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Akinyemiju T, Do AN, Patki A, Aslibekyan S, Zhi D, Hidalgo B, Tiwari HK, Absher D, Geng X, Arnett DK, Irvin MR. Epigenome-wide association study of metabolic syndrome in African-American adults. Clin Epigenetics 2018; 10:49. [PMID: 29643945 PMCID: PMC5891946 DOI: 10.1186/s13148-018-0483-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 03/27/2018] [Indexed: 01/10/2023] Open
Abstract
Background The high prevalence of obesity among US adults has resulted in significant increases in associated metabolic disorders such as diabetes, dyslipidemia, and high blood pressure. Together, these disorders constitute metabolic syndrome, a clinically defined condition highly prevalent among African-Americans. Identifying epigenetic alterations associated with metabolic syndrome may provide additional information regarding etiology beyond current evidence from genome-wide association studies. Methods Data on metabolic syndrome and DNA methylation was assessed on 614 African-Americans from the Hypertension Genetic Epidemiology Network (HyperGEN) study. Metabolic syndrome was defined using the joint harmonized criteria, and DNA methylation was assessed using the Illumina HumanMethylation450K Bead Chip assay on DNA extracted from buffy coat. Linear mixed effects regression models were used to examine the association between CpG methylation at > 450,000 CpG sites and metabolic syndrome adjusted for study covariates. Replication using DNA from a separate sample of 69 African-Americans, as well as meta-analysis combining both cohorts, was conducted. Results Two differentially methylated CpG sites in the IGF2BP1 gene on chromosome 17 (cg06638433; p value = 3.10 × 10− 7) and the ABCG1 gene on chromosome 21 (cg06500161; p value = 2.60 × 10− 8) were identified. Results for the ABCG1 gene remained statistically significant in the replication dataset and meta-analysis. Conclusion Metabolic syndrome was consistently associated with increased methylation in the ABCG1 gene in the discovery and replication datasets, a gene that encodes a protein in the ATP-binding cassette transporter family and is involved in intra- and extra-cellular signaling and lipid transport. Electronic supplementary material The online version of this article (10.1186/s13148-018-0483-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tomi Akinyemiju
- 1Department of Epidemiology, University of Kentucky, Lexington, KY USA
| | - Anh N Do
- 2Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Amit Patki
- 3Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL USA
| | - Stella Aslibekyan
- 2Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Degui Zhi
- 4School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX USA.,5School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Bertha Hidalgo
- 2Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
| | - Hemant K Tiwari
- 3Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL USA
| | - Devin Absher
- 6HudsonAlpha Institute for Biotechnology, Huntsville, AL USA
| | - Xin Geng
- 4School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Donna K Arnett
- 7College of Public Health, University of Kentucky, Lexington, KY USA
| | - Marguerite R Irvin
- 2Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL USA
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Abstract
PURPOSE OF REVIEW It is becoming increasingly evident that epigenetic mechanisms, particularly DNA methylation, play a role in the regulation of blood lipid levels and lipid metabolism-linked phenotypes and diseases. RECENT FINDINGS Recent genome-wide methylation and candidate gene studies of blood lipids have highlighted several robustly replicated methylation markers across different ethnicities. Furthermore, many of these lipid-related CpG sites associated with blood lipids are also linked to lipid-related phenotypes and diseases. Integrating epigenome-wide association studies (EWAS) data with other layers of molecular data such as genetics or the transcriptome, accompanied by relevant statistical methods (e.g. Mendelian randomization), provides evidence for causal relationships. Recent data suggest that epigenetic changes can be consequences rather than causes of dyslipidemia. There is sparse information on many lipid classes and disorders of lipid metabolism, and also on the interplay of DNA methylation with other epigenetic layers such as histone modifications and regulatory RNAs. SUMMARY The current review provides a literature overview of epigenetic modifications in lipid metabolism and other lipid-related phenotypes and diseases focusing on EWAS of DNA methylation from January 2016 to September 2017. Recent studies strongly support the importance of epigenetic modifications, such as DNA methylation, in lipid metabolism and related diseases for relevant biological insights, reliable biomarkers, and even future therapeutics.
