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Ackerman WE, Rigo MM, DaSilva-Arnold SC, Do C, Tariq M, Salas M, Castano A, Zamudio S, Tycko B, Illsley NP. Epigenetic changes regulating the epithelial-mesenchymal transition in human trophoblast differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.02.601748. [PMID: 39005325 PMCID: PMC11244995 DOI: 10.1101/2024.07.02.601748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The phenotype of human placental extravillous trophoblast (EVT) at the end of pregnancy reflects both first trimester differentiation from villous cytotrophoblast (CTB) and later gestational changes, including loss of proliferative and invasive capacity. Invasion abnormalities are central to two major placental pathologies, preeclampsia and placenta accreta spectrum, so characterization of the corresponding normal processes is crucial. In this report, our gene expression analysis, using purified human CTB and EVT cells, highlights an epithelial-mesenchymal transition (EMT) mechanism underlying CTB-EVT differentiation and provides a trophoblast-specific EMT signature. In parallel, DNA methylation profiling shows that CTB cells, already hypomethylated relative to non-trophoblast cell lineages, show further genome-wide hypomethylation in the transition to EVT. However, a small subgroup of genes undergoes gains of methylation (GOM) in their regulatory regions or gene bodies, associated with differential mRNA expression (DE). Prominent in this GOM-DE group are genes involved in the EMT, including multiple canonical EMT markers and the EMT-linked transcription factor RUNX1, for which we demonstrate a functional role in modulating the migratory and invasive capacities of JEG3 trophoblast cells. This analysis of DE associated with locus-specific GOM, together with functional studies of an important GOM-DE gene, highlights epigenetically regulated genes and pathways acting in human EVT differentiation and invasion, with implications for obstetric disorders in which these processes are dysregulated.
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Affiliation(s)
- William E. Ackerman
- Department of Obstetrics and Gynecology and AI.Health4All Center for Health Equity Using Machine Learning and Artificial Intelligence, University of Illinois College of Medicine, Chicago, USA
| | - Mauricio M. Rigo
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
| | - Sonia C. DaSilva-Arnold
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack NJ
| | - Catherine Do
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
| | - Mariam Tariq
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
| | - Martha Salas
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
| | - Angelica Castano
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
| | - Stacy Zamudio
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack NJ
| | - Benjamin Tycko
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ
| | - Nicholas P. Illsley
- Department of Obstetrics and Gynecology, Hackensack University Medical Center, Hackensack NJ
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2
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De Ridder K, Che H, Leroy K, Thienpont B. Benchmarking of methods for DNA methylome deconvolution. Nat Commun 2024; 15:4134. [PMID: 38755121 PMCID: PMC11099101 DOI: 10.1038/s41467-024-48466-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
Defining the number and abundance of different cell types in tissues is important for understanding disease mechanisms as well as for diagnostic and prognostic purposes. Typically, this is achieved by immunohistological analyses, cell sorting, or single-cell RNA-sequencing. Alternatively, cell-specific DNA methylome information can be leveraged to deconvolve cell fractions from a bulk DNA mixture. However, comprehensive benchmarking of deconvolution methods and modalities was not yet performed. Here we evaluate 16 deconvolution algorithms, developed either specifically for DNA methylome data or more generically. We assess the performance of these algorithms, and the effect of normalization methods, while modeling variables that impact deconvolution performance, including cell abundance, cell type similarity, reference panel size, method for methylome profiling (array or sequencing), and technical variation. We observe differences in algorithm performance depending on each these variables, emphasizing the need for tailoring deconvolution analyses. The complexity of the reference, marker selection method, number of marker loci and, for sequencing-based assays, sequencing depth have a marked influence on performance. By developing handles to select the optimal analysis configuration, we provide a valuable source of information for studies aiming to deconvolve array- or sequencing-based methylation data.
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Affiliation(s)
- Kobe De Ridder
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Huiwen Che
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Kaat Leroy
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, 3000, Leuven, Belgium.
- KU Leuven Institute for Single Cell Omics (LISCO), KU Leuven, 3000, Leuven, Belgium.
- KU Leuven Cancer Institute (LKI), KU Leuven, 3000, Leuven, Belgium.
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3
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Sah N, Soncin F. Conserved and divergent features of trophoblast stem cells. J Mol Endocrinol 2024; 72:e230131. [PMID: 38276878 PMCID: PMC11008758 DOI: 10.1530/jme-23-0131] [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: 11/01/2023] [Accepted: 01/26/2024] [Indexed: 01/27/2024]
Abstract
Trophoblast stem cells (TSCs) are a proliferative multipotent population derived from the trophectoderm of the blastocyst, which will give rise to all the functional cell types of the trophoblast compartment of the placenta. The isolation and culture of TSCs in vitro represent a robust model to study mechanisms of trophoblast differentiation into mature cells both in successful and diseased pregnancy. Despite the highly conserved functions of the placenta, there is extreme variability in placental morphology, fetal-maternal interface, and development among eutherian mammals. This review aims to summarize the establishment and maintenance of TSCs in mammals such as primates, including human, rodents, and nontraditional animal models with a primary emphasis on epigenetic regulation of their origin while defining gaps in the current literature and areas of further development. FGF signaling is critical for mouse TSCs but dispensable for derivation of TSCs in other species. Human, simian, and bovine TSCs have much more complicated requirements of signaling pathways including activation of WNT and inhibition of TGFβ cascades. Epigenetic features such as DNA and histone methylation as well as histone acetylation are dynamic during development and are expressed in cell- and gestational age-specific pattern in placental trophoblasts. While TSCs from different species seem to recapitulate some select epigenomic features, there is a limitation in the comprehensive understanding of TSCs and how well TSCs retain placental epigenetic marks. Therefore, future studies should be directed at investigating epigenomic features of global and placental-specific gene expression in primary trophoblasts and TSCs.
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Affiliation(s)
- Nirvay Sah
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
| | - Francesca Soncin
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium for Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
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4
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Chang C, Chen YL, Wang YW, Chen HW, Hsu CW, Lin KC, Ou YC, Liu T, Chen WL, Chu CA, Ho CL, Lee CT, Chow NH. Aberrant trophoblastic differentiation in human cancer: An emerging novel therapeutic target (Review). Oncol Rep 2024; 51:43. [PMID: 38240107 PMCID: PMC10823338 DOI: 10.3892/or.2024.8701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/15/2023] [Indexed: 01/23/2024] Open
Abstract
Various types of human cancer may develop aberrant trophoblastic differentiation, including histological changes and altered expression of β‑human chorionic gonadotropin (β‑hCG). Aberrant trophoblastic differentiation in epithelial cancer is usually associated with poor differentiation, tumor metastasis, unfavorable prognosis and treatment resistance. Since β‑hCG‑targeting vaccines have failed in an early phase II trial, it is crucial to obtain a better understanding of the molecular pathogenesis of trophoblastic differentiation in human cancer. The present review summarizes the clinical and translational research on this topic with the aim of accelerating the development of an effective targeted therapy. Ectopic expression of β‑hCG promotes proliferation, migration, invasion, vasculogenesis and epithelial‑mesenchymal transition (EMT) in vitro, and enhances metastatic and tumorigenic capabilities in vivo. Signaling cascades modulated by β‑hCG include the TGF‑β receptor pathway, EMT‑related pathways, the c‑MET receptor tyrosine kinase and mitogen‑activated protein kinase/ERK pathways, and the SMAD2/4 pathway. Taken together, these findings indicated that TGF‑β receptors, c‑MET and ERK1/2 are potential therapeutic targets. Nevertheless, further investigation on the molecular basis of aberrant trophoblastic differentiation is mandatory to improve the design of precision therapy for this aggressive type of human cancer.
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Affiliation(s)
- Chen Chang
- Department of Pathology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Yi-Lin Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Yi-Wen Wang
- Department of Dental Technology, Shu-Zen Junior College of Medicine and Management, Kaohsiung 821, Taiwan, R.O.C
| | - Hui-Wen Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Che-Wei Hsu
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Kun-Che Lin
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Yin-Chien Ou
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Tsunglin Liu
- The Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Bioinformatics Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Wan-Li Chen
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Chien-An Chu
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
| | - Chung-Liang Ho
- Department of Pathology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
| | - Chung-Ta Lee
- Department of Pathology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
| | - Nan-Haw Chow
- Department of Pathology, College of Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
- Department of Pathology, National Cheng Kung University Hospital, Tainan 704, Taiwan, R.O.C
- Molecular Medicine Core Laboratory, Research Center of Clinical Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
- Molecular Diagnostics Laboratory, Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan, R.O.C
- The Institute of Molecular Medicine, National Cheng Kung University, Tainan 701, Taiwan, R.O.C
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5
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Nakamura A, Broséus L, Tost J, Vaiman D, Martins S, Keyes K, Bonello K, Fekom M, Strandberg-Larsen K, Sutter-Dallay AL, Heude B, Melchior M, Lepeule J. Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age. Int J Mol Sci 2023; 24:11772. [PMID: 37511531 PMCID: PMC10380531 DOI: 10.3390/ijms241411772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 07/04/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
The placenta is a key organ for fetal and brain development. Its epigenome can be regarded as a biochemical record of the prenatal environment and a potential mechanism of its association with the future health of the fetus. We investigated associations between placental DNA methylation levels and child behavioral and emotional difficulties, assessed at 3 years of age using the Strengths and Difficulties Questionnaire (SDQ) in 441 mother-child dyads from the EDEN cohort. Hypothesis-driven and exploratory analyses (on differentially methylated probes (EWAS) and regions (DMR)) were adjusted for confounders, technical factors, and cell composition estimates, corrected for multiple comparisons, and stratified by child sex. Hypothesis-driven analyses showed an association of cg26703534 (AHRR) with emotional symptoms, and exploratory analyses identified two probes, cg09126090 (intergenic region) and cg10305789 (PPP1R16B), as negatively associated with peer relationship problems, as well as 33 DMRs, mostly positively associated with at least one of the SDQ subscales. Among girls, most associations were seen with emotional difficulties, whereas in boys, DMRs were as much associated with emotional than behavioral difficulties. This study provides the first evidence of associations between placental DNA methylation and child behavioral and emotional difficulties. Our results suggest sex-specific associations and might provide new insights into the mechanisms of neurodevelopment.
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Affiliation(s)
- Aurélie Nakamura
- Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences (IAB), University Grenoble Alpes, INSERM, 38700 La Tronche, France;
| | - Lucile Broséus
- Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences (IAB), University Grenoble Alpes, INSERM, 38700 La Tronche, France;
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA—Institut de Biologie François Jacob, University Paris Saclay, 91057 Evry, France;
| | - Daniel Vaiman
- From Gametes to Birth, Institut Cochin, U1016 INSERM, UMR 8104 CNRS, Paris Cité University, 75014 Paris, France;
| | - Silvia Martins
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (S.M.); (K.K.)
| | - Katherine Keyes
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA; (S.M.); (K.K.)
| | - Kim Bonello
- Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Equipe de Recherche en Epidémiologie Sociale (ERES), Sorbonne Université, INSERM, 75571 Paris, France; (K.B.); (M.F.); (M.M.)
