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Maugeri A. The Effects of Dietary Interventions on DNA Methylation: Implications for Obesity Management. Int J Mol Sci 2020; 21:ijms21228670. [PMID: 33212948 PMCID: PMC7698434 DOI: 10.3390/ijms21228670] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/28/2020] [Accepted: 11/16/2020] [Indexed: 12/13/2022] Open
Abstract
Previous evidence from in vivo and observational research suggested how dietary factors might affect DNA methylation signatures involved in obesity risk. However, findings from experimental studies are still scarce and, if present, not so clear. The current review summarizes studies investigating the effect of dietary interventions on DNA methylation in the general population and especially in people at risk for or with obesity. Overall, these studies suggest how dietary interventions may induce DNA methylation changes, which in turn are likely related to the risk of obesity and to different response to weight loss programs. These findings might explain the high interindividual variation in weight loss after a dietary intervention, with some people losing a lot of weight while others much less so. However, the interactions between genetic, epigenetic, environmental and lifestyle factors make the whole framework even more complex and further studies are needed to support the hypothesis of personalized interventions against obesity.
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Affiliation(s)
- Andrea Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, 95123 Catania, Italy
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Shade DC, Park HJ, Hausman DB, Hohos N, Meagher RB, Kauwell GPA, Kilaru V, Lewis RD, Smith AK, Bailey LB. DNA Methylation Changes in Whole Blood and CD16+ Neutrophils in Response to Chronic Folic Acid Supplementation in Women of Childbearing Age. INT J VITAM NUTR RES 2018; 87:271-278. [PMID: 30499755 DOI: 10.1024/0300-9831/a000491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Folate, a water-soluble vitamin, is a key source of one-carbon groups for DNA methylation, but studies of the DNA methylation response to supplemental folic acid yield inconsistent results. These studies are commonly conducted using whole blood, which contains a mixed population of white blood cells that have been shown to confound results. The objective of this study was to determine if CD16+ neutrophils may provide more specific data than whole blood for identifying DNA methylation response to chronic folic acid supplementation. The study was performed in normal weight (BMI 18.5 - 24.9 kg/m2) women (18 - 35 y; n = 12), with blood samples taken before and after 8 weeks of folic acid supplementation at 800 μg/day. DNA methylation patterns from whole blood and isolated CD16+ neutrophils were measured across >485,000 CpG sites throughout the genome using the Infinium HumanMethylation450 BeadChip. Over the course of the 8-week supplementation, 6746 and 7513 CpG sites changed (p < 0.05) in whole blood and CD16+ neutrophils, respectively. DNA methylation decreased in 68.4% (whole blood) and 71.8% (CD16+ neutrophils) of these sites. There were only 182 CpG sites that changed in both the whole blood and CD16+ neutrophils, 139 of which changed in the same direction. These results suggest that the genome-wide DNA methylation response to chronic folic acid supplementation is different between whole blood and CD16+ neutrophils and that a single white blood cell type may function as a more specific epigenetic reporter of folate status than whole blood.
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Affiliation(s)
- Deanna C Shade
- a Co-first authors; these authors contributed equally.,1 Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Hea Jin Park
- a Co-first authors; these authors contributed equally.,1 Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Dorothy B Hausman
- 1 Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Natalie Hohos
- 1 Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | | | - Gail P A Kauwell
- 3 Food Science and Human Nutrition Department, University of Florida, Gainesville, FL, USA
| | - Varun Kilaru
- 4 Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Richard D Lewis
- 1 Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Alicia K Smith
- 4 Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Lynn B Bailey
- 1 Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
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Chan MA, Ciaccio CE, Gigliotti NM, Rezaiekhaligh M, Siedlik JA, Kennedy K, Barnes CS. DNA methylation levels associated with race and childhood asthma severity. J Asthma 2016; 54:825-832. [PMID: 27929694 DOI: 10.1080/02770903.2016.1265126] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Asthma is a common chronic childhood disease worldwide. Socioeconomic status, genetic predisposition and environmental factors contribute to its incidence and severity. A disproportionate number of children with asthma are economically disadvantaged and live in substandard housing with potential indoor environmental exposures such as cockroaches, dust mites, rodents and molds. These exposures may manifest through epigenetic mechanisms that can lead to changes in relevant gene expression. We examined the association of global DNA methylation levels with socioeconomic status, asthma severity and race/ethnicity. METHODS We measured global DNA methylation in peripheral blood of children with asthma enrolled in the Kansas City Safe and Healthy Homes Program. Inclusion criteria included residing in the same home for a minimum of 4 days per week and total family income of less than 80% of the Kansas City median family income. DNA methylation levels were quantified by an immunoassay that assessed the percentage of 5-methylcytosine. RESULTS Our results indicate that overall, African American children had higher levels of global DNA methylation than children of other races/ethnicities (p = 0.029). This difference was more pronounced when socioeconomic status and asthma severity were coupled with race/ethnicity (p = 0.042) where low-income, African American children with persistent asthma had significantly elevated methylation levels relative to other races/ethnicities in the same context (p = 0.006, Hedges g = 1.14). CONCLUSION Our study demonstrates a significant interaction effect among global DNA methylation levels, asthma severity, race/ethnicity, and socioeconomic status.
