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Cantarero-Cuenca A, Gonzalez-Jimenez A, Martínez-Núñez GM, Garrido-Sánchez L, Ranea JAG, Tinahones FJ. Epigenetic profiles in blood and adipose tissue: identifying strong correlations in morbidly obese and non-obese patients. J Mol Med (Berl) 2024:10.1007/s00109-024-02475-z. [PMID: 39225820 DOI: 10.1007/s00109-024-02475-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 07/02/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024]
Abstract
Epigenetic alterations play a pivotal role in conditions influenced by environmental factors such as overweight and obesity. Many of these changes are tissue-specific, which entails a problem in its study since obtaining human tissue is a complex and invasive practice. While blood is widely used as a surrogate biomarker, it cannot directly extrapolate the evidence found in blood to tissue. Moreover, the intricacies of metabolic diseases add a new layer of complexity, as obesity leads to significant alterations in adipose tissue, potentially causing associated pathologies that can disrupt existing correlations seen in healthy individuals. Here, our objective was to determine which epigenetic markers exhibit correlations between blood and adipose tissue, regardless of the metabolic status. We collected paired blood and adipose tissue samples from 64 patients with morbidity obesity and non-obese and employed the MethylationEPIC 850 K array for analysis. We found that only a small fraction, specifically 4.3% (corresponding to 34,825 CpG sites), of the sites showed statistically significant correlations (R ≥ 0.6) between blood and adipose tissue. Within this subset, 5327 CpG sites exhibited a strong correlation (R ≥ 0.8) between blood and adipose tissue. Our findings suggest that the majority of epigenetic markers in peripheral blood do not reliably reflect changes occurring in visceral adipose tissues. However, it is important to note that there exists a distinct set of epigenetic markers that can indeed mirror changes in adipose tissue within blood samples. KEY MESSAGES: More than 8% of methylation sites exhibit similarity between blood and adipose tissues, regardless of BMI The correlation percentage between blood and adipose tissue is strongly influenced by gender The principal genes implicated in this correlation are related to metabolism or the immunological system.
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Affiliation(s)
- Antonio Cantarero-Cuenca
- Bioinformatic Platform, Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), 29590, Málaga, Spain
| | - Andres Gonzalez-Jimenez
- Bioinformatic Platform, Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), 29590, Málaga, Spain.
| | - Gracia M Martínez-Núñez
- Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), Málaga, Spain
- Centro de Investigación Biomédica en Red de La Fisiopatología de La Obesidad y La Nutrición (CIBERObn), ISCIII, Madrid, Spain
| | - Lourdes Garrido-Sánchez
- Department of Endocrinology and Nutrition, Virgen de La Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), 29010, Málaga, Spain.
- Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), Málaga, Spain.
- Centro de Investigación Biomédica en Red de La Fisiopatología de La Obesidad y La Nutrición (CIBERObn), ISCIII, Madrid, Spain.
| | - Juan A G Ranea
- Bioinformatic Platform, Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), 29590, Málaga, Spain
- Department of Biochemistry and Molecular Biology, University of Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Spanish National Bioinformatics Institute (INB/ELIXIR-ES), 08034, Barcelona, Spain
| | - Francisco J Tinahones
- Department of Endocrinology and Nutrition, Virgen de La Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), 29010, Málaga, Spain
- Instituto de Investigación Biomédica de Málaga (IBIMA - Plataforma Bionand), Málaga, Spain
- Faculty of Medicine, University of Málaga, Málaga, Spain
- Centro de Investigación Biomédica en Red de La Fisiopatología de La Obesidad y La Nutrición (CIBERObn), ISCIII, Madrid, Spain
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Lastialno MP, Bashari MH, Ariyanto EF. Current Updates on the Understanding of the Role of DNA Methylation on Obesity. Diabetes Metab Syndr Obes 2024; 17:3177-3186. [PMID: 39220797 PMCID: PMC11365516 DOI: 10.2147/dmso.s471348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/10/2024] [Indexed: 09/04/2024] Open
Abstract
Obesity is a condition in which there is an accumulation of excess body fat leading to a weight far above the normal range that poses significant health risks. According to WHO, 8 billion people in the world were obese in 2022. Consequently, obesity has become a pandemic with negative impacts on both global health and economies. Obesity is influenced by various factors including environmental influences, lifestyle choices, gut microbiota, genetic factors, and epigenetic mechanisms such as DNA methylation. DNA methylation can affect an individual's phenotype and condition without altering their DNA sequence. It is the most extensively studied epigenetic alteration and it plays an important part in controlling gene activity associated with obesity. Numerous studies have indicated that DNA methylation is implicated in obesity, thus this review aims to elaborate the roles of DNA methylation to inform the development of preventive measures for obesity.
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Affiliation(s)
- Mohammad Parezal Lastialno
- Program of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, 40161, Indonesia
| | - Muhammad Hasan Bashari
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
| | - Eko Fuji Ariyanto
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Sumedang, West Java, 45363, Indonesia
- Study Center for Medical Genetics, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, 40161, Indonesia
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Khodasevich D, Holland N, Harley KG, Eskenazi B, Barcellos LF, Cardenas A. Prenatal exposure to environmental phenols and phthalates and altered patterns of DNA methylation in childhood. ENVIRONMENT INTERNATIONAL 2024; 190:108862. [PMID: 38972116 DOI: 10.1016/j.envint.2024.108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 06/13/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Epigenetic marks are key biomarkers linking the prenatal environment to health and development. However, DNA methylation associations and persistence of marks for prenatal exposure to multiple Endocrine Disrupting Chemicals (EDCs) in human populations have not been examined in great detail. METHODS We measured Bisphenol-A (BPA), triclosan, benzophenone-3 (BP3), methyl-paraben, propyl-paraben, and butyl-paraben, as well as 11 phthalate metabolites, in two pregnancy urine samples, at approximately 13 and 26 weeks of gestation in participants of the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study (N = 309). DNA methylation of cord blood at birth and child peripheral blood at ages 9 and 14 years was measured with 450K and EPIC arrays. Robust linear regression was used to identify differentially methylated probes (DMPs), and comb-p was used to identify differentially methylated regions (DMRs) in association with pregnancy-averaged EDC concentrations. Quantile g-computation was used to assess associations of the whole phenol/phthalate mixture with DMPs and DMRs. RESULTS Prenatal BPA exposure was associated with 1 CpG among males and Parabens were associated with 10 CpGs among females at Bonferroni-level significance in cord blood. Other suggestive DMPs (unadjusted p-value < 1 × 10-6) and several DMRs associated with the individual phenols and whole mixture were also identified. A total of 10 CpG sites at least suggestively associated with BPA, Triclosan, BP3, Parabens, and the whole mixture in cord blood were found to persist into adolescence in peripheral blood. CONCLUSIONS We found sex-specific associations between prenatal phenol exposure and DNA methylation, particularly with BPA in males and Parabens in females. Additionally, we found several DMPs that maintained significant associations with prenatal EDC exposures at age 9 and age 14 years.
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Affiliation(s)
- Dennis Khodasevich
- Division of Environmental Health Sciences, Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Nina Holland
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Kim G Harley
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Lisa F Barcellos
- Division of Epidemiology, Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
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Elliott HR, Bennett CL, Caramaschi D, English S. Negative association between higher maternal pre-pregnancy body mass index and breastfeeding outcomes is not mediated by DNA methylation. Sci Rep 2024; 14:14675. [PMID: 38918574 PMCID: PMC11199553 DOI: 10.1038/s41598-024-65605-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 06/27/2024] Open
Abstract
The benefits of breastfeeding for the health and wellbeing of both infants and mothers are well documented, yet global breastfeeding rates are low. One factor associated with low breast feeding is maternal body mass index (BMI), which is used as a measure of obesity. The negative relationship between maternal obesity and breastfeeding is likely caused by a variety of social, psychological, and physiological factors. Maternal obesity may also have a direct biological association with breastfeeding through changes in maternal DNA methylation. Here, we investigate this potential biological association using data from a UK-based cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC). We find that pre-pregnancy body mass index (BMI) is associated with lower initiation to breastfeed and shorter breastfeeding duration. We conduct epigenome-wide association studies (EWAS) of pre-pregnancy BMI and breastfeeding outcomes, and run candidate-gene analysis of methylation sites associated with BMI identified via previous meta-EWAS. We find that DNA methylation at cg11453712, annotated to PHTP1, is associated with pre-pregnancy BMI. From our results, neither this association nor those at candidate-gene sites are likely to mediate the link between pre-pregnancy BMI and breastfeeding.
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Affiliation(s)
- Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
| | - Chloe L Bennett
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Doretta Caramaschi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Faculty of Health and Life Sciences, Department of Psychology, University of Exeter, Exeter, UK
| | - Sinead English
- School of Biological Sciences, University of Bristol, Bristol, UK.
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Smith HM, Ng HK, Moodie JE, Gadd DA, McCartney DL, Bernabeu E, Campbell A, Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. Methylome-wide studies of six metabolic traits. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308103. [PMID: 38853823 PMCID: PMC11160850 DOI: 10.1101/2024.05.29.24308103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Exploring the molecular correlates of metabolic health measures may identify the shared and unique biological processes and pathways that they track. Here, we performed epigenome-wide association studies (EWASs) of six metabolic traits: body mass index (BMI), body fat percentage, waist-hip ratio (WHR), and blood-based measures of glucose, high-density lipoprotein (HDL) cholesterol, and total cholesterol. We considered blood-based DNA methylation (DNAm) from >750,000 CpG sites in over 17,000 volunteers from the Generation Scotland (GS) cohort. Linear regression analyses identified between 304 and 11,815 significant CpGs per trait at P<3.6×10-8, with 37 significant CpG sites across all six traits. Further, we performed a Bayesian EWAS that jointly models all CpGs simultaneously and conditionally on each other, as opposed to the marginal linear regression analyses. This identified between 3 and 27 CpGs with a posterior inclusion probability ≥ 0.95 across the six traits. Next, we used elastic net penalised regression to train epigenetic scores (EpiScores) of each trait in GS, which were then tested in the Lothian Birth Cohort 1936 (LBC1936; European ancestry) and Health for Life in Singapore (HELIOS; Indian-, Malay- and Chinese-ancestries). A maximum of 27.1% of the variance in BMI was explained by the BMI EpiScore in the subset of Malay-ancestry Singaporeans. Four metabolic EpiScores were associated with general cognitive function in LBC1936 in models adjusted for vascular risk factors (Standardised βrange: 0.08 - 0.12, PFDR < 0.05). EpiScores of metabolic health are applicable across ancestries and can reflect differences in brain health.
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Affiliation(s)
- Hannah M. Smith
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Joanna E. Moodie
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Paul Redmond
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Adele Taylor
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Danielle Page
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Janie Corley
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Darwin Tay
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Matthew R. Robinson
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
| | - John C. Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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Li W, Xia M, Zeng H, Lin H, Teschendorff AE, Gao X, Wang S. Longitudinal analysis of epigenome-wide DNA methylation reveals novel loci associated with BMI change in East Asians. Clin Epigenetics 2024; 16:70. [PMID: 38802969 PMCID: PMC11131215 DOI: 10.1186/s13148-024-01679-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 05/11/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Obesity is a global public health concern linked to chronic diseases such as cardiovascular disease and type 2 diabetes (T2D). Emerging evidence suggests that epigenetic modifications, particularly DNA methylation, may contribute to obesity. However, the molecular mechanism underlying the longitudinal change of BMI has not been well-explored, especially in East Asian populations. METHODS This study performed a longitudinal epigenome-wide association analysis of DNA methylation to uncover novel loci associated with BMI change in 533 individuals across two Chinese cohorts with repeated DNA methylation and BMI measurements over four years. RESULTS We identified three novel CpG sites (cg14671384, cg25540824, and cg10848724) significantly associated with BMI change. Two of the identified CpG sites were located in regions previously associated with body shape and basal metabolic rate. Annotation of the top 20 BMI change-associated CpGs revealed strong connections to obesity and T2D. Notably, these CpGs exhibited active regulatory roles and located in genes with high expression in the liver and digestive tract, suggesting a potential regulatory pathway from genome to phenotypes of energy metabolism and absorption via DNA methylation. Cross-sectional and longitudinal EWAS comparisons indicated different mechanisms between CpGs related to BMI and BMI change. CONCLUSION This study enhances our understanding of the epigenetic dynamics underlying BMI change and emphasizes the value of longitudinal analyses in deciphering the complex interplay between epigenetics and obesity.
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Affiliation(s)
- Wenran Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mingfeng Xia
- Department of Endocrinology and Metabolism, Zhongshan Hospital and Fudan Institute for Metabolic Diseases, Fudan University, Shanghai, China
- Department of Endocrinology and Metabolism, Wusong Branch of Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hailuan Zeng
- Department of Endocrinology and Metabolism, Zhongshan Hospital and Fudan Institute for Metabolic Diseases, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Huandong Lin
- Department of Endocrinology and Metabolism, Zhongshan Hospital and Fudan Institute for Metabolic Diseases, Fudan University, Shanghai, China
| | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin Gao
- Department of Endocrinology and Metabolism, Zhongshan Hospital and Fudan Institute for Metabolic Diseases, Fudan University, Shanghai, China.
- Human Phenome Institute, Fudan University, Shanghai, China.
| | - Sijia Wang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
- Taizhou Institute of Health Sciences, Fudan University, Taizhou, Jiangsu, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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Lee HS, Kim B, Park T. Genome- and epigenome-wide association studies identify susceptibility of CpG sites and regions for metabolic syndrome in a Korean population. Clin Epigenetics 2024; 16:60. [PMID: 38685121 PMCID: PMC11059751 DOI: 10.1186/s13148-024-01671-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND While multiple studies have investigated the relationship between metabolic syndrome (MetS) and its related traits (fasting glucose, triglyceride, HDL cholesterol, blood pressure, waist circumference) and DNA methylation, our understanding of the epigenetic mechanisms in MetS remains limited. Therefore, we performed an epigenome-wide meta-analysis of blood DNA methylation to identify differentially methylated probes (DMPs) and differentially methylated regions (DMRs) associated with MetS and its components using two independent cohorts comprising a total of 2,334 participants. We also investigated the specific genetic effects on DNA methylation, identified methylation quantitative trait loci (meQTLs) through genome-wide association studies and further utilized Mendelian randomization (MR) to assess how these meQTLs subsequently influence MetS status. RESULTS We identified 40 DMPs and 27 DMRs that are significantly associated with MetS. In addition, we identified many novel DMPs and DMRs underlying inflammatory and steroid hormonal processes. The most significant associations were observed in 3 DMPs (cg19693031, cg26974062, cg02988288) and a DMR (chr1:145440444-145441553) at the TXNIP, which are involved in lipid metabolism. These CpG sites were identified as coregulators of DNA methylation in MetS, TG and FAG levels. We identified a total of 144 cis-meQTLs, out of which only 13 were found to be associated with DMPs for MetS. Among these, we confirmed the identified causal mediators of genetic effects at CpG sites cg01881899 at ABCG1 and cg00021659 at the TANK genes for MetS. CONCLUSIONS This study observed whether specific CpGs and methylated regions act independently or are influenced by genetic effects for MetS and its components in the Korean population. These associations between the identified DNA methylation and MetS, along with its individual components, may serve as promising targets for the development of preventive interventions for MetS.
