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Mitochondrial DNA damage


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#31 Michael

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Posted 20 February 2005 - 08:01 PM

All:

[quote]
Let's go back to the evidence you are presenting:

- 8-oxodG amount is higher in mtDNA than in nDNA

If this is all then it is hardly evidence to support your hypothesis.[/quote]

I agree. I already emphasized that the simple fact of higher mtDNA than nuDNA damage was not the issue. The contention that mt, but not nuclear, DNA damage is causally related to aging lies, as I indicated, in the interspecies and CR data relating the former, but not the latter, to species maximum lifespan:

[quote]
The rate of aging in mammals is, on good interspecies evidence ([references renumbered (8,9) -- Prometheus, please don't snip references!]), related to the rate of accumulation of mt, but not nuclear, DNA damage and esp deletions ... "long-lived animals show lower levels of oxidative damage in their mitochondrial DNA (mtDNA) than short-lived ones, whereas this does not occur in nuclear DNA (nDNA)." (8) This means longevous species, not individual organisms, and is measured in terms of max LS. Likewise, "the rates of mitochondrial oxygen radical generation [and] oxidative damage to mitochondrial DNA" "are negatively correlated with maximum longevity." (9) This originally goes back to a series of comparative studies, most notably (10):

[quote] If oxidative damage to DNA is involved in aging, long-lived animals (which age slowly) should show lower levels of markers of this kind of damage than short-lived ones. ... In this study, steady-state levels of ... (8-oxodG) referred to deoxyguanosine (dG) were measured ... in the mitochondrial (mtDNA) and nuclear (nDNA) DNA from the heart of eight and the brain of six mammalian species ranging in maximum life span (MLSP) from 3.5 to 46 years. ... 8-oxodG/dG in nDNA did not correlate with MLSP across species either in the heart (r=-0.68; P<0.06) or brain (r = 0.53; P<0.27). However, 8-oxodG/dG in mtDNA was inversely correlated with MLSP both in heart (r=-0.92; P<0.001) and brain (r=-0.88; P<0.016) tissues following the power function y = a(.)x(b), where y is 8-oxodG/dG and x is the MLSP.[/quote]
... and (11) also finds a more consistent relationship of mtDNA than nuDNA damage to maximum LS, somewhat more weakly because based on comparisons across 2 different orders of vertebrates who already show unexpected differences in rate of mtROS generation based on body size and metabolic rate, rather than within one order as in (10):

[quote] Lower steady-state 8-oxodG values were observed in all cases in the heart mtDNA in birds than in mammals. 8-oxodG levels were also lower in brain mtDNA in pigeons than in rats, in brain nDNA in canaries than in mice, and in heart nDNA in parakeets compared with mice. The rest of the comparisons did not show significant differences between species. These results taken together indicate that oxidative damage to DNA tends to be lower in birds (highly long-lived species) than in short-lived mammals, especially in the case of mtDNA.[/quote]

The fact that CR does not lower mtDNA deletions brain (12,13), unlike in mucle, heart, and liver, may also be important to interpreting this finding...

To observe the fact that some kind of damage increases, and even accumulates, with age is distinct from showing that the rate at which this happens it is related to the rate of aging. To show the latter, we need evidence either from intervention (interventions that reduce a particular kind of damage with age increase max LS, and interventions that do not do the former do not do the latter) or from interspecies comparisons (more longevous spp suffer less of this damage with age than more short-lived ones). Barja and others have shown that this is true of oxidative mtDNA and not of nuDNA.[/quote]

[quote]
Also, there is no new evidence that you have presented in your previous post despite the number of references you cite. [/quote]
Quite correct, as I believe that the originally-cited data are quite adeqate to make the point. My original post laid out the nature of the evidence; my last post simply quoted the material explicitly, since it seemed that you had missed the key points in the citations given, and clarified some points in response to your specific questions. I apologize for largely repeating myself here.

[quote]
To show you the weakness of this evidence for your claim I will demonstrate how it can be used against your claim:

Hypothesis: Increasing  nDNA damage is the driver of the aging phenotype. 
Key Evidence: Increasing 8-oxodG amounts especially in mtDNA
Interpretation: It is known that the nuclear environment contains far less ROS than the mitochondrial matrix. It is thus expected that ROS induced DNA damage will be higher in mtDNA than in nDNA. It is known that the mtDNA repair activity from nuclear encoded but mitochondrially acting enzymes such as 8-oxodG glycosylase decline with aging (1). Consequently, any damage to the nuclear genome, that impairs the regulation or the synthesis of mitochondrial genome stabilizers will manifest as increasing damage in mtDNA.