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Affiliation(s)
- Marcia A Chan
- a Division of Allergy, Asthma and Immunology , Children's Mercy Hospital , Kansas City , MO , USA
| | - Christina E Ciaccio
- b Department of Pediatrics , University of Chicago Medicine, Comer Comer Children's Hospital , Chicago , IL , USA
| | - Nicole M Gigliotti
- a Division of Allergy, Asthma and Immunology , Children's Mercy Hospital , Kansas City , MO , USA
| | - Mo Rezaiekhaligh
- a Division of Allergy, Asthma and Immunology , Children's Mercy Hospital , Kansas City , MO , USA
| | - Jacob A Siedlik
- c Department of Exercise Science and Pre-Health Professions , Creighton University , Omaha , NE , USA
| | - Kevin Kennedy
- d Center for Environmental Health, Children's Mercy Hospital , Kansas City , MO , USA
| | - Charles S Barnes
- a Division of Allergy, Asthma and Immunology , Children's Mercy Hospital , Kansas City , MO , USA
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DNA methylation-based variation between human populations. Mol Genet Genomics 2016; 292:5-35. [PMID: 27815639 DOI: 10.1007/s00438-016-1264-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022]
Abstract
Several studies have proved that DNA methylation affects regulation of gene expression and development. Epigenome-wide studies have reported variation in methylation patterns between populations, including Caucasians, non-Caucasians (Blacks), Hispanics, Arabs, and numerous populations of the African continent. Not only has DNA methylation differences shown to impact externally visible characteristics, but is also a potential biomarker for underlying racial health disparities between human populations. Ethnicity-related methylation differences set their mark during early embryonic development. Genetic variations, such as single-nucleotide polymorphisms and environmental factors, such as age, dietary folate, socioeconomic status, and smoking, impacts DNA methylation levels, which reciprocally impacts expression of phenotypes. Studies show that it is necessary to address these external influences when attempting to differentiate between populations since the relative impacts of these factors on the human methylome remain uncertain. The present review summarises several reported attempts to establish the contribution of differential DNA methylation to natural human variation, and shows that DNA methylation could represent new opportunities for risk stratification and prevention of several diseases amongst populations world-wide. Variation of methylation patterns between human populations is an exciting prospect which inspires further valuable research to apply the concept in routine medical and forensic casework. However, trans-generational inheritance needs to be quantified to decipher the proportion of variation contributed by DNA methylation. The future holds thorough evaluation of the epigenome to understand quantification, heritability, and the effect of DNA methylation on phenotypes. In addition, methylation profiling of the same ethnic groups across geographical locations will shed light on conserved methylation differences in populations.
