Annotation and evaluation of base editing outcomes in multiple cell types using CRISPRbase.

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• CRISPR-Cas base editing (BE) offers precise genome editing but varies in efficiency and accuracy.
• Different base editing systems exhibit distinct editing efficiencies, product purities, and off-target effects.

Purpose of the Study:

• To develop CRISPRbase, a comprehensive database of base editing outcomes.
• To enable evaluation of base editing precision, efficiency, and purity across diverse systems.
• To assess the impact of off-target mutations in cancer-related contexts.

Main Methods:

• Integrated 1,252,935 base editing records from 17 species and over 50 cell types.
• Developed a platform incorporating annotations, functional predictions, and sequence blasting for SgRNA analysis.
• Systematically assessed editing windows, efficiency, and product purity of various BE systems.

Main Results:

• CRISPRbase provides a resource for evaluating and comparing different base editing systems.
• Analysis revealed that over half of cancer-related off-target mutations were non-synonymous and potentially damaging.
• Most identified cancer-related off-target mutations were passenger rather than driver mutations, suggesting a limited role in carcinogenesis.

Conclusions:

• CRISPRbase is a valuable tool for researchers studying base editor outcomes.
• The database aids in selecting optimal base editor designs for specific functional studies.
• Understanding off-target mutation profiles is crucial for safe and effective genome editing applications.