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Affiliation(s)
- Kirstin Mittelstraß
- Research Unit of Molecular Epidemiology
- Institute of Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology
- Institute of Epidemiology, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany
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Titus AJ, Gallimore RM, Salas LA, Christensen BC. Cell-type deconvolution from DNA methylation: a review of recent applications. Hum Mol Genet 2018; 26:R216-R224. [PMID: 28977446 PMCID: PMC5886462 DOI: 10.1093/hmg/ddx275] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023] Open
Abstract
Recent advances in cell-type deconvolution approaches are adding to our understanding of the biology underlying disease development and progression. DNA methylation (DNAm) can be used as a biomarker of cell types, and through deconvolution approaches, to infer underlying cell type proportions. Cell-type deconvolution algorithms have two main categories: reference-based and reference-free. Reference-based algorithms are supervised methods that determine the underlying composition of cell types within a sample by leveraging differentially methylated regions (DMRs) specific to cell type, identified from DNAm measures of purified cell populations. Reference-free algorithms are unsupervised methods for use when cell-type specific DMRs are not available, allowing scientists to estimate putative cellular proportions or control for potential confounding from cell type. Reference-based deconvolution is typically applied to blood samples and has potentiated our understanding of the relation between immune profiles and disease by allowing estimation of immune cell proportions from archival DNA. Bioinformatic analyses using DNAm to infer immune cell proportions, part of a new field known as Immunomethylomics, provides a new direction for consideration in epigenome wide association studies (EWAS).
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Affiliation(s)
- Alexander J Titus
- Program in Quantitative Biomedical Sciences.,Department of Epidemiology
| | | | | | - Brock C Christensen
- Department of Epidemiology.,Department of Molecular and Systems Biology.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
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Abstract
PURPOSE OF REVIEW Postprandial lipemia (PPL), the prolonged increase in plasma triglyceride-rich lipoproteins following food consumption, is an independent risk factor for cardiovascular disease. Genetic variation, environment and the interplay between these direct an individual's postprandial lipid response. From such interplay, inducible and reversible epigenetic changes arise. Increasing evidence suggests epigenetic variation contributes to postprandial response in lipids and risk. RECENT FINDINGS Diet and exercise are central agents affecting postprandial lipemia - triglyceride, but heterogeneity of the findings warrant more and larger studies. Several epigenetic loci identified from a human intervention study account for a substantial proportion of PPL phenotype variation, but the burden to conduct an intervention study of postprandial responses likely limits translation to personalized nutrition. SUMMARY The impact of both DNA methylation patterns and environmental factors such as diet, exercise, sleep and medication on PPL is multifaceted. Discovery of interactions that modify the association between CpG (oligodeoxydinucleotide) methylation and postprandial phenotypes is unfolding.
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Affiliation(s)
| | - Jose M Ordovas
- Jean Mayer-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, Massachusetts, USA
- IMDEA Food Institute, CEI UAM + CSIC
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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Sayols-Baixeras S, Subirana I, Fernández-Sanlés A, Sentí M, Lluís-Ganella C, Marrugat J, Elosua R. DNA methylation and obesity traits: An epigenome-wide association study. The REGICOR study. Epigenetics 2017; 12:909-916. [PMID: 29099282 DOI: 10.1080/15592294.2017.1363951] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Obesity is associated with increased risk of several diseases and has become epidemic. Obesity is highly heritable but the genetic variants identified by genome-wide association studies explain only limited variability. Epigenetics could contribute to explain the missing variability. The study aim was to discover differential methylation patterns related to obesity. We designed an epigenome-wide association study with a discovery phase in a subsample of 641 REGICOR study participants, validated by analysis of 2,515 participants in the Framingham Offspring Study. Blood DNA methylation was assessed using Illumina HumanMethylation450 BeadChip. Next, we meta-analyzed the data using the fixed effects method and performed a functional and pathway analysis using the Ingenuity Pathway Analysis software. We were able to validate 94 CpGs associated with body mass index (BMI) and 49 CpGs associated with waist circumference, located in 95 loci. In addition, we newly discovered 70 CpGs associated with BMI and 33 CpGs related to waist circumference. These CpGs explained 25.94% and 29.22% of the variability of BMI and waist circumference, respectively, in the REGICOR sample. We also evaluated 65 of the 95 validated loci in the GIANT genome-wide association data; 10 of them had Tag SNPs associated with BMI. The top-ranked diseases and functions identified in the functional and pathway analysis were neurologic, psychological, endocrine, and metabolic.