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Bailey LB, Stover PJ, McNulty H, Fenech MF, Gregory JF, Mills JL, Pfeiffer CM, Fazili Z, Zhang M, Ueland PM, Molloy AM, Caudill MA, Shane B, Berry RJ, Bailey RL, Hausman DB, Raghavan R, Raiten DJ. Biomarkers of Nutrition for Development-Folate Review. J Nutr 2015; 145:1636S-1680S. [PMID: 26451605 PMCID: PMC4478945 DOI: 10.3945/jn.114.206599] [Citation(s) in RCA: 350] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/11/2014] [Accepted: 04/14/2015] [Indexed: 12/13/2022] Open
Abstract
The Biomarkers of Nutrition for Development (BOND) project is designed to provide evidence-based advice to anyone with an interest in the role of nutrition in health. Specifically, the BOND program provides state-of-the-art information and service with regard to selection, use, and interpretation of biomarkers of nutrient exposure, status, function, and effect. To accomplish this objective, expert panels are recruited to evaluate the literature and to draft comprehensive reports on the current state of the art with regard to specific nutrient biology and available biomarkers for assessing nutrients in body tissues at the individual and population level. Phase I of the BOND project includes the evaluation of biomarkers for 6 nutrients: iodine, iron, zinc, folate, vitamin A, and vitamin B-12. This review represents the second in the series of reviews and covers all relevant aspects of folate biology and biomarkers. The article is organized to provide the reader with a full appreciation of folate's history as a public health issue, its biology, and an overview of available biomarkers (serum folate, RBC folate, and plasma homocysteine concentrations) and their interpretation across a range of clinical and population-based uses. The article also includes a list of priority research needs for advancing the area of folate biomarkers related to nutritional health status and development.
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Affiliation(s)
- Lynn B Bailey
- Department of Foods and Nutrition, University of Georgia, Athens, GA;
| | - Patrick J Stover
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Helene McNulty
- Northern Ireland Centre for Food and Health, Biomedical Sciences Research Institute, University of Ulster, Londonderry, United Kingdom
| | - Michael F Fenech
- Genome Health Nutrigenomics Laboratory, Food, Nutrition, and Bioproducts Flagship, Commonwealth Scientific and Industrial Research Organization, Adelaide, Australia
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | | | - Zia Fazili
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Mindy Zhang
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Per M Ueland
- Department of Clinical Science, Univeristy of Bergen, Bergen, Norway
| | - Anne M Molloy
- Institute of Molecular Medicine, Trinity College, Dublin, Ireland
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA
| | - Robert J Berry
- National Center on Birth Defects and Developmental Disabilities, CDC, Atlanta, GA; and
| | | | - Dorothy B Hausman
- Department of Foods and Nutrition, University of Georgia, Athens, GA
| | - Ramkripa Raghavan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | - Daniel J Raiten
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD;
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Straughen JK, Sipahi L, Uddin M, Misra DP, Misra VK. Racial differences in IGF1 methylation and birth weight. Clin Epigenetics 2015; 7:47. [PMID: 25945130 PMCID: PMC4419394 DOI: 10.1186/s13148-015-0080-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/06/2015] [Indexed: 11/30/2022] Open
Abstract
Background The birth weight of Black neonates in the United States is consistently smaller than that of their White counterparts. Epigenetic differences between the races may be involved in such disparities. The goal of these analyses was to model the role of IGF1 methylation in mediating the association between race and birth weight. Data was collected on a cohort of 87 live born infants. IGF1 methylation was measured in DNA isolated from the mononuclear fraction of umbilical cord blood collected after delivery. Quantitative, loci-specific methylation was assessed using the Infinium HumanMethylation27 BeadArray (Illumina Inc., San Diego, CA). Locus specific methylation of the IGF1 CpG site was validated on a subset of the original sample (N = 61) using pyrosequencing. Multiple linear regression was used to examine relationships between IGF1 methylation, race, and birth weight. A formal mediation analysis was then used to estimate the relationship of IGF1 methylation to race and birth weight. Results Black race was associated with a 7.45% decrease in gestational age-adjusted birth weight (aBW) (P = 0.04) and Black infants had significantly higher IGF1 methylation than non-Black infants (P < 0.05). A one standard deviation increase in IGF1 methylation was associated with a 3.32% decrease in aBW (P = 0.02). Including IGF1 methylation as a covariate, the effect of Black race on aBW was attenuated. A formal mediation analysis showed that the controlled direct effect of Black race on aBW was −6.26% (95% CI = −14.15, 1.06); the total effect of Black race on IGF1 methylation was −8.12% (95% CI = −16.08, −0.55); and the natural indirect effect of Black race on aBW through IGF1 methylation was −1.86% (95% CI = −5.22, 0.18) Conclusion The results of the mediation analysis along with the multivariable regression analyses suggest that IGF1 methylation may partially mediate the relationship between Black race and aBW. Such epigenetic differences may be involved in racial disparities observed in perinatal outcomes.
