Snapshot: What Does Success Mean in Clinical Trials with Antisense Oligonucleotides (ASO)?

Research is rapidly moving from the bench to the bedside to treat neurological inherited disorders of all types, including spinocerebellar ataxias. SCAsource has previously gone over the science behind ASO therapy. These diseases share a common theory that the DNA mutation leads to the formation of an altered protein that is toxic. ASO therapy is meant to stop the formation of the toxic protein by “shooting the messenger”.

What is involved in these clinical trials?

To see what might happen in ataxia trials, let’s look at ASO trials happening right now in related polyglutamine diseases. In Huntington’s disease (HD), there are two programs that are currently in clinical trials. Regulatory authorities view ASOs as drugs and require that the product be shown to be both safe and effective in patients.

ASOs cannot be given as pills and they are currently injected into the spinal fluid. This is called intrathecal administration to get the drug directly in the fluid space where it can circulate back to the brain. Patients in phase 1 studies in HD are asked to have up to 7 injections and one phase 3 program requires injections every second month for 2 years. This involves a large commitment to the study and is asking a lot from patients and their families.

The only published phase 1 double-blind, placebo-controlled study in HD (Tabrizi et al., New England Journal of Medicine, 2019) has identified that a series of 4 injections were safe. They measured changes of the “bad” protein in the spinal fluid as a proof of concept that ASOs could lower protein levels. The good news was that they found that there was a dose-related reduction in this protein of about 40%. Patients from this study were offered “open label” monthly injections and this has shown a 60% reduction in the abnormal protein according to a recent presentation. Open label extensions are when patients can continue taking a drug after the formal time of the clinical trial is over.

medical doctor in blue scrubs and a white lab coat holding a stethoscope. They are off to one side, so only have their body can be seen, not inclduing their face.
What will ataxia clinical trials involving ASOs look like in the future? What will success look like?

So, what does success mean?

The phase 3 studies that are currently ongoing in HD are designed to see if there is a slowing of disease progression. This is being measured by assessing motor, cognitive and behavioral symptom change over time. Changes occur slowly in HD and SCA. Therefore, large numbers of patients are required over a relatively long study time.

The bottom line is that a successful study that shows slowing disease progression is likely to mean that the patients may not experience any obvious improvement while receiving the treatment and that they will continue to have progressive symptoms over time. Hopefully, this will be at a slower rate compared to the placebo group. Since there are no treatments available for SCA or HD, this will be welcome. It is by no means considered to be a cure or likely to stop the progression. True cures in medicine are rare, where a cure is defined as a drug ending disease.

Graphs of symptoms vs time. The "typical progression" line has more symptoms more quickly. The "delayed progression after potential treatment" line has fewer symptoms, but still increases over time.
Graph explaining how a potential ASO treatment might work in the future. Although it might not make symptoms go away completely, it could reduce how severe symptoms are, the number of symptoms, and/or delay when symptoms first appear. Illustration by Celeste Suart.

In the HD research community, we are asking questions that include:

  1. Is it a good idea to reduce the good protein that is part of our normal brain chemistry? In the current phase 3 study, the ASO reduces both the “good” and the “bad” HD protein. Another program in phase 1 uses an ASO that only reduces the “bad” protein.
  2. When is the best time to use ASO therapy? Since these conditions are associated with nerve cell damage and loss, it makes sense to use these types of therapy very early, even before damage occurs. This will mean that patients with moderate or advanced symptoms may not be good candidates for ASO therapy.
  3. Should we consider treatment in people who have had predictive genetic testing before symptoms start? This is being actively discussed but it is too early to consider this. We have to show that ASOs are safe and effective in symptomatic patients. We need to have good measures to determine if treatments are working. Regulatory authorities have required evidence that treatments have a positive effect on patients lives. This may be difficult to show in a short study. We must consider that it takes patients decades to get these diseases: slowing or stopping this could take just as long.

We can only figure out the answers to these questions in clinical trials. The goals of these trials are to improve people’s quality of life. To do this we need information from real people with these diseases, and not just models of disease. This is a process that will take time but will tell us which approach has the most promise and is worth pursuing faster. Thus, the patients and families at this point are just as important as the researchers in lab coats working together to treat these diseases.

If you would like to learn more about clinical trials, take a look at this resource by the FDA or our previous Snapshot on the subject.

Snapshot written by Dr. Mark Guttman and edited by Dr. Ray Truant.

Snapshot: What is Gene Therapy?

Gene therapy is using nucleic acids to treat a genetic disorder.  These nucleic acids can be designed in a variety of ways to achieve the same therapeutic outcome. Gene therapy tools can be used to correct a mutant gene by one of three ways:

  1. Expressing a healthy copy of a gene
  2. Silencing or inactivating the mutant gene transcript
  3. Using genome editing tools to repair or turn-off the mutated gene.
computer desk laptop stethoscope
Photo of a stethoscope by Negative Space on

How is gene therapy used?