- Department of General Practice, School of Medicine, Sorbonne University, 75013 Paris, France
| | - Mathilde Fekom
- Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Equipe de Recherche en Epidémiologie Sociale (ERES), Sorbonne Université, INSERM, 75571 Paris, France; (K.B.); (M.F.); (M.M.)
| | - Katrine Strandberg-Larsen
- Section of Epidemiology, Department of Public Health, University of Copenhagen, 1165 Copenhagen, Denmark;
| | - Anne-Laure Sutter-Dallay
- Bordeaux Population Health, Bordeaux University, INSERM, UMR 1219, 33076 Bordeaux, France;
- University Department of Child and Adolescent Psychiatry, Charles Perrens Hospital, 33000 Bordeaux, France
| | - Barbara Heude
- Center for Research in Epidemiology and Statistics (CRESS), Université Paris Cité and Université Sorbonne Paris Nord, INSERM, INRAE, 75004 Paris, France;
| | - Maria Melchior
- Institut Pierre Louis d’Epidémiologie et de Santé Publique (IPLESP), Equipe de Recherche en Epidémiologie Sociale (ERES), Sorbonne Université, INSERM, 75571 Paris, France; (K.B.); (M.F.); (M.M.)
| | - Johanna Lepeule
- Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences (IAB), University Grenoble Alpes, INSERM, 38700 La Tronche, France;
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6
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Orellana-Guerrero D, Uribe-Salazar JM, El-Sheikh Ali H, Scoggin KE, Ball B, Daels P, Finno CJ, Dini P. Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation. Int J Mol Sci 2023; 24:ijms24087084. [PMID: 37108254 PMCID: PMC10139181 DOI: 10.3390/ijms24087084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The placenta is a temporary organ that is essential for the survival of the fetus, with a lifelong effect on the health of both the offspring and the dam. The functions of the placenta are controlled by its dynamic gene expression during gestation. In this study, we aimed to investigate the equine placental DNA methylome as one of the fundamental mechanisms that controls the gene expression dynamic. Chorioallantois samples from four (4M), six (6M), and ten (10M) months of gestation were used to map the methylation pattern of the placenta. Globally, methylation levels increased toward the end of gestation. We identified 921 differentially methylated regions (DMRs) between 4M and 6M, 1225 DMRs between 4M and 10M, and 1026 DMRs between 6M and 10M. A total of 817 genes carried DMRs comparing 4M and 6M, 978 comparing 4M and 10M, and 804 comparing 6M and 10M. We compared the transcriptomes between the samples and found 1381 differentially expressed genes (DEGs) when comparing 4M and 6M, 1428 DEGs between 4M and 10M, and 741 DEGs between 6M and 10M. Finally, we overlapped the DEGs and genes carrying DMRs (DMRs-DEGs). Genes exhibiting (a) higher expression, low methylation and (b) low expression, high methylation at different time points were identified. The majority of these DMRs-DEGs were located in introns (48.4%), promoters (25.8%), and exons (17.7%) and were involved in changes in the extracellular matrix; regulation of epithelial cell migration; vascularization; and regulation of minerals, glucose, and metabolites, among other factors. Overall, this is the first report highlighting the dynamics in the equine placenta methylome during normal pregnancy. The findings presented serve as a foundation for future studies on the impact of abnormal methylation on the outcomes of equine pregnancies.
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Affiliation(s)
- Daniela Orellana-Guerrero
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | | | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
- College of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Barry Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Peter Daels
- Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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7
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Sanyal T, Das A, Bhowmick P, Bhattacharjee P. Interplay between environmental exposure and mitochondrial DNA methylation in disease susceptibility and cancer: a comprehensive review. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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8
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Jedynak P, Tost J, Calafat AM, Bourova-Flin E, Busato F, Forhan A, Heude B, Jakobi M, Rousseaux S, Schwartz J, Slama R, Vaiman D, Philippat C, Lepeule J. Pregnancy exposure to synthetic phenols and placental DNA methylation - An epigenome-wide association study in male infants from the EDEN cohort. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 290:118024. [PMID: 34523531 PMCID: PMC8590835 DOI: 10.1016/j.envpol.2021.118024] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 08/20/2021] [Indexed: 05/14/2023]
Abstract
In utero exposure to environmental chemicals, such as synthetic phenols, may alter DNA methylation in different tissues, including placenta - a critical organ for fetal development. We studied associations between prenatal urinary biomarker concentrations of synthetic phenols and placental DNA methylation. Our study involved 202 mother-son pairs from the French EDEN cohort. Nine phenols were measured in spot urine samples collected between 22 and 29 gestational weeks. We performed DNA methylation analysis of the fetal side of placental tissues using the IlluminaHM450 BeadChips. We evaluated methylation changes of individual CpGs in an adjusted epigenome-wide association study (EWAS) and identified differentially methylated regions (DMRs). We performed mediation analysis to test whether placental tissue heterogeneity mediated the association between urinary phenol concentrations and DNA methylation. We identified 46 significant DMRs (≥5 CpGs) associated with triclosan (37 DMRs), 2,4-dichlorophenol (3), benzophenone-3 (3), methyl- (2) and propylparaben (1). All but 2 DMRs were positively associated with phenol concentrations. Out of the 46 identified DMRs, 7 (6 for triclosan) encompassed imprinted genes (APC, FOXG1, GNAS, GNASAS, MIR886, PEG10, SGCE), which represented a significant enrichment. Other identified DMRs encompassed genes encoding proteins responsible for cell signaling, transmembrane transport, cell adhesion, inflammatory, apoptotic and immunological response, genes encoding transcription factors, histones, tumor suppressors, genes involved in tumorigenesis and several cancer risk biomarkers. Mediation analysis suggested that placental cell heterogeneity may partly explain these associations. This is the first study describing the genome-wide modifications of placental DNA methylation associated with pregnancy exposure to synthetic phenols or their precursors. Our results suggest that cell heterogeneity might mediate the effects of triclosan exposure on placental DNA methylation. Additionally, the enrichment of imprinted genes within the DMRs suggests mechanisms by which certain exposures, mainly to triclosan, could affect fetal development.
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Affiliation(s)
- Paulina Jedynak
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Antonia M Calafat
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ekaterina Bourova-Flin
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Florence Busato
- Laboratory for Epigenetics and Environment, Centre National de Recherche en Génomique Humaine, CEA - Institut de Biologie François Jacob, University Paris Saclay, Evry, France
| | - Anne Forhan
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Milan Jakobi
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Sophie Rousseaux
- University Grenoble Alpes, Inserm, CNRS, EpiMed Group, Institute for Advanced Biosciences, Grenoble, France
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rémy Slama
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Vaiman
- Genomics, Epigenetics and Physiopathology of Reproduction, Institut Cochin, U1016 Inserm - UMR 8104 CNRS - Paris-Descartes University, Paris, France
| | - Claire Philippat
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
| | - Johanna Lepeule
- University Grenoble Alpes, Inserm, CNRS, Team of Environmental Epidemiology Applied to Development and Respiratory Health, Institute for Advanced Biosciences, Grenoble, France
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9
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Lecorguillé M, Charles MA, Lepeule J, Lioret S, de Lauzon-Guillain B, Forhan A, Tost J, Suderman M, Heude B. Association between dietary patterns reflecting one-carbon metabolism nutrients intake before pregnancy and placental DNA methylation. Epigenetics 2021; 17:715-730. [PMID: 34461807 DOI: 10.1080/15592294.2021.1957575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The preconception period represents an important window for foetal and epigenetic programming. Some micronutrients (B vitamins, choline, betaine, methionine) implicated in one-carbon metabolism (OCM) are essential for major epigenetic processes that take place in early pregnancy. However, few studies have evaluated the implication of the micronutrients in placental DNA methylation. We investigated whether intake of OCM nutrients in the year before pregnancy was associated with placental DNA methylation in the EDEN mother-child cohort. Maternal dietary intake was assessed with a food-frequency questionnaire. Three dietary patterns, 'varied and balanced diet,' 'vegetarian tendency,' and 'bread and starchy food,' were used to characterize maternal OCM dietary intake. The Illumina Infinium HumanMethylation450 BeadChip was used to measure placental DNA methylation of 573 women included in the analyses. We evaluated the association of dietary patterns with global DNA methylation. Then, we conducted an agnostic epigenome-wide association study (EWAS) and investigated differentially methylated regions (DMRs) associated with each dietary pattern. We found no significant association between the three dietary patterns and global DNA methylation or individual CpG sites. DMR analyses highlighted associations between the 'varied and balanced' or 'vegetarian tendency' pattern and DMRs located at genes previously implicated in functions essential for embryonic development, such as neurodevelopment. The 'bread and starchy food' pattern was associated with regions related to genes whose functions involve various metabolic and cell synthesis-related processes. In mainly well-nourished French women without major deficiencies, OCM intake before pregnancy was not associated with major variation in DNA methylation.
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Affiliation(s)
| | - Marie-Aline Charles
- Université De Paris, Cress, Inserm, Inrae, Paris, France.,Ined, Inserm, EFS, ELFE Joint Unit, 93322, Aubervilliers, France
| | - Johanna Lepeule
- Inserm, CNRS, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, IAB, Université Grenoble Alpes, Grenoble, France
| | | | | | - Anne Forhan
- Université De Paris, Cress, Inserm, Inrae, Paris, France
| | - Jörg Tost
- Laboratory for Epigenetics and Environment, Centre National De Recherche En Génomique Humaine, CEA - Institut De Biologie François Jacob, Evry, France
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Barbara Heude
- Université De Paris, Cress, Inserm, Inrae, Paris, France
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10
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Yuan V, Hui D, Yin Y, Peñaherrera MS, Beristain AG, Robinson WP. Cell-specific characterization of the placental methylome. BMC Genomics 2021; 22:6. [PMID: 33407091 PMCID: PMC7788826 DOI: 10.1186/s12864-020-07186-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epigenetically distinct cell populations. Here, we present the first methylome-wide analysis of first trimester (n = 9) and term (n = 19) human placental samples of four cell populations: trophoblasts, Hofbauer cells, endothelial cells, and stromal cells, using the Illumina EPIC methylation array, which quantifies DNAm at > 850,000 CpGs. RESULTS The most distinct DNAm profiles were those of placental trophoblasts, which are central to many pregnancy-essential functions, and Hofbauer cells, which are a rare fetal-derived macrophage population. Cell-specific DNAm occurs at functionally-relevant genes, including genes associated with placental development and preeclampsia. Known placental-specific methylation marks, such as those associated with genomic imprinting, repetitive element hypomethylation, and placental partially methylated domains, were found to be more pronounced in trophoblasts and often absent in Hofbauer cells. Lastly, we characterize the cell composition and cell-specific DNAm dynamics across gestation. CONCLUSIONS Our results provide a comprehensive analysis of DNAm in human placental cell types from first trimester and term pregnancies. This data will serve as a useful DNAm reference for future placental studies, and we provide access to this data via download from GEO (GSE159526), through interactive exploration from the web browser ( https://robinsonlab.shinyapps.io/Placental_Methylome_Browser/ ), and through the R package planet, which allows estimation of cell composition directly from placental DNAm data.
