Caloric restriction slows brain aging
Lou Pagnucco
Nature Genetics which demonstrates that genes
(at least in lab mice) that are upregulated during
aging in the brain (associated with inflammation and
the stress response) are repressed by caloric
restriction. Presumably, CR should retard brain
senescence.
It is interesting that gene chips were central to this
analysis. The secrets of the aging process are finally
being unraveled.
Regards,
L. Pagnucco
From URL:
http://unisci.com/stories/20002/0627002.htm
Eating Less Seems To Fend Off Brain Diseases
Eating less may be good for the health of your brain, and
may help keep debilitating ailments such as Alzheimer's
and Parkinson's diseases at bay.
That is the message derived from a pathbreaking study
that employed a powerful new gene-scanning technique
to analyze activity in thousands of genes to create a
molecular portrait of the aging brain in mice.
The new study focuses on genetic activity related to two
critical regions of the brain: the cerebral cortex, the part
of the brain involved in the higher functions of thought, and
the cerebellum, the brain structure that helps coordinate
motor and muscle function.
Conducted by scientists at the University of Wisconsin-
Madison and to be reported in July in the British scientific
journal Nature Genetics, the study provides new insight into
the cognitive and motor skill deficits that occur with age.
The results may also help to explain the basis of common
neurological disorders such as Parkinson's and Alzheimer's
diseases.
Cheol-Koo Lee, Richard Weindruch and Tomas A. Prolla,
all of UW-Madison, profiled the action of 6,347 genes. The
scientists charted changes in genetic activity in two groups of
aging mice, one group on a standard diet and another group
whose diet had been trimmed to 76 percent of the standard diet.
The study builds on similar work of aging skeletal muscle by the
same group of Wisconsin scientists and reported last year in the
journal Science.
The new Wisconsin study shows that a reduced-calorie diet
selectively lowers the age-associated increase in the activity of
genes that encode inflammatory and free-radical-generated
stress responses, says Weindruch, a UW-Madison professor
of medicine.
Free radicals are highly reactive molecules that circulate in the
body and can damage cells over time. Previous studies suggest
that both inflammation and free-radical damage may play a role
in the onset of Alzheimer's and Parkinson's disease.
The study's findings, Weindruch notes, add to mounting evidence
that a reduced-calorie diet, the only known method of slowing
aging in several species of animals, not only extends life, but
confers health benefits that contribute significantly to a better
quality of life in old age.
The study also suggests that basic aging mechanisms in the
brain, including inflammation and free radical damage, are
shared among different species of animals, including mice,
monkeys and humans.
Scientific opinion on the value of the mouse as a model for
human neurological disorders is divided, says Prolla, a
UW-Madison professor of genetics. But the Wisconsin study
shows that many genes related to inflammation become more
active with normal aging, a phenomenon suppressed in mice
placed on a low-calorie diet.
"Although it is known that caloric restriction retards certain
aspects of aging in the brain, the mechanism is not known,"
says Weindruch, an authority on caloric restriction and aging.
"However, these new findings advance our understanding of
caloric restriction's effects on aging in the brain."
Prolla says this new understanding of the relationship between
genes and brain health in mice could take on importance as a
testing ground for new drugs: "It means we can use mice to
screen for drugs that might prevent these processes in humans,"
Prolla says.
"Gene expression changes observed with aging in the two
brain regions can be used to measure the aging process on
a tissue-specific and molecular basis," Weindruch says.
"This should facilitate the development of interventions --
drugs, dietary modifications -- to retard aging in the brain."
Prolla says the study also indicates that diet alterations may
lower the risk of developing some of the most common and
debilitating age-associated neurological disorders.
The Wisconsin study depended on a powerful new technology
known as the "gene chip," a small DNA-laden plate that, when
read with a laser, reveals activity levels for thousands of
individual genes at once. The technique can show which genes
are in play in a given circumstance. The more than 6,000
genes surveyed for the new Wisconsin study represent
5 percent to 20 percent of the mouse genome.
The Wisconsin group is extending its gene chip studies
to monkeys and humans. UW-Madison, at its Wisconsin
Regional Primate Research Center, is the site of a decade-
old study of rhesus macaques on a reduced-calorie diet.
- By Terry Devitt
[Contact: Richard Weindruch, Tomas A. Prolla, Terry Devitt ]
27-Jun-2000
Aubrey de Grey
Lou Pagnucco wrote:
> Below is a summary of a paper just published in Nature Genetics which
> demonstrates that genes (at least in lab mice) that are upregulated
> during aging in the brain (associated with inflammation and the stress
> response) are repressed by caloric restriction. Presumably, CR should
> retard brain senescence.
>
> It is interesting that gene chips were central to this analysis. The
> secrets of the aging process are finally being unraveled.
While I agree with the widespread sentiment that microarray and other
genomic analysis techniques can tell us a great deal about cell biology
in general and aging in particular, I think it may be worth pointing out
the limitations of such work. I participated last weekend in a small
meeting ostensibly focused on reversing human aging; Weindruch also took
part and several other participants were also genomics afficionadios.
I found it necessary to spell out rather forcefully that what we get by
microarray and related experiments is a picture of the **coordinated**
gene-expression changes which occur during aging, and that such changes
are almost entirely descriptive of what cells are doing to *compensate*
for the primary, accumulated losses of function that define the process
of aging and its rate. Those primary processes themselves, by contrast,
are either non-genetic (such as accumulation of protein cross-links or
of lipofuscin), or non-coordinated (such as nuclear or mitochondrial
mutations, which affect different genes (if any) in each cell), or both
(such as cell loss in glands, muscle, heart, some brain areas, etc.).
Even changes that one might guess are moderately uniform within a given
tissue, such as telomere shortening, are now known not to be (such that
one in 10,000 or so dermal fibroblasts shows senescent gene expression
in old age but the rest don't, for example). Moreover, microarray data
give virtually no clue as to the relative importance of these various
primary processes, because the changes they reveal are compensations for
the cumulative effect of all the primary processes mixed together.
