title: Validation of gene signatures that predict the response of breast cancer to neoadjuvant chemotherapy: a substudy of the EORTC 10994/BIG 00-01 clinical trial.
abstract: BACKGROUND
  We have previously described gene-expression signatures that predict growth inhibitory and cytotoxic effects of common chemotherapeutic drugs in vitro. The aim of this study was to confirm the validity of these gene-expression signatures in a large series of patients with oestrogen-receptor-negative breast tumours who were treated in a phase III neoadjuvant clinical trial.
  
  
  METHODS
  This trial compares a non-taxane regimen (fluorouracil, epirubicin, and cyclophosphamide [FEC] for six cycles) with a taxane regimen (docetaxel for three cycles followed by epirubicin plus docetaxel [TET] for three cycles) in women with oestrogen-receptor-negative breast cancer. The primary endpoint of the study is the difference in progression-free survival based on TP53 status and will be reported later. Predicting response with gene signatures was a planned secondary endpoint of the trial and is reported here. Pathological complete response, defined as complete disappearance of the tumour with no more than a few scattered tumour cells detected by the pathologist in the resection specimen, was used to assess chemosensitivity. RNA was prepared from sections of frozen biopsies taken at diagnosis and hybridised to Affymetrix X3P microarrays. In-vitro single-agent drug sensitivity signatures were combined to obtain FEC and TET regimen-specific signatures. This study is registered on the clinical trials site of the US National Cancer Institute website http://www.clinicaltrials.gov/ct/show/NCT00017095.
  
  
  RESULTS
  Of 212 patients with oestrogen-receptor-negative tumours assessed, 87 patients were excluded. 125 oestrogen-receptor-negative tumours (55 that showed pathological complete responses) were tested: 66 in the FEC group (28 that showed pathological complete responses) and 59 in the TET group (27 that showed pathological complete responses). The regimen-specific signatures significantly predicted pathological complete response in patients treated with the appropriate regimen (p<0.0001). The FEC predictor had a sensitivity of 96% (27 of 28 patients [95% CI 82-99]), specificity of 66% (25 of 38 patients [50-79]), positive predictive value (PPV) of 68% (27 of 40 patients [52-80]), and negative predictive value (NPV) of 96% (25 of 26 patients [81-99]). The TET predictor had a sensitivity of 93% (25 of 27 patients [77-98]), specificity 69% (22 of 32 patients [51-82]), PPV of 71% (25 of 35 patients [55-84]), and NPV of 92% (22 of 24 patients [74-98]). Analysis of tumour size, grade, nodal status, age, and regimen-specific signatures showed that the genomic signatures were the only independent variables predicting pathological complete response at p<0.01. Selection of patients with these signatures would increase the proportion of patients with pathological complete responses from 44% to around 70% in the patients studied here.
  
  
  CONCLUSIONS
  We have validated the use of regimen-specific drug sensitivity signatures in the context of a multicentre randomised trial. The high NPV of both signatures may allow early selection of patients with breast cancer who should be considered for trials with new drugs.
authors.affiliation: Geneva University Hospital, Geneva, Switzerland; European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium; Swiss Group for Clinical Cancer Research (SAKK), Berne, Switzerland. Electronic address: bonnefoi@bergonie.org.
authors.forename: Hervé
authors.initials: H
authors.lastname: Bonnefoi
authors.affiliation: Duke Institute for Genome Sciences and Policy, and Duke University Medical Center, Durham, NC, USA.
authors.forename: Anil
authors.initials: A
authors.lastname: Potti
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), National Centre of Competence in Research (NCCR), Epalinges, Switzerland; Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Mauro
authors.initials: M
authors.lastname: Delorenzi
authors.affiliation: Bergonié Institute, Bordeaux, France.
authors.forename: Louis
authors.initials: L
authors.lastname: Mauriac
authors.affiliation: René Gauducheau Centre, Nantes, France.
authors.forename: Mario
authors.initials: M
authors.lastname: Campone
authors.affiliation: René Huguenin Centre, St-Cloud, France.
authors.forename: Michèle
authors.initials: M
authors.lastname: Tubiana-Hulin
authors.affiliation: Paul Strauss Centre, Strasbourg, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Petit
authors.affiliation: Paul Lamarque Centre, Montpellier, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Rouanet
authors.affiliation: Medical University, Gdansk, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Jassem
authors.affiliation: Henri Becquerel Centre, Rouen, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Blot
authors.affiliation: René Huguenin Centre, St-Cloud, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Becette
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), National Centre of Competence in Research (NCCR), Epalinges, Switzerland; Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland.
authors.forename: Pierre
authors.initials: P
authors.lastname: Farmer
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), National Centre of Competence in Research (NCCR), Epalinges, Switzerland.
authors.forename: Sylvie
authors.initials: S
authors.lastname: André
authors.affiliation: Duke Institute for Genome Sciences and Policy, and Duke University Medical Center, Durham, NC, USA.
authors.forename: Chaitanya R
authors.initials: CR
authors.lastname: Acharya
authors.affiliation: Duke Institute for Genome Sciences and Policy, and Duke University Medical Center, Durham, NC, USA.
authors.forename: Sayan
authors.initials: S
authors.lastname: Mukherjee
authors.affiliation: Anglo-Celtic Cooperative Oncology Group (ACCOG), Edinburgh University, Edinburgh, UK.
authors.forename: David
authors.initials: D
authors.lastname: Cameron
authors.affiliation: Swedish Breast Cancer Group (SweBCG), Karolinska Institute and Radiumhemmet, Karolinska University Hospital, Stockholm, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Bergh
authors.affiliation: Duke Institute for Genome Sciences and Policy, and Duke University Medical Center, Durham, NC, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Nevins
authors.affiliation: Swiss Institute for Experimental Cancer Research (ISREC), National Centre of Competence in Research (NCCR), Epalinges, Switzerland; University of St Andrews, Scotland, UK.
authors.forename: Richard D
authors.initials: RD
authors.lastname: Iggo
mesh_terms: D000328:Adult; D000368:Aged; D000971:Antineoplastic Combined Chemotherapy Protocols / Q000627:therapeutic use*; D001943:Breast Neoplasms / Q000737:chemistry / Q000175:diagnosis / Q000188:drug therapy* / Q000235:genetics; D017024:Chemotherapy, Adjuvant; D003520:Cyclophosphamide / Q000008:administration & dosage; D018572:Disease-Free Survival; D000077143:Docetaxel; D015251:Epirubicin / Q000008:administration & dosage; D005260:Female; D005472:Fluorouracil / Q000008:administration & dosage; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D008875:Middle Aged; D020360:Neoadjuvant Therapy; D009367:Neoplasm Staging; D020411:Oligonucleotide Array Sequence Analysis; D018579:Patient Selection; D011237:Predictive Value of Tests; D012372:ROC Curve; D011960:Receptors, Estrogen / Q000032:analysis; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D043823:Taxoids / Q000008:administration & dosage; D016896:Treatment Outcome
chemical_list: D011960:Receptors, Estrogen; D043823:Taxoids; D000077143:Docetaxel; D015251:Epirubicin; D003520:Cyclophosphamide; D005472:Fluorouracil