However, the evidence is far more compelling than this little exercise. An excellent review (2) is attached to this post. I suggest you read it before debating this matter further.[/quote]
But neither of these points addresses the key issue of mtDNA deletions, which are the key to de Grey's MiFRA (the only "mitochondrial free radical theory of aging" actually consistent with the data, with the semi-exceptions of Brunk's (13) and Aiken's (12) -- and deletions are still key to Aiken's work), which actually accumulate with age, and which are reduced by CR, as documented previously. Again, DNA deletions -- unlike point mutations -- cannot be repaired.

[quote]
But that does not prevent me from responding to claims you have already made:

[quote]
Note that this isn't actually a contradiction. To observe the fact that some kind of damage increases, and even accumulates, with age is distinct from showing that the rate at which this happens it is related to the rate of aging. To show the latter, we need evidence either from intervention (interventions that reduce a particular kind of damage with age increase max LS, and interventions that do not do the former do not do the latter) or from interspecies comparisons (more longevous spp suffer less of this damage with age than more short-lived ones). Barja and others have shown that this is true of oxidative mtDNA and not of nuDNA.[/quote]

What specifically has Barja shown that cannot be explained by altered regulatory mechanisms of mtDNA repair vs nDNA repair?[/quote]

That mitochondrial, but not nuclear, DNA damage is related to normal mammalian aging.

[quote]
[quote]
On this front, it should be noted that while individual cells and their progeny certainly can be expected to become dysfunctional when their nuDNA aquire mutations, the low rate of cell division in vivo in most tissues -- and the virtual nonexistance of same in postmitotic tissues like heart and brain -- means that individual cell's mutations get little chance to "take over" the tissue and render the whole dysfunctional.[/quote]
Do I see backpedaling?[/quote]
Not as far as I can see. It remains my position -- having been convinced by Aubrey's arguments and Barja's data -- that damage to mtDNA but not nuclear DNA are causal to aging itself, although the latter does contribute to cancer.

[quote]
You're saying that it is possible for cell nDNA to acquire mutations that result in dysfunction but that it is so rare an event and unlikely have any effect on the overall tissue physiology because of the low mitotic potential of the cell with damage?[/quote]
Yes.

[quote]
This implies that nuclear genome integrity is maintained relatively intact in the vast majority of cells which contradicts numerous gene expression studies that show dramatically altered transcription profiles in between young and old organisms (3,4,5,6).[/quote]

But changes in gene expression need not imply changes in gene structure ((epi)mutation). As I indicated,

[quote]
And indeed, the most useful investigations into such shifts -- those in which shifts in gene expression associated with normal aging are compared with those undergone in animals subjected to calorie restriction (CR) ([14]), which (as Estep well knows) is the sole intervention known to retard biological aging in mammals. These studies have found that the most prominent classes of genes undergoing shifts which both occur with aging are retarded by CR (and which are thus most likely related, as cause or as effect, to primary aging processes) are those involved in inflammation and antioxidant defense -- gene classes, that is, whose natures imply precisely that their expression has been altered in response to underlying, [primary] molecular lesion(s). [Compare the parallel findings in humans ([15])].[/quote]

[quote]
You say that such changes are secondary to other "primary lesions" (I am at this stage hoping you are not going to say cancer so I am awaiting to hear what these other lesions are). Then you back to the tired old argument that the main effect of nDNA mutations is cancer. Oh dear.[/quote]

I'm not sure what you're getting at, here. Cells suffer a shift in REDOX tone with age, convincingly explained by de Grey's MiFRA (and see also Nick Lane's "double agent" theory (16). This leads to an expected increase in expression of genes which protect the cell against oxidative injury and inflammation. CR prevents the original lesions leading to the secondary increase in oxidative stress and the resulting changes in gene expression either don't occur in the first place by lowering mtROS generation and mtDNA deletions; allotopic expresion would sever the link between deletions and increased oxidative stress.

