An international study 13 years in the making demonstrates for the first time that degradation
in the way DNA is organized and regulated — known as epigenetics — can drive aging
in an organism, independently of changes to the genetic code itself.
The work shows that a breakdown in epigenetic information causes mice to age and that restoring
the integrity of the epigenome reverses those signs of aging.
Findings are published online in the journal Cell.
Paper’s senior author, David Sinclair says this is the first study to show epigenetic
change as a primary driver of aging in mammals.
The team’s extensive series of experiments provide long-awaited confirmation that DNA
changes are not the only, or even the main, cause of aging.
Rather, the findings show, chemical and structural changes to chromatin — the complex of DNA
and proteins that forms chromosomes — fuel aging without altering the genetic code itself.
The authors say that because it’s easier to manipulate the molecules that control epigenetic
processes than to reverse DNA mutations, the work points to new avenues that focus on epigenetics
rather than genetics to prevent or treat age-related damage.
First, the results need to be replicated in larger mammals and in humans.
Studies in nonhuman primates are currently underway.
The researchers hope these results are seen as a turning point in their ability to control
aging.
This is the first study showing that they can have precise control of the biological
age of a complex animal; that they can drive it forwards and backwards at will.
Perhaps the most burning question for those who study aging is what causes it.
For decades, a reigning theory in the field was that aging arises from an accumulation
of changes to DNA, primarily genetic mutations, which over time prevent more and more genes
from functioning properly.
These malfunctions, in turn, cause cells to lose their identity, so that tissues and organs
break down, leading to disease and, ultimately, death.
In recent years, however, studies have increasingly hinted that there’s more to the story.
For instance, some researchers found that some people and mice with high mutation rates
don’t show signs of premature aging.
Others observed that many types of aged cells have few or no mutations.
Researchers started wondering what else works with or instead of DNA changes to cause aging.
A list of possible culprits grew.
Among them were epigenetic changes.
A component of epigenetics is the physical structures such as histones that bundle DNA
into tightly compacted chromatin and unspool portions of that DNA when needed.
Genes are inaccessible when they’re bundled up but available to be copied and used to
produce proteins when they’re unspooled.
Thus, epigenetic factors regulate which genes are active or inactive in any given cell at
any given time.
By acting as a toggle for gene activity, these epigenetic molecules help define cell type
and function.
Since each cell in an organism has basically the same DNA, it’s the on-off switching
of particular genes that differentiates a nerve cell from a muscle cell from a lung
cell.
Epigenetics is like a cell’s operating system, telling it how to use the same genetic material
differently.
In the late 1990s and early 2000s, Sinclair’s lab and others showed in yeast and mammals
that epigenetic changes accompany aging.
Yet they couldn’t tell whether these changes drove aging or were a consequence of it.
It wasn’t until the current study that Sinclair’s team was able to disentangle epigenetic from
genetic changes and confirm that a breakdown in epigenetic information does, in fact, contribute
to aging in mice.
The team’s main experiment involved creating temporary, fast-healing cuts in the DNA of
lab mice.
These breaks mimicked the low-grade, ongoing breaks in chromosomes that mammalian cells
experience every day in response to things like breathing, exposure to sunlight and cosmic
rays, and contact with certain chemicals.
In the study, to test whether aging results from this process, the researchers sped the
number of breaks to simulate life on fast-forward.
The team also ensured that most of the breaks were not made within the coding regions of
the mice’s DNA — the segments that make up genes.
This prevented the animals’ genes from developing mutations.
Instead, the breaks altered the way DNA is folded.
Sinclair and colleagues called their system ICE, short for inducible changes to the epigenome.
At first, epigenetic factors paused their normal job of regulating genes and moved to
the DNA breaks to coordinate repairs.
Afterward, the factors returned to their original locations.
But as time passed, things changed.
The researchers noticed that these factors got “distracted” and did not return home
after repairing breaks.
The epigenome grew disorganized and began to lose its original information.
Chromatin got condensed and unspooled in the wrong patterns, a hallmark of epigenetic malfunction.
As the mice lost their youthful epigenetic function, they began to look and act old.
The researchers saw a rise in biomarkers that indicate aging.
Cells lost their identities as, for example, muscle or skin cells.
Tissue function faltered.
Organs failed.
The team used a recent tool developed by Sinclair’s lab to measure how old the mice were, not
chronologically, in days or months, but “biologically,” based on how many sites across the genome
lost the methyl groups normally attached to them.
Compared to untreated mice born at the same time, the ICE mice had aged significantly
more.
Next, the researchers gave the mice a gene therapy that reversed the epigenetic changes
they’d caused.
It’s like rebooting a malfunctioning computer.
The therapy delivered a trio of genes — Oct4, Sox2, and Klf4, together named OSK — that
are active in stem cells and can help rewind mature cells to an earlier state.
Sinclair’s lab used this cocktail to restore sight in blind mice in 2020.
The ICE mice’s organs and tissues resumed a youthful state.
The therapy set in motion an epigenetic program that led cells to restore the epigenetic information
they had when they were young.
