251
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Meirelles FV, Bressan FF, Smith LC, Perecin F, Chiaratti MR, Ferraz JBS. Cytoplasmatic inheritance, epigenetics and reprogramming DNA as tools in animal breeding. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.05.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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252
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Paul DS, Beck S. Advances in epigenome-wide association studies for common diseases. Trends Mol Med 2014; 20:541-3. [PMID: 25092140 PMCID: PMC4186777 DOI: 10.1016/j.molmed.2014.07.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 07/14/2014] [Indexed: 12/21/2022]
Abstract
Epigenome-wide association studies (EWASs) provide a systematic approach to uncovering epigenetic variants underlying common diseases. Discoveries have shed light on novel molecular mechanisms of disease and enabled the application of epigenetic variants as biomarkers. Here, we highlight the recent advances in this emerging line of research and discuss key challenges for current and future studies.
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Affiliation(s)
- Dirk S Paul
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, WC1E 6BT, UK.
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253
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Voisin S, Almén MS, Moschonis G, Chrousos GP, Manios Y, Schiöth HB. Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents. Eur J Hum Genet 2014; 23:654-62. [PMID: 25074463 PMCID: PMC4402618 DOI: 10.1038/ejhg.2014.139] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 06/16/2014] [Accepted: 06/20/2014] [Indexed: 12/04/2022] Open
Abstract
The type and the amount of dietary fat have a significant influence on the metabolic pathways involved in the development of obesity, metabolic syndrome, diabetes type 2 and cardiovascular diseases. However, it is unknown to what extent this modulation is achieved through DNA methylation. We assessed the effects of cholesterol intake, the proportion of energy intake derived from fat, the ratio of polyunsaturated fatty acids (PUFA) to saturated fatty acids (SFA), the ratio of monounsaturated fatty acids (MUFA) to SFA, and the ratio of MUFA+PUFA to SFA on genome-wide DNA methylation patterns in normal-weight and obese children. We determined the genome-wide methylation profile in the blood of 69 Greek preadolescents (∼10 years old) as well as their dietary intake for two consecutive weekdays and one weekend day. The methylation levels of one CpG island shore and four sites were significantly correlated with total fat intake. The methylation levels of 2 islands, 11 island shores and 16 sites were significantly correlated with PUFA/SFA; of 9 islands, 26 island shores and 158 sites with MUFA/SFA; and of 10 islands, 40 island shores and 130 sites with (MUFA+PUFA)/SFA. We found significant gene enrichment in 34 pathways for PUFA/SFA, including the leptin pathway, and a significant enrichment in 5 pathways for (MUFA+PUFA)/SFA. Our results suggest that specific changes in DNA methylation may have an important role in the mechanisms involved in the physiological responses to different types of dietary fat.
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Affiliation(s)
- Sarah Voisin
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - Markus S Almén
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
| | - George Moschonis
- Department of Nutrition and Dietetics, Harokopio University, Athens, Greece
| | - George P Chrousos
- First Department of Pediatrics, Athens University Medical School, Aghia Sophia Children's Hospital, Athens, Greece
| | - Yannis Manios
- Department of Nutrition and Dietetics, Harokopio University, Athens, Greece
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, Uppsala, Sweden
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254
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Li X, Baker-Andresen D, Zhao Q, Marshall V, Bredy TW. Methyl CpG Binding Domain Ultra-Sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation. GENES BRAIN AND BEHAVIOR 2014; 13:721-31. [DOI: 10.1111/gbb.12150] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 05/06/2014] [Accepted: 06/11/2014] [Indexed: 12/16/2022]
Affiliation(s)
- X. Li
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
| | - D. Baker-Andresen
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
| | - Q. Zhao
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
| | - V. Marshall
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
- Murdoch Children's Research Institute (MCRI); Royal Children's Hospital; Melbourne Australia
| | - T. W. Bredy
- Psychiatric Epigenomics Laboratory, Queensland Brain Institute; The University of Queensland; Brisbane
- Center for Neurobiology of Learning & Memory; University of California Irvine; Irvine CA USA
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255
