Functional <i>Ex Vivo</i> Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects.

Abstract

Tumors of germline <i>BRCA1/2</i> mutated carriers show homologous recombination (HR) deficiency (HRD), resulting in impaired DNA double-strand break (DSB) repair and high sensitivity to PARP inhibitors. Although this therapy is expected to be effective beyond germline <i>BRCA1/2</i> mutated carriers, a robust validated test to detect HRD tumors is lacking. In this study, we therefore evaluated a functional HR assay exploiting the formation of RAD51 foci in proliferating cells after <i>ex vivo</i> irradiation of fresh breast cancer tissue: the recombination REpair CAPacity (RECAP) test. Fresh samples of 170 primary breast cancer were analyzed using the RECAP test. The molecular explanation for the HRD phenotype was investigated by exploring <i>BRCA</i> deficiencies, mutational signatures, tumor-infiltrating lymphocytes (TIL), and microsatellite instability (MSI). RECAP was completed successfully in 148 of 170 samples (87%). Twenty-four tumors showed HRD (16%), whereas six tumors were HR intermediate (HRi; 4%). HRD was explained by <i>BRCA</i> deficiencies (mutations, promoter hypermethylation, deletions) in 16 cases, whereas seven HRD tumors were non-BRCA related. HRD tumors showed an increased incidence of high TIL counts (<i>P</i> = 0.023) compared with HR proficient (HRP) tumors and MSI was more frequently observed in the HRD group (2/20, 10%) than expected in breast cancer (1%; <i>P</i> = 0.017). RECAP is a robust functional HR assay detecting both <i>BRCA1/2</i>-deficient and <i>BRCA1/2</i>-proficient HRD tumors. Functional assessment of HR in a pseudo-diagnostic setting is achievable and produces robust and interpretable results.