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Mortillo M, Kennedy EG, Hermetz KM, Burt AA, Marsit CJ. Epigenetic landscape of 5-hydroxymethylcytosine and associations with gene expression in placenta. Epigenetics 2024; 19:2326869. [PMID: 38507502 PMCID: PMC10956631 DOI: 10.1080/15592294.2024.2326869] [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: 09/28/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
5-hydroxymethylcystosine (5hmC), is an intermediate product in the DNA demethylation pathway, but may act as a functional epigenetic modification. We have conducted the largest study of site-specific 5hmC in placenta to date using parallel bisulphite and oxidative bisulphite modification with array-based assessment. Incorporating parallel RNA-sequencing data allowed us to assess associations between 5hmC and gene expression, using expression quantitative trait hydroxymethylation (eQTHM) analysis. We identified ~ 47,000 loci with consistently elevated (systematic) 5hmC proportions. Systematic 5hmC was significantly depleted (p < 0.0001) at CpG islands (CGI), and enriched (p < 0.0001) in 'open sea' regions (CpG >4 kb from CGI). 5hmC was most and least abundant at CpGs in enhancers and active transcription start sites (TSS), respectively (p < 0.05). We identified 499 significant (empirical-p <0.05) eQTHMs within 1 MB of the assayed gene. At most (75.4%) eQTHMs, the proportion of 5hmC was positively correlated with transcript abundance. eQTHMs were significantly enriched among enhancer CpGs and depleted among CpGs in active TSS (p < 0.05 for both). Finally, we identified 107 differentially hydroxymethylated regions (DHMRs, p < 0.05) across 100 genes. Our study provides insight into placental distribution of 5hmC, and sheds light on the functional capacity of this epigenetic modification in placenta.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Elizabeth G. Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Karen M. Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Amber A. Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
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Mortillo M, Kennedy E, Hermetz K, Burt A, Marsit C. Associations between placental hydroxymethylation and birthweight. EPIGENETICS REPORTS 2024; 2:1-7. [PMID: 39091447 PMCID: PMC11290493 DOI: 10.1080/28361512.2024.2376954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 07/02/2024] [Indexed: 08/04/2024]
Abstract
5-hydroxymethylcytosine (5hmC), formed through the ten-eleven translocation (TET) methylcytosine dioxygenase mediated oxidation of 5-methylcytosine (5mC) at cytosine-phosphate-guanine (CpG) dinucleotides, is believed to mainly serve as an intermediate in the DNA demethylation pathway, though recent evidence suggests that 5hmC may also play a functionally relevant role. We have conducted an epigenome-wide association study (EWAS) to assess the association between placenta 5hmC, obtained through parallel bisulfite and oxidative bisulfite modification of DNA and array-based assessment, and newborn birthweight in the Rhode Island Child Health Study (RICHS). We also assessed whether the removal of 5hmC signal impacts the observed results from traditional epigenome-wide studies that rely on BS modification-based (combined 5mC and 5hmC) assessment alone. We identified 5hmC at one CpG in the CUBN gene to be significantly associated with birthweight (FDR < 0.05) and demonstrate that expression of that gene was also associated with birthweight. Comparison of 5hmC+5mC and 5mC EWAS effect estimates reveal a strong correlation (r = 0.77, p < 0.0001). Our study suggests that traditional assessment of 5mC through bisulfite modification alone provides an accurate assessment of CpG-specific DNA methylation for EWAS studies but was unable to provide evidence of widespread associations between placental 5hmC and birthweight.
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Affiliation(s)
- Michael Mortillo
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Elizabeth Kennedy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Karen Hermetz
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Amber Burt
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
| | - Carmen Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University
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Vasconcelos S, Caniçais C, Chuva de Sousa Lopes SM, Marques CJ, Dória S. The role of DNA hydroxymethylation and TET enzymes in placental development and pregnancy outcome. Clin Epigenetics 2023; 15:66. [PMID: 37095555 PMCID: PMC10127343 DOI: 10.1186/s13148-023-01483-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
The placenta is a temporary organ that is essential for supporting mammalian embryo and fetal development. Understanding the molecular mechanisms underlying trophoblast differentiation and placental function may contribute to improving the diagnosis and treatment of obstetric complications. Epigenetics plays a significant role in the regulation of gene expression, particularly at imprinted genes, which are fundamental in the control of placental development. The Ten-Eleven-Translocation enzymes are part of the epigenetic machinery, converting 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). DNA hydroxymethylation is thought to act as an intermediate in the DNA demethylation mechanism and potentially be a stable and functionally relevant epigenetic mark on its own. The role of DNA hydroxymethylation during differentiation and development of the placenta is not fully understood but increasing knowledge in this field will help to evaluate its potential role in pregnancy complications. This review focuses on DNA hydroxymethylation and its epigenetic regulators in human and mouse placental development and function. Additionally, we address 5hmC in the context of genomic imprinting mechanism and in pregnancy complications, such as intrauterine growth restriction, preeclampsia and pregnancy loss. The cumulative findings show that DNA hydroxymethylation might be important for the control of gene expression in the placenta and suggest a dynamic role in the differentiation of trophoblast cell types during gestation.
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Affiliation(s)
- Sara Vasconcelos
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Carla Caniçais
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | | | - C Joana Marques
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal.
