title: Exon-array profiling unlocks clinically and biologically relevant gene signatures from formalin-fixed paraffin-embedded tumour samples.
abstract: BACKGROUND
  Degradation and chemical modification of RNA in formalin-fixed paraffin-embedded (FFPE) samples hamper their use in expression profiling studies. This study aimed to show that useful information can be obtained by Exon-array profiling archival FFPE tumour samples.
  
  
  METHODS
  Nineteen cervical squamous cell carcinoma (SCC) and 9 adenocarcinoma (AC) FFPE samples (10-16-year-old) were profiled using Affymetrix Exon arrays. The gene signature derived was tested on a fresh-frozen non-small cell lung cancer (NSCLC) series. Exploration of biological networks involved gene set enrichment analysis (GSEA). Differential gene expression was confirmed using Quantigene, a multiplex bead-based alternative to qRT-PCR.
  
  
  RESULTS
  In all, 1062 genes were higher in SCC vs AC, and 155 genes higher in AC. The 1217-gene signature correctly separated 58 NSCLC into SCC and AC. A gene network centered on hepatic nuclear factor and GATA6 was identified in AC, suggesting a role in glandular cell differentiation of the cervix. Quantigene analysis of the top 26 differentially expressed genes correctly partitioned cervix samples as SCC or AC.
  
  
  CONCLUSIONS
  FFPE samples can be profiled using Exon arrays to derive gene expression signatures that are sufficiently robust to be applied to independent data sets, identify novel biology and design assays for independent platform validation.
authors.affiliation: Translational Radiobiology Group, School of Cancer and Enabling Sciences, Manchester Academic Health Science Centre, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
authors.forename: J S
authors.initials: JS
authors.lastname: Hall
authors.forename: H S
authors.initials: HS
authors.lastname: Leong
authors.forename: L S C
authors.initials: LS
authors.lastname: Armenoult
authors.forename: G E
authors.initials: GE
authors.lastname: Newton
authors.forename: H R
authors.initials: HR
authors.lastname: Valentine
authors.forename: J J
authors.initials: JJ
authors.lastname: Irlam
authors.forename: C
authors.initials: C
authors.lastname: Möller-Levet
authors.forename: K A
authors.initials: KA
authors.lastname: Sikand
authors.forename: S D
authors.initials: SD
authors.lastname: Pepper
authors.forename: C J
authors.initials: CJ
authors.lastname: Miller
authors.forename: C M L
authors.initials: CM
authors.lastname: West
mesh_terms: D000230:Adenocarcinoma / Q000235:genetics / Q000473:pathology; D001706:Biopsy; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics / Q000473:pathology; D002294:Carcinoma, Squamous Cell / Q000145:classification / Q000235:genetics / Q000473:pathology; D005091:Exons; D005260:Female; D005404:Fixatives / Q000494:pharmacology; D005557:Formaldehyde / Q000494:pharmacology; D020869:Gene Expression Profiling; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D009369:Neoplasms / Q000235:genetics* / Q000473:pathology*; D016612:Paraffin Embedding / Q000379:methods; D013997:Time Factors; D016707:Tissue Fixation / Q000379:methods; D014021:Tissue Preservation / Q000379:methods*; D002583:Uterine Cervical Neoplasms / Q000145:classification / Q000235:genetics / Q000473:pathology
chemical_list: D005404:Fixatives; D005557:Formaldehyde