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Affiliation(s)
- Sergi Sayols-Baixeras
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,b Universitat Pompeu Fabra (UPF) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
| | - Isaac Subirana
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,d CIBER Epidemiology and Public Health (CIBERESP) , Barcelona , Catalonia , Spain
| | - Alba Fernández-Sanlés
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,b Universitat Pompeu Fabra (UPF) , Barcelona , Catalonia , Spain
| | - Mariano Sentí
- b Universitat Pompeu Fabra (UPF) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
| | - Carla Lluís-Ganella
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain
| | - Jaume Marrugat
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
| | - Roberto Elosua
- a Cardiovascular Epidemiology and Genetics Research Group , IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Catalonia , Spain.,c CIBER Cardiovascular diseases (CIBERCV) , Barcelona , Catalonia , Spain
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Nano J, Ghanbari M, Wang W, de Vries PS, Dhana K, Muka T, Uitterlinden AG, van Meurs JBJ, Hofman A, Franco OH, Pan Q, Murad SD, Dehghan A. Epigenome-Wide Association Study Identifies Methylation Sites Associated With Liver Enzymes and Hepatic Steatosis. Gastroenterology 2017. [PMID: 28624579 DOI: 10.1053/j.gastro.2017.06.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Epigenetic mechanisms might be involved in the regulation of liver enzyme level. We aimed to identify CpG sites at which DNA methylation levels are associated with blood levels of liver enzymes and hepatic steatosis. METHODS We conducted an epigenome-wide association study in whole blood for liver enzyme levels, including gamma-glutamyl transferase (GGT), alanine aminotransferase (ALT), and aspartate aminotransferase (AST), among a discovery set of 731 participants of the Rotterdam Study and sought replication in a non-overlapping sample of 719 individuals. Significant DNA methylation changes were further analyzed to evaluate their relation with hepatic steatosis. Expression levels of the top identified gene were measured in 9 human liver cell lines and compared with expression profiles of its potential targets associated with lipid traits. The candidate gene was subsequently knocked down in human hepatoma cells using lentiviral vectors expressing small hairpin RNAs. RESULTS Eight probes annotated to SLC7A11, SLC1A5, SLC43A1, PHGDH, PSORS1C1, SREBF1, ANKS3 were associated with GGT and 1 probe annotated to SLC7A11 was associated with ALT after Bonferroni correction (1.0 × 10-7). No probe was identified for AST levels. Four probes for GGT levels including cg06690548 (SLC7A11), cg11376147 (SLC43A1), cg22304262 (SLC1A5), and cg14476101 (PHGDH), and 1 for ALT cg06690548 (SLC7A11) were replicated. DNA methylation at SLC7A11 was associated with reduced risk of hepatic steatosis in participants (odds ratio, 0.69; 95% CI= 0.55-0.93; P value: 2.7 × 10-3). In functional experiments, SLC7A11 was highly expressed in human liver cells; its expression is positively correlated with expression of a panel of lipid-associated genes, indicating a role of SLC7A11 in lipid metabolism. CONCLUSIONS Our results provide new insights into epigenetic mechanisms associated with markers of liver function and hepatic steatosis, laying the groundwork for future diagnostic and therapeutic applications.
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Affiliation(s)
- Jana Nano
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Wenshi Wang
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Paul S de Vries
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas
| | - Klodian Dhana
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Taulant Muka
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | | | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sarwa Darwish Murad
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Abbas Dehghan
- Department of Biostatistics and Epidemiology, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London.