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
| | - Sofia Dória
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Porto, Portugal.
- i3S - Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
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Tung PW, Kennedy EM, Burt A, Hermetz K, Karagas M, Marsit CJ. Prenatal lead (Pb) exposure is associated with differential placental DNA methylation and hydroxymethylation in a human population. Epigenetics 2022; 17:2404-2420. [PMID: 36148884 PMCID: PMC9665158 DOI: 10.1080/15592294.2022.2126087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 09/02/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022] Open
Abstract
Prenatal lead (Pb) exposure is associated with adverse developmental outcomes and to epigenetic alterations such as DNA methylation and hydroxymethylation in animal models and in newborn blood. Given the importance of the placenta in foetal development, we sought to examine how prenatal Pb exposure was associated with differential placental DNA methylation and hydroxymethylation and to identify affected biological pathways linked to developmental outcomes. Maternal (n = 167) and infant (n = 172) toenail and placenta (n = 115) samples for prenatal Pb exposure were obtained from participants in a US birth cohort, and methylation and hydroxymethylation data were quantified using the Illumina Infinium MethylationEPIC BeadChip. An epigenome-wide association study was applied to identify differential methylation and hydroxymethylation associated with Pb exposure. Biological functions of the Pb-associated genes were determined by overrepresentation analysis through ConsensusPathDB. Prenatal Pb quantified from maternal toenail, infant toenail, and placenta was associated with 480, 27, and 2 differentially methylated sites (q < 0.05), respectively, with both increases and decreases associated with exposure. Alternatively, we identified 2, 1, and 14 differentially hydroxymethylated site(s) associated with maternal toenail, infant toenail, and placental Pb, respectively, with most showing increases in hydroxymethylation with exposure. Significantly overrepresented pathways amongst genes associated with differential methylation and hydroxymethylation (q < 0.10) included mechanisms pertaining to nervous system and organ development, calcium transport and regulation, and signalling activities. Our results suggest that both methylation and hydroxymethylation in the placenta can be variable based on Pb exposure and that the pathways impacted could affect placental function.
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Affiliation(s)
- Pei Wen Tung
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA, USA
| | - Elizabeth M. Kennedy
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA, USA
| | - Amber Burt
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA, USA
| | - Karen Hermetz
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA, USA
| | - Margaret Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, Lebanon
| | - Carmen J. Marsit
- Gangarosa Department of Environmental Health, Emory University, Atlanta, GA, USA
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Hjort L, Novakovic B, Cvitic S, Saffery R, Damm P, Desoye G. Placental DNA Methylation in pregnancies complicated by maternal diabetes and/or obesity: State of the Art and research gaps. Epigenetics 2022; 17:2188-2208. [PMID: 35950598 DOI: 10.1080/15592294.2022.2111755] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
SUMMARYMaternal diabetes and/or obesity in pregnancy are undoubtedly associated with later disease-risk in the offspring. The placenta, interposed between the mother and the fetus, is a potential mediator of this risk through epigenetic mechanisms, including DNA methylation. In recent years, multiple studies have identified differentially methylated CpG sites in the placental tissue DNA in pregnancies complicated by diabetes and obesity. We reviewed all published original research relevant to this topic and analyzed our findings with the focus of identifying overlaps, contradictions and gaps. Most studies focused on the association of gestational diabetes and/or hyperglycemia in pregnancy and DNA methylation in placental tissue at term. We identified overlaps in results related to specific candidate genes, but also observed a large research gap of pregnancies affected by type 1 diabetes. Other unanswered questions relate to analysis of specific placental cell types and the timing of DNA methylation change in response to diabetes and obesity during pregnancy. Maternal metabolism is altered already in the first trimester involving structural and functional changes in the placenta, but studies into its effects on placental DNA methylation during this period are lacking and urgently needed. Fetal sex is also an important determinant of pregnancy outcome, but only few studies have taken this into account. Collectively, we provide a reference work for researchers working in this large and evolving field. Based on the results of the literature review, we formulate suggestions for future focus of placental DNA methylation studies in pregnancies complicated by diabetes and obesity.
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Affiliation(s)
- Line Hjort
- Dept. of Obstetrics, Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Environmental Epigenetics Group, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Boris Novakovic
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.,Dept. of Pediatrics, Melbourne University, Melbourne, VIC, Australia
| | - Silvija Cvitic
- Department of Pediatrics and Adolescent Medicine, Research Unit of Analytical Mass Spectrometry, Cell Biology and Biochemistry of Inborn Errors of Metabolism, Medical University of Graz, Austria
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria 3052, Australia.,Dept. of Pediatrics, Melbourne University, Melbourne, VIC, Australia
| | - Peter Damm
- Dept. of Obstetrics, Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark.,Dept of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Gernot Desoye
- Dept. of Obstetrics, Center for Pregnant Women with Diabetes, Rigshospitalet, Copenhagen, Denmark.,Dept. of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
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Zhang Z, Lee MK, Perreard L, Kelsey KT, Christensen BC, Salas LA. Navigating the hydroxymethylome: experimental biases and quality control tools for the tandem bisulfite and oxidative bisulfite Illumina microarrays. Epigenomics 2022; 14:139-152. [PMID: 35029129 PMCID: PMC8914583 DOI: 10.2217/epi-2021-0490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.
