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Ma H, Wang X, Liang Z, Li X, Heianza Y, He J, Chen W, Bazzano L, Qi L. BMI change during childhood, DNA methylation change at TXNIP, and glucose change during midlife. Obesity (Silver Spring) 2023; 31:2150-2158. [PMID: 37415079 PMCID: PMC10524171 DOI: 10.1002/oby.23806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/28/2023] [Accepted: 04/29/2023] [Indexed: 07/08/2023]
Abstract
OBJECTIVE This study investigated whether changes in DNA methylation (DNAm) at TXNIP are associated with glycemic changes and whether such an association differs with early-life adiposity changes. METHODS A total of 594 Bogalusa Heart Study participants who had blood DNAm measurements at two time points in midlife were included. Of them, 353 participants had at least four BMI measurements during childhood and adolescence. The incremental area under the curve was calculated as a measure of long-term trends of BMI during childhood and adolescence. RESULTS Increase in DNAm at TXNIP was significantly associated with decrease in fasting plasma glucose (FPG) independent of covariates (p < 0.001). The study found that the strength of this relationship was significantly modified by a trend of increasing BMI during childhood and adolescence (p-interaction = 0.003). Each 1% increase in DNAm at TXNIP was associated with a 2.90- (0.77) mg/dL decrease in FPG among participants with the highest tertile of BMI incremental area under the curve and a 0.96- (0.38) mg/dL decrease among those with the middle tertile, whereas no association was observed among participants with the lowest tertile. CONCLUSIONS These results indicate that changes in blood DNAm at TXNIP are significantly associated with changes in FPG in midlife, and this association was modified by BMI trends during childhood and adolescence.
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Affiliation(s)
- Hao Ma
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Xuan Wang
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Zhaoxia Liang
- Obstetrical Department, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiang Li
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Yoriko Heianza
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Jiang He
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Wei Chen
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Lydia Bazzano
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA
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2
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Janoš T, Ottenbros I, Bláhová L, Šenk P, Šulc L, Pálešová N, Sheardová J, Vlaanderen J, Čupr P. Effects of pesticide exposure on oxidative stress and DNA methylation urinary biomarkers in Czech adults and children from the CELSPAC-SPECIMEn cohort. ENVIRONMENTAL RESEARCH 2023; 222:115368. [PMID: 36716809 PMCID: PMC10009299 DOI: 10.1016/j.envres.2023.115368] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 05/13/2023]
Abstract
Current-use pesticide (CUP) exposure occurs mainly through diet and environmental application in both agricultural and urban settings. While pesticide exposure has been associated with many adverse health outcomes, the intermediary molecular mechanisms are still not completely elucidated. Among others, their roles in epigenetics (DNA methylation) and DNA damage due to oxidative stress are presumed. Scientific evidence on urinary biomarkers of such body response in general population is limited, especially in children. A total of 440 urine samples (n = 110 parent-child pairs) were collected during the winter and summer seasons in order to describe levels of overall DNA methylation (5-mC, 5-mdC, 5-hmdC, 7-mG, 3-mA) and oxidative stress (8-OHdG) biomarkers and investigate their possible associations with metabolites of pyrethroids (3-PBA, t/c-DCCA), chlorpyrifos (TCPY), and tebuconazole (TEB-OH). Linear mixed-effects models accounting for intraindividual and intrahousehold correlations were utilized. We applied false discovery rate procedure to account for multiplicity and adjusted for potential confounding variables. Higher urinary levels of most biological response biomarkers were measured in winter samples. In adjusted repeated measures models, interquartile range (IQR) increases in pyrethroid metabolites were associated with higher oxidative stress. t/c-DCCA and TCPY were associated with higher urinary levels of cytosine methylation biomarkers (5-mC and/or 5-mdC). The most robust association was observed for tebuconazole metabolite with 3-mA (-15.1% change per IQR increase, 95% CI = -23.6, -5.69) suggesting a role of this pesticide in reduced demethylation processes through possible DNA glycosylase inhibition. Our results indicate an urgent need to extend the range of analyzed environmental chemicals such as azole pesticides (e.g. prothioconazole) in human biomonitoring studies. This is the first study to report urinary DNA methylation biomarkers in children and associations between CUP metabolites and a comprehensive set of biomarkers including methylated and oxidized DNA alterations. Observed associations warrant further large-scale research of these biomarkers and environmental pollutants including CUPs.