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Janssen BG, Byun HM, Cox B, Gyselaers W, Izzi B, Baccarelli AA, Nawrot TS. Variation of DNA methylation in candidate age-related targets on the mitochondrial-telomere axis in cord blood and placenta. Placenta 2014; 35:665-72. [PMID: 25047690 DOI: 10.1016/j.placenta.2014.06.371] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 06/20/2014] [Accepted: 06/24/2014] [Indexed: 01/19/2023]
Abstract
BACKGROUND Epigenetics is tissue-specific and potentially even cell-specific, but little information is available from human reproductive studies about the concordance of DNA methylation patterns in cord blood and placenta, as well as within-placenta variations. We evaluated methylation levels at promoter regions of candidate genes in biological ageing pathways (SIRT1, TP53, PPARG, PPARGC1A, and TFAM), a subtelomeric region (D4Z4) and the mitochondrial genome (MT-RNR1, D-loop). METHODS Ninety individuals were randomly chosen from the ENVIRONAGE birth cohort to evaluate methylation concordance between cord blood and placenta using highly quantitative bisulfite-PCR pyrosequencing. In a subset of nineteen individuals, a more extensive sampling scheme was performed to examine within-placenta variation. RESULTS The DNA methylation levels of the subtelomeric region and mitochondrial genome showed concordance between cord blood and placenta with correlation coefficients ranging from r = 0.31 to 0.43, p ≤ 0.005, and also between the maternal and foetal sides of placental tissue (r = 0.53 to 0.72, p ≤ 0.05). For the majority of targets, an agreement in methylation levels between four foetal biopsies was found (with intra-class correlation coefficients ranging from 0.16 to 0.72), indicating small within-placenta variation. CONCLUSIONS The methylation levels of the subtelomeric region (D4Z4) and mitochondrial genome (MT-RNR1, D-loop) showed concordance between cord blood and placenta, suggesting a common epigenetic signature of these targets between tissues. Concordance was lacking between the other genes that were studied. In placental tissue, methylation patterns of most targets on the mitochondrial-telomere axis were not strongly influenced by sample location.
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Affiliation(s)
- B G Janssen
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - H M Byun
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, USA
| | - B Cox
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - W Gyselaers
- Department of Obstetrics, East-Limburg Hospital, Genk, Belgium; Department of Physiology, Hasselt University, Diepenbeek, Belgium
| | - B Izzi
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven (KULeuven), Leuven, Belgium
| | - A A Baccarelli
- Laboratory of Environmental Epigenetics, Exposure Epidemiology and Risk Program, Harvard School of Public Health, Boston, MA, USA
| | - T S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium; Department of Public Health & Primary Care, Occupational and Environmental Medicine, Leuven University (KULeuven), Leuven, Belgium.
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256
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Saffery R, Novakovic B. Epigenetics as the mediator of fetal programming of adult onset disease: what is the evidence? Acta Obstet Gynecol Scand 2014; 93:1090-8. [DOI: 10.1111/aogs.12431] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 05/12/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Richard Saffery
- Cancer and Disease Epigenetics; Murdoch Childrens Research Institute; Royal Children's Hospital; Parkville Victoria Australia
- Department of Paediatrics; University of Melbourne; Parkville Victoria Australia
| | - Boris Novakovic
- Cancer and Disease Epigenetics; Murdoch Childrens Research Institute; Royal Children's Hospital; Parkville Victoria Australia
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257
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Liang L, Cookson WOC. Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies. Hum Mol Genet 2014; 23:R83-8. [PMID: 24927738 PMCID: PMC4170720 DOI: 10.1093/hmg/ddu284] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Platform technologies for measurement of CpG methylation at multiple loci across the genome have made ambitious epigenome-wide association studies affordable and practicable. In contrast to genetic studies, which estimate the effects of structural changes in DNA, and transcriptomic studies, which measure genomic outputs, epigenetic studies can access states of regulation of genome function in particular cells and in response to specific stimuli. Although many factors complicate the interpretation of epigenetic variation in human disease, cell-specific methylation patterns and the cellular heterogeneity present in peripheral blood and tissue biopsies are anticipated to cause the most problems. In this review, we suggest that the difficulties may be exaggerated and we explore how cellular heterogeneity may be embraced with appropriate study designs and analytical tools. We further suggest that systematic mapping of the loci influenced by age, sex and genetic polymorphisms will bring important biological insights as well as improved control of epigenome-wide association studies.
