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Shorey-Kendrick LE, McEvoy CT, Milner K, Harris J, Brownsberger J, Tepper RS, Park B, Gao L, Vu A, Morris CD, Spindel ER. Improvements in lung function following vitamin C supplementation to pregnant smokers are associated with buccal DNA methylation at 5 years of age. Clin Epigenetics 2024; 16:35. [PMID: 38413986 PMCID: PMC10900729 DOI: 10.1186/s13148-024-01644-8] [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: 10/17/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND We previously reported in the "Vitamin C to Decrease the Effects of Smoking in Pregnancy on Infant Lung Function" randomized clinical trial (RCT) that vitamin C (500 mg/day) supplementation to pregnant smokers is associated with improved respiratory outcomes that persist through 5 years of age. The objective of this study was to assess whether buccal cell DNA methylation (DNAm), as a surrogate for airway epithelium, is associated with vitamin C supplementation, improved lung function, and decreased occurrence of wheeze. METHODS We conducted epigenome-wide association studies (EWAS) using Infinium MethylationEPIC arrays and buccal DNAm from 158 subjects (80 placebo; 78 vitamin C) with pulmonary function testing (PFT) performed at the 5-year visit. EWAS were performed on (1) vitamin C treatment, (2) forced expiratory flow between 25 and 75% of expired volume (FEF25-75), and (3) offspring wheeze. Models were adjusted for sex, race, study site, gestational age at randomization (≤ OR > 18 weeks), proportion of epithelial cells, and latent covariates in addition to child length at PFT in EWAS for FEF25-75. We considered FDR p < 0.05 as genome-wide significant and nominal p < 0.001 as candidates for downstream analyses. Buccal DNAm measured in a subset of subjects at birth and near 1 year of age was used to determine whether DNAm signatures originated in utero, or emerged with age. RESULTS Vitamin C treatment was associated with 457 FDR significant (q < 0.05) differentially methylated CpGs (DMCs; 236 hypermethylated; 221 hypomethylated) and 53 differentially methylated regions (DMRs; 26 hyper; 27 hypo) at 5 years of age. FEF25-75 was associated with one FDR significant DMC (cg05814800), 1,468 candidate DMCs (p < 0.001), and 44 DMRs. Current wheeze was associated with 0 FDR-DMCs, 782 candidate DMCs, and 19 DMRs (p < 0.001). In 365/457 vitamin C FDR significant DMCs at 5 years of age, there was no significant interaction between time and treatment. CONCLUSIONS Vitamin C supplementation to pregnant smokers is associated with buccal DNA methylation in offspring at 5 years of age, and most methylation signatures appear to be persistent from the prenatal period. Buccal methylation at 5 years was also associated with current lung function and occurrence of wheeze, and these functionally associated loci are enriched for vitamin C associated loci. Clinical trial registration ClinicalTrials.gov, NCT01723696 and NCT03203603.
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA.
| | - Cindy T McEvoy
- Department of Pediatrics, Pape Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Kristin Milner
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Julia Harris
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Julie Brownsberger
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Robert S Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland State University School of Public Health, Portland, OR, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland State University School of Public Health, Portland, OR, USA
| | - Annette Vu
- Oregon Clinical & Translational Research Institute, Oregon Health and Science; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia D Morris
- Oregon Clinical & Translational Research Institute, Oregon Health and Science; Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
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2
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Mallick R, Duttaroy AK. Epigenetic modification impacting brain functions: Effects of physical activity, micronutrients, caffeine, toxins, and addictive substances. Neurochem Int 2023; 171:105627. [PMID: 37827244 DOI: 10.1016/j.neuint.2023.105627] [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: 08/23/2023] [Revised: 10/06/2023] [Accepted: 10/07/2023] [Indexed: 10/14/2023]
Abstract
Changes in gene expression are involved in many brain functions. Epigenetic processes modulate gene expression by histone modification and DNA methylation or RNA-mediated processes, which is important for brain function. Consequently, epigenetic changes are also a part of brain diseases such as mental illness and addiction. Understanding the role of different factors on the brain epigenome may help us understand the function of the brain. This review discussed the effects of caffeine, lipids, addictive substances, physical activity, and pollutants on the epigenetic changes in the brain and their modulatory effects on brain function.
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Affiliation(s)
- Rahul Mallick
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Finland
| | - Asim K Duttaroy
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, POB 1046 Blindern, Oslo, Norway.
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3
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Wang H, Wang J, Li D, Zhu Z, Pei D. A functional polymorphism within the distal promoter of RUNX3 confers risk of colorectal cancer. Int J Biol Markers 2022; 37:40-46. [DOI: 10.1177/17246008211073342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background Accumulating evidence has indicated that runt-related transcription factor 3 ( RUNX3) gene polymorphism (rs7528484) is associated with an alimentary system cancer risk. However, the role of rs7528484 in colorectal cancer is still unclear. The present study aimed to explore the association between rs7528484 and colorectal cancer susceptibility in a Chinese Han population. Material and methods We firstly investigated the effect of the polymorphism rs7528484 in distal promoter of RUNX3 polymorphism on colorectal cancer risk in a Chinese Han population comprising 427 colorectal cancer patients and 503 controls. We then carried out a phenotype–genotype association analysis to validate its influence on the adjacent gene RUNX3. Results Logistic regression analysis demonstrated that the T allele of rs7528484 was significantly associated with an increased risk for colorectal cancer occurrence in our case-control study (odds ratio = 1.33; 95% confidence interval = 1.09–1.65; P = 0.005). In stratified analysis, the susceptibility of colorectal cancer in the T allele carriers increased among the smokers, III and IV tumor stage, and at the rectum. Furthermore, the T allele was significantly correlated with lower expression of RUNX3 in vitro. Conclusion In summary, the current case-control and genotype–phenotype study provides convincing evidence that functional RUNX3 polymorphism (rs7528484) is related to colorectal cancer risk and is a plausible marker for the prediction of colorectal cancer.
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Affiliation(s)
- Huiping Wang
- Xuzhou Engineering Research Center of Medical Genetics and Transformation, Laboratory of Genetic Foundation and Clinical Application, Department of Genetics, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Jin Wang
- Laboratory of Experimental and Clinical Pathology, Departments of Pathology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Danhua Li
- Laboratory of Experimental and Clinical Pathology, Departments of Pathology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Zhansheng Zhu
- Laboratory of Experimental and Clinical Pathology, Departments of Pathology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Dongsheng Pei
- Laboratory of Experimental and Clinical Pathology, Departments of Pathology, School of Basic Medical Sciences, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, China
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4
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Li C, Cao M, Zhou X. Role of epigenetics in parturition and preterm birth. Biol Rev Camb Philos Soc 2021; 97:851-873. [PMID: 34939297 DOI: 10.1111/brv.12825] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 11/29/2021] [Accepted: 12/02/2021] [Indexed: 12/19/2022]
Abstract
Preterm birth occurs worldwide and is associated with high morbidity, mortality, and economic cost. Although several risk factors associated with parturition and preterm birth have been identified, mechanisms underlying this syndrome remain unclear, thereby limiting the implementation of interventions for prevention and management. Known triggers of preterm birth include conditions related to inflammatory and immunological pathways, as well as genetics and maternal history. Importantly, epigenetics, which is the study of heritable phenotypic changes that occur without alterations in the DNA sequence, may play a role in linking social and environmental risk factors for preterm birth. Epigenetic approaches to the study of preterm birth, including analyses of the effects of microRNAs, long non-coding RNAs, DNA methylation, and histone modification, have contributed to an improved understanding of the molecular bases of both term and preterm birth. Additionally, epigenetic modifications have been linked to factors already associated with preterm birth, including obesity and smoking. The prevention and management of preterm birth remains a challenge worldwide. Although epigenetic analysis provides valuable insights into the causes and risk factors associated with this syndrome, further studies are necessary to determine whether epigenetic approaches can be used routinely for the diagnosis, prevention, and management of preterm birth.
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Affiliation(s)
- Chunjin Li
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Maosheng Cao
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
| | - Xu Zhou
- College of Animal Sciences, Jilin University, Changchun, Jilin, 130062, China
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5
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Rosenfeld CS. Transcriptomics and Other Omics Approaches to Investigate Effects of Xenobiotics on the Placenta. Front Cell Dev Biol 2021; 9:723656. [PMID: 34631709 PMCID: PMC8497882 DOI: 10.3389/fcell.2021.723656] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/31/2021] [Indexed: 12/25/2022] Open
Abstract
The conceptus is most vulnerable to developmental perturbation during its early stages when the events that create functional organ systems are being launched. As the placenta is in direct contact with maternal tissues, it readily encounters any xenobiotics in her bloodstream. Besides serving as a conduit for solutes and waste, the placenta possesses a tightly regulated endocrine system that is, of itself, vulnerable to pharmaceutical agents, endocrine disrupting chemicals (EDCs), and other environmental toxicants. To determine whether extrinsic factors affect placental function, transcriptomics and other omics approaches have become more widely used. In casting a wide net with such approaches, they have provided mechanistic insights into placental physiological and pathological responses and how placental responses may impact the fetus, especially the developing brain through the placenta-brain axis. This review will discuss how such omics technologies have been utilized to understand effects of EDCs, including the widely prevalent plasticizers bisphenol A (BPA), bisphenol S (BPS), and phthalates, other environmental toxicants, pharmaceutical agents, maternal smoking, and air pollution on placental gene expression, DNA methylation, and metabolomic profiles. It is also increasingly becoming clear that miRNA (miR) are important epigenetic regulators of placental function. Thus, the evidence to date that xenobiotics affect placental miR expression patterns will also be explored. Such omics approaches with mouse and human placenta will assuredly provide key biomarkers that may be used as barometers of exposure and can be targeted by early mitigation approaches to prevent later diseases, in particular neurobehavioral disorders, originating due to placental dysfunction.
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Affiliation(s)
- Cheryl S Rosenfeld
- Biomedical Sciences, University of Missouri, Columbia, MO, United States.,MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO, United States.,Thompson Center for Autism and Neurobehavioral Disorders, University of Missouri, Columbia, MO, United States.,Genetics Area Program, University of Missouri, Columbia, MO, United States
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6
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Luo R, Zhang H, Mukherjee N, Karmaus W, Patil V, Arshad H, Mzayek F. Association of grandmaternal smoking during pregnancy with DNA methylation of grandchildren: the Isle of Wight study. Epigenomics 2021; 13:1473-1483. [PMID: 34596434 DOI: 10.2217/epi-2020-0433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Background: To investigate the intergenerational effects of grandmaternal smoking during pregnancy (GMSDP) on the DNA methylation of grandchildren. Methods: Data from the Isle of Wight birth cohort with information regarding GMSDP and DNA methylation profiling at the birth of grandchildren (n = 161) were used. Differentially methylated CpG sites related to GMSDP were identified using testing-training screening, analysis of variance and multivariate analysis of covariance. The association between identified CpG sites and expression levels of neighboring genes was tested by linear regression. Results: Twenty-three CpG sites were differentially methylated in grandchildren because of GMSDP, and eight of these were associated with expression levels of 13 neighboring genes. Conclusion: GMSDP has an intergenerational effect on the DNA methylation profile of grandchildren independent of maternal smoking during pregnancy.
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Affiliation(s)
- Rui Luo
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
| | - Veeresh Patil
- David Hide Asthma and Allergy Research Centre, Newport, PO30 5TG, UK
| | - Hasan Arshad
- David Hide Asthma and Allergy Research Centre, Newport, PO30 5TG, UK.,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, UK
| | - Fawaz Mzayek
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152, USA
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7
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Shorey-Kendrick LE, McEvoy CT, O'Sullivan SM, Milner K, Vuylsteke B, Tepper RS, Haas DM, Park B, Gao L, Vu A, Morris CD, Spindel ER. Impact of vitamin C supplementation on placental DNA methylation changes related to maternal smoking: association with gene expression and respiratory outcomes. Clin Epigenetics 2021; 13:177. [PMID: 34538263 PMCID: PMC8451157 DOI: 10.1186/s13148-021-01161-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/28/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Maternal smoking during pregnancy (MSDP) affects development of multiple organ systems including the placenta, lung, brain, and vasculature. In particular, children exposed to MSDP show lifelong deficits in pulmonary function and increased risk of asthma and wheeze. Our laboratory has previously shown that vitamin C supplementation during pregnancy prevents some of the adverse effects of MSDP on offspring respiratory outcomes. Epigenetic modifications, including DNA methylation (DNAm), are a likely link between in utero exposures and adverse health outcomes, and MSDP has previously been associated with DNAm changes in blood, placenta, and buccal epithelium. Analysis of placental DNAm may reveal critical targets of MSDP and vitamin C relevant to respiratory health outcomes. RESULTS DNAm was measured in placentas obtained from 72 smokers enrolled in the VCSIP RCT: NCT03203603 (37 supplemented with vitamin C, 35 with placebo) and 24 never-smokers for reference. Methylation at one CpG, cg20790161, reached Bonferroni significance and was hypomethylated in vitamin C supplemented smokers versus placebo. Analysis of spatially related CpGs identified 93 candidate differentially methylated regions (DMRs) between treatment groups, including loci known to be associated with lung function, oxidative stress, fetal development and growth, and angiogenesis. Overlap of nominally significant differentially methylated CpGs (DMCs) in never-smokers versus placebo with nominally significant DMCs in vitamin C versus placebo identified 9059 candidate "restored CpGs" for association with placental transcript expression and respiratory outcomes. Methylation at 274 restored candidate CpG sites was associated with expression of 259 genes (FDR < 0.05). We further identified candidate CpGs associated with infant lung function (34 CpGs) and composite wheeze (1 CpG) at 12 months of age (FDR < 0.05). Increased methylation in the DIP2C, APOH/PRKCA, and additional candidate gene regions was associated with improved lung function and decreased wheeze in offspring of vitamin C-treated smokers. CONCLUSIONS Vitamin C supplementation to pregnant smokers ameliorates changes associated with maternal smoking in placental DNA methylation and gene expression in pathways potentially linked to improved placental function and offspring respiratory health. Further work is necessary to validate candidate loci and elucidate the causal pathway between placental methylation changes and outcomes of offspring exposed to MSDP. Clinical trial registration ClinicalTrials.gov, NCT01723696. Registered November 6, 2012. https://clinicaltrials.gov/ct2/show/record/NCT01723696 .