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Affiliation(s)
- Ho-Sun Lee
- Forensic Toxicology Division, Daegu Institute, National Forensic Service, Chilgok-gun, 39872, Gyeongsangbuk-do, Korea.
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea.
| | - Boram Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea
| | - Taesung Park
- Forensic Toxicology Division, Daegu Institute, National Forensic Service, Chilgok-gun, 39872, Gyeongsangbuk-do, Korea
- Department of Statistics, Seoul National University, Seoul, 08826, Korea
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8
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Zeng Q, Song J, Sun X, Wang D, Liao X, Ding Y, Hu W, Jiao Y, Mai W, Aini W, Wang F, Zhou H, Xie L, Mei Y, Tang Y, Xie Z, Wu H, Liu W, Deng T. A negative feedback loop between TET2 and leptin in adipocyte regulates body weight. Nat Commun 2024; 15:2825. [PMID: 38561362 PMCID: PMC10985112 DOI: 10.1038/s41467-024-46783-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
Ten-eleven translocation (TET) 2 is an enzyme that catalyzes DNA demethylation to regulate gene expression by oxidizing 5-methylcytosine to 5-hydroxymethylcytosine, functioning as an essential epigenetic regulator in various biological processes. However, the regulation and function of TET2 in adipocytes during obesity are poorly understood. In this study, we demonstrate that leptin, a key adipokine in mammalian energy homeostasis regulation, suppresses adipocyte TET2 levels via JAK2-STAT3 signaling. Adipocyte Tet2 deficiency protects against high-fat diet-induced weight gain by reducing leptin levels and further improving leptin sensitivity in obese male mice. By interacting with C/EBPα, adipocyte TET2 increases the hydroxymethylcytosine levels of the leptin gene promoter, thereby promoting leptin gene expression. A decrease in adipose TET2 is associated with obesity-related hyperleptinemia in humans. Inhibition of TET2 suppresses the production of leptin in mature human adipocytes. Our findings support the existence of a negative feedback loop between TET2 and leptin in adipocytes and reveal a compensatory mechanism for the body to counteract the metabolic dysfunction caused by obesity.
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Affiliation(s)
- Qin Zeng
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Jianfeng Song
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Xiaoxiao Sun
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Dandan Wang
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Xiyan Liao
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yujin Ding
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Wanyu Hu
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yayi Jiao
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Wuqian Mai
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Wufuer Aini
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Fanqi Wang
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Hui Zhou
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Limin Xie
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Ying Mei
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Yuan Tang
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Wei Liu
- Department of Biliopancreatic Surgery and Bariatric Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, and Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Key Laboratory of Diabetes Immunology, Ministry of Education, and Metabolic Syndrome Research Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
- Clinical Immunology Center, The Second Xiangya Hospital of Central South University, Changsha, Hunan, 410011, China.
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9
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Domínguez-Barragán J, Fernández-Sanlés A, Hernáez Á, Llauradó-Pont J, Marrugat J, Robinson O, Tzoulaki I, Elosua R, Lassale C. Blood DNA methylation signature of diet quality and association with cardiometabolic traits. Eur J Prev Cardiol 2024; 31:191-202. [PMID: 37793095 PMCID: PMC10809172 DOI: 10.1093/eurjpc/zwad317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/06/2023]
Abstract
AIMS Diet quality might influence cardiometabolic health through epigenetic changes, but this has been little investigated in adults. Our aims were to identify cytosine-phosphate-guanine (CpG) dinucleotides associated with diet quality by conducting an epigenome-wide association study (EWAS) based on blood DNA methylation (DNAm) and to assess how diet-related CpGs associate with inherited susceptibility to cardiometabolic traits: body mass index (BMI), systolic blood pressure (SBP), triglycerides, type 2 diabetes (T2D), and coronary heart disease (CHD). METHODS AND RESULTS Meta-EWAS including 5274 participants in four cohorts from Spain, the USA, and the UK. We derived three dietary scores (exposures) to measure adherence to a Mediterranean diet, to a healthy plant-based diet, and to the Dietary Approaches to Stop Hypertension. Blood DNAm (outcome) was assessed with the Infinium arrays Human Methylation 450K BeadChip and MethylationEPIC BeadChip. For each diet score, we performed linear EWAS adjusted for age, sex, blood cells, smoking and technical variables, and BMI in a second set of models. We also conducted Mendelian randomization analyses to assess the potential causal relationship between diet-related CpGs and cardiometabolic traits. We found 18 differentially methylated CpGs associated with dietary scores (P < 1.08 × 10-7; Bonferroni correction), of which 12 were previously associated with cardiometabolic traits. Enrichment analysis revealed overrepresentation of diet-associated genes in pathways involved in inflammation and cardiovascular disease. Mendelian randomization analyses suggested that genetically determined methylation levels corresponding to lower diet quality at cg02079413 (SNORA54), cg02107842 (MAST4), and cg23761815 (SLC29A3) were causally associated with higher BMI and at cg05399785 (WDR8) with greater SBP, and methylation levels associated with higher diet quality at cg00711496 (PRMT1) with lower BMI, T2D risk, and CHD risk and at cg0557921 (AHRR) with lower CHD risk. CONCLUSION Diet quality in adults was related to differential methylation in blood at 18 CpGs, some of which related to cardiometabolic health.
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Affiliation(s)
- Jorge Domínguez-Barragán
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
| | - Alba Fernández-Sanlés
- MRC Unit for Lifelong Health and Ageing, University College London, London WC1E 7HB, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Álvaro Hernáez
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo 0463, Norway
- Blanquerna School of Health Sciences, Universitat Ramon Llull, 08025 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
| | - Joana Llauradó-Pont
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
| | - Jaume Marrugat
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Oliver Robinson
- μedical Research Council Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Ioanna Tzoulaki
- Centre for Systems Biology, Biomedical Research Foundation of the Academy of Athens, 115 27 Athens, Greece
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Roberto Elosua
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Medicine, University of Vic—Central University of Catalunya, Ctra. de Roda, 70, 08500 Vic, Spain
| | - Camille Lassale
- Hospital del Mar Research Institute (IMIM), Programme of Epidemiology and Public Health, Dr Aiguader, 88, 08003 Barcelona, Spain
- Consortium for Biomedical Research—Pathophysiology of Obesity and Nutrition (CIBEROBN), Instituto de Salud Carlos III, Monforte de Lemos 3-5, 08029 Madrid, Spain
- Barcelona Institute of Global Health (ISGlobal), Dr Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, 08003, Barcelona, Spain
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10
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Viola TW, Danzer C, Mardini V, Szobot C, Chrusciel JH, Stertz L, Schmitz JM, Walss-Bass C, Fries GR, Grassi-Oliveira R. Prenatal cocaine exposure and its influence on pediatric epigenetic clocks and epigenetic scores in humans. Sci Rep 2024; 14:1946. [PMID: 38253635 PMCID: PMC10803757 DOI: 10.1038/s41598-024-52433-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
The investigation of the effects of prenatal cocaine exposure (PCE) on offspring has been inconsistent, with few studies investigating biological outcomes in humans. We profiled genome-wide DNA methylation (DNAm) of umbilical cord blood (UCB) from newborns with (n = 35) and without (n = 47) PCE. We used DNAm data to (1) assess pediatric epigenetic clocks at birth and (2) to estimate epigenetic scores (ES) for lifetime disorders. We generated gestational epigenetic age estimates (DNAmGA) based on Knight and Bohlin epigenetic clocks. We also investigated the association between DNAmGA and UCB serum brain-derived neurotrophic factor (BDNF) levels. Considering the large-scale DNAm data availability and existing evidence regarding PCE as a risk for health problems later in life, we generated ES for tobacco smoking, psychosis, autism, diabetes, and obesity. A gene ontology (GO) analysis on the CpGs included in the ES with group differences was performed. PCE was associated with lower DNAmGA in newborns, and this effect remained significant when controlling for potential confounders, such as blood cell type composition predicted by DNAm and obstetric data. DNAmGA was negatively correlated with BDNF levels in the serum of UCB. Higher tobacco smoking, psychosis, and diabetes ES were found in the PCE group. The GO analysis revealed GABAergic synapses as a potential pathway altered by PCE. Our findings of decelerated DNAmGA and ES for adverse phenotypes associated with PCE, suggest that the effects of gestational cocaine exposure on the epigenetic landscape of human newborns are detectable at birth.
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Affiliation(s)
- Thiago Wendt Viola
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Christina Danzer
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 11, A701-129, 8200, Aarhus, Denmark
| | - Victor Mardini
- Clinical Hospital of Porto Alegre, Porto Alegre, RS, Brazil
| | - Claudia Szobot
- Clinical Hospital of Porto Alegre, Porto Alegre, RS, Brazil
| | - João Henrique Chrusciel
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Laura Stertz
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Joy M Schmitz
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Consuelo Walss-Bass
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Gabriel R Fries
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Rodrigo Grassi-Oliveira
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil.
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 11, A701-129, 8200, Aarhus, Denmark.
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11
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Harris HA, Friedman C, Starling AP, Dabelea D, Johnson SL, Fuemmeler BF, Jima D, Murphy SK, Hoyo C, Jansen PW, Felix JF, Mulder RH. An epigenome-wide association study of child appetitive traits and DNA methylation. Appetite 2023; 191:107086. [PMID: 37844693 PMCID: PMC11156223 DOI: 10.1016/j.appet.2023.107086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
The etiology of childhood appetitive traits is poorly understood. Early-life epigenetic processes may be involved in the developmental programming of appetite regulation in childhood. One such process is DNA methylation (DNAm), whereby a methyl group is added to a specific part of DNA, where a cytosine base is next to a guanine base, a CpG site. We meta-analyzed epigenome-wide association studies (EWASs) of cord blood DNAm and early-childhood appetitive traits. Data were from two independent cohorts: the Generation R Study (n = 1,086, Rotterdam, the Netherlands) and the Healthy Start study (n = 236, Colorado, USA). DNAm at autosomal methylation sites in cord blood was measured using the Illumina Infinium HumanMethylation450 BeadChip. Parents reported on their child's food responsiveness, emotional undereating, satiety responsiveness and food fussiness using the Children's Eating Behaviour Questionnaire at age 4-5 years. Multiple regression models were used to examine the association of DNAm (predictor) at the individual site- and regional-level (using DMRff) with each appetitive trait (outcome), adjusting for covariates. Bonferroni-correction was applied to adjust for multiple testing. There were no associations of DNAm and any appetitive trait when examining individual CpG-sites. However, when examining multiple CpGs jointly in so-called differentially methylated regions, we identified 45 associations of DNAm with food responsiveness, 7 associations of DNAm with emotional undereating, 13 associations of DNAm with satiety responsiveness, and 9 associations of DNAm with food fussiness. This study shows that DNAm in the newborn may partially explain variation in appetitive traits expressed in early childhood and provides preliminary support for early programming of child appetitive traits through DNAm. Investigating differential DNAm associated with appetitive traits could be an important first step in identifying biological pathways underlying the development of these behaviors.
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Affiliation(s)
- Holly A Harris
- Department of Child & Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Erasmus University Rotterdam, Department of Psychology, Education & Child Studies, Rotterdam, the Netherlands.
| | - Chloe Friedman
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Anne P Starling
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pediatrics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Susan L Johnson
- Department of Pediatrics, Section of Nutrition, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Bernard F Fuemmeler
- Virginia Commonwealth University, Massey Comprehensive Cancer Center, Richmond, VA, USA.
| | - Dereje Jima
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA; Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
| | - Susan K Murphy
- Duke University Medical Center, Department of Obstetrics and Gynecology, Reproductive Sciences, Durham, NC, USA.
| | - Cathrine Hoyo
- Department of Biological Sciences, Center for Human Health and the Environment, North Carolina State University, Raleigh, NC, USA.
| | - Pauline W Jansen
- Department of Child & Adolescent Psychiatry/Psychology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Erasmus University Rotterdam, Department of Psychology, Education & Child Studies, Rotterdam, the Netherlands.
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
| | - Rosa H Mulder
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands; Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands.
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12
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Keller M, Svensson SIA, Rohde-Zimmermann K, Kovacs P, Böttcher Y. Genetics and Epigenetics in Obesity: What Do We Know so Far? Curr Obes Rep 2023; 12:482-501. [PMID: 37819541 DOI: 10.1007/s13679-023-00526-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE OF REVIEW Enormous progress has been made in understanding the genetic architecture of obesity and the correlation of epigenetic marks with obesity and related traits. This review highlights current research and its challenges in genetics and epigenetics of obesity. RECENT FINDINGS Recent progress in genetics of polygenic traits, particularly represented by genome-wide association studies, led to the discovery of hundreds of genetic variants associated with obesity, which allows constructing polygenic risk scores (PGS). In addition, epigenome-wide association studies helped identifying novel targets and methylation sites being important in the pathophysiology of obesity and which are essential for the generation of methylation risk scores (MRS). Despite their great potential for predicting the individual risk for obesity, the use of PGS and MRS remains challenging. Future research will likely discover more loci being involved in obesity, which will contribute to better understanding of the complex etiology of human obesity. The ultimate goal from a clinical perspective will be generating highly robust and accurate prediction scores allowing clinicians to predict obesity as well as individual responses to body weight loss-specific life-style interventions.
