Toward improving the proteomic analysis of formalin-fixed, paraffin-embedded tissue

Abstract

Archival formalin-fixed, paraffin-embedded (FFPE) tissue and their associated diagnostic records represent an invaluable source of retrospective proteomic information on diseases for which the clinical outcome and response to treatment are known. However, analysis of archival FFPE tissues by high-throughput proteomic methods has been hindered by the adverse effects of formaldehyde fixation and subsequent tissue histology. This review examines recent methodological advances for extracting proteins from FFPE tissue suitable for proteomic analysis. These methods, based largely upon heat-induced antigen retrieval techniques borrowed from immunohistochemistry, allow at least a qualitative analysis of the proteome of FFPE archival tissues. The authors also discuss recent advances in the proteomic analysis of FFPE tissue; including liquid-chromatography tandem mass spectrometry, reverse phase protein microarrays and imaging mass spectrometry.

Keywords::

• antigen retrieval
• formalin-fixed, paraffin-embedded
• liquid chromatography-tandem mass spectrometry
• matrix-assisted, laser desorption/ionization-imaging mass spectrometry
• protein extraction
• proteomics
• reverse-phase protein array

Financial & competing interests disclosure

The authors have been funded, in part, with federal funds under grant 1R21 CA134359 from the NCI Innovative Molecular Analysis Technologies (IMAT) Program, and the Veterans Health Administration under a Merit Review award. The content of this publication does not necessarily reflect the views or policies of the Veterans Health Administration nor does the mention of trade names, commercial products or organization(s) imply endorsement by the US Government. The authors are named as co-inventors in patent number US 8,288,122 B2, ‘pressure-assisted molecular recovery (PAMR) of biomolecules, pressure-assisted antigen retrieval (PAAR) and pressure-assisted tissue histology (PATH)’. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.