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Affiliation(s)
- Lyndsey E Shorey-Kendrick
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA.
| | - Cindy T McEvoy
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Shannon M O'Sullivan
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
| | - Kristin Milner
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Brittany Vuylsteke
- Department of Pediatrics, Oregon Health and Science University, Portland, OR, USA
| | - Robert S Tepper
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - David M Haas
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Byung Park
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
- School of Public Health, Oregon Health and Science University-Portland State University, Portland, OR, USA
| | - Lina Gao
- Biostatistics Shared Resources, Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Bioinformatics and Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Portland, OR, USA
| | - Annette Vu
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia D Morris
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR, USA
- Oregon Clinical and Translational Research Institute, Oregon Health and Science, Portland, OR, USA
| | - Eliot R Spindel
- Division of Neuroscience, Oregon National Primate Research Center, Oregon Health and Science University, 505 NW 185th Ave, Beaverton, OR, 97006, USA
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8
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Buck JM, Yu L, Knopik VS, Stitzel JA. DNA methylome perturbations: an epigenetic basis for the emergingly heritable neurodevelopmental abnormalities associated with maternal smoking and maternal nicotine exposure†. Biol Reprod 2021; 105:644-666. [PMID: 34270696 PMCID: PMC8444709 DOI: 10.1093/biolre/ioab138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/29/2021] [Accepted: 07/14/2021] [Indexed: 11/13/2022] Open
Abstract
Maternal smoking during pregnancy is associated with an ensemble of neurodevelopmental consequences in children and therefore constitutes a pressing public health concern. Adding to this burden, contemporary epidemiological and especially animal model research suggests that grandmaternal smoking is similarly associated with neurodevelopmental abnormalities in grandchildren, indicative of intergenerational transmission of the neurodevelopmental impacts of maternal smoking. Probing the mechanistic bases of neurodevelopmental anomalies in the children of maternal smokers and the intergenerational transmission thereof, emerging research intimates that epigenetic changes, namely DNA methylome perturbations, are key factors. Altogether, these findings warrant future research to fully elucidate the etiology of neurodevelopmental impairments in the children and grandchildren of maternal smokers and underscore the clear potential thereof to benefit public health by informing the development and implementation of preventative measures, prophylactics, and treatments. To this end, the present review aims to encapsulate the burgeoning evidence linking maternal smoking to intergenerational epigenetic inheritance of neurodevelopmental abnormalities, to identify the strengths and weaknesses thereof, and to highlight areas of emphasis for future human and animal model research therein.
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Affiliation(s)
- Jordan M Buck
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder, CO, USA
| | - Li Yu
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - Valerie S Knopik
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - Jerry A Stitzel
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Boulder, CO, USA
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9
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Everson TM, Vives-Usano M, Seyve E, Cardenas A, Lacasaña M, Craig JM, Lesseur C, Baker ER, Fernandez-Jimenez N, Heude B, Perron P, Gónzalez-Alzaga B, Halliday J, Deyssenroth MA, Karagas MR, Íñiguez C, Bouchard L, Carmona-Sáez P, Loke YJ, Hao K, Belmonte T, Charles MA, Martorell-Marugán J, Muggli E, Chen J, Fernández MF, Tost J, Gómez-Martín A, London SJ, Sunyer J, Marsit CJ, Lepeule J, Hivert MF, Bustamante M. Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth. Nat Commun 2021; 12:5095. [PMID: 34429407 PMCID: PMC8384884 DOI: 10.1038/s41467-021-24558-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Maternal smoking during pregnancy (MSDP) contributes to poor birth outcomes, in part through disrupted placental functions, which may be reflected in the placental epigenome. Here we present a meta-analysis of the associations between MSDP and placental DNA methylation (DNAm) and between DNAm and birth outcomes within the Pregnancy And Childhood Epigenetics (PACE) consortium (N = 1700, 344 with MSDP). We identify 443 CpGs that are associated with MSDP, of which 142 associated with birth outcomes, 40 associated with gene expression, and 13 CpGs are associated with all three. Only two CpGs have consistent associations from a prior meta-analysis of cord blood DNAm, demonstrating substantial tissue-specific responses to MSDP. The placental MSDP-associated CpGs are enriched for environmental response genes, growth-factor signaling, and inflammation, which play important roles in placental function. We demonstrate links between placental DNAm, MSDP and poor birth outcomes, which may better inform the mechanisms through which MSDP impacts placental function and fetal growth.
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Affiliation(s)
- Todd M Everson
- Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA.
| | - Marta Vives-Usano
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Emie Seyve
- University Grenoble Alpes, Inserm, CNRS, IAB, Grenoble, France
| | - Andres Cardenas
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Marina Lacasaña
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Andalusian School of Public Health, Granada, Spain
- Instituto de Investigación Biosantaria (ibs.GRANADA), Granada, Spain
| | - Jeffrey M Craig
- Epigenetics Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- IMPACT - the Institute for Mental and Physical Health and Clinical Translation, Deakin University, Geelong, VIC, Australia
| | - Corina Lesseur
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Emily R Baker
- Department of Obstetrics & Gynecology, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Nora Fernandez-Jimenez
- University of the Basque Country (UPV/EHU), Leioa, Spain
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain
- Public Health Division of Gipuzkoa, Basque Government, San Sebastian, Spain
| | - Barbara Heude
- Université de Paris, CRESS, INSERM, INRAE, Paris, France
| | - Patrice Perron
- Department of Medicine, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Beatriz Gónzalez-Alzaga
- Andalusian School of Public Health, Granada, Spain
- Instituto de Investigación Biosantaria (ibs.GRANADA), Granada, Spain
| | - Jane Halliday
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Reproductive Epidemiology, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Maya A Deyssenroth
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Carmen Íñiguez
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Department of Statistics and Computational Research, Universitat de València, València, Spain
- Epidemiology and Environmental Health Joint Research Unit, FISABIO-Universitat Jaume I-Universitat de València, València, Spain
| | - Luigi Bouchard
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, QC, Canada
| | - Pedro Carmona-Sáez
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Statistics, Faculty of Sciences, University of Granada, Granada, Spain
| | - Yuk J Loke
- Epigenetics Group, Murdoch Children's Research Institute, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Jordi Martorell-Marugán
- Bioinformatics Unit, GENYO. Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Atrys Health S.A., Barcelona, Spain
| | - Evelyne Muggli
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Reproductive Epidemiology, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Jia Chen
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mariana F Fernández
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Instituto de Investigación Biosantaria (ibs.GRANADA), Granada, Spain
- Biomedical Research Centre (CIBM) and School of Medicine, University of Granada, Granada, Spain
| | - Jorg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, Evry, France
| | - Antonio Gómez-Martín
- Genomics Unit, GENYO. Centre for Genomics and Oncological Research, Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Stephanie J London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC, USA
| | - Jordi Sunyer
- Universitat Pompeu Fabra, Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health at Emory University, Atlanta, GA, USA
- Department of Epidemiology, Rollins School of Public health at Emory University, Atlanta, GA, USA
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, IAB, Grenoble, France
| | - Marie-France Hivert
- Department of Population Medicine, Harvard Medical School, Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mariona Bustamante
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain.
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10
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Franzago M, Fraticelli F, Marchioni M, Di Nicola M, Di Sebastiano F, Liberati M, Stuppia L, Vitacolonna E. Fat mass and obesity-associated (FTO) gene epigenetic modifications in gestational diabetes: new insights and possible pathophysiological connections. Acta Diabetol 2021; 58:997-1007. [PMID: 33743080 PMCID: PMC8272710 DOI: 10.1007/s00592-020-01668-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/26/2020] [Indexed: 12/16/2022]
Abstract
AIMS Gestational diabetes mellitus (GDM) can lead to short- and long-term complications for the child. Epigenetic alterations could contribute to explaining the metabolic disturbances associated with foetal programming. Although the role of the FTO gene remains unclear, it affects metabolic phenotypes probably mediated by epigenetic mechanisms. The aim of this study was to assess whether placental DNA epigenetic modifications at FTO promoter-associated cysteine-phosphate-guanine (CpG) sites are correlated with GDM. A secondary aim was to evaluate the association between the placental FTO DNA methylation and the maternal metabolic traits in women with and without GDM. METHODS Socio-demographic characteristics, clinical parameters at the third trimester of pregnancy, Mediterranean diet adherence, and physical activity were assessed in 33 GDM women and 27 controls. Clinical information about the newborns was registered at birth. The FTO rs9939609 (T > A) was genotyped. RESULTS No association between FTO DNA methylation and GDM was found. DNA methylation on the maternal side at the CpG1 was associated with maternal smoking in GDM (p = 0.034), and DNA methylation at the CpG3 was correlated with smoking or former smoking in controls (p = 0.023). A higher level of TGs was correlated with higher foetal placental DNA methylation at the CpG2 (p = 0.036) in GDM. An inverse association between HDL-C and maternal placental DNA methylation at the CpG3 in controls (p = 0.045) was found. An association between FTO rs9939609 and neonatal birthweight (p = 0.033) was detected. CONCLUSIONS In the awareness that the obesity pathophysiology is complex, the study adds a piece to this intricate mosaic.
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Affiliation(s)
- Marica Franzago
- Department of Medicine and Aging, School of Medicine and Health Sciences, "G. D'Annunzio" University, Chieti-Pescara, Via dei Vestini, 66100, Chieti, Italy
- Center for Advanced Studies and Technology (CAST), "G. D'Annunzio" University, Chieti-Pescara, Chieti, Italy
| | - Federica Fraticelli
- Department of Medicine and Aging, School of Medicine and Health Sciences, "G. D'Annunzio" University, Chieti-Pescara, Via dei Vestini, 66100, Chieti, Italy
| | - Michele Marchioni
- Laboratory of Biostatistics, Department of Medical, Oral and Biotechnological Sciences, "G.D'Annunzio" University, Chieti-Pescara, Chieti, Italy
| | - Marta Di Nicola
- Laboratory of Biostatistics, Department of Medical, Oral and Biotechnological Sciences, "G.D'Annunzio" University, Chieti-Pescara, Chieti, Italy
| | - Francesca Di Sebastiano
- Department of Obstetric and Gynaecology, SS. Annunziata Hospital, "G. D'Annunzio" University, Chieti-Pescara, Chieti, Italy
| | - Marco Liberati
- Department of Medicine and Aging, School of Medicine and Health Sciences, "G. D'Annunzio" University, Chieti-Pescara, Via dei Vestini, 66100, Chieti, Italy
| | - Liborio Stuppia
- Center for Advanced Studies and Technology (CAST), "G. D'Annunzio" University, Chieti-Pescara, Chieti, Italy
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, "G. D'Annunzio" University, Chieti-Pescara, Chieti, Italy
| | - Ester Vitacolonna
- Department of Medicine and Aging, School of Medicine and Health Sciences, "G. D'Annunzio" University, Chieti-Pescara, Via dei Vestini, 66100, Chieti, Italy.
- Center for Advanced Studies and Technology (CAST), "G. D'Annunzio" University, Chieti-Pescara, Chieti, Italy.
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11
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von Ehrenstein OS, Cui X, Yan Q, Aralis H, Ritz B. Maternal Prenatal Smoking and Autism Spectrum Disorder in Offspring: A California Statewide Cohort and Sibling Study. Am J Epidemiol 2021; 190:728-737. [PMID: 32830844 DOI: 10.1093/aje/kwaa182] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 05/31/2020] [Accepted: 06/03/2020] [Indexed: 12/18/2022] Open
Abstract
We examined associations between maternal smoking and autism spectrum disorder (ASD) in children in a statewide population-based cohort and sibling-comparison design using California birth records (n = 2,015,104) with information on maternal smoking, demographic factors, and pregnancy (2007-2010). ASD cases (n = 11,722) were identified through California Department of Developmental Services records with diagnoses based on the Diagnostic and Statistical Manual of Mental Disorders-IV-TR. We estimated odds ratios for ASD with and without intellectual disability in the full cohort using logistic regression and in a sibling comparison using conditional logistic regression. In the full cohort, the adjusted odds ratio for ASD and maternal smoking 3 months before/during pregnancy compared with nonsmoking was 1.15 (95% confidence interval (CI): 1.04, 1.26), and it was similar in cases with (odds ratio = 1.12, 95% CI: 0.84, 1.49) and without intellectual disability (odds ratio = 1.15, 95% CI: 1.04, 1.27). Heavy prenatal smoking (≥20 cigarettes/day in any trimester) was related to an odds ratio of 1.55 (95% CI: 1.21, 1.98). In the sibling comparison, the odds ratio for heavy smoking was similarly elevated but the confidence interval was wide. Our findings are consistent with an increased risk for ASD in offspring of mothers who smoked ≥20 cigarettes/day during pregnancy; associations with lighter smoking were weaker.