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Affiliation(s)
- Victor Yuan
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Desmond Hui
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Yifan Yin
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Maria S. Peñaherrera
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
| | - Alexander G. Beristain
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, Vancouver, BC Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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11
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Jayalekshmi VS, Ramachandran S. Maternal cholesterol levels during gestation: boon or bane for the offspring? Mol Cell Biochem 2020; 476:401-416. [PMID: 32964393 DOI: 10.1007/s11010-020-03916-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/15/2020] [Indexed: 02/08/2023]
Abstract
An increase in cholesterol levels is perceived during pregnancy and is considered as a normal adaptive response to the development of the fetus. In some pregnancies, excessive increase in total cholesterol with high levels of Low-Density Lipoprotein leads to maladaptation by the fetus to cholesterol demands, resulting in a pathological condition termed as maternal hypercholesterolemia (MH). MH is considered clinically irrelevant and therefore cholesterol levels are not routinely checked during pregnancy, as a consequence of which there is scarce information on its global prevalence in pregnant women. Studies have reported that MH during pregnancy can cause atherogenesis in adults emphasizing the concept of in utero programming of fetus. Moreover, Gestational Diabetes Mellitus, obesity and Polycystic Ovary Syndrome are potential risk factors which strengthen combined pathologies in placenta and fetuses of mothers with MH. However, lack of conclusive evidence on cholesterol transport and underlying programming demand substantial research to develop population-based life style strategies for women in their childbearing years. The current review focuses on the mechanisms and outcomes of MH from existing epidemiological as well as experimental data and presents a detailed insight on this novel risk factor of cardiovascular diseases.
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Affiliation(s)
- V S Jayalekshmi
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.,PhD Program in Biotechnology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Surya Ramachandran
- Cardiovascular Diseases and Diabetes Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, India.
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12
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The tissue-specific aspect of genome-wide DNA methylation in newborn and placental tissues: implications for epigenetic epidemiologic studies. J Dev Orig Health Dis 2020; 12:113-123. [PMID: 32327008 DOI: 10.1017/s2040174420000136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Epigenetic programming is essential for lineage differentiation, embryogenesis and placentation in early pregnancy. In epigenetic association studies, DNA methylation is often examined in DNA derived from white blood cells, although its validity to other tissues of interest remains questionable. Therefore, we investigated the tissue specificity of epigenome-wide DNA methylation in newborn and placental tissues. Umbilical cord white blood cells (UC-WBC, n = 25), umbilical cord blood mononuclear cells (UC-MNC, n = 10), human umbilical vein endothelial cells (HUVEC, n = 25) and placental tissue (n = 25) were obtained from 36 uncomplicated pregnancies. Genome-wide DNA methylation was measured by the Illumina HumanMethylation450K BeadChip. Using UC-WBC as a reference tissue, we identified 3595 HUVEC tissue-specific differentially methylated regions (tDMRs) and 11,938 placental tDMRs. Functional enrichment analysis showed that HUVEC and placental tDMRs were involved in embryogenesis, vascular development and regulation of gene expression. No tDMRs were identified in UC-MNC. In conclusion, the extensive amount of genome-wide HUVEC and placental tDMRs underlines the relevance of tissue-specific approaches in future epigenetic association studies, or the use of validated representative tissues for a certain disease of interest, if available. To this purpose, we herewith provide a relevant dataset of paired, tissue-specific, genome-wide methylation measurements in newborn tissues.
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13
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Dwi Putra SE, Reichetzeder C, Hasan AA, Slowinski T, Chu C, Krämer BK, Kleuser B, Hocher B. Being Born Large for Gestational Age is Associated with Increased Global Placental DNA Methylation. Sci Rep 2020; 10:927. [PMID: 31969597 PMCID: PMC6976643 DOI: 10.1038/s41598-020-57725-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/31/2019] [Indexed: 02/01/2023] Open
Abstract
Being born small (SGA) or large for gestational age (LGA) is associated with adverse birth outcomes and metabolic diseases in later life of the offspring. It is known that aberrations in growth during gestation are related to altered placental function. Placental function is regulated by epigenetic mechanisms such as DNA methylation. Several studies in recent years have demonstrated associations between altered patterns of DNA methylation and adverse birth outcomes. However, larger studies that reliably investigated global DNA methylation are lacking. The aim of this study was to characterize global placental DNA methylation in relationship to size for gestational age. Global DNA methylation was assessed in 1023 placental samples by LC-MS/MS. LGA offspring displayed significantly higher global placental DNA methylation compared to appropriate for gestational age (AGA; p < 0.001). ANCOVA analyses adjusted for known factors impacting on DNA methylation demonstrated an independent association between placental global DNA methylation and LGA births (p < 0.001). Tertile stratification according to global placental DNA methylation levels revealed a significantly higher frequency of LGA births in the third tertile. Furthermore, a multiple logistic regression analysis corrected for known factors influencing birth weight highlighted an independent positive association between global placental DNA methylation and the frequency of LGA births (p = 0.001).
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Affiliation(s)
- S E Dwi Putra
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany.,Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Faculty of Biotechnology, University of Surabaya, Surabaya, Indonesia
| | - C Reichetzeder
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.
| | - A A Hasan
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany.,Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany.,Department of Biochemistry, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt.,UP Transfer GmbH, University of Potsdam, Potsdam, Germany
| | - T Slowinski
- Department of Nephrology, Campus Charité Mitte, University Hospital Charité, Berlin, Germany
| | - C Chu
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - B K Krämer
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany
| | - B Kleuser
- Department of Nutritional Toxicology, Institute of Nutritional Science, University of Potsdam, Nuthetal, Germany
| | - B Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Heidelberg, Germany. .,Department of Basic Medicine, Medical College of Hunan Normal University, Changsha, China. .,Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, China.
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14
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Vizitiu AC, Stambouli D, Pavel AG, Muresan MC, Anastasiu DM, Bejinar C, Alexa A, Marian C, Sirbu IO, Sima L. Mature miR-99a Upregulation in the Amniotic Fluid Samples from Female Fetus Down Syndrome Pregnancies: A Pilot Study. ACTA ACUST UNITED AC 2019; 55:medicina55110728. [PMID: 31703316 PMCID: PMC6915350 DOI: 10.3390/medicina55110728] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023]
Abstract
Background and Objective: Although Down syndrome is the most frequent aneuploidy, its pathogenic molecular mechanisms are not yet fully understood. The aim of our study is to quantify-by qRT-PCR-the expression levels of both the mature forms and the pri-miRNAs of the microRNAs resident on chromosome 21 (miR(21)) in the amniotic fluid samples from Down syndrome singleton pregnancies and to estimate the impact of the differentially expressed microRNAs on Down syndrome fetal heart and amniocytes transcriptomes. Materials and methods: We collected amniotic fluid samples harvested by trained obstetricians as part of the second trimester screening/diagnostic procedure for aneuploidies to assess the trisomy 21 status by QF-PCR and karyotyping. Next, we evaluated-by Taqman qRT-PCR-the expression levels of both the mature forms and the pri-miRNA precursors of the microRNAs resident on chromosome 21 in amniotic fluid samples from singleton Down syndrome and euploid pregnancies. Further, we combined miRWalk 3.0 microRNA target prediction with GEO DataSets analysis to estimate the impact of hsa-miR-99a abnormal expression on Down syndrome heart and amniocytes transcriptome. Results: We found a statistically significant up-regulation of the mature form of miR-99a, but not pri-miR-99a, in the amniotic fluid samples from Down syndrome pregnancies with female fetuses. GATHER functional enrichment analysis of miRWalk3.0-predicted targets from Down syndrome amniocytes and fetal hearts transcriptome GEODataSets outlined both focal adhesion and cytokine-cytokine receptor interaction signaling as novel signaling pathways impacted by miR-99a and associated with cardiac defects in female Down syndrome patients. Conclusions: The significant overexpression of miR-99a, but not pri-miR-99a, points towards an alteration of the post-transcriptional mechanisms of hsa-miR-99a maturation and/or stability in the female trisomic milieu, with a potential impact on signaling pathways important for proper development of the heart.
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Affiliation(s)
- Anda-Cornelia Vizitiu
- Doctoral School, Victor Babes University of Medicine and Pharmacy Timisoara, Eftimie Murgu Nr. 2, Timisoara 300041, Romania;
| | - Danae Stambouli
- CytoGenomic Medical Laboratory, Calea Floreasca Nr. 35, Sector 1, Bucharest 014451, Romania; (D.S.); (A.-G.P.)
| | - Anca-Gabriela Pavel
- CytoGenomic Medical Laboratory, Calea Floreasca Nr. 35, Sector 1, Bucharest 014451, Romania; (D.S.); (A.-G.P.)
| | - Maria-Cezara Muresan
- Obstetrics and Gynecology Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania (D.M.A.)
| | - Diana Maria Anastasiu
- Obstetrics and Gynecology Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania (D.M.A.)
| | - Cristina Bejinar
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
| | - Anda Alexa
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
| | - Catalin Marian
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
| | - Ioan Ovidiu Sirbu
- Biochemistry Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania; (C.B.); (A.A.); (C.M.)
- Correspondence: ; Tel.: +40-756-136-272
| | - Laurentiu Sima
- Surgical Semiology Department, Victor Babes University of Medicine and Pharmacy, Eftimie Murgu Nr. 2, Timisoara 300041, Romania;
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15
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Loiseau C, Cooper MM, Doolan DL. Deciphering host immunity to malaria using systems immunology. Immunol Rev 2019; 293:115-143. [PMID: 31608461 DOI: 10.1111/imr.12814] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 09/18/2019] [Accepted: 09/20/2019] [Indexed: 12/11/2022]
Abstract
A century of conceptual and technological advances in infectious disease research has changed the face of medicine. However, there remains a lack of effective interventions and a poor understanding of host immunity to the most significant and complex pathogens, including malaria. The development of successful interventions against such intractable diseases requires a comprehensive understanding of host-pathogen immune responses. A major advance of the past decade has been a paradigm switch in thinking from the contemporary reductionist (gene-by-gene or protein-by-protein) view to a more holistic (whole organism) view. Also, a recognition that host-pathogen immunity is composed of complex, dynamic interactions of cellular and molecular components and networks that cannot be represented by any individual component in isolation. Systems immunology integrates the field of immunology with omics technologies and computational sciences to comprehensively interrogate the immune response at a systems level. Herein, we describe the system immunology toolkit and report recent studies deploying systems-level approaches in the context of natural exposure to malaria or controlled human malaria infection. We contribute our perspective on the potential of systems immunity for the rational design and development of effective interventions to improve global public health.
