Functional proteomics outlines the complexity of breast cancer molecular subtypes

Breast cancer is a heterogeneous disease comprising a variety of entities with various genetic backgrounds. Estrogen receptor-positive, human epidermal growth factor receptor 2-negative tumors typically have a favorable outcome; however, some patients eventually relapse, which suggests some heterogeneity within this category. In the present study, we used proteomics and miRNA profiling techniques to characterize a set of 102 either estrogen receptor-positive (ER+)/progesterone receptor-positive (PR+) or triple-negative formalin-fixed, paraffin-embedded breast tumors. Protein expression-based probabilistic graphical models and flux balance analyses revealed that some ER+/PR+ samples had a protein expression profile similar to that of triple-negative samples and had a clinical outcome similar to those with triple-negative disease. This probabilistic graphical model-based classification had prognostic value in patients with luminal A breast cancer. This prognostic information was independent of that provided by standard genomic tests for breast cancer, such as MammaPrint, OncoType Dx and the 8-gene ScoreThe authors would like to acknowledge funding from grants PI12/00444, PI12/01016 and PI15/01310 from the Instituto de Salud Carlos III, Spanish Economy and Competitiveness Ministry, Spain, and co-funded by the FEDER program, “Una forma de hacer Europa”. This study has also been supported by the PRIME-XS project, grant agreement number 262067, funded by the EU’s Seventh Framework Program for Research. AG-P and RL-V are supported by Instituto de Salud Carlos III, and the Spanish Economy and Competitiveness Ministry grants, CA12/00258 and CA12/00264, respectively. . We want to particularly acknowledge the patients in this study for their participation and to the IdiPAZ, I+12 and O+EHUN Biobanks for the generous gifts of clinical samples used in this study. LT-F is supported by the Spanish Economy and Competitiveness Ministry (DI-15-07614). IdiPAZ, I+12 and O+EHUN Biobanks are supported by Instituto de Salud Carlos III, Spanish Economy and Competitiveness Ministry (RD09/0076/00073, RD09/0076/00118 and RD09/0076/00140, respectively) and FarmaIndustria, through the Cooperation Program in Clinical and Translational Research of the Community of Madrid and Basque Autonomous Communit