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Affiliation(s)
- Ze Zhang
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Laurent Perreard
- Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Karl T Kelsey
- Department of Epidemiology, Department of Pathology & Laboratory Medicine, Brown University School of Public Health, Providence, 02912 RI, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Department of Molecular & Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, 03756 NH, USA,Author for correspondence: Tel.: 603 646 5496;
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Joshi P, Vijaykumar A, Enkhmandakh B, Mina M, Shin DG, Bayarsaihan D. Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors. J Biochem 2021; 171:123-129. [PMID: 34676418 DOI: 10.1093/jb/mvab114] [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] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 12/25/2022] Open
Abstract
The dental pulp is critical for the production of odontoblasts to create reparative dentin. In recent years dental pulp has become a promising source of mesenchymal stem cells that are capable of differentiating into multiple cell types. To elucidate the transcriptional control mechanisms specifying the early phases of odontoblast differentiation, we analyzed the DNA demethylation pattern associated with 5-hydroxymethylcytosine (5hmC) in the primary murine dental pulp. 5hmC plays an important role in chromatin accessibility and transcriptional control by modeling a dynamic equilibrium between DNA methylation and demethylation. Our research revealed 5hmC enrichment along genes and non-coding regulatory regions associated with specific developmental pathways in the genome of mouse incisor and molar dental pulp. Although the overall distribution of 5hmC is similar, the intensity and location of the 5hmC peaks significantly differs between the incisor and molar pulp genome, indicating cell type-specific epigenetic variations. Our study suggests that the differential DNA demethylation pattern could account for the distinct regulatory mechanisms underlying the tooth-specific ontogenetic programs.
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Affiliation(s)
- Pujan Joshi
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269, USA
| | - Anushree Vijaykumar
- Department of Craniofacial Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Badam Enkhmandakh
- Center for Regenerative Medicine & Skeletal Development, Department of Reconstructive Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Mina Mina
- Department of Craniofacial Sciences, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
| | - Dong-Guk Shin
- Computer Science and Engineering Department, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269, USA
| | - Dashzeveg Bayarsaihan
- Institute for System Genomics & Center for Regenerative Medicine & Skeletal Development, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030, USA
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DNA 5-hydroxymethylcytosine in pediatric central nervous system tumors may impact tumor classification and is a positive prognostic marker. Clin Epigenetics 2021; 13:176. [PMID: 34538273 PMCID: PMC8451154 DOI: 10.1186/s13148-021-01156-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 08/18/2021] [Indexed: 01/05/2023] Open
Abstract
Background Nucleotide-specific 5-hydroxymethylcytosine (5hmC) remains understudied in pediatric central nervous system (CNS) tumors. 5hmC is abundant in the brain, and alterations to 5hmC in adult CNS tumors have been reported. However, traditional approaches to measure DNA methylation do not distinguish between 5-methylcytosine (5mC) and its oxidized counterpart 5hmC, including those used to build CNS tumor DNA methylation classification systems. We measured 5hmC and 5mC epigenome-wide at nucleotide resolution in glioma, ependymoma, and embryonal tumors from children, as well as control pediatric brain tissues using tandem bisulfite and oxidative bisulfite treatments followed by hybridization to the Illumina Methylation EPIC Array that interrogates over 860,000 CpG loci.
Results Linear mixed effects models adjusted for age and sex tested the CpG-specific differences in 5hmC between tumor and non-tumor samples, as well as between tumor subtypes. Results from model-based clustering of tumors was used to test the relation of cluster membership with patient survival through multivariable Cox proportional hazards regression. We also assessed the robustness of multiple epigenetic CNS tumor classification methods to 5mC-specific data in both pediatric and adult CNS tumors. Compared to non-tumor samples, tumors were hypohydroxymethylated across the epigenome and tumor 5hmC localized to regulatory elements crucial to cell identity, including transcription factor binding sites and super-enhancers. Differentially hydroxymethylated loci among tumor subtypes tended to be hypermethylated and disproportionally found in CTCF binding sites and genes related to posttranscriptional RNA regulation, such as DICER1. Model-based clustering results indicated that patients with low 5hmC patterns have poorer overall survival and increased risk of recurrence. Our results suggest 5mC-specific data from OxBS-treated samples impacts methylation-based tumor classification systems giving new opportunities for further refinement of classifiers for both pediatric and adult tumors. Conclusions We identified that 5hmC localizes to super-enhancers, and genes commonly implicated in pediatric CNS tumors were differentially hypohydroxymethylated. We demonstrated that distinguishing methylation and hydroxymethylation is critical in identifying tumor-related epigenetic changes. These results have implications for patient prognostication, considerations of epigenetic therapy in CNS tumors, and for emerging molecular neuropathology classification approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01156-9.