[quote]
[quote]
It seems obvious to me (and I expect that Aubrey agrees) that it is likely that nuDNA mutations would eventually become pathological if not repaired over the course of a greatly extended LS, as eventually all cells would have accumulated a great many true mutations; however, evidence to hand indicates that they are not accumulating at high enough levels over the course of a "normal" lifespan to significantly contribute to aging per se.[/quote]
So finally the point of contention is when and not if nDNA damage is going to lead to altered cell function.[/quote]

Not quite: the point of contention is when and not if non-cancer nDNA mutations are going to lead to meaningful increases in pathology and to contributing to aging per se (as opposed to cancer) in a way that is not obviable by the existing SENS interventions. Aubrey has never claimed that the "Seven Deadlies" include all of the lesions that would ever become pathological in a greatly-extended lifespan -- just that they include all of the lesions that contribute to pathology in a current, "normal" lifetime. After we correct these defects, other, more subtle forms of damage which are irrelevant to pathology within a current, normal lifetime will emerge, and require increasingly refined therapies to correct in order to further push back aging. Fortunately, as time goes on we will have increasingly powerful tools with which to identify and then obviate these newly-hazardous forms of damage or de-link them from pathology. See his "actuarial escape velocity" paper (17), and also his chapter in the Immortality Institute's book (18):

[quote]
As I have discussed extensively elsewhere, [refs] there seem to be only seven broad categories of molecular and cellular difference between older and younger people that we have any reason to believe we need to fix to achieve two decades of human life extension, even of those already in middle age. ...

The above considerations constitute an acknowledgement that aging will never be cured in the sense that a bacterial infection is cured, i.e. entirely eliminated from the body. Rather, it will be cured in the sense that malaria or AIDS can presently be cured: it can be controlled very well given access to appropriate medication whenever needed, but that medication can never be confidently dispensed with forever. It may not be clear to the reader, however, that what I have said above allows even that degree of “cure” of aging.

The reason it does so can be summed up in one word: bootstrapping. The second-generation therapies that will eventually be needed to bear down even more effectively on the “seven deadly things” than our already-foreseeable first attempts do will not be needed for at least two decades after the firstgeneration therapies arrive ... The key point here is that two decades is an eternity in science, especially in well-funded science (which life extension will certainly be at this time): the second-generation therapies are thus virtually certain to arrive in time. Hence, as soon as we reach the point of extending life expectancy by even a couple of decades, we can be confident that most beneficiaries of such therapies will survive to benefit from subsequent ones. Those people’s life expectancy will thus be indefinite, even though they are still aging. ...

For the reasons surveyed above, I consider it appropriate to regard the WOA [Waro on Aging] as ending when first generation SENS therapies become widely available. Thus far, however, I have only discussed specific, identifiable problems—which are, necessarily, unimaginatively similar to the targets of the first-generation therapies. What about things we haven’t thought of?

This entirely valid point will, I predict, motivate—starting as the WOA nears its end—a research project that will dwarf even the WOA itself. Our unarguably limited ability to predict what aging will throw at us next could, it would seem, only be addressed reliably by clairvoyance. Or could it? Could we metaphorically press the fast-forward button to discover what the future holds? We are exceedingly fortunate that such an option is indeed available.

Specifically, I predict that humanity will at that time create, and maintain indefinitely, a very large colony of non-human primates  ... on which to test novel life extension therapies. ... a large colony of primates maintained under conditions very similar to those under which we maintain ourselves—the same range of diets, the same lack of exercise, and of course the same medical care, including all life-extension treatments in use at the time—will be virtually certain to display any health-threatening characteristic of aging that we ourselves exhibit, at an age at most half that at which it appears in us. These primates will be the experimental recipients of succeeding generations of rejuvenation therapies. ... Splendidly, this becomes progressively easier as time passes: we may only just have 80-year-old primates before we have 160-year-old humans, but we will certainly have 100-year-old primates some years before we have 200-year-old humans, and the lead-time improves forever thereafter. This strategy will be our most powerful defence against the unforeseeable biomedical challenges that our attainment of unprecedented ages will create.[/quote]

Likewise, and specifically on the point of nuclear DNA mutations, Aubrey added this caveat in previous discussion in these forums ($(%$*!! Forum post links won't hook directly -- see his post of an 24, 2005):

[quote]
- My reason for not mentioning other nuclear mutations is that I think they don't matter in anytrhing like a normal lifetime; our DNA repair and maintenance machinery has evolved to be good enough to stop us from dying of cancer before middle age, and the rest of our genes, in which dysfunction has to occur not just in one cell but in a fair proportion of the cells in a tissue in order to be harmful, get a free ride. Jan Vijg has been trying to prove this logic wrong for a decade or more and has so far only provided a lot of evidence that it's correct.[/quote]

Same thread, post of Jan 25, 2005:
[quote]
- Premature aging syndromes (humans or mice) caused by faster DNA damage accumulation say nothing at all about whether that accumulation does any damage to us at its normal rate in a normal lifetime.[/quote]

