Publication

Kelder T. (1,11), Summer G. (1,2), Caspers M. (1), van Schothorst E.M. (3), Keijer J. (3), Duivenvoorde L. (3), Klaus S. (4), Voigt A. (4), Bohnert L. (4), Pico C. (5,6), Palou A. (5,6), Bonet M.L. (5,6), Dembinska-Kiec A. (7), Malczewska-Malec M. (7), Kie?-Wilk B. (8), Del Bas J.M. (9), Caimari A. (9), Arola L. (9,10), van Erk M. (1), van Ommen B. (1), Radonjic M. (1)

Genes Nutr. 2015;10(1):439.

(1) Microbiology & Systems Biology, TNO, Zeist, The Netherlands; (2) CARIM, Maastricht University, Maastricht, The Netherlands; (3) Human and Animal Physiology, Wageningen University, Wageningen, The Netherlands; (4) Group of Energy Metabolism, German Institute of Human Nutrition in Potsdam, Nuthetal, Germany; (5) Molecular Biology, Nutrition and Biotechnology (Nutrigenomics), University of the Balearic Islands (UIB), Palma de Mallorca, Spain; (6) CIBER Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Palma de Mallorca, Spain; (7) Department of Clinical Biochemistry, Jagiellonian University Medical College, Krakow, Poland; (8) Department of Metabolic Disorders, Jagiellonian University Medical College, Krakow, Poland; (9) Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, Reus, Spain; (10) Rovira i Virgili University, Tarragona, Spain; and (11) EdgeLeap B.V., Hooghiemstraplein 15, 3514 AX, Utrecht, The Netherlands.

Abstract

Optimal health is maintained by interaction of multiple intrinsic and environmental factors at different levels of complexity-from molecular, to physiological, to social. Understanding and quantification of these interactions will aid design of successful health interventions. We introduce the reference network concept as a platform for multi-level exploration of biological relations relevant for metabolic health, by integration and mining of biological interactions derived from public resources and context-specific experimental data. A White Adipose Tissue Health Reference Network (WATRefNet) was constructed as a resource for discovery and prioritization of mechanism-based biomarkers for white adipose tissue (WAT) health status and the effect of food and drug compounds on WAT health status. The WATRefNet (6,797 nodes and 32,171 edges) is based on (1) experimental data obtained from 10 studies addressing different adiposity states, (2) seven public knowledge bases of molecular interactions, (3) expert's definitions of five physiologically relevant processes key to WAT health, namely WAT expandability, Oxidative capacity, Metabolic state, Oxidative stress and Tissue inflammation, and (4) a collection of relevant biomarkers of these processes identified by BIOCLAIMS ( http://bioclaims.uib.es ). The WATRefNet comprehends multiple layers of biological complexity as it contains various types of nodes and edges that represent different biological levels and interactions. We have validated the reference network by showing overrepresentation with anti-obesity drug targets, pathology-associated genes and differentially expressed genes from an external disease model dataset. The resulting network has been used to extract subnetworks specific to the above-mentioned expert-defined physiological processes. Each of these process-specific signatures represents a mechanistically supported composite biomarker for assessing and quantifying the effect of interventions on a physiological aspect that determines WAT health status. Following this principle, five anti-diabetic drug interventions and one diet intervention were scored for the match of their expression signature to the five biomarker signatures derived from the WATRefNet. This confirmed previous observations of successful intervention by dietary lifestyle and revealed WAT-specific effects of drug interventions. The WATRefNet represents a sustainable knowledge resource for extraction of relevant relationships such as mechanisms of action, nutrient intervention targets and biomarkers and for assessment of health effects for support of health claims made on food products. 

doi: 10.1007/s12263-014-0439-x.

Event date: 03/12/2014

Publication date: Mon May 25 13:45:00 CEST 2015