This article is based on a poster I presented on “Forschungsforum HTW Berlin” in October 2021. The poster is available in German language on DOI: 10.13140/RG.2.2.26595.43048.
What’s so cool about Telomeres?
Telomeres are relevant to both aging and cancer. Drugs elongating or stabilizing them could delay aging. Drugs that shorten them could be used in cancer therapy.
Drug development that affects Telomere length and dynamics requires systems to screen for these parameters. In such a system the influence of thousands of substances on Telomeres has to be examined in parallel. It has to be cheap, quick and easy.
Idea: A high-throughput system that uses optical signals to estimate the telomere lengths of living yeast cells. For this purpose, proteins that naturally bind to Telomeres will be labeled fluorescently and/or luminescently.
Problem: Yeast use Telomerase to keep their Telomeres constant. In addition to the marking the Telomers, I need to integrate a switch on the Telomerase of the yeast to activate and deactivate it.
Markers for Telomer Length
Methods for Marking
The marking is done in the genomic code of the target proteins (RAP1, RIF1 and RIF2) by fusion with reporter proteins. The genetic code of the reporter (a fluorescent or luminescent protein) is attached to the code for the target protein in the genome by means of transformation and recombination.
Methods to turn Telomerase on/off
In order to make the Telomerase switchable the promoter of one of the genes that together form the Telomerase is exchanged. A promoter is a regulatory sequence in front of the actual gene (the blueprint of a protein). It controls how and when the encoded protein is produced.
The natural promoter of the EST2 gene, which is one of the components of yeast Telomerase, is replaced with the promoter of the DDI2 gene. While Telomerase is always active in yeast, the DDI2 gene is only activated under certain chemical stimuli. If the promoter is successfully exchanged the Telomerase is inactive but can be activated by adding small amounts of the chemical cyanamide.
One way to achieve this is to exchange the promoter directly in the yeast genome via recombination.
Another slightly simpler method would be to destroy (knock-out) the gene in the yeast genome and introduce a functional version with the exchanged promoter on an artificial chromosome (plasmid) into the cell.
Status of work after year 1 of 4
Libraries of yeast strains with GFP-tagged proteins are available. These were used to carry out the first preliminary tests to establish the measurement methods.
A DNA construct was designed and produced that makes it possible to replace the promoter of the EST2 gene. The construct was transformed into strains with different GFP tags.
Transformed colonies are currently being examined to determine whether and where the construct is integrated in the genome. It is also checked at the protein level whether the control works. This has just been confirmed by a Western blot which I will explain in one of my next articles.
Next the new strain will be tested in the fluorescence assay.
The good news is, slowing aging and gaining more than ten years is absolutely possible and doesn’t cost you anything except some discipline (yeah, I know, that’s the bad news here). However, to keep you reading, I’ll tell you a little later how that works. Whether it is possible to slow or even reverse aging is currently the topic of a lot of research. But let’s start at the beginning. If you want to treat something, you first need to define it clearly. The most obvious definition for aging is chronological. However, changing the actual flow of time falls more into the realm of physics and is probably not very practical. What we want to influence is the biological age. To measure this, we use a lot of different methods, called “clocks,” and they work with blood parameters, heart rate variability, epigenetics, simple photos of your face, or other data. Clocks are all somewhat linked to chronological age but can generally tell you how one (or several) aspects of your biological age compare to the average person your age. So they tell you if you’re younger or older than you actually are.
What is aging?
The specific unpleasant cellular effects of aging are summed up as the 9 Hallmarks of Aging that you see above. I won’t go into detail, but they are all interconnected and lead to what we recognize as aging, like wrinkles, grey hair, loss of muscle mass, frailty, dementia, decreasing bone density, and all the other stuff that you’re not keen on having.
Reading this list, you might already guess why treating aging might have other perks than just living longer. The biggest deal, not only for the individual but also for society, would be increasing the so-called healthspan. It can be argued that while in the last 100 years we have already more than doubled the average life span, the healthspan, the time lived in good health, hasn’t grown accordingly. Our current medicine has become very good at treating most of the countless ailments that old age brings; however, many are more managed than cured. So wouldn’t it be better (and cheaper, by the way) to treat the underlying cause of most illnesses instead of each of them at a time? The results of healthspan research could revolutionize medicine and bring us from fixing what’s broken to preventing the breaking.