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Affiliation(s)
- Maria Keller
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig, University Hospital Leipzig, 04103, Leipzig, Germany
| | - Stina Ingrid Alice Svensson
- EpiGen, Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway
| | - Kerstin Rohde-Zimmermann
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig, University Hospital Leipzig, 04103, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III-Endocrinology, Nephrology, Rheumatology, Medical Center, University of Leipzig, 04103, Leipzig, Germany
| | - Yvonne Böttcher
- EpiGen, Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0316, Oslo, Norway.
- EpiGen, Medical Division, Akershus University Hospital, 1478, Lørenskog, Norway.
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13
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Silva-Ochoa AD, Velasteguí E, Falconí IB, García-Solorzano VI, Rendón-Riofrio A, Sanguña-Soliz GA, Vanden Berghe W, Orellana-Manzano A. Metabolic syndrome: Nutri-epigenetic cause or consequence? Heliyon 2023; 9:e21106. [PMID: 37954272 PMCID: PMC10637881 DOI: 10.1016/j.heliyon.2023.e21106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 09/08/2023] [Accepted: 10/16/2023] [Indexed: 11/14/2023] Open
Abstract
Metabolic syndrome is a cluster of conditions that results from the interplay of genetic and environmental factors, which increase the comorbidity risk of obesity, hyperglycemia, dyslipidemia, arterial hypertension, stroke, and cardiovascular disease. In this article, we review various high-impact studies which link epigenetics with metabolic syndrome by comparing each study population, methylation effects, and strengths and weaknesses of each research. We also discuss world statistical data on metabolic syndrome incidence in developing countries where the metabolic syndrome is common condition that has significant public health implications.
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Affiliation(s)
- Alfonso D. Silva-Ochoa
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- Licenciatura en Nutrición y Dietética, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Erick Velasteguí
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- Departamento de Ciencias de Alimentos y Biotecnología, Escuela Politécnica Nacional, Quito, Ecuador
| | - Isaac B. Falconí
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Valeria I. García-Solorzano
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Angie Rendón-Riofrio
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Gabriela A. Sanguña-Soliz
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Agua y Desarrollo Sustentable, CADS, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
| | - Wim Vanden Berghe
- Epigenetic signaling PPES lab, Department Biomedical Sciences, University Antwerp, Antwerp, Belgium
| | - Andrea Orellana-Manzano
- Laboratorio para Investigaciones Biomédicas, Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Campus Gustavo Galindo Km. 30.5 Vía Perimetral, P.O. Box 09-01-5863, Guayaquil, Ecuador
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14
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Patel P, Selvaraju V, Babu JR, Geetha T. Association of the DNA Methylation of Obesity-Related Genes with the Dietary Nutrient Intake in Children. Nutrients 2023; 15:2840. [PMID: 37447167 DOI: 10.3390/nu15132840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
The occurrence of obesity stems from both genetic and external influences. Despite thorough research and attempts to address it through various means such as dietary changes, physical activity, education, and medications, a lasting solution to this widespread problem remains elusive. Nutrients play a crucial role in various cellular processes, including the regulation of gene expression. One of the mechanisms by which nutrients can affect gene expression is through DNA methylation. This modification can alter the accessibility of DNA to transcription factors and other regulatory proteins, thereby influencing gene expression. Nutrients such as folate and vitamin B12 are involved in the one-carbon metabolism pathway, which provides the methyl groups necessary for DNA methylation. Studies have shown that the inadequate intake of these nutrients can lead to alterations in DNA methylation patterns. For this study, we aim to understand the differences in the association of the dietary intake between normal weight and overweight/obese children and between European American and African American children with the DNA methylation of the three genes NRF1, FTO, and LEPR. The research discovered a significant association between the nutritional intake of 6-10-years-old children, particularly the methyl donors present in their diet, and the methylation of the NRF1, FTO, and LEPR genes. Additionally, the study emphasizes the significance of considering health inequalities, particularly family income and maternal education, when investigating the epigenetic impact of methyl donors in diet and gene methylation.
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Affiliation(s)
- Priyadarshni Patel
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
| | | | - Jeganathan Ramesh Babu
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
| | - Thangiah Geetha
- Department of Nutritional Sciences, Auburn University, Auburn, AL 36849, USA
- Boshell Metabolic Diseases and Diabetes Program, Auburn University, Auburn, AL 36849, USA
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15
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Wu YL, Lin ZJ, Li CC, Lin X, Shan SK, Guo B, Zheng MH, Li F, Yuan LQ, Li ZH. Epigenetic regulation in metabolic diseases: mechanisms and advances in clinical study. Signal Transduct Target Ther 2023; 8:98. [PMID: 36864020 PMCID: PMC9981733 DOI: 10.1038/s41392-023-01333-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 01/02/2023] [Accepted: 01/18/2023] [Indexed: 03/04/2023] Open
Abstract
Epigenetics regulates gene expression and has been confirmed to play a critical role in a variety of metabolic diseases, such as diabetes, obesity, non-alcoholic fatty liver disease (NAFLD), osteoporosis, gout, hyperthyroidism, hypothyroidism and others. The term 'epigenetics' was firstly proposed in 1942 and with the development of technologies, the exploration of epigenetics has made great progresses. There are four main epigenetic mechanisms, including DNA methylation, histone modification, chromatin remodelling, and noncoding RNA (ncRNA), which exert different effects on metabolic diseases. Genetic and non-genetic factors, including ageing, diet, and exercise, interact with epigenetics and jointly affect the formation of a phenotype. Understanding epigenetics could be applied to diagnosing and treating metabolic diseases in the clinic, including epigenetic biomarkers, epigenetic drugs, and epigenetic editing. In this review, we introduce the brief history of epigenetics as well as the milestone events since the proposal of the term 'epigenetics'. Moreover, we summarise the research methods of epigenetics and introduce four main general mechanisms of epigenetic modulation. Furthermore, we summarise epigenetic mechanisms in metabolic diseases and introduce the interaction between epigenetics and genetic or non-genetic factors. Finally, we introduce the clinical trials and applications of epigenetics in metabolic diseases.
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Affiliation(s)
- Yan-Lin Wu
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Zheng-Jun Lin
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Chang-Chun Li
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Xiao Lin
- Department of Radiology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Su-Kang Shan
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Bei Guo
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Ming-Hui Zheng
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Fuxingzi Li
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Ling-Qing Yuan
- National Clinical Research Center for Metabolic Disease, Department of Metabolism and Endocrinology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Zhi-Hong Li
- Department of Orthopaedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
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Woldemariam S, Dorner TE, Wiesinger T, Stein KV. Multi-omics approaches for precision obesity management : Potentials and limitations of omics in precision prevention, treatment and risk reduction of obesity. Wien Klin Wochenschr 2023; 135:113-124. [PMID: 36717394 PMCID: PMC10020295 DOI: 10.1007/s00508-022-02146-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 12/12/2022] [Indexed: 02/01/2023]
Abstract
INTRODUCTION Obesity is a multifactorial chronic disease that cannot be addressed by simply promoting better diets and more physical activity. To date, not a single country has successfully been able to curb the accumulating burden of obesity. One explanation for the lack of progress is that lifestyle intervention programs are traditionally implemented without a comprehensive evaluation of an individual's diagnostic biomarkers. Evidence from genome-wide association studies highlight the importance of genetic and epigenetic factors in the development of obesity and how they in turn affect the transcriptome, metabolites, microbiomes, and proteomes. OBJECTIVE The purpose of this review is to provide an overview of the different types of omics data: genomics, epigenomics, transcriptomics, proteomics, metabolomics and illustrate how a multi-omics approach can be fundamental for the implementation of precision obesity management. RESULTS The different types of omics designs are grouped into two categories, the genotype approach and the phenotype approach. When applied to obesity prevention and management, each omics type could potentially help to detect specific biomarkers in people with risk profiles and guide healthcare professionals and decision makers in developing individualized treatment plans according to the needs of the individual before the onset of obesity. CONCLUSION Integrating multi-omics approaches will enable a paradigm shift from the one size fits all approach towards precision obesity management, i.e. (1) precision prevention of the onset of obesity, (2) precision medicine and tailored treatment of obesity, and (3) precision risk reduction and prevention of secondary diseases related to obesity.
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Affiliation(s)
- Selam Woldemariam
- Karl Landsteiner Institute for Health Promotion Research, 3062, Kirchstetten, Austria
| | - Thomas E Dorner
- Karl Landsteiner Institute for Health Promotion Research, 3062, Kirchstetten, Austria
- Academy for Ageing Research, House of Mercy, 1160, Vienna, Austria
| | - Thomas Wiesinger
- Karl Landsteiner Institute for Health Promotion Research, 3062, Kirchstetten, Austria
| | - Katharina Viktoria Stein
- Karl Landsteiner Institute for Health Promotion Research, 3062, Kirchstetten, Austria.
- Department of Public Health and Primary Care, Leiden University Medical Centre, 2511 DP, The Hague, The Netherlands.
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Esteban-Cantos A, Rodríguez-Centeno J, Silla JC, Barruz P, Sánchez-Cabo F, Saiz-Medrano G, Nevado J, Mena-Garay B, Jiménez-González M, de Miguel R, Bernardino JI, Montejano R, Cadiñanos J, Marcelo C, Gutiérrez-García L, Martínez-Martín P, Wallet C, Raffi F, Rodés B, Arribas JR. Effect of HIV infection and antiretroviral therapy initiation on genome-wide DNA methylation patterns. EBioMedicine 2023; 88:104434. [PMID: 36640455 PMCID: PMC9842861 DOI: 10.1016/j.ebiom.2022.104434] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/09/2022] [Accepted: 12/22/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Previous epigenome-wide association studies have shown that HIV infection can disrupt the host DNA methylation landscape. However, it remains unclear how antiretroviral therapy (ART) affects the HIV-induced epigenetic modifications. METHODS 184 individuals with HIV from the NEAT001/ANRS143 clinical trial (with pre-ART and post-ART samples [96 weeks of follow-up]) and 44 age-and-sex matched individuals without HIV were included. We compared genome-wide DNA methylation profiles in whole blood between groups adjusting for age, sex, batch effects, and DNA methylation-based estimates of leucocyte composition. FINDINGS We identified 430 differentially methylated positions (DMPs) between HIV+ pre-ART individuals and HIV-uninfected controls. In participants with HIV, ART initiation modified the DNA methylation levels at 845 CpG positions and restored 49.3% of the changes found between HIV+ pre-ART and HIV-uninfected individuals. We only found 15 DMPs when comparing DNA methylation profiles between HIV+ post-ART individuals and participants without HIV. The Gene Ontology enrichment analysis of DMPs associated with untreated HIV infection revealed an enrichment in biological processes regulating the immune system and antiviral responses. In participants with untreated HIV infection, DNA methylation levels at top HIV-related DMPs were associated with CD4/CD8 ratios and viral loads. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio. INTERPRETATION Control of HIV viraemia after 96 weeks of ART initiation partly restores the host DNA methylation changes that occurred before antiretroviral treatment of HIV infection. FUNDING NEAT-ID Foundation and Instituto de Salud Carlos III, co-funded by European Union.
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Affiliation(s)
- Andrés Esteban-Cantos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Javier Rodríguez-Centeno
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Juan C Silla
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Pilar Barruz
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Spanish National Centre for Cardiovascular Research (CNIC), Madrid, Spain
| | - Gabriel Saiz-Medrano
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julián Nevado
- Genomics Laboratory, Institute of Medical and Molecular Genetics, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Beatriz Mena-Garay
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - María Jiménez-González
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rosa de Miguel
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Jose I Bernardino
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Rocío Montejano
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Julen Cadiñanos
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cristina Marcelo
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Lucía Gutiérrez-García
- HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Patricia Martínez-Martín
- Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain
| | - Cédrick Wallet
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, CHU de Bordeaux, Bordeaux, France
| | - François Raffi
- Centre Hospitalier Universitaire de Nantes and CIC 1413 INSERM, Nantes, France
| | - Berta Rodés
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; HIV/AIDS and Infectious Diseases Research Group, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
| | - José R Arribas
- CIBER of Infectious Diseases (CIBERINFEC), Madrid, Spain; Department of Internal Medicine, Infectious Diseases Unit, La Paz University Hospital, Hospital La Paz Institute for Health Research (IdiPAZ), Madrid, Spain.
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18
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Taylor JY, Huang Y, Zhao W, Wright ML, Wang Z, Hui Q, Potts‐Thompson S, Barcelona V, Prescott L, Yao Y, Crusto C, Kardia SLR, Smith JA, Sun YV. Epigenome-wide association study of BMI in Black populations from InterGEN and GENOA. Obesity (Silver Spring) 2023; 31:243-255. [PMID: 36479596 PMCID: PMC10107734 DOI: 10.1002/oby.23589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Obesity is a significant public health concern across the globe. Research investigating epigenetic mechanisms related to obesity and obesity-associated conditions has identified differences that may contribute to cellular dysregulation that accelerates the development of disease. However, few studies include Black women, who experience the highest incidence of obesity and early onset of cardiometabolic disorders. METHODS The association of BMI with epigenome-wide DNA methylation (DNAm) was examined using the 850K Illumina EPIC BeadChip in two Black populations (Intergenerational Impact of Genetic and Psychological Factors on Blood Pressure [InterGEN], n = 239; and The Genetic Epidemiology Network of Arteriopathy [GENOA] study, n = 961) using linear mixed-effects regression models adjusted for batch effects, cell type heterogeneity, population stratification, and confounding factors. RESULTS Cross-sectional analysis of the InterGEN discovery cohort identified 28 DNAm sites significantly associated with BMI, 24 of which had not been previously reported. Of these, 17 were replicated using the GENOA study. In addition, a meta-analysis, including both the InterGEN and GENOA cohorts, identified 658 DNAm sites associated with BMI with false discovery rate < 0.05. In a meta-analysis of Black women, we identified 628 DNAm sites significantly associated with BMI. Using a more stringent significance threshold of Bonferroni-corrected p value 0.05, 65 and 61 DNAm sites associated with BMI were identified from the combined sex and female-only meta-analyses, respectively. CONCLUSIONS This study suggests that BMI is associated with differences in DNAm among women that can be identified with DNA extracted from salivary (discovery) and peripheral blood (replication) samples among Black populations across two cohorts.
