ASOs and Fragile X: Addressing the Most Asked Questions

Fragile X Antisense Oligonucleotide therapy

With funding from FRAXA, Drs. Joel Richter and Sneha Shah at UMass Chan Medical School and Dr. Elizabeth Berry-Kravis at Rush University Medical Center have made a breakthrough discovery which points to using an antisense oligonucleotide (ASO) to treat Fragile X syndrome. They published their findings, "Antisense oligonucleotide rescue of CGG expansion–dependent FMR1 mis-splicing in fragile X syndrome restores FMRP" in the Proceedings of the National Academy of Sciences.

This Q&A is to clarify what ASOs are and how they might be used to treat Fragile X syndrome and FXTAS.

An Introduction to ASOs

The novel finding here is that the Fragile X gene is not silent, as had been thought for decades. Messenger RNA is being transcribed. However, this RNA is abnormal and it is not translated into protein. What's really remarkable in these findings is that many people with a full mutation of the Fragile X gene also produce a fair amount of normal FMR1 messenger RNA, along with the abnormally spliced version, but none of this is translated into protein. That suggests that the mutant splice variant is somehow gumming up the works. Removing it allows for normal translation of a normal protein, at least in cells in the lab.

An ASO (or antisense oligonucleotide) is a short strand of DNA or RNA that binds to a complementary RNA sequence. It's like a puzzle piece that fits perfectly into the target RNA. When these researchers discovered that the Fragile X gene was indeed producing messenger RNA (a defective variant which could not produce protein), they designed an ASO to fit into that variant and block it. Then something unexpected happened: the gene proceeded to churn out the correct messenger RNA, which was able to produce protein. Why? The ASO removed (or blocked) the mutant RNA and it no longer got in the way.

Each ASO is a custom made sequence which fits into the target RNA. So an ASO would be developed specifically for patients with Fragile X syndrome. Each of the existing ASOs is tailor made to address a specific disorder.

The methods developed in treating other brain disorders will certainly help us to treat Fragile X, especially the delivery methods. But it is the specific coding sequence of the ASO that gives each treatment its selective, targeted, and powerful effects. These sequences are specific to the condition, but they are fairly easy to engineer once you know the target. So, it's kind of a plug-and-play system. Once you have the basic methods developed, you can swap out the specific sequence of the ASO at will.

It's theoretically possible, especially if the ASO is a very short sequence. That's part of the testing process and a good reason not to have a very short ASO. It's like a password in that sense.

ASOs for Fragile X have only been tested in blood cells in the lab, so far. Much more testing is needed, and that presents problems. What it really needs is testing in postmortem brain tissue from individuals with Fragile X. FRAXA has established a collaboration with the Autism Brain Net to address the issue. It also needs testing in Fragile X mice, and for that, we need a custom mouse model. The "standard" Fragile X mouse model will not be helpful in testing this because it is a knockout, meaning that the entire Fragile X gene has been deleted from the mouse genome. There is no gene there to apply the ASO to. FRAXA is supporting another lab that is developing mice which have the human Fragile X gene. Testing will likely be done on those mice.

It does! These findings explain why the previous studies have been unable to provide any significant degree of reactivation; it's all about the abnormal splicing!

While the findings from the Richter lab don't necessarily mean that any other specific kind of treatment will not work, these findings do explain why previous reactivation studies have been unsuccessful. The abnormally spliced version of the Fragile X mRNA is interfering with translation and needs to be eliminated from the cell.

Currently the thinking is that ASOs would be needed primarily in brain cells. The administration of these treatments is not trivial. You need to inject them into the central nervous system somehow. The most common way this is done in current clinical trials is via intrathecal administration. This is like getting spinal anesthesia, only instead of injecting an anesthetic, these ASOs are introduced. Systems being developed that can make the process easier and more like getting IV fluids.

It would probably require lifelong treatment, but we don’t know that. So far, treatment every 3-4 months has been typical for other ASO therapies which target the central nervous system. This has been surprisingly well-tolerated in the trials done so far.

There is a chance that could happen. There is some evidence from previous research that the presence of FMRP itself appears to promote expression of the Fragile X gene. This is preliminary and will certainly be investigated.

Understanding ASO Treatment in Fragile X: What to Expect

This should be effective against a broad range of symptoms, including speech, since we are talking about expressing the missing protein and reversing the defect at the cellular level. However, we will just need to wait and see how actual human subjects respond.

This probably would not address physical symptoms or autoimmune conditions, since the treatment would be injected directly into the central nervous system.

One of the nice things about this approach is that the ASO only binds to the abnormal mRNA, so this treatment could be given to females or highly mosaic males and the treatment would only affect the abnormal cells. It would have no effect on normally functioning cells. This is not true for therapeutics like gene therapy, where you necessarily treat every cell, whether you want to or not. This is very highly targeted, and that's a very good thing!

