In two recent studies, researchers looked at how different parts of the brain are affected by CAG expansions in Huntington’s disease (HD) at the level of individual brain cells. The scientists looked at post-mortem brains from people with and without HD to track molecular changes in different brain regions called the cortex and striatum. These studies have provided new insights into what contributes to HD. Let’s get into it!

Specific brain areas are prone to damage in HD

For a long time now, we have known that some areas of the brain are affected more than others in people with HD. Specific types of brain cells in these vulnerable parts of the brain tend to die off more quickly than others, in a process known as degeneration.

However, the underlying reasons for why some cells are affected more than others are not very clear. Lots of researchers from around the world have been trying to figure this out, as it might shine a light on exactly how HD progresses and give us clues as to how we might treat it.

In two recent papers coming from the same laboratory at Rockefeller University in New York, scientists have looked very closely at molecular changes which happen in different types of brain cells in HD. Using generously donated post-mortem brain samples from people with or without HD, the team carefully separated the brain tissue into individual cells.

The two studies focused on different parts of the brain; the first concentrating on a region called the cortex, and the second looking into cells which make up the striatum and cerebellum. Each brain region is made up of lots of different types of cells so they used special markers to sort all the cells and work out which cells were which type. They were then able to measure all sorts of molecular changes from the different types of cells using cutting-edge genetics technologies.

Linking somatic expansion to when symptom start

One of the changes the scientists looked at in each cell was the CAG number in the huntingtin gene. HD is defined at the genetics level as people who have more than 36 repeating C-A-G DNA letters in their huntingtin gene, with most folks with HD having 40-50 CAGs compared to people without HD who have somewhere around 18 CAGs.

For some time now we have known that in certain types of cells this CAG number is not stable and will change over the course of someone’s lifetime, often getting much longer. This process of CAG increases in some cells is known as somatic expansion. It’s important to note that blood cells happen to be a cell type with stable CAG repeat numbers compared to other cell types. So if you received a genetic test when you were 18, that number will almost surely be the same if you were to get tested again at age 50.

Somatic expansion became a hot topic in HD research when studies of genetic modifiers, traits which change the age of symptom onset, pointed to the exact genes which we think control somatic expansion. Together, this suggests there is a link between how big a CAG number gets during the lifetime of someone with HD and how early they will experience symptoms of the disease.

Thanks to tremendous advances in DNA sequencing technology, we can now look at how long the CAG number is in each individual cell. In fact, this is exactly what the team from Rockefeller did. So what did they find?

Cool conclusions from the cortex

In the first study published at the start of this year, the scientists zoomed into a part of the brain called the cortex – the outer part of the brain with all the wrinkles. Studies which have done detailed brain scans of people with HD have shown a thinning of this part of the brain. They’ve also found that connections between brain cells are lost in this part of the brain over the course of the disease and that the cells tend to die early on. Changes in the cortex cause cognitive decline and psychiatric symptoms that many people with HD experience.

The scientists found that a specific type of brain cell, called Layer 5a corticostriatal projection neurons (phew, what a mouthful!), is lost in people with HD. These cells die early during the disease, in both humans and monkeys. While these cells are found in the wrinkly cortex, they connect all the way to the centre of the brain, to the striatum, the region that’s most vulnerable in HD.

Interestingly, the team found that increases in the CAG number happen in many different types of nerve cells in the cortex, including those that remain relatively healthy. CAG increases were seen in the vulnerable Layer 5a brain cells but also in other cells called Betz cells, which aren’t so badly affected by HD. This pointed the researchers to the conclusion that having an increase in CAG number is not enough on its own to cause cells to get sick.

Study surprises from the striatum

In the second study, the researchers focused on the striatum, a brain region in the very center of our heads and the part of the brain most affected by HD. A type of brain cell, called medium spiny neurons or MSNs, are found in this part of the brain and are known by researchers to be the most vulnerable to death in folks with HD.

When the team looked at the CAG number in individual cell types from this part of the brain, they found that the MSNs had the biggest increase in their CAG number. However, other cells in the striatum which are not so affected in HD, such as a type of nerve cell called ChAT+, also had big changes in their CAG number.

The researchers looked at cells from the brain of someone with a similar brain disease to HD called SCA3 (spinocerebellar ataxia type 3), which is caused by an increase in CAGs in a gene called Ataxin3. Folks with SCA3 suffer loss of brain cells but this is not specific to the MSN cell type like it is in HD.

In this disease, they also found that the CAG number increased in the MSN cells, but not other types of brain cells, even though the MSN cells in these folks’ brains weren’t so affected. This means that MSNs may just be particularly prone to expanding CAG repeats, regardless of what gene has the long CAG repeats. However the ever expanding CAG repeat may not be the direct reason that those cells die.

So what does this all mean?

What both of these studies point to is the idea that increasing CAG number in HD could be just one of the necessary steps towards cells getting sick. On its own, somatic expansion might be insufficient to cause that cell to die, as the researchers report CAG expansions in cells not vulnerable to death in HD, like the Betz cells.

Both studies also looked at other features of these cells. They did a deep dive into the genes that are turned on or off in every cell in brains of people with and without HD. What they found is that HD causes global changes in the types of genes that are on or off. This has also been shown by many other researcher groups before. Researchers think that these changes may cause toxicity, affecting the health of the cells, eventually contributing to their death.

The researchers think that connection issues could also be contributing to cell death. In the cortex, they found alterations in vulnerable cells that change the way they can connect and communicate with cells in other areas of the brain. This disconnection not only reduces the ability of one brain area to communicate with another, but it also weakens the cells themselves over time.

Other research groups are still testing the hypothesis that somatic expansion is the major driver of HD. Different scientists are using different technologies to measure the CAG numbers and early previews of these datasets at the recent therapeutics meeting suggest that this can lead to different results. We expect to see a lot more work in this space in the future.

Science only made possible by patient families

It is really important to note that nearly all of the findings of these two very important studies were made possible by the researchers having access to extremely precious post-mortem brain samples. In both studies, the scientists compared brain material from people either with or without HD, who had passed, who generously donated their brains to science to further research. This is an amazing selfless act that has tremendous impacts for research to better understand HD, with the ultimate aim of one day finding a drug to slow, stop, or reverse the disease.

Whilst brain donation is not something that everyone might be comfortable or able to do, if this is something you are interested in doing, the HDSA, HSC, the Brain Donor Project, and other patient organisations, have information and resources about what this decision involves and next steps.

HDBuzz is back for Day 2 of the CHDI HD Therapeutics Conference: Wednesday February 28th in Palm Springs, California. This article summarizes our real-time updates of the conference in community-friendly language.

It’s a brain disease

This morning’s session is titled “It’s a brain disease” and will feature talks about BRAINSSSS! HD scientists are a bit like zombies – they love brains! The session chairs posed big questions to the audience, such as: why does HD affect the brain? Why does it affect certain cells in the brain? And why does HD affect people at the time in their life that it does. This season’s talks tried to address these questions from a variety of different angles.

Christopher Walsh: DNA “signatures” of brain cells in aging and disease

The first speaker of the day was Dr. Christopher Walsh from Boston Children’s Hospital & Harvard Medical School who spoke to us about somatic expansion in the brain. We mentioned that somatic expansion was a hot topic in HD as of late, and many of the talks at CHDI proved that true! Somatic expansion is the increase in the CAG number in some types of cells over the course of someone’s lifetime. There seems to be a link between the amount of somatic expansion and disease progression. Lots of scientists are pursuing this to understand how and why this occurs and also how we might treat it.

Chris’s team look at human brains, generously donated by folks to science. They examine individual cells in those brains, then try to identify single letter changes in the DNA code that are linked to somatic instability.

Over their lifetime, cells accumulate changes in their DNA code, forming “signatures” that scientists can use to classify those cells. Different diseases and cell types have different DNA “signatures,” which researchers can track and categorise. In nerve cells, these changes in DNA signatures happen with age. Chris says this is a bit like a molecular “clock” which gives insight to that person’s degree of aging.

