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Cancer cells share several metabolic traits, including aerobic production of lactate from glucose (Warburg effect), extensive glutamine utilization and impaired mitochondrial electron flow. It is still unclear how these metabolic rearrangements, which may involve different molecular events in different cells, contribute to a selective advantage for cancer cell proliferation. To ascertain which metabolic pathways are used to convert glucose and glutamine to balanced energy and biomass production, we performed systematic constraint-based simulations of a model of human central metabolism. Sampling of the feasible flux space allowed us to obtain a large number of randomly mutated cells simulated at different glutamine and glucose uptake rates. We observed that, in the limited subset of proliferating cells, most displayed fermentation of glucose to lactate in the presence of oxygen. At high utilization rates of glutamine, oxidative utilization of glucose was decreased, while the production of lactate from glutamine was enhanced. This emergent phenotype was observed only when the available carbon exceeded the amount that could be fully oxidized by the available oxygen. Under the latter conditions, standard Flux Balance Analysis indicated that: this metabolic pattern is optimal to maximize biomass and ATP production; it requires the activity of a branched TCA cycle, in which glutamine-dependent reductive carboxylation cooperates to the production of lipids and proteins; it is sustained by a variety of redox-controlled metabolic reactions. In a K-ras transformed cell line we experimentally assessed glutamine-induced metabolic changes. We validated computational results through an extension of Flux Balance Analysis that allows prediction of metabolite variations. Taken together these findings offer new understanding of the logic of the metabolic reprogramming that underlies cancer cell growth., Author summary Hallmarks describing common key events in initiation, maintenance and progression of cancer have been identified. One hallmark deals with rewiring of metabolic reactions required to sustain enhanced cell proliferation. The availability of molecular, mechanistic models of cancer hallmarks will mightily improve optimized personal treatment and new drug discovery. Metabolism is the only hallmark for which it is currently possible to derive large scale mathematical models, which have predictive ability. In this paper, we exploit a constraint-based model of the core metabolism required for biomass conversion of the most relevant nutrients—glucose and glutamine—to clarify the logic of control of cancer metabolism. We newly report that, when available oxygen is not sufficient to fully oxidize available glucose and glutamine carbons–a situation compatible with that observed under normal oxygen conditions in human and in cancer cells growing in vitro—utilization of glutamine by reductive carboxylation and conversion of glucose and glutamine to lactate confer advantage for biomass production. Redox homeostasis can be maintained through the use of different alternative pathways. In conclusion, this paper offers a logic interpretation to the link between metabolic rewiring and enhanced proliferation, which may offer new approaches to targeted drug discovery and utilization.

Common Processes. (PDF 66 kb)

Aims: Mitochondria are very dynamic organelles. Mitochondrial dynamics (alternation of fission/fusion cycles and their axonal transport) and biogenesis are crucial for neuronal homeostasis and synaptic function; moreover, alteration of the balance between fission and fusion can determine the fate of neuronal cells. Fission processes require the intervention of Fis1 and the active form of Drp1, whereas fusion is primarily regulated by Opa1 and Mfn1/2. We here focused on correlation between oxidative stress and mitochondrial dynamics and biogenesis. Materials and Methods: We compared the effect of hydrogen peroxide and Rotenone (a neurotoxin that inhibits the Complex-I of electrons transport chain), on primary cortical neurons or models of neurodegeneration based on neuroblastoma or PC12 cells. Protein levels and distribution (cytoplasm, mitochondria or nuclei) were assessed by western blots and immunofluorescence imaging. Results: Exposure of neurons or neuroblastoma to Rotenone determined a dose-dependent (200-400-800 nM) decrease of P-Drp1 and a biphasic trend of Opa1 and Mfn2 in a time-dependent manner (1-3-6-24h). In PC12 cells, alterations of mitochondrial proteins in response to hydrogen peroxide was paralleled by differential distribution (cytoplasm/nuclei) of oxidative-stress sensors (DJ-1, Nrf2) and proteins regulating mitochondrial biogenesis (mtTFAM and PGC1a), while determining a dose- and time-dependent increase of ROS and ATP depletion. Interestingly, human fibroblasts showed similar changes in response to rotenone but a different trend in response to Amyloid-beta oligomers. Discussion/Conclusions: These studies suggest 1) the existence of a complex cross-talk underlying mitochondrial dynamics and biogenesis, 2) alteration of mitochondrial dynamic proteins as biomarkers of mitochondrial dysfunction in neurodegenerative processes.

Pathology Specific Processes. (PDF 66 kb)

ISBE published its business plan at the end of July 2015, which sets out the long term proposed organisation, governance and legal structure of ISBE to be implemented as it establishes itself as a legal entity from 2018 onwards. This report sets out the steps taken to develop this proposed structure and determine its suitability for providing the most appropriate framework for ISBE to operate as a sustainable transnational research infrastructure. In developing this structure, ISBE WP11 consulted with a broad range of representatives from national ministries and funding agencies. The first step in establishing the long term structure was to develop a set of guiding principles that were endorsed by the ISBE steering committee. WP11 then drew on best practice from across the ESFRI Research Infrastructures, both planned and in place, to develop the structure presented. We believe that the resultant model provides a viable mechanism for ensuring suitable overview by member states supporting it, together with involvement of researchers providing the resources, services and activities for the community. The structure also provides a robust way of ensuring independent advice, most notably in assessing and monitoring institutions that will deliver the operational activities for ISBE. Finally, the model sets out a modest but efficient executive function that can ensure coordination of operations, development of strategic direction and most crucially, the outreach needed to expand the breadth of provision being set out for ISBE

Work Package 11 (WP11) was established to deliver a proposal for “a long-term funding and governance strategy that supports the objectives and priorities of funding organisations participating in ISBE.” Based on project partners’ prior experience from other ESFRIs, ISBE identified the need to consider an interim phase immediately following the preparatory phase prior to the legal phase. A key aspect for the structure of the interim phase was what opportunities for greater coherence and cohesion to maximise links across existing infrastructure elements it might enable. Any agreement for this phase would also need to encompass existing cross-border and potential bi/multilateral funding and legal agreements. Significantly, the Systems Biology community provides scope to build on activities supported through existing European funding programmes (e.g. ERANETS), and synergies with other ESFRI BMS projects. For these goals, WP11 has developed an initial funding structure and legal mechanism for ISBE to immediately follow the preparatory phase, being the “Interim Phase”. This is intended to include elements for early investment for delivering a pilot phase infrastructure resource, and developing associated co-ordination structure. This interim phase could aide identification and integration of potential ministries and funding agencies expressing their interest in long term strategic support. This is intended to be a combined process of transitional steps to establish operations in advance of the legal phase of ISBE, and engage in negotiations with funding agencies and other bodies previously expressing an interest in supporting ISBE. WP11 identified the establishment of a Memorandum of Understanding as the best form of agreement to support the interim phase. Finally, WP11 outlined a process whereby expressions of interest and/or the identification of ISBE candidate national systems biology centres could be approved through transparent review that also responded to the strategic and financial expectations of ISBE funding organisations. Plans for developing this interim phase were developed through discussions with WP11 Funding Governance and Legal Advisory Committee (FGLAC), then via Focus Group 5 (2014) followed by joint Focus Groups 4 and 5 (2015).

Between September 2012 and December 2013, ISBE project WP11 staff engaged representatives from a range of national funding agencies through one-to-one engagement, and via updates and the twice yearly meetings of the Work Package 11 meetings. Input following interviews was received from 16 Countries and further information on roadmap activities was obtained for a further 6 countries. The summary of those discussions is provided within this document.