This has very profound implications for the utility of microarray data
in anti-aging research. For example, an intervention which restored
the expression levels of many (or all) genes in an elderly individual
to youthful levels in an elderly individual would be predicted to be
*harmful*, because it would be stopping the body from making the best
of a bad job (i.e. reacting, by gene-expression tuning, to the primary
changes listed above). The value of such analyses may in reality be
restricted to the (important, but limited) field of biomarkers of
"biological age". The Nature Genetics study, for example, identifies
"selective" attenuation by CR of gene expression changes which occur
during aging, thereby providing evidence that those genes whose change
in expression was not attenuated are less good markers of biological
age than the ones which did change. Another application which follows
from this is that a candidate CR mimetic (a chemical proposed to trick
the body into thinking it's on CR when it isn't, and thence -- with luck
-- extending one's lifespan) could be evaluated for its likely efficacy
by determining how similar its effects on gene expression are to those
seen in CR. A wider applicability to anti-aging research -- especially
reversal of aging -- is, by contrast, very hard to see. It is therefore
regrettable that many of those involved in such work are allowing this
distinction to become blurred in the public mind -- and, I increasingly
find, in their own.
Aubrey de Grey
ta...@keydatatech.com
wrote:
>I found it necessary to spell out rather forcefully that what we get by
>microarray and related experiments is a picture of the **coordinated**
>gene-expression changes which occur during aging, and that such changes
>are almost entirely descriptive of what cells are doing to *compensate*
>for the primary, accumulated losses of function that define the process
>of aging and its rate.
Is any thought being given to the possibility that these changes
aren't compensation at all but nature's built in obsolescence so that
there will be room for future, supposedly superior, generations? Or am
I way off the mark here?
Lou Pagnucco
Thanks for the very informative reply.
I hope, though, that you are at least somewhat too pessimistic.
See my remarks below.
Cheers,
Lou Pagnucco
Aubrey de Grey wrote in message <8jl101$949$1...@pegasus.csx.cam.ac.uk>...
>
>Lou Pagnucco wrote:
>
>> Below is a summary of a paper just published in Nature Genetics which
>> demonstrates that genes (at least in lab mice) that are upregulated
>> during aging in the brain (associated with inflammation and the stress
>> response) are repressed by caloric restriction. Presumably, CR should
>> retard brain senescence.
>>
>> It is interesting that gene chips were central to this analysis. The
>> secrets of the aging process are finally being unraveled.
>
>While I agree with the widespread sentiment that microarray and other
>genomic analysis techniques can tell us a great deal about cell biology
>in general and aging in particular, I think it may be worth pointing out
>the limitations of such work. I participated last weekend in a small
>meeting ostensibly focused on reversing human aging; Weindruch also took
>part and several other participants were also genomics afficionadios.
>I found it necessary to spell out rather forcefully that what we get by
>microarray and related experiments is a picture of the **coordinated**
>gene-expression changes which occur during aging, and that such changes
>are almost entirely descriptive of what cells are doing to *compensate*
>for the primary, accumulated losses of function that define the process
>of aging and its rate.
IMHO (as a layman), I tend to agree that many of these changes in gene
transcription are indeed compensatory. However, I am inclined to think
that many are causal given that modifications of single genes have been
found which significantly increase maximum lifespan in mice, drosophila
and worms.
>Those primary processes themselves, by contrast,
>are either non-genetic (such as accumulation of protein cross-links or
>of lipofuscin), or non-coordinated (such as nuclear or mitochondrial
>mutations, which affect different genes (if any) in each cell), or both
>(such as cell loss in glands, muscle, heart, some brain areas, etc.).
Definitely. Nevertheless, those "non-genetic" changes appear to be
down range results of genetic programs activated earlier. Why else
would such changes be so species-specific?
The DNA arrays should allow us to spot these precursors.
>Even changes that one might guess are moderately uniform within a given
>tissue, such as telomere shortening, are now known not to be (such that
>one in 10,000 or so dermal fibroblasts shows senescent gene expression
>in old age but the rest don't, for example).
Nevertheless, there are eminent gerontologists who surmise that the
increasing fraction of senescent and near-senescent fibroblasts does indeed
have deleterious effects on the extra-cellular matrix which, in turn, has
damaging effects on the cells which must rely on the ECM to maintain
their proper state of differentiation.
>Moreover, microarray data
>give virtually no clue as to the relative importance of these various
>primary processes, because the changes they reveal are compensations for
>the cumulative effect of all the primary processes mixed together.
Amen. This will certainly require the most powerful of supercomputers.
Such a complex multifactorial process may be too intricate for the unaided
human brain to disentangle.
>
>This has very profound implications for the utility of microarray data
>in anti-aging research. For example, an intervention which restored
>the expression levels of many (or all) genes in an elderly individual
>to youthful levels in an elderly individual would be predicted to be
>*harmful*, because it would be stopping the body from making the best
>of a bad job (i.e. reacting, by gene-expression tuning, to the primary
>changes listed above).
Some compensatory changes must be beneficial.
Still, I would bet that many are detrimental.
[...]
\>Aubrey de Grey
mik...@my-deja.com
In article <24uslss799n9nr7nd...@aol.com>,
ta...@keydatatech.com wrote:
> On 1 Jul 2000 14:59:13 GMT, ag...@mole.bio.cam.ac.uk (Aubrey de Grey)
> wrote:
>
> >I found it necessary to spell out rather forcefully that what we get by
> >microarray and related experiments is a picture of the **coordinated**
> >gene-expression changes which occur during aging, and that such changes
> >are almost entirely descriptive of what cells are doing to *compensate*
> >for the primary, accumulated losses of function that define the process
> >of aging and its rate.
>
> Is any thought being given to the possibility that these changes
> aren't compensation at all but nature's built in obsolescence so that
> there will be room for future, supposedly superior, generations? Or am
> I way off the mark here?
Yes :). Analysis with evolutionary theory demonstrates that "planned
obsolescence" genes will always be powerfully selected AGAINST, because
of the nature of natural selection. Such genes yield benefits to all
competing organisms, but only accrue costs to those bearing them;
organisms not bearing such genes will thus leave more young behind in the
spaces left by the "altruistic," and the whole scheme will fall apart at
the hands of the "tragedy of the commons." For an excellent, highly
readable discussion of the point, see _Why We Age: What Science Is
Discovering about the Body's Journey Through Life_ by Steven N. Austad.
Paperback - 256 pages 1 edition (March 11, 1999) John Wiley & Sons;
ISBN: 0471296465.
