The effects of timing of fine needle aspiration biopsies on gene expression profiles in breast cancers.

Author(s): Wong V, Wang DY, Warren K, Kulkarni S, Boerner S, Done SJ, Leong WL

Publication: BMC Cancer, 2008, Vol. 8, Page 277

PubMed ID: 18826606 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to assess the effect of surgery on gene expression by comparing sixteen case-matched biopsy specimens collected before surgery with those collected after surgical resection. Gene expression was quantified by microarray and validated by real-time quantitative RT-PCR (qRT-PCR).

   Summary of Findings:

   Of the 4, 056 cDNA probes evaluated by microarray, 14 probes differed among biopsies procured before surgery and those procured from surgically resected specimens. Hierarchical clustering analysis revealed 12 unique genes (CDC42, SLC25A20, CSRP2, CSTA, COX7A2, LOC145758, UBE2Q2, AKAP13, SAT1, MEF2C, FOS, TMEM49) and an expressed sequence tag that differed among biopsies procured before or after surgical resection. Using PathwayAssist software, 9 of the 12 genes were linked directly or indirectly to the gene FOS.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • None (Fresh)

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   RNA	Real-time qRT-PCR
   Protein	Immunohistochemistry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Time of biospecimen collection	Before surgery Post surgical excision
   Real-time qRT-PCR Specific	Targeted nucleic acid	FOS GAPDH
   DNA microarray Specific	Targeted nucleic acid	CDC42 SLC25A20 CSRP2 CSTA COX7A2 EST LOC145758 UBE2Q2 AKAP13 SAT1 MEF2C FOS TMEM49

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2. Study Purpose

   In order to determine if the differences in gene expression observed among case-matched biopsy specimens collected pre- and post-surgery were attributable to differences in cold ischemia, analysis of FOS expression was expanded to include 10 biobanked breast specimens subjected to at least 30 min of cold ischemia prior to frozen storage. Importantly, specimens procured prospectively were collected as fine needle aspirates and processed immediately, while retrospective biobanked specimens were surgically resected and stored at an unspecified temperature for an unspecified period of time.

   Summary of Findings:

   FOS expression was significantly higher both in specimens procured after surgical resection and those that were biobanked after a minimum of 30 min of cold ischemia when compared to those procured before surgery. Findings were verified by qRT-PCR. The authors infer that FOS expression is sensitive to cold ischemia.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   RNA	Real-time qRT-PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Time of biospecimen collection	Before surgery Post surgical excision
   Biospecimen Acquisition	Cold ischemia time	0 min > 30 min Not specified
   DNA microarray Specific	Targeted nucleic acid	FOS
   Real-time qRT-PCR Specific	Targeted nucleic acid	FOS
   Biospecimen Acquisition	Method of tissue acquisition	Fine needle aspiration Surgical resection

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