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Affiliation(s)
- Liming Liang
- Department of Epidemiology and Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA and
| | - William O C Cookson
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK
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258
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Shojaei Saadi HA, O'Doherty AM, Gagné D, Fournier É, Grant JR, Sirard MA, Robert C. An integrated platform for bovine DNA methylome analysis suitable for small samples. BMC Genomics 2014; 15:451. [PMID: 24912542 PMCID: PMC4092217 DOI: 10.1186/1471-2164-15-451] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/28/2014] [Indexed: 01/16/2023] Open
Abstract
Background Oocytes and early embryos contain minute amounts of DNA, RNA and proteins, making the study of early mammalian development highly challenging. The study of the embryo epigenome, in particular the DNA methylome, has been made accessible thanks to the possibility of amplifying specific sequences according to their initial methylation status. This paper describes a novel platform dedicated to the genome-wide study of bovine DNA methylation, including a complete pipeline for data analysis and visualization. The platform allows processing and integrating of DNA methylome and transcriptome data from the same sample. Procedures were optimized for genome-wide analysis of 10 ng of DNA (10 bovine blastocysts). Bovine sperm and blastocysts were compared as a test of platform capability. Results The hypermethylation of bovine sperm DNA compared to the embryo genome was confirmed. Differentially methylated regions were distributed across various classes of bovine sperm genomic feature including primarily promoter, intronic and exonic regions, non-CpG-island regions (shore, shelf and open-sea) and CpG islands with low-to-intermediate CpG density. The blastocyst genome bore more methylation marks than sperm DNA only in CpG islands with high CpG density. Long-terminal-repeat retrotransposons (LTR), LINE and SINE were more methylated in sperm DNA, as were low-complexity repetitive elements in blastocysts. Conclusions This is the first early embryo compatible genome-wide epigenetics platform for bovine. Such platforms should improve the study of the potential epigenetic risks of assisted reproductive technologies (ART), the establishment sequence of embryonic cell lines and potential deviations in both gene expression and DNA methylation capable of having long-term impact. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-451) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Claude Robert
- Laboratory of Functional Genomics of Early Embryonic Development, Institut des nutraceutiques et des aliments fonctionnels, Faculté des sciences de l'agriculture et de l'alimentation, Pavillon des services, Université Laval, Québec G1V 0A6, Canada.
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259
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Infinium monkeys: Infinium 450K array for the Cynomolgus macaque (Macaca fascicularis). G3-GENES GENOMES GENETICS 2014; 4:1227-34. [PMID: 24815017 PMCID: PMC4455772 DOI: 10.1534/g3.114.010967] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The Infinium Human Methylation450 BeadChip Array (Infinium 450K) is a robust and cost-efficient survey of genome-wide DNA methylation patterns. Macaca fascicularis (Cynomolgus macaque) is an important disease model; however, its genome sequence is only recently published, and few tools exist to interrogate the molecular state of Cynomolgus macaque tissues. Although the Infinium 450K is a hybridization array designed to the human genome, the relative conservation between the macaque and human genomes makes its use in macaques feasible. Here, we used the Infinium 450K array to assay DNA methylation in 11 macaque muscle biopsies. We showed that probe hybridization efficiency was related to the degree of sequence identity between the human probes and the macaque genome sequence. Approximately 61% of the Human Infinium 450K probes could be reliably mapped to the Cynomolgus macaque genome and contain a CpG site of interest. We also compared the Infinium 450K data to reduced representation bisulfite sequencing data generated on the same samples and found a high level of concordance between the two independent methodologies, which can be further improved by filtering for probe sequence identity and mismatch location. We conclude that the Infinium 450K array can be used to measure the DNA methylome of Cynomolgus macaque tissues using the provided filters. We also provide a pipeline for validation of the array in other species using a simple BLAST-based sequence identify filter.
