title: Utility of formalin-fixed, paraffin-embedded liver biopsy specimens for global proteomic analysis in nonalcoholic steatohepatitis.
abstract: OBJECTIVE
  To compare the proteomic profiles of formalin-fixed, paraffin-embedded (FFPE) liver biopsy material and matched frozen liver tissue from patients with nonalcoholic steatohepatitis (NASH).
  
  
  METHODS
  A label-free mass spectrometry-based approach was used to profile global protein expression in FFPE and frozen liver biopsy specimens from five patients with NASH.
  
  
  RESULTS
  Eight hundred and sixty proteins were identified with >75% confidence: 225 common proteins were identified in both the FFPE and frozen tissues, and an additional 142 and 493 proteins were identified in the FFPE and frozen tissues, respectively. Functional analyses revealed a general, nonspecific reduction in the number of proteins identified in FFPE tissue compared with frozen tissue. No bias toward proteins located in any specific subcellular compartments or implicated in any particular biological functions was observed. The relative abundance of several proteins with functions relating to the pathogenesis of NASH (peroxiredoxin-1, fatty acid binding protein 1, fatty acid synthase, vimentin, catalase, and glutathione S-transferase A1) was similar in FFPE and frozen liver tissues.
  
  
  CONCLUSIONS
  FFPE liver biopsy material from NASH patients can be used for global proteomic analysis and biomarker identification studies, although a universal reduction in the number of identified proteins compared with frozen tissue is likely.
authors.affiliation: Division of Gastroenterology/Hepatology, Indiana University, Indianapolis, IN 46202, USA. lnbell@iupui.edu
authors.forename: Lauren N
authors.initials: LN
authors.lastname: Bell
authors.forename: Romil
authors.initials: R
authors.lastname: Saxena
authors.forename: Samer G
authors.initials: SG
authors.lastname: Mattar
authors.forename: Jinsam
authors.initials: J
authors.lastname: You
authors.forename: Mu
authors.initials: M
authors.lastname: Wang
authors.forename: Naga
authors.initials: N
authors.lastname: Chalasani
mesh_terms: D015415:Biomarkers / Q000032:analysis; D001706:Biopsy; D002853:Chromatography, Liquid; D005234:Fatty Liver / Q000175:diagnosis* / Q000473:pathology; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D005615:Freezing; D055106:Genome-Wide Association Study; D006801:Humans; D008099:Liver / Q000737:chemistry*; D065626:Non-alcoholic Fatty Liver Disease; D016612:Paraffin Embedding / Q000379:methods; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D013194:Staining and Labeling / Q000379:methods* / Q000706:statistics & numerical data; D053719:Tandem Mass Spectrometry
chemical_list: D015415:Biomarkers; D005404:Fixatives; D011506:Proteins; D005557:Formaldehyde