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Rosenkrantz JL, Gaffney JE, Roberts VHJ, Carbone L, Chavez SL. Transcriptomic analysis of primate placentas and novel rhesus trophoblast cell lines informs investigations of human placentation. BMC Biol 2021; 19:127. [PMID: 34154587 PMCID: PMC8218487 DOI: 10.1186/s12915-021-01056-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Proper placentation, including trophoblast differentiation and function, is essential for the health and well-being of both the mother and baby throughout pregnancy. Placental abnormalities that occur during the early stages of development are thought to contribute to preeclampsia and other placenta-related pregnancy complications. However, relatively little is known about these stages in humans due to obvious ethical and technical limitations. Rhesus macaques are considered an ideal surrogate for studying human placentation, but the unclear translatability of known human placental markers and lack of accessible rhesus trophoblast cell lines can impede the use of this animal model. RESULTS Here, we performed a cross-species transcriptomic comparison of human and rhesus placenta and determined that while the majority of human placental marker genes (HPGs) were similarly expressed, 952 differentially expressed genes (DEGs) were identified between the two species. Functional enrichment analysis of the 447 human-upregulated DEGs, including ADAM12, ERVW-1, KISS1, LGALS13, PAPPA2, PGF, and SIGLEC6, revealed over-representation of genes implicated in preeclampsia and other pregnancy disorders. Additionally, to enable in vitro functional studies of early placentation, we generated and thoroughly characterized two highly pure first trimester telomerase (TERT) immortalized rhesus trophoblast cell lines (iRP-D26 and iRP-D28A) that retained crucial features of isolated primary trophoblasts. CONCLUSIONS Overall, our findings help elucidate the molecular translatability between human and rhesus placenta and reveal notable expression differences in several HPGs and genes implicated in pregnancy complications that should be considered when using the rhesus animal model to study normal and pathological human placentation.
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Affiliation(s)
- Jimi L. Rosenkrantz
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Jessica E. Gaffney
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Victoria H. J. Roberts
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
| | - Lucia Carbone
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Genetics, Oregon National Primate Research Center, Beaverton, OR 97006 USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239 USA
- Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR 97239 USA
| | - Shawn L. Chavez
- Department of Molecular and Medical Genetics, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239 USA
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, 505 NW 185th Avenue, Beaverton, OR 97006 USA
- Department of Obstetrics and Gynecology, Oregon Health and Science University School of Medicine, Portland, OR 97239 USA
- Department of Biomedical Engineering, Oregon Health and Science University School of Medicine, Portland, OR 97239 USA
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Caniçais C, Vasconcelos S, Ramalho C, Marques CJ, Dória S. Deregulation of imprinted genes expression and epigenetic regulators in placental tissue from intrauterine growth restriction. J Assist Reprod Genet 2021; 38:791-801. [PMID: 33389447 PMCID: PMC8079450 DOI: 10.1007/s10815-020-02047-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 12/21/2020] [Indexed: 12/27/2022] Open
Abstract
PURPOSE Intrauterine growth restriction (IUGR) is a fetal growth complication that can be caused by ineffective nutrient transfer from the mother to the fetus via the placenta. Abnormal placental development and function have been correlated with abnormal expression of imprinted genes, which are regulated by epigenetic modifications at imprinting control regions (ICRs). In this study, we analyzed the expression of imprinted genes known to be involved in fetal growth and epigenetic regulators involved in DNA methylation, as well as DNA methylation at the KvDMR1 imprinting control region and global levels of DNA hydroxymethylation, in IUGR cases. METHODS Expression levels of imprinted genes and epigenetic regulators were analyzed in term placental samples from 21 IUGR cases and 9 non-IUGR (control) samples, by RT-qPCR. Additionally, KvDMR1 methylation was analyzed by bisulfite sequencing and combined bisulfite restriction analysis (COBRA) techniques. Moreover, global DNA methylation and hydroxymethylation levels were also measured. RESULTS We observed increased expression of PHLDA2, CDKN1C, and PEG10 imprinted genes and of DNMT1, DNMT3A, DNMT3B, and TET3 epigenetic regulators in IUGR placentas. No differences in methylation levels at the KvDMR1 were observed between the IUGR and control groups; similarly, no differences in global DNA methylation and hydromethylation were detected. CONCLUSION Our study shows that deregulation of epigenetic mechanisms, namely increased expression of imprinted genes and epigenetic regulators, might be associated with IUGR etiology. Therefore, this study adds knowledge to the molecular mechanisms underlying IUGR, which may contribute to novel prediction tools and future therapeutic options for the management of IUGR pregnancies.
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Affiliation(s)
- Carla Caniçais
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Sara Vasconcelos
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
| | - Carla Ramalho
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal
- Department of Obstetrics and Gynecology, Faculty of Medicine, Hospital São João, Porto, Portugal
| | - C Joana Marques
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
| | - Sofia Dória
- Department of Genetics, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.
- i3S-Instituto de Investigação e Inovação em Saúde, Porto, Portugal.
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Palli SR. Epigenetic regulation of post-embryonic development. CURRENT OPINION IN INSECT SCIENCE 2021; 43:63-69. [PMID: 33068783 PMCID: PMC8044252 DOI: 10.1016/j.cois.2020.09.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/09/2020] [Accepted: 09/18/2020] [Indexed: 05/02/2023]
Abstract
Modifications to DNA and core histones influence chromatin organization and expression of the genome. DNA methylation plays a significant role in the regulation of multiple biological processes that regulate behavior and caste differentiation in social insects. Histone modifications play significant roles in the regulation of development and reproduction in other insects. Genes coding for acetyltransferases, deacetylases, methyltransferases, and demethylases that modify core histones have been identified in genomes of multiple insects. Studies on the function and mechanisms of action of some of these enzymes uncovered their contribution to post-embryonic development. The results from studies on epigenetic modifiers could help in the identification of inhibitors of epigenetic modifiers that could be developed to control pests and disease vectors.
