DNA Repair - the shortest route to longevity

DNA in the nucleus (nDNA) and mitochondria (mtDNA) is subject to constant damage from a variety of insults including endogenous factors such as free radicals and exogenous factors such as UV radiation, man-made mutagens. The damage reaction rate of occurrence has been estimated to be as much as 100,000 individual events per cell per day. This is balanced by the collective of repair mechanisms, such that an equilibrium is achieved between DNA damage (DD) and repair (DR).

The rate of DD must be counterbalanced by the rate DR lest an accumulation of errors overwhelm the cell and result in senescence, apoptosis or cancer. Syndromes associated with faulty DR functioning result in premature aging and increased sensitivity to carcinogens. Studies in animals where DR genes are knocked out show similar disease profiles.

On the other hand, organisms with enhanced DR systems such as Deinococcus radiodurans exhibit unusual resistance to lethal dosages of radiation. In humans, Japanese centenarians have been found to have a common mitochondrial genotype which predisposes them to reduced mtDNA damage.

Low DR has been postulated as a reflection of the competition for energy resources. Whilst accuracy in germline cells is vital to the genome for survival, accuracy in somatic cells is not. Both brain and muscle cells exhibit depressed DR and the survival mechanisms compensating for DD are based on cellular redundancy and transiently rapid division of cell populations rather than optimal DR.

Just like the balance between DD and DR, the equilibrium eventually shifts towards more cells dying than being created resulting in tissue function impairment and ultimately the demise of the organism.

Considering that the vast majority of life is not able to reach anywhere near the maximal lifespan in the wild, selection has not pressed for longevity.

There are numerous lines of evidence that converge on DD as the cause of aging. These include observations of reduced transcription and protein synthesis and reduction of cell viability and function. Also observed are increases in the rate of senesce, apoptosis and cancer. In fact, DD is the single most prevalent factor in the abnormal functioning of cells, aging or otherwise.

In light of the countless knockout studies that have been conducted to support these views, it is strange that research is now not focused on overexpression studies to determine by how much cellular, tissue and whole animal lifespan can be extended.

Adjusting the balance between DD and DR in somatic cells presents the most rapid and achievable, by today's technological capabilities, method of extending human lifespan.

Illustration of the ideas presented in previous post.

A layman's introduction to DNA repair here.

Considering that the vast majority of life is not able to reach anywhere near the maximal lifespan in the wild, selection has not pressed for longevity.

I think it might not be just that, but that it could actually be they've been purposely designed to deteriorate. The body might just be rigged to do this.
aging is an evolved characteristic

Also since I've heard of some of the negligible senescence species, and how close relatives to some are actually short-lived. It might be that the actual changes to allow the engineering of this, might not be too drastic. (yeah, It's a bit optimistic.)

Very interesting stuff. Apocalypse, thanks for the link. And Prometheus, thanks for the Wikipedia link.

Prometheus, given that you are such a proponent of the DNA-repair route to aging medicine, would you care to comment on de Grey's SENS approach? I'm sure you already have, so if you perhaps remember somewhere where you've commented on it before (in depth), you could point me in that direction? (rather than go through it all over again; I know I've already taken up so much of your time in other topics.)

I think I remember that you mentioned your own version of a SENS-like approach that was simpler in certain ways. Have you posted this anywhere?

Jay Fox

For those who choose to read the following I suggest you go brew a cup of coffee, because it's a long one, even by my standards.

Firstly, Aubrey de Grey (AG) has to be congratulated for the effort he has put towards shifting the inertia in the biogerontology community on treating aging as a disorder and coming up with real and practical solutions. He is an articulate, committed and resilient advocate for legitimate anti-aging research. Thanks to his strategies for engineered negligible senescence (SENS) he has brought credibility in using practical solutions for solving the aging problem and has fired the imagination of even the most conservative scientists and laymen (whether they choose to admit it or not). Furthermore he has rejuvenated the classic scientific approach of inventing new methods for solving problems as opposed to validating hypotheses for their own sake- what he calls the engineering approach. He has done much and we should all be grateful.