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12
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Lkhagvadorj K, Zeng Z, Meyer KF, Verweij LP, Kooistra W, Reinders-Luinge M, Dijkhuizen HW, de Graaf IAM, Plösch T, Hylkema MN. Postnatal Smoke Exposure Further Increases the Hepatic Nicotine Metabolism in Prenatally Smoke Exposed Male Offspring and Is Linked with Aberrant Cyp2a5 Methylation. Int J Mol Sci 2020; 22:ijms22010164. [PMID: 33375250 PMCID: PMC7795156 DOI: 10.3390/ijms22010164] [Citation(s) in RCA: 3] [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: 11/20/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/16/2022] Open
Abstract
Prenatal smoke exposure (PreSE) is a risk factor for nicotine dependence, which is further enhanced by postnatal smoke exposure (PostSE). One susceptibility gene to nicotine dependence is Cytochrome P450 (CYP) 2A6, an enzyme responsible for the conversion of nicotine to cotinine in the liver. Higher CYP2A6 activity is associated with nicotine dependence and could be regulated through DNA methylation. In this study we investigated whether PostSE further impaired PreSE-induced effects on nicotine metabolism, along with Cyp2a5, orthologue of CYP2A6, mRNA expression and DNA methylation. Using a mouse model where prenatally smoke-exposed adult offspring were exposed to cigarette smoke for 3 months, enzyme activity, mRNA levels, and promoter methylation of hepatic Cyp2a5 were evaluated. We found that in male offspring, PostSE increased PreSE-induced cotinine levels and Cyp2a5 mRNA expression. In addition, both PostSE and PreSE changed Cyp2a5 DNA methylation in male groups. PreSE however decreased cotinine levels whereas it had no effect on Cyp2a5 mRNA expression or methylation. These adverse outcomes of PreSE and PostSE were most prominent in males. When considered in the context of the human health aspects, the combined effect of prenatal and adolescent smoke exposure could lead to an accelerated risk for nicotine dependence later in life.
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Affiliation(s)
- Khosbayar Lkhagvadorj
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
- Department of Pulmonology and Allergology, Mongolian National University of Medical Sciences, Ulaanbaatar 14210, Mongolia
| | - Zhijun Zeng
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Karolin F. Meyer
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Laura P. Verweij
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Wierd Kooistra
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Marjan Reinders-Luinge
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
| | - Henk W. Dijkhuizen
- Faculty of Science and Engineering, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Inge A. M. de Graaf
- Department of Pharmacokinetics, Toxicology and Targeting, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV Groningen, The Netherlands;
| | - Torsten Plösch
- University Medical Center Groningen, Department of Obstetrics and Gynecology, University of Groningen, 9713 GZ Groningen, The Netherlands;
| | - Machteld N. Hylkema
- University Medical Center Groningen, Department of Pathology and Medical Biology, University of Groningen, 9713 GZ Groningen, The Netherlands; (K.L.); (Z.Z.); (K.F.M.); (L.P.V.); (W.K.); (M.R.-L.)
- GRIAC Research Institute, University of Groningen, 9713 AV Groningen, The Netherlands
- Correspondence:
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13
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Wang XM, Tian FY, Xie CB, Niu ZZ, Chen WQ. Abnormal placental DNA methylation variation in spontaneous preterm birth. J Matern Fetal Neonatal Med 2020; 35:4704-4712. [PMID: 33327822 DOI: 10.1080/14767058.2020.1863357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Preterm birth (PTB) has become a major public health concern as the leading cause of neonatal death, but little is understood about its etiology. Children born preterm are also at increased risk of long-term consequences such as neurodevelopmental disorders, adulthood hypertension and diabetes. Recent studies have indicated that DNA methylation may be involved in the occurrence of PTB as well as related adverse outcomes. The latest Infinium EPIC BeadChip extends the coverage of the genome and provides a better tool to help investigate the involvement of DNA methylation in these conditions. METHODS We conducted this case-control study in three Women and Children's hospitals in South China, and enrolled 32 spontaneous preterm births and 16 term births. We assessed placental DNA methylation profiling of these participants with the Infinium EPIC BeadChip. We identified PTB and gestational age (GA)-associated CpG sites with limma regression model, and applied seqlm to identify PTB-associated regions. We performed gene ontology analysis to further interpret functional enrichment of the identified differentially methylated genes in PTB. RESULTS We identified a total of 8 differentially methylated positions (DMPs) that were significantly associated with PTB (FDR < 0.1) and a total of 15 DMPs that were associated with GA (FDR < 0.1). In the regional analysis, one differentially methylated region in the SLC23A1 gene overlapped with PTB-associated CpG site. The differentially methylated CpG sites in PTB were mapped to the genes involving in biological processes mainly regarding neurodevelopment, regulation of inflammation and metabolism. CONCLUSION Our findings suggested that preterm placenta have distinct DNA methylation alterations, and these alteration patterns established at birth provide insight into the long-term consequences of preterm birth.
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Affiliation(s)
- Xi-Meng Wang
- Department of Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China.,Department of Epidemiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Fu-Ying Tian
- Department of Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Chuan-Bo Xie
- Department of Cancer Prevention Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhong-Zheng Niu
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, State University of New York at Buffalo, Buffalo, NY, USA
| | - Wei-Qing Chen
- Department of Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, China.,Department of Information Management, Xinhua College, Sun Yat-sen University, Guangzhou, China
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14
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Collier ARY, Ledyard R, Montoya-Williams D, Qiu M, Dereix AE, Farrokhi MR, Hacker MR, Burris HH. Racial and ethnic representation in epigenomic studies of preterm birth: a systematic review. Epigenomics 2020; 13:1735-1746. [PMID: 33264049 DOI: 10.2217/epi-2020-0007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Aim: We conducted a systematic review evaluating race/ethnicity representation in DNA methylomic studies of preterm birth. Data sources: PubMed, EMBASE, CINHAL, Scopus and relevant citations from 1 January 2000 to 30 June 2019. Study appraisal & synthesis methods: Two authors independently identified abstracts comparing DNA methylomic differences between term and preterm births that included race/ethnicity data. Results: 16 studies were included. Black and non-Hispanic Black deliveries were well represented (28%). However, large studies originating from more than 95% White populations were excluded due to unreported race/ethnicity data. Most studies were cross-sectional, allowing for reverse causation. Most studies were also racially/ethnically homogeneous, preventing direct comparison of DNA methylomic differences across race/ethnicities. Conclusion: In DNA methylomic studies, Black women and infants were well represented. However, the literature has limitations and precludes drawing definitive conclusions.
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Affiliation(s)
- Ai-Ris Y Collier
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Obstetrics, Gynecology, & Reproductive Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Rachel Ledyard
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Diana Montoya-Williams
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Maylene Qiu
- Biomedical Library, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexandra E Dereix
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Loyola University Chicago Stritch School of Medicine, Maywood, IL 60153, USA
| | - Minou Raschid Farrokhi
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.,Colby College, Waterville, ME 04901, USA
| | - Michele R Hacker
- Department of Obstetrics & Gynecology, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA.,Department of Obstetrics, Gynecology, & Reproductive Biology, Harvard Medical School, Boston, MA 02115, USA.,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Heather H Burris
- Division of Neonatology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
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15
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Lkhagvadorj K, Meyer KF, Verweij LP, Kooistra W, Reinders-Luinge M, Dijkhuizen HW, de Graaf IAM, Plösch T, Hylkema MN. Prenatal smoke exposure induces persistent Cyp2a5 methylation and increases nicotine metabolism in the liver of neonatal and adult male offspring. Epigenetics 2020; 15:1370-1385. [PMID: 32573327 PMCID: PMC7678918 DOI: 10.1080/15592294.2020.1782655] [Citation(s) in RCA: 3] [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: 02/05/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 02/08/2023] Open
Abstract
Prenatal smoke exposure (PSE) is a risk factor for nicotine dependence. One susceptibility gene for nicotine dependence is Cytochrome P450 (CYP) 2A6, an enzyme responsible for the conversion of nicotine to cotinine and nicotine clearance in the liver. Higher activity of the CYP2A6 enzyme is associated with nicotine dependence, but no research has addressed the PSE effects on the CYP2A6 gene or its mouse homologue Cyp2a5. We hypothesized that PSE affects Cyp2a5 promoter methylation, Cyp2a5 mRNA levels, and nicotine metabolism in offspring. We used a smoke-exposed pregnant mouse model. RNA, DNA, and microsomal protein were isolated from liver tissue of foetal, neonatal, and adult offspring. Enzyme activity, Cyp2a5 mRNA levels, and Cyp2a5 methylation status of six CpG sites within the promoter region were analysed via HPLC, RT-PCR, and bisulphite pyrosequencing. Our data show that PSE induced higher cotinine levels in livers of male neonatal and adult offspring compared to controls. PSE-induced cotinine levels in neonates correlated with Cyp2a5 mRNA expression and promoter methylation at CpG-7 and CpG+45. PSE increased methylation in almost all CpG sites in foetal offspring, and this effect persisted at CpG-74 in male neonatal and adult offspring. Our results indicate that male offspring of mothers which were exposed to cigarette smoke during pregnancy have a higher hepatic nicotine metabolism, which could be regulated by DNA methylation. Given the detected persistence into adulthood, extrapolation to the human situation suggests that sons born from smoking mothers could be more susceptible to nicotine dependence later in life.
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Affiliation(s)
- Khosbayar Lkhagvadorj
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pulmonology and Allergology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Karolin F. Meyer
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Laura P. Verweij
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wierd Kooistra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjan Reinders-Luinge
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Henk W. Dijkhuizen
- Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Inge A. M. de Graaf
- Department of Pharmacokinetics, Toxicology, and Targeting, Groningen Research Institute of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Machteld N. Hylkema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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16
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Merid SK, Novoloaca A, Sharp GC, Küpers LK, Kho AT, Roy R, Gao L, Annesi-Maesano I, Jain P, Plusquin M, Kogevinas M, Allard C, Vehmeijer FO, Kazmi N, Salas LA, Rezwan FI, Zhang H, Sebert S, Czamara D, Rifas-Shiman SL, Melton PE, Lawlor DA, Pershagen G, Breton CV, Huen K, Baiz N, Gagliardi L, Nawrot TS, Corpeleijn E, Perron P, Duijts L, Nohr EA, Bustamante M, Ewart SL, Karmaus W, Zhao S, Page CM, Herceg Z, Jarvelin MR, Lahti J, Baccarelli AA, Anderson D, Kachroo P, Relton CL, Bergström A, Eskenazi B, Soomro MH, Vineis P, Snieder H, Bouchard L, Jaddoe VW, Sørensen TIA, Vrijheid M, Arshad SH, Holloway JW, Håberg SE, Magnus P, Dwyer T, Binder EB, DeMeo DL, Vonk JM, Newnham J, Tantisira KG, Kull I, Wiemels JL, Heude B, Sunyer J, Nystad W, Munthe-Kaas MC, Räikkönen K, Oken E, Huang RC, Weiss ST, Antó JM, Bousquet J, Kumar A, Söderhäll C, Almqvist C, Cardenas A, Gruzieva O, Xu CJ, Reese SE, Kere J, Brodin P, Solomon O, Wielscher M, Holland N, Ghantous A, Hivert MF, Felix JF, Koppelman GH, London SJ, Melén E. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. Genome Med 2020; 12:25. [PMID: 32114984 PMCID: PMC7050134 DOI: 10.1186/s13073-020-0716-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. METHODS We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. RESULTS We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. CONCLUSIONS We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
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Affiliation(s)
- Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leanne K Küpers
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ritu Roy
- Computational Biology And Informatics, University of California, San Francisco, San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Isabella Annesi-Maesano
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Pooja Jain
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Michelle Plusquin
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Florianne O Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomic of Complex diseases, School of Public Health, Imperial College London, London, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Nour Baiz
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Tim S Nawrot
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellen Aagaard Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Shanshan Zhao
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Terence Dwyer
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Murdoch Children's Research Institute, Australia Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - John Newnham
- Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Inger Kull
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Barbara Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Josep Maria Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France
- Department of Dermatology, Charité, Berlin, Germany
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Sarah E Reese
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsa Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki Finland, Helsinki, Finland
| | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Nina Holland
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
- Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.