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Affiliation(s)
- Jacquelyn Y. Taylor
- Center for Research on People of ColorColumbia University School of NursingNew YorkNew YorkUSA
| | - Yunfeng Huang
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | - Wei Zhao
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | | | - Zeyuan Wang
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | - Qin Hui
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | | | - Veronica Barcelona
- Center for Research on People of ColorColumbia University School of NursingNew YorkNew YorkUSA
| | - Laura Prescott
- Center for Research on People of ColorColumbia University School of NursingNew YorkNew YorkUSA
| | - Yutong Yao
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
| | - Cindy Crusto
- Department of PsychiatryYale School of MedicineNew HavenConnecticutUSA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public HealthUniversity of MichiganAnn ArborMichiganUSA
- Survey Research CenterInstitute for Social Research, University of MichiganAnn ArborMichiganUSA
| | - Yan V. Sun
- Department of EpidemiologyEmory University Rollins School of Public HealthAtlantaGeorgiaUSA
- Atlanta VA Healthcare SystemDecaturGeorgiaUSA
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19
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Chu DT, Bui NL, Vu Thi H, Nguyen Thi YV. Role of DNA methylation in diabetes and obesity. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:153-170. [PMID: 37019591 DOI: 10.1016/bs.pmbts.2023.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
Abstract
Due to the fact that the upward trend of several metabolic disorders such as diabetes and obesity, in individuals especially monozygotic twins, who are under the same effects from the environment, are not similar, the role of epigenetic elements like DNA methylation needs taking into account. In this chapter, emerging scientific evidence supporting the strong relationship between changes in DNA methylation and those diseases' development was summarized. Changing in the expression level of diabetes/obesity-related genes through being silenced by methylation can be the underlying mechanism of this phenomenon. Genes with abnormal methylation status are potential biomarkers for early prediction and diagnosis. Moreover, methylation-based molecular targets should be investigated as a new treatment for both T2D and obesity.
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Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
| | - Nhat-Le Bui
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Yen-Vy Nguyen Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
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20
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Talukdar FR, Escobar Marcillo DI, Laskar RS, Novoloaca A, Cuenin C, Sbraccia P, Nisticò L, Guglielmi V, Gheit T, Tommasino M, Dogliotti E, Fortini P, Herceg Z. Bariatric surgery-induced weight loss and associated genome-wide DNA-methylation alterations in obese individuals. Clin Epigenetics 2022; 14:176. [PMID: 36528638 PMCID: PMC9759858 DOI: 10.1186/s13148-022-01401-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Obesity is a multifactorial and chronic condition of growing universal concern. It has recently been reported that bariatric surgery is a more successful treatment for severe obesity than other noninvasive interventions, resulting in rapid significant weight loss and associated chronic disease remission. The identification of distinct epigenetic patterns in patients who are obese or have metabolic imbalances has suggested a potential role for epigenetic alterations in causal or mediating pathways in the development of obesity-related pathologies. Specific changes in the epigenome (DNA methylome), associated with metabolic disorders, can be detected in the blood. We investigated whether such epigenetic changes are reversible after weight loss using genome-wide DNA methylome analysis of blood samples from individuals with severe obesity (mean BMI ~ 45) undergoing bariatric surgery. RESULTS Our analysis revealed 41 significant (Bonferroni p < 0.05) and 1169 (false discovery rate p < 0.05) suggestive differentially methylated positions (DMPs) associated with weight loss due to bariatric surgery. Among the 41 significant DMPs, 5 CpGs were replicated in an independent cohort of BMI-discordant monozygotic twins (the heavier twin underwent diet-induced weight loss). The effect sizes of these 5 CpGs were consistent across discovery and replication sets (p < 0.05). We also identified 192 differentially methylated regions (DMRs) among which SMAD6 and PFKFB3 genes were the top hypermethylated and hypomethylated regions, respectively. Pathway enrichment analysis of the DMR-associated genes showed that functional pathways related to immune function and type 1 diabetes were significant. Weight loss due to bariatric surgery also significantly decelerated epigenetic age 12 months after the intervention (mean = - 4.29; p = 0.02). CONCLUSIONS We identified weight loss-associated DNA-methylation alterations targeting immune and inflammatory gene pathways in blood samples from bariatric-surgery patients. The top hits were replicated in samples from an independent cohort of BMI-discordant monozygotic twins following a hypocaloric diet. Energy restriction and bariatric surgery thus share CpGs that may represent early indicators of response to the metabolic effects of weight loss. The analysis of bariatric surgery-associated DMRs suggests that epigenetic regulation of genes involved in endothelial and adipose tissue function is key in the pathophysiology of obesity.
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Affiliation(s)
- Fazlur Rahman Talukdar
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - David Israel Escobar Marcillo
- Section of Mechanisms, Biomarkers and Models, Dept Environment and Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
- Obesity Center-Internal Medicine Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Ruhina Shirin Laskar
- Nutrition and Metabolism Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Alexei Novoloaca
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Paolo Sbraccia
- Obesity Center-Internal Medicine Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lorenza Nisticò
- Centre for Behavioral Sciences and Mental Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
| | - Valeria Guglielmi
- Obesity Center-Internal Medicine Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Tarik Gheit
- Early Detection, Prevention, and Infections Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | | | - Eugenia Dogliotti
- Section of Mechanisms, Biomarkers and Models, Dept Environment and Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
| | - Paola Fortini
- Section of Mechanisms, Biomarkers and Models, Dept Environment and Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
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21
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Wu Y, Tian H, Wang W, Li W, Duan H, Zhang D. DNA methylation and waist-to-hip ratio: an epigenome-wide association study in Chinese monozygotic twins. J Endocrinol Invest 2022; 45:2365-2376. [PMID: 35882828 DOI: 10.1007/s40618-022-01878-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 07/19/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Epigenetic signatures such as DNA methylation may be associated with specific obesity traits. We performed an epigenome-wide association study (EWAS) by combining with the waist-to-hip ratio (WHR)-discordant monozygotic (MZ) twin design in an attempt to identify genetically independent DNA methylation marks associated with abdominal obesity in Northern Han Chinese and to determine the causation underlying. METHODS A total of 60 WHR discordant MZ twin pairs were selected from the Qingdao Twin Registry, China. Generalized estimated equation (GEE) model was used to regress the methylation level of CpG sites on WHR. The Inference about Causation through Examination of FAmiliaL CONfounding (ICE FALCON) was used to assess the temporal relationship between methylation and WHR. Gene expression analysis was conducted to validate the results of differentially methylated analyses. RESULTS EWAS identified 92 CpG sites with the level of P < 10 - 4 which were annotated to 32 genes, especially CADPS2, TUSC5, ZCCHC14, CORO7, COL23A1, CACNA1C, CYP26B1, and BCAT1. ICE FALCON showed significant causality between DNA methylation of several genes and WHR (P < 0.05). In region-based analysis, 14 differentially methylated regions (DMRs) located at 15 genes (slk-corrected P < 0.05) were detected. The gene expression analysis identified the significant correlation between expression levels of 5 differentially methylated genes and WHR (P < 0.05). CONCLUSIONS Our study identifies the associations between specific epigenetic variations and WHR in Northern Han Chinese. These DNA methylation signatures may have value as diagnostic biomarkers and provide novel insights into the molecular mechanisms of pathogenesis.
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Affiliation(s)
- Y Wu
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, NO. 308 Ningxia Road, 266071, Qingdao, Shandong, China.
| | - H Tian
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, NO. 308 Ningxia Road, 266071, Qingdao, Shandong, China
| | - W Wang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, NO. 308 Ningxia Road, 266071, Qingdao, Shandong, China
| | - W Li
- Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - H Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong, China
| | - D Zhang
- Department of Epidemiology and Health Statistics, Public Health College, Qingdao University, NO. 308 Ningxia Road, 266071, Qingdao, Shandong, China
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22
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Blostein FA, Fisher J, Dou J, Schneper L, Ware EB, Notterman DA, Mitchell C, Bakulski KM. Polymethylation scores for prenatal maternal smoke exposure persist until age 15 and are detected in saliva in the Fragile Families and Child Wellbeing cohort. Epigenetics 2022; 17:2223-2240. [PMID: 35980258 PMCID: PMC9665138 DOI: 10.1080/15592294.2022.2112815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/05/2022] [Indexed: 01/18/2023] Open
Abstract
Prenatal maternal smoking is associated with low birthweight, neurological disorders, and asthma in exposed children. DNA methylation signatures can function as biomarkers of prenatal smoke exposure. However, the robustness of DNA methylation signatures across child ages, genetic ancestry groups, or tissues is not clear. Using coefficients from a meta-analysis of prenatal smoke exposure and DNA methylation in newborn cord blood, we created polymethylation scores of saliva DNA methylation from children at ages 9 and 15 in the Fragile Families and Child Wellbeing study. In the full sample at age 9 (n = 753), prenatal smoke exposure was associated with a 0.51 (95%CI: 0.35, 0.66) standard deviation higher polymethylation score. The direction and magnitude of the association was consistent in European and African genetic ancestry samples. In the full sample at age 15 (n = 747), prenatal smoke exposure was associated with a 0.48 (95%CI: 0.32, 0.63) standard deviation higher polymethylation score, and the association was attenuated among the European and Admixed-Latin genetic ancestry samples. The polymethylation score classified prenatal smoke exposure accurately (AUC age 9 = 0.77, age 15 = 0.76). Including the polymethylation score increased the AUC of base model covariates by 5 (95% CI: (2.1, 7.2)) percentage points, while including a single candidate site in the AHRR gene did not (P-value = 0.19). Polymethylation scores for prenatal smoking were portable across genetic ancestries and more accurate than an individual DNA methylation site. Polymethylation scores from saliva samples could serve as robust and practical biomarkers of prenatal smoke exposure.
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Affiliation(s)
- Freida A. Blostein
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jonah Fisher
- Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - John Dou
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Lisa Schneper
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Erin B. Ware
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Daniel A. Notterman
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Colter Mitchell
- Institute for Social Research, University of Michigan, Ann Arbor, Michigan, USA
| | - Kelly M. Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
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Abstract
Nowadays, obesity is one of the largest public health problems worldwide. In the last few decades, there has been a marked increase in the obesity epidemic and its related comorbidities. Worldwide, more than 2.2 billion people (33%) are affected by overweight or obesity (712 million, 10%) and its associated metabolic complications. Although a high heritability of obesity has been estimated, the genetic variants conducted from genetic association studies only partially explain the variation of body mass index. This has led to a growing interest in understanding the potential role of epigenetics as a key regulator of gene-environment interactions on the development of obesity and its associated complications. Rapid advances in epigenetic research methods and reduced costs of epigenome-wide association studies have led to a great expansion of population-based studies. The field of epigenetics and metabolic diseases such as obesity has advanced rapidly in a short period of time. The main epigenetic mechanisms include DNA methylation, histone modifications, microRNA (miRNA)-mediated regulation and so on. DNA methylation is the most investigated epigenetic mechanism. Preliminary evidence from animal and human studies supports the effect of epigenetics on obesity. Studies of epigenome-wide association studies and genome-wide histone modifications from different biological specimens such as blood samples (newborn, children, adolescent, youth, woman, man, twin, race, and meta-analysis), adipose tissues, skeletal muscle cells, placenta, and saliva have reported the differential expression status of multiple genes before and after obesity interventions and have identified multiple candidate genes and biological markers. These findings may improve the understanding of the complex etiology of obesity and its related comorbidities, and help to predict an individual's risk of obesity at a young age and open possibilities for introducing targeted prevention and treatment strategies.
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Affiliation(s)
- Feng-Yao Wu
- Department of Comprehensive Internal Medicine, Affiliated Infectious Disease Hospital of Nanning (The Fourth People’s Hospital of Nanning), Guangxi Medical University, No. 1 Erli, Changgang Road, Nanning, 530023 Guangxi People’s Republic of China
| | - Rui-Xing Yin
- Department of Comprehensive Internal Medicine, Affiliated Infectious Disease Hospital of Nanning (The Fourth People’s Hospital of Nanning), Guangxi Medical University, No. 1 Erli, Changgang Road, Nanning, 530023 Guangxi People’s Republic of China
- Department of Cardiology, Institute of Cardiovascular Diseases, The First Affiliated Hospital, Guangxi Medical University, 6 Shuangyong Road, Nanning, 530021 Guangxi People’s Republic of China
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Zhang X, Ammous F, Lin L, Ratliff SM, Ware EB, Faul JD, Zhao W, Kardia SLR, Smith JA. The Interplay of Epigenetic, Genetic, and Traditional Risk Factors on Blood Pressure: Findings from the Health and Retirement Study. Genes (Basel) 2022; 13:1959. [PMID: 36360196 PMCID: PMC9689874 DOI: 10.3390/genes13111959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/19/2022] [Indexed: 01/21/2023] Open
Abstract
The epigenome likely interacts with traditional and genetic risk factors to influence blood pressure. We evaluated whether 13 previously reported DNA methylation sites (CpGs) are associated with systolic (SBP) or diastolic (DBP) blood pressure, both individually and aggregated into methylation risk scores (MRS), in 3070 participants (including 437 African ancestry (AA) and 2021 European ancestry (EA), mean age = 70.5 years) from the Health and Retirement Study. Nine CpGs were at least nominally associated with SBP and/or DBP after adjusting for traditional hypertension risk factors (p < 0.05). MRSSBP was positively associated with SBP in the full sample (β = 1.7 mmHg per 1 standard deviation in MRSSBP; p = 2.7 × 10-5) and in EA (β = 1.6; p = 0.001), and MRSDBP with DBP in the full sample (β = 1.1; p = 1.8 × 10-6), EA (β = 1.1; p = 7.2 × 10-5), and AA (β = 1.4; p = 0.03). The MRS and BP-genetic risk scores were independently associated with blood pressure in EA. The effects of both MRSs were weaker with increased age (pinteraction < 0.01), and the effect of MRSDBP was higher among individuals with at least some college education (pinteraction = 0.02). In AA, increasing MRSSBP was associated with higher SBP in females only (pinteraction = 0.01). Our work shows that MRS is a potential biomarker of blood pressure that may be modified by traditional hypertension risk factors.
