An atlas of human metabolism

Jonathan L Robinson; Pınar Kocabaş; Hao Wang; Pierre-Etienne Cholley; Daniel Cook; Avlant Nilsson; Mihail Anton; Raphael Ferreira; Iván Domenzain; Virinchi Billa; Angelo Limeta; Alex Hedin; Johan Gustafsson; Eduard J Kerkhoven; L Thomas Svensson; Bernhard O Palsson; Adil Mardinoglu; Lena Hansson; Mathias Uhlén; Jens Nielsen

doi:10.1126/scisignal.aaz1482

An atlas of human metabolism

Sci Signal. 2020 Mar 24;13(624):eaaz1482. doi: 10.1126/scisignal.aaz1482.

Authors

Jonathan L Robinson^{1

2}, Pınar Kocabaş^{1

2}, Hao Wang^{1

3

4}, Pierre-Etienne Cholley⁴, Daniel Cook¹, Avlant Nilsson¹, Mihail Anton⁴, Raphael Ferreira¹, Iván Domenzain^{1

2}, Virinchi Billa¹, Angelo Limeta¹, Alex Hedin¹, Johan Gustafsson^{1

2}, Eduard J Kerkhoven¹, L Thomas Svensson⁴, Bernhard O Palsson^{5

6

7}, Adil Mardinoglu^{8

9}, Lena Hansson^{4

10}, Mathias Uhlén^{5

8

11}, Jens Nielsen^{12

2

5

13}

Affiliations

¹ Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41258 Gothenburg, Sweden.
² Wallenberg Center for Protein Research, Chalmers University of Technology, Kemivägen 10, SE-41258 Gothenburg, Sweden.
³ Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Kemivägen 10, SE-41258 Gothenburg, Sweden.
⁴ Department of Biology and Biological Engineering, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Chalmers University of Technology, Kemivägen 10, SE-41258 Gothenburg, Sweden.
⁵ Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark.
⁶ Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA.
⁷ Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
⁸ Department of Protein Science, Science for Life Laboratory, KTH-Royal Institute of Technology, SE-10044 Stockholm, Sweden.
⁹ Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London WC2R 2LS, UK.
¹⁰ Novo Nordisk Research Centre Oxford, Oxford OX3 7FZ, UK.
¹¹ Wallenberg Center for Protein Research, KTH-Royal Institute of Technology, SE-10044 Stockholm, Sweden.
¹² Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-41258 Gothenburg, Sweden. nielsenj@chalmers.se.
¹³ BioInnovation Institute, Ole Maaløes Vej 3, DK-2200 Copenhagen, Denmark.

Abstract

Genome-scale metabolic models (GEMs) are valuable tools to study metabolism and provide a scaffold for the integrative analysis of omics data. Researchers have developed increasingly comprehensive human GEMs, but the disconnect among different model sources and versions impedes further progress. We therefore integrated and extensively curated the most recent human metabolic models to construct a consensus GEM, Human1. We demonstrated the versatility of Human1 through the generation and analysis of cell- and tissue-specific models using transcriptomic, proteomic, and kinetic data. We also present an accompanying web portal, Metabolic Atlas (https://www.metabolicatlas.org/), which facilitates further exploration and visualization of Human1 content. Human1 was created using a version-controlled, open-source model development framework to enable community-driven curation and refinement. This framework allows Human1 to be an evolving shared resource for future studies of human health and disease.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology*
Humans
Metabolome*
Software*

Grants and funding

F32 CA220848/CA/NCI NIH HHS/United States