Analyzing Sirtuins Impact on the Epigenome and Activation Pathways
My younger brother just finished the second book in the Harry Potter series. As some of you may remember (spoiler alert), the book spectacularly ends with Harry destroying the diary of Voldemort in the Chamber of Secrets. Inside the diary was a piece of Voldemorts soul — a “Horcrux” in Harry Potter lore. As long as the diary was never destroyed, Voldemort would be immortal.
Voldemort was obsessed with immortality, and so were a lot of people in the history of our species. Countless books, movies, and mythology revolve around the idea of “everlasting youth”. I’m here to tell you immortality is (probably) not possible in the current timeframe we live in. However, extending our health and lifespans is totally possible.
Time as a healthy individual is an extremely valuable resource each person has at an individual level. You can ask the 80-year old billionaires of the world and I would put money if, given the choice, they would turn back the clock to when they were 25 without the amassed wealth and wisdom to regain their health.
What if we lived in a world 62 is the midpoint of your life, instead of a day to begin collecting Social Security. This is conceivable with the inter-disciplinary progress that has been made in human longevity research. In this article, I’ll highlight a specific area of the longevity puzzle that has garnered a lot of attention: Sirtuins.
Sirtuins: An Essential Part of the Puzzle
To understand Sirtuins we first start in yeast. The sirtuin gene was first found in yeast cells in the 1970s by Dr. Amy Klar. The gene was called Sir2 standing for — “silent mating-type information regulation 2”. The gene coded for a protein of the same name and that was heavily studied in the 1990s by Dr. Leonard Guarante of MIT.
The functionality of the protein is what gave it its name. Sir2 primarily acted as a histone deacetylase (HDAC). Histone tails are positively charged because of amine groups attached to the tails which causes it to bond with phosphates on DNA make it tight. If left unchanged, this will create heterochromatin. Heterochromatin is tightly bound chromatin that is not available to be transcribed making it silent.
Histone acetylation is when an acetyl group is added to the histone tail it neutralizes its charge. This means the histone tails do not react to the phosphates in the DNA and the DNA becomes transcribable. This accessible chromatin is called euchromatin. Basically :
Acetylation -> Euchromatin -> genes are accessible
No acetylation -> Heterochromatin -> genes are silenced.
Regulating the expression of genes falls under the umbrella of epigenetics. Epigenetics is all about gene expression in which genes will be transcribed. The collective processes that facilitate turning genes “on and off” is called the epigenome.
Coming back to Sir2 in yeast, The Sir2 protein is a histone deacetylase so its primary functionality is to remove acetyl groups which make the gene that was targeted silenced. An important gene that Sir2 regulated is HML and HMR mating genes.
Yeast comes in two sexes: a and α ( standing for alpha, I know they look very alike). Oddly enough, a yeast cell that is either a or α has access to both the genes to become a or α type. The catch is that only one should be expressed by a given yeast. The other should be silenced because of Sir2’s deacetylase functionality.
This is all well and good but one thing needs to be mentioned about Sir2. Deactalting histones are not its only functionality. Another big functionality is that Sir2 plays a part in DNA damage repair.
DNA damage is any physical abnormality in DNA. DNA damage should not be confused with DNA mutations. A DNA mutation is the actual change of the base sequence. Like a point mutation where an A changes to a G. DNA change is any to the structure of the DNA.
A few examples of DNA damage are :
- single and double-strand breaks, where the strands of DNA become severed
- oxidative stress ie. free radicals
- pyrimidine dimers — when two cytosines or thymines conjoin because of UV radiation
DNA damage can be caused by a variety of things. Some endogenous, or internal, causes are the reactive oxidative species (free radicals) that were produced from metabolism, and errors created in DNA replication. However, DNA damage can also be caused by environmental factors like toxins in cigarettes and UV radiation along with other frequencies of radiation.