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Affiliation(s)
- Xinman Zhang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lisha Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Scott M. Ratliff
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erin B. Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48104, USA
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25
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Wu P, Guo L, Li X, Du Y, Lin X, Ma X, Lin Y, Wen C, Yang C, Liu N, Feng Q, Xue Y, Guan M. Comprehensive analysis of epigenomics and transcriptome data to identify potential target genes associated with obesity. Front Genet 2022; 13:1024300. [PMID: 36313453 PMCID: PMC9614047 DOI: 10.3389/fgene.2022.1024300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
DNA methylation is closely related to the occurrence and development of many diseases, but its role in obesity is still unclear. This study aimed to find the potential differentially methylated genes associated with obesity occurrence and development. By combining methylation and transcriptome analysis, we identified the key genes in adipose tissue affecting the occurrence and development of obesity and revealed the possible molecular mechanisms involved in obesity pathogenesis. We first screened 14 methylation-related differential genes and verified their expression in adipose tissue by quantitative polymerase chain reaction (qPCR). Seven genes with the same expression pattern were identified as key genes, namely, CCRL2, GPT, LGALS12, PC, SLC27A2, SLC4A4, and TTC36. Then, the immune microenvironment of adipose tissue was quantified by CIBERSORT, and we found that the content of M0 macrophages and T follicular helper cells in adipose tissue was significantly increased and decreased, respectively, in the obese group. Furthermore, the relationship between key genes and the immune microenvironment was analyzed. Additionally, the metabolic pathway activity of each sample was calculated based on the ssGSEA algorithm, and the key gene–metabolic network was constructed. Moreover, we performed a CMAP analysis based on the differential genes in adipose tissue to screen out drugs potentially effective in obesity treatment. In conclusion, we identified seven methylation-related key genes closely related to obesity pathogenesis and explored the potential mechanism of their role in obesity. This study provided novel insights into the molecular mechanisms and management of obesity.
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Affiliation(s)
- Peili Wu
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Lei Guo
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xuelin Li
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yuejun Du
- Department of Urology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaochun Lin
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Xiaoqin Ma
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yingbei Lin
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Churan Wen
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Chuyi Yang
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Nannan Liu
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Qijian Feng
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Yaoming Xue
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Meiping Guan
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- *Correspondence: Meiping Guan,
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Abstract
DNA methylation is an epigenetic modification that has consistently been shown to be linked with a variety of human traits and diseases. Because DNA methylation is dynamic and potentially reversible in nature and can reflect environmental exposures and predict the onset of diseases, it has piqued interest as a potential disease biomarker. DNA methylation patterns are more stable than transcriptomic or proteomic patterns, and they are relatively easy to measure to track exposure to different environments and risk factors. Importantly, technologies for DNA methylation quantification have become increasingly cost effective-accelerating new research in the field-and have enabled the development of novel DNA methylation biomarkers. Quite a few DNA methylation-based predictors for a number of traits and diseases already exist. Such predictors show potential for being more accurate than self-reported or measured phenotypes (such as smoking behavior and body mass index) and may even hold potential for applications in clinics. In this review, we will first discuss the advantages and challenges of DNA methylation biomarkers in general. We will then review the current state and future potential of DNA methylation biomarkers in two human traits that show rather consistent alterations in methylome-obesity and smoking. Lastly, we will briefly speculate about the future prospects of DNA methylation biomarkers, and possible ways to achieve them.
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Affiliation(s)
- Aino Heikkinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Sailalitha Bollepalli
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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27
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Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, Pospisilik JA. Independent phenotypic plasticity axes define distinct obesity sub-types. Nat Metab 2022; 4:1150-1165. [PMID: 36097183 PMCID: PMC9499872 DOI: 10.1038/s42255-022-00629-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/29/2022] [Indexed: 01/04/2023]
Abstract
Studies in genetically 'identical' individuals indicate that as much as 50% of complex trait variation cannot be traced to genetics or to the environment. The mechanisms that generate this 'unexplained' phenotypic variation (UPV) remain largely unknown. Here, we identify neuronatin (NNAT) as a conserved factor that buffers against UPV. We find that Nnat deficiency in isogenic mice triggers the emergence of a bi-stable polyphenism, where littermates emerge into adulthood either 'normal' or 'overgrown'. Mechanistically, this is mediated by an insulin-dependent overgrowth that arises from histone deacetylase (HDAC)-dependent β-cell hyperproliferation. A multi-dimensional analysis of monozygotic twin discordance reveals the existence of two patterns of human UPV, one of which (Type B) phenocopies the NNAT-buffered polyphenism identified in mice. Specifically, Type-B monozygotic co-twins exhibit coordinated increases in fat and lean mass across the body; decreased NNAT expression; increased HDAC-responsive gene signatures; and clinical outcomes linked to insulinemia. Critically, the Type-B UPV signature stratifies both childhood and adult cohorts into four metabolic states, including two phenotypically and molecularly distinct types of obesity.
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Affiliation(s)
- Chih-Hsiang Yang
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | | | - Vanessa Wegert
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Kathrin Landgraf
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
| | - Ilaria Panzeri
- Van Andel Institute, Grand Rapids, MI, USA
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Erez Dror
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Steffen Heyne
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Roche Diagnostics Deutschland, Mannheim, Germany
| | - Till Wörpel
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Di Lu
- Van Andel Institute, Grand Rapids, MI, USA
| | - Tao Yang
- Van Andel Institute, Grand Rapids, MI, USA
| | - Elizabeth Gibbons
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Martin Thomasen
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
| | - Louise G Grunnet
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
| | - Allan A Vaag
- Department of Endocrinology, Rigshospitalet, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Herlev, Denmark
- Lund University Diabetes Centre, Lund University, Malmö, Sweden
| | - Linn Gillberg
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Elin Grundberg
- Genomic Medicine Center, Children's Mercy Research Institute, Children's Mercy Kansas City, MO, USA
| | - Ana Conesa
- Institute for Integrative Systems Biology, Spanish National Research Council (CSIC), Paterna, Valencia, Spain
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, USA
| | - Antje Körner
- Medical Faculty, University of Leipzig, University Hospital for Children & Adolescents, Center for Pediatric Research Leipzig, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Zentrum München at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - J Andrew Pospisilik
- Van Andel Institute, Grand Rapids, MI, USA.
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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28
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Rathod R, Zhang H, Karmaus W, Ewart S, Mzayek F, Arshad SH, Holloway JW. Association of childhood BMI trajectory with post-adolescent and adult lung function is mediated by pre-adolescent DNA methylation. Respir Res 2022; 23:194. [PMID: 35906571 PMCID: PMC9335987 DOI: 10.1186/s12931-022-02089-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Body mass index (BMI) has been shown to be associated with lung function. Recent findings showed that DNA methylation (DNAm) variation is likely to be a consequence of changes in BMI. However, whether DNAm mediates the association of BMI with lung function is unknown. We examined the mediating role of DNAm on the association of pre-adolescent BMI trajectories with post-adolescent and adulthood lung function (forced expiratory volume (FEV1), forced vital capacity (FVC), and FEV1/FVC). METHODS Analyses were undertaken in the Isle of Wight birth cohort (IOWBC). Group-based trajectory modelling was applied to infer latent BMI trajectories from age 1 to 10 years. An R package, ttscreening, was applied to identify CpGs at 10 years potentially associated with BMI trajectories for each sex. Linear regressions were implemented to further screen CpGs for their association with lung function at 18 years. Path analysis, stratified by sex, was applied to each screened CpG to assess its role of mediation. Internal validation was applied to further examine the mediation consistency of the detected CpGs based on lung function at 26 years. Mendelian randomization (MR-base) was used to test possible causal effects of the identified CpGs. RESULTS Two BMI trajectories (high vs. low) were identified. Of the 442,475 CpG sites, 18 CpGs in males and 33 in females passed screening. Eight CpGs in males and 16 CpGs in females (none overlapping) were identified as mediators. For subjects with high BMI trajectory, high DNAm at all CpGs in males were associated with decreased lung function, while 8 CpGs in females were associated with increased lung function at 18 years. At 26 years, 6 CpGs in males and 14 CpGs in females showed the same direction of indirect effects as those at 18 years. DNAm at CpGs cg19088553 (GRIK2) and cg00612625 (HPSE2) showed a potential causal effect on FEV1. CONCLUSIONS The effects of BMI trajectory in early childhood on post-adolescence lung function were likely to be mediated by pre-adolescence DNAm in both males and females, but such mediation effects were likely to diminish over time.
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Affiliation(s)
- Rutu Rathod
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, 38152-0001, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, 38152-0001, USA.
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, 38152-0001, USA
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Fawaz Mzayek
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN, 38152-0001, USA
| | - S Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - John W Holloway
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
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29
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Zheng Y, Joyce B, Hwang SJ, Ma J, Liu L, Allen N, Krefman A, Wang J, Gao T, Nannini D, Zhang H, Jacobs DR, Gross M, Fornage M, Lewis CE, Schreiner PJ, Sidney S, Chen D, Greenland P, Levy D, Hou L, Lloyd-Jones D. Association of Cardiovascular Health Through Young Adulthood With Genome-Wide DNA Methylation Patterns in Midlife: The CARDIA Study. Circulation 2022; 146:94-109. [PMID: 35652342 PMCID: PMC9348746 DOI: 10.1161/circulationaha.121.055484] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cardiovascular health (CVH) from young adulthood is strongly associated with an individual's future risk of cardiovascular disease (CVD) and total mortality. Defining epigenomic biomarkers of lifelong CVH exposure and understanding their roles in CVD development may help develop preventive and therapeutic strategies for CVD. METHODS In 1085 CARDIA study (Coronary Artery Risk Development in Young Adults) participants, we defined a clinical cumulative CVH score that combines body mass index, blood pressure, total cholesterol, and fasting glucose measured longitudinally from young adulthood through middle age over 20 years (mean age, 25-45). Blood DNA methylation at >840 000 methylation markers was measured twice over 5 years (mean age, 40 and 45). Epigenome-wide association analyses on the cumulative CVH score were performed in CARDIA and compared in the FHS (Framingham Heart Study). We used penalized regression to build a methylation-based risk score to evaluate the risk of incident coronary artery calcification and clinical CVD events. RESULTS We identified 45 methylation markers associated with cumulative CVH at false discovery rate <0.01 (P=4.7E-7-5.8E-17) in CARDIA and replicated in FHS. These associations were more pronounced with methylation measured at an older age. CPT1A, ABCG1, and SREBF1 appeared as the most prominent genes. The 45 methylation markers were mostly located in transcriptionally active chromatin and involved lipid metabolism, insulin secretion, and cytokine production pathways. Three methylation markers located in genes SARS1, SOCS3, and LINC-PINT statistically mediated 20.4% of the total effect between CVH and risk of incident coronary artery calcification. The methylation risk score added information and significantly (P=0.004) improved the discrimination capacity of coronary artery calcification status versus CVH score alone and showed association with risk of incident coronary artery calcification 5 to 10 years later independent of cumulative CVH score (odds ratio, 1.87; P=9.66E-09). The methylation risk score was also associated with incident clinical CVD in FHS (hazard ratio, 1.28; P=1.22E-05). CONCLUSIONS Cumulative CVH from young adulthood contributes to midlife epigenetic programming over time. Our findings demonstrate the role of epigenetic markers in response to CVH changes and highlight the potential of epigenomic markers for precision CVD prevention, and earlier detection of subclinical CVD, as well.
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Affiliation(s)
- Yinan Zheng
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Brian Joyce
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shih-Jen Hwang
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiantao Ma
- Tufts University Friedman School of Nutrition Science and Policy, Boston, Massachusetts, USA
| | - Lei Liu
- Division of Biostatistics, Washington University, St. Louis, Missouri, USA
| | - Norrina Allen
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Amy Krefman
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jun Wang
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tao Gao
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Drew Nannini
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Haixiang Zhang
- Center for Applied Mathematics, Tianjin University, Tianjin, China
| | - David R. Jacobs
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Myron Gross
- Department of Laboratory Medicine and Pathology, Medical School, University of Minnesota, Minneapolis, Minnesota, USA
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Cora E. Lewis
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Division of Preventive Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Pamela J. Schreiner
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Stephen Sidney
- Division of Research, Kaiser Permanente Northern California, Oakland, California, USA
| | - Dongquan Chen
- Department of Medicine, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Philip Greenland
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Daniel Levy
- Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Donald Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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30
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Holzapfel C, Waldenberger M, Lorkowski S, Daniel H. Genetics and Epigenetics in Personalized Nutrition: Evidence, Expectations and Experiences. Mol Nutr Food Res 2022; 66:e2200077. [PMID: 35770348 DOI: 10.1002/mnfr.202200077] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 05/17/2022] [Indexed: 11/10/2022]
Abstract
With the presentation of the blueprint of the first human genome in 2001 and the advent of technologies for high-throughput genetic analysis, personalized nutrition (PN) became a new scientific field and the first commercial offerings of genotype-based nutrition advice emerged at the same time. Here, we summarize the state of evidence for the effect of genetic and epigenetic factors in the development of obesity, the metabolic syndrome and resulting illnesses such as non-insulin-dependent diabetes mellitus and cardiovascular diseases. We also critically value the concepts of PN that were built around the new genetic avenue from both the academic and a commercial perspective and their effectiveness in causing sustained changes in diet, lifestyle and for improving health. Despite almost 20 years of research and commercial direct-to-consumer offerings, evidence for the success of gene-based dietary recommendations is still generally lacking. This calls for new concepts of future PN solutions that incorporate more phenotypic measures and provide a panel of instruments (e.g., self- and bio-monitoring tools, feedback systems, algorithms based on artificial intelligence) that increases compliance based on the individual´s physical and social environment and value system. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christina Holzapfel
- Institute for Nutritional Medicine, Technical University of Munich, School of Medicine, Munich, Germany
| | - Melanie Waldenberger
- Research Unit Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, German Research Center for Environmental Health, Neuherberg, Germany.,German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Stefan Lorkowski
- Institute of Nutritional Sciences and Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, Friedrich Schiller University, Jena, Germany
| | - Hannelore Daniel
- Professor emeritus, Technical University of Munich, Freising, Germany
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31
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Abstract
Healthcare is undergoing large transformations, and it is imperative to leverage new technologies to support the advent of personalized medicine and disease prevention. It is now well accepted that the levels of certain biological molecules found in blood and other bodily fluids, as well as in exhaled breath, are an indication of the onset of many human diseases and reflect the health status of the person. Blood, urine, sweat, or saliva biomarkers can therefore serve in early diagnosis of diseases such as cancer, but also in monitoring disease progression, detecting metabolic disfunctions, and predicting response to a given therapy. For most point-of-care sensors, the requirement that patients themselves can use and apply them is crucial not only regarding the diagnostic part, but also at the sample collection level. This has stimulated the development of such diagnostic approaches for the non-invasive analysis of disease-relevant analytes. Considering these timely efforts, this review article focuses on novel, sensitive, and selective sensing systems for the detection of different endogenous target biomarkers in bodily fluids as well as in exhaled breath, which are associated with human diseases.
