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Raitoharju E, Rajić S, Marttila S. Non-coding 886 ( nc886/ vtRNA2-1), the epigenetic odd duck - implications for future studies. Epigenetics 2024; 19:2332819. [PMID: 38525792 DOI: 10.1080/15592294.2024.2332819] [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: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 03/26/2024] Open
Abstract
Non-coding 886 (nc886, vtRNA2-1) is the only human polymorphically imprinted gene, in which the methylation status is not determined by genetics. Existing literature regarding the establishment, stability and consequences of the methylation pattern, as well as the nature and function of the nc886 RNAs transcribed from the locus, are contradictory. For example, the methylation status of the locus has been reported to be stable through life and across somatic tissues, but also susceptible to environmental effects. The nature of the produced nc886 RNA(s) has been redefined multiple times, and in carcinogenesis, these RNAs have been reported to have conflicting roles. In addition, due to the bimodal methylation pattern of the nc886 locus, traditional genome-wide methylation analyses can lead to false-positive results, especially in smaller datasets. Herein, we aim to summarize the existing literature regarding nc886, discuss how the characteristics of nc886 give rise to contradictory results, as well as to reinterpret, reanalyse and, where possible, replicate the results presented in the current literature. We also introduce novel findings on how the distribution of the nc886 methylation pattern is associated with the geographical origins of the population and describe the methylation changes in a large variety of human tumours. Through the example of this one peculiar genetic locus and RNA, we aim to highlight issues in the analysis of DNA methylation and non-coding RNAs in general and offer our suggestions for what should be taken into consideration in future analyses.
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Affiliation(s)
- Emma Raitoharju
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
| | - Sonja Rajić
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Tays Research Services, Wellbeing Services County of Pirkanmaa, Tampere University Hospital, Tampere, Finland
- Gerontology Research Center, Tampere University, Tampere, Finland
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2
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Kok DE, Saunders R, Nelson A, Smith D, Ford D, Mathers JC, McKay JA. Influence of maternal folate depletion on Art3 DNA methylation in the murine adult brain; potential consequences for brain and neurocognitive health. Mutagenesis 2024; 39:196-204. [PMID: 38417824 PMCID: PMC11040152 DOI: 10.1093/mutage/geae007] [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: 10/04/2023] [Accepted: 02/27/2024] [Indexed: 03/01/2024] Open
Abstract
The developmental origins of health and disease hypothesis suggest early-life environment impacts health outcomes throughout the life course. In particular, epigenetic marks, including DNA methylation, are thought to be key mechanisms through which environmental exposures programme later-life health. Adequate maternal folate status before and during pregnancy is essential in the protection against neural tube defects, but data are emerging that suggest early-life folate exposures may also influence neurocognitive outcomes in childhood and, potentially, thereafter. Since folate is key to the supply of methyl donors for DNA methylation, we hypothesize that DNA methylation may be a mediating mechanism through which maternal folate influences neurocognitive outcomes. Using bisulphite sequencing, we measured DNA methylation of five genes (Art3, Rsp16, Tspo, Wnt16, and Pcdhb6) in the brain tissue of adult offspring of dams who were depleted of folate (n = 5, 0.4 mg folic acid/kg diet) during pregnancy (~19-21 days) and lactation (mean 22 days) compared with controls (n = 6, 2 mg folic acid/kg diet). Genes were selected as methylation of their promoters had previously been found to be altered by maternal folate intake in mice and humans across the life course, and because they have potential associations with neurocognitive outcomes. Maternal folate depletion was significantly associated with Art3 gene hypomethylation in subcortical brain tissue of adult mice at 28 weeks of age (mean decrease 6.2%, P = .03). For the other genes, no statistically significant differences were found between folate depleted and control groups. Given its association with neurocognitive outcomes, we suggest Art3 warrants further study in the context of lifecourse brain health. We have uncovered a potential biomarker that, once validated in accessible biospecimens and human context, may be useful to track the impact of early-life folate exposure on later-life neurocognitive health, and potentially be used to develop and monitor the effects of interventions.
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Affiliation(s)
- Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, P.O. Box 17, 6700 AA Wageningen Stippeneng 4, 6708 WE Wageningen Wageningen Campus l Building 124 (Helix), Wageningen, The Netherlands
| | - Rachael Saunders
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Northumberland Building, Newcastle Upon Tyne, NE1 8ST, United Kingdom
| | - Andrew Nelson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Northumberland Building, Newcastle Upon Tyne, NE1 8ST, United Kingdom
| | - Darren Smith
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Northumberland Building, Newcastle Upon Tyne, NE1 8ST, United Kingdom
| | - Dianne Ford
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Northumberland Building, Newcastle Upon Tyne, NE1 8ST, United Kingdom
| | - John C Mathers
- Human Nutrition & Exercise Research Centre, Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Room M2.060, 2nd floor William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Jill A McKay
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Northumberland Building, Newcastle Upon Tyne, NE1 8ST, United Kingdom
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3
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Qiao H, Tan J, Yan J, Sun C, Yin X, Li Z, Wu J, Guan H, Wen S, Zhang M, Xu S, Jin L. A comprehensive evaluation of the phenotype-first and data-driven approaches in analyzing facial morphological traits. iScience 2024; 27:109325. [PMID: 38487017 PMCID: PMC10937830 DOI: 10.1016/j.isci.2024.109325] [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: 11/08/2023] [Revised: 01/17/2024] [Accepted: 02/20/2024] [Indexed: 03/17/2024] Open
Abstract
The phenotype-first approach (PFA) and data-driven approach (DDA) have both greatly facilitated anthropological studies and the mapping of trait-associated genes. However, the pros and cons of the two approaches are poorly understood. Here, we systematically evaluated the two approaches and analyzed 14,838 facial traits in 2,379 Han Chinese individuals. Interestingly, the PFA explained more facial variation than the DDA in the top 100 and 1,000 except in the top 10 phenotypes. Accordingly, the ratio of heterogeneous traits extracted from the PFA was much greater, while more homogenous traits were found using the DDA for different sex, age, and BMI groups. Notably, our results demonstrated that the sex factor accounted for 30% of phenotypic variation in all traits extracted. Furthermore, we linked DDA phenotypes to PFA phenotypes with explicit biological explanations. These findings provide new insights into the analysis of multidimensional phenotypes and expand the understanding of phenotyping approaches.
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Affiliation(s)
- Hui Qiao
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Jun Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Chang Sun
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Xing Yin
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Zijun Li
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Jiazi Wu
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Haijuan Guan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
| | - Shaoqing Wen
- Institute of Archaeological Science, Fudan University, Shanghai 200433, China
| | - Menghan Zhang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 201203, China
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai 200433, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Sciences, Fudan University, Shanghai 200438, China
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4
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Socha MW, Flis W, Wartęga M. Epigenetic Genome Modifications during Pregnancy: The Impact of Essential Nutritional Supplements on DNA Methylation. Nutrients 2024; 16:678. [PMID: 38474806 DOI: 10.3390/nu16050678] [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: 01/28/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Pregnancy is an extremely stressful period in a pregnant woman's life. Currently, women's awareness of the proper course of pregnancy and its possible complications is constantly growing. Therefore, a significant percentage of women increasingly reach for various dietary supplements during gestation. Some of the most popular substances included in multi-ingredient supplements are folic acid and choline. Those substances are associated with positive effects on fetal intrauterine development and fewer possible pregnancy-associated complications. Recently, more and more attention has been paid to the impacts of specific environmental factors, such as diet, stress, physical activity, etc., on epigenetic modifications, understood as changes occurring in gene expression without the direct alteration of DNA sequences. Substances such as folic acid and choline may participate in epigenetic modifications by acting via a one-carbon cycle, leading to the methyl-group donor formation. Those nutrients may indirectly impact genome phenotype by influencing the process of DNA methylation. This review article presents the current state of knowledge on the use of folic acid and choline supplementation during pregnancy, taking into account their impacts on the maternal-fetal unit and possible pregnancy outcomes, and determining possible mechanisms of action, with particular emphasis on their possible impacts on epigenetic modifications.
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Affiliation(s)
- Maciej W Socha
- Department of Perinatology, Gynecology and Gynecologic Oncology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Łukasiewicza 1, 85-821 Bydgoszcz, Poland
- Department of Obstetrics and Gynecology, St. Adalbert's Hospital in Gdańsk, Copernicus Healthcare Entity, Jana Pawła II 50, 80-462 Gdańsk, Poland
| | - Wojciech Flis
- Department of Perinatology, Gynecology and Gynecologic Oncology, Faculty of Health Sciences, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Łukasiewicza 1, 85-821 Bydgoszcz, Poland
- Department of Obstetrics and Gynecology, St. Adalbert's Hospital in Gdańsk, Copernicus Healthcare Entity, Jana Pawła II 50, 80-462 Gdańsk, Poland
| | - Mateusz Wartęga
- Department of Pathophysiology, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, M. Curie-Skłodowskiej 9, 85-094 Bydgoszcz, Poland
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5
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Derakhshan M, Kessler NJ, Hellenthal G, Silver MJ. Metastable epialleles in humans. Trends Genet 2024; 40:52-68. [PMID: 38000919 DOI: 10.1016/j.tig.2023.09.007] [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: 05/22/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 11/26/2023]
Abstract
First identified in isogenic mice, metastable epialleles (MEs) are loci where the extent of DNA methylation (DNAm) is variable between individuals but correlates across tissues derived from different germ layers within a given individual. This property, termed systemic interindividual variation (SIV), is attributed to stochastic methylation establishment before germ layer differentiation. Evidence suggests that some putative human MEs are sensitive to environmental exposures in early development. In this review we introduce key concepts pertaining to human MEs, describe methods used to identify MEs in humans, and review their genomic features. We also highlight studies linking DNAm at putative human MEs to early environmental exposures and postnatal (including disease) phenotypes.
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Affiliation(s)
- Maria Derakhshan
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Noah J Kessler
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | | | - Matt J Silver
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, Banjul, The Gambia.
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6
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Verscheure E, Stierum R, Schlünssen V, Lund Würtz AM, Vanneste D, Kogevinas M, Harding BN, Broberg K, Zienolddiny-Narui S, Erdem JS, Das MK, Makris KC, Konstantinou C, Andrianou X, Dekkers S, Morris L, Pronk A, Godderis L, Ghosh M. Characterization of the internal working-life exposome using minimally and non-invasive sampling methods - a narrative review. ENVIRONMENTAL RESEARCH 2023; 238:117001. [PMID: 37683788 DOI: 10.1016/j.envres.2023.117001] [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: 04/13/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023]
Abstract
During recent years, we are moving away from the 'one exposure, one disease'-approach in occupational settings and towards a more comprehensive approach, taking into account the totality of exposures during a life course by using an exposome approach. Taking an exposome approach however is accompanied by many challenges, one of which, for example, relates to the collection of biological samples. Methods used for sample collection in occupational exposome studies should ideally be minimally invasive, while at the same time sensitive, and enable meaningful repeated sampling in a large population and over a longer time period. This might be hampered in specific situations e.g., people working in remote areas, during pandemics or with flexible work hours. In these situations, using self-sampling techniques might offer a solution. Therefore, our aim was to identify existing self-sampling techniques and to evaluate the applicability of these techniques in an occupational exposome context by conducting a literature review. We here present an overview of current self-sampling methodologies used to characterize the internal exposome. In addition, the use of different biological matrices was evaluated and subdivided based on their level of invasiveness and applicability in an occupational exposome context. In conclusion, this review and the overview of self-sampling techniques presented herein can serve as a guide in the design of future (occupational) exposome studies while circumventing sample collection challenges associated with exposome studies.
