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Cancer Cellular Metabolism across Space and Time

Periodic Reporting for period 2 - CancerFluxome (Cancer Cellular Metabolism across Space and Time)

Reporting period: 2018-08-01 to 2020-01-31

Cancer cells develop remarkably distinct metabolism compared to normal cells. Evidence for alterations in metabolic activity in malignant cells goes back almost a century ago to the discovery of the ‘Warburg effect’. The recent resurgence of interest in the field of cancer metabolism involved numerous findings of metabolic alterations in a variety of pathways in cancer cells, evidence for oncogenes and tumour suppressors regulating metabolic enzymes and specific oncogenic mutations in metabolic genes. While extensively studied, our current view of cancer cellular metabolism is fundamentally limited by lack of information on variability in metabolic activity between distinct subcellular compartments and cells. Specifically, while mitochondrial bioenergetics and biosynthesis play a major role in tumorigenesis, we lack basic understanding of the metabolic interplay between cytoplasm is and mitochondria; and how cells adapt central metabolic fluxes to fulfil the changing energetic and anabolic demands throughout the cell-cycle. Analysing the rate of metabolic reactions (i.e. metabolic flux) via isotope tracing is a central technique in cancer metabolic research. However, applied on a population of cells that are heterogeneous in terms of cell-cycle phase and not accounting for subcellular compartments confounds flux estimations and provides an overly simplified view of cellular metabolism

The CancerFluxome project aims to develop a spatio-temporal fluxomics approach for quantifying metabolic fluxes in the cytoplasm vs. mitochondria as well as their cell-cycle dynamics, combining a variety of experimental and computational techniques – including, mass-spectrometry based isotope tracing with cell synchronization, rapid cellular fractionation, and metabolic network modelling. This will be used to investigate fundamental questions regarding spatio-temporal metabolic dynamics, regulation, and design principles; and investigate how cells adapt their spatio-temporal flux program in response to oncogenic mutations.

Scientifically, the proposed research challenges our current view of cancer cellular metabolism, zooming in from the level of population/whole cellular fluxes, to a high-resolution, spatio-temporal view of metabolic activity. This will profoundly affect our understanding of the phenotypic advantage that metabolic adaptations confer to cancer cells. From a technical front, the project addresses a major open challenge in metabolic research of Eukaryotic cells - quantifying subcellular and cell-cycle dependent flux. The development of a spatio-temporal fluxomics method is a highly timely endeavor, considering the ever-growing interest in cancer metabolism. From a clinical front, a comprehensive view of metabolic adaptations to oncogenic mutations will facilitate finding of induced essentiality of metabolic genes – suggesting targets for anti-cancer drugs.
We developed an approach, temporal-fluxomics, to derive a comprehensive and quantitative view of alterations in metabolic fluxes throughout the mammalian cell cycle – combining experimental and computational techniques. Applied to cultured mammalian cells, we find major oscillations in flux in central energy metabolism (i.e. the Krebs Cycle) as cells progress through the cell cycle; with complementary oscillations of glucose versus glutamine-derived fluxes. We show that these metabolic oscillations play an important role in cell cycle progression and cell proliferation. These results are described in Ahn et al., Molecular Systems Biology, 13 (11), 2017.

We further developed a spatial-fluxomics approach for inferring metabolic fluxes in mitochondria and cytosol combining a variety of experimental and computational methods. Applying this method highlighted a non-canonical pathway for fatty acid biosynthesis in cells (through reductive IDH1 as the sole net contributor of carbons to under standard conditions). Applied to study how metabolism is rewired in cancer cells which lost the tumor suppressor SDH, we find a novel route through which these cell support nucleotide biosynthesis - through reversed mitochondrial citrate synthase flux. This is suggested to provide novel means to selectively target such cancer cells for therapeutic purposes. This work is described in Lee et al., Nature Communications 10 (1), 2019.

We provide an overview of metabolic flux inference techniques and the above recent developments in a review paper by Lagziel et al., BMC Biology, 17: 51, 2019.
The developed Systems Biology techniques enables to increase the resolution in which we can observe metabolic flux in mammalian cells, zooming in from the level of population/whole cellular fluxes, to a spatial and temporal view of metabolic activity.

Our work on probing metabolic flux specifically in mitochondria versus in cytosol focused on Krebs cycle and specifically on the glutamine-derived fluxes. Extending this to obtain a more comprehensive view of compartmentalized flux in central carbon metabolism raises substantial computational challenges that we are currently addressing. We expect to finalize this work until the completion of the ERC project and provide an approach for deriving a comprehensive and quantitative view of subcellular level metabolic fluxes. Ongoing research further involves the application of the developed techniques in a variety of cancer cells, investigating cancer specific reprogramming and regulation of cytosolic and mitochondrial flux and induced dependence on specific enzymes that can be therapeutically targeted.