It turns out that the majority of these DNA signature changes are happening in genes that are most important for nerve cells. It also looks like these changes are fairly unique to neurons over other types of brain cells. What’s rather cool about these signatures is that it gives scientists clues about the birth of brain cells, and the common stem cells that gave rise to nerve cells with different DNA signatures. This helps us understand how the brain is formed and how it changes over someone’s lifetime.

Folks in Chris’s team are also using this tracking system to look at how the brain changes in diseases like Alzheimer’s and other neurological disorders, and how this trajectory differs from healthy brains. For example, they were able to use their molecular clock to figure out that brain cells from some people with Alzheimer’s had DNA changes equivalent to around 10 additional years of age compared to people without Alzheimer’s.

Although most of this talk was focused on findings in other diseases, the methods this lab has developed could be an asset to the HD community as scientists continue to pursue DNA repair for HD therapeutics and understand how HD changes the brain.

Mark Bevan: electrical activity in the HD brain

Next on the roster was Mark Bevan from Northwestern University. Mark’s team study HD mice to understand how their brains are affected by the HD mutation, especially an area called the STN, which is thought to suppress movements. Mark recapped some of what we know about CAG repeat expansion: that it may play a role in brain cells getting sick, and that long repeats trigger even more expansion. HD mice with really long CAG repeats have measurable signs of HD – they move and behave differently.

Mark’s lab measures the electrical activity between neurons to understand the activity of different types of cells as mice move around. These techniques involve implanting an electrode into the brain. With this technique, they can get into the nitty gritty of which cells are firing in HD mice and in non-HD mice to unpick exactly what is working and what is going wrong. This is helping them to understand why the HD mice have movement symptoms.

In fact, using special genetic trickery, they were able to make mice without HD move like mice with HD, by stimulating similar patterns of brain cell firing. The challenge is to do the reverse: getting HD mice to move like mice that don’t model HD.

Another interesting finding is that huntingtin-lowering techniques help to restore normal brain activity in some cells but not in others. It also helps to ease the movement symptoms Mark’s team see in the HD mice.

Mark’s work focuses on brain regions that are not normally thought of as top targets for drugs, because they are affected later, or less, in HD. He reminds us that therapies will need to reach widespread areas of the brain. As an electrophysiologist (a scientist who studies electrical brain activity), Mark asks the audience to consider that changes in electrical activity could play a role in damage to neurons. It’s a reminder that a wide variety of techniques give us a clearer picture of changes to the HD brain.

Osama Al-Dalahmah: how HD affects astrocytes

Osama Al-Dalahmah is a neuropathologist based at Columbia University Irving Medical Center. He shared his work looking at how different cells and regions of the brain are affected in HD. There are over 100 different types of cells in the brain! Osama is interested in a type of cell called an astrocyte – a star-shaped cell that helps maintain health and function of neurons.

Osama and his team looked at brains which had been generously donated by folks with and without HD who had passed. There’s been so much data from human tissue this year! This highlights the collaboration between researchers and the HD community. It also gets us closer to understanding HD in the only species we care about – people!

They looked at which genes had been switched on and off in different parts of each brain. They also delved into what was happening at the level of individual cells. Armed with all of this data they could see which genes may track with increasing CAG number and other factors.

The star-shaped astrocytes have genes switched on which suggest they are responding to stress, which we know is happening as brain cells get sick. In fact, Osama’s team found that the more sick brain cells there are, the more the astrocytes are trying to make things better again. As astrocytes work to keep neurons healthy, understanding more about how HD affects them may help us understand how to improve the health of the whole brain.

Osama is trying to identify molecules that might improve the health of both astrocytes and neurons. Its early stages but it looks like his team might have found a molecule that appears to protect HD neurons in a dish!

Matthew Baffuto: understanding CAG expansion through decorations on DNA

Next we heard from Matthew Baffuto from Rockefeller University who spoke about his work on understanding changes to the CAG number in different types of brain cells. One part of this analysis is looking at an area of biology called epigenetics. Essentially, there are inherited decorations on the genetic code that make it easier or harder for a gene to be made into a message or protein.

Matthew’s research uses a special method of sorting out different types of brain cells so they can look at each type in lots of detail and see what molecular changes are happening with disease. As you may have gathered by now, there were a ton of talks using cutting edge technologies to really get into the nitty gritty of what each cell is doing in HD. This is a great example of how HD research benefits from technology developments in other fields.

One of the things Matthew wanted to tease out was which cell types have increasing CAG repeats due to somatic expansion. He looked at the decorative epigenetic markers on genes known to control this, like MSH3 and FAN1, which may sound familiar. The different decorative marks will let Matthew know if levels of MSH3, FAN1, and other DNA repair genes, are likely to be higher or lower in those cell types with somatic expansion. This is a way to examine the cause of lengthening CAG repeats.

Overall, the cells which get sicker in HD had a different array of decorative marks on DNA than cells which are less affected. Many of these decorative mark differences occur on genes known to be important in HD.

Matthew highlighted that changes in these decorative marks aren’t responsible for all the changes in HD in cells. However, his work shines light on how epigenetics can be used to understand how HD affects some drivers of disease, like somatic expansion. We need many different approaches to explain everything that’s going wrong in the cell!

Bob Handsaker – which cells gain CAGs and why?

The final talk of the morning was from Bob Handsaker who is based at Harvard Medical School and the Broad Institute. He studies the very long CAG repeats caused by somatic expansion in the brain. He began by recapping work from Peggy Shelbourne and Vanessa Wheeler who were some of the first researchers to detail that massive expansions can happen in some cells of the brain – up to 1000 CAGs in some cases!

What many researchers are trying to figure out is whether somatic expansion is the main thing that drives HD progression or whether it is involved in another way. Bob’s team uses a fancy type of DNA sequencing which means they can measure CAG numbers up to 1000 CAGs long. Impressive! Bob and his fellow researchers see that somatic expansion really only happens in cell types which get sick in HD. This is one explanation for the vulnerability of certain cells, but it’s a bit different from what other researchers have seen.

Bob shows us a model for how a CAG repeat tract might change from ~42 repeats to 100 repeats and then gets bigger at a faster rate as the person ages. In cells with less than ~150 CAGs, Bob’s team sees very few changes in the genes that are switched on or off. In their analysis, widespread changes only seem to happen when repeats get very large.

They also looked at the speed at which cells gain CAG repeats – it takes decades to reach rapid expansion. By 80 CAGs, it seems cells start gaining more CAGs rapidly, on the order of years. And once they reach 150 CAGs, the cells gain CAGs within a matter of months. In the rapid phase, at 150+ CAGs, the cells become dysregulated. Genes that should be off are turned on and others that should be on are turned off. Bob thinks this leads to toxicity and eventually death of the neurons that undergo this rapid CAG expansion.

Bob and his team are using their model to try and map the trajectory of HD: how many brain cells are lost when different symptoms start to happen? This is a new way of looking at HD and how the disease progresses, enabled by brand new technologies. He shared data from another area called the cortex (the wrinkly outer part of the brain). In these cells they saw a similar two-phase change in CAG numbers – slow and then much faster. This suggests that the process happens across brain regions. It also looks like somatic expansion could be linked to toxic huntingtin protein clumps. Cells which have really long CAGs are also the ones which show clumps.

After so many fascinating talks on somatic expansion, there are some contrasting ideas emerging in the research space. Some scientists believe that CAG repeat expansion is the number one driver of cell vulnerability in the striatum. Others believe CAG expansion kicks off a process that leads to toxicity, but isn’t necessarily the primary player.

Although Bob, Matthew, and other folks have different ideas about what is happening with somatic instability and HD progression, this is not necessarily bad news for the HD research community. In fact this happens all the time in science! Folks have different findings and they battle it out with genuine camaraderie in meetings. Researchers can weigh the strengths and limitations of each piece of data to figure out who might be right. An enthusiastic Q&A followed this talk!