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Affiliation(s)
- Eline Verscheure
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rob Stierum
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Vivi Schlünssen
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Anne Mette Lund Würtz
- Department of Public Health, Research unit for Environment, Occupation and Health, Danish Ramazzini Centre, Aarhus University, Aarhus, Denmark
| | - Dorian Vanneste
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Manolis Kogevinas
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Barbara N Harding
- Environment and Health over the Lifecourse Program, ISGlobal, Barcelona, Spain
| | - Karin Broberg
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden; Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Mrinal K Das
- National Institute of Occupational Health, Oslo, Norway
| | - Konstantinos C Makris
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Corina Konstantinou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Xanthi Andrianou
- Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus
| | - Susan Dekkers
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | | | - Anjoeka Pronk
- Netherlands Organisation for Applied Scientific Research TNO, Risk Analysis for Products in Development, Utrecht, the Netherlands
| | - Lode Godderis
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium; Idewe, External Service for Prevention and Protection at work, Heverlee, Belgium.
| | - Manosij Ghosh
- Department of Public Health and Primary Care, Centre for Environment and Health, Katholieke Universiteit Leuven, Leuven, Belgium.
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7
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Fardous AM, Heydari AR. Uncovering the Hidden Dangers and Molecular Mechanisms of Excess Folate: A Narrative Review. Nutrients 2023; 15:4699. [PMID: 37960352 PMCID: PMC10648405 DOI: 10.3390/nu15214699] [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: 09/29/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
This review delves into the intricate relationship between excess folate (vitamin B9) intake, especially its synthetic form, namely, folic acid, and its implications on health and disease. While folate plays a pivotal role in the one-carbon cycle, which is essential for DNA synthesis, repair, and methylation, concerns arise about its excessive intake. The literature underscores potential deleterious effects, such as an increased risk of carcinogenesis; disruption in DNA methylation; and impacts on embryogenesis, pregnancy outcomes, neurodevelopment, and disease risk. Notably, these consequences stretch beyond the immediate effects, potentially influencing future generations through epigenetic reprogramming. The molecular mechanisms underlying these effects were examined, including altered one-carbon metabolism, the accumulation of unmetabolized folic acid, vitamin-B12-dependent mechanisms, altered methylation patterns, and interactions with critical receptors and signaling pathways. Furthermore, differences in the effects and mechanisms mediated by folic acid compared with natural folate are highlighted. Given the widespread folic acid supplementation, it is imperative to further research its optimal intake levels and the molecular pathways impacted by its excessive intake, ensuring the health and well-being of the global population.
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Affiliation(s)
- Ali M. Fardous
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, USA;
| | - Ahmad R. Heydari
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI 48202, USA;
- Barbara Ann Karmanos Cancer Institute, Wayne State University, Detroit, MI 48202, USA
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Clementson M, Hurley L, Coonrod S, Bennett C, Marella P, Pascual AS, Pull K, Wasek B, Bottiglieri T, Malysheva O, Caudill MA, Jadavji NM. Maternal dietary deficiencies in folic acid or choline worsen stroke outcomes in adult male and female mouse offspring. Neural Regen Res 2023; 18:2443-2448. [PMID: 37282475 PMCID: PMC10360112 DOI: 10.4103/1673-5374.371375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Abstract
Maternal one-carbon metabolism plays an important role in early life programming. There is a well-established connection between the fetal environment and the health status of the offspring. However, there is a knowledge gap on how maternal nutrition impacts stroke outcomes in offspring. The aim of our study was to investigate the role of maternal dietary deficiencies in folic acid or choline on stroke outcomes in 3-month-old offspring. Adult female mice were fed a folic acid-deficient diet, choline-deficient diet, or control diet 4 weeks before pregnancy. They were continued on diets during pregnancy and lactation. Male and female offspring were weaned onto a control diet and at 2 months of age were subjected to ischemic stroke within the sensorimotor cortex via photothrombotic damage. Mothers maintained on either a folic acid-deficient diet or choline-deficient diet had reduced levels of S-adenosylmethionine in the liver and S-adenosylhomocysteine in the plasma. After ischemic stroke, motor function was impaired in 3-month-old offspring from mothers receiving either a folic acid-deficient diet or choline-deficient diet compared to the animals receiving a control diet. In brain tissue, there was no difference in ischemic damage volume. When protein levels were assessed in ischemic brain tissue, there were lower levels of active caspase-3 and hypoxia-inducible factor 1α in males compared to females and betaine levels were reduced in offspring from the mothers receiving a choline-deficient diet. Our results demonstrate that a deficient maternal diet at critical time points in neurodevelopment results in worse stroke outcomes. This study emphasizes the importance of maternal diet and the impact it can have on offspring health.
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Affiliation(s)
- McCoy Clementson
- Department of Biomedical Sciences; College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Lauren Hurley
- Department of Biomedical Sciences; College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
| | - Sarah Coonrod
- Department of Biomedical Sciences; College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA
| | - Calli Bennett
- Department of Biomedical Sciences; College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Purvaja Marella
- Department of Biomedical Sciences; College of Osteopathic Medicine, Midwestern University, Glendale, AZ, USA
| | - Agnes S Pascual
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Kasey Pull
- Department of Biomedical Sciences, Midwestern University, Glendale, AZ, USA
| | - Brandi Wasek
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Olga Malysheva
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | - Nafisa M Jadavji
- Department of Biomedical Sciences; College of Osteopathic Medicine; College of Veterinary Medicine, Midwestern University, Glendale, AZ, USA; Department of Neuroscience, Carleton University, Ottawa, ON, Canada; Department of Child Health, College of Medicine - Phoenix, University of Arizona, Phoenix, AZ, USA
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9
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Turck D, Bohn T, Castenmiller J, de Henauw S, Hirsch‐Ernst K, Knutsen HK, Maciuk A, Mangelsdorf I, McArdle HJ, Pentieva K, Siani A, Thies F, Tsabouri S, Vinceti M, Crous‐Bou M, Molloy A, Ciccolallo L, de Sesmaisons Lecarré A, Fabiani L, Horvath Z, Karavasiloglou N, Naska A. Scientific opinion on the tolerable upper intake level for folate. EFSA J 2023; 21:e08353. [PMID: 37965303 PMCID: PMC10641704 DOI: 10.2903/j.efsa.2023.8353] [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] [Indexed: 11/16/2023] Open
Abstract
Following a request from the European Commission (EC), the EFSA Panel on Nutrition, Novel Foods and Food Allergens (NDA) was asked to deliver a scientific opinion on the revision of the tolerable upper intake level (UL) for folic acid/folate. Systematic reviews of the literature were conducted to assess evidence on priority adverse health effects of excess intake of folate (including folic acid and the other authorised forms, (6S)-5-methyltetrahydrofolic acid glucosamine and l-5-methyltetrahydrofolic acid calcium salts), namely risk of cobalamin-dependent neuropathy, cognitive decline among people with low cobalamin status, and colorectal cancer and prostate cancer. The evidence is insufficient to conclude on a positive and causal relationship between the dietary intake of folate and impaired cognitive function, risk of colorectal and prostate cancer. The risk of progression of neurological symptoms in cobalamin-deficient patients is considered as the critical effect to establish an UL for folic acid. No new evidence has been published that could improve the characterisation of the dose-response between folic acid intake and resolution of megaloblastic anaemia in cobalamin-deficient individuals. The ULs for folic acid previously established by the Scientific Committee on Food are retained for all population groups, i.e. 1000 μg/day for adults, including pregnant and lactating women, 200 μg/day for children aged 1-3 years, 300 μg/day for 4-6 years, 400 μg/day for 7-10 years, 600 μg/day for 11-14 years and 800 μg/day for 15-17 years. A UL of 200 μg/day is established for infants aged 4-11 months. The ULs apply to the combined intake of folic acid, (6S)-5-methyltetrahydrofolic acid glucosamine and l-5-methyltetrahydrofolic acid calcium salts, under their authorised conditions of use. It is unlikely that the ULs for supplemental folate are exceeded in European populations, except for regular users of food supplements containing high doses of folic acid/5-methyl-tetrahydrofolic acid salts.
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10
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Gaml-Sørensen A, Brix N, Lunddorf LLH, Ernst A, Høyer BB, Olsen SF, Granström C, Toft G, Henriksen TB, Ramlau-Hansen CH. Maternal intake of folate and folic acid during pregnancy and pubertal timing in girls and boys: A population-based cohort study. Paediatr Perinat Epidemiol 2023; 37:618-629. [PMID: 37132131 DOI: 10.1111/ppe.12981] [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: 10/03/2022] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023]
Abstract
BACKGROUND Folate is essential for normal foetal development as it plays an important role for gene expression during different periods of foetal development. Thus, prenatal exposure to folate may have a programming effect on pubertal timing. OBJECTIVES To study the association between maternal intake of folate during pregnancy and pubertal timing in girls and boys. METHODS We studied 6585 girls and 6326 boys from a Danish population-based Puberty Cohort, 2000-2021. Information on maternal intake of folate from diet and folic acid from supplements was obtained from a food-frequency questionnaire in mid-pregnancy, and total folate was calculated as dietary folate equivalents. Information on age at menarche in girls, age at first ejaculation and voice break in boys, and Tanner stages, acne and axillary hair in both girls and boys was obtained every 6 months throughout puberty. We estimated mean monthly differences according to exposure groups for each pubertal milestone in addition to a combined estimate for the average age at attaining all pubertal milestones using multivariable interval-censored regression models. Total folate was analysed in quintiles, continuous and as restricted cubic splines. RESULTS Maternal intake of total folate in mid-pregnancy was not associated with pubertal timing in girls (combined estimate for overall pubertal timing per standard deviation (SD 325 μg/day) decrease in maternal intake of total folate: -0.14 months (95% confidence interval [CI] -0.51, 0.22)). Boys had slightly later overall pubertal timing per standard deviation (SD 325 μg/day) decrease in maternal intake of total folate (combined estimate: 0.40 months, 95% CI 0.01, 0.72). Spline plots supported these findings. CONCLUSIONS Prenatal exposure to low maternal intake of total folate in mid-pregnancy was not associated with pubertal timing in girls but associated with slightly later pubertal timing in boys. This minor delay is likely not of clinical importance.
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Affiliation(s)
| | - Nis Brix
- Department of Public Health, Aarhus University, Aarhus C, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
| | | | - Andreas Ernst
- Department of Public Health, Aarhus University, Aarhus C, Denmark
- Department of Urology, Aarhus University Hospital, Aarhus N, Denmark
| | - Birgit Bjerre Høyer
- Open Patient Data Explorative Network, Odense University Hospital, Odense, Denmark
| | - Sjurdur Frodi Olsen
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen S, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen K, Denmark
| | - Charlotta Granström
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen S, Denmark
| | - Gunnar Toft
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus N, Denmark
| | - Tine Brink Henriksen
- Perinatal Epidemiology Research Unit, Department of Paediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus N, Denmark
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11
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Xu R, Hong X, Ladd-Acosta C, Buckley JP, Choi G, Wang G, Hou W, Wang X, Liang L, Ji H. Contrasting Association of Maternal Plasma Biomarkers of Smoking and 1-Carbon Micronutrients with Offspring DNA Methylation: Evidence of Aryl Hydrocarbon Receptor Repressor Gene-Smoking-Folate Interaction. J Nutr 2023; 153:2339-2351. [PMID: 37156443 PMCID: PMC10447613 DOI: 10.1016/j.tjnut.2023.05.002] [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: 01/12/2023] [Revised: 04/11/2023] [Accepted: 05/01/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Maternal prenatal smoking is known to alter offspring DNA methylation (DNAm). However, there are no effective interventions to mitigate smoking-induced DNAm alteration. OBJECTIVES This study investigated whether 1-carbon nutrients (folate, vitamins B6, and B12) can protect against prenatal smoking-induced offspring DNAm alterations in the aryl hydrocarbon receptor repressor (AHRR) (cg05575921), GFI1 (cg09935388), and CYP1A1 (cg05549655) genes. METHODS This study included mother-newborn dyads from a racially diverse US birth cohort. The cord blood DNAm at the above 3 sites were derived from a previous study using the Illumina Infinium MethylationEPIC BeadChip. Maternal smoking was assessed by self-report and plasma biomarkers (hydroxycotinine and cotinine). Maternal plasma folate, and vitamins B6 and B12 concentrations were obtained shortly after delivery. Linear regressions, Bayesian kernel machine regression, and quantile g-computation were applied to test the study hypothesis by adjusting for covariables and multiple testing. RESULTS The study included 834 mother-newborn dyads (16.7% of newborns exposed to maternal smoking). DNAm at cg05575921 (AHRR) and at cg09935388 (GFI1) was inversely associated with maternal smoking biomarkers in a dose-response fashion (all P < 7.01 × 10-13). In contrast, cg05549655 (CYP1A1) was positively associated with maternal smoking biomarkers (P < 2.4 × 10-6). Folate concentrations only affected DNAm levels at cg05575921 (AHRR, P = 0.014). Regression analyses showed that compared with offspring with low hydroxycotinine exposure (<0.494) and adequate maternal folate concentrations (quartiles 2-4), an offspring with high hydroxycotinine exposure (≥0.494) and low folate concentrations (quartile 1) had a significant reduction in DNAm at cg05575921 (M-value, ß ± SE = -0.801 ± 0.117, P = 1.44 × 10-11), whereas adequate folate concentrations could cut smoking-induced hypomethylation by almost half. Exposure mixture models further supported the protective role of adequate folate concentrations against smoking-induced aryl hydrocarbon receptor repressor (AHRR) hypomethylation. CONCLUSIONS This study found that adequate maternal folate can attenuate maternal smoking-induced offspring AHRR cg05575921 hypomethylation, which has been previously linked to a range of pediatric and adult diseases.