So it is with great respect and greater reluctance that I will deconstruct and criticize some of his theories, but in the spirit of science and with the hope that with critical analysis the objective that we all anticipate will be achieved sooner rather than later.

AG has admitted that he came up with what he calls "seven deadly things" during a sleepless night due to jet lag whilst he was visiting the states. They are derived from the book "Understanding Aging" by another famous aging researcher, Robin Holliday, after whom the term "Holliday junction", a DNA structure associated with recombination, is named after. The seven deadly things and his solutions can be summed up as follows:

1. Cell loss - treatable by stem cells
2. Cancer - treatable by WILT (Whole-body Interdiction of Lengthening of Telomeres)
3. Mitochondrial DNA damage - treatable by Allotopic expression of the 13 mitochondrial proteins
4. Cell senescence - treatable by destruction of unwanted cells
5. Extracellular cross-links - treatable by AGE-breaking molecules/enzymes
6. Extracellular junk - treatable by phagocytosis
7. Intracellular junk - treatable by transgenic microbial hydrolases

The strategies I have issue with are (2) and (3).

(2) concerns AG's remedy for cancer which is to prevent telomere maintenance throughout every cell in the body. His theory is since cancer cells are able to maintain their telomere length, by preventing them from doing so would eradicate the incidence of cancer. Aside from the fantastic difficulty of implementing this without having to resort to germline therapy, which would present further problems in development, it is an entirely unnecessary and physiologically incompatible strategy.

A telomerase primer: in the ends of eukaryotic chromosomes, are specialized structures called telomeres (in humans it consists of the sequence TTAGGG repeated thousands of times) that provide structural stability by preventing the ends of chromosomes from fusing with each other and from being degraded by nucleolytic enzymes. Furthermore, each time a cell undergoes division, due to the way DNA polymerase functions, it is unable to replicate the end of one side of the DNA strand (3' end). Consequently, a portion of the chromosome becomes lost with each cell division leading eventually to cell senescence and death due to chromosome instability. Some cells express an enzyme called telomerase that rebuilds the portion of telomere that is lost with each cell division, allowing a cell to divide indefinitely provided nothing else goes wrong with the cell. Telomerase positive cells include germline cells, and every stem cell type in the body including those that are constantly rebuilding epithelial structures (e.g. lining of the mouth, stomach, intestine, colon, hair follicle and skin), the hematopoietic system (all cells of the blood and immune system), those of the brain (e.g. in the hypothalamus and olfactory node) and many more stem cell reservoirs that regeneratively sustain various tissues and organs in the body. Cancer cells, however, also are telomerase positive.

A cancer primer: cancer is the result of a breakdown in the tight controls that regulate normal cell activity. For a cell to become carcinogenic, a multi-step process is involved, that can be generally summarized by the following cell behavior:
- independant of external growth signals
- insensitive to external anti-growth signals
- no longer able to elicit apoptosis
- able to divide indefinately
- able to induce angiogenesis
- able to migrate and invade other tissues
These changes come about as a result of alterations in such things as DNA methylation, oncogene activation and tumor suppressor gene mutation (loss of function). In other words, multiple changes must occur for a cell to become completely out of line with its intended destiny. One of these changes is that, at some stage, it will begin to express telomerase and consequently have the same ability as stem cells - that of being capable of indefinite division.

AG has chosen the step associated with the cell becoming telomerase positive as the mark for death. In doing so, however, he has also chosen every single other cell that gives life, namely stem cells. One of the conventional cancer strategies used today involves whole body irradiation or chemotherapy which specifically targets cells that rapidly divide and destroys them. This includes rapidly dividing cancer cells and healthy stem cells. When stem cells die, however, the patient endures tremendous side effects: the one's we see are the loss of hair, drop in weight, and constant fatigue. What we don't see are the constant body pains, burning throughout the entire alimentary canal (from mouth to anus and everything in between), severe nausea, vomiting, diarrhea, unusual pain and numbing (when nerves start to die), wart formation, anemia and of course drop in immunity. If the treatment has to be severe then the patient must have a stem cell transplant ready or else death ensues. The treatment relies on the body's capability to regenerate after being brought to the brink of cellular annihilation.

