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An Analysis of DNA Methylation in Human Adipose Tissue Reveals Differential Modification of Obesity Genes Before and After Gastric Bypass and Weight Loss Miles C

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An Analysis of DNA Methylation in Human Adipose Tissue Reveals Differential Modification of Obesity Genes Before and After Gastric Bypass and Weight Loss Miles C Himmelfarb Health Sciences Library, The George Washington University Health Sciences Research Commons Genomics and Precision Medicine Faculty Genomics and Precision Medicine Publications 1-22-2015 An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss Miles C. Benton Alice Johnstone David Eccles Brennan Harmon Mark T. Hayes See next page for additional authors Follow this and additional works at: http://hsrc.himmelfarb.gwu.edu/smhs_intsysbio_facpubs Part of the Systems Biology Commons Recommended Citation Benton, M.C., Johnstone, A., Eccles, D., Harmon, B., Hayes, M.T. et al. (2015). An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss. Genome Biology, 16:8. This Journal Article is brought to you for free and open access by the Genomics and Precision Medicine at Health Sciences Research Commons. It has been accepted for inclusion in Genomics and Precision Medicine Faculty Publications by an authorized administrator of Health Sciences Research Commons. For more information, please contact [email protected]. Authors Miles C. Benton, Alice Johnstone, David Eccles, Brennan Harmon, Mark T. Hayes, Rod A. Lea, Lyn Griffiths, Eric P. Hoffman, Richard S. Stubbs, and Donia Macartney-Coxson This journal article is available at Health Sciences Research Commons: http://hsrc.himmelfarb.gwu.edu/smhs_intsysbio_facpubs/ 112 Benton et al. Genome Biology (2015) 16:8 DOI 10.1186/s13059-014-0569-x RESEARCH Open Access An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss Miles C Benton1,2, Alice Johnstone1,5, David Eccles1, Brennan Harmon4, Mark T Hayes3,5, Rod A Lea2, Lyn Griffiths2, Eric P Hoffman4, Richard S Stubbs3,5 and Donia Macartney-Coxson1* Abstract Background: Environmental factors can influence obesity by epigenetic mechanisms. Adipose tissue plays a key role in obesity-related metabolic dysfunction, and gastric bypass provides a model to investigate obesity and weight loss in humans. Results: Here, we investigate DNA methylation in adipose tissue from obese women before and after gastric bypass and significant weight loss. In total, 485,577 CpG sites were profiled in matched, before and after weight loss, subcutaneous and omental adipose tissue. A paired analysis revealed significant differential methylation in omental and subcutaneous adipose tissue. A greater proportion of CpGs are hypermethylated before weight loss and increased methylation is observed in the 3′ untranslated region and gene bodies relative to promoter regions. Differential methylation is found within genes associated with obesity, epigenetic regulation and development, such as CETP, FOXP2, HDAC4, DNMT3B, KCNQ1 and HOX clusters. We identify robust correlations between changes in methylation and clinical trait, including associations between fasting glucose and HDAC4, SLC37A3 and DENND1C in subcutaneous adipose. Genes investigated with differential promoter methylation all show significantly different levels of mRNA before and after gastric bypass. Conclusions: This is the first study reporting global DNA methylation profiling of adipose tissue before and after gastric bypass and associated weight loss. It provides a strong basis for future work and offers additional evidence for the role of DNA methylation of adipose tissue in obesity. Background differing natures of the depots themselves [9-11]. Increased Obesity is a major public health problem and a risk factor intra-abdominal adipose tissue has been correlated with for type-2 diabetes, hypertension and cardiovascular disease an increased risk of obesity-related co-morbidities such [1-4]. Adipose tissue is an endocrine organ [5] and plays a as cardiovascular disease, atherosclerosis and type-2 fundamental role in obesity-related metabolic dysfunction diabetes [12-14]. [6]. Different adipose tissue depots within the body have Causal genetic variants of obesity and type-2 diabetes distinct structural and biochemical properties [7,8]. In have been identified through candidate gene, family-based humans, these depots can broadly be divided into two linkage and large scale association analyses. However, categories, subcutaneous and intra-abdominal. Metabolic apart from the small number of rare monogenic disease risk is affected by both the distribution of body fat between variants application of genetics to clinical management different adipose tissue depots within an individual and the has not occurred. Reasons for this include the relatively small effect size of common genetic variants, the location * Correspondence: [email protected] of a large number of disease associated loci in intergenic 1 Biomarkers Group, Environmental Health, Institute of Environmental Science regions of the genome, and the likelihood that additional and Research (ESR), Wellington 5022, New Zealand Full list of author information is available at the end of the article causal variants are yet to be identified [15,16]. © 2015 Benton et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. 