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32
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Barbosa P, Landes RD, Graw S, Byrum SD, Bennuri S, Delhey L, Randolph C, MacLeod S, Reis A, Børsheim E, Rose S, Carvalho E. Effect of excess weight and insulin resistance on DNA methylation in prepubertal children. Sci Rep 2022; 12:8430. [PMID: 35589784 PMCID: PMC9120504 DOI: 10.1038/s41598-022-12325-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
Epigenetic mechanisms, such as DNA methylation, regulate gene expression and play a role in the development of insulin resistance. This study evaluates how the BMI z-score (BMIz) and the homeostatic model assessment of insulin resistance (HOMA-IR), alone or in combination, relate to clinical outcomes and DNA methylation patterns in prepubertal children. DNA methylation in peripheral blood mononuclear cells (PBMCs) and clinical outcomes were measured in a cohort of 41 prepubertal children. Children with higher HOMA-IR had higher blood pressure and plasma lactate levels while children with higher BMIz had higher triglycerides levels. Moreover, the DNA methylation analysis demonstrated that a 1 unit increase in the BMIz was associated with a 0.41 (95% CI: 0.29, 0.53) increase in methylation of a CpG near the PPP6R2 gene. This gene is important in the regulation of NF-kB expression. However, there was no strong evidence that the BMIz and the HOMA-IR were synergistically related to any clinical or DNA methylation outcomes. In summary, the results suggest that obesity and insulin resistance may impact metabolic health both independently in prepubertal children. In addition, obesity also has an impact on the DNA methylation of the PPP6R2 gene. This may be a novel underlying starting point for the systemic inflammation associated with obesity and insulin resistance, in this population.
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Affiliation(s)
- Pedro Barbosa
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
| | - Reid D Landes
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Arkansas Children's Research Institute, Little Rock, AR, USA.,Everest Clinical Research Corporation, Markham, ON, Canada
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Sirish Bennuri
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Leanna Delhey
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Chris Randolph
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Stewart MacLeod
- Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Andreia Reis
- Department of Medical Sciences (DCM), Institute for Research in Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Elisabet Børsheim
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Arkansas Children's Nutrition Center, Little Rock, AR, USA.,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shannon Rose
- Arkansas Children's Research Institute, Little Rock, AR, USA.,Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eugenia Carvalho
- Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal. .,Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal. .,Arkansas Children's Research Institute, Little Rock, AR, USA. .,Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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33
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Sasaki A, Murphy KE, Briollais L, McGowan PO, Matthews SG. DNA methylation profiles in the blood of newborn term infants born to mothers with obesity. PLoS One 2022; 17:e0267946. [PMID: 35500004 PMCID: PMC9060365 DOI: 10.1371/journal.pone.0267946] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/19/2022] [Indexed: 01/03/2023] Open
Abstract
Maternal obesity is an important risk factor for childhood obesity and influences the prevalence of metabolic diseases in offspring. As childhood obesity is influenced by postnatal factors, it is critical to determine whether children born to women with obesity during pregnancy show alterations that are detectable at birth. Epigenetic mechanisms such as DNA methylation modifications have been proposed to mediate prenatal programming. We investigated DNA methylation signatures in male and female infants from mothers with a normal Body Mass Index (BMI 18.5-24.9 kg/m2) compared to mothers with obesity (BMI≥30 kg/m2). BMI was measured during the first prenatal visit from women recruited into the Ontario Birth Study (OBS) at Mount Sinai Hospital in Toronto, ON, Canada. DNA was extracted from neonatal dried blood spots collected from heel pricks obtained 24 hours after birth at term (total n = 40) from women with a normal BMI and women with obesity matched for parity, age, and neonatal sex. Reduced representation bisulfite sequencing was used to identify genomic loci associated with differentially methylated regions (DMRs) in CpG-dense regions most likely to influence gene regulation. DMRs were predominantly localized to intergenic regions and gene bodies, with only 9% of DMRs localized to promoter regions. Genes associated with DMRs were compared to those from a large publicly available cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC; total n = 859). Hypergeometric tests revealed a significant overlap in genes associated with DMRs in the OBS and ALSPAC cohorts. PTPRN2, a gene involved in insulin secretion, and MAD1L1, which plays a role in the cell cycle and tumor suppression, contained DMRs in males and females in both cohorts. In males, KEGG pathway analysis revealed significant overrepresentation of genes involved in endocytosis and pathways in cancer, including IGF1R, which was previously shown to respond to diet-induced metabolic stress in animal models and in lymphocytes in the context of childhood obesity. These preliminary findings are consistent with Developmental Origins of Health and Disease paradigm, which posits that adverse prenatal exposures set developmental health trajectories.
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Affiliation(s)
- Aya Sasaki
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kellie E. Murphy
- Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Laurent Briollais
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Patrick O. McGowan
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Department of Psychology, University of Toronto, Toronto, Ontario, Canada
- Departments of Biological Sciences and Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Stephen G. Matthews
- Department of Physiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Obstetrics & Gynecology, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
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Ping Z, Guo Z, Lu M, Chen Y, Liu L. Association of CIDEB gene promoter methylation with overweight or obesity in adults. Aging (Albany NY) 2022; 14:3607-3616. [PMID: 35475772 PMCID: PMC9085220 DOI: 10.18632/aging.204032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/25/2022] [Indexed: 12/02/2022]
Abstract
Objective: To explore the association of the methylation level of cell death-inducing DFF45-like effector B (CIDEB) gene promoter with overweight or obesity in the abdominal subcutaneous adipose tissue (SAT) and omental adipose tissue (OAT) of adults. Methods: A total of 61 patients undergoing abdominal surgery in the hospital were selected with an average age of 51.87 years. According to the diagnostic criteria of Chinese adult obesity, the subjects were divided into normal-weight group (n = 28) and overweight/obesity group (n = 33). CIDEB promoter methylation level in abdominal SAT and OAT was detected by the MethylTarget technology, then its relationship with overweight or obesity was analyzed. Results: (1) There were no statistical differences between the normal-weight group and overweight/obesity group in Methylation levels of 16 CpG sites in the CIDEB gene promoter sequence. (2) The methylation level of OAT was higher than that of SAT, and there were significant differences in 16 CpG sites. (3) There were 3 statistically significant haplotypes between the normal-weight group and overweight/obesity group (2 in SAT and 1 in OAT). Conclusions: The methylation level of CIDEB gene promoter in abdominal SAT and OAT may be related to overweight or obesity in adults, and the specific regulatory mechanism needs to be further studied.
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Affiliation(s)
- Zhiguang Ping
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhaoyan Guo
- College of Public Health, Zhengzhou University, Zhengzhou, Henan, China
| | - Ming Lu
- Nursing Department of Jiaozuo People's Hospital, Jiaozuo, Henan, China
| | - Yanzi Chen
- Henan Huapu Pharmaceutical Technology Co., Ltd., Zhengzhou, Henan, China
| | - Li Liu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Black Tea Reduces Diet-Induced Obesity in Mice via Modulation of Gut Microbiota and Gene Expression in Host Tissues. Nutrients 2022; 14:nu14081635. [PMID: 35458198 PMCID: PMC9027533 DOI: 10.3390/nu14081635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/06/2022] [Accepted: 04/08/2022] [Indexed: 12/17/2022] Open
Abstract
Black tea was reported to alter the microbiome populations and metabolites in diet-induced obese mice and displays properties that prevent obesity, but the underlying mechanism of the preventative effect of black tea on high-fat diet (HFD) induced obesity has not been elucidated. Epigenetic studies are a useful tool for determining the relationship between obesity and environment. Here, we show that the water extract of black tea (Lapsang souchong, LS) reverses HFD-induced gut dysbiosis, alters the tissue gene expression, changes the level of a major epigenetic modification (DNA methylation), and prevents obesity in HFD feeding mice. The anti-obesity properties of black tea are due to alkaloids, which are the principal active components. Our data indicate that the anti-obesity benefits of black tea are transmitted via fecal transplantation, and the change of tissue gene expression and the preventative effects on HFD-induced obesity in mice of black tea are dependent on the gut microbiota. We further show that black tea could regulate the DNA methylation of imprinted genes in the spermatozoa of high-fat diet mice. Our results show a mechanistic link between black tea, changes in the gut microbiota, epigenetic processes, and tissue gene expression in the modulation of diet-induced metabolic dysfunction.
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Lorenzo PM, Izquierdo AG, Rodriguez-Carnero G, Fernández-Pombo A, Iglesias A, Carreira MC, Tejera C, Bellido D, Martinez-Olmos MA, Leis R, Casanueva FF, Crujeiras AB. Epigenetic Effects of Healthy Foods and Lifestyle Habits from the Southern European Atlantic Diet Pattern: A Narrative Review. Adv Nutr 2022; 13:1725-1747. [PMID: 35421213 PMCID: PMC9526853 DOI: 10.1093/advances/nmac038] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/21/2022] [Indexed: 01/28/2023] Open
Abstract
Recent scientific evidence has shown the importance of diet and lifestyle habits for the proper functioning of the human body. A balanced and healthy diet, physical activity, and psychological well-being have a direct beneficial effect on health and can have a crucial role in the development and prognosis of certain diseases. The Southern European Atlantic diet, also named the Atlantic diet, is a unique dietary pattern that occurs in regions that present higher life expectancy, suggesting that this specific dietary pattern is associated with positive health effects. In fact, it is enriched with nutrients of high biological value, which, together with its cooking methods, physical activity promotion, reduction in carbon footprint, and promoting of family meals, promote these positive effects on health. The latest scientific advances in the field of nutri-epigenetics have revealed that epigenetic markers associated with food or nutrients and environmental factors modulate gene expression and, therefore, are involved with both health and disease. Thus, in this review, we evaluated the main aspects that define the Southern European Atlantic diet and the potential epigenetic changes associated with them based on recent studies regarding the main components of these dietary patterns. In conclusion, based on the information existing in the literature, we postulate that the Southern European Atlantic diet could promote healthy aging by means of epigenetic mechanisms. This review highlights the necessity of performing longitudinal studies to demonstrate this proposal.
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Affiliation(s)
- Paula M Lorenzo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Andrea G Izquierdo
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Gemma Rodriguez-Carnero
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,Endocrinology and Nutrition Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Antía Fernández-Pombo
- Endocrinology and Nutrition Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Alba Iglesias
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Marcos C Carreira
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Molecular and Cellular Endocrinology Group. Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain
| | - Cristina Tejera
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,Endocrinology and Nutrition Unit, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS), Ferrol, Spain
| | - Diego Bellido
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,Endocrinology and Nutrition Unit, Complejo Hospitalario Universitario de Ferrol (CHUF/SERGAS), Ferrol, Spain
| | - Miguel A Martinez-Olmos
- Epigenomics in Endocrinology and Nutrition Group, Epigenomics Unit, Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain,CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Endocrinology and Nutrition Division, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Rosaura Leis
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Department of Pediatrics, Complejo Hospitalario Universitario de Santiago de Compostela (CHUS); Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain,Fundacion Dieta Atlántica, Santiago de Compostela, Spain
| | - Felipe F Casanueva
- CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain,Molecular and Cellular Endocrinology Group. Instituto de Investigacion Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago de Compostela (CHUS) and Santiago de Compostela University (USC), Santiago de Compostela, Spain,Fundacion Dieta Atlántica, Santiago de Compostela, Spain
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Noble AJ, Purcell RV, Adams AT, Lam YK, Ring PM, Anderson JR, Osborne AJ. A Final Frontier in Environment-Genome Interactions? Integrated, Multi-Omic Approaches to Predictions of Non-Communicable Disease Risk. Front Genet 2022; 13:831866. [PMID: 35211161 PMCID: PMC8861380 DOI: 10.3389/fgene.2022.831866] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/19/2022] [Indexed: 12/26/2022] Open
Abstract
Epidemiological and associative research from humans and animals identifies correlations between the environment and health impacts. The environment-health inter-relationship is effected through an individual's underlying genetic variation and mediated by mechanisms that include the changes to gene regulation that are associated with the diversity of phenotypes we exhibit. However, the causal relationships have yet to be established, in part because the associations are reduced to individual interactions and the combinatorial effects are rarely studied. This problem is exacerbated by the fact that our genomes are highly dynamic; they integrate information across multiple levels (from linear sequence, to structural organisation, to temporal variation) each of which is open to and responds to environmental influence. To unravel the complexities of the genomic basis of human disease, and in particular non-communicable diseases that are also influenced by the environment (e.g., obesity, type II diabetes, cancer, multiple sclerosis, some neurodegenerative diseases, inflammatory bowel disease, rheumatoid arthritis) it is imperative that we fully integrate multiple layers of genomic data. Here we review current progress in integrated genomic data analysis, and discuss cases where data integration would lead to significant advances in our ability to predict how the environment may impact on our health. We also outline limitations which should form the basis of future research questions. In so doing, this review will lay the foundations for future research into the impact of the environment on our health.
