#apaperaday: Preparing for Patient-Customized N-of-1 Antisense Oligonucleotide Therapy to Treat Rare Diseases

In today’s #apaperaday, Prof. Aartsma-Rus reads and comments on the paper titled:  Preparing for Patient-Customized N-of-1 Antisense Oligonucleotide Therapy to Treat Rare Diseases

Today’s pick is by Wilton-Clark and @toshifumiyokota on N-of-1 antisense oligonucleotides (ASOs) in FDA jurisdiction, from @Genes_MDPI. DOI: 10.3390/genes15070821. The authors introduce rare disease, which are individually rare but combined affect ~5% of the population.

The rarity means studying the disease is more challenging, and drug development is more challenging, because costs are similar to common drug development, but the cost have to be divided over a lot less patients. Furthermore, getting sufficient numbers in trials is a challenge.

Authors suggest this is why researchers started doing N-of-1 treatment development, so they could bypass challenges. I would argue the reason for N-of-1 is that an approach is only applicable to 1 individual (or very few), so you cannot follow the traditional development path.

Authors introduce that ASOs are perfect tools for individualized treatments. Here I agree with the authors :). ASOs can be used to cleave transcripts for toxic gain of function variants, and to modulate splicing to restore/increase production of (partially) functional protein.

Because ASOs have been tested and approved for more common rare diseases with the intended route of administration (intrathecal), one can extrapolate from these ASOs (nusinersen and tofersen) with regards to safety and dosing.

Also while development can be quicker, with reduced safety studies in a single species, development is still expensive. Currently, money is obtained mainly via fundraising. My own addition: the hope is that costs will go down in the future when development is more streamlined.

Authors mention efforts from the N1Collaborative to provide guidelines and expertise and to streamline. They also list the different N-of-1 ASOs that are currently reported: milasen and atipeksen have been published. For milasen there was a treatment effect (less seizures).

Atipeksen treatment was started in a patient with ataxia telangiectasia before the onset of symptoms. Here the challenge is that the onset of symptoms can vary between patients, so longer follow up is needed to establish whether symptom onset is delayed.

Authors also list so far unpublished cases: valeriasen, which was used in 2 patients with a severely progressive disease, where seizures were reduced after treatment, but the treatment did induce hydrocephalus. Authors outline only the Valeria case, where Valeria sadly passed away.

The other patient where treatment was initiated later, survived & hydrocephalus was treated with a shunt. However, after stopping with valeriasen treatment, the seizures came back. Currently, the goal is to develop a new ASO for treatment of this disease caused by KCNT1 variants.

Authors also list a patient with another epileptic syndrome, caused by TNPO2 variants, where allele-specific ASOs with LNAs are used in a single patient since 2023. So far, treatment is tolerated well, and there are reported signs of efficacy (not yet published).

Finally, authors mention the as yet unpublished results from the first n_lorem case, a girl with KIF1A pathogenic variants. Also, there are reported signs of efficacy by the parents. Authors do not mention it but this is an allele-specific ASO as well.

Authors then outline the regulatory guidelines as stipulated by FDA for N=1 ASOs developed by academics. Single species toxicity studies are sufficient, and when diseases are very severely progressive, shorter safety studies are acceptable.

Reduced toxicity studies increase the risk—however, this has to be balanced with the risk of the diseases and the risk of not treating. Preclinical studies to show that the ASOs are efficient are crucial. Chemical modifications ideally should be well characterized.

This is why most of the current N=1 ASOs are of the nusinersen and tofersen chemistries (except the Creyon Bio ASO which has LNAs). CMC should make sure of sufficient purity and low endotoxin levels, etc.

A plan to monitor clinical effects (safety and beneficial effects) should be in place before treatment is initiated. Also, approval from the local ethics board needs to be in place and consent from the patient/family where the risks need to be clearly outlined.

The risks for N=1 treatment are multiple fold: there is a risk of safety issues but also there is a risk of the treatment not working. Authors suggest also having discussions with ethicists about potential ethical concerns. I think this is a good suggestion indeed.

Authors conclude ASOs are in a unique position for N=1 development. I agree but want to flag efforts to develop N=1 gene therapy and gene editing. These developments face similar challenges. The hope is by sharing expertise we can all benefit and streamline future developments.