51
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Zhang S, Zeng T, Hu B, Zhang YH, Feng K, Chen L, Niu Z, Li J, Huang T, Cai YD. Discriminating Origin Tissues of Tumor Cell Lines by Methylation Signatures and Dys-Methylated Rules. Front Bioeng Biotechnol 2020; 8:507. [PMID: 32528944 PMCID: PMC7264161 DOI: 10.3389/fbioe.2020.00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 04/30/2020] [Indexed: 12/18/2022] Open
Abstract
DNA methylation is an essential epigenetic modification for multiple biological processes. DNA methylation in mammals acts as an epigenetic mark of transcriptional repression. Aberrant levels of DNA methylation can be observed in various types of tumor cells. Thus, DNA methylation has attracted considerable attention among researchers to provide new and feasible tumor therapies. Conventional studies considered single-gene methylation or specific loci as biomarkers for tumorigenesis. However, genome-scale methylated modification has not been completely investigated. Thus, we proposed and compared two novel computational approaches based on multiple machine learning algorithms for the qualitative and quantitative analyses of methylation-associated genes and their dys-methylated patterns. This study contributes to the identification of novel effective genes and the establishment of optimal quantitative rules for aberrant methylation distinguishing tumor cells with different origin tissues.
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Affiliation(s)
- Shiqi Zhang
- School of Life Sciences, Shanghai University, Shanghai, China.,Department of Biostatistics, University of Copenhagen, Copenhagen, Denmark
| | - Tao Zeng
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China
| | - Bin Hu
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yu-Hang Zhang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kaiyan Feng
- Department of Computer Science, Guangdong AIB Polytechnic, Guangzhou, China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, China
| | - Zhibin Niu
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jianhao Li
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tao Huang
- Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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52
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Salas-Pérez F, Ramos-Lopez O, Mansego ML, Milagro FI, Santos JL, Riezu-Boj JI, Martínez JA. DNA methylation in genes of longevity-regulating pathways: association with obesity and metabolic complications. Aging (Albany NY) 2020; 11:1874-1899. [PMID: 30926763 PMCID: PMC6461164 DOI: 10.18632/aging.101882] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/20/2019] [Indexed: 12/28/2022]
Abstract
Aging is the main risk factor for most chronic diseases. Epigenetic mechanisms, such as DNA methylation (DNAm) plays a pivotal role in the regulation of physiological responses that can vary along lifespan. The aim of this research was to analyze the association between leukocyte DNAm in genes involved in longevity and the occurrence of obesity and related metabolic alterations in an adult population. Subjects from the MENA cohort (n=474) were categorized according to age (<45 vs 45>) and the presence of metabolic alterations: increased waist circumference, hypercholesterolemia, insulin resistance, and metabolic syndrome. The methylation levels of 58 CpG sites located at genes involved in longevity-regulating pathways were strongly correlated (FDR-adjusted< 0.0001) with BMI. Fifteen of them were differentially methylated (p<0.05) between younger and older subjects that exhibited at least one metabolic alteration. Six of these CpG sites, located at MTOR (cg08862778), ULK1 (cg07199894), ADCY6 (cg11658986), IGF1R (cg01284192), CREB5 (cg11301281), and RELA (cg08128650), were common to the metabolic traits, and CREB5, RELA, and ULK1 were statistically associated with age. In summary, leukocyte DNAm levels of several CpG sites located at genes involved in longevity-regulating pathways were associated with obesity and metabolic syndrome traits, suggesting a role of DNAm in aging-related metabolic alterations.
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Affiliation(s)
- Francisca Salas-Pérez
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain
| | - Omar Ramos-Lopez
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain
| | - María L Mansego
- Department of Bioinformatics, Making Genetics S.L, Pamplona, 31002, Spain
| | - Fermín I Milagro
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain.,CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, 28029, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
| | - José L Santos
- IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
| | - José I Riezu-Boj
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain.,CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, 28029, Spain.,IdiSNA, Navarra Institute for Health Research, Pamplona, 31008, Spain
| | - J Alfredo Martínez
- Department of Nutrition, Food Science and Physiology; Center for Nutrition Research, University of Navarra, Pamplona, 31008, Spain.,CIBERobn, Fisiopatología de la Obesidad y la Nutrición, Carlos III Health Institute, Madrid, 28029, Spain.,Department of Nutrition, Diabetes and Metabolism, School of Medicine, Pontificia Universidad Católica de Chile, Santiago, 8331150, Chile.,Institute IMDEA Food, Madrid, 28049, Spain
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53
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Han W, Zhang C, Shi CT, Gao XJ, Zhou MH, Shao QX, Shen XJ, Wu CJ, Cao F, Hu YW, Yuan JL, Ding HZ, Wang QH, Wang HN. Roles of eIF3m in the tumorigenesis of triple negative breast cancer. Cancer Cell Int 2020; 20:141. [PMID: 32368187 PMCID: PMC7191806 DOI: 10.1186/s12935-020-01220-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background Without targets, triple negative breast cancer (TNBC) has the worst prognosis in all subtypes of breast cancer (BC). Recently, eukaryotic translation initiation factor 3 m (eIF3m) has been declared to be involved in the malignant progression of various neoplasms. The aim of this study is to explore biological functions of eIF3m in TNBC. Methods Multiple databases, including Oncomine, KM-plotter and so on, were performed to analyze prognosis and function of eIF3m in TNBC. After transfection of eIF3m-shRNA lentivirus, CCK-8, colony formation assay, cell cycle analysis, wound healing assay, transwell assays, mitochondrial membrane potential assay and cell apoptosis analysis were performed to explore the roles of eIF3m in TNBC cell bio-behaviors. In addition, western blotting was conducted to analyze the potential molecular mechanisms of eIF3m. Results In multiple databases, up-regulated eIF3m had lower overall survival, relapse-free survival and post progression survival in BC. EIF3m expression in TNBC was obviously higher than in non-TNBC or normal breast tissues. Its expression in TNBC was positively related to differentiation, lymph node invasion and distant metastasis. After knockdown of eIF3m, cell proliferation, migration, invasion and levels of mitochondrial membrane potential of MDA-MB-231 and MDA-MB-436 were all significantly suppressed, while apoptosis rates of them were obviously increased. In addition, eIF3m could regulate cell-cycle, epithelial–mesenchymal transition and apoptosis-related proteins. Combined with public databases and RT-qPCR, 14 genes were identified to be modulated by eIF3m in the development of TNBC. Conclusions eIF3m is an unfavorable indicator of TNBC, and plays a vital role in the process of TNBC tumorigenesis.
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Affiliation(s)
- Wei Han
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Cong Zhang
- Department of Pharmacy, Kunshan Hospital of Traditional Chinese Medicine, Kunshan Jiangsu, 215300 People's Republic of China
| | - Chun-Tao Shi
- Department of General Surgery, Wuxi Xishan People's Hospital, Kunshan Wuxi Jiangsu, 214000 People's Republic of China
| | - Xiao-Jiao Gao
- 4Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Ming-Hui Zhou
- 5Centralab, Kunshan First People's Hospital Affiliated to Jiangsu University, Jiangsu, 215300 Kunshan People's Republic of China
| | - Qi-Xiang Shao
- 6Department of Immunology, Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang Jiangsu, 212013 People's Republic of China
| | - Xiao-Jun Shen
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Cheng-Jiang Wu
- 7Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou Jiangsu, 215000 People's Republic of China
| | - Fang Cao
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Yong-Wei Hu
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Jian-Liang Yuan
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Hou-Zhong Ding
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Qing-Hua Wang
- 1Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan Jiangsu, 215300 People's Republic of China
| | - Hao-Nan Wang
- Oncology Department, Wuxi Fifth People's Hospital, Wuxi Jiangsu, 214000 People's Republic of China
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54
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Hossan T, Kundu S, Alam SS, Nagarajan S. Epigenetic Modifications Associated with the Pathogenesis of Type 2 Diabetes Mellitus. Endocr Metab Immune Disord Drug Targets 2020; 19:775-786. [PMID: 30827271 DOI: 10.2174/1871530319666190301145545] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Type 2 diabetes mellitus (T2DM) is a multifactorial metabolic disorder. Pancreatic β-cell dysfunction and insulin resistance are the most common and crucial events of T2DM. Increasing evidence suggests the association of epigenetic modifications with the pathogenesis of T2DM through the changes in important biological processes including pancreatic β- cell differentiation, development and maintenance of normal β-cell function. Insulin sensitivity by the peripheral glucose uptake tissues is also changed by the altered epigenetic mechanisms. In this review, we discussed the major epigenetic alterations and their effects on β-cell function, insulin secretion and insulin resistance in context of T2DM. METHODS We investigated the presently available epigenetic modifications including DNA methylation, posttranslational histone modifications, ATP-dependent chromatin remodeling and non-coding RNAs related to the pathogenesis of T2DM. Published literatures on this topic were searched both on Google Scholar and Pubmed with related keywords and investigated for relevant information. RESULTS The epigenetic modifications introduce changes in gene expression which are essential for appropriate β-cell development and functions, insulin secretion and sensitivity resulting in the pathogenesis of T2DM. Interestingly, T2DM could also be a prominent reason for the mentioned epigenetic alterations. CONCLUSION This review article emphasized on the epigenetic modifications associated with T2DM and discussed the consequences in deterioration of the disease condition.
