title: Proteomic analysis of laser-captured paraffin-embedded tissues: a molecular portrait of head and neck cancer progression.
abstract: OBJECTIVE
  Squamous cell carcinoma of the head and neck (HNSCC), the sixth most prevalent cancer among men worldwide, is associated with poor prognosis, which has improved only marginally over the past three decades. A proteomic analysis of HNSCC lesions may help identify novel molecular targets for the early detection, prevention, and treatment of HNSCC.
  
  
  METHODS
  Laser capture microdissection was combined with recently developed techniques for protein extraction from formalin-fixed paraffin-embedded (FFPE) tissues and a novel proteomics platform. Approximately 20,000 cells procured from FFPE tissue sections of normal oral epithelium and well, moderately, and poorly differentiated HNSCC were processed for mass spectrometry and bioinformatic analysis.
  
  
  RESULTS
  A large number of proteins expressed in normal oral epithelium and HNSCC, including cytokeratins, intermediate filaments, differentiation markers, and proteins involved in stem cell maintenance, signal transduction, migration, cell cycle regulation, growth and angiogenesis, matrix degradation, and proteins with tumor suppressive and oncogenic potential, were readily detected. Of interest, the relative expression of many of these molecules followed a distinct pattern in normal squamous epithelia and well, moderately, and poorly differentiated HNSCC tumor tissues. Representative proteins were further validated using immunohistochemical studies in HNSCC tissue sections and tissue microarrays.
  
  
  CONCLUSIONS
  The ability to combine laser capture microdissection and in-depth proteomic analysis of FFPE tissues provided a wealth of information regarding the nature of the proteins expressed in normal squamous epithelium and during HNSCC progression, which may allow the development of novel biomarkers of diagnostic and prognostic value and the identification of novel targets for therapeutic intervention in HNSCC.
authors.affiliation: Oral and Pharyngeal Cancer Branch, National Institute of Craniofacial and Dental Research, NIH, Bethesda, Maryland 20892, USA.
authors.forename: Vyomesh
authors.initials: V
authors.lastname: Patel
authors.forename: Brian L
authors.initials: BL
authors.lastname: Hood
authors.forename: Alfredo A
authors.initials: AA
authors.lastname: Molinolo
authors.forename: Norman H
authors.initials: NH
authors.lastname: Lee
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Conrads
authors.forename: John C
authors.initials: JC
authors.lastname: Braisted
authors.forename: David B
authors.initials: DB
authors.lastname: Krizman
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Veenstra
authors.forename: J Silvio
authors.initials: JS
authors.lastname: Gutkind
mesh_terms: D000368:Aged; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D019295:Computational Biology; D018450:Disease Progression; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D006258:Head and Neck Neoplasms / Q000235:genetics*; D006801:Humans; D007150:Immunohistochemistry; D007834:Lasers; D008297:Male; D042282:Microdissection; D008875:Middle Aged; D016612:Paraffin Embedding; D040901:Proteomics / Q000379:methods