Three Technologies to Watch

1. Thymus Regrowth with FOXN1

The thymus gland is a time bomb that would kill us at a certain age, if nothing else got us first.  It shrinks (the medical word is “involution”) gradually through life, beginning in childhood and culminating in disastrous results in old age.

The thymus is a small gland located just behind the top of the breastbone.  Among your white blood cells, your first-defense cells are the T-cells, named for their association with the thymus.  The thymus is training ground for the T-cells, where they learn to distinguish friend from foe.  The body has many types of cells, and the T-cells must not attack any of them; but they also must reliably identify invading microbes.

These immune functions are related to many aspects of health, and not just attacking invasive microbes.  The immune system is continually eliminating errant, pre-cancerous cells before they can become cancers, as well as cells in the body that have been taken over by a viral infection.  Rampant inflammation and auto-immune disorders are the consequence when the immune system begins to turn against self late in life.

As the thymus shrinks year by year, the immune system breaks down.  A 90-year-old thymus may be one tenth the size it was in the bloom of childhood, and this goes a long way toward explaining the vulnerability of older people to viral infections that would not be serious for a young person.  Arthritis is well-characterized as an auto-immune disease, but there are auto-immune aspects of other diseases including Alzheimer’s

There is good reason to think that if we can preserve or even regrow the shrinking thymus, then there will be benefits that echo through many or all the diseases of old age.  Human growth hormone has been used with some success, but reactions to HGH vary, and there is reason to worry about its long-term effects.  There is a recent breakthrough in treatment for the thymus that looks very promising.  A transcription factor is a coded chemical signal capable of switching the expression of many genes at once, turning some on and others off in one sweep.  FOXN1 is a transcription factor that has been isolated from the thymus of young mice, and by re-introducing it to old mice, a Scottish research team succeeded in consistently stimulating the thymus to regrow [ref].  The larger thymus looked and functioned much like the thymus of a young mouse.

The most glaring absence in the blood as we age is naive T-cells, cells that are not pre-trained to fight any specific infection from the past, but are primed to look out for new invaders.  So it is most promising that the thymus glands regenerated with FOXN1 produced copious naive T cells.

In the Scottish experiments, mice were genetically engineered with extra copies of the FOXN1 gene that could be turned on with a drug as trigger.  You and I don’t have these extra copies, so we need another means to get FOXN1 into our aging thymi.  FOXN1 is not something we can take in a pill, because it is a large protein molecule that is routinely chopped up for recycling during digestion.  A research group at University of Texas is injecting little snippets of DNA (called plasmids) containing the FOXN1 gene directly into the thymus with some success [ref].  Turning on the cell’s own FOXN1 gene would be ideal, and there are already candidates that can do this.  There is no reason to doubt the feasibility of FOXN1 drugs, but for now we have only rumors that they are under development.


2. New Anti-Inflammatory Drugs based on ARF6 Inhibitors

Inflammation has been a recurring theme in this blog, because inflammation is the most obvious and ubiquitous mode by which the body destroys itself.

The fact that simple, “dumb” NSAIDs lower mortality in older people and increase life expectancy is very promising, but the promise is limited because inflammation has an important positive function as well as its self-destructive role.  That’s why the more powerful NSAIDs have side-effects that limit their use.  To make real progress in this area, we will need smart anti-inflammatories that go selectively after the destructive role, and leave the protective function intact.

Dean Li and his research group at University of Utah have been addressing just this challenge.  Their breakthrough paper came in 2012, when they announced the discovery of a signaling pathway that controls just the destructive inflammation, and is not involved in the good kind.  In petri dishes, they identified a target signal called ARF6, and for therapy they constructed a protein that contained the last 12 units at the tail end of ARF6.

Have you ever broken off half a key inside a doorknob?  Not only can’t you turn the knob, you can’t pull the key out, and you can’t get another key in there either.  You may have to give up on the lock and get a new doorknob.  The tail end of ARF6 works like half a key.  It fits neatly into the same receptor as the full ARF6 molecule, but once inside it doesn’t change the conformation of the receptor the way that the full molecule does.  It won’t open the lock, and it stays stuck in the keyhole, blocking access to the real, working key.