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Affiliation(s)
- Richard Xu
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Xiumei Hong
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States.
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Jessie P Buckley
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Giehae Choi
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Guoying Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States
| | - Wenpin Hou
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, United States
| | - Xiaobin Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States; Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, United States
| | - Liming Liang
- Department of Epidemiology, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States; Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, United States.
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12
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Gu YJ, Qian HY, Zhou F, Zhang L, Chen L, Song Y, Chen YN, Zhang HL. Folic acid relieves bone cancer pain by downregulating P2X2/3 receptors in rats. Brain Res 2023; 1811:148405. [PMID: 37164174 DOI: 10.1016/j.brainres.2023.148405] [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: 12/27/2022] [Revised: 05/04/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]
Abstract
BACKGROUND Bone cancer pain (BCP) remains a clinical challenge due to the limited and side effects of therapeutic methods. Folic acid has been known as an FDA approved dietary supplement and proved to have an analgesic effect in neuropathic pain. Here we investigate the role and mechanism of folic acid in bone cancer pain of a rat model. METHODS Walker 256 tumor cells were inoculated into the left tibia of rats to induce bone cancer pain model. Pain reflex were assessed by paw withdrawal threshold (PWT) response to Von Frey filaments and paw withdrawal latency (PWL) response to thermal stimulation. Folic acid was injected intraperitoneally to evaluate its analgesic effect in rats with bone cancer pain. Western blotting and qPCR were used to determine P2X2/3 receptor protein and mRNA levels in ipsilateral L4-6 dorsal root ganglion (DRG) and spinal dorsal horn (SDH). RESULTS The PWT and PWL of rats with bone cancer pain were obviously decreased compared to the naïve and sham rats. Interestingly, continuous folic acid treatment significantly increased the PWT and PWL of rats with bone cancer pain. P2X2 and P2X3 receptors were clearly upregulated at both mRNA and protein expression in L4-6 DRG and SDH of rats with bone cancer pain. P2X2 and P2X3 receptors were mainly localized with CGRP (calcitonin gene-related peptide) or IB4 (isolectin B4) positive neurons in L4-6 DRG of rats with bone cancer pain. Notably, continuous folic acid treatment significantly reduced the expression of P2X2 and P2X3 receptors in L4-6 DRG and SDH of rats with bone cancer pain. Finally, intrathecal injection of A317491 (a selective antagonist of P2X2/3 receptors) markedly elevated the PWT and PWL of rats with bone cancer pain. CONCLUSION These results suggest that folic acid has an effective antinociceptive effect on bone cancer pain, which is mediated by downregulating P2X2/3 receptors in L4-6 DRG and SDH of rats with bone cancer pain. Folic acid may be a novel therapeutic strategy in cancer patients for pain relief.
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Affiliation(s)
- Yong-Juan Gu
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China; Department of Oncology, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China
| | - He-Ya Qian
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China; Department of Oncology, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China
| | - Fang Zhou
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China; Department of Oncology, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China
| | - Ling Zhang
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China
| | - Long Chen
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China
| | - Yu Song
- Department of Oncology, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China
| | - Ya-Nan Chen
- Department of Oncology, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China.
| | - Hai-Long Zhang
- Center for Translational Medicine, Affiliated Zhangjiagang Hospital of Soochow University, Zhangjiagang 215600, China; Jiangsu Key Laboratory of Neuropsychiatric Diseases and Institute of Neuroscience, Soochow University, Suzhou 215123, China.
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13
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Gaml‐Sørensen A, Brix N, Høyer BB, Tøttenborg SS, Hougaard KS, Bonde JPE, Clemmensen PJ, Ernst A, Arendt LH, Olsen SF, Granström C, Henriksen TB, Toft G, Ramlau‐Hansen CH. Maternal intake of folate and folic acid during pregnancy and markers of male fecundity: A population-based cohort study. Andrology 2023; 11:537-550. [PMID: 36524586 PMCID: PMC10947439 DOI: 10.1111/andr.13364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/18/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Poor male fecundity is of concern, and a prenatal origin has been proposed. Folate, a methyl donor involved in DNA methylation, is essential for normal fetal development by regulating gene expression during different periods of fetal development. Thus, prenatal exposure to low maternal folate intake might have a programing function of the developing reproductive organs. OBJECTIVES To examine the association between maternal intake of folate from diet and folic acid from supplements during pregnancy and markers of fecundity in young men. MATERIALS AND METHODS We conducted a follow-up study using a Danish mother-son cohort of 787 young men born 1998-2000. Percentage differences in semen characteristics, testes volume, and reproductive hormone levels were analyzed according to total folate calculated as dietary folate equivalents from diet and supplements in midpregnancy, using multivariable negative binomial regression models. Total folate was analyzed in quintiles, continuous per standard deviation decrease (SD: 318 μg/day) and as restricted cubic splines. RESULTS Low maternal intake of total folate was associated with lower total sperm count (-5% (95% confidence intervals [CI]: -11%; 2%)), a lower proportion of non-progressive and immotile spermatozoa (-5% [95% CI: -8%; -3%]), and lower testes volume (-4% [95% CI: -6%; -2%]) per SD decrease in total folate intake. Spline plots supported these findings. DISCUSSION The finding of a lower proportion of non-progressive and immotile spermatozoa, and hence a higher proportion of motile spermatozoa, in men of mothers with a lower intake of total folate in midpregnancy was surprising and may be a chance finding. CONCLUSION Lower maternal intake of total folate in midpregnancy was associated with lower sperm count and lower testes volume, however, also with a lower proportion of non-progressive and immotile spermatozoa in adult men. Whether this actually affects the ability to obtain a pregnancy warrants further investigation.
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Affiliation(s)
- Anne Gaml‐Sørensen
- Department of Public HealthResearch Unit for EpidemiologyAarhus UniversityAarhus CDenmark
| | - Nis Brix
- Department of Public HealthResearch Unit for EpidemiologyAarhus UniversityAarhus CDenmark
- Department of Clinical GeneticsAarhus University HospitalAarhus NDenmark
| | - Birgit Bjerre Høyer
- Department of Occupational and Environmental MedicineBispebjerg and Frederiksberg HospitalUniversity of CopenhagenCopenhagen NVDenmark
- Open Patient data Explorative NetworkOdense University HospitalOdenseDenmark
| | - Sandra Søgaard Tøttenborg
- Department of Occupational and Environmental MedicineBispebjerg and Frederiksberg HospitalUniversity of CopenhagenCopenhagen NVDenmark
- Department of Public HealthUniversity of CopenhagenCopenhagen KDenmark
| | - Karin Sørig Hougaard
- Department of Public HealthUniversity of CopenhagenCopenhagen KDenmark
- National Research Centre for the Working EnvironmentCopenhagen OestDenmark
| | - Jens Peter Ellekilde Bonde
- Department of Occupational and Environmental MedicineBispebjerg and Frederiksberg HospitalUniversity of CopenhagenCopenhagen NVDenmark
- Department of Public HealthUniversity of CopenhagenCopenhagen KDenmark
| | | | - Andreas Ernst
- Department of Public HealthResearch Unit for EpidemiologyAarhus UniversityAarhus CDenmark
- Department of UrologyAarhus University HospitalAarhus NDenmark
| | - Linn Håkonsen Arendt
- Department of Public HealthResearch Unit for EpidemiologyAarhus UniversityAarhus CDenmark
- Department of Obstetrics and GynecologyAarhus University HospitalAarhus NDenmark
| | - Sjurdur Frodi Olsen
- Department of Public HealthUniversity of CopenhagenCopenhagen KDenmark
- Department of Epidemiology ResearchStatens Serum InstitutCopenhagen SDenmark
| | - Charlotta Granström
- Department of Epidemiology ResearchStatens Serum InstitutCopenhagen SDenmark
| | - Tine Brink Henriksen
- Department of Clinical MedicineAarhus UniversityAarhus CDenmark
- Department of PaediatricsAarhus University HospitalAarhus NDenmark
| | - Gunnar Toft
- Steno Diabetes Center AarhusAarhus University HospitalAarhus NDenmark
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14
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Steane SE, Cuffe JSM, Moritz KM. The role of maternal choline, folate and one-carbon metabolism in mediating the impact of prenatal alcohol exposure on placental and fetal development. J Physiol 2023; 601:1061-1075. [PMID: 36755527 PMCID: PMC10952912 DOI: 10.1113/jp283556] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 01/30/2023] [Indexed: 02/10/2023] Open
Abstract
Prenatal alcohol consumption (PAE) may be associated with a broad spectrum of impacts, ranging from no overt effects, to miscarriage, fetal growth restriction and fetal alcohol spectrum disorder. A major mechanism underlying the effects of PAE is considered to be altered DNA methylation and gene expression. Maternal nutritional status may be an important factor in determining the extent to which PAE impacts pregnancy outcomes, particularly the dietary micronutrients folate and choline because they provide methyl groups for DNA methylation via one carbon metabolism. This review summarises the roles of folate and choline in development of the blastocyst, the placenta and the fetal brain, and examines the evidence that maternal intake of these micronutrients can modify the effects of PAE on development. Studies of folate or choline deficiency have found reduced blastocyst development and implantation, reduced placental invasion, vascularisation and nutrient transport capability, impaired fetal brain development, and abnormal neurodevelopmental outcomes. PAE has been shown to reduce absorption and/or metabolism of folate and choline and to produce similar outcomes to maternal choline/folate deficiency. A few studies have demonstrated that the effects of PAE on brain development can be ameliorated by folate or choline supplementation; however, there is very limited evidence on the effects of supplementation in early pregnancy on the blastocyst and placenta. Further studies are required to support these findings and to determine optimal supplementation parameters.
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Affiliation(s)
- Sarah E. Steane
- School of Biomedical SciencesThe University of QueenslandSt LuciaQLDAustralia
| | - James S. M. Cuffe
- School of Biomedical SciencesThe University of QueenslandSt LuciaQLDAustralia
| | - Karen M. Moritz
- School of Biomedical SciencesThe University of QueenslandSt LuciaQLDAustralia
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15
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Crider KS, Wang A, Ling H, Potischman N, Bailey RL, Lichen Y, Pfeiffer CM, Killian JK, Rose C, Sampson J, Zhu L, Berry RJ, Linet M, Yu W, Su LJ. Maternal Periconceptional Folic Acid Supplementation and DNA Methylation Patterns in Adolescent Offspring. J Nutr 2023; 152:2669-2676. [PMID: 36196007 PMCID: PMC9839994 DOI: 10.1093/jn/nxac184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Folate, including the folic acid form, is a key component of the one-carbon metabolic pathway used for DNA methylation. Changes in DNA methylation patterns during critical development periods are associated with disease outcomes and are associated with changes in nutritional status in pregnancy. The long-term impact of periconceptional folic acid supplementation on DNA methylation patterns is unknown. OBJECTIVES To determine the long-term impact of periconceptional folic acid supplementation on DNA methylation patterns, we examined the association of the recommended dosage (400 μg/d) and time period (periconceptional before pregnancy through first trimester) of folic acid supplementation with the DNA methylation patterns in the offspring at age 14-17 y compared with offspring with no supplementation. METHODS Two geographic sites in China from the 1993-1995 Community Intervention Program of folic acid supplementation were selected for the follow-up study. DNA methylation at 402,730 CpG sites was assessed using saliva samples from 89 mothers and 179 adolescents (89 male). The mean age at saliva collection was 40 y among mothers (range: 35-54 y) and 15 y among adolescents (range: 14-17 y). Epigenome-wide analyses were conducted to assess the interactions of periconceptional folic acid exposure, the 5,10-methylenetetrahydrofolate reductase (MTHFR)-C677T genotype, and epigenome-wide DNA methylation controlling for offspring sex, geographic region, and background cell composition in the saliva. RESULTS In the primary outcome, no significant differences were observed in epigenome-wide methylation patterns between adolescents exposed and those non-exposed to maternal periconceptional folic acid supplementation after adjustment for potential confounders [false discovery rate (FDR) P values < 0.05]. The MTHFR-C677T genotype did not modify this lack of association (FDR P values < 0.05). CONCLUSIONS Overall, there were no differences in DNA methylation between adolescents who were exposed during the critical developmental window and those not exposed to the recommended periconceptional/first-trimester dosage of folic acid.
