Quantitative proteomic analysis of formalin-fixed, paraffin-embedded clear cell renal cell carcinoma tissue using stable isotopic dimethylation of primary amines

Abstract: Background

Formalin-fixed, paraffin-embedded (FFPE) tissues represent the most abundant resource of archived human specimens in pathology. Such tissue specimens are emerging as a highly valuable resource for translational proteomic studies. In quantitative proteomic analysis, reductive di-methylation of primary amines using stable isotopic formaldehyde variants is increasingly used due to its robustness and cost-effectiveness.

Results

In the present study we show for the first time that isotopic amine dimethylation can be used in a straightforward manner for the quantitative proteomic analysis of FFPE specimens without interference from formalin employed in the FFPE process. Isotopic amine dimethylation of FFPE specimens showed equal labeling efficiency as for cryopreserved specimens. For both FFPE and cryopreserved specimens, differential labeling of identical samples yielded highly similar ratio distributions within the expected range for dimethyl labeling. In an initial application, we profiled proteome changes in clear cell renal cell carcinoma (ccRCC) FFPE tissue specimens compared to adjacent non–malignant renal tissue. Our findings highlight increased levels of glyocolytic enzymes, annexins as well as ribosomal and proteasomal proteins.

Conclusion

Our study establishes isotopic amine dimethylation as a versatile tool for quantitative proteomic analysis of FFPE specimens and underlines proteome alterations in ccRCC.

Keywords

Dimethylation - Formalin-fixation - Paraffin-embedment clear cell renal cell carcinoma

Object Details

• Location: Deutsche Nationalbibliothek Frankfurt am Main
• Extent: Online-Ressource
• Language: Englisch
• Notes: BMC Genomics. 16 (2015), 559, DOI 10.1186/s12864-015-1768-x, issn: 1471-2164 ; IN COPYRIGHT http://rightsstatements.org/page/InC/1.0 rs

Classification and Topics

• Keyword: Paraffinkrebs ; Hypernephrom ; Krebs ; Onkologie

Contributors, Places and Time

• Event: Veröffentlichung
• (where): Freiburg
• (who): Universität
• (when): 2015
• Creator: Weißer, Juliane ; Lai, Zon Weng ; Bronsert, Peter ; Kühs, Markus ; Drendel, Vanessa ; Timme-Bronsert, Sylvia ; Küsters, Simon ; Jilg, Cordula ; Wellner, Ulrich ; Laßmann, Silke ; Werner, Martin ; Biniossek, Martin Lothar ; Schilling, Oliver
• Contributor: Universitätsklinikum Freiburg. Institut für Klinische Pathologie ; Albert-Ludwigs-Universität Freiburg. Institut für Molekulare Medizin und Zellforschung ; Tumorzentrum Freiburg - CCCF ; DKTK German Cancer Consortium ; Klinik für Allgemein- und Viszeralchirurgie. Freiburg im Breisgau ; Universitätsklinikum Freiburg. Zentrale Klinische Forschung ; Universitätsklinikum Freiburg. Klinik für Urologie ; Albert-Ludwigs-Universität Freiburg. Medizinische Fakultät ; Deutsches Krebsforschungszentrum ; Albert-Ludwigs-Universität Freiburg. Centre for Biological Signalling Studies ; Albert-Ludwigs-Universität Freiburg. Fakultät für Biologie ; Albert-Ludwigs-Universität Freiburg

Further information

• DOI: 10.1186/s12864-015-1768-x
• URN: urn:nbn:de:bsz:25-freidok-125565
• Rights: Der Zugriff auf das Objekt ist unbeschränkt möglich.
• Last update: 25.03.2025, 1:47 PM CET