David Altshuler – learning from the Vertex approach to drug discovery

Wednesday afternoon involved a poster session where more than 100 scientists had the chance to present their work to one another, followed by a keynote presentation from David Altshuler, who is the Chief Scientific Officer at Vertex Pharmaceuticals. He is an experienced researcher and pharmaceutical executive who spoke about his work developing drugs for various diseases.

David shared the timeline of discoveries in HD research, mentioning how far we’ve come from the 1980s when some researchers thought we could learn everything we need to know from mice. Slow progress isn’t unique to HD, it’s just really hard to make good medicines for human diseases! Despite tremendous advances, there is still so much we don’t know about human health and disease.

Making new drugs is also super expensive, and many drugs fail during clinical trials, costing time and money to companies and governments, whilst leaving patients waiting without effective treatments. 75% of new medicines fail, and on average it takes more than 12 years to make a drug. That said, David made a key point that it’s encouraging that we have many different technologies available now for the development of medicines. We see this in the HD field with splicing modulators, ASOs, gene therapies and other types of drugs which are all being tested in the clinic – most of these are fairly recent technologies.

As an example of how drug discovery can be successful, he notes Vertex’s efforts on Cystic Fibrosis. The factors that got them to multiple effective drugs are many of the things we already have in the HD field – care centers, natural history studies, and funding agencies that focus on moving research forward. He cited that after 25 years of Vertex working on Cystic Fibrosis, they now have multiple drugs, several of which they developed in just 3 years and can be used in patients as young as 1 month old.

An important point David makes is that genetic therapies should not be the endpoint. These expensive and inaccessible therapies do not serve global patient populations. Vertex is committed to drug modalities which could treat many more people, such as a pill.

David ended with a strong message of hope by saying, “I know this group will find a cure for Huntington’s disease. I don’t know when, but I know you will.”

That’s all for Day 2! Stay tuned for research updates from the last day of the 2024 CHDI HD Therapeutics Conference.

HDBuzz is back for the last day of the CHDI HD Therapeutics Conference: Thursday February 29th in Palm Springs, California. This article summarizes our real-time updates of the conference in community-friendly language.

From genes to medicines

The morning session will focus on how human genetics is driving the development of therapeutics. “Genetic modifiers” are genes that influence when HD symptoms onset, and human data is extremely valuable to discover new drug targets.

Scientists can only find these modifiers when they have access to huge amounts of genetic data, so every single person from an HD family who contributed samples and signed those consent forms played an important role in all of these discoveries.

Vanessa Wheeler: expansion of CAGs and HD modifiers

The first speaker of the morning is Vanessa Wheeler, from Massachusetts General Hospital & Harvard Medical School. Vanessa’s team are experts on somatic instability (expansion of CAGs) and have been busy researching modifiers.

Vanessa is telling us about the work of a large consortium of scientists who all collaborated in a big team effort to do the best science possible. A lot of what we know about the genes that affect HD onset has come from these genome-wide association studies (GWAS). They first looked at modifiers in a very large dataset – from over 12,000 people from HD families! With such large amounts of data, they can start to parse out which modifier genes may contribute to which HD symptoms, such as movement or thinking.

The newest study highlighted familiar modifier genes, like FAN1 and MSH3, as well as a whole host of new ones, like MED15 and POLD. This is very exciting for HD researchers who are always looking for new possible drug targets or ways to alter the progress of HD. Based on this new data, Vanessa proposes a 2 stage model of HD – CAG expansion first due to faulty DNA repair, followed by the harmful effects of other proteins that mess up the normal biology of cells.

Vanessa and her colleagues at Harvard are looking to see how the human modifiers influence CAG expansions in mouse models of HD. Getting rid of these modifier genes in the mouse can have lengthening or shortening effects on CAG repeats. One of the new modifiers in Vanessa’s mouse model is a gene called HMGB1. Other HD scientists have already been working on HMGB1 because it sticks to huntingtin and plays a role in DNA repair – this is a cool connection.

Vanessa is proposing different roles for her favorite modifiers in the process of CAG repeat expansion and in other parts of HD biology. When science enters new territory, it’s interesting to hear many perspectives at global meetings like this one!

Darren Monckton: HD biomarkers to track disease progression

Next up is Darren Monckton from the University of Glasgow. Darren will be presenting his team’s recent work on HD biomarkers – different measurements scientists and clinicians can use to track how disease progresses over time or how it is affected by a treatment.

One of the challenges of creating drugs that combat somatic expansion is measuring whether the drug is working over time. Somatic expansion happens very slowly throughout a person’s lifetime, so how can we measure differences in a shorter timeframe, like in a clinical trial? Even more tricky is that changes in HD are happening in the brain! We can’t take out a piece of the brain to measure the effects of a drug, like we can with organs like the liver. Darren’s team have been investigating blood samples to see if this might work as a convenient, safe and reliable proxy.

Darren’s team are experts at doing very detailed analyses of the genetic code. They developed a cool technology to measure tiny changes in the CAG number which happen over time. Using blood from folks who generously donated samples to ENROLL-HD, they can see general patterns of somatic expansion as HD worsens. When they look at the level of individual people, they see there is actually a lot of variation in how their CAG numbers change.

The key thing to measure is how the CAG number changes in an individual over a reasonable timeframe, such as 1-3 years. This is not easy! To figure this all out they used a lot of different samples from the amazing and generous HD community. Darren’s team have been doing all kinds of cool science math to figure out exactly how many measurements they need to accurately and reliably detect a change in CAG number from blood samples, no matter the person’s age or initial CAG repeat number.

The most reliable measurements come from people with very long CAG repeats, such as those that cause juvenile HD. Darren and his team are working to ensure that they can make good measurements across the board, which would be important for clinical trial recruitment. Darren is also exploring these ideas in other diseases caused by CAG repeat expansions, like movement and balance disorders called ataxias.

The conference has featured so much work in the field of somatic instability. The ability to reliably measure how CAG length changes in blood, and connect it to what happens in brain, will be invaluable when research efforts lead to clinical trials.

Alice Davidson: insights from Fuchs’ disease

Next up is Alice Davidson. She’s an ophthalmologist who studies Fuchs disease, an eye disorder caused by a triplet repeat. Her work on genetic modifiers could inform HD research – it’s always fantastic to see the exchange of ideas across disciplines!

Fuchs’ disease is caused by a repeat of CTG letters in the DNA code. Alice has found that these CTGs get longer over time, just like the CAGs in HD. Her team discovered this using eye tissue donated by people with Fuchs’. Alice and her team use lots of cool technology to really get into the details of changes to the DNA code throughout the entire genomes of different Fuchs models. The CTG expansions seem to be happening in the types of eye cells that are most vulnerable in Fuchs’.

In HD, superlong CAG repeats are found in the most vulnerable brain cells. In Fuchs’, this is happening in the eyes. Similar findings about repeat expansion across different diseases lends strength to a new hypothesis that somatic instability is a major driver of symptoms. Alice’s team even found that some of the same modifier genes discovered by HD researchers seem to be coming up for Fuchs’ disease too.

Another line of research in her lab reveals that changes in the way that genes turn on and off in eye cells can also contribute to Fuchs’ disease. Some of yesterday’s talks suggest that this is also happening in HD. There are lots of interesting parallels here in techniques and findings from researchers in two different fields! The more the merrier.

Carlos Bustamante: tailored healthcare and medicines for all

Carlos Bustamante, Founder and CEO of Galatea Bio, spoke about how we might work towards the possibility of tailored healthcare and medicines for all people.

Carlos starts by reminding us how powerful DNA sequencing can be and how much we’ve learned about world relationships and diseases as technologies have evolved. He also stresses the importance of diversity in large-scale human research. As we’ve heard this morning, genetic studies can lead to drug targets, but Carlos shares the statistic that about 95% of what we know comes from studying white European populations. This is not only an ethical and moral problem, but a scientific problem, if we want to make sure we have all the information needed to design drugs.

Carlos suggests that we may learn completely new things and find new paths towards therapy, if we commit to studying the genetics of more HD families in Africa and Asia, and more diverse populations in North America, South America, and Europe. He uses the example of studies in transmission of COVID-19 to show that not only social factors, but genetic factors, contributed to who was getting sick when the virus began to spread in the USA.