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Affiliation(s)
- Krista S Crider
- National Center on Birth Defects and Developmental Disabilities, US CDC, Atlanta, GA, USA
| | - Arick Wang
- National Center on Birth Defects and Developmental Disabilities, US CDC, Atlanta, GA, USA
| | - Hao Ling
- US CDC China Office, Beijing, China
| | | | - Regan L Bailey
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Yang Lichen
- National Center for Nutrition and Health, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Christine M Pfeiffer
- Division of Laboratory Sciences, National Center for Environmental Health, US CDC, Atlanta, GA, USA
| | - J Keith Killian
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Charles Rose
- National Center on Birth Defects and Developmental Disabilities, US CDC, Atlanta, GA, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Li Zhu
- School of Public Health, Peking University Health Science Center, Beijing, China (retired)
| | - Robert J Berry
- National Center on Birth Defects and Developmental Disabilities, US CDC, Atlanta, GA, USA
| | - Martha Linet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Wang Yu
- Director General (former), Chinese Center for Disease Control and Prevention, Beijing, China
| | - L Joseph Su
- Cancer Prevention and Population Sciences Program, Division of Epidemiology, University of Arkansas, Little Rock, AR, USA
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16
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Schrott R, Song A, Ladd-Acosta C. Epigenetics as a Biomarker for Early-Life Environmental Exposure. Curr Environ Health Rep 2022; 9:604-624. [PMID: 35907133 DOI: 10.1007/s40572-022-00373-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE OF REVIEW There is interest in evaluating the developmental origins of health and disease (DOHaD) which emphasizes the role of prenatal and early-life environments on non-communicable health outcomes throughout the life course. The ability to rigorously assess and identify early-life risk factors for later health outcomes, including those with childhood onset, in large population samples is often limited due to measurement challenges such as impractical costs associated with prospective studies with a long follow-up duration, short half-lives for some environmental toxicants, and lack of biomarkers that capture inter-individual differences in biologic response to external environments. RECENT FINDINGS Epigenomic patterns, and DNA methylation in particular, have emerged as a potential objective biomarker to address some of these study design and exposure measurement challenges. In this article, we summarize the literature to date on epigenetic changes associated with specific prenatal and early-life exposure domains as well as exposure mixtures in human observational studies and their biomarker potential. Additionally, we highlight evidence for other types of epigenetic patterns to serve as exposure biomarkers. Evidence strongly supports epigenomic biomarkers of exposure that are detectable across the lifespan and across a range of exposure domains. Current and future areas of research in this field seek to expand these lines of evidence to other environmental exposures, to determine their specificity, and to develop predictive algorithms and methylation scores that can be used to evaluate early-life risk factors for health outcomes across the life span.
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Affiliation(s)
- Rose Schrott
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ashley Song
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205, USA.
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17
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Xu FX, Chen X, Zhang H, Fan YJ, Song YP, Lv JW, Xie YL, Huang Y, Chen DZ, Wang H, Xu DX. Association between gestational arsenic exposure and intrauterine growth restriction: the role of folate content. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:89652-89661. [PMID: 35857162 DOI: 10.1007/s11356-022-21961-w] [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: 03/26/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Gestational arsenic (As) exposure is associated with intrauterine growth restriction (IUGR). This study explored the association among gestational As exposure, IUGR, and reduction of folate content in maternal and umbilical plasma from 530 mother-and-singleton-offspring pairs. Birth weight (BW) was negatively correlated with As in maternal plasma (r=-0.194, P<0.001) and umbilical plasma (r=-0.235, P<0.001). By contrast, a positive correlation was found between BW and maternal folate content (r=0.198, P<0.001). The subjects were divided into As-L and As-H groups. The influence of As-H on small for gestational age (SGA) infants, a marker of IUGR, was evaluated by multivariate logistic regression that excludes interferences of gestational age, infant sex, and other confounding factors. Mothers with As-H had an elevated risk of SGA infants (adjusted OR, 2.370; P<0.05). Interestingly, maternal folate content was lower in subjects with As-H than those with As-L (22.4±10.7 vs 11.2±6.7 nmol/L, P<0.001). Linear correlation models show that As level was negatively correlated with folate content in maternal plasma (r=-0.615, P<0.001) and umbilical plasma (r=-0.209, P<0.001). Moreover, maternal folate reduction has an obvious mediating effect between increased As and decreased BW (β=-0.078, P<0.05). Our results indicate that folate reduction may be a mediator between gestational As exposure and IUGR.
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Affiliation(s)
- Fei-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Xu Chen
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Heng Zhang
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
- Wuxi Maternity and Child Health Care Hospital, Wuxi, 214122, Jiangsu Province, China
| | - Yi-Jun Fan
- Second Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Ya-Ping Song
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Jin-Wei Lv
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Ya-Li Xie
- Department of Nutrition, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Yichao Huang
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - Dao-Zhen Chen
- Wuxi Maternity and Child Health Care Hospital, Wuxi, 214122, Jiangsu Province, China
| | - Hua Wang
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China
| | - De-Xiang Xu
- Department of Toxicology, Anhui Medical University, Hefei, 230032, Anhui Province, China.
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18
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Charoenvicha C, Sirimaharaj W, Khwanngern K, Chattipakorn N, Chattipakorn SC. Alterations in DNA Methylation in Orofacial Clefts. Int J Mol Sci 2022; 23:ijms232112727. [PMID: 36361518 PMCID: PMC9654384 DOI: 10.3390/ijms232112727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Orofacial clefts are among the most common craniofacial anomalies with multifactorial etiologies, including genetics and environments. DNA methylation, one of the most acknowledged mechanisms of epigenetics, is involved in the development of orofacial clefts. DNA methylation has been examined in patients with non-syndromic cleft lip with cleft palate (nsCL/P) from multiple specimens, including blood, saliva, lip, and palate, as well as experimental studies in mice. The results can be reported in two different trends: hypomethylation and hypermethylation. Both hypomethylation and hypermethylation can potentially increase the risk of nsCL/P depending on the types of specimens and the specific regions on each gene and chromosome. This is the most up-to-date review, intending to summarize evidence of the alterations of DNA methylation in association with the occurrence of orofacial clefts. To make things straightforward to understand, we have systematically categorized the data into four main groups: human blood, human tissues, animal models, and the factors associated with DNA methylation. With this review, we are moving closer to the core of DNA methylation associated with nsCL/P development; we hope this is the initial step to find a genetic tool for early detection and prevention of the occurrence of nsCL/P.
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Affiliation(s)
- Chirakan Charoenvicha
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Clinical Surgical Research Center, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wimon Sirimaharaj
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Krit Khwanngern
- Plastic and Reconstructive Surgery Unit, Department of Surgery, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nipon Chattipakorn
- Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Siriporn C. Chattipakorn
- Center of Excellence in Cardiac Electrophysiology Research, Chiang Mai University, Chiang Mai 50200, Thailand
- Neurophysiology Unit, Cardiac Electrophysiology Research and Training Center, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Department of Oral Biology and Diagnostic Sciences, Faculty of Dentistry, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence: ; Tel.: +011-66-53-944-451; Fax: +011-66-53-222-844
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19
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Derakhshan M, Kessler NJ, Ishida M, Demetriou C, Brucato N, Moore G, Fall CHD, Chandak GR, Ricaut FX, Prentice A, Hellenthal G, Silver M. Tissue- and ethnicity-independent hypervariable DNA methylation states show evidence of establishment in the early human embryo. Nucleic Acids Res 2022; 50:6735-6752. [PMID: 35713545 PMCID: PMC9749461 DOI: 10.1093/nar/gkac503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/06/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs ('hvCpGs') with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.
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Affiliation(s)
| | - Noah J Kessler
- Department of Genetics, University of Cambridge,
Cambridge CB2 3EH, UK
| | - Miho Ishida
- UCL Great Ormond Street Institute of Child Health, UK
| | | | - Nicolas Brucato
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton,
Southampton, UK
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR-Centre for Cellular
and Molecular Biology,Hyderabad, India
| | - Francois-Xavier Ricaut
- Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université
de Toulouse Midi-Pyrénées, CNRS, IRD, UPS,Toulouse, France
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
| | - Garrett Hellenthal
- UCL Genetics Institute, University College London,
Gower Street, London WC1E 6BT, UK
| | - Matt J Silver
- London School of Hygiene and Tropical Medicine, UK
- Medical Research Council Unit The Gambia at the London School of Hygiene
and Tropical Medicine, The Gambia
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20
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Moderate Folic Acid Supplementation in Pregnant Mice Results in Altered Sex-Specific Gene Expression in Brain of Young Mice and Embryos. Nutrients 2022; 14:nu14051051. [PMID: 35268026 PMCID: PMC8912750 DOI: 10.3390/nu14051051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/22/2022] [Accepted: 02/26/2022] [Indexed: 02/07/2023] Open
Abstract
Food fortification and increased vitamin intake have led to higher folic acid (FA) consumption by many pregnant women. We showed that FA-supplemented diet in pregnant mice (fivefold higher FA than the recommended level (5xFASD)) led to hyperactivity-like behavior and memory impairment in pups. Disturbed choline/methyl metabolism and altered placental gene expression were identified. The aim of this study was to examine the impact of 5xFASD on the brain at two developmental stages, postnatal day (P) 30 and embryonic day (E) 17.5. Female C57BL/6 mice were fed a control diet or 5xFASD for 1 month before mating. Diets were maintained throughout the pregnancy and lactation until P30 or during pregnancy until E17.5. The 5xFASD led to sex-specific transcription changes in P30 cerebral cortex and E17.5 cerebrum, with microarrays showing a total of 1003 and 623 changes, respectively. Enhanced mRNA degradation was observed in E17.5 cerebrum. Expression changes of genes involved in neurotransmission, neuronal growth and development, and angiogenesis were verified by qRT-PCR; 12 and 15 genes were verified at P30 and E17.5, respectively. Hippocampal collagen staining suggested decreased vessel density in FASD male embryos. This study provides insight into the mechanisms of neurobehavioral alterations and highlights potential deleterious consequences of moderate folate oversupplementation during pregnancy.