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Affiliation(s)
- Jennifer K Straughen
- Department of Family Medicine and Public Health Sciences, The Wayne State University School of Medicine, 3939 Woodward Avenue, Detroit, MI 48201 USA ; Current address: Department of Public Health Sciences, Henry Ford Hospital, One Ford Place, Detroit, MI 48202 USA
| | - Levent Sipahi
- Center for Molecular Medicine and Genetics, The Wayne State University School of Medicine, 540 East Canfield, Detroit, MI 48201 USA
| | - Monica Uddin
- Department of Psychology, University of Illinois at Urbana-Champaign, 603 E. Daniel Street, Champaign, IL 61820 USA
| | - Dawn P Misra
- Department of Family Medicine and Public Health Sciences, The Wayne State University School of Medicine, 3939 Woodward Avenue, Detroit, MI 48201 USA
| | - Vinod K Misra
- Department of Pediatrics, Division of Genetic and Metabolic Disorders, The Wayne State University School of Medicine, 3901 Beaubien Blvd, Detroit, MI 48201 USA ; Children's Hospital of Michigan, Division of Genetic and Metabolic Disorders, The Wayne State University School of Medicine, 3950 Beaubien Blvd, Detroit, MI 48201 USA
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Sun YV, Smith AK, Conneely KN, Chang Q, Li W, Lazarus A, Smith JA, Almli LM, Binder EB, Klengel T, Cross D, Turner ST, Ressler KJ, Kardia SLR. Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans. Hum Genet 2013; 132:1027-37. [PMID: 23657504 PMCID: PMC3744600 DOI: 10.1007/s00439-013-1311-6] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2013] [Accepted: 05/01/2013] [Indexed: 12/31/2022]
Abstract
Cigarette smoking is an environmental risk factor for many chronic diseases, and disease risk can often be managed by smoking control. Smoking can induce cellular and molecular changes, including epigenetic modification, but the short- and long-term epigenetic modifications caused by cigarette smoking at the gene level have not been well understood. Recent studies have identified smoking-related DNA methylation (DNAm) sites in Caucasians. To determine whether the same DNAm sites associate with smoking in African Americans, and to identify novel smoking-related DNAm sites, we conducted a methylome-wide association study of cigarette smoking using a discovery sample of 972 African Americans, and a replication sample of 239 African Americans with two array-based methods. Among 15 DNAm sites significantly associated with smoking after correction for multiple testing in our discovery sample, 5 DNAm sites are replicated in an independent cohort, and 14 sites in the replication sample have effects in the same direction as in the discovery sample. The top two smoking-related DNAm sites in F2RL3 (factor II receptor-like 3) and GPR15 (G-protein-coupled receptor 15) observed in African Americans are consistent with previous findings in Caucasians. The associations between the replicated DNAm sites and smoking remain significant after adjusting for genetic background. Despite the distinct genetic background between African Americans and Caucasians, the DNAm from the two ethnic groups shares common associations with cigarette smoking, which suggests a common molecular mechanism of epigenetic modification influenced by environmental exposure.
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Affiliation(s)
- Yan V Sun
- Department of Epidemiology, Rollins School of Public Health, Emory University, 1518 Clifton Road NE #3049, Atlanta, GA, 30322, USA.
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Subramanyam MA, Diez-Roux AV, Pilsner JR, Villamor E, Donohue KM, Liu Y, Jenny NS. Social factors and leukocyte DNA methylation of repetitive sequences: the multi-ethnic study of atherosclerosis. PLoS One 2013; 8:e54018. [PMID: 23320117 PMCID: PMC3539988 DOI: 10.1371/journal.pone.0054018] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 12/05/2012] [Indexed: 12/29/2022] Open
Abstract
Epigenetic changes are a potential mechanism contributing to race/ethnic and socioeconomic disparities in health. However, there is scant evidence of the race/ethnic and socioeconomic patterning of epigenetic marks. We used data from the Multi-Ethnic Study of Atherosclerosis Stress Study (N = 988) to describe age- and gender- independent associations of race/ethnicity and socioeconomic status (SES) with methylation of Alu and LINE-1 repetitive elements in leukocyte DNA. Mean Alu and Line 1 methylation in the full sample were 24% and 81% respectively. In multivariable linear regression models, African-Americans had 0.27% (p<0.01) and Hispanics 0.20% (p<0.05) lower Alu methylation than whites. In contrast, African-Americans had 0.41% (p<0.01) and Hispanics 0.39% (p<0.01) higher LINE-1 methylation than whites. These associations remained after adjustment for SES. In addition, a one standard deviation higher wealth was associated with 0.09% (p<0.01) higher Alu and 0.15% (p<0.01) lower LINE-1 methylation in age- and gender- adjusted models. Additional adjustment for race/ethnicity did not alter this pattern. No associations were observed with income, education or childhood SES. Our findings, from a large community-based sample, suggest that DNA methylation is socially patterned. Future research, including studies of gene-specific methylation, is needed to understand better the opposing associations of Alu and LINE-1 methylation with race/ethnicity and wealth as well as the extent to which small methylation changes in these sequences may influence disparities in health.