The tail stub of ARF6 worked like a broken key to interfere with the real ARF6, preventing it from doing its job.  The Li lab was able to block the inflammatory reaction that responds to ARF6 without affecting the course of inflammation that is beneficial and protective.

They went on to inject their tail stub molecule intravenously in mice.  They report exciting initial successes, treating mouse arthritis without gumming up the other important functions of inflammation.

Some bacteria kill the host not directly but by inducing such a violent inflammatory reaction that the patient dies of his own inflammation.  Dr Li’s team challenged mice with LPS, which is the chemical that induces this fatal inflammation.  Mice protected with their ARF6 tail stub had reduced inflammatory responses, and mostly survived, while those without the tail stub mostly died after being poisoned with LPS. [ref]

This is a discovery that has yet to make front page headlines, but Dr Li’s team is fully aware of the potential for changing the way we treat the inflammatory basis of arthritis and other diseases of old age, especially coronary artery disease.


3. Telomere Length Directly Affects Gene Expression

Short telomeres cause cell senescence, which pulls a stem cell out of circulation and, worse, causes the cell to emit signals that damage neighboring tissues and the body as a whole.  This has been the basis of the theory that telomeres act as a kind of fuse for an epigenetic time bomb.  This month, a paper came out of Woody Wright’s Univ of Texas lab that adds a mechanism by which telomeres can affect aging even before cells become senescent.  Telomeres affect gene expression, which is the epigenetic state of a cell.  The same chromosome tends to express and repress different sets of genes depending on length of its telomeres.

It has long been suspected that telomere length affects gene expression.  As far back as 1990, Telomere Position Effect (TPE) was noted as affecting gene regulation.  But until this month’s study, there was no coherent idea how this occurs.  In order to study the effect systematically, the Wright team had to create a culture of cells all with the same telomere length.  They were both able to image the conformation of the chromosomes and also measure the genes they expressed as a function of telomere length.  Wright introduces the acronym TPE-OLD, for Telomere Position Effect Over Long Distances.  What they found was that

  • Telomere length affects the folding and conformation of the DNA
  • Telomeres wrap back over coding DNA and have effects extending at least 10MB from the end
  • Telomere length affects the transcription of at least hundreds, perhaps thousands of genes.

(To have a sense of the scale, keep in mind that a human chromosome is hundreds of millions of base pairs long (108), that the length of a telomere is only about 10 thousand BP (104), and that there are about 25,000 genes in the human genome.  So, even though telomeres are 0.01% of the length of the chromosome, they may affect the transcription of 3% of all genes.)

Gene expression changes with age in some ways that are regular and others that are random.  I would say that as we age, our epigenetic state changes toward a self-destructive, inflammatory mode, and also drifts randomly out of tight regulation.

Telomere length varies greatly from one tissue to another, from one cell to another within a tissue, and from chromosome to chromosome within a cell.  It is difficult to make sense of this within a picture of a tightly-regulated aging program.  But the idea that the random portion of telomere length contributes to epigenetic drift seems plausible to me.

In any case, the present study opens a door to a new science, and gives added credibility to the idea that telomere length plays a fundamental role in human aging.

Nicotinamide Riboside — Where’s the Beef?

NR is a supplement that affects energy generation in mitochondria and gene regulation through the same pathway as resveratrol and caloric restriction.  It has been promoted in recent months, and this month is featured in Life Extension Magazine.  But evidence for its life expectancy benefit is indirect.  There have been no positive results for fruit flies, let alone mice.  If it works in humans, benefits will likely be limited to people who are overweight.  And there are reasons to expect only limited benefits from the pathways through which NR works.

Reading about a new life extension supplement, I get excited when I see “we fed it to mice and they lived X% longer”, or better yet, “In preliminary human trials, mortality was found to be Y% lower.”  The articles about NR are full of biochemical pathways and chains of genes that promote other genes.  In my way of thinking, all the biochemistry is important for generating ideas, but the proof of the pudding is in life extension trials.  Lab experiments on live mice run hundreds of thousands of dollars to test a single compound.  We can’t be testing everything under the sun, so we rely on biochemistry for plausible candidates.  But jumping from biochemical theory to marketing of a supplement is a leap of faith that leaves me behind.