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Affiliation(s)
- Tareq Hossan
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Shoumik Kundu
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sayeda Sadia Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sankari Nagarajan
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
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55
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Ciuculete DM, Voisin S, Kular L, Welihinda N, Jonsson J, Jagodic M, Mwinyi J, Schiöth HB. Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression. Epigenetics 2019; 15:646-663. [PMID: 31852353 PMCID: PMC7574381 DOI: 10.1080/15592294.2019.1700628] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Unrecognized depression during adolescence can result in adult suicidal behaviour. The aim of this study was to identify, replicate and characterize DNA methylation (DNAm) shifts in depression aetiology, using a longitudinal, multi-tissue (blood and brain) and multi-layered (genetics, epigenetics, transcriptomics) approach. We measured genome-wide blood DNAm data at baseline and one-year follow-up, and imputed genetic variants, in 59 healthy adolescents comprising the discovery cohort. Depression and suicidal symptoms were determined using the Development and Well-Being Assessment (DAWBA) depression band, Montgomery-Åsberg Depression Rating Scale-Self (MADRS-S) and SUicide Assessment Scale (SUAS). DNAm levels at follow-up were regressed against depression scores, adjusting for sex, age and the DNAm residuals at baseline. Higher methylation levels of 5% and 13% at cg24627299 within the MET gene were associated with higher depression scores (praw<1e-4) and susceptibility for suicidal symptoms (padj.<0.005). The nearby rs39748 was discovered to be a methylation and expression quantitative trait locus in blood cells. mRNA levels of hepatocyte growth factor (HGF) expression, known to strongly interact with MET, were inversely associated with methylation levels at cg24627299, in an independent cohort of 1180 CD14+ samples. In an open-access dataset of brain tissue, lower methylation at cg24627299 was found in 45 adults diagnosed with major depressive disorder compared with matched controls (padj.<0.05). Furthermore, lower MET expression was identified in the hippocampus of depressed individuals compared with controls in a fourth, independent cohort. Our findings reveal methylation changes at MET in the pathology of depression, possibly involved in downregulation of HGF/c-MET signalling the hippocampal region.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University , Footscray, Australian
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Nipuni Welihinda
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Jörgen Jonsson
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet , Stockholm, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University , Uppsala, Sweden.,Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University , Moscow, Russia
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56
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Melnik BC. Milk exosomal miRNAs: potential drivers of AMPK-to-mTORC1 switching in β-cell de-differentiation of type 2 diabetes mellitus. Nutr Metab (Lond) 2019; 16:85. [PMID: 31827573 PMCID: PMC6898964 DOI: 10.1186/s12986-019-0412-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) steadily increases in prevalence since the 1950's, the period of widespread distribution of refrigerated pasteurized cow's milk. Whereas breastfeeding protects against the development of T2DM in later life, accumulating epidemiological evidence underlines the role of cow's milk consumption in T2DM. Recent studies in rodent models demonstrate that during the breastfeeding period pancreatic β-cells are metabolically immature and preferentially proliferate by activation of mechanistic target of rapamycin complex 1 (mTORC1) and suppression of AMP-activated protein kinase (AMPK). Weaning determines a metabolic switch of β-cells from a proliferating, immature phenotype with low insulin secretion to a differentiated mature phenotype with glucose-stimulated insulin secretion, less proliferation, reduced mTORC1- but increased AMPK activity. Translational evidence presented in this perspective implies for the first time that termination of milk miRNA transfer is the driver of this metabolic switch. miRNA-148a is a key inhibitor of AMPK and phosphatase and tensin homolog, crucial suppressors of mTORC1. β-Cells of diabetic patients return to the postnatal phenotype with high mTORC1 and low AMPK activity, explained by continuous transfer of bovine milk miRNAs to the human milk consumer. Bovine milk miRNA-148a apparently promotes β-cell de-differentiation to the immature mTORC1-high/AMPK-low phenotype with functional impairments in insulin secretion, increased mTORC1-driven endoplasmic reticulum stress, reduced autophagy and early β-cell apoptosis. In contrast to pasteurized cow's milk, milk's miRNAs are inactivated by bacterial fermentation, boiling and ultra-heat treatment and are missing in current infant formula. Persistent milk miRNA signaling adds a new perspective to the pathogenesis of T2DM and explains the protective role of breastfeeding but the diabetogenic effect of continued milk miRNA signaling by persistent consumption of pasteurized cow's milk.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Am Finkenhügel 7A, D-49076 Osnabrück, Germany
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57
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Chavira-Suárez E, Ramírez-Mendieta AJ, Martínez-Gutiérrez S, Zárate-Segura P, Beltrán-Montoya J, Espinosa-Maldonado NC, de la Cerda-Ángeles JC, Vadillo-Ortega F. Influence of pre-pregnancy body mass index (p-BMI) and gestational weight gain (GWG) on DNA methylation and protein expression of obesogenic genes in umbilical vein. PLoS One 2019; 14:e0226010. [PMID: 31794592 PMCID: PMC6890247 DOI: 10.1371/journal.pone.0226010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 11/17/2019] [Indexed: 01/14/2023] Open
Abstract
Understanding the regulatory mechanisms that affect obesogenic genes expression in newborns is essential for early prevention efforts, but they remain unclear. Our study aimed to explore whether the maternal p-BMI and GWG were associated with regulatory single-locus DNA methylation in selected obesogenic genes. For this purpose, DNA methylation was assayed by Methylation-Sensitive High Resolution Melting (MS-HRM) technique and Sanger allele-bisulfite sequencing in fifty samples of umbilical vein to evaluate glucosamine-6-phosphate deaminase 2 (GNPDA2), peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC1α), and leptin receptor (LEPR) genes. Correlations between DNA methylation levels and indicators of maternal nutritional status were carried out. Western blotting was used to evaluate protein expression in extracts of the same samples. Results indicated that GNPDA2 and PGC1α genes have the same level of DNA methylation in all samples; however, a differential DNA methylation of LEPR gene promoter was found, correlating it with GWG and this correlation is unaffected by maternal age or unhealthy habits. Furthermore, leptin receptor (Lep-Rb) was upregulated in samples that showed the lowest levels of DNA methylation. This study highlights the association between poor GWG and adjustments on obesogenic genes expression in newborn tissues with potential consequences for development of obesity in the future.
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Affiliation(s)
- Erika Chavira-Suárez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Unidad de Vinculación Científica de la Facultad de Medicina, Universidad Nacional Autónoma de México en el Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Angélica Jazmín Ramírez-Mendieta
- Unidad de Vinculación Científica de la Facultad de Medicina, Universidad Nacional Autónoma de México en el Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sofía Martínez-Gutiérrez
- Unidad de Vinculación Científica de la Facultad de Medicina, Universidad Nacional Autónoma de México en el Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Paola Zárate-Segura
- Laboratorio de Medicina Traslacional, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Jorge Beltrán-Montoya
- Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Mexico City, Mexico
| | | | | | - Felipe Vadillo-Ortega
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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58
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Wu X, Chen W, Lin F, Huang Q, Zhong J, Gao H, Song Y, Liang H. DNA methylation profile is a quantitative measure of biological aging in children. Aging (Albany NY) 2019; 11:10031-10051. [PMID: 31756171 PMCID: PMC6914436 DOI: 10.18632/aging.102399] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/26/2019] [Indexed: 12/21/2022]
Abstract
DNA methylation changes within the genome can be used to predict human age. However, the existing biological age prediction models based on DNA methylation are predominantly adult-oriented. We established a methylation-based age prediction model for children (9-212 months old) using data from 716 blood samples in 11 DNA methylation datasets. Our elastic net model includes 111 CpG sites, mostly in genes associated with development and aging. The model performed well and exhibited high precision, yielding a 98% correlation between the DNA methylation age and the chronological age, with an error of only 6.7 months. When we used the model to assess age acceleration in children based on their methylation data, we observed the following: first, the aging rate appears to be fastest in mid-childhood, and this acceleration is more pronounced in autistic children; second, lead exposure early in life increases the aging rate in boys, but not in girls; third, short-term recombinant human growth hormone treatment has little effect on the aging rate of children. Our child-specific methylation-based age prediction model can effectively detect epigenetic changes and health imbalances early in life. This may thus be a useful model for future studies of epigenetic interventions for age-related diseases.
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Affiliation(s)
- Xiaohui Wu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.,Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China
| | - Weidan Chen
- Department of Cardiovascular Surgery, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Fangqin Lin
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Qingsheng Huang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jiayong Zhong
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huan Gao
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yanyan Song
- The Guangdong Early Childhood Development Applied Engineering and Technology Research Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangdong, China
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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59
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Juvinao-Quintero DL, Hivert MF, Sharp GC, Relton CL, Elliott HR. DNA Methylation and Type 2 Diabetes: the Use of Mendelian Randomization to Assess Causality. CURRENT GENETIC MEDICINE REPORTS 2019; 7:191-207. [PMID: 32274260 PMCID: PMC7145450 DOI: 10.1007/s40142-019-00176-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purpose of Review This review summarises recent advances in the field of epigenetics in order to understand the aetiology of type 2 diabetes (T2D). Recent Findings DNA methylation at a number of loci has been shown to be robustly associated with T2D, including TXNIP, ABCG1, CPT1A, and SREBF1. However, due to the cross-sectional nature of many epidemiological studies and predominant analysis in samples derived from blood rather than disease relevant tissues, inferring causality is difficult. We therefore outline the use of Mendelian randomisation (MR) as one method able to assess causality in epigenetic studies of T2D. Summary Epidemiological studies have been fruitful in identifying epigenetic markers of T2D. Triangulation of evidence including utilisation of MR is essential to delineate causal from non-causal biomarkers of disease. Understanding the causality of epigenetic markers in T2D more fully will aid prioritisation of CpG sites as early biomarkers to detect disease or in drug development to target epigenetic mechanisms in order to treat patients.
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Affiliation(s)
- Diana L Juvinao-Quintero
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Marie-France Hivert
- Division of Chronic Disease Research Across the Lifecourse, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care, Boston, USA
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
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60
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Prats-Puig A, Xargay-Torrent S, Carreras-Badosa G, Mas-Parés B, Bassols J, Petry CJ, Girardot M, D E Zegher F, Ibáñez L, Dunger DB, Feil R, López-Bermejo A. Methylation of the C19MC microRNA locus in the placenta: association with maternal and chilhood body size. Int J Obes (Lond) 2019; 44:13-22. [PMID: 31554916 DOI: 10.1038/s41366-019-0450-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 06/18/2019] [Accepted: 07/07/2019] [Indexed: 12/20/2022]
Abstract
OBJECTIVES To study DNA methylation at the C19MC locus in the placenta and its association with (1) parental body size, (2) transmission of haplotypes for the C19MC rs55765443 SNP, and (3) offspring's body size and/or body composition at birth and in childhood. SUBJECTS AND METHODS Seventy-two pregnant women-infant pairs and 63 fathers were included in the study. Weight and height of mothers, fathers and newborns were registered during pregnancy or at birth (n = 72). Placental DNA methylation at the C19MC imprinting control region (ICR) was quantified by bisulfite pyrosequencing. Genotyping of the SNP was performed using restriction fragment length polymorphisms. The children's body size and composition were reassessed at age 6 years (n = 32). RESULTS Lower levels of placental C19MC methylation were associated with increased body size of mother, specifically with higher pregestational and predelivery weights and height of the mother (β from -0.294 to -0.371; R2 from 0.04 to 0.10 and all p < 0.019), and with higher weight, height, waist and hip circumferences, and fat mass of the child (β from -0.428 to -0.552; R2 from 0.33 to 0.56 and all p < 0.009). Parental transmission of the SNP did not correlate with an altered placental methylation status at the C19MC ICR. CONCLUSIONS Increased maternal size is associated with reduced placental C19MC methylation, which, in turn, relate to larger body size of the child.
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Affiliation(s)
- Anna Prats-Puig
- Department of Pediatrics, Girona Institute for Biomedical Research (IDIBGI), Salt, Spain.,Department of Physical Therapy, EUSES University of Girona, Salt Girona, Spain
| | - Sílvia Xargay-Torrent
- Department of Pediatrics, Girona Institute for Biomedical Research (IDIBGI), Salt, Spain
| | - Gemma Carreras-Badosa
- Department of Pediatrics, Girona Institute for Biomedical Research (IDIBGI), Salt, Spain
| | - Berta Mas-Parés
- Department of Pediatrics, Girona Institute for Biomedical Research (IDIBGI), Salt, Spain
| | - Judit Bassols
- Department of Pediatrics, Girona Institute for Biomedical Research (IDIBGI), Salt, Spain
| | - Clive J Petry
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Michael Girardot
- Institute of Molecular Genetics (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Francis D E Zegher
- Department of Development & Regeneration, University of Leuven, Leuven, Belgium
| | - Lourdes Ibáñez
- Endocrinology, Institut de Recerca Pediàtrica Sant Joan de Déu, University of Barcelona, Esplugues, Spain.,Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - David B Dunger
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Robert Feil
- Institute of Molecular Genetics (IGMM), CNRS, University of Montpellier, Montpellier, France
| | - Abel López-Bermejo
- Department of Pediatrics, Girona Institute for Biomedical Research (IDIBGI), Salt, Spain. .,Department of Pediatrics, Dr. Josep Trueta Hospital, Girona, Spain.