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Affiliation(s)
- Alexandra J. Noble
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Rachel V. Purcell
- Department of Surgery, University of Otago Christchurch, Christchurch, New Zealand
| | - Alex T. Adams
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Ying K. Lam
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, University of Oxford, Oxford, United Kingdom
| | - Paulina M. Ring
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Jessica R. Anderson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Amy J. Osborne
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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Lee YC, Christensen JJ, Parnell LD, Smith CE, Shao J, McKeown NM, Ordovás JM, Lai CQ. Using Machine Learning to Predict Obesity Based on Genome-Wide and Epigenome-Wide Gene-Gene and Gene-Diet Interactions. Front Genet 2022; 12:783845. [PMID: 35047011 PMCID: PMC8763388 DOI: 10.3389/fgene.2021.783845] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022] Open
Abstract
Obesity is associated with many chronic diseases that impair healthy aging and is governed by genetic, epigenetic, and environmental factors and their complex interactions. This study aimed to develop a model that predicts an individual's risk of obesity by better characterizing these complex relations and interactions focusing on dietary factors. For this purpose, we conducted a combined genome-wide and epigenome-wide scan for body mass index (BMI) and up to three-way interactions among 402,793 single nucleotide polymorphisms (SNPs), 415,202 DNA methylation sites (DMSs), and 397 dietary and lifestyle factors using the generalized multifactor dimensionality reduction (GMDR) method. The training set consisted of 1,573 participants in exam 8 of the Framingham Offspring Study (FOS) cohort. After identifying genetic, epigenetic, and dietary factors that passed statistical significance, we applied machine learning (ML) algorithms to predict participants' obesity status in the test set, taken as a subset of independent samples (n = 394) from the same cohort. The quality and accuracy of prediction models were evaluated using the area under the receiver operating characteristic curve (ROC-AUC). GMDR identified 213 SNPs, 530 DMSs, and 49 dietary and lifestyle factors as significant predictors of obesity. Comparing several ML algorithms, we found that the stochastic gradient boosting model provided the best prediction accuracy for obesity with an overall accuracy of 70%, with ROC-AUC of 0.72 in test set samples. Top predictors of the best-fit model were 21 SNPs, 230 DMSs in genes such as CPT1A, ABCG1, SLC7A11, RNF145, and SREBF1, and 26 dietary factors, including processed meat, diet soda, French fries, high-fat dairy, artificial sweeteners, alcohol intake, and specific nutrients and food components, such as calcium and flavonols. In conclusion, we developed an integrated approach with ML to predict obesity using omics and dietary data. This extends our knowledge of the drivers of obesity, which can inform precision nutrition strategies for the prevention and treatment of obesity. Clinical Trial Registration: [www.ClinicalTrials.gov], the Framingham Heart Study (FHS), [NCT00005121].
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Affiliation(s)
- Yu-Chi Lee
- USDA ARS, Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| | - Jacob J. Christensen
- Department of Nutrition, Norwegian National Advisory Unit on FH, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Laurence D. Parnell
- USDA ARS, Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| | - Caren E. Smith
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
| | - Jonathan Shao
- Statistical and Bioinformatics Group, Northeast Area, USDA ARS, Beltsville, MD, United States
| | - Nicola M. McKeown
- Nutritional Epidemiology Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - José M. Ordovás
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
- CEI UAM + CSIC, IMDEA Food Institute, Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Chao-Qiang Lai
- USDA ARS, Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, United States
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Panera N, Mandato C, Crudele A, Bertrando S, Vajro P, Alisi A. Genetics, epigenetics and transgenerational transmission of obesity in children. Front Endocrinol (Lausanne) 2022; 13:1006008. [PMID: 36452324 PMCID: PMC9704419 DOI: 10.3389/fendo.2022.1006008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Sedentary lifestyle and consumption of high-calorie foods have caused a relentless increase of overweight and obesity prevalence at all ages. Its presently epidemic proportion is disquieting due to the tight relationship of obesity with metabolic syndrome and several other comorbidities which do call for urgent workarounds. The usual ineffectiveness of present therapies and failure of prevention campaigns triggered overtime a number of research studies which have unveiled some relevant aspects of obesity genetic and epigenetic inheritable profiles. These findings are revealing extremely precious mainly to serve as a likely extra arrow to allow the clinician's bow to achieve still hitherto unmet preventive goals. Evidence now exists that maternal obesity/overnutrition during pregnancy and lactation convincingly appears associated with several disorders in the offspring independently of the transmission of a purely genetic predisposition. Even the pre-conception direct exposure of either father or mother gametes to environmental factors can reprogram the epigenetic architecture of cells. Such phenomena lie behind the transfer of the obesity susceptibility to future generations through a mechanism of epigenetic inheritance. Moreover, a growing number of studies suggests that several environmental factors such as maternal malnutrition, hypoxia, and exposure to excess hormones and endocrine disruptors during pregnancy and the early postnatal period may play critical roles in programming childhood adipose tissue and obesity. A deeper understanding of how inherited genetics and epigenetics may generate an obesogenic environment at pediatric age might strengthen our knowledge about pathogenetic mechanisms and improve the clinical management of patients. Therefore, in this narrative review, we attempt to provide a general overview of the contribution of heritable genetic and epigenetic patterns to the obesity susceptibility in children, placing a particular emphasis on the mother-child dyad.
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Affiliation(s)
- Nadia Panera
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Claudia Mandato
- Pediatrics Section, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salermo, Italy
- *Correspondence: Anna Alisi, ; Claudia Mandato,
| | - Annalisa Crudele
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Sara Bertrando
- Pediatrics Clinic, San Giovanni di Dio e Ruggi d’Aragona University Hospital, Salerno, Italy
| | - Pietro Vajro
- Pediatrics Section, Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, Baronissi, Salermo, Italy
| | - Anna Alisi
- Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- *Correspondence: Anna Alisi, ; Claudia Mandato,
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Li J, Zhu J, Zhang Q, Chen L, Ma S, Lu Y, Shen B, Zhang R, Zhang M, He Y, Wu L, Peng H. NPPA Promoter Hypomethylation Predicts Central Obesity Development: A Prospective Longitudinal Study in Chinese Adults. Obes Facts 2022; 15:257-270. [PMID: 34875662 PMCID: PMC9021652 DOI: 10.1159/000521295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 11/26/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Atrial natriuretic peptide plays a potential role in obesity with unclear molecular mechanisms. The objective of this study was to examine the association between its coding gene (natriuretic peptide A [NPPA]) methylation and obesity. METHODS Peripheral blood DNA methylation of NPPA promoter was quantified at baseline by targeted bisulfite sequencing for 2,497 community members (mean aged 53 years, 38% men) in the Gusu cohort. Obesity was repeatedly assessed by body mass index (BMI) and waist circumference (WC) at baseline and follow-up examinations. The cross-sectional, longitudinal, and prospective associations between NPPA promoter methylation and obesity were examined. RESULTS Of the 9 CpG loci assayed, DNA methylation levels at 6 CpGs were significantly lower in participants with central obesity than those without (all p < 0.05 for permutation test). These CpG methylation levels at baseline were also inversely associated with dynamic changes in BMI or WC during follow-up (all p < 0.05 for permutation test). After an average 4 years of follow-up, hypermethylation at the 6 CpGs (CpG2 located at Chr1:11908348, CpG3 located at Chr1:11908299, CpG4 located at Chr1:11908200, CpG5 located at Chr1:11908182, CpG6 located at Chr1:11908178, and CpG8 located at Chr1:11908165) was significantly associated with a lower risk of incident central obesity (all p < 0.05 for permutation test). CONCLUSIONS Hypomethylation at NPPA promoter was associated with increased future risk of central obesity in Chinese adults. Aberrant DNA methylation of the NPPA gene may participate in the mechanisms of central obesity.
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Affiliation(s)
- Jing Li
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Jinhua Zhu
- Department of Chronic Disease Management, Center for Disease Prevention and Control of Wujiang District, Suzhou, China
| | - Qiu Zhang
- Department of Chronic Disease Management, Center for Disease Prevention and Control of Gusu District, Suzhou, China
| | - Linan Chen
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Shengqi Ma
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Ying Lu
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Bin Shen
- Department of Chronic Disease Management, Center for Disease Prevention and Control of Wujiang District, Suzhou, China
| | - Rongyan Zhang
- Department of Chronic Disease Management, Center for Disease Prevention and Control of Wujiang District, Suzhou, China
| | - Mingzhi Zhang
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Yan He
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou, China
| | - Lei Wu
- Department of Maternal and Child Health, Suzhou Industrial Park Center for Disease Control and Prevention, Suzhou, China
- *Lei Wu,
| | - Hao Peng
- Department of Epidemiology, School of Public Health, Medical College of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou, China
- ** Hao Peng,
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Bhat B, Jones GT. Data Analysis of DNA Methylation Epigenome-Wide Association Studies (EWAS): A Guide to the Principles of Best Practice. Methods Mol Biol 2022; 2458:23-45. [PMID: 35103960 DOI: 10.1007/978-1-0716-2140-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Array-based EWAS have become an increasingly popular technique to identify population epigenetic effects, particularly in humans. With the arrival of nonhuman species arrays, such as the mouse, this is likely to become an even more widely used technology. This chapter provides the less experienced researcher a guide to the analysis of data from the most widely used platform, the Illumina Infinium Methylation assay. This includes an overview of quality filtering, data normalization, analysis options, and techniques to improve the interpretation of results.
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Affiliation(s)
- Basharat Bhat
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gregory T Jones
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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Do WL, Nguyen S, Yao J, Guo X, Whitsel EA, Demerath E, Rotter JI, Rich SS, Lange L, Ding J, Van Den Berg D, Liu Y, Justice AE, Guan W, Horvath S, Assimes TL, Bhatti P, Jordahl K, Shadyab A, Valencia CI, Stein AD, Smith A, Staimez LR, Conneely K, Narayan KMV. Associations between DNA methylation and BMI vary by metabolic health status: a potential link to disparate cardiovascular outcomes. Clin Epigenetics 2021; 13:230. [PMID: 34937574 PMCID: PMC8697469 DOI: 10.1186/s13148-021-01194-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/01/2021] [Indexed: 11/26/2022] Open
Abstract
Background Body mass index (BMI), a well-known risk factor for poor cardiovascular outcomes, is associated with differential DNA methylation (DNAm). Similarly, metabolic health has also been associated with changes in DNAm. It is unclear how overall metabolic health outside of BMI may modify the relationship between BMI and methylation profiles, and what consequences this may have on downstream cardiovascular disease. The purpose of this study was to identify cytosine-phosphate-guanine (CpG) sites at which the association between BMI and DNAm could be modified by overall metabolic health. Results The discovery study population was derived from three Women’s Health Initiative (WHI) ancillary studies (n = 3977) and two Atherosclerosis Risk in Communities (ARIC) ancillary studies (n = 3520). Findings were validated in the Multi-Ethnic Study of Atherosclerosis (MESA) cohort (n = 1200). Generalized linear models regressed methylation β values on the interaction between BMI and metabolic health Z score (BMI × MHZ) adjusted for BMI, MHZ, cell composition, chip number and location, study characteristics, top three ancestry principal components, smoking, age, ethnicity (WHI), and sex (ARIC). Among the 429,566 sites examined, differential associations between BMI × MHZ and DNAm were identified at 22 CpG sites (FDR q < 0.05), with one site replicated in MESA (cg18989722, in the TRAPPC9 gene). Three of the 22 sites were associated with incident coronary heart disease (CHD) in WHI. For each 0.01 unit increase in DNAm β value, the risk of incident CHD increased by 9% in one site and decreased by 6–10% in two sites over 25 years. Conclusions Differential associations between DNAm and BMI by MHZ were identified at 22 sites, one of which was validated (cg18989722) and three of which were predictive of incident CHD. These sites are located in several genes related to NF-kappa-B signaling, suggesting a potential role for inflammation between DNA methylation and BMI-associated metabolic health. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01194-3.
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Affiliation(s)
- Whitney L Do
- Nutrition and Health Sciences Program, Laney Graduate School, Emory University, 1518 Clifton Rd, Atlanta, GA, 30322, USA.
| | - Steve Nguyen
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, CA, USA
| | - Jie Yao
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Eric A Whitsel
- Departments of Epidemiology and Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Ellen Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Jerome I Rotter
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Leslie Lange
- Division of Biomedical Informatics & Personalized Medicine, School of Medicine, Colorado University Anschutz Medical Campus, Aurora, CO, USA
| | - Jingzhong Ding
- Gerontology and Geriatric Medicine, School of Medicine, Wake Forest, Winston-Salem, NC, USA
| | - David Van Den Berg
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA, USA
| | - Yongmei Liu
- Duke Molecular Physiology Institute, Duke University, Durham, NC, USA
| | - Anne E Justice
- Center for Biomedical and Translational Informatics, Geisinger, Wilkes-Barre, PA, USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
| | - Steve Horvath
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Parveen Bhatti
- Cancer Control Research, BC Cancer, Vancouver, BC, Canada
| | - Kristina Jordahl
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Aladdin Shadyab
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, CA, USA
| | - Celina I Valencia
- College of Medicine, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Aryeh D Stein
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Alicia Smith
- Department of Gynecology and Obstetrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Lisa R Staimez
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karen Conneely
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - K M Venkat Narayan
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Abstract
The intestinal tract is the entry gate for nutrients and symbiotic organisms, being in constant contact with external environment. DNA methylation is one of the keys to how environmental conditions, diet and nutritional status included, shape functionality in the gut and systemically. This review aims to summarise findings on the importance of methylation to gut development, differentiation and function. Evidence to date on how external factors such as diet, dietary supplements, nutritional status and microbiota modifications modulate intestinal function through DNA methylation is also presented.
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Do WL, Gohar J, McCullough LE, Galaviz KI, Conneely KN, Narayan KMV. Examining the association between adiposity and DNA methylation: A systematic review and meta-analysis. Obes Rev 2021; 22:e13319. [PMID: 34278703 DOI: 10.1111/obr.13319] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/26/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022]
Abstract
Obesity is associated with widespread differential DNA methylation (DNAm) patterns, though there have been limited overlap in the obesity-associated cytosine-guanine nucleotide pair (CpG) sites that have been identified in the literature. We systematically searched four databases for studies published until January 2020. Eligible studies included cross-sectional, longitudinal, or intervention studies examining adiposity and genome-wide DNAm in non-pregnant adults aged 18-75 in all tissue types. Study design and results were extracted in the descriptive review. Blood-based DNAm results in body mass index (BMI) and waist circumference (WC) were meta-analyzed using weighted sum of Z-score meta-analysis. Of the 10,548 studies identified, 46 studies were included in the systematic review with 18 and nine studies included in the meta-analysis of BMI and WC, respectively. In the blood, 77 and four CpG sites were significant in three or more studies of BMI and WC, respectively. Using a genome-wide threshold for significance, 52 blood-based CpG sites were significantly associated with BMI. These sites have previously been associated with many obesity-related diseases including type 2 diabetes, cardiovascular disease, Crohn's disease, and depression. Our study shows that DNAm at 52 CpG sites represent potential mediators of obesity-associated chronic diseases and may be novel intervention or therapeutic targets to protect against obesity-associated chronic diseases.