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17
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Shen Y, Zhang H, Jiang Y, Mzayek F, Arshad H, Karmaus W. Maternal Birth Weight and BMI Mediate the Transgenerational Effect of Grandmaternal BMI on Grandchild's Birth Weight. Obesity (Silver Spring) 2020; 28:647-654. [PMID: 32012478 PMCID: PMC7042056 DOI: 10.1002/oby.22680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/26/2019] [Indexed: 12/25/2022]
Abstract
OBJECTIVE The aims of this study are to examine the potential association between grandmaternal BMI and grandchild's birth weight (BW) and whether maternal BW and BMI mediate this association. METHODS Data of 209 grandmother-mother pairs and 355 grandchildren from the Isle of Wight birth cohort in the UK were analyzed using path analysis. RESULTS An indirect effect of grandmaternal BMI on increasing grandchild's BW was mediated by maternal BW and BMI at age 18 years (indirect effects: β = 2.3 g/unit increase in grandmaternal BMI via maternal BW and β = 4.4 g via maternal BMI; P = 0.04). These two mediating effects of maternal BW and BMI confounded one another. Grandmaternal smoking during pregnancy had an indirect effect on decreasing grandchild's BW, dependent on maternal smoking during pregnancy and BW (indirect effects: β = -36.1 g compared with nonsmoking grandmothers via maternal smoking during pregnancy and β = -27.2 g via maternal BW; P = 0.005). Neither direct effect between grandmaternal BMI and grandchild's BW nor that between grandmaternal smoking during pregnancy and grandchild's BW was statistically significant. CONCLUSIONS Larger grandmaternal BMI indirectly increased grandchild's BW via maternal BW and BMI. Grandmaternal smoking during pregnancy indirectly reduced grandchild's BW via maternal smoking during pregnancy and BW.
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Affiliation(s)
- Yan Shen
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Fawaz Mzayek
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hampshire, UK
- David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Science, School of Public Health, University of Memphis, Memphis, TN, USA
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18
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Barišić A, Kolak M, Peterlin A, Tul N, Gašparović Krpina M, Ostojić S, Peterlin B, Pereza N. DNMT3B rs1569686 and rs2424913 gene polymorphisms are associated with positive family history of preterm birth and smoking status. Croat Med J 2020; 61:8-17. [PMID: 32118373 PMCID: PMC7063552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2023] Open
Abstract
AIM To evaluate the association between spontaneous preterm birth (SPTB) and DNA methyltransferase (DNMT)1, 3A, 3B, and 3L gene polymorphisms, and their contribution to the clinical characteristics of women with SPTB and their newborns. METHODS This case-control study, conducted in 2018, enrolled 162 women with SPTB and 162 women with term delivery. DNMT1 rs2228611, DNMT3A rs1550117, DNMT3B rs1569686, DNMT3B rs2424913, and DNMT3L rs2070565 single nucleotide polymorphisms were genotyped using polymerase chain reaction and restriction fragment length polymorphism methods. The clinical characteristics included in the analysis were family history of preterm birth, maternal smoking, maternal age, gestational week at delivery, and fetal birth weight. RESULTS DNMT gene polymorphisms were not significantly associated with SPTB. DNMT3B rs1569686 and rs2424913 minor alleles (T) were significantly more frequent in women with familial PTB than in women with non-familial PTB, increasing the odds for familial PTB 3.30 and 3.54 times under dominant genetic models. They were also significantly more frequent in women with SPTB who smoked before pregnancy, reaching the most significant association under additive genetic models (odds ratio 6.86, 95% confidence interval 2.25-20.86, P<0.001; odds ratio 3.77, 95% confidence interval 1.36-10.52, P=0.011, respectively). CONCLUSIONS DNMT3B rs1569686 and rs2424913 gene polymorphisms might be associated with positive family history of PTB and smoking status.
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Affiliation(s)
| | | | | | | | | | | | | | - Nina Pereza
- Nina Pereza, Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia,
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19
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Dwi Putra SE, Reichetzeder C, Hasan AA, Slowinski T, Chu C, Krämer BK, Kleuser B, Hocher B. Being Born Large for Gestational Age is Associated with Increased Global Placental DNA Methylation. Sci Rep 2020; 10:927. [PMID: 31969597 PMCID: PMC6976643 DOI: 10.1038/s41598-020-57725-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/31/2019] [Indexed: 02/01/2023] Open
Abstract
Being born small (SGA) or large for gestational age (LGA) is associated with adverse birth outcomes and metabolic diseases in later life of the offspring. It is known that aberrations in growth during gestation are related to altered placental function. Placental function is regulated by epigenetic mechanisms such as DNA methylation. Several studies in recent years have demonstrated associations between altered patterns of DNA methylation and adverse birth outcomes. However, larger studies that reliably investigated global DNA methylation are lacking. The aim of this study was to characterize global placental DNA methylation in relationship to size for gestational age. Global DNA methylation was assessed in 1023 placental samples by LC-MS/MS. LGA offspring displayed significantly higher global placental DNA methylation compared to appropriate for gestational age (AGA; p < 0.001). ANCOVA analyses adjusted for known factors impacting on DNA methylation demonstrated an independent association between placental global DNA methylation and LGA births (p < 0.001). Tertile stratification according to global placental DNA methylation levels revealed a significantly higher frequency of LGA births in the third tertile. Furthermore, a multiple logistic regression analysis corrected for known factors influencing birth weight highlighted an independent positive association between global placental DNA methylation and the frequency of LGA births (p = 0.001).
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Affiliation(s)
- S E Dwi Putra
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany.,Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Faculty of Biotechnology, University of Surabaya, Surabaya, Indonesia
| | - C Reichetzeder
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.
| | - A A Hasan
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany.,Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt.,UP Transfer GmbH, University of Potsdam, Potsdam, Germany
| | - T Slowinski
- Department of Nephrology, Campus Charité Mitte, University Hospital Charité, Berlin, Germany
| | - C Chu
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - B K Krämer
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - B Kleuser
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - B Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany. .,Department of Basic Medicine, Medical College of Hunan Normal University, Changsha, China. .,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.
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20
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Park B, Khanam R, Vinayachandran V, Baqui AH, London SJ, Biswal S. Epigenetic biomarkers and preterm birth. ENVIRONMENTAL EPIGENETICS 2020; 6:dvaa005. [PMID: 32551139 PMCID: PMC7293830 DOI: 10.1093/eep/dvaa005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 05/06/2023]
Abstract
Preterm birth (PTB) is a major public health challenge, and novel, sensitive approaches to predict PTB are still evolving. Epigenomic markers are being explored as biomarkers of PTB because of their molecular stability compared to gene expression. This approach is also relatively new compared to gene-based diagnostics, which relies on mutations or single nucleotide polymorphisms. The fundamental principle of epigenome diagnostics is that epigenetic reprogramming in the target tissue (e.g. placental tissue) might be captured by more accessible surrogate tissue (e.g. blood) using biochemical epigenome assays on circulating DNA that incorporate methylation, histone modifications, nucleosome positioning, and/or chromatin accessibility. Epigenomic-based biomarkers may hold great potential for early identification of the majority of PTBs that are not associated with genetic variants or mutations. In this review, we discuss recent advances made in the development of epigenome assays focusing on its potential exploration for association and prediction of PTB. We also summarize population-level cohort studies conducted in the USA and globally that provide opportunities for genetic and epigenetic marker development for PTB. In addition, we summarize publicly available epigenome resources and published PTB studies. We particularly focus on ongoing genome-wide DNA methylation and epigenome-wide association studies. Finally, we review the limitations of current research, the importance of establishing a comprehensive biobank, and possible directions for future studies in identifying effective epigenome biomarkers to enhance health outcomes for pregnant women at risk of PTB and their infants.
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Affiliation(s)
- Bongsoo Park
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Rasheda Khanam
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, International Center for Maternal and Newborn Health, Baltimore, MD 21205, USA
| | - Vinesh Vinayachandran
- School of Medicine, Cardiovascular Research Institute, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, International Center for Maternal and Newborn Health, Baltimore, MD 21205, USA
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Shyam Biswal
- Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
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21
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Scarpato R, Testi S, Colosimo V, Garcia Crespo C, Micheli C, Azzarà A, Tozzi MG, Ghirri P. Role of oxidative stress, genome damage and DNA methylation as determinants of pathological conditions in the newborn: an overview from conception to early neonatal stage. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 783:108295. [DOI: 10.1016/j.mrrev.2019.108295] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 11/25/2019] [Accepted: 12/24/2019] [Indexed: 12/15/2022]
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22
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Ding T, Mokshagundam S, Rinaudo PF, Osteen KG, Bruner-Tran KL. Paternal developmental toxicant exposure is associated with epigenetic modulation of sperm and placental Pgr and Igf2 in a mouse model. Biol Reprod 2019; 99:864-876. [PMID: 29741588 DOI: 10.1093/biolre/ioy111] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 05/04/2018] [Indexed: 01/16/2023] Open
Abstract
Preterm birth (PTB), parturition prior to 37 weeks' gestation, is the leading cause of neonatal mortality. The causes of spontaneous PTB are poorly understood; however, recent studies suggest that this condition may arise as a consequence of the parental fetal environment. Specifically, we previously demonstrated that developmental exposure of male mice (F1 animals) to the environmental endocrine disruptor 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) was associated with reduced sperm quantity/quality in adulthood and control female partners frequently delivered preterm. Reproductive defects persisted in the F2 and F3 descendants, and spontaneous PTB was common. Reproductive changes in the F3 males, the first generation without direct TCDD exposure, suggest the occurrence of epigenetic alterations in the sperm, which have the potential to impact placental development. Herein, we conducted an epigenetic microarray analysis of control and F1 male-derived placentae, which identified 2171 differentially methylated regions, including the progesterone receptor (Pgr) and insulin-like growth factor (Igf2). To assess if Pgr and Igf2 DNA methylation changes were present in sperm and persist in future generations, we assessed methylation and expression of these genes in F1/F3 sperm and F3-derived placentae. Although alterations in methylation and gene expression were observed, in most tissues, only Pgr reached statistical significance. Despite the modest gene expression changes in Igf2, offspring of F1 and F3 males consistently exhibited IUGR. Taken together, our data indicate that paternal developmental TCDD exposure is associated with transgenerational placental dysfunction, suggesting epigenetic modifications within the sperm have occurred. An evaluation of additional genes and alternative epigenetic mechanisms is warranted.
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Affiliation(s)
- Tianbing Ding
- Women's Reproductive Health Research Center, Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Shilpa Mokshagundam
- Women's Reproductive Health Research Center, Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Paolo F Rinaudo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California, USA
| | - Kevin G Osteen
- Women's Reproductive Health Research Center, Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA.,VA Tennessee Valley Healthcare System, Nashville Tennessee, USA
| | - Kaylon L Bruner-Tran
- Women's Reproductive Health Research Center, Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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23
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Peng Z, Xueb G, Chen W, Xia S. Environmental inhibitors of the expression of cytochrome P450 17A1 in mammals. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2019; 69:16-25. [PMID: 30921671 DOI: 10.1016/j.etap.2019.02.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 02/09/2019] [Accepted: 02/14/2019] [Indexed: 05/23/2023]
Abstract
Cytochrome P450 17A1 (CYP17A1; EC: 1.14.14.19) is a critically important bifunctional enzyme with nicotinamide adenine dinucleotide phosphate (NADPH) as its cofactor that catalyzes the formation of all endogenous androgens. Its hydroxylase activity catalyzes the 17α-hydroxylation of pregnenolone (PREG)/progesterone (P4) to 17α-OH-pregnenolone/17α-OH-progesterone, and its 17,20-lyase activity converts 17α-OH-pregnenolone/17α-OH-progesterone to dehydroepiandrosterone/androstenedione. Androgens are required for male reproductive development, so androgen deficiency resulting from CYP17A1 inhibition may lead to reproductive disorders. There has been some advances on the study of environmental chemicals inhibiting mammalian CYP17A1 expression but no related review was available so we think it now necessary to review their characteristics and inhibiting properties.
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Affiliation(s)
- Zhiheng Peng
- Department of Clinical Laboratory Center, The second Hospital of Lanzhou University, Lanzhou, Gansu 730000, China.
| | - Guoqiang Xueb
- Second Provincial People's Hospital of Gansu, Lanzou, Gansu 730000, China.
| | - Wenci Chen
- Wenzhou Hospital of Integrated Traditional Chinese and Western Medicine, Wenzhou, Zhejiang, 32500, China.
| | - Shenglong Xia
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 32500, China.
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Schuster J, Uzun A, Stablia J, Schorl C, Mori M, Padbury JF. Effect of prematurity on genome wide methylation in the placenta. BMC MEDICAL GENETICS 2019; 20:116. [PMID: 31253109 PMCID: PMC6599230 DOI: 10.1186/s12881-019-0835-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/24/2019] [Indexed: 12/12/2022]
Abstract
Background Preterm birth is a significant clinical problem and an enormous burden on society, affecting one in eight pregnant women and their newborns. Despite decades of research, the molecular mechanism underlying its pathogenesis remains unclear. Many studies have shown that preterm birth is associated with health risks across the later life course. The “fetal origins” hypothesis postulates that adverse intrauterine exposures are associated with later disease susceptibility. Our recent studies have focused on the placental epigenome at term. We extended these studies to genome-wide placental DNA methylation across a wide range of gestational ages. We applied methylation dependent immunoprecipitation/DNA sequencing (MeDIP-seq) to 9 placentas with gestational age from 25 weeks to term to identify differentially methylated regions (DMRs). Results Enrichment analysis revealed 427 DMRs with nominally significant differences in methylation between preterm and term placentas (p < 0.01) and 21 statistically significant DMRs after multiple comparison correction (FDR p < 0.05), of which 62% were hypo-methylated in preterm placentas vs term placentas. The majority of DMRs were in distal intergenic regions and introns. Significantly enriched pathways identified by Ingenuity Pathway Analysis (IPA) included Citrulline-Nitric Oxide Cycle and Fcy Receptor Mediated Phagocytosis in macrophages. The DMR gene set overlapped placental gene expression data, genes and pathways associated evolutionarily with preterm birth. Conclusion These studies form the basis for future studies on the epigenetics of preterm birth, “fetal programming” and the impact of environment exposures on this important clinical challenge. Electronic supplementary material The online version of this article (10.1186/s12881-019-0835-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Schuster
- Pediatrics, Women & Infants Hospital, Providence, Rhode Island, 02905, USA
| | - Alper Uzun
- Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA
| | - Joan Stablia
- Pediatrics, Women & Infants Hospital, Providence, Rhode Island, 02905, USA
| | - Christoph Schorl
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, 02906, USA
| | - Mari Mori
- Pediatrics and Genetics, Hasbro Children's Hospital, Providence, Rhode Island, 02905, USA
| | - James F Padbury
- Pediatrics, Center for Computational Molecular Biology, Brown Medical School, Brown University, Providence, Rhode Island, 02906, USA. .,, Providence, USA.
