Winding the Biological Clock
Imagine that you’re a scientist working on a new drug to combat ageing. You start moving up the ladder of laboratory organisms. It works in yeast. Then in C. elegans. Then in fruit flies. And, finally, in mice too. You’re very excited. After some speculation, you decide to take the leap and bet on this drug. Years go by with safety tests, fundraising, dosage experiments and a lot of bureaucracy. But eventually, you’re ready to answer the big question: will your new drug work in humans? You sit down to plan the trial. How are you going to find out? Are you going to give your drug to a bunch of middle-aged people? Then you’ll have to wait for decades to find out if they lived longer than usual. Instead, you could give your drug to people who are already old. But even this trial will take many years – and by using old people, you’re giving your drug less time to work. You could end up in a situation where the trial fails but is still suggestive of some benefit. Then you either have to give up, or revert to the original plan: giving your drug to middle-aged people while waiting the rest of your career to see what happens.
As you might imagine, this ‘waiting dilemma’ is extremely annoying to biomedical scientists. It’s one of the main obstacles for anyone trying to develop preventative medicine. If you want to prevent, say, dementia or cancer, it will take years before you know if a potential drug works. Only then can you adjust your approach accordingly. And mind you, even making it to the point where you can test a drug takes many years and costs millions of dollars. So it is really no surprise that progress in medicine tends to be slower than in many other areas of science and technology.
The huge time investment required for drug development is why researchers are excited by what are called biomarkers. A biomarker is a surrogate indicator for some important biological outcome. It’s something you can easily measure that helps tell you about a particular biological state. For instance, during a fever, your temperature rises. That means we can use body temperature as a biomarker for fever intensity. If we give you a new drug, and your body temperature starts falling, it might be because the drug is treating whatever is causing your fever.
You can imagine another biomarker that, instead of ‘tracking’ the progression of a fever, tracks biological age. That is, it describes how old you are biologically as opposed to the number of candles on your birthday cake. In more morbid words, a biomarker for biological age would accurately describe how close you are to death. We’re well aware that two people who might be the same age chronologically can have bodies in wildly different physical conditions. Some seventy-year-olds are busy running marathons, while others are struggling to walk to the corner shop. In this case, the first person might be fifty-five biologically, while the other person is eighty-five biologically.
So, if you had a biological clock, your drug-development efforts would be much easier. At the start of your trial, you’d get baseline measurements. Then, you’d make two groups with similar characteristics and give the subjects in one group your drug. Now, instead of waiting for years until people die, you’d occasionally measure their biological ages. If your drug really works, it will slow down the biological ageing of those receiving it. That means they would be biologically younger at later measurements than the control group, who would continue to age normally. And in that way, you’d save yourself a whole lot of time.
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Among the first ‘biological clocks’ proposed were telomeres. At first glance, they seem a good match. As you might remember, our telomeres gradually get shorter throughout our lives, and shorter telomeres tend to correlate with an earlier death. For this reason, many studies do use telomeres as a biological clock, and they are better than nothing. However, telomere-shortening is not as reliable a biological clock as we might wish. Yes, on average, people with shorter telomeres tend to die younger but the correlation is far from perfect. And if we zoom out, away from just humans, the picture gets murkier still. Mice, as we’ve seen, have longer telomeres than humans, yet live much shorter lives. And scientists have even found a seabird, Leach’s storm petrel, that has telomeres that get longer as it ages (interestingly, this bird also has a long lifespan for its size). Clearly, telomeres don’t reflect the whole phenomenon we call ageing.
In 2013, the German-American scientist Steve Horvath presented a new biological clock that beats telomere-shortening, along with pretty much everything else we have. This new biological clock is often called ‘the epigenetic clock’, and the way it works is a little complicated. But let’s give it a shot.