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Li R, Liang F, Li M, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z. MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res 2019; 46:D288-D295. [PMID: 29161430 PMCID: PMC5753180 DOI: 10.1093/nar/gkx1139] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022] Open
Abstract
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals. Additionally, it is enhanced by improving the functionalities for data annotation, which accordingly enables systematic identification of methylation sites closely associated with age, sites with constant methylation levels across different ages, differentially methylated promoters, age-specific differentially methylated cytosines/regions, and methylated CpG islands. Moreover, MethBank provides tools to estimate human methylation age online and to identify differentially methylated promoters, respectively. Taken together, MethBank is upgraded with significant improvements and advances over the previous version, which is of great help for deciphering DNA methylation regulatory mechanisms for epigenetic studies.
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Affiliation(s)
- Rujiao Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fang Liang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengwei Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shixiang Sun
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongbing Zhao
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenming Zhao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
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62
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Ling C, Rönn T. Epigenetics in Human Obesity and Type 2 Diabetes. Cell Metab 2019; 29:1028-1044. [PMID: 30982733 PMCID: PMC6509280 DOI: 10.1016/j.cmet.2019.03.009] [Citation(s) in RCA: 487] [Impact Index Per Article: 97.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/05/2019] [Accepted: 03/18/2019] [Indexed: 12/16/2022]
Abstract
Epigenetic mechanisms control gene activity and the development of an organism. The epigenome includes DNA methylation, histone modifications, and RNA-mediated processes, and disruption of this balance may cause several pathologies and contribute to obesity and type 2 diabetes (T2D). This Review summarizes epigenetic signatures obtained from human tissues of relevance for metabolism-i.e., adipose tissue, skeletal muscle, pancreatic islets, liver, and blood-in relation to obesity and T2D. Although this research field is still young, these comprehensive data support not only a role for epigenetics in disease development, but also epigenetic alterations as a response to disease. Genetic predisposition, as well as aging, contribute to epigenetic variability, and several environmental factors, including exercise and diet, further interact with the human epigenome. The reversible nature of epigenetic modifications holds promise for future therapeutic strategies in obesity and T2D.
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Affiliation(s)
- Charlotte Ling
- Epigenetics and Diabetes Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden.
| | - Tina Rönn
- Epigenetics and Diabetes Unit, Department of Clinical Sciences Malmö, Lund University Diabetes Centre, Scania University Hospital, Malmö, Sweden
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63
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Jia X, Yang Y, Chen Y, Xia Z, Zhang W, Feng Y, Li Y, Tan J, Xu C, Zhang Q, Deng H, Shi X. Multivariate analysis of genome-wide data to identify potential pleiotropic genes for type 2 diabetes, obesity and coronary artery disease using MetaCCA. Int J Cardiol 2019; 283:144-150. [DOI: 10.1016/j.ijcard.2018.10.102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 10/17/2018] [Accepted: 10/29/2018] [Indexed: 01/26/2023]
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Rohde K, Keller M, la Cour Poulsen L, Blüher M, Kovacs P, Böttcher Y. Genetics and epigenetics in obesity. Metabolism 2019; 92:37-50. [PMID: 30399374 DOI: 10.1016/j.metabol.2018.10.007] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/15/2018] [Accepted: 10/21/2018] [Indexed: 12/20/2022]
Abstract
Obesity is among the most threatening health burdens worldwide and its prevalence has markedly increased over the last decades. Obesity maybe considered a heritable trait. Identifications of rare cases of monogenic obesity unveiled that hypothalamic circuits and the brain-adipose axis play an important role in the regulation of energy homeostasis, appetite, hunger and satiety. For example, mutations in the leptin gene cause obesity through almost unsuppressed overeating. Common (multifactorial) obesity, most likely resulting from a concerted interplay of genetic, epigenetic and environmental factors, is clearly linked to genetic predisposition by multiple risk variants, which, however only account for a minor part of the general BMI variability. Although GWAS opened new avenues in elucidating the complex genetics behind common obesity, understanding the biological mechanisms relative to the specific risk contributing to obesity remains poorly understood. Non-genetic factors such as eating behavior or physical activity strongly modulate the individual risk for developing obesity. These factors may interact with genetic predisposition for obesity through epigenetic mechanisms. Thus, here, we review the current knowledge about monogenic and common (multifactorial) obesity highlighting the important recent advances in our knowledge on how epigenetic regulation is involved in the etiology of obesity.
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Affiliation(s)
- Kerstin Rohde
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany; University of Oslo, Institute of Clinical Medicine, Oslo 0316, Norway.
| | - Maria Keller
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany.
| | - Lars la Cour Poulsen
- Akershus University Hospital, Department of Clinical Molecular Biology, Medical Division, Lørenskog 1478, Norway.
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig 04103, Germany.
| | - Peter Kovacs
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany.
| | - Yvonne Böttcher
- Leipzig University Medical Center, IFB Adiposity Diseases, Leipzig 04103, Germany; University of Oslo, Institute of Clinical Medicine, Oslo 0316, Norway; Akershus University Hospital, Department of Clinical Molecular Biology, Medical Division, Lørenskog 1478, Norway.
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65
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Carullo NVN, Day JJ. Genomic Enhancers in Brain Health and Disease. Genes (Basel) 2019; 10:E43. [PMID: 30646598 PMCID: PMC6357130 DOI: 10.3390/genes10010043] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 01/18/2023] Open
Abstract
Enhancers are non-coding DNA elements that function in cis to regulate transcription from nearby genes. Through direct interactions with gene promoters, enhancers give rise to spatially and temporally precise gene expression profiles in distinct cell or tissue types. In the brain, the accurate regulation of these intricate expression programs across different neuronal classes gives rise to an incredible cellular and functional diversity. Newly developed technologies have recently allowed more accurate enhancer mapping and more sophisticated enhancer manipulation, producing rapid progress in our understanding of enhancer biology. Furthermore, identification of disease-linked genetic variation in enhancer regions has highlighted the potential influence of enhancers in brain health and disease. This review outlines the key role of enhancers as transcriptional regulators, reviews the current understanding of enhancer regulation in neuronal development, function and dysfunction and provides our thoughts on how enhancers can be targeted for technological and therapeutic goals.
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Affiliation(s)
- Nancy V N Carullo
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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66
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Melnik BC, Schmitz G. Exosomes of pasteurized milk: potential pathogens of Western diseases. J Transl Med 2019; 17:3. [PMID: 30602375 PMCID: PMC6317263 DOI: 10.1186/s12967-018-1760-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 12/21/2018] [Indexed: 12/16/2022] Open
Abstract
Milk consumption is a hallmark of western diet. According to common believes, milk consumption has beneficial effects for human health. Pasteurization of cow's milk protects thermolabile vitamins and other organic compounds including bioactive and bioavailable exosomes and extracellular vesicles in the range of 40-120 nm, which are pivotal mediators of cell communication via systemic transfer of specific micro-ribonucleic acids, mRNAs and regulatory proteins such as transforming growth factor-β. There is compelling evidence that human and bovine milk exosomes play a crucial role for adequate metabolic and immunological programming of the newborn infant at the beginning of extrauterine life. Milk exosomes assist in executing an anabolic, growth-promoting and immunological program confined to the postnatal period in all mammals. However, epidemiological and translational evidence presented in this review indicates that continuous exposure of humans to exosomes of pasteurized milk may confer a substantial risk for the development of chronic diseases of civilization including obesity, type 2 diabetes mellitus, osteoporosis, common cancers (prostate, breast, liver, B-cells) as well as Parkinson's disease. Exosomes of pasteurized milk may represent new pathogens that should not reach the human food chain.
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Affiliation(s)
- Bodo C. Melnik
- Department of Dermatology, Environmental Medicine and Health Theory, University of Osnabrück, Am Finkenhügel 7A, 49076 Osnabrück, Germany
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, University of Regensburg, Josef-Strauss-Allee 11, 93053 Regensburg, Germany
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Diseases and their clinical heterogeneity – Are we ignoring the SNiPers and micRomaNAgers? An illustration using Beta-thalassemia clinical spectrum and fetal hemoglobin levels. Genomics 2019; 111:67-75. [DOI: 10.1016/j.ygeno.2018.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/18/2017] [Accepted: 01/03/2018] [Indexed: 12/18/2022]
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68
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Malipatil N, Lunt M, Narayanan RP, Siddals K, Cortés Moreno GY, Gibson MJ, Gu HF, Heald AH, Donn RP. Assessment of global long interspersed nucleotide element-1 (LINE-1) DNA methylation in a longitudinal cohort of type 2 diabetes mellitus (T2DM) individuals. Int J Clin Pract 2018; 73:e13270. [PMID: 30345607 DOI: 10.1111/ijcp.13270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 09/06/2018] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION Recent studies have indicated that methylation of the LINE-1 elements is associated with an increased risk of worsening carbohydrate metabolism. It has been shown that overall DNA methylation of LINE-1 elements could be considered as a risk factor for T2DM and its complications, independent of other established risk factors. METHODS A total of 794 T2DM individuals from Salford, UK were included in this study (60% men n = 470). All patients had clinical and metabolic variables measured in 2002 (baseline outcomes) and annually through to 2016. Global LINE-1 DNA methylation was measured at four CpG sites. The QIAGEN PyroMark Q96 MD pyrosequencer was used to quantify methylation. RESULTS The overall mean ± SD global LINE-1 methylation was 75.81 ± 3.25%. Cross-sectional linear regression analysis at baseline year 2002 showed that LINE-1 methylation was a significant predictor of diastolic BP (adjusted beta coefficient β = -0.25), estimated glomerular filtration rate (eGFR) (β = -0.48) and cholesterol HDL ratio (β = -0.04). A 10% increase in LINE-1 methylation was associated with a lower diastolic BP by 2.5 mm Hg, a lower eGFR by 4.8 ml/min/1.73 m2 and decreased cholesterol/HDL ratio by 0.4 mmol/L. Longitudinal analysis over the 14-year-follow-up periods showed that global LINE-1 methylation at baseline was associated with lower BMI in women [β = -0.25] and lower cholesterol: HDL ratio [β = -0.07]. A 10% increase in LINE-1 methylation was associated with reduction in BMI by 2.5 kg/m2 in women and reduction in cholesterol:HDL ratio by 0.7 mmol/L. CONCLUSION In a 14-year longitudinal cohort of T2DM individuals, relations between global LINE-1 DNA methylation status and specific metabolic markers were seen. Also, a higher degree of DNA methylation was predictive of less weight gain over time in women.
