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Abstract
Arsenic is a major public health concern worldwide. While it is an established carcinogen and associated with a number of other adverse health outcomes, the molecular mechanisms underlying arsenic toxicity are not completely clarified. There is mounting evidence from human studies suggesting that arsenic exposure is associated with epigenetic alterations, including DNA methylation. In this review, we summarize several recent human studies that have evaluated arsenic exposure using the Illumina HumanMethylation 450K BeadChip, which interrogates more than 485,000 methylation sites across the genome. Many of these studies have observed novel regions of the genome associated with arsenic exposure. However, few studies have evaluated the biological and functional relevance of these DNA methylation changes, which are still needed. We emphasize the need for future studies to replicate the identified DNA methylation signals as well as assess whether these markers are associated with risk of arsenic-related diseases.
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Affiliation(s)
- Maria Argos
- Division of Epidemiology and Biostatistics, School of Public Health, University of Illinois at Chicago, 1603 West Taylor Street, MC923, Chicago, IL, 60612, USA,
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Slieker RC, Bos SD, Goeman JJ, Bovée JVMG, Talens RP, van der Breggen R, Suchiman HED, Lameijer EW, Putter H, van den Akker EB, Zhang Y, Jukema JW, Slagboom PE, Meulenbelt I, Heijmans BT. Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin 2013; 6:26. [PMID: 23919675 PMCID: PMC3750594 DOI: 10.1186/1756-8935-6-26] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/28/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation has been recognized as a key mechanism in cell differentiation. Various studies have compared tissues to characterize epigenetically regulated genomic regions, but due to differences in study design and focus there still is no consensus as to the annotation of genomic regions predominantly involved in tissue-specific methylation. We used a new algorithm to identify and annotate tissue-specific differentially methylated regions (tDMRs) from Illumina 450k chip data for four peripheral tissues (blood, saliva, buccal swabs and hair follicles) and six internal tissues (liver, muscle, pancreas, subcutaneous fat, omentum and spleen with matched blood samples). RESULTS The majority of tDMRs, in both relative and absolute terms, occurred in CpG-poor regions. Further analysis revealed that these regions were associated with alternative transcription events (alternative first exons, mutually exclusive exons and cassette exons). Only a minority of tDMRs mapped to gene-body CpG islands (13%) or CpG islands shores (25%) suggesting a less prominent role for these regions than indicated previously. Implementation of ENCODE annotations showed enrichment of tDMRs in DNase hypersensitive sites and transcription factor binding sites. Despite the predominance of tissue differences, inter-individual differences in DNA methylation in internal tissues were correlated with those for blood for a subset of CpG sites in a locus- and tissue-specific manner. CONCLUSIONS We conclude that tDMRs preferentially occur in CpG-poor regions and are associated with alternative transcription. Furthermore, our data suggest the utility of creating an atlas cataloguing variably methylated regions in internal tissues that correlate to DNA methylation measured in easy accessible peripheral tissues.
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Affiliation(s)
- Roderick C Slieker
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Steffan D Bos
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
| | - Jelle J Goeman
- Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Judith VMG Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rudolf P Talens
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ruud van der Breggen
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - H Eka D Suchiman
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric-Wubbo Lameijer
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hein Putter
- Medical Statistics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik B van den Akker
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- The Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | - Yanju Zhang
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - P Eline Slagboom
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
| | - Ingrid Meulenbelt
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Netherlands Consortium for Healthy Aging, PO Box 9600, Leiden 2300, RC, The Netherlands
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Koestler DC, Avissar-Whiting M, Houseman EA, Karagas MR, Marsit CJ. Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in utero. Environ Health Perspect 2013; 121:971-7. [PMID: 23757598 PMCID: PMC3733676 DOI: 10.1289/ehp.1205925] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 06/07/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND There is increasing epidemiologic evidence that arsenic exposure in utero, even at low levels found throughout much of the world, is associated with adverse reproductive outcomes and may contribute to long-term health effects. Animal models, in vitro studies, and human cancer data suggest that arsenic may induce epigenetic alterations, specifically by altering patterns of DNA methylation. OBJECTIVES In this study we aimed to identify differences in DNA methylation in cord blood samples of infants with in utero, low-level arsenic exposure. METHODS DNA methylation of cord-blood derived DNA from 134 infants involved in a prospective birth cohort in New Hampshire was profiled using the Illumina Infinium Methylation450K array. In utero arsenic exposure was estimated using maternal urine samples collected at 24-28 weeks gestation. We used a novel cell mixture deconvolution methodology for examining the association between inferred white blood cell mixtures in infant cord blood and in utero arsenic exposure; we also examined the association between methylation at individual CpG loci and arsenic exposure levels. RESULTS We found an association between urinary inorganic arsenic concentration and the estimated proportion of CD8+ T lymphocytes (1.18; 95% CI: 0.12, 2.23). Among the top 100 CpG loci with the lowest p-values based on their association with urinary arsenic levels, there was a statistically significant enrichment of these loci in CpG islands (p = 0.009). Of those in CpG islands (n = 44), most (75%) exhibited higher methylation levels in the highest exposed group compared with the lowest exposed group. Also, several CpG loci exhibited a linear dose-dependent relationship between methylation and arsenic exposure. CONCLUSIONS Our findings suggest that in utero exposure to low levels of arsenic may affect the epigenome. Long-term follow-up is planned to determine whether the observed changes are associated with health outcomes.
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Affiliation(s)
- Devin C Koestler
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA
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