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Quantifying Nuclear DNA Mutation Rates in Stem Cells Doesn't Tell Us the Degree to which those Mutations Contribute to Aging

The study noted here provides numbers for the mutation rates in muscle stem cells, the stochastic damage that occurs over time as small numbers of errors slip past the highly efficient molecular machinery of cellular replication and DNA repair. The researchers used single cell genomic sequencing, a very useful and still comparatively new capability. It produces a much more detailed view of the state of nuclear DNA inside a cell population, showing the enormous variations in stochastic mutational damage that takes place over the years. Every cell has thousands of different areas of damage in their DNA, and it is becoming apparent that the damage in stem cell populations is cloned out into tissues. Stem cells maintain tissues by providing a supply of somatic cells, and those somatic cells divide many times before they reach the Hayflick limit. So the mutations present in a stem cell will over time propagate into a fraction of the supported tissue.

Is this important? Mutation in nuclear DNA is certainly a contributing cause of cancer, though it can be argued that the decline of the immune system - responsible for killing cancers before it gets underway - is actually more significant than mutations when it comes to the age-related nature of cancer risk. One can look at the numbers for mutational damage in old cells and it sounds fairly horrific out of context, but everything irelated cells and cellular biochemistry involves huge numbers. We know that nuclear DNA becomes more mutated over time, and we know that many of the methods of slowing aging, such as calorie restriction, produce reduced levels of mutation at a given age in comparison to normally aging individuals. However: at present there is no compelling causal evidence to show that nuclear DNA damage alone has a significant effect over the present human life span in comparison to other contributions to degenerative aging. If anything, the slight tilt in the present indirect evidence is in the opposite direction, towards skepticism for a significant role over the present human life span.

Nonetheless, it is the present consensus that nuclear DNA damage does cause meaningful metabolic dysfunction; a lot of research proceeds upon this assumption. The authors of the open access paper here are quite ready to theorize a connection between stem cell mutation level and age-related declines in muscle mass and strength, but their data only shows a correlation. A great many things happen over the course of aging, and not all are directly connected to one another: aging is a tree, a spreading set of damage and issues stemming from a few root causes. The far branches will appear correlated even if they have little to do with one another.

I'm in the camp of those who would like to see more work directed towards the production of a compelling demonstration to show that nuclear DNA damage either is or is not a major factor in aging beyond cancer risk. The best way to do that is to repair a significant amount of the damaged DNA, but that is exceptionally challenging, beyond present capabilities. It might be possible in the near future to use one of the new forms of genetic technology to tackle the clonal expansions of specific mutations, provided there are only a few of them and they are present in large numbers of cells. Once we start talking about scores or hundreds of mutations, however, then that is just not a near term prospect. So a less direct approach is called for, something clever yet to be assembled, that will be obvious in hindsight to the rest of us.

Stem cell study may result in stronger muscles in old age

It has already been established that natural ageing impairs the function of our skeletal muscles. We also know that the number and the activity of the muscles' stem cells decline with age. However, the reasons for this has not been fully understood. In a new study, researchers have investigated the number of mutations that accumulate in the muscle's stem cells (satellite cells). "What is most surprising is the high number of mutations. We have seen how a healthy 70-year-old has accumulated more than 1,000 mutations in each stem cell in the muscle, and that these mutations are not random but there are certain regions that are better protected."

The researchers have benefited from new methods to complete the study. The study was performed using single stem cells cultivated to provide sufficient DNA for whole genome sequencing. The mutations occur during natural cell division, and the regions that are protected are those that are important for the function or survival of the cells. Nonetheless, the researchers were able to identify that this protection declines with age. "We can demonstrate that this protection diminishes the older you become, indicating an impairment in the cell's capacity to repair their DNA. And this is something we should be able to influence with new drugs."

"We achieved this in the skeletal muscle tissue, which is absolutely unique. We have also found that there is very little overlap of mutations, despite the cells being located close to each other, representing an extremely complex mutational burden." The researchers will now continue their work to investigate whether physical exercise can affect the number of accumulated mutations. Is it true that physical exercise from a young age clears out cells with many mutations, or does it result in the generation of a higher number of such cells?

