Inter-Tissue Gene Co-Expression Networks between Metabolically Healthy and Unhealthy Obese Individuals

RESEARCH ARTICLE Inter-Tissue Gene Co-Expression Networks between Metabolically Healthy and Unhealthy Obese Individuals Lisette J. A. Kogelman1, Jingyuan Fu2,3, Lude Franke2, Jan Willem Greve4, Marten Hofker5, Sander S. Rensen6, Haja N. Kadarmideen1* a11111 1 Department of Large Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark, 2 University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands, 3 University of Groningen, University Medical Center Groningen, Department of Paediatrics, Groningen, The Netherlands, 4 Department of General Surgery, Atrium Medical Center Parkstad, Heerlen, the Netherlands, 5 Pediatrics Molecular Genetics, University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands, 6 Department of Surgery, NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, The Netherlands * OPEN ACCESS Citation: Kogelman LJA, Fu J, Franke L, Greve JW, Hofker M, Rensen SS, et al. (2016) Inter-Tissue Gene Co-Expression Networks between Metabolically Healthy and Unhealthy Obese Individuals. PLoS ONE 11(12): e0167519. doi:10.1371/journal.pone.0167519 Editor: Guillermo López Lluch, Universidad Pablo de Olavide, SPAIN Received: June 23, 2016 Accepted: November 15, 2016 Published: December 1, 2016 Copyright: © 2016 Kogelman et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All raw data are publicly available at Gene Expression Omnibus (GSE22070). Funding: Lisette J. A. Kogelman is funded by a post-doctoral fellowship within Biochild project (http://biochild.ku.dk/) with grant (0603-00457B) from the Programme Commission on Individuals, Disease and Society under the Danish Council for Strategic Research (Innovationsfonden). Haja N. Kadarmideen thanks EU-FP7 Marie Curie Actions – Career Integration Grant (CIG-293511) for partially funding his time spent on this research. Abstract Background Obesity is associated with severe co-morbidities such as type 2 diabetes and nonalcoholic steatohepatitis. However, studies have shown that 10–25 percent of the severely obese individuals are metabolically healthy. To date, the identification of genetic factors underlying the metabolically healthy obese (MHO) state is limited. Systems genetics approaches have led to the identification of genes and pathways in complex diseases. Here, we have used such approaches across tissues to detect genes and pathways involved in obesity-induced disease development. Methods Expression data of 60 severely obese individuals was accessible, of which 28 individuals were MHO and 32 were metabolically unhealthy obese (MUO). A whole genome expression profile of four tissues was available: liver, muscle, subcutaneous adipose tissue and visceral adipose tissue. Using insulin-related genes, we used the weighted gene co-expression network analysis (WGCNA) method to build within- and inter-tissue gene networks. We identified genes that were differentially connected between MHO and MUO individuals, which were further investigated by homing in on the modules they were active in. To identify potentially causal genes, we integrated genomic and transcriptomic data using an eQTL mapping approach. Results Both IL-6 and IL1B were identified as highly differentially co-expressed genes across tissues between MHO and MUO individuals, showing their potential role in obesity-induced disease PLOS ONE | DOI:10.1371/journal.pone.0167519 December 1, 2016 1 / 15 Inter-Tissue Gene Networks in Obesity Competing Interests: The authors have declared that no competing interests exist. development. WGCNA showed that those genes were clustering together within tissues, and further analysis showed different co-expression patterns between MHO and MUO subnetworks. A potential causal role for metabolic differences under similar obesity state was detected for PTPRE, IL-6R and SLC6A5. Conclusions We used a novel integrative approach by integration of co-expression networks across tissues to elucidate genetic factors related to obesity-induced metabolic disease development. The identified genes and their interactions give more insight into the genetic architecture of obesity and the association with co-morbidities. Introduction Obesity, characterized by an excessive accumulation of adipose tissue in the body, has major consequences for human health, like type 2 diabetes (T2D) and nonalcoholic steatohepatitis (NASH). However, it has now been acknowledged that (extremely) obese individuals may also be metabolically and cardiorespiratory fit, so called metabolic healthy obese (MHO) [1, 2]. It is estimated that 10 − 25 percent of the obese individuals are MHO [1]. The excessive accumulation of adipose tissue in case of obesity disturbs the endocrine balance. Already in 1968, it was indicated that the functioning of insulin metabolism is dependent upon adipose cell size and that adaptive functioning of adipose cells is linked to the metabolic condition of individuals [3]. The expandability of the adipose tissue to be able to store large amounts of fat may be an important factor determining obesity-induced metabolic disturbances [4]. However, expandability is not an unlimited process; in fact, adipose tissue storage capacity may become saturated, resulting in excess of fat “overspilled” to non-adipose tissues and subsequent lipotoxicity which can lead to metabolic syndrome [5]. In such cases, obesity results in elevated levels of free fatty acids (FFA) affecting the pancreatic beta cells, and in the secretion of a group of adipose tissue derived cytokines, the adipokines. The direct effect of FFA is thought to be the result of activation of multiple intracellular signals in the beta cell, eventually leading to apoptosis and reduced insulin secretion [6]. To date, involved genetic factors and pathways are largely unknown. Here, we aim to find genetic and molecular mechanisms important for human obesityinduced disease development by comparing inter-tissue gene co-expression of MHO and metabolically unhealthy obese (MUO) individuals. A study in mice showed important dynamic inter-tissue crosstalk in obesity development, with a key role for inflammatory pathways [7]. Also, the inter-tissue crosstalk of adipose tissue and skeletal tissue has shown its importance in obesity [8] and insulin resistance [9]. Weighted Gene Co-expression Network Analysis (WGCNA) [10] clusters genes based on gene-gene interactions and is used to unravel genetic mechanisms of complex diseases, including obesity [11–14]. We here use this approach to create an inter-tissue network, giving the potential of studying the inter-tissue gene co-expression (...truncated)