ArticlePLoS computational biology2014
A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Metabolic reprogramming and immunosenescence: a new sight for glioma therapy.Frontiers in cell and developmental biology · 2026Review
- Impact of IDH Mutations on Ligand Unbinding: Insights from Steered Molecular Dynamics.Current topics in medicinal chemistry · 2026Article
- A constraint-based framework for exploring the impact of multireaction dependencies on metabolic functions.NPJ systems biology and applications · 2025Article
- Unraveling the metabolic heterogeneity and commonality in senescent cells using systems modeling.Life medicine · 2025Article
- Genome-scale models in human metabologenomics.Nature reviews. Genetics · 2025Review
- The metabolic-epigenetic interface: lysine succinylation orchestrates bidirectional crosstalk in neurodegenerative disorders.Frontiers in neurology · 2025Review
- Prediction of metabolites associated with somatic mutations in cancers by using genome-scale metabolic models and mutation data.Genome biology · 2024Article
- Genome-scale metabolic models applied for human health and biopharmaceutical engineering.Quantitative biology (Beijing, China) · 2023Review
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- Crosstalk between Metabolite Production and Signaling Activity in Breast Cancer.International journal of molecular sciences · 2023Article
- System-level metabolic modeling facilitates unveiling metabolic signature in exceptional longevity.Aging cell · 2022Article
- A mechanistic modeling framework reveals the key principles underlying tumor metabolism.PLoS computational biology · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Metabostemness in cancer: Linking metaboloepigenetics and mitophagy in remodeling cancer stem cells.Stem cell reviews and reports · 2022Review
- Mitochondrial Dysfunction Pathway Alterations Offer Potential Biomarkers and Therapeutic Targets for Ovarian Cancer.Oxidative medicine and cellular longevity · 2022Review
- Genome Scale Modeling to Study the Metabolic Competition between Cells in the Tumor Microenvironment.Cancers · 2021Review
- Thermodynamic Genome-Scale Metabolic Modeling of Metallodrug Resistance in Colorectal Cancer.Cancers · 2021Article
- Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models.Journal of personalized medicine · 2021Article
- DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks.PLoS computational biology · 2021Article
- Construction, comparison and evolution of networks in life sciences and other disciplines.Journal of the Royal Society, Interface · 2020Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation. However, this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases (IDH), succinate dehydrogenase (SDH), and fumarate hydratase (FH) that produce oncometabolites that competitively inhibit epigenetic regulation. In this study, we demonstrate in silico predictions of oncometabolites that have the potential to dysregulate epigenetic controls in nine types of cancer by incorporating massive scale genetic mutation information (collected from more than 1,700 cancer genomes), expression profiling data, and deploying Recon 2 to reconstruct context-specific genome-scale metabolic models. Our analysis predicted 15 compounds and 24 substructures of potential oncometabolites that could result from the loss-of-function and gain-of-function mutations of metabolic enzymes, respectively. These results suggest a substantial potential for discovering unidentified oncometabolites in various forms of cancers.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.