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Affiliation(s)
- Claire Loiseau
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Martha M Cooper
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
| | - Denise L Doolan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Qld, Australia
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16
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Śliwa A, Kubiczak M, Szczerba A, Walkowiak G, Nowak-Markwitz E, Burczyńska B, Butler S, Iles R, Białas P, Jankowska A. Regulation of human chorionic gonadotropin beta subunit expression in ovarian cancer. BMC Cancer 2019; 19:746. [PMID: 31362717 PMCID: PMC6664497 DOI: 10.1186/s12885-019-5960-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Expression of human chorionic gonadotropin beta subunit by cancers is extensively documented, yet regulation of the multiple genes that can code for this protein is poorly understood. The aim of the study was to examine the mechanisms regulating CGB gene expression in ovarian cancer. METHODS Expression of CGB genes and SP1, SP3, TFAP2A transcription factor genes was evaluated by RT-qPCR. The methylation status of CGB genes promoter regions was examined by methylation-specific PCR. RESULTS mRNA arising from multiple CGB genes was detected in both ovarian control and malignant tissues. However, expression of CGB3-9 genes was shown to be significantly higher in malignant than healthy ovarian tissues. CGB1 and CGB2 transcripts were shown to be present in 20% of ovarian cancers, but were not detected in any of the control samples. Malignant tissues were characterized by DNA demethylation of CGB promoter regions. In ovarian cancer CGB expression positively correlated with TFAP2A transcripts level and expression of TFAP2A transcription factor was significantly higher in cancer than in control tissues. In contrast SP3 expression level was significantly lower in ovarian tumours than in control ovarian tissue. CONCLUSIONS In ovarian cancers increased expression of human chorionic gonadotropin beta subunit is associated with demethylation of CGB promoter regions. CGB3-9 expression level strongly correlates with expression of the TFAP2A transcription factor. Presence of mRNA arising from CGB1 and CGB2 genes appears to be a unique feature of a subset of ovarian cancers.
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Affiliation(s)
- Aleksandra Śliwa
- Department of Cell Biology, Poznan University of Medical Sciences, 5D Rokietnicka Street, 60-806, Poznan, Poland.
| | - Marta Kubiczak
- Department of Cell Biology, Poznan University of Medical Sciences, 5D Rokietnicka Street, 60-806, Poznan, Poland
| | - Anna Szczerba
- Department of Cell Biology, Poznan University of Medical Sciences, 5D Rokietnicka Street, 60-806, Poznan, Poland
| | - Grzegorz Walkowiak
- Department of Cell Biology, Poznan University of Medical Sciences, 5D Rokietnicka Street, 60-806, Poznan, Poland
| | - Ewa Nowak-Markwitz
- Gynaecologic Oncology Department, Poznan University of Medical Sciences, 33 Polna Street, 60-101, Poznan, Poland
| | - Beata Burczyńska
- Centre for Investigative and Diagnostic Oncology, Middlesex University, The Burroughs, London, NW4 4BT, UK
| | - Stephen Butler
- MAP Diagnostics Ltd, The iLAB, Stannard Way, Bedford, Bedfordshire, MK44 3RZ, UK
| | - Ray Iles
- MAP Diagnostics Ltd, The iLAB, Stannard Way, Bedford, Bedfordshire, MK44 3RZ, UK.,College of Health, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Piotr Białas
- Department of Cell Biology, Poznan University of Medical Sciences, 5D Rokietnicka Street, 60-806, Poznan, Poland
| | - Anna Jankowska
- Department of Cell Biology, Poznan University of Medical Sciences, 5D Rokietnicka Street, 60-806, Poznan, Poland
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17
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Gamage TKJB, Schierding W, Tsai P, Ludgate JL, Chamley LW, Weeks RJ, Macaulay EC, James JL. Human trophoblasts are primarily distinguished from somatic cells by differences in the pattern rather than the degree of global CpG methylation. Biol Open 2018; 7:bio.034884. [PMID: 30026266 PMCID: PMC6124577 DOI: 10.1242/bio.034884] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The placenta is a fetal exchange organ connecting mother and baby that facilitates fetal growth in utero. DNA methylation is thought to impact placental development and function. Global DNA methylation studies using human placental lysates suggest that the placenta is uniquely hypomethylated compared to somatic tissue lysates, and this hypomethylation is thought to be important in conserving the unique placental gene expression patterns required for successful function. In the placental field, methylation has frequently been examined in tissue lysates, which contain mixed cell types that can confound results. To better understand how DNA methylation influences placentation, DNA from isolated first trimester trophoblast populations underwent reduced representation bisulfite sequencing and was compared to publicly available data of blastocyst-derived and somatic cell populations. First, this revealed that, unlike murine blastocysts, human trophectoderm and inner cell mass samples did not have significantly different levels of global methylation. Second, our work suggests that differences in global CpG methylation between trophoblasts and somatic cells are much smaller than previously reported. Rather, our findings suggest that different patterns of CpG methylation may be more important in epigenetically distinguishing the placenta from somatic cell populations, and these patterns of methylation may contribute to successful placental/trophoblast function. Summary: The placenta may not be as uniquely hypomethylated as previously reported, rather differences in the pattern of CpG methylation are what make it epigenetically distinct.
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Affiliation(s)
- Teena K J B Gamage
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - William Schierding
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - Peter Tsai
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - Jackie L Ludgate
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Lawrence W Chamley
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
| | - Robert J Weeks
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Erin C Macaulay
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand
| | - Joanna L James
- Department of Obstetrics and Gynaecology, The University of Auckland, Auckland 1142, New Zealand
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18
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Kang J, Lee CN, Li HY, Hsu KH, Wang SH, Lin SY. Association of Interleukin-10 Methylation Levels With Gestational Diabetes in a Taiwanese Population. Front Genet 2018; 9:222. [PMID: 29988451 PMCID: PMC6024195 DOI: 10.3389/fgene.2018.00222] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/04/2018] [Indexed: 11/13/2022] Open
Abstract
Objective: Gestational diabetes mellitus (GDM) is defined as glucose intolerance with onset during pregnancy, which is also associated with future metabolic diseases in both patients and their offspring. The mechanisms underlying this condition remain largely unknown and may be partly related to epigenetics. The aim of this study was to compare the methylation levels of the cytokine interleukin-10 (IL-10) in pregnant women and their fetuses under both hyperglycemic and euglycemic environments, as those levels may be a clue to the epigenetic mechanisms underlying pathogenesis of GDM. Methods: We analyzed the methylation levels of the IL-10 gene in maternal blood, cord blood, and placental tissue in both a GDM group (n = 8) and a control group (n = 24) using a LightCycler LC480 (Roche, Rotkreuz, Switzerland). IL-10 concentrations in maternal blood and THP-1 cells were measured by enzyme-linked immunosorbent assay (ELISA) using BD OptEIA Human IL-10 ELISA kits (BD Biosciences Pharmingen, San Diego, CA, United States). Results: The maternal blood IL-10 methylation levels in the GDM group and the control group were 0.23 ± 0.04 and 0.26 ± 0.04, respectively (p = 0.03), but there were no significant differences between the levels of the two groups in the cord blood or placental tissue. Increased IL-10 plasma concentrations were discovered under hyperglycemic environments and were confirmed via the THP-1 cell line. Conclusion: Hypomethylation of maternal blood and increased plasma IL-10 concentrations before birth were found in the GDM group.
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Affiliation(s)
- Jessica Kang
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Nan Lee
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
| | - Hung-Yuan Li
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Kai-Han Hsu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shu-Huei Wang
- Department of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shin-Yu Lin
- Department of Obstetrics and Gynecology, National Taiwan University Hospital, Taipei, Taiwan
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19
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DNA methylation of the glucocorticoid receptor gene promoter in the placenta is associated with blood pressure regulation in human pregnancy. J Hypertens 2018; 35:2276-2286. [PMID: 28817493 DOI: 10.1097/hjh.0000000000001450] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Blood pressure (BP) regulation during pregnancy is influenced by hormones of placental origin. It was shown that the glucocorticoid system is altered in hypertensive pregnancy disorders such as preeclampsia. Epigenetic mechanism might influence the activity of genes involved in placental hormone/hormone receptor synthesis/action during pregnancy. METHOD In the current study, we analyzed the association of 5'-C-phosphate-G-3' (CpG) site methylation of different glucocorticoid receptor gene (NR3C1) promoter regions with BP during pregnancy. The study was performed as a nested case-control study (n = 80) out of 1045 mother/child pairs from the Berlin Birth Cohort. Placental DNA was extracted and bisulfite converted. Nested PCR products from six NR3C1 proximal promoter regions [glucocorticoid receptor gene promotor region B (GR-1B), C (GR-1C), D (GR-1D), E (GR-1E), F (GR-1F), and H (GR-1H)] were analyzed by next generation sequencing. RESULTS NR3C1 promoter regions GR-1D and GR-1E had a much higher degree of DNA methylation as compared to GR-1B, GR-1F or GR-1H when analyzing the entire study population. Comparison of placental NR3C1 CpG site methylation among hypotensive, normotensive and hypertensive mothers revealed several differently methylated CpG sites in the GR-1F promoter region only. Both hypertension and hypotension were associated with increased DNA methylation of GR-1F CpG sites. These associations were independent of confounding factors, such as family history of hypertension, smoking status before pregnancy and prepregnancy BMI. Assessment of placental glucocorticoid receptor expression by western blot showed that observed DNA methylation differences were not associated with altered levels of placental glucocorticoid receptor expression. However, correlation matrices of all NR3C1 proximal promoter regions demonstrated different correlation patterns of intraregional and interregional DNA methylation in the three BP groups, putatively indicating altered transcriptional control of glucocorticoid receptor isoforms. CONCLUSION Our study provides evidence of an independent association between placental NR3C1 proximal promoter methylation and maternal BP. Furthermore, we observed different patterns of NR3C1 promoter methylation in normotensive, hypertensive and hypotensive pregnancy.
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20
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Wen Y, Wei Y, Zhang S, Li S, Liu H, Wang F, Zhao Y, Zhang D, Zhang Y. Cell subpopulation deconvolution reveals breast cancer heterogeneity based on DNA methylation signature. Brief Bioinform 2017; 18:426-440. [PMID: 27016391 DOI: 10.1093/bib/bbw028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Tumour heterogeneity describes the coexistence of divergent tumour cell clones within tumours, which is often caused by underlying epigenetic changes. DNA methylation is commonly regarded as a significant regulator that differs across cells and tissues. In this study, we comprehensively reviewed research progress on estimating of tumour heterogeneity. Bioinformatics-based analysis of DNA methylation has revealed the evolutionary relationships between breast cancer cell lines and tissues. Further analysis of the DNA methylation profiles in 33 breast cancer-related cell lines identified cell line-specific methylation patterns. Next, we reviewed the computational methods in inferring clonal evolution of tumours from different perspectives and then proposed a deconvolution strategy for modelling cell subclonal populations dynamics in breast cancer tissues based on DNA methylation. Further analysis of simulated cancer tissues and real cell lines revealed that this approach exhibits satisfactory performance and relative stability in estimating the composition and proportions of cellular subpopulations. The application of this strategy to breast cancer individuals of the Cancer Genome Atlas's identified different cellular subpopulations with distinct molecular phenotypes. Moreover, the current and potential future applications of this deconvolution strategy to clinical breast cancer research are discussed, and emphasis was placed on the DNA methylation-based recognition of intra-tumour heterogeneity. The wide use of these methods for estimating heterogeneity to further clinical cohorts will improve our understanding of neoplastic progression and the design of therapeutic interventions for treating breast cancer and other malignancies.
