Initial Development and Validation of a Novel Extraction Method for Quantitative Mining of the Formalin-Fixed, Paraffin-Embedded Tissue Proteome for Biomarker Investigations
Open Access
- 23 December 2010
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of Proteome Research
- Vol. 10 (2), 896-906
- https://doi.org/10.1021/pr100812d
Abstract
Annotated formalin-fixed, paraffin-embedded (FFPE) tissue archives constitute a valuable resource for retrospective biomarker discovery. However, proteomic exploration of archival tissue is impeded by extensive formalin-induced covalent cross-linking. Robust methodology enabling proteomic profiling of archival resources is urgently needed. Recent work is beginning to support the feasibility of biomarker discovery in archival tissues, but further developments in extraction methods which are compatible with quantitative approaches are urgently needed. We report a cost-effective extraction methodology permitting quantitative proteomic analyses of small amounts of FFPE tissue for biomarker investigation. This surfactant/heat-based approach results in effective and reproducible protein extraction in FFPE tissue blocks. In combination with a liquid chromatography−mass spectrometry-based label-free quantitative proteomics methodology, the protocol enables the robust representative and quantitative analyses of the archival proteome. Preliminary validation studies in renal cancer tissues have identified typically 250−300 proteins per 500 ng of tissue with 1D LC−MS/MS with comparable extraction in FFPE and fresh frozen tissue blocks and preservation of tumor/normal differential expression patterns (205 proteins, r = 0.682; p < 10−15). The initial methodology presented here provides a quantitative approach for assessing the potential suitability of the vast FFPE tissue archives as an alternate resource for biomarker discovery and will allow exploration of methods to increase depth of coverage and investigate the impact of preanalytical factors.Keywords
This publication has 29 references indexed in Scilit:
- Systematic Comparative Protein Expression Profiling of Clear Cell Renal Cell CarcinomaMolecular & Cellular Proteomics, 2009
- Equivalence of Protein Inventories Obtained from Formalin-fixed Paraffin-embedded and Frozen Tissue in Multidimensional Liquid Chromatography-Tandem Mass Spectrometry Shotgun Proteomic AnalysisMolecular & Cellular Proteomics, 2009
- Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass SpectrometryJournal of Histochemistry & Cytochemistry, 2009
- Grade-dependent Proteomics Characterization of Kidney CancerMolecular & Cellular Proteomics, 2009
- LC/MS-Based Quantitative Proteomic Analysis of Paraffin-Embedded Archival Melanomas Reveals Potential Proteomic Biomarkers Associated with MetastasisPLOS ONE, 2009
- Evaluation of Archival Time on Shotgun Proteomics of Formalin-Fixed and Paraffin-Embedded TissuesJournal of Proteome Research, 2009
- Optimization of Mass Spectrometry-Compatible Surfactants for Shotgun ProteomicsJournal of Proteome Research, 2007
- Contribution of oncoproteomics to cancer biomarker discoveryMolecular Cancer, 2007
- Protein biomarker discovery and validation: the long and uncertain path to clinical utilityNature Biotechnology, 2006
- Serological and proteomic evaluation of antibody responses in the identification of tumor antigens in renal cell carcinomaProteomics, 2003