A combined laser microdissection and mass spectrometry method for proteomic analysis of tissue sections for the identification of tumor signatures

  • Clinical research
  • Proteomics
Université de Bordeaux - Carreire Nord GREF INSERM U1053



A combined laser microdissection and mass spectrometry method for proteomic analysis of Formalin-fixed, Paraffin-embedded (FFPE) tissue sections. Mass spectrometry is the method of choice to identify, characterize and quantify proteins in a complex sample. Resulting from a know-how acquired during the development of a new procedure of subcellular proteomic analysis that has been the object of a patent registration, we propose a method combining laser microdissection and mass spectrometry analysis to compare the levels of protein expression between tumoral and non tumoral tissue derived from the same patient. This procedure can be applied to classical FFPE tumor sections and compatible to biopsies.
It is possible with this method to identify signature biomarkers in tumors and thus provide a new tool for clinicians that increase the quantity of clinical data and improve the prognosis for an equivalent or lesser cost. This procedure can be applied in many types of cancers and other pathologies.


  1. for a more precise classification of the different stages of tumors
  2. to study the heterogeneousness of tumors and identify more aggressive clones.
  3. to estimate the level of aggressiveness of benign tumors
  4. to discriminate patients good and bad responders to chemotherapies.
  5. to isolate metastatic cells for a targeted study.
  6. development of targeted quantification by mass spectrometry of set of choice of known biomarkers.

Infrastructure and equipment

  • PALM type 4 automated laser microdissector (Zeiss) on the laser microdissection platform of the Magendie Neurocenter (INSERM U 862)
  • Q-Exactive mass spectrometer (Thermo) of the Proteome Plateform of the Functional Genomic Center of Bordeaux


  1. Raymond AA, Benhamouche S, Neaud V, Di Martino J, Javary J, Rosenbaum J. Reptin regulates DNA double strand breaks repair in human hepatocellular carcinoma. PLoS One 2015
  2. Marza E, Taouji S*, Barroso K*, Raymond AA*, Guignard L, Bonneu M, Pallares-Lupon N, Dupuy JW, Fernandez-Zapico ME, Rosenbaum J, Palladino F, Dupuy D, Chevet E. Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription. EMBO Rep 2015 *equal work
  3. Vigneron S, Gharbi-Ayachi A, Raymond AA, Burgess A, Labbé JC, Labesse G, Monsarrat B, Lorca T, Castro A. Characterization of the mechanisms controlling Greatwall activity. Mol Cell Biol 2011
  4. Hsu CY, Henry J, Raymond AA, Méchin MC, Pendaries V, Nassar D, Hansmann B, Balica S, Burlet-Schiltz O, Schmitt AM, Takahara H, Paul C, Serre G, Simon M.Deimination of human filaggrin-2 promotes its proteolysis by calpain 1. J Biol Chem 2011
  5. Patent registration : Ezzoukhry Z, Raymond AA and Saltel F, July 2015, BNT219885FR00


  • Nault JC, Mallet M, Pilati C, Calderaro J, Bioulac-Sage P, Laurent C, Laurent A, Cherqui D, Balabaud C, Zucman-Rossi J. High frequency of telomerase reverse-transcriptase promoter somatic mutations in hepatocellular carcinoma and preneoplastic lesions. Nat Commun. 2013
  • Nault JC, Bioulac-Sage P, Zucman-Rossi J. Hepatocellular benign tumors-from molecular classification to personalized clinical care. Gastroenterology. 2013
  • Nault JC, De Reyniès A, Villanueva A, Calderaro J, Rebouissou S, Couchy G, Decaens T, Franco D, Imbeaud S, Rousseau F, Azoulay D, Saric J, Blanc JF, Balabaud C, Bioulac-Sage P, Laurent A, Laurent-Puig P, Llovet JM, Zucman-Rossi J. A hepatocellular carcinoma 5-gene score associated with survival of patients after liver resection. Gastroenterology. 2013
  • Guichard C, Amaddeo G, Imbeaud S, Ladeiro Y, Pelletier L, Maad IB, Calderaro J, Bioulac-Sage P, Letexier M, Degos F, Clément B, Balabaud C, Chevet E, Laurent A, Couchy G, Letouzé E, Calvo F, Zucman-Rossi J. Integrated analysis of somatic mutations and focal copy-number changes identifies key genes and pathways in hepatocellular carcinoma. Nat Genet. 2012