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21
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Herzog EM, Eggink AJ, Willemsen SP, Slieker RC, Wijnands KP, Felix JF, Chen J, Stubbs A, van der Spek PJ, van Meurs JB, Steegers-Theunissen RP. Early- and late-onset preeclampsia and the tissue-specific epigenome of the placenta and newborn. Placenta 2017; 58:122-132. [DOI: 10.1016/j.placenta.2017.08.070] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 08/18/2017] [Accepted: 08/28/2017] [Indexed: 01/22/2023]
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22
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Seki Y, Suzuki M, Guo X, Glenn AS, Vuguin PM, Fiallo A, Du Q, Ko YA, Yu Y, Susztak K, Zheng D, Greally JM, Katz EB, Charron MJ. In Utero Exposure to a High-Fat Diet Programs Hepatic Hypermethylation and Gene Dysregulation and Development of Metabolic Syndrome in Male Mice. Endocrinology 2017; 158:2860-2872. [PMID: 28911167 PMCID: PMC5659663 DOI: 10.1210/en.2017-00334] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/16/2017] [Indexed: 12/12/2022]
Abstract
Exposure to a high-fat (HF) diet in utero is associated with increased incidence of cardiovascular disease, diabetes, and metabolic syndrome later in life. However, the molecular basis of this enhanced susceptibility for metabolic disease is poorly understood. Gene expression microarray and genome-wide DNA methylation analyses of mouse liver revealed that exposure to a maternal HF milieu activated genes of immune response, inflammation, and hepatic dysfunction. DNA methylation analysis revealed 3360 differentially methylated loci, most of which (76%) were hypermethylated and distributed preferentially to hotspots on chromosomes 4 [atherosclerosis susceptibility quantitative trait loci (QTLs) 1] and 18 (insulin-dependent susceptibility QTLs 21). Interestingly, we found six differentially methylated genes within these hotspot QTLs associated with metabolic disease that maintain altered gene expression into adulthood (Arhgef19, Epha2, Zbtb17/Miz-1, Camta1 downregulated; and Ccdc11 and Txnl4a upregulated). Most of the hypermethylated genes in these hotspots are associated with cardiovascular system development and function. There were 140 differentially methylated genes that showed a 1.5-fold increase or decrease in messenger RNA levels. Many of these genes play a role in cell signaling pathways associated with metabolic disease. Of these, metalloproteinase 9, whose dysregulation plays a key role in diabetes, obesity, and cardiovascular disease, was upregulated 1.75-fold and hypermethylated in the gene body. In summary, exposure to a maternal HF diet causes DNA hypermethylation, which is associated with long-term gene expression changes in the liver of exposed offspring, potentially contributing to programmed development of metabolic disease later in life.
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Affiliation(s)
- Yoshinori Seki
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Masako Suzuki
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Xingyi Guo
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Alan Scott Glenn
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Patricia M. Vuguin
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Ariana Fiallo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Quan Du
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Yi-An Ko
- Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Yiting Yu
- Department of Oncology, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York 10461
| | - John M. Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Ellen B. Katz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
| | - Maureen J. Charron
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461
- Departments of Obstetrics and Gynecology and Women’s Health, Albert Einstein College of Medicine, Bronx, New York 10461
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23
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Janssen BG, Byun HM, Roels HA, Gyselaers W, Penders J, Baccarelli AA, Nawrot TS. Regulating role of fetal thyroid hormones on placental mitochondrial DNA methylation: epidemiological evidence from the ENVIR ONAGE birth cohort study. Clin Epigenetics 2017. [PMID: 28649287 PMCID: PMC5479026 DOI: 10.1186/s13148-017-0366-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Fetal development largely depends on thyroid hormone availability and proper placental function with an important role played by placental mitochondria. The biological mechanisms by which thyroid hormones exert their effects on mitochondrial function are not well understood. We investigated the role of fetal thyroid hormones on placental mitochondrial DNA (mtDNA) content and mtDNA methylation. We collected placental tissue and cord blood from 305 mother-child pairs that were enrolled between February 2010 and June 2014 in the ENVIRONAGE (ENVIRonmental influence ON early AGEing) birth cohort (province of Limburg, Belgium). Placental mtDNA content was determined by qPCR and placental mtDNA methylation by bisulfite-pyrosequencing in two regions, i.e., the D-loop control region and 12S ribosomal RNA (MT-RNR1). The levels of free thyroid hormones (FT3, FT4) and thyroid-stimulating hormone (TSH) were measured in cord blood. RESULTS Cord blood FT3 and FT4 were inversely associated with placental mtDNA methylation at the MT-RNR1 (p ≤ 0.01) and D-loop (p ≤ 0.05) regions, whereas a positive association was observed for both hormones with placental mtDNA content (p ≤ 0.04). Assuming causality, we estimated that MT-RNR1 and D-loop methylation mediated, respectively, 77% [indirect effect +14.61% (95% CI 2.64 to 27.98%, p = 0.01)] and 47% [indirect effect +8.60% (95% CI 1.23 to 16.50%, p = 0.02] of the positive association between FT3 and placental mtDNA content. Mediation models with FT4 gave similar results but the estimated effect proportions were smaller compared with those of FT3 (54% and 24%, respectively). CONCLUSIONS We showed that epigenetic modification at specific loci of the mitochondrial genome could intervene with the thyroid-dependent regulation of mitochondrial DNA copy numbers.
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Affiliation(s)
- Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Hyang-Min Byun
- Human Nutrition Research Centre, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, NE4 5PL UK
| | - Harry A Roels
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.,Louvain Centre for Toxicology and Applied Pharmacology (LTAP), Université catholique de Louvain, Brussels, Belgium
| | - Wilfried Gyselaers
- Department of Obstetrics, East-Limburg Hospital, Genk, 3600 Belgium.,Biomedical Research Institute, Hasselt University, Diepenbeek, 3590 Belgium
| | - Joris Penders
- Biomedical Research Institute, Hasselt University, Diepenbeek, 3590 Belgium.,Laboratory of Clinical Biology, East-Limburg Hospital, Genk, 3600 Belgium
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY 10032 USA
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium.,Department of Public Health & Primary Care, Occupational & Environmental Medicine, Leuven University, Leuven, Belgium
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24
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van den Berg CB, Chaves I, Herzog EM, Willemsen SP, van der Horst GTJ, Steegers-Theunissen RPM. Early- and late-onset preeclampsia and the DNA methylation of circadian clock and clock-controlled genes in placental and newborn tissues. Chronobiol Int 2017; 34:921-932. [DOI: 10.1080/07420528.2017.1326125] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- C. B. van den Berg
- Department of Obstetrics and Gynecology, Division of Obstetrics & Prenatal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - I. Chaves
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - E. M. Herzog
- Department of Obstetrics and Gynecology, Division of Obstetrics & Prenatal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - S. P. Willemsen
- Department of Obstetrics and Gynecology, Division of Obstetrics & Prenatal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Biostatistics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - G. T. J. van der Horst
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - R. P. M. Steegers-Theunissen
- Department of Obstetrics and Gynecology, Division of Obstetrics & Prenatal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Division of Neonatology, Erasmus University Medical Center, Rotterdam, The Netherlands
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25
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The influence of in vitro fertilization and embryo culture on the embryo epigenetic constituents and the possible consequences in the bovine model. J Dev Orig Health Dis 2017; 8:411-417. [PMID: 28260557 DOI: 10.1017/s2040174417000125] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Medically assisted reproductive technologies, such as in vitro embryo production, are increasingly being used to palliate infertility. Eggs are produced following a hormonal regimen that stimulates the ovaries to produce a large number of oocytes. Collected oocytes are then fertilized in vitro and allowed to develop in vitro until they are either frozen or transferred to mothers. There are controversial reports on the adverse impacts of these technologies on early embryos and their potential long-term effects. Using newly developed technological platforms that enable global gene expression and global DNA methylation profiling, we evaluated gene perturbations caused by such artificial procedures. We know that cells in the early embryo produce all cells in the body and are able to respond to their in vitro environment. However, it is not known whether gene perturbations are part of a normal response to the environment or are due to distress and will have long-term impacts. While the mouse is an established genetic model used for quality control of culture media in clinics, the bovine is a large mono-ovulating mammal with similar embryonic kinetics as humans during the studied developmental window. These model systems are critical to understand the effects of assisted reproduction without the confounding impact of infertility and without the limitations imposed by the scarcity of donated human samples and ethical issues. The data presented in this review come mostly from our own experimentation, publications, and collaborations. Together they demonstrate that the in vitro environment has a significant impact on embryos at the transcriptomic level and at the DNA methylation level.
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26
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de Goede OM, Lavoie PM, Robinson WP. Characterizing the hypomethylated DNA methylation profile of nucleated red blood cells from cord blood. Epigenomics 2016; 8:1481-1494. [PMID: 27687885 DOI: 10.2217/epi-2016-0069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
AIM To provide insight into fetal nucleated red blood cell (nRBC) development using genome-wide DNA methylation (DNAm) profiling. MATERIALS & METHODS The DNAm profile (Illumina 450K array) of cord blood (n = 7) derived nRBCs was compared with B cells, CD4 and CD8 T cells, natural killer cells, granulocytes, monocytes and placenta (n = 5). RESULTS nRBCs and placenta had similarly low array-wide DNAm compared with white blood cells, but their patterns of hypomethylation differed at biologically relevant subsets of the array. High interindividual variability in nRBC DNAm was driven by a negative association between DNAm and nRBC count. CONCLUSION nRBC hypomethylation is likely an epigenetic signature of erythropoiesis rather than of early development. Variability in nRBC DNAm may stem from differences in the cell population's maturity or hematopoietic source.
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Affiliation(s)
- Olivia M de Goede
- Child & Family Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Pascal M Lavoie
- Child & Family Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Wendy P Robinson
- Child & Family Research Institute, Vancouver, British Columbia, V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
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27
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Rahat B, Thakur S, Hamid A, Bagga R, Kaur J. Association of aberrant methylation at promoter regions of tumor suppressor genes with placental pathologies. Epigenomics 2016; 8:767-87. [PMID: 27337502 DOI: 10.2217/epi.16.7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: The resemblance between invasive behavior of cancer cells and placental trophoblasts and the role of aberrant epigenetic regulation in cancer development is well known. Methods: We analyzed the role of promoter region CpG-methylation and H3K9/27me3 of tumor suppressor genes in normal and pathological pregnancies and utilized their CpG-methylation data to search for fetal DNA epigenetic marker in maternal blood. Results: CpG and H3K9/27-methylation associated decreased expression of RASSF1A and APC and increased expression of P16, RB1 and PRKCDBP was observed with advancing normal gestation. Gestational trophoblastic diseases and preeclampsia revealed gene-specific epigenetic deregulation of candidate tumor suppressor genes. Furthermore, APC and PRKCDBP showed the potential to act as fetal DNA epigenetic markers, similar to RASSF1A. Conclusion: Deregulation of methylation of tumor suppressor genes contributes to the development of preeclampsia and gestational trophoblastic diseases. APC and PRKCDBP may act as fetal DNA epigenetic markers for prenatal diagnosis.