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Affiliation(s)
- Subba Reddy Palli
- Department of Entomology, College of Agriculture, Food and Environment, University of Kentucky, S225 Ag. Science N, Lexington, KY 40546, United States.
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12
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Oxidative Bisulfite Sequencing: An Experimental and Computational Protocol. Methods Mol Biol 2020. [PMID: 32822043 DOI: 10.1007/978-1-0716-0876-0_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Bisulfite sequencing (BS-seq) remains the gold standard technique to quantitively map DNA methylation at a single-base resolution. However, BS-seq cannot discriminate between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Oxidative bisulfite sequencing (oxBS-seq) was one of the first techniques that enabled absolute quantification of 5mC and 5hmC at single-base resolution. OxBS-seq uses chemical oxidation of 5hmC prior to bisulfite treatment to provide a direct readout of 5mC; comparison with BS-seq data can then be used to infer 5hmC levels. Here we describe in detail an updated version of our laboratory's oxBS-seq protocol, which uses potassium perruthenate (KRuO4) as an oxidant. We also describe a bioinformatics pipeline designed to handle Illumina short read sequencing data from whole-genome oxBS-seq.
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13
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Roque-Jiménez JA, Mendoza-Martínez GD, Vázquez-Valladolid A, Guerrero-González MDLL, Flores-Ramírez R, Pinos-Rodriguez JM, Loor JJ, Relling AE, Lee-Rangel HA. Supplemental Herbal Choline Increases 5-hmC DNA on Whole Blood from Pregnant Ewes and Offspring. Animals (Basel) 2020; 10:ani10081277. [PMID: 32727060 PMCID: PMC7460248 DOI: 10.3390/ani10081277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 11/24/2022] Open
Abstract
Simple Summary DNA hydroxymethylation (5-hmC) is an epigenetic mechanism that modifies the five positions of cytosine through the addition of a hydroxymethyl group to DNA. In the last decade, the use of herbal products, marketed as dietary supplements or “nutraceuticals” in some countries, has increased rapidly; however, there is a lack of evidence on the extent to which formulas used during pregnancy cause epigenetic changes in the fetus. The aim of this study was to characterize the effects of supplementing an herbal choline source (BCho) on 5-hmC DNA in whole blood from gestating ewes and their offspring. Such data would provide evidence of nutritional programming effects. Abstract Herbal formulas during pregnancy have been used in developing countries. Despite that, the potential effects on the mother and offspring and whether those supplements elicit epigenetic modifications is still unknown. Therefore, our objectives were to determine the effects of supplemental herbal choline source (BCho) on the percentage of 5-hmC in whole blood from gestating ewes and their offspring, as well as determining the milk quality and growth of the offspring. Thirty-five gestating Rambouillet ewes were randomly assigned to five treatments: T1, supplementation of 4 g per day (gd−1) of BCho during the first third of gestation; T2, supplementation of 4 gd−1 of BCho during the second third of gestation; T3, supplementation of 4 gd−1 of BCho during the last third of gestation; T4, supplementation of 4 gd−1 of BCho throughout gestation; and T5, no BCho supplementation (control). For the 5-hmC DNA analysis, whole blood from ewes was sampled before pregnancy and at each third of gestation (50 days). Whole blood from lambs was sampled five weeks after birth. The evaluation of the nutritional programming effects was conducted through the percentages of 5-hmC in the lambs. Compared with other treatments, the whole blood from ewes supplemented during T1 and T4 had the greatest 5-hmC percentages (p < 0.05). However, only ewes fed BCho throughout gestation (T4) maintained the greatest percentages of 5-hmC (p < 0.05). The lamb growth performance indicated that the BCho maternal supplementation did not affect the nutritional programming. However, the lambs born from ewes supplemented during T2 had the greatest 5-hmC percentages (p < 0.05). Our data suggest that ewes supplemented during T4 with BCho increase and maintain the percentages of 5-hmC in whole blood, and the offspring born from ewes supplemented with BCho during T2 maintained the greatest percentages of 5-hmC 35 d after they were born.
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Affiliation(s)
- José Alejandro Roque-Jiménez
- Facultad de Agronomía y Veterinaria, Universidad Autonoma de San Luis Potosí, Carretera Federal 57 Km 14.5, Ejido Palma de la Cruz, Soledad de Graciano Sánchez, San Luis Potosí 78321, Mexico; (J.A.R.-J.); (A.V.-V.); (M.d.l.L.G.-G.)
| | | | - Anayeli Vázquez-Valladolid
- Facultad de Agronomía y Veterinaria, Universidad Autonoma de San Luis Potosí, Carretera Federal 57 Km 14.5, Ejido Palma de la Cruz, Soledad de Graciano Sánchez, San Luis Potosí 78321, Mexico; (J.A.R.-J.); (A.V.-V.); (M.d.l.L.G.-G.)
