Oxidation


(previous session)

At the end of the meeting, Martin Brand and Stuart Kim led a group discussion about the free radical theory of aging. Martin began the discussion by pointing out that “after 50 years, you would expect a theory to accumulate enough evidence to convince us that it’s true or false – but the fact that we’re still discussing it today means that hasn’t happened.” I’m paraphrasing slightly, but that’s the general idea.

Martin Brand (who doesn’t, by the way, adhere to this theory) started by summarizing the evidence in favor of FRTA:

  • “50 million Frenchmen can’t be wrong” (i.e., there are lots of correlative experiments)
  • SOD2 knockout is bad
  • catalase overexpression is good

Stuart rejoined with some contradicting evidence:

  • Superoxide dismutase protects against oxidative stress but has little effect on lifespan in mice
  • Deletion of mitochondrial SOD extends lifespan in C. elegans
  • High oxidative damage levels in the longest-living rodent, the naked mole-rat.

To the last of which, others answered:

  • The naked mole rat isn’t suffering from a global increase in oxidative damage – rather, there are a small number of proteins with increased damage, which may represent antioxidant proteins protecting the rest of the cell
  • There’s no evidence that naked mole rats increase damage with age, which is a more relevant metric

The first two pieces of Stuart’s contradicting evidence were more difficult to challenge. Some ideas:

  • Overexpressing an antioxidant enzyme in the wrong subcellular compartment wouldn’t be predicted to have any effect on lifespan

Martin also asked questions about whether FRTA is even falsifiable, and lamented the absence of an alternative clear, single-sentence “singular” theory of aging.

No final resolution but on the balance it seems like the theory is on the ropes, as we’ve discussed here before.

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(previous session)

Matt Hirschey (Verdin Lab, UCSF-Gladstone): Lack of SIRT3 results in the metabolic syndrome. SIRT3 is a mitochondrial sirtuin (NAD+-dependent deacetylase) that is upregulated in liver upon fasting; knockout mice (SIRT3KO) are grossly normal but have trouble with lipid metabolism (specifically, beta-oxidation). Hershey identified several mitochondrial proteins involved in lipid oxidation that are deacetylated in response to fasting, in wildtype but not SIRT3KO. The knockouts are prone to developing obesity and metabolic syndrome with age.

Kate Brown (Chen lab, UC-Berkeley): Calorie restriction reduces oxidative stress by inducing SIRT3. Beginning with an invocation of the free radical theory of aging, and the observation that calorie restriction (CR) reduces oxidative stress, Brown asked whether the mitochondrial sirtuin SIRT3 could be involved in resistance to reactive oxygen species. She showed that CR induces SIRT3 expression, and that the SIRT3 protein deacetylates the mitochondrial antioxidant enzyme SOD2. Furthermore, consistent with Subhash Katewa’s talk in the first session, she demonstrated that CR reduces oxidative stress by switching from glucose to fatty acid oxidation, and that this switch requires SIRT3 activity.

(We’ve discussed SIRT3 before, most recently regarding its role as a tumor suppressor and also with respect to its relationship with exercise).

Ruth Tennen (Chua lab, Stanford): Insight into SIRT6 function at telomeres and beyond. Another member of the sirtuin family, SIRT6, is not localized to mitochondria but rather to telomeres, where it maintains telomeric chromatin in a healthy state and regulates the activity of the senescence-associated transcription factor NF-κB – for more background, see this previous post.) Tennen has shown that SIRT6 is involved in regulating the telomere position effect (TPE) – the silencing of gene expression caused by proximity to a telomere. The TPE has been implicated in age-related changes in gene expression: as telomeres shorten over time, telomere-proximal genes are aberrantly expressed — meanwhile, silencing factors are liberated to wander throughout the genome, repressing genes that should be turned on; similar logic has been applied to the relationship between DNA damage and transcriptional dysregulation.

Jue Lin (Blackburn Lab, UCSF): Telomere length maintenance and aging-related diseases. This talk described work that builds on significant progress, from this lab and others, demonstrating relationships between telomere length and stress, psychological outlook, and lifespan. Lin reviewed evidence that perceived stress is correlated with telomere length in white blood cells (consistent with previous results showing a relationship with intrusive thoughts). New-to-me data included a demonstration that people who increased omega-3 levels or made favorable lifestyle changes exhibited a slower rate of telomere shortening.

(next session)

An overwhelming number of natural products and nutraceuticals vie for our attention. Each is associated with a variety of claims of health benefits, often without any reference to the experimental evidence (if any) supporting those claims – or with reference only to dubious, poorly controlled studies in backwater journals. I don’t spend a lot of time following these compounds, but occasionally one gets mentioned often enough that is breaks through into the literature (e.g., resveratrol, green tea, carnitine/lipoate, or other supplements) and I discuss it here.

