A guide to 13C metabolic flux analysis for the cancer biologist

[1]  Christian M. Metallo,et al.  Reverse engineering the cancer metabolic network using flux analysis to understand drivers of human disease. , 2018, Metabolic engineering.

[2]  Christopher P. Long,et al.  Hexokinase-2 depletion inhibits glycolysis and induces oxidative phosphorylation in hepatocellular carcinoma and sensitizes to metformin , 2018, Nature Communications.

[3]  Christopher P. Long,et al.  13C metabolic flux analysis of three divergent extremely thermophilic bacteria: Geobacillus sp. LC300, Thermus thermophilus HB8, and Rhodothermus marinus DSM 4252. , 2017, Metabolic engineering.

[4]  G. Stephanopoulos,et al.  Review of metabolic pathways activated in cancer cells as determined through isotopic labeling and network analysis. , 2017, Metabolic engineering.

[5]  Avlant Nilsson,et al.  Genome scale metabolic modeling of cancer. , 2017, Metabolic engineering.

[6]  R. Deberardinis,et al.  Engineering approaches to study cancer metabolism. , 2017, Metabolic engineering.

[7]  J. Marini,et al.  Exo-MFA - A 13C metabolic flux analysis framework to dissect tumor microenvironment-secreted exosome contributions towards cancer cell metabolism. , 2017, Metabolic engineering.

[8]  F. Chiaradonna,et al.  Analysis of mitochondrial metabolism in situ: Combining stable isotope labeling with selective permeabilization. , 2017, Metabolic engineering.

[9]  R. Deberardinis,et al.  Quantitative metabolic flux analysis reveals an unconventional pathway of fatty acid synthesis in cancer cells deficient for the mitochondrial citrate transport protein. , 2017, Metabolic engineering.

[10]  Kevin D. Smith,et al.  Application of 13C flux analysis to identify high-productivity CHO metabolic phenotypes. , 2017, Metabolic engineering.

[11]  Matthew G. Vander Heiden,et al.  Understanding the Intersections between Metabolism and Cancer Biology , 2017, Cell.

[12]  Christopher P. Long,et al.  Enzyme I facilitates reverse flux from pyruvate to phosphoenolpyruvate in Escherichia coli , 2017, Nature Communications.

[13]  Christopher P. Long,et al.  Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis. , 2017, Metabolic engineering.

[14]  Christopher P. Long,et al.  13C metabolic flux analysis of microbial and mammalian systems is enhanced with GC-MS measurements of glycogen and RNA labeling. , 2016, Metabolic engineering.

[15]  Christopher P. Long,et al.  Optimal tracers for parallel labeling experiments and 13C metabolic flux analysis: A new precision and synergy scoring system. , 2016, Metabolic engineering.

[16]  Karen H. Vousden,et al.  Serine and one-carbon metabolism in cancer , 2016, Nature Reviews Cancer.

[17]  Scott B. Crown,et al.  Evidence for transketolase-like TKTL1 flux in CHO cells based on parallel labeling experiments and (13)C-metabolic flux analysis. , 2016, Metabolic engineering.

[18]  Christopher P. Long,et al.  Characterization of physiological responses to 22 gene knockouts in Escherichia coli central carbon metabolism. , 2016, Metabolic engineering.

[19]  Scott B. Crown,et al.  Comprehensive metabolic modeling of multiple 13C-isotopomer data sets to study metabolism in perfused working hearts. , 2016, American journal of physiology. Heart and circulatory physiology.

[20]  D. Sabatini,et al.  Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism , 2016, Cell.

[21]  P. Carmeliet,et al.  A key role for transketolase-like 1 in tumor metabolic reprogramming , 2016, Oncotarget.

[22]  J. Rabinowitz,et al.  Malic enzyme tracers reveal hypoxia-induced switch in adipocyte NADPH pathway usage. , 2016, Nature chemical biology.

[23]  M. Antoniewicz,et al.  Measuring the Composition and Stable-Isotope Labeling of Algal Biomass Carbohydrates via Gas Chromatography/Mass Spectrometry. , 2016, Analytical chemistry.