As the name implies, the epigenetic clock is based on something called epigenetics. You can think of epigenetics as a control system inside your cells. Remember, all your cells (except red blood cells) have all of your DNA – the entire genetic recipe for making you. But for the most part, your cells only need a tiny fraction of the recipe at any given time. Your muscle cells need to use genes that help make muscle fibres, but they don’t need the genes that make dental enamel or taste receptors. Cells that make your teeth, on the other hand, do need the genes for making dental enamel but not the genes for making muscle fibres. And besides, even if a cell needs a specific gene, it doesn’t necessarily need it all the time.
The solution to this is a control system that can manage which genes are used in the cell at any given time. When the cell needs a gene, it can turn it on. When it doesn’t, it can shut it down.
Part of this control system is epigenetics: reversible chemical changes to your DNA. You can imagine the cell putting different tags on genes – ‘turn on’, ‘turn on soon’, ‘switch off temporarily’, ‘switch off permanently’, and so on. It’s pretty ingenious, actually. In this way, our cells can use the same genetic recipe to make brain cells, immune cells, cells in your pinkie and everything in between.
Epigenetics are especially useful during development, when we grow from a tiny ball of cells to an infant, a child and later an adult. Some genes are only needed during early development, some are needed to become a certain type of cell, and some are useful for growing up and becoming a mature adult. However, at that point, we would then expect our epigenetics to stay relatively set. After all, once you’ve become an adult, the programme has successfully run to completion. But surprisingly, epigenetic changes keep happening, even later in life. Scientists used to believe this was simply due to cellular machinery getting faulty with age. They imagined cells slowly losing control and ending up putting essentially random tags on genes. To support this, most of the age-related epigenetic changes are loss of the ability to turn genes off effectively. This becomes a hazard when genes involved in growth are activated even though we finished growing long ago, because this growth promotion can stimulate the growth of cancers.
Despite this neat story, Steve Horvath has proved that epigenetic changes later in life are not random after all. They keep following a specific pattern, almost as if the developmental programme continues. Programmed ageing? In order to remain sane, scientists have resolved to call this pattern ‘quasi-
programmed’. Whatever the reason, though, the predictability of epigenetic changes can be used to determine the biological age of a cell. The epigenetic clock uses a particular epigenetic ‘tag’ called methylation which is used to turn genes off. Scientists measure the amount of methylation in specific genetic places and because the age-related changes follow a pattern, they can use statistics to determine biological age with high accuracy. For instance, people whose epigenetic age is higher than their actual age are at greater risk of dying early. They also have a greater risk of getting age-related diseases, such as cardiovascular disease, cancer and Alzheimer’s. And they even seem older, performing worse on cognitive tests and being physically weaker. On the other hand, centenarians reliably turn out to be younger biologically than their actual age, which is probably why they are still alive: their actual age might be 106, while the biological state of their body is much younger than that.
In fact, newer versions of the epigenetic clock work so well that they can even be used in other species. First, this was done in chimpanzees, but now there are epigenetic clocks that work for all other mammals, too. That suggests these clocks measure something very fundamental about the ageing process.
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Since their creation, researchers have been busy using epigenetic clocks to peek into all sorts of interesting aspects of ageing. One example is the way ageing works in different parts of the body. You see, chronologically, all your cells and tissues are the same age. Some cell types might have short individual lifespans, but these cells are recently descended from stem cells – the cells that make other cells. And in the end, all your cells descend from the first cell that was uniquely you, the fertilised egg. The epigenetic clock corroborates this, as all cells have roughly the same biological age. This means you can use all sorts of different cell types from the same person – brain cells, liver cells, skin cells – and the epigenetic clock will show the same biological age. However, there are a few exceptions, and these tell us some fascinating things about ageing. Most notably, women’s breast tissue tends to be biologically older than any other tissue studied. This is thought-provoking, because breast cancer is the most common cancer in women, costing millions of lives each year. We’re all aware that breast cancer is a big menace, because there are so many support groups and fundraisers for it. But I’m not sure someone completely naive would have guessed one of the most common cancers to be in the breasts. Why there and not one of the dozen other organs? If the reason is that breast tissue ages more rapidly, that at least gives a little bit of an explanation. In fact, premature cellular ageing must be involved: studies show that the higher the epigenetic age of a woman’s breast tissue compared to her actual age, the greater her risk of breast cancer. Of course, this only raises the next big question: why does breast tissue tend to age more rapidly? We don’t really know. But once we find the answer, we might be able to use it in the development of breast cancer therapies and preventative medicine. And in the process, we might also learn some things about cellular ageing that can be broadly applicable.