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57
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Truong V, Huang S, Dennis J, Lemire M, Zwingerman N, Aïssi D, Kassam I, Perret C, Wells P, Morange PE, Wilson M, Trégouët DA, Gagnon F. Blood triglyceride levels are associated with DNA methylation at the serine metabolism gene PHGDH. Sci Rep 2017; 7:11207. [PMID: 28894120 PMCID: PMC5593822 DOI: 10.1038/s41598-017-09552-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/18/2017] [Indexed: 12/14/2022] Open
Abstract
Efficient interventions to reduce blood triglycerides are few; newer and more tolerable intervention targets are needed. Understanding the molecular mechanisms underlying blood triglyceride levels variation is key to identifying new therapies. To explore the role of epigenetic mechanisms on triglyceride levels, a blood methylome scan was conducted in 199 individuals from 5 French-Canadian families ascertained on venous thromboembolism, and findings were replicated in 324 French unrelated patients with venous thromboembolism. Genetic context and functional relevance were investigated. Two DNA methylation sites associated with triglyceride levels were identified. The first one, located in the ABCG1 gene, was recently reported, whereas the second one, located in the promoter of the PHGDH gene, is novel. The PHGDH methylation site, cg14476101, was found to be associated with variation in triglyceride levels in a threshold manner: cg14476101 was inversely associated with triglyceride levels only when triglyceride levels were above 1.12 mmol/L (discovery P-value = 8.4 × 10-6; replication P-value = 0.0091). Public databases findings supported a functional role of cg14476101 on PHGDH expression. PHGDH catalyses the first step in the serine biosynthesis pathway. These findings highlight the role of epigenetic regulation of the PHGDH gene in triglyceride metabolism, providing novel insights on putative intervention targets.
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Affiliation(s)
- Vinh Truong
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Siying Huang
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Jessica Dennis
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | | | - Nora Zwingerman
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Dylan Aïssi
- Sorbonne Universités, UPMC Univ. Paris 06, INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Irfahan Kassam
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Claire Perret
- Sorbonne Universités, UPMC Univ. Paris 06, INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - Philip Wells
- Department of Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | | | - Michael Wilson
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Canada
| | - David-Alexandre Trégouët
- Sorbonne Universités, UPMC Univ. Paris 06, INSERM, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris, France
- ICAN Institute for Cardiometabolism and Nutrition, Paris, France
| | - France Gagnon
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada.
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Aslibekyan S, Ruiz-Narváez EA. The State of Cardiovascular Genomics: Abundant Data, Limited Information. REVISTA ESPANOLA DE CARDIOLOGIA (ENGLISH ED.) 2017; 70:696-698. [PMID: 28400104 PMCID: PMC5821493 DOI: 10.1016/j.rec.2017.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/10/2017] [Indexed: 06/07/2023]
Affiliation(s)
- Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States.
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59
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Situación actual en genómica cardiovascular: muchos datos, poca información. Rev Esp Cardiol (Engl Ed) 2017. [DOI: 10.1016/j.recesp.2017.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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60
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Suchacki KJ, Roberts F, Lovdel A, Farquharson C, Morton NM, MacRae VE, Cawthorn WP. Skeletal energy homeostasis: a paradigm of endocrine discovery. J Endocrinol 2017; 234:R67-R79. [PMID: 28455432 DOI: 10.1530/joe-17-0147] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 04/28/2017] [Indexed: 12/15/2022]
Abstract
Throughout the last decade, significant developments in cellular, molecular and mouse models have revealed major endocrine functions of the skeleton. More recent studies have evolved the interplay between bone-specific hormones, the skeleton, marrow adipose tissue, muscle and the brain. This review focuses on literature from the last decade, addressing the endocrine regulation of global energy metabolism via the skeleton. In addition, we will highlight several recent studies that further our knowledge of new endocrine functions of some organs; explore remaining unanswered questions; and, finally, we will discuss future directions for this more complex era of bone biology research.
