Exploiting Transcriptional Adaptation to Develop New Genetic Compensation-based Therapies

Organisms display various mechanisms to compensate for the deleterious effects of harmful mutations. One such mechanism is transcriptional adaptation (TA), a recently identified mode of gene regulation whereby mutant mRNA decay triggers the transcriptional modulation of so-called adapting genes, independently of protein loss (Rossi et al., Nature 2015; El-Brolosy et al., Nature 2019). In some cases, TA can lead to functional compensation by upregulating genes that are functionally redundant with the mutated gene. In our funded project, Transcriptional Adaptation and Genetic Compensation (TAaGC), we are investigating the mechanisms underlying TA and its relevance to human health and disease. We have now observed TA in human cells and found that splice-switching antisense oligonucleotides (ASOs) can be used as tools to induce TA (Falcucci et al., Nature 2025). By causing the skipping of out-of-frame exons, these ASOs disrupt the reading frame, thereby triggering mutant mRNA decay and the upregulation of functional paralogs. Using this approach, we have induced the upregulation of functional paralogs for both the DMD and LMNA genes, mutations in which cause Duchenne muscular dystrophy and laminopathies, respectively. ASOs have been approved by regulatory agencies, including the FDA, for the treatment of multiple diseases, altogether suggesting that splice-switching ASOs constitute a viable therapeutic approach to induce functional compensation via TA. In this PoC project, we first aim to further optimize the sequence of TA-inducing ASOs for DMD and LMNA in human and mouse cells in culture. The optimized human ASOs will then be fully investigated in relevant human cells in regards to their effect on the transcriptome and proteome; the optimized mouse ASOs will be tested in wild-type and mutant mice. Together, these studies will identify lead ASO candidates ready for further preclinical and clinical development in the treatment of DMD and laminopathies.