If only because of the size of the heap, I nonetheless still suspect that there’s a pony in there somewhere; I’ve often wished I had the time to do a comprehensive literature review of my own, so that I could identify the compounds whose associated claims are supported by the best evidence. Now it looks like I can start wishing for something else, because someone did it for me.

At the (amazing) blog Information is Beautiful, David McCandless and Andy Perkins have assembled a “generative data-visualisation of all the scientific evidence for popular health supplements“. In David’s words:

I’m a bit of a health nut. Keeping fit. Streamlining my diet. I plan to live to the age of 150 in fact. But I get frustrated by constant, conflicting reports and studies about health supplements.

Is Vitamin C worth taking or not? Does Echinacea kill colds? Am I missing out not drinking litres of Goji juice, wheatgrass extract and flaxseed oil every day?

In an effort to give myself a quick reference guide, I dove into the scientific evidence and created a visualization for my book. And then worked with the awesome Andy Perkins on a further interactive, generative “living image”.

The image itself is dynamic with respect to both user input about what information is desired, and introduction of new data – it is based on the information in a spreadsheet, which can be updated (new compounds, or information about compounds already mentioned), altering the visual rendering the dynamic image. You can play with the image here; I’ve attached a still snapshot below.

The rendering is imperfect (as also discussed elsewhere): More reliable claims are near the top, and more dubious claims are near the bottom, but this positioning is the result of a single variable, “evidence,” which may the based largely on a citation count. This is a problem because not all citations that mention a compound should be weighted equally; furthermore, it’s not clear how conflicting claims end up getting counted. The abstraction of a complex body of data into a single number unquestionably involves some judgment calls that could be made differently – that’s not necessarily a lethal criticism, but the process should be as transparent as possible.

On a visual level, the image is attractive, but color is mostly a wasted variable: position along the color spectrum is synonymous with height — except in the case of orange, which indicates a compound with “low evidence, promising results”. The orange compounds are still assigned an evidentiary weight, according to an algorithm I can’t fathom; this is particularly confusing at both ends: beta-glucan is in the “high evidence” position, which seems to contradict the label’s definition (“low evidence”); whereas noni and astragalus are in the “no evidence” position, raising questions about how there could be “promising results”.

The strength of the project, however, is that it can evolve; the creators are already enthusiastically updating it. So far the changes (as detailed in this log) are content-oriented; one hopes that the methodology of generative data visualization will also enjoy improvements as time goes by.

(For another example of user-driven visualization, see the Timeline of Discoveries in the Science of aging, which we discussed here previously (1 2). That piece hasn’t been updated in a while – perhaps it could use some new contributors.)

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Yesterday we learned that the most well-characterized mammalian sirtuin, SIRT1, is involved in the control of behavior in response to food availability. SIRT1 is just one of seven sirtuins in mammalian genomes, each of which has a characteristic expression pattern, subcellular localization, and physiological importance.

Today we’re going to talk about another member of the sirtuin family, SIRT3, which has been known for a while now to localize to the mitochondria. Now, Kim et al. have shown that the SIRT3 protein acts as a tumor suppressor:

SIRT3 Is a Mitochondria-Localized Tumor Suppressor Required for Maintenance of Mitochondrial Integrity and Metabolism during Stress

The sirtuin gene family (SIRT) is hypothesized to regulate the aging process and play a role in cellular repair. This work demonstrates that SIRT3−/− mouse embryonic fibroblasts (MEFs) exhibit abnormal mitochondrial physiology as well as increases in stress-induced superoxide levels and genomic instability. Expression of a single oncogene (Myc or Ras) in SIRT3−/− MEFs results in in vitro transformation and altered intracellular metabolism. Superoxide dismutase prevents transformation by a single oncogene in SIRT3−/− MEFs and reverses the tumor-permissive phenotype as well as stress-induced genomic instability. In addition, SIRT3−/− mice develop ER/PR-positive mammary tumors. Finally, human breast and other human cancer specimens exhibit reduced SIRT3 levels. These results identify SIRT3 as a genomically expressed, mitochondria-localized tumor suppressor.

So, the absence of the SIRT3 gene disrupts mitochondrial function and destabilizes the mitochondrial genome, but the causal relationship is unclear: one can imagine a derangement of mitochondrial morphology or physiology causing the genomic instability, but one can also imagine a primary defect in DNA metabolism causing the physiological defects — and one could also imagine both, operating in a vicious cycle.

The significance of the “single oncogene” observation requires a bit of explanation: In a normal cell, simply turning on a single tumor-promoting gene isn’t sufficient to transform the cell, i.e., create a tumor — if a cell detects a hyperphysiological level of a growth factor or internally generated mitogenic signal, it will undergo senescence, a permanent cell cycle arrest that (among other things) prevents mutated cells from turning into cancers.