Monogenic disorders, like some spinocerebellar ataxias (SCAs), are excellent targets for gene therapy approaches. Gene therapies are currently being used throughout ataxia research for studying disease mechanisms and for preclinical therapeutic application.

Overview of how gene therapy works. First, Package the healthy gene, RNAi, or gene editing tools into the AAV (can also deliver as naked DNA or in a nanoparticle). Second, Inject the packaged AAV into the tissue of interest. Third, AAV will enter the cell and release the genetic material. The cell will become healthy by either 1) expressing the normal gene, 2) repressing the mutant RNA, or by 3) correcting the mutant gene.
Overview of gene therapy, designed by Stephanie Coffin using Biorender.

One gene therapy approach for rescuing SCA1 phenotypes involves overexpressing a healthy gene, ataxin-1-like, which competes with the mutant ATXN1 protein for complex formation. This work, conducted by Keiser and colleagues in 2016, showed phenotypic rescue in a mouse model of SCA1.

There are two common technologies for silencing or inactivating disease genes: RNA interference (RNAi) or antisense oligonucleotides (ASOs). RNAi strategies utilize small RNA molecules to knock down the expression of target mutant RNA transcripts, while ASOs are DNA molecules used to knock down or correct mutant RNA transcripts. Both therapeutic approaches are being pursued in SCAs. For example, Carmo and colleagues in 2013 showed that using RNAi against the SCA3 disease gene, ATXN3, could longitudinally decrease mutant ATXN3 levels. See the SCAsource snapshot on ASOs for further information about their use in SCAs.

The most common genome editing tool is the CRISPR/Cas9 system, which uses an RNA guide to direct the Cas9 nuclease to the region of the genome to be edited. One can then knockout that gene or correct the mutant gene. It is early days for this technology as a potential therapeutic option due to the challenges of delivery and the risk of off-target editing.

How is gene therapy delivered?

One of the most difficult aspects of gene therapy is how to deliver these various molecules to the cells of interest. One of the most common delivery methods is through viral delivery.  The “drug” nucleic acid is transferred into the disease cells by a vector, which is a virus that has been modified to remove viral components. The most common viral vectors for gene therapies currently are adeno-associated viruses (AAVs). Other delivery methods include non-viral vectors such as naked DNA and nanoparticles.

How long-lasting is gene therapy?

Viral delivery of gene therapy products provides a longitudinal expression of the nucleic acid, while naked DNA and nanoparticles express the nucleic acid drug transiently, thus typically requiring ongoing treatment.

If you would like to learn more about gene therapy, take a look at these resources by the National Institutes of Health and KidsHealth.

Snapshot written by Stephanie Coffin and edited by Dr.Hayley McLoughlin.

Snapshot: What is an antisense oligonucleotide (ASO/AON)?

Antisense Oligonucleotides (also known as ASOs or AONs) are small molecules that can be used to prevent or alter the production of proteins. Proteins are the workforce of the cell, taking care of most cellular processes. They are generally made in a two-step process: first, a specific protein-coding gene is converted into an instruction file, called the messenger RNA (mRNA). The mRNA carries the information from that gene to the compartment of the cell that builds proteins. There, the mRNA’s information then gets converted into the protein. ASOs are short single stranded pieces of DNA that match the complementary sequence of a specific mRNA. Based on the type of chemical modifications, the ASO can have two different effects on the mRNA. Some modifications of ASOs trigger the destruction of the mRNA. This will result in the loss of the corresponding protein. Other modifications can mask only certain parts of the mRNA leading to a modified version of the protein.

diagram showing how ASOs can bind or snip mRNA to create alternative forms of protein or prevent protein synthesis
How ASOs work in the human body. Image by Larissa Nitschke, Created with BioRender.

The majority of Spinocerebellar Ataxias (SCAs) are caused by the accumulation of toxic proteins in certain regions of the brain. The primary goal of ASO treatments for SCAs is therefore to prevent the production of the toxic protein altogether. One example is work from Dr. Harry Orr’s group at the University of Minnesota. His lab studies Spinocerebellar Ataxia Type 1 (SCA1), which is caused by the toxic accumulation of the Atxn1 protein. Injections of ASOs into a SCA1 animal model decreased Atxn1 levels and rescued the SCA1 motor incoordination symptoms. Another way of using ASOs as treatment for SCAs is the modification of the mRNAs information to produce a modified version of the protein. This approach has been tested in Spinocerebellar Ataxia Type 3 (SCA3), in which an expansion in the Atxn3 gene renders the Atxn3 protein toxic. The van Roon-Mom group from the Netherlands, for instance, used ASOs to only remove the expansion from Atxn3 while leaving the remaining protein structure and function intact.