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Satellite cells (SCs) are a heterogeneous population of stem and progenitor cells that have been demonstrated to play a pivotal role in skeletal muscle (SkM) regeneration. The SCs are normally kept in a quiescent state and activated upon exposure to stimuli, such as exercise or SkM injury. When committed to myogenic differentiation, SCs proliferate further, fuse to existing SkM fibers, and contribute new nuclei to the growing and regenerating fibers. Aged human SkMs show a decline in the number and proliferative potential of the SCs. As a consequence, a dysfunctional SC compartment is envisaged as a major contributor to age-related defects, including reduced capacity to respond to hypertrophic stimuli such as exercise and impaired recovery from muscle disuse and injury.

A well-known factor in the decline of stem cell function is the loss of genome integrity, for example, caused by the appearance of somatic mutations. These modifications of the genome range from single-base changes (single-nucleotide variants) to insertions or deletions of a few bases (indels) to chromosomal rearrangements and occur during the whole life, starting from the first division of the embryo. In contrast to germline variants, somatic variants are not propagated to the whole individual but to a subpopulation of cells in the body, with the final consequence that adult human tissues are a mosaic of genetically different cells. Moreover, somatic mutation burden increases during a lifetime as a result of accumulating errors occurring either during cell division or because of environment-induced DNA damage. At present, nothing is known about somatic mutation burden in human SCs or SkM.

Here, we investigate the genetic changes that occur with aging in the genome of human adult SCs and use the results to elucidate mutational processes and SC replication rate occurring in vivo in adult human muscles. We assess the functional effects of somatic mutations on SC proliferation and differentiation and predict the global consequence on muscle aging and sarcopenia. Our analyses reveal an accumulation of 13 mutations per genome per year that results in a 2-3-fold higher mutation load in active genes and promoters in aged SCs. High mutation burden correlates with defective SC function. Overall, our work points to the accumulation of somatic mutations as an intrinsic factor contributing to impaired muscle function with aging.

Comments

What about rebooting the stem cell populations with fresh engineered stem cells periodically?

If nuclear DNA damage does contribute to metabolic dysfunction, then keeping it below a certain threshold should work to prevent aging?

Posted by: Jim at February 23rd, 2018 9:15 PM

Hi there ! Just a 2 cent.

I wondr too, nDNA mutation load must not be this consequential.
Although in certain disease state it might be, such as progeria.
nDNA deleterious mutation could cause sufficiently enough genomic instability
to matter. The fact that animals can reach centuries lifespans, not develop cancer
and most likely accumulate some small nDNA deleterious mutation load over time could mean that nDNA mutation are not as deleterious as say mtDNA deletions mutation. We will know in time.
Currently I think on aging point, the word rejuvenation does not mean what it means anymore, it means more repair damage and it will make you live longer by eeping your health and damage level low(er).
Though it will not rejuvenate you in the litteral sense of 'reverting aging to a young phenotype'.
This is only achievable via epigenetic reprogramming and replicative senescence hayflick limi tsolving.
Thus it is not true rejuvenation but damage repair which will manifest as health improving, but not as cell age reversed.
And thus, LEV is not possible until these cell imposed limits are solvd. Our MLSP of 122 years will stand despite the SENS therapyd, they must be clmbined with Other therapynto cover all bases and biological limits..it is not 'rejuvenation', true one but damage repair only not aging reversal (unless limits solved).

Just a 2 cent.

Posted by: CANanonymity at February 23rd, 2018 9:19 PM

Jim: That's WILT (well, half of it).

Posted by: Antonio at February 24th, 2018 3:23 AM

@Jim, that is what was proposed as WICT --

Whole-body Induced Cell Turnover (WICT) consists of the qualitative and quantitative coordination of targeted cell ablation with exogenous cell administration so as to effect the replacement of a patient's entire set of endogenous cells with exogenous cells (of the same quantity and cell type as the ablated endogenous cells they are replacing) derived from human pluripotent stem cells and directionally differentiated in vitro prior to their administration. The idea of WICT was firstly proposed in 2016 and improved in 2017 year.

The aim of WICT is the removal from the organismal environment of accumulated cellular and intracellular damage present in the patient's endogenous cells, including telomere depletion, nuclear DNA damage and mutations, mitochondrial DNA damage and mutations, replicative senescence, functionally-deleterious age-related changes in gene expression and accumulated cellular and intracellular aggregates.

