Homologous Recombination Deficiency Across Subtypes of Primary Breast Cancer

Abstract

Homologous recombination; Primary breast cancer

Recombinació homòloga; Càncer de mama primari

Recombinación homóloga; Cáncer de mama primario

PURPOSE Homologous recombination deficiency (HRD) is highly prevalent in triple-negative breast cancer (TNBC) and associated with response to PARP inhibition (PARPi). Here, we studied the prevalence of HRD in non-TNBC to assess the potential for PARPi in a wider group of patients with breast cancer. METHODS HRD status was established using targeted gene panel sequencing (360 genes) and BRCA1 methylation analysis of pretreatment biopsies from 201 patients with primary breast cancer in the phase II PETREMAC trial (ClinicalTrials.gov identifier: NCT02624973). HRD was defined as mutations in BRCA1, BRCA2, BRIP1, BARD1, or PALB2 and/or promoter methylation of BRCA1 (strict definition; HRD-S). In secondary analyses, a wider definition (HRD-W) was used, examining mutations in 20 additional genes. Furthermore, tumor BRCAness (multiplex ligation-dependent probe amplification), PAM50 subtyping, RAD51 nuclear foci to test functional HRD, tumor-infiltrating lymphocyte (TIL), and PD-L1 analyses were performed. RESULTS HRD-S was present in 5% of non-TNBC cases (n = 9 of 169), contrasting 47% of the TNBC tumors (n = 15 of 32). HRD-W was observed in 23% of non-TNBC (n = 39 of 169) and 59% of TNBC cases (n = 19 of 32). Of 58 non-TNBC and 30 TNBC biopsies examined for RAD51 foci, 4 of 4 (100%) non-TNBC and 13 of 14 (93%) TNBC cases classified as HRD-S had RAD51 low scores. In contrast, 4 of 17 (24%) non-TNBC and 15 of 19 (79%) TNBC biopsies classified as HRD-W exhibited RAD51 low scores. Of nine non-TNBC tumors with HRD-S status, only one had a basal-like PAM50 signature. There was a high concordance between HRD-S and either BRCAness, high TIL density, or high PD-L1 expression (each P < .001). CONCLUSION The prevalence of HRD in non-TNBC suggests that therapy targeting HRD should be evaluated in a wider breast cancer patient population. Strict HRD criteria should be implemented to increase diagnostic precision with respect to functional HRD.

Supported by unrestricted grants from The K.G. Jebsen Foundation [SKGJ-MED-020 to H.P.E., S.K., P.E.L.], Helse Vest [912008 to P.E.L.], The Norwegian Research Council [273354 to P.E.L.] and The Norwegian Cancer Society [190281-2017 to S.K., 190275-2017 to P.E.L.]. Research funding was provided by Grieg Foundation (to H.P.E. and T.A.), Helse Vest [912252; Clinical researcher fellowship to H.P.E.], Generalitat de Catalunya [PERIS, SLT017/20/000081 to A.H.R.], “la Caixa” Foundation and European Institute of Innovation and Technology/Horizon 2020 [LCF/TR/CC19/52470003 to A.L.G.], Asociación Española Contra el Cáncer [AECC, INVES20095LLOP to A.L.G.], Generalitat de Catalunya (PERIS Fellowship SLT002/16/00477 to A.L.G.) ERA PerMed [2019-215 to V.S.] and Miguel Servet fellowship (CPII19/00033 to V.S.). Additional funding and study medication was provided by Illumina [grant number 9529854], Pfizer [WI206347] and AstraZeneca [ESR-14-10077] to H.P.E., S.K., P.E.L.