Combined Tumor Sequencing and Case-Control Analyses of RAD51C in Breast Cancer

Abstract

Background: Loss-of-function variants in RAD51C are associated with familial ovarian cancer, but its role in hereditary breast cancer remains unclear. The aim of this study was to couple breast tumor sequencing with case-control data to clarify the contribution of RAD51C to hereditary breast cancer.

Methods: RAD51C was sequenced in 3080 breast cancer index cases that were negative in BRCA1/2 clinical tests and 4840 population-matched cancer-free controls. Pedigree and pathology data were analyzed. Nine breast cancers and one ovarian cancer from RAD51C variant carriers were sequenced to identify biallelic inactivation of RAD51C, copy number variation, mutational signatures, and the spectrum of somatic mutations in breast cancer driver genes. The promoter of RAD51C was analyzed for DNA methylation.

Results: A statistically significant excess of loss-of-function variants was identified in 3080 cases (0.4%) compared with 2 among 4840 controls (0.04%; odds ratio = 8.67, 95% confidence interval = 1.89 to 80.52, P< .001), with more than half of the carriers having no personal or family history of ovarian cancer. In addition, the association was highly statistically significant among cases with estrogen-negative (P <. 001) or triple-negative cancer (P < .001), but not in estrogen-positive cases. Tumor sequencing from carriers confirmed bi-allelic inactivation in all the triple-negative cases and was associated with high homologous recombination deficiency scores and mutational signature 3 indicating homologous recombination repair deficiency.

Conclusions: This study provides evidence that germline loss-of-function variants of RAD51C are associated with hereditary breast cancer, particularly triple-negative type. RAD51C-null breast cancers possess similar genomic and clinical features to BRCA1-null cancers and may also be vulnerable to DNA double-strand break inducing chemotherapies and poly ADP-ribose polymerase inhibitors.

Figure 1.

Genomic characterization of breast and ovarian cancers from carriers of RAD51C germline loss-of-function variants. A) Germline variants, bi-allelic inactivation events, somatic mutations, and genomic alterations of RAD51C-associated tumors. Germline and somatic mutation types are color-coded according to the legend. The phenobar (top) provides information about estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) status, basal-like subtype, loss of heterozygosity (LOH) of the wild-type allele, and somatic mutations in TP53 and PIK3CA. The fraction of the genome altered (FGA) and homologous recombination deficiency (HRD) score are shown for each case below. B) The weighted contribution of mutational signatures from breast cancers of RAD51C germline variant carriers. C) HRD scores of RAD51C-null (n = 7), RAD51C-het (n = 2), sporadic TN breast cancers (n = 10), and sporadic non-TN breast cancers (n = 105). P values were calculated using Mann–Whitney test, 2-tailed. ER = estrogen receptor; FGA = fraction of genome altered; HER2 = human epidermal growth factor receptor 2; HRD = homologous recombination deficiency; LOH = loss of heterozygosity; PR = progesterone receptor; TN = triple-negative.