[24]  Christian M. Metallo,et al.  Reductive carboxylation supports redox homeostasis during anchorage-independent growth , 2016, Nature.

[25]  D. Sabatini,et al.  A PHGDH inhibitor reveals coordination of serine synthesis and 1-carbon unit fate , 2016, Nature chemical biology.

[26]  Adam M. Feist,et al.  Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology , 2016, PloS one.

[27]  J. Locasale,et al.  The Warburg Effect: How Does it Benefit Cancer Cells? , 2016, Trends in biochemical sciences.

[28]  B. Faubert,et al.  Metabolic Heterogeneity in Human Lung Tumors , 2016, Cell.

[29]  Abhishek K. Jha,et al.  Environment Impacts the Metabolic Dependencies of Ras-Driven Non-Small Cell Lung Cancer. , 2016, Cell metabolism.

[30]  C. Thompson,et al.  The Emerging Hallmarks of Cancer Metabolism. , 2016, Cell metabolism.

[31]  Christian M. Metallo,et al.  Branched chain amino acid catabolism fuels adipocyte differentiation and lipogenesis , 2015, Nature chemical biology.

[32]  Scott B. Crown,et al.  Catabolism of Branched Chain Amino Acids Contributes Significantly to Synthesis of Odd-Chain and Even-Chain Fatty Acids in 3T3-L1 Adipocytes , 2015, PloS one.

[33]  Maciek R. Antoniewicz,et al.  Parallel labeling experiments for pathway elucidation and (13)C metabolic flux analysis. , 2015, Current opinion in biotechnology.

[34]  Averina Nicolae,et al.  Identification of active elementary flux modes in mitochondria using selectively permeabilized CHO cells. , 2015, Metabolic engineering.

[35]  Maciek R Antoniewicz,et al.  (13)C-metabolic flux analysis of co-cultures: A novel approach. , 2015, Metabolic engineering.

[36]  Joerg M. Buescher,et al.  A roadmap for interpreting (13)C metabolite labeling patterns from cells. , 2015, Current opinion in biotechnology.

[37]  Jamey D. Young,et al.  Mass spectrometry-based microassay of (2)H and (13)C plasma glucose labeling to quantify liver metabolic fluxes in vivo. , 2015, American journal of physiology. Endocrinology and metabolism.

[38]  R. Deberardinis,et al.  Metabolic pathways promoting cancer cell survival and growth , 2015, Nature Cell Biology.

[39]  Christopher P. Long,et al.  Integrated 13C-metabolic flux analysis of 14 parallel labeling experiments in Escherichia coli. , 2015, Metabolic engineering.

[40]  M. Antoniewicz Methods and advances in metabolic flux analysis: a mini-review , 2015, Journal of Industrial Microbiology & Biotechnology.

[41]  A. Harris,et al.  Acetyl-CoA Synthetase 2 Promotes Acetate Utilization and Maintains Cancer Cell Growth under Metabolic Stress , 2015, Cancer cell.

[42]  R. Hammer,et al.  Acetate Dependence of Tumors , 2014, Cell.

[43]  R. Deberardinis,et al.  Acetate Is a Bioenergetic Substrate for Human Glioblastoma and Brain Metastases , 2014, Cell.

[44]  J. Rabinowitz,et al.  Quantitative analysis of acetyl-CoA production in hypoxic cancer cells reveals substantial contribution from acetate , 2014, Cancer & Metabolism.

[45]  Christopher P. Long,et al.  Quantifying biomass composition by gas chromatography/mass spectrometry. , 2014, Analytical chemistry.

[46]  Vitaly A. Selivanov,et al.  13C metabolic flux analysis shows that resistin impairs the metabolic response to insulin in L6E9 myotubes , 2014, BMC Systems Biology.

[47]  N. Hay,et al.  The pentose phosphate pathway and cancer. , 2014, Trends in biochemical sciences.