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Affiliation(s)
- Malavika A Subramanyam
- Social Epidemiology, Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat, India.
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Jung AY, Botma A, Lute C, Blom HJ, Ueland PM, Kvalheim G, Midttun Ø, Nagengast F, Steegenga W, Kampman E. Plasma B vitamins and LINE-1 DNA methylation in leukocytes of patients with a history of colorectal adenomas. Mol Nutr Food Res 2012; 57:698-708. [PMID: 23132835 DOI: 10.1002/mnfr.201200069] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Revised: 07/23/2012] [Accepted: 09/10/2012] [Indexed: 12/21/2022]
Abstract
SCOPE Low concentrations of folate, other B vitamins, and methionine are associated with colorectal cancer risk, possibly by changing DNA methylation patterns. Here, we examine whether plasma concentrations of B vitamins and methionine are associated with methylation of long interspersed nuclear element-1 (LINE-1) among those at high risk of colorectal cancer, i.e. patients with at least one histologically confirmed colorectal adenoma (CRA) in their life. METHODS AND RESULTS We used LINE-1 bisulfite pyrosequencing to measure global DNA methylation levels in leukocytes of 281 CRA patients. Multivariable linear regression was used to assess associations between plasma B vitamin concentrations and LINE-1 methylation levels. Plasma folate was inversely associated with LINE-1 methylation in CRA patients, while plasma methionine was positively associated with LINE-1 methylation. CONCLUSION This study does not provide evidence that in CRA patients, plasma folate concentrations are positively related to LINE-1 methylation in leukocytes but does suggest a direct association between plasma methionine and LINE-1 methylation in leukocytes.
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Affiliation(s)
- Audrey Y Jung
- Department of Epidemiology, Biostatistics, and HTA, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
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Perng W, Rozek LS, Mora-Plazas M, Duchin O, Marin C, Forero Y, Baylin A, Villamor E. Micronutrient status and global DNA methylation in school-age children. Epigenetics 2012; 7:1133-41. [PMID: 22918385 DOI: 10.4161/epi.21915] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aberrations in global LINE-1 DNA methylation have been related to risk of cancer and cardiovascular disease. Micronutrients including methyl-donors and retinoids are involved in DNA methylation pathways. We investigated associations of micronutrient status and LINE-1 methylation in a cross-sectional study of school-age children from Bogotá, Colombia. Methylation of LINE-1 repetitive elements was quantified in 568 children 5-12 years of age using pyrosequencing technology. We examined the association of LINE-1 methylation with erythrocyte folate, plasma vitamin B12, vitamin A ferritin (an indicator of iron status) and serum zinc concentrations using multivariable linear regression. We also considered associations of LINE-1 methylation with socio-demographic and anthropometric characteristics. Mean (± SD) LINE-1 methylation was 80.25 (± 0.65) percentage of 5-mC (%5-mC). LINE-1 methylation was inversely related to plasma vitamin A. After adjustment for potential confounders, children with retinol levels higher than or equal to 1.05 µmol/L showed 0.19% 5-mC lower LINE-1 methylation than children with retinol levels lower than 0.70 µmol/L. LINE-1 methylation was also inversely associated with C-reactive protein, a marker of chronic inflammation, and female sex. We identified positive associations of maternal body mass index and socioeconomic status with LINE-1 methylation. These associations were not significantly different by sex. Whether modification of these exposures during school-age years leads to changes in global DNA methylation warrants further investigation.
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Affiliation(s)
- Wei Perng
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA.