DNA damage is constantly occurring in our cells. Oxidative DNA damage will occur around 10,000 times per cell per day. With trillions of cells in your body, this is literally quintillions of DNA damage processes happening to your cell every day. 🤯
Sir2 plays a role in DNA damage repair. When there are double-strand breaks the deacetylation function stabilizes the DNA and allows other enzymes like PARP-1 to facilitate DNA repair.
Recall that Sir2 controlled the expression of the mating genes in yeast cells. However, when large amounts of DNA damage accumulated, Sir2 proteins moved from their post of the mating genes and began to work on DNA repair. While they were gone fixing the DNA damage both the a and α mating genes become expressed. This renders the cell infertile which meant they couldn’t mate and they die. (since yeast are unicellular their lifespan is calculated by how many times they produce daughter cells).
In his book Lifespan — Why We Age and Why We Don’t Have To, David Sinclair, a longevity researcher at Harvard and the man who got me interested in geroscience, compares this phenomenon to emergency workers leaving their normal posts. When the forest fires occurred in Australia earlier this year many firefighters from California flew there to help mitigate the fires. While they were in Australia who was taking care of things in California? Even the everyday tasks that the firefighters would do: mowing the lawn, cleaning the gutter, and coaching the baseball team would be left devoid.
When they come back some things would be different. The grass would be taller and the gutter would be clogged. The same thing happens to our cells with sirtuins. While they are busy with DNA repair the gene expression they are normally doing has some “epigenetic noise”. The expression levels are different than they were left.
So far we have been using the example of yeast and Sir2, namely because that is where sirtuin experiments were first conducted. Lets transition now to humans. Humans have 7 sirtuins and they all have unique functionalities that expand on histone deacetylating. SIRT 1,6, and 7 are all nuclear. SIRT 3, 4, and 5 are found in the mitochondria and SIRT 2 is found in the cytoplasm. For the purpose of this article, I’m only going to focus on nuclear sirtuins.
SIRT1 still deacetylates histones but it has further functionality. It also modifies transcription factors (p53, NF-κB, and PGC-1α) and DNA repair proteins (Ku70, PARP1). SIRT1 also plays a big part in homologous recombination which is a way to fix DNA double-strand breaks.
With its processes of gene expression and DNA repair (along with more metabolic responsibilities as well), SIRT1 is very similar to Sir2 in yeast. In fact, SIRT1 is the mammalian ortholog of Sir2 in yeast. This means they are very similar in structure and function and were descended from a common ancestor.
SIRT6 enzymes are more involved in DNA repair. They play a part in the initial steps of double-strand break repairs and they help in repair short patches of broken nucleotides (base excision repair).
Overall, if you add all 7 of the sirtuins processes they play a large role in the functions of a cell. There main responsibilities though still lie in gene expression and DNA repair. And as shown with Sir2 in yeast, if lots of DNA damage begins to accumulate then the gene expression becomes altered.
The Information Theory of Aging
This is what David Sinclair says is the primary cause of aging. A loss of epigenetic information. As we go on more DNA damage gradually accumulates and over time our gene expression begins to change. It is important to keep in mind that DNA damage is not all accumulating at once — if that were to happen it would be hard for the cell to manage that. Instead, day in and day out as we go through damage that slightly alters our expression more and more.
In 1948, Claude Shannon proposed Information Theory. He was fascinated with communication over a noisy channel. To my understanding, he said that information loss was due to entropy — the introduction of noise to the channel. In our bodies, our epigenetic information travels through the channel of time with noise accumulating as we go through life.
Also in Shannon’s theory was a way to recover lost information due to noise. He said the way to make sure the data is sent to the receiver is also store a backup copy of the data in what is called the observer. The observer can send that data to a correcting device to correct the received data.
As Sinclair noted, this way of sending data back and forth, and keeping back up copies of the data is the protocol on how the internet works.
In biology, this may seem non-analogous. The way a cell works, intuitively would probably not be keeping a backup set of the data because what good would it do for it? However, more attention is now being shown to this theory with the recent emergence of epigenetic reprogramming.