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Li S, Chen M, Li Y, Tollefsbol TO. Prenatal epigenetics diets play protective roles against environmental pollution. Clin Epigenetics 2019; 11:82. [PMID: 31097039 PMCID: PMC6524340 DOI: 10.1186/s13148-019-0659-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
It is thought that germ cells and preimplantation embryos during development are most susceptible to endogenous and exogenous environmental factors because the epigenome in those cells is undergoing dramatic elimination and reconstruction. Exposure to environmental factors such as nutrition, climate, stress, pathogens, toxins, and even social behavior during gametogenesis and early embryogenesis has been shown to influence disease susceptibility in the offspring. Early-life epigenetic modifications, which determine the expression of genetic information stored in the genome, are viewed as one of the general mechanisms linking prenatal exposure and phenotypic changes later in life. From atmospheric pollution, endocrine-disrupting chemicals to heavy metals, research increasingly suggests that environmental pollutions have already produced significant consequences on human health. Moreover, mounting evidence now links such pollution to relevant modification in the epigenome. The epigenetics diet, referring to a class of bioactive dietary compounds such as isothiocyanates in broccoli, genistein in soybean, resveratrol in grape, epigallocatechin-3-gallate in green tea, and ascorbic acid in fruits, has been shown to modify the epigenome leading to beneficial health outcomes. This review will primarily focus on the causes and consequences of prenatal environment pollution exposure on the epigenome, and the potential protective role of the epigenetics diet, which could play a central role in neutralizing epigenomic aberrations against environmental pollutions.
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Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Min Chen
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yuanyuan Li
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, USA.
- Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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Fragou D, Pakkidi E, Aschner M, Samanidou V, Kovatsi L. Smoking and DNA methylation: Correlation of methylation with smoking behavior and association with diseases and fetus development following prenatal exposure. Food Chem Toxicol 2019; 129:312-327. [PMID: 31063835 DOI: 10.1016/j.fct.2019.04.059] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/13/2022]
Abstract
Among epigenetic mechanisms, DNA methylation has been widely studied with respect to many environmental factors. Smoking is a common factor which affects both global and gene-specific DNA methylation. It is supported that smoking directly affects DNA methylation, and these effects contribute to the development and progression of various diseases, such as cancer, lung and cardiovascular diseases and male infertility. In addition, prenatal smoking influences the normal development of the fetus via DNA methylation changes. The DNA methylation profile and its smoking-induced alterations helps to distinguish current from former smokers and non-smokers and can be used to predict the risk for the development of a disease. This review summarizes the DNA methylation changes induced by smoking, their correlation with smoking behavior and their association with various diseases and fetus development.
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Affiliation(s)
- Domniki Fragou
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece
| | - Eleni Pakkidi
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Michael Aschner
- Departments of Molecular Pharmacology, Neuroscience, and Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Victoria Samanidou
- Laboratory of Analytical Chemistry, Department of Chemistry, Aristotle University of Thessaloniki, Greece
| | - Leda Kovatsi
- Laboratory of Forensic Medicine and Toxicology, School of Medicine, Aristotle University of Thessaloniki, Greece.
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27
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Franzago M, Fraticelli F, Stuppia L, Vitacolonna E. Nutrigenetics, epigenetics and gestational diabetes: consequences in mother and child. Epigenetics 2019; 14:215-235. [PMID: 30865571 PMCID: PMC6557546 DOI: 10.1080/15592294.2019.1582277] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Gestational Diabetes Mellitus (GDM) is the most common metabolic condition during pregnancy and may result in short- and long-term complications for both mother and offspring. The complexity of phenotypic outcomes seems influenced by genetic susceptibility, nutrient-gene interactions and lifestyle interacting with clinical factors. There is strong evidence that not only the adverse genetic background but also the epigenetic modifications in response to nutritional and environmental factors could influence the maternal hyperglycemia in pregnancy and the foetal metabolic programming. In this view, the correlation between epigenetic modifications and their transgenerational effects represents a very interesting field of study. The present review gives insight into the role of gene variants and their interactions with nutrients in GDM. In addition, we provide an overview of the epigenetic changes and their role in the maternal-foetal transmission of chronic diseases. Overall, the knowledge of epigenetic modifications induced by an adverse intrauterine and perinatal environment could shed light on the potential pathophysiological mechanisms of long-term disease development in the offspring and provide useful tools for their prevention.
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Affiliation(s)
- Marica Franzago
- a Department of Medicine and Aging, School of Medicine and Health Sciences , "G. d'Annunzio" University, Chieti-Pescara , Chieti , Italy.,b Molecular Genetics, Unit , CeSI-Met , Chieti , Italy
| | - Federica Fraticelli
- a Department of Medicine and Aging, School of Medicine and Health Sciences , "G. d'Annunzio" University, Chieti-Pescara , Chieti , Italy
| | - Liborio Stuppia
- b Molecular Genetics, Unit , CeSI-Met , Chieti , Italy.,c Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences , "G. d'Annunzio" University, Chieti-Pescara , Chieti , Italy
| | - Ester Vitacolonna
- a Department of Medicine and Aging, School of Medicine and Health Sciences , "G. d'Annunzio" University, Chieti-Pescara , Chieti , Italy
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28
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Wang XM, Tian FY, Fan LJ, Xie CB, Niu ZZ, Chen WQ. Comparison of DNA methylation profiles associated with spontaneous preterm birth in placenta and cord blood. BMC Med Genomics 2019; 12:1. [PMID: 30606219 PMCID: PMC6318854 DOI: 10.1186/s12920-018-0466-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/21/2018] [Indexed: 11/13/2022] Open
Abstract
Background The etiology and mechanism of spontaneous preterm birth (sPTB) are still unclear. Accumulating evidence has documented that various environmental exposure scenarios may cause maternal and fetal epigenetic changes, which initiates the focus on whether epigenetics can contribute to the occurrence of sPTB. Therefore, we conducted the current study to examine and compare the DNA methylation changes associated with sPTB in placenta and cord blood. Methods This hospital-based case-control study was carried out at three Women and Children’s hospitals in South China, where 32 spontaneous preterm births and 16 term births were recruited. Genome-wide DNA methylation profiles of the placenta and cord blood from these subjects were measured using the Illumina HumanMethylation EPIC BeadChip, and sPTB-associated differential methylated CpG sites were identified using limma regression model, after controlling for major maternal and infant confounders. Further Gene Ontology analysis was performed with PANTHER in order to assess different functional enrichment of the sPTB-associated genes in placenta and cord blood. Results After controlling for potential confounding factors, one differentially methylated position (DMP) in placenta and 31 DMPs in cord blood were found significantly associated with sPTB (Bonferroni corrected p < 0.05). The sPTB-associated CpG sites in placenta were mapped to genes that showed higher enrichment on biological processes including biological regulation, multicellular organismal process, and especially response to stimulus, while those in cord blood were mapped to genes that had higher enrichment on biological processes concerning cellular process, localization, and particularly metabolic process. Conclusion Findings of this study indicated that DNA methylation alteration in both placenta and cord blood are associated with sPTB, yet the DNA methylation modification patterns may appear differently in placenta and cord blood. Electronic supplementary material The online version of this article (10.1186/s12920-018-0466-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xi-Meng Wang
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Fu-Ying Tian
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China.,Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Li-Jun Fan
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Chuan-Bo Xie
- Department of Cancer Prevention Research, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, No 21 Qingcaigang, Jianshe Road 6, Guangzhou, 510600, Guangdong, China
| | - Zhong-Zheng Niu
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, State University of New York at Buffalo, 265 Farber Hall, Buffalo, NY, 14214, USA
| | - Wei-Qing Chen
- Department of Medical Statistics and Epidemiology, Guangzhou Key Laboratory of Environmental Pollution and Health Assessment, Guangdong Provincial Key Laboratory of Food, Nutrition and Health. School of Public Health, Sun Yat-sen University, Guangzhou, Guangdong, China. .,Department of Information Management, Xinhua College, Sun Yat-sen University, Guangzhou, Guangdong, China.
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29
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Choukrallah MA, Sewer A, Talikka M, Sierro N, Peitsch MC, Hoeng J, Ivanov NV. Epigenomics in tobacco risk assessment: Opportunities for integrated new approaches. CURRENT OPINION IN TOXICOLOGY 2018. [DOI: 10.1016/j.cotox.2019.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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30
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Zhang B, Hong X, Ji H, Tang WY, Kimmel M, Ji Y, Pearson C, Zuckerman B, Surkan PJ, Wang X. Maternal smoking during pregnancy and cord blood DNA methylation: new insight on sex differences and effect modification by maternal folate levels. Epigenetics 2018; 13:505-518. [PMID: 29945474 PMCID: PMC6140808 DOI: 10.1080/15592294.2018.1475978] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022] Open
Abstract
Maternal smoking during pregnancy may affect newborn DNA methylation (DNAm). However, little is known about how these associations vary by a newborn's sex and/or maternal nutrition. To fill in this research gap, we investigated epigenome-wide DNAm associations with maternal smoking during pregnancy in African American mother-newborn pairs. DNAm profiling in cord (n = 379) and maternal blood (n = 300) were performed using the Illumina HumanMethylation450 BeadChip array. We identified 12 CpG sites whose DNAm levels in cord blood were associated with maternal smoking, at a false discovery rate <5%. The identified associations in the GFI1 gene were more pronounced in male newborns than in females (P = 0.002 for maternal smoking × sex interaction at cg18146737). We further observed that maternal smoking and folate level may interactively affect cord blood DNAm level at cg05575921 in the AHRR gene (P = 5.0 × 10-4 for interaction): compared to newborns unexposed to maternal smoking and with a high maternal folate level (>19.2 nmol/L), the DNAm level was about 0.03 lower (P = 3.6 × 10-4) in exposed newborns with a high maternal folate level, but was 0.08 lower (P = 1.2 × 10-8) in exposed newborns with a low maternal folate level. Our data suggest that adequate maternal folate levels may partly counteract the impact of maternal smoking on DNAm. These findings may open new avenues of inquiry regarding sex differences in response to environmental insults and novel strategies to mitigate their intergenerational health effects through optimization of maternal nutrition.
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Affiliation(s)
- Boyang Zhang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hongkai Ji
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Wan-yee Tang
- Department of Environmental Health and Engineering, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mary Kimmel
- Department of Psychiatry, University of North Carolina at Chapel Hill’s School of Medicine, Chapel Hill, NC, USA
| | - Yuelong Ji
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Colleen Pearson
- Department of Pediatrics, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Barry Zuckerman
- Department of Pediatrics, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Pamela J. Surkan
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on the Early Life Origins of Disease, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Division of General Pediatrics & Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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31
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Nguyen T, Li GE, Chen H, Cranfield CG, McGrath KC, Gorrie CA. Maternal E-Cigarette Exposure Results in Cognitive and Epigenetic Alterations in Offspring in a Mouse Model. Chem Res Toxicol 2018; 31:601-611. [PMID: 29863869 DOI: 10.1021/acs.chemrestox.8b00084] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electronic cigarette (e-cigarette) use is on the rise worldwide and is particularly attractive to young people and as a smoking substitute by pregnant woman. There is a perception in pregnant women and women of child-bearing age that the use of e-cigarettes (vaping) is safer than smoking tobacco cigarettes during pregnancy. However, there is little evidence to support this perception. Here, we examined the offspring from mouse dams that had been exposed during and after pregnancy to ambient air (sham) ( n = 8), e-cigarette aerosols with nicotine ( n = 8), or e-cigarette aerosols without nicotine ( n = 8). Offspring underwent cognitive testing at 12 weeks of age and epigenetic testing of brain tissues at 1 day, 20 days, and 13 weeks after birth. The findings showed deficits in short-term memory, reduced anxiety, and hyperactivity in offspring following maternal e-cigarette exposure using the novel object recognition and elevated plus maze tests. In addition, global DNA methylation was increased in the brains of offspring soon after birth. Using a quantitative-PCR array specific to chromatin modification enzymes on genomic DNA and histones,13 key genes were identified to be significantly altered in the offspring brains from the e-cigarette groups compared to the nonexposed groups. The changes to genes Aurka, Aurkb, Aurkc, Kdm5c, Kdm6b, Dnmt3a, Dnmt3b, and Atf2, all associated with modulating neurological activity, were validated using RT-qPCR. In conclusion, in a mouse model, maternal exposure to e-cigarette aerosols resulted in both cognitive and epigenetic changes in offspring. This suggests that the use of e-cigarettes during pregnancy may have hitherto undetected neurological consequences on newborns.
