Low Efficiency of Homology-Independent Targeted Integration for CRISPR/Cas9 Correction in the Vicinity of SLC26A4 c.919–2A>G Variant

Abstract Recessive variants of SLC26A4 are a common cause of hereditary hearing impairment and are responsible for non-syndromic enlarged vestibular aqueducts and Pendred syndrome. Patients with bi-allelic SLC26A4 variants often suffer from fluctuating hearing loss and recurrent vertigo, ultimately leading to severe to profound hearing impairment. However, there are currently no satisfactory prevention or treatment options for this condition. The CRISPR/Cas9 genome-editing technique is a well-known tool for correcting point mutations or manipulating genes and shows potential therapeutic application for hereditary disorders. In this study, we attempted to use the homology-independent targeted integration (HITI) strategy to correct the SLC26A4 c.919-2A > G variant, the most common SLC26A4 variant in the Han Chinese population. Next-generation sequencing was performed to evaluate the editing efficiency of the HITI strategy. The results showed that only 0.15% of the reads successfully exhibited HITI integration, indicating that the c.919-2 region may not be a suitable region for HITI selection and that other site selection or insertion strategies may be needed to improve the efficiency of correcting the SLC26A4 c.919-2A > G variant. This experience may serve as a valuable reference for other researchers considering CRISPR target design in this region.