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

Most chemotherapy regimens used for breast cancer in the adjuvant, neoadjuvant, or advanced settings contain agents that directly damage DNA, such as anthracyclines (epirubicin or doxorubicin) and alkylating agents (cyclophosphamide). Approximately 20% to 40% of early breast cancer patients have a complete clinical response and 10% have a complete pathological response (pCR) to these regimens (1–3), most likely because of a deficiency in normal DNA damage response (DDR) pathways (4,5). Many patients, however, do not respond and may not gain any benefit from this type of chemotherapy. In spite of this, there is no reliable method for predicting DDR deficiency from diagnostic material for the purpose of patient treatment selection. One of the major DDR pathways disrupted in breast cancer is the Fanconi anemia (FA)/BRCA pathway (6). This pathway was first described as lost in a rare autosomal recessive condition characterized by extreme sensitivity to DNA-damaging agents (7). The FA/BRCA pathway coordinates the repair of stalled DNA replication after DNA damage and is therefore important for cancer cell survival after therapeutic DNA-damaging agents such as anthracyclines and cyclophosphamide (5,8). It is estimated to be deficient in approximately 25% of breast cancer patients through mutation or epigenetic silencing of several key components, including the BRCA1 and BRCA2 genes (9). Although identification of FA/BRCA pathway–deficient, and therefore DDR-deficient, tumors could allow the selection of patients for anthracycline/cyclophosphamide–based chemotherapy treatment, the multiple mechanisms through which the pathway can be lost has made it difficult to develop assays suitable for clinical use. In this study, it was hypothesized that although the FA/BRCA pathway can be compromised by multiple mutational or epigenetic events, the resultant accumulation of DNA damage might activate common genetic processes, thereby defining a distinct molecular subgroup. Furthermore, an assay that identified this subgroup could predict which patients would benefit from chemotherapy. Taking this approach, a novel DDR deficiency (DDRD) assay that can be applied prospectively to patient samples has been developed and independently validated.