NEWS & VIEWS Epigenetic mechanisms underlying type 2 diabetes mellitus Mark A. Hanson and Keith M. Godfrey Refers to Multhaup, M. L. et al. Mouse–human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab. 21, 136–129 (2015)
The aetiology of type 2 diabetes mellitus (T2DM) involves interactions between genetic, developmental and lifestyle environmental risk factors, which are partly influenced by epigenetic processes. Multhaup and colleagues have combined genome-wide analysis with analyses of an animal model of insulin resistance and tissues from individuals with obesity obtained before and after gastric bypass surgery to identify novel potential pathways that contribute to T2DM pathogenesis. The rising prevalence of type 2 diabetes mellitus (T2DM) is of great concern, especially as the disease increasingly presents in young people and in low-to-middle income countries that are undergoing socioeconomic transition. The increase in the prevalence of T2DM has occurred in parallel with the obesity epidemic, at a rate that rules out a purely genetic basis for the disease, and this increase has been confirmed by genomewide association studies (GWAS). 1 For example, a study of 63 newly discovered and established autosomal loci found that together these genetic variants accounted for only 5.7% of variance in T2DM susceptibility.1 Across the life course, however, the condition has a heritability of 21%, 2 which suggests that although some aspects of susceptibility are passed across generations, a major environmental component of risk also exists. Such effects are now widely believed to involve epigenetic processes, whereby variations in external influences affect gene expression and, thus, functional phenotypic differences between individuals. In childhood, epigenetic DNA modifications associated with the risk of metabolic disease can be stable over many years and variations measured at birth can explain a substantial proportion of the variance in adiposity that can occur in later life.3 In addition, experimental studies show that early-life environmental exposures can change epigenetic processes in different tissues within the same individual in a stable manner across the life course without affecting the
inherited genetic sequence.4 Multhaup and colleagues have used this e pigenetic concept as the basis of their study.5 Using an array-based method for measuring relative levels of DNA methylation across the genome, Multhaup et al. first identified a number of differentially methylated regions (DMRs) in adipose tissue from mice in which obesity was induced by a high-fat diet; one of the DMRs identified in this way was the Pck1 gene,5 which, in rats, is known to be epi genetically regulated by maternal diet in the liver of offspring.4 Additional analyses examined body weight and glucose and/or insulin homeostasis, as well as the expected inverse relationship between demethylation and gene expression in pancreatic islets and liver tissue.5 Given that replication in independent samples is essential in epigenetic studies, the authors repeated these analyses for a subset of DMRs in adipose and islet tissues obtained from another group of mice.5 An important scientific advance of the study is the replication in humans of findings derived in mice, which was achieved by comparing subcutaneous adipose tissue from individuals with obesity and age-matched lean male individuals, as well as with adipose tissue from a subgroup of the individuals with obesity after gastric bypass surgery. Of the 625 DMRs found to be linked to the diet-induced phenotype in mice, 249 DMRs at sites that are homologous in mouse and human were conserved in the comparison tissues from lean men and from individuals with obesity, and 170 of these DMRs showed
NATURE REVIEWS | ENDOCRINOLOGY
methylation changes in the same direction.5 Many of these DMRs were also associated with levels of obesity and glucose and/or insulin homeostasis. The number of these homologous sites was reduced when the acceptable limits of the level of methylation change and direction were more rigorously defined; however, a substantial number of loci in individuals with obesity who underwent gastric bypass surgery showed methy lation changes that moved towards those of samples from lean individuals.5 This finding is important as it suggests that, at least in principle, some epigenetic processes associ ated with T2DM might be reversible in adult patients with obesity. Multhaup and colleagues next examined the overlap between known fixed genetic regions associated with human T2DM and the panel of DMRs that was identified in mice fed a high-fat diet and in humans with obesity. Other studies have identified methy lation quantitative trait loci and provided estimates of the relative contribution of fixed genetic variants compared with environ ment to methylome variation.6 Multhaup et al. used two complementary GWAS techniques to hone the number of DMRs to 30, of which 27 loci together accounted for up to
Risk of obesity, T2DM and metabolic disease
GENETICS
Fixed genetic effect Unhealthy lifestyle effect Developmental effect Potentially reversible epigenetic processes
Gastric bypass surgery
Gastric bypass surgery
Time
Figure 1 | The risk of noncommunicable Nature Reviews | Endocrinology diseases such as T2DM increases in a nonlinear fashion throughout the life course, with contributions from fixed genetic effects, lifestyle and development, which are partially reversible by gastric bypass surgery. The effects of genetic predisposition are increased by an unhealthy lifestyle and further still by developmental factors. Abbreviation: T2DM, type 2 diabetes mellitus.