AG says that we can compensate for the loss in stem cells by having a replacement treatment every 10 years. This, of course, is not physiologically possible with extremely high cell turnover tissues such as the lining of the stomach wall, which requires new cells every 24 hours. Other obstacles include how every cell can have this modification made outside of using germline interventions. And even if germline interventions are used, what effect having no endogenous population of dividing stem cells would have on a developing human. Where will the necessary biomass of cells come from to build the growing body from embryo to fetus etc.

Naturally, one cannot walk away without offering an alternative solution. I have two. The first concerns the fundamental root of the cause for cancer: altered gene expression. We know that the changes associated with cancer commence with altered gene expression which has its origins in DNA damage. We know this from numerous studies where normal cells will turn cancerous providing they are exposed to sufficient mutagens either in the form of UV irradiation or chemicals. We also know that cells not exposed to these mutagens but that have their DNA repair systems knocked out will act as if they are exposed to mutagens and become cancerous. Finally we know that cells that are made to over-express certain DNA repair factors will be able to withstand higher concentrations of mutagens for longer periods without becoming affected. It is not unreasonable to suspect that by increasing the expression of specific DNA repair factors (I repeat some - not all - since some DNA repair factors can also be mutagenic) that we can reduce the probability of altered gene expression.

But the benefit does not lie solely with cancer prevention but with the process of aging itself. We know that cumulative oxidative and other damage in DNA results in senescence and cell death (or cancer). By reducing DNA damage we also keep cells alive and healthy for a longer period of time. Here too it is not unreasonable to suspect that the tissues from which those cells are composed of - and ultimately the entire organism would also remain healthier for a longer period.

Now for the second solution. This should run parallel with the first, however, we are a tad further from realizing it technologically until we have a more mature knowledge of immunological molecular interactions (not as far however as the fantastically ambitious WILT). This solution concerns a customized method of programming the adaptive immune response. It is effectively a step up from the use of vaccines which train our adaptive immune system to recognize and subsequently kill foreign cells based on antigen being processing from material delivered in the vaccine. By using immune stem cells that can be programmed genetically in the lab to respond to any target including any infective agent our immune response can be kept constantly optimized. This would include targeting cancer cells which are known to express alternative proteins on their cell surface once they "turn".

The second strategy I have issue with is (3). It involves the wholesale migration of the entire DNA apparatus of mitochondria to the nucleus. For those that may not be aware, mitochondria have their own DNA in a circular form, and whilst the majority of proteins that are utilized in mitochondria are actually encoded for by the nucleus and then transported to mitochondria, 13 mitochondrial proteins are encoded for by the mitochondrial genome. The mitochondria being the biggest producer of oxidants in the cell is also prone to the most damage. Some cells have up to 1,000 mitochondria at any one time. Consequently, the mitochondrion has become the achilles heel of the cell and it is the main cause of apoptosis. Also the rate of mutation inside mitochondria is increased due to the oxidative environment and even if mitochondria do not send the "death signal" they can still become sluggishly ineffective at doing their job and thereby making the entire cell ineffective. If that sounds mild, imagine all your heart cells and brain cells becoming "ineffective" and you get a clearer picture of the physiological consequences.

AG thinks that the best way to prevent mitochondrial damage from occurring is to shift the mitochndrial genes into the oxidation-wise relatively safer environment of the nucleus. The first problem we encounter is that the proteins that the mitochondrial genes encode for are fiercely hydrophobic and would not take too well to being transported around and end up in nonfunctioning conformations. The second is that the special mitochndrial gate that lets the nuclear encoded proteins in, the TIM/TOM complex, is itself compromised by oxidants and becomes less efficient at letting the necessary proteins in. Finally, if we are talking about replacing the production of the proteins in up to 1,000 mitochondria, we are talking about a very large scale production of mRNA from the nucleus and protein from the endoplasmic reticulum, the consequences of which we do not know.