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260
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Martino D, Joo JE, Sexton-Oates A, Dang T, Allen K, Saffery R, Prescott S. Epigenome-wide association study reveals longitudinally stable DNA methylation differences in CD4+ T cells from children with IgE-mediated food allergy. Epigenetics 2014; 9:998-1006. [PMID: 24762976 DOI: 10.4161/epi.28945] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED Food allergy is mediated by a combination of genetic and environmental risk factors, potentially mediated by epigenetic mechanisms. CD4+ T-cells are key drivers of the allergic response, and may therefore harbor epigenetic variation in association with the disease phenotype. Here we retrospectively examined genome-wide DNA methylation profiles (~450,000 CpGs) from CD4+ T-cells on a birth cohort of 12 children with IgE-mediated food allergy diagnosed at 12-months, and 12 non-allergic controls. DNA samples were available at two time points, birth and 12-months. CASE control comparisons of CD4+ methylation profiles identified 179 differentially methylated probes (DMP) at 12-months and 136 DMP at birth (FDR-adjusted P value<0.05, delta β>0.1). Approximately 30% of DMPs were coincident with previously annotated SNPs. A total of 92 [corrected] allergy-associated non-SNP DMPs were present at birth when individuals were initially disease-free, potentially implicating these loci in the causal pathway. Pathway analysis of differentially methylated genes identified several MAP kinase signaling molecules. Mass spectrometry was used to validate 15 CpG sites at 3 candidate genes. Combined analysis of differential methylation with gene expression profiles revealed gene expression differences at some but not all allergy associated differentially methylated genes. Thus, dysregulation of DNA methylation at MAPK signaling-associated genes during early CD4+ T-cell development may contribute to suboptimal T-lymphocyte responses in early childhood associated with the development of food allergy.
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Affiliation(s)
- David Martino
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia; NHMRC Centre for Food and Allergy Research; Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia; Honorary Fellow University of Melbourne; Melbourne, VIC Australia
| | - Jihoon E Joo
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia
| | - Alexandra Sexton-Oates
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia
| | - Thanh Dang
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia
| | - Katrina Allen
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia; NHMRC Centre for Food and Allergy Research; Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia
| | - Richard Saffery
- Murdoch Childrens Research Institute; Royal Children's Hospital; Melbourne, VIC Australia
| | - Susan Prescott
- Childhood Allergy and Immunology Research; School of Paediatrics and Child Health; University of Western Australia; Crawley, WA Australia
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261
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Teh AL, Pan H, Chen L, Ong ML, Dogra S, Wong J, MacIsaac JL, Mah SM, McEwen LM, Saw SM, Godfrey KM, Chong YS, Kwek K, Kwoh CK, Soh SE, Chong MFF, Barton S, Karnani N, Cheong CY, Buschdorf JP, Stünkel W, Kobor MS, Meaney MJ, Gluckman PD, Holbrook JD. The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes. Genome Res 2014; 24:1064-74. [PMID: 24709820 PMCID: PMC4079963 DOI: 10.1101/gr.171439.113] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Integrating the genotype with epigenetic marks holds the promise of better understanding the biology that underlies the complex interactions of inherited and environmental components that define the developmental origins of a range of disorders. The quality of the in utero environment significantly influences health over the lifecourse. Epigenetics, and in particular DNA methylation marks, have been postulated as a mechanism for the enduring effects of the prenatal environment. Accordingly, neonate methylomes contain molecular memory of the individual in utero experience. However, interindividual variation in methylation can also be a consequence of DNA sequence polymorphisms that result in methylation quantitative trait loci (methQTLs) and, potentially, the interaction between fixed genetic variation and environmental influences. We surveyed the genotypes and DNA methylomes of 237 neonates and found 1423 punctuate regions of the methylome that were highly variable across individuals, termed variably methylated regions (VMRs), against a backdrop of homogeneity. MethQTLs were readily detected in neonatal methylomes, and genotype alone best explained ∼25% of the VMRs. We found that the best explanation for 75% of VMRs was the interaction of genotype with different in utero environments, including maternal smoking, maternal depression, maternal BMI, infant birth weight, gestational age, and birth order. Our study sheds new light on the complex relationship between biological inheritance as represented by genotype and individual prenatal experience and suggests the importance of considering both fixed genetic variation and environmental factors in interpreting epigenetic variation.