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Affiliation(s)
- Tomáš Janoš
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Ilse Ottenbros
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands; Center for Sustainability, Environment and Health, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lucie Bláhová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Petr Šenk
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Libor Šulc
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Nina Pálešová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Jessica Sheardová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Pavel Čupr
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
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Xu Y, Lindh CH, Fletcher T, Jakobsson K, Engström K. Perfluoroalkyl substances influence DNA methylation in school-age children highly exposed through drinking water contaminated from firefighting foam: a cohort study in Ronneby, Sweden. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac004. [PMID: 35308102 PMCID: PMC8931254 DOI: 10.1093/eep/dvac004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/04/2022] [Indexed: 05/31/2023]
Abstract
Perfluoroalkyl substances (PFASs) are widespread synthetic substances with various adverse health effects. A potential mechanism of toxicity for PFASs is via epigenetic changes, such as DNA methylation. Previous studies have evaluated associations between PFAS exposure and DNA methylation among newborns and adults. However, no study has evaluated how PFASs influence DNA methylation among children of school age. In this exploratory study with school-age children exposed to PFASs through drinking water highly contaminated from firefighting foams, we aimed to investigate whether exposure to PFASs was associated with alteration in DNA methylation and epigenetic age acceleration. Sixty-three children aged 7-11 years from the Ronneby Biomarker Cohort (Sweden) were included. The children were either controls with only background exposure (n = 32; perfluorooctane sulfonic acid: median 2.8 and range 1-5 ng/ml) or those exposed to very high levels of PFASs (n = 31; perfluorooctane sulfonic acid: median 295 and range 190-464 ng/ml). These two groups were matched on sex, age, and body mass index. Genome-wide methylation of whole-blood DNA was analyzed using the Infinium MethylationEPIC BeadChip kit. Epigenetic age acceleration was derived from the DNA methylation data. Twelve differentially methylated positions and seven differentially methylated regions were found when comparing the high-exposure group to the control group. There were no differences in epigenetic age acceleration between these two groups (P = 0.66). We found that PFAS exposure was associated with DNA methylation at specific genomic positions and regions in children at school age, which may indicate a possible mechanism for linking PFAS exposure to health effects.
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Affiliation(s)
- Yiyi Xu
- School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Medicinaregatan 18A, Gothenburg 413 90, Sweden
| | - Christian H Lindh
- Department of Laboratory Medicine, Division of Occupational and Environmental Medicine, Lund University, Scheelevägen 2, Lund 223 63, Sweden
| | - Tony Fletcher
- Department of Social and Environmental Health Research, London School of Hygiene & Tropical Medicine, Keppel St, London WC1E 7HT, UK
| | - Kristina Jakobsson
- School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Medicinaregatan 18A, Gothenburg 413 90, Sweden
- Occupational and Environmental Medicine, Sahlgrenska University Hospital, Medicinaregatan 16 A, Gothenburg 413 90, Sweden
| | - Karin Engström
- **Correspondence address. Department of Laboratory Medicine, EPI@LUND, Division of Occupational and Environmental Medicine, Lund University, Biskopsgatan 9, Lund 223 62, Sweden. Tel: +46 46 222 16 38; E-mail:
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4
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Kananen L, Marttila S. Ageing-associated changes in DNA methylation in X and Y chromosomes. Epigenetics Chromatin 2021; 14:33. [PMID: 34215292 PMCID: PMC8254238 DOI: 10.1186/s13072-021-00407-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ageing displays clear sexual dimorphism, evident in both morbidity and mortality. Ageing is also associated with changes in DNA methylation, but very little focus has been on the sex chromosomes, potential biological contributors to the observed sexual dimorphism. Here, we sought to identify DNA methylation changes associated with ageing in the Y and X chromosomes, by utilizing datasets available in data repositories, comprising in total of 1240 males and 1191 females, aged 14–92 years. Results In total, we identified 46 age-associated CpG sites in the male Y, 1327 age-associated CpG sites in the male X, and 325 age-associated CpG sites in the female X. The X chromosomal age-associated CpGs showed significant overlap between females and males, with 122 CpGs identified as age-associated in both sexes. Age-associated X chromosomal CpGs in both sexes were enriched in CpG islands and depleted from gene bodies and showed no strong trend towards hypermethylation nor hypomethylation. In contrast, the Y chromosomal age-associated CpGs were enriched in gene bodies, and showed a clear trend towards hypermethylation with age. Conclusions Significant overlap in X chromosomal age-associated CpGs identified in males and females and their shared features suggest that despite the uneven chromosomal dosage, differences in ageing-associated DNA methylation changes in the X chromosome are unlikely to be a major contributor of sex dimorphism in ageing. While age-associated CpGs showed good replication across datasets in the present study, only a limited set of previously reported age-associated CpGs were replicated. One contributor to the limited overlap are differences in the age range of individuals included in each data set. Further study is needed to identify biologically significant age-associated CpGs in the sex chromosomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00407-6.