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Affiliation(s)
- Nagaraj Malipatil
- The School of Medicine and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal Hospital, Salford, UK
| | - Mark Lunt
- Department of Diabetes and Endocrinology, Salford Royal Hospital, Salford, UK
| | | | - Kirk Siddals
- The School of Medicine and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal Hospital, Salford, UK
| | | | - Martin J Gibson
- Department of Diabetes and Endocrinology, Salford Royal Hospital, Salford, UK
- NorthWest EHealth Ltd, Manchester, UK
| | - Harvest F Gu
- Center for Molecular Medicine, Karolinska University Hospital, Solna, Stockholm, Sweden
| | - Adrian H Heald
- The School of Medicine and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
- Department of Diabetes and Endocrinology, Salford Royal Hospital, Salford, UK
| | - Rachelle P Donn
- The School of Medicine and Manchester Academic Health Sciences Centre, University of Manchester, Manchester, UK
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Sun R, Weng H, Men R, Xia X, Chong KC, Wu WKK, Zee BCY, Wang MH. Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment. BMC Proc 2018; 12:53. [PMID: 30263051 PMCID: PMC6156903 DOI: 10.1186/s12919-018-0143-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
An increasing number of studies are focused on the epigenetic regulation of DNA to affect gene expression without modifications to the DNA sequence. Methylation plays an important role in shaping disease traits; however, previous studies were mainly experiment, based, resulting in few reports that measured gene-methylation interaction effects via statistical means. In this study, we applied the data set adaptive W-test to measure gene-methylation interactions. Performance was evaluated by the ability to detect a given set of causal markers in the data set obtained from the GAW20. Results from simulation data analyses showed that the W-test was able to detect most markers. The method was also applied to chromosome 11 of the experimental data set and identified clusters of genes with neuronal and retinal functions, including MPPED2I, GUCY2E, NAV2, and ZBTB16. Genes from the TRIM family were also identified; these genes are potentially related to the regulation of triglyceride levels. Our results suggest that the W-test could be an efficient and effective method to detect gene-methylation interactions. Furthermore, the identified genes suggest an interesting relationship between lipid levels and the etiology of neurological disorders.
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Affiliation(s)
- Rui Sun
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Haoyi Weng
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Ruoting Men
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Xiaoxuan Xia
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Ka Chun Chong
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - William K K Wu
- Department of Anaesthesia and Intensive Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China
| | - Benny Chung-Ying Zee
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Maggie Haitian Wang
- Division of Biostatistics, Centre for Clinical Research and Biostatistics, JC School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, N.T., Hong Kong, Hong Kong, Special Administrative Region of China.,2The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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Abstract
Obesity is a complex disease which has reached epidemic dimensions. Thus, prevention of excessive weight gain and associated metabolic and cardiovascular diseases has to start as early in life as possible. The impact of epigenetic mechanisms on the regulation of genes involved in obesity is increasingly recognized. On the other hand, it is well known that socioeconomic factors influence the risk for obesity. These factors can also have an impact on epigenetic gene regulation. There is increasing body of evidence that several factors and interventions addressing extragenetic causes of obesity may not only improve individual health, but also the health of future generations by epigenetic alterations. Our current understanding of epigenetic changes has shown that many of them are potentially reversible, i.e. by physical exercise, by pharmacological treatment, by environmental factors or nutrition, or even by influencing socioeconomic factors, which might have impact on improving health in future generations by avoiding epigenetic dysregulation. In this review we present the current state of the art with regard to the interplay between social determinants, weight status and epigenetic alterations.
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Affiliation(s)
- Susann Weihrauch-Blüher
- Department of Pediatrics I, University Hospital of the Martin Luther University Halle-Wittenberg, Germany; Leipzig University Medical Center, IFB Adiposity Diseases, University of Leipzig, Germany.
| | - Matthias Richter
- Institute of Medical Sociology, Martin Luther University Halle-Wittenberg, Germany
| | - Martin S Staege
- Department of Pediatrics I, University Hospital of the Martin Luther University Halle-Wittenberg, Germany
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Keller M, Klös M, Rohde K, Krüger J, Kurze T, Dietrich A, Schön MR, Gärtner D, Lohmann T, Dreßler M, Stumvoll M, Blüher M, Kovacs P, Böttcher Y. DNA methylation of SSPN is linked to adipose tissue distribution and glucose metabolism. FASEB J 2018; 32:fj201800528R. [PMID: 29932866 DOI: 10.1096/fj.201800528r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
DNA methylation is a crucial epigenetic mechanism in obesity and fat distribution. We explored the Sarcospan ( SSPN) gene locus by using genome-wide data sets comprising methylation and expression data, pyrosequencing analysis in the promoter region, and genetic analysis of an SNP variant rs718314, which was previously reported to associate with waist-to-hip ratio. We found that DNA methylation influences several clinical variables related to fat distribution and glucose metabolism, while SSPN mRNA levels showed directionally opposite effects on these traits. Complete DNA methylation of the SSPN promoter construct suppressed the gene expression of firefly luciferase in MCF7 cells. Moreover, rs718314 was associated with waist and with DNA methylation at CpG sites. Our data strongly support the role of the SSPN locus in body fat composition and glucose homeostasis, and suggest that this is most likely the result of changes in DNA methylation of SSPN in adipose tissue.-Keller, M., Klös, M., Rohde, K., Krüger, J., Kurze, T., Dietrich, A., Schön, M. R., Gärtner, D., Lohmann, T., Dreßler, M., Stumvoll, M., Blüher, M., Kovacs, P., Böttcher, Y. DNA methylation of SSPN is linked to adipose tissue distribution and glucose metabolism.
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Affiliation(s)
- Maria Keller
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University Diabetes Centre, Skåne University Hospital, Malmö, Sweden
| | - Matthias Klös
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany
| | - Kerstin Rohde
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Medicine, Akershus University Hospital, University of Oslo, Lørenskog, Norway
| | | | - Tabea Kurze
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Arne Dietrich
- Department of Surgery, University of Leipzig, Leipzig, Germany
| | - Michael R Schön
- Städtisches Klinikum Karlsruhe, Clinic of Visceral Surgery, Karlsruhe, Germany; and
| | - Daniel Gärtner
- Städtisches Klinikum Karlsruhe, Clinic of Visceral Surgery, Karlsruhe, Germany; and
| | | | | | | | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Yvonne Böttcher
- Integrated Research and Treatment Center (IFB) Adiposity Diseases, University of Leipzig, Leipzig, Germany
- Institute of Clinical Medicine, Akershus University Hospital, University of Oslo, Lørenskog, Norway
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Li W, Tang R, Ma F, Ouyang S, Liu Z, Wu J. Folic acid supplementation alters the DNA methylation profile and improves insulin resistance in high-fat-diet-fed mice. J Nutr Biochem 2018; 59:76-83. [PMID: 29986310 DOI: 10.1016/j.jnutbio.2018.05.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/20/2018] [Accepted: 05/31/2018] [Indexed: 12/11/2022]
Abstract
Folic acid (FA) supplementation may protect from obesity and insulin resistance, the effects and mechanism of FA on chronic high-fat-diet-induced obesity-related metabolic disorders are not well elucidated. We adopted a genome-wide approach to directly examine whether FA supplementation affects the DNA methylation profile of mouse adipose tissue and identify the functional consequences of these changes. Mice were fed a high-fat diet (HFD), normal diet (ND) or an HFD supplemented with folic acid (20 μg/ml in drinking water) for 10 weeks, epididymal fat was harvested, and genome-wide DNA methylation analyses were performed using methylated DNA immunoprecipitation sequencing (MeDIP-seq). Mice exposed to the HFD expanded their adipose mass, which was accompanied by a significant increase in circulating glucose and insulin levels. FA supplementation reduced the fat mass and serum glucose levels and improved insulin resistance in HFD-fed mice. MeDIP-seq revealed distribution of differentially methylated regions (DMRs) throughout the adipocyte genome, with more hypermethylated regions in HFD mice. Methylome profiling identified DMRs associated with 3787 annotated genes from HFD mice in response to FA supplementation. Pathway analyses showed novel DNA methylation changes in adipose genes associated with insulin secretion, pancreatic secretion and type 2 diabetes. The differential DNA methylation corresponded to changes in the adipose tissue gene expression of Adcy3 and Rapgef4 in mice exposed to a diet containing FA. FA supplementation improved insulin resistance, decreased the fat mass, and induced DNA methylation and gene expression changes in genes associated with obesity and insulin secretion in obese mice fed a HFD.
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Affiliation(s)
- Wei Li
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China; Department of Biochemistry & Immunology, Capital Institute of Pediatrics, No. 2, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Renqiao Tang
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China; Department of Biochemistry & Immunology, Capital Institute of Pediatrics, No. 2, Yabao Road, Chaoyang District, Beijing 100020, China
| | - Feifei Ma
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China
| | - Shengrong Ouyang
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China
| | - Zhuo Liu
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China
| | - Jianxin Wu
- Graduate School of Peking Union Medical College, No. 9, Dongdansantiao, Dongcheng District, Beijing 100730, China; Department of Biochemistry & Immunology, Capital Institute of Pediatrics, No. 2, Yabao Road, Chaoyang District, Beijing 100020, China.
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73
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Chen Y, Hong T, Wang S, Mo J, Tian T, Zhou X. Epigenetic modification of nucleic acids: from basic studies to medical applications. Chem Soc Rev 2018; 46:2844-2872. [PMID: 28352906 DOI: 10.1039/c6cs00599c] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The epigenetic modification of nucleic acids represents one of the most significant areas of study in the field of nucleic acids because it makes gene regulation more complex and heredity more complicated, thus indicating its profound impact on aspects of heredity, growth, and diseases. The recent characterization of epigenetic modifications of DNA and RNA using chemical labelling strategies has promoted the discovery of these modifications, and the newly developed single-base or single-cell resolution mapping strategies have enabled large-scale epigenetic studies in eukaryotes. Due to these technological breakthroughs, several new epigenetic marks have been discovered that have greatly extended the scope and impact of epigenetic modifications in nucleic acids over the past few years. Because epigenetics is reversible and susceptible to environmental factors, it could potentially be a promising direction for clinical medicine research. In this review, we have comprehensively discussed how these epigenetic marks are involved in disease, including the pathogenesis, prevention, diagnosis and treatment of disease. These findings have revealed that the epigenetic modification of nucleic acids has considerable significance in various areas from methodology to clinical medicine and even in biomedical applications.
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Affiliation(s)
- Yuqi Chen
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Hubei, Wuhan 430072, P. R. China.
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74
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Tang Y, Jin B, Zhou L, Lu W. MeQTL analysis of childhood obesity links epigenetics with a risk SNP rs17782313 near MC4R from meta-analysis. Oncotarget 2018; 8:2800-2806. [PMID: 27926527 PMCID: PMC5356842 DOI: 10.18632/oncotarget.13742] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/23/2016] [Indexed: 02/06/2023] Open
Abstract
Earlier GWAS has identified that rs17782313 near MC4R was associated with obesity. However, subsequent studies showed conflicting results, especially among childhood. Besides, the mechanisms underlying the association between rs17782313 and childhood obesity remain largely unexplored, and genetic and epigenetic may interact and together affect the development of childhood obesity. We conducted a comprehensive meta-analysis to assess the association between rs17782313 and childhood obesity. MeQTL and eQTL analysis was applied to explore the effect of rs17782313 on DNA methylation and MC4R expression. We found that rs17782313 near MC4R was associated with increased childhood obesity risk and BMI z-score in several inheritable models (P < 0.05). Additionally, the similar trend was observed among subgroups of Asians, Caucasian. Furthermore, meQTL and eQTL analysis indicated that individuals carrying rs17782313 TT genotype were significantly associated with increased methylation level of cg10097150 located in MC4R promoter and decreased expression of MC4R than those with CT/CC genotype (P = 1.7 × 10−4 and P = 1.9 × 10−3 respectively). Our results strongly confirmed that rs17782313 was associated with increased risk of childhood obesity. Furthermore, rs17782313 T allele was correlated with promoter hypermethylation and decreased expression of MC4R, thus involved in the development of childhood obesity.
