eSkip2 prioritizes exon-skipping antisense oligonucleotide target regions across exon--intron contexts

Abstract

Exon-skipping antisense oligonucleotides (ASOs) can restore productive transcripts, but identifying effective binding regions remains difficult because splicing regulation extends across exons, introns and splice junctions. Here we develop eSkip2, a genome-informed framework that ranks target regions within a unified exon-intron sequence context. eSkip2 combines a genome-pretrained sequence model with ASO-induced exon-skipping data and single-nucleotide-variant splicing perturbations, followed by target-locus adaptation that requires no experimental ASO labels from the locus being designed. Across benchmarks comprising canonical exons and pseudoexons, multiple cell types and chemistries, and exonic, intronic and exon-intron-spanning targets, eSkip2 prioritized active regions and showed a higher median AUROC than applicable exon-restricted models. Prospective application to the combinatorial design of dual-targeting ASOs for DMD exon 46 enriched active candidates near the top of the ranking: the two most active new ASOs ranked within the top three and produced dose-dependent dystrophin restoration in patient-derived cells. These results support eSkip2 as a practical first-pass strategy for reducing experimental search space in exon-skipping ASO discovery.