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21
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Kok DE, Richmond RC, Adriaens M, Evelo CT, Ford D, Mathers JC, Robinson N, McKay JA. Impact of In Utero Folate Exposure on DNA Methylation and Its Potential Relevance for Later-Life Health-Evidence from Mouse Models Translated to Human Cohorts. Mol Nutr Food Res 2022; 66:e2100789. [PMID: 34850562 PMCID: PMC7614326 DOI: 10.1002/mnfr.202100789] [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: 08/24/2021] [Revised: 10/29/2021] [Indexed: 11/08/2022]
Abstract
SCOPE Persistent DNA methylation changes may mediate effects of early-life exposures on later-life health. Human lifespan is challenging for prospective studies, therefore data from longitudinal studies are limited. Projecting data from mouse models of early-life exposure to human studies offers a tool to address this challenge. METHODS AND RESULTS C57BL/6J mice were fed low/normal folate diets before and during pregnancy and lactation. Genome-wide promoter methylation was measured in male offspring livers at 17.5 days gestation and 28 weeks. Eight promoters were concurrently hypermethylated by folate depletion in fetuses and adults (>1.10 fold-change; p < 0.05). Processes/pathways potentially influenced by global changes, and function of these eight genes, suggest neurocognitive effects. Human observational and randomized controlled trial data were interrogated for translation. Methylation at birth was inversely associated with maternal plasma folate in six genes (-1.15% to -0.16% per nmol L-1 ; p < 0.05), while maternal folic acid supplementation was associated with differential methylation of four genes in adulthood. Three CpGs were persistently hypermethylated with lower maternal folate (p = 0.04). CONCLUSION Some persistent folate-induced methylation changes in mice are mirrored in humans. This demonstrates utility of mouse data in identifying human loci for interrogation as biomarkers of later-life health.
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Affiliation(s)
- Dieuwertje E Kok
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, The Netherlands
| | - Rebecca C Richmond
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Michiel Adriaens
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands
| | - Chris T Evelo
- Maastricht Centre for Systems Biology, Maastricht University, Maastricht, The Netherlands.,Department of Bioinformatics - BiGCaT, NUTRIM Research School, Maastricht University, Maastricht, The Netherlands
| | - Dianne Ford
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - John C Mathers
- Centre for Healthier Lives, Population Health Sciences Institute, Newcastle University, Human Nutrition Research Centre, Newcastle upon Tyne, UK
| | - Natassia Robinson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jill A McKay
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
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22
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OUP accepted manuscript. Nutr Rev 2022; 80:2178-2197. [DOI: 10.1093/nutrit/nuac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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23
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Candler T, Kessler N, Gunasekara C, Ward K, James P, Laritsky E, Baker M, Dyer R, Elango R, Jeffries D, Waterland R, Moore S, Ludgate M, Prentice A, Silver M. DNA methylation at a nutritionally sensitive region of the PAX8 gene is associated with thyroid volume and function in Gambian children. SCIENCE ADVANCES 2021; 7:eabj1561. [PMID: 34739318 PMCID: PMC8570597 DOI: 10.1126/sciadv.abj1561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 09/16/2021] [Indexed: 05/13/2023]
Abstract
PAX8 is a key thyroid transcription factor implicated in thyroid gland differentiation and function, and PAX8 gene methylation is reported to be sensitive to the periconceptional environment. Using a novel recall-by-epigenotype study in Gambian children, we found that PAX8 hypomethylation at age 2 years is associated with a 21% increase in thyroid volume and an increase in free thyroxine (T4) at 5 to 8 years, the latter equivalent to 8.4% of the normal range. Free T4 was associated with a decrease in DXA-derived body fat and bone mineral density. Furthermore, offspring PAX8 methylation was associated with periconceptional maternal nutrition, and methylation variability was influenced by genotype, suggesting that sensitivity to environmental exposures may be under partial genetic control. Together, our results demonstrate a possible link between early environment, PAX8 gene methylation and thyroid gland development and function, with potential implications for early embryonic programming of thyroid-related health and disease.
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Affiliation(s)
- Toby Candler
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Noah Kessler
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Chathura Gunasekara
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Kate Ward
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- MRC Lifecourse Epidemiology, University of Southampton, Southampton, UK
| | - Philip James
- Department of Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Eleonora Laritsky
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Maria Baker
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Roger Dyer
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Rajavel Elango
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - David Jeffries
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Robert Waterland
- USDA/ARS Children’s Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sophie Moore
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
- Department of Women and Children’s Health, King’s College London, London, UK
| | - Marian Ludgate
- Thyroid Research Group, School of Medicine, Cardiff University, Cardiff, UK
| | - Andrew Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
| | - Matt Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, UK
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24
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Oocyte age and preconceptual alcohol use are highly correlated with epigenetic imprinting of a noncoding RNA ( nc886). Proc Natl Acad Sci U S A 2021; 118:2026580118. [PMID: 33723081 PMCID: PMC8000112 DOI: 10.1073/pnas.2026580118] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Genomic imprinting occurs before fertilization, impacts every cell of the developing child, and may be sensitive to environmental perturbations. The noncoding RNA, nc886 (also called VTRNA2-1) is the only known example of the ∼100 human genes imprinted by DNA methylation, that shows polymorphic imprinting in the population. The nc886 gene is part of an ∼1.6-kb differentially methylated region (DMR) that is methylated in the oocyte and silenced on the maternal allele in about 75% of humans worldwide. Here, we show that the presence or absence of imprinting at the nc886 DMR in an individual is consistent across different tissues, confirming that the imprint is established before cellular differentiation and is maintained into adulthood. We investigated the relationships between the frequency of imprinting in newborns and maternal age, alcohol consumption and cigarette smoking before conception in more than 1,100 mother/child pairs from South Africa. The probability of imprinting in newborns was increased in older mothers and decreased in mothers who drank alcohol before conception. On the other hand, cigarette smoking had no apparent relationship with the frequency of imprinting. These data show an epigenetic change during oocyte maturation which is potentially subject to environmental influence. Much focus has been placed on avoiding alcohol consumption during pregnancy, but our data suggest that drinking before conception may affect the epigenome of the newborn.
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25
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Fort RS, Duhagon MA. Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology. F1000Res 2021; 10:182. [PMID: 34354812 PMCID: PMC8287541 DOI: 10.12688/f1000research.28510.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.
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Affiliation(s)
- Rafael Sebastián Fort
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Montevideo, 11600, Uruguay
| | - María Ana Duhagon
- Laboratorio de Interacciones Moleculares, Facultad de Ciencias, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay.,Depto. de Genética, Facultad de Medicina, Universidad de la República, Montevideo, Montevideo, 11400, Uruguay
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26
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VTRNA2-1: Genetic Variation, Heritable Methylation and Disease Association. Int J Mol Sci 2021; 22:ijms22052535. [PMID: 33802562 PMCID: PMC7961504 DOI: 10.3390/ijms22052535] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/28/2022] Open
Abstract
VTRNA2-1 is a metastable epiallele with accumulating evidence that methylation at this region is heritable, modifiable and associated with disease including risk and progression of cancer. This study investigated the influence of genetic variation and other factors such as age and adult lifestyle on blood DNA methylation in this region. We first sequenced the VTRNA2-1 gene region in multiple-case breast cancer families in which VTRNA2-1 methylation was identified as heritable and associated with breast cancer risk. Methylation quantitative trait loci (mQTL) were investigated using a prospective cohort study (4500 participants with genotyping and methylation data). The cis-mQTL analysis (334 variants ± 50 kb of the most heritable CpG site) identified 43 variants associated with VTRNA2-1 methylation (p < 1.5 × 10−4); however, these explained little of the methylation variation (R2 < 0.5% for each of these variants). No genetic variants elsewhere in the genome were found to strongly influence VTRNA2-1 methylation. SNP-based heritability estimates were consistent with the mQTL findings (h2 = 0, 95%CI: −0.14 to 0.14). We found no evidence that age, sex, country of birth, smoking, body mass index, alcohol consumption or diet influenced blood DNA methylation at VTRNA2-1. Genetic factors and adult lifestyle play a minimal role in explaining methylation variability at the heritable VTRNA2-1 cluster.
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27
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van der Windt M, Schoenmakers S, van Rijn B, Galjaard S, Steegers-Theunissen R, van Rossem L. Epidemiology and (Patho)Physiology of Folic Acid Supplement Use in Obese Women before and during Pregnancy. Nutrients 2021; 13:331. [PMID: 33498674 PMCID: PMC7911986 DOI: 10.3390/nu13020331] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/11/2022] Open
Abstract
Preconception folic acid supplement use is a well-known method of primary prevention of neural tube defects (NTDs). Obese women are at a higher risk for having a child with a NTD. As different international recommendations on folic acid supplement use for obese women before and during pregnancy exist, this narrative review provides an overview of epidemiology of folate deficiency in obese (pre)pregnant women, elaborates on potential mechanisms underlying folate deficiency, and discusses considerations for the usage of higher doses of folic acid supplements. Women with obesity more often suffer from an absolute folate deficiency, as they are less compliant to periconceptional folic acid supplement use recommendations. In addition, their dietary folate intake is limited due to an unbalanced diet (relative malnutrition). The association of obesity and NTDs also seems to be independent of folate intake, with studies suggesting an increased need of folate (relative deficiency) due to derangements involved in other pathways. The relative folate deficiency, as a result of an increased metabolic need for folate in obese women, can be due to: (1) low-grade chronic inflammation (2) insulin resistance, (3) inositol, and (4) dysbiotic gut microbiome, which plays a role in folate production and uptake. In all these pathways, the folate-dependent one-carbon metabolism is involved. In conclusion, scientific evidence of the involvement of several folate-related pathways implies to increase the recommended folic acid supplementation in obese women. However, the physiological uptake of synthetic folic acid is limited and side-effects of unmetabolized folic acid in mothers and offspring, in particular variations in epigenetic (re)programming with long-term health effects, cannot be excluded. Therefore, we emphasize on the urgent need for further research and preconception personalized counseling on folate status, lifestyle, and medical conditions.
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Affiliation(s)
| | | | | | | | - Régine Steegers-Theunissen
- Department of Obstetrics and Gynecology, Erasmus MC, University Medical Center, 3000 CA Rotterdam, The Netherlands; (M.v.d.W.); (S.S.); (B.v.R.); (S.G.); (L.v.R.)
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28
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Maude H, Sanchez-Cabanillas C, Cebola I. Epigenetics of Hepatic Insulin Resistance. Front Endocrinol (Lausanne) 2021; 12:681356. [PMID: 34046015 PMCID: PMC8147868 DOI: 10.3389/fendo.2021.681356] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 04/20/2021] [Indexed: 01/14/2023] Open
Abstract
Insulin resistance (IR) is largely recognized as a unifying feature that underlies metabolic dysfunction. Both lifestyle and genetic factors contribute to IR. Work from recent years has demonstrated that the epigenome may constitute an interface where different signals may converge to promote IR gene expression programs. Here, we review the current knowledge of the role of epigenetics in hepatic IR, focusing on the roles of DNA methylation and histone post-translational modifications. We discuss the broad epigenetic changes observed in the insulin resistant liver and its associated pathophysiological states and leverage on the wealth of 'omics' studies performed to discuss efforts in pinpointing specific loci that are disrupted by these changes. We envision that future studies, with increased genomic resolution and larger cohorts, will further the identification of biomarkers of early onset hepatic IR and assist the development of targeted interventions. Furthermore, there is growing evidence to suggest that persistent epigenetic marks may be acquired over prolonged exposure to disease or deleterious exposures, highlighting the need for preventative medicine and long-term lifestyle adjustments to avoid irreversible or long-term alterations in gene expression.
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Affiliation(s)
| | | | - Inês Cebola
- *Correspondence: Hannah Maude, ; Inês Cebola,
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29
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He Q, Zou T, Chen J, Jian L, He J, Xia Y, Xie F, Wang Z, You J. Maternal Methyl-Donor Micronutrient Supplementation During Pregnancy Promotes Skeletal Muscle Differentiation and Maturity in Newborn and Weaning Pigs. Front Nutr 2020; 7:609022. [PMID: 33330599 PMCID: PMC7734050 DOI: 10.3389/fnut.2020.609022] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/27/2020] [Indexed: 12/17/2022] Open
Abstract
Adequate maternal methyl-donor micronutrient (MET) intake is an important determinant of the organ development and metabolic renovation of offspring. The mechanism involved in skeletal myogenesis and the effect of MET supplementation during pregnancy on the maternal body remain unclear. Thus, this study aimed to investigate the potential effect of methyl donor micronutrients (MET) on skeletal muscle development and metabolism in offspring using pig models. Forty-three Duroc × Erhualian gilts were assigned to two dietary groups during gestation: control diet (CON) and CON diet supplemented with MET (folic acid, methionine, choline, vitamin B6, and vitamin B12). The results showed that maternal MET exposure during pregnancy significantly increased the concentrations of protein, triiodothyronine (T3), and thyroxine (T4) in colostrum and methyl metabolites, including S-adenosylmethionine (SAM), S-adenosyl-L-homocysteine (SAH), 5-methyl-tetrahydrofolate (5-MTHF), and betaine, in the maternal and offspring umbilical vein serum. A similar pattern was demonstrated in the body weight gain and myofiber diameters in offspring. In addition, maternal MET supplementation significantly increased the concentration of offspring serum insulin-like growth factor 1 (IGF-1), T3, and T4; upregulated the mRNA expression of IGF-1 and IGF-1 receptor (IGF-1r) and the phosphorylation level of protein kinases in offspring longissimus dorsi muscle; and upregulated the expression of myogenic genes and fast myosin heavy chain (fast MyHC) in offspring skeletal muscle. Supplementing sows with higher levels of MET during gestation may promote skeletal muscle differentiation and maturity and improve the skeletal muscle mass of the piglets.