Whilst this is not as difficult to envisage as WILT, it can be dealt with by a far more elegant solution. Considering once more that the primary causative factor of mitochondrial failure is oxidation-induced DNA damage, I propose the targeting of specific DNA repair factors and anti-oxidant factors directly into the mitochondrion. It is much easier to implement as this has already been demonstrated experimentally and and I suspect would be more effective.

In conclusion it is quite obvious by now that I am a great believer in enhancing the rate of DNA repair and believe that the positive effects would be multi-faceted particularly as DNA damage seems to be the primary factor associated with altered gene regulation that manifests as aging. Once more, this post should not be in any way interpreted as being negatively judgmental of AG's fine work. It is based on scientific fact and my conclusions drawn from those facts.

As always, please feel free to challenge.

I have a question to pose in relation to studying potential aging treatments in flies and mice.

Allow me to sum up how I'm interpreting this: in comparison to Dr. de Grey, you look more towards reducing DNA damage, whereas Dr. de Grey seems to focus more on circumventing the need for such repair capabilities.

To wit:
Dr. de Grey: WILT. Even if cancerous cells forms, the tumors can only grow so much before their telomeres are used up. Given the limited lifespan of a tumor( and its "progeny" should it escape into the system), trying to fight cancer would no longer be a losing battle; it becomes a battle of attrition. Depending on how quickly a tumor uses up its telomeres, it might not even be that bad of a battle.

Prometheus: Better repair facilities, prevent cancers from forming in the first place. Supplement with more a programmable immune system. Runs the risk (however small) that a cancer forms that we cannot beat in time. However, if that risk is sufficiently small, then the death rate from cancer can still be lowered enough to make it a negligible risk in life expectancy.

Dr. de Grey: Move mitochondrial DNA to the safer harbor of the nucleus, with modifications necessary to cooperate with TIM/TOM mechanism. By the way, this is favoring better DNA repair, in a way.

Prometheus: Improve DNA repair within the mitochondria. By the way, of the three methods (better DNA repair factors, increased anti-oxidant production/availability, and decreased oxidant production), how would you rank the ease of implementing these, and how would you rank the effectiveness, given technology available now, or in fifteen years?


I suppose there are a few questions here that are open from where I sit (the biologists may disagree).

First, how effective will therapies targetting DNA damage directly be? That is, to what degree can we increase DNA repair effectiveness. Put another way, to what degree can we reduce the damage that slips through the repair facilities? A factor of 2? 5? 10? 100?

As for the other two factors: How much can we reduce DNA damage with anti-oxidants without severely impairing feedback mechanisms that have evolved to use anti-oxidants for signalling? How much can we reduce oxidant production before reaching a point of diminishing returns?

On the other side of the aisle, I have to admit that WILT seems quite extreme. I don't like the idea of frequent therapies being necessary to maintain basic functionality. Let's assume that for whatever reason, attaining a 200+ year lifespan requires periodic treatments (whether every year, or every 10). At the worst, I would expect that if I stopped taking the treatments, I would simply age at what would otherwise be a "normal" rate given my physiological age at the time. In other words, if I start treatments at age 40; and if by the time I'm 100, my body is that of a 50 year old; then if I stop the treatments, I expect there to be remaining about 30 years of life expectancy.

Put another way, if my son starts the treatments at age 20; and if by age 100, his body is that of a 30 year old; then if he stops the treatments, I expect he should have at least a 40-50 year life expectancy remaining.

Now maybe I'm reading this wrong, but if all cells, even stem cells, have their telomere lengthening capabilities removed, we'll die much sooner. We'll lose critical organs with high cell turnover rates.

If I'm wrong, let me know where. If I'm right, then why would we consider WILT as a viable option? It certainly would make a neat academic solution, and it might be fine for the rich, but for the common person, I think it's completely unacceptable.

Dr. de Grey, if you're around, would you care to comment? While WILT would seem to work when taken at face value, are there perhaps less elegant solutions that make more practical sense?

