title: Gene expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer.
abstract: BACKGROUND
  Systemic chemotherapy for operable breast cancer substantially decreases the risk of death. Patients often have de novo resistance or incomplete response to docetaxel, one of the most active agents in this disease. We postulated that gene expression profiles of the primary breast cancer can predict the response to docetaxel.
  
  
  METHODS
  We took core biopsy samples from primary breast tumours in 24 patients before treatment and then assessed tumour response to neoadjuvant docetaxel (four cycles, 100 mg/m2 daily for 3 weeks) by cDNA analysis of RNA extracted from biopsy samples using HgU95-Av2 GeneChip.
  
  
  RESULTS
  From the core biopsy samples, we extracted sufficient total RNA (3-6 microg) for cDNA array analysis using HgU95-Av2 GeneChip. Differential patterns of expression of 92 genes correlated with docetaxel response (p=0.001). Sensitive tumours had higher expression of genes involved in cell cycle, cytoskeleton, adhesion, protein transport, protein modification, transcription, and stress or apoptosis; whereas resistant tumours showed increased expression of some transcriptional and signal transduction genes. In leave-one-out cross-validation analysis, ten of 11 sensitive tumours (90% specificity) and 11 of 13 resistant tumours (85% sensitivity) were correctly classified, with an accuracy of 88%. This 92-gene predictor had positive and negative predictive values of 92% and 83%, respectively. Correlation between RNA expression measured by the arrays and semiquantitative RT-PCR was also ascertained, and our results were validated in an independent set of six patients.
  
  
  CONCLUSIONS
  If validated, these molecular profiles could allow development of a clinical test for docetaxel sensitivity, thus reducing unnecessary treatment for women with breast cancer.
authors.affiliation: Breast Center and the Departments of Medicine, Pathology, and Molecular and Cellular Biology, Baylor College of Medicine, and the Methodist Hospital, Houston, TX 77030, USA. jcchang@breastcenter.tmc.edu <jcchang@breastcenter.tmc.edu>
authors.forename: Jenny C
authors.initials: JC
authors.lastname: Chang
authors.forename: Eric C
authors.initials: EC
authors.lastname: Wooten
authors.forename: Anna
authors.initials: A
authors.lastname: Tsimelzon
authors.forename: Susan G
authors.initials: SG
authors.lastname: Hilsenbeck
authors.forename: M Carolina
authors.initials: MC
authors.lastname: Gutierrez
authors.forename: Richard
authors.initials: R
authors.lastname: Elledge
authors.forename: Syed
authors.initials: S
authors.lastname: Mohsin
authors.forename: C Kent
authors.initials: CK
authors.lastname: Osborne
authors.forename: Gary C
authors.initials: GC
authors.lastname: Chamness
authors.forename: D Craig
authors.initials: DC
authors.lastname: Allred
authors.forename: Peter
authors.initials: P
authors.lastname: O'Connell
mesh_terms: D000328:Adult; D000972:Antineoplastic Agents, Phytogenic / Q000627:therapeutic use*; D001707:Biopsy, Needle; D001940:Breast / Q000473:pathology; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics* / Q000473:pathology; D000077143:Docetaxel; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects / Q000235:genetics*; D052138:Genes, Neoplasm / Q000235:genetics; D006801:Humans; D020360:Neoadjuvant Therapy / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D017239:Paclitaxel / Q000031:analogs & derivatives* / Q000627:therapeutic use*; D011379:Prognosis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D043823:Taxoids; D016896:Treatment Outcome
chemical_list: D000972:Antineoplastic Agents, Phytogenic; D043823:Taxoids; D000077143:Docetaxel; D017239:Paclitaxel