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Affiliation(s)
- Qin He
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Tiande Zou
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Jun Chen
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Li Jian
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Jia He
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Yingying Xia
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Fei Xie
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Zirui Wang
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
| | - Jinming You
- Key Laboratory of Animal Nutrition in Jiangxi Province, Jiangxi Agricultural University, Nanchang, China.,Key Innovation Center for Industry-Education Integration of High-Quality and Safety Livestock Production in Jiangxi Province, Nanchang, China
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30
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Maruvada P, Stover PJ, Mason JB, Bailey RL, Davis CD, Field MS, Finnell RH, Garza C, Green R, Gueant JL, Jacques PF, Klurfeld DM, Lamers Y, MacFarlane AJ, Miller JW, Molloy AM, O'Connor DL, Pfeiffer CM, Potischman NA, Rodricks JV, Rosenberg IH, Ross SA, Shane B, Selhub J, Stabler SP, Trasler J, Yamini S, Zappalà G. Knowledge gaps in understanding the metabolic and clinical effects of excess folates/folic acid: a summary, and perspectives, from an NIH workshop. Am J Clin Nutr 2020; 112:1390-1403. [PMID: 33022704 PMCID: PMC7657327 DOI: 10.1093/ajcn/nqaa259] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/20/2020] [Indexed: 12/21/2022] Open
Abstract
Folate, an essential nutrient found naturally in foods in a reduced form, is present in dietary supplements and fortified foods in an oxidized synthetic form (folic acid). There is widespread agreement that maintaining adequate folate status is critical to prevent diseases due to folate inadequacy (e.g., anemia, birth defects, and cancer). However, there are concerns of potential adverse effects of excess folic acid intake and/or elevated folate status, with the original concern focused on exacerbation of clinical effects of vitamin B-12 deficiency and its role in neurocognitive health. More recently, animal and observational studies have suggested potential adverse effects on cancer risk, birth outcomes, and other diseases. Observations indicating adverse effects from excess folic acid intake, elevated folate status, and unmetabolized folic acid (UMFA) remain inconclusive; the data do not provide the evidence needed to affect public health recommendations. Moreover, strong biological and mechanistic premises connecting elevated folic acid intake, UMFA, and/or high folate status to adverse health outcomes are lacking. However, the body of evidence on potential adverse health outcomes indicates the need for comprehensive research to clarify these issues and bridge knowledge gaps. Three key research questions encompass the additional research needed to establish whether high folic acid or total folate intake contributes to disease risk. 1) Does UMFA affect biological pathways leading to adverse health effects? 2) Does elevated folate status resulting from any form of folate intake affect vitamin B-12 function and its roles in sustaining health? 3) Does elevated folate intake, regardless of form, affect biological pathways leading to adverse health effects other than those linked to vitamin B-12 function? This article summarizes the proceedings of an August 2019 NIH expert workshop focused on addressing these research areas.
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Affiliation(s)
- Padma Maruvada
- National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, USA
| | - Patrick J Stover
- Texas A&M University College of Agriculture and Life Sciences, Texas A&M University AgriLife, College Station, TX, USA
| | - Joel B Mason
- Jean Mayer USDA Human Nutrition Research Center on Aging, Friedman School of Nutrition Science and Policy, and School of Medicine, Tufts University, Boston, MA, USA
| | - Regan L Bailey
- Department of Nutrition Science, Purdue University, West Lafayette, IN, USA
| | - Cindy D Davis
- Office of Dietary Supplements, NIH, Bethesda, MD, USA
| | - Martha S Field
- Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, NY, USA
| | - Richard H Finnell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Cutberto Garza
- Professor Emeritus, Division of Nutritional Sciences, College of Human Ecology, Cornell University, Ithaca, NY, USA
| | - Ralph Green
- Department of Pathology and Laboratory Medicine, University of California, Davis Medical Center, Sacramento, CA, USA
| | - Jean-Louis Gueant
- University of Lorraine and University Regional Hospital Centre of Nancy, Nancy, France
| | - Paul F Jacques
- Tufts University Friedman School of Nutritional Science and Policy and the Jean Mayer USDA Human Nutrition Research Center, Boston, MA, USA
| | - David M Klurfeld
- Department of Nutrition, Food Safety, and Quality, USDA Agricultural Research Service, Beltsville, MD, USA
| | - Yvonne Lamers
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Anne M Molloy
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Deborah L O'Connor
- Department of Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
| | | | | | | | - Irwin H Rosenberg
- Jean Mayer USDA Human Nutrition Research Center on Aging, Friedman School of Nutrition Science and Policy, and School of Medicine, Tufts University, Boston, MA, USA
| | | | - Barry Shane
- Department of Nutritional Sciences & Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Jacob Selhub
- Tufts University Friedman School of Nutritional Science and Policy and the Jean Mayer USDA Human Nutrition Research Center, Boston, MA, USA
| | | | | | - Sedigheh Yamini
- Office of Nutrition and Food Labeling, Center for Food Safety and Applied Nutrition, US FDA, College Park, MD, USA
| | - Giovanna Zappalà
- Division of Geriatrics and Clinical Gerontology, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
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31
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Saffari A, Shrestha S, Issarapu P, Sajjadi S, Betts M, Sahariah SA, Tomar AS, James P, Dedaniya A, Yadav DK, Kumaran K, Prentice AM, Lillycrop KA, Fall CHD, Chandak GR, Silver MJ. Effect of maternal preconceptional and pregnancy micronutrient interventions on children's DNA methylation: Findings from the EMPHASIS study. Am J Clin Nutr 2020; 112:1099-1113. [PMID: 32889533 PMCID: PMC7528567 DOI: 10.1093/ajcn/nqaa193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Maternal nutrition in pregnancy has been linked to offspring health in early and later life, with changes to DNA methylation (DNAm) proposed as a mediating mechanism. OBJECTIVE We investigated intervention-associated DNAm changes in children whose mothers participated in 2 randomized controlled trials of micronutrient supplementation before and during pregnancy, as part of the EMPHASIS (Epigenetic Mechanisms linking Preconceptional nutrition and Health Assessed in India and sub-Saharan Africa) study (ISRCTN14266771). DESIGN We conducted epigenome-wide association studies with blood samples from Indian (n = 698) and Gambian (n = 293) children using the Illumina EPIC array and a targeted study of selected loci not on the array. The Indian micronutrient intervention was food based, whereas the Gambian intervention was a micronutrient tablet. RESULTS We identified 6 differentially methylated CpGs in Gambians [2.5-5.0% reduction in intervention group, all false discovery rate (FDR) <5%], the majority mapping to ESM1, which also represented a strong signal in regional analysis. One CpG passed FDR <5% in the Indian cohort, but overall effect sizes were small (<1%) and did not have the characteristics of a robust signature. We also found strong evidence for enrichment of metastable epialleles among subthreshold signals in the Gambian analysis. This supports the notion that multiple methylation loci are influenced by micronutrient supplementation in the early embryo. CONCLUSIONS Maternal preconceptional and pregnancy micronutrient supplementation may alter DNAm in children measured at 7-9 y. Multiple factors, including differences between the nature of the intervention, participants, and settings, are likely to have contributed to the lack of replication in the Indian cohort. Potential links to phenotypic outcomes will be explored in the next stage of the EMPHASIS study.
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Affiliation(s)
- Ayden Saffari
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Smeeta Shrestha
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, India
| | - Prachand Issarapu
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Sara Sajjadi
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Modupeh Betts
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Ashutosh Singh Tomar
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Philip James
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Dilip K Yadav
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
- Department of Physiology, Boston University, School of Medicine, Boston, MA, USA
| | - Kalyanaraman Kumaran
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- CSI Holdsworth Memorial Hospital, Mysore, India
| | - Andrew M Prentice
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia
| | | | - Caroline H D Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
| | - Giriraj R Chandak
- Genomic Research on Complex Diseases (GRC Group), CSIR–Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Matt J Silver
- MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, London, United Kingdom
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32
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Maternal Folic Acid Supplementation Mediates Offspring Health via DNA Methylation. Reprod Sci 2020; 27:963-976. [PMID: 32124397 DOI: 10.1007/s43032-020-00161-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 09/09/2019] [Indexed: 10/24/2022]
Abstract
The clinical significance of periconceptional folic acid supplementation (FAS) in the prevention of neonatal neural tube defects (NTDs) has been recognized for decades. Epidemiological data and experimental findings have consistently been indicating an association between folate deficiency in the first trimester of pregnancy and poor fetal development as well as offspring health (i.e., NTDs, isolated orofacial clefts, neurodevelopmental disorders). Moreover, compelling evidence has suggested adverse effects of folate overload during perinatal period on offspring health (i.e., immune diseases, autism, lipid disorders). In addition to several single-nucleotide polymorphisms (SNPs) in genes related to folate one-carbon metabolism (FOCM), folate concentrations in maternal serum/plasma/red blood cells must be considered when counseling FAS. Epigenetic information encoded by 5-methylcytosines (5mC) plays a critical role in fetal development and offspring health. S-adenosylmethionine (SAM), a methyl donor for 5mC, could be derived from FOCM. As such, folic acid plays a double-edged sword role in offspring health via mediating DNA methylation. However, the underlying epigenetic mechanism is still largely unclear. In this review, we summarized the link across DNA methylation, maternal FAS, and offspring health to provide more evidence for clinical guidance in terms of precise FAS dosage and time point. Future studies are, therefore, required to set up the reference intervals of folate concentrations at different trimesters of pregnancy for different populations and to clarify the epigenetic mechanism for specific offspring diseases.
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Maia CS, Menezes KMCD, Tenorio FDCAM, Queiroz Júnior JRAD, Maciel GEDS. Transtorno do espectro autista e a suplementação por ácido fólico antes e durante a gestação. JORNAL BRASILEIRO DE PSIQUIATRIA 2019. [DOI: 10.1590/0047-2085000000251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
RESUMO Objetivo Elucidar se a suplementação com ácido fólico pouco antes da concepção e/ou durante a gestação pode estar realmente atrelado ao desenvolvimento do transtorno do espectro autista (TEA). Metódos Foi realizada uma revisão de literatura em base de dados, nos idiomas português e inglês, durante o período de novembro de 2017 até abril de 2018, com ênfase nas publicações mais recentes. Resultados Do total de 174 artigos, 87 compuseram este trabalho. Pesquisas apontam que o aumento dos casos de TEA se deve ao fato de que mais fatores genéticos estejam implicados na etiopatogênese neural. No entanto, a grande maioria dos artigos ressalta com maior precisão que há mais efeitos benéficos do uso de ácido fólico antes da concepção e durante a gestação na prevenção do TEA, assim como de outras anormalidades relacionadas aos defeitos do tubo neural. Conclusão Quando se analisa o risco-benefício da suplementação com ácido fólico nas doses recomendadas, 0,4 a 0,8 mg/dia, conclui-se que os benefícios sobrepujam os possíveis riscos de desenvolver o TEA.