That is the beauty of this approach. You can treat people with any kind of mosaicism, male or female, and the ASO is so specific that it will only target the abnormal messenger RNA. Cells that are functioning normally and producing FMRP should not be affected.

One fine point of this research that could easily be overlooked is that the Richter lab saw this same abnormal splicing in pre-mutations cells with more than 140 repeats. There's still a bit more work to be done, but this suggests that the same ASO which would be used to treat Fragile X syndrome might actually have positive effects in people with FXTAS. The original discovery was quite serendipitous, and this might be even more serendipity! But neurodegenerative disorders have proven to be difficult to treat, so the conventional wisdom would say that this treatment would arrest the progress but recovery would be slow.

Only clinical trials will tell us how completely we can rescue all the features of Fragile X syndrome at any given age. We still need to see if it is possible to restore production of the protein to the levels seen in these cells in Dr. Richter's lab, but the remarkable thing about these results is that the investigators are seeing a lot of protein produced. We are not talking about small amounts in partial expression, we are talking about normal levels of protein.

We think that this will be a very effective treatment for adults, but that a period of rehabilitation and rewiring of the brain will be required, and other medications may still be very helpful during this time.

It will almost certainly be tested in adults first. This is for ethical reasons, primarily, but also for practical reasons, as adults with Fragile X tend to be easier to work with. There is absolutely no reason to think that reinstating FMRP production in the brains of adults with Fragile X would not have a positive effect. Many experts in the field would guess that this would be even more effective if done at a younger age, but that's only a guess right now. We really don't know for sure.

It can be expected to see different effects in different people and at different ages. If we are seeing cognitive improvement in adults using small molecules like the Tetra Therapeutics compound, then it is reasonable to expect significant cognitive improvements in adults, if we can reactivate production of the missing protein.

Yes, females should benefit as well as males.

The initial study of Fragile X blood samples showed that about 75% of full mutation males produce the abnormally spliced messenger RNA which is the target for this ASO therapeutic. Those patients would be the best candidates for initial treatment.

However, further studies showed that treating cells which do not produce the abnormally spliced messenger RNA with a simple demethylating agent rendered these cells susceptible to the ASO therapeutic. In practice, this might mean that one quarter of patients would have a two step therapeutic protocol, and this might take a while longer to develop.

They can detect that from blood, although it's a specialized nonstandard test.

Your daughter does have a good question! If her autism is because of Fragile X, then over time her autism should fade away.

If it works, it should have a genuinely transformative effect. In other words, people with Fragile X won't have autism anymore. We would expect all aspects of an individual's condition to improve, with the exception of purely somatic effects like macroorchidism or lax connective tissue. In most cases, it seems that autism is just one symptom of more severe Fragile X, so I would expect that to improve significantly. However, even in the best case scenario we would expect that this would take some time, perhaps years to achieve a full response. As with all other treatments, only the research and ultimately the trials will be able to tell for sure.

This is highly specific to Fragile X. Many of the treatments that we are developing for Fragile X will have crossover applications for other forms of autism. This is especially true of the small molecules (drugs) that target pathways which are affected in many developmental disorders. For example, phosphodiesterase inhibitors like the new drug from Tetra Therapeutics will probably benefit many people with autism and other developmental disabilities. However, treatments aimed at reactivating the FMR1 gene are highly selective and will only work in people with classical Fragile X, with a trinucleotide repeat expansion.

So far this has only been done in cells, but the effect is quite rapid. How long it takes to see an effect in human subjects remains to be seen. But probably what you would see is continuing improvement over time. That would be a wonder to watch! There might be quite a lot of teaching to be done then!

The Role of ASOs for the Treatment of Other Disorders

Among neurodevelopmental disorders, the best known success of ASOs has been in the treatment of spinal muscular atrophy (SMA) where a life-saving ASO has been approved and is on the market. However, there are many more treatments in clinical trials.

A number of ASO drugs have been approved for rare genetic diseases, and ASO therapy is being used to address heart disease, cancer, and some eye conditions.

There are two trials of ASOs for Angelman syndrome, a couple for muscular dystrophy, and many others for other brain diseases. Dr. Elizabeth Berry-Kravis is conducting ASO clinical trials in Angelman syndrome right now, but results have not yet been reported. One of these is an ASO developed by a pharma company, Ionis Pharmaceuticals, Inc.

The n-Lorem Foundation is a non-profit organization that develops personalized ASO treatments for people with extremely rare neurodevelopmental conditions. n-Lorem has launched three n-of-1 trials and it aims to start seven more by the end of 2023.

When and Where would ASO Treatment for Fragile X Syndrome Become Available?

