a blog post today about rewinding epigentics:

https://www.linkedin...-sinclair-ph-d-

 

 

So then, what do I think about how cellular reprogramming research might change the field of aging science and the future of human health?

 

Ask me in five weeks.

 

 

Edited by HaplogroupW, 19 September 2018 - 01:39 AM.

[OP2040]

Sinclair made a blog post today about rewinding epigentics:

https://www.linkedin...-sinclair-ph-d-

 

That's a fantastic post, I encourage everyone to read it and keep their spirits up.  The great thing about David is he doesn't shy away from being an advocate as well as a great scientist. 

[albedo]

Sinclair made a blog post today about rewinding epigentics:

https://www.linkedin...-sinclair-ph-d-

 

Thank you. In a recent tweet (9/9) Sinclair points to the recent Belmonte's work on in-vivo reprogramming in wound healing I pointed out earlier in this thread and indicates a soon to come publication on results on reprogramming at Harvard on the track of Belmonte's work. I am very curious to read that. I wonder about his possible focus on small molecules and more important to me is knowing more about results of his collaboration with George Church.

[albedo]

My recent participation to a conference session, chaired by Judith Campisi, triggered a bit more investigation between reprogramming and senescence.

 

I was mostly intrigued by a talk by Manuel Serrano whose work was pointed to in my previous post (see the Mosteiro et al reference therein). Provided I got it right, I wondered about the (paracrine) sort of homeostatic interplay between OSKM induced reprogramming and senescence:

• OSKM > reprogramming > “reduced” senescence > “reduced” inflammasome
• “increased” inflammasome > “increased” senescence > OSKM induction > reprogramming

This can be resumed into “small inflammation is good, chronic is bad” as emphasized in the previously mentioned Giuliano’s post pointed to by Harkijn. And chronic inflammation is associated to cancer.

 

Inflammation seems (also mentioned during Campisi’s own talk) having evolved as a response to wound healing and this supports what found in Belmonte’s work pointed to in my previous post.

 

Work by Milanovic, Schmitt et al. found SAS (Senescence Associated Stemness) has been equipping cells as a response to wound healing and its works by epigenetic in-vivo reprogramming but turns to be highly detrimental when the mechanism is hijacked by cancer. SAS occurs in vivo reprogramming and tissue repair. The key role is played by inflammatory IL-6 paracrine release. The 3 quoted papers on this were:

 

Milanovic M, Fan DNY, Belenki D, et al. Senescence-associated reprogramming promotes cancer stemness. Nature. 2018;553(7686):96-100

Mosteiro L, Pantoja C, De martino A, Serrano M. Senescence promotes in vivo reprogramming through p16 and IL-6. Aging Cell. 2018;17(2)

Ritschka B, Storer M, Mas A, et al. The senescence-associated secretory phenotype induces cellular plasticity and tissue regeneration. Genes Dev. 2017;31(2):172-183.

 

All this resounded profoundly to what I recalled since some time from Judith Campisi’s work on the link between senescence/aging and cancer.

 

Now, the completely brand new information to me during Serrano’s talk, though not yet published, is an hypothesis made by a post-doc in his team on the key role of iron in senescence. Intuitively I also linked this to what some of us (me included) are trying to do when measuring ferritin levels as a marker of inflammation and reducing it with potential natural iron chelators (I am using IP6 for that with some success). In summary the hypothesis is:

• Senescence associated pathologies have abnormal level of iron
• Iron triggers senescence and associated pathologies
• Iron chelators might prevent senescence and associated pathologies

The mechanism is mediated by an inflating cascade of iron induced vascular damage in a self-reinforcing loop. The damage goes like:

• iron > senescence > SASP > fibrosis > damaged endothelium > red blood cells leakage > iron > ….

It is just an hypothesis but recouping with other concepts in this Forum and knowing the quality of the Serrano’s team it might possibly turn to be a fruitful path as therapeutic drugs acting as iron chelators are known (e.g. deferiprone).

 

Sorry for the log post ….....

[Fafner55]

“Partial reprogramming induces a steady decline in epigenetic 2 age before loss of somatic identity” (2018) https://www.biorxiv....8/09/03/292680 

Induced pluripotent stem cells (IPSCs), with their unlimited regenerative capacity, carry the promise for tissue replacement to counter age-related decline. However, attempts to realise in vivo iPSC have invariably resulted in the formation of teratomas. Partial reprogramming in prematurely aged mice has shown promising results in alleviating age-related symptoms without teratoma formation. Does partial reprogramming lead to rejuvenation (i.e. "younger" cells), rather than dedifferentiation, which bears the risk of cancer? Here we analyse the dynamics of cellular age during human iPSC reprogramming and find that partial reprogramming leads to a reduction in the epigenetic age of cells. We also find that the loss of somatic gene expression and epigenetic age follow different kinetics, suggesting that they can be uncoupled and there could be a safe window where rejuvenation can be achieved with a minimised risk of cancer.

[albedo]

I just pop into this review which, while a bit old (2012) and coming before the Belmonte's work on the "in vivo amelioration ...", does put all in context. I liked in particular the metaphor of rejuvenation seen through the "lens" of epigenetic reprogramming. I apologize if this is well know to you already but found it useful to log the review also here:

 

Rando TA, Chang HY. Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock. Cell. 2012;148(1-2):46-57.

 

 epigenetic lens.PNG   161.35KB   0 downloads

 

"...Clearly, epigenetic changes are both responsive to and effectors of the aging process. With DNA damage and environmental stresses like inflammation leading to changes in chromatin, the epigenome clearly adapts to age-related changes in the genome and the local milieu. Perhaps the epigenome is a general sensor of cellular dysfunction, sensing metabolic and proteomic changes that accompany aging as well. However, the epigenome is also an effector of the aging process, enforcing different patterns of gene expression in old cells and young cells and, in many cases, resulting in cellular phenotypes associated with aging such as senescence and metaplasia (Martin, 2009). In that sense, the epigenome is rather like a lens through which genomic information is filtered (Figure 3), a lens that deteriorates with age because of both loss of integrity of genomic information and direct environmental stresses within and outside of the cell. Within the “epigenome as lens” metaphor, the process of rejuvenation is the restoration of a youthful state by actions on the epigenomic lens (Figure 3). The loss of integrity of the genomic information remains, but the rejuvenating interventions are sufficient to overcome and possibly reverse at least some of the age-related epigenetic changes..."