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. Benton et al. Genome Biology (2015) 16:8 Page 2 of 21 It is now recognised that epigenetics plays a significant Given this increasing evidence for the involvement of role in complex disease, and provides mechanisms epigenetics in complex disease and obesity in particular whereby environmental factors can influence complex [17,18], together with the role that adipose tissue plays diseases such as obesity and type-2 diabetes [17,18]. in disease progression, we hypothesised that epigenetic Thus, epigenetics may explain some of the ‘missing changes would be present in this tissue in the context of heritability’ of complex disease, and, because of effects obesity and weight loss. Roux en Y gastric bypass surgery on regulation, provide a functional role for some of the (from now on referred to as gastric bypass) is used to intergenic loci associated with disease. treat morbid obesity and results in marked weight loss Animal and human studies have shown that the DNA [43,44]. Therefore, we use gastric bypass as a model for methylation status of genes in offspring can be altered significant weight loss. Two studies have investigated in utero by the maternal dietary environment [19-23]. global DNA methylation before and after gastric bypass, Godfrey et al. [24] further reported that the child’s one in skeletal muscle and the other in liver [45,46]. methylation status correlated with adiposity in later life. Here we extend this to two adipose tissue depots and Feinberg et al. [25] identified four variably methylated present the first high density DNA methylation profile of regions in lymphocytes which correlated with body subcutaneous abdominal and intra-abdominal omental mass index (BMI); these regions were located in or near adipose tissue before and after gastric bypass and weight genes previously implicated in body weight regulation or loss. diabetes. Obesity has also been associated with genome- wide DNA methylation changes in peripheral blood Results [26-28], and methylation differences have been reported Differential methylation of adipose tissue before and in peripheral blood in response to caloric restriction [29] after weight loss and weight loss intervention [30]. In addition, a recent Global differential methylation genome-wide analysis of peripheral blood revealed type-2 DNA methylation was analysed independently in subcuta- diabetes related DNA methylation variations [31], and an- neous abdominal adipose and intra-abdominal omental other investigated associations between methylation and adipose (referred to as subcutaneous adipose and omen- fasting glucose, insulin and insulin resistance [32]. tum, respectively, from this point) before and after gastric Epigenetic signatures are acquired by cells during deve- bypass and weight loss in 15 women (clinical and an- lopment and differentiation. DNA methylation changes, thropometric data presented in Table 1). We investigated such as demethylation of specific sequences within the global DNA methylation (450,315 CpG sites passing qual- leptin and GLUT4 gene promoters is observed during ity filtering) and plotted this at the level of genomic gene adipogenesis [33,34] and adipose tissue precursor cells annotation (Figure 1). This revealed a clear pattern of retain their DNA methylation profile through generations methylation across the genome with least methylation in of culture [35]. In addition, women with a lower baseline promoter regions and greatest methylation in the 3′ UTRs methylation of the leptin and TNF-alpha gene promoters (untranslated regions) and gene bodies. While the overall in subcutaneous adipose tissue responded better to dietary pattern was the same in both adipose tissues, significantly intervention [36]. more methylation was observed before than after weight AsmallnumberofstudieshavereportedDNA loss for all gene regions in subcutaneous adipose and all methylation
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