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Affiliation(s)
- Yuping Tang
- Department of Orthopaedic, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Bo Jin
- Department of Neurology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Lingling Zhou
- Department of Orthopaedic, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Weifeng Lu
- Surgical Intensive Care Unite, Children's Hospital of Nanjing Medical University, Nanjing, China
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75
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Loss-of-function mutations in ADCY3 cause monogenic severe obesity. Nat Genet 2018; 50:175-179. [DOI: 10.1038/s41588-017-0023-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 11/14/2017] [Indexed: 12/26/2022]
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76
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Willmer T, Johnson R, Louw J, Pheiffer C. Blood-Based DNA Methylation Biomarkers for Type 2 Diabetes: Potential for Clinical Applications. Front Endocrinol (Lausanne) 2018; 9:744. [PMID: 30564199 PMCID: PMC6288427 DOI: 10.3389/fendo.2018.00744] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/23/2018] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) is a leading cause of death and disability worldwide. It is a chronic metabolic disorder that develops due to an interplay of genetic, lifestyle, and environmental factors. The biological onset of the disease occurs long before clinical symptoms develop, thus the search for early diagnostic and prognostic biomarkers, which could facilitate intervention strategies to prevent or delay disease progression, has increased considerably in recent years. Epigenetic modifications represent important links between genetic, environmental and lifestyle cues and increasing evidence implicate altered epigenetic marks such as DNA methylation, the most characterized and widely studied epigenetic mechanism, in the pathogenesis of T2D. This review provides an update of the current status of DNA methylation as a biomarker for T2D. Four databases, Scopus, Pubmed, Cochrane Central, and Google Scholar were searched for studies investigating DNA methylation in blood. Thirty-seven studies were identified, and are summarized with respect to population characteristics, biological source, and method of DNA methylation quantification (global, candidate gene or genome-wide). We highlight that differential methylation of the TCF7L2, KCNQ1, ABCG1, TXNIP, PHOSPHO1, SREBF1, SLC30A8, and FTO genes in blood are reproducibly associated with T2D in different population groups. These genes should be prioritized and replicated in longitudinal studies across more populations in future studies. Finally, we discuss the limitations faced by DNA methylation studies, which include including interpatient variability, cellular heterogeneity, and lack of accounting for study confounders. These limitations and challenges must be overcome before the implementation of blood-based DNA methylation biomarkers into a clinical setting. We emphasize the need for longitudinal prospective studies to support the robustness of the current findings of this review.
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Affiliation(s)
- Tarryn Willmer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- *Correspondence: Tarryn Willmer
| | - Rabia Johnson
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Johan Louw
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, South Africa
| | - Carmen Pheiffer
- Biomedical Research and Innovation Platform, South African Medical Research Council, Tygerberg, South Africa
- Division of Medical Physiology, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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77
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Stryjecki C, Alyass A, Meyre D. Ethnic and population differences in the genetic predisposition to human obesity. Obes Rev 2018; 19:62-80. [PMID: 29024387 DOI: 10.1111/obr.12604] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 06/17/2017] [Accepted: 08/02/2017] [Indexed: 12/22/2022]
Abstract
Obesity rates have escalated to the point of a global pandemic with varying prevalence across ethnic groups. These differences are partially explained by lifestyle factors in addition to genetic predisposition to obesity. This review provides a comprehensive examination of the ethnic differences in the genetic architecture of obesity. Using examples from evolution, heritability, admixture, monogenic and polygenic studies of obesity, we provide explanations for ethnic differences in the prevalence of obesity. The debate over definitions of race and ethnicity, the advantages and limitations of multi-ethnic studies and future directions of research are also discussed. Multi-ethnic studies have great potential to provide a better understanding of ethnic differences in the prevalence of obesity that may result in more targeted and personalized obesity treatments.
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Affiliation(s)
- C Stryjecki
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - A Alyass
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada
| | - D Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
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78
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Jokinen J, Boström AE, Dadfar A, Ciuculete DM, Chatzittofis A, Åsberg M, Schiöth HB. Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents. EBioMedicine 2017; 27:123-133. [PMID: 29277323 PMCID: PMC5828554 DOI: 10.1016/j.ebiom.2017.12.018] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/15/2017] [Accepted: 12/15/2017] [Indexed: 12/11/2022] Open
Abstract
The aim of this study, comprising 88 suicide attempters, was to identify hypothalamic-pituitary-adrenal (HPA) -axis coupled CpG-sites showing methylation shifts linked to severity of the suicide attempt. Candidate methylation loci were further investigated as risk loci for a general psychiatric risk score in two cohorts of adolescents (cohort 1 and 2). The genome-wide methylation pattern was measured in whole blood using the Illumina Infinium Methylation EPIC BeadChip. Subjects were stratified into high-risk and low-risk groups based on the severity of the suicidal behavior. We included CpG sites located within 2000 basepairs away from transcriptional start site of the following HPA-axis coupled genes: corticotropin releasing hormone (CRH), corticotropin releasing hormone binding protein (CRHBP), corticotropin releasing hormone receptor 1 (CRHR1), corticotropin releasing hormone receptor 2 (CRHR2), FK506-binding protein 51 (FKBP5) and the glucocorticoid receptor (NR3C1). The methylation state of two corticotropin releasing hormone (CRH)-associated CpG sites were significantly hypomethylated in the high-risk group of suicide attempters (n = 31) (cg19035496 and cg23409074) (p < 0.001). Adolescent cohort 1 and 2 consisted of 129 and 93 subjects, respectively, and were stratified by the in silico generated DAWBA measurements of a general psychiatric risk score into high-risk group (>~50% risk) or controls. In adolescent cohort 2, cg19035496 was hypermethylated in subjects with a high general psychiatric risk score. Our results show epigenetic changes in the CRH gene related to severity of suicide attempt in adults and a general psychiatric risk score in adolescents. Two CRH-associated CpG sites were significantly hypomethylated in the high-risk group of suicide attempters. In adolescent cohort, cg19035496 was hypermethylated in subjects with a high general psychiatric risk score. Epigenetic modulatory effects on the HPA axis dysregulation are associated with psychiatric illness and suicidal behavior.
In this study, comprising 88 suicide attempters, we aimed to identify epigenetic changes in stress system linked to severity of the suicide attempt. In the next step, we investigated if the same epigenetic changes could be detected in adolescents with high risk for psychiatric illness. The methylation pattern was measured in blood and subjects were stratified into high-risk and low-risk groups based on the severity of the suicidal behavior. One corticotropin releasing hormone (CRH)-a key regulator of stress system-associated CpG site showed less methylation in the high-risk group and was hypermethylated in adolescents with a high general psychiatric risk score. Epigenetic changes in the CRH gene were related to severity of suicide attempt in adults and a general psychiatric risk score in adolescents.
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Affiliation(s)
- Jussi Jokinen
- Department of Clinical Neuroscience/Center for Psychiatric Research, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden.
| | - Adrian E Boström
- Department of Neuroscience/Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Ali Dadfar
- Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden
| | - Diana M Ciuculete
- Department of Neuroscience/Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Andreas Chatzittofis
- Department of Clinical Neuroscience/Center for Psychiatric Research, Karolinska Institutet, Stockholm, Sweden; Medical School, University of Cyprus, Nicosia, Cyprus
| | - Marie Åsberg
- Department of Clinical Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience/Functional Pharmacology, Uppsala University, Uppsala, Sweden
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79
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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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80
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Gao L, Millstein J, Siegmund KD, Dubeau L, Maguire R, Gilliland FD, Murphy SK, Hoyo C, Breton CV. Epigenetic regulation of AXL and risk of childhood asthma symptoms. Clin Epigenetics 2017; 9:121. [PMID: 29177020 PMCID: PMC5688797 DOI: 10.1186/s13148-017-0421-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/01/2017] [Indexed: 12/14/2022] Open
Abstract
Background AXL is one of the TAM (TYRO3, AXL and MERTK) receptor tyrosine kinases and may affect numerous immune-related health conditions. However, the role for AXL in asthma, including its epigenetic regulation, has not been extensively studied. Methods We investigated the association between AXL DNA methylation at birth and risk of childhood asthma symptoms at age 6 years. DNA methylation of multiple CpG loci across the regulatory regions of AXL was measured in newborn bloodspots using the Illumina HumanMethylation450 array on a subset of 246 children from the Children's Health Study (CHS). Logistic regression models were fitted to assess the association between asthma symptoms and DNA methylation. Findings were evaluated for replication in a separate population of 1038 CHS subjects using Pyrosequencing on newborn bloodspot samples. AXL genotypes were extracted from genome-wide data. Results Higher average methylation of CpGs in the AXL gene at birth was associated with higher risk of parent-reported wheezing, and the association was stronger in girls than in boys. This relationship reflected the methylation status of the gene-body region near the 5' end, for which a 1% higher methylation level was significantly associated with a 72% increased risk of ever having wheezed by 6 years. The association of one CpG locus, cg00360107 was replicated using Pyrosequencing. Increased AXL methylation was also associated with lower mRNA expression level of this gene in lung tissue from the Cancer Genome Atlas (TCGA) dataset. Furthermore, AXL DNA methylation was strongly linked to underlying genetic polymorphisms. Conclusions AXL DNA methylation at birth was associated with higher risk for asthma-related symptoms in early childhood.