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Abstract
SIGNIFICANCE The progressive, dose-dependent, and potentially reversible epigenetic changes observed in cancer present new opportunities in cancer risk modification and prevention using dietary and lifestyle factors. Folate, a water-soluble B vitamin, has been of intense interest because of an inverse association between folate status and the risk of several malignancies (particularly colorectal cancer) and its potential to modulate DNA methylation. Aberrant patterns and dysregulation of DNA methylation are mechanistically related to carcinogenesis. RECENT ADVANCES The effects of folate on DNA methylation patterns have recently been investigated in two important life stages: pre- and early postnatal life and aging. Recent studies have demonstrated that folate exposure in the intrauterine environment and early life and during the aging process may have profound effects on DNA methylation with significant functional ramifications, including the risk of cancer. CRITICAL ISSUES Evidence from animal, human, and in vitro studies suggest that the epigenetic effects of folate on DNA methylation are highly complex. The effects are gene and site specific and appear to depend on cell type, target organ, stage of transformation, the degree and duration of folate manipulations, interactions with other methyl group donors and dietary factors, and genetic variants in the folate metabolic pathways. FUTURE DIRECTIONS The potential for folate to modulate DNA methylation and, thus, modify the risk of cancer in humans is worthy of further investigation. Due to the complex relationship between folate exposure and DNA methylation, more elaborate epidemiological, clinical, and mechanistic studies that determine the clinical, biological, and molecular effects of folate are warranted.
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Affiliation(s)
- Anna Ly
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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Terry MB, Delgado-Cruzata L, Vin-Raviv N, Wu HC, Santella RM. DNA methylation in white blood cells: association with risk factors in epidemiologic studies. Epigenetics 2011; 6:828-37. [PMID: 21636973 PMCID: PMC3154425 DOI: 10.4161/epi.6.7.16500] [Citation(s) in RCA: 265] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 05/16/2011] [Indexed: 12/14/2022] Open
Abstract
Alterations in DNA methylation patterns, both at specific loci and overall in the genome, have been associated with many different health outcomes. In cancer and other diseases, most of these changes have been observed at the tissue level. Data on whether DNA methylation changes in white blood cells (WBC) can serve as a useful biomarker for different health outcomes are much more limited, but rapidly emerging. Epidemiologic studies have reported associations between global WBC methylation and several different cancers including cancers of the colon, bladder, stomach, breast and head and neck, as well as schizophrenia and myelodysplastic syndrome. Evidence for WBC methylation at specific loci and disease risk is more limited, but increasing. Differences in WBC DNA methylation by selected risk factors including demographic (age, gender, race), environmental exposures (benzene, persistent organic pollutants, lead, arsenic, and air pollution), and other risk factors (cigarette smoke, alcohol drinking, body size, physical activity and diet) have been observed in epidemiologic studies though the patterns are far from consistent. Challenges in inferences from the existing data are primarily due to the cross-sectional and small size of most studies to date as well as the differences in results across assay type and source of DNA. Large, prospective studies will be needed to understand whether changes in risk factors are associated with changes in DNA methylation patterns, and if changes in DNA methylation patterns are associated with changes in disease endpoints.
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Affiliation(s)
- Mary Beth Terry
- Department of Epidemiology, Columbia University Medical Center, Mailman School of Public Health, New York, NY, USA.
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Zhang FF, Morabia A, Carroll J, Gonzalez K, Fulda K, Kaur M, Vishwanatha JK, Santella RM, Cardarelli R. Dietary patterns are associated with levels of global genomic DNA methylation in a cancer-free population. J Nutr 2011; 141:1165-71. [PMID: 21525250 PMCID: PMC3095144 DOI: 10.3945/jn.110.134536] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Animal studies have provided direct evidence that dietary factors induce changes in DNA methylation patterns. In humans, studies on diet and DNA methylation have yielded inconsistent findings. Because humans tend to consume foods and nutrients that are highly interrelated, study of dietary patterns may have improved the power of detecting the effect of diet on DNA methylation. Using data collected from 149 participants aged 45-75 y in the North Texas Healthy Heart Study, we examined the relationship between dietary patterns and levels of genomic DNA methylation in peripheral blood leukocytes. Dietary data were collected from study participants using the Block FFQ. Genomic DNA methylation was measured using bisulfite conversion of DNA and real-time PCR (MethyLight) for LINE-1. Two dietary patterns were identified using factor analysis: a "prudent" dietary pattern characterized by a high intake of vegetables and fruits, and a "Western" dietary pattern characterized by a high intake of meats, grains, dairy, oils, and potatoes. The prudent dietary pattern was associated with a lower prevalence of DNA hypomethylation (Q(4) vs. Q(1); OR = 0.33, 95% CI: 0.12-0.92) and the association was dose dependent (P-trend = 0.04). There was no apparent association between the Western dietary pattern and global leukocyte DNA methylation (Q(4) vs. Q(1); OR = 1.28, 95% CI: 0.47-3.47; P-trend = 0.55). Thus, a dietary pattern characterized by a high intake of vegetables and fruits may protect against global DNA hypomethylation. Future studies with a larger sample size need to confirm that this association holds longitudinally.