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NEWS & VIEWS 2.69% of genetic predisposition to T2DM.5 In addition to pathway analysis, the researchers sought functional evidence of involvement of these alleles in disease risk using adipocyte cell lines. Candidate genes that were hypermethylated and hypomethylated in mice fed a high-fat diet were knocked down and overexpressed, respectively, in the adipocyte cell line; cell responses were quantified by measuring insulin-stimulated glucose uptake. Four of five candidate genes showed changes in the expected direction.5 Although these data seem to build a case for a causal link, possibly through epigenetic control of gene enhancer activity, as the authors correctly point out, these findings do not directly establish a role for methylation in T2DM aetiology. Nonetheless, the power of this cross-species genome–epigenome– functional approach is demonstrated by revelation of novel evidence for the involvement of changes in methylation of Mkl1, Plekho1 and Tnfaip8l2 in insulin resistance.5 These are genes that have not been previously identified using GWAS, but that show epigenetic change after gastric bypass sur gery. This discovery is interesting as gastric bypass surgery can produce rapid improvements in cardiometabolic health, even with the persistence of a degree of obesity.7 What are the wider implications of this work? As Multhaup et al. suggest, at the physiological level, both positive and negative feedback loops are present in most complex living systems, and, thus, deeper investigations than simple association studies must be conducted to determine the epigenetic contributions to human disease. Present studies are inevitably complicated by the
tissues available. For example, different fat depots can have different functional roles.8 In addition to the genetic, lifestyle and associ ated epigenetic components of risk (the last two of which might be partially reversible), the contribution of early-life development to risk, which also has environmental and epigenetic components, sets the scene for res ponses to challenges in late life,9 which necessitates taking a broad life-course perspective (Figure 1). Substantial experimental evidence now exists that an unbalanced diet, such as a diet with high fat or low protein content in relation to carbohydrate intake, in pregnant rodents produces lasting effects on the meta bolic phenotype of the offspring,10 which might partly result from epigenetic processes. Alongside the work from Multhaup et al. these observations suggest a model in which genetic variants, the developmental environment and the adult environment can influence epigenetic signatures with downstream effects on phenotypes. Much work now needs to be done in order to determine whether there are critical windows of plasticity in which the environment interacts with the genome, as well as to determine the nature of the environmental exposures that drive these epigenetic changes, and whether or not the effects of such exposures can be prevented or reversed. Academic Unit of Human Development and Health (M.A.H.), MRC Lifecourse Epidemiology Unit (K.M.G.), University of Southampton, University Road, Southampton SO17 1BJ, UK. Correspondence to: M.A.H. [email protected] doi:10.1038/nrendo.2015.31 Published online 10 March 2015
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Acknowledgements The authors are supported by The British Heart Foundation and the NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Trust, Southampton, UK. Competing interests The authors declare no competing interests. 1.
Morris, A. P. et al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat. Genet. 44, 981–990 (2012). 2. Almgren, P. et al. Heritability and familiality of type 2 diabetes and related quantitative traits in the Botnia Study. Diabetologia 54, 2811–2819 (2011). 3. Godfrey, K. M. et al. Epigenetic gene promoter methylation at birth is associated with child’s later adiposity. Diabetes 60, 1528–1534 (2011). 4. Hanson M., Godfrey K. M., Lillycrop, K. A., Burdge, G. C. & Gluckman, P. D. Developmental plasticity and developmental origins of noncommunicable disease: theoretical considerations and epigenetic mechanisms. Prog. Biophys. Mol. Biol. 106, 272–280 (2011). 5. Multhaup, M. L. et al. Mouse–human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab. 21, 138–149 (2015). 6. Teh, A. L. et. al. The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. Genome Res. 24, 1064–1074 (2014). 7. Adams, T. D. et al. Health benefits of gastric bypass surgery after 6 years. JAMA 308, 1122–1131 (2012). 8. Tchkonia, T. et al. Mechanisms and metabolic implications of regional differences among fat depots. Cell Metab. 17, 644–656 (2013). 9. Hanson, M. A. & Gluckman, P. D. Early developmental conditioning of later health and disease: physiology or pathophysiology? Physiol. Rev. 94, 1027–1076 (2014). 10. Poston, L., Taylor, P. D. & Nathanielsz, P. in Maternal Obesity Ch. 10 (eds Gillman, M. W. & Poston, L.) 100–114 (Cambridge University Press, 2012).
