Transcriptional adaptation drives utrophin upregulation in Duchenne muscular dystrophy

Duchenne muscular dystrophy (DMD) is a muscle-degenerating disease caused by mutations in DMD/dystrophin. Utrophin (UTRN), the functional paralog of DMD, is upregulated in DMD nonsense alleles, suggesting a potential therapy for DMD. We developed an inducible mRNA degradation system for DMD by introducing a premature termination codon (PTC) in one of its alternatively spliced exons. Inclusion of the PTC-containing exon triggers DMD mutant mRNA decay and UTRN upregulation. Notably, blocking nonsense-mediated mRNA decay results in the reversal of UTRN upregulation, whereas overexpressing DMD does not. Furthermore, overexpressing DMD PTC minigenes in wild-type cells causes UTRN upregulation, as does a DMD WT minigene containing a self-cleaving ribozyme. To place these findings in a therapeutic context, we used splice-switching antisense oligonucleotides (ASOs) to induce the skipping of out-of-frame exons of DMD, aiming to introduce PTCs. We found that these ASOs cause UTRN upregulation. In addition, when using an ASO to restore the DMD reading frame, an actual DMD treatment, in myotubes derived from a DMD patient with an exon 52 deletion, which leads to a PTC, UTRN upregulation is blocked. Altogether, these results indicate that UTRN upregulation in DMD nonsense alleles is not due to dystrophin protein loss but rather to an mRNA decay-based mechanism called transcriptional adaptation (TA), and highlight an unexplored therapeutic application of ASOs in inducing genetic compensation via TA.