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Affiliation(s)
- Lu Gao
- 0000 0001 2156 6853grid.42505.36Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Los Angeles, CA 90032 USA
| | - Joshua Millstein
- 0000 0001 2156 6853grid.42505.36Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Los Angeles, CA 90032 USA
| | - Kimberly D. Siegmund
- 0000 0001 2156 6853grid.42505.36Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Los Angeles, CA 90032 USA
| | - Louis Dubeau
- 0000 0001 2156 6853grid.42505.36Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Los Angeles, CA 90032 USA
| | - Rachel Maguire
- 0000 0001 2173 6074grid.40803.3fDepartment of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695 USA
| | - Frank D. Gilliland
- 0000 0001 2156 6853grid.42505.36Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Los Angeles, CA 90032 USA
| | - Susan K. Murphy
- 0000 0004 1936 7961grid.26009.3dDivision of Gynecologic Oncology, Department of Obstetrics and Gynecology, Duke University School of Medicine, Durham, NC 27710 USA
| | - Cathrine Hoyo
- 0000 0001 2173 6074grid.40803.3fDepartment of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC 27695 USA
| | - Carrie V. Breton
- 0000 0001 2156 6853grid.42505.36Department of Preventive Medicine, USC Keck School of Medicine, 2001 N. Soto Street, Los Angeles, CA 90032 USA
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81
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DNA methylation in blood from neonatal screening cards and the association with BMI and insulin sensitivity in early childhood. Int J Obes (Lond) 2017; 42:28-35. [PMID: 29064478 DOI: 10.1038/ijo.2017.228] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/13/2017] [Accepted: 08/27/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND/OBJECTIVES There is increasing evidence that metabolic diseases originate in early life, and epigenetic changes have been implicated as key drivers of this early life programming. This led to the hypothesis that epigenetic marks present at birth may predict an individual's future risk of obesity and type 2 diabetes. In this study, we assessed whether epigenetic marks in blood of newborn children were associated with body mass index (BMI) and insulin sensitivity later in childhood. SUBJECTS/METHODS DNA methylation was measured in neonatal blood spot samples of 438 children using the Illumina Infinium 450 k BeadChip. Associations were assessed between DNA methylation at birth and BMI z-scores, body fat mass, fasting plasma glucose, insulin and homeostatic model assessment of insulin resistance (HOMA-IR) at age 5 years, as well as birth weight, maternal BMI and smoking status. RESULTS No individual methylation sites at birth were associated with obesity or insulin sensitivity measures at 5 years. DNA methylation in 69 genomic regions at birth was associated with BMI z-scores at age 5 years, and in 63 regions with HOMA-IR. The methylation changes were generally small (<5%), except for a region near the non-coding RNA nc886 (VTRNA2-1) where a clear link between methylation status at birth and BMI in childhood was observed (P=0.001). Associations were also found between DNA methylation, maternal smoking and birth weight. CONCLUSIONS We identified a number of DNA methylation regions at birth that were associated with obesity or insulin sensitivity measurements in childhood. These findings support the mounting evidence on the role of epigenetics in programming of metabolic health. Whether many of these small changes in DNA methylation are causally related to the health outcomes, and of clinical relevance, remains to be determined, but the nc886 region represents a promising obesity risk marker that warrants further investigation.
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82
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Albuquerque D, Nóbrega C, Manco L, Padez C. The contribution of genetics and environment to obesity. Br Med Bull 2017; 123:159-173. [PMID: 28910990 DOI: 10.1093/bmb/ldx022] [Citation(s) in RCA: 147] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 06/23/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Obesity is a global health problem mainly attributed to lifestyle changes such as diet, low physical activity or socioeconomics factors. However, several evidences consistently showed that genetics contributes significantly to the weight-gain susceptibility. SOURCES OF DATA A systematic literature search of most relevant original, review and meta-analysis, restricted to English was conducted in PubMed, Web of Science and Google scholar up to May 2017 concerning the contribution of genetics and environmental factors to obesity. AREAS OF AGREEMENT Several evidences suggest that obesogenic environments contribute to the development of an obese phenotype. However, not every individual from the same population, despite sharing the same obesogenic environment, develop obesity. AREAS OF CONTROVERSY After more than 10 years of investigation on the genetics of obesity, the variants found associated with obesity represent only 3% of the estimated BMI-heritability, which is around 47-80%. Moreover, genetic factors per se were unable to explain the rapid spread of obesity prevalence. GROWING POINTS The integration of multi-omics data enables scientists having a better picture and to elucidate unknown pathways contributing to obesity. AREAS TIMELY FOR DEVELOPING RESEARCH New studies based on case-control or gene candidate approach will be important to identify new variants associated with obesity susceptibility and consequently unveiling its genetic architecture. This will lead to an improvement of our understanding about underlying mechanisms involved in development and origin of the actual obesity epidemic. The integration of several omics will also provide insights about the interplay between genes and environments contributing to the obese phenotype.
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Affiliation(s)
- David Albuquerque
- Research Center for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Fundación Investigación Hospital General Universitario de Valencia, Genomics group, Valencia, Spain
| | - Clévio Nóbrega
- Department of Biomedical Sciences and Medicine (DCBM), University of Algarve, Faro, Portugal.,Centre for Biomedical Research (CBMR), University of Algarve, Faro, Portugal.,Algarve Biomedical Center (ABC), University of Algarve, Faro, Portugal
| | - Licínio Manco
- Research Center for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Cristina Padez
- Research Center for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal.,Faculty of Sciences and Technology, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Association of variants in SH2B1 and RABEP1 with worsening of low-density lipoprotein and glucose parameters in patients treated with psychotropic drugs. Gene 2017; 628:8-15. [DOI: 10.1016/j.gene.2017.07.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 05/11/2017] [Accepted: 07/02/2017] [Indexed: 12/22/2022]
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84
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Huang JY, King NB. Epigenetics Changes Nothing: What a New Scientific Field Does and Does Not Mean for Ethics and Social Justice. Public Health Ethics 2017; 11:69-81. [PMID: 30619507 DOI: 10.1093/phe/phx013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Recently, ethicists have posited that consideration of epigenetic mechanisms presents novel challenges to concepts of justice and equality of opportunity, such as elevating the importance of environments in bioethics and providing a counterpoint to gross genetic determinism. We argue that new findings in epigenetic sciences, including those regarding intergenerational health effects, do not necessitate reconceptualization of theories of justice or the environment. To the contrary, such claims reflect a flawed understanding of epigenetics and its relation to genetics that may unintentionally undermine appeals to social justice. We provide a brief summary of epigenetic sciences, focusing on phenomena central to the current ethical discourse. We identify three fallacious modes of reasoning arising from the emergent literature on the ethical and policy implications of epigenetics, including mischaracterization, undue extrapolation, and exceptionalism. We end by discussing how these issues may work against mobilizing health equity policies and present a more modest claim regarding the value of new epigenetic knowledge to health justice by setting this discourse within the context of known themes in biomedical ethics and health policy.
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Affiliation(s)
- Jonathan Y Huang
- Institute for Health and Social Policy, Department of Epidemiology, Biostatistics, and Occupational Health, McGill University
| | - Nicholas B King
- Department of Epidemiology, Biostatistics, and Occupational Health, Department of the Social Studies of Medicine, Biomedical Ethics Unit, McGill University
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85
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Wang S, Song J, Yang Y, Zhang Y, Chawla NV, Ma J, Wang H. Interaction between obesity and the Hypoxia Inducible Factor 3 Alpha Subunit rs3826795 polymorphism in relation with plasma alanine aminotransferase. BMC MEDICAL GENETICS 2017; 18:80. [PMID: 28754107 PMCID: PMC5534125 DOI: 10.1186/s12881-017-0437-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 07/13/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Hypoxia Inducible Factor 3 Alpha Subunit (HIF3A) DNA has been demonstrated to be associated with obesity in the methylation level, and it also has a Body Mass Index (BMI)-independent association with plasma alanine aminotransferase (ALT). However, the relation among obesity, plasma ALT, HIF3A polymorphism and methylation remains unclear. This study aims to identify the association between HIF3A polymorphism and plasma ALT, and further to determine whether the effect of HIF3A polymorphism on ALT could be modified by obesity or mediated by DNA methylation. METHODS The HIF3A rs3826795 polymorphism was genotyped in a case-control study including 2030 Chinese children aged 7-18 years (705 obese cases and 1325 non-obese controls). Furthermore, the HIF3A DNA methylation of the peripheral blood was measured in 110 severely obese children and 110 age- and gender- matched normal-weight controls. RESULTS There was no overall association between the HIF3A rs3826795 polymorphism and ALT. A significant interaction between obesity and rs3826795 in relation with ALT was found (P inter = 0.042), with rs3826795 G-allele number elevating ALT significantly only in obese children (β' = 0.075, P = 0.037), but not in non-obese children (β' = -0.009, P = 0.741). Additionally, a mediation effect of HIF3A methylation was found in the association between the HIF3A rs3826795 polymorphism and ALT among obese children (β' = 0.242, P = 0.014). CONCLUSION This is the first study to report the interaction between obesity and HIF3A gene in relation with ALT, and also to reveal a mediation effect among the HIF3A polymorphism, methylation and ALT. This study provides new evidence to the function of HIF3A gene, which would be helpful for future risk assessment and personalized treatment of liver diseases.
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Affiliation(s)
- Shuo Wang
- Institute of Child and Adolescent Health of Peking University, School of Public Health, Peking University Health Science Center, Beijing, 100191, China.,Interdisciplinary Center for Network Science and Applications (iCeNSA), University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jieyun Song
- Institute of Child and Adolescent Health of Peking University, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Yide Yang
- Institute of Child and Adolescent Health of Peking University, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Yining Zhang
- Institute of Child and Adolescent Health of Peking University, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Nitesh V Chawla
- Interdisciplinary Center for Network Science and Applications (iCeNSA), University of Notre Dame, Notre Dame, IN, 46556, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Jun Ma
- Institute of Child and Adolescent Health of Peking University, School of Public Health, Peking University Health Science Center, Beijing, 100191, China.
| | - Haijun Wang
- Division of Maternal and Child Health, School of Public Health, Peking University Health Science Center, Beijing, 100191, China.
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86
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The importance of gene-environment interactions in human obesity. Clin Sci (Lond) 2017; 130:1571-97. [PMID: 27503943 DOI: 10.1042/cs20160221] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
The worldwide obesity epidemic has been mainly attributed to lifestyle changes. However, who becomes obese in an obesity-prone environment is largely determined by genetic factors. In the last 20 years, important progress has been made in the elucidation of the genetic architecture of obesity. In parallel with successful gene identifications, the number of gene-environment interaction (GEI) studies has grown rapidly. This paper reviews the growing body of evidence supporting gene-environment interactions in the field of obesity. Heritability, monogenic and polygenic obesity studies provide converging evidence that obesity-predisposing genes interact with a variety of environmental, lifestyle and treatment exposures. However, some skepticism remains regarding the validity of these studies based on several issues, which include statistical modelling, confounding, low replication rate, underpowered analyses, biological assumptions and measurement precision. What follows in this review includes (1) an introduction to the study of GEI, (2) the evidence of GEI in the field of obesity, (3) an outline of the biological mechanisms that may explain these interaction effects, (4) methodological challenges associated with GEI studies and potential solutions, and (5) future directions of GEI research. Thus far, this growing body of evidence has provided a deeper understanding of GEI influencing obesity and may have tremendous applications in the emerging field of personalized medicine and individualized lifestyle recommendations.
