Utility of formalin-fixed, paraffin-embedded liver biopsy specimens for global proteomic analysis in nonalcoholic steatohepatitis

Lauren N. Bell, Romil Saxena, Samer G. Mattar, Jinsam You, Mu Wang, Naga Chalasani

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

Purpose: 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). Experimental design: 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 and clinical relevance: 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.

Original languageEnglish
Pages (from-to)397-404
Number of pages8
JournalProteomics - Clinical Applications
Volume5
Issue number7-8
DOIs
StatePublished - Aug 2011

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Biopsy
Liver
Paraffin
Proteomics
Formaldehyde
Tissue
Proteins
Peroxiredoxins
Fatty Acid Synthases
Fatty Acid-Binding Proteins
Non-alcoholic Fatty Liver Disease
Biomarkers
Vimentin
Glutathione Transferase
Catalase
Design of experiments
Mass spectrometry
Labels
Mass Spectrometry
Research Design

Keywords

  • Biomarkers
  • Formalin-fixed
  • Mass spectrometry
  • Nonalcoholic steatohepatitis
  • Paraffin-embedded

ASJC Scopus subject areas

  • Clinical Biochemistry

Cite this

Utility of formalin-fixed, paraffin-embedded liver biopsy specimens for global proteomic analysis in nonalcoholic steatohepatitis. / Bell, Lauren N.; Saxena, Romil; Mattar, Samer G.; You, Jinsam; Wang, Mu; Chalasani, Naga.

In: Proteomics - Clinical Applications, Vol. 5, No. 7-8, 08.2011, p. 397-404.

Research output: Contribution to journalArticle

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