Epigenetic reprogramming, which I wrote an article on a while ago, has been shown to reverse the age of eye tissue in mice. The reprogramming factors are these transcription factors called Yamanaka factors. The factors code for proteins that wipe some of the methylation (an epigenetic factor) off the genome and restores youthful gene expression.
The correcting device has been found but how did the partial Yamanaka factors know which methylation groups to wipe off? Longevity researchers hypothesize there must be an observer that we carry with us that provides the correcting data that the correcting device — the reprogramming factors use. For now what the observer is remains…. unsolved.
Back to Sirtuins
Sirtuins’ job is to limit the amount of epigenetic noise that accumulates as we age. However, as I have shown the accumulation of DNA damage distracts their ability to do this. Sinclair says it concisely in his book :
Youth → broken DNA → genome instability → disruption of DNA packaging and gene regulation (the epigenome) → loss of cell identity → cellular senescence → disease → death
A key argument against this is: why doesn’t the body just make more sirtuins so they can have enough to repair DNA damage and maintain youthful gene expression?
Sinclair explains that we are evolutionarily evolved to only produce so many sirtuins to live long enough to proliferate. Historically we only needed to survive until we were old enough to have and nurture kids. Then our time was up. Mother Nature had no intent on creating us to live for hundreds of years. The energy required to produce sirtuins could be better used elsewhere. If we go back to our first example in yeast, as Sinclair notes, it is not evolutionarily advantaged to remain fertile for 28 cell divisions as opposed to 24.
That does not mean we have to go by Mother Nature’s restriction. The process in which our epigenome begins to deteriorate does not have a “correct timing”. We as a society have been anchored to a certain expectation of what we think a normal life expectancy could be. With new science, this definitely could change to a new upper bound.
There is a whole section dedicated to the Lifespan Book that deals with the question — Should we Age? It goes into the political, economic, and social implications of what a longer lifespan would look like. How it would impact our institutions like healthcare, government, and universities. This is a very loaded question that a lot of bioethicists have been thinking about. I plan to write an article covering that in the future but now I want to focus my energy on the science of aging; how we are pursuing truth and knowledge to extend longevity.
Activating Sirtuins and expressing sirtuins more is a key part of increasing longevity. They play a key intermediary part in the main two causes of aging: DNA damage and loss of epigenetic information. Researchers in labs have been successful in their endeavors. When researchers increased the expression of SIRT1 in mice and there lifespan increased by 30%. Researchers increased the expression of SIRT6 and in male mice, lifespan increased by 15%.
These methods were done with gene therapy which in humans is not as viable to do. Instead, there are a few molecules that could activate the sirtuins.
One of the most hyped anti-aging intervention in NAD — Nicotinamide adenine dinucleotide. NAD, as you may remember from high school biology, is used in redox reactions in metabolism most notably: glycolysis, the Krebs cycle, and electron transport chain. All of these processes are crucial in the formation of ATP; the energy currency of the cell.
But NAD has another very important job. NAD acts as a coenzyme to a lot of proteins, including the Sirtuins. Sirtuins are dependent on NAD to function. Without NAD the sirtuins would not be able to catalyze the necessary reactions.
As we age our NAD levels deplete, it could be because more of it is being used up by certain enzymes like CD38 or less of it is being produced. A way to boost the activity of sirtuins is to replenish the levels of NAD.
NAD cannot be directly transported into the cell. There is no transport protein for it to enter. Instead, researchers have found the NAD precursors that become NAD through certain pathways.
NAD Precursors — NR and NMN
The two NAD precursors that have been highly studied are NR — Nicotinamide Riboside and NMN — Nicotinamide mononucleotide. Both of these can be supplemented into our bodies either through a pill or an IV.
NR and NMN are converted into NAD through the salvage pathway. Basically the salvage pathway is a way to recycle the remains of NAD after a reaction — NAM (nicotinamide) and convert it back into NAD. Certain enzymes catalyze these transformations (NAMPT).
