Transcriptomic analysis of cultured myotonic dystrophy type 1 myoblasts treated with blocking or gapmer AONs

Antisense oligonucleotides (AONs) have gained momentum as therapeutics for neuromuscular disorders with the clinical approval of nusinersen and eteplirsen. For microsatellite repeat expansion disorders, AONs have not reached the clinic yet. Oligonucleotide therapies in such disorders are based on preventing translation of expanded repeats or sequestration of RNA-binding proteins. This can be achieved both by steric hindrance and by degradation of the transcript, and it is unknown which approach is superior. Here, we directly compared blocking AONs with RNase H-recruiting gapmers in a myotonic dystrophy type 1 cell model. Two target sequences were selected: the triplet repeat, which offers many identical binding sites, and a unique sequence upstream of the repeat. We performed RNA sequencing to investigate both on- and off-target effects on a transcriptome-wide level. Overall design: Immortalized DM1 patient-derived myoblasts (DM11) were treated with (CAG)5 repeat blocking AONs, (CAG)6 repeat gapmer AONs, or DMPK-specific gapmer AONs. As negative controls, non-targeting (GAC)5 blocking, (GAC)6 gapmer AONs and untreated cells were included. As positive reference, untreated healthy control myoblasts (C25) were included. The negative controls were grouped for the analysis to exclude non-specific effects of AON treatment.