It’s a permanent reset.
How exactly OSK treatment achieved that remains unclear.
At this stage, Sinclair says the discovery supports the hypothesis that mammalian cells
maintain a kind of backup copy of epigenetic software that, when accessed, can allow an
aged, epigenetically scrambled cell to reboot into a youthful, healthy state.
For now, the extensive experiments led the team to conclude that by manipulating the
epigenome, aging can be driven forwards and backwards.
The ICE method offers researchers a new way to explore the role of epigenetics in aging
and other biological processes.
Because signs of aging developed in the ICE mice after only six months rather than toward
the end of the average mouse life span of two and a half years, the approach also saves
time and money for researchers studying aging.
Researchers can also look beyond OSK gene therapy in exploring how lost epigenetic information
might be restored in aged organisms.
There are other ways to manipulate the epigenome, like drugs and small molecule chemicals that
induce gentle stress.
This work opens a door for applying those other methods to rejuvenate cells and tissues.
Sinclair hopes the work inspires other scientists to study how to control aging to prevent and
eliminate age-related diseases and conditions in humans, such as cardiovascular disease,
type 2 diabetes, neurodegeneration, and frailty.
The goal would be to address the root causes of aging to extend human health span: the
number of years that a person remains not just alive but well.
Medical applications are a long way off and will take extensive experiments in multiple
cell and animal models.
But, Sinclair said, scientists should think big and keep trying in order to achieve such
dreams.
For about the past fifty years, popular theory has held that the process of aging is caused
in large part by an accumulation of mutations.
There’s growing evidence, however, that aging has a significant epigenetic component.
That is, the process by which stretches of DNA – or the genes – are turned on and
off.
My colleagues and I believe that not only are epigenetic changes a primary cause of
aging, but these changes are driven by the ongoing
process of DNA breakage and repair.
Why do we think this?
Here we have two mice from the same litter – essentially twins.
We checked, so we know that they have the same DNA sequence.
The only difference between the two is that, for the older-looking one, the break and repair
process was accelerated.
And this caused epigenetic changes.
Part of the epigenetic process involves the packaging of DNA.
When genes are not active they’re packed tightly in chromatin but sometimes this packaging
loosens, giving the cell access to appropriate genes.
This process happens all the time, and it has to for a cell to function properly.
Certain areas of the DNA structure within a liver cell, for example, need to loosen
to allow access to liver-specific genes.
Unfortunately, naturally occurring DNA breaks cause changes in the chromatin structure And
over time, this happens a lot.
Our bodies experience a million DNA breaks a minute.
And as cells try to repair the broken DNA, the chromatin structure loosens in some areas,
including the area around the break, and it tightens in other areas.
And if it loosens an area that it’s not supposed to, a wrong gene might be expressed.
This is important because if, for example, liver cells accidentally activate wrong genes,
the organ as a whole will begin to show signs of aging.
We wanted to test our theory that aging results from DNA break and repair, so we engineered
a new strain of transgenic mice.
These mice are genetically altered to let us turn on and off a special enzyme.
When we turn the enzyme on, the DNA within many of the mouse cells are cut at a number
of locations – at a rate that is about three times the natural frequency of DNA breakage.
And each breaking of the DNA initiates a repair.
Special proteins that regulate chromatin structure and gene expression move to the cut DNA.
The proteins loosen the chromatin and recruit other proteins that repair the DNA.
When their work is done, the proteins usually move back to their original locations, and
the chromatin structure – the packaging – usually resets to its original tightness.
In our mouse, as long as the enzyme is on, cuts are initiated in the DNA.
With many breaks happening, the repair proteins are very busy.
And this is an issue.
With each successive fix, the proteins don’t always return to their original locations,
and the chromatin structures at the repair locations don’t always reset to their original
tightness.
Actually, the process is a bit more complicated.
There are other proteins involved, and these proteins, in addition to assisting with DNA
repair, are also responsible for turning genes on
and off.
With each successive fix, the proteins become more jumbled.
This jumbling results in some genes that were initially turned on to turn off and other
genes that were turned off to turn on.
Changes like these alter the cells enough to cause them to become more dysfunctional.
By the way, just to be sure we weren’t disrupting the function of cells, we didn't cut in random
places.
Instead, we avoided locations that code for genes.
So what did we find?
Here are the two mice I showed you earlier.
They are both 10 months old.
The older-looking mouse had the cutting enzyme turned on for three weeks when it was young.
The other didn’t.
To verify that the aging we see isn’t the result of mutations, we sequence – or “read”
– the entire chromosome of each mouse.
So really, the only difference between these mice is epigenetic.
To test our theory further we experimented with resetting epigenetic
structures in our aged mice, and we found that we could safely reverse blindness and
rejuvenate kidneys and muscle.
We used to think that aging was like parts of a recipe being erased – once a mutation
occurred, the DNA code was lost forever.
But now we know that cells still have the DNA intact, we just need to teach them how
to read that code again.
And if we can do that, aging may be much more reversible than we ever thought.