For wich I propose Original Genome Restoration Procedure --

Most cells with critical mutations in nuclear DNA (a) undergo apoptosis, (b) become senescent or (c) become cancerous (and we have already discussed how to address each of these problems). But if the mutations are not critical, the cells will live, divide and accumulate them. Over time, these cells will increase in numbers. One wrong protein here, another one there. Finally, there will be too many of them, and they will lead to the malfunctioning of the body.

Fortunately, experiments done by Dr. Jan Vijg at the Albert Einstein College of Medicine and others on mutations (changes in base sequence in DNA) and additional studies commissioned by SENS Research Foundation on epimutations (changes in the arrangement of methyl groups) suggest that these latter kinds of alterations - the kind that accumulate in cells without triggering apoptosis or senescence or contributing to cancer - accumulate too slowly to make a difference with the current lifespan. Apparently, most (epi)mutations in the cell are recognized as critical and trigger the apoptosis program, or make the cell senescent - and the rest, unfortunately, do contribute to cancer.

But what if the scientists in SENS RF are wrong, and the accumulation of small mutations plays a role now? And in the future we still have to solve this problem. It will be very unpleasant to live three hundred years and die because of brain failure, because we did not take into account the accumulation of small mutations. Houston, it looks like we have a problem! And because each cell has its own unique set of mutations, we cannot solve them with the methods of gene therapy in the adult organism either today or tomorrow.

Of course, in three hundreds (and even fifty) years, we will have completely different technologies (and other problems), but our goal is to show you that even with current technologies the problem of accumulating small mutations is completely solvable.

The point at which these become a problem can also be delayed by the RepleniSENS and OncoSENS programs. As we know, some of the tissues are regularly updated, and a regimen of regularly destroying old, mutated stem cell populations and reseed them with new and healthy ones will slow the rate of accumulation of cells bearing these disabling mutations.

With slowly updated or not renewing at all tissues which do not have their own pools of specialized stem cells, everything is a little more complicated and at the same time easier. On the one hand, the less often the cell divides, the less mutations it accumulates, because most of them are formed in the process of DNA replication. On the other hand, such cells usually accumulate physical and chemical damage in the DNA - chain breaks, oxidized or otherwise modified bases. Over time, the repair system in the cell works worse, and much of this damage either is not corrected at all, disrupting the expression of genes, or converted into mutations. And since such cells usually live for a long time, the accumulated damage and mutations in DNA can exceed the critical level.

To our happiness (I would never have thought that brain degradation would play a good role!) these cells still die, and, as we said above, some long-lived tissues lose about 30% of their cells in 80 years of life. We can replace these dying cells with new healthy cells, and thus dilute the overall level of damage and mutations. However, due to the lack of stem cells in these tissues, we will have to tinker a bit and grow the proper amount of the progenitors or mature cells and integrate them into the tissue. But this is a solvable problem. Recently, scientists have grown mature neurons and transplanted them into the brain of a rat. New neurons successfully integrated into the rat brain and generally behave very well. Similar experiments with the heart muscle also showed good results in restoring it after a heart attack.

Moreover, some tissues (for example, skeletal muscles and skin) will soon be easier to print or grow in a bioreactor than to mess with their cell therapy. Of course, non-invasive methods are always better, so their rejuvenation will still need to be done.

While these rejuvenation biotechnologies give us much reassurance even about the hypothetical dysfunctional mutations, someone should ask the question: where will we take these new healthy cells that we plan to use in cell therapy? In the chapter on RepleniSENS, we discussed in detail the preparation of pluripotent stem and adult cells by reprogramming and transdifferentiation, but ignored the accumulation of small mutations. Now it's time to take them into account.

For example, we took skin cells or more convenient mesenchymal stem cells and sowed them on a nutrient medium. A colony will grow from each cell. We will choose from them the best by their phenotype, sequencing their genomes and discover that they all differ slightly in unique sets of mutations! Which of them we should take as a basis for future cell therapy? Well, probably, the one whose genome is closer to the original, and therefore accumulated fewer mutations. But we do not have the original! The original is a fertilized egg, and it has long grown and turned into 100 trillion cells of an adult human, each of which has its own unique set of mutations. Houston, it seems, we have a problem again and now is much more serious. We have nothing to compare our cells!

