Cancer Diagnosis Program | Biorepositories and Biospecimen Research Branch

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Total RNA yield and microarray gene expression profiles from fine-needle aspiration biopsy and core-needle biopsy samples of breast carcinoma.

Author(s): Symmans WF, Ayers M, Clark EA, Stec J, Hess KR, Sneige N, Buchholz TA, Krishnamurthy S, Ibrahim NK, Buzdar AU, Theriault RL, Rosales MF, Thomas ES, Gwyn KM, Green MC, Syed AR, Hortobagyi GN, Pusztai L

Publication: Cancer, 2003, Vol. 97, Page 2960-71

PubMed ID: 12784330 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   This study compared the cellular make-up and gene expression of CNB and FNA specimens of breast carcinoma. Of the 68 patients, 48 underwent 23 or 25-gauge FNA only, three patients underwent 14-gauge CNB only, and 17 patients underwent both FNA and CNB. Four FNA specimens were obtained from each patient; the first was prepared as Diff-Quick cytological smears, two were placed in RNAlater and frozen at -80˚C after 20 min, and one was snap-frozen and placed at -80˚C. Of the six CNB collected from each patient, three were formalin-fixed and paraffin-embedded (FFPE), two were placed in RNAlater and frozen at -80˚C after 20 min, and one was snap-frozen and stored at -80˚C. RNA was extracted from specimens stored in RNAlater using the RNeasy kit and quality was assessed by Bioanalyzer. Expression was evaluated using Millennium Pharmaceuticals high density cDNA microarrays in 38 FNA and 12 CNBs (10 matched cases). 

   Summary of Findings:

   Compared to the FNA specimens, CNB specimens contained more stromal cells (30% versus 5%) and fewer tumor cells (50% versus 80%). Two FNA and one CNB did not contain adequate cellularity and thus were not used for RNA extraction.  Eleven FNA and two CNB in RNAlater resulted in RNA of insufficient quality for hybridization and RNA of sufficient quality was obtained in a follow-up extraction of a second biopsy for only two FNA and one CNB The RNA yield was comparable from FNA and CNB specimens (mean of 3.6 µg and 2.8 µg, respectively) and RNA of sufficient quality was obtained from 46 of the 65 (71%) FNA and 15 of the 20 (75%) CNB.  The correlation in gene expression between matched CNB and FNA ranged from 0.34-0.90. While expression in seven of the 10 pairs clustered by patient, the remaining three did not cluster by patient. Interestingly, the three CNB that did not cluster with their respective FNA had comparable stromal content and histopathologic appearance to CNB that clustered with their respective FNA. Fifty-one genes were found to have consistently higher expression in CNB than FNA which consisted mostly of genes expressed in nonlymphoid stromal cells, smooth muscle cells, histiocytes, and adipocytes and those involved in angiogenesis, fibrosis, tissue remodeling, myocontractility, and phagocytosis. However, the three CNB with the lowest proportion of stromal calls and those with the highest had comparable expression of these 51 genes. Analysis of published microarray data from 78 patients with invasive breast carcinoma showed that expression of 120 stromal genes was not found to be different between patients who developed metastasis within five years and those who did not develop metastasis within five years. 

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin
   • Frozen
   • RNAlater

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   Cell count/volume	H-and-E microscopy
   Cell count/volume	Light microscopy
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Method of tissue acquisition	Core needle biopsy Fine needle aspiration

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