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87
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Jokinen J, Boström AE, Chatzittofis A, Ciuculete DM, Öberg KG, Flanagan JN, Arver S, Schiöth HB. Methylation of HPA axis related genes in men with hypersexual disorder. Psychoneuroendocrinology 2017; 80:67-73. [PMID: 28319850 DOI: 10.1016/j.psyneuen.2017.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/26/2017] [Accepted: 03/03/2017] [Indexed: 12/21/2022]
Abstract
Hypersexual Disorder (HD) defined as non-paraphilic sexual desire disorder with components of compulsivity, impulsivity and behavioral addiction, and proposed as a diagnosis in the DSM 5, shares some overlapping features with substance use disorder including common neurotransmitter systems and dysregulated hypothalamic-pituitary-adrenal (HPA) axis function. In this study, comprising 67 HD male patients and 39 male healthy volunteers, we aimed to identify HPA-axis coupled CpG-sites, in which modifications of the epigenetic profile are associated with hypersexuality. The genome-wide methylation pattern was measured in whole blood using the Illumina Infinium Methylation EPIC BeadChip, measuring the methylation state of over 850K CpG sites. Prior to analysis, the global DNA methylation pattern was pre-processed according to standard protocols and adjusted for white blood cell type heterogeneity. We included CpG sites located within 2000bp of the transcriptional start site of the following HPA-axis coupled genes: Corticotropin releasing hormone (CRH), corticotropin releasing hormone binding protein (CRHBP), corticotropin releasing hormone receptor 1 (CRHR1), corticotropin releasing hormone receptor 2 (CRHR2), FKBP5 and the glucocorticoid receptor (NR3C1). We performed multiple linear regression models of methylation M-values to a categorical variable of hypersexuality, adjusting for depression, dexamethasone non-suppression status, Childhood Trauma Questionnaire total score and plasma levels of TNF-alpha and IL-6. Of 76 tested individual CpG sites, four were nominally significant (p<0.05), associated with the genes CRH, CRHR2 and NR3C1. Cg23409074-located 48bp upstream of the transcription start site of the CRH gene - was significantly hypomethylated in hypersexual patients after corrections for multiple testing using the FDR-method. Methylation levels of cg23409074 were positively correlated with gene expression of the CRH gene in an independent cohort of 11 healthy male subjects. The methylation levels at the identified CRH site, cg23409074, were significantly correlated between blood and four different brain regions. CRH is an important integrator of neuroendocrine stress responses in the brain, with a key role in the addiction processes. Our results show epigenetic changes in the CRH gene related to hypersexual disorder in men.
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Affiliation(s)
- Jussi Jokinen
- Department of Clinical Neuroscience/Psychiatry, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Sciences/Psychiatry, Umeå University, Umeå, Sweden.
| | | | - Andreas Chatzittofis
- Department of Clinical Neuroscience/Psychiatry, Karolinska Institutet, Stockholm, Sweden; Medical School, University of Cyprus, Nicosia, Cyprus
| | | | | | - John N Flanagan
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Arver
- Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
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88
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Samy MD, Yavorski JM, Mauro JA, Blanck G. Impact of SNPs on CpG Islands in the MYC and HRAS oncogenes and in a wide variety of tumor suppressor genes: A multi-cancer approach. Cell Cycle 2017; 15:1572-8. [PMID: 27074591 DOI: 10.1080/15384101.2016.1164360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) that occur within CpG Islands may lead to increased hypermethylation if a SNP allele has the potential to form a CpG dinucleotide, as well as potentially lead to hypomethylation if a SNP allele eliminates a CpG dinucleotide. We analyzed CpG-related SNP allele frequencies in whole genome sequences (WGS) across 5 TCGA cancer datasets, thereby exploiting a more recent appreciation for signaling pathway degeneracy in cancer. The cancer data sets were analyzed for SNPs in CpG islands associated with the oncogenes, HRAS and MYC, and in the CpG islands associated with the tumor suppressor genes, APC, DCC, and RB1. We determined that one SNP allele (rs3824120) in a CpG island associated with MYC which eliminated a CpG was more common in the cancer datasets than in the 100Genomes databases (p < 0.01). For HRAS, 2 SNP alleles (rs112690925, rs7939028) that created CpG's occurred significantly less frequently in the cancer data sets than in the general SNP databases (e.g., rs7939028, p < 0.0002, in comparison with AllSNPs(142)). Also, one SNP allele (rs4940177) that created a CpG in a CpG island associated with the DCC tumor suppressor gene, was more common in the cancer datasets (p < 0.0007). To understand a broader picture of the potential of SNP alleles to create CpG's in CpG islands of tumor suppressor genes, we developed a scripted algorithm to assess the SNP alleles associated with the CpG islands of 43 tumor suppressor genes. The following tumor suppressor genes have the possibility of significant, percent increases in their CpG counts, depending on which SNP allele(s) is present: VHL, BRCA1, BRCA2, CHEK2, PTEN and RB1.
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Affiliation(s)
- Mohammad D Samy
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA
| | - John M Yavorski
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA
| | - James A Mauro
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA
| | - George Blanck
- a Department of Molecular Medicine , Morsani College of Medicine, University of South Florida , Tampa , FL , USA.,b Immunology Program, Moffitt Cancer Center and Research Institute , Tampa , FL , USA
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Recent progress in genetics, epigenetics and metagenomics unveils the pathophysiology of human obesity. Clin Sci (Lond) 2017; 130:943-86. [PMID: 27154742 DOI: 10.1042/cs20160136] [Citation(s) in RCA: 227] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/24/2016] [Indexed: 12/19/2022]
Abstract
In high-, middle- and low-income countries, the rising prevalence of obesity is the underlying cause of numerous health complications and increased mortality. Being a complex and heritable disorder, obesity results from the interplay between genetic susceptibility, epigenetics, metagenomics and the environment. Attempts at understanding the genetic basis of obesity have identified numerous genes associated with syndromic monogenic, non-syndromic monogenic, oligogenic and polygenic obesity. The genetics of leanness are also considered relevant as it mirrors some of obesity's aetiologies. In this report, we summarize ten genetically elucidated obesity syndromes, some of which are involved in ciliary functioning. We comprehensively review 11 monogenic obesity genes identified to date and their role in energy maintenance as part of the leptin-melanocortin pathway. With the emergence of genome-wide association studies over the last decade, 227 genetic variants involved in different biological pathways (central nervous system, food sensing and digestion, adipocyte differentiation, insulin signalling, lipid metabolism, muscle and liver biology, gut microbiota) have been associated with polygenic obesity. Advances in obligatory and facilitated epigenetic variation, and gene-environment interaction studies have partly accounted for the missing heritability of obesity and provided additional insight into its aetiology. The role of gut microbiota in obesity pathophysiology, as well as the 12 genes associated with lipodystrophies is discussed. Furthermore, in an attempt to improve future studies and merge the gap between research and clinical practice, we provide suggestions on how high-throughput '-omic' data can be integrated in order to get closer to the new age of personalized medicine.
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90
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San-Cristobal R, Navas-Carretero S, Milagro FI, Riezu-Boj JI, Guruceaga E, Celis-Morales C, Livingstone KM, Brennan L, Lovegrove JA, Daniel H, Saris WH, Traczyk I, Manios Y, Gibney ER, Gibney MJ, Mathers JC, Martinez JA. Gene methylation parallelisms between peripheral blood cells and oral mucosa samples in relation to overweight. J Physiol Biochem 2017; 73:465-474. [DOI: 10.1007/s13105-017-0560-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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91
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A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels. Int J Obes (Lond) 2017; 41:990-994. [PMID: 28194012 DOI: 10.1038/ijo.2017.43] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 12/30/2016] [Accepted: 01/31/2017] [Indexed: 02/07/2023]
Abstract
We investigated five methylation markers recently linked to body mass index, for their role in the neuropathology of obesity. In neuroimaging experiments, our analysis involving 23 participants showed that methylation levels for the cg07814318 site, which lies within the KLF13 gene, correlated with brain activity in the claustrum, putamen, cingulate gyrus and frontal gyri, some of which have been previously associated to food signaling, obesity or reward. Methylation levels at cg07814318 also positively correlated with ghrelin levels. Moreover, expression of KLF13 was augmented in the brains of obese and starved mice. Our results suggest the cg07814318 site could be involved in orexigenic processes, and also implicate KLF13 in obesity. Our findings are the first to associate methylation levels in blood with brain activity in obesity-related regions, and further support previous findings between ghrelin, brain activity and genetic differences.
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92
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A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score. Transl Psychiatry 2017; 7:e1002. [PMID: 28094813 PMCID: PMC5545735 DOI: 10.1038/tp.2016.275] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/25/2016] [Accepted: 11/27/2016] [Indexed: 12/28/2022] Open
Abstract
Genome-wide association studies have identified a number of single-nucleotide polymorphisms (SNPs) that are associated with psychiatric diseases. Increasing body of evidence suggests a complex connection of SNPs and the transcriptional and epigenetic regulation of gene expression, which is poorly understood. In the current study, we investigated the interplay between genetic risk variants, shifts in methylation and mRNA levels in whole blood from 223 adolescents distinguished by a risk for developing psychiatric disorders. We analyzed 37 SNPs previously associated with psychiatric diseases in relation to genome-wide DNA methylation levels using linear models, with Bonferroni correction and adjusting for cell-type composition. Associations between DNA methylation, mRNA levels and psychiatric disease risk evaluated by the Development and Well-Being Assessment (DAWBA) score were identified by robust linear models, Pearson's correlations and binary regression models. We detected five SNPs (in HCRTR1, GAD1, HADC3 and FKBP5) that were associated with eight CpG sites, validating five of these SNP-CpG pairs. Three of these CpG sites, that is, cg01089319 (GAD1), cg01089249 (GAD1) and cg24137543 (DIAPH1), manifest in significant gene expression changes and overlap with active regulatory regions in chromatin states of brain tissues. Importantly, methylation levels at cg01089319 were associated with the DAWBA score in the discovery group. These results show how distinct SNPs linked with psychiatric diseases are associated with epigenetic shifts with relevance for gene expression. Our findings give a novel insight on how genetic variants may modulate risks for the development of psychiatric diseases.
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93
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Wu L, Shen C, Seed Ahmed M, Östenson CG, Gu HF. Adenylate cyclase 3: a new target for anti-obesity drug development. Obes Rev 2016; 17:907-14. [PMID: 27256589 DOI: 10.1111/obr.12430] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/06/2016] [Accepted: 04/19/2016] [Indexed: 12/14/2022]
Abstract
Obesity has become epidemic worldwide, and abdominal obesity has a negative impact on health. Current treatment options on obesity, however, still remain limited. It is then of importance to find a new target for anti-obesity drug development based upon recent molecular studies in obesity. Adenylate cyclase 3 (ADCY3) is the third member of adenylyl cyclase family and catalyses the synthesis of cAMP from ATP. Genetic studies with candidate gene and genome-wide association study approaches have demonstrated that ADCY3 genetic polymorphisms are associated with obesity in European and Chinese populations. Epigenetic studies have indicated that increased DNA methylation levels in the ADCY3 gene are involved in the pathogenesis of obesity. Furthermore, biological analyses with animal models have implicated that ADCY3 dysfunction resulted in increased body weight and fat mass, while reduction of body weight is partially explained by ADCY3 activation. In this review, we describe genomic and biological features of ADCY3, summarize genetic and epigenetic association studies of the ADCY3 gene with obesity and discuss dysfunction and activation of ADCY3. Based upon all data, we suggest that ADCY3 is a new target for anti-obesity drug development. Further investigation on the effectiveness of ADCY3 activator and its delivery approach to treat abdominal obesity has been taken into our consideration.
