Molecular characterization of breast cancer cell response to metabolic drugs

// Lucia Trilla-Fuertes 1, 2 , Angelo Gamez-Pozo 1, 2 , Jorge M. Arevalillo 3 , Mariana Diaz-Almiron 4 , Guillermo Prado-Vazquez 1 , Andrea Zapater-Moros 1 , Hilario Navarro 3 , Rosa Aras-Lopez 5 , Irene Dapia 6, 7 , Rocio Lopez-Vacas 1 , Paolo Nanni 8 , Sara Llorente-Armijo 1 , Pedro Arias 6, 7 , Alberto M. Borobia 9 , Paloma Main 10 , Jaime Feliu 11, 12, 13 , Enrique Espinosa 11, 12 and Juan Angel Fresno Vara 1, 2, 12 1 Molecular Oncology and Pathology Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Madrid, Spain 2 Biomedica Molecular Medicine SL, Madrid, Spain 3 Operational Research and Numerical Analysis, National Distance Education University (UNED), Madrid, Spain 4 Biostatistics Unit, La Paz University Hospital-IdiPAZ, Madrid, Spain 5 Congenital Malformations Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital, IdiPAZ, Madrid, Spain 6 Pharmacogenetics Lab, Institute of Medical and Molecular Genetics-INGEMM, La Paz University Hospital-IdiPAZ, Autonomous University of Madrid, Madrid, Spain 7 Biomedical Research Networking Center on Rare Diseases-CIBERER, ISCIII, Madrid, Spain 8 Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, Switzerland 9 Clinical Pharmacology Department, La Paz University Hospital School of Medicine, IdiPAZ, Autonomous University of Madrid, Madrid, Spain 10 Department of Statistics and Operations Research, Faculty of Mathematics, Complutense University of Madrid, Madrid, Spain 11 Medical Oncology Service, La Paz University Hospital-IdiPAZ, Madrid, Spain 12 Biomedical Research Networking Center on Oncology-CIBERONC, ISCIII, Madrid, Spain 13 Catedra UAM-AMGEN, Universidad Autonoma de Madrid, Madrid, Spain Correspondence to: Juan Angel Fresno Vara, email: juanangel.fresno@salud.madrid.org Keywords: breast cancer; flux balance analysis; metabolism; perturbation experiments; proteomics Received: October 29, 2017      Accepted: January 03, 2018      Published: January 08, 2018 ABSTRACT Metabolic reprogramming is a hallmark of cancer. It has been described that breast cancer subtypes present metabolism differences and this fact enables the possibility of using metabolic inhibitors as targeted drugs in specific scenarios. In this study, breast cancer cell lines were treated with metformin and rapamycin, showing a heterogeneous response to treatment and leading to cell cycle disruption. The genetic causes and molecular effects of this differential response were characterized by means of SNP genotyping and mass spectrometry-based proteomics. Protein expression was analyzed using probabilistic graphical models, showing that treatments elicit various responses in some biological processes such as transcription. Moreover, flux balance analysis using protein expression values showed that predicted growth rates were comparable with cell viability measurements and suggesting an increase in reactive oxygen species response enzymes due to metformin treatment. In addition, a method to assess flux differences in whole pathways was proposed. Our results show that these diverse approaches provide complementary information and allow us to suggest hypotheses about the response to drugs that target metabolism and their mechanisms of action.