-Michael
>
Sent via Deja.com http://www.deja.com/
Before you buy.
ta...@keydatatech.com
>Yes :). Analysis with evolutionary theory demonstrates that "planned
>obsolescence" genes will always be powerfully selected AGAINST, because
>of the nature of natural selection. Such genes yield benefits to all
>competing organisms, but only accrue costs to those bearing them;
>organisms not bearing such genes will thus leave more young behind in the
>spaces left by the "altruistic," and the whole scheme will fall apart at
>the hands of the "tragedy of the commons." For an excellent, highly
>readable discussion of the point, see _Why We Age: What Science Is
>Discovering about the Body's Journey Through Life_ by Steven N. Austad.
>Paperback - 256 pages 1 edition (March 11, 1999) John Wiley & Sons;
>ISBN: 0471296465.
>
>-Michael
An excellent point, and it sounds very reasonable. But even so there
are obvious signs that built in obsolescence is at work at least to
some extent. At least they seem obvious to me. If nothing else
consider menopause in women. After she has had her chance to have
children her body just kind of says to heck with it and starts it's
inevitable decline. It's nature's way of discarding what is no longer
useful after it has served it's purpose.
Maybe I'm using a term that doesn't really apply in calling it
obsolesence(we as self-aware thinking beings never really become
obsolete, at least to ourselves even if we have passed our
reproductive years), let's call it a built in self destruct instead
that isn't activated until the organism is no longer useful to nature.
Thanks for the reference, I'll try to find it at the local library or
if not there at Amazon.
mik...@my-deja.com
ta...@keydatatech.com wrote:
> On Sun, 02 Jul 2000 00:39:33 GMT, mik...@my-deja.com wrote:
>
> >Yes :). Analysis with evolutionary theory demonstrates that "planned
> >obsolescence" genes will always be powerfully selected AGAINST, because
> >of the nature of natural selection. Such genes yield benefits to all
> >competing organisms, but only accrue costs to those bearing them;
> >organisms not bearing such genes will thus leave more young behind in the
> >spaces left by the "altruistic," and the whole scheme will fall apart at
> >the hands of the "tragedy of the commons." For an excellent, highly
> >readable discussion of the point, see _Why We Age: What Science Is
> >Discovering about the Body's Journey Through Life_ by Steven N. Austad.
> >Paperback - 256 pages 1 edition (March 11, 1999) John Wiley & Sons;
> >ISBN: 0471296465.
> >
> >-Michael
>
> An excellent point, and it sounds very reasonable. But even so there
> are obvious signs that built in obsolescence is at work at least to
> some extent. At least they seem obvious to me. If nothing else
> consider menopause in women. After she has had her chance to have
> children her body just kind of says to heck with it and starts it's
> inevitable decline. It's nature's way of discarding what is no longer
> useful after it has served it's purpose.
It seems that way; that's why programmed obsolescence (or "built in self
destruct" -- same thing) theories have found so many adherents outside of
evolutionary theorists per se. But menopause is not a programmed
destruction. The evils of the pause come from endocrine disruptions
arising from the fact that the hormone feedback loops are all dependent
on ova-releasing ovaries. when the ovaries run out of eggs, FSH & LH go
NUTS trying to stimulate ovulation, which suppresses estrogen &
progesterone (if I have this slightly off, anyone, feel free to correct
me, but this is the basic picture).
"But," you say, "doesn't this mean that the lack of eggs is a clock?" In
a sense, yes -- but the organism wasn't built with a limited supply of
eggs to kill it off: again, this would be counterproductive. rather, the
organism is built with enough eggs to ensure that it will have enough to
last its natural life. Emphasis on "natural." remember, until this
century, nearly all cultures had an av'g age of death of <25, and even
welthier nations were under 40. Designing an organism with all the
preservation resources and supplies (such as ova) to last indefinitely is
a waste of resources if the organism is almost sure to die of malaria,
accidents, predation, or warfare long before. Those resources are instead
spent making the organism maximally reproductively fit for its extrinsic
LS. IOW, Nature doesn't design us to die ("you've served your purpose,
but now you're a drain and must go") -- it just doesn't build us to last
forever.
ta...@keydatatech.com
>Nature doesn't design us to die ("you've served your purpose,
>but now you're a drain and must go") -- it just doesn't build us to last
>forever.
Well then, let's fix it... : )
This makes sense when put that way. It just seems to me that there are
so many complicated systems that must be ramped up in the organism to
reverse any kind of aging that it is nearly impossible... Or it has to
be done at a fundamantal genetic level. This of course would leave
most already mature organisms(you and I for example) out in the cold.
As an aside. I was watching This Week this morning and one of the two
gentlemen taking credit for was asked when we would have extended
lifespan as a result af this. His response was that he didn't forsee
any kind of life extension resulting form the tinkering of genes in
the near future if ever. He went on to say that if any kind of
lifespan increases came from this it would be in the area of
mechanical improvements like organ transplants for the dying on the
waiting lists and other such advances. I'm paraphrasing here
obviously, but that's about the gist of what was said.
Aubrey de Grey
Lou Pagnucco wrote:
> Thanks for the very informative reply.
> I hope, though, that you are at least somewhat too pessimistic.
I don't consider my view pessimistic! Microarray and related work is
easily overinterpretable, that's all. Since it's in its infancy, that's
no surprise.
> IMHO (as a layman), I tend to agree that many of these changes in gene
> transcription are indeed compensatory. However, I am inclined to think
> that many are causal given that modifications of single genes have been
> found which significantly increase maximum lifespan in mice, drosophila
> and worms.
That logic is seductive but very fragile. I recommend Gordon Lithgow's
recent article in Nature 405:296-297. To paraphrase: the best-studied
life-extending mutant in C. elegans shows no compensatory diminution of
fitness (such as lowered fertility) in the normal lab environment, so
evolutionary theory predicts that it would enjoy a selective advantage
relative to wild-type, which would make it become the wild-type (i.e.
take over the natural population) once it arose naturally. It's not
very attractive to argue that the mutation simply never HAS arisen
naturally -- basically, anything one can induce in the lab by random
mutagenesis using a comparatively tiny number of flies is certain to
arise often in nature. Lithgow resolved the paradox by growing mutant
worms in conditions that mimicked nature more faithfully than standard
lab conditions do: specifically, he alternated them between food-rich
and starvation conditions. The long-lived mutants rapidly lost out in
coculture with wild-type worms. Everyone predicts that the same thing
will be found with all the other long-lived mutants in C. elegans and
other species, once we find sufficiently natural conditions. Since we
do not ourselves live in natural conditions, the implications of such
mutants for human longevity are less clear... but it would be extremely
surprising if similar-sized life-extensions were found from single-gene
mutations in long-lived species. Most of my colleagues are doubtful
that November's mouse result (Nature 402:309) will repeat even in long-
lived mouse strains, let alone long-lived species. (Ever the optimist,
I have a princely five dollars with George Martin that C57BL6 will be
longevised at least 20%.... I should add that I am unaware that such
an experiment is yet in progress.)
