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We used a 2D-electrophoresis (2-DE) proteomic approach to identify novelbiomarkers in node-negative breast cancers. This retrospective study focused ona population of patients with ductal pN0M0 tumours. A subset of patients who developedmetastases and in whose tumours were found high levels of uPA and PAI-1 (metastaticrelapse, MR: n=20) were compared to another subset in whom no metastatic relapseoccurred and whose tumours were found to have low levels of uPA and PAI-1 (norelapse, NR: n=21). We used a 2-DE coupled with MS approach to screen cytosolfractions using two pH-gradient scales, a broad scale (3.0-11.0) and a narrowerscale focussing in on a protein rich region (5.0-8.0). This study was conductedon 41 cytosol specimens analyzed in duplicate on two platforms. The differentialanalysis of more than 2,000 spots in 2-DE gels, obtained on the two platforms,allowed the identification of 13 proteins which were confirmed by western blotting.Two proteins, GPDA and FABP4 were down-regulated in the MR subset whereas allthe others were up-regulated. An in silico analysis revealed that GMPS (GUAA),GAPDH (G3P), CFL1 (COF1) and FTL (FRIL), the most informative genes, displayeda proliferation profile (high expression in basal-like, HER2+ and luminal B molecularsubtypes). Inversely, similar to FABP4, GPD1 [GPDA] displayed a high expressionin luminal A subtype, a profile characteristic of tumour suppressor genes. Despitethe small size of our cohort, the 2-DE analysis gave interesting results whichwere confirmed by the in silico analysis showing that some of the correspondinggenes had a strong prognostic impact in breast cancer, mostly because of theirlink with proliferation: GMPS, GAPDH, FTL and GPD1. A validation phase on a largercohort is now needed before these biomarkers could be considered for use in clinicalpractice.

Identification of potential prognostic biomarkers for node-negative breast tumours by proteomic analysis: A multicentric 2004 national PHRC study