ArticleBioinformatics (Oxford, England)2017
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis.
Article in Bioinformatics (Oxford, England), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.PLoS computational biology · 2023Review
- Understanding Antimicrobial Resistance Using Genome-Scale Metabolic Modeling.Antibiotics (Basel, Switzerland) · 2023Review
- Systems Biology in ELIXIR: modelling in the spotlight.F1000Research · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Elucidating Plant-Microbe-Environment Interactions Through Omics-Enabled Metabolic Modelling Using Synthetic Communities.Frontiers in plant science · 2022Article
- SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems.Bioinformatics (Oxford, England) · 2021Article
- GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.PLoS computational biology · 2021Article
- Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment.Cancers · 2021Review
- On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples.Current genomics · 2021Article
- MaREA4Galaxy: Metabolic reaction enrichment analysis and visualization of RNA-seq data within Galaxy.Computational and structural biotechnology journal · 2020Article
- Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.PLoS computational biology · 2019Article
- Human Systems Biology and Metabolic Modelling: A Review-From Disease Metabolism to Precision Medicine.BioMed research international · 2019Review
- A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect.PLoS computational biology · 2017Article
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Authors and funding
6 authors.
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Abstract
motivationIntratumour heterogeneity poses many challenges to the treatment of cancer. Unfortunately, the transcriptional and metabolic information retrieved by currently available computational and experimental techniques portrays the average behaviour of intermixed and heterogeneous cell subpopulations within a given tumour. Emerging single-cell genomic analyses are nonetheless unable to characterize the interactions among cancer subpopulations. In this study, we propose popFBA , an extension to classic Flux Balance Analysis, to explore how metabolic heterogeneity and cooperation phenomena affect the overall growth of cancer cell populations.
resultsWe show how clones of a metabolic network of human central carbon metabolism, sharing the same stoichiometry and capacity constraints, may follow several different metabolic paths and cooperate to maximize the growth of the total population. We also introduce a method to explore the space of possible interactions, given some constraints on plasma supply of nutrients. We illustrate how alternative nutrients in plasma supply and/or a dishomogeneous distribution of oxygen provision may affect the landscape of heterogeneous phenotypes. We finally provide a technique to identify the most proliferative cells within the heterogeneous population. AVAILABILITY AND IMPLEMENTATION: the popFBA MATLAB function and the SBML model are available at https://github.com/BIMIB-DISCo/popFBA . CONTACT: chiara.damiani@unimib.it.
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