Anti-gene oligonucleotides targeting Friedreichs ataxia expanded GAA:TTC repeats increase Frataxin expression

Friedreichs ataxia (FRDA) is a progressive, autosomal recessive ataxia caused, in the majority of cases, by homozygous expansion of GAA*TTC triplet-repeats in the first intron of the frataxin (FXN) gene. GAA*TTC repeat expansion results in the formation of non-B DNA intramolecular triplex structure (H-DNA) as well as changes in the epigenetic landscape at FXN loci and heterochromatin formation. Expansion of intronic GAA*TTC repeats is associated with reduced levels of FXN mRNA and protein resulting in disease development. Previously, we reported that DNA-binding anti-gene oligonucleotides (AGOs) targeting the GAA*TTC repeat expansion abolished H-DNA formation. Here, we demonstrate that targeting repeat-expanded chromosomal DNA using single-strand locked nucleic acid (LNA)-DNA mixmer AGOs increases FXN mRNA and protein expression in patient-derived cells. We examined numerous LNA-DNA AGOs and found that the design, length and their LNA composition have a high impact on the effectiveness of the treatment. Collectively, our results demonstrate the unique capability of specifically designed ONs targeting the GAA*TTC DNA repeats to upregulate FXN gene expression.