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Affiliation(s)
- Whitney L Do
- Nutrition and Health Sciences Program, Laney Graduate School, Emory University, Atlanta, Georgia, USA
| | - Jazib Gohar
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Lauren E McCullough
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
| | - Karla I Galaviz
- Department of Applied Health Science, School of Public Health, Indiana University Bloomington, Bloomington, Indiana, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - K M Venkat Narayan
- Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA
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Redox Imbalance and Methylation Disturbances in Early Childhood Obesity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:2207125. [PMID: 34457110 PMCID: PMC8387800 DOI: 10.1155/2021/2207125] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/13/2021] [Accepted: 08/02/2021] [Indexed: 11/29/2022]
Abstract
Obesity is increasing worldwide in prepubertal children, reducing the age of onset of associated comorbidities, including type 2 diabetes. Sulfur-containing amino acids, methionine, cysteine, and their derivatives play important roles in the transmethylation and transsulfuration pathways. Dysregulation of these pathways leads to alterations in the cellular methylation patterns and an imbalanced redox state. Therefore, we tested the hypothesis that one-carbon metabolism is already dysregulated in prepubertal children with obesity. Peripheral blood was collected from 64 children, and the plasma metabolites from transmethylation and transsulfuration pathways were quantified by HPLC. The cohort was stratified by BMI z-scores and HOMA-IR indices into healthy lean (HL), healthy obese (HO), and unhealthy obese (UHO). Fasting insulin levels were higher in the HO group compared to the HL, while the UHO had the highest. All groups presented normal fasting glycemia. Furthermore, high-density lipoprotein (HDL) was lower while triglycerides and lactate levels were higher in the UHO compared to HO subjects. S-adenosylhomocysteine (SAH) and total homocysteine levels were increased in the HO group compared to HL. Additionally, glutathione metabolism was also altered. Free cystine and oxidized glutathione (GSSG) were increased in the HO as compared to HL subjects. Importantly, the adipocyte secretory function was already compromised at this young age. Elevated circulating leptin and decreased adiponectin levels were observed in the UHO as compared to the HO subjects. Some of these alterations were concomitant with alterations in the DNA methylation patterns in the obese group, independent of the impaired insulin levels. In conclusion, our study informs on novel and important metabolic alterations in the transmethylation and the transsulfuration pathways in the early stages of obesity. Moreover, the altered secretory function of the adipocyte very early in life may be relevant in identifying early metabolic markers of disease that may inform on the increased risk for specific future comorbidities in this population.
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Adipose Tissue Hypoxia Correlates with Adipokine Hypomethylation and Vascular Dysfunction. Biomedicines 2021; 9:biomedicines9081034. [PMID: 34440238 PMCID: PMC8394952 DOI: 10.3390/biomedicines9081034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 01/10/2023] Open
Abstract
Obesity is characterized by the accumulation of dysfunctional adipose tissues, which predisposes to cardiometabolic diseases. Our previous in vitro studies demonstrated a role of hypoxia in inducing adipokine hypomethylation in adipocytes. We sought to examine this mechanism in visceral adipose tissues (VATs) from obese individuals and its correlation with cardiometabolic risk factors. We propose an involvement of the hypoxia-inducible factor, HIF1α, and the DNA hydroxymethylase, TET1. Blood samples and VAT biopsies were obtained from obese and non-obese subjects (n = 60 each) having bariatric and elective surgeries, respectively. The analyses of VAT showed lower vascularity, and higher levels of HIF1α and TET1 proteins in the obese subjects than controls. Global hypomethylation and hydroxymethylation were observed in VAT from obese subjects along with promoter hypomethylation of several pro-inflammatory adipokines. TET1 protein was enriched near the promotor of the hypomethylated adipokines. The average levels of adipokine methylation correlated positively with vascularity and arteriolar vasoreactivity and negatively with protein levels of HIF1α and TET1 in corresponding VAT samples, serum and tissue inflammatory markers, and other cardiometabolic risk factors. These findings suggest a role for adipose tissue hypoxia in causing epigenetic alterations, which could explain the increased production of adipocytokines and ultimately, vascular dysfunction in obesity.
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Awada Z, Bouaoun L, Nasr R, Tfayli A, Cuenin C, Akika R, Boustany RM, Makoukji J, Tamim H, Zgheib NK, Ghantous A. LINE-1 methylation mediates the inverse association between body mass index and breast cancer risk: A pilot study in the Lebanese population. ENVIRONMENTAL RESEARCH 2021; 197:111094. [PMID: 33839117 DOI: 10.1016/j.envres.2021.111094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/28/2021] [Accepted: 03/24/2021] [Indexed: 06/12/2023]
Abstract
INTRODUCTION Lebanon is among the top countries worldwide in combined incidence and mortality of breast cancer, which raises concern about risk factors peculiar to this country. The underlying molecular mechanisms of breast cancer require elucidation, particularly epigenetics, which is recognized as a molecular sensor to environmental exposures. PURPOSE We aim to explore whether DNA methylation levels of AHRR (marker of cigarette smoking), SLC1A5 and TXLNA (markers of alcohol consumption), and LINE-1 (a genome-wide repetitive retrotransposon) can act as molecular mediators underlying putative associations between breast cancer risk and pertinent extrinsic (tobacco smoking and alcohol consumption) and intrinsic factors [age and body mass index (BMI)]. METHODS This is a cross-sectional pilot study which includes breast cancer cases (N = 65) and controls (N = 54). DNA methylation levels were measured using bisulfite pyrosequencing on available peripheral blood samples (N = 119), and Multivariate Imputation by Chained Equations (MICE) was used to impute missing DNA methylation values in remaining samples. Multiple mediation analysis was performed to assess direct and indirect (via DNA methylation) effects of intrinsic and extrinsic factors on breast cancer risk. RESULTS In relation to exposure, AHRR hypo-methylation was associated with cigarette but not waterpipe smoking, suggesting potentially different biomarkers of these two forms of tobacco use; SLC1A5 and TXLNA methylation were not associated with alcohol consumption; LINE-1 methylation was inversely associated with BMI (β-value [95% confidence interval (CI)] = -0.04 [-0.07, -0.02]), which remained significant after adjustment for age, smoking and alcohol consumption. In relation to breast cancer, there was no detectable association between AHRR, SLC1A5 or TXLNA methylation and cancer risk, but LINE-1 methylation was significantly higher in breast cancer cases when compared to controls (mean ± SD: 72.00 ± 0.66 versus 70.89 ± 0.73, P = 4.67 × 10-14). This difference remained significant after adjustment for confounders (odds ratio (OR) [95% CI] = 9.75[3.74, 25.39]). Moreover, LINE-1 hypo-methylation mediated 83% of the inverse effect of BMI on breast cancer risk. CONCLUSION This pilot study demonstrates that alterations in blood LINE-1 methylation mediate the inverse effect of BMI on breast cancer risk. This warrants large scale studies and stratification based on clinic-pathological types of breast cancer.
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Affiliation(s)
- Zainab Awada
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon; International Agency for Research on Cancer, Lyon, France
| | | | - Rihab Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Arafat Tfayli
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Cyrille Cuenin
- International Agency for Research on Cancer, Lyon, France
| | - Reem Akika
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Rose-Mary Boustany
- Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine, Beirut, Lebanon; Department of Neurology, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Joelle Makoukji
- Department of Biochemistry and Molecular Genetics, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Hani Tamim
- Department of Internal Medicine and Clinical Research Institute, American University of Beirut Faculty of Medicine, Beirut, Lebanon
| | - Nathalie K Zgheib
- Department of Pharmacology and Toxicology, American University of Beirut Faculty of Medicine, Beirut, Lebanon.
| | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France.
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Chen N, Miao L, Lin W, Zou D, Huang L, Huang J, Shi W, Li L, Luo Y, Liang H, Pan S, Peng J. Integrated DNA Methylation and Gene Expression Analysis Identified S100A8 and S100A9 in the Pathogenesis of Obesity. Front Cardiovasc Med 2021; 8:631650. [PMID: 34055926 PMCID: PMC8163519 DOI: 10.3389/fcvm.2021.631650] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/30/2021] [Indexed: 12/19/2022] Open
Abstract
Background: To explore the association of DNA methylation and gene expression in the pathology of obesity. Methods: (1) Genomic DNA methylation and mRNA expression profile of visceral adipose tissue (VAT) were performed in a comprehensive database of gene expression in obese and normal subjects. (2) Functional enrichment analysis and construction of differential methylation gene regulatory networks were performed. (3) Validation of the two different methylation sites and corresponding gene expression was done in a separate microarray dataset. (4) Correlation analysis was performed on DNA methylation and mRNA expression data. Results: A total of 77 differentially expressed mRNAs matched with differentially methylated genes. Analysis revealed two different methylation sites corresponding to two unique genes—s100a8-cg09174555 and s100a9-cg03165378. Through the verification test of two interesting different expression positions [differentially methylated positions (DMPs)] and their corresponding gene expression, we found that methylation in these genes was negatively correlated to gene expression in the obesity group. Higher S100A8 and S100A9 expressions in obese subjects were validated in a separate microarray dataset. Conclusion: This study confirmed the relationship between DNA methylation and gene expression and emphasized the important role of S100A8 and S100A9 in the pathogenesis of obesity.
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Affiliation(s)
- Ningyuan Chen
- Department of Pathophysiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Liu Miao
- Department of Cardiology, Liuzhou People's Hospital, Guangxi Medical University, Liuzhou, China
| | - Wei Lin
- Department of Neurological Rehabilitation, Guangxi Jiangbin Hospital, Nanning, China
| | - Donghua Zou
- Department of Neurology, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ling Huang
- Department of Pathophysiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Jia Huang
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Wanxin Shi
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Lilin Li
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Yuxing Luo
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Hao Liang
- The First Clinical Medical School, Guangxi Medical University, Nanning, China
| | - Shangling Pan
- Department of Pathophysiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, China
| | - Junhua Peng
- Department of Pathophysiology, School of Preclinical Medicine, Guangxi Medical University, Nanning, China
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Cao VT, Lea RA, Sutherland HG, Benton MC, Pishva RS, Haupt LM, Griffiths LR. A genome-wide methylation study of body fat traits in the Norfolk Island isolate. Nutr Metab Cardiovasc Dis 2021; 31:1556-1563. [PMID: 33810959 DOI: 10.1016/j.numecd.2021.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND AND AIMS Natural variation in body fat is explained by both genetic and environmental effects. Epigenetic mechanisms such as DNA methylation can mediate these effects causing changes in gene expression leading to onset of obesity. Studies of genetic isolates have the potential to provide new epigenetic insights with advantages such as reduced genetic diversity and environmental exposures. METHODS AND RESULTS This was an exploratory study of genome-wide DNA methylation in relation to body fat traits in 47 healthy adults from the genetic isolate of Norfolk Island. Quantitative body fat traits (body fat percentage, body mass index, hip circumference, waist circumference, waist-hip-ratio and weight) were carefully measured. DNA methylation data was obtained from peripheral blood using Illumina 450K arrays. Multi-trait analysis was performed using Principal Component Analysis (PCA). CpG by trait association testing was performed using stepwise linear regressions. Two components were identified that explained approximately 89% of the phenotypic variance. In total, 5 differential methylated positions (DMPs) were identified at genome-wide significance (P≤ 2.4 × 10-7), which mapped to GOT2-CDH8, LYSMD3, HIBADH, ADGRD1 and EBF4 genes. Gene set enrichment analysis of 848 genes containing suggestive DMPs (P≤ 1.0 × 10-4) implicated the Cadherin (28 genes, Padj = 6.76 × 10-7) and Wnt signaling pathways (38 genes, Padj = 7.78 × 10-6). CONCLUSION This study provides new insights into the epigenetically influenced genes and pathways underlying body fat variation in a healthy cohort and provides targets for consideration in future studies of obesity risk.
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Affiliation(s)
- Van T Cao
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Rodney A Lea
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Heidi G Sutherland
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Miles C Benton
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia; Human Genomics, Institute of Environmental Science and Research, Kenepuru, Wellington, New Zealand.
| | - Reza S Pishva
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Institute of Health and Biomedical Innovation, 60 Musk Ave., Kelvin Grove, Queensland 4059, Australia.
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Li G, Meng H, Bai Y, Wei W, Feng Y, Li M, Li H, He M, Zhang X, Wei S, Li Y, Guo H. DNA methylome analysis identifies BMI-related epigenetic changes associated with non-small cell lung cancer susceptibility. Cancer Med 2021; 10:3770-3781. [PMID: 33939316 PMCID: PMC8178488 DOI: 10.1002/cam4.3906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Background Body mass index (BMI) has been reported to be inversely associated with incident risk of non‐small cell lung cancer (NSCLC). However, the underlying mechanism is still unclear. This study aimed to investigate the role of DNA methylation in the relationship between BMI and NSCLC. Methods We carried out a genome‐wide DNA methylation study of BMI in peripheral blood among 2266 Chinese participants by using Illumina Methylation arrays. For the BMI‐related DNA methylation changes, their associations with NSCLC risk were further analyzed and their mediation effects on BMI‐NSCLC association were also evaluated. Results The methylation levels of four CpGs (cg12593793, cg17061862, cg11024682, and cg06500161, annotated to LMNA, ZNF143, SREBF1, and ABCG1, respectively) were found to be significantly associated with BMI. Methylation levels of cg12593793, cg11024682, and cg06500161 were observed to be inversely associated with NSCLC risk [OR (95%CI) =0.22 (0.16, 0.31), 0.39 (0.30, 0.50), and 0.66 (0.53, 0.82), respectively]. Additionally, cg11024682 in SREBF1 and cg06500161 in ABCG1 mediated 45.3% and 19.5% of the association between BMI and decreased NSCLC risk, respectively. Conclusions In this study, we identified four DNA methylation sites associated with BMI in the Chinese populations at the genome‐wide significant level. We also found that the BMI‐related methylations of SREBF1 and ABCG1 could mediate about a quintile‐to‐half of the effect of BMI on reduced NSCLC risk, which adds a potential mechanism underlying this association.
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Affiliation(s)
- Guyanan Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hua Meng
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yansen Bai
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wei Wei
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yue Feng
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mengying Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hang Li
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Meian He
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sheng Wei
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yangkai Li
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Huan Guo
- Department of Occupational and Environmental Health, Key Laboratory of Environment & Health, Ministry of Education; State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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