Galatea Bio is building a large database and biobank that focuses on a more diverse population. This is allowing them to more accurately make predictions about people’s risk factors for heart disease and other disorders, based on their genetics. Although Galatea focuses on health issues relevant to a much wider population, the HD research community can learn from this more inclusive approach to strengthen the genetic information that fuels our drug discovery pipeline.

Sahar Gelfman: how the huntingtin gene varies across a million people

Sahar Gelfman shared work from the Regeneron Genetics Center. Regeneron has been looking at how the huntingtin gene varies across almost a million different folks!

Regeneron’s approach will allow us to better understand how often the HD mutation occurs across people from different ancestries from around the world, and what range of CAG numbers they see. They are using genetic techniques and fancy statistics in lots of samples to identify when people may have been mis-diagnosed with HD and other repeat disorders. They see a similar incidence of HD and variation in CAG numbers as others have previously reported.

Although we often see HD being reported as occurring in around 1 in 10,000 people, from this study with lots and lots of data, it actually looks closer to 1 in 2000 people with 40 or more CAGs in this particular dataset. They also see higher levels of HD in folks of European ancestry. However, there aren’t a lot of samples from people outside of Europe and North America, because of historical biases and exclusion. Lots of folks are working to correct this sampling bias so we can have insight to the true numbers.

What’s happening in the clinic

The best was saved for last, with the final session covering UPDATE ON CLINICAL TRIALS!

David Margolin: uniQure’s ongoing Phase1/2 trial of AMT-130

First up is an update from David Margolin from uniQure on their ongoing Phase ½ trial of AMT-130, a gene therapy for lowering huntingtin that involves a brain surgery to deliver the drug to deep areas of the brain that are affected by HD. The drug is packaged in a harmless virus which is injected into specific areas of the brain through a well-controlled surgery. This is a one-shot therapy so folks who are treated will only have the surgery once and then their huntingtin levels should be lowered permanently.

This is exciting as it means that if this drug works, it could be a one-and-done approach. On the other hand, if things don’t pan out as we all hope, it could be bad news. Because of this, uniQure did a ton of safety testing in all sorts of HD animals and their trial in people proceeded very slowly to make sure everything was going ok.

UniQure are running two trials at the same time in the US and in Europe. Both trials are testing out a high dose and a low dose of the drug but only the US trial has a placebo arm – people who have the surgery but don’t receive the drug.

David is summarizing results from the most important question this trial will answer: whether the drug is safe and tolerable. The drug seems to generally be safe and side effects that did occur could be managed with treatment. We wrote about most of these findings back at the end of last year which you can find here: https://en.hdbuzz.net/355

UniQure next explored preliminary results asking whether the drug may have beneficial effects on slowing the signs and symptoms of HD. Things seem to look ok but it’s tricky to tell as not many folks in the trial have been on the drug very long. So we can’t expect a conclusive difference quite yet. Other measurements uniQure looked at were ok too, and there were possibly some positive effects…. However, it’s too soon to say for sure with such a small number of folks in this trial.

The key message is that nothing really bad has happened in people who received the drug. This is a big deal since this is the first gene therapy for HD to move to the clinic and we had very little idea how a one-shot therapy like this might work in people with HD. David shared that uniQure will have another update with more data in June.

Amy-Lee Bredlau: PTC Therapeutics’ update on the Phase2 trial for PTC-518

Amy-Lee Bredlau from PTC Therapeutics shared an update on a Phase 2 trial for PTC-518, a drug taken by mouth to lower huntingtin.

The oral drug that PTC is developing for HD is called a splicing modulator; this works to lower huntingtin by targeting its message copy and sending the message molecule to the cell’s trash can so the huntingtin protein is not made.

Before trialing this drug in people, the PTC team tested whether it could lower huntingtin in different cell models of HD as well as in the brains of mice that model HD. They found lower huntingtin levels in the blood and in the brain – this is important as getting drugs to work in the brain can be very tricky.

The next step is to test if the drug is safe in people, which they are doing in the PIVOT-HD trial. PTC was one of the first companies to adopt the HD-ISS staging system and recruited folks into their trials in stages 2 and 3. We previously wrote about the HD-ISS staging system, which you can read about here: https://en.hdbuzz.net/325

People in the trial received either 5 or 10 mg of the drug, while some folks only received a placebo. The study is taking place across North America, Europe, and Australia. We are now seeing interim data from a small group of just 33 folks who participated in the trial. It looks like PTC-518 was pretty safe and there were no significant changes to the levels of NfL – a biomarker which tells us about overall brain health.

Importantly, they see that huntingtin levels are lowered in the blood in a dose-dependent manner – this means that folks who got more drug had more huntingtin lowering. No data was shown for whether lowering is happening in the central nervous system, such as the brain or fluid that bathes the brain, but we hope PTC will share that in their next formal update, which is promised soon.

Peter McColgan, Jonas Dorn, and Marcelo Boareto from Roche

Up next were two talks from three scientists: Peter McColgan, Jonas Dorn, and Marcelo Boareto from Roche.

Peter is starting by focusing on biomarkers in CSF, the fluid that bathes the brain. Levels of different biomarker proteins found in this fluid can give us information about different aspects of brain health. Peter and the folks at Roche are looking at these biomarkers from the spinal fluid they collected in the GENERATION-HD1 clinical trial which was sadly halted back in 2021 because of safety concerns. That trial was testing the HTT lowering drug tominersen.

Folks who received a low dose of tominersen had lower levels of huntingtin, but flat levels of NfL, YKL-40 and other markers of brain health. People receiving much more drug had more huntingtin lowering, but increased levels of NfL and brain markers indicating the brain was sick. These results have helped Roche decide on doses to use in their ongoing trial for tominersen, GENERATION-HD2, so that they get good levels of huntingtin lowering but without making brain cells sick. GENERATION-HD2 is well underway at many sites around the world, and is now more than 50% recruited.

Digital biomarkers, such as an app measuring finger tapping speed or shape drawing, allow data to be collected every day, not just when someone goes to the clinic for testing. Jonas tells about how these frequent digital biomarker measurements can give us a different picture of how folks are doing and how their disease progression might be affected by the drug.

In the future this may enable the same amount of information to be drawn from smaller groups of people so lots of different trials might take place more quickly and get us to treatments for HD faster. Jonas and the team are comparing the digital biomarkers they have measured with other traditional measures like brain imaging. They see some promising results! The data suggests these digital biomarkers are robust measures of how HD progresses.

In the Roche triple bill, we are now hearing from Marcelo Boareto, who will tell us about natural history studies. These studies don’t test the effect of a drug, but rather follow people with and without HD to see how the disease progresses as they age. Natural history studies help researchers understand what to expect in terms of changes in disease trajectory in HD clinical trials. The more we understand the normal course of HD, the better we can measure if a drug is changing the progression of HD and if it is helping folks with HD.

For many measures, people in the placebo group of GENERATION-HD1 not taking drug initially looked like they were improving. But then they proceeded to follow the same course as what we would expect from the natural history study – the placebo effect can be strong! Now that Roche has analyzed the placebo effect and how it compares to the natural disease progression, this information can be used to better design future trials to account for the placebo effect.

Swati Sathe: updates from the SHIELD-HD natural history study

Swati Sathe from CHDI shared data from SHIELD-HD, a natural history study that was initiated by Triplet Therapeutics. They were working on somatic instability but the company unfortunately closed down.

This study was designed to look at people with HD before they started to show symptoms and follow them for 120 weeks. They collected lots of different samples from the people in this study, like the fluid that bathes the brain, blood, and MRIs. The main purpose of the study was to understand how CAG repeat numbers change over time and track progression of HD with the different samples collected and tests performed. It was run in 9 sites in 5 different countries.