This thread, post of Jan 28, 2005:
[quote]
nuclear mutations and/or DNA damage do not contribute to aging in a currently normal lifetime in mammals except to the extent that they promote cancer, and possibly arthritis. Of course nuclear DNA damage causes senescence, but we have hardly any senescent cells in any tissue yet found except chondrocytes in the articular cartilage (Martin and Buckwalter, various papers). [and IAC, the SENS platform addresses senescent cells direcly, via restoration or ablation -MR][/quote]

Also this post:

[quote]
Non-DNA damage: see my previous answers, they will matter in the end but I claim not for many tiimes a currently normal lifetime.[/quote]

Emphasis above is mine; on Vijg's efforts, see his own recent reviews (19,20), and then Aubrey's analysis in these three posts showing the surprising implications of this work:

[quote]
A somewhat stronger argument against nuclear-DNA mutation theories is that we have fabulous DNA repair/maintenance capacity to avoid cancer, and it's evolutionarily cheaper to apply that system genome-wide in all cells (even though that is overkill) than to have a second, less fabulous, system most of the time and a better one just for genes that are involved in cell cycle control. This is also a bit weak though, because it may be easier to tune up/down a system tissue-specifically than gene-specifically -- i.e. the "postmitotic tissues might matter" argument above might apply because postmitotic cells can't develop into cancer. However, it does mean we can't extrapolate to mammals from insects or other very short-lived animals that don't get cancer.

So what we really need is data. Much the most useful work on this is from Jan Vijg's group. They developed a clever assay for mutation rate involving disruption of a transgene (many papers; a quite recent review is Mech Ageing Dev 123:907). Their basic conclusion was that there are indeed not nearly enough point mutations to matter, but that in some tissues there are quite a lot of chromosomal rearrangements. What is "quite a lot"? Well, actually only about the same number as point mutations. But Vijg and colleagues have argued that this is a lot more important than the point mutations, because of gene dosage and position effect changes -- i.e. any one mutation can affect many genes. However, their most recent paper (Genome Res 12:1732) seems to me to argue against that, because they now establish that most such rearrangements do not involve heterochromatin.

This means that the scope for position effects on gene expression is quite limited and thus that probably the only mutations that could matter are deletions. Deletions can potentially be very bad for the cell because they take out an arbitrary number of genes (potentially thousands). But here, there is a big problem: a big deletion on the X chromosome will very probably be fatal for the cell because it removes the only active copy of the gene (presuming that the deleted DNA is degraded -- the other option, in postmitotic cells, is that it survives as a circular extrachromosomal fragment. But then it will still be expressible, so we can ignore this case.) So, the cell has to take pretty good care not to suffer big deletions on the X. But then it will use the same machinery for the other chromosomes (qv the cancer argument above).

So in sum, even though Vijg and colleagues are doing terrific work in this area, I remain pretty sure that the chances of nuclear mutations mattering for aging other than via promotion of cancer are very slim.

Michael Price wrote:

> Surely the DNA errors will also cause other dysfunctions
> (errors in enzyme coding, other genetic malfunctions etc). I don't
> have any quantitive insights, but qualitatively wouldn't we would
> expect these dysfunctions to contribute to mitotic aging? I.e. the
> cancer is correlative with mitotic aging?

Absolutely right. What this means, though, is that we are in fact very *fortunate* to have a body plan that allows us to get cancer, because the necessity to reproduce before you die of cancer has forced evolution to make our DNA maintenance and repair systems so incredibly good that most of the time not a single cell will turn cancerous and kill us before we're middle-aged. The rest of our genome gets that same quality control as a free ride.

This logic may sound too good to be true, but it seems to be supported by the evidence: the most careful work evaluating the frequency of somatic mutations, by Jan Vijg's group, has concluded that typical cells get only about ten (not necessarily in coding regions) in a normal lifetime, far too little to cause the tissue any trouble. What's even better about this result is that (a) Vijg is a very talented scientist and (b) he really doesn't like this result, so he's spent the past few years doing his level best to save the somatic mutation theory without success. His main theme, which you may remember from IABG 10, is that the point mutations may be harmless but there are also chromosomal rearrangements, at about the same frequency, which may do a lot more harm by affecting the level of expression of genes in a fairly large region around the new DNA junction.

There are two big problems with this concept: (a) such long-range effects are only known (in genetically well-studied species) when euchromatin is put next to heterochromatin, which is not what he mainly sees, and (b) even ten rearrangements per cell would cause havoc for cell division so it is generally felt that this must be a big overestimate. This also means that somatic mutations may indeed be inportant for life span in flies, worms and other such species that have essentially no mitotically competent cells.

