title: Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation.
abstract: Qualitative proteome profiling of formalin-fixed, paraffin-embedded (FFPE) tissue is advancing the field of clinical proteomics. However, quantitative proteome analysis of FFPE tissue is hampered by the lack of an efficient labelling method. The usage of conventional protein labelling on FFPE tissue has turned out to be inefficient. Classical labelling targets lysine residues that are blocked by the formalin treatment. The aim of this study was to establish a quantitative proteomics analysis of FFPE tissue by combining the label-free approach with optimised protein extraction and separation conditions. As a model system we used FFPE heart tissue of control and exposed C57BL/6 mice after total body irradiation using a gamma ray dose of 3 gray. We identified 32 deregulated proteins (p≤0.05) in irradiated hearts 24h after the exposure. The proteomics data were further evaluated and validated by bioinformatics and immunoblotting investigation. In good agreement with our previous results using fresh-frozen tissue, the analysis indicated radiation-induced alterations in three main biological pathways: respiratory chain, lipid metabolism and pyruvate metabolism. The label-free approach enables the quantitative measurement of radiation-induced alterations in FFPE tissue and facilitates retrospective biomarker identification using clinical archives.
authors.affiliation: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Radiation Biology, Neuherberg, Germany. omid.azimzadeh@helmholtz-muenchen.de
authors.forename: Omid
authors.initials: O
authors.lastname: Azimzadeh
authors.forename: Harry
authors.initials: H
authors.lastname: Scherthan
authors.forename: Ramesh
authors.initials: R
authors.lastname: Yentrapalli
authors.forename: Zarko
authors.initials: Z
authors.lastname: Barjaktarovic
authors.forename: Marius
authors.initials: M
authors.lastname: Ueffing
authors.forename: Marcus
authors.initials: M
authors.lastname: Conrad
authors.forename: Frauke
authors.initials: F
authors.lastname: Neff
authors.forename: Julia
authors.initials: J
authors.lastname: Calzada-Wack
authors.forename: Michaela
authors.initials: M
authors.lastname: Aubele
authors.forename: Christian
authors.initials: C
authors.lastname: Buske
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Atkinson
authors.forename: Stefanie M
authors.initials: SM
authors.lastname: Hauck
authors.forename: Soile
authors.initials: S
authors.lastname: Tapio
mesh_terms: D000818:Animals; D005404:Fixatives / Q000494:pharmacology; D005557:Formaldehyde / Q000494:pharmacology; D006321:Heart / Q000187:drug effects / Q000528:radiation effects*; D053858:Metabolic Networks and Pathways / Q000187:drug effects / Q000528:radiation effects; D055442:Metabolome / Q000502:physiology; D051379:Mice; D008810:Mice, Inbred C57BL; D008929:Mitochondria, Heart / Q000737:chemistry / Q000187:drug effects / Q000378:metabolism / Q000528:radiation effects*; D024101:Mitochondrial Proteins / Q000032:analysis / Q000187:drug effects / Q000528:radiation effects; D009124:Muscle Proteins / Q000032:analysis / Q000187:drug effects / Q000378:metabolism* / Q000528:radiation effects; D009206:Myocardium / Q000737:chemistry / Q000378:metabolism*; D016612:Paraffin Embedding / Q000379:methods; D011839:Radiation, Ionizing; D013194:Staining and Labeling / Q000379:methods
chemical_list: D005404:Fixatives; D024101:Mitochondrial Proteins; D009124:Muscle Proteins; D005557:Formaldehyde