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Affiliation(s)
- Laura Kananen
- Faculty of Social Sciences (Health Sciences), Tampere University, Tampere, Finland. .,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Saara Marttila
- Gerontology Research Center, Tampere University, Tampere, Finland. .,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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5
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Olstad EW, Nordeng HME, Gervin K. Prenatal medication exposure and epigenetic outcomes: a systematic literature review and recommendations for prenatal pharmacoepigenetic studies. Epigenetics 2021; 17:357-380. [PMID: 33926354 PMCID: PMC8993058 DOI: 10.1080/15592294.2021.1903376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
When used during pregnancy, analgesics and psychotropics pass the placenta to enter the foetal circulation and may induce epigenetic modifications. Where such modifications occur and whether they disrupt normal foetal developme nt, are currently unanswered questions. This field of prenatal pharmacoepigenetics has received increasing attention, with several studies reporting associations between in utero medication exposure and offspring epigenetic outcomes. Nevertheless, no recent systematic review of the literature is available. Therefore, the objectives of this review were to (i) provide an overview of the literature on the association of prenatal exposure to psychotropics a nd analgesics with epigenetic outcomes, and (ii) suggest recommendations for future studies within prenatal pharmacoepigenetics. We performed systematic literature searches in five databases. The eligible studies assessed human prenatal exposure to psychotropics or analgesics, with epigenetic analyses of offspring tissue as an outcome. We identified 18 eligible studies including 4,419 neonates exposed to either antidepressants, antiepileptic drugs, paracetamol, acetylsalicylic acid, or methadone. The epigenetic outcome in all studies was DNA methylation in cord blood, placental tissue or buccal cells. Although most studies found significant differences in DNA methylation upon medication exposure, almost no differences were persistent across studies for similar medications and sequencing methods. The reviewed studies were challenging to compare due to poor transparency in reporting, and heterogeneous methodology, design, genome coverage, and statistical modelling. We propose 10 recommendations for future prenatal pharmacoepigenetic studies considering both epidemiological and epigenetic perspectives. These recommendations may improve the quality, comparability, and clinical relevance of such studies. PROSPERO registration ID: CRD42020166675.
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Affiliation(s)
- Emilie Willoch Olstad
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Hedvig Marie Egeland Nordeng
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.,Department of Research, Innovation and Education, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
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6
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Bicho RC, Scott-Fordsmand JJ, Amorim MJB. Developing an epigenetics model species - From blastula to mature adult, life cycle methylation profile of Enchytraeus crypticus (Oligochaete). THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:139079. [PMID: 32428769 DOI: 10.1016/j.scitotenv.2020.139079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/07/2020] [Accepted: 04/26/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is an epigenetic mechanism of particular importance in developmental biology, but methylation also varies along organisms' life cycle. Recent studies have deliberated copper (Cu) exposure induced epigenetic changes in Enchytraeus crypticus, a standard species belonging to one of the most common and important genera of soil invertebrates in many ecosystems. There is however no information on how DNA methylation levels change within the life cycle of this species. We here investigate the global DNA methylation profile along the life cycle of E. crypticus and compare this to the expression of target genes involved in methylation. Results showed that after the lowest DNA methylation level at day 3 (early embryonic stage, blastula) there was an increase by day 7 (organogenesis) after which levels were maintained at days 11, 18 and 25. DNA methyltransferase associated protein 1 (DMPA1) and Methyl Binding Domain 2 (MBD2) gene expression was highest during embryo stages (3 to 7 days), then decreasing (11, 18 days) and finally unregulated in adults (25 days). Hence, we here show that DNA methylation in E. crypticus changes among the different life stages, from cocoons to adults. Such information is a key knowledge to use this endpoint and tool in an ecotoxicology context. This means that it is almost implicit that gene expression levels are age specific for a given stressor. It seems logic to recommend to always compare individuals with the same age between treatments, and to be careful when extrapolating results among life stages. Once, we understand more of these effects we may even be able to predict which life stage is more sensitive to specific stressors. An experimental design that aims to cover epigenetics of stressors in a multigenerational exposure, including transgenerational effects, should ensure the synchronous age of organisms for sampling analysis purposes.
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Affiliation(s)
- Rita C Bicho
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Janeck J Scott-Fordsmand
- Department of Bioscience, Aarhus University, Vejlsovej 25, PO Box 314, DK-8600 Silkeborg, Denmark
| | - Mónica J B Amorim
- Department of Biology & CESAM, University of Aveiro, 3810-193 Aveiro, Portugal.
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7
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Almstrup K, Frederiksen H, Andersson AM, Juul A. Levels of endocrine-disrupting chemicals are associated with changes in the peri-pubertal epigenome. Endocr Connect 2020; 9:845-857. [PMID: 32755991 PMCID: PMC7487188 DOI: 10.1530/ec-20-0286] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 08/04/2020] [Indexed: 12/23/2022]
Abstract
Puberty marks a transition period, which leads to the attainment of adult sexual maturity. Timing of puberty is a strongly heritable trait. However, large genetic association studies can only explain a fraction of the observed variability and striking secular trends suggest that lifestyle and/or environmental factors are important. Using liquid-chromatography tandem-mass-spectrometry, we measured endocrine-disrupting chemicals (EDCs; triclosan, bisphenol A, benzophenone-3, 2,4-dichlorophenol, 11 metabolites from 5 phthalates) in longitudinal urine samples obtained biannually from peri-pubertal children included in the COPENHAGEN puberty cohort. EDC levels were associated with blood DNA methylation profiles from 31 boys and 20 girls measured both pre- and post-pubertally. We found little evidence of single methylation sites that on their own showed association with urinary excretion levels of EDCs obtained either the same-day or measured as the yearly mean of dichotomized EDC levels. In contrast, methylation of several promoter regions was found to be associated with two or more EDCs, overlap with known gene-chemical interactions, and form a core network with genes known to be important for puberty. Furthermore, children with the highest yearly mean of dichotomized urinary phthalate metabolite levels were associated with higher promoter methylation of the thyroid hormone receptor interactor 6 gene (TRIP6), which again was mirrored by lower circulating TRIP6 protein levels. In general, the mean TRIP6 promoter methylation was mirrored by circulating TRIP6 protein levels. Our results provide a potential molecular mode of action of how exposure to environmental chemicals may modify pubertal development.