In the case of the SIRT3 knockout, however, a single oncogene is enough to transform an otherwise normal cell, i.e., the loss of SIRT3 function appears to potentiate the transformation process. Furthermore, this implies that the mitochondria are involved in the decision to undergo senescence. This is not to say that SIRT3 is directly involved in the senescence fate decision: the SIRT3 knockout has broadly deranged mitochondria, and it’s not clear which mitochondrial function is involved in senescence.

While this report does not fully elucidate the mechanism of SIRT3 action, it is clear that oxidation must be central to the issue: reactive oxygen species (ROS) levels are high in the SIRT3 knockout, but increasing the dose of an antioxidant enzyme prevents the single-oncogene transformation. We don’t yet know whether the ROS themselves are causing oncogenic mutations, or the loss of the mitochondrial function in senescence is allowing cells that would have arrested to progress further down the path to cancer. (Could be both, obviously, but it’s likely that one of the two is more important.)

These findings are consistent with what we already know about the connection between mitochondrial ROS, cellular damage and lifespan (ideas that are central to one strategy for developing longevity-enhancing drug compounds by targeting antioxidants to mitochondria), but they raise a question: how much of the “longevity regulation” we owe to antioxidant genes can be attributed to tumor suppression?

ResearchBlogging.orgKim, H., Patel, K., Muldoon-Jacobs, K., Bisht, K., Aykin-Burns, N., Pennington, J., van der Meer, R., Nguyen, P., Savage, J., & Owens, K. (2010). SIRT3 Is a Mitochondria-Localized Tumor Suppressor Required for Maintenance of Mitochondrial Integrity and Metabolism during Stress Cancer Cell, 17 (1), 41-52 DOI: 10.1016/j.ccr.2009.11.023

There’s lots more about SIRT3 in a recent post at @ging.

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A prominent scholar of the CLK-1 story has called the coroner on the mitochondrial free radical theory of aging (MFRTA). From Lapointe & Hekimi:

When a theory of aging ages badly

According to the widely acknowledged mitochondrial free radical theory of aging (MFRTA), the macromolecular damage that results from the production of toxic reactive oxygen species (ROS) during cellular respiration is the cause of aging. However, although it is clear that oxidative damage increases during aging, the fundamental question regarding whether mitochondrial oxidative stress is in any way causal to the aging process remains unresolved. An increasing number of studies on long-lived vertebrate species, mutants and transgenic animals have seriously challenged the pervasive MFRTA. Here, we describe some of these new results, including those pertaining to the phenotype of the long-lived Mclk1 +/− mice, which appear irreconcilable with the MFRTA. Thus, we believe that it is reasonable to now consider the MFRTA as refuted and that it is time to use the insight gained by many years of testing this theory to develop new views as to the physiological causes of aging.

MFRTA recently turned 50, and consequently has received a lot of attention lately; q.v. this review and this retrospective by Denham Harman, the originator of the theory. The thesis of most pieces seems to be that the theory hasn’t been demonstrated to explain the bulk of age-related decline, but that there’s still life in the idea. In contrast, the authors of this review argue that the relevant experiments have been performed and that the theory has been falsified — in other words, we’ve done our scientific duty and it’s now time to move on.

I doubt very much that this article will put a permanent end to the controversy. Data reported fairly recently have breathed new life into oxidative theories in general and the MFRTA in particular. While these authors contend that the CLK-1 mouse mutant contradicts the underlying mechanisms of the MFRTA, other recently reported work on this pathway supports the claim that inhibiting mitochondrial respiration delays aging, a key prediction of MFRTA.

Furthermore, if mitochondrially generated oxidative radicals are truly not playing a causative role in aging, it becomes much harder to explain how mitochondrially targeted antioxidants can extend lifespan in mammals.

ResearchBlogging.orgLapointe, J., & Hekimi, S. (2009). When a theory of aging ages badly Cellular and Molecular Life Sciences DOI: 10.1007/s00018-009-0138-8

I’m sitting in the Drexler Auditorium of the Buck Institute, where I’ve been working over the last six months. Today we’re being treated to an off-schedule “Special Institute Lecture” by Harvard’s Gregory Verdine. These are my notes about the talk; below, I’m paraphrasing Verdine’s words, not writing my own.

To fix it you have to find it: Repairing oxidative damage to DNA.

Mitochondrial metabolism generates oxygen radicals, which damage DNA and increase the risk of mutation. The primary oxidative adduct of guanine, 8-oxoG, differs by only two atoms from the original guanine, but this small difference is still enough to change the residue’s base-pairing characteristics (i.e., from G=C to 8-oxoG=A). 8-oxoG is repaired by the enzyme Ogg1, which displaces the damaged residue by covalently bonding to the DNA backbone.

