Despite decades of research, cancer remains a leading cause of death and calls for novel treatment approaches. An emerging therapeutic target is the altered metabolism in cancer cells. However, the altered metabolism, known as the Warburg effect, remains a mystery for almost a century, and has not led to any therapeutic successes so far. A recent discovery, made in microorganisms, might open up a new avenue to hit cancer cells at the foundation of their altered metabolism. In this project, we will investigate whether cancer cells, similarly to microorganisms, are constrained by the rate with which they can dissipate Gibbs energy to the environment. To this end, we will develop and use a new computational model, combining our expertise in systems biology with input from medical collaborators. If we find that cancer cells indeed have a thermodynamic Achilles’ heel, this will establish the grounds for exciting new fundamental and applied research on how to tackle cancer via its metabolism.

Life leads to death, which is arguably the sole universal characteristic of life. The association between the rate of living and the rate of dying has fascinated biologists for a century, but the principal causes of ageing in humans and other organisms are still not resolved. Life span and rates of senescence vary distinctly, even between closely related species of similar size. Yet, for many organisms an intriguing relation between metabolic rate and lifespan is observed: when summed over lifetime, the metabolic rate per unit body mass is remarkably constant. This relation spans a wide range of organisms from yeast to elephant, and includes humans. Also within species, metabolism seems to be causally related with ageing, since caloric (or dietary) restriction typically enhances life expectancy. Despite intense research efforts, the nature of the relationship between metabolism and ageing remains enigmatic. By establishing a Systems Biology Centre called Energy Metabolism and Ageing (SBC-EMA), we will apply a systems biology approach to shed new light on metabolism, ageing, and their interaction. The metabolic rate of an organism is the result of the complex interplay of biochemical and physiological processes acting at various levels of organisation (mitochondria, cells, tissues, organs). Similarly, the physiological and molecular deterioration that characterizes ageing reflects the failure of networks of interacting cells, tissues and organs. Hence, by their very nature both metabolism and ageing require a systems biology approach in order to achieve a full understanding of their nature and their interaction. To unravel the complex relationship between energy metabolism and lifespan, SBC-EMA will combine large-scale data generation efforts with both data-driven top-down approaches and hypothesis-driven bottom-up approaches. In the first phase of its development, the Centre will focus on two model systems: the yeast Saccharomyces cerevisiae and mice Mus musculus. Metabolism and ageing in unicellular yeast and mice shows many similarities as well as differences, but the existence of a universal relation between metabolic rate and ageing suggests that key mechanisms underlying the ageing process are conserved from microorganisms to humans. We aim to discover these general mechanisms and this is an important motivation to study mouse and yeast next to each other. Yeast allows detailed investigations at the level of cells and organelles and they age rapidly. Moreover, a plethora of ?omics? information and techniques is already available, also within the University of Groningen, and metabolic and signalling pathways have been well characterised. Mice will be used to generate and test hypotheses involving intercellular and inter-organ relationships that are critical in higher organisms including humans. By applying similar manipulations (caloric restriction) in two model systems, we will simultaneously study intracellular (yeast) and higher-order (mice) processes in unprecedented detail with the aim to uncover the fundamental ageing processes shared by all life. This proposal is a joint research initiative of two faculties of the University of Groningen, the Faculty of Mathematics and the Natural Sciences (FMNS) and the Faculty of Medical Sciences (FMS). To achieve our ambitious goal, SBC-EMA brings together leading groups from both faculties, with expertise ranging from biochemistry, (molecular) biology, physiology and medicine to mathematics, statistics, bioinformatics and theoretical biology. The research theme of SBC-EMA builds on a rich history in both energetics and ageing research in both faculties. The University of Groningen has identified Healthy Ageing as one of its central research themes, and has founded the European Research Institute on the Biology of Ageing (ERIBA), which will focus on fundamental aspects of the biology of ageing. SBC-EMA will be physically and scientifically embedded within ERIBA together with other facilities like the Groningen Genomics Coordination Centre. By creating first-class infrastructure and by their recruitment policy, the University already demonstrates its commitment to systems biology. They also show a commitment to this proposal by providing 12 PhD student positions in addition to the positions requested in this proposal. SBC-EMA will be a vibrant Centre where scientists with diverse backgrounds will meet and collaborate on a daily basis to understand the fundamentals of ageing. Although research in SBC-EMA is predominantly fundamental, the topic of (healthy) ageing is of major societal relevance. Our research program on yeast and mice will therefore interact closely with Lifelines (and the complementary Systems Genetics endeavours), which will become the largest longitudinal population study in the Netherlands, involving more than 150,000 individuals. SBC-EMA will also have considerable scientific and educational outreach, by making data and results available to the scientific community, by developing user-friendly systems biology software, and by launching attractive systems biology courses for graduate and postgraduate students.