After Triplet closed down, the HD research foundation CHDI (which is hosting this conference) took over the study to ensure these precious samples and all of the data gathered so far would not be wasted and could be used to help inform future trials. The HD-ISS staging system was also used in this study. Incorporating it in clinical trials and natural history studies will help researchers target specific disease stages to hopefully move drugs forward faster by matching them to the people that will benefit most.

The CHDI team looked at which measurements changed over the course of the study, such as scores on movement tests, volume of vulnerable brain areas, and other metrics. They also compared their data with other studies, like TRACK-HD. The great wealth of data generated from all of the SHIELD-HD participants will inform which tests and measurements are the best ones to use over the length of a drug trial so there is the best chance of detecting whether a treatment is working.

That’s all from us for this year! The 2024 HD Therapeutics Conference was a fantastic look at ongoing trials, upcoming research, and fantastic data. We hope you all follow along next year!

The HDBuzz team recently convened in Palm Springs, California, along with hundreds of other scientists from all over the globe, for the 19th Annual HD Therapeutics Conference, hosted by the HD research foundation CHDI. From Tuesday February 27th through Thursday February 29th, we live-tweeted dozens of scientific talks by world experts in Huntington’s disease research, from bench scientists to clinicians. We’ve compiled our tweets into a summary of the entire conference, beginning with Day 1.

Huntingtin Homework: Teaching an Old Dogma New Tricks

The first session of the conference focused on huntingtin, the gene that expands to cause HD. The meeting kicked off with Gill Bates, who reviewed what we know about the genetics of HD, which is that the length of CAG repeats in the huntingtin gene dictates whether people will develop HD. More recently, lengthening of the CAG repeat in some brain cells, known as somatic expansion, has been implicated in driving the disease.

There are many unanswered questions about exactly how the CAG expansion results in the death of brain cells. This session addressed a wide range of approaches, at the epigenetic, RNA, and protein levels.

Karine Merienne: DNA tags in the striatum

The first speaker of the conference was Karine Merienne from the University of Strasbourg who told us about changes in certain types of markers in HD associated with aging. Karine reminded us that it is still a mystery why the nerve cells of the striatum are so vulnerable to the CAG expansion in the huntingtin gene. One hypothesis she is investigating are changes in how genes are turned on and off.

Karine’s research looks into how so-called epigenetic changes occur in HD. These aren’t changes to the DNA code itself but certain markers which affect how DNA is packaged. This in turn changes which genes are switched on or off, which affects the properties of cells, making a nerve cell a nerve cell, or a skin cell a skin cell.

The epigenetic markers change with age in all people, not just folks with HD. Karine’s team found that certain epigenetic markers are altered further in mouse models of HD. Using cutting-edge technologies, they were able to look at changes to markers at the level of single brain cells from a mouse. They saw that nerve cells from the striatum, the vulnerable brain region in HD, were missing an important epigenetic mark.

This gives us insight into why cells in the striatum might be more likely to get sick in people with HD. Perhaps if we can fix these epigenetic marks, we could make the cells better again? We will see; there are a lot of smart folks working on this!

Yinsheng Wang: chemical tags wreaking havoc

The next talk of the morning came from Yinsheng Wang, who is based at the University of California, Riverside. Yinsheng investigates how genetic message molecules are modified with chemical tags in HD and other CAG diseases.

The repeating CAGs in the message of the huntingtin gene can be “tagged” with extra molecules. In the course of HD, the extra tags can inappropriately recruit proteins in the cell, sopping them up and keeping them from their normal jobs. Interestingly, these changes to the tags on the huntingtin message molecule seem to happen most often in the striatum in HD mice. Could this be another reason why these brain cells get the most sick?

Special molecular machines add or remove these tags from the huntingtin message molecule. Yinsheng and colleagues figured out which of these machines was responsible for the changes they could measure. If they got rid of the machine, the message molecule tags went back to normal.

They also found that changes in molecular tags alter the ability of the huntingtin message to stick to a protein called TDP-43, which plays a role in other neurodegenerative diseases. (Like huntingtin, TDP-43 can also form clumps.) Huntingtin along with its CAG repeats and tags can affect formation of these clumps. This team’s data suggest that expanded repeats on the huntingtin message molecule led to clumping of TDP-43.

Yinsheng explains yet another way that chemical tags on the huntingtin message molecule may wreak havoc in the cell: by causing the message molecule to get off kilter and make toxic proteins it is not meant to encode. Maybe if we can restore the way the HD message molecule is tagged by these molecular machines, brain cells will get less sick. This is an interesting new avenue for drug discovery research in the HD field.

Jeff Carroll: how low should we go?

We also heard from HDBuzz’s very own Jeff Carroll. Jeff’s lab, which is based at University of Washington, has been busy investigating HTT-lowering in mouse models of HD. Jeff’s lab is asking what they can do to help speed up and improve upon clinical huntingtin lowering strategies. One major question is how much to reduce huntingtin and in which types of cells to improve symptoms of HD without negative effects.

Key questions Jeff’s team is trying to answer are how low is too low for huntingtin lowering, and how low do we have to go to have a positive effect. Experiments in mice have shown that going too low might not be very good. One of the projects Jeff’s lab has been working on is looking at huntingtin lowering in adult mice. This represents what we are doing in the clinic, giving adult people with HD different types of drugs to lower huntingtin protein levels.

Jeff’s lab showed that it was not safe to completely remove huntingtin in the brains of mice – they literally had holes in their brains! Of course, complete removal of huntingtin in human brains is not what clinical trials are aiming for. The trick is probably going to be getting the balance right. Jeff reiterates this does not mean that huntingtin lowering is a bad idea per se, we just need to figure out how low to go.

We know from genetic studies that 50% (what most clinical trials are aiming for) seems to be ok in people and animal models of HD, but perhaps below that is not a good idea. One interesting thing Jeff’s group noticed was that lowering huntingtin with ASOs in mice seems to alter somatic instability, the expansion of the CAG repeat in some cells. This seems to happen in the liver at very high ASO doses. Figuring out why this is the case has been complicated!

More importantly, would the clinical approaches, which use lower amounts of ASOs, do the same? It doesn’t appear so. But it’s probably something scientists should keep an eye on moving forward.

Next Jeff’s team looked at selective lowering approaches – therapies which only target the toxic huntingtin and leave the regular huntingtin levels untouched. Again they saw that somatic instability seemed to be blocked by these treatments – this could be a cool two for the price of one therapy!

Altogether, Jeff’s work is helping us better understand what huntingtin-lowering means at a molecular level, which will help us better understand what’s happening in the current clinical trials, and any extra considerations we might need to think about to give this approach its best shot.

Ileana Cristea: huntingtin and its dance partners

We’re back and up next is Ileana Cristea who leads a research group at Princeton University. They study the huntingtin protein and the other proteins it likes to hang out with in cells, and how these relationships change in HD. This work lies in the area of “omics” research where researchers look at changes in proteins and how they interact across many cells, tissues, and brain areas. There’s tremendous collaborative effort!

Ileana’s talk continues the theme of figuring out why some cells get sick in HD, while others seem to be ok. Her lab looks at the locations of different proteins and which ones hang out together. They are trying to address what drives disease, and what are the consequences of lowering huntingtin levels with drugs. They are doing so by studying what proteins interact in the presence and absence of huntingtin.

They found that in cells from mice which don’t have huntingtin protein, the levels of all sorts of proteins were changed, as well as which proteins were hanging out together. The biggest changes occurred in proteins with jobs in energy generation and DNA repair. The next step was to understand how these changes lead to disease, so they zeroed in on the striatum of HD mice, since this is the region of the brain most affected in HD.

They narrowed down a list of proteins involved in specific cell functions that may give us clues to what goes wrong in HD. After getting a bird’s eye view of networks that interact, they confirmed some of their “hits” in collaboration with scientists who work on other models and techniques, like cells and fruit flies. In different types of cells, different protein buddies of huntingtin are altered, which once again could explain why different cells are affected in different ways in HD.