Ogg1 has a tough job: oxoG-C base pairs are perfectly stable, and from the outside they look just like G-C pairs, so the detection of rare lesions within the genome poses a tremendous challenge. In crystallographic studies that exploited a catalytically dead Ogg1 enzyme (which can recognize but not cleave DNA), Verdine’s lab has shown that the binding of Ogg1 at a G-C base pair results in the extrusion of G or oxoG to the exterior of the double helix, setting the stage for repair — but how does Ogg1 find the lesion site in the first place? To answer this question, Verdine’s group visualized single molecules of Ogg1 diffusing in one dimension along a double helix. They observed that Ogg1 moves so quickly that it can’t be checking every G-C base pair along its path. Instead, Ogg1 (and other lesion-repair proteins) may exploit subtle rearrangements in the DNA backbones near lesion sites. The enzyme amplifies these local structural changes into substantial conformational changes, leading to base extrusion and starting the process of repair.

We want a new drug: Synthetic biologicals as novel pharmaceuticals

Small-molecule drugs have “good geography,” in the sense that they can cross cell membranes. However, they’re limited, in that they can only target proteins that engulf them (e.g., in hydrophobic pockets or active sites). Proteins, on the other hand, have much more diverse function, but terrible geography — they simply can’t get into cells, and they’re therefore useless for intracellular targets. Both classes of drug can attack (generously) only ~10% of prospective targets. Therefore, we need an entirely new class of drug: synthetic biologics like stapled peptides and RIPtides, which combine the bioavailability of small molecules with the functional diversity of proteins.

Stapled peptides are essentially the interaction domains of proteins, conformationally restrained in such a way that they still retain the active structure. (Think of a protein as a delivery system for an interaction domain, in which the non-interacting portions serve primarily to hold the ID in place.) An interaction domain alone would be too floppy to have a biological effect; conversely, the intact protein has the desired function but can’t cross the membrane. Solution: replace the main body of the protein with a hydrocarbon “staple” that keeps the interactive domain in the active conformation, without substantially increasing its size. Surprisingly, stapled peptides are taken up by cells via an energy-dependent active transport process, one upshot of which is that they don’t need to be uncharged and hydrophobic in order to cross the membrane. Drugs of this kind have already been used in animal studies to suppress leukemia by activating apoptotic factors in tumor cells.

Declaring open season on transcription factors

A brief concluding note: Transcription factors are among the most well-validated prospective targets, but they have historically been outside the scope of drug developers. TFs function primarily by protein-protein interactions that aren’t amenable to interference by small-molecule drugs. Recently, however, Verdine and others have been able to use synthetic biologicals to interfere with a specific oncogenic transcription factors.

My own comments

OK, so, not a lot of specific about either aging or cancer, but the idea of a novel class of pharmaceuticals that could be used to attack the “missing 80%” of validated prospective drug targets is still very exciting.

The free radical theory of aging (FRTA) was first advanced by Denham Harman more than 50 years ago. The theory proceeds logically from a small number of straightforward assumptions, based on observations from radiation biology. From the Science of Aging Timeline:

Harman’s logic proceeds from three observations: (1) irradiation causes premature aging; (2) irradiation creates oxygen radicals, which may mediate its effects; and (3) cells produce oxygen radicals under normal conditions. From these premises, he theorized that aging could be caused by endogenously generated oxygen radicals.

Over a half-century, the FRTA has evolved substantially (eventually focusing on the mitochondria as a major source of the initially postulated endogenous radicals), and has lately been the subject of several reviews evaluating its explanatory power and extent of current acceptance.

A unique perspective on the FRTA’s history has recently been provided by none other than its initiator, Denham Harman, who is retired but still intellectually active. From his review:

Origin and evolution of the free radical theory of aging: a brief personal history, 1954–2009

Aging is the progressive accumulation in an organism of diverse, deleterious changes with time that increase the chance of disease and death. The basic chemical process underlying aging was first advanced by the free radical theory of aging (FRTA) in 1954: the reaction of active free radicals, normally produced in the organisms, with cellular constituents initiates the changes associated with aging. The involvement of free radicals in aging is related to their key role in the origin and evolution of life. The initial low acceptance of the FRTA by the scientific community, its slow growth, manifested by meetings and occasional papers based on the theory, prompted this account of the intermittent growth of acceptance of the theory over the past nearly 55 years.

It’s a very personal account, starting with the educational experiences that Harman credits with putting him in the right place at the right time, continuing with a description of the origins of the theory, and paying a great deal of attention to the “fits-and-starts” advancement of the theory toward broad acceptance (though not without effort and extensive modification). Pieces like these, in which the originator of a hugely influential theory provides their individual perspective on the consequences of their work, are rare indeed — hence this is a must-read for students and practitioners of biogerontology.

ResearchBlogging.orgHarman, D. (2009). Origin and evolution of the free radical theory of aging: a brief personal history, 1954–2009 Biogerontology DOI: 10.1007/s10522-009-9234-2

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