Growth of cells is inherently connected with the origin of life. Despite 4 billion years of evolution there seems to be an upper limit to how fast cells can grow. However, it is poorly understood what physical principles constrain growth. A recent discovery opens a new perspective on what limits cell growth: growth might be limited by the rate at which cells can dissipate Gibbs energy to the environment. Similar to a mechanical machine, which should not be operated above an upper rate, cells apparently also do not function above a critical Gibbs energy dissipation rate. Insight in life’s boundaries forms one of the most pressing scientific challenges in biology, but is also highly relevant for industrial biotechnology. In this project, we aim to unravel the molecular basis for the upper Gibbs energy dissipation limit. We hypothesize that the energy released in enzymatic reactions of living cells is partly dissipated as work, leading to molecule movement inside cells, too much of which compromises biomolecular functions. Through concerted efforts of industrial stakeholders and academic partners drawing on physics, biology and chemistry, and exploiting in vitro and in vivo experiments and computational analyses, we will investigate how catalysis-induced molecule movement constrains cellular metabolism and growth, leading to fundamental understanding of the limits of cell growth. Beyond, through a novel ‘pull strategy’ for basic science communication, which we will co-develop between scientists and artists/media designers, this forefront scientific research will also be used to engage with Dutch citizens in an unprecedented manner. Thus, the project will deliver new fundamental insights into the very basics of cellular functioning, which is of key importance to understand the origin of life and for the bio-based economy, but will also involve the broader public in the process of scientific research.

Cell division is one of the most fundamental processes of life. When cell division fails, the loss or gain of genomic information can result in cell death or worse promote unregulated cell proliferation. It is therefore essential that the multitude of biochemical and morphological processes underlying cell division are tightly regulated in space and time. The anaphase promoting complex/cyclosome (APC/C-Cdc20) is the central regulator of mitotic progression. The phospho-regulation and activation of the APC/C-Cdc20 is a highly dynamic, multi-layered process. Progressive phosphorylation of the APC/C-Cdc20 at over a hundred residues has been hypothesized to act as a molecular timer to provide sufficient time delay between mitotic entry and APC/C-Cdc20 activation for the mitotic spindle to assemble and thereby ensure faithful chromosome segregation. However, our current understanding of APC/C phosphorylation and activation is largely an interpolation of studying the APC/C-Cdc20 in two defined states, interphase or mitosis. How exactly all the phosphorylations synergize to ensure the timely activation of the APC/C has remained unclear. In this project, my team and I will unravel the temporal dimension of APC/C-Cdc20 regulation by phosphorylation. Specifically, by combining the powerful frog egg extract system with quantitative mass spectrometry we will derive a kinetic model of APC/C phosphorylation of unprecedented temporal and single residue resolution. We will establish the direct connection between these phosphorylation events and APC/C activation dynamics using microfluidics and fluorescence microscopy. Lastly, we will demonstrate the impact of disrupting the temporal regulation of APC/C activity on mitotic progression in human cells. Protein regulation by reversible phosphorylation is a universal mechanism of cellular signal transduction. Therefore, the project will not only significantly deepen our knowledge about the critical cell cycle regulator APC/C-Cdc20, but more generally provide fundamental insights into how multisite phosphorylation contributes to the temporal regulation of enzyme function.

Metabolism and cell division are both crucial for life, and not surprisingly major contributing factors in many pathologies, such as cancer. As metabolism is linked to cell growth, and growth is part of the cell cycle, there should be coordination between metabolism and cell division. However, until today, the interplay between metabolism and the cell-cycle machinery is largely enigmatic. Recent findings from my lab shed light on the complex crosstalk between both processes. Using novel single-cell techniques, we demonstrated that metabolism of budding yeast, even under constant conditions and across nutrients, oscillates in strict synchrony with the cell cycle. Stunningly, the metabolic oscillations continued when we halted the cell-cycle machinery, suggesting that metabolism might be an autonomous oscillator. We also discovered that the oscillations co-coordinate the cell cycle by setting the moment for cell cycle entry and exit, in a clock-like manner. However, it is completely unclear which metabolic pathways change in activity during the cell cycle and which mechanism generates the metabolic oscillations. Exploiting single-cell microscopy, we generated exciting novel data indicating that the oscillations might arise from a temporal segregation of protein and lipid biosynthesis, as opposed to previous hypotheses. In this project I aim to unravel the clockwork of cellular metabolism, working towards a novel layer of knowledge on cell cycle control. Specifically, my team will identify how metabolic fluxes in metabolism change during the cell cycle and establish the mechanism that generates the metabolic oscillations. We will combine a unique set of tools: time-lapse microscopy and single-cell perturbations, multi-layer omics analyses, and a powerful computational method for metabolic flux modeling that we recently developed. This project will be foundational to determine how the metabolic oscillator exerts control on the cell cycle and will generate fundamental new insights of significant value for biomedicine and biotechnology.