Not only can Ileana’s team work out which proteins huntingtin hangs out with, but through which surfaces they might all stick together, giving a very detailed molecular view of what is going on in HD. Although this type of study can feel a bit granular, it is actually very important to help us understand exactly what goes wrong in HD. It also helps us identify new genes and proteins which might be good targets for future drug discovery efforts.

Tony Reiner: patterns of huntingtin clumps

The final talk of the morning came from Tony Reiner, who is based at the University of Tennessee Health Science Center. His team have been looking at where the disease form of the huntingtin protein is found in HD human and mouse brains.

Tony first reminded us about the specific parts of the brain which are most vulnerable in HD. The striatum, which is at the very center of the brain, is one of the most affected brain regions, but nerve cells in the cortex and thalamus are also affected. The regions of the brain that make a lot of huntingtin protein are not necessarily those most affected in HD. Regular huntingtin is really found everywhere, so this does not seem to explain why cells in the striatum are so vulnerable.

Huntingtin proteins come in lots of different flavours – expanded, fragmented, clumped, and others. Tony’s group uses antibodies as tools to visualize the different forms of the huntingtin protein in the brain. They started by looking in HD mouse brains, and tried to match that up with tissue from people with HD who generously donated their brains to research after passing away. This selfless act has been critical for generating data that lets us know what’s going on with HD in human brains.

If you’re interested, you can learn more about brain donations from the Brain Donor Project (https://braindonorproject.org/), HDSA, HSC, HD organizations in your home country, and through local academic institutions.

We can measure lots of changes in brain cells over time but which changes are actually causing cells to get sick is still not very clear. Tony’s work shows that increased protein clumps and other measurements don’t always seem to match up with the cells we know get sick. Work from Tony’s lab and others really get into these measurements at the level of different cell types that might one day help us better understand cause and effect.

Targeting the DNA Repair Machinery to Modulate Somatic Instability

Session 2 of the conference focused on ways to combat the expansion of CAG repeats. This happens in some cells as HD symptoms worsen. Lots of new evidence points to the lengthening of CAG repeats as an important driver of cell loss in the striatum, pushing symptom onset earlier. Using blood donated by thousands of individuals with HD, scientists have been able to perform large genetic studies (known as GWAS) to determine other genes that affect HD onset. Notably, many of these genes are involved in something called DNA repair.

DNA repair is a process where little molecular machines repair mistakes or changes in the spelling code of DNA. One of those changes that happens in HD is the increase of the CAG repeat. Some people have DNA repair machines that are great at catching mistakes, while others have machines that aren’t so good. When the DNA repair machinery fails, the CAG repeat can lengthen in some cells over time.

Many HD scientists now believe that by targeting DNA repair genes, it could be possible to slow down the lengthening of CAG repeats in vulnerable brain cells, ultimately delaying onset or slowing the worsening of HD symptoms. More and more scientists and companies are now seeking, confirming, and testing different players within the machinery that repairs DNA, to determine what goes wrong when CAG repeats get longer, and try to prevent it.

We’ll be throwing around lots of acronyms and names of proteins known to be involved in the DNA repair process. These proteins work together to repair DNA in different ways and may go awry in HD. Scientists are developing genetic drugs to increase or decrease their levels and stop CAG expansion.

Maren Thomsen: the shape of DNA repair machines

The afternoon’s first speaker was a structural biologist, Maren Thomsen from a company called Proteros Biostructures. She is studying the shape of a protein called MutSꞵ which is involved in DNA repair. Using special microscopes they can see exactly how the protein is organised in 3D space which can help scientists figure out how it works.

Ideally we would like to stop the activity of MutSꞵ, and there are different ways to do this. Maren uses the analogy of trying to stop the movement of a bicycle: you could stop the pedals, or put a barricade in front of it, or block the wheel from turning. Knowing the details of the MutSꞵ structure allows them to come up with different ways to stop its activity.

Cool microscopes allow Maren and her team to figure out precisely where each atom of the protein is, and how this changes as MutSꞵ goes about its job sliding along and repairing DNA. With this high resolution of information, they can create a super detailed model of how this molecular machine works. It can really move, gripping and opening around DNA like a clamp! When Maren’s team makes changes to the MutSꞵ machine, this changes its grip and motion, and they are learning more about which parts of the protein stick to other players in the DNA repair process.

Maren is also investigating a protein called FAN1, along with its “dance partners.” FAN1 is also involved in DNA repair, and her group has been able to visualize it in new ways with the goal of harnessing it for drug development. With these detailed insights into how all these molecules work together, we can begin to understand why certain mutations found in GWAS might delay or hasten the age of onset of symptoms in HD.

Structural biology techniques illuminate the shape and movement of critical molecules so that we can better understand where and how to intervene in the faulty biology of Huntington’s disease and design drugs that precisely target proteins like MutSꞵ.

Wei Yang: MutSꞵ and long CAG repeats

We heard next from another structural biologist, Wei Yang, who is based at the National Institutes of Health, and is also studying MutSꞵ. The MutSꞵ molecular machine acts on all kinds of repeating DNA sequences, not just CAG repeats. Wei’s team worked to figure out exactly how MutSꞵ binds to these repeating DNA letters using structural biology approaches.

An interesting conundrum is why there is a threshold of CAGs at which the repeats continue to expand over time. Understanding this requires neat experiments looking at CAG repeating DNA and how it binds onto MutSꞵ. Wei and her team found that MutSꞵ much prefers binding onto longer CAG repeats than shorter ones. In fact, if the CAG stretch is long enough, more than one MutSꞵ molecule will bind onto the CAG DNA.

When they look at the CAG DNA stuck to MutSꞵ, they see that MutSꞵ contorts the CAG repeating DNA to look like non-repeating DNA. It works like a vice to bend the DNA into this different shape. Unsurprisingly, this requires a lot of energy. But what does this all mean for HD? Well, when the CAGs repeat enough, like they do in folks with HD, more and more MutSꞵ molecules bind on. Wei thinks this may unintentionally encourage CAG expansion.

Structural biology studies help us confirm findings from people that have revealed the importance of DNA repair in HD. We are learning more about the genes and machinery involved in somatic instability and how it might be linked to symptom onset. Armed with this kind of knowledge, drug hunters can work to find ways to stop MutSꞵ from making mistakes that lengthen CAGs, with the goal of slowing or stopping HD.

In fact, Wei and her team have identified a compound which changes how MutSꞵ sticks onto CAG DNA. Although this molecule is not likely to be a drug, it could be a helpful starting point for drug hunters.

Sarah Tabrizi: exploring DNA repair in human cells

Next up was the legendary Sarah Tabrizi, a physician and scientist from University College London who is involved in lots of basic and clinical HD research. Sarah is using human cells grown in a dish to further test many of the genes identified as important for DNA repair and CAG repeat expansion. There are lots of DNA repair proteins which look like good targets for therapies.

Sarah and her team are using genetic techniques like CRISPR to lower the levels of DNA repair proteins that go awry in HD. Then they see how this affects the levels of other genes, to tease out relationships among the DNA repair machinery. After changing the levels of different DNA repair proteins, Sarah’s team then looked to see how this affected CAG repeat expansion. They targeted genes called MSH2 and MSH3. Lowering these (and others) reduced the level of somatic expansion.

In stem cells coaxed to become brain cells, lowering of one specific DNA repair gene called MLH1 reduced somatic expansion by 78% – wow! She’s also exploring other targets, including a gene called MSH3, which she calls “an ideal therapeutic target.” Her work highlights two repair proteins called MLH1 and PMS1 as potentially interesting drug targets. Working on targets beyond the MutSꞵ complex could be really handy to increase our odds of finding drugs that work.

Nonetheless, Sarah reiterates that MSH3 is her favourite drug target, as knocking it out seems to slow CAG repeat expansion. Furthermore, depleting this protein does not seem to have too many bad side effects, at least in models. Sarah’s lab uses ASOs to lower levels of MSH3, the same type of drug that some companies (like Roche) are using to lower huntingtin. When they lowered MSH3 levels, this slowed down somatic expansion. When they completely removed MSH3, CAG repeats got smaller. This did not affect other DNA repair proteins, which is positive news for MSH3 drug discovery.