> those "non-genetic" changes appear to be
> down range results of genetic programs activated earlier. Why else
> would such changes be so species-specific?
I'm not sure I understand you. Which ones are species-specific? The
RATE of such changes is species-specific, to be sure, but that doesn't
make them programmed. For example, most such differences can plausibly
be attributed to variations in the rate of mitochondrial superoxide
production as a percentage of oxygen consumption; that's under genetic
control, to the extent that it can be affected by the precise shape of
some of the enzymes in the electron transport chain, which is of course
a consequence of their amino acid sequence, but one can't really call
oxidative damage a programmed process.
> there are eminent gerontologists who surmise that the increasing
> fraction of senescent and near-senescent fibroblasts does indeed have
> deleterious effects on the extra-cellular matrix which, in turn, has
> damaging effects on the cells which must rely on the ECM to maintain
> their proper state of differentiation.
Actually that view is losing ground at present. Judy Campisi, who first
identified senescent gene expression in vivo, now suggests that the most
important secreted products of near-senescent are growth factors, which
could promote tumours. (I believe she first set this out in J Am Geriatr
Soc 1997; 45(4):482.) But dysdifferentiation of the sort you describe
could also potentially have that effect, yes. However, my point was that
this process is uneven -- some cells of a given type are affected a lot
more than others. The stochastic element may be due to random choice
of which cells divide and which don't during growth (since the cells we
are talking about here are skin cells, dermal fibroblasts); it may also,
to a large extent, be oxidative, since telomeres shorten as a result of
oxidative damage as well as incomplete end-replication.
> >Moreover, microarray data
> >give virtually no clue as to the relative importance of these various
> >primary processes, because the changes they reveal are compensations
> >for the cumulative effect of all the primary processes mixed together.
>
> Amen. This will certainly require the most powerful of supercomputers.
> Such a complex multifactorial process may be too intricate for the
> unaided human brain to disentangle.
Hm... A contrary sentiment, which I share, is that a lot of the work we
could do now to intervene in aging is being held back by reluctance to
invest effort in projects that are not based on detailed understanding
of the system being manipulated (i.e. the aging human). Ultimately we
must appreciate that there is a trade-off here -- the longer we wait for
more data and better theory, the surer we are to succeed when we try, but
the surer we are not to succeed soon. I am in favour of being ambitious
now and hoping to get lucky, even if quite a lot of effort is likely to
be wasted in the process.
Aubrey de Grey
Aubrey de Grey
tateg wrote:
> This makes sense when put that way. It just seems to me that there are
> so many complicated systems that must be ramped up in the organism to
> reverse any kind of aging that it is nearly impossible...
That is by no means clear. The complexity of the human body may work in
our favour in such an endeavour, because of the synergistic interactions
that comprise most of that complexity: identification and reversal of the
few most influential primary degradative molecular processes in aging may
retard or reverse nearly the entire panoply of secondary symptoms.
> Or it has to
> be done at a fundamantal genetic level. This of course would leave
> most already mature organisms(you and I for example) out in the cold.
Not once we develop comprehensive somatic gene therapy (i.e. the ability
to get engineered DNA into any chosen cell type).
> I was watching This Week this morning and one of the two
> gentlemen taking credit for was asked when we would have extended
> lifespan as a result af this. His response was that he didn't forsee
> any kind of life extension resulting form the tinkering of genes in
> the near future if ever.
Yes, many of my colleagues still prefer to err on the side of pessimism
when speaking to the media. The "if ever" part of the view you quote is
not remotely compatible with known facts, however. The "near future"
part is a matter of opinion -- and of definition of "near", of course.
Aubrey de Grey
ta...@keydatatech.com
wrote:
>I am in favour of being ambitious
>now and hoping to get lucky, even if quite a lot of effort is likely to
>be wasted in the process.
Well sure. For we have little to lose an everything to gain...
Ultimately.
Tom Matthews
>
> Lou Pagnucco wrote:
>
> > Below is a summary of a paper just published in Nature Genetics which
> > demonstrates that genes (at least in lab mice) that are upregulated
> > during aging in the brain (associated with inflammation and the stress
> > response) are repressed by caloric restriction. Presumably, CR should
> > retard brain senescence.
> >
> > It is interesting that gene chips were central to this analysis. The
> > secrets of the aging process are finally being unraveled.
>
> genomic analysis techniques can tell us a great deal about cell biology
> in general and aging in particular, I think it may be worth pointing out
> the limitations of such work. I participated last weekend in a small
> meeting ostensibly focused on reversing human aging; Weindruch also took
> part and several other participants were also genomics afficionadios.
> microarray and related experiments is a picture of the **coordinated**
> gene-expression changes which occur during aging, and that such changes
> are almost entirely descriptive of what cells are doing to *compensate*
> for the primary, accumulated losses of function that define the process
> are either non-genetic (such as accumulation of protein cross-links or
> of lipofuscin), or non-coordinated (such as nuclear or mitochondrial
> mutations, which affect different genes (if any) in each cell), or both
> (such as cell loss in glands, muscle, heart, some brain areas, etc.).
> tissue, such as telomere shortening, are now known not to be (such that
> one in 10,000 or so dermal fibroblasts shows senescent gene expression
> give virtually no clue as to the relative importance of these various
> primary processes, because the changes they reveal are compensations for
> the cumulative effect of all the primary processes mixed together.
>
> in anti-aging research. For example, an intervention which restored
> the expression levels of many (or all) genes in an elderly individual
> to youthful levels in an elderly individual would be predicted to be
> *harmful*, because it would be stopping the body from making the best
> of a bad job (i.e. reacting, by gene-expression tuning, to the primary
> changes listed above).