Lifestyle Interventions to Slow Aging
But how far along are we? Will we still get old like our grandparents? That depends. To cite one of the leading minds in this field of science, Professor David Sinclair: “It’s easy to expand your lifespan. […] If you do the right things, which is: Don’t overeat, eat less often during the day, do some exercise, don’t smoke, don’t drink! That alone gives you, compared to people who don’t do that, 14 extra years. So living longer isn’t hard, it just takes some discipline.” Well, I told you, it’s not too easy, but it’s doable.
Especially the eating less often part seems to be important. Intermittent fasting (best more than 16 hours without food) gives the cells a feeling of food scarcity and switches on certain survival programs. Probably the most important is autophagy which let’s cells recycle accumulated proteins and other reserves. This kind of a cleaning helps get rid of things that can cause trouble when they accumulate too much.
The other main effect is a reduction in metabolism and especially on cell division. Since cell division is on multiple levels the main reason for mutation (errors in the DNA) it is also the main reason for aging. Avoiding strong mutagens like smoking, excessive drinking (one drink a day seems to be positive) and sun bathing is helpful for the same reason.
Enough sleep and some exercise have also been shown to positively affect aging in human studies.
However, there is obviously more to aging research than the typical advice on living a more healthy lifestyle.
Supplements and Drugs
First of all, there are drugs and supplements that (at least in animal models) show a huge potential to give another few healthy years like Nicotinamide Mononucleotide (NMN), α-Ketoglutarate (AKG), Resveratrol, Metformin, and Rapamycin. I won’t go into detail on those now, but I’ll write some more articles about that on my blog soon.
Most of these, however, seem to work mainly as a prevention and not a cure. And while they show a lot of promise in animal models, so far reliable data from humans is scarce. Most of them work through mimicking food scarcity which can also be reached through fasting.
But there are other measures in the pipeline. An interesting idea is the so-called “Senolytics.” Instead of killing themselves as damaged cells normally do, some become senescent. Senescence occurs when cells sense an instability of their chromosomes after having divided a certain number of times or because of high stress (due to their Telomers), so they permanently stop dividing. Senescent cells also secrete signals that lead to inflammation, changing the development of their surrounding cells and the extracellular matrix.
The more senescent cells in an organ, the less vital and functional the organ becomes. Senolytics like Dasatinib and Quercetin are substances that target and remove these senescent cells to rejuvenate the organ. There are ongoing clinical studies on human patients with these substances on several age-related diseases, and they show some promise, but there is still a lot of research to do.
The idea that sounds probably most impossible but has the potential to slow the clock and actually reverse aging is cellular reprogramming. Each cell in our body has basically the same genetic information, the same construction plans packed into our DNA organized in chromosomes. But how does a cell in your brain know that it’s not in your foot and has to behave differently? And, even more important, how does a cell know that it’s not supposed to copy itself as often as possible or try to build a new complete clone of you? The answer is epigenetics (mostly). Epigenetics is quite a young field that has made huge progress in the last 15 years. Epigenetics determines which of the genes of a cell’s genome are switched on and switched off by modifying the DNA or proteins associated with the DNA. These bookmarks make a cell behave as it does. They are changed by environmental influences like sunshine, smoking, food, no food, or a thousand other things. Most of these factors and time itself lead to an overall decrease in these bookmarks, although certain areas of the genome also acquire more of them with time. So the idea is to reset these bookmarks to a “younger” state.
In 2006 a set of four transcription factors (regulators for genes) were identified that can reset a differentiated cell from being part of a certain tissue to a very similar state to that of the cells you find in an embryo. The cells treated with the transcription factors become stem cells and can be reprogrammed into almost any cell type within the body. These transcription factors are called Yamanaka Factors after one of the authors of this study from 2006. Using the Yamanaka Factors, there have been successful reprogramming studies on animals. The aim is to reset the epigenetics of cells to young without dedifferentiating the cells, making the tissues they form fall apart. This technique is currently tested to restore vision in primates after successful tests on mice that have gone blind because of glaucoma. David Sinclair’s group carrying out these experiments expects it to be ready for human clinical trials within this year. If this is successful, it would be a new hope for many blind people and be a proof of concept for rejuvenating a tissue by epigenetic reprogramming.
