A dynamic multi-tissue model to study human metabolism.
Journal
NPJ systems biology and applications
ISSN: 2056-7189
Titre abrégé: NPJ Syst Biol Appl
Pays: England
ID NLM: 101677786
Informations de publication
Date de publication:
22 01 2021
22 01 2021
Historique:
received:
03
06
2019
accepted:
19
10
2020
entrez:
23
1
2021
pubmed:
24
1
2021
medline:
5
10
2021
Statut:
epublish
Résumé
Metabolic modeling enables the study of human metabolism in healthy and in diseased conditions, e.g., the prediction of new drug targets and biomarkers for metabolic diseases. To accurately describe blood and urine metabolite dynamics, the integration of multiple metabolically active tissues is necessary. We developed a dynamic multi-tissue model, which recapitulates key properties of human metabolism at the molecular and physiological level based on the integration of transcriptomics data. It enables the simulation of the dynamics of intra-cellular and extra-cellular metabolites at the genome scale. The predictive capacity of the model is shown through the accurate simulation of different healthy conditions (i.e., during fasting, while consuming meals or during exercise), and the prediction of biomarkers for a set of Inborn Errors of Metabolism with a precision of 83%. This novel approach is useful to prioritize new biomarkers for many metabolic diseases, as well as for the integration of various types of personal omics data, towards the personalized analysis of blood and urine metabolites.
Identifiants
pubmed: 33483512
doi: 10.1038/s41540-020-00159-1
pii: 10.1038/s41540-020-00159-1
pmc: PMC7822846
doi:
Substances chimiques
Biomarkers
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
5Références
Front Physiol. 2016 Jan 22;6:410
pubmed: 26834640
Nat Protoc. 2011 Aug 04;6(9):1290-307
pubmed: 21886097
Proc Natl Acad Sci U S A. 2007 Feb 6;104(6):1777-82
pubmed: 17267599
Annu Int Conf IEEE Eng Med Biol Soc. 2016 Aug;2016:1417-1421
pubmed: 28268592
Nat Biotechnol. 2013 May;31(5):419-25
pubmed: 23455439
Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6
pubmed: 17202168
Sci Rep. 2018 Aug 21;8(1):12504
pubmed: 30131500
Biotechnol Bioeng. 1996 May 5;50(3):299-318
pubmed: 18626958
Nucleic Acids Res. 2014 Jan;42(Database issue):D938-43
pubmed: 24271388
Nucleic Acids Res. 2011 Jan;39(Database issue):D1011-5
pubmed: 21177656
BMC Syst Biol. 2011 Oct 31;5:180
pubmed: 22041191
Mol Syst Biol. 2007;3:119
pubmed: 17625511
Nat Commun. 2014;5:3083
pubmed: 24419221
J Appl Physiol (1985). 2007 Oct;103(4):1227-33
pubmed: 17656631
Am J Physiol Endocrinol Metab. 2000 Jan;278(1):E65-75
pubmed: 10644538
Mol Biosyst. 2012 Oct;8(10):2545-58
pubmed: 22699794
Proc Natl Acad Sci U S A. 2009 Oct 20;106(42):17787-92
pubmed: 19805130
Science. 2012 May 25;336(6084):1040-4
pubmed: 22628656
BMC Genomics. 2015 Oct 19;16:809
pubmed: 26480823
J Physiol. 2005 Nov 1;568(Pt 3):941-50
pubmed: 16020461
Mol Syst Biol. 2009;5:263
pubmed: 19401675
Curr Opin Microbiol. 2010 Jun;13(3):344-9
pubmed: 20430689
Nat Methods. 2007 Nov;4(11):911-3
pubmed: 17906632
PLoS One. 2016 Feb 23;11(2):e0150006
pubmed: 26906900
J Physiol. 2001 Oct 1;536(Pt 1):295-304
pubmed: 11579177
Metabolomics. 2016;12:109
pubmed: 27358602
Biophys J. 2002 Sep;83(3):1331-40
pubmed: 12202358
Mol Syst Biol. 2007;3:135
pubmed: 17882155
Nat Commun. 2016 Feb 03;7:8994
pubmed: 26839171
Compr Physiol. 2014 Jan;4(1):177-97
pubmed: 24692138
Physiol Meas. 2004 Aug;25(4):905-20
pubmed: 15382830
Mol Syst Biol. 2013;9:649
pubmed: 23511207
Nucleic Acids Res. 2018 Jan 4;46(D1):D608-D617
pubmed: 29140435
J Clin Invest. 1997 Sep 1;100(5):1305-19
pubmed: 9276749
Nucleic Acids Res. 2009 Jan;37(Database issue):D603-10
pubmed: 18953024
J Strength Cond Res. 2009 Oct;23(7):2090-5
pubmed: 19855335
J Inherit Metab Dis. 2015 Nov;38(6):1029-39
pubmed: 25875217
Am J Clin Nutr. 2000 Aug;72(2 Suppl):558S-63S
pubmed: 10919960
NPJ Syst Biol Appl. 2017 Jan 31;3:3
pubmed: 28649430
PLoS Comput Biol. 2012;8(10):e1002750
pubmed: 23133351
Med Sci Sports Exerc. 2002 Jan;34(1):92-7
pubmed: 11782653
Am J Physiol Endocrinol Metab. 2009 Sep;297(3):E578-91
pubmed: 19531645
Nucleic Acids Res. 2013 Jan;41(Database issue):D801-7
pubmed: 23161693
Mol Syst Biol. 2011 Jun 21;7:501
pubmed: 21694718
J Inherit Metab Dis. 2018 May;41(3):337-353
pubmed: 29453510
Genome Biol. 2005;6(6):R49
pubmed: 15960801
Am J Physiol Endocrinol Metab. 2016 Sep 1;311(3):E543-53
pubmed: 27436612
Nat Biotechnol. 2018 Mar;36(3):272-281
pubmed: 29457794
Mol Syst Biol. 2010 Sep 7;6:411
pubmed: 20823849
J Nutr Health Aging. 2015 Oct;19(8):839-45
pubmed: 26412288
J Physiol. 2000 May 1;524 Pt 3:919-28
pubmed: 10790168
Front Physiol. 2011 Dec 30;2:112
pubmed: 22232606
Acta Physiol Scand. 2003 Aug;178(4):385-90
pubmed: 12864743
J Physiol. 2004 Dec 15;561(Pt 3):871-82
pubmed: 15498802