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Affiliation(s)
- Tara Nguyen
- School of Life Sciences, Faculty of Science , University of Technology Sydney , Sydney , New South Wales , Australia
| | - Gerard E Li
- School of Life Sciences, Faculty of Science , University of Technology Sydney , Sydney , New South Wales , Australia
| | - Hui Chen
- School of Life Sciences, Faculty of Science , University of Technology Sydney , Sydney , New South Wales , Australia
| | - Charles G Cranfield
- School of Life Sciences, Faculty of Science , University of Technology Sydney , Sydney , New South Wales , Australia
| | - Kristine C McGrath
- School of Life Sciences, Faculty of Science , University of Technology Sydney , Sydney , New South Wales , Australia
| | - Catherine A Gorrie
- School of Life Sciences, Faculty of Science , University of Technology Sydney , Sydney , New South Wales , Australia
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Gentilini D, Somigliana E, Pagliardini L, Rabellotti E, Garagnani P, Bernardinelli L, Papaleo E, Candiani M, Di Blasio AM, Viganò P. Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception. Clin Epigenetics 2018; 10:77. [PMID: 29930742 PMCID: PMC5994106 DOI: 10.1186/s13148-018-0510-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/29/2018] [Indexed: 12/24/2022] Open
Abstract
Background An increased incidence of imprint-associated disorders has been reported in babies born from assisted reproductive technology (ART). However, previous studies supporting an association between ART and an altered DNA methylation status of the conceived babies have been often conducted on a limited number of methylation sites and without correction for critical potential confounders. Moreover, all the previous studies focused on the identification of methylation changes shared among subjects while an evaluation of stochastic differences has never been conducted. This study aims to evaluate the effect of ART and other common behavioral or environmental factors associated with pregnancy on stochastic epigenetic variability using a multivariate approach. Results DNA methylation levels of cord blood from 23 in vitro and 41 naturally conceived children were analyzed using the Infinium HumanMethylation450 BeadChips. After multiple testing correction, no statistically significant difference emerged in the number of cord blood stochastic epigenetic variations or in the methylation levels between in vitro- and in vivo-conceived babies. Conversely, four multiple factor analysis dimensions summarizing common phenotypic, behavioral, or environmental factors (cord blood cell composition, pre or post conception supplementation of folates, birth percentiles, gestational age, cesarean section, pre-gestational mother’s weight, parents’ BMI and obesity status, presence of adverse pregnancy outcomes, mother’s smoking status, and season of birth) were significantly associated with stochastic epigenetic variability. The stochastic epigenetic variation analysis allowed the identification of a rare imprinting defect in the locus GNAS in one of the babies belonging to the control population, which would not have emerged using a classical case-control association analysis. Conclusions We confirmed the effect of several common behavioral or environmental factors on the epigenome of newborns and described for the first time an epigenetic effect related to season of birth. Children born after ART did not appear to have an increased risk of genome-wide changes in DNA methylation either at specific loci or randomly scattered throughout the genome. The inability to identify differences between cases and controls suggests that the number of stochastic epigenetic variations potentially induced by ART was not greater than that naturally produced in response to maternal behavior or other common environmental factors. Electronic supplementary material The online version of this article (10.1186/s13148-018-0510-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- D Gentilini
- 1Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy.,5Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - E Somigliana
- 2Infertility Unit, Fondazione Ca' Granda, Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - L Pagliardini
- 3Reproductive Sciences Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - E Rabellotti
- 3Reproductive Sciences Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - P Garagnani
- 4Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - L Bernardinelli
- 5Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - E Papaleo
- 3Reproductive Sciences Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
| | - M Candiani
- 6Obstetrics and Gynaecology Unit, IRCCS Ospedale San Raffaele, 20132 Milan, Italy
| | - A M Di Blasio
- 1Istituto Auxologico Italiano IRCCS, 20095 Cusano Milanino, Italy
| | - P Viganò
- 3Reproductive Sciences Laboratory, Division of Genetics and Cell Biology, IRCCS Ospedale San Raffaele, Via Olgettina 58, 20132 Milan, Italy
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33
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Um SW, Kim Y, Lee BB, Kim D, Lee KJ, Kim HK, Han J, Kim H, Shim YM, Kim DH. Genome-wide analysis of DNA methylation in bronchial washings. Clin Epigenetics 2018; 10:65. [PMID: 29796116 PMCID: PMC5960087 DOI: 10.1186/s13148-018-0498-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/09/2018] [Indexed: 12/03/2022] Open
Abstract
Background The objective of this study was to discover DNA methylation biomarkers for detecting non-small lung cancer (NSCLC) in bronchial washings and understanding the association between DNA methylation and smoking cessation. Methods DNA methylation was analyzed in bronchial washing samples from 70 NSCLCs and 53 hospital-based controls using Illumina HumanMethylation450K BeadChip. Methylation levels in these bronchial washings were compared to those in 897 primary lung tissues of The Cancer Genome Atlas (TCGA) data. Results Twenty-four CpGs (p < 1.03E−07) were significantly methylated in bronchial washings from 70 NSCLC patients compared to those from 53 controls. The CpGs also had significant methylation in the TCGA cohort. The 123 participants were divided into a training set (N = 82) and a test set (N = 41) to build a classification model. Logistic regression model showed the best performance for classification of lung cancer in bronchial washing samples: the sensitivity and specificity of a marker panel consisting of seven CpGs in TFAP2A, TBX15, PHF11, TOX2, PRR15, PDGFRA, and HOXA11 genes were 87.0 and 83.3% in the test set, respectively. The area under the curve (AUC) was equal to 0.87 (95% confidence interval = 0.73–0.96, p < 0.001). Methylation levels of two CpGs in RUNX3 and MIR196A1 genes were inversely associated with duration of smoking cessation in the controls, but not in NSCLCs, after adjusting for pack-years of smoking. Conclusions The present study suggests that NSCLC may be detected by analyzing methylation changes of seven CpGs in bronchial washings. Furthermore, smoking cessation may lead to decreased DNA methylation in nonmalignant bronchial epithelial cells in a gene-specific manner. Electronic supplementary material The online version of this article (10.1186/s13148-018-0498-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sang-Won Um
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Yujin Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Bo Bin Lee
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Dongho Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea
| | - Kyung-Jong Lee
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Hong Kwan Kim
- 3Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Joungho Han
- 4Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Hojoong Kim
- 1Department of Internal Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Young Mog Shim
- 3Department of Thoracic and Cardiovascular Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, 135-710 South Korea
| | - Duk-Hwan Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon, 440-746 South Korea.,Samsung Medical Center, Research Institute for Future Medicine, #50 Ilwon-dong, Kangnam-gu, Professor Rm #5, Seoul, 135-710 South Korea
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Affiliation(s)
- Sharvari S. Deshpande
- Department of Neuroendocrinology, National Institute for Research in Reproductive Health (ICMR), Parel, Mumbai, India
| | - Nafisa H. Balasinor
- Department of Neuroendocrinology, National Institute for Research in Reproductive Health (ICMR), Parel, Mumbai, India
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Knopik VS, Marceau K, Bidwell LC, Rolan E. Prenatal substance exposure and offspring development: Does DNA methylation play a role? Neurotoxicol Teratol 2018; 71:50-63. [PMID: 29408446 DOI: 10.1016/j.ntt.2018.01.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 01/12/2018] [Accepted: 01/24/2018] [Indexed: 12/17/2022]
Abstract
The period of in utero development is one of the most critical windows during which adverse conditions and exposures may influence the growth and development of the fetus as well as its future postnatal health and behavior. Maternal substance use during pregnancy remains a relatively common but nonetheless hazardous in utero exposure. For example, previous epidemiological studies have associated prenatal substance exposure with reduced birth weight, poor developmental and psychological outcomes, and increased risk for diseases and behavioral disorders (e.g., externalizing behaviors like ADHD, conduct disorder, and substance use) later in life. Researchers are now learning that many of the mechanisms whereby adverse in utero exposures may affect key pathways crucial for proper fetal growth and development are epigenetic in nature, with the majority of work in humans considering DNA methylation specifically. This review will explore the research to date on epigenetic alterations tied to maternal substance use during pregnancy and will also discuss the possible role of DNA methylation in the robust relationship between maternal substance use and later behavioral and developmental sequelae in offspring.
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Affiliation(s)
- Valerie S Knopik
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA.
| | - Kristine Marceau
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
| | - L Cinnamon Bidwell
- Institute of Cognitive Science, University of Colorado, Boulder, CO, USA
| | - Emily Rolan
- Department of Human Development and Family Studies, Purdue University, West Lafayette, IN, USA
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Tehranifar P, Wu HC, McDonald JA, Jasmine F, Santella RM, Gurvich I, Flom JD, Terry MB. Maternal cigarette smoking during pregnancy and offspring DNA methylation in midlife. Epigenetics 2018; 13:129-134. [PMID: 28494218 DOI: 10.1080/15592294.2017.1325065] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Maternal smoking in pregnancy (MSP) has been associated with DNA methylation in specific CpG sites (CpGs) in infants and children. We investigated whether MSP, independent of own personal active smoking, was associated with midlife DNA methylation in CpGs that were previously identified in studies of MSP-DNA methylation in children. We used data on MSP collected from pregnant mothers of 89 adult women born in 1959-1964 and measured DNA methylation in blood (granulocytes) collected in 2001-2007 (mean age: 43 years). Seventeen CpGs were differentially methylated by MSP, with multiple CpGs mapping to CYP1A1, MYO1G, AHRR, and GFI1. These associations were consistent in direction with prior studies (e.g., MSP associated with more and less methylation in AHRR and CYP1A1, respectively) and, with the exception of AHRR CpGs, were not substantially altered by adjustment for active smoking. These preliminary results confirm prior prospective reports that MSP influences the offspring DNA methylation, and extends the timeframe to midlife, and suggest that these effects may persist into adulthood, independently of active smoking.
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Affiliation(s)
- Parisa Tehranifar
- a Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA.,b Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Hui-Chen Wu
- c Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Jasmine A McDonald
- a Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA.,b Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Farzana Jasmine
- d Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Regina M Santella
- b Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.,c Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Irina Gurvich
- c Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Julie D Flom
- a Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Mary Beth Terry
- a Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA.,b Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
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Toure DM, ElRayes W, Barnes-Josiah D, Hartman T, Klinkebiel D, Baccaglini L. Epigenetic modifications of human placenta associated with preterm birth: a systematic review. J Matern Fetal Neonatal Med 2018; 31:530-541. [PMID: 28282769 DOI: 10.1080/14767058.2017.1291620] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 02/01/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Preterm birth (PTB) is one of the leading causes of neonatal mortality and morbidity around the world. Epigenetic alterations of the human placenta may be involved in the causal chain of adverse pregnancy outcomes specifically PTB. In this systematic review, we investigated whether epigenetic dysregulation of the human placenta is associated with PTB. METHODS We searched MEDLINE and EMBASE and systematically reviewed all relevant studies on epigenetic placental modifications in PTB. Two independent reviewers selected controlled human studies published in any language, evaluated their quality, and graded them using the Newcastle-Ottawa Quality Assessment Scale. We resolved disagreements by consensus with a third reviewer. RESULTS Eleven observational studies of low to moderate quality met the eligibility criteria out of 60 unique studies. Most studies reported an association between placental epigenetic changes (methylation, mRNA and miRNA) and PTB, although research methods were highly heterogeneous. CONCLUSIONS Studies reported various associations between specific epigenetic findings and PTB, although methodological concerns limited results' validity. Additional high quality studies are needed to assess the repeatability of these findings. The STROBE guidelines can be used to improve the quality of reporting.
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Affiliation(s)
- Drissa M Toure
- a Department of Health Promotion, Social and Behavioral Health , College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - Wael ElRayes
- b Department of Environmental, Agricultural and Occupational Health , College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - Debora Barnes-Josiah
- c Department of Epidemiology , College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
| | - Teresa Hartman
- d McGoogan Library of Medicine , University of Nebraska Medical Center , Omaha , NE , USA
| | - David Klinkebiel
- e Department of Biochemistry and Molecular Biology , University of Nebraska Epigenomics Core Facility , Omaha , NE , USA
| | - Lorena Baccaglini
- c Department of Epidemiology , College of Public Health, University of Nebraska Medical Center , Omaha , NE , USA
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Martin EM, Fry RC. Environmental Influences on the Epigenome: Exposure- Associated DNA Methylation in Human Populations. Annu Rev Public Health 2018; 39:309-333. [PMID: 29328878 DOI: 10.1146/annurev-publhealth-040617-014629] [Citation(s) in RCA: 364] [Impact Index Per Article: 60.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA methylation is the most well studied of the epigenetic regulators in relation to environmental exposures. To date, numerous studies have detailed the manner by which DNA methylation is influenced by the environment, resulting in altered global and gene-specific DNA methylation. These studies have focused on prenatal, early-life, and adult exposure scenarios. The present review summarizes currently available literature that demonstrates a relationship between DNA methylation and environmental exposures. It includes studies on aflatoxin B1, air pollution, arsenic, bisphenol A, cadmium, chromium, lead, mercury, polycyclic aromatic hydrocarbons, persistent organic pollutants, tobacco smoke, and nutritional factors. It also addresses gaps in the literature and future directions for research. These gaps include studies of mixtures, sexual dimorphisms with respect to environmentally associated methylation changes, tissue specificity, and temporal stability of the methylation marks.