This is the same (logically sound) argument used by those who suggest
that hormone replacement may be life shortening while at the same time
increasing the quality of life in the earlier aged years.
> The value of such analyses may in reality be
> restricted to the (important, but limited) field of biomarkers of
> "biological age". The Nature Genetics study, for example, identifies
> "selective" attenuation by CR of gene expression changes which occur
> during aging, thereby providing evidence that those genes whose change
> in expression was not attenuated are less good markers of biological
> age than the ones which did change. Another application which follows
> from this is that a candidate CR mimetic (a chemical proposed to trick
> the body into thinking it's on CR when it isn't, and thence -- with luck
> -- extending one's lifespan) could be evaluated for its likely efficacy
> by determining how similar its effects on gene expression are to those
> seen in CR.
This is very similar, but of shorter duration, to the manner in which
CR'ed animals are nowadays used as a second set of "controls" during
studies of other antiaging interventions (such as a particular nutrient
or mix of nutrients).
> A wider applicability to anti-aging research -- especially
> reversal of aging -- is, by contrast, very hard to see.
Even though I am an extreme optimist with respect to conquering aging
and supremely desirous of an unbounded life-length, I want to say how
delighted that I am to read Aubrey's cogent and lucid interpretation of
the value, and lack thereof, for the new microassay technique. I have
subconsciously "known" this to be true since I first read about this
technique and had said so to many people, but I had never got down to
attempting to construct a fully worked out explanation for that
"feeling". Aubrey has now saved me the trouble and, of course, stated it
much better than I possibly could with my current level of knowledge.
> It is therefore
> regrettable that many of those involved in such work are allowing this
> distinction to become blurred in the public mind -- and, I increasingly
> find, in their own.
I very much agree, but I think that "regrettable" is inappropriately
weak.
Both too much optimistic, unrealistic hype, and too much pessimism are
counterproductive to real progress toward any goal. But when the goal is
so momentous as human lifespan extension such errors of judgment are
potentially fatal to many people and almost certainly fatal to some.
--Tom
Tom Matthews
The LIFE EXTENSION FOUNDATION - http://www.lef.org - 800-544-4440
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Mike Reilly
>Not once we develop comprehensive somatic gene therapy (i.e. the ability
>to get engineered DNA into any chosen cell type).
Does this mean that the recent successes with beta (islet) cells is
indicative of a potential breakthrough in aging research. My understanding
is that they have succesfully inserted insulin production using somatic cell
therapy. Not only was it succesfull, but it has already been done with
humans.
Randall Parker
Your sentiment (which any good _engineer_ would share <g>) matches my
own. It raises a question however: What sorts of efforts ought to be
launched now to develop and test interventions without an understanding
of what is going on?
What are the top 5 or 10 things you'd like to see tried?
In news:<8jo0ka$q37$1...@pegasus.csx.cam.ac.uk>, ag...@mole.bio.cam.ac.uk
says...
Steven B. Harris
>changes listed above). The value of such analyses may in reality be
>restricted to the (important, but limited) field of biomarkers of
>"biological age". The Nature Genetics study, for example, identifies
>"selective" attenuation by CR of gene expression changes which occur
>during aging, thereby providing evidence that those genes whose change
>in expression was not attenuated are less good markers of biological
>age than the ones which did change. Another application which follows
>from this is that a candidate CR mimetic (a chemical proposed to trick
>the body into thinking it's on CR when it isn't, and thence -- with
luck
>-- extending one's lifespan) could be evaluated for its likely
efficacy
>by determining how similar its effects on gene expression are to those
>seen in CR. A wider applicability to anti-aging research --
especially
>reversal of aging -- is, by contrast, very hard to see.
Oh, man, it's worse than you think. For one thing, the gene
expression changes brought about by CR are far larger than the changes
induced by normal aging, indeed "old age," itself. That makes CR as
normally done more or less worthless as a tool for studying what genes
are important to aging-- the noise is several times worse than the
phenomena.
And that's even if we *could* somehow guess which of the normal
age-associated gene-expression change phenomena were causal, and which
were merely (as you point out) markers/confounders. Which we can't.
One might get rid of some of the noise in both systems by refeeding
long-restricted animals, so as to turn off some of the acute
starvation-response-genes, and see what (if anything) is left. That
might have some hope of leaving you with a smaller set of things that
stay tweaked up by restriction BUT (mirablile dictu) aren't normally
changed in that direction by aging-- which changes would then be
candidates for being things to look at more, as possible special
antiaging effects of CR. This lets you get around the causal vs
confounder thing for those genes that are changed by a history of CR,
but not by normal aging, because any genes that go the other way on CR
from what they do in normal aging, are certainly not exagerated
confounder-type age-adjustment responses. If they are age-damage
responses, they are more likely not passive, because they are reponding
more to less aging. That suggests that the horse here comes before
cart.
Of course, if you don't get lucky, and there are only genetic
expression things involved in the antiaging effect of CR which go the
same way as in normal aging, or (worse) which which go away the moment
you refeed, you'll never find them this way. Indeed, it's hard to see
how you're going to sort them out of the noise at all.
But it's worth a try. I've been arguing for a short refeed control
for CR experiments for years, but nobody really wanted to do it,
because I think they were all half-afraid that they'd get no
differences at all in biomarkers between CR and control, and thus have
nothing to report. Now, with all the junk and crap coming out of the
gene expression chips in CR mice, at last people seem willing to do
something drastic to find some way to cut through the noise. Steve
Spindler tells me he's gearing up to at last try a refeed control (not
particularly because I asked, either-- the messy results now sort of
dictate it). If I were running the NIA I'd have made them do this years
ago. But, of course, I'm not.
Steven B. Harris
COMMENT
Oh, man, it's worse than that. For one thing, the gene
expression changes brought about by CR are far larger than the changes
induced by normal aging, indeed "old age," itself! That makes CR, as
heretofore done, more or less worthless as a tool for studying what
something drastic to find some way to cut through the noise. I am told
by one worker that they are gearing up to at last try a refeed control
Aubrey de Grey
Mike Reilly wrote:
> Does this mean that the recent successes with beta (islet) cells is
> indicative of a potential breakthrough in aging research.