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Affiliation(s)
- Kristian Almstrup
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- Correspondence should be addressed to K Almstrup:
| | - Hanne Frederiksen
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anna-Maria Andersson
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
- International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
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8
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Hwang SH, Yeom H, Han BI, Ham BJ, Lee YM, Han MR, Lee M. Predicting Carcinogenic Mechanisms of Non-Genotoxic Carcinogens via Combined Analysis of Global DNA Methylation and In Vitro Cell Transformation. Int J Mol Sci 2020; 21:ijms21155387. [PMID: 32751172 PMCID: PMC7432388 DOI: 10.3390/ijms21155387] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/17/2020] [Accepted: 07/27/2020] [Indexed: 12/13/2022] Open
Abstract
An in vitro cell transformation assay (CTA) is useful for the detection of non-genotoxic carcinogens (NGTXCs); however, it does not provide information on their modes of action. In this study, to pursue a mechanism-based approach in the risk assessment of NGTXCs, we aimed to develop an integrated strategy comprising an in vitro Bhas 42 CTA and global DNA methylation analysis. For this purpose, 10 NGTXCs, which were also predicted to be negative through Derek/Sarah structure-activity relationship analysis, were first tested for transforming activity in Bhas 42 cells. Methylation profiles using reduced representation bisulfite sequencing were generated for seven NGTXCs that were positive in CTAs. In general, the differentially methylated regions (DMRs) within promoter regions showed slightly more bias toward hypermethylation than the DMRs across the whole genome. We also identified 13 genes associated with overlapping DMRs within the promoter regions in four NGTXCs, of which seven were hypermethylated and six were hypomethylated. Using ingenuity pathway analysis, the genes with DMRs at the CpG sites were found to be enriched in cancer-related categories, including "cell-to-cell signaling and interaction" as well as "cell death and survival". Moreover, the networks related to "cell death and survival", which were considered to be associated with carcinogenesis, were identified in six NGTXCs. These results suggest that epigenetic changes supporting cell transformation processes occur during non-genotoxic carcinogenesis. Taken together, our combined system can become an attractive component for an integrated approach for the testing and assessment of NGTXCs.
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Affiliation(s)
- Sung-Hee Hwang
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
| | - Hojin Yeom
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
| | - Byeal-I Han
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
| | - Byung-Joo Ham
- Department of Psychiatry, Korea University Anam Hospital, Korea University College of Medicine, Seoul 02841, Korea;
| | - Yong-Moon Lee
- College of Pharmacy and Medical Research Center, Chungbuk National University, Cheoungju-si, Chungcheongbuk-do 28160, Korea;
| | - Mi-Ryung Han
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
- INU Human Genome Center, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (M.L.); Tel.: +82-32-835-8247 (M.L.)
| | - Michael Lee
- Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea; (S.-H.H.); (H.Y.)
- Institute for New Drug Development, Incheon National University, Incheon 22012, Korea;
- INU Human Genome Center, Incheon National University, Incheon 22012, Korea
- Correspondence: (M.-R.H.); (M.L.); Tel.: +82-32-835-8247 (M.L.)
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9
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Lee E, Kang MJ, Kim JH, Lee SH, Lee SY, Cho HJ, Yoon J, Jung S, Park Y, Oh DK, Hong SB, Hong SJ. NOTCH1 Pathway is Involved in Polyhexamethylene Guanidine-Induced Humidifier Disinfectant Lung Injuries. Yonsei Med J 2020; 61:186-191. [PMID: 31997628 PMCID: PMC6992453 DOI: 10.3349/ymj.2020.61.2.186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/29/2019] [Accepted: 12/26/2019] [Indexed: 12/17/2022] Open
Abstract
An outbreak of fatal humidifier disinfectant lung injuries (HDLI) occurred in Korea. Human studies on mechanisms underlying HDLI have yet to be conducted. This study aimed to investigate methylation changes and their potential role in HDLI after exposure to HDs containing polyhexamethylene guanidine-phosphate. DNA methylation analysis was performed in blood samples from 10 children with HDLI and 10 healthy children using Infinium Human MethylationEPIC BeadChip. Transcriptome analysis was performed using lung tissues from 5 children with HDLI and 5 controls. Compared to healthy controls, 92 hypo-methylated and 79 hyper-methylated CpG sites were identified in children with HDLI at the statistical significance level of |Δβ|>0.2 and p<0.05. NOTCH1 was identified as a candidate network hub gene in cases. NOTCH1 transcripts significantly increased in lung tissues from HDLI cases compared to unexposed controls (p=0.05). NOTCH1 may play an important role in pulmonary fibrosis of HDLI.
