Background The lack of standardized guidelines for
protein analysis of archival tissues (AT) seems to have
hampered the use of such samples in molecular analyses.
IMPACTS is a new European consortium aiming to
establish guidelines for AT analyses. Here we focus on the
evaluation of protein analysis in AT, fixed with formalin or
new fixatives, for research and diagnostic use.
Methods Tissue samples were fixed with formalin (FFPE)
or a new fixative (FineFix, Milestone Srl) and inspected by
histology. Five sections from three matched samples of
each tissue were distributed within the consortium in order
to compare the efficiency of protein recovery by immunohistochemistry,
Western blot, and protein lysate microarray
technology.
Results By applying an optimized protocol, proteins can be
successfully extracted from FFPE and FineFix tissues.
Moreover, we could show a correlation between immunohistochemical,
Western blot, and protein lysate microarray
results for each of the tissue fixation procedures. Differences
between methods, however, were observed in the
total protein yield and staining intensities for antibodies
detecting membrane proteins, including E-cadherin, EGFR,
and HER2.
Conclusion(s) Analysing proteins from fixed tissue samples
can provide critical information for clinical decision
making. Although long-term studies for formalinsubstitutes
such as FineFix are still missing, formalin-free
tissue fixation represents a reliable alternative for protein
preservation, regarding quality and quantity, as compared to
FFPE tissue. The IMPACTS consortium is working towards
evaluating AT sample processing for protein analysis and
tap into the vast treasure chest of archived samples