title: Gene expression pathway analysis to predict response   to neoadjuvant docetaxel and capecitabine for breast cancer.
abstract: Neoadjuvant chemotherapy has been shown to be equivalent to post-operative treatment for breast cancer, and allows for assessment of chemotherapy response. In a pilot trial of docetaxel (T) and capecitabine (X) neoadjuvant chemotherapy for Stage II/III BC, we assessed correlation between baseline gene expression and tumor response to treatment, and examined changes in gene expression associated with treatment. Patients received four cycles of TX. Tumor tissue obtained from Mammotome core biopsies pretreatment (BL) and post-cycle 1 (C1) of TX was FLash frozen and stored at -70 degrees C until processing. Gene expression analysis utilized Affymetrix HG-U133 Plus 2.0 GeneChip arrays. Statistical analysis was performed using BRB Array Tools after RMA normalization. Gene ontology (GO) pathway analysis used random variance t tests with a significance level of P\0.005. For gene categories identified byGO pathway analysis as significant, expression levels of individual genes within those pathways were compared between classes using univariate t tests; those genes with significance level of P\0.05 were reported. PAM50 analyses were performed on tumor samples to investigate biologic subtype and risk of relapse (ROR). Using GO pathway analysis, 39 gene categories discriminated between responders and non-responders,most notably genes involved in microtubule assembly and regulation. When comparing pre- and post-chemotherapy specimens, we identified 71 differentially expressed gene categories, including DNA repair and cell proliferation regulation. There were 45 GO pathways in which the change in expression after one cycle of chemotherapy was significantly different among responders and nonresponders. The majority of tumor samples fell into the basal like and luminal B categories. ROR scores decreased in response to chemotherapy; this change was more evident in samples from patients classified as responders by clinical criteria. GO pathway analysis identified a number of gene categories pertinent to therapeutic response, and may be an informative method for identifying genes important in response to chemotherapy. Larger studies using the methods described here are necessary to fully evaluate gene expression changes in response to chemotherapy.
authors.affiliation: Division of Medical Oncology, Department of Medicine University of Washington/Seattle Cancer Care Alliance, G3639, 825 Eastlake Ave, E, Seattle, WA 98109, USA. lkorde@u.washington.edu
authors.forename: Larissa A
authors.initials: LA
authors.lastname: Korde
authors.forename: Lara
authors.initials: L
authors.lastname: Lusa
authors.forename: Lisa
authors.initials: L
authors.lastname: McShane
authors.forename: Peter F
authors.initials: PF
authors.lastname: Lebowitz
authors.forename: LuAnne
authors.initials: L
authors.lastname: Lukes
authors.forename: Kevin
authors.initials: K
authors.lastname: Camphausen
authors.forename: Joel S
authors.initials: JS
authors.lastname: Parker
authors.forename: Sandra M
authors.initials: SM
authors.lastname: Swain
authors.forename: Kent
authors.initials: K
authors.lastname: Hunter
authors.forename: Jo Anne
authors.initials: JA
authors.lastname: Zujewski
mesh_terms: D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use*; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics* / Q000473:pathology; D000069287:Capecitabine; D016000:Cluster Analysis; D003841:Deoxycytidine / Q000008:administration & dosage / Q000031:analogs & derivatives; D000077143:Docetaxel; D019008:Drug Resistance, Neoplasm / Q000235:genetics*; D005472:Fluorouracil / Q000008:administration & dosage / Q000031:analogs & derivatives; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D020360:Neoadjuvant Therapy; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D010865:Pilot Projects; D043823:Taxoids / Q000008:administration & dosage
chemical_list: D043823:Taxoids; D003841:Deoxycytidine; D000077143:Docetaxel; D000069287:Capecitabine; D005472:Fluorouracil