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Affiliation(s)
- Eun Lee
- Department of Pediatrics, Chonnam National University Hospital, Chonnam National University Medical School, Gwangju, Korea
| | - Mi Jin Kang
- Asan Medical Center, Asan Institute for Life Sciences, Environmental Health Center, Seoul, Korea
| | - Jeong Hyun Kim
- Department of Medicine, University of Ulsan Collage of Medicine, Seoul, Korea
| | - Seung Hwa Lee
- Asan Medical Center, Asan Institute for Life Sciences, Environmental Health Center, Seoul, Korea
| | - So Yeon Lee
- Department of Pediatrics, Childhood Asthma Atopy Center, Environmental Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyun Ju Cho
- Department of Pediatrics, International St. Mary's hospital, Catholic Kwandong University College of Medicine, Incheon, Korea
| | - Jisun Yoon
- Department of Pediatrics, Mediplex Hospital, Incheon, Korea
| | - Sungsu Jung
- Department of Pediatrics, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Yangsoon Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dong Kyu Oh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, Seoul, Korea
| | - Sang Bum Hong
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Soo Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Environmental Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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10
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Wikenius E, Moe V, Smith L, Heiervang ER, Berglund A. DNA methylation changes in infants between 6 and 52 weeks. Sci Rep 2019; 9:17587. [PMID: 31772264 PMCID: PMC6879561 DOI: 10.1038/s41598-019-54355-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Infants undergo extensive developments during their first year of life. Although the biological mechanisms involved are not yet fully understood, changes in the DNA methylation in mammals are believed to play a key role. This study was designed to investigate changes in infant DNA methylation that occurs between 6 and 52 weeks. A total of 214 infant saliva samples from 6 or 52 weeks were assessed using principal component analyses and t-distributed stochastic neighbor-embedding algorithms. Between the two time points, there were clear differences in DNA methylation. To further investigate these findings, paired two-sided student’s t-tests were performed. Differently methylated regions were defined as at least two consecutive probes that showed significant differences, with a q-value < 0.01 and a mean difference > 0.2. After correcting for false discovery rates, changes in the DNA methylation levels were found in 42 genes. Of these, 36 genes showed increased and six decreased DNA methylation. The overall DNA methylation changes indicated decreased gene expression. This was surprising because infants undergo such profound developments during their first year of life. The results were evaluated by taking into consideration the extensive development that occurs during pregnancy. During the first year of life, infants have an overall three-fold increase in weight, while the fetus develops from a single cell into a viable infant in 9 months, with an 875-million-fold increase in weight. It is possible that the findings represent a biological slowing mechanism in response to extensive fetal development. In conclusion, our study provides evidence of DNA methylation changes during the first year of life, representing a possible biological slowing mechanism. We encourage future studies of DNA methylation changes in infants to replicate the findings by using a repeated measures model and less stringent criteria to see if the same genes can be found, as well as investigating whether other genes are involved in development during this period.
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Affiliation(s)
- Ellen Wikenius
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA. .,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Vibeke Moe
- Department of Psychology, Faculty of Social Sciences, University of Oslo, Oslo, Norway.,The Center for Child and Adolescent Mental Health, Eastern and Southern Norway (RBUP), Oslo, Norway
| | - Lars Smith
- Department of Psychology, Faculty of Social Sciences, University of Oslo, Oslo, Norway
| | - Einar R Heiervang
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.,Oslo University Hospital, Oslo, Norway
| | - Anders Berglund
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
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11
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Odintsova VV, Hagenbeek FA, Suderman M, Caramaschi D, van Beijsterveldt CEM, Kallsen NA, Ehli EA, Davies GE, Sukhikh GT, Fanos V, Relton C, Bartels M, Boomsma DI, van Dongen J. DNA Methylation Signatures of Breastfeeding in Buccal Cells Collected in Mid-Childhood. Nutrients 2019; 11:E2804. [PMID: 31744183 PMCID: PMC6893543 DOI: 10.3390/nu11112804] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/12/2019] [Accepted: 11/12/2019] [Indexed: 12/11/2022] Open
Abstract
Breastfeeding has long-term benefits for children that may be mediated via the epigenome. This pathway has been hypothesized, but the number of empirical studies in humans is small and mostly done by using peripheral blood as the DNA source. We performed an epigenome-wide association study (EWAS) in buccal cells collected around age nine (mean = 9.5) from 1006 twins recruited by the Netherlands Twin Register (NTR). An age-stratified analysis examined if effects attenuate with age (median split at 10 years; n<10 = 517, mean age = 7.9; n>10 = 489, mean age = 11.2). We performed replication analyses in two independent cohorts from the NTR (buccal cells) and the Avon Longitudinal Study of Parents and Children (ALSPAC) (peripheral blood), and we tested loci previously associated with breastfeeding in epigenetic studies. Genome-wide DNA methylation was assessed with the Illumina Infinium MethylationEPIC BeadChip (Illumina, San Diego, CA, USA) in the NTR and with the HumanMethylation450 Bead Chip in the ALSPAC. The duration of breastfeeding was dichotomized ('never' vs. 'ever'). In the total sample, no robustly associated epigenome-wide significant CpGs were identified (α = 6.34 × 10-8). In the sub-group of children younger than 10 years, four significant CpGs were associated with breastfeeding after adjusting for child and maternal characteristics. In children older than 10 years, methylation differences at these CpGs were smaller and non-significant. The findings did not replicate in the NTR sample (n = 98; mean age = 7.5 years), and no nearby sites were associated with breastfeeding in the ALSPAC study (n = 938; mean age = 7.4). Of the CpG sites previously reported in the literature, three were associated with breastfeeding in children younger than 10 years, thus showing that these CpGs are associated with breastfeeding in buccal and blood cells. Our study is the first to show that breastfeeding is associated with epigenetic variation in buccal cells in children. Further studies are needed to investigate if methylation differences at these loci are caused by breastfeeding or by other unmeasured confounders, as well as what mechanism drives changes in associations with age.
