Final Report Summary - METAFLUX (Metabolic Flux Analysis and Cancer)
METAFLUX examines the hypothesis that cancer causes significant and mechanistically important changes to the flux of cellular metabolites, and that these metabolites can be used a markers in disease diagnoses, based on an understanding of cellular metabolic pathways and their responses to drug intervention, both in vitro and in vivo.
METAFLUX aims to address this problem by developing state of the art technologies to measure and model metabolic flux in the context of Cancer.
The research objectives of METAFLUX include:
1) Establishment of model cancer cell systems to study metabolic flux in vitro.
2) To compare the metabolic flux measurements in cellular models using different technologies.
3) To study the influence of drugs in various cancer models
4) To build computational models that help understand mechanisms underlying cancer.
5) To test new hypotheses arising from the combination of different flux measurements and computational modelling, focussing on new cancer biomarkers and drug targets.
METAFLUX focuses on the training of young researchers, to enable them to go on to successful research careers. Training objectives of Metaflux include:
- Delivering a structured training programme taught by leading international scientists in the state-of-the art infrastructure, which covers a portfolio of interdisciplinary techniques.
- To provide academic, industrial and public sector employers with researchers skilled in a wide range of techniques and direct experience of interaction across disciplines and sectors.
- To produce researchers with excellent transferable skills, and able to transform abstract ideas into influential outcomes.
- To create an active, long-term network of young researchers whose personal contacts, support and expertise will help Europe shape the future of metabolomics research.
- Delivering European researchers able to become leaders in the field in the near future.
At the completion of the project, 21 ESRs and 2 ERs have been employed on the project. The researchers recruited to the project initially received training in relevant laboratory and research skills, and now after 48 months of the project, the scientific highlights of the project include:
Development and optimisation of the novel method of measuring metabolic activity of living primary cells using the NMR spectroscopy (UBham).
CLL cells exhibit high metabolic plasticity and are able to alter their metabolism depending on the oxygen condition (UbHam).
Metabolic fluxes in MCF7 breast cancer cell lines reveal a mechanism of altered pentose phosphate cycle and increased pyruvate carboxylase activity under hypoxic conditions (UBham).
In a mouse model residual breast cancer metabolism post chemotherapy has been studied using metabolic fluxes, showing a more aggressive Warburg effect in the cells that survive paclitaxel treatment (Ubham).
A DNP high-pressure dissolution kit has been developed that works with the Hypersense DNP system (OI/ UBHam).
Imaging of tumour glycolysis using hyperpolarized 13C-labelled glucose and detection of pentose phosphate pathway activity (published in Nature Medicine). (UCam).
Early detection of pancreatic cancer using hyperpolarized [1-13C]pyruvate. Translation of this technique to the clinic may enable detection of pancreatic cancer at a stage that is still curable by resection.Detection of the singlet state of hyperpolarized [1-13C] pyruvate in a mouse in vivo. This is the first time that a singlet state has been detected in vivo. Accessing the singlet state in other metabolites may be used to extend their polarization lifetimes, thus increasing the applicability of the technique (Ucam).
Models of metabolic flux network reprogramming in cancer cell lines have been established in joint efforts between fellows in partners MTASZBK, BIOCRATES and UB (UB).
Hypothesis arising from the different flux measurements and computational modelling focusing on new drug targets has been tested using siRNA or appropriate drugs targeting the key steps identified from flux measurements (UB).
Metabolic flux reprogramming accompanying angiogenic activation has been characterized and glycogen phosphorylase was identified as a putative drug target to impair tumour angiogenesis (UB).
Enzymes in pentose phosphate pathway and glutamine metabolism have been identified as putative drug targets in lung, breast cancer and prostate cancer models (UB).
A new a chain search based method for prioritization and contextualization of biological subnetworks has been developed (UB partner fellow) in collaboration with an SME in the field of software development (Biomax, Germany) (UB).
A computer program that separates natural from assayed artificial mass isotopomer distributions, and offers different ways of corrections for overlapping peaks depending of the nature of such peaks have been developed. This program has been submitted for publication and can be available for internal use to the consortia even pending to be published (UB.
Identify how metabolic pathways are modified to promote glioblastoma growth and invasiveness (EPFL)The hepatic metabolic fluxes are estimated using 13C labelling of TCA cycle intermediates within a single 1-min experiment, enabling comparative studies of different metabolic states like hepatocellular carcinoma (HCC) (EPFL).
Identify potential biomarkers for glioblastoma (EPFL)
Directly compare the neurochemical profile of glioblastoma in the human patient and in the animal model to ensure the highest significance of the results derived by the animal model (EPFL)
Technical developments in DNP in vivo protocols to be able to probe metabolic precursors . especially to understand cancer metabolism (EPFL).
