Modulation of pre-mRNA splicing using antisense oligonucleotides (ASOs) is a clinically validated therapeutic strategy, with multiple FDA-approved drugs. Current splice-switching ASOs (SSOs), primarily based on phosphorodiamidate morpholino oligomer (PMO) and 2'-O-methoxyethyl phosphorothioate (2'-MOE PS) chemistries, have certain limitations. Our laboratory focuses on developing innovative SSO designs and chemistries to overcome these challenges and enhance therapeutic efficacy. Here, we present our recent advances in developing next-generation SSOs for therapeutic applications.

Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by TCF4 haploinsufficiency. Integrating genomic datasets with strand-specific RNA analysis identified transcribed promoter regions suitable for activating double-stranded RNAs (dsRNAs). Screening identified a hotspot increasing TCF4 expression, retained by a lead dsRNA with therapeutic modifications. Anti-AGO2 immunoprecipitation enriched targeted-promoter RNA; dsRNA activation increased RNA polymerase II occupancy. These findings establish chemically tractable promoter-targeted dsRNAs as a mutation-independent strategy for treating haploinsufficient disease.

SECN-15 is a high-affinity-modified antisense oligonucleotide (ASO) targeting NRP1, a tumor-promoting factor expressed by multiple cell types within the tumor microenvironment. In preclinical models, systemic administration of SECN-15 achieved sustained tumor exposure, resulting in potent target knockdown in relevant cell populations and durable suppression of soluble NRP1 in plasma. Moreover, SECN-15 demonstrated robust antitumor activity both as a monotherapy and in combination with anti-PD-1 therapy, supporting further clinical development.

Wave’s PRISM platform enables the generation of chimeric phosphoryl guanidine (PN) backbone-containing stereopure oligonucleotides with position-controlled chemistry and stereochemical configuration. Examples provided will include where stereopure design and incorporation of PN linkages improve the pharmacological properties of oligonucleotides designed for distinct genetic targets, modalities, and tissues. Ongoing clinical trial data suggests that the improved pharmacological properties of investigational PN-containing oligonucleotides are translating into the clinic.