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Affiliation(s)
- Ai Ling Teh
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Hong Pan
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609; School of Computer Engineering, Nanyang Technological University (NTU), Singapore 639798
| | - Li Chen
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Mei-Lyn Ong
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Shaillay Dogra
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Johnny Wong
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Julia L MacIsaac
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - Sarah M Mah
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - Lisa M McEwen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - Seang-Mei Saw
- Saw Swee Hock School of Public Health, NUS, Singapore 117597
| | - Keith M Godfrey
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, United Kingdom
| | - Yap-Seng Chong
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609; Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore 119228
| | - Kenneth Kwek
- KK Women's and Children's Hospital, Singapore 229899
| | - Chee-Keong Kwoh
- School of Computer Engineering, Nanyang Technological University (NTU), Singapore 639798
| | - Shu-E Soh
- Saw Swee Hock School of Public Health, NUS, Singapore 117597; Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore 119228
| | - Mary F F Chong
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609; Yong Loo Lin School of Medicine, National University of Singapore, National University Health System, Singapore 119228
| | - Sheila Barton
- MRC Lifecourse Epidemiology Unit and NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton, SO16 6YD, United Kingdom
| | - Neerja Karnani
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Clara Y Cheong
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Jan Paul Buschdorf
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Walter Stünkel
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4 Canada
| | - Michael J Meaney
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609; Ludmer Centre for Neuroinformatics and Mental Health, Douglas University Mental Health Institute, McGill University, Montreal, (Quebec) H4H 1R3 Canada
| | - Peter D Gluckman
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609; Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland 1142, New Zealand
| | - Joanna D Holbrook
- Singapore Institute of Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, Singapore 117609
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262
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Possible molecular mechanisms linking air pollution and asthma in children. BMC Pulm Med 2014; 14:31. [PMID: 24581224 PMCID: PMC3941253 DOI: 10.1186/1471-2466-14-31] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/03/2014] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Air pollution has many effects on the health of both adults and children, but children's vulnerability is unique. The aim of this review is to discuss the possible molecular mechanisms linking air pollution and asthma in children, also taking into account their genetic and epigenetic characteristics. RESULTS Air pollutants appear able to induce airway inflammation and increase asthma morbidity in children. A better definition of mechanisms related to pollution-induced airway inflammation in asthmatic children is needed in order to find new clinical and therapeutic strategies for preventing the exacerbation of asthma. Moreover, reducing pollution-induced oxidative stress and consequent lung injury could decrease children's susceptibility to air pollution. This would be extremely useful not only for the asthmatic children who seem to have a genetic susceptibility to oxidative stress, but also for the healthy population. In addition, epigenetics seems to have a role in the lung damage induced by air pollution. Finally, a number of epidemiological studies have demonstrated that exposure to common air pollutants plays a role in the susceptibility to, and severity of respiratory infections. CONCLUSIONS Air pollution has many negative effects on pediatric health and it is recognised as a serious health hazard. There seems to be an association of air pollution with an increased risk of asthma exacerbations and acute respiratory infections. However, further studies are needed in order to clarify the specific mechanism of action of different air pollutants, identify genetic polymorphisms that modify airway responses to pollution, and investigate the effectiveness of new preventive and/or therapeutic approaches for subjects with low antioxidant enzyme levels. Moreover, as that epigenetic changes are inheritable during cell division and may be transmitted to subsequent generations, it is very important to clarify the role of epigenetics in the relationship between air pollution and lung disease in asthmatic and healthy children.