Network-driven discovery of mechanisms underlying calcitriol and fatty acid oxidation as therapeutic targets in metastatic prostate cancer (1) (MTASZBK)
Developing a new algorithm to efficiently identify and sample unbiased metabolic pathways in genome-scale metabolic networks. Application to identify novel pathways formed by enzyme side activities (2) (MTASZBK)
Fellows have also presented their work at more than 14 international conferences, including at the Radiology Society of North America, Chicago, USA 2012 (E. Serrao, UCam, Young Investigator award in Molecular Imaging), 21st meeting of International Society of Magnetic Resonance in Medicine (ISMRM), Salt Lake City, USA, 2013, (Irene Marco-Ruis, Ucam, Prize for best poster presentation); and 3rd International Conference on Constraint-based Reconstruction and Analysis (Wintergreen, VA, USA 2014)(F. Pal, MTASZBK, Best Poster Presentation Award).
In addition, fellows have undertaken transferable skills training in areas such as communication and listening skills, Scientific Writing, and Computer programming.
By the end of the project, we have held 3 Workshops (ATC), and 4 Lab-based courses (LBC). The first METAFLUX workshop was held in April 2012, and the program highlighted the projects involved in METAFLUX. Talks from PI's and external speakers were insightful about cellular metabolic networks and the various techniques used for the analysis of fluxes. The workshop introduced various techniques like NMR, DNP-NMR, PET, and GC-MS, and demonstrated the importance of communication among the network. The second Workshop was held in Hungary in October 2013, and focused on Computational Flux Modelling, with topics including things such as as principles of constraint-based modelling of large-scale metabolic networks and integration of heterogeneous omics data.. The final workshop was held in Barcelona in July 2014 and covered topics including gene expression data (computational tools to convert raw microarray data to usable data) and DNP-NMR technique (basics of technique, sample preparation and examples of its use in in vivo studies).
4 LBC for the METAFLUX fellows have also been run, the first of these covered metabolism, metabolic flux analysis (MFA), and NMR-based analytical methods. The second course was a practical course in mass spectrometry. The third course, run alongside the workshop in Hungary, covered an introduction to computational methods for metabolic modelling. The final LBC covered DNP-NMR and analysis of gene expression data.
The Metaflux website is at http://http/beregond.bham.ac.uk/METAFLUX/Home.html. The contacts for the Metaflux project are Prof. Ulrich Günther (Project Co-ordinator: u.l.gunther@bham.ac.uk) and Dr. Karen Atkins (Project Manager: k.l.atkins@bham.ac.uk).
METAFLUX aims to address this problem by developing state of the art technologies to measure and model metabolic flux in the context of Cancer.
The research objectives of METAFLUX include:
1) Establishment of model cancer cell systems to study metabolic flux in vitro.
2) To compare the metabolic flux measurements in cellular models using different technologies.
3) To study the influence of drugs in various cancer models
4) To build computational models that help understand mechanisms underlying cancer.
5) To test new hypotheses arising from the combination of different flux measurements and computational modelling, focussing on new cancer biomarkers and drug targets.
METAFLUX focuses on the training of young researchers, to enable them to go on to successful research careers. Training objectives of Metaflux include:
- Delivering a structured training programme taught by leading international scientists in the state-of-the art infrastructure, which covers a portfolio of interdisciplinary techniques.
- To provide academic, industrial and public sector employers with researchers skilled in a wide range of techniques and direct experience of interaction across disciplines and sectors.
- To produce researchers with excellent transferable skills, and able to transform abstract ideas into influential outcomes.
- To create an active, long-term network of young researchers whose personal contacts, support and expertise will help Europe shape the future of metabolomics research.
- Delivering European researchers able to become leaders in the field in the near future.
At the completion of the project, 21 ESRs and 2 ERs have been employed on the project. The researchers recruited to the project initially received training in relevant laboratory and research skills, and now after 48 months of the project, the scientific highlights of the project include:
Development and optimisation of the novel method of measuring metabolic activity of living primary cells using the NMR spectroscopy (UBham).
CLL cells exhibit high metabolic plasticity and are able to alter their metabolism depending on the oxygen condition (UbHam).
Metabolic fluxes in MCF7 breast cancer cell lines reveal a mechanism of altered pentose phosphate cycle and increased pyruvate carboxylase activity under hypoxic conditions (UBham).
In a mouse model residual breast cancer metabolism post chemotherapy has been studied using metabolic fluxes, showing a more aggressive Warburg effect in the cells that survive paclitaxel treatment (Ubham).
A DNP high-pressure dissolution kit has been developed that works with the Hypersense DNP system (OI/ UBHam).
Imaging of tumour glycolysis using hyperpolarized 13C-labelled glucose and detection of pentose phosphate pathway activity (published in Nature Medicine). (UCam).