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Affiliation(s)
- Fang Fang Zhang
- Department of Nutrition Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111, USA.
| | - Alfredo Morabia
- Center for the Biology of Natural System, Queens College at City University of New York, Flushing, NY 11365
| | - Joan Carroll
- Department of Integrated Physiology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Health Science Center, Fort Worth, TX 76107
| | - Karina Gonzalez
- Department of Environmental Health, Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Kimberly Fulda
- Primary Care Research Institute, University of North Texas Health Science Center, Health Science Center, Fort Worth, TX 76107
| | - Manleen Kaur
- Department of Epidemiology, School of Public Health, University of North Texas Health Science Center, Health Science Center, Fort Worth, TX 76107
| | - Jamboor K. Vishwanatha
- Department of Molecular Biology and Immunology, Graduate School of Biomedical Sciences, University of North Texas Health Science Center, Health Science Center, Fort Worth, TX 76107
| | - Regina M. Santella
- Department of Environmental Health, Mailman School of Public Health, Columbia University, New York, NY 10032
| | - Roberto Cardarelli
- Primary Care Research Institute, University of North Texas Health Science Center, Health Science Center, Fort Worth, TX 76107
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15
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Wu HC, Delgado-Cruzata L, Flom JD, Kappil M, Ferris JS, Liao Y, Santella RM, Terry MB. Global methylation profiles in DNA from different blood cell types. Epigenetics 2011; 6:76-85. [PMID: 20890131 DOI: 10.4161/epi.6.1.13391] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA methylation measured in white blood cell DNA is increasingly being used as in studies of cancer susceptibility. However, little is known about the correlation between different assays to measure global methylation and whether the source of DNA matters when examining methylation profiles in different blood cell types. Using information from 620 women, 217 and 403 women with DNA available from granulocytes (Gran), and total white blood cells (WBC), respectively, and 48 women with DNA available from four different sources (WBC, Gran, mononuclear (MN), and lymphoblastoid cell lines (LCL)), we compared DNA methylation for three repetitive elements (LINE1, Sat2, Alu) by MethyLight, luminometric methylation assay (LUMA), and [(3)H]-methyl acceptance assay. For four of the five assays, DNA methylation levels measured in Gran were not correlated with methylation in LBC, MN, or WBC; the exception was Sat2. DNA methylation in LCL was correlated with methylation in MN and WBC for the [(3)H]-methyl acceptance, LINE1, and Alu assays. Methylation in MN was correlated with methylation in WBC for the [(3)H]-methyl acceptance and LUMA assays. When we compared the five assays to each other by source of DNA, we observed statistically significant positive correlations ranging from 0.3-0.7 for each cell type with one exception (Sat2 and Alu in MN). Among the 620 women stratified by DNA source, correlations among assays were highest for the three repetitive elements (range 0.39-0.64). Results from the LUMA assay were modestly correlated with LINE1 (0.18-0.20). These results suggest that both assay and source of DNA are critical components in the interpretation of global DNA methylation patterns from WBC.