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263
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Izzi B, Binder AM, Michels KB. Pyrosequencing Evaluation of Widely Available Bisulfite Conversion Methods: Considerations for Application. ACTA ACUST UNITED AC 2014; 2:28-36. [PMID: 24944560 PMCID: PMC4058339 DOI: 10.1159/000358882] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Introduction Bisulfite treatment of DNA introduces methylation-dependent sequence changes through selective chemical conversion of nonmethylated cytosine to uracil and serves as pretreatment step for the majority of DNA methylation analysis methods. Methods We have evaluated the conversion performance of five of the most commonly used bisulfite treatment kits [MethylDetector (Active Motif), Epitect+ (Qiagen), Zymo Methylation, Zymo Gold and Zymo Lightning (all from Zymo Research)] by pyrosequencing four different regions with variable methylation levels, including: a repetitive element (ALUSX), a gene with low levels of methylation (IL6ST), an imprinted gene expected to be approximately 50% methylated (IGF2), and a fully methylated gene (ST3GAL2). In addition, we have studied the influence of duration (3 vs. 16 h) and type (fixed temperature vs. cycling program) of incubation protocol on the conversion efficiency of each evaluated kit. Results All kits produced similar conversion rates of ALUSX, IGF2 and ST3GAL2, while the conversion of the low methylated IL6ST gene was variable between kits. The Zymo kits were highly consistent in their performance even when different protocols of incubation were applied, generating full conversion at the low methylated gene IL6; this was not true for the MethylDetector and Epitect+ kits. However, long-cycling incubation could produce similar conversion rates for the same locus in combination with Active Motif and Qiagen kits. Conclusions The selection of a long-cycling protocol during conversion permits standardization of protocols, improving the reproducibility of methylation estimates across laboratories for gene-specific, genome-wide and bisulfite-based sequencing analyses.
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Affiliation(s)
- Benedetta Izzi
- Institute for Prevention and Cancer Epidemiology, Freiburg Medical Center, University of Freiburg, Freiburg, Germany ; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass., USA
| | - Alexandra M Binder
- Harvard School of Public Health, Department of Epidemiology, Boston, Mass., USA
| | - Karin B Michels
- Institute for Prevention and Cancer Epidemiology, Freiburg Medical Center, University of Freiburg, Freiburg, Germany ; Obstetrics and Gynecology Epidemiology Center, Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, Mass., USA ; Harvard School of Public Health, Department of Epidemiology, Boston, Mass., USA
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264
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Paul DS, Guilhamon P, Karpathakis A, Butcher LM, Thirlwell C, Feber A, Beck S. Assessment of RainDrop BS-seq as a method for large-scale, targeted bisulfite sequencing. Epigenetics 2014; 9:678-84. [PMID: 24518816 PMCID: PMC4063826 DOI: 10.4161/epi.28041] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We present a systematic assessment of RainDrop BS-seq, a novel method for large-scale, targeted bisulfite sequencing using microdroplet-based PCR amplification coupled with next-generation sequencing. We compared DNA methylation levels at 498 target loci (1001 PCR amplicons) in human whole blood, osteosarcoma cells and an archived tumor tissue sample. We assessed the ability of RainDrop BS-seq to accurately measure DNA methylation over a range of DNA quantities (from 10 to 1500 ng), both with and without whole-genome amplification (WGA) following bisulfite conversion. DNA methylation profiles generated using at least 100 ng correlated well (median R = 0.92) with those generated on Illumina Infinium HumanMethylation450 BeadChips, currently the platform of choice for epigenome-wide association studies (EWAS). WGA allowed for testing of samples with a starting DNA amount of 10 and 50 ng, although a reduced correlation was observed (median R = 0.79). We conclude that RainDrop BS-seq is suitable for measuring DNA methylation levels using nanogram quantities of DNA, and can be used to study candidate epigenetic biomarker loci in an accurate and high-throughput manner, paving the way for its application to routine clinical diagnostics.