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Moody L, Shao J, Chen H, Pan YX. Maternal Low-Fat Diet Programs the Hepatic Epigenome despite Exposure to an Obesogenic Postnatal Diet. Nutrients 2019; 11:nu11092075. [PMID: 31484384 PMCID: PMC6769607 DOI: 10.3390/nu11092075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 12/22/2022] Open
Abstract
Obesity and metabolic disease present a danger to long-term health outcomes. It has been hypothesized that epigenetic marks established during early life might program individuals and have either beneficial or harmful consequences later in life. In the present study, we examined whether maternal diet alters DNA methylation and whether such modifications persist after an obesogenic postnatal dietary challenge. During gestation and lactation, male Sprague-Dawley rats were exposed to either a high-fat diet (HF; n = 10) or low-fat diet (LF; n = 10). After weaning, all animals were fed a HF diet for an additional nine weeks. There were no differences observed in food intake or body weight between groups. Hepatic DNA methylation was quantified using both methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylation-sensitive restriction enzyme sequencing (MRE-seq). Overall, 1419 differentially methylated regions (DMRs) were identified. DMRs tended to be located in CpG shores and were enriched for genes involved in metabolism and cancer. Gene expression was measured for 31 genes in these pathways. Map3k5 and Igf1r were confirmed to be differentially expressed. Finally, we attempted to quantify the functional relevance of intergenic DMRs. Using chromatin contact data, we saw that conserved DMRs were topologically associated with metabolism genes, which were associated with differential expression of Adh5, Enox1, and Pik3c3. We show that although maternal dietary fat is unable to reverse offspring weight gain in response to a postnatal obesogenic diet, early life diet does program the hepatic methylome. Epigenetic alterations occur primarily in metabolic and cancer pathways and are associated with altered gene expression, but it is unclear whether they bear consequence later in life.
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Affiliation(s)
- Laura Moody
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Justin Shao
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Exeter High School, 1 Blue Hawk Drive, Exeter, NH 03833, USA
| | - Hong Chen
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yuan-Xiang Pan
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, and Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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35
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Khan MFJ, Little J, Aleotti V, Mossey PA, Steegers-Theunissen RPM, Autelitano L, Meazzini MC, Ravaei A, Rubini M. LINE-1 methylation in cleft lip tissues: Influence of infant MTHFR c.677C>T genotype. Oral Dis 2019; 25:1668-1671. [PMID: 31161688 DOI: 10.1111/odi.13136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 05/06/2019] [Accepted: 05/24/2019] [Indexed: 12/17/2022]
Abstract
OBJECTIVE To investigate the influence of MTHFR c.677C>T genotype on LINE-1 methylation in lateral and medial tissues from cleft lip (CL). METHODS Forty-five consecutive non-syndromic cleft lip with or without cleft palate (nsCL/P) cases were included in the study. Genomic DNA was extracted from tissues at both sides of cleft lip, and LINE-1 methylation was detected by bisulfite conversion and pyrosequencing. MTHFR c.677C>T genotyping was carried out using the TaqMan genotyping assay. RESULTS LINE-1 methylation level was significantly higher on medial side of cleft lip compared with lateral side (p = 0.001). This difference was not significantly influenced by the case's sex or cleft type. However, MTHFR c.677C>T genotyping revealed that the difference in LINE-1 methylation across cleft lip was restricted to carriers of C allele of MTHFR c.677C>T and was not apparent in TT homozygous cases (p = 0.027). CONCLUSION This integrated analysis supports the previous finding of differences in DNA methylation across the two sides of cleft lip and further suggests a possible role of MTHFR c.677C>T genotype in establishing this difference.
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Affiliation(s)
- Mohammad Faisal J Khan
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy.,Epidemiology Research Group, Department of Public Health and Primary Care, Faculty of Medicine, KU Leuven - University, Leuven, Belgium
| | - Julian Little
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Valentina Aleotti
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Peter A Mossey
- Craniofacial Development at the World Health Organization-collaborating Centre for Oral and Craniofacial Research, Dental Hospital and School, University of Dundee, Dundee, UK
| | - Régine P M Steegers-Theunissen
- Department of Obstetrics and Gynaecology, University Medical Center, Rotterdam, The Netherlands.,Division Neonatology Erasmus MC, Department of Pediatrics, University Medical Center, Rotterdam, The Netherlands
| | - Luca Autelitano
- Smile House, Regional Centre for Orofacial Clefts and Craniofacial Anomalies, Department of Cranio-Maxillo-Facial Surgery, San Paolo Hospital, University of Milan, Milan, Italy
| | - Maria C Meazzini
- Smile House, Regional Centre for Orofacial Clefts and Craniofacial Anomalies, Department of Cranio-Maxillo-Facial Surgery, San Paolo Hospital, University of Milan, Milan, Italy
| | - Amin Ravaei
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Michele Rubini
- Department of Biomedical and Specialty Surgical Sciences, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
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36
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Pre-natal folic acid and iron supplementation and atopic dermatitis in the first 6 years of life. Arch Dermatol Res 2019; 311:361-367. [PMID: 30923900 DOI: 10.1007/s00403-019-01911-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 02/07/2019] [Accepted: 03/20/2019] [Indexed: 12/16/2022]
Abstract
Exposure in utero has been suggested to influence health later in life. The aim of this study was to investigate, if the use of prenatal food supplements was associated with atopic dermatitis in the offspring. Mothers who gave birth in the hospital G. B. Grassi were invited to participate in the study (n = 395). Information on socio-demographic characteristics, clinical data of the mothers and babies, vegetables and fruit intake, food avoidance, and food supplements use during pregnancy, depression status, and environmental exposure was obtained for all subjects in the hospital at the time of delivery. Data on breastfeeding practice, introduction of weaning foods, day care attendance, and atopic dermatitis were collected in the postnatal follow-ups. Logistic regression was applied to estimate odds ratio (OR) and 95% confidence intervals (CI). Children in which mothers used both iron and folic acid supplementation had a fourfold decreased risk of developing atopic dermatitis [OR = 0.22; 95% confidence interval (CI) 0.06-0.79, p = 0.02], after adjusting for possible confounding factors. Findings suggest an independent and protective effect of prenatal folic acid and iron supplementation for atopic dermatitis in children.
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37
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Gonseth S, Shaw GM, Roy R, Segal MR, Asrani K, Rine J, Wiemels J, Marini NJ. Epigenomic profiling of newborns with isolated orofacial clefts reveals widespread DNA methylation changes and implicates metastable epiallele regions in disease risk. Epigenetics 2019; 14:198-213. [PMID: 30870065 PMCID: PMC6557558 DOI: 10.1080/15592294.2019.1581591] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Cleft lip with or without cleft palate (CL/P) is a common human birth defect whose etiologies remain largely unknown. Several studies have demonstrated that periconceptional supplementation of folic acid can reduce risk of CL/P in offspring. In this study, we tested the hypothesis that the preventive effect of folic acid is manifested through epigenetic modifications by determining whether DNA methylation changes are associated with CL/P. To more readily observe the potential effects of maternal folate on the offspring epigenome, we focused on births prior to mandatory dietary folate fortification in the United States (i.e. birth year 1997 or earlier). Genomic DNA methylation levels were assessed from archived newborn bloodspots in a 182-member case-control study using the Illumina® Human Beadchip 450K array. CL/P cases displayed striking epigenome-wide hypomethylation relative to controls: 63% of CpGs interrogated had lower methylation levels in case newborns, a trend which held up in racially stratified sub-groups. 28 CpG sites reached epigenome-wide significance and all were case-hypomethylated. The most significant CL/P-associated differentially methylated region encompassed the VTRNA2-1 gene, which was also hypomethylated in cases (FWER p = 0.014). This region has been previously characterized as a nutritionally-responsive, metastable epiallele and CL/P-associated methylation changes, in general, were greater at or near putative metastable epiallelic regions. Gene Set Enrichment Analysis of CL/P-associated DMRs showed an over-representation of genes involved in palate development such as WNT9B, MIR140 and LHX8. CL/P-associated DNA methylation changes may partly explain the mechanism by which orofacial clefts are responsive to maternal folate levels.
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Affiliation(s)
- Semira Gonseth
- a School of Public Health , University of California , Berkeley , CA , USA.,b Institute of Social and Preventive Medicine , Lausanne University Hospital , Lausanne , Switzerland
| | - Gary M Shaw
- c Department of Pediatrics , Stanford University School of Medicine , Stanford , CA , USA
| | - Ritu Roy
- d Cancer Research Institute , University of California , San Francisco , CA , USA
| | - Mark R Segal
- e Department of Epidemiology and Biostatistics , University of California , San Francisco , CA , USA
| | - Kripa Asrani
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Jasper Rine
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
| | - Joseph Wiemels
- g Center for Genetic Epidemiology , University of Southern California School of Medicine , Los Angeles , CA , USA
| | - Nicholas J Marini
- f California Institute for Quantitative Biosciences , University of California , Berkeley , CA , USA
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38
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Walton E, Relton CL, Caramaschi D. Using Openly Accessible Resources to Strengthen Causal Inference in Epigenetic Epidemiology of Neurodevelopment and Mental Health. Genes (Basel) 2019; 10:E193. [PMID: 30832291 PMCID: PMC6470715 DOI: 10.3390/genes10030193] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
The recent focus on the role of epigenetic mechanisms in mental health has led to several studies examining the association of epigenetic processes with psychiatric conditions and neurodevelopmental traits. Some studies suggest that epigenetic changes might be causal in the development of the psychiatric condition under investigation. However, other scenarios are possible, e.g., statistical confounding or reverse causation, making it particularly challenging to derive conclusions on causality. In the present review, we examine the evidence from human population studies for a possible role of epigenetic mechanisms in neurodevelopment and mental health and discuss methodological approaches on how to strengthen causal inference, including the need for replication, (quasi-)experimental approaches and Mendelian randomization. We signpost openly accessible resources (e.g., "MR-Base" "EWAS catalog" as well as tissue-specific methylation and gene expression databases) to aid the application of these approaches.
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Affiliation(s)
- Esther Walton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
- Department of Psychology, University of Bath, BA2 7AY Bath, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
| | - Doretta Caramaschi
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, BS8 2BN Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, BS8 2BN Bristol, UK.
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39
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Irwin RE, Thursby SJ, Ondičová M, Pentieva K, McNulty H, Richmond RC, Caffrey A, Lees-Murdock DJ, McLaughlin M, Cassidy T, Suderman M, Relton CL, Walsh CP. A randomized controlled trial of folic acid intervention in pregnancy highlights a putative methylation-regulated control element at ZFP57. Clin Epigenetics 2019; 11:31. [PMID: 30777123 PMCID: PMC6380035 DOI: 10.1186/s13148-019-0618-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 01/21/2019] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Maternal blood folate concentrations during pregnancy have been previously linked with DNA methylation patterns, but this has been done predominantly through observational studies. We showed recently in an epigenetic analysis of the first randomized controlled trial (RCT) of folic acid supplementation specifically in the second and third trimesters (the EpiFASSTT trial) that methylation at some imprinted genes was altered in cord blood samples in response to treatment. Here, we report on epigenome-wide screening using the Illumina EPIC array (~ 850,000 sites) in these same samples (n = 86). RESULTS The top-ranked differentially methylated promoter region (DMR) showed a gain in methylation with folic acid (FA) and was located upstream of the imprint regulator ZFP57. Differences in methylation in cord blood between placebo and folic acid treatment groups at this DMR were verified using pyrosequencing. The DMR also gains methylation in maternal blood in response to FA supplementation. We also found evidence of differential methylation at this region in an independent RCT cohort, the AFAST trial. By altering methylation at this region in two model systems in vitro, we further demonstrated that it was associated with ZFP57 transcription levels. CONCLUSIONS These results strengthen the link between folic acid supplementation during later pregnancy and epigenetic changes and identify a novel mechanism for regulation of ZFP57. This trial was registered 15 May 2013 at www.isrctn.com as ISRCTN19917787.
