Genomic signatures for paclitaxel and gemcitabine resistance in breast cancer derived by machine learning. Issue 1 (22nd August 2015)

• Record Type: Journal Article
• Authors: Dorman, Stephanie N.; Baranova, Katherina; Knoll, Joan H.M.; Urquhart, Brad L.; Mariani, Gabriella; Carcangiu, Maria Luisa; Rogan, Peter K.
• Is Part Of: Molecular oncology. Volume 10:Issue 1(2016:Jan.)
• Page Start: 85
• Page End: 100
• Publication Date: 2015-08-22
• Subjects: Paclitaxel -- Gemcitabine -- Resistance -- Drug sensitivity -- Genomic profiles -- Breast cancer; Cancer -- Molecular aspects -- Periodicals; 616.994005
• DOI: 10.1016/j.molonc.2015.07.006
• Languages: English
• ISSNs: 1574-7891

Abstract

Abstract : Increasingly, the effectiveness of adjuvant chemotherapy agents for breast cancer has been related to changes in the genomic profile of tumors. We investigated correspondence between growth inhibitory concentrations of paclitaxel and gemcitabine (GI50) and gene copy number, mutation, and expression first in breast cancer cell lines and then in patients. Genes encoding direct targets of these drugs, metabolizing enzymes, transporters, and those previously associated with chemoresistance to paclitaxel (n = 31 genes) or gemcitabine (n = 18) were analyzed. A multi‐factorial, principal component analysis (MFA) indicated expression was the strongest indicator of sensitivity for paclitaxel, and copy number and expression were informative for gemcitabine. The factors were combined using support vector machines (SVM). Expression of 15 genes (ABCC10, BCL2, BCL2L1, BIRC5, BMF, FGF2, FN1, MAP4, MAPT, NFKB2, SLCO1B3, TLR6, TMEM243, TWIST1, and CSAG2) predicted cell line sensitivity to paclitaxel with 82% accuracy. Copy number profiles of 3 genes (ABCC10, NT5C, TYMS) together with expression of 7 genes (ABCB1, ABCC10, CMPK1, DCTD, NME1, RRM1, RRM2B), predicted gemcitabine response with 85% accuracy. Expression and copy number studies of two independent sets of patients with known responses were then analyzed with these models. These included tumor blocks from 21 patients that were treated with both paclitaxel and gemcitabine, and 319 patients on paclitaxel and anthracycline therapy. A new paclitaxel SVM was derived from an 11‐gene subset since data for 4 of the original genes was unavailable. The accuracy of this SVM was similar in cell lines and tumor blocks (70–71%). The gemcitabine SVM exhibited 62% prediction accuracy for the tumor blocks due to the presence of samples with poor nucleic acid integrity. Nevertheless, the paclitaxel SVM predicted sensitivity in 84% of patients with no or minimal residual disease. Highlights: Cell line genomic signatures of paclitaxel and gemcitabine resistance were derived. Paclitaxel signature accurately predicts resistant cell lines with 82% accuracy. Gemcitabine signature accurately predicts resistant cell lines with 84% accuracy. Paclitaxel signature predicted sensitive patients with 84% accuracy. Gemcitabine signature predicted response in FFPE tumor blocks with 62% accuracy.