> wouldn't evolution provide us with good
> DNA repair mechanisms for all the other, non-cancerous
> reasons, for instance general protein (including enzyme)
> mis-coding.

Sure, but the necessary quality of that repair is far less (i.e. it can fail without killing the organism far more often in a given period of time), since so many cells must be hit.

> Just let me check what Vijg is saying.  That germ and soma are equally
> protected against mutation?  Wow.  This would be a surprise, according
> to the disposable soma viewpoint.

Oh no, he's definitely not saying that, he's just saying that the soma is only as well protected as the genes need to be, i.e. that the rate of nuclear mutations in general (not just cancer-causing ones) is one of the things that would kill us sooner if it were higher. 

> By mutations, is he including the chromosomal rearrangements you
> mentioned earlier, or just talking about the point mutations?

Yes he is -- in fact, he relies entirely on rearrangements, because he accepts that the level of point mutations he sees is indeed far too low to cause anything except cancer.

> let me make another stab at recapitulating
> your encapsulation of Vijg's work and its relevance to aging.
>
> The existence of cancer drives the evolution of v. effective genomic
> repair mechanisms (for which we should be thankful!). Consequently,
> in massively multicellular organisms, such as ourselves, the average
> somatic cell has such few few mutational hits that tissue aging can not
> be driven by mutations -- although the mutation rate is sufficient to
> explain post-middle age cancer (where a single cell gets unlucky with
> multiple hits in the wrong places).

All correct.

> Vijg is trying to save the
> mutational-soma-aging theory by including chromosomal rearrangements
> in the picture

Yes.

> (is he theorising they don't cause cancer but do generally
> degrade cellular performance and induce tissue aging?).

No; that would be a hard argument to make, because cancers tend to have plenty of chromosomal rearrangements.

> I gather you
> think there are holes in Vijg's theory to do with hetero/eu-chromatin (I
> must look that up) and that the rate of rearrangements he sees is too
> large.

Right. First of all, most rearrangements should not affect all that many genes (only ones actually disrupted by the breakpoints), unless they are deletions (as opposed to inversions, transpositions etc that do not involve loss of any DNA). In flies, the only rearrangements that exhibit "position effect variegation" -- the alteration of expression of genes relatively far from the breaks -- are those that juxtapose euchromatin with heterochromatin. Second, as you say, the number of rearrangements he sees seems to be far too many to be compatible with any cell division, as they would far too often create dicentric or acentric chromosomes that would misbehave at mitosis.[/quote]

Aubrey has not presented this analysis in any detail on Imminst AFAICS; perhaps this is part of the logjam in your previous discussions with him.

[quote]
Where is this evidence to hand? I am still awaiting it from Aubrey![/quote]

The evidence is the interspecies and CR data I've already provided, as well as Aubrey's analysis of Vijg's results. I think that if you weigh all of this together, you will conclude the case is sufficiently strong to agree that non-cancer nuDNA mutations do not significantly contribute to aging per se in a current, normal lifespan.

-Michael

(1) Age-dependent decline of DNA repair activity for oxidative lesions in rat brain mitochondria.
Chen D, Cao G, Hastings T, Feng Y, Pei W, O'Horo C, Chen J.
Neurochem. 2002 Jun;81(6):1273-84.

(2) Maintenance of mitochondrial DNA integrity: repair and degradation.
Kang D, Hamasaki N.
Curr Genet. 2002 Aug;41(5):311-22.

(3) Gene regulation and DNA damage in the ageing human brain.
Lu T, Pan Y, Kao SY, Li C, Kohane I, Chan J, Yankner BA.
Nature. 2004 Jun 24;429(6994):883-91.

(4) Transcriptional mechanisms of hippocampal aging.
Lund PK, Hoyt EC, Bizon J, Smith DR, Haberman R, Helm K, Gallagher M.
Exp Gerontol. 2004 Nov-Dec;39(11-12):1613-22.

(5) A transcriptional profile of aging in the human kidney.
Rodwell GE, Sonu R, Zahn JM, Lund J, Wilhelmy J, Wang L, Xiao W, Mindrinos M, Crane E, Segal E, Myers BD, Brooks JD, Davis RW, Higgins J, Owen AB, Kim SK.
PLoS Biol. 2004 Dec;2(12):e427

(6) Gene expression profile of aging in human muscle.
Welle S, Brooks AI, Delehanty JM, Needler N, Thornton CA.
Physiol Genomics. 2003 Jul 07;14(2):149-59.