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Affiliation(s)
- L Wu
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing, 210009, China
| | - C Shen
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - M Seed Ahmed
- Unit for Medical Education, Centre for Learning and Knowledge, Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, 17177, Sweden
| | - C-G Östenson
- Rolf Luft Center for Diabetes Research and Endocrinology, Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital, Solna, Stockholm, 17176, Sweden
| | - H F Gu
- Department of Clinical Science, Intervention and Technologies, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, 14157, Sweden.,Center of Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Solna, Stockholm, 17176, Sweden
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94
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Yu J, Qiu Y, Yang J, Bian S, Chen G, Deng M, Kang H, Huang L. DNMT1-PPARγ pathway in macrophages regulates chronic inflammation and atherosclerosis development in mice. Sci Rep 2016; 6:30053. [PMID: 27530451 PMCID: PMC4987643 DOI: 10.1038/srep30053] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/29/2016] [Indexed: 01/26/2023] Open
Abstract
The DNA methyltransferase-mediated proinflammatory activation of macrophages is causally linked to the development of atherosclerosis (AS). However, the role of DNMT1, a DNA methylation maintenance enzyme, in macrophage polarization and AS development remains obscure. Here, we established transgenic mice with macrophage-specific overexpression of DNMT1 (TgDNMT1) or PPAR-γ (TgPPAR-γ) to investigate their effects on AS progression in ApoE-knockout mice fed an atherogenic diet. Primary macrophages were extracted to study the role of the DNMT1/PPAR-γ pathway in regulating inflammatory cytokine production. We demonstrated that TgDNMT1 significantly increased proinflammatory cytokine production in macrophages and plasma, and it accelerated the progression of AS in the atherogenic diet-treated ApoE-knockout mice. Further, we found that the DNA methylation status of the proximal PPAR-γ promoter was regulated by DNMT1 in macrophages. Notably, additional TgPPAR-γ or pharmacological activation of PPAR-γ effectively prevented TgDNMT1-induced proinflammatory cytokine production in macrophages and AS development in the mouse model. Finally, we demonstrated that elevated DNMT1 was correlated with decreased PPAR-γ, and increased proinflammatory cytokine production in the peripheral blood monocytes isolated from the patients with AS, compared to those of healthy donors. Our findings shed light on a novel strategy for the prevention and therapy of AS.
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Affiliation(s)
- Jie Yu
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Youzhu Qiu
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Jie Yang
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Shizhu Bian
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Guozhu Chen
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Mengyang Deng
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Huali Kang
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
| | - Lan Huang
- Institute of Cardiovascular Diseases of the PLA , Xinqiao Hospital, Third Military Medical University, Chongqing, 400037, China
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95
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Sport participation in pediatric age affects modifications in diabetes markers in adulthood. Int J Diabetes Dev Ctries 2016. [DOI: 10.1007/s13410-016-0516-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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96
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Painter JN, Kaufmann S, O'Mara TA, Hillman KM, Sivakumaran H, Darabi H, Cheng THT, Pearson J, Kazakoff S, Waddell N, Hoivik EA, Goode EL, Scott RJ, Tomlinson I, Dunning AM, Easton DF, French JD, Salvesen HB, Pollock PM, Thompson DJ, Spurdle AB, Edwards SL. A Common Variant at the 14q32 Endometrial Cancer Risk Locus Activates AKT1 through YY1 Binding. Am J Hum Genet 2016; 98:1159-1169. [PMID: 27259051 PMCID: PMC4908177 DOI: 10.1016/j.ajhg.2016.04.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/19/2016] [Indexed: 11/21/2022] Open
Abstract
A recent meta-analysis of multiple genome-wide association and follow-up endometrial cancer case-control datasets identified a novel genetic risk locus for this disease at chromosome 14q32.33. To prioritize the functional SNP(s) and target gene(s) at this locus, we employed an in silico fine-mapping approach using genotyped and imputed SNP data for 6,608 endometrial cancer cases and 37,925 controls of European ancestry. Association and functional analyses provide evidence that the best candidate causal SNP is rs2494737. Multiple experimental analyses show that SNP rs2494737 maps to a silencer element located within AKT1, a member of the PI3K/AKT/MTOR intracellular signaling pathway activated in endometrial tumors. The rs2494737 risk A allele creates a YY1 transcription factor-binding site and abrogates the silencer activity in luciferase assays, an effect mimicked by transfection of YY1 siRNA. Our findings suggest YY1 is a positive regulator of AKT1, mediating the stimulatory effects of rs2494737 increasing endometrial cancer risk. Identification of an endometrial cancer risk allele within a member of the PI3K/AKT signaling pathway, more commonly activated in tumors by somatic alterations, raises the possibility that well tolerated inhibitors targeting this pathway could be candidates for evaluation as chemopreventive agents in individuals at high risk of developing endometrial cancer.
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Affiliation(s)
- Jodie N Painter
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Susanne Kaufmann
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Tracy A O'Mara
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Kristine M Hillman
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Haran Sivakumaran
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Hatef Darabi
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Timothy H T Cheng
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - John Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Erling A Hoivik
- Centre for Cancer Biomarkers, Department of Clinical Science, The University of Bergen, N5020 Bergen, Norway; Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway
| | - Ellen L Goode
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Rodney J Scott
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, NSW 2305, Australia; Pathology North (Newcastle) John Hunter Hospital, Newcastle, NSW 2305, Australia; Centre for Information Based Medicine, University of Newcastle, NSW 2308, Australia; School of Biomedical Sciences and Pharmacy, University of Newcastle, NSW 2308, Australia
| | - Ian Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Juliet D French
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Helga B Salvesen
- Centre for Cancer Biomarkers, Department of Clinical Science, The University of Bergen, N5020 Bergen, Norway; Department of Obstetrics and Gynecology, Haukeland University Hospital, N5021 Bergen, Norway
| | - Pamela M Pollock
- Institute of Health and Biomedical Innovation and School of Biomedical Science, Queensland University of Technology at the Translation Research Institute, Brisbane 4102, Australia
| | - Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Stacey L Edwards
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.
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Clark AJL. 60 YEARS OF POMC: The proopiomelanocortin gene: discovery, deletion and disease. J Mol Endocrinol 2016; 56:T27-37. [PMID: 26643913 DOI: 10.1530/jme-15-0268] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 12/04/2015] [Indexed: 11/08/2022]
Abstract
The cloning of the bovine proopiomelanocortin (POMC) cDNA in 1978 by Nakanishi and colleagues was the result of a remarkable series of exacting and ingenious experiments. With this work, they instantly confirmed the single precursor hypothesis for adrenocorticotrophic hormone-β-lipotropin, as it was then known, and in so doing revealed the existence of additional, largely unpredicted, N-terminal peptides that together formed the POMC precursor peptide. This work paved the way for a host of additional studies into the physiology of these peptides and their regulation. Furthermore, the cloning of the murine Pomc gene was essential for subsequent studies, in which Pomc was intentionally deleted in the mouse illuminating its substantial role in body weight regulation and adrenal function. Contemporaneously with this work, naturally occurring mutations in human POMC came to light underlining the vital role of this gene in appetite regulation. This article reviews each of these aspects of POMC with the benefit of several decades of hindsight and informed by more recent genomic and transcriptomic data.
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Affiliation(s)
- Adrian J L Clark
- Centre for EndocrinologyWilliam Harvey Research Institute, Queen Mary University of London, Charterhouse Square, London, UK
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98
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Lemche E, Chaban OS, Lemche AV. Neuroendocrinological and Epigenetic Mechanisms Subserving Autonomic Imbalance and HPA Dysfunction in the Metabolic Syndrome. Front Neurosci 2016; 10:142. [PMID: 27147943 PMCID: PMC4830841 DOI: 10.3389/fnins.2016.00142] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/21/2016] [Indexed: 12/18/2022] Open
Abstract
Impact of environmental stress upon pathophysiology of the metabolic syndrome (MetS) has been substantiated by epidemiological, psychophysiological, and endocrinological studies. This review discusses recent advances in the understanding of causative roles of nutritional factors, sympathomedullo-adrenal (SMA) and hypothalamic-pituitary adrenocortical (HPA) axes, and adipose tissue chronic low-grade inflammation processes in MetS. Disturbances in the neuroendocrine systems for leptin, melanocortin, and neuropeptide Y (NPY)/agouti-related protein systems have been found resulting directly in MetS-like conditions. The review identifies candidate risk genes from factors shown critical for the functioning of each of these neuroendocrine signaling cascades. In its meta-analytic part, recent studies in epigenetic modification (histone methylation, acetylation, phosphorylation, ubiquitination) and posttranscriptional gene regulation by microRNAs are evaluated. Several studies suggest modification mechanisms of early life stress (ELS) and diet-induced obesity (DIO) programming in the hypothalamic regions with populations of POMC-expressing neurons. Epigenetic modifications were found in cortisol (here HSD11B1 expression), melanocortin, leptin, NPY, and adiponectin genes. With respect to adiposity genes, epigenetic modifications were documented for fat mass gene cluster APOA1/C3/A4/A5, and the lipolysis gene LIPE. With regard to inflammatory, immune and subcellular metabolism, PPARG, NKBF1, TNFA, TCF7C2, and those genes expressing cytochrome P450 family enzymes involved in steroidogenesis and in hepatic lipoproteins were documented for epigenetic modifications.
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Affiliation(s)
- Erwin Lemche
- Section of Cognitive Neuropsychiatry, Department of Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience, King's College London London, UK
| | - Oleg S Chaban
- Section of Psychosomatic Medicine, Bogomolets National Medical University Kiev, Ukraine
| | - Alexandra V Lemche
- Department of Medical Science, Institute of Clinical Research Berlin, Germany
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99
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Luo Z, Lin C. Enhancer, epigenetics, and human disease. Curr Opin Genet Dev 2016; 36:27-33. [DOI: 10.1016/j.gde.2016.03.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 03/24/2016] [Indexed: 02/09/2023]
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100
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Kronenberg F, Paulweber B, Lamina C. [Genomwide association studies on obesity: what can we learn from these studies]. Wien Med Wochenschr 2016; 166:88-94. [PMID: 26795628 DOI: 10.1007/s10354-015-0429-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 12/30/2015] [Indexed: 01/10/2023]
Abstract
The introduction of genome-wide association studies resulted in a tremendous increase in the number of genes associated with obesity and related phenotypes (BMI, waist and waist-hip-ratio). Despite this enormous gain in knowledge the search for genes is only started since only a small fraction of the heritability of these phenotypes is explained yet: each single gene of the 97 hitherto known BMI-associated genes and 49 waist-hip-ratio-associated genes explains only a tiny fraction of the variance of these phenotypes. Sex-specific differences are mainly known for waist-hip-ratio and ̴40% of the genes showed only an effect in women but no or a markedly smaller effect in men. The functional characterization of the identified genes will take a lot of time. It is unclear whether and how fast the findings will result in therapeutic consequences. It is of utmost importance that we understand the involved mechanisms before new therapeutic strategies can be developed.
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Affiliation(s)
- Florian Kronenberg
- Division für Genetische Epidemiologie, Department für Medizinische Genetik, Molekulare and Klinische Pharmakologie, Medizinische Universität Innsbruck, Schöpfstr. 41, 6020, Innsbruck, Österreich.
| | - Bernhard Paulweber
- Universitätsklinik für Innere Medizin I der Paracelsus Medizinischen Privatuniversität Salzburg, St. Johanns-Spital, Müllner Hauptstraße 48, 5020, Salzburg, Österreich
| | - Claudia Lamina
- Division für Genetische Epidemiologie, Department für Medizinische Genetik, Molekulare and Klinische Pharmakologie, Medizinische Universität Innsbruck, Schöpfstr. 41, 6020, Innsbruck, Österreich
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