It's a breakthrough in aging research, but not for reasons connected
with gene therapy - see below.
> My understanding is that they have succesfully inserted insulin
> production using somatic cell therapy.
Right - not somatic GENE therapy. Many aspects of aging are due to
depletion in the number we have of a particular type of cell, and this
is an example; in many such cases it should be possible to replenish
that cell type by introducing cells grown ex vivo. Gene therapy means
introducing DNA synthesised ex vivo into cells that are already in vivo.
This is what Geron, Roslin, ACT etc are pursuing and it's definitely
of enormous value in anti-aging research. But there are aspects of
aging that somatic cell therapy is fundamentally inapplicable to,
namely those which are not related to cell loss: these include the
accumulation of intracellular junk (particularly lipofuscin), and
also accumulation of mutations (including mitochondrial ones). Gene
therapy approaches to reversing much of this have been suggested, but
not cell therapy ones.
Aubrey de Grey
Paul S. Brookes.
WRT the comments on CR and gene arrays, the whole idea that identifying genes changed in CR and then changing them by a pharmaco / genetic CR mimicry approach is more than a little shortsighted, since many of the effects of CR at the cellular level (e.g. decreased mitochondrial ROS production) can be attributed to phenomena that appear to have no genetic basis.
_________________________________________
Dr. Paul S. Brookes. (bro...@uab.edu)
UAB Department of Pathology, G004 Volker Hall
1670 University Blvd., Birmingham AL 35294 USA
Tel (001) 205 934 1915 Fax (001) 205 934 1775
http://peir.path.uab.edu/brookes
The quality of e-mails can go down as well as up
Randall Parker
Has anyone done "de-feeding" where they took aged animals on a normal
diet and switched them to CR to see what changed?
In news:<8juq7m$5oo$1...@slb3.atl.mindspring.net>, sbha...@ix.netcom.com
says...
Steven B. Harris
<rgpa...@west.net> writes:
>
>Steve,
>
>Has anyone done "de-feeding" where they took aged animals on a normal
>diet and switched them to CR to see what changed?
No, since this tends to kill them. You can do it VERY, VERY gently,
but not much as been done to see biochemically what happens. Weindruch
is the guy who's done most of those studies. He was most successful
starting with animals at only about half MLS-- say 40 or 45 for humans
(figuring that our MSL in cages with no medical care and in small
groups would be 80 or 90).
Aubrey de Grey
Randall Parker wrote:
> What are the top 5 or 10 things you'd like to see tried?
They fall into two categories: direct development of the interventions
and conclusive demonstrations that the interventions wouldn't work. I
consider that the most conclusive experiment showing that a process
does not contribute to mammalian aging during a normal lifetime is to
speed it up and observe no reduction in lifespan. Such results are
often downplayed - characterised as "negative results", which is really
a misuse of a term that should be restricted to cases where the result
could have occurred just because the experiment was done carelessly.
Also, unlike the other type of conclusive experiment (trying to retard
aging by intervention), the result that is informative actually OCCURS
every so often, whereas successful and reproducible life-extension in
mammals is decidedly hard to come by.
So, what follows is a list of what I see as main candidates for crucial
degenerative processes underlying aging, followed by (a) an experiment
doable now (when I can think of one) that would show it wasn't such a
process, and (b) a project doable now (albeit usually rather ambitious)
that would result in reversal of that process in mice.
1. Accumulation of mutant mitochondrial DNA
Falsification experiment: Mutate an appropriate mtDNA repair and/or
replication gene so as to increase, modestly, the rate of accumulation
of such mutations. If lifespan is unaffected, mtDNA mutations do not
determine the rate of mouse aging. This is very close indeed -- see
Ann N Y Acad Sci 893:353-357. I think all that is needed now is a
somewhat milder mutation than Zassenhaus's group has isolated.
Intervention: Allotopic expression of mtDNA-encoded proteins (making
transgenic copies placed in the nucleus and suitably modified so that
the proteins would get back into mitochondria). I've discussed this
in the past so I won't go into more details now; it's a big subject
which has been under consideration for 15 years. See Medline, and
also a review I have in press in Trends in Biotechnology which will
be out in a few months. I am very confident this could be achieved
in mice in under five years with appropriate funding (say $1m/year).
2. Accumulation of lipofuscin
Falsification experiment: Speed it up by dietary manipulation. This
has sort of already been done, in that vitamin E deficiency is said
to have this effect (and does not have much effect on lifespan), but
that result is controversial, because others say that the stuff that
accumulated when vitamin E is low isn't real lipofuscin. I'm hoping
that this will be resolved soon, but very few people work on it at
the moment.
Intervention: I'm currently collaborating with a colleague here in
Cambridge on a very ambitious idea: to find bacteria that can break
down lipofuscin, identify the relevant genes and get them into mice.
The first part is going well - my colleague works on a type of bug
that eats essentially anything (including TNT, for example) and it
seems to eat lipofuscin.
3. Replicative senescence
Falsification experiment: We already know that telomere length does
not limit mouse lifespan (Blasco 1997 etc). Where this leaves the
replicative senescence theory of aging is with two major hypotheses:
(a) that what matters is telomere length relative to some kind of
marker set down early in embryogenesis, as opposed to absolute
telomere length, and (b) that replicative senescence is not driven
by telomere shortening in mouse, even though it is in humans, so it
might drive mammalian aging in general after all. Theory (a) is not
completely out of the question, but would be forcefully eliminated
by showing that mouse cells underwent replicative senescence without
telomere shortening: on present data we can't quite say that, but
mouse cells with high constitutive telomerase should be around soon.
Theory (b) would be best tested by exploring what process determines
mouse replicative senescence, proving it does so by eliminating that
senescence (analogous to constitutive telomerase), and then making
it go faster in a live mouse (analogous to the telomerase knockouts).
Then, if lifespan is unaffected we can forget about replicative
senescence as a player in mammalian aging. Experts on replicative
senescence in mice that I have talked to (the UK is especially
strong in this area) consider this a few-year project (again, with
adequate funding).
Intervention: Doing in vivo what was found to eliminate replicative
senescence in vitro (in mice). Such therapy in humans is of course
being energetically pursued already, but we still need to do the
mouse experiment in order to assess side-effects.
