Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches

Spatial-fluxomics provides a subcellular-compartmentalized view of reductive glutamine metabolism in cancer cells

(2019) Won Dong Lee et al.   Nature Communications

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis

(2018) Dongxin Zhao et al.   MOLECULAR CELL

Recon3D enables a three-dimensional view of gene variation in human metabolism

(2018) Elizabeth Brunk et al.   NATURE BIOTECHNOLOGY

Increased formate overflow is a hallmark of oxidative cancer

(2018) Johannes Meiser et al.   Nature Communications

Structural absorption by barbule microstructures of super black bird of paradise feathers

(2018) Dakota E. McCoy et al.   Nature Communications

Constraint based modeling of metabolism allows finding metabolic cancer hallmarks and identifying personalized therapeutic windows

(2018) Sergio Bordel   Oncotarget

Understanding metabolism with flux analysis: From theory to application

(2017) Ziwei Dai et al.   METABOLIC ENGINEERING

Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis

(2017) Wentao Dong et al.   METABOLIC ENGINEERING

Quantitative metabolic flux analysis reveals an unconventional pathway of fatty acid synthesis in cancer cells deficient for the mitochondrial citrate transport protein

(2017) Lei Jiang et al.   METABOLIC ENGINEERING

Temporal fluxomics reveals oscillations in TCA cycle flux throughout the mammalian cell cycle

(2017) Eunyong Ahn et al.   Molecular Systems Biology

An integrated computational and experimental study uncovers FUT9 as a metabolic driver of colorectal cancer

(2017) Noam Auslander et al.   Molecular Systems Biology

Personal model‐assisted identification of NAD + and glutathione metabolism as intervention target in NAFLD

(2017) Adil Mardinoglu et al.   Molecular Systems Biology

Glucose feeds the TCA cycle via circulating lactate

(2017) Sheng Hui et al.   NATURE

Synthetic lethality and cancer

(2017) Nigel J. O'Neil et al.   NATURE REVIEWS GENETICS

An in-silico approach to predict and exploit synthetic lethality in cancer metabolism

(2017) Iñigo Apaolaza et al.   Nature Communications

A systems approach reveals distinct metabolic strategies among the NCI-60 cancer cell lines

(2017) Maike K. Aurich et al.   PLoS Computational Biology

A Systematic Evaluation of Methods for Tailoring Genome-Scale Metabolic Models

(2017) Sjoerd Opdam et al.   Cell Systems

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

The Emerging Hallmarks of Cancer Metabolism

(2016) Natalya N. Pavlova et al.   Cell Metabolism

Environment Impacts the Metabolic Dependencies of Ras-Driven Non-Small Cell Lung Cancer

(2016) Shawn M. Davidson et al.   Cell Metabolism

Optimal tracers for parallel labeling experiments and 13 C metabolic flux analysis: A new precision and synergy scoring system

(2016) Scott B. Crown et al.   METABOLIC ENGINEERING

Reductive carboxylation supports redox homeostasis during anchorage-independent growth

(2016) Lei Jiang et al.   NATURE

Metabolite concentrations, fluxes and free energies imply efficient enzyme usage

(2016) Junyoung O Park et al.   Nature Chemical Biology

Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage

(2016) Ling Liu et al.   Nature Chemical Biology

The Warburg Effect: How Does it Benefit Cancer Cells?

(2016) Maria V. Liberti et al.   TRENDS IN BIOCHEMICAL SCIENCES

Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease

(2016) Tuulia Hyötyläinen et al.   Nature Communications

Breast Cancer-Derived Lung Metastases Show Increased Pyruvate Carboxylase-Dependent Anaplerosis

(2016) Stefan Christen et al.   Cell Reports

Fundamentals of cancer metabolism

(2016) R. J. DeBerardinis et al.   Science Advances

A roadmap for interpreting 13 C metabolite labeling patterns from cells

(2015) Joerg M Buescher et al.   CURRENT OPINION IN BIOTECHNOLOGY

Identification of active elementary flux modes in mitochondria using selectively permeabilized CHO cells

(2015) Averina Nicolae et al.   METABOLIC ENGINEERING

13C metabolic flux analysis at a genome-scale

(2015) Saratram Gopalakrishnan et al.   METABOLIC ENGINEERING

Modeling cancer metabolism on a genome scale

(2015) K. Yizhak et al.   Molecular Systems Biology

Synthetic dosage lethality in the human metabolic network is highly predictive of tumor growth and cancer patient survival

(2015) Wout Megchelenbrink et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

(2015) Katarzyna Tomczak et al.   Wspolczesna Onkologia-Contemporary Oncology

A Method to Constrain Genome-Scale Models with 13C Labeling Data

(2015) Héctor García Martín et al.   PLoS Computational Biology

Quantitation of Cellular Metabolic Fluxes of Methionine

(2014) Tomer Shlomi et al.   ANALYTICAL CHEMISTRY

INCA: a computational platform for isotopically non-stationary metabolic flux analysis