At the other end of the spectrum, there’s also a specific tissue that tends to age more slowly than the rest of the body. The part of the brain called the cerebellum usually has the lowest epigenetic age in a person. The cerebellum is not a part of the body non-scientists hear that much about. Perhaps one reason is that not much stuff tends to go wrong here – at least, the cerebellum is far less afflicted by age-related diseases than the rest of the brain. Again, we don’t really know why, but maybe studies of ageing in the cerebellum can help us learn how to slow down ageing in the rest of the brain, and decrease the risk of neurodegenerative diseases.
The female advantage
Women tend to live longer than men, and they also have lower epigenetic ages on average. In fact, this is already evident by the age of two. The female advantage is especially evident before menopause. Until then, women seem partially protected against age-related diseases. And only after menopause does the female risk profile slowly start to converge with the male one. Interestingly, women who go through menopause later than average also tend to live longer than average. And the epigenetic clock gives us an idea why. Women who have their ovaries removed surgically – and thus enter menopause artificially early – have higher biological ages than expected. On the other hand, women who delay menopause using hormone therapy have lower biological ages than expected.
Unfortunately, hormone therapy increases the risk of breast cancer, so this area is a bit like the telomeres. If only we had better cancer therapies, we might have a highly beneficial anti-ageing therapy.
You started your life as a single cell – the result of a fusion between the egg cell provided by your mother and the sperm cell provided by your father. After the fusion, the fertilised egg quickly began to divide, forming a little ball of cells. All these early cells were what scientists called ‘pluripotent’, which means they were cells retaining the ability to morph into any of the more than 200 cell types that make up your body today. However, as you developed, your cells continuously specialised, closing off options as they went. You can imagine it like climbing up a big tree. At the trunk, the cell retains the ability to climb out on any branch that it wants. Then, at one point, the cell chooses a major branch, and this limits the cell types it can later become. Continuing up the tree, options are limited by each further choice until the cell ends up on a particular branch: the ‘finished product’, such as brain cells, muscle cells or skin cells. This is what’s called terminally differentiated cells.
Scientists once thought that this climb was a one-way thing: that once a cell had committed to a particular fate, there was no way to reverse the decision. But then Japanese scientist Shinya Yamanaka proved everyone wrong (and later won the Nobel Prize in Medicine in 2012). Yamanaka showed that terminally differentiated cells can be made back into pluripotent cells. That is, we could take one of your skin cells and coax it into crawling all the way back to the trunk of our hypothetical tree. Yamanaka and his research group reset development this way by using four proteins, which are now called ‘the Yamanaka factors’. Once these are activated in the cell, ‘de-development’ takes place, and the resulting cell is called an ‘induced pluripotent stem cell’. That is, a cell that has been induced by researchers into becoming a pluripotent stem cell, and which can now give rise to all other cells.
As we’ve discussed, natural pluripotent stem cells are found at the beginning of life. This means their biological age is pretty much zero. So, scientists wondered whether induced pluripotent stem cells were young as well, or if they were still the same age as the adult cells from which they were derived. Using the epigenetic clock, it is clear that the Yamanaka factors do, in fact, turn back biological age. When scientists use the Yamanaka factors in an adult cell, and the cell gradually transitions into an induced pluripotent stem cell, its biological age moves towards zero. Just like the age of a natural pluripotent stem cell. This is the closest we get to the backwards ageing of the jellyfish Turritopsis which is actually believed to happen with a similar mechanism.
Think about it for a second. The Yamanaka factors essentially turn back the biological clock. We could take a cell from your skin right now and use the Yamanaka factors to make it much younger than the rest of you. Again, cellular anti-ageing and immortality is a current reality.
