RNA-based discovery and correction of splicing defects caused by POLR3A missense mutations

RNA polymerase III-related disorders represent a clinically diverse spectrum of diseases. While pathogenic variants in the POLR3A subunit are most commonly associated with hypomyelinating leukodystrophies, they also contribute to other neurological or systemic deficiencies. Despite this phenotypic variability, many disease-causing POLR3A variants converge mechanistically on altered RNA expression that can impair oligodendrocyte maturation and their myelination capacity. Using CRISPR-dCas13Rx, we investigated whether regions containing disease-causing missense mutations in POLR3A affect RNA splicing in EcR293 and oligodendroglioma cell lines. Our analysis indicates that 20% of the interrogated exon regions of POLR3A harboring disease-causing missense mutations induce significant splicing changes when targeted by an interfering guide RNA (gRNA)/dCas13Rx complex. Minigene assays confirmed that mutations residing in these regions caused splicing aberrations. We then used the CRISPR-dCas13Rx system to identify intron elements that, when targeted with gRNAs, alleviated the splicing defect caused by missense mutations in exon 14 and exon 26. Antisense oligonucleotides (ASOs) derived from these active gRNAs also improved correct splicing in EcR293 and oligodendroglioma cell lines. These findings not only highlight the therapeutic promise of gRNAs and ASOs in rescuing splicing defects caused by POLR3A missense mutations but also establish CRISPR-dCas13Rx as a useful tool for identifying and correcting disease-causing splicing aberrations.