4. Cell loss (various cell types, including glands)
5. Glycation-induced cross-linking
These are being energetically and successfully addressed (somatic
cell therapy and AGE-breakers, respectively) and I have nothing to
add to what's been discussed extensively here.
6. Accumulation of nuclear mutations not related to cancer
7. Dysregulation of nuclear genes (loss/gain of methylation, etc)
Falsification experiment: I doubt that it will be possible to
get a true assessment of the role of non-cancer-related nuclear
DNA damage (whether mutations or dysregulation) until we have very
effective anti-cancer interventions in mice. Angiostatins may
provide that soon; then a number of interventions known to cause
more mutations (such as folate deficiency) will be informative.
Intervention: Nothing presently seems to me to be anywhere near as
feasible for this as for the other types of degeneration discussed
above. Suggestions welcome....
Aubrey de Grey
Aubrey de Grey
Paul Brookes wrote:
> WRT the comments on CR and gene arrays, the whole idea that identifying
> genes changed in CR and then changing them by a pharmaco / genetic CR
> mimicry approach is more than a little shortsighted, since many of the
> effects of CR at the cellular level (e.g. decreased mitochondrial ROS
> production) can be attributed to phenomena that appear to have no genetic
> basis.
Hang on: What is your preferred interpretation of how CR decreases
mitochondrial ROS production? All the proposals I know of ARE based
on gene-expression changes.
Aubrey de Grey
Aubrey de Grey
Steve Harris wrote:
> I've been arguing for a short refeed control
> for CR experiments for years, but nobody really wanted to do it
> ...
> I am told by one worker that they are gearing up to at last try a
> refeed control
That's excellent news -- I entirely support your reasoning for it.
However, I think what you wrote at the top:
> the gene
> expression changes brought about by CR are far larger than the changes
> induced by normal aging, indeed "old age," itself! That makes CR, as
> heretofore done, more or less worthless as a tool for studying what
> genes are important to aging-- the noise is several times worse than
> the phenomena.
is misinterpretable, because it reads as though the only interesting
effects of CR are the retardations of the changes that normally happen
in aging, whereas I think everyone agrees that these retardations are a
result of big changes which don't normally occur in aging at all, and
moreover that those big, causative changes are the ones one would seek
to mimic pharmacologically for life-extension purposes. I see what you
mean, but I think that such changes are still reasonably describable as
important to aging, even if they're not important to ad-lib aging. In
other words, the "noise" you refer to is a perfectly meaningful part of
the signal -- just that it's a different signal.
Aubrey de Grey
Mike Reilly
reply... (see end of message for further comments).
>> My understanding is that they have succesfully inserted insulin
>> production using somatic cell therapy.
>
>Right - not somatic GENE therapy. Many aspects of aging are due to
>depletion in the number we have of a particular type of cell, and this
>is an example; in many such cases it should be possible to replenish
>that cell type by introducing cells grown ex vivo. Gene therapy means
>introducing DNA synthesised ex vivo into cells that are already in vivo.
>This is what Geron, Roslin, ACT etc are pursuing and it's definitely
>of enormous value in anti-aging research. But there are aspects of
>aging that somatic cell therapy is fundamentally inapplicable to,
>namely those which are not related to cell loss: these include the
>accumulation of intracellular junk (particularly lipofuscin), and
>also accumulation of mutations (including mitochondrial ones). Gene
>therapy approaches to reversing much of this have been suggested, but
>not cell therapy ones.
>
>Aubrey de Grey
Perhaps I'm wrong, but I was under the impression that the work in Edmonton
was both somatic gene and cell therapy - the beta cells were removed from a
patient, insulin production was re-instated, the cells cultured and then
re-introduced.
Mike Reilly
http://www.nhgri.nih.gov/Policy_and_public_affairs/Communications/Press_rele
ases/clinical_trial.html
Aubrey de Grey
Mike Reilly wrote:
> Perhaps I'm wrong, but I was under the impression that the work in
> Edmonton was both somatic gene and cell therapy - the beta cells were
> removed from a patient, insulin production was re-instated, the cells
> cultured and then re-introduced.
You're absolutely right. My mistake was not in mis-remembering what
was done, but in the terminology -- I always forget that introducing
engineered DNA into cells in vitro (which are then put back into the
body) still counts as gene therapy. So, to restate my point: there
are aspects of aging that might be addressed by in situ gene therapy,
but which cannot easily be addressed by ex vivo gene therapy, because
the number of cells that need to be altered in order to affect the
phenotype is too large and the cells in question are postmitotic (so
their number can't be increased after reimplantation).
Aubrey de Grey
Paul S. Brookes.
mitochondrial ROS production? All the proposals I know of ARE based
on gene-expression changes.
Also, in yur list of proposed experiments, under #1 you said...
Intervention: Allotopic expression of mtDNA-encoded proteins (making
transgenic copies placed in the nucleus and suitably modified so that
the proteins would get back into mitochondria). I've discussed this
in the past so I won't go into more details now; it's a big subject
which has been under consideration for 15 years.
A better way to go around this might be to try and get "simpler" versions of the respiratory proteins in, for example bacterial or yeast complexes with less sub-units, which might be easier to transport/import. Alternatively, some mechanism for preventing mtDNA mutation in the first place, or expediting its repair, such as mito' targetted plasmids containing DNA repair enzymes, or coding for antioxidant enzymes, or maybe just whole "replacement mtDNA" plasmids to correct the damage. The nuclear replacement route seems a long way off currently.
Regards
Paul
Aubrey de Grey
Paul Brookes wrote:
> > What is your preferred interpretation of how CR decreases
> > mitochondrial ROS production?
>
> Right now I don't have a specific interpretation, although one could
> invoke a number of things such as fatty acid compositional changes in
> mitochondrial membranes bought about by selective loss of a particular
> species during CR. I don't think it would be unreasonable to say that
> reducing overall food intake would result in loss (or retention) of
> some things more than others.
Agreed; however, that really only works for things we don't synthesise.
For fatty acids that we make, gene-expression changes to desaturases etc
would seem to be the more likely adaptation.
> > Intervention: Allotopic expression of mtDNA-encoded proteins
>
> There's a very good reason its been discussed for 15 years and not much
> done so far - mitochondria have been in existance for millions of years,
> and therefore there must be a very good reason that they haven't lost all
> their genes to the nucleus yet.