www.nature.com/nrendo © 2015 Macmillan Publishers Limited. All rights reserved
The aetiology of type 2 diabetes mellitus (T2DM) involves interactions between genetic, developmental and lifestyle environmental risk factors, which are partly influenced by epigenetic processes. Multhaup and colleagues have combined genome-wide analysis with analyses of an animal model of insulin resistance and tissues from individuals with obesity obtained before and after gastric bypass surgery to identify novel potential pathways that contribute to T2DM pathogenesis. The rising prevalence of type 2 diabetes mellitus (T2DM) is of great concern, especially as the disease increasingly presents in young people and in low-to-middle income countries that are undergoing socioeconomic transition. The increase in the prevalence of T2DM has occurred in parallel with the obesity epidemic, at a rate that rules out a purely genetic basis for the disease, and this increase has been confirmed by genomewide association studies (GWAS). 1 For example, a study of 63 newly discovered and established autosomal loci found that together these genetic variants accounted for only 5.7% of variance in T2DM susceptibility.1 Across the life course, however, the condition has a heritability of 21%, 2 which suggests that although some aspects of susceptibility are passed across generations, a major environmental component of risk also exists. Such effects are now widely believed to involve epigenetic processes, whereby variations in external influences affect gene expression and, thus, functional phenotypic differences between individuals. In childhood, epigenetic DNA modifications associated with the risk of metabolic disease can be stable over many years and variations measured at birth can explain a substantial proportion of the variance in adiposity that can occur in later life.3 In addition, experimental studies show that early-life environmental exposures can change epigenetic processes in different tissues within the same individual in a stable manner across the life course without affecting the
inherited genetic sequence.4 Multhaup and colleagues have used this e pigenetic concept as the basis of their study.5 Using an array-based method for measuring relative levels of DNA methylation across the genome, Multhaup et al. first identified a number of differentially methylated regions (DMRs) in adipose tissue from mice in which obesity was induced by a high-fat diet; one of the DMRs identified in this way was the Pck1 gene,5 which, in rats, is known to be epi genetically regulated by maternal diet in the liver of offspring.4 Additional analyses examined body weight and glucose and/or insulin homeostasis, as well as the expected inverse relationship between demethylation and gene expression in pancreatic islets and liver tissue.5 Given that replication in independent samples is essential in epigenetic studies, the authors repeated these analyses for a subset of DMRs in adipose and islet tissues obtained from another group of mice.5 An important scientific advance of the study is the replication in humans of findings derived in mice, which was achieved by comparing subcutaneous adipose tissue from individuals with obesity and age-matched lean male individuals, as well as with adipose tissue from a subgroup of the individuals with obesity after gastric bypass surgery. Of the 625 DMRs found to be linked to the diet-induced phenotype in mice, 249 DMRs at sites that are homologous in mouse and human were conserved in the comparison tissues from lean men and from individuals with obesity, and 170 of these DMRs showed
NATURE REVIEWS | ENDOCRINOLOGY
methylation changes in the same direction.5 Many of these DMRs were also associated with levels of obesity and glucose and/or insulin homeostasis. The number of these homologous sites was reduced when the acceptable limits of the level of methylation change and direction were more rigorously defined; however, a substantial number of loci in individuals with obesity who underwent gastric bypass surgery showed methy lation changes that moved towards those of samples from lean individuals.5 This finding is important as it suggests that, at least in principle, some epigenetic processes associ ated with T2DM might be reversible in adult patients with obesity. Multhaup and colleagues next examined the overlap between known fixed genetic regions associated with human T2DM and the panel of DMRs that was identified in mice fed a high-fat diet and in humans with obesity. Other studies have identified methy lation quantitative trait loci and provided estimates of the relative contribution of fixed genetic variants compared with environ ment to methylome variation.6 Multhaup et al. used two complementary GWAS techniques to hone the number of DMRs to 30, of which 27 loci together accounted for up to
Risk of obesity, T2DM and metabolic disease
GENETICS
Fixed genetic effect Unhealthy lifestyle effect Developmental effect Potentially reversible epigenetic processes
Gastric bypass surgery
Gastric bypass surgery
Time
Figure 1 | The risk of noncommunicable Nature Reviews | Endocrinology diseases such as T2DM increases in a nonlinear fashion throughout the life course, with contributions from fixed genetic effects, lifestyle and development, which are partially reversible by gastric bypass surgery. The effects of genetic predisposition are increased by an unhealthy lifestyle and further still by developmental factors. Abbreviation: T2DM, type 2 diabetes mellitus.