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Affiliation(s)
- Veronika V. Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 101000, Russia
| | - Fiona A. Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol BS8 1TH, UK
| | - Doretta Caramaschi
- MRC Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol BS8 1TH, UK
| | | | - Noah A. Kallsen
- Avera Institute for Human Genetics, Sioux Falls, SD 57101, USA
| | - Erik A. Ehli
- Avera Institute for Human Genetics, Sioux Falls, SD 57101, USA
| | | | - Gennady T. Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow 101000, Russia
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU and University of Cagliari, 09121 Cagliari, Italy
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, Bristol Medical School, Population Health Science, University of Bristol, Bristol BS8 1TH, UK
| | - Meike Bartels
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081 BT Amsterdam, The Netherlands (D.I.B.)
- Amsterdam Public Health Research Institute, 1081 BT Amsterdam, The Netherlands
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12
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Zhang P, Li T, Liu YQ, Zhang H, Xue SM, Li G, Cheng HYM, Cao JM. Contribution of DNA methylation in chronic stress-induced cardiac remodeling and arrhythmias in mice. FASEB J 2019; 33:12240-12252. [PMID: 31431066 DOI: 10.1096/fj.201900100r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
It is recognized that stress can induce cardiac dysfunction, but the underlying mechanisms are not well understood. The present study aimed to test the hypothesis that chronic negative stress leads to alterations in DNA methylation of certain cardiac genes, which in turn contribute to pathologic remodeling of the heart. We found that mice that were exposed to chronic restraint stress (CRS) for 4 wk exhibited cardiac remodeling toward heart failure, as characterized by ventricular chamber dilatation, wall thinning, and decreased contractility. CRS also induced cardiac arrhythmias, including intermittent sinus tachycardia and bradycardia, frequent premature ventricular contraction, and sporadic atrioventricular conduction block. Circulating levels of stress hormones were elevated, and the cardiac expression of tyrosine hydroxylase, a marker of sympathetic innervation, was increased in CRS mice. Using reduced representation bisulfite sequencing, we found that although CRS did not lead to global changes in DNA methylation in the murine heart, it nevertheless altered methylation at specific genes that are associated with the dilated cardiomyopathy (DCM) (e.g., desmin) and adrenergic signaling of cardiomyocytes (ASPC) (e.g., adrenergic receptor-α1) pathways. We conclude that CRS induces cardiac remodeling and arrhythmias, potentially through altered methylation of myocardial genes associated with the DCM and ASPC pathways.-Zhang, P., Li, T., Liu, Y.-Q., Zhang, H., Xue, S.-M., Li, G., Cheng, H.-Y.M., Cao, J.-M. Contribution of DNA methylation in chronic stress-induced cardiac remodeling and arrhythmias in mice.
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Affiliation(s)
- Peng Zhang
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Tao Li
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Ya-Qin Liu
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Hao Zhang
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Si-Meng Xue
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Guang Li
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Hai-Ying Mary Cheng
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Ji-Min Cao
- Institute of Cardiovascular Research, Key Laboratory of Medical Electrophysiology, Ministry of Education-Medical Electrophysiological Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China.,Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Southwest Medical University, Luzhou, China.,Key Laboratory of Cellular Physiology, Ministry of Education, Department of Physiology, Shanxi Medical University, Taiyuan, China
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13
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Sherwood WB, Bion V, Lockett GA, Ziyab AH, Soto-Ramírez N, Mukherjee N, Kurukulaaratchy RJ, Ewart S, Zhang H, Arshad SH, Karmaus W, Holloway JW, Rezwan FI. Duration of breastfeeding is associated with leptin (LEP) DNA methylation profiles and BMI in 10-year-old children. Clin Epigenetics 2019; 11:128. [PMID: 31464656 PMCID: PMC6716837 DOI: 10.1186/s13148-019-0727-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 08/16/2019] [Indexed: 02/07/2023] Open
Abstract