The timeframe will greatly depend on results from ongoing basic research and preclinical studies. The method itself (ASO therapy) has been approved by the FDA, so we don't have to reinvent the wheel. But the specific sequence of this ASO is unique to Fragile X, and that needs to be tested further.

It is realistic to expect initial clinical trials in 2 to 3 years, but these would likely be small scale. Larger trials would probably take something like five years, and approval depends on how those trials go and the general state of the technology at that point.

Trials almost always start with adults. The first subjects will probably be those who express the target mRNA abnormal splice variant in their blood.

Clinical trials will probably start in the US first, but we would not be surprised to see many International companies pick up on these findings and start competing programs. Even if the trials are done exclusively in the US there is no doubt that any company developing this kind of treatment will attempt to market in as many countries as possible.

This is a very active area of interest in the biotech world, so there is little doubt that there will be many more ASO-based treatments on the market five years from now. Hopefully this will be one of them.

Yes. We are fortunate that an established path to FDA approval for ASO therapies is being developed now. Many of the basic methods have been worked out and tested in human subjects for other diseases, and we just need to put it in the specific sequence that targets the Fragile X abnormally spliced RNA. That greatly shortens the development time and it also means that we don't need to use as many subjects in each clinical trial.

Generally speaking clinical trials for ASOs are relatively small. While they are technically challenging to do, they do not require a large number of subjects and many trial sites. So instead of 150 to 200 subjects in a typical drug trial, many ASO trials only have 15 or 20 subjects in each age group.

The FDA is quite receptive to this type of clinical research and if the results are positive we could probably expect relatively rapid approval.

It is too soon to know what the clinical trial protocols will look like, but I would imagine that most subjects would be able to continue on their regular medications and there would be no particular interaction with this type of treatment. If sedation or anesthesia are to be used for the infusion, there might need to be some temporary adjustment of medications, but that is all to be determined. One general issue, which is worth considering, is that it is always helpful for folks with Fragile X to get used to having their blood drawn or having an EKG, or just taking pills. All of these things are easy for most of our kids if they've done them before, but can be really difficult if they haven't.

This treatment is not really a drug, it is a biological molecule which only interacts with a RNA, so most medications would be fine. There may be some sedation involved which might require a minor adjustment of medications, but only temporarily.

We don't know yet where the first clinical trials would happen. For this research to get to clinical trials, it is going to need to have large-scale funding: a pharma company will take it forward. So it depends where that company is based and where they are able to run the trials. Everyone wants to get their drugs approved in the US for the very simple reason that prices are higher here than anywhere else and there is much more profit potential. However, once the technology is established it can be expected to spread rapidly around the world.

If it is approved in the US by the FDA, some countries will accept that US approval whereas others will want additional trials done.

I'm sorry to say that ASO therapy will be hideously expensive, which is one of the reasons that biotech companies are so interested in ASOs. However, it should be covered by insurance, perhaps with a bit of negotiation at first. Like any other new technology, the cost should come down dramatically over time.

FRAXA is funding much of the work now but we do not have the resources to develop this treatment, so the cost will be determined later on by whatever pharma company ultimately develops the treatment. Pharmaceutical companies generally work with insurance companies when they set the treatment prices. These treatments are usually covered by most insurance companies in the United States and many national health services in other countries.

How You Can Help and the Next Steps

While this treatment is being developed, there are two phase 3 clinical trials of promising medications that are accepting participants right now. Both trials offer a continuation phase after the double blind phase, meaning that your child/adult would be offered the medicine.

Research is critically important and we should all be helping to move it forward one way or another. At each step along the way, there are things we can do to speed up that step. Right now, FRAXA has doubled our funding for the Richter lab, raising it to $100K per year. Once this has backing from a commercial entity such as a pharma company, funding should flow which will speed things up. We will do everything we can to accelerate the process at every step!

Yes, several are interested! The conversations are happening now and I hope they come to a quick resolution! We at FRAXA have little to no control over that process though. In the meantime we are continuing to fund this research.

Thank you very much for your help! FRAXA is funding this project at $100,000 per year, as well as related projects These related initiatives, which include the development of organoids and new mouse models to test ASOs, each receive $50,000 per year. Those are the amounts we are talking about. When this ASO development work gets picked up by a pharma company, funding should follow that project. FRAXA will certainly keep funding other projects, until we reach the goal - a cure!

Yes! Funds would speed up the research! The caveat is that there could be an unexpected research finding along the way that slows things down. It's a path we have to follow and we don't know what barriers are there until we get there.

Artificial intelligence is already accelerating progress and it does so more all the time. AI is woven through everything that happens in labs. It's amazing to see how much progress is accelerating, and that's one thing that should give us all hope!