This is however a very ambitious time line and I dare say it won’t happen. The main reason is that the Yamanaka factors used here are some of the most potent oncogenes. Those are genes responsible for the transformation of a cell into a cancer cell. It is to be expected that therapies working on a thin line between dedifferentiation and cancer will be looked upon with extreme scrutiny by the authorities before being accepted for human trials.
A possible future application of this could be to treat a patient’s cells outside the body to become stem cells and then inject them to regenerate damaged tissue or to rejuvenate the patient as a whole.
Much is unclear about reversing aging. Many studies in the field show contradicting results, but what would have seemed impossible 20 years ago is rapidly evolving from promising basic research to clinical trials. Currently, you still need some discipline and changes to your lifestyle if you want to increase your lifespan and healthspan. However, the more life and health you win through your life choices, the closer scientists might be to real solutions to all the unpleasant effects of aging and maybe to aging itself.
This post has first been published as a guest post on the blog BoldedScience.com and has since been modified and updated.
In the last article I ended having a DNA template thanks to Prof. Yu Fu and I had a DNA sequence of the region where I want to integrate my DNA construct. So to now I need to copy a piece of the DNA plasmid (ring) that I have and add a stretch of DNA sequence (~ 50 bases) that are complementary to to the point in the yeast genome where I want to integrate that peace. I can do both in one step with a technique called Polymerase Chain Reaction or PCR.
A PCR is a method to produce DNA without using living cells to do it. It is something like a molecular copy machine. The main ingredients for a PCR are an enzyme called DNA-polymerase, which does the copying, dNTPs, which are the building blocks of DNA, the template DNA from which I want to copy and primers. Primers are small DNA peaces (normally about 20-25 bases long) that define the DNA stretch I want to copy. The forward primer (the start signal) is complementary to the sequence where I want to start the copy and the reverse primer is identical to the sequence where I want to stop the copy.
The picture above is from the Wikipedia article on PCR that also explains it really well in detail. As you see the first step of a PCR is making the DNA accessible for the copying by heating it until the typical double-strand structure splits up into two single strands. For this you heat it to something around 95 °C. Then you cool it down to the annealing temperature which depends on your primers but is normally a bit above 50 °C. To start the DNA-polymerase you now heat it again to something around 72 °C. This sounds like a very high temperature for an enzyme and it is. The trick is that the polymerase comes from the bacterium Thermophilus Aquaticus (or others) that lives around hydrothermal vents that spew water, smoke, acid and other stuff at temperatures of more than 100 °C. So their enzymes are optimized to work in extremely hot and unpleasant conditions.
Now you repeat these three steps over and over again and with each repeat the number of your DNA constructs doubles. This means you have an exponential growth from 1 to 2 to 4 to 8… to a bit more than a million after 20 cycles to a bit more than a billion after 30 cycles. So you create a lot of identical DNA in quite a short time (normally 1 to 4 hours).
The machine that adjusts the temperature in a programmed manner is called a Thermocycler and looks quite unspectacular.
This explains how I copy the stretch of DNA from the plasmid but I also wanted to add some sequence to the ends. That’s actually quite easy. I just add the sequence to the primers because they are the beginning and the end of my newly created DNA constructs. Now you might ask: And how do you get these primers? Well like most things today. I order them online. There are companies specialized in producing custom DNA. Basically I could also save myself the whole work and just order my whole construct online but that is still quite expensive. While my exceptionally long primers (primer + sequence are about 60 bases long) cost something between 20 and 50 $, my whole 2500 bases long construct would cost about 1.000 $ to order. That is still quite a difference but it gets cheaper and in a few years biologists will probably order a lot more DNA than they create using molecular techniques like PCR and cloning.
