Stem Cells: The Key to Reversing Biological Age

Using Yamanaka Factors to Reverse Epigenetic Noise and Regenerate Aged Tissues

Akshaj Darbar
11 min readJun 23, 2020

In 2006, Dr. Shinya Yamanaka, a Japanese stem cell researcher, published his paper on induced pluripotent stem cells, and it changed the medical world. Dr. Yamanaka had found a way to convert a mature skin cell into a stem cell by injecting just a few genes. And for this, Dr. Yamanaka received the Nobel Prize in Physiology or Medicine in 2012, sharing it with another Sir John B. Gurdon, who found another method of inducing pluripotency.

Dr. Yamanaka giving a lecture at the Nobel Prize Inspiration Initiative

Thirteen years after this paper was published (in 2019), Dr. Yuancheng Lu from the Sinclair Lab at Harvard University authored another paper (still being peer-reviewed) where he had used Dr. Yamanaka’s breakthrough to reverse aging.

Stem Cells Are SUPER Important

To first explain what stem cells are (for those of you that don’t have much biology experience), we’re going to go back in time to when you were just a small mass of cells in your mother’s womb.

Embryonic Stem Cells

Unlike the adult human, which has skin cells, muscle cells, brain cells (or neurons), or any of the other hundreds of cell types, the embryonic mass has unspecialized cells without a specific “type”. These cells are said to be undifferentiated (no specific type or function), and are referred to as embryonic stem cells (ES cells). You can think of them as a bunch of kids that don’t have a specific job or function in society.

As the development process continues, these stem cells begin to differentiate or turn into cells that carry out only specific functions, based on their different chemical signals that they’re exposed to. It’s like when a child gets a bunch of spaceships as toys, watches lots of YouTube videos on space exploration, and (when they grow up) attends university and studies space exploration. Based on these signals or experiences, the child is now most likely to enter a career in space exploration, whether that involves becoming an astronaut or becoming a researcher at NASA or SpaceX or another space institution. Similarly, based on which chemical signals an ES cell is exposed to, it will specialize into a specific cell type.

Even after we have fully developed, adult stem cells stick around and work on regenerating tissues as they are damaged. But, as we age, these stem cells are depleted in the body, due to a variety of causes. This is actually a defining hallmark of aging, leading to tissues not being repaired and sustaining damage. And so, researchers were looking frantically into uses of stem cells to treat various disorders, such as Parkinson’s disease, spinal cord injury, or diabetes.

Side Note: Check out my article on the nine hallmarks of aging to find out more about why we age:

iPS Cells Breakthrough

The only problem was, these stem cells could only be obtained from embryos. Other stem cells in adult bodies were already somewhat specialized so that they could only transform into a few different types of cells. But there is obviously a huge ethical problem with obtaining stem cells from embryos.

And so, Dr. Yamanaka set out to find a way to obtain stem cells without having to extract them from the embryo. From previous experiments, Dr. Yamanaka had realized that somatic cells (or normal, differentiated cells of the body) could be reprogrammed by either transferring their genetic material into oocytes (egg cells) or by fusing them with embryonic stem cells. From this, he inferred that there must be some factors in these undifferentiated cells that maintain the pluripotent (capable of differentiating into many other cell types) state, and hypothesized that these same factors could also induce pluripotency in somatic cells.

First, Dr. Yamanaka’s team recognized a host of genes (24 in total) that were involved in the maintenance of ES cell phenotypes and genes that were only expressed in ES cells. Next, they used vectors known as retroviruses to introduce these genes into cells, after which they tested pluripotency by observing the reaction of the cell to specific compounds.

After repeated trials, the researchers finally settled on four main genes: Oct3/4, Sox2, c-Myc, and Klf-4. Oct3/4 and Sox2 code for key transcription factors important for inducing pluripotency to cause the development of what they call induced pluripotent stem cells (iPS cells).

A Colony of Induced Pluripotent Stem Cells (iPS Cells)

c-Myc has many downstream targets that enhance cell proliferation and transformation, which may also play a major role in iPS cell generation. Specifically, c-Myc associates with histone acetyltransferase (HAT) which might induce global histone acetylation (more on this later), allowing Oct3/4 and Sox2 to bind to their specific targets.