But once more, the big question is to what degree we can transfer it to the whole organism. Using the four Yamanaka factors in all our cells is not a viable solution – that would make every cell climb all the way down our developmental tree and end up at the ‘ball of cells’ state. There’d be no muscle cells, brain cells and so on, and the body would simply disintegrate. Instead, scientists are trying to use the Yamanaka factors in short pulses. The idea is that cells would then be rejuvenated, but not so far that they end up as pluripotent cells. This is called ‘cellular reprogramming’, and so far, it has shown promising results in mice. For instance, the first scientists using the technique found that it could increase the regenerative ability of old mice. Since then, other scientists have used cellular reprogramming to restore youthful vision in old mice. These scientists adjusted the normal protocol, though, in an effort to decrease cancer risk. You see, cellular reprogramming suffers from the same risk as the experiments with telomerase. Only this time, the cancer is far more horrific. What happens is that cells that are ‘de-developed’ too far end up as pluripotent cells. These can then start development anew, forming a cancer called a teratoma in the process. This cancer mimics the growth of a new organism, which gives it some terrifying characteristics. The tumour consists of all kinds of tissue. It will often grow strands of hair and, for some reason, teratomas often end up having teeth growing inside them as well. High risk, high reward, right?
Many scientists and companies are, in fact, ready to take the bet on cellular reprogramming. It’s not hard to see why. A lot of the other therapies we’ve discussed involve decreasing some kind of damage or improving the ability to repair. That means they might be able to postpone ageing or increase health a little. Cellular reprogramming, on the other hand, suggests some form of programmed ageing and a way to control the programme. That means it promises the ability to turn age back and forth at will. We don’t know how this is going to pan out yet, but even the possibility is like a million dollars lying on the sidewalk. And of course, if you ever see that, I’d suggest you run really fast to get there first. Not surprisingly, this sidewalk race already has many contestants. Several companies backed by billionaires and big-name scientists have launched within a couple of years in the pursuit of cellular reprogramming in humans. Of particular note is the Silicon Valley start-up Altos Labs, which is potentially the biggest shot at fighting ageing anyone has ever taken. Investors have put $3 billion into the company, though exactly who is behind the money is unknown. Several of the richest people in the world, among them Jeff Bezos, are rumoured to be involved. As a result, the employee roll at Altos Labs is hard to distinguish from the literature list in the back of this book. The company has hired many of the best researchers of ageing in the world, and is betting that, given sufficient funds, they will be able to turn cellular reprogramming into an actual Fountain of Youth.
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Cellular reprogramming is not the only way in which the Yamanaka factors and pluripotent stem cells are relevant to the fight against ageing. As we’ve discussed, pluripotent stem cells have the ability to become any cell type in the body. So what if we learned how cells normally turn into, say, heart muscle cells, and then coaxed the pluripotent stem cells in that direction? Then we could essentially make spare parts for the body. We could take our pluripotent stem cells and, with the right knowledge, turn them into any cell type we need. Getting a kidney replacement would no longer be dependent on the kindness of family members, friends or strangers: instead, a new one could be made with your own cells. And we could potentially create ‘replacement’ organs for old age instead of tirelessly trying to rejuvenate the ones we have.
While this stuff might sound like science fiction, the research has actually been going on for decades already. Scientists are trying to make any cell or tissue type you can think of – even brain cells. Like so much of biology, though, this stuff is really hard. The stem cells are difficult to make, they are time-
consuming to take care of, and the signalling molecules used to coax their development are often extremely expensive. So progress has been slow. But it is there. In fact, the decades of work are now finally starting to come to fruition. It will be a while before we can make entire replacement organs consisting of complex structures with many different cell types. But there has been a lot of progress in making individual types of cells. For instance, scientists at Harvard have succeeded in making what are called beta cells. These are cells of the pancreas that produce the hormone insulin. In type 1 diabetes, the beta cells are attacked by the immune system, which ultimately kills them. This used to be deadly, but today we can make artificial insulin so that patients themselves can take over the job of the beta cells. Tracking blood sugar and injecting insulin is a big nuisance, though, and merely treats the symptoms; it’s not a cure. But with the development of beta cells from pluripotent stem cells, the cure is near. In fact, the first patient has already had ‘artificial’ beta cells transplanted and been cured of his type 1 diabetes.