Now that I have my PCR product I want to verify if it is the right one. The easiest way to do that is to put it on a gel that lets short DNA pass quicker than long DNA. Than you add voltage and the negatively charged DNA wanders towards the positive electrode and splits up by size. If you add a marker that includes DNA pieces of known size and a compound that makes DNA visible under UV-light (ethidium bromide) you can see what size the fragments that you produced have. That normally gives you a good idea if the experiment ran as expected.
I did all of that and on the first try the result was no visible DNA at all. Than I changed a few parameters and tried again and saw a very thin band where I expected it and a few others where they shouldn’t be. So I changed some more parameters and on the third try I got this wonderful picture of a gel with a strong band at exactly the position where I expected it.
This made me quite happy but now I had to do something with it. I wanted to put this DNA into a yeast cell and make it integrate into the genome. This is called transformation and is quite tricky as well. I’ll explain that the next time.
In my last post I explained how to get a bag of 4 yeast spores of which one hopefully has the two mutations I want in my new yeast strain. Now comes the really tricky part: You have to find this spore.
Before I explain the method you have to get an idea on how small one yeast cell is. The average yeast cell is about 3 to 4 micrometers. The smallest distance between two dots to still see them as two with the naked eye is 0.1 mm which is about 300 times a yeast cell. A human hair is on average between 0.06 an 0.08 mm thick, which is 20 times a yeast cell. If you look at the picture above, depicting yeast cells magnified 1000x, the whole frame is about the thickness of a hair.
OK, so they are really small and not visible with the naked eye but we want to find a single spore (that is again smaller than a normal cell) and identify it. The method we use for that is called micromanipulation. A micromanipulator is basically a microscope with a stage (on which you fix the plate with your cells) that can be moved in tiny increments. And it has a lever with a very thin glas needle fixed to it that through some mechanics can also be moved in a very small scale.
My lab has quite a cool and modern micromipulator that has a joystick to move the stage and a computer driving you to positions on a virtual grid on your plate where you can put single cells. What you now do is you look through a patch on your plate where you’ve put some of your cells. Once you’ve found a bag with 4 spores (which is called a Tetrad) you move the tiny needle really close to it. A moment before the needle would actually touch the plate a meniscus of water forms between the needle tip and the plate that scoops up the Tetrad and hopefully nothing else. Then you move to an empty position on the grid and, by moving and shaking the needle while it almost touches the surface, you try to deposit one of those 4 spores. Then you go to the next spot and do that again. So in the end you get a plate full of 4 spots in a row where you deposited single spores. You can see how it works in the following video.
After finishing the sorting I put the plate to 30 °C for one or two days to give the cells time to grow. The result looks like this:
As you see not all cells I’ve laid out have grown. That is quite normal because not all spores are viable after the procedure. On the left side was the reservoir, where I’ve put a lot of cells to look for Tetrads. I’ve cut that off with a clean scalpel so the cells do not overgrow the rest of the plate.
In the next step now I have to identify which of these cells are really derived from spores (and are haploid) and which of them are actually just normal diploid cells that accidentally lay around with 3 buddies and looked like Tetrads. To do this you use another nice feature of yeast. Wild yeast can live of a lt of things and can make everything it needs (like amino-acids and bases for DNA) semselves. The labstrains you normally use however have some genes they need for this knocked-out. This means to let them grow you need to add some amino-acids and other things to the medium. Now the trick is, that the genetic traits that I want to breed together here are marked with the genetic code that the laboratory strain needs to make these amio-acids themselves. That means I take this plate and stamp it over to a plate where the medium is missing two special amino-acids, only those cells can grow that have both genetic traits that I need. This is called selection.
The problem here is that the diploid cells I mistook for Tetrads also have both markers and can also grow. Here however the statistic can help. Since I always put all 4 cells that were together in one row and in a Tetrad only one of those 4 can have both of the genetic markers, I now have to check my selection plate for rows where only one of the 4 cells has grown. Another test that I can do afterwards is to see if the cells of such a colony mate with other haploid cells of either mating type. Diploid cells won’t do that.