Klf4 represses another protein known as p53, which plays a major role in preventing cells from turning cancerous. In normal cells, p53 levels are low, which allows the cells to continue living and dividing. However, DNA damage or stress on the cell could trigger an increase in p53 protein levels, which could cause growth arrest (no more cellular division) or even apoptosis (cellular death) as a last resort. As such, Klf4 might function as an inhibitor of c-Myc-induced apoptosis by suppressing the p53 proteins.

Using these genes, Dr. Yamanaka converted skin fibroblasts (or skin cells) into iPS cells in both humans and mice.

Note: It was later found that c-Myc is dispensable, and iPS cells can be generated with just Oct3/4, Sox2, and Klf4.

With this, scientists could now generate stem cells very easily without any ethical concerns. And soon, tons and tons of papers and research that showed the beneficial use of these stem cells in curing various disorders appeared.

The Epigenome

Before we get into how Dr. Lu used iPS cells to reverse aging, we need a quick review of epigenetics.

Every cell in your body has the same exact genome or DNA code. So then what differentiates a skin cell from a nerve cell? That’s where the epigenome comes in. The epigenome, simply put, is the chemical system that regulates how your genome is read, and how different genes are expressed. It does so with many different mechanisms, but two common mechanisms involve DNA methylation and histone acetylation.

DNA methylation involves binding methyl groups (single carbon bonded to three hydrogens) to cytosine nucleotides at specific points on the gene. These methyl groups prevent DNA transcription molecules from binding to the gene and expressing it.

Histone acetylation acts on the histone proteins that DNA is bound around. These proteins coil the super long DNA strands into the chromatin and chromosomes that can fit inside a cell. By adding an acetyl group to these histones, the chromatin can be uncoiled, allowing access to the genes and increasing expression. Meanwhile, the deacetylation of histones causes the DNA to be wound up tighter and limits access to those genes, repressing them in the process.

And so, with this epigenetic control of which genes are expressed, a skin cell would only express genes that are important for being a skin cell. A nerve cell, on the other hand, would only express the genes necessary for being a nerve cell (such as genes needed for producing electrical signals).

But this epigenome begins to get damaged and break down as we age, due to what is called epigenetic noise. This essentially involves random changes in the epigenetic landscape (ex. removal or addition of methyls, (de)acetylation of histones) where genes that are meant to be off turn on, whereas genes that are meant to be on turn off. This has been linked to the progression of aging and development of the several hallmarks of aging.

Dr. David Sinclair, Author of Lifespan and Longevity Researcher at Harvard Medical School

And so, many researchers have been investigating the potential of reversing this epigenetic noise, and in the process, reversing aging. This includes Dr. David Sinclair, who developed the Information Theory of Aging that establishes this loss in epigenetic information as the main cause behind aging, and runs the Sinclair lab where Dr. Lu carried out the experiment.

The Epigenetic Correction System

Dr. Sinclair and other researchers in this field often compare the epigenetic information system in our bodies to the mathematically-developed information system proposed by Dr. Claude Shannon in the 1940s.

The correction system proposed by Dr. Shannon | Harvard Mathematics

In Shannon’s system, which actually serves as the backbone for how the Internet operates, the information from the source is not only directly sent through the transmitter to the receiver, but also copied by a secondary observer node. This is because many problems can arise during the transmission process (ex. loss or corruption of data, etc.) that might compromise the data. To work around this, the receiver compares the data it receives to the observer node. If a discrepancy exists, the data from the observer node is used as a reference by the correcting device, which fixes the received data and finally sends wherever it might be needed (ex. for you to see on your computer screen).

Dr. Sinclair’s book Lifespan, which discusses the science behind aging, and ways that aging can be avoided or even reversed

Dr. Sinclair, in his book Lifespan, compares this to epigenetic information in a cell. The source would be the initial epigenetic state for a stem cell, or the epigenome right after a cell has differentiated. The transmitter and receiver can instead be replaced by just the progression of life for the cell, over the course of which it accumulates epigenetic noise. But when it comes to the observer and the correction device, no one knows which cellular components might play a similar role.

