Individualized Antisense Oligonucleotide Therapy for SCN2A-Related Epilepsy

Researchers have successfully designed and administered patient-specific antisense oligonucleotides (ASOs) to treat two individuals with intractable epilepsy caused by pathogenic variants in the SCN2A gene. By utilizing whole-genome sequencing and induced pluripotent stem cell (iPSC) models, investigators developed allele-selective therapies that target the mutant transcript while sparing the wild-type allele, according to a report.

Precision Design of Allele-Selective ASOs

The therapeutic approach for these patients relied on identifying single-nucleotide polymorphisms (SNPs) to distinguish between the pathogenic and wild-type alleles. Because the patients possessed different causal variants associated with Developmental and Epileptic Encephalopathy 11 (DEE11), a “one-size-fits-all” treatment was not feasible.

Scientists mapped informative heterozygous SNPs using long-read sequencing. They then screened over 500 2’-methoxyethyl gapmers to identify those capable of recruiting RNase H1 to selectively degrade the mutant SCN2A transcript. In vitro assays using patient-derived iPSC neurons demonstrated significant allele selectivity, with the lead ASOs achieving 42-fold and 53-fold selectivity for the mutant transcripts in Patient 1 and Patient 2, respectively.

Safety and Toxicology Profile

Before clinical administration, the ASOs underwent rigorous safety assessments. Researchers evaluated the potential for innate immune activation by measuring CCL22 levels in BJAB cells and conducted in silico analysis to identify potential off-target effects. While some dose-dependent reduction was observed in off-target genes such as ANKS1B and TXK, these were deemed to carry a low risk based on existing genetic data from the gnomAD database and mouse models.

Repeat-dose toxicology studies were conducted in rats over 13 weeks. According to the study data, the ASOs were well-tolerated at doses up to 1 mg. While some transient clinical observations—such as abnormal gait or reduced activity—were noted at the highest doses, these findings were considered nonadverse and consistent with the profiles of other commercial ASO therapies.

Clinical Trial Implementation and Monitoring

The FDA authorized investigator-initiated, open-label clinical trials for both patients. Patient 1 began treatment in June 2023, while Patient 2 was enrolled in February 2024. The therapies were delivered via intrathecal lumbar injection.

The protocols were highly individualized, with endpoints tailored to each patient’s specific neurodevelopmental and seizure phenotype. For Patient 2, researchers expanded the clinical assessment to include:
* Neurodevelopmental scores: Measured via the Vineland Adaptive Behavior Scales (Vineland-3) and Bayley Scales of Infant and Toddler Development (BSID-4).
* Motor function: Assessed using the Dyskinetic Cerebral Palsy Functional Impact Scale (D-FIS).
* Gastrointestinal health: Tracked via the Bristol Stool Form Scale.

Amendments to the trial protocols allowed for flexible dosing intervals of 60 to 90 days, adjusted based on real-time clinical data regarding seizure control and developmental gains. As of the data cutoff in June 2025, both clinical trials remain active at their respective institutions, Rush University and the University of California San Diego (UCSD).

Future Implications for Rare Genetic Epilepsy

This study highlights the potential for “n-of-1” medicine in treating ultra-rare genetic disorders. By targeting the specific molecular cause of a patient’s epilepsy rather than broad symptoms, this approach offers a template for future individualized genetic therapies. The researchers noted that the SNPs utilized for allele selectivity in these patients had population frequencies of 27% and 18%, suggesting that these specific ASOs could potentially be applied to other patients harboring the same pathogenic variants.