Figure S3 from Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects

Meijer, Titia G.; Verkaik, Nicole S.; Sieuwerts, Anieta M.; van Riet, Job; Naipal, Kishan A.T.; van Deurzen, Carolien H.M.; den Bakker, Michael A.; Sleddens, Hein F.B.M.; Dubbink, Hendrikus-Jan; den Toom, T. Dorine; Dinjens, Winand N.M.; Lips, Esther; Nederlof, Petra M.; Smid, Marcel; van de Werken, Harmen J.G.; Kanaar, Roland; Martens, John W.M.; Jager, Agnes; van Gent, Dik C.

doi:10.1158/1078-0432.22467971.v1

Figure S3 from Functional Ex Vivo Assay Reveals Homologous Recombination Deficiency in Breast Cancer Beyond BRCA Gene Defects

journal contribution

posted on 2023-03-31, 20:24 authored by Titia G. Meijer, Nicole S. Verkaik, Anieta M. Sieuwerts, Job van Riet, Kishan A.T. Naipal, Carolien H.M. van Deurzen, Michael A. den Bakker, Hein F.B.M. Sleddens, Hendrikus-Jan Dubbink, T. Dorine den Toom, Winand N.M. Dinjens, Esther Lips, Petra M. Nederlof, Marcel Smid, Harmen J.G. van de Werken, Roland Kanaar, John W.M. Martens, Agnes Jager, Dik C. van Gent

Comparison of mutational signature analysis using all WGS-derived somatic mutations versus using somatic mutations present on SureSelect v5 target regions only.

Funding

Dutch Cancer Society

History

ARTICLE ABSTRACT

Tumors of germline BRCA1/2 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 BRCA1/2 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 ex vivo 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 BRCA deficiencies, mutational signatures, tumor-infiltrating lymphocytes (TIL), and microsatellite instability (MSI). RECAP was completed successfully in 125 of 170 samples (74%). Twenty-four tumors showed HRD (19%), whereas six tumors were HR intermediate (HRi; 5%). HRD was explained by BRCA 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 (P = 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%; P = 0.017). RECAP is a robust functional HR assay detecting both BRCA1/2-deficient and BRCA1/2-proficient HRD tumors. Functional assessment of HR in a pseudo-diagnostic setting is achievable and produces robust and interpretable results.