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

Background – The DNA damage response (DDR) safeguards genome integrity, and its disruption contributes to cancer development, therapy response, and resistance. Large-scale sequencing has identified thousands of DDR gene variants in tumors, but the functional consequences of most remain unclear, limiting their clinical interpretation and application. Results – We previously developed CRISPR-dependent base editing screens to functionally characterize DDR variants in breast-derived cell lines. Here, we extend this work to triple-negative breast cancer by performing a large-scale base editing screen in MDA-MB-231 cells. We assessed the impact on cellular fitness of ∼11, 000 single-guide RNAs (sgRNAs) targeting the coding sequences of 27 DDR genes, primarily involved in homologous recombination (HR) and inter-strand crosslink repair (ICLR). The resulting dataset integrates mutation-associated effects with clinical annotations, enabling functional stratification of variants of uncertain significance. Conclusion – Combined with our previous datasets from MCF7 and MCF10A breast-derived cell lines, these results create a standardized, cross-comparable data that uncover both shared and context-specific genetic dependencies. Ultimately, we anticipate this resource will advance the functional interpretation of DDR variants, thereby facilitating the development of precision oncology approaches.