title: The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers.
abstract: BACKGROUND
  DNA microarray analysis has great potential to become an important clinical tool to individualize prognostication and treatment for breast cancer patients. However, with any emerging technology, there are many variables one must consider before bringing the technology to the bedside. There are already concerted efforts to standardize protocols and to improve reproducibility of DNA microarray. Our study examines one variable that is often overlooked, the timing of tissue acquisition, which may have a significant impact on the outcomes of DNA microarray analyses especially in studies that compare microarray data based on biospecimens taken in vivo and ex vivo.
  
  
  METHODS
  From 16 patients, we obtained paired fine needle aspiration biopsies (FNABs) of breast cancers taken before (PRE) and after (POST) their surgeries and compared the microarray data to determine the genes that were differentially expressed between the FNABs taken at the two time points. qRT-PCR was used to validate our findings. To examine effects of longer exposure to hypoxia on gene expression, we also compared the gene expression profiles of 10 breast cancers from clinical tissue bank.
  
  
  RESULTS
  Using hierarchical clustering analysis, 12 genes were found to be differentially expressed between the FNABs taken before and after surgical removal. Remarkably, most of the genes were linked to FOS in an early hypoxia pathway. The gene expression of FOS also increased with longer exposure to hypoxia.
  
  
  CONCLUSIONS
  Our study demonstrated that the timing of fine needle aspiration biopsies can be a confounding factor in microarray data analyses in breast cancer. We have shown that FOS-related genes, which have been implicated in early hypoxia as well as the development of breast cancers, were differentially expressed before and after surgery. Therefore, it is important that future studies take timing of tissue acquisition into account.
authors.affiliation: Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Canada. viettyw@uhnresearch.ca
authors.forename: Vietty
authors.initials: V
authors.lastname: Wong
authors.forename: Dong-Yu
authors.initials: DY
authors.lastname: Wang
authors.forename: Keisha
authors.initials: K
authors.lastname: Warren
authors.forename: Supriya
authors.initials: S
authors.lastname: Kulkarni
authors.forename: Scott
authors.initials: S
authors.lastname: Boerner
authors.forename: Susan Jane
authors.initials: SJ
authors.lastname: Done
authors.forename: Wey Liang
authors.initials: WL
authors.lastname: Leong
mesh_terms: D000328:Adult; D014408:Biomarkers, Tumor; D044963:Biopsy, Fine-Needle / Q000379:methods*; D001940:Breast / Q000378:metabolism / Q000473:pathology; D001943:Breast Neoplasms / Q000235:genetics*; D015687:Cell Hypoxia; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D016762:Genes, fos; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013997:Time Factors
chemical_list: D014408:Biomarkers, Tumor