Rapid and scalable preclinical evaluation of personalized antisense oligonucleotide therapeutics using organoids derived from rare disease patients

Abstract Personalized antisense oligonucleotides (ASOs) have achieved positive results in the treatment of rare genetic disease. As clinical sequencing technologies continue to advance, the ability to identify rare disease patients harboring pathogenic genetic variants amenable to this therapeutic strategy will likely improve. Here, we describe a scalable platform for generating patient-derived cellular models and demonstrate that these personalized models can be used for preclinical evaluation of patient-specific ASOs. We establish robust protocols for delivery of ASOs to patient-derived organoid models and confirm reversal of disease-associated phenotypes in cardiac organoids derived from a Duchenne muscular dystrophy (DMD) patient harboring a structural deletion in the dystrophin gene amenable to treatment with existing ASO therapeutics. Furthermore, we design novel patient-specific ASOs for two additional DMD patients (siblings) harboring a deep intronic variant in the dystrophin gene that gives rise to a novel splice acceptor site, incorporation of a cryptic exon, and premature transcript termination. We show that treatment of patient-derived cardiac organoids with patient-specific ASOs results in restoration of DMD expression and reversal of disease-associated phenotypes. The approach outlined here provides the foundation for an expedited path towards the design and preclinical evaluation of personalized ASO therapeutics for a broad range of rare diseases.