The only problem is that the enzymes that are used to catalyze the reactions are subject to the feedback inhibition from the reduced form of NAD called NADH. What this means is that only a certain concentration of NAD can be produced from the salvage pathway because there has to a right ratio of NAD to NADH for metabolic reactions.
NR has been more highly studied than NMN. From the review articles I have seen, it seems that NR is more effective at producing NAD. When either NMN or NR is taken intravenously it is more effective than taken orally. This testing is done in mice so in humans it is not as viable to use IVs to administer the supplements.
Also, a note that I have seen, and one that Dr. Rhonda Patrick noted out on her video about NAD is that the precursors have to be taken in quite high dosages to be effective. For example, one of the studies used 400 grams per kg of NR supplement in mice. For a 180 lb human that is a 2.6 gram dosage which is quite high.
Studies have shown the NR and NMN supplementation have increased cardiovascular, metabolic, and cognitive abilities in mice. It still needs to be further tested on humans though.
Currently, there are companies like Elysium Health that are selling NR as a supplement. They have people like Leonard Guarante, who was there at the beginning with Sir2 leading the charge.
It should also be noted though, that NMN and possibly NR have been linked to cancer. Studies have shownthat NAD increases the quality of senescent cells which are linked to cancer because of the toxins they produce. NAD is used in the senescent cells’ metabolism which makes them more tumorogenic. However, this was only shown for a specific type of cancer — Pancreatic and may be unique to that cell type. Just because that occurred in the pancreas does not mean it will occur in other organs.
Resveratrol and other STACS
In the 1990s when sirtuins were first found to be connected to linked to longevity researchers searched to look for molecules that would either activate or inhibit the sirtuins (by inhibiting it slightly it would cause the body to react and produce more).
Generally, it is harder to find molecules that activate proteins than inhibit them. If you can find a molecule that activates something it is really good because it works 10x faster.
Dr. Konrad Howitz from Cornell found two STACS or SIRT1-activating compounds: fisetin and butein. Resveratrol was found because of fisetin and butein because it has a similar structure to them.
Resveratrol is a substance that is found in red wine. It is an example of a xenohormetic molecule. A xenohormetic molecule is a chemical that plants produce during stressed times otherwise known as xenohormesis. Sinclair describes in his book that the plants are activating their “survival circuit” to tell the body to hunker down.
Activating your survival circuit is probably the most proven way, as of right now to extend your longevity. Caloric restriction (intermittent fasting), HIIT exercise, hot/cold therapies have all been shown to trigger the survival circuit. Of course, doing these things is hard work and not exactly fun. That is why people are much more willing to take a pill that replicates the molecular experience without the extra work.
It is unconfirmed in which pathways that resveratrol impacts sirtuins and researchers are currently working on that now. It has been shown by research by Joseph Baur and Rafael De Cabo, that resveratrol has an increase in lifespan on mice.
TL;DR I know it was a long 🙂
- Sirtuins in our body play an important role in gene expression and DNA repair. We first found out about sirtuins by studying an ortholog in yeast called Sir2
- Cumulative DNA damage causes sirtuins to leave their post of gene expression and causes a loss of information in our epigenome. Creation of “epigenetic noise”
- All goes into the information theory of aging. Aging = loss of information. Has been shown with epigenetic reprogramming we can return cells to a youthful gene expression
- Another way to mitigate epigenetic noise is by activating the sirtuins. More sirtuins = less epigenetic noise = longer life and healthspan
- Ways to activate sirtuins: NAD through NR or NMN. Or use resveratrol or another sirtuin-activating compound.
Thanks for reading this article I hope you learned something from it. If you have some background in longevity you may know that I left out some potential sirtuin-activating pathways like AMPK and metformin. My next article will be all about AMPK and mTOR, and my next article after that will be about senolytics — how to eradicate senescent cells. Thanks for tuning in and peace out ✌.
Hey y’all! 👋 I’m Aaron, a 16-year-old who’s super passionate about the intersection between artificial intelligence and human longevity. Feel free to connect with me on Linkedin or check out my full portfolio