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Affiliation(s)
- Beenish Rahat
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Shilpa Thakur
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Abid Hamid
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Rashmi Bagga
- Department of Obstetrics & Gynecology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Jyotdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
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28
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Lendvai Á, Deutsch MJ, Plösch T, Ensenauer R. The peroxisome proliferator-activated receptors under epigenetic control in placental metabolism and fetal development. Am J Physiol Endocrinol Metab 2016; 310:E797-810. [PMID: 26860983 DOI: 10.1152/ajpendo.00372.2015] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/02/2016] [Indexed: 01/09/2023]
Abstract
The placental metabolism can adapt to the environment throughout pregnancy to both the demands of the fetus and the signals from the mother. Such adaption processes include epigenetic mechanisms, which alter gene expression and may influence the offspring's health. These mechanisms are linked to the diversity of prenatal environmental exposures, including maternal under- or overnutrition or gestational diabetes. The peroxisome proliferator-activated receptors (PPARs) are nuclear receptors that contribute to the developmental plasticity of the placenta by regulating lipid and glucose metabolism pathways, including lipogenesis, steroidogenesis, glucose transporters, and placental signaling pathways, thus representing a link between energy metabolism and reproduction. Among the PPAR isoforms, PPARγ appears to be the main modulator of mammalian placentation. Certain fatty acids and lipid-derived moieties are the natural activating PPAR ligands. By controlling the amounts of maternal nutrients that go across to the fetus, the PPARs play an important regulatory role in placenta metabolism, thereby adapting to the maternal nutritional status. As demonstrated in animal studies, maternal nutrition during gestation can exert long-term influences on the PPAR methylation pattern in offspring organs. This review underlines the current state of knowledge on the relationship between environmental factors and the epigenetic regulation of the PPARs in placenta metabolism and offspring development.
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Affiliation(s)
- Ágnes Lendvai
- Center for Liver, Digestive, and Metabolic Diseases, Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Manuel J Deutsch
- Research Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Torsten Plösch
- Department of Obstetrics and Gynecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands;
| | - Regina Ensenauer
- Research Center, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-Universität München, Munich, Germany; Experimental Pediatrics, Department of General Pediatrics, Pediatric Cardiology, and Neonatology, Heinrich-Heine-University Düsseldorf, Dusseldorf, Germany
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29
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Bianco-Miotto T, Mayne BT, Buckberry S, Breen J, Rodriguez Lopez CM, Roberts CT. Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction 2016; 152:R23-30. [PMID: 27026712 PMCID: PMC5064761 DOI: 10.1530/rep-16-0014] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 03/29/2016] [Indexed: 12/20/2022]
Abstract
Epigenetic modifications, and particularly DNA methylation, have been studied in many tissues, both healthy and diseased, and across numerous developmental stages. The placenta is the only organ that has a transient life of 9 months and undergoes rapid growth and dynamic structural and functional changes across gestation. Additionally, the placenta is unique because although developing within the mother, its genome is identical to that of the foetus. Given these distinctive characteristics, it is not surprising that the epigenetic landscape affecting placental gene expression may be different to that in other healthy tissues. However, the role of epigenetic modifications, and particularly DNA methylation, in placental development remains largely unknown. Of particular interest is the fact that the placenta is the most hypomethylated human tissue and is characterized by the presence of large partially methylated domains (PMDs) containing silenced genes. Moreover, how and why the placenta is hypomethylated and what role DNA methylation plays in regulating placental gene expression across gestation are poorly understood. We review genome-wide DNA methylation studies in the human placenta and highlight that the different cell types that make up the placenta have very different DNA methylation profiles. Summarizing studies on DNA methylation in the placenta and its relationship with pregnancy complications are difficult due to the limited number of studies available for comparison. To understand the key steps in placental development and hence what may be perturbed in pregnancy complications requires large-scale genome-wide DNA methylation studies coupled with transcriptome analyses.
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Affiliation(s)
- Tina Bianco-Miotto
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Benjamin T Mayne
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Sam Buckberry
- Harry Perkins Institute of Medical ResearchThe University of Western Australia, Crawley, Western Australia, Australia Plant Energy BiologyARC Centre of Excellence, The University of Western Australia, Crawley, Western Australia, Australia
| | - James Breen
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia Bioinformatics HubUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Carlos M Rodriguez Lopez
- School of Agriculture, Food and WineUniversity of Adelaide, Adelaide, South Australia, Australia
| | - Claire T Roberts
- Robinson Research InstituteUniversity of Adelaide, Adelaide, South Australia, Australia School of MedicineUniversity of Adelaide, Adelaide, South Australia, Australia
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30
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Januar V, Desoye G, Novakovic B, Cvitic S, Saffery R. Epigenetic regulation of human placental function and pregnancy outcome: considerations for causal inference. Am J Obstet Gynecol 2015; 213:S182-96. [PMID: 26428498 DOI: 10.1016/j.ajog.2015.07.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetic mechanisms, often defined as regulating gene activity independently of underlying DNA sequence, are crucial for healthy development. The sum total of epigenetic marks within a cell or tissue (the epigenome) is sensitive to environmental influence, and disruption of the epigenome in utero has been associated with adverse pregnancy outcomes. Not surprisingly, given its multifaceted functions and important role in regulating pregnancy outcome, the placenta shows unique epigenetic features. Interestingly however, many of these are only otherwise seen in human malignancy (the pseudomalignant placental epigenome). Epigenetic variation in the placenta is now emerging as a candidate mediator of environmental influence on placental functioning and a key regulator of pregnancy outcome. However, replication of findings is generally lacking, most likely due to small sample sizes and a lack of standardization of analytical approaches. Defining DNA methylation "signatures" in the placenta associated with maternal and fetal outcomes offers tremendous potential to improve pregnancy outcomes, but care must be taken in interpretation of findings. Future placental epigenetic research would do well to address the issues present in epigenetic epidemiology more generally, including careful consideration of sample size, potentially confounding factors, issues of tissue heterogeneity, reverse causation, and the role of genetics in modulating epigenetic profile. The importance of animal or in vitro models in establishing a functional role of epigenetic variation identified in human beings, which is key to establishing causation, should not be underestimated.
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Affiliation(s)
- Vania Januar
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Boris Novakovic
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Silvija Cvitic
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Pediatrics, University of Melbourne, Parkville, Australia.
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31
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Guo J, He H, Liu Q, Zhang F, Lv J, Zeng T, Gu N, Wu Q. Identification and Epigenetic Analysis of a Maternally Imprinted Gene Qpct. Mol Cells 2015; 38:859-65. [PMID: 26447138 PMCID: PMC4625067 DOI: 10.14348/molcells.2015.0098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 11/27/2022] Open
Abstract
Most imprinted genes are concerned with embryonic development, especially placental development. Here, we identified a placenta-specific imprinted gene Qpct. Our results show that Qpct is widely expressed during early embryonic development and can be detected in the telecephalon, midbrain, and rhombencephalon at E9.5b-E11.5. Moreover, Qpct is strikingly expressed in the brain, lung and liver in E15.5. Expression signals for Qpct achieved a peak at E15.5 during placental development and were only detected in the labyrinth layer in E15.5 placenta. ChIP assay results suggest that the modification of histone H3K4me3 can result in maternal activating of Qpct.
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Affiliation(s)
- Jing Guo
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Hongjuan He
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Qi Liu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Fengwei Zhang
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Jie Lv
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Tiebo Zeng
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Ning Gu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
| | - Qiong Wu
- School of Life Science and Technology, State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology, 150001, Heilongjiang,
China
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32
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Shan N, Zhang X, Xiao X, Zhang H, Tong C, Luo X, Chen Y, Liu X, Yin N, Deng Q, Qi H. Laminin α4 (LAMA4) expression promotes trophoblast cell invasion, migration, and angiogenesis, and is lowered in preeclamptic placentas. Placenta 2015; 36:809-20. [DOI: 10.1016/j.placenta.2015.04.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/28/2015] [Accepted: 04/15/2015] [Indexed: 12/11/2022]
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33
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Abstract
This review provides an overview of the unique features of DNA methylation in the human placenta. We discuss the importance of understanding placental development, structure, and function in the interpretation of DNA methylation data. Examples are given of how DNA methylation is important in regulating placental-specific gene expression, including monoallelic expression and X-chromosome inactivation in the placenta. We also discuss studies of global DNA methylation changes in the context of placental pathology and environmental exposures.
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Affiliation(s)
- Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - E Magda Price
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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34
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Babenko O, Kovalchuk I, Metz GAS. Stress-induced perinatal and transgenerational epigenetic programming of brain development and mental health. Neurosci Biobehav Rev 2014; 48:70-91. [PMID: 25464029 DOI: 10.1016/j.neubiorev.2014.11.013] [Citation(s) in RCA: 324] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 09/19/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Research efforts during the past decades have provided intriguing evidence suggesting that stressful experiences during pregnancy exert long-term consequences on the future mental wellbeing of both the mother and her baby. Recent human epidemiological and animal studies indicate that stressful experiences in utero or during early life may increase the risk of neurological and psychiatric disorders, arguably via altered epigenetic regulation. Epigenetic mechanisms, such as miRNA expression, DNA methylation, and histone modifications are prone to changes in response to stressful experiences and hostile environmental factors. Altered epigenetic regulation may potentially influence fetal endocrine programming and brain development across several generations. Only recently, however, more attention has been paid to possible transgenerational effects of stress. In this review we discuss the evidence of transgenerational epigenetic inheritance of stress exposure in human studies and animal models. We highlight the complex interplay between prenatal stress exposure, associated changes in miRNA expression and DNA methylation in placenta and brain and possible links to greater risks of schizophrenia, attention deficit hyperactivity disorder, autism, anxiety- or depression-related disorders later in life. Based on existing evidence, we propose that prenatal stress, through the generation of epigenetic alterations, becomes one of the most powerful influences on mental health in later life. The consideration of ancestral and prenatal stress effects on lifetime health trajectories is critical for improving strategies that support healthy development and successful aging.
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Affiliation(s)
- Olena Babenko
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4; Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4
| | - Gerlinde A S Metz
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, 4401 University Drive, Lethbridge, AB, Canada T1K 3M4
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Głodek A, Kubiczak MJ, Walkowiak GP, Nowak-Markwitz E, Jankowska A. Methylation status of human chorionic gonadotropin beta subunit promoter and TFAP2A expression as factors regulating CGB gene expression in placenta. Fertil Steril 2014; 102:1175-1182.e8. [PMID: 25063728 DOI: 10.1016/j.fertnstert.2014.06.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 06/09/2014] [Accepted: 06/11/2014] [Indexed: 12/26/2022]
Abstract
OBJECTIVE To evaluate mechanisms regulating the expression of CGB genes in placental tissues from uncomplicated pregnancies and chorionic samples from spontaneous miscarriages. DESIGN Molecular analyses in human samples. SETTING Laboratory of molecular biology. PATIENT(S) Nine placental samples from term deliveries and 21 chorionic samples from miscarriages at 7-13 weeks of gestation. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) The expression level of CGBs and genes encoding SP1, SP3, and AP2 transcription factors was analyzed using quantitative polymerase chain reaction (qPCR). The methylation status of the CGBs' promoter regions was determined using methylation-specific PCR. RESULT(S) The experiments showed significant differences in CGBs' expression and their regulation between placental and chorionic tissues. In placental tissues and chorionic tissues from 7 to 9 weeks of gestation, the expression level of CGBs was shown to be associated with the amount of TFAP2A transcripts. It was also demonstrated that variation in the expression level of CGB genes relies on changes in methylation of CGB3-9 and CGB1-2 promoter sequences. CONCLUSION(S) During pregnancy, regulation of hCG beta subunit genes expression correlates with both methylation of their promoters and TFAP2A expression level. The results suggest that these factors may be very influential in the early stages of pregnancy and may be associated with pregnancy outcome.