| | - María de la Luz Guerrero-González
- Facultad de Agronomía y Veterinaria, Universidad Autonoma de San Luis Potosí, Carretera Federal 57 Km 14.5, Ejido Palma de la Cruz, Soledad de Graciano Sánchez, San Luis Potosí 78321, Mexico; (J.A.R.-J.); (A.V.-V.); (M.d.l.L.G.-G.)
| | - Rogelio Flores-Ramírez
- Centro de Investigación Aplicada en Ambiente y Salud, CIACYT—Medicina, Universidad Autonoma de San Luis Potosí, Lomas de San Luis 78210, Mexico;
| | | | - Juan J. Loor
- Department of Animal Sciences, Division of Nutritional Sciences, University of Illinois, 262 Animal Sciences Laboratory, Urbana, IL 61801, USA;
| | - Alejandro Enrique Relling
- Department of Animal Science, The Ohio State University, Ohio Agricultural Research and Development Center (OARDC), Wooster, OH 44691, USA;
| | - Héctor Aarón Lee-Rangel
- Facultad de Agronomía y Veterinaria, Universidad Autonoma de San Luis Potosí, Carretera Federal 57 Km 14.5, Ejido Palma de la Cruz, Soledad de Graciano Sánchez, San Luis Potosí 78321, Mexico; (J.A.R.-J.); (A.V.-V.); (M.d.l.L.G.-G.)
- Correspondence: ; Tel.: +52-444-852-4056
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14
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Zhang Y, Zheng D, Fang Q, Zhong M. Aberrant hydroxymethylation of ANGPTL4 is associated with selective intrauterine growth restriction in monochorionic twin pregnancies. Epigenetics 2020; 15:887-899. [PMID: 32114885 DOI: 10.1080/15592294.2020.1737355] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Selective intrauterine growth restriction (sIUGR) is a severe complication in monochorionic (MC) twin pregnancies, and it carries increased risks of poor prognosis. Current data suggest that vascular anastomoses and unequal placental sharing may be the key contributor to discordant foetal growth. While MC twins derive from a single zygote and have almost identical genetic information, the precise mechanisms remain unknown. DNA hydroxymethylation is a newly discovered epigenetic feature associated with gene regulation and modification. Here, we investigate discordant hydroxymethylation patterns between two placental shares of sIUGR and analyse the potential role of aberrant hydroxymethylation of angiopoietin-like 4 (ANGPTL4) in placental dysplasia. Hydroxymethylation DNA immunoprecipitation (hMeDIP)-chip and mRNA sequencing were performed to identify hydroxymethylation-associated genes. Real-time qPCR, western blotting, and immunohistochemistry were used to confirm ANGPTL4 expression. The mechanisms regulating ANGPTL4 were investigated by cell migration assay, invasion assay, viability assay, and apoptotic ratio assays, western blotting and hMeDIP-qPCR. Decreased ANGPTL4 was detected in the smaller placental shares of sIUGR. ANGPTL4 knockdown suppressed trophoblast invasiveness and migration, which possibly occurred through hypoxia inducible factor 1α (HIF-1α) and HIF-1 signalling pathway. Hypoxia leads to aberrant expression of ANGPTL4 and HIF-1α, positively correlated with their aberrant hydroxymethylation levels in promoter regions. Aberrant hydroxymethylation of ANGPTL4 may contribute to placental impairment by the HIF-1 signalling pathway in smaller placental shares of sIUGR.
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Affiliation(s)
- Yi Zhang
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Dezhong Zheng
- Department of Cardiology, The Third Affiliated Hospital of Southern Medical University, Southern Medical University , Guangzhou, China.,Department of Cardiology, Nanfang Hospital, Southern Medical University , Guangzhou, China
| | - Qun Fang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Sun Yat-sen University, Sun Yat-sen University , Guangzhou, China
| | - Mei Zhong
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University , Guangzhou, China
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15
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Wilkins OM, Johnson KC, Houseman EA, King JE, Marsit CJ, Christensen BC. Genome-wide characterization of cytosine-specific 5-hydroxymethylation in normal breast tissue. Epigenetics 2019; 15:398-418. [PMID: 31842685 PMCID: PMC7153548 DOI: 10.1080/15592294.2019.1695332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Despite recent evidence that 5-hydroxymethylcytosine (5hmC) possesses roles in gene regulation distinct from 5-methylcytosine (5mC), relatively little is known regarding the functions of 5hmC in mammalian tissues. To address this issue, we utilized an approach combining both paired bisulfite (BS) and oxidative bisulfite (oxBS) DNA treatment, to resolve genome-wide patterns of 5hmC and 5mC in normal breast tissue from disease-free women. Although less abundant than 5mC, 5hmC was differentially distributed, and consistently enriched among breast-specific enhancers and transcriptionally active chromatin. In contrast, regulatory regions associated with transcriptional inactivity, such as heterochromatin and repressed Polycomb regions, were relatively depleted of 5hmC. Gene regions containing abundant 5hmC were significantly associated with lactate oxidation, immune cell function, and prolactin signaling pathways. Furthermore, genes containing abundant 5hmC were enriched among those actively transcribed in normal breast tissue. Finally, in independent data sets, normal breast tissue 5hmC was significantly enriched among CpG loci demonstrated to have altered methylation in pre-invasive breast cancer and invasive breast tumors. Primarily, our findings identify genomic loci containing abundant 5hmC in breast tissues and provide a genome-wide map of nucleotide-level 5hmC in normal breast tissue. Additionally, these data suggest 5hmC may participate in gene regulatory programs that are dysregulated during breast-related carcinogenesis.
