A community-driven global reconstruction of human metabolism
Ines Thiele,Neil Swainston,Ronan M. T. Fleming,Andreas Hoppe,Swagatika Sahoo,Maike K. Aurich,Hulda S. Haraldsdóttir,Monica L. Mo,Ottar Rolfsson,Miranda D. Stobbe,Miranda D. Stobbe,Stefan Gretar Thorleifsson,Rasmus Agren,Christian Bölling,Sergio Bordel,Arvind K. Chavali,Paul D. Dobson,Warwick B. Dunn,Warwick B. Dunn,Lukas Endler,David Hala,Michael Hucka,Duncan Hull,Daniel Jameson,Neema Jamshidi,Jon J. Jonsson,Nick Juty,Sarah M. Keating,Intawat Nookaew,Nicolas Le Novère,Nicolas Le Novère,Naglis Malys,Naglis Malys,Alexander Mazein,Jason A. Papin,Nathan D. Price,Evgeni Selkov,Martin I. Sigurdsson,Evangelos Simeonidis,Evangelos Simeonidis,Nikolaus Sonnenschein,Kieran Smallbone,Anatoly Sorokin,Anatoly Sorokin,Johannes H. G. M. van Beek,Dieter Weichart,Igor Goryanin,Jens Nielsen,Hans V. Westerhoff,Douglas B. Kell,Pedro Mendes,Pedro Mendes,Bernhard O. Palsson,Bernhard O. Palsson +53 more
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TLDR
Recon 2, a community-driven, consensus 'metabolic reconstruction', is described, which is the most comprehensive representation of human metabolism that is applicable to computational modeling and has improved topological and functional features.Abstract:
Multiple models of human metabolism have been reconstructed, but each represents only a subset of our knowledge. Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling. Compared with its predecessors, the reconstruction has improved topological and functional features, including ~2× more reactions and ~1.7× more unique metabolites. Using Recon 2 we predicted changes in metabolite biomarkers for 49 inborn errors of metabolism with 77% accuracy when compared to experimental data. Mapping metabolomic data and drug information onto Recon 2 demonstrates its potential for integrating and analyzing diverse data types. Using protein expression data, we automatically generated a compendium of 65 cell type–specific models, providing a basis for manual curation or investigation of cell-specific metabolic properties. Recon 2 will facilitate many future biomedical studies and is freely available at http://humanmetabolism.org/.read more
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Improving lipid mapping in Genome Scale Metabolic Networks using ontologies.
Nathalie Poupin,Florence Vinson,Arthur Moreau,Aurélie Batut,Maxime Chazalviel,Benoit Colsch,Laetitia Fouillen,Sarah Guez,Spiro Khoury,Jessica Dalloux-Chioccioli,Anthony Tournadre,Pauline Le Faouder,Corinne Pouyet,Pierre van Delft,Fanny Viars,Justine Bertrand-Michel,Fabien Jourdan +16 more
TL;DR: A new matching method based on the ChEBI ontology that can be applied to any metabolomics data and therefore improve the comprehension of metabolic modulations and provide ways for improvements in terms of network curation and lipidomics data annotation.
Journal ArticleDOI
Genome-wide metabolic model to improve understanding of CD4+ T cell metabolism, immunometabolism and application in drug design
TL;DR: This work reconstructed the genome-wide metabolic network of naïve CD4(+) T cells, CD4T1670, by integrating transcriptome and metabolism data and found that depletion of either glucose or glutamine did not significantly affect ATP production and biomass, but dramatically unbalanced the metabolic network and increased the release of some inflammation or anti-inflammation related factors.
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Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism.
Filmon Eyassu,Claudio Angione +1 more
TL;DR: A constraint-based metabolic model is developed and manually curated to investigate the mechanism of pyruvate dehydrogenase under hypoxia and results in lactate accumulation, consistent with recenthypoxia studies and a well-known feature in cancer metabolism.
Journal ArticleDOI
Integrating Extracellular Flux Measurements and Genome-Scale Modeling Reveals Differences between Brown and White Adipocytes
Alfred K. Ramirez,Alfred K. Ramirez,Matthew D. Lynes,Farnaz Shamsi,Ruidan Xue,Yu-Hua Tseng,C. Ronald Kahn,Simon Kasif,Jonathan M. Dreyfuss,Jonathan M. Dreyfuss +9 more
TL;DR: The XF Analyzer's metabolic profile from human white and brown adipocytes is integrated with a genome-scale metabolic model to predict flux differences across the metabolic map and uncovered a difference in how adipocytes dispose of nitrogenous waste.
Journal ArticleDOI
Quantitative constraint-based computational model of tumor-to-stroma coupling via lactate shuttle
Fabrizio Capuani,Daniele De Martino,Daniele De Martino,Enzo Marinari,Andrea De Martino,Andrea De Martino +5 more
TL;DR: In this article, a large-scale in silico metabolic model of interacting human cells was analyzed and it was shown that synergistic multi-cell effects play a central role in cancer sustainment.
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