Tareen et al. Genes & Nutrition (2018) 13:17 https://doi.org/10.1186/s12263-018-0609-3 REVIEW Open Access Exploring the cellular network of metabolic flexibility in the adipose tissue Samar H. K. Tareen1* , Martina Kutmon1,2, Michiel E. Adriaens1, Edwin C. M. Mariman3, Theo M. de Kok1,4, Ilja C. W. Arts1,5 and Chris T. Evelo1,2 Abstract Background: Metabolic flexibility is the ability of cells to change substrates for energy production based on the nutrient availability and energy requirement. It has been shown that metabolic flexibility is impaired in obesity and chronic diseases such as type 2 diabetes mellitus, cardiovascular diseases, and metabolic syndrome, although, whether it is a cause or an effect of these conditions remains to be elucidated. Main body: In this paper, we have reviewed the literature on metabolic flexibility and curated pathways and processes resulting in a network resource to investigate the interplay between these processes in the subcutaneous adipose tissue. The adipose tissue has been shown to be responsible, not only for energy storage but also for maintaining energy homeostasis through oxidation of glucose and fatty acids. We highlight the role of pyruvate dehydrogenase complex–pyruvate dehydrogenase kinase (PDC-PDK) interaction as a regulatory switch which is primarily responsible for changing substrates in energy metabolism from glucose to fatty acids and back. Baseline gene expression of the subcutaneous adipose tissue, along with a publicly available obesity data set, are visualised on the cellular network of metabolic flexibility to highlight the genes that are expressed and which are differentially affected in obesity. Conclusion: We have constructed an abstracted network covering glucose and fatty acid oxidation, as well as the PDC-PDK regulatory switch. In addition, we have shown how the network can be used for data visualisation and as a resource for follow-up studies. Keywords: Obesity, Metabolic flexibility, Regulation, Networks, Pathways, Metabolism Background Given that metabolic flexibility is associated with Metabolic flexibility is defined as the ability of an organ- maintaining a dynamic and shifting balance between the ism to adapt its substrate for energy production in cellular two sources of energy, it may have a prominent role in respiration, based on the availability of the substrates [1]. the development of metabolic diseases and associated The primary substrates are glucose and fatty acids, which conditions. The inability or impairment of the organism are converted to acetyl-coenzyme A (acetyl-CoA) for use to change its source as per requirements is called meta- in the tricarboxylic acid cycle (TCA cycle). Cellular respir- bolic inflexibility. A number of recent studies have ation for most tissues and organs utilises only one energy started focusing on its association with conditions substrate at a given time; glucose during the fed state and pertaining to malfunctioning metabolism, including fatty acids during the fasted state (exceptions include the obesity, type 2 diabetes mellitus (T2DM), cardiovascu- brain for example). However, it has been observed that lar diseases (CVD) and metabolic syndrome (MetS) under stress and severe energy deprivation conditions, this [2–5]. Considering the implication of metabolic flexi- exclusivity can be broken and both glucose and fatty acids bility in disease development, we focus on curating are consumed for energy production [1]. the underlying cellular/molecular mechanisms in this study, specifically in the adipose tissue as several adi- * Correspondence: [email protected] pose tissue gene expression markers have linked it 1Maastricht Centre for Systems Biology (MaCSBio), Maastricht University, Maastricht, the Netherlands with reduced metabolic flexibility [6]. Full list of author information is available at the end of the article © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Tareen et al. Genes & Nutrition (2018) 13:17 Page 2 of 8 Adipose tissue holds a central role in metabolic flexi- of the subcutaneous adipose tissue [14] along with expres- bility and energy metabolism with major regulatory sion data from a publicly available obesity dataset [15]are mechanisms and roles, both tissue- and organism-wide mapped onto the network as a use case showing the [7, 8]. Although adipose tissue stores the majority of the expression of the components of the network under fat in the body, most of the fat is synthesised de novo by baseline/non-diseased and obese conditions. the liver. The adipose tissue ends up storing both the synthesised fat released by the liver, as well as dietary fat Biochemical pathways of metabolic flexibility [9]. In addition, the adipose tissue only takes up 10–15% In this review, we have curated an abstracted network of circulating glucose [10]. However, this interplay and representing pathways of cellular metabolic flexibility balance between glucose uptake as well fatty acid uptake through literature review and querying the WikiPath- and later release is the result of metabolic flexibility in ways database [16]. We started with biochemical reac- the adipose tissue. Indeed, metabolic inflexibility in the tions involved in glucose and fatty acid oxidation in the adipose tissue has been known to cause impaired adi- adipose tissue, namely the glycolysis and fatty acid pokine signalling, as well as impaired non-esterified β-oxidation processes, and expanded them to link them fatty acid (NEFA) clearance from circulation, trigger- to each other via the TCA cycle. Next, rate-limiting ing NEFA-mediated signalling cascades in other tis- enzymes as well as transport, signalling and regulatory sues (reviewed in [11, 12]). Thus, the impairment of proteins were included to expand upon the biochemical metabolic flexibility in the adipose tissue can cause processes, along with their respective interactions with systemic effects with regard to energy provision and other components already in the network. This was related processes. followed by the addition of fatty acid synthesis down- In this review, we summarise the cellular mechanisms stream of the TCA cycle as a feedback mechanism to pertaining to metabolic flexibility in a network of fatty acid β-oxidation. Furthermore, cellular signalling cas- interacting molecular species and processes. The major cades known to affect cellular oxidation were also added. benefit of this approach is that it allows further study of Finally, to give a simplified overview and ease its un- the various cellular processes involved in metabolic flexi- derstanding, the network was abstracted by only leaving bility to pinpoint crucial elements in the said systems. in rate-limiting steps, major metabolites between the Similar approaches have previously been employed, for said steps, and associated regulatory proteins. The exact example in [13] where data and existing knowledge were procedure and order of reduction differs from network collectively used to identify seemingly unrelated processes to network; however, the basic idea remains the same, involved in adipogenesis in culture. In our review, we em- i.e. to represent multiple nodes and/or edges by a single ploy existing knowledge in terms of known pathways to node and/or edge. Figure 1 illustrates this procedure. As curate a network representing cellular metabolic flexibility an example, consider the procedure of fatty acid break- in the adipocytes. Subsequently, baseline expression data down to release multiple Acyl-CoA molecules, which is Fig. 1 Methodology overview showing the workflow to construct the abstracted network. (i) Known knowledge in the form of published literature and databases is queried regarding cellular metabolism. (ii) Base biological processes are isolated and then expanded by adding regulators and other related processes as long as they are related to cellular metabolism. (iii) The expanded network is then abstracted by merging edges such that only major components and rate-limiting steps remain Tareen et al. Genes & Nutrition (2018) 13:17 Page 3 of 8 a multi-step process involving multiple sets of enzymes pathways are interacting with each other, in particular and reactions. However, unless we are specifically targeting how the various products of the TCA cycle are playing astepwithinthisprocedure,oroneofthestepsisa roles in activating or inhibiting different pathways through rate-limiting step under scrutiny, we can represent the feedback mechanisms. We define any interaction that acti- whole breakdown process in an abstracted manner using a vates or continues a process in the network as a positive fatty acid node, linked to an Acyl-CoA node with an edge. interaction. In the network shown in Fig. 2, these positive The resultant abstracted cellular network of metabolic interactions cover transcriptional activation, allosteric flexibility is shown in Fig. 2. The colour coded sections activation, biochemical reactions (substrate consumption identify the major pathways