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Affiliation(s)
- Elizabeth M Martin
- Department of Environmental Sciences and Engineering, and Curriculum in Toxicology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, USA; ,
| | - Rebecca C Fry
- Department of Environmental Sciences and Engineering, and Curriculum in Toxicology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina 27599, USA; ,
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Palma-Gudiel H, Cirera F, Crispi F, Eixarch E, Fañanás L. The impact of prenatal insults on the human placental epigenome: A systematic review. Neurotoxicol Teratol 2018; 66:80-93. [PMID: 29307795 DOI: 10.1016/j.ntt.2018.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/20/2017] [Accepted: 01/01/2018] [Indexed: 02/07/2023]
Abstract
The placenta is the first human organ to reach full development during pregnancy. It serves as a barrier but also as an interchange surface. Epigenetic changes observed in placental tissue may reflect intrauterine insults while also pointing to physiological pathways altered under exposure to such environmental threats. By means of a systematic search of the literature, 39 papers assessing human placental epigenetic signatures in association with either (i) psychosocial stress, (ii) maternal psychopathology, (iii) maternal smoking during pregnancy, and (iv) exposure to environmental pollutants, were identified. Their findings revealed placental tissue as a unique source of epigenetic variability that does not correlate with epigenetic patterns observed in maternal or newborn blood, tissues which are typically analyzed regarding prenatal stress. Studies regarding prenatal stress and psychopathology during pregnancy were scarce and exploratory in nature revealing inconsistent findings. Of note, there was a marked tendency towards placental hypomethylation in studies assessing either tobacco use during pregnancy or exposure to environmental pollutants suggesting the interaction between contaminant-derived metabolites and epigenetic machinery. This review highlights the need for further prospective longitudinal studies assessing long-term health effects of placental epigenetic signatures derived from exposure to several prenatal stressors.
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Affiliation(s)
- Helena Palma-Gudiel
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain
| | - Flors Cirera
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain
| | - Fátima Crispi
- Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Barcelona, Spain; Centre for Biomedical Research on Rare Diseases (CIBER-ER), Madrid, Spain
| | - Elisenda Eixarch
- Fetal i+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Deu), Barcelona, Spain; Centre for Biomedical Research on Rare Diseases (CIBER-ER), Madrid, Spain
| | - Lourdes Fañanás
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona, Spain; Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Spain.
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van Otterdijk SD, Binder AM, Michels KB. Locus-specific DNA methylation in the placenta is associated with levels of pro-inflammatory proteins in cord blood and they are both independently affected by maternal smoking during pregnancy. Epigenetics 2017; 12:875-885. [PMID: 28820654 DOI: 10.1080/15592294.2017.1361592] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
We investigated the impact of maternal smoking during pregnancy on placental DNA methylation and how this may mediate the association between maternal smoking and pro-inflammatory proteins in cord blood. The study population consisted of 27 individuals exposed to maternal smoking throughout pregnancy, 32 individuals exposed during a proportion of the pregnancy, and 61 unexposed individuals. Methylation of 11 regions within 6 genes in placenta tissue was assessed by pyrosequencing. Levels of 7 pro-inflammatory proteins in cord blood were assessed by electrochemiluminescence. Differential methylation was observed in the CYP1A1 promoter and AHRR gene body regions between women who smoked throughout pregnancy and non-smokers on the fetal-side of the placenta and in the GFI1 promoter between women who quit smoking while pregnant and non-smokers on the maternal-side of the placenta. Maternal smoking resulted in elevated levels of IL-8 protein in cord blood, which was not mediated by DNA methylation of our candidate regions at either the maternal or the fetal side of the placenta. Placental DNA methylation was associated with levels of inflammatory proteins in cord blood. Our observations suggest that maternal smoking during pregnancy affects both placental DNA methylation and the neonate's immune response.
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Affiliation(s)
- Sanne D van Otterdijk
- a Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center , University of Freiburg , Freiburg , Germany.,b Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology , Brigham and Women's Hospital, Harvard Medical School , Boston , MA
| | - Alexandra M Binder
- b Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology , Brigham and Women's Hospital, Harvard Medical School , Boston , MA.,c Department of Epidemiology , Harvard School of Public Health , Boston , MA , USA
| | - Karin B Michels
- a Institute for Prevention and Cancer Epidemiology, Faculty of Medicine and Medical Center , University of Freiburg , Freiburg , Germany.,b Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology , Brigham and Women's Hospital, Harvard Medical School , Boston , MA.,c Department of Epidemiology , Harvard School of Public Health , Boston , MA , USA
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Marjonen H, Kahila H, Kaminen-Ahola N. rs10732516 polymorphism at the IGF2/H19 locus associates with a genotype-specific trend in placental DNA methylation and head circumference of prenatally alcohol-exposed newborns. Hum Reprod Open 2017; 2017:hox014. [PMID: 30895230 PMCID: PMC6276671 DOI: 10.1093/hropen/hox014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 08/31/2017] [Accepted: 09/11/2017] [Indexed: 12/20/2022] Open
Abstract
Study Question Does prenatal alcohol exposure (PAE) affect regulation of the insulin-like growth factor 2 (IGF2)/H19 locus in placenta and the growth-restricted phenotype of newborns? Summary Answer PAE results in genotype-specific trends in both placental DNA methylation at the IGF2/H19 locus and head circumference (HC) of newborns. What is Known Already PAE can disturb development of the nervous system and lead to restricted growth of the head, even microcephaly. To clarify the etiology of alcohol-induced growth restriction, we focused on the imprinted IGF2/H19 locus known to be important for normal placental and embryonic growth. The expression of IGF2 and a negative growth controller H19 are regulated by the H19 imprinting control region (H19 ICR) with seven-binding sites for the methylation-sensitive zinc-finger regulatory protein CTCF. A single nucleotide polymorphism rs10732516 G/A in the sixth-binding site has shown to associate with genotype-specific DNA methylation profiles at the H19 ICR. Study Design, Size, Duration By grouping 39 alcohol-exposed and 100 control samples according to rs10732516 polymorphism we explored alcohol-induced, genotype-specific changes in DNA methylation at the H19 ICR and the promoter region of H19 (H19 differentially methylated region). Also, IGF2 and H19 mRNA expression level in placenta as well as the phenotypes of newborns were examined. Participants/Materials, Setting, Methods We explored alcohol-induced, genotype-specific changes in placental DNA methylation by MassARRAY EpiTYPER and allele-specific changes by bisulphite sequencing. IGF2 and H19 expression in placenta were analyzed by quantitative PCR and the HC, birthweight and birth length of newborns were examined using national growth charts. Main Results and the Role of Chance We observed a consistent trend in genotype-specific changes in DNA methylation at H19 ICR in alcohol-exposed placentas. DNA methylation level in the normally highly methylated paternal allele of rs10732516 paternal A/maternal G genotype was decreased in alcohol-exposed placentas. In addition to decreased IGF2 mRNA expression in alcohol-exposed placentas of this specific genotype (P = 0.03), we observed significantly increased expression of H19 in relation to IGF2 when comparing all alcohol-exposed placentas to unexposed controls (P = 0.006). Furthermore, phenotypic examination showed a significant genotype-specific association between the alcohol exposure and HC of newborns (P = 0.001). Limitations Reasons for Caution Owing to the exceptional character of the alcohol-exposed human samples collected in this study, the sample size is restricted. An increased sample size and functional studies are needed to confirm these data and clarify the biological significance or causality of the observed associations. Wider Implications of the Findings Our results suggest that the rs10732516 polymorphism associates with the alcohol-induced alterations in DNA methylation profiles and head growth in a parent-of-origin manner. We also introduce a novel genotype-specific approach for exploring environmental effects on the IGF2/H19 locus and ultimately on embryonic growth. Study Funding/Competing Interest(s) This work was supported by the Academy of Finland (258304), The Finnish Foundation for Alcohol Studies, Finnish Cultural Foundation, Juho Vainio Foundation, Yrjö Jahnsson Foundation and Arvo and Lea Ylppö Foundation. No competing interests are declared.
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Affiliation(s)
- Heidi Marjonen
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Hanna Kahila
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Nina Kaminen-Ahola
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
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Shorey-Kendrick LE, McEvoy CT, Ferguson B, Burchard J, Park BS, Gao L, Vuylsteke BH, Milner KF, Morris CD, Spindel ER. Vitamin C Prevents Offspring DNA Methylation Changes Associated with Maternal Smoking in Pregnancy. Am J Respir Crit Care Med 2017; 196:745-755. [PMID: 28422514 DOI: 10.1164/rccm.201610-2141oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
RATIONALE Infants whose mothers smoked during pregnancy demonstrate lifelong decreases in pulmonary function. DNA methylation changes associated with maternal smoking during pregnancy have been described in placenta and cord blood at delivery, in fetal lung, and in buccal epithelium and blood during childhood. We demonstrated in a randomized clinical trial ( ClinicalTrials.gov identifier, NCT00632476) that vitamin C supplementation to pregnant smokers can lessen the impact of maternal smoking on offspring pulmonary function and decrease the incidence of wheeze at 1 year of age. OBJECTIVES To determine whether vitamin C supplementation reduces changes in offspring methylation in response to maternal smoking and whether methylation at specific CpGs is also associated with respiratory outcomes. METHODS Targeted bisulfite sequencing was performed with a subset of placentas, cord blood samples, and buccal samples collected during the NCT00632476 trial followed by independent validation of selected cord blood differentially methylated regions, using bisulfite amplicon sequencing. MEASUREMENTS AND MAIN RESULTS The majority (69.03%) of CpGs with at least 10% methylation difference between placebo and nonsmoker groups were restored (by at least 50%) toward nonsmoker levels with vitamin C treatment. A significant proportion of restored CpGs were associated with phenotypic outcome with greater enrichment among hypomethylated CpGs. CONCLUSIONS We identified a pattern of normalization in DNA methylation by vitamin C supplementation across multiple loci. The consistency of this pattern across tissues and time suggests a systemic and persistent effect on offspring DNA methylation. Further work is necessary to determine how genome-wide changes in DNA methylation may mediate or reflect persistent effects of maternal smoking on lung function.
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Affiliation(s)
| | - Cindy T McEvoy
- 2 Oregon Health and Science University, Portland, Oregon
| | - Betsy Ferguson
- 1 Oregon National Primate Research Center, Beaverton, Oregon; and
| | - Julja Burchard
- 2 Oregon Health and Science University, Portland, Oregon
| | - Byung S Park
- 1 Oregon National Primate Research Center, Beaverton, Oregon; and.,2 Oregon Health and Science University, Portland, Oregon
| | - Lina Gao
- 1 Oregon National Primate Research Center, Beaverton, Oregon; and.,2 Oregon Health and Science University, Portland, Oregon
| | | | | | | | - Eliot R Spindel
- 1 Oregon National Primate Research Center, Beaverton, Oregon; and
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Banik A, Kandilya D, Ramya S, Stünkel W, Chong YS, Dheen ST. Maternal Factors that Induce Epigenetic Changes Contribute to Neurological Disorders in Offspring. Genes (Basel) 2017; 8:E150. [PMID: 28538662 PMCID: PMC5485514 DOI: 10.3390/genes8060150] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/06/2017] [Accepted: 05/19/2017] [Indexed: 12/12/2022] Open
Abstract
It is well established that the regulation of epigenetic factors, including chromatic reorganization, histone modifications, DNA methylation, and miRNA regulation, is critical for the normal development and functioning of the human brain. There are a number of maternal factors influencing epigenetic pathways such as lifestyle, including diet, alcohol consumption, and smoking, as well as age and infections (viral or bacterial). Genetic and metabolic alterations such as obesity, gestational diabetes mellitus (GDM), and thyroidism alter epigenetic mechanisms, thereby contributing to neurodevelopmental disorders (NDs) such as embryonic neural tube defects (NTDs), autism, Down's syndrome, Rett syndrome, and later onset of neuropsychological deficits. This review comprehensively describes the recent findings in the epigenetic landscape contributing to altered molecular profiles resulting in NDs. Furthermore, we will discuss potential avenues for future research to identify diagnostic markers and therapeutic epi-drugs to reverse these abnormalities in the brain as epigenetic marks are plastic and reversible in nature.
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Affiliation(s)
- Avijit Banik
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
| | - Deepika Kandilya
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
| | - Seshadri Ramya
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
| | - Walter Stünkel
- Singapore Institute of Clinical Sciences, A*STAR, Singapore 117609, Singapore.
| | - Yap Seng Chong
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore.
| | - S Thameem Dheen
- Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117594, Singapore.
