HOPE-Fixation of Lung Tissue Allows Retrospective Proteome and Phosphoproteome Studies

Hepes-glutamic
acid buffer-mediated organic solvent protection
effect (HOPE)-fixation has been introduced as an alternative to formalin
fixation of clinical samples. Beyond preservation of morphological
structures for histology, HOPE-fixation was demonstrated to be compatible
with recent methods for RNA and DNA sequencing. However, the suitability
of HOPE-fixed materials for the inspection of proteomes by mass spectrometry
so far remained undefined. This is of particular interest, since proteins
constitute a prime resource for drug research and can give valuable
insights into the activity status of signaling pathways. In this study,
we extracted proteins from human lung tissue and tested HOPE-treated
and snap-frozen tissues comparatively by proteome and phosphoproteome
analyses. High confident data from accurate mass spectrometry allowed
the identification of 2603 proteins and 3036 phosphorylation sites.
HOPE-fixation did not hinder the representative extraction of proteins,
and investigating their biochemical properties, covered subcellular
localizations, and cellular processes revealed no bias caused by the
type of fixation. In conclusion, proteome as well as phosphoproteome
data of HOPE lung samples were qualitatively equivalent to results
obtained from snap-frozen tissues. Thus, HOPE-treated tissues match
clinical demands in both histology and retrospective proteome analyses
of patient samples by proteomics.