The results look relatively promising but further analysis showed that this actually hasn’t worked. However this is an important part of science: Things don’t work. After trying this a couple of times I decided to first try another way to teach my yeast cells to age that is a bit more elegant and hopefully works better: I will put a switch on the gene for Telomerase so I can turn it on and off as I want. I’ll explain how this works the next time.
Well if that’s not one of the click baitiest titles you’ve ever seen. But that’s what I hope being part of with my PhD project.
In the last article I explained what Telomeres are and why they are important as one of the possible keys to aging on one and cancer on the other side. If you haven’t read the article yet, you can find it here.
When it comes to Telomeres it’s all about their length and its changes over time. If Telomeres degrade it is a sign of cellular stress (in some cases the opposite is true) or strong proliferation and if they reach a certain critical length they stop the cell from division and send it into senescence. If a cancer cell wants to divide further it has to overcome this brink and find a way to elongate its Telomeres.
This shows you why drugs that influence Telomere length (in either way) have a huge potential. But how do you find these drugs? There are several answers to this question however often the answer is high throughput screening. Which is a nice word for trial and error.
In high throughput screens you develope a system that gives you an easy, reproducible and cheap read-out for the effect you hope for and then you make tens or even hundreds of thousands of experiments in parallel with huge libraries of chemical compounds. If some of them show a promising effect you try to reproduce that effect first in the same and later in other experimental setups. Then you try to find out how your candidate compounds work, if they are toxic and other questions before you can start developing a drug from them.
For Telomere length there is currently already a problem in the first step. There is currently not yet a really easy, cheap, quick way to measure Telomere length in high throughput assays. For an overview on the currently available options you can read this review paper by Lai et al. 2011
My idea seems to be an easy (if probably not very accurate) option. Telomeres are normally quite tightly packed with proteins. I want to use this Telosome as a molecular ruler. My idea is to optically tag one or more of these proteins and look for a correlation between an optical read out from these tags and the length of the Telomeres. If I find this correlation I only have to calibrate it and I’m ready to screen for the pill against aging or cancer.
In the first step I’m using the bakers yeast Saccharomyces Cerevisiae as a model. I’ll explain a little more about the advantages and disadvantages of this system in another article. For now one of the advantages is that my lab has a library of yeast strains with tagged proteins. These tagged proteins are fusion proteins that were made by adding the genetic code code for Green Fluorescent Protein (GFP) to end of the code for (basically all) yeast proteins.
So in the first step I’m just taking yeast stains out of the – 80 °C freezer and revive them. Now I only have to check the fluorescence signal from cells with different Telomere lengths and see if there is a difference.
It could be so easy but there’s a problem with yeast. It doesn’t age or at least it keeps it’s Telomeres very constant in length using Telomerase. So I first have to teach my yeast to age like our somatic cells. I do this by disabling their Telomerase. I thought about three different methods of doing this that I’m currently working on but I’ll explain them in other articles.
On the other hand I can not only make their Telomeres shorter but also longer. This is interestingly done by cultivating the cells in 5 % alcohol.
If I don’t see a correlation in this easy system I have a few more elegant ideas that I’ll explain in other articles.
To explain what I’m doing I’ll first explain what Telomeres are and why their length is relatively important.
Telomeres are solving a problem that came up when bacteria became eucariots (plants, mushrooms and animals). At this point they stopped storing their genetic information on DNA-rings and instead developed linear chromosomes. This brings some structural advantages for bigger chromosomes but has a huge disadvantage. Each time a cell divides (which most cells do a lot) it has to replicate it’s genome so each daughter can have a copy. This is done by enzymes called DNA-polymerases. The process only works in one direction on the DNA-string and doesn’t start at the beginning.
For a circular genome this is no problem but for a linear genome this means the loss of a few bases (the building blocks of DNA) at each devision. For a while this is not a huge problem if you don’t write important stuff at the beginning (or end) of the chromosome. And that is already the first function of Telomeres. Aside from mechanically stabilizing the chromosome ends, they are a peace of genetic code at the ends of chromosomes that do not contain vital information.