Worms and flies are much cheaper to breed than mice, and the experiments last weeks instead of years.  Furthermore, genetics of these lower animals is well-understood, and easy to manipulate.  Experiments with worms and flies provide an intermediate proving ground for ideas before the expensive life span trials with rodents.  The ultimate yield is low.  There are many interventions that work well to extend life in flies that don’t work in mammals.


NR and Resveratrol

Resveratrol, which works along similar biochemical pathways to NR, was all the rage from about 2003 to 2006.  First discovered in yeast, its mechanism of action was mapped out.  Len Guarente at MIT and others from his lab put the SIR gene on the  map, and coined the term “sirtuins” for substances that activate these genes.

Excitement mounted as resveratrol was shown to extend life span in worms, and then flies.  A young scientist in Italy launched his career by introducing a short-lived African fish to laboratory genetics.  Nothobranchius lives only a few months, one of the shortest life spans of any vertebrate.  For his PhD dissertation, Dario Ricardo Valenzano (2006) safaried to Africa to bring back samples of Nothobranchius, figured out how to breed them in the lab, and demonstrated they live 60% longer with resveratrol in their food.

Incidentally: Valenzano found best results for an intermediate dose of resveratrol, not the highest or the lowest dose.  This has been a recurrent theme in resveratrol research: a little is better than none, but a lot isn’t better than a little.

Soon after Valenzano’s fish, it was reported that resveratrol failed to extend life span in mice.  We were all disappointed.  The result came from the Harvard lab of David Sinclair, Guarente’s most famous student, who was highly motivated to get good results because he had commercial ambitions for resveratrol derivatives.  Sinclair reported that overweight mice that were fed a high-fat diet could be brought back to a normal life expectancy with resveratrol, but that normal-weight mouse received no life extension from the same treatment.


NR in experiments with lab animals

Almost all the literature on NR is about yeast cells.  I can’t find a single study on flies or fish.  I found one study of Alzheimer’s Disease in mice that did not look at life span, but the measured the plaques in the brain that are a symptom of AD.  These are mice that are genetically engineered to be vulnerable to AD, because normally AD is absent in mice.  They showed that feeding these mice NR slowed the progress of their mental decline, a good result that traces dietary cause all the way to behavioral effect, its ultimate benefit.  Another mouse study showed metabolic benefits for mice that were fed to obesity.  This was similar to the result for resveratrol, but not as strong because life extension for obese mice was recorded from resveratrol, but not from NR.  The only study in worms showed a 16% life extension.  This kind of performance would be impressive in mice, but there are many ways to double and triple the life span of worms that don’t work in mammals.  (the record is tenfold increase in a genetically modified worms).;


Biochemistry of NR and NAD+ / NADH

Biomolecules are a huge variety of different geometric structures, based mostly on covalent bonds between carbon and carbon or between carbon and hydrogen.  But the body’s energy metabolism is based on ionic bonds, because they store more energy in each bond.  Ionic bonds form between atoms that are very different from each other, like sodium and chlorine in table salt.  The standard biological energy repository is in phosphate bonds.

Every cell has hundreds of mitochondria, which are tiny energy factories that burn sugar and produce  phosphates for the cell’s use.  This energy generation process is an ancient biochemical trick called the Krebs Cycle, and is shared by all plants and animals today.  NAD+ has a role to play in the Krebs Cycle, where it absorbs an electron to become NADH, and then is recycled to NAD+ again.

As we age, we lose mitochondria, and the mitochondria we have become less active.  We have less of all the chemical intermediates of the Krebs Cycle, including CoQ10 and NADH.  CoQ10 is an important anti-oxidant, soaking up ROS and converting their energy to useful form.  CoQ10 has been found to improve heart health, but it has failed to extend life span in mice.