Background Breastfeeding is protective against many long-term diseases, yet the mechanisms involved are unknown. Leptin gene (LEP) is reported to be associated with body mass index (BMI). On the other hand, breastfeeding duration has been found to be associated with DNA methylation (DNAm) of the LEP gene. Therefore, epigenetic regulation of LEP may represent the mechanism underlying the protective effect of breastfeeding duration against obesity. Methods In the Isle of Wight Birth Cohort, peripheral blood DNAm at 23 cytosine-phosphate-guanine sites (CpGs) in the LEP locus in 10-year-old (n = 297) samples and 16 CpGs in 18-year-old (n = 305) samples, were generated using the Illumina Infinium MethylationEPIC and HumanMethylation450 Beadchips respectively and tested for association with breastfeeding duration (total and exclusive) using linear regression. To explore the association between breastfeeding durations and genome-wide DNAm, epigenome-wide association studies (EWASs) and differential methylation region (DMR) analyses were performed. BMI trajectories spanning the first 18 years of life were used as the outcome to test the association with breastfeeding duration (exposure) using multi-nominal logistic regression. Mediation analysis was performed for significant CpG sites. Results Both total and exclusive breastfeeding duration were associated with DNAm at four LEP CpG sites at 10 years (P value < 0.05), and not at 18 years. Though no association was observed between breastfeeding duration and genome-wide DNAm, DMR analyses identified five significant differentially methylated regions (Sidak adjusted P value < 0.05). Breastfeeding duration was also associated with the early transient overweight trajectory. Furthermore, DNAm of LEP was associated with this trajectory at one CpG site and early persistent obesity at another, though mediation analysis was not significant. Conclusions Breastfeeding duration is associated with LEP methylation at age 10 years and BMI trajectory. LEP DNAm is also significantly associated with BMI trajectories throughout childhood, though sample sizes were small. However, mediation analysis did not demonstrate that DNAm of LEP explained the protective effect of breastfeeding against childhood obesity. Electronic supplementary material The online version of this article (10.1186/s13148-019-0727-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- William B Sherwood
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK
| | - Victoria Bion
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK
| | - Gabrielle A Lockett
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK
| | - Ali H Ziyab
- Department of Community Medicine and Behavioral Sciences, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | - Nandini Mukherjee
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN, 38152, USA
| | - Ramesh J Kurukulaaratchy
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN, 38152, USA
| | - S Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,The David Hide Asthma and Allergy Research Centre, Isle of Wight, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, 236A Robison Hall, Memphis, TN, 38152, USA
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK.,Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University Hospital Southampton, University of Southampton, Duthie Building, MP808, Tremona Road, Southampton, Hampshire, SO16 6YD, UK.
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14
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Whyte JM, Ellis JJ, Brown MA, Kenna TJ. Best practices in DNA methylation: lessons from inflammatory bowel disease, psoriasis and ankylosing spondylitis. Arthritis Res Ther 2019; 21:133. [PMID: 31159831 PMCID: PMC6547594 DOI: 10.1186/s13075-019-1922-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Advances in genomic technology have enabled a greater understanding of the genetics of common immune-mediated diseases such as ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. The substantial overlap in genetically identified pathogenic pathways has been demonstrated between these diseases. However, to date, gene discovery approaches have only mapped a minority of the heritability of these common diseases, and most disease-associated variants have been found to be non-coding, suggesting mechanisms of disease-association through transcriptional regulatory effects. Epigenetics is a major interface between genetic and environmental modifiers of disease and strongly influence transcription. DNA methylation is a well-characterised epigenetic mechanism, and a highly stable epigenetic marker, that is implicated in disease pathogenesis. DNA methylation is an under-investigated area in immune-mediated diseases, and many studies in the field are affected by experimental design limitations, related to study design, technical limitations of the methylation typing methods employed, and statistical issues. This has resulted in both sparsity of investigations into disease-related changes in DNA methylation, a paucity of robust findings, and difficulties comparing studies in the same disease. In this review, we cover the basics of DNA methylation establishment and control, and the methods used to examine it. We examine the current state of DNA methylation studies in AS, IBD and psoriasis; the limitations of previous studies; and the best practices for DNA methylation studies. The purpose of this review is to assist with proper experimental design and consistency of approach in future studies to enable a better understanding of the functional role of DNA methylation in immune-mediated disease.
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Affiliation(s)
- Jessica M Whyte
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Jonathan J Ellis
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia. .,Translational Research Institute, Princess Alexandra Hospital, 37 Kent Street, Woolloongabba, Queensland, 4102, Australia.