Early detection of pancreatic cancer using hyperpolarized [1-13C]pyruvate. Translation of this technique to the clinic may enable detection of pancreatic cancer at a stage that is still curable by resection.Detection of the singlet state of hyperpolarized [1-13C] pyruvate in a mouse in vivo. This is the first time that a singlet state has been detected in vivo. Accessing the singlet state in other metabolites may be used to extend their polarization lifetimes, thus increasing the applicability of the technique (Ucam).
Models of metabolic flux network reprogramming in cancer cell lines have been established in joint efforts between fellows in partners MTASZBK, BIOCRATES and UB (UB).
Hypothesis arising from the different flux measurements and computational modelling focusing on new drug targets has been tested using siRNA or appropriate drugs targeting the key steps identified from flux measurements (UB).
Metabolic flux reprogramming accompanying angiogenic activation has been characterized and glycogen phosphorylase was identified as a putative drug target to impair tumour angiogenesis (UB).
Enzymes in pentose phosphate pathway and glutamine metabolism have been identified as putative drug targets in lung, breast cancer and prostate cancer models (UB).
A new a chain search based method for prioritization and contextualization of biological subnetworks has been developed (UB partner fellow) in collaboration with an SME in the field of software development (Biomax, Germany) (UB).
A computer program that separates natural from assayed artificial mass isotopomer distributions, and offers different ways of corrections for overlapping peaks depending of the nature of such peaks have been developed. This program has been submitted for publication and can be available for internal use to the consortia even pending to be published (UB.
Identify how metabolic pathways are modified to promote glioblastoma growth and invasiveness (EPFL)The hepatic metabolic fluxes are estimated using 13C labelling of TCA cycle intermediates within a single 1-min experiment, enabling comparative studies of different metabolic states like hepatocellular carcinoma (HCC) (EPFL).
Identify potential biomarkers for glioblastoma (EPFL)
Directly compare the neurochemical profile of glioblastoma in the human patient and in the animal model to ensure the highest significance of the results derived by the animal model (EPFL)
Technical developments in DNP in vivo protocols to be able to probe metabolic precursors . especially to understand cancer metabolism (EPFL).
Network-driven discovery of mechanisms underlying calcitriol and fatty acid oxidation as therapeutic targets in metastatic prostate cancer (1) (MTASZBK)
Developing a new algorithm to efficiently identify and sample unbiased metabolic pathways in genome-scale metabolic networks. Application to identify novel pathways formed by enzyme side activities (2) (MTASZBK)
Fellows have also presented their work at more than 14 international conferences, including at the Radiology Society of North America, Chicago, USA 2012 (E. Serrao, UCam, Young Investigator award in Molecular Imaging), 21st meeting of International Society of Magnetic Resonance in Medicine (ISMRM), Salt Lake City, USA, 2013, (Irene Marco-Ruis, Ucam, Prize for best poster presentation); and 3rd International Conference on Constraint-based Reconstruction and Analysis (Wintergreen, VA, USA 2014)(F. Pal, MTASZBK, Best Poster Presentation Award).
In addition, fellows have undertaken transferable skills training in areas such as communication and listening skills, Scientific Writing, and Computer programming.
By the end of the project, we have held 3 Workshops (ATC), and 4 Lab-based courses (LBC). The first METAFLUX workshop was held in April 2012, and the program highlighted the projects involved in METAFLUX. Talks from PI's and external speakers were insightful about cellular metabolic networks and the various techniques used for the analysis of fluxes. The workshop introduced various techniques like NMR, DNP-NMR, PET, and GC-MS, and demonstrated the importance of communication among the network. The second Workshop was held in Hungary in October 2013, and focused on Computational Flux Modelling, with topics including things such as as principles of constraint-based modelling of large-scale metabolic networks and integration of heterogeneous omics data.. The final workshop was held in Barcelona in July 2014 and covered topics including gene expression data (computational tools to convert raw microarray data to usable data) and DNP-NMR technique (basics of technique, sample preparation and examples of its use in in vivo studies).
4 LBC for the METAFLUX fellows have also been run, the first of these covered metabolism, metabolic flux analysis (MFA), and NMR-based analytical methods. The second course was a practical course in mass spectrometry. The third course, run alongside the workshop in Hungary, covered an introduction to computational methods for metabolic modelling. The final LBC covered DNP-NMR and analysis of gene expression data.
The Metaflux website is at http://http/beregond.bham.ac.uk/METAFLUX/Home.html. The contacts for the Metaflux project are Prof. Ulrich Günther (Project Co-ordinator: u.l.gunther@bham.ac.uk) and Dr. Karen Atkins (Project Manager: k.l.atkins@bham.ac.uk).