Quantitative Analysis of Energy Metabolic Pathways in MCF-7 Breast Cancer Cells by Selected Reaction Monitoring Assay

Abstract

To investigate the quantitative response of energy metabolic pathways in human MCF-7 breast cancer cells to hypoxia, glucose deprivation, and estradiol stimulation, we developed a targeted proteomics assay for accurate quantification of protein expression in glycolysis/gluconeogenesis, TCA cycle, and pentose phosphate pathways. Cell growth conditions were selected to roughly mimic the exposure of cells in the cancer tissue to the intermittent hypoxia, glucose deprivation, and hormonal stimulation. Targeted Adaptation of cancer cells to hypoxia, lack of nutrients, and abnormal hormonal stimulation is known to alter their metabolism (1, 2). "Aerobic glycolysis," also referred as the Warburg effect, is a unique characteristic of rapidly proliferating cancer cells (3). Deregulating cellular energetics and reprogramming of metabolism are the emerging hallmarks of cancer (4). There is also an increasing number of epidemiologic evidence that link cancer risk with metabolic disorders such as diabetes and obesity (5).Until recently, the metabolic transformation of cancer cells was studied primarily at the level of genome (6), transcriptome (7), and metabolome (8). These studies discovered new mutations (9, 10), cancer-related alternative splicing isoforms (11), and altered enzyme activities in human cancers (2). Subsequent clinical applications included diagnostic imaging (12), prognosis (13), and identification of compounds targeting tumor metabolism (14).To fully understand the events and outcomes of metabolic transformation of cancer cells, quantitative proteomic approaches are required to complement existing genomic, transcriptomic, and metabolomic approaches. Proteomic methods provide additional levels of information, such as protein abundances, post-translational modifications, dynamics of protein turn-over, which cannot be accurately predicted using other -omic approaches.Typically, expression of enzymes in cellular metabolic pathways is measured by ELISA or immunoblot assays, which provide information for a very limited number of enzymes. Multiplex proteomic assays, on the contrary, could reveal simultaneous rearrangement of protein expression in entire metabolic pathways. Mass spectrometry-based proteomics, complemented with chemical and metabolic labeling approaches, is a powerful tool for global analysis of protein expression. However, these approaches have very limited throughput and require extensive sample preparation, complex data analysis, and verification of their results by independent assays. Besides, metabolic labeling is applicable to actively dividing cell lines, but not to the primary cells.Targeted proteomic assays present an attractive complementary tool devoid of the abovementioned limitations. SeFrom the ‡Samuel Lunenfeld Research Institute, Mount Sinai Hospital,

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