Gene expression profile of BRCAness that correlates with responsiveness to chemotherapy and with outcome in patients with epithelial ovarian cancer

Abstract

Purpose: To define a gene expression profile of BRCAness that correlates with chemotherapy response and outcome in epithelial ovarian cancer (EOC).

Methods: A publicly available microarray data set including 61 patients with EOC with either sporadic disease or BRCA(1/2) germline mutations was used for development of the BRCAness profile. Correlation with platinum responsiveness was assessed in platinum-sensitive and platinum-resistant tumor biopsy specimens from six patients with BRCA germline mutations. Association with poly-ADP ribose polymerase (PARP) inhibitor responsiveness and with radiation-induced RAD51 foci formation (a surrogate of homologous recombination) was assessed in Capan-1 cell line clones. The BRCAness profile was validated in 70 patients enriched for sporadic disease to assess its association with outcome.

Results: The BRCAness profile accurately predicted platinum responsiveness in eight out of 10 patient-derived tumor specimens, and between PARP-inhibitor sensitivity and resistance in four out of four Capan-1 clones. [corrected] When applied to the 70 patients with sporadic disease, patients with the BRCA-like (BL) profile had improved disease-free survival (34 months v 15 months; log-rank P = .013) and overall survival (72 months v 41 months; log-rank P = .006) compared with patients with a non-BRCA-like (NBL) profile, respectively. The BRCAness profile maintained independent prognostic value in multivariate analysis, which controlled for other known clinical prognostic factors.

Conclusion: The BRCAness profile correlates with responsiveness to platinum and PARP inhibitors and identifies a subset of sporadic patients with improved outcome. Additional evaluation of this profile as a predictive tool in patients with sporadic EOC is warranted.

Fig 1.

Expression plot of the 60 genes that comprise the BRCAness profile. Columns represent set samples; rows, gene expression levels (normalized). Complete information regarding gene identity is provided in Appendix Table A1. Red indicates overexpressed genes; green, underexpressed genes. The gene expression signature that correlates with BRCA-like tumors is defined as the BL profile, and the signature that correlates with non–BRCA-like tumors is defined as the NBL profile.

Fig 2.

BRCAness profile distinguishes between platinum-sensitive and platinum-resistant tumor biopsy specimens in patients with known BRCA germline mutation status. (A) Hierarchical clustering that is based on the expression pattern of the 60 genes of the BRCAness profile distinguished between platinum-resistant and platinum-sensitive tumor biopsy samples. Platinum sensitivity was defined as a complete response to treatment maintained without progression for at least 6 months after platinum therapy. Platinum resistance was defined as progressive disease on platinum therapy, or less than a complete response to platinum therapy, or progression within 6 months of completing platinum therapy. (B) Correlation of BRCAness profile with platinum sensitivity and BRCA germline mutation status. The BRCAness profile accurately distinguished between platinum sensitivity and platinum resistance in eight of 10 tumor specimens, which in turn correlated with the presence of mutated versus functional BRCA gene status, respectively. NBL, non–BRCA-like; BL, BRCA-like.

Fig 3.

Association of BRCAness profile with disease-free survival (DFS) and overall survival (OS) in the combined patient cohort (N = 70). (A) DFS in the combined patient cohort. The median DFS times for patients with either the BRCA-like (BL) or non–BRCA-like (NBL) profile were 34 months and 15 months, respectively (log-rank P = .013). (B) OS in the combined patient cohort. The median OS times for patients with either the BL or NBL profile were 72 months and 41 months, respectively (log-rank P = .006).

Fig A1.

Development of the BRCAness gene expression profile. Previous investigators have described gene expression differences between BRCA-mutated and sporadic cancers, although these studies have typically grouped all sporadic tumors together without taking into consideration that some of these sporadic tumors might indeed have a BRCAness phenotype (Hedenfalk IA: J Natl Cancer Inst 94:960-961, 2002; Jazaeri AA, Awtrey CS, Chandramouli GV, et al: Clin Cancer Res 11:6300-6310, 2005). Thus, the group of patients with sporadic disease in such analyses is potentially diluted by patients who may exhibit a gene expression profile more consistent with a BRCA1 or BRCA2 germline mutation carrier, and vice versa. To address this issue, we first performed genome-wide hierarchical clustering of all 61 tumors. We found that patients clustered into three groups, (A) which represeted BRCA1, BRCA2, and sporadic clusters, respectively. The BRCA1 cluster contained 22 patients, of which nine actually had sporadic (ie, nonmutated) disease. The BRCA2 cluster contained 14 patients, of which four had sporadic disease. The sporadic cluster contained 25 patients, of which six had BRCA1 and five had BRCA2 germline mutation. The clustering reproducibility index (R) was 0.934, and the three clusters did not change even if clear cell or mucinous samples were excluded from the analysis. For the purpose of defining the profile, these outliers (eg, a patient with BRCA1 contaminating the sporadic cluster, or a patient with sporadic disease contaminating the BRCA cluster) were removed from the analysis. We then proceeded to develop a 60-gene, diagonal linear discriminant predictor (B) that distinguished the BRCA clusters (ie, BRCA-like tumors) from the sporadic cluster (ie, non–BRCA-like tumors).

Fig A2.

Association of BRCAness profile with disease-free survival (DFS) and overall survival (OS) in the sequenced patient cohort (n = 35). (A) DFS in the sequenced patient cohort. The median DFS times for patients with the BRCA-like (BL) and non–BRCA-like (NBL) profiles were not yet reached at median follow-up times of 53.5 months and 20 months, respectively (log-rank P = .03). (B) OS in the sequenced patient cohort. The median OS times for patients with the BL and NBL profiles were 72 months and 48 months, respectively (log-rank P = .1).

Fig A3.

Association of BRCAness profile with disease-free survival (DFS) and overall survival (OS) in the nonsequenced patient cohort (n = 35). (A) DFS in the nonsequenced patient cohort. The median DFS times for patients with the BL and NBL profiles were 22 and 7 months, respectively, (log-rank P = .013). (B) OS in the nonsequenced patient cohort. The median OS times for patients with the BL and NBL profiles were not yet reached and 30 months, respectively, (log-rank P = .009).