Correction of multiple splicing mutations associated with CFTR exon 18 using a single exon-specific U1 snRNA

ABSTRACT Splice site mutations represent a major class of pathogenic mutations in many diseases, as these changes disrupt normal splicing leading to gene expression changes. Cystic fibrosis (CF) results from mutations to the cystic fibrosis transmembrane conductance regulator (CFTR) gene that encodes an essential ion channel. Approximately 13% of the over 2,100 known CFTR mutations disrupt 3’ or 5’ splice sites and are predicted to cause splicing defects. Because each splicing mutation is rare, developing individualized therapies to treat each one is financially challenging. Exon specific U1 snRNA (ExSpeU1) targets the non-conserved intronic region downstream the 5’ splice site (ss) to rescue exon skipping. Because this approach is exon-rather than mutation-specific, a single agent can potentially rescue multiple mutations. In this study, we have developed a platform to systematically classify all patient variants associated with an exon that are predicted to affect splicing and then determine their rescue potential using ExSpeU1. Here we report the results of these studies. Our minigene reporter study shows that 7 of 10 exon 18 variants resulted in exon skipping. Four mutations at the 3’ and 5’ ss were rescued at least partially using a single ExSpeU1. Using a luciferase reporter, we observe that the splicing rescue is reflected at the protein level. Lastly, we demonstrate exon-targeting ExSpeU1s can also rescue 3’ and 5’ ss mutations. Overall, this study exemplifies the power of our platform to screen and rescue multiple patient-derived splicing mutations using a single agent.