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Affiliation(s)
- Hui-Chen Wu
- Department of Epidemiology, Mailman School of Public Health of Columbia University, New York, NY, USA
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16
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de Montera B, El Zeihery D, Müller S, Jammes H, Brem G, Reichenbach HD, Scheipl F, Chavatte-Palmer P, Zakhartchenko V, Schmitz OJ, Wolf E, Renard JP, Hiendleder S. Quantification of leukocyte genomic 5-methylcytosine levels reveals epigenetic plasticity in healthy adult cloned cattle. Cell Reprogram 2010; 12:175-81. [PMID: 20677931 DOI: 10.1089/cell.2009.0062] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Successful somatic cell nuclear transfer (SCNT) requires epigenetic reprogramming of a differentiated donor cell nucleus. Incorrect reprogramming of epigenetic markings such as DNA methylation is associated with compromised prenatal development and postnatal abnormalities. Clones that survive into adulthood, in contrast, are assumed to possess a normalized epigenome corresponding to their normal phenotype. To address this point, we used capillary electrophoresis to measure 5-methylcytosine (5mC) levels in leukocyte DNA of 38 healthy female bovine clones that represented five genotypes from the Simmental breed and four genotypes from the Holstein breed. The estimated variance in 5mC level within clone genotypes of both breeds [0.104, 95% confidence interval (CI): 0.070-0.168] was higher than between clone genotypes (0, CI: 0-0.047). We quantified the contribution of SCNT to this unexpected variability by comparing the 19 Simmental clones with 12 female Simmental monozygotic twin pairs of similar age. In Simmental clones, the estimated variability within genotype (0.0636, CI: 0.0358-0.127) was clearly higher than in twin pairs (0.0091, CI: 0.0047-0.0229). In clones, variability within genotype (0.0636) was again higher than between genotypes (0, CI: 0-0.077). Twins, in contrast, showed lower variability within genotypes (0.0091) than between genotypes (0.0136, CI: 0.00250-0.0428). Importantly, the absolute deviations of 5mC values of individual SCNT clones from their genotype means were fivefold increased in comparison to twins. Further comparisons with noncloned controls revealed DNA hypermethylation in most of the clones. The clone-specific variability in DNA methylation and DNA hypermethylation clearly show that healthy adult SCNT clones must be considered as epigenome variants.
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Affiliation(s)
- Béatrice de Montera
- INRA , UMR 1198 Biologie du Développement et Reproduction, Jouy en Josas, France
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17
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Figueiredo JC, Grau MV, Wallace K, Levine AJ, Shen L, Hamdan R, Chen X, Bresalier RS, McKeown-Eyssen G, Haile RW, Baron JA, Issa JPJ. Global DNA hypomethylation (LINE-1) in the normal colon and lifestyle characteristics and dietary and genetic factors. Cancer Epidemiol Biomarkers Prev 2009; 18:1041-9. [PMID: 19336559 PMCID: PMC2712652 DOI: 10.1158/1055-9965.epi-08-0926] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Global loss of methylated cytosines in DNA, thought to predispose to chromosomal instability and aneuploidy, has been associated with an increased risk of colorectal neoplasia. Little is known about the relationships between global hypomethylation and lifestyle, demographics, dietary measures, and genetic factors. METHODS Our data were collected as part of a randomized clinical trial testing the efficacy of aspirin and folic acid for the prevention of colorectal adenomas. At a surveillance colonoscopy approximately 3 years after the qualifying exam, we obtained two biopsies of the normal-appearing mucosa from the right colon and two biopsies from the left colon. Specimens were assayed for global hypomethylation using a pyrosequencing assay for LINE-1 (long interspersed nucleotide elements) repeats. RESULTS The analysis included data from 388 subjects. There was relatively little variability in LINE methylation overall. Mean LINE-1 methylation levels in normal mucosa from the right bowel were significantly lower than those on the left side (P < 0.0001). No significant associations were found between LINE-1 methylation and folate treatment, age, sex, body mass index, smoking status, alcohol use, dietary intake, or circulating levels of B vitamins, homocysteine, or selected genotypes. Race, dietary folic acid, and plasma B(6) showed associations with global methylation that differed between the right and the left bowel. The effect of folic acid on risk of adenomas did not differ according to extent of LINE-1 methylation, and we found no association between LINE-1 methylation and risk of adenomas. CONCLUSIONS LINE-1 methylation is not influenced by folic acid supplementation but differs by colon subsite.
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Affiliation(s)
- Jane C Figueiredo
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
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Abratte CM, Wang W, Li R, Axume J, Moriarty DJ, Caudill MA. Choline status is not a reliable indicator of moderate changes in dietary choline consumption in premenopausal women. J Nutr Biochem 2009; 20:62-9. [DOI: 10.1016/j.jnutbio.2007.12.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 11/30/2007] [Accepted: 12/12/2007] [Indexed: 01/13/2023]
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