title: Differentially expressed genes in window trials are influenced by the wound-healing process: lessons learned from a pilot study with anastrozole.
abstract: BACKGROUND
  Perioperative window trials provide an opportunity to obtain intact tumor samples at two different time-points for evaluation of potential surrogate biomarkers. We report results of a pilot trial designed to determine if treatment-mediated changes in gene expression can be detected in formalin-fixed paraffin-embedded (FFPE) samples after 10-d exposure to anastrozole in estrogen receptor (ER)-positive breast cancer compared with untreated controls.
  
  
  METHODS
  Paired tumor samples (biopsy, surgical) were obtained from 26 postmenopausal women with ER-positive breast cancer. Patients were assigned anastrozole (1 mg/d) for 10 d immediately prior to surgery (13 cases) or no treatment (13 controls). Five hundred two cancer-related genes were examined by the Illumina cDNA-mediated annealing, selection, extension, and ligation, FFPE cDNA array (moderated t-test, P ≤ 0.005). Surrogate biomarkers reflecting changes in gene expression were examined by immunohistochemistry (Wilcoxon rank-based test, P < 0.05).
  
  
  RESULTS
  Sufficient RNA was available from 19 paired samples (8 controls, 11 cases). Frozen tissue and FFPE showed good correlation (r = 0.82). Within each group, 18 genes, reflecting roles in proliferation, angiogenesis, and apoptosis, showed differential expression from biopsy to surgery (P < 0.005). Estrogen-related genes were dysregulated in the treated group only. A reduction in Ki-67 was observed in 7 (54%) treated cases and in 1 (7.7%) control patient.
  
  
  CONCLUSIONS
  10-d exposure to anastrozole resulted in dysregulation of 18/502 cancer-related genes, and Ki-67 was reduced in 54% of cases. FFPE samples demonstrated good correlation with frozen samples. However, changes in gene expression and increased Ki-67 in the control group suggest local effects of wound healing may represent a confounding factor in the interpretation of perioperative window trials.
authors.affiliation: Breast Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
authors.forename: Mary
authors.initials: M
authors.lastname: Morrogh
authors.forename: Victor P
authors.initials: VP
authors.lastname: Andrade
authors.forename: Asawari J
authors.initials: AJ
authors.lastname: Patil
authors.forename: Li-Xuan
authors.initials: LX
authors.lastname: Qin
authors.forename: Qianxing
authors.initials: Q
authors.lastname: Mo
authors.forename: Rita
authors.initials: R
authors.lastname: Sakr
authors.forename: Crispinita D
authors.initials: CD
authors.lastname: Arroyo
authors.forename: Edi
authors.initials: E
authors.lastname: Brogi
authors.forename: Monica
authors.initials: M
authors.lastname: Morrow
authors.forename: Tari A
authors.initials: TA
authors.lastname: King
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000077384:Anastrozole; D018952:Antigens, CD34 / Q000378:metabolism; D047072:Aromatase Inhibitors / Q000494:pharmacology; D014408:Biomarkers, Tumor / Q000378:metabolism; D001943:Breast Neoplasms / Q000378:metabolism* / Q000473:pathology / Q000601:surgery; D004305:Dose-Response Relationship, Drug; D005260:Female; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects* / Q000502:physiology*; D006801:Humans; D019394:Ki-67 Antigen / Q000378:metabolism; D008875:Middle Aged; D009570:Nitriles / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D010865:Pilot Projects; D057234:Preoperative Period; D014230:Triazoles / Q000494:pharmacology*; D014945:Wound Healing / Q000187:drug effects* / Q000502:physiology*
chemical_list: D018952:Antigens, CD34; D047072:Aromatase Inhibitors; D014408:Biomarkers, Tumor; D019394:Ki-67 Antigen; D009570:Nitriles; D014230:Triazoles; D000077384:Anastrozole