The effects of oligomycin administration and glutamine deprivation on metabolic profile of MCF7 breast cancer cell line measured using [1,2-13C2]-D-glucose and [U-13C5]-L-glutamine as tracers

This study aims to establish a comprehensive, genome-scale metabolic model (GSMM) combining different omics data of different regulatory levels of breast cancer cells in order to elucidate the way that these regulatory levels affect or determine each other. Together with transcriptomics, proteomics and metabolomics data obtained, fluxomics data was also to be integrated. In order to get the fluxomics data, MCF cells were incubated with either the medium containing [1,2-13C2]-D-glucose or [U-13C5]-L-glutamine for 8 or 24 hours. A good GSMM should answer any perturbations applied; therefore, different incubation conditions should be applied to generate different metabolic profiles that will help to test if the model of breast cancer works well. To this end, MCF cells were either administered oligomycine, which is an ATP synthase inhibitor, or were deprived of glutamine. Cells were counted before and after each incubation time so as to get the cell proliferation curve. Later, at the corresponding time points, cells and media were frozen to measure the concentrations of glucose, glutamine and lactate (not shown in the file) and the mass isotopomer distributions of glutamate, ribose, lactate, amino acids and TCA cycle intermediates (shown in the file). Finally, all these data was combined in order to estimate the flux rates of various reactions within the central carbon metabolism (not shown in the file). The fluxomics data obtained in this way is to be introduced in the GSMM designed.