Nearly all of this work was done in nerve cells in a dish, which had been created from a blood sample generously donated by a young patient that Sarah was treating before they passed. These discoveries and many others in the realm of somatic instability would have been impossible without the dedication of HD families and their willingness to participate in research. Sarah’s team are continuing this work in a mouse model to see how their MSH3 ASOs fare in a more complex system. Watch this space!

Ricardo Mouro Pinto: exploring DNA repair genes as potential targets

Ricardo Mouro Pinto is based at Massachusetts General Hospital & Harvard Medical School. His team also studies somatic expansion. Patients with increased somatic instability start to have HD symptoms earlier. The genes that influence the onset of symptoms are known as genetic modifiers. Ricardo and others are testing the theory that changing the levels of these modifiers can delay or stop the onset of HD.

Ricardo is using CRISPR to change levels of these modifiers in mice that model HD. He’s screened 60 different genes in mice – that’s a lot of work! What all that work found is that DNA repair genes have a large effect on the length of CAG repeats. This confirms what many others in the field have found. Anytime results are replicated in various labs across the world it strengthens the field’s confidence in that data.

He then moved to human cells grown in a dish to confirm their own and others’ data. They found that lowering MSH3 slows the rate of expansion and lowering FAN1 increases it. They also found that reducing levels of MLH3 and PMS1 halt expansions. Ricardo is also working to check these modifier targets in other diseases. HD isn’t the only disease affected by somatic expansion. So he’s screening the targets he identified in HD in mice that model other diseases, like Frederich’s Ataxia.

Targeting the same protein that is involved in multiple diseases not only benefits more people, but could speed up trial enrollment and drug development. But before we get ahead of ourselves, these targets have to be tested more to ensure they’re having the effect we want! One point researchers have to be aware of is that DNA repair genes are also involved in cancer. Ricardo is being mindful of this and choosing potential drug targets with the lowest chances of leading to cancer in people.

One target Ricardo’s team is particularly interested in is called MLH3. They did some detailed studies to see exactly what part of the MLH3 gene is responsible for somatic expansion in HD. Knowing exactly what part of the gene is responsible for influencing CAG length lets researchers know which spot they would need to target if they designed a drug against MLH3.

Using cool genetic techniques, Ricardo is able to make cells that produce a version of MLH3 that excludes the part of the code that leads to CAG repeat expansion. When he did this, he was able to suppress CAG expansions. He’s now working to use CRISPR to change a single letter in the sequence of MLH3. This is a precise approach that will stop MLH3 from increasing the CAG number while leaving the rest of the MLH3’s functions alone.

This is important because proteins in cells have lots of different functions. Targeting a single function reduces the chances of having unintended consequences. Something that’s critical for drug design! Ricardo’s next steps are to use his new CRISPR approaches to alter MLH3 in mice and human cells in a dish. For this, Ricardo was recently awarded a $1,000,000 grant from the Hereditary Disease Foundation!

Karen Usdin: somatic expansion in other diseases

Karen Usdin from the National Institutes of Health spoke about her team’s work looking at somatic expansion in different types of diseases caused by DNA repeats, beyond HD. There are many diseases caused by repetitive sequences of DNA. Karen’s team primarily focuses on one of those diseases called Fragile X, which is caused by a repeating CGG. However, she’s now also beginning to focus on HD. Woohoo!

Fragile X also has somatic expansion controlled by DNA repair genes. Karen has used mice that model Fragile X to identify which DNA repair genes are important for this process in Fragile X. Karen has focused on parts of the DNA repair machinery called MutL complexes.

Her lab eliminated a piece of the MutL complex, called PMS2. Lowering PMS2 levels stopped repeat expansions in human cells and mice with other genetic diseases. She found similar results with another part of the MutL complex called PMS1. Lowering levels of PMS1 reduced expansions in Fragile X. Combined with data from other diseases, this suggests that PMS1 plays a role in expansion across repeat diseases.

Now Karen is getting to the good stuff – her work in HD! She made a mouse model that had genes for both HD and Fragile X. With this mouse, she was able to look at repeat expansion in both genes at the same time. She wanted to know if expansion of one gene affected expansion of the other gene. Put simply – no. Expansions of the HD gene didn’t influence the gene for Fragile X and vice versa.

She suggests that expansions depend on the balance between different types of DNA repair machinery in different cells. Some of the ideas she is putting forward are purely theory, but she welcomed other scientists to engage in conversation about it over a beverage! Conferences like this one are a fantastic place to exchange ideas.

Rgenta Therapeutics: oral drugs targeting DNA repair

The final talk of the day came from Travis Wager of Rgenta Therapeutics. Travis told us about drugs his team is developing which can be taken by mouth to target the modifier PMS1, with the aim of slowing down somatic expansion in human clinical trials.

Rgenta has spent the last 4 years thinking about how they can go after targets that have traditionally been considered “undruggable”. Others have tried to target genes that control somatic expansion, like PMS1 and MSH3, in the past without success. Rgenta’s drugs act like glues that create a stronger bond between disease-causing RNA messages and the proteins that bind to them, in order to change how proteins are made, or to get rid of a faulty message or protein.

Travis highlighted the various diseases that they’re trying to target with their drugs against genes that control somatic expansion. This includes HD, myotonic dystrophy, Fragile X, and Fredreich’s ataxia: all repeat expansion diseases. Rgenta’s interest in HD is driven by the availability of huge amounts of data from both humans and animals, a testament to the collaboration and dedication of scientists and HD families. The HD field draws many companies for this reason.

Rgenta has targeted PMS1, because higher levels of PMS1 in people are associated with earlier HD symptom onset. Using mice, they’ve shown that changing levels of PMS1 seems safe and isn’t associated with cancer. Rgenta tested thousands of different chemicals known to change levels of RNAs, then measured which ones were best at changing the levels of PMS1, their target. So cool!

Their drug molecule that targets PMS1 is something called a “splice modulator.” It works by altering the PMS1 message molecule, which results in lower levels of the PMS1 protein. They’ve shown their drug works in lots of different cell and animal models. They then tested their PMS1-targeting drug in HD cells grown in a dish. In theory, lowering PMS1 should reduce somatic expansion. And that’s exactly what they found! Lowering PMS1 by about 90% essentially halted somatic expansion.

Rgenta’s compound also appears to only really target PMS1 levels without affecting other proteins. They also shared data which suggests that the compound works well in animal models, and does a good job getting into the brain. Right now Rgenta only has data showing that lowering PMS1 reduces somatic expansions in HD cells in a dish. But they’re marching forward with this approach, planning to test their drug in other models of HD. However, this is exciting news as it means there is another promising drug in the pipeline which might one day make it into the clinic if the animal studies continue to look good.

We are very happy to end Day 1 after reporting on so many cool things happening in labs at universities and companies around the world! Stay tuned for Day 2, coming shortly!

You’ve likely heard of CRISPR. By now, you also may have heard that CRISPR has been used to produce a revolutionary new treatment for Sickle Cell Disease. Just 4 years after the Nobel Prize for the discovery of CRISPR was awarded, we have an approved treatment using this technology. This may have you wondering if this approach is being used in Huntington’s disease (HD) research and when a similar drug for HD might come to the clinic. Let’s discuss!

Genetic scissors transform science

CRISPR is short for “clustered regularly interspaced short palindromic repeats” – quite a mouthful! That’s essentially just science-speak for short strings of DNA letters that break up repeating parts of genetic code. These so-called CRISPR sequence interruptions were first noticed in bacteria. The unique strings of DNA letters which make up these sequences appear to have come from viruses, which scientists think might be part of an immune system that protects bacteria against viruses that they previously encountered.