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Affiliation(s)
- Karla J Suchacki
- The Queen's Medical Research InstituteThe University of Edinburgh, Edinburgh, UK
| | - Fiona Roberts
- The Roslin InstituteThe University of Edinburgh, Easter Bush, Midltohian, UK
| | - Andrea Lovdel
- The Queen's Medical Research InstituteThe University of Edinburgh, Edinburgh, UK
| | - Colin Farquharson
- The Roslin InstituteThe University of Edinburgh, Easter Bush, Midltohian, UK
| | - Nik M Morton
- The Queen's Medical Research InstituteThe University of Edinburgh, Edinburgh, UK
| | - Vicky E MacRae
- The Roslin InstituteThe University of Edinburgh, Easter Bush, Midltohian, UK
| | - William P Cawthorn
- The Queen's Medical Research InstituteThe University of Edinburgh, Edinburgh, UK
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61
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Current epigenetic aspects the clinical kidney researcher should embrace. Clin Sci (Lond) 2017; 131:1649-1667. [DOI: 10.1042/cs20160596] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/17/2017] [Accepted: 04/19/2017] [Indexed: 02/06/2023]
Abstract
Chronic kidney disease (CKD), affecting 10–12% of the world’s adult population, is associated with a considerably elevated risk of serious comorbidities, in particular, premature vascular disease and death. Although a wide spectrum of causative factors has been identified and/or suggested, there is still a large gap of knowledge regarding the underlying mechanisms and the complexity of the CKD phenotype. Epigenetic factors, which calibrate the genetic code, are emerging as important players in the CKD-associated pathophysiology. In this article, we review some of the current knowledge on epigenetic modifications and aspects on their role in the perturbed uraemic milieu, as well as the prospect of applying epigenotype-based diagnostics and preventive and therapeutic tools of clinical relevance to CKD patients. The practical realization of such a paradigm will require that researchers apply a holistic approach, including the full spectrum of the epigenetic landscape as well as the variability between and within tissues in the uraemic milieu.
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Fall T, Mendelson M, Speliotes EK. Recent Advances in Human Genetics and Epigenetics of Adiposity: Pathway to Precision Medicine? Gastroenterology 2017; 152:1695-1706. [PMID: 28214526 PMCID: PMC5576453 DOI: 10.1053/j.gastro.2017.01.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/26/2017] [Accepted: 01/30/2017] [Indexed: 12/26/2022]
Abstract
Obesity is a heritable trait that contributes to substantial global morbidity and mortality. Here, we summarize findings from the past decade of genetic and epigenetic research focused on unravelling the underpinnings of adiposity. More than 140 genetic regions now are known to influence adiposity traits. The genetics of general adiposity, as measured by body mass index, and that of abdominal obesity, as measured by waist-to-hip ratio, have distinct biological backgrounds. Gene expression associated with general adiposity is enriched in the nervous system. In contrast, genes associated with abdominal adiposity function in adipose tissue. Recent population-based epigenetic analyses have highlighted additional distinct loci. We discuss how associated genetic variants can lead to understanding causal mechanisms, and to disentangling reverse causation in epigenetic analyses. Discoveries emerging from population genomics are identifying new disease markers and potential novel drug targets to better define and combat obesity and related diseases.