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Affiliation(s)
- Aleksandra Głodek
- Department of Cell Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Marta J Kubiczak
- Department of Cell Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Grzegorz P Walkowiak
- Department of Cell Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewa Nowak-Markwitz
- Gynecologic Oncology Department, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Jankowska
- Department of Cell Biology, Poznan University of Medical Sciences, Poznan, Poland.
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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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Reamon-Buettner SM, Buschmann J, Lewin G. Identifying placental epigenetic alterations in an intrauterine growth restriction (IUGR) rat model induced by gestational protein deficiency. Reprod Toxicol 2014; 45:117-24. [PMID: 24607647 DOI: 10.1016/j.reprotox.2014.02.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 02/04/2014] [Accepted: 02/26/2014] [Indexed: 12/13/2022]
Abstract
Poor maternal nutrition during gestation can lead to intrauterine growth retardation (IUGR), a main cause of low birth weight associated with high neonatal morbidity and mortality. Such early uterine environmental exposures can impact the neonatal epigenome to render later-in-life disease susceptibility. We established in Wistar Han rats a mild IUGR model induced by gestational protein deficiency (i.e. 9% crude protein in low protein diet vs. 21% in control, from GD 0 to 21) to identify alterations in gene expression and methylation patterns in certain genes implicated in human IUGR or in placental development. We found differential gene expression of Wnt2 and Dlk1 between IUGR and control. Notably, Wnt2 exhibited significant decrease while Dlk1 increase in IUGR placentas, correlating to decrease in fetal and placental weight. Methylation patterns encompassing 30 CpGs in the Wnt2 promoter region revealed variability in both IUGR and control placentas, but a site-specific hypomethylation was evident in IUGR placentas. Our present findings further support a key role of maternal gestational nutrition in defining the neonatal epigenome.
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Affiliation(s)
- Stella Marie Reamon-Buettner
- Toxicology and Environmental Hygiene, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany.
| | - Jochen Buschmann
- Toxicology and Environmental Hygiene, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany
| | - Geertje Lewin
- Toxicology and Environmental Hygiene, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs Strasse 1, 30625 Hannover, Germany
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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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Logan PC, Mitchell MD, Lobie PE. DNA methyltransferases and TETs in the regulation of differentiation and invasiveness of extra-villous trophoblasts. Front Genet 2013; 4:265. [PMID: 24363660 PMCID: PMC3849743 DOI: 10.3389/fgene.2013.00265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/15/2013] [Indexed: 01/21/2023] Open
Abstract
Specialized cell types of trophoblast cells form the placenta in which each cell type has particular properties of proliferation and invasion. The placenta sustains the growth of the fetus throughout pregnancy and any aberrant trophoblast differentiation or invasion potentially affects the future health of the child and adult. Recently, the field of epigenetics has been applied to understand differentiation of trophoblast lineages and embryonic stem cells (ESC), from fertilization of the oocyte onward. Each trophoblast cell-type has a distinctive epigenetic profile and we will concentrate on the epigenetic mechanism of DNA methyltransferases and TETs that regulate DNA methylation. Environmental factors affecting the mother potentially regulate the DNA methyltransferases in trophoblasts, and so do steroid hormones, cell cycle regulators, such as p53, and cytokines, especially interlukin-1β. There are interesting questions of why trophoblast genomes are globally hypomethylated yet specific genes can be suppressed by hypermethylation (in general, tumor suppressor genes, such as E-cadherin) and how invasive cell-types are liable to have condensed chromatin, as in metastatic cancer cells. Future work will attempt to understand the interactive nature of all epigenetic mechanisms together and their effect on the complex biological system of trophoblast differentiation and invasion in normal as well as pathological conditions.
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Affiliation(s)
- Philip C Logan
- The Liggins Institute, The University of Auckland Auckland, New Zealand
| | - Murray D Mitchell
- University of Queensland Centre for Clinical Research, University of Queensland Brisbane, QLD, Australia
| | - Peter E Lobie
- Cancer Science Institute of Singapore, National University of Singapore Singapore, Singapore
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40
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Vilahur N, Baccarelli AA, Bustamante M, Agramunt S, Byun HM, Fernandez MF, Sunyer J, Estivill X. Storage conditions and stability of global DNA methylation in placental tissue. Epigenomics 2013; 5:341-8. [PMID: 23750648 DOI: 10.2217/epi.13.29] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
AIM The placenta is an informative and easily available tissue for many epidemiological studies. We analyzed the extent to which storage delay affects DNA methylation. MATERIAL & METHODS Biopsies from two placentas were sequentially stored at -80°C after standing at room temperature for 30 min, 1 h, 2 h, 6 h and 24 h. Global DNA methylation was measured by bisulfite pyrosequencing of repetitive elements and the luminometric methylation assay. RESULTS Small changes in global DNA methylation in relation to time-to-storage were observed by pyrosequencing, with a coefficient of variation (COV) of 2.49% (placenta 1) and 2.86% (placenta 2), similar to the mean technical variation observed for pyrosequencing (COV: 1.91 and 1.51%, respectively). A luminometric methylation assay yielded more variable results in the two placentas analyzed, both among time points (COV: 9.13 and 10.35%, respectively) and technical replicates (COV: 11.60 and 9.80%, respectively). CONCLUSION Global DNA methylation is stable at room temperature. However, some techniques to measure methylation might be confounded by DNA degradation caused by a delay in storage.
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Affiliation(s)
- Nadia Vilahur
- Center for Research in Environmental Epidemiology CREAL, Barcelona, Catalonia, Spain.
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Hernandez VJ, Weng J, Ly P, Pompey S, Dong H, Mishra L, Schwarz M, Anderson RGW, Michaely P. Cavin-3 dictates the balance between ERK and Akt signaling. eLife 2013; 2:e00905. [PMID: 24069528 PMCID: PMC3780650 DOI: 10.7554/elife.00905] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 08/14/2013] [Indexed: 12/22/2022] Open
Abstract
Cavin-3 is a tumor suppressor protein of unknown function. Using both in vivo and in vitro approaches, we show that cavin-3 dictates the balance between ERK and Akt signaling. Loss of cavin-3 increases Akt signaling at the expense of ERK, while gain of cavin-3 increases ERK signaling at the expense Akt. Cavin-3 facilitates signal transduction to ERK by anchoring caveolae to the membrane skeleton of the plasma membrane via myosin-1c. Caveolae are lipid raft specializations that contain an ERK activation module and loss of the cavin-3 linkage reduces the abundance of caveolae, thereby separating this ERK activation module from signaling receptors. Loss of cavin-3 promotes Akt signaling through suppression of EGR1 and PTEN. The in vitro consequences of the loss of cavin-3 include induction of Warburg metabolism (aerobic glycolysis), accelerated cell proliferation, and resistance to apoptosis. The in vivo consequences of cavin-3 knockout are increased lactate production and cachexia. DOI:http://dx.doi.org/10.7554/eLife.00905.001.
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Affiliation(s)
- Victor J Hernandez
- Department of Cell Biology , University of Texas Southwestern Medical Center , Dallas , United States
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Aldinger KA, Plummer JT, Levitt P. Comparative DNA methylation among females with neurodevelopmental disorders and seizures identifies TAC1 as a MeCP2 target gene. J Neurodev Disord 2013; 5:15. [PMID: 23759142 PMCID: PMC3700820 DOI: 10.1186/1866-1955-5-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 05/22/2013] [Indexed: 12/26/2022] Open
Abstract
Background Several proteins involved in epigenetic regulation cause syndromic neurodevelopmental disorders when human genes are mutated. More general involvement of epigenetic mechanisms in neurodevelopmental phenotypes is unclear. Methods In an attempt to determine whether DNA methylation differentiates clinical subgroups, profiling was performed on bisulfite converted DNA from lymphoblastoid cell lines (LCLs) in discovery (n = 20) and replication (n = 40) cohorts of females with Rett syndrome (RTT; n = 18), autism (AUT; n = 17), seizure disorder (SEZ; n = 6), and controls (CTL; n = 19) using Illumina HumanMethylation27 arrays. TAC1 CpGs were validated using a Sequenom EpiTYPER assay and expression was measured in LCLs and postmortem brain. Chromatin immunoprecipitation was performed in HEK cells. Cells were treated with valproic acid and MeCP2 binding was assessed. Results Two female-only cohorts were analyzed. DNA methylation profiling in a discovery cohort identified 40 CpGs that exhibited statistically significant differential methylation (≥15%) between clinical groups (P <0.01). Hierarchical clustering and principal components analysis suggested neurodevelopmental groups were distinct from CTL, but not from each other. In a larger and more heterogeneous replication cohort, these 40 CpG sites suggested no clear difference between clinical groups. Pooled analysis of DNA methylation across all 60 samples suggested only four differentially methylated CpG sites (P <0.0005), including TAC1. TAC1 promoter CpG hypermethylation was validated in AUT and SEZ (P <0.005). Analyzed for the first time in postmortem brain, TAC1 expression was reduced in cingulate cortex in RTT and AUT+SEZ (P = 0.003). However, no significant difference in TAC1 promoter CpG methylation was detected in RTT and AUT+SEZ brains. Additional molecular analyses revealed that MeCP2 binds directly to the TAC1 promoter and is sensitive to antiepileptic drug treatment. Conclusion These data suggest that DNA methylation is not widely altered in RTT, consistent with subtle changes in gene expression previously observed. However, TAC1 may be an important target for further functional analyses in RTT. Studies of larger sample cohorts using primary cells that also consider shared clinical features and drug treatments may be required to address apparent subtle disruptions of DNA methylation in neurodevelopmental disorders.
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Affiliation(s)
- Kimberly A Aldinger
- Zilkha Neurogenetic Institute, Keck School of Medicine of USC, 1501 San Pablo Street, Los Angeles, CA 90089, USA.
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Janssen BG, Godderis L, Pieters N, Poels K, Kiciński M, Cuypers A, Fierens F, Penders J, Plusquin M, Gyselaers W, Nawrot TS. Placental DNA hypomethylation in association with particulate air pollution in early life. Part Fibre Toxicol 2013; 10:22. [PMID: 23742113 PMCID: PMC3686623 DOI: 10.1186/1743-8977-10-22] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 05/27/2013] [Indexed: 12/13/2022] Open
Abstract
Background There is evidence that altered DNA methylation is an important epigenetic mechanism in prenatal programming and that developmental periods are sensitive to environmental stressors. We hypothesized that exposure to fine particles (PM2.5) during pregnancy could influence DNA methylation patterns of the placenta. Methods In the ENVIRONAGE birth cohort, levels of 5’-methyl-deoxycytidine (5-mdC) and deoxycytidine (dC) were quantified in placental DNA from 240 newborns. Multiple regression models were used to study placental global DNA methylation and in utero exposure to PM2.5 over various time windows during pregnancy. Results PM2.5 exposure during pregnancy averaged (25th-75th percentile) 17.4 (15.4-19.3) μg/m3. Placental global DNA methylation was inversely associated with PM2.5 exposures during whole pregnancy and relatively decreased by 2.19% (95% confidence interval [CI]: -3.65, -0.73%, p = 0.004) for each 5 μg/m3 increase in exposure to PM2.5. In a multi-lag model in which all three trimester exposures were fitted as independent variables in the same regression model, only exposure to PM2.5 during trimester 1 was significantly associated with lower global DNA methylation (-2.13% per 5 μg/m3 increase, 95% CI: -3.71, -0.54%, p = 0.009). When we analyzed shorter time windows of exposure within trimester 1, we observed a lower placental DNA methylation at birth during all implantation stages but exposure during the implantation range (6-21d) was strongest associated (-1.08% per 5 μg/m3 increase, 95% CI: -1.80, -0.36%, p = 0.004). Conclusions We observed a lower degree of placental global DNA methylation in association with exposure to particulate air pollution in early pregnancy, including the critical stages of implantation. Future studies should elucidate genome-wide and gene-specific methylation patterns in placental tissue that could link particulate exposure during in utero life and early epigenetic modulations.