The real secret sauce that transformed CRISPR into a powerful tool with the potential to treat many diseases are proteins called Cas – “CRISPR-associated sequence” proteins. If the CRISPR system as a whole is thought of as “genetic scissors”, the Cas proteins are the scissors themselves – they are the enzyme that actually cuts the DNA. The CRISPR sequences are the guide that show where the DNA should be cut. For this discovery in 2012, Drs. Emmanuelle Charpentier and Jennifer Doudna won the Nobel Prize in Chemistry in 2020 for the use of the CRISPR/Cas system to precisely edit DNA. An all-female Nobel team!

The CRISPR system wasn’t the first tool that allowed researchers to cut DNA, but it took off like wildfire throughout research labs around the world because it was easier, cheaper, and more accurate. Having an easy to use system to precisely edit DNA has revolutionized how researchers work in the lab. It can not only be used to turn genes on or off, but can also edit their DNA letter code. This holds a lot of promise for genetic diseases like HD where changes to the DNA letter code are the root cause of the disease.

Targeting Sickle Cell Disease with CRISPR

Once scientists knew how easy it was to edit DNA with the CRISPR system, lots of different companies began working with the technology to target various diseases. So why did the first approved CRISPR-based treatment focus on Sickle Cell and what exactly is it? Let’s focus on what Sickle Cell Disease is first.

Sickle Cell Disease is a blood disorder that gives red blood cells a sickle shape, like the letter “C”. Genetically, this is caused by mutation of a gene called hemoglobin that allows red blood cells to hold oxygen. If red blood cells aren’t carrying oxygen to parts of the body where it’s needed, this can lead to a stroke. The sickle-shaped red blood cells get all clumped together, leading to clogged blood vessels. With fewer red blood cells, people with Sickle Cell Disease are anemic, experience swelling of the hands and feet, and extreme fatigue. Sickle Cell Disease is recessively inherited. This means that both parents must have a faulty copy of the gene to pass the disease on to their kids, who have a 25% chance of inheriting the condition.

Drug discovery companies looking for a way to use CRISPR in the clinic focused on Sickle Cell Disease for several reasons:

• 1) The genetic cause is known. Sickle Cell Disease was first described all the way back in 1870. Hemoglobin as the cause was first noted in 1927 and the genetic basis was first described in 1949. So it has a long history!

• 2) The cure is already known! Increasing levels of hemoglobin essentially erases symptoms of the disease. So companies already knew what they had to do to treat the disease.

• 3) It affects red blood cells, which only live for about 120 days and new ones are constantly being made by the body. Additionally, red blood cells are made in bone marrow. Bone marrow transplants have a long medical history and have been well studied.

• 4) Genetic editing can be done outside the body. Because bone marrow transplants have been successful for other applications, researchers planned to take bone marrow stem cells out, treat them with CRISPR technology, and then put them back again. This is a lower risk approach than treating cells still inside the body because they could start over if something went wrong with the CRISPR editing process, and no one would be harmed.

How the drug works

With a disease in their targets, CRISPR Therapeutics and Vertex Pharmaceuticals tested their first CRISPR-based treatment for Sickle Cell Disease in a person in 2019. The drug, Casgevy, received approval in the United Kingdom and United States in November and December of 2023, respectively.

Once a patient is identified, bone marrow stem cells are removed. They are taken back to a lab where they are edited using CRISPR therapy. This editing modifies the faulty hemoglobin gene that prevents red blood cells from holding their shape and carrying oxygen. After editing, the cells have to be “grown” in the lab – essentially scientists feed them nutrients and watch over them closely to take care of them while they multiply, allowing the few cells they edited to divide into many cells.

With Casgevy-treated cells in hand, the cells are then returned back to the patient using an infusion. Now the Casgevy-treated cells can attach and turn from stem cells to red blood cells, producing new cells that have the corrected version of hemoglobin.

The good, the bad, and the ugly

As with all drugs, there will be pros and cons. The pro here (and it’s a big one) is that this is the first ever lifetime or one-shot treatment for Sickle Cell Disease! Casgevy is essentially a cure for Sickle Cell Disease which is a fantastic achievement for this community. However, even when a drug is the first or best in class, there can still be large drawbacks. In this case, Casgevy is complex to manufacture, will have a slow roll-out, and is very expensive.

Editing and growing the bone marrow stem cells has to happen in a specific facility with very strict manufacturing rules in place. These rules also require scientists with very specific training and skill sets. This reduces how fast the treatment can be produced and increases costs associated with the drug. The overall treatment takes about 6 months.

Prior to the infusion of the Casgevy-treated cells, the patient has to undergo high-dose chemotherapy in preparation of receiving the treatment. This can cause lots of side effects, like exhaustion, hair loss, and nausea. Chemotherapy is needed to remove blood stem cells that are left in the bone marrow. With the old blood cells gone, only the Casgevy-treated cells will be able to produce new red blood cells.

There are limitations on how fast this type of treatment can be rolled out. For instance, in the United States, there are currently about 25,000 bone marrow transplantations performed every year, but there are 100,000 people living with Sickle Cell Disease in the US. The current transplantations will still need to take place along with the new Casgevy treatments. So there is an issue with scaling up this treatment and finding the capacity to add to the current system.

Lastly, and perhaps most importantly for many people, Casgevy is very expensive. With the intense hands-on processing that Casgevy requires, it has a hefty price tag – $2.2 million according to Vertex. High price tags are likely to be the norm for one-shot drugs.

With all that in mind, Casgevy is still a massive leap forward for the Sickle Cell community and science as a whole. The first patient to be treated in the 2019 clinical trial was going to the hospital every 4 to 6 weeks for blood transfusions and her kids started struggling in school because they were worried about her dying if she didn’t receive treatment. After treatment with Casgevy, she no longer needs blood transfusions and her blood counts are stabilized; she’s essentially cured.

Where do CRISPR-based drugs stand for HD?

Sickle Cell and other blood disorders aren’t the only diseases that pharmaceutical companies are eyeing for CRISPR-based treatments. Any disease with a known genetic cause is a candidate for a CRISPR approach. This includes HD.

There is lots of work currently being done in cells and animal models to test CRISPR therapies that target various aspects of HD. Some researchers are directly going after the HTT gene that causes HD, while others are going after modifier genes that control age of onset. Having a diversity in approaches is a great thing!

There are also pharmaceutical companies that have committed to using a CRISPR-based approach for treating HD. Life Edit Therapeutics is a company that is working to use harmless viruses to deliver CRISPR machinery that will target only the expanded copy of HTT to lower expression. So far, they’ve tested this in different kinds of mice that model HD and have looked at different drug doses. While many people are currently working on CRISPR-based treatments for HD, none of these are currently in clinical trials.

Why aren’t CRISPR trials for HD in the clinic right now?

Having commercial approval for a CRISPR-based drug paves the way for similar drugs for other diseases, like HD. However, treating a blood disease is very different from treating a disease that primarily affects the brain. There are many aspects of Sickle Cell Disease that made it the perfect candidate for the first ever CRISPR-based drug. The other side of the coin is that there are many aspects of HD that make it a challenging disease to treat with CRISPR.

A major difference is that Sickle Cell Disease affects red blood cells while HD primarily affects brain cells. Blood cells are easy to access and blood sampling can be used to let doctors know if editing was successful. Brain cells can’t be sampled to get a picture of how the treatment is going.

Sickle Cell affects bone marrow that’s comparatively easy to manipulate and there’s lots of precedent for successful bone marrow transplantations. HD affects the brain, which requires invasive procedures to access and we don’t have a similar precedent for successful treatment of the brain.

Sickle Cell is caused by the lack of a protein, which many studies have shown can be added back to erase symptoms. We don’t yet know what will erase symptoms of HD. Researchers also have to weigh targeting both copies of HTT or only the expanded copy.

While this is a massive leap forward for using CRISPR to treat disease, we also want to manage expectations about when CRISPR-based treatments will be available for HD. Companies went for the low hanging fruit first with Sickle Cell Disease. However, none of this is to say that CRISPR won’t work for HD! On paper, this is a great strategy, HD fits the genetic requirement for such a treatment, and scientists love a good challenge. CRISPR-based treatments for brain diseases are certainly heading toward the clinic, but we have various other hurdles to clear first before they can be applied to HD.