Novel base editor fusions for safer genome editing with reduced genomic rearrangements

Overview

This technology addresses a critical safety challenge in base editing, a precise genome editing approach that converts single DNA bases without cutting both strands. Current base editors can inadvertently trigger unwanted double-strand breaks (DSBs) during DNA repair, leading to genomic rearrangements that limit therapeutic safety. The proposed solution fuses NHEJ-inhibitory effectors directly to base editors, confining protective activity to the target site while leaving normal cellular DNA repair processes undisturbed.

This site-restricted safety mechanism offers a significant advantage over systemic NHEJ inhibitors (chemical compounds or transient mRNA-based inhibitors), which can disrupt physiological DNA repair throughout the cell. The technology builds on a recently published Cas9 fusion platform that promotes homology-directed repair while suppressing error-prone non-homologous end-joining (NHEJ).

Technical specifications

• Core innovation: Fusion of NHEJ-inhibitory protein domains to base editors (Cas9 nickase + deaminase effector) to prevent nick-to-DSB conversion during repair
• Delivery format: mRNA encapsulated in lipid nanoparticles (LNPs), compatible with in vivo therapeutic applications
• Validation system: GFP-to-BFP reporter assay that distinguishes successful base conversion (color change) from unwanted NHEJ events (fluorescence loss)
• Established capabilities: All screening assays and primary cell testing protocols are already operational in the lab
• Application scope: Therapeutic gene editing in primary human cells and in vivo liver disease models

Technology readiness level

The concept is supported by a published Cas9 fusion platform demonstrating successful modulation of DNA repair outcomes (PMID: 37070192). The team has extensive experience with DNA repair modulation in both cell lines and primary cells. The current project focuses on a 6-month screening phase to identify optimal NHEJ-inhibitory fusion partners for base editors, followed by validation in primary human cells. In vivo testing in mouse models of liver disease via LNP delivery is planned beyond the current scope. The platform is at an early-to-mid research stage with strong foundational validation in adjacent technology.