This is already enough for many of our somatic cells (those cells in the body that form most of our body) they only divide a certain number of times until a tissue (like a muscle or your brain) is formed and then just work and do not or only rarely divide.
Only cells that need to divide unlimited or often (germ line or stem cells but also unicellular life) need another trick. This trick is called Telomerase and earned it’s discoverers a Nobel Prize. Telomerase is an enzyme complex that uses an RNA-template to elongate Telomeres and so completely solve the so called End-Replication-Problem.
The fact that most somatic cells are not using this trick and have telomerase switched off has an interesting implication. It makes Telomeres something like a cellular clock of aging. They limit the number of times a cell can divide and rejuvenate a tissue before it goes into a state called senescence. The more cells of an organ are in this state, the less likely the whole organ gets to repair itself and to function correctly.
Another type of cell that needs to replicate a lot is cancer. This is why about 4 out of 5 cancer cells have Telomerase switched on.
The full picture of the connection between Telomeres, aging and cancer are quite complicated and still under discussion but it is quite clear that influencing Telomere length has quite some potential to treat cancer on one side and influence aging on the other.
Why do we age? What seems like a biological necessity is actually not. Single cell organisms in most cases could be called immortal although the definition is somewhat problematic since for most it is hard to distinguish between mother and daughter, between individual and a population of clones.
There are however also more complex life forms that are not aging as we do. The only really biological immortal animal we know of is the jellyfish Turritopsis dohrnii. It can rejuvenate itself by re-entering the polyp stage and re-emerging as a jellyfish. But there are also mammals that defy our traditional understanding of aging: The naked mole rat.
The naked mole rat is a funny animal through and through. They look like sausages with teeth that could use a dentist. They live underground in insect like states where only the queen is able to breed. Becoming the queen normally means beating the current queen in a bloody usurpation. They have an amazing immune system that basically completely protects them from illness, cancer and infection. And they do not age like we do.
Aging for us is mostly defined by a decrease in physical fitness, the slow loss of function of our bodies after the end of the reproductive phase. It is also an increase in mortality rate (the probability to die within a fixed amount of time). Naked mole rats however show neither an end to reproduction, a decrease in health or fitness nor an increase in mortality with age. That doesn’t mean that mole rats are immortal. On average they become 15 years old but that is mostly because of injuries from fights or predators.
If aging is not mandatory, why is it so common in nature? There are two main theories. The first is that aging is a genetic function that is selected evolutionary since it purges individuals after their reproductive phase which means when it doesn’t affect their evolutionary fitness anymore. However this is already the first problem with this theory. Why should something so consequently be selected in so many? An argument could be that it is an advantage to make room and save resources for your offspring but that’s not really realistic in this case. The selective pressure would be different depending on the scarcity of resources but life spans are not.
The second theory is aging is just an effect of wear and unrepairable damages that accumulate. So is a body just like a car that, no mater how much you put into into repairs at some point it’s not worth it anymore? Obviously this is a factor there are measurable accumulations especially in genomic damages and epigenetic deregulation.
What speaks clearly against pure random damage leading to biological aging, is that it has a clearly distinguishable phenotype. We all are able to tell if a person is old. This seems like there are biological integrators and common pathways activated by different kinds of damage. There are two kinds of those pathways. Those that repair or prevent the damage like stress responses. And those that in case the damage becomes too much and bears the risk of turning the cell into a cancer cell. Those can be programmed cell death in extreme cases but also senescence. Senescence means that cells permanently stop deviding behave differently but stay alive.
This is responsible for many of the observable phenotypes of old age. The more senescent cells an organ contains the older the whole organ behaves.
Back to the main question: Why do we age? The answer is, that we don’t know yet. It seems however that it is a mix of wear and tear that is integrated by molecular responses to the damage and a deregulation that is due to the loss of selective pressure after the end of the reproductive phase.
If you want a deeper dive into the topic from a scientific perspective a good starting point could be the review article by Shufei Song and F. Brad Johnson (2018).
In case you’re not sure how to get scientific publications without paying the horrendous sums many publishers charge for them, stay tuned there will be an article on this topic soon.