Upregulation of a CFTR mRNA isoform has therapeutic potential for the treatment of 3′ CFTR PTC variants

Nonsense or premature termination codon (PTC) variants of the CFTR gene are pathogenic and found in ∼10% of North American people with cystic fibrosis. In addition to encoding incomplete proteins, PTC variants induce nonsense-mediated mRNA decay (NMD), leading to ∼80%-90% reduction in full-length mRNA. This reduction is a contributor to PTC mutation-related pathology. E22 trunc is a naturally occurring truncated CFTR mRNA that terminates before the W1282X PTC variant and is resistant to NMD. To induce its expression, antisense oligonucleotides (ASOs) were tiled across intron 22 splice donor (SD) and splice acceptor (SA) sites. Top SD/SA ASO pairs were assessed for their impact on e22 trunc mRNA, e22 trunc protein, and CFTR-mediated chloride (Cl^-) transport in immortalized and primary human bronchial epithelial (hBE) cell cultures. We demonstrate that e22 trunc mRNA generates a truncated CFTR protein whose Cl^- transport function can be enhanced with elexacaftor/tezacaftor/ivacaftor (ETI) treatment. ASO and ETI treatment in combination restore ∼20% and 25% of wild-type CFTR Cl^- transport function in immortalized epithelial and primary hBE cells homozygous for CFTR W1282X, respectively. This study provides a foundation for advancing ASO-mediated upregulation of e22 trunc mRNA and protein as a therapeutic approach for cystic fibrosis caused by 3'-terminal CFTR PTC mutations.