But do not panic! If we do not have the original, we will recreate it! How? In the same way in which scientists recreate the original versions of the ancient books, having only a number of slightly different copies. Differences in them, as mutations in cells, arose because of the inevitable mistakes in copying. But scientists have found a way out! The probability of the same error in the same phrase in several books at once is small, and it decreases with the number of copies. In other words, the more times a certain phrase occurs, the more likely it is that it was in the original. With such a simple method, scientists can restore the version of the book closest to the original. And of course, computer programs have been written already, automating the comparison of copies and recreating the original.

Similarly, comparing the sequenced genomes of different cell lines, we can recreate the most closest genome to the original one by using computer. And then we will choose the most genetically close cell line to it and, consistently applying methods of modern genetic engineering, we will correct all found mutations, recreating the cell closest to the original. In the first round, we can not pay attention to the non-coding regions of DNA (which is more than half of the entire genome) and, thus, we will make our work much easier. Cloning the cell, we will get a master line, which we put in the freezer and will use in the cell therapy of our patient. In principle, it is enough to conduct such a procedure only once, but no one forbids us from iteratively improving our master line with the advances of new technologies, using more cells for comparison, better algorithms and methods of genetic engineering.

Posted by: Ariel at February 24th, 2018 9:21 AM

Ariel: That is from a book?

Posted by: Antonio at February 24th, 2018 1:24 PM

If we have to solve this problem in the future anyway, why don't begin now? We have all technology we need. That is really hard to prove the role of nuclear mutations in ageing, it may take 10 years or more, so it would be much better to put all efforts in prepare for solving.

Posted by: Ariel at February 24th, 2018 2:45 PM

Thanks! I will look forward to your essay :)

Posted by: Antonio at February 24th, 2018 2:53 PM

So skeletal muscle, which is mostly quiescent and not replaced in a lifetime, is the subject of a study into DNA damage, but skin or stomach lining is not, despite being turned over really quickly....anyone else see a problem with this?!? LOL

Posted by: Mark at February 24th, 2018 3:38 PM

Stem cell pools are protected by the FOXO3A gene, so for longevity, it is important to have the right SNP alleles that best protect and maintain the stem cell pool. There are about 15 FOXO3A SNP's that have alleles that have been shown by various studies to have longevity benefits. I have searched my own genome and found that I am homozygous for at least 12 of these longevity FOXO3A SNP alleles, though I don't have data on the rest of them. Also, it is important to have good DNA repair genes, particularly to repair the double-stranded DNA breaks. The PARP1 gene SNP rs1136410 AA alleles is especially important in repair of the double-stranded breaks, but also the FOXO3A and SIRT6 genes. The BubR1 gene is important for protection of chromosome stability, along with Vitamin D. Magnesium is necessary to repair R-loop mutations. With age, NAD+ levels in the cell decline, as do various enzymes necessary for efficient energy production. Thus, with age there are many things that can decline, so supplementation with various nutrients and supplements, and CR and adequate exercise and sleep may help extend your life span somewhat.

Posted by: Biotechy at February 24th, 2018 6:14 PM

PS: The mitochondria also play an important role in muscle wasting with age or sedentary lifestyle. The generation of ROS during energy production increases with aging and increased inflammation levels. CR can help reduce ROS by reducing fuel source and body temp (CR practitioners have a body temp 2-3 degrees below normal, mine is around 96 in the morning after waking). Also, it is good if you have good alleles for the UCP3 gene SNP rs1800849 AA alleles (uncoupling protein 3), that gets rid of excess heat in skeletal muscle mitochondria membranes, thus reducing ROS stress.

Posted by: Biotechy at February 24th, 2018 6:59 PM

The SENS therapies would reduce the mutation rate significantly. My main concern is the potentially damaging mutations evolution has left us with. About thirteen percent of my genome is probably or possibly harmful.

Posted by: Tj Green at February 25th, 2018 7:51 AM

@Tj Green

How did you calculate such an exact number of 13 percent?

Kind regards,
K.

Posted by: K. at February 26th, 2018 3:57 AM

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