8. Barja G.
Endogenous oxidative stress: relationship to aging, longevity and caloric restriction.
Ageing Res Rev. 2002 Jun;1(3):397-411. Review.
PMID: 12067594 [PubMed - indexed for MEDLINE]

9. Barja G.
Rate of generation of oxidative stress-related damage and animal longevity.
Free Radic Biol Med. 2002 Nov 1;33(9):1167-72. Review.
PMID: 12398924 [PubMed - indexed for MEDLINE]
0. Barja G, Herrero A.
Oxidative damage to mitochondrial DNA is inversely related to maximum life span
in the heart and brain of mammals.
FASEB J. 2000 Feb;14(2):312-8.
PMID: 10657987 [PubMed - indexed for MEDLINE]

11. Herrero A, Barja G.
8-oxo-deoxyguanosine levels in heart and brain mitochondrial and nuclear DNA of
two mammals and three birds in relation to their different rates of aging.
Aging (Milano). 1999 Oct;11(5):294-300.
PMID: 10631878 [PubMed - indexed for MEDLINE]

12: McKenzie D, Bua E, McKiernan S, Cao Z, Aiken JM; Jonathan Wanagat.
Mitochondrial DNA deletion mutations: a causal role in sarcopenia.
Eur J Biochem. 2002 Apr;269(8):2010-5. Review.
PMID: 11985577 [PubMed - indexed for MEDLINE]

13: Brunk UT, Terman A.
The mitochondrial-lysosomal axis theory of aging: accumulation of damaged
mitochondria as a result of imperfect autophagocytosis.
Eur J Biochem. 2002 Apr;269(8):1996-2002. Review.
PMID: 11985575 [PubMed - indexed for MEDLINE]
14. Weindruch R, Kayo T, Lee CK, Prolla TA.
Gene expression profiling of aging using DNA microarrays.
Mech Ageing Dev. 2002 Jan;123(2-3):177-93.
PMID: 11718811 [PubMed - indexed for MEDLINE]

15. Lu T, Pan Y, Kao SY, Li C, Kohane I, Chan J, Yankner BA.
Gene regulation and DNA damage in the ageing human brain.
Nature. 2004 Jun 24;429(6994):883-91. Epub 2004 Jun 09.
PMID: 15190254 [PubMed - indexed for MEDLINE]

16: Lane N.
A unifying view of ageing and disease: the double-agent theory.
J Theor Biol. 2003 Dec 21;225(4):531-40.
PMID: 14615212 [PubMed - indexed for MEDLINE]
17. de Grey AD
Escape Velocity: Why the Prospect of Extreme Human Life Extension Matters Now.
PLoS Biol 2(6): e187.
http://www.plosbiolo...al.pbio.0020187

18. de Grey AD
After the war on aging: speculations on some future chapters in the never-ending story of human life extension.
In Immortality Institute (ed). The Scientific Conquest of Death: Essays on Infinite Lifespans.
2004; Libros en Red. ISBN: 9875611352

19. J. Vijg, R. Bahar, K. Rodriguez, R. Busuttil, M. Dolle, H. van Steeg, J. Campisi, J. Hoeijmakers
Genomic instability in cancer and aging
http://www.gen.cam.a...10/abs/Vijg.htm
http://www.gen.cam.a...0/ppts/Vijg.ppt


20. Vijg J.
Impact of genome instability on transcription regulation of aging and
senescence.
Mech Ageing Dev. 2004 Oct-Nov;125(10-11):747-53.
PMID: 15541769 [PubMed - in process]

#32 jaydfox

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Posted 21 February 2005 - 03:50 PM

Michael, to your knowledge, has de Grey published his analysis of Vijg's work with respect to its pertinence to somatic nuDNA mutation theories of aging?

#33

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Posted 23 February 2005 - 08:05 AM

Michael, thanks for your reply. I came across the attached study which I believe has strong bearing on any data that relies on 8-oxoG as a mtDNA damage indicator in the context of mitochondrial dysfunction.

I await your response since it places the studies you mention into question in the way you are interpreting them and thereby compromises your entire argument.

#34

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Posted 23 February 2005 - 08:55 AM

Aubrey has not presented this analysis in any detail on Imminst AFAICS; perhaps this is part of the logjam in your previous discussions with him.