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Affiliation(s)
- Dirk S Paul
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Paul Guilhamon
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Anna Karpathakis
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Lee M Butcher
- UCL Cancer Institute; University College London; London, United Kingdom
| | | | - Andrew Feber
- UCL Cancer Institute; University College London; London, United Kingdom
| | - Stephan Beck
- UCL Cancer Institute; University College London; London, United Kingdom
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265
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Friemel C, Ammerpohl O, Gutwein J, Schmutzler AG, Caliebe A, Kautza M, von Otte S, Siebert R, Bens S. Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in PIWIL1 and PIWIL2. Fertil Steril 2014; 101:1097-1103.e1. [PMID: 24524831 DOI: 10.1016/j.fertnstert.2013.12.054] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2013] [Revised: 12/13/2013] [Accepted: 12/26/2013] [Indexed: 12/31/2022]
Abstract
OBJECTIVE To identify CpG sites differentially methylated in peripheral blood of men with idiopathic infertility due to impaired spermatogenesis as compared with fertile controls. DESIGN DNA methylation profiling on peripheral blood samples using the HumanMethylation450 BeadChip (Illumina) in patients and controls, single-nucleotide polymorphism (SNP) typing by Sanger sequencing. SETTING University institute in cooperation with genetic and infertility clinics. PATIENT(S) 30 infertile men with normal CFTR and AZF tests and karyotype, and 10 fertile male controls. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) DNA methylation levels at CpG sites. RESULT(S) We identified 471 CpGs (287 genes) as differentially methylated between patients and controls. These were significantly enriched for the gene ontology functions MHC class II receptor activity and piwi-interacting (piRNA) binding. The latter was associated with two methylation-sensitive SNPs in the genes PIWIL1 and PIWIL2, respectively, which showed significant allele distribution skewing in the infertile cohort. We found that 445 (94.5%) of 471 differentially methylated CpGs were associated with SNPs, but 26 (15 genes) were not genomically templated, including the ENO1, MTA2, BRSK2, and LBX2 genes previously associated with fertility and spermatogenesis. CONCLUSION(S) Our study identifies surrogate DNA methylation markers for idiopathic infertility in peripheral blood and suggests that allele-specific DNA methylation differences at regulatory sites of genes involved in piRNA regulation are associated with disturbed spermatogenesis.
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Affiliation(s)
- Carolin Friemel
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ole Ammerpohl
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jana Gutwein
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andreas G Schmutzler
- Department of Gynecology and Obstetrics, Center of Reproductive Medicine, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Almuth Caliebe
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Monika Kautza
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Sören von Otte
- Department of Gynecology and Obstetrics, Center of Reproductive Medicine, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanne Bens
- Institute of Human Genetics, Christian-Albrechts-University Kiel and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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266
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Hogg K, Price EM, Robinson WP. Improved reporting of DNA methylation data derived from studies of the human placenta. Epigenetics 2014; 9:333-7. [PMID: 24394602 DOI: 10.4161/epi.27648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Epigenetic variation is increasingly hypothesized as a mechanism underlying the effect of the in utero environment on long-term postnatal health; however, there is currently little clear data to support this in humans. A number of biological and technical factors provide challenges for the design of clinical epigenetic studies: from the type of cells or tissues that are available to the large range of predicted confounders that may impact findings. The human placenta, in addition to other neonatal tissues and whole blood, is commonly sampled for the study of epigenetic modifications. However there is little conformity for the most appropriate methods for study design, data analysis, and importantly, data interpretation. Here we present general recommendations for the reporting of DNA methylation in biological samples, with specific focus on the placenta. We outline key guidelines for: (1) placental sampling, (2) data analysis and presentation, and (3) interpretation of DNA methylation data. We emphasize the need to consider methodological noise, increase statistical power and to ensure appropriate adjustment for biological covariates. Finally, we highlight that epigenetic changes may be non-pathological and not necessarily translate into disease-associated changes. Improved reporting of DNA methylation data will be critical to identify epigenetic-based effects and to better understand the full phenotypic impact of these widely-reported epigenomic changes.
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Affiliation(s)
- Kirsten Hogg
- Department of Medical Genetics; University of British Columbia; Vancouver, BC Canada; Child & Family Research Institute; Vancouver, BC Canada
| | - E Magda Price
- Department of Medical Genetics; University of British Columbia; Vancouver, BC Canada; Child & Family Research Institute; Vancouver, BC Canada; Department of Obstetrics and Gynaecology; University of British Columbia; Vancouver, BC Canada
| | - Wendy P Robinson
- Department of Medical Genetics; University of British Columbia; Vancouver, BC Canada; Child & Family Research Institute; Vancouver, BC Canada
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