AON-based degradation of c.151C>T mutant COCH transcripts associated with dominantly inherited hearing impairment DFNA9

Abstract

The c.151C>T founder mutation in COCH is a frequent cause of late-onset, dominantly inherited hearing impairment and vestibular dysfunction (DFNA9) in the Dutch/Belgian population. The initial clinical symptoms only manifest between the 3rd and 5th decade of life, which leaves ample time for therapeutic intervention. The dominant inheritance pattern and established non-haploinsufficiency disease mechanism indicate that suppressing translation of mutant COCH transcripts has high therapeutic potential. Single-molecule real-time (SMRT) sequencing resulted in the identification of 11 variants with a low population frequency (<10%) that are specific to the c.151C>T mutant COCH allele. Proof of concept was obtained that gapmer antisense oligonucleotides (AONs), directed against the c.151C>T mutation or mutant allele-specific intronic variants, are able to induce mutant COCH transcript degradation when delivered to transgenic cells expressing COCH minigenes. The most potent AON, directed against the c.151C>T mutation, was able to induce a 60% decrease in mutant COCH transcripts without affecting wild-type COCH transcript levels. Allele specificity decreased when increasing concentrations of AON were delivered to the cells. With the proven safety of AONs in humans, and rapid advancements in inner ear drug delivery, our in vitro studies indicate that AONs offer a promising treatment modality for DFNA9.

Genotype-Phenotype Correlations of Pathogenic COCH Variants in DFNA9: A HuGE Systematic Review and Audiometric Meta-Analysis

“…The results of the present study are also important because of recent promising developments in the evolving field of genetic therapies for hereditary hearing loss. The first preclinical study [ 74 ] on the development of such a therapy for DFNA9 was recently published. The results of the present meta-analysis can be used as a baseline to assess the efficacy of such novel therapeutics in future clinical trials.…”

Splicing mutations in the CFTR gene as therapeutic targets

“…Ribose sugar can contain 2′-O-methyl or 2′-O-methoxyethyl substitutions that increase the oligonucleotide stability [ 75 ]. AON modifications at sugar positions include also phosphorodiamidate morpholino, peptide nucleic acids, and Locked Nucleic Acids (LNA) that increases binding affinity to the target and resistance to nucleases [ 76 ]. LNA are artificial analogs in which the ribose contains a bridge connecting the 2′-O with the 4′-C position.…”

Antisense RNA Therapeutics: A Brief Overview

“…The therapeutic gapmer targets the mutant allele to reduce the amount of tetramers containing the mutant protein, and therefore prevent the aforementioned depositions [42,43]. Another recent example is the use of gapmers to specifically degrade the mutant allele introduced by a mutation in the COCH gene, which causes autosomal dominant hearing impairment [44]. In this study, two strategies were used to degrade the mutant transcript: directly targeting the mutation or other single-nucleotide polymorphisms (SNPs) in cis with the mutation that are part of the mutant haplotype.…”