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Affiliation(s)
- Owen M Wilkins
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - E Andres Houseman
- Department of Biostatistics, College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA
| | - Jessica E King
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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16
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Kochmanski J, Savonen C, Bernstein AI. A Novel Application of Mixed Effects Models for Reconciling Base-Pair Resolution 5-Methylcytosine and 5-Hydroxymethylcytosine Data in Neuroepigenetics. Front Genet 2019; 10:801. [PMID: 31552098 PMCID: PMC6748167 DOI: 10.3389/fgene.2019.00801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/31/2019] [Indexed: 12/01/2022] Open
Abstract
Epigenetic marks operate at multiple chromosomal levels to regulate gene expression, from direct covalent modification of DNA to three-dimensional chromosomal structure. Research has shown that 5-methylcytosine (5-mC) and its oxidized form, 5-hydroxymethylcytosine (5-hmC), are stable epigenetic marks with distinct genomic distributions and separate regulatory functions. In addition, recent data indicate that 5-hmC plays a critical regulatory role in the mammalian brain, emphasizing the importance of considering this alternative DNA modification in the context of neuroepigenetics. Traditional bisulfite (BS) treatment-based methods to measure the methylome are not able to distinguish between 5-mC and 5-hmC, meaning much of the existing literature does not differentiate these two DNA modifications. Recently developed methods, including Tet-assisted bisulfite treatment and oxidative bisulfite treatment, allow for differentiation of 5-hmC and/or 5-mC levels at base-pair resolution when combined with next-generation sequencing or methylation arrays. Despite these technological advances, there remains a lack of clarity regarding the appropriate statistical methods for integration of 5-mC and 5-hmC data. As a result, it can be difficult to determine the effects of an experimental treatment on 5-mC and 5-hmC dynamics. Here, we propose a statistical approach involving mixed effects to simultaneously model paired 5-mC and 5-hmC data as repeated measures. We tested this approach using publicly available BS/oxidative bisulfite-450K array data and showed that our new approach detected far more CpG probes with paired changes in 5-mC and 5-hmC by Alzheimer’s disease status (n = 14,183 probes) compared with the overlapping differential probes generated from separate models for each epigenetic mark (n = 68). Of note, all 68 of the overlapping probe IDs from the separate models were also significant in our new modeling approach, supporting the sensitivity of our new analysis method. Using the proposed approach, it will be possible to determine the effects of an experimental treatment on both 5-mC and 5-hmC at the base-pair level.
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Affiliation(s)
- Joseph Kochmanski
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Candace Savonen
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Alison I Bernstein
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
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17
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Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, Marsit C, Lu AT, Ritz B, Bohlin J, Gjessing HK, Harris JR, Magnus P, Binder AM, Robinson WP, Jugessur A, Horvath S. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging (Albany NY) 2019; 11:4238-4253. [PMID: 31235674 PMCID: PMC6628997 DOI: 10.18632/aging.102049] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
The human pan-tissue epigenetic clock is widely used for estimating age across the entire lifespan, but it does not lend itself well to estimating gestational age (GA) based on placental DNAm methylation (DNAm) data. We replicate previous findings demonstrating a strong correlation between GA and genome-wide DNAm changes. Using substantially more DNAm arrays (n=1,102 in the training set) than a previous study, we present three new placental epigenetic clocks: 1) a robust placental clock (RPC) which is unaffected by common pregnancy complications (e.g., gestational diabetes, preeclampsia), and 2) a control placental clock (CPC) constructed using placental samples from pregnancies without known placental pathology, and 3) a refined RPC for uncomplicated term pregnancies. These placental clocks are highly accurate estimators of GA based on placental tissue; e.g., predicted GA based on RPC is highly correlated with actual GA (r>0.95 in test data, median error less than one week). We show that epigenetic clocks derived from cord blood or other tissues do not accurately estimate GA in placental samples. While fundamentally different from Horvath's pan-tissue epigenetic clock, placental clocks closely track fetal age during development and may have interesting applications.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Samantha L. Wilson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Victor Yuan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Amber Burt
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Carmen Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K. Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexandra M. Binder
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Wendy P. Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
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18
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Slynko A, Benner A. Statistical methods for classification of 5hmC levels based on the Illumina Inifinium HumanMethylation450 (450k) array data, under the paired bisulfite (BS) and oxidative bisulfite (oxBS) treatment. PLoS One 2019; 14:e0218103. [PMID: 31194780 PMCID: PMC6563990 DOI: 10.1371/journal.pone.0218103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 05/27/2019] [Indexed: 12/22/2022] Open
Abstract
Hydroxymethylcytosine (5hmC) methylation is a well-known epigenetic mark that is involved in gene regulation and may impact genome stability. To investigate a possible role of 5hmC in cancer development and progression, one must be able to detect and quantify its level first. In this paper, we address the issue of 5hmC detection at a single base resolution, starting with consideration of the well-established 5hmC measure Δβ and, in particular, with an analysis of its properties, both analytically and empirically. Then we propose several alternative hydroxymethylation measures and compare their properties with those of Δβ. In the absence of a gold standard, the (pairwise) resemblance of those 5hmC measures to Δβ is characterized by means of a similarity analysis and relative accuracy analysis. All results are illustrated on matched healthy and cancer tissue data sets as derived by means of bisulfite (BS) and oxidative bisulfite converting (oxBS) procedures.
