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

Giuseppe Leuzzi^1*Raquel Cuella-Martin^2*Samuel B. Hayward³Vincent Chapdelaine-Trépanier²Wei He⁴Han Xu⁴Alberto Ciccia^3*

• ¹IFOM ETS, the AIRC Institute of Molecular Oncology, Milan, Italy
• ²McGill University, Montreal, Canada
• ³Columbia University, New York, United States
• ⁴The University of Texas MD Anderson Cancer Center, Houston, United States

ABSTRACT 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.