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A laser microdissection-based workflow for FFPE tissue microproteomics: important considerations for small sample processing

Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no meth...

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Main Authors: Longuespée, Rémi (Author) , Alberts, Deborah (Author) , Pottier, Charles (Author) , Smargiasso, Nicolas (Author) , Mazzucchelli, Gabriel (Author) , Baiwir, Dominique (Author) , Kriegsmann, Mark (Author) , Herfs, Michael (Author) , Kriegsmann, Jörg (Author) , Delvenne, Philippe (Author) , De Pauw, Edwin (Author)
Format: Article (Journal)
Language:English
Published: 15 July 2016
In: Methods
Year: 2015, Volume: 104, Pages: 154-162
ISSN:1095-9130
DOI:10.1016/j.ymeth.2015.12.008
Online Access:Verlag, Volltext: https://doi.org/10.1016/j.ymeth.2015.12.008
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Author Notes:Rémi Longuespée, Deborah Alberts, Charles Pottier, Nicolas Smargiasso, Gabriel Mazzucchelli, Dominique Baiwir, Mark Kriegsmann, Michael Herfs, Jörg Kriegsmann, Philippe Delvenne, Edwin De Pauw
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Summary:Proteomic methods are today widely applied to formalin-fixed paraffin-embedded (FFPE) tissue samples for several applications in research, especially in molecular pathology. To date, there is an unmet need for the analysis of small tissue samples, such as for early cancerous lesions. Indeed, no method has yet been proposed for the reproducible processing of small FFPE tissue samples to allow biomarker discovery. In this work, we tested several procedures to process laser microdissected tissue pieces bearing less than 3000 cells. Combined with appropriate settings for liquid chromatography mass spectrometry-mass spectrometry (LC-MS/MS) analysis, a citric acid antigen retrieval (CAAR)-based procedure was established, allowing to identify more than 1400 proteins from a single microdissected breast cancer tissue biopsy. This work demonstrates important considerations concerning the handling and processing of laser microdissected tissue samples of extremely limited size, in the process opening new perspectives in molecular pathology. A proof of the proposed method for biomarker discovery, with respect to these specific handling considerations, is illustrated using the differential proteomic analysis of invasive breast carcinoma of no special type and invasive lobular triple-negative breast cancer tissues. This work will be of utmost importance for early biomarker discovery or in support of matrix-assisted laser desorption/ionization (MALDI) imaging for microproteomics from small regions of interest.
Item Description:Available online 12 December 2015
Gesehen am 14.05.2020
Physical Description:Online Resource
ISSN:1095-9130
DOI:10.1016/j.ymeth.2015.12.008

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