Targeted antisense oligonucleotide therapy rescues PRPF31 expression in retinitis pigmentosa caused by a splicing mutation

Pathogenic variants in splicing factors are the second most common cause of autosomal dominant retinitis pigmentosa, with mutations in PRPF31 being the most prevalent. Here, we characterize a novel intronic variant in PRPF31 (c.1074-11C>G) that creates a cryptic 3' splice site, resulting in an aberrantly spliced transcript predicted to encode a protein with an altered C terminus. However, the pathogenic protein is unstable and undetectable in patient-derived induced pluripotent stem cells (iPSCs). In addition, expression of the full-length PRPF31 protein was reduced in patient-derived retinal pigment epithelium (RPE). To correct the splicing defect, we designed a panel of antisense oligonucleotides (ASOs) targeting putative RNA-binding sites in exon 10 and intron 10 and identified a candidate that corrects PRPF31 splicing in a minigene reporter system as well as in patient-derived iPSCs and RPE. We further showed that ASO treatment enhances PRPF31 protein expression in patient-derived iPSC and RPE carrying the intronic mutation, supporting the potential of the ASO-based approach to restore PRPF31 expression in patients with the same or similar splicing defects.