A base editing resource for functional annotation of DNA repair variants in breast-derived cell models

Area of Science:

• Genomics
• Cancer Biology
• Molecular Biology

Background:

• The DNA damage response (DDR) is crucial for maintaining genome integrity.
• Disruptions in DDR genes are implicated in cancer development and treatment resistance.
• Thousands of DDR gene variants in tumors lack clear functional interpretation, hindering clinical application.

Purpose of the Study:

• To functionally characterize DNA damage response (DDR) gene variants in triple-negative breast cancer (TNBC).
• To extend previous CRISPR-based screening efforts to a new cell line model (MDA-MB-231).
• To create a dataset for stratifying variants of uncertain significance and advancing precision oncology.

Main Methods:

• Performed a large-scale CRISPR-dependent base editing screen in MDA-MB-231 cells.
• Assessed the impact of approximately 11,000 single-guide RNAs (sgRNAs) on cellular fitness.
• Targeted the coding sequences of 27 DDR genes, focusing on homologous recombination (HR) and inter-strand crosslink repair (ICLR) pathways.

Main Results:

• Generated a dataset of functional consequences for thousands of DDR variants in TNBC.
• Integrated mutation-associated effects with clinical annotations for variant stratification.
• Identified shared and context-specific genetic dependencies across different breast cancer cell lines.

Conclusions:

• The study provides a standardized, cross-comparable resource for interpreting DDR variants.
• This resource is expected to facilitate the development of precision oncology strategies.
• Advances the functional understanding of DDR variants in cancer, aiding clinical decision-making.