I am afraid that had he presented it, it would not have made much difference except to provide more substrate for debate. For all of Vijg's terrific work and despite the fact that he supports the nDNA damage model of aging, the lacZ plasmid mutation assay system, does not agree with other published estimates of nDNA mutation frequency. For example the lacZ system shows no increase in mutation in the brain whereas 8-oxoG findings show a two fold increase. His data show a two fold increase in heart, whereas 8-oxoG studies show a three fold increase. Finally, the small intestine shows the greatest rate of mutation in contrast to clinical observations which show a comparatively lower incidence of cancer in in this tissue in contrast to other tissue/organ types.

#35 Michael

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Posted 24 February 2005 - 09:27 PM

All:

Michael, thanks for your reply. I came across the attached study which I believe has strong bearing on any data that relies on 8-oxoG as a mtDNA damage indicator in the context of mitochondrial dysfunction.

I await your response since it places the studies you mention into question in the way you are interpreting them and thereby compromises your entire argument.


Remember, neither I nor Aubrey is claiming that 8-oxoDG is itself pathological, let alone that it contributes to mt dysfunction which is what this study confirms it does not. This is as you'd expect, as it is a steady-state marker rather than something that actually accumulates (as a proper SENS target does). As I said in a previous post,

And one more thing, you may be interested to know that your mentor is not fond of 8-oxodG as an indicator of DNA damage:

One of the most pervasive errors in DNA analysis is to presume that rises in the amount of a pre-mutagenic lesion translate to proportional rises in that of bona fide mutations: in fact the relationship is nowhere near that, because the chance of a given 8oxodG becoming a mutation depends on its halflife, i.e. how long on average before it is repaired.


Aubrey is not saying that 8-OHdG is not an indicator of any damage to DNA, but hat it is not a reliable proxy of actual mutations. 8-OHdG is not an accumulating lesion but a steady-state damage snap shot, and in fact it directly measures the rate of repair of oxidative DNA lesions rather than their rate of formation. But you have to swallow the whole pill. It's fortunate that the evidence from the CR model avaialable, as it has drawn the link to actual damage accumulation in the form of mtDNA deletions (5-9, 12, 13). Likewise, the fact that 8-OHdG is more readily repaired in nuDNA than mtDNA further strengthens the non-relevance of the former in aging (although, of course, it causes cancer).


Similarly:

Aubrey has not presented this analysis [of Jan Vijg's data on the incidence of mutations in somatic cells with aging] in any detail on Imminst AFAICS; perhaps this is part of the logjam in your previous discussions with him.


I am afraid that had he presented it, it would not have made much difference except to provide more substrate for debate. For all of Vijg's terrific work and despite the fact that he supports the nDNA damage model of aging, the lacZ plasmid mutation assay system, does not agree with other published estimates of nDNA mutation frequency. For example the lacZ system shows no increase in mutation in the brain whereas 8-oxoG findings show a two fold increase. His data show a two fold increase in heart, whereas 8-oxoG studies show a three fold increase. Finally, the small intestine shows the greatest rate of mutation in contrast to clinical observations which show a comparatively lower incidence of cancer in in this tissue in contrast to other tissue/organ types.


Again, 8-oxoG is not a mutation, and does not accumulate. You would expect the level of actual mutations in a cell to be significantly lower than the level of 8-oxoG.

-Michael


5. Barja G.
Endogenous oxidative stress: relationship to aging, longevity and caloric restriction.
Ageing Res Rev. 2002 Jun;1(3):397-411. Review.
PMID: 12067594 [PubMed - indexed for MEDLINE]

6. Lee CM, Aspnes LE, Chung SS, Weindruch R, Aiken JM.
Influences of caloric restriction on age-associated skeletal muscle fiber characteristics and mitochondrial changes in rats and mice.
Ann N Y Acad Sci. 1998 Nov 20;854:182-91. Review.
PMID: 9928429 [PubMed - indexed for MEDLINE]

7. Barja G.
Rate of generation of oxidative stress-related damage and animal longevity.
Free Radic Biol Med. 2002 Nov 1;33(9):1167-72. Review.
PMID: 12398924 [PubMed - indexed for MEDLINE]

9. Bua E, McKiernan SH, Aiken JM.
Calorie restriction limits the generation but not the progression of
mitochondrial abnormalities in aging skeletal muscle.
FASEB J. 2004 Mar;18(3):582-4. Epub 2004 Jan 20.
PMID: 14734641 [PubMed - indexed for MEDLINE]

12: Kang CM, Kristal BS, Yu BP.
Age-related mitochondrial DNA deletions: effect of dietary restriction.
Free Radic Biol Med. 1998 Jan 1;24(1):148-54.
PMID: 9436624 [PubMed - indexed for MEDLINE]

13: Cassano P, Lezza AM, Leeuwenburgh C, Cantatore P, Gadaleta MN.
Measurement of the 4,834-bp mitochondrial DNA deletion level in aging rat liver and brain subjected or not to caloric restriction diet.
Ann N Y Acad Sci. 2004 Jun;1019:269-73. Review.
PMID: 15247027 [PubMed - indexed for MEDLINE]

#36

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Posted 25 February 2005 - 06:07 AM

Well, then.

