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Updated: Jul 30, 2025
Characterizing Exon Skipping Efficiency in DMD Patient Samples in Clinical Trials of Antisense Oligonucleotides
Published on: May 7, 2020
Block or degrade? Balancing on- and off-target effects of antisense strategies against transcripts with expanded
Najoua El Boujnouni1, M Leontien van der Bent1, Marieke Willemse1
1Department of Medical BioSciences, Research Institute for Medical Innovation, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands.
Abstract:
Antisense oligonucleotide (ASO) therapies for myotonic dystrophy type 1 (DM1) are based on elimination of transcripts containing an expanded repeat or inhibition of sequestration of RNA-binding proteins. This activity is achievable by both degradation of expanded transcripts and steric hindrance, although it is unknown which approach is superior. We compared blocking ASOs with RNase H-recruiting gapmers of equivalent chemistries. Two DMPK target sequences were selected: the triplet repeat and a unique sequence upstream thereof. We assessed ASO effects on transcript levels, ribonucleoprotein foci and disease-associated missplicing, and performed RNA sequencing to investigate on- and off-target effects. Both gapmers and the repeat blocker led to significant DMPK knockdown and a reduction in (CUG)exp foci. However, the repeat blocker was more effective in MBNL1 protein displacement and had superior efficiency in splicing correction at the tested dose of 100 nM. By comparison, on a transcriptome level, the blocking ASO had the fewest off-target effects. In particular, the off-target profile of the repeat gapmer asks for cautious consideration in further therapeutic development. Altogether, our study demonstrates the importance of evaluating both on-target and downstream effects of ASOs in a DM1 context, and provides guiding principles for safe and effective targeting of toxic transcripts.
Insights
Antisense oligonucleotide (ASO) therapies for myotonic dystrophy type 1 (DM1) were compared. Repeat blockers showed superior splicing correction and fewer off-target effects than gapmers, guiding safer DM1 therapeutic development.
Area of Science:
- Molecular Biology
- Genetics
- Pharmacology
Background:
- Myotonic dystrophy type 1 (DM1) therapies utilize antisense oligonucleotides (ASOs) to eliminate toxic transcripts or inhibit RNA-binding proteins.
- Two primary ASO mechanisms exist: transcript degradation and steric hindrance, with their comparative efficacy in DM1 remaining unclear.
Purpose of the Study:
- To compare the efficacy and safety of blocking ASOs versus RNase H-recruiting gapmers for DM1 treatment.
- To evaluate ASO effects on DMPK transcript levels, RNA foci, splicing, and off-target effects.
Main Methods:
- Comparison of blocking ASOs and gapmers with equivalent chemistries targeting two DMPK sequences.
- Assessment of ASO effects on transcript levels, ribonucleoprotein foci, and missplicing.
- RNA sequencing to identify on- and off-target effects.
Main Results:
- Both ASO types reduced DMPK transcripts and (CUG)exp foci.
- Repeat blockers demonstrated superior MBNL1 protein displacement and splicing correction efficiency at 100 nM.
- Blocking ASOs exhibited fewer transcriptome-wide off-target effects compared to repeat gapmers.
Conclusions:
- The study highlights the importance of evaluating both on-target and downstream effects of ASOs in DM1.
- Repeat blockers may offer a safer and more effective therapeutic strategy for DM1 by minimizing off-target impacts.
- Guiding principles for safe and effective targeting of toxic transcripts in DM1 are provided.