[48]  Christopher P. Long,et al.  Metabolic flux analysis of Escherichia coli knockouts: lessons from the Keio collection and future outlook. , 2014, Current opinion in biotechnology.

[49]  M. Antoniewicz,et al.  Metabolic network reconstruction, growth characterization and 13C-metabolic flux analysis of the extremophile Thermus thermophilus HB8. , 2014, Metabolic engineering.

[50]  T. Shlomi,et al.  Quantitative flux analysis reveals folate-dependent NADPH production , 2014, Nature.

[51]  Adam M. Feist,et al.  Tracing compartmentalized NADPH metabolism in the cytosol and mitochondria of mammalian cells. , 2014, Molecular cell.

[52]  Jamey D. Young,et al.  INCA: a computational platform for isotopically non-stationary metabolic flux analysis , 2014, Bioinform..

[53]  M. Cleary,et al.  New methodologies for studying lipid synthesis and turnover: looking backwards to enable moving forwards. , 2014, Biochimica et biophysica acta.

[54]  Maciek R Antoniewicz,et al.  13C metabolic flux analysis: optimal design of isotopic labeling experiments. , 2013, Current opinion in biotechnology.

[55]  M. Antoniewicz Dynamic metabolic flux analysis--tools for probing transient states of metabolic networks. , 2013, Current opinion in biotechnology.

[56]  Jamey D. Young Metabolic flux rewiring in mammalian cell cultures. , 2013, Current opinion in biotechnology.

[57]  Maciek R Antoniewicz,et al.  Publishing 13C metabolic flux analysis studies: a review and future perspectives. , 2013, Metabolic engineering.

[58]  Gregory Stephanopoulos,et al.  Kinetic isotope effects significantly influence intracellular metabolite [superscript 13]C labeling patterns and flux determination , 2013 .

[59]  J. Locasale Serine, glycine and one-carbon units: cancer metabolism in full circle , 2013, Nature Reviews Cancer.

[60]  G. Stephanopoulos,et al.  Metformin decreases glucose oxidation and increases the dependency of prostate cancer cells on reductive glutamine metabolism. , 2013, Cancer research.

[61]  Ronan M. T. Fleming,et al.  A community-driven global reconstruction of human metabolism , 2013, Nature Biotechnology.

[62]  Scott B. Crown,et al.  Parallel labeling experiments and metabolic flux analysis: Past, present and future methodologies. , 2013, Metabolic engineering.

[63]  Christian M. Metallo,et al.  Understanding metabolic regulation and its influence on cell physiology. , 2013, Molecular cell.

[64]  Karsten Hiller,et al.  Profiling metabolic networks to study cancer metabolism. , 2013, Current opinion in biotechnology.

[65]  Maciek R Antoniewicz,et al.  Parallel labeling experiments with [1,2-(13)C]glucose and [U-(13)C]glutamine provide new insights into CHO cell metabolism. , 2013, Metabolic engineering.

[66]  R. Deberardinis,et al.  Cellular Metabolism and Disease: What Do Metabolic Outliers Teach Us? , 2012, Cell.

[67]  Maciek R Antoniewicz,et al.  Selection of tracers for 13C-metabolic flux analysis using elementary metabolite units (EMU) basis vector methodology. , 2012, Metabolic engineering.

[68]  M. Antoniewicz,et al.  Towards dynamic metabolic flux analysis in CHO cell cultures , 2012, Biotechnology journal.

[69]  Christian M. Metallo,et al.  Reductive glutamine metabolism by IDH1 mediates lipogenesis under hypoxia , 2011, Nature.

[70]  Scott B. Crown,et al.  Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells , 2012, BMC Systems Biology.

[71]  M. Antoniewicz,et al.  Dynamic metabolic flux analysis (DMFA): a framework for determining fluxes at metabolic non-steady state. , 2011, Metabolic engineering.

[72]  R. Deberardinis Serine metabolism: some tumors take the road less traveled. , 2011, Cell metabolism.

[73]  M. Antoniewicz,et al.  Metabolic flux analysis of CHO cells at growth and non-growth phases using isotopic tracers and mass spectrometry. , 2011, Metabolic engineering.