But first off, to even test the hypothesis that the cellular epigenetic information management system might have a backup data correction system similar to Dr. Shannon’s proposal, Dr. Lu set off to correct eye injuries with the Yamanaka genes.

Resetting the Epigenetic Age — Dr. Lu’s Research

To test the hypothesis, Dr. Lu and his team first introduced the expression of Oct3/4, Sox2, and Klf4 (collectively referred to as OSK) in fibroblasts from old mice. They then measured the effects of OSK treatment on the RNA levels of genes known to be altered by age. They found that OSK-treated old fibroblasts promoted youthful levels of these genes without loss of cellular identity. They also observed no induction of Nanog, an early embryonic transcription factor that can induce tumours.

To truly test the regenerative abilities, however, the team tested the ability to regenerate retinal ganglion cells (RGCs) in mice. RGCs are part of the central nervous system, the first organ system to lose regenerative potential, that project axons from the retina to the brain. RGCs can regenerate when damaged during embryogenesis and in newborns, but the capacity to regenerate RGCs is lost within a few days after birth.

The vitreous body consists of the gel-like vitreous humor between the lens and the retina

Dr. Lu’s team tested the effects of OSK induction in an optic nerve crush injury model where the optic nerve is precisely crushed to eliminate sight. The team also introduced the OSK genes into adeno-associated viruses (AAVs) developed to target RGCs, which were then injected into the vitreous body.

They found that the induction of all three genes with a single AAV resulted in the greatest extent of axon regeneration in the damaged eye and that the greatest effects were observed if the gene induction was carried out post-injury. The researchers also found that injured RGCs experienced accelerated epigenetic aging in the cells (accumulation of epigenetic noise at a higher rate) and that OSK expression counteracted this effect to maintain a younger epigenome to allow axon regeneration.

Regeneration of axons (stained orange/yellow) without (top) and with (bottom) OSK expression post-injury. Blue asterisks indicate optic nerve crush site

The experiment was also applied on human neuronal cultures, where the damage involved induction of vincristine (VCS), a chemotherapic agent. The cells were allowed 9 days of recovery, after which the DNA methylation age was measured. Just like the mice RGCs, DNA methylation age was increased significantly after the injury/damage, and OSK expression not only prevented this increase, it also restored a younger DNA methylation age without reducing global DNA methylation levels.

This means that OSK expression was able to precisely reverse epigenetic noise to a younger state, instead of just randomly reducing methylation throughout the genome. This suggests that there may be a backup of the original, pre-epigenetic noise genome as expected with the correction system proposed by Dr. Shannon.

And that discovery comes as amazing news to all longevity researchers and fanatics (like me!). It suggests that it is entirely possible to reverse aging in cells with the use of a molecular mechanism already present in the cells. And so, scientists are now off to the races in the hopes of finding this cellular mechanism, and ways to activate this correction system in living beings without requiring OSK gene induction.

This same procedure could, in the future, be used to treat various disorders that require regeneration of cells (ex. Alzheimer’s Disease, types of diabetes, glaucoma, and many more).

But even more importantly, this breakthrough opens up the possibility of taking some medication and reversing your biological, or epigenetic age. You could, theoretically, go into the doctor’s office when you’re 40, get a pill, and become 20 years younger. You could even do this multiple times in your life, and live a healthy life for much much longer, or even forever!!!

Now that’s a future I’m excited about.


Dr. Yuancheng Lu’s Paper on his Research (Still Unpublished)

Dr. Yamanaka’s First Paper on iPS Cells

Lifespan — Book by Dr. David Sinclair

On A More Personal Note:
I am a
17-year old currently obsessed with the science behind aging, and if we could live forever (because, let’s be honest, no one wants to die).
I do have more articles coming up on the
coronavirus vaccine research right now, and on cancer stem cells (super excited for this one), so if you want to read more of my articles, follow me here on Medium. And check out some of the other articles I have written, on various topics from AI, to gene editing, to life and philosophy.
To find out more about me and what I’m working on, check out my
website, and my Twitter.

That’s all for me now. See you next time!



Akshaj Darbar

MD Candidate at McMaster University. Researching blood cancer detection.