On the contrary, this is an absolutely rotten reason. Evolution has to
rely on mutations, whereas we can make arbitrary alterations to sequences
rather easily. This is a perfectly sufficient explanation for why there
has been no gene transfer since animals diverged from plants and fungi,
because at about that time the mitochondrial genetic code began to treat
UGA as tryptophan rather than STOP, with the result that our mitochondrial
genes rapidly became littered with TGA's that were previously TGG's, which
caused any later gene transfer to the nucleus to encode brutally truncated
proteins. This could only be overcome by the astronomically unlikely
back-mutation of the TGA's prior to any other mutations elsewhere in the
gene. A prediction of this interpretation is that in plants, where the
mitochondrial genetic code has stayed standard, there should be plenty of
variability of gene complement between taxa, including nuclear versions of
our "dirty baker's dozen", and that is indeed what's found (Chlamydomonas
being the current record-holder). No one has even got around to cloning
most of these genes, let alone working out how the proteins get into the
mitochondrion despite their hydrophobicity, but that may change soon.
The sad situation is that Bill Martin (author of the TIG piece) and the
other people who have explored this topic are almost all evolutionists,
not biotechnologists. The TIG article, in particular, is very heavily
focused on chloroplasts, in which for all we know there are indeed other
forces retaining genes in the organelle.
The cytosolic toxicity idea is of course also rendered dead on arrival by
(among other arguments) the very example you give, cytochrome c, which is
nuclear-coded in all species yet examined: the problem is entirely solved
by making the heme in the mitochondrion and attaching it after import.
> A better way to go around this might be to try and get "simpler" versions
> of the respiratory proteins in, for example bacterial or yeast complexes
> with less sub-units, which might be easier to transport/import.
This is rendered problematic by the fact that the mt-coded subunits are
(with only one exception, ATP8, the one which was most easily expressed
allotopically as long ago as 1986) all still present in the corresponding
bacterial enzymes, with comparable hydrophobicity. Yeast doesn't have
Complex I at all -- it uses a non-proton-pumping NADH dehydrogenase that
has only one, nuclear-coded, polypeptide -- and Yagi's group are looking
at rescuing Complex I mutations with that enzyme, with astonishingly
promising initial results (see Seo et al., 1998 PNAS and 1999 BBA), so
that may be a solution to half the problem.
> Alternatively, some mechanism for preventing mtDNA mutation in the
> first place, or expediting its repair, such as mito' targetted plasmids
> containing DNA repair enzymes, or coding for antioxidant enzymes
These are fine ideas for retarding the rate of accumulation of damage,
but I'm focusing on reversing it.
> or maybe just whole "replacement mtDNA" plasmids to correct the damage
This is being pursued by Seibel's group; I thnk it's unlikely to work
because of the selective advantage of dysfunctional mitochondria.
> The nuclear replacement route seems a long way off currently.
Let's see what you say when you've seen my Tibtech paper :-)
Aubrey de Grey
Mike Reilly
engineering them, and re-implanting them is being done, we are not yet at
the stage where we can manipulate the vast majority of cells that are in the
body. We have not yet developed the techniques required to safely access
these cells (especially those in regions with minimal circulation).
I agree that this is an area that is in _real_ need of addressing. I have
heard of some interesting work in terms of delivery of proteins to cells in
vivo, which may prove a boon both to ageing research as well as the
pharmaceutical industry.
One point I haven't seen much research on is the effect of lipofuschin on
cellular metabolism and function. The correlation between it's buildup and
cellular age is unmistakable. Any idea of the actual percentage of cellular
volume that is being consumed by liposomes?
Aubrey de Grey wrote in message <8kcg73$8e$1...@pegasus.csx.cam.ac.uk>...
Aubrey de Grey
Mike Reilly wrote:
> If I'm reading you correctly, you are saying that while removing cells,
> engineering them, and re-implanting them is being done, we are not yet
> at the stage where we can manipulate the vast majority of cells that
> are in the body.
Sort of. In situ gene therapy is also moving forward (and ex vivo gene
therapy still has plenty of problems), so it's not black and white, but
I think it's safe to say that in situ gene therapy is lagging.
> One point I haven't seen much research on is the effect of lipofuschin
> on cellular metabolism and function.
Right. Ulf Brunk is virtually the only person working on this. Look
him up in Medline.
> Any idea of the actual percentage of cellular volume that is being
> consumed by liposomes?
Lysosomes, not liposomes. In the heart it approaches 10% by old age:
see Nakano et al, Mech Ageing Dev 66:243 as a representative study.
In the brain it is very variable between different regions and there is
also in some cases controversy about what is and is not lipofuscin, but
some areas surely get amounts comparable to the heart.
Aubrey de Grey
Paul S. Brookes.
Aubrey de Grey
Paul Brookes wrote:
> Surely if man can develop such technology on a short timescale
> then nature would have done so already.
This is indeed the argument everyone uses, and I think it's quite
persuasive, but wrong. Animals have a second barrier to transfer
of genes during evolution, namely the disparity of genetic codes;
that barrier is probably even more insurmountable by evolution than
the hydrophobicity one (judging from the plant successes I noted).
But humans have got round it easily, because we've got a tool that
nature hasn't, i.e. site-directed mutagenesis. So I agree that we
will probably only get around the problem of hydrophobicity by use
of a tool hugely different from what evolution has had available,
but I don't agree that such tools are inconceivable. In fact, the
second half of my Tibtech paper is just such a proposal, concerning
using inteins to reform the correct protein after import of a much
less hydrophobic precursor. If you don't know what inteins are,
you're very far from alone; see http://www.neb.com/neb/inteins.html
> Any chance of a tibtech article preprint?
I'm told I will receive my proofs as a PDF file tomorrow; I'll send
it along.
> assuming its possible that flux control exists between the
> individual sub-units of a protein but that's another story.
Hm... and not one I've ever thought about. No comment :-)
> Is it just that these proteins have to be on mtDNA so they're readily
> up/down-regulated in response to mitochondria-specific stimuli?
I think that such considerations very probably make gene transfers
somewhat harder than they would be otherwise, but only somewhat: they
aren't the sort of all-out showstoppers that the hydrophobicity and
genetic code issues are. Otherwise we wouldn't see such variability
of gene content in plants.
Aubrey de Grey