title: Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores.
abstract: BACKGROUND
  Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection.
  
  
  METHODS
  In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR.
  
  
  RESULTS
  Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan(R) Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient.
  
  
  CONCLUSIONS
  We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen.
authors.affiliation: Department of Clinical Research, University of Bern, Murtenstrasse 35, CH-3010 Bern, Switzerland. martina.schobesberger@dkf.unibe.ch
authors.forename: Martina
authors.initials: M
authors.lastname: Schobesberger
authors.forename: Anna
authors.initials: A
authors.lastname: Baltzer
authors.forename: Andrea
authors.initials: A
authors.lastname: Oberli
authors.forename: Andreas
authors.initials: A
authors.lastname: Kappeler
authors.forename: Mathias
authors.initials: M
authors.lastname: Gugger
authors.forename: Hana
authors.initials: H
authors.lastname: Burger
authors.forename: Rolf
authors.initials: R
authors.lastname: Jaggi
mesh_terms: D001940:Breast; D001943:Breast Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D018270:Carcinoma, Ductal, Breast / Q000175:diagnosis / Q000235:genetics / Q000473:pathology; D002285:Carcinoma, Intraductal, Noninfiltrating / Q000175:diagnosis / Q000235:genetics / Q000473:pathology; D049109:Cell Proliferation; D005260:Female; D018734:Genes, erbB-2; D014644:Genetic Variation; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D011379:Prognosis; D012334:RNA, Neoplasm / Q000032:analysis / Q000302:isolation & purification; D011960:Receptors, Estrogen / Q000235:genetics
chemical_list: D012334:RNA, Neoplasm; D011960:Receptors, Estrogen