Both studies as well as other studies performed for additional SCAs are highlighting the potential use of ASOs as therapeutics for SCAs. While ASO research for SCA is mostly in the pre-clinical phase, ASO treatment for other diseases, including Duchenne muscular dystrophy and spinal muscular atrophy, have already gained approval by the US Food and Drug Administration (FDA). Further clinical trials will need to be performed to measure the therapeutic benefit of ASOs in SCA patients.

If you would like to learn more about antisense oligonucelotides, take a look at this article in HDBuzz about ASOs in development for Huntington’s Disease.

Snapshot written by Larissa Nitschke edited by Dr. Hayley McLoughlin



Approaching the age of clinical therapy for spinocerebellar ataxia type 1

Written by Dr. Marija Cvetanovic Edited by Dr. Maxime W. Rousseaux

New research (published Nov. 2018) reveals promising potential genetic therapy for SCA1.

A research team comprised of scientists from academia and industry have tested a new treatment for Spinocerebellar ataxia type 1 (SCA1), bringing disease-modifying therapy one step closer to the clinic. SCA1 is a dominantly-inherited ataxia that is currently untreatable. Symptoms of the disease include progressive loss of balance, slurring of speech, difficulties with swallowing and coughing, mild cognitive impairments, and depression. With a life expectancy after diagnosis of only 10-15 years, SCA1 is one of the fastest-progressing SCAs: after symptoms first appear, patients typically have just over a decade before these symptoms become so severe that they cause death (often due to respiratory failure). In 1993, collaborative efforts from the laboratories of Drs. Harry T. Orr and Huda Y. Zoghbi discovered that SCA1 is caused by the expansion of a CAG repeat somewhere in a patient’s DNA. CAG repeats cause a polyglutamine expansion in the protein that the mutated gene encodes; in this case, the group later identified that this had occurred in Ataxin-1 (ATXN1), the gene that encodes the ATXN1 protein. The SCA1 mouse models that Drs. Orr and Zoghbi generated (and graciously shared with the scientific community) have allowed for significant advances in the understanding of SCA1 pathogenesis over the years. Now, they provide preclinical evidence of a promising therapy to alter the progressive motor deficits and fatal outcome of SCA1.

stethoscope on top of laptop
Photo by Pixabay on

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A novel therapeutic approach for the treatment of SCA3

Written by Larissa Nitschke Edited by Dr. Gülin Öz

Researchers in the Netherlands uncover a new way to treat SCA3

Upon receiving a conclusive diagnosis of Spinocerebellar Ataxia (SCA), hundreds of questions can appear in a patient’s mind: What is Spinocerebellar Ataxia? Why am I affected? How will my symptoms progress? What is the ultimate prognosis? Thankfully, years of research have enabled us to answer many of these questions for patients affected by Spinocerebellar Ataxia Type 3 (SCA3), also known as Machado-Joseph Disease. Still, the most important question a patient could ask – How can I be healthy again? – has remained unanswered.

SCA3 is the most common form of Spinocerebellar Ataxia worldwide. It is passed down from generation to generation in affected families. Initial symptoms typically appear around midlife, but cases of much earlier and much later onset have been reported. At first, problems with movement coordination are the most noticeable, leading to an increase in stumbles and falls. At later stages, speech difficulties, muscle stiffness, and sleeping problems appear, leaving the patient fatigued during the day. The symptoms worsen over the course of 10 to 20 years, at which point affected individuals typically succumb to the disease. As with other SCAs, current options for SCA3 treatment are mainly limited to symptom management rather than treating the direct cause of the disease.

Artist's representation of DNA
Artist’s representation of DNA. Photo from Pixabay.

The genetic cause of SCA3 is the presence of excess copies of the DNA building blocks cytosine (C), adenine (A), and guanine (G) in the Ataxin-3 gene (Atxn3). Scientists refer to this type of mutation as an expansion of a triplet repeat, since the C, A, and G copies appear as sets of back-to-back CAGs. Because the CAG triplet is responsible for coding the amino acid glutamine (Gln or Q) in the Ataxin-3 protein, the repeat expansion results in an elongated glutamine (polyQ) tract. This faulty protein accumulates in cells and causes toxicity in specific regions of the brain. Since the 1994 discovery that SCA3 is caused by a polyQ expansion in Atxn3, scientists and physicians all over the world have been humbled by the question of how to help patients affected with SCA3. One specific angle of research has focused on the removal of the toxic protein altogether. However, one downside of this approach is that it would also cause the loss of normal Atxn3 function in patients. Atxn3 is critical for the degradation of unwanted proteins, which is necessary for the healthy functioning of all our body’s cells. It normally binds to little marks on proteins called ubiquitin chains (which tag proteins for removal), then cleaves these chains to facilitate the entry of proteins into the cell’s destruction machinery. Since treatment will need to be sustained over the span of a patient’s lifetime, the complete removal of Atxn3 might be harmful.

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