Purpose To identify biomarkers within the breast cancer genome that may predict chemosensitivity in breast cancer. Introduction Expression array analyses in breast cancer have revealed multiple subtypes of breast cancer, each with distinct clinical prognosis and response to treatments (1C4). Every tumor acquires a complex combination of somatic mutations that contribute to the cancer phenotype. Large-scale sequencing of multiple cancers has reported thousands of genes that have low frequency mutation rates in cancer (5C9). This poses a tremendous challenge for finding novel therapeutic targets and identifying patient subgroups that may benefit from specific treatment regimens. Furthermore, besides sequence mutations, there are numerous chromosomal alterations, copy number variations, miRNA dysregulations, and epigenetic events that are frequently found in human cancers (10C12). Successful therapy depends on the identification of critical genes in the oncogenic network where pharmacologic inhibition can result in death of cancer cells while sparing normal cells. Clinical trials in breast cancer so far have often shown that the most effective treatment is when chemotherapy is combined with targeted therapies rather than chemotherapy or targeted therapies alone (13C15). We used a combinatorial approach using RNA interference (RNAi; short hairpin RNA; shRNA) against a cohort of candidate breast cancer genes identified via whole-genome cancer sequencing along with docetaxel to identify gene targets whose loss-of-function would augment chemosensitivity. We conducted the chemosensitivity screen against a well-characterized estrogen receptorCnegative, progesterone receptorCnegative, and Her2-negative (ER?PR?Her2?), “triple-negative,” claudin-low breast cancer cell line, MDA-MB-231, as it represents the clinical subtype that has the worst prognosis (16, 17). We used docetaxel as it is one of the most 86307-44-0 IC50 common chemotherapies given for breast cancer. Although response rates are high to taxanes, toxicities including neuropathy and myelosuppression often preclude use of these drugs at high doses or for prolonged periods of time. Identification of novel targets that would enhance docetaxel chemosensitivity and enable lower effective dosages may allow patients a better quality of life and perhaps improved prognosis. Materials and Methods Cells MDA-MB-231, HCC38, Hs578T, and MCF7 cells were kindly provided by M. White (Department of Cell Biology, University of Texas Southwestern Medical 86307-44-0 IC50 School, Dallas, TX). T47D and HCC1428 cells were 86307-44-0 IC50 kindly provided by G. Pearson (Department of Pharmacology, Simmons Comprehensive Cancer Center, Dallas, TX). HME2424 cells were a gift from D. Euhus and were originally immortalized by retroviral infection with human telomerase reverse transcriptase (hTERT) by D. Euhus (Department of Surgery, Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX). The 2800delAA of in HME2424 was sequence verified. SUM190PT cells were purchased from Asterand. HCC1937 cells were originally derived by A. Gazdar (University of Texas Southwestern Medical Center, Dallas, TX) and are available from American Type Culture Collection (ATCC) Cell Systems. Human mammary epithelial cells (HMEC; HME1) were originally 86307-44-0 IC50 immortalized by retroviral infection with hTERT by J.W. Shay (University of Texas Southwestern Medical Center, Dallas, TX) and 86307-44-0 IC50 are available from ATCC Cell Systems (Gaithsburg, MD). HME50 cells were originally derived by J.W. Shay from the noncancerous breast tissue of a female diagnosed with Li-Fraumeni syndrome as previously described (18). BMP7 The missense mutation (M133T) in HME50 was sequence verified. All cancer cell lines were cultured in basal medium supplemented with 10% fetal calf serum. All benign cells were cultured in serum-free conditions as described elsewhere (19). Chemicals Doxorubicin and docetaxel were obtained from Sigma. PP2 and SB203580 were obtained from Tocris Bioscience. Expression array analysis and statistics Five publically available breast cancer expression datasets (3, 20, 21) were separately normalized then pooled for analysis (=.