Stopping the Genetic Snowball: How a simple genetic interruption slows Huntington’s disease

While the genetic change that causes Huntington’s disease (HD) leads to several problems for cells, researchers believe they could stem from one core issue: the length of the genetic change increasing over time, like a snowball gaining mass as it rolls downhill. This genetic phenomenon, known as somatic instability or somatic expansion, seems to be a key driver of disease progression. In a recent study, scientists developed a new variant of CRISPR, a powerful gene editing tool, to interrupt this genetic expansion, potentially paving the way to new therapeutic opportunities. 

A Genetic Snowball

HD is caused by a change in a gene called HTT, specifically where the genetic letters C-A-G are repeated several times. In people with HD, this CAG section is longer than normal, jump-starting a deadly chain reaction inside brain cells. Unlike most mutations, which remain the same throughout life, the CAG repeats in HTT grow longer with age, like a snowball picking up speed as it barrels downhill. 

At birth, most people with HD have around 40 to 50 CAG repeats in their HTT gene. Over time, that number grows exponentially inside cells, sometimes surpassing 500 repeats by the time symptoms develop! If the initial repeat is above a critical threshold (36 repeats), the expansion turns into a kind of genetic snowball over time and begins growing out of control.

However, HD is not alone; it belongs to a broader category of diseases called trinucleotide repeat disorders – a fancy term for 3 (tri) genetic letters (nucleotide) that repeat (repeat – ok that one was obvious…). These disorders all share a similar problem with snowballing mutations. One such example is Friedrich’s Ataxia, which is driven by a growing CTG repeat that also worsens over time. 

The observation that several brain diseases are caused by a growing trinucleotide repeat raises a key question: Why are growing trinucleotide sequences so toxic to brain cells? Normally, genes like HTT are used to produce messenger RNA, also called mRNA, a temporary copy of DNA that is used to make proteins, the machines of the cell. However, long trinucleotide repeats cause the RNA to twist into super-tangled and stable knots, clogging the cell’s protein-making machinery. As these tangled RNAs grow longer and more abundant, they increasingly disrupt protein production, eventually contributing to cell death.

Interrupting the Instability

What if there were a way to break this snowball effect before it spirals out of control? Scientists at Harvard University, led by Dr. David Liu, hypothesized that they could interrupt the repeating CAG sequence by simply replacing one of the CAGs with a similar, but harmless, CAA sequence. 

By interrupting the repeating CAGs, even with a similar CAA sequence, the underlying pathway that leads to the CAGs growing with age might get blocked! In other words, inserting a CAA sequence is like placing a patch of rocks on the hill, causing the snowball to smash into them and break its momentum! 

Liu and his team were inspired by previous research showing that CAA interruptions seem to delay disease onset. Typically, the number of CAG repeats strongly predicts when someone will develop HD, but genetic studies identified people with long repeats but delayed ages of onset. 

Examined more closely, these genetic outliers were discovered to contain short CAA interruptions within their CAG stretch. Remarkably, these simple interruptions were linked to a 12-year delay in disease onset! Motivated by these observations, Liu and his team wondered if they could intentionally insert CAA sequences into cells with the gene for HD, and if this could recreate the protective effect. 

CRISPR Cracks the Snowball

Precision genetic changes, like swapping a CAG to CAA, are simple in theory, but extremely challenging in practice. Liu and his team turned to CRISPR, a gene-editing tool that acts like molecular scissors to alter specific DNA sequences. They developed a special type of CRISPR, called base editing, that looks for CAG repeats and swaps some of them out for CAAs. 

Using human cells growing in petri dishes, they found that their CRISPR base editing strategy successfully modified the HTT CAG repeat in about 80% of cells, with no signs of toxicity. Even more promising, they found these simple CAA interruptions seemed to stop the CAG repeat expansions after 30 days. They even noticed the CRISPR-edited cells appeared to grow faster and look healthier!  