(2014) J. D. Young   BIOINFORMATICS

Non-stationary 13C metabolic flux analysis of Chinese hamster ovary cells in batch culture using extracellular labeling highlights metabolic reversibility and compartmentation

(2014) Averina Nicolae et al.   BMC Systems Biology

IDH1 Mutations Alter Citric Acid Cycle Metabolism and Increase Dependence on Oxidative Mitochondrial Metabolism

(2014) A. R. Grassian et al.   CANCER RESEARCH

Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells

(2014) Caroline A. Lewis et al.   MOLECULAR CELL

Regulation of Substrate Utilization by the Mitochondrial Pyruvate Carrier

(2014) Nathaniel M. Vacanti et al.   MOLECULAR CELL

Quantitative flux analysis reveals folate-dependent NADPH production

(2014) Jing Fan et al.   NATURE

Constraint-based models predict metabolic and associated cellular functions

(2014) Aarash Bordbar et al.   NATURE REVIEWS GENETICS

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

(2014) Nikos Vlassis et al.   PLoS Computational Biology

Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer

(2014) Keren Yizhak et al.   eLife

Genome-scale modeling of human metabolism - a systems biology approach

(2013) Adil Mardinoglu et al.   Biotechnology Journal

Isotopically non-stationary metabolic flux analysis: complex yet highly informative

(2013) Wolfgang Wiechert et al.   CURRENT OPINION IN BIOTECHNOLOGY

Fatty Acid Labeling from Glutamine in Hypoxia Can Be Explained by Isotope Exchange without Net Reductive Isocitrate Dehydrogenase (IDH) Flux

(2013) Jing Fan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Understanding Metabolic Regulation and Its Influence on Cell Physiology

(2013) Christian M. Metallo et al.   MOLECULAR CELL

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Metabolic targets for cancer therapy

(2013) Lorenzo Galluzzi et al.   NATURE REVIEWS DRUG DISCOVERY

Contribution of serine, folate and glycine metabolism to the ATP, NADPH and purine requirements of cancer cells

(2013) P M Tedeschi et al.   Cell Death & Disease

Model-based identification of drug targets that revert disrupted metabolism and its application to ageing

(2013) Keren Yizhak et al.   Nature Communications

Reductive glutamine metabolism is a function of the α-ketoglutarate to citrate ratio in cells

(2013) Sarah-Maria Fendt et al.   Nature Communications

13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

(2012) Michael Weitzel et al.   BIOINFORMATICS

Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE

(2012) Yuliang Wang et al.   BMC Systems Biology

Isotopically nonstationary 13C flux analysis of Myc-induced metabolic reprogramming in B-cells

(2012) Taylor A. Murphy et al.   METABOLIC ENGINEERING

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Constraining the metabolic genotype–phenotype relationship using a phylogeny of in silico methods

(2012) Nathan E. Lewis et al.   NATURE REVIEWS MICROBIOLOGY

Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation

(2012) M. Jain et al.   SCIENCE

Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT

(2012) Rasmus Agren et al.   PLoS Computational Biology

Integration of expression data in genome-scale metabolic network reconstructions

(2012) Anna S. Blazier et al.   Frontiers in Physiology

Functional genomics reveal that the serine synthesis pathway is essential in breast cancer

(2011) Richard Possemato et al.   NATURE

Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase

(2011) Christian Frezza et al.   NATURE

Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia

(2011) Christian M. Metallo et al.   NATURE

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

Molecular Crowding Defines a Common Origin for the Warburg Effect in Proliferating Cells and the Lactate Threshold in Muscle Physiology

(2011) Alexei Vazquez et al.   PLoS One

Genome-Scale Metabolic Modeling Elucidates the Role of Proliferative Adaptation in Causing the Warburg Effect

(2011) Tomer Shlomi et al.   PLoS Computational Biology

iMAT: an integrative metabolic analysis tool

(2010) Hadas Zur et al.   BIOINFORMATICS

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

Stationary versus non-stationary 13C-MFA: A comparison using a consistent dataset

(2010) Stephan Noack et al.   JOURNAL OF BIOTECHNOLOGY

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Decomposing complex reaction networks using random sampling, principal component analysis, and basis rotation

(2009) Christian L Barrett et al.   BMC Systems Biology

Novel biological insights through metabolomics and 13C-flux analysis

(2009) Nicola Zamboni et al.   CURRENT OPINION IN MICROBIOLOGY

Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation

(2009) M. G. Vander Heiden et al.   SCIENCE

Quantifying Reductive Carboxylation Flux of Glutamine to Lipid in a Brown Adipocyte Cell Line

(2008) Hyuntae Yoo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Network-based prediction of human tissue-specific metabolism

(2008) Tomer Shlomi et al.   NATURE BIOTECHNOLOGY

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

Kinetic flux profiling for quantitation of cellular metabolic fluxes

(2008) Jie Yuan et al.   Nature Protocols

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology