New insights into cell metabolism and how it is altered in disease conditions While cell metabolism is what helps cancer cells grow and proliferate, it may also hold the key to developing new ways to diagnose and treat the disease. But this requires that we first fully understand the inner workings of this hugely complex system – which is exactly what the EU-funded CancerFluxome project set out to do. Health © peterschreiber.media/stock.adobe.com Cellular metabolism is a hugely complex dynamic system involving the function of thousands of enzymes. “Exploring metabolic activities in cells has typically involved measuring average quantities across multiple subcellular compartments, which mask important information on how metabolite concentrations differ between distinct organelles,” explains Tomer Shlomi, a researcher at the Israel Institute of Technology and CancerFluxome project coordinator. As if missing subcellular-level information wasn’t challenging enough, Shlomi says that metabolic measurements are typically only possible on large populations of cells, further complicating the ability to infer potential cell-to-cell variability in metabolic activities. Seeing metabolic activity in high spatial-temporal resolution To overcome these challenges, the European Research Council supported project used an innovative systems biology method capable of assessing metabolite concentration and flux (the actual rate that metabolic enzymes work) in distinct subcellular compartments. The method can also explore the dynamics of metabolites and fluxes across the cell cycle. “Being able to explore metabolic activities in high spatial-temporal resolution is expected to fundamentally contribute to our understanding of cell metabolism and how it is altered in disease conditions – including cancer,” says Shlomi. For example, using a method that combined cell synchronisation with computational deconvolution, isotope tracing, mass spectrometry, and metabolic network modelling, the Shlomi Lab was able to explore the dynamics of metabolic flux as cells progressed throughout the cell line. “Applying this method to a commonly studied cell line added another temporal dimension to our understanding of a fundamentally important metabolic system in cells,” adds Shlomi. “Namely, we found that metabolic flux through this system oscillates as a cell progresses through the cell cycle, adapting its activity to changing anabolic requirements.” Previously unknown pathway Turning to the even more technically challenging task of inferring metabolic flux at a subcellular level and under physiological conditions, the project developed a method for the rapid fractionation of cells. “This process isolates mitochondria from cells in a matter of seconds, essentially snap-freezing it, and then follows up with measurements and computational modelling,” notes Shlomi. When used to probe central metabolic activities, researchers at the Shlomi Lab discovered a previously unknown pathway where several mitochondrial enzymes in the Krebs cycle showed reversed activity in specific tumours to support anabolic activities and cancer cell proliferation. A new target for treating cancer Another important finding involved a mitochondrial enzyme whose activity is essential for growth of liver cancer cells. Following up on this finding, researchers were able to demonstrate that genetic silencing of this enzyme-coding gene inhibits the growth of hepatocellular carcinoma tumours in mice – suggesting a novel target for treating the disease. “The methods developed as part of this project provide fundamental tools for metabolic researchers, as well as advance our understanding of how cellular metabolism is reprogrammed by cancer cells and how this reprogramming could possibly be targeted by drugs,” concludes Shlomi. Although the CancerFluxome project is now finished, the Shlomi Lab continues to work on new methods for obtaining an even more comprehensive view of cellular metabolism, its regulation, and how it can all go awry in disease conditions. Keywords CancerFluxome, high spatial-temporal resolution, cell metabolism, disease, cancer, cancer cells, metabolites, metabolic flux, tumours