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Affiliation(s)
- Rachelle E. Irwin
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
| | - Sara-Jayne Thursby
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
| | - Miroslava Ondičová
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
| | - Kristina Pentieva
- Nutrition Innovation Centre for Food and Health, School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health, School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - Rebecca C. Richmond
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Aoife Caffrey
- Nutrition Innovation Centre for Food and Health, School of Biomedical Sciences, Ulster University, Coleraine, UK
| | - Diane J. Lees-Murdock
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
| | | | - Tony Cassidy
- Psychology Institute, Ulster University, Coleraine, UK
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Colum P. Walsh
- Genomic Medicine Research Group, School of Biomedical Sciences, Ulster University, Coleraine BT52 1SA, UK
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Abstract
Purpose of review This review demonstrates the growing body of evidence connecting DNA methylation to prior exposure. It highlights the potential to use DNA methylation patterns as a feasible, stable, and accurate biomarker of past exposure, opening new opportunities for environmental and gene-environment interaction studies among existing banked samples. Recent findings We present the evidence for association between past exposure, including prenatal exposures, and DNA methylation measured at a later time in the life course. We demonstrate the potential utility of DNA methylation-based biomarkers of past exposure using results from multiple studies of smoking as an example. Multiple studies show the ability to accurately predict prenatal smoking exposure based on DNA methylation measured at birth, in childhood, and even adulthood. Separate sets of DNA methylation loci have been used to predict past personal smoking exposure (postnatal) as well. Further, it appears that these two types of exposures, prenatal and previous personal exposure, can be isolated from each other. There is also a suggestion that quantitative methylation scores may be useful for estimating dose. We highlight the remaining needs for rigor in methylation biomarker development including analytic challenges as well as the need for development across multiple developmental windows, multiple tissue types, and multiple ancestries. Summary If fully developed, DNA methylation-based biomarkers can dramatically shift our ability to carry out environmental and genetic-environmental epidemiology using existing biobanks, opening up unprecedented opportunities for environmental health.
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Mother-child transmission of epigenetic information by tunable polymorphic imprinting. Proc Natl Acad Sci U S A 2018; 115:E11970-E11977. [PMID: 30509985 PMCID: PMC6304996 DOI: 10.1073/pnas.1815005115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
First, our work provides critical biological interpretation of intermediate DNA methylation readouts at the nc886 differentially methylated region (DMR). nc886 was identified in multiple large-scale epigenome-wide association studies (EWAS) that did not recognize that this region acts as a contiguous DMR imposed by genomic imprinting, highlighting the need to reexamine several 450k data sets. Second, strict control of genomic imprinting was thought to be required for organismal viability. Reports of polymorphic imprinting are limited to specific tissue types such as placenta and brain. In blood and somatic tissues, we show nc886 imprinting is mosaic in the population and influenced by maternal environment. Genomic imprinting mediated by DNA methylation restricts gene expression to a single allele determined by parental origin and is not generally considered to be under genetic or environmental influence. Here, we focused on a differentially methylated region (DMR) of approximately 1.9 kb that includes a 101-bp noncoding RNA gene (nc886/VTRNA2-1), which is maternally imprinted in ∼75% of humans. This is unlike other imprinted genes, which demonstrate monoallelic methylation in 100% of individuals. The DMR includes a CTCF binding site on the centromeric side defining the DMR boundary and is flanked by a CTCF binding site on the telomeric side. The centromeric CTCF binding site contains an A/C polymorphism (rs2346018); the C allele is associated with less imprinting. The frequency of imprinting of the nc886 DMR in infants was linked to at least two nongenetic factors, maternal age at delivery and season of conception. In a separate cohort, nc886 imprinting was associated with lower body mass index in children at 5 y of age. Thus, we propose that the imprinting status of the nc886 DMR is “tunable” in that it is associated with maternal haplotype and prenatal environment. This provides a potential mechanism for transmitting information, with phenotypic consequences, from mother to child.
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Boyd A, Woollard M, Macleod J, Park A. The destruction of the 'Windrush' disembarkation cards: a lost opportunity and the (re)emergence of Data Protection regulation as a threat to longitudinal research. Wellcome Open Res 2018; 3:112. [PMID: 30345387 PMCID: PMC6171557 DOI: 10.12688/wellcomeopenres.14796.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2018] [Indexed: 11/30/2022] Open
Abstract
Historical records and the research databases of completed studies have the potential either to establish new research studies or to inform follow-up studies assessing long-term health and social outcomes. Yet, such records are at risk of destruction resulting from misconceptions about data protection legislation and research ethics. The recent destruction of the Windrush disembarkation cards, which potentially could have formed the basis of a retrospective cohort study, illustrates this risk. As organisations across Europe transition to the EU General Data Protection Regulation (GDPR), this risk is being amplified due to uncertainty as to how to comply with complex new rules, and the requirement under GDPR that data owners catalogue their data and set data retention and destruction rules. The combination of these factors suggests there is a new meaningful risk that scientifically important historical records will be destroyed, despite the fact that GDPR provides a clear legal basis to hold historical records and to repurpose them for research for the public good. This letter describes this risk; details the legal basis enabling the retention and repurposing of these data; makes recommendations as to how to alleviate this risk; and finally encourages the research and research-active clinical community to contact their ‘Data Protection Officers’ to promote safe-keeping of historical records.
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Affiliation(s)
- Andy Boyd
- ALSPAC, University of Bristol, Bristol, BS8 2BN, UK.,CLOSER, UCL Institute of Education, London, WC1H 0NU, UK
| | | | - John Macleod
- Population Health Science, University of Bristol, Bristol, BS8 2BN, UK
| | - Alison Park
- CLOSER, UCL Institute of Education, London, WC1H 0NU, UK
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Ding K, Jiang J, Chen L, Xu X. Methylenetetrahydrofolate Dehydrogenase 1 Silencing Expedites the Apoptosis of Non-Small Cell Lung Cancer Cells via Modulating DNA Methylation. Med Sci Monit 2018; 24:7499-7507. [PMID: 30343310 PMCID: PMC6206813 DOI: 10.12659/msm.910265] [Citation(s) in RCA: 12] [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: 03/28/2018] [Accepted: 05/25/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) accounts for about 85% of all types of lung cancer. Methylenetetrahydrofolate dehydrogenase 1 (MTHFD1) is involved in DNA methylation, and DNA methylation is related to tumorigenesis. The role of MTHFD1 in NSCLC was examined in our study. MATERIAL AND METHODS The correlation between the expression of MTHFD1 and the clinicopathological features of patients diagnosed with lung cancer was investigated using the chi-square test. The viability and apoptosis of NCI-H1299 cells was respectively detected using cell counting kit-8 and flow cytometry assays. The expression levels of MTHFD1, apoptosis-related factors and DNA methyltransferase-related factors were assessed by quantitative real-time PCR (qRT-PCR) and western blot assays. RESULTS We found that MTHFD1 expression in the tumor tissues and cells was higher than that of adjacent normal tissues and cells. The survival time of patients with high MTHFD1 expression was shorter than those with low MTHFD1 expression. The expression level of MTHFD1 was related to tumor size, TNM stage, histologic grade, and metastasis, but not linked to gender and age. Besides, si-MTHFD1 significantly decreased the viability of cells in a time-dependent manner, and increased cell apoptosis. When cells were transfected with MTHFD1-siRNA, the levels of surviving and B-cell lymphoma-2 (Bcl-2) were attenuated, while p53 and Bcl-2 associated X protein (Bax) levels were enhanced. Moreover, si-MTHFD1 markedly downregulated the expression levels of DNA methyltransferase 1 (DNMT1), DNMT3a, and DNMT3b. CONCLUSIONS Collectively, our results proved that MTHFD1 silencing obviously reduced the proliferation and enhanced the apoptosis of NSCLC via suppressing DNA methylation.
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Affiliation(s)
- Ke Ding
- Dispensary of Traditional Chinese Medicine, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P.R. China
| | - Jianyang Jiang
- Department of Respiration, Quzhou People’s Hospital, Quzhou, Zhejiang, P.R. China
| | - Liang Chen
- Zhejiang Chinese Medical University, Hangzhou, Zhejiang, P.R. China
| | - Xiaohua Xu
- Department of Respiration, Quzhou People’s Hospital, Quzhou, Zhejiang, P.R. China
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Richmond S, Howe LJ, Lewis S, Stergiakouli E, Zhurov A. Facial Genetics: A Brief Overview. Front Genet 2018; 9:462. [PMID: 30386375 PMCID: PMC6198798 DOI: 10.3389/fgene.2018.00462] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 09/20/2018] [Indexed: 12/20/2022] Open
Abstract
Historically, craniofacial genetic research has understandably focused on identifying the causes of craniofacial anomalies and it has only been within the last 10 years, that there has been a drive to detail the biological basis of normal-range facial variation. This initiative has been facilitated by the availability of low-cost hi-resolution three-dimensional systems which have the ability to capture the facial details of thousands of individuals quickly and accurately. Simultaneous advances in genotyping technology have enabled the exploration of genetic influences on facial phenotypes, both in the present day and across human history. There are several important reasons for exploring the genetics of normal-range variation in facial morphology. - Disentangling the environmental factors and relative parental biological contributions to heritable traits can help to answer the age-old question "why we look the way that we do?" - Understanding the etiology of craniofacial anomalies; e.g., unaffected family members of individuals with non-syndromic cleft lip/palate (nsCL/P) have been shown to differ in terms of normal-range facial variation to the general population suggesting an etiological link between facial morphology and nsCL/P. - Many factors such as ancestry, sex, eye/hair color as well as distinctive facial features (such as, shape of the chin, cheeks, eyes, forehead, lips, and nose) can be identified or estimated using an individual's genetic data, with potential applications in healthcare and forensics. - Improved understanding of historical selection and adaptation relating to facial phenotypes, for example, skin pigmentation and geographical latitude. - Highlighting what is known about shared facial traits, medical conditions and genes.
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Affiliation(s)
- Stephen Richmond
- Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Laurence J. Howe
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- Institute of Cardiovascular Science, University College London, London, United Kingdom
| | - Sarah Lewis
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
| | - Evie Stergiakouli
- MRC Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
- School of Oral and Dental Sciences, University of Bristol, Bristol, United Kingdom
| | - Alexei Zhurov
- Applied Clinical Research and Public Health, School of Dentistry, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
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Dugué PA, Dowty JG, Joo JE, Wong EM, Makalic E, Schmidt DF, English DR, Hopper JL, Pedersen J, Severi G, MacInnis RJ, Milne RL, Giles GG, Southey MC. Heritable methylation marks associated with breast and prostate cancer risk. Prostate 2018; 78:962-969. [PMID: 30133758 DOI: 10.1002/pros.23654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/02/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND DNA methylation can mimic the effects of germline mutations in cancer predisposition genes. Recently, we identified twenty-four heritable methylation marks associated with breast cancer risk. As breast and prostate cancer share genetic risk factors, including rare, high-risk mutations (eg, in BRCA2), we hypothesized that some of these heritable methylation marks might also be associated with the risk of prostate cancer. METHODS We studied 869 incident prostate cancers (430 aggressive and 439 non-aggressive) and 869 matched controls nested within a prospective cohort study. DNA methylation was measured in pre-diagnostic blood samples using the Illumina Infinium HM450K BeadChip. Conditional logistic regression models, adjusted for prostate cancer risk factors and blood cell composition, were used to estimate odds ratios and 95% confidence intervals for the association between the 24 methylation marks and the risk of prostate cancer. RESULTS Five methylation marks within the VTRNA2-1 promoter region (cg06536614, cg00124993, cg26328633, cg25340688, and cg26896946), and one in the body of CLGN (cg22901919) were associated with the risk of prostate cancer. In stratified analyses, the five VTRNA2-1 marks were associated with the risk of aggressive prostate cancer. CONCLUSIONS This work highlights a potentially important new area of investigation for prostate cancer susceptibility and adds to our knowledge about shared risk factors for breast and prostate cancer.
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Affiliation(s)
- Pierre-Antoine Dugué
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Victoria, Australia
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - James G Dowty
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Jihoon E Joo
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
| | - Ee M Wong
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Enes Makalic
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Daniel F Schmidt
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Faculty of Information Technology, Monash University, Victoria, Australia
| | - Dallas R English
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Victoria, Australia
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - John L Hopper
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | | | - Gianluca Severi
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Victoria, Australia
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Robert J MacInnis
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Victoria, Australia
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Roger L Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Victoria, Australia
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Victoria, Australia
- Centre for Epidmiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Victoria, Australia
| | - Melissa C Southey
- Genetic Epidemiology Laboratory, Department of Clinical Pathology, The University of Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
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