Identification and Validation of an Anthracycline/Cyclophosphamide–Based Chemotherapy Response Assay in Breast Cancer

Abstract

BackgroundThere is no method routinely used to predict response to anthracycline and cyclophosphamide–based chemotherapy in the clinic; therefore patients often receive treatment for breast cancer with no benefit. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA damage response (DDR) pathway occurs in approximately 25% of breast cancer patients through several mechanisms and results in sensitization to DNA-damaging agents. The aim of this study was to develop an assay to detect DDR-deficient tumors associated with loss of the FA/BRCA pathway, for the purpose of treatment selection.MethodsDNA microarray data from 21 FA patients and 11 control subjects were analyzed to identify genetic processes associated with a deficiency in DDR. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples, and a molecular subgroup was identified that was defined by the molecular processes represented within FA patients. A 44-gene microarray-based assay (the DDR deficiency assay) was developed to prospectively identify this subgroup from formalin-fixed, paraffin-embedded samples. All statistical tests were two-sided.ResultsIn a publicly available independent cohort of 203 patients, the assay predicted complete pathologic response vs residual disease after neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline, and cyclophosphamide) with an odds ratio of 3.96 (95% confidence interval [Cl] =1.67 to 9.41; P = .002). In a new independent cohort of 191 breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin, and cyclophosphamide, a positive assay result predicted 5-year relapse-free survival with a hazard ratio of 0.37 (95% Cl = 0.15 to 0.88; P = .03) compared with the assay negative population.ConclusionsA formalin-fixed, paraffin-embedded tissue-based assay has been developed and independently validated as a predictor of response and prognosis after anthracycline/cyclophosphamide–based chemotherapy in the neoadjuvant and adjuvant settings. These findings warrant further validation in a prospective clinical study.

Up-regulation of the interferon-related genes in BRCA2 knockout epithelial cells

“…In breast cancer, an immune response gene expressing subgroup has been identified, and is associated with improved prognosis in triple negative breast cancers [46,47]. Recently, activated immune response has been associated with the loss of Fanconi anemia/BRCA (FA/BRCA) pathway in breast cancer patients, and has been validated as a biomarker of increased sensitivity to DNA damaging chemotherapy [48]. Our cell line model and knockdown experimental results are consistent with these clinical data, supporting that aberrations in BRCA2 or other components in BRCA DNA damage repair pathway result in the direct activation of immune response.…”

Biology and Management of Patients With Triple-Negative Breast Cancer

“…It is estimated that if these factors beyond germline BRCA mutations are comprehensively evaluated, 50%-60% of TNBC will demonstrate HR deficiency or BRCAness, making it an attractive selection and response biomarker for DNA-damaging therapy, such as platinum compounds and PARPi (Fig. 2) [58,68,80,81,85]. It is speculated that DNA-damaging therapy may be most active in tumors with germline BRCA mutations and in BRCA wild-type tumors that harbor the BRCAness phenotype.…”

Homologous recombination deficiency and host anti-tumor immunity in triple-negative breast cancer

“…The 'DDR deficiency assay' is a 44-gene expression signature derived to identify loss of the Fanconi anemia/BRCA DNA repair pathways [38]. In two independent datasets of patients treated with (neo)adjuvant fluorouracil, anthracycline and cyclophosphamide, the DDR deficiency assay was significantly associated with pCR and relapse-free survival.…”