I guess the above mentioned study refutes any argument which relies on 8-oxodeoxyguanine as an indicator of mutagenesis in mitochondria. Note of course that it has no bearing on studies which use 8-oxodeoxyguanine as an indicator of mutagenesis in the nucleus. So what non-proxy (so-called SENS-target) indicator can you use to support rates of mutation in mitochondria?

#37 circuitblue

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Posted 05 March 2005 - 04:08 PM

Hi there,

I very much agree with Michael's statement: "The immortality and agelessness of the germ line has been rather misrepresented. One of the main reasons that the germ line is retained intact is that the body is so much more rigorous in apoptosing (neologism!) defective cells in the line -- not that the cells themselves are individually retained pristine."

While many specific details on the mechanisms responsible for different facets of germline immortality remain unclear, it appears as though selection is a majorly-employed and efficacious one. The existence of, and selection against, damaged or unviable germ cells is indicative that the germline does not "select qualifying cells to *hold pristine*," but rather it seems the germline doesn't know which cells have accumulated damaged until it selects against them. Thus, the germline likely both creates some "cells with slightly faulty systems" and also incurs additional accumulated damage with age, both of which need to be selected against for viable healthy embryos. The specific role of mitochondria in this process is very much ambiguous at present, and I am currently investigating this genetically under Dr. Ahmed at Chapel Hill (hopefully I'll have some results soon :)).

If anyone is more interested in germline immorality, check out the following review paper on Germline Immortality I wrote with my boss:

Smelick C, Ahmed S.
Achieving immortality in the C. elegans germline.
Ageing Res Rev. 2005 Jan;4(1):67-82. Epub 2004 Dec 10.
http://www.ncbi.nlm....t_uids=15619471

cheers,

-chris

#38

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Posted 06 March 2005 - 01:00 PM

Hi Chris, and thanks for your input and the link to your paper!

For those interested in C. elegans as a model organism for studying aging it provides good background.

Attached Files



#39

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Posted 10 March 2005 - 02:44 PM

Another study where overexpression of a DNA repair enzyme, in this case hOGG1, is able to repair mitochondrial DNA damage and rescue a cell from apoptosis.

Am J Physiol Lung Cell Mol Physiol. 2005 Mar;288(3):L530-5.
Mitochondrial DNA damage triggers mitochondrial dysfunction and apoptosis in oxidant-challenged lung endothelial cells.
Ruchko M, Gorodnya O, LeDoux SP, Alexeyev MF, Al-Mehdi AB, Gillespie MN.

Oxidant-induced death and dysfunction of pulmonary vascular cells play important roles in the evolution of acute lung injury. In pulmonary artery endothelial cells (PAECs), oxidant-mediated damage to mitochondrial DNA (mtDNA) seems to be critical in initiating cytotoxicity inasmuch as overexpression of the mitochondrially targeted human DNA repair enzyme, human Ogg1 (hOgg1), prevents both mtDNA damage and cell death (Dobson AW, Grishko V, LeDoux SP, Kelley MR, Wilson GL, and Gillespie MN. Am J Physiol Lung Cell Mol Physiol 283: L205-L210, 2002). The mechanism by which mtDNA damage leads to PAEC death is unknown, and the present study tested the specific hypothesis that enhanced mtDNA repair suppresses PAEC mitochondrial dysfunction and apoptosis evoked by xanthine oxidase (XO). PAECs transfected either with an adenoviral vector encoding hOgg1 linked to a mitochondrial targeting sequence or with empty vector were challenged with ascending doses of XO plus hypoxanthine. Quantitative Southern blot analyses revealed that, as expected, hOgg1 overexpression suppressed XO-induced mtDNA damage. Mitochondrial overexpression of hOgg1 also suppressed the XO-mediated loss of mitochondrial membrane potential. Importantly, hOgg1 overexpression attenuated XO-induced apoptosis as detected by suppression of caspase-3 activation, by reduced DNA fragmentation, and by a blunted appearance of condensed, fragmented nuclei. These observations suggest that mtDNA damage serves as a trigger for mitochondrial dysfunction and apoptosis in XO-treated PAECs.




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