[74]  Elmar Heinzle,et al.  Eukaryotic metabolism: Measuring compartment fluxes , 2011, Biotechnology journal.

[75]  A. Caudy,et al.  Riboneogenesis in Yeast , 2011, Cell.

[76]  U. Sauer,et al.  Large-scale 13C-flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli , 2011, Molecular systems biology.

[77]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[78]  Maciek R Antoniewicz,et al.  Resolving the TCA cycle and pentose-phosphate pathway of Clostridium acetobutylicum ATCC 824: Isotopomer analysis, in vitro activities and expression analysis. , 2011, Biotechnology journal.

[79]  이연수 Functional genomics reveal that the serine synthesis pathway is essential in breast cancer , 2011 .

[80]  Jason W. Locasale,et al.  Evidence for an Alternative Glycolytic Pathway in Rapidly Proliferating Cells , 2010, Science.

[81]  Elmar Heinzle,et al.  Metabolic flux analysis in eukaryotes. , 2010, Current opinion in biotechnology.

[82]  Gregory Stephanopoulos,et al.  Evaluation of 13C isotopic tracers for metabolic flux analysis in mammalian cells. , 2009, Journal of biotechnology.

[83]  H. Mori,et al.  Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism , 2009, Molecular systems biology.

[84]  Alexander Bauer,et al.  Quantification of statin effects on hepatic cholesterol synthesis by transient (13)C-flux analysis. , 2009, Metabolic engineering.

[85]  Bing Wu,et al.  Characterization of the Central Metabolic Pathways in Thermoanaerobacter sp. Strain X514 via Isotopomer-Assisted Metabolite Analysis , 2009, Applied and Environmental Microbiology.

[86]  Gregory Stephanopoulos,et al.  Quantifying Reductive Carboxylation Flux of Glutamine to Lipid in a Brown Adipocyte Cell Line* , 2008, Journal of Biological Chemistry.

[87]  Jamey D. Young,et al.  An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis , 2008, Biotechnology and bioengineering.

[88]  R. Deberardinis,et al.  Beyond aerobic glycolysis: Transformed cells can engage in glutamine metabolism that exceeds the requirement for protein and nucleotide synthesis , 2007, Proceedings of the National Academy of Sciences.

[89]  G. Stephanopoulos,et al.  Metabolic flux analysis in a nonstationary system: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol. , 2007, Metabolic engineering.

[90]  G. Stephanopoulos,et al.  Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. , 2007, Metabolic engineering.

[91]  Gregory Stephanopoulos,et al.  Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. , 2006, Metabolic engineering.

[92]  Gregory Stephanopoulos,et al.  Evaluation of regression models in metabolic physiology: predicting fluxes from isotopic data without knowledge of the pathway , 2006, Metabolomics.

[93]  Wolfgang Wiechert,et al.  From stationary to instationary metabolic flux analysis. , 2005, Advances in biochemical engineering/biotechnology.

[94]  P. Schubert,et al.  Mutations in the transketolase-like gene TKTL1: clinical implications for neurodegenerative diseases, diabetes and cancer. , 2005, Clinical laboratory.

[95]  W. Wiechert,et al.  Bidirectional reaction steps in metabolic networks: III. Explicit solution and analysis of isotopomer labeling systems. , 1999, Biotechnology and bioengineering.

[96]  J. Villadsen,et al.  Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. , 1997, Biotechnology and bioengineering.

[97]  J. Wahren,et al.  Contributions of gluconeogenesis to glucose production in the fasted state. , 1996, The Journal of clinical investigation.

[98]  G. Stephanopoulos,et al.  Intracellular flux analysis in hybridomas using mass balances and in vitro 13C nmr , 1995, Biotechnology and bioengineering.

[99]  J. Kelleher,et al.  Isotopomer spectral analysis of triglyceride fatty acid synthesis in 3T3-L1 cells. , 1992, The American journal of physiology.

[100]  O. Warburg [Origin of cancer cells]. , 1956, Oncologia.