The beta cell effort, and others like it, did not actually use induced pluripotent stem cells, though. Instead, they used what is called embryonic stem cells. These cells are not from the patient themselves, but actual cells from the ‘ball of cells’ state – the embryo. Because they are not the person’s own cells, they can cause problems with the immune system. If the immune system discovers foreign cells, it will attack and kill them. This can be dangerous – even deadly – to the patient. And of course, it also defeats the purpose a little. If the immune system kills the new cells, we won’t have much use of them. However, fortunately, we have lots of experience with organ transplantation, so we know how to keep the immune system at bay. And scientists are also working to modify the stem cells so that the immune system won’t recognise and attack them. This still leaves one final concern, though. The embryonic stem cells are often derived from leftover embryos created for artificial insemination. This means they are from a potential human who was not born which raises an ethical dilemma: is it okay to use these cells, which are, in essence, from another human? It’s a similar discussion to that concerning the cells of Henrietta Lacks. Both types of cells have helped tremendously in the development of medical therapies, saving countless lives in the process. But as always, technological development forces us to make ethical trade-offs and reflect on our values.
Besides the pluripotent stem cells present during development, there are also stem cells in the adult body. The vast majority of these are not ‘pluripotent’, though, but ‘multipotent’. This means they can create several cell types but not all. The adult stem cells are tasked with replacing the cells that are continuously lost, either to damage or due to normal cell turnover. For instance, the outermost layer of your gut is replaced every four days, skin cells are replaced every ten to thirty days and red blood cells live approximately 120 days. Not all cell types are replaced this often; for instance, only ten per cent of the cells in your bones are replaced each year, and some cells, like your brain cells, typically last your entire life. But the general rule is that your cells need to be replaced occasionally, and that makes adult stem cells important.
In fact, your stem cells determine your ability to regenerate at tissue level. Autophagy and similar recycling or repair processes help individual cells recover from damage. But on a tissue level, repair and maintenance is taken care of by stem cells. Like so many other repair mechanisms in the body, though, the ability of your stem cells deteriorates over time. As we age, stem cells become passive and worse at making new cells to replace lost ones. This phenomenon is usually called ‘stem cell exhaustion’. The result is that we get worse at recovering from injury as we age, and eventually even normal maintenance cannot be upheld. For instance, the stem cells responsible for making new immune cells get worse over time, and that is one of the reasons old people have weaker immune systems. They also take longer to recover from injuries or surgeries, while having a higher risk of long-term complications, all because the ability to regenerate worsens as stem cells give up.
So while we envision replacing entire organs with new ones made from pluripotent stem cells, we could also replace adult stem cells to increase regenerative ability. Even though it sounds like a scammy procedure from Hollywood, you can imagine getting stem cell injections to fight ageing. This approach is especially developed for what is called mesenchymal stem cells. These are stem cells that make cells of bone, muscle, cartilage and fat. In one experiment, researchers isolated mesenchymal stem cells from young mice and injected them into old mice. Originally, the research was meant to examine if mesenchymal stem cell injections could be a treatment for osteoporosis, a disease of old age in which bones lose density and become weaker. One reason for this disease could be that stem cells don’t produce the cells required for maintenance. To the researchers’ surprise, though, their treatment didn’t just affect bone health. It actually also made the mice live longer. While that doesn’t necessarily mean it would help people in the same way, some plastic surgeons actually already use mesenchymal stem cells to regenerate sun-damaged skin, while there are clinics that offer treatments for various sports injuries with mesenchymal stem cells.
So, whether we’re talking cellular reprogramming, organ replacements or stem cell injections, there is no doubt stem cell research will be delivering a lot of future therapies against ageing.