Because this type of CRISPR targets all CAG repeats (not just the one in HTT) and introduces CAA interruptions into them as well, they needed to confirm that other genes were not disrupted by accident. In total, they found about 250 other genes changed by CRISPR, likely because they contained similar CAG repeats. However, only about 50 of them are active in brain cells, and just one appeared to be significantly disrupted. While this finding doesn’t rule out risk, it does suggest that unintended edits are unlikely to cause serious issues. Regardless, minimizing accidental edits will be a top priority moving forward!

Interrupting CAGs with CRISPR

Now comes the big challenge: Can the team get the CRISPR machinery into cells in a living brain and successfully edit CAG sequences? Liu’s team used a mouse model of HD that carries 110 CAG repeats in its HTT gene, and this repeat grows rapidly as the mice age (repeat instability). To deliver CRISPR to the brain, the team packaged up CRISPR into a harmless virus, which acts like a gene delivery service, injecting the genetic editing tools directly into cells. 

Four weeks after injecting the CRISPR-loaded viruses into the mice, the researchers found that about 30% of the cells seemed to have picked up the gene editing tool. Of the 30% of cells containing CRISPR, around 75% appeared to have at least one CAA interruption in their HTT gene. That means about 1 in 5 brain cells successfully received the protective genetic change – not perfect, but a promising start! After 12 more weeks, the researchers examined the length of CAG repeats and found that expansion seemed to not only stop, but some CAG repeats may have even shortened! 

To investigate if their approach worked beyond HD, the researchers repeated their experiments in cell and mouse models of Friedreich’s Ataxia, another repeat expansion disorder. Excitingly, they observed similar results: up to 55% of brain cells seemed to contain repeat interruptions, and the repeats appeared stable over time, showing no signs of expansion with age. 

Will CRISPR Break the Ice?

Collectively, these findings seem to show that the snowballing repeat expansion in HTT can be stopped, and this approach might even apply to other repeat disorders. However, there are a couple of reasons for caution. This study focused on whether CRISPR could insert CAA interruptions and halt repeat growth, but it did not assess whether this intervention improves symptoms or delays disease. Knowing the impact of this type of therapeutic approach on HD signs and symptoms is essential for determining if it should move forward.

Additionally, reducing unintended changes to genes other than HTT will be critical before moving to human trials. Another issue is delivery – human brains are much bigger than mouse brains, and getting CRISPR into enough brain cells to make a difference will be particularly challenging. 

Regardless of these current limitations, these results are a major step forward. With advances in gene editing accuracy and more effective delivery methods, CRISPR is likely to become a powerful tool in the fight against HD and other trinucleotide repeat diseases. 

TL;DR: The Big Takeaways

• The problem: HD is caused by a mutation in the HTT gene, where CAG repeats grow over time, a process called somatic expansion. This “genetic snowball” seems to worsen brain cell function and drive disease progression.
• The insight: Even a small interruption in the repeating sequence, like swapping a CAG for a similar and harmless CAA, may be able to slow or stop expansion and delay symptom onset.
• The breakthrough: Scientists used a refined CRISPR tool (called base editing) to insert these potentially protective CAA interruptions into the HTT gene.
• In the lab: In human cells, CRISPR base editing worked in ~80% of cells, seeming to halt expansion and improve cell health.
• In mice: After CRISPR was delivered via viral injection, about 20% of brain cells had protective changes and CAG repeats appeared to stop growing.
• Bonus: Similar success was seen in mouse models of another repeat disorder, Friedreich’s Ataxia.
• The catch: More work is needed to:
  • Prove symptom improvement
  • Minimize unintended effects
  • Scale delivery to the much larger human brain
• Why it matters: This work shows that CRISPR could be used to interrupt repeat expansions in living brain tissue, offering real hope for treating HD and similar genetic disorders.

Learn More

Original research article, “Base editing of trinucleotide repeats that cause Huntington’s disease and Friedreich’s ataxia reduces somatic repeat expansions in patient cells and in mice” (open access).