Homologous Recombination Deficiency Across Subtypes of Primary Breast Cancer

Abstract

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.

FIG 1.

Oncoplot of HRR mutations, HRD status, response, and surgical outcome in the PETREMAC trial. All breast cancers with HRD-W are displayed. The HRD-S subset includes tumors with HRR mutations by strict definition (listed above the dotted line) and/or BRCA1 methylation and includes gene silencing on the opposite allele. BRCAness was assessed by MLPA analysis. Objective response (combined) and patients with a partial or complete response to treatment based on combined radiological and clinical evaluation. HRD, homologous recombination deficiency; HRD-S, HRD-strict definition; HRD-W, HRD scored by wide definition; HRP, homologous recombination proficiency; HRR, homologous recombination repair; LOH, loss-of-heterozygosity; MLPA, multiplex ligation-dependent probe amplification; NA, not analyzed; pCR, pathological complete response; TNBC, triple-negative breast cancer; wt, wild type.

FIG 2.

Signaling molecules involved in homologous recombination to repair DNA DSBs. HRR of DNA DSB. HRD results from germline, somatic, or epigenetic gene alterations inactivating either of the key proteins: BRCA1, BRCA2, PALB2, RAD51C, RAD51D, BARD1, and BRIP1. The HRR proteins localize to the DSB site, acting as a helicase and opening the chromatin to allow pairing of BRCA2 and RAD51 with the undamaged DNA strand from the alternate chromosome. The undamaged copy serves as a template for DNA polymerase and PCNA to repair the damaged strand. DSB, double-strand break; HRD, homologous recombination deficiency; HRR, homologous recombination repair. Figure created with BioRender.com.