The Breakome of BRCA1 and BRCA2 Mutation Carriers Reveals Early Processes in Breast Oncogenesis

DNA double-strand breaks (DSBs) can lead to genome instability in cancer. Cells rely on an efficient DNA damage response (DDR) to maintain their DNA integrity and prevent oncogenic transformation. However, the early events that connect recurrent DNA damage to oncogenesis are not yet fully understood. Here, we employed in-suspension Breaks Labeling in-situ and Sequencing (sBLISS) to identify DSBs in primary cells of non-malignant carriers of BRCA1 and BRCA2 mutations (BRCAmut), categorized as high-risk patients, to characterize the effects of homologous recombination (HR) loss on cancer initiation. We demonstrate that the landscape of physiological DSBs in BRCAmut samples differs from that in healthy controls, and resemble more the pattern observed in cancer cells. Our results reveal that proto-oncogenes and tumor suppressors contain more breaks in BRCAmut samples, and that highly broken genes tend to be more highly expressed. These highly broken genes are also often mutated in breast cancer tumors. Finally, differentially broken genes in BRCAmut samples exhibit a strong correlation with homologous recombination repair. Together, our findings underscore the impact of BRCA loss on the early stages of carcinogenesis and highlight future possibilities for early cancer detection. Overall design: sBLISS (in-suspension Breaks Labeling in-situ and Sequencing) of epithelial primary cells derived from non-malignant BRCA1 and BRCA2 mutation carriers at high risk of developing breast cancer or non-carrier average risk controls, and sBLISS of non-malignant and breast cancer cell lines. All samples are non-treated.