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Barcelona de Mendoza V, Wright ML, Agaba C, Prescott L, Desir A, Crusto CA, Sun YV, Taylor JY. A Systematic Review of DNA Methylation and Preterm Birth in African American Women. Biol Res Nurs 2017; 19:308-317. [PMID: 27646016 PMCID: PMC5357599 DOI: 10.1177/1099800416669049] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND The causes of many cases of preterm birth (PTB) remain enigmatic. Increased understanding of how epigenetic factors are associated with health outcomes has resulted in studies examining DNA methylation (DNAm) as a contributing factor to PTB. However, few studies on PTB and DNAm have included African American women, the group with the highest rate of PTB. METHODS The objective of this review was to systematically analyze the existing studies on DNAm and PTB among African American women. RESULTS Studies ( N = 10) were limited by small sample size, cross-sectional study designs, inconsistent methodologies for epigenomic analysis, and evaluation of different tissue types across studies. African Americans comprised less than half of the sample in 50% of the studies reviewed. Despite these limitations, there is evidence for an association between DNAm patterns and PTB. CONCLUSIONS Future research on DNAm patterns and PTB should use longitudinal study designs, repeated DNAm testing, and a clinically relevant definition of PTB and should include large samples of high-risk African American women to better understand the mechanisms for PTB in this population.
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Affiliation(s)
| | | | | | | | | | - Cindy A. Crusto
- Yale School of Medicine, New Haven, CT, USA
- Department of Psychology, University of Pretoria, Pretoria, South Africa
| | - Yan V. Sun
- Emory University Rollins School of Public Health, Atlanta, GA, USA
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Wang S, He Z, Li D, Zhang B, Li M, Li W, Zhu W, Xing X, Zeng X, Wang Q, Dong G, Xiao Y, Chen W, Chen L. Aberrant methylation of RUNX3 is present in Aflatoxin B 1-induced transformation of the L02R cell line. Toxicology 2017; 385:1-9. [PMID: 28458013 DOI: 10.1016/j.tox.2017.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 04/22/2017] [Accepted: 04/23/2017] [Indexed: 12/13/2022]
Abstract
Chronic exposure to aflatoxin B1 (AFB1) is linked to the development of hepatocellular carcinoma (HCC). To identify differentially methylated genes involved in AFB1-induced cell transformation, we analyzed DNA methylation patterns in immortal human hepatocyte L02 cells expressing an oncogenic H-Ras allele (L02R cells) and AFB1-transformed L02R (L02RT-AFB1) cells by performing genome-wide methylation profiling. We treated L02R cells with 0.3μM AFB1 weekly and observed a transformed phenotype at the 17th week post-treatment. The transformed cells (L02RT-AFB1) could grow in an anchorage independent fashion and form tumors in immunodeficient mice. qRT-PCR was performed to examine whether gene methylation led to a reduction in gene expression of methylated candidate genes. As a result, the expression of the following seven genes including JUNB, RUNX3, NAV1, CXCR4, RARRES1, INTS1, and POLL was down-regulated in transformed L02RT-AFB1 cells. The reduction of gene expression of these genes could be reversed by treatment of 5-azadeoxycytidine. The methylated CpG sites of RUNX3 genes were verified using bisulfite sequencing PCR (BSP) assay. Furthermore, a dynamic change in RUNX3 methylation was observed over the course of AFB1-induced cell transformation, which was corresponded to the alteration of gene expression and the extent of DNA damage. In vitro study showed that methylation of RUNX3 tended to abate in L02R cells treated with AFB1 for a short-term period of time. Notably, hypermethylation of RUNX3 appeared in 70% (14/20) of human hepatocellular carcinomas. Moreover, LINE-1 hypomethylation and dynamic changes of DNMTs, TETs and MeCP2 expression were also observed during AFB1-induced transformation. Taken together, these observations suggest that aberrant methylation of RUNX3 and LINE-1 might be involved in AFB1-induced carcinogenesis.
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Affiliation(s)
- Shan Wang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Zhini He
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Daochuan Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Bo Zhang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Miao Li
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wenxue Li
- Departmant of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Wei Zhu
- Departmant of Toxicology, Guangzhou Center for Disease Control and Prevention, Guangzhou, China
| | - Xiumei Xing
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Xiaowen Zeng
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Qing Wang
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Guanghui Dong
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Yongmei Xiao
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China
| | - Wen Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Liping Chen
- Department of Toxicology, Guangzhou Key Laboratory of Environmental Pollution and Health Risk Assessment, School of Public Health, Sun Yat-sen University, Guangzhou, China.
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46
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Richmond RC, Joubert BR. Contrasting the effects of intra-uterine smoking and one-carbon micronutrient exposures on offspring DNA methylation. Epigenomics 2017; 9:351-367. [PMID: 28234021 PMCID: PMC5331918 DOI: 10.2217/epi-2016-0135] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 12/22/2016] [Indexed: 12/11/2022] Open
Abstract
Maternal smoking and micronutrient intake during pregnancy are two strong biological candidates for impacting the developing epigenome. The extent to which DNA methylation in offspring is modified by these intrauterine exposures has not been presented in parallel. In this review, we summarize human studies which have investigated genome-wide DNA methylation in the offspring in relation to maternal smoking and one-carbon micronutrient exposure during pregnancy. We contrast the primarily independent efforts for these two categories of exposure, and potential explanations for these differences. We emphasize methodological considerations such as power to detect methylation signals, exposure assessment, control of sources of variability, causal inference and the role of observed methylation changes in mediating downstream outcomes in the offspring.
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Affiliation(s)
- Rebecca C Richmond
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, BS8 2BN, UK
| | - Bonnie R Joubert
- National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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47
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Majchrzak-Celińska A, Kosicka K, Paczkowska J, Główka FK, Bręborowicz GH, Krzyścin M, Siemiątkowska A, Szaumkessel M, Baer-Dubowska W. HSD11B2, RUNX3, and LINE-1 Methylation in Placental DNA of Hypertensive Disorders of Pregnancy Patients. Reprod Sci 2017; 24:1520-1531. [PMID: 29017438 DOI: 10.1177/1933719117692043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Hypertensive Disorders of Pregnancy (HDsP) remain leading causes of maternal and perinatal morbidity and mortality. Growing evidence suggests the involvement of epigenetic factors, such as gene-specific and global DNA methylation changes, both in the etiology and as an effect of HDsP. In this study, we investigated the potential association between placental DNA methylation status in selected CpGs of HSD11B2 cortisol level controlling gene, RUNX3 tumor suppressor gene, and long interspersed nucleotide element-1 (LINE-1) repetitive elements and HDsP-preeclampsia (PE), gestational hypertension (GH), and chronic hypertension (CH). Methylation-specific polymerase chain reaction (MSP) and pyrosequencing (PSQ) were used to analyze placental DNA methylation. Plasma and urine cortisol and cortisone levels were measured using high performance liquid chromatography with fluorescence detection (HPLC-FLD), whereas serum progesterone level was determined by electrochemiluminescence immunoassay. The mean percentage of HSD11B2, RUNX3, and LINE-1 methylation was not altered in the placentas of patients with HDsP, as compared to the controls. However, among patients from PE, GH, and CH groups, several significant correlations were observed between the methylation status of HSD11B2, RUNX3, or LINE-1 and children's birth weight, gestational age at delivery, mother's age, and body mass index as well as hormones levels. These results indicate lack of association between methylation status of HSD11B2, RUNX3, or LINE-1 repetitive elements and HDsP. However, association of these parameters with some clinical variables may suggest the role of placental DNA methylation in fetal development and should be further explored.
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Affiliation(s)
| | - Katarzyna Kosicka
- 2 Department of Physical Pharmacy and Pharmacokinetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Julia Paczkowska
- 3 Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Franciszek K Główka
- 2 Department of Physical Pharmacy and Pharmacokinetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Grzegorz H Bręborowicz
- 4 Department of Perinatology and Gynecology, Poznan University of Medical Sciences, Poznań, Poland
| | - Mariola Krzyścin
- 4 Department of Perinatology and Gynecology, Poznan University of Medical Sciences, Poznań, Poland
| | - Anna Siemiątkowska
- 2 Department of Physical Pharmacy and Pharmacokinetics, Poznan University of Medical Sciences, Poznań, Poland
| | - Marcin Szaumkessel
- 3 Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Wanda Baer-Dubowska
- 1 Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
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48
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Current Issues in Developmental Immunotoxicity. IMMUNOPATHOLOGY IN TOXICOLOGY AND DRUG DEVELOPMENT 2017. [DOI: 10.1007/978-3-319-47377-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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49
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Schmidt RJ, Schroeder DI, Crary-Dooley FK, Barkoski JM, Tancredi DJ, Walker CK, Ozonoff S, Hertz-Picciotto I, LaSalle JM. Self-reported pregnancy exposures and placental DNA methylation in the MARBLES prospective autism sibling study. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw024. [PMID: 28781890 PMCID: PMC5538262 DOI: 10.1093/eep/dvw024] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/10/2016] [Accepted: 10/11/2016] [Indexed: 05/30/2023]
Abstract
Human placenta is a fetal-derived tissue that offers a unique sample of epigenetic and environmental exposures present in utero. In the MARBLES prospective pregnancy study of high-risk younger siblings of children with autism spectrum disorder (ASD), pregnancy and environmental factors collected by maternal interviews were examined as predictors of placental DNA methylation, including partially methylated domains (PMDs), an embryonic feature of the placental methylome. DNA methylation data from MethylC-seq analysis of 47 placentas of children clinically diagnosed at 3 years with ASD or typical development using standardized assessments were examined in relation to: child's gestational age, birth-weight, and diagnosis; maternal pre-pregnancy body mass index, smoking, education, parity, height, prenatal vitamin and folate intake; home ownership; pesticides professionally applied to lawns or gardens or inside homes, pet flea/tick pouches, collars, or soaps/shampoos used in the 3 months prior to or during pregnancy. Sequencing run, order, and coverage, and child race and sex were considered as potential confounders. Akaike information criterion was used to select the most parsimonious among candidate models. Final prediction models used sandwich estimators to produce homoscadisticity-robust estimates of the 95% confidence interval (CI) and P-values controlled the false discovery rate at 5%. The strongest, most robust associations were between pesticides professionally applied outside the home and higher average methylation over PMDs [0.45 (95% CI 0.17, 0.72), P = 0.03] and a reduced proportion of the genome in PMDs [-0.42 (95% CI - 0.67 to -0.17), P = 0.03]. Pesticide exposures could alter placental DNA methylation more than other factors.
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Affiliation(s)
- Rebecca J. Schmidt
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, CA, USA
- MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Diane I. Schroeder
- Department of Medical Microbiology and Immunology, Genome Center, UC Davis School of Medicine, Davis, CA, USA
| | - Florence K. Crary-Dooley
- Department of Medical Microbiology and Immunology, Genome Center, UC Davis School of Medicine, Davis, CA, USA
| | | | | | - Cheryl K. Walker
- MIND Institute, UC Davis School of Medicine, Davis, CA, USA
- Department of Obstetrics and Gynecology, UC Davis School of Medicine, Davis, CA, USA
| | - Sally Ozonoff
- MIND Institute, UC Davis School of Medicine, Davis, CA, USA
- Department of Psychiatry and Behavioral Sciences, UC Davis School of Medicine, Davis, CA, USA
| | - Irva Hertz-Picciotto
- Department of Public Health Sciences, UC Davis School of Medicine, Davis, CA, USA
- MIND Institute, UC Davis School of Medicine, Davis, CA, USA
| | - Janine M. LaSalle
- MIND Institute, UC Davis School of Medicine, Davis, CA, USA
- Department of Medical Microbiology and Immunology, Genome Center, UC Davis School of Medicine, Davis, CA, USA
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50
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Mayne BT, Leemaqz SY, Smith AK, Breen J, Roberts CT, Bianco-Miotto T. Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation. Epigenomics 2016; 9:279-289. [PMID: 27894195 PMCID: PMC6040051 DOI: 10.2217/epi-2016-0103] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Aim: To determine whether dynamic DNA methylation changes in the human placenta can be used to predict gestational age. Materials & methods: Publicly available placental DNA methylation data from 12 studies, together with our own dataset, using Illumina Infinium Human Methylation BeadChip arrays. Results & conclusion: We developed an accurate tool for predicting gestational age of placentas using 62 CpG sites. There was a higher predicted gestational age for placentas from early onset preeclampsia cases, but not term preeclampsia, compared with their chronological age. Therefore, early onset preeclampsia is associated with placental aging. Gestational age acceleration prediction from DNA methylation array data may provide insight into the molecular mechanisms of pregnancy disorders.
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Affiliation(s)
- Benjamin T Mayne
- Robinson Research Institute, University of Adelaide, SA, 5005, Australia.,Adelaide Medical School, University of Adelaide, SA, 5005, Australia
| | - Shalem Y Leemaqz
- Robinson Research Institute, University of Adelaide, SA, 5005, Australia.,Adelaide Medical School, University of Adelaide, SA, 5005, Australia
| | - Alicia K Smith
- Department of Gynecology and Obstetrics & Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - James Breen
- Robinson Research Institute, University of Adelaide, SA, 5005, Australia.,Bioinformatics Hub, School of Biological Sciences, University of Adelaide, SA, 5005, Australia
| | - Claire T Roberts
- Robinson Research Institute, University of Adelaide, SA, 5005, Australia.,Adelaide Medical School, University of Adelaide, SA, 5005, Australia
| | - Tina Bianco-Miotto
- Robinson Research Institute, University of Adelaide, SA, 5005, Australia.,Waite Research Institute, School of Agriculture, Food & Wine, University of Adelaide, SA, 5005, Australia
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