In addition to its role in the Krebs Cycle, NAD+ works through sirtuins.  These are high-level chemical signals that can close up DNA into tight balls (facultative heterochromatin) selectively in certain places to block expression of many genes at once.  NAD+ can turn on sirtuins in order to turn off a panoply of pro-aging genes.  This has been shown to work well to slow aging in obese lab animals, but not normal animals.  It works by some of the same pathways as caloric restriction, but without the restriction.


Saturation of the CR pathway

Life span is programmed in a flexible way, so as to respond to external mortality.  Famine is one of the deadliest dangers for populations in nature, and so evolution has provided extra ruggedness in the face of starvation.  Death from aging takes a vacation just when the death rate from starvation is highest, helping to level out the overall death rate and protect against extinction.

The fact that life span is extended by hunger was first discovered in the 1930s, and many years later, the genes and biochemical pathways associated with sensing food scarcity have proven to be the most accessible, the easiest to manipulate.

Underfeeding, and tricking the body into thinking it is underfed, are the simplest, most fertile, and most reliable strategies for extending life span.  On a percentage basis, these strategies work best in short-lived species.  With caloric restriction we can double the life span of worms, add 40% to the life span of mice, but only 15% to dogs and 5% or less in Rhesus monkey experiments reported last year.  So 3 to 5 years is an optimistic range for the available flexibility in humans via the caloric restriction pathway.

There are many ways to activate this pathway, either by eating less, exercising, or taking metformin or resveratrol, for example.  The benefit you get from each of these do not add together; rather you are getting the same 3 years over and over again.  So NR is likely to work best for people who are overweight and not taking metformin or resveratrol.


The bottom line

It may be that there have already been experiments feeding NR to mice or rats, but sometimes negative results don’t get published.  I am going to wait and see before jumping on the NR bandwagon.

Quick Notes from Quebec

 (or “Short Takes from Sherbrooke”),
Center for Research on Aging, Symposium Nov 2-4

Why does the cell appear to be shooting itself in the foot?” asked Andres Kriete of Drexel Bioengineering Dept.  All through the conference, I heard people puzzle that our bodies seem to miss opportunities to save themselves from aging, or worse, that they seem to be pouring gasoline on the fire.  Invariably, researchers sought to reconcile what they were seeing with their faith that the body really is evolved to protect itself as best it can.  Everything that looks on its face like a suicide mechanism is re-interpreted to have some hidden benefit.

I was invited to the conference as an advocate of programmed aging, the only one in the room.  I found everyone to be more than polite–listening with an open mind and eagerly engaging with me.  I spoke on a subject that I find exciting, and which has seen an explosion of results in recent months: the possibility that aging is controlled by a biological clock based on epigenetic programming.


Experts in diverse fields, hailing from La Jolla to Poland were represented, and I made several new friends, while renewing acquaintance with Siegfried Hekimi, whose lab I visited four years ago.  I woke up this morning visited by a muse, and penned this before I got out of bed.

Ballad of the Sherbrook Gerontologists

When joints and arteries become inflamed,
The body yields to nature’s conflagration
The standard culprit (as always) is blamed.
The problem must be some dysregulation

We scratch our heads, we wonder what went wrong.
To clearly programmed death we pay no heed…
And comfort find we in familiar song:
“Respect the body’s wisdom” is our creed.

The muscle’s satellites that proudly grew
Retire now and yield to cell senescence
Forsake their given mission, to renew…
But we question not their motives nor their essence.

We scratch our heads, we wonder what went wrong.
To clearly programmed death we pay no heed…
And find we comfort in familiar song:
“Respect the body’s wisdom” is our creed.

And even in the face of apoptosis,
The body’s good intent we must abide.
We tender our familiar diagnosis
And whisper not the phrase “cell suicide”.

For evolution is our benefactor
And we must never question her intent
We blame some tradeoff, or an unknown factor
Though on our own demise she is hell-bent.

We scratch our heads, we wonder what went wrong.
To clearly programmed death we pay no heed…
And comfort find we in familiar song:
“Respect the body’s wisdom” is our creed.