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Wang L, Feng Y, Zou S, Brännström M, He L, Billig H, Shao R. Linking DNA methylation to the onset of human tubal ectopic pregnancy. Am J Transl Res 2013; 5:116-125. [PMID: 23573357 PMCID: PMC3612508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Accepted: 03/02/2013] [Indexed: 06/02/2023]
Abstract
Ectopic pregnancy is a common reproductive disorder of unknown etiology and is a leading cause of maternal and fetal mortality. Because of the asymptomatic nature of early tubal ectopic pregnancy and the lack of specific biomarkers for early diagnosis, a better understanding of the complex cellular and molecular interactions that contribute to tubal ectopic pregnancy is required. DNA methylation is the most studied epigenetic process in various tissues and cells, and the goal of this article is to provide a brief review of recent work describing the potential mechanisms of DNA methylation and the biological function of such methylation in normal intrauterine pregnancy. Further, novel findings from our laboratory highlight the possible role of DNA methylation in human Fallopian tube dysfunction and suggest a possible correlation between methylation of estrogen receptor α in women and the occurrence of tubal ectopic pregnancies.
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Affiliation(s)
- Lei Wang
- Institutes of Biomedical Sciences at Fudan UniversityShanghai 200032, China
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong UniversityShanghai 200032, China
| | - Yi Feng
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of GothenburgGothenburg 40530, Sweden
- Department of Integrative Medicine and Neurobiology, State Key Lab of Medical Neurobiology, Shanghai Medical College and Institute of Acupuncture Research (WHO Collaborating Center for Traditional Medicine), Institute of Brain Science, Fudan UniversityShanghai 200032, China
| | - Shien Zou
- Department of Gynecology, Obstetrics and Gynecology Hospital of Fudan UniversityShanghai 200011, China
| | - Mats Brännström
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, The Sahlgrenska Academy, University of GothenburgGothenburg 41345, Sweden
| | - Lin He
- Institutes of Biomedical Sciences at Fudan UniversityShanghai 200032, China
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong UniversityShanghai 200032, China
| | - Håkan Billig
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of GothenburgGothenburg 40530, Sweden
| | - Ruijin Shao
- Department of Physiology/Endocrinology, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of GothenburgGothenburg 40530, Sweden
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Abstract
Tissue-specific DNA methylation is found at promoters, enhancers, and CpG islands but also over larger genomic regions. In most human tissues, the vast majority of the genome is highly methylated (>70%). Recently, sequencing of bisulfite-treated DNA (MethylC-seq) has revealed large partially methylated domains (PMDs) in some human cell lines. PMDs cover up to 40% of the genome and are associated with gene repression and inactive chromatin marks. However, to date, only cultured cells and cancers have shown evidence for PMDs. Here, we performed MethylC-seq in full-term human placenta and demonstrate it is the first known normal tissue showing clear evidence of PMDs. We found that PMDs cover 37% of the placental genome, are stable throughout gestation and between individuals, and can be observed with lower sensitivity in Illumina 450K Infinium data. RNA-seq analysis confirmed that genes in PMDs are repressed in placenta. Using a hidden Markov model to map placental PMDs genome-wide and compare them to PMDs in other cell lines, we found that genes within placental PMDs have tissue-specific functions. For regulatory regions, methylation levels in promoter CpG islands are actually higher for genes within placental PMDs, despite the lower overall methylation of surrounding regions. Similar to PMDs, polycomb-regulated regions are hypomethylated but smaller and distinct from PMDs, with some being hypermethylated in placenta compared with other tissues. These results suggest that PMDs are a developmentally dynamic feature of the methylome that are relevant for understanding both normal development and cancer and may be of use as epigenetic biomarkers.
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Rull K, Christiansen OB, Nagirnaja L, Steffensen R, Margus T, Laan M. A modest but significant effect of CGB5 gene promoter polymorphisms in modulating the risk of recurrent miscarriage. Fertil Steril 2013; 99:1930-6.e6. [PMID: 23499152 PMCID: PMC3698440 DOI: 10.1016/j.fertnstert.2013.02.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 02/08/2013] [Accepted: 02/08/2013] [Indexed: 11/25/2022]
Abstract
Objective To confirm the effect of single nucleotide polymorphisms (SNPs) in chorionic gonadotropin beta (CGB) genes in modulating the susceptibility to recurrent miscarriage (RM) in Danes and in a meta-analysis across Danes and the discovery samples from Estonia and Finland. Design Case-control association study, restriction fragment length polymorphism genotyping, resequencing. Setting Fertility clinics at the Rigshospitalet, Copenhagen, and Aalborg Hospital, Aalborg, Denmark. Patient(s) Four hundred fifty Danish women and men from couples with RM and 119 women with children and no miscarriages in new study. A total of 634 women and men from RM couples and 314 female controls in a combined study of Estonians, Finns, and Danes. Intervention(s) None. Main Outcome Measure(s) Distribution of CGB5 and CGB8 allele and haplotype frequencies in patients and controls. Result(s) For the majority of studied SNPs, the allelic and haplotypic distribution differed statistically between the Danish and the previous Estonian-Finnish sample. In Danes, two CGB5 promoter SNPs (c5-155; c5-142) exhibited a nonsignificant trend for higher allele frequency in fertile women compared with RM patients. The meta-analysis of results from three populations confirmed a modest but significant effect on carriage of c5-155C (odds ratio = 0.64; 95% confidence interval [CI] 0.44–0.94) and c5-142A (odds ratio = 0.66; 95% CI, 0.45–0.94) variants in reducing the risk of RM. None of the investigated genetic variants in the CGB8 gene was associated with RM. Conclusion(s) Carriage of particular variants in the promoter of the CGB5 gene seems to protect against RM. No common genetic variants in CGB5 and CGB8 were associated with increased RM susceptibility in the studied North European populations.
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Affiliation(s)
- Kristiina Rull
- Human Molecular Genetics Research Group, Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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Koestler DC, Christensen BC, Marsit CJ, Kelsey KT, Houseman EA. Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures. Stat Appl Genet Mol Biol 2013; 12:225-40. [PMID: 23468465 DOI: 10.1515/sagmb-2012-0068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation is a well-recognized epigenetic mechanism that has been the subject of a growing body of literature typically focused on the identification and study of profiles of DNA methylation and their association with human diseases and exposures. In recent years, a number of unsupervised clustering algorithms, both parametric and non-parametric, have been proposed for clustering large-scale DNA methylation data. However, most of these approaches do not incorporate known biological relationships of measured features, and in some cases, rely on unrealistic assumptions regarding the nature of DNA methylation. Here, we propose a modified version of a recursively partitioned mixture model (RPMM) that integrates information related to the proximity of CpG loci within the genome to inform correlation structures from which subsequent clustering analysis is based. Using simulations and four methylation data sets, we demonstrate that integrating biologically informative correlation structures within RPMM resulted in improved goodness-of-fit, clustering consistency, and the ability to detect biologically meaningful clusters compared to methods which ignore such correlation. Integrating biologically-informed correlation structures to enhance modeling techniques is motivated by the rapid increase in resolution of DNA methylation microarrays and the increasing understanding of the biology of this epigenetic mechanism.
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Affiliation(s)
- Devin C Koestler
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, 1 Medical Center Dr., Lebanon, NH 03756, USA.
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Abstract
Epigenetic modifications to chromatin are essential for the specification and maintenance of cell fate, enabling the same genome to programme a variety of cellular outcomes. Epigenetic modulation of gene expression is also a critical mechanism by which cells stabilize their responses to environmental stimuli, including both nutritional cues and hormonal signalling. Unsurprisingly, epigenetics is proving to be vitally important in fetal development, and this review addresses our current understanding of the roles of epigenetic regulation in the prenatal phase. It is striking that while there has been a major interest in the intersection of fetal health with epigenetics, there has been relatively little discussion in the literature on epigenetic changes in the pregnant woman, and we attempt to redress this balance, drawing on the fragmented but intriguing experimental literature in this field.
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Affiliation(s)
- Jonathan D Best
- CellCentric, Chesterford Research Park, Little Chesterford CB10 1XL, UK
| | - Nessa Carey
- CellCentric, Chesterford Research Park, Little Chesterford CB10 1XL, UK
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5-Aza-dC treatment induces mesenchymal-to-epithelial transition in 1st trimester trophoblast cell line HTR8/SVneo. Biochem Biophys Res Commun 2013; 432:116-22. [PMID: 23376068 DOI: 10.1016/j.bbrc.2013.01.075] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Accepted: 01/18/2013] [Indexed: 11/20/2022]
Abstract
Placental trophoblast invasion involves a cellular transition from epithelial to mesenchymal phenotype. Cytotrophoblasts undergo epithelial to mesenchymal transition (EMT) when differentiating into extravillous trophoblasts and gaining the capacity of invasion. In this research, we investigated the role of DNA methylation in trophoblasts during this EMT. First, using BeWo and HTR8/SVneo cell lines as models of cytotrophoblasts and extravillous trophoblasts, respectively, we analyzed the gene expression and DNA methylation status of the known epithelial marker genes, E-Cadherin and Cytokeratin7. We found that, in HTR8/SVneo cells, both genes were silenced and their promoters hypermethylated, as compared with the high-level gene expression and promoter hypomethylation observed in BeWo cells. This result suggests that dynamic DNA methylation of epithelial marker genes plays a critical role in the trophoblast EMT process. To verify these results, we treated HTR8/SVneo cells with 5-aza-dC, a known inhibitor of DNA methyltransferase, for three days. Five-Aza-dC treatment significantly increased the expression of epithelial marker genes and slightly decreased the expression of mesenchymal genes, as detected by qRT-PCR, immunocytochemistry and Western blot. Furthermore, 5-aza-dC treated HTR8/SVneo cells changed their morphology from mesenchymal into epithelial phenotype, indicating that 5-aza-dC induced mesenchymal to epithelial transition. Lastly, we examined the effect of 5-aza-dC on trophoblast migration and invasion capacity. We applied 5-aza-dC to HTR8/SVneo cells in trans-well cell migration and invasion assays and found that 5-aza-dC treatment decreased trophoblast migration and invasion capacity. In conclusion, DNA methylation of epithelial marker genes represents a molecular mechanism for the process of trophoblast EMT.
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Novakovic B, Saffery R. The ever growing complexity of placental epigenetics – Role in adverse pregnancy outcomes and fetal programming. Placenta 2012; 33:959-70. [DOI: 10.1016/j.placenta.2012.10.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/02/2012] [Accepted: 10/06/2012] [Indexed: 02/01/2023]
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