The challenges for molecular nutrition research 4: the “nutritional systems biology level”

Ommen, Ben van; Cavallieri, Duccio; Roche, Helen M.; Klein, Ulla I.; Daniel, Hannelore

doi:10.1007/s12263-008-0090-5

Cited by 21 publications

(14 citation statements)

References 26 publications

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“…The application of systems biology to nutrition aims at highlighting molecular links between diet and health in an integrated manner (van Ommen et al 2008). Interactome models have been increasingly used, especially proteinprotein interaction (PPI) networks which provide an abstraction of the complex relationships among different molecular components-spanning from nutrients and their metabolites to diet-modulated transcription factors (Nguyen et al 2011).…”

Section: Discussionmentioning

confidence: 99%

Zinc proteome interaction network as a model to identify nutrient-affected pathways in human pathologies

et al. 2014

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Zinc is an essential micronutrient playing fundamental roles in cellular metabolism. It acts mostly through binding a wide range of proteins, thus affecting a broad spectrum of biological processes, which include cell division, growth and differentiation. Full annotation of zinc-binding proteins showed them to represent about 10 % of the human proteome, with over 300 enzymes containing zinc ions within their catalytic domains. Also, hundreds of key regulatory proteins, including transcription factors, require zinc for their activity. In this study, the whole set of zinc-binding proteins together with their direct interactors was listed and defined as the zinc proteome (ZNP). We interrogated pathway analysis tools to identify the cellular processes that are predicted to be affected by zinc availability. Network and functional enrichment analyses highlighted biological processes potentially affected by deregulated zinc homeostasis. This computational approach was also tested on a real case study: The possible involvement of ZNP network proteins in Crohn's disease pathogenesis was assessed on genes transcriptionally regulated in the intestine of patients affected by this condition. The analysis produced a network of pathways likely to be influenced by zinc and associated with Crohn's disease. These results highlight a central role for zinc in the tissue remodeling process which occurs upon gut inflammation, pointing at novel disease pathways whose effect could be worsened by zinc dyshomeostasis and impaired zinc fluxes in specific damaged areas. Overall, our computational approach could provide novel insights into pathological conditions and could therefore be used to drive mechanistic research in under-investigated fields of research. An interactive version of the determined ZNP network is available at URL http://93.63.165.11/ZNnetwork/.

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Section: Discussionmentioning

confidence: 99%

Zinc proteome interaction network as a model to identify nutrient-affected pathways in human pathologies

et al. 2014

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“…A thorough understanding of the association between nutrients and disease requires the use of approaches to integrate information derived from a multitude of molecular entities and pathways involved. Recently, nutritional systems biology has emerged as a powerful approach to address challenges in nutritional research using advanced omics technologies (de Graaf et al, 2009; Kaput and Morine, 2012; Panagiotou and Nielsen, 2009; van Ommen et al, 2008; Zhao et al, 2015). In principle, nutritional systems biology purposes to assess the interactions and influences of nutritional intake at multiple molecular layers involved in information processing in cells, tissues, and organ systems.…”

Section: Challenges Posed By the Multiple Effects Of Diet On Brain Camentioning

confidence: 99%

System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders

Gómez‐Pinilla

Yang

2018

Progress in Neurobiology

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The surge in meals high in calories has prompted an epidemic of metabolic disorders around the world such that the elevated incidence of obese and diabetic individuals is alarming. New research indicates that metabolic disorders pose a risk for neurological and psychiatric conditions including stroke, Alzheimer’s disease, Huntington’s disease, and depression, all of which have a metabolic component. These relationships are rooted to a dysfunctional interaction between molecular processes that regulate energy metabolism and synaptic plasticity. The strong adaptive force of dietary factors on shaping the brain during evolution can be manipulated to trans form the interaction between cell bioenergetics and epigenome with the aptitude to promote long-lasting brain healthiness. A thorough understanding of the association between the broad action of nutrients and brain fitness requires high level data processing empowered with the capacity to integrate information from a multitude of molecular entities and pathways. Nutritional systems biology is emerging as a viable approach to elucidate the multiple molecular layers involved in information processing in cells, tissues, and organ systems in response to diet. Information about the wide range of cellular and molecular interactions elicited by foods on the brain and cognitive plasticity is crucial for the design of public health initiatives for curtailing the epidemic of metabolic and brain disorders.

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“…We now understand that pathways interact with regulatory elements, with one another, and with systems critical to the endocrine, circulatory, digestive, nervous, and immune function (Afacan et al 2012;MacLellan et al 2012;Slikker et al 2007;van Ommen et al 2008a, b;Zhao et al 2012). As an example, a map of the central immunity pathway linking the toll-like receptor 4 to the transcription factor NFjB (a master regulator responsive to nutrients) contains only 20 core components, but adding just the main interacting elements of these 20 core proteins expands the network to more than 800 proteins (Gardy et al 2009).…”

Section: The Slow Application Of Systems Thinking To Biomedical Researchmentioning

confidence: 99%

“…The goal of systems nutrition (Fairweather-Tait 2003;van Ommen et al 2008avan Ommen et al , 2009de Graaf et al 2009;Morine et al 2010Morine et al , 2011Morine et al , 2012Fu et al 2011), systems Fig. 1 Examples of experimental variables for systems nutrition research.…”

Section: Conceptual Framework Of Systems Nutritionmentioning

confidence: 99%

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

Kaput

Ommen²,

Kremer³

et al. 2013

Genes Nutr

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Nutrition research, like most biomedical disciplines, adopted and often uses experimental approaches based on Beadle and Tatum's one gene-one polypeptide hypothesis, thereby reducing biological processes to single reactions or pathways. Systems thinking is needed to understand the complexity of health and disease processes requiring measurements of physiological processes, as well as environmental and social factors, which may alter the expression of genetic information. Analysis of physiological processes with omics technologies to assess systems' responses has only become available over the past decade and remains costly. Studies of environmental and social conditions known to alter health are often not connected to biomedical research. While these facts are widely accepted, developing and conducting comprehensive research programs for health are often beyond financial and human resources of single research groups. We propose a new research program on essential nutrients for optimal underpinning of growth and health (ENOUGH) that will use systems approaches with more comprehensive measurements and biostatistical analysis of the many biological and environmental factors that influence undernutrition. Creating a knowledge base for nutrition and health is a necessary first step toward developing solutions targeted to different populations in diverse social and physical environments for the two billion undernourished people in developed and developing economies.

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The challenges for molecular nutrition research 4: the “nutritional systems biology level”

Cited by 21 publications

References 26 publications

Zinc proteome interaction network as a model to identify nutrient-affected pathways in human pathologies

Zinc proteome interaction network as a model to identify nutrient-affected pathways in human pathologies

System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders

Consensus statement understanding health and malnutrition through a systems approach: the ENOUGH program for early life

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