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Affiliation(s)
- Tove Fall
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Michael Mendelson
- The Framingham Heart Study, Framingham, Massachusetts,Population Sciences Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland,Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts
| | - Elizabeth K. Speliotes
- Department of Internal Medicine, Division of Gastroenterology,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan
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63
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Mendelson MM, Marioni RE, Joehanes R, Liu C, Hedman ÅK, Aslibekyan S, Demerath EW, Guan W, Zhi D, Yao C, Huan T, Willinger C, Chen B, Courchesne P, Multhaup M, Irvin MR, Cohain A, Schadt EE, Grove ML, Bressler J, North K, Sundström J, Gustafsson S, Shah S, McRae AF, Harris SE, Gibson J, Redmond P, Corley J, Murphy L, Starr JM, Kleinbrink E, Lipovich L, Visscher PM, Wray NR, Krauss RM, Fallin D, Feinberg A, Absher DM, Fornage M, Pankow JS, Lind L, Fox C, Ingelsson E, Arnett DK, Boerwinkle E, Liang L, Levy D, Deary IJ. Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach. PLoS Med 2017; 14:e1002215. [PMID: 28095459 PMCID: PMC5240936 DOI: 10.1371/journal.pmed.1002215] [Citation(s) in RCA: 202] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 12/08/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND The link between DNA methylation, obesity, and adiposity-related diseases in the general population remains uncertain. METHODS AND FINDINGS We conducted an association study of body mass index (BMI) and differential methylation for over 400,000 CpGs assayed by microarray in whole-blood-derived DNA from 3,743 participants in the Framingham Heart Study and the Lothian Birth Cohorts, with independent replication in three external cohorts of 4,055 participants. We examined variations in whole blood gene expression and conducted Mendelian randomization analyses to investigate the functional and clinical relevance of the findings. We identified novel and previously reported BMI-related differential methylation at 83 CpGs that replicated across cohorts; BMI-related differential methylation was associated with concurrent changes in the expression of genes in lipid metabolism pathways. Genetic instrumental variable analysis of alterations in methylation at one of the 83 replicated CpGs, cg11024682 (intronic to sterol regulatory element binding transcription factor 1 [SREBF1]), demonstrated links to BMI, adiposity-related traits, and coronary artery disease. Independent genetic instruments for expression of SREBF1 supported the findings linking methylation to adiposity and cardiometabolic disease. Methylation at a substantial proportion (16 of 83) of the identified loci was found to be secondary to differences in BMI. However, the cross-sectional nature of the data limits definitive causal determination. CONCLUSIONS We present robust associations of BMI with differential DNA methylation at numerous loci in blood cells. BMI-related DNA methylation and gene expression provide mechanistic insights into the relationship between DNA methylation, obesity, and adiposity-related diseases.
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Affiliation(s)
- Michael M. Mendelson
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Boston University School of Medicine, Boston, Massachusetts, United States of America
- Department of Cardiology, Boston Children’s Hospital, Boston, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Roby Joehanes
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Hebrew SeniorLife, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Chunyu Liu
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biostatistics, Boston University, Boston, Massachusetts, United States of America
| | - Åsa K. Hedman
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ellen W. Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Degui Zhi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Chen Yao
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christine Willinger
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian Chen
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Paul Courchesne
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Multhaup
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Ariella Cohain
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Eric E. Schadt
- Icahn Institute for Genomics and Multiscale Biology and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Megan L. Grove
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Jan Bressler
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Kari North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Johan Sundström
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Stefan Gustafsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Sonia Shah
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Allan F. McRae
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jude Gibson
- Wellcome Trust Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - Paul Redmond
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Janie Corley
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Lee Murphy
- Wellcome Trust Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh, United Kingdom
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - Erica Kleinbrink
- Center for Molecular Medicine and Genetics and Department of Neurology, Wayne State University, Detroit, Michigan, United States of America
| | - Leonard Lipovich
- Center for Molecular Medicine and Genetics and Department of Neurology, Wayne State University, Detroit, Michigan, United States of America
| | - Peter M. Visscher
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Naomi R. Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Ronald M. Krauss
- Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
| | - Daniele Fallin
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew Feinberg
- Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Myriam Fornage
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Brown Foundation Institute of Molecular Medicine, University of Texas, Houston, Texas, United States of America
| | - James S. Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Caroline Fox
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Erik Ingelsson
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, United States of America
| | - Donna K. Arnett
- College of Public Health, University of Kentucky, Lexington, Kentucky, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Liming Liang
- Departments of Epidemiology and Biostatistics, School of Public Health, Harvard University, Boston, Massachusetts, United States of America
| | - Daniel Levy
- Framingham Heart Study, Framingham, Massachusetts, United States of America
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
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