Jay Fox

There is no evidence to suggest that decreasing the concentration of oxidants in the nucleus or mitochondria would negatively impact any signaling mechanism reliant upon them (I did not say extinguish). Note that the signaling mechanisms that are known are generally associated with senescence and apoptosis. Indeed apoptosis is a fundamental requirement for development and any interference of that signaling mechanism would be catastrophic.

Oxidative signaling has become an integral means of cells being aware of the impending damage that oxidation is going to bring about and anticipating more disastrous consequences (such as cancer) decide to switch cellular proliferative pathways off.

In order to understand what I mean about reducing oxidants in the cell you need to visualize the oxidant state of a youthful cell, say one belonging to an 8 year old child. In such a cell you would find relatively more robust systems of oxidative protection and DNA repair. Oxidant species would still be present but they would not be overwhelming the cells ability to mop them up and repair any damage.

In terms of what I propose, the overall aim would be genomic integrity maintenance (GIM). This is a multi-factorial approach towards reducing the DNA damage which induces alterations in gene expression and consequently bring about disease and aging phenotypes. This involves different approaches for nuclear GIM versus mitochondrial GIM due to the differences between intranuclear and intramitochondrial environment and and genome structures. In nuclear GIM (nGIM) the emphasis is in increasing the presence of substrate specific DNA repair factors and preventing negative changes to histone acetylation and DNA methylation and whereas in mitochondrial GIM (mGIM) the aim is to reduce the concentration of oxidants and increasing DNA repair function.

The efficacy of the GIM strategy can only be determined by getting experimental data. Peripheral investigations suggest that we have to focus on isolating DNA repair factors that are very specific in the mode of action. For instance we know that overexpression of certain DNA repair enzymes that have a broad range of specificity can destabilize the genome if overexpressed. Highly specific DNA repair enzymes, however will continue to only interact with sites of damage when overexpressed. An example of a DNA repair enzyme with fine substrate specificity is hOGG1 which will only interact with 8-oxo-G type DNA perturbations.

To answer your question about how long it would take to convert the GIM theory into therapy - well most of the important groundwork has already been done. What remains is delivering selected overexpressable gene constructs into model organisms and sitting back. Naturally we select for maximum efficacy with maximum safety. Using the technology that we have available today it is hardly a sophisticated experiment and only needs run of the mill molecular biology lab resources. You can probably understand now why I see some of the research proposed as a waste of time when this type of investigation is being neglected simply because of the "anti-aging" stain.

The question of when treatments should be started is one that concerns many, particularly. those over 40. To answer this question we really need to ask is it possible to reverse aging. You will find a post in the biotech forum titled "reprogramming the transcriptome" that explains it rather well. The short answer is that we can definitely stimulate a cell to turn from one type of into another demonstrating that we can totally alter gene expression and regulation. But can we can turn the developmental clock back? This of course is a function of the extent of damage - if the DNA is damaged irreversibly (both strands damaged in each chromosome in homologous regions) we do not want to get the cell dividing again because of the potential for cancer. But if the problem is something reversible than we want to get the cell back up on its feet and acting young again and this may simply be a matter of giving it access to the resources it needs to reduce oxidant levels and repair its damaged DNA.

Improve DNA repair within the mitochondria. By the way, of the three methods (better DNA repair factors, increased anti-oxidant production/availability, and decreased oxidant production), how would you rank the ease of implementing these, and how would you rank the effectiveness, given technology available now, or in fifteen years?

I never mentioned anything about decreasing oxidant production. But it is possible, that if more efficient enzymes were engineered or transfected from other organisms they could output the same workload but with less oxidative byproduct.

I would say that anti-oxidant delivery is probably easier to implement than substrate specific DNA repair because we need to hone down on only certain DNA repair factors and pathways. But ultimately we will still need to find ways to keep the cell in its youthful state before it becomes overwhelmed by damage and this can only be achieved by enhanced DNA repair.

But any longevity solution will still need to rely on increasing the regenerative function of youth and that means a highly active system of stem cell reservoirs throughout the body that are able to proliferate and migrate to the site of damage quickly and efficiently.

After much lobotomizing the wikipedia DNA repair article made it to "featured articles".