– JJM, 2014 Nov 4

Here are some teasers for things I found most interesting in this brief symposium:

One study in Scotland found diabetics who take metformin live longer than non-diabetics who don’t!  (There’s no data on non-diabetics taking metformin, because there are so few of us.  But in studies with normal, non-diabetic mice, metformin extends life span.) (from presentation of Nir Barzilai)

Centennarians don’t have healthy eating habits, don’t exercise more than others in their cohort or smoke or drink less.  They also don’t have genes that are associated with protection from cancer or heart disease or AD.  What they do have is genetic pre-disposition to long life, and it is specific genes that slow aging.  There are specific genes that are necessary to make to age 100, and without them your chances are slim.  (This is different from longevity between ages 70 and 90, which is affected much more by life choices, environment, etc.) (also from Nir Barzilai)

During the last 2 years of life of a centennarian, health costs are ⅓ what they are for the last 2 years of someone who dies at 75. (also from Nir Barzilai)

Burning ketone fuel instead of sugar helps protect the brain against Alzheimer’s Disease.  Fasting a few days, of course, shifts the body to ketosis.  A low-carb diet is ketogenic, but even better are medium-chain triglycerides, often refined from coconut oil for experimental diets. (presented by Alex Castellano)

The Free Radical Theory of aging has it all backwards, says Siegfried Hekimi.  ROS are not a cause of the oxidative damage that accumulates with age, but rather a signal that turns on the body’s protection against that damage.  In his McGill laboratory, worm life span has been increased almost twofold by exposing them to a strong pro-oxidant chemical.  In biology experiments, it is called “paraquat”, but the Vietnamese knew it as Agent Orange.  Of course, large doses of paraquat poison the worms, and their lives are shortened.  But a range of low doses is beneficial.  This result comports with genetic experiments.  The all-time record for long-lived, genetically altered worms is a worm that lacks the ubiquinone gene, so that its energy metabolism is completely disrupted and it is unprotected from ROS.

Children conceived to starving women in Netherlands 1944 had higher rates of metabolic syndrome 50 and 60 years later, due presumably to epigenetic patterns of methylation laid down at conception. (presentation of Irene Maeve Rea)

Michael Kobor of UBritColumbia shared my enthusiasm for the epigenetic clock. He cited recent work of Steve Horvath, demonstrating a set of epigenetic changes that are characteristic of the aging human.  Some of his own work documents the influence of childhood deprivation on epigenetics that affect health, psychology and longevity much later.

And in preparing my own presentation, I un-learned something that I been taught long ago.  DNA is supposed to be the same in every cell in our body (except for a small number of random mutations).  But a recent paper actually samples tissue from different organs and finds big differences.  Could it be that the body is re-configuring its own DNA, as well as epigenetics, when differentiating?  If this is real, it implies an ability we didn’t know cells possess.

Rumors are the most fun

Alan Cohen (from the home team at University of Sherbrooke) told me that he was in touch with Vaupel, whose work I wrote about back in January.  Vaupel had just published a paper comparing the aging patterns of 48 different animals and plants, mostly animals.  Some age gradually, some hardly age at all until the end, and they all die suddenly.  Some age “backwards” in that they become less and less likely to die as time goes on.  Alan told me that Vaupel and his group at Max Planck Inst have been expanding this list, drawing a more representative sample of 10,000 species, and there is a great deal more “non-aging” than anyone expected.

For at least 10 years, it has been known that senescent cells are “bad actors”, not just shirking their duty to the body but spewing out toxins that destroy neighboring cells and contribute to systemic inflammation, ultimately to cancer. In 2011, Jan van Deursen of Mayo Clinic in Minnesota published a paper that demonstrated this dramatically.  Mice were genetically modified to attach a self-destruct signal to the p16 gene, which is a marker of senescence.  The mice could then be dosed with a signal, and the senescent cells would eliminate themselves cleanly via apoptosis.  The mice with their senescent cells removed had a 20 to 30% greater mean life span and even better results for health span.  Even though these cells are less than 1 in 10,000, they do damage far out of proportion to their numbers.  (To my way of thinking, cell senescence is clearly part of the aging program.)

Van Deursen was there to explain and update his work.  The rumor is that there are at least five companies around the world working on drugs that will remove senescent cells without harming other cells, and that these drugs show promise for treating all the major diseases of old age.