| | - Tony J Kenna
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Woolloongabba, Queensland, Australia
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15
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Wan M, Bennett BD, Pittman GS, Campbell MR, Reynolds LM, Porter DK, Crowl CL, Wang X, Su D, Englert NA, Thompson IJ, Liu Y, Bell DA. Identification of Smoking-Associated Differentially Methylated Regions Using Reduced Representation Bisulfite Sequencing and Cell type-Specific Enhancer Activation and Gene Expression. ENVIRONMENTAL HEALTH PERSPECTIVES 2018; 126:047015. [PMID: 29706059 PMCID: PMC6071796 DOI: 10.1289/ehp2395] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 03/22/2018] [Accepted: 03/22/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Cigarette smoke is a causal factor in cancers and cardiovascular disease. Smoking-associated differentially methylated regions (SM-DMRs) have been observed in disease studies, but the causal link between altered DNA methylation and transcriptional change is obscure. OBJECTIVE Our objectives were to finely resolve SM-DMRs and to interrogate the mechanistic link between SM-DMRs and altered transcription of enhancer noncoding RNA (eRNA) and mRNA in human circulating monocytes. METHOD We integrated SM-DMRs identified by reduced representation bisulfite sequencing (RRBS) of circulating CD14+ monocyte DNA collected from two independent human studies [n=38 from Clinical Research Unit (CRU) and n=55 from the Multi-Ethnic Study of Atherosclerosis (MESA), about half of whom were active smokers] with gene expression for protein-coding genes and noncoding RNAs measured by RT-PCR or RNA sequencing. Candidate SM-DMRs were compared with RRBS of purified CD4+ T cells, CD8+ T cells, CD15+ granulocytes, CD19+ B cells, and CD56+ NK cells (n=19 females, CRU). DMRs were validated using pyrosequencing or bisulfite amplicon sequencing in up to 85 CRU volunteers, who also provided saliva DNA. RESULTS RRBS identified monocyte SM-DMRs frequently located in putative gene regulatory regions. The most significant monocyte DMR occurred at a poised enhancer in the aryl-hydrocarbon receptor repressor gene (AHRR) and it was also detected in both granulocytes and saliva DNA. To our knowledge, we identify for the first time that SM-DMRs in or near AHRR, C5orf55-EXOC-AS, and SASH1 were associated with increased noncoding eRNA as well as mRNA in monocytes. Functionally, the AHRR SM-DMR appeared to up-regulate AHRR mRNA through activating the AHRR enhancer, as suggested by increased eRNA in the monocytes, but not granulocytes, from smokers compared with nonsmokers. CONCLUSIONS Our findings suggest that AHRR SM-DMR up-regulates AHRR mRNA in a monocyte-specific manner by activating the AHRR enhancer. Cell type-specific activation of enhancers at SM-DMRs may represent a mechanism driving smoking-related disease. https://doi.org/10.1289/EHP2395.
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Affiliation(s)
- Ma Wan
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Brian D Bennett
- Integrative Bioinformatics Support Group, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - Gary S Pittman
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Michelle R Campbell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Lindsay M Reynolds
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Devin K Porter
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Christopher L Crowl
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Xuting Wang
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Dan Su
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Neal A Englert
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Isabel J Thompson
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Douglas A Bell
- Environmental Epigenomics and Disease Group, Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
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16
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Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer's Disease. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2018; 2018:6918797. [PMID: 29849909 PMCID: PMC5904768 DOI: 10.1155/2018/6918797] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/14/2018] [Accepted: 02/04/2018] [Indexed: 12/11/2022]
Abstract
Epigenetic mechanisms play an important role in the development and progression of various neurodegenerative diseases. Abnormal methylation of numerous genes responsible for regulation of transcription, DNA replication, and apoptosis has been linked to Alzheimer's disease (AD) pathology. We have recently performed whole transcriptome profiling of familial early-onset Alzheimer's disease (fEOAD) patient-derived fibroblasts. On this basis, we demonstrated a strong dysregulation of cell cycle checkpoints and DNA damage response (DDR) in both fibroblasts and reprogrammed neurons. Here, we show that the aging-correlated hypermethylation of KLF14 and TRIM59 genes associates with abnormalities in DNA repair and cell cycle control in fEOAD. Based on the resulting transcriptome networks, we found that the hypermethylation of KLF14 might be associated with epigenetic regulation of the chromatin organization and mRNA processing followed by hypermethylation of TRIM59 likely associated with the G2/M cell cycle phase and p53 role in DNA repair with BRCA1 protein as the key player. We propose that the hypermethylation of KLF14 could constitute a superior epigenetic mechanism for TRIM59 hypermethylation. The methylation status of both genes affects genome stability and might contribute to proapoptotic signaling in AD. Since this study combines data obtained from various tissues from AD patients, it reinforces the view that the genetic methylation status in the blood may be a valuable predictor of molecular processes occurring in affected tissues. Further research is necessary to define a detailed role of TRIM59 and KLF4 in neurodegeneration of neurons.
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17
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DNA methylation in ELOVL2 and C1orf132 correctly predicted chronological age of individuals from three disease groups. Int J Legal Med 2017; 132:1-11. [PMID: 28725932 PMCID: PMC5748441 DOI: 10.1007/s00414-017-1636-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Improving accuracy of the available predictive DNA methods is important for their wider use in routine forensic work. Information on age in the process of identification of an unknown individual may provide important hints that can speed up the process of investigation. DNA methylation markers have been demonstrated to provide accurate age estimation in forensics, but there is growing evidence that DNA methylation can be modified by various factors including diseases. We analyzed DNA methylation profile in five markers from five different genes (ELOVL2, C1orf132, KLF14, FHL2, and TRIM59) used for forensic age prediction in three groups of individuals with diagnosed medical conditions. The obtained results showed that the selected age-related CpG sites have unchanged age prediction capacity in the group of late onset Alzheimer’s disease patients. Aberrant hypermethylation and decreased prediction accuracy were found for TRIM59 and KLF14 markers in the group of early onset Alzheimer’s disease suggesting accelerated aging of patients. In the Graves’ disease patients, altered DNA methylation profile and modified age prediction accuracy were noted for TRIM59 and FHL2 with aberrant hypermethylation observed for the former and aberrant hypomethylation for the latter. Our work emphasizes high utility of the ELOVL2 and C1orf132 markers for prediction of chronological age in forensics by showing unchanged prediction accuracy in individuals affected by three diseases. The study also demonstrates that artificial neural networks could be a convenient alternative for the forensic predictive DNA analyses.
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