ADVANCE ONLINE PUBLICATION | 1 © 2015 Macmillan Publishers Limited. All rights reserved
NEWS & VIEWS 2.69% of genetic predisposition to T2DM.5 In addition to pathway analysis, the researchers sought functional evidence of involvement of these alleles in disease risk using adipocyte cell lines. Candidate genes that were hypermethylated and hypomethylated in mice fed a high-fat diet were knocked down and overexpressed, respectively, in the adipocyte cell line; cell responses were quantified by measuring insulin-stimulated glucose uptake. Four of five candidate genes showed changes in the expected direction.5 Although these data seem to build a case for a causal link, possibly through epigenetic control of gene enhancer activity, as the authors correctly point out, these findings do not directly establish a role for methylation in T2DM aetiology. Nonetheless, the power of this cross-species genome–epigenome– functional approach is demonstrated by revelation of novel evidence for the involvement of changes in methylation of Mkl1, Plekho1 and Tnfaip8l2 in insulin resistance.5 These are genes that have not been previously identified using GWAS, but that show epigenetic change after gastric bypass sur gery. This discovery is interesting as gastric bypass surgery can produce rapid improvements in cardiometabolic health, even with the persistence of a degree of obesity.7 What are the wider implications of this work? As Multhaup et al. suggest, at the physiological level, both positive and negative feedback loops are present in most complex living systems, and, thus, deeper investigations than simple association studies must be conducted to determine the epigenetic contributions to human disease. Present studies are inevitably complicated by the
tissues available. For example, different fat depots can have different functional roles.8 In addition to the genetic, lifestyle and associ ated epigenetic components of risk (the last two of which might be partially reversible), the contribution of early-life development to risk, which also has environmental and epigenetic components, sets the scene for res ponses to challenges in late life,9 which necessitates taking a broad life-course perspective (Figure 1). Substantial experimental evidence now exists that an unbalanced diet, such as a diet with high fat or low protein content in relation to carbohydrate intake, in pregnant rodents produces lasting effects on the meta bolic phenotype of the offspring,10 which might partly result from epigenetic processes. Alongside the work from Multhaup et al. these observations suggest a model in which genetic variants, the developmental environment and the adult environment can influence epigenetic signatures with downstream effects on phenotypes. Much work now needs to be done in order to determine whether there are critical windows of plasticity in which the environment interacts with the genome, as well as to determine the nature of the environmental exposures that drive these epigenetic changes, and whether or not the effects of such exposures can be prevented or reversed. Academic Unit of Human Development and Health (M.A.H.), MRC Lifecourse Epidemiology Unit (K.M.G.), University of Southampton, University Road, Southampton SO17 1BJ, UK. Correspondence to: M.A.H. [email protected] doi:10.1038/nrendo.2015.31 Published online 10 March 2015
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Acknowledgements The authors are supported by The British Heart Foundation and the NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Trust, Southampton, UK. Competing interests The authors declare no competing interests. 1.
Morris, A. P. et al. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat. Genet. 44, 981–990 (2012). 2. Almgren, P. et al. Heritability and familiality of type 2 diabetes and related quantitative traits in the Botnia Study. Diabetologia 54, 2811–2819 (2011). 3. Godfrey, K. M. et al. Epigenetic gene promoter methylation at birth is associated with child’s later adiposity. Diabetes 60, 1528–1534 (2011). 4. Hanson M., Godfrey K. M., Lillycrop, K. A., Burdge, G. C. & Gluckman, P. D. Developmental plasticity and developmental origins of noncommunicable disease: theoretical considerations and epigenetic mechanisms. Prog. Biophys. Mol. Biol. 106, 272–280 (2011). 5. Multhaup, M. L. et al. Mouse–human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab. 21, 138–149 (2015). 6. Teh, A. L. et. al. The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. Genome Res. 24, 1064–1074 (2014). 7. Adams, T. D. et al. Health benefits of gastric bypass surgery after 6 years. JAMA 308, 1122–1131 (2012). 8. Tchkonia, T. et al. Mechanisms and metabolic implications of regional differences among fat depots. Cell Metab. 17, 644–656 (2013). 9. Hanson, M. A. & Gluckman, P. D. Early developmental conditioning of later health and disease: physiology or pathophysiology? Physiol. Rev. 94, 1027–1076 (2014). 10. Poston, L., Taylor, P. D. & Nathanielsz, P. in Maternal Obesity Ch. 10 (eds Gillman, M. W. & Poston, L.) 100–114 (Cambridge University Press, 2012).
www.nature.com/nrendo © 2015 Macmillan Publishers Limited. All rights reserved