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Affiliation(s)
- Alla Slynko
- Department of Statistics and Actuarial Science, University of Waterloo, Waterloo, Canada
- * E-mail:
| | - Axel Benner
- Division of Biostatistics, German Cancer Research Center, Heidelberg, Germany
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19
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Apicella C, Ruano CSM, Méhats C, Miralles F, Vaiman D. The Role of Epigenetics in Placental Development and the Etiology of Preeclampsia. Int J Mol Sci 2019; 20:ijms20112837. [PMID: 31212604 PMCID: PMC6600551 DOI: 10.3390/ijms20112837] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/03/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022] Open
Abstract
In this review, we comprehensively present the function of epigenetic regulations in normal placental development as well as in a prominent disease of placental origin, preeclampsia (PE). We describe current progress concerning the impact of DNA methylation, non-coding RNA (with a special emphasis on long non-coding RNA (lncRNA) and microRNA (miRNA)) and more marginally histone post-translational modifications, in the processes leading to normal and abnormal placental function. We also explore the potential use of epigenetic marks circulating in the maternal blood flow as putative biomarkers able to prognosticate the onset of PE, as well as classifying it according to its severity. The correlation between epigenetic marks and impacts on gene expression is systematically evaluated for the different epigenetic marks analyzed.
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Affiliation(s)
- Clara Apicella
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Camino S M Ruano
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Céline Méhats
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Francisco Miralles
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
| | - Daniel Vaiman
- Institut Cochin, U1016 INSERM, UMR8104 CNRS, Université Paris Descartes, 24 rue du faubourg St Jacques, 75014 Paris, France.
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20
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Wilson RL, François M, Jankovic-Karasoulos T, McAninch D, McCullough D, Leifert WR, Roberts CT, Bianco-Miotto T. Characterization of 5-methylcytosine and 5-hydroxymethylcytosine in human placenta cell types across gestation. Epigenetics 2019; 14:660-671. [PMID: 31038385 DOI: 10.1080/15592294.2019.1609866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The placenta is an important organ in pregnancy, however, very little is understood about placental development at a molecular level. This includes the role of epigenetic mechanisms and how they change throughout gestation. DNA methylation studies in this organ are complicated by the different cell types that make up the placenta, each with their own unique transcriptome and epigenome. Placental dysfunction is often associated with pregnancy complications such as preeclampsia (PE). Aberrant DNA methylation in the placenta has been identified in pregnancy complications. We used immunohistochemistry (IHC) and immunofluorescence (IF) to localize 5-methylcytosine (5-mC) and 5-hydroxymethylcytosine (5-hmC) in placenta tissue from first and second trimester as well as uncomplicated term and PE samples. IHC analysis of whole placental tissues showed 5-mC increased across gestation. When cytotrophoblasts (CTB) and syncytiotrophoblasts (STB) were isolated and assessed using IF, both 5-mC and 5-hmC increased in term CTBs compared to first/second-trimester samples. Staining intensity of 5-hmC was higher in first/second trimester STBs compared to CTBs (P = 0.0011). Finally, IHC staining of term tissue from PE and uncomplicated pregnancies revealed higher 5-mC staining intensity in placentas from PE pregnancies (P = 0.028). Our study has shown increased 5-mC and 5-hmC staining intensities across gestation and differed between two trophoblast populations. Differences in DNA methylation profiles between placental cell types may be indicative of different functions and requires further study to elucidate what changes accompany placental pathologies.
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Affiliation(s)
- Rebecca L Wilson
- a Center for Fetal and Placental Research , Cincinnati Children's Hospital and Medical Research Center , Cincinnati , OH , USA.,b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Maxime François
- d CSIRO Health and Biosecurity , Future Science Platforms Probing Biosystems , Adelaide , Australia.,e School of Biological Sciences , University of Adelaide , Adelaide , Australia
| | - Tanja Jankovic-Karasoulos
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Dale McAninch
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Dylan McCullough
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Wayne R Leifert
- d CSIRO Health and Biosecurity , Future Science Platforms Probing Biosystems , Adelaide , Australia.,e School of Biological Sciences , University of Adelaide , Adelaide , Australia
| | - Claire T Roberts
- b Adelaide Medical School , University of Adelaide , Adelaide , Australia.,c Robinson Research Institute , University of Adelaide , Adelaide , Australia
| | - Tina Bianco-Miotto
- c Robinson Research Institute , University of Adelaide , Adelaide , Australia.,f School of Agriculture, Food and Wine, Waite Research Institute , University of Adelaide , Adelaide , Australia
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21
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Li L, Gao Y, Wu Q, Cheng ASL, Yip KY. New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation. Genome Res 2019; 29:543-553. [PMID: 30782641 PMCID: PMC6442395 DOI: 10.1101/gr.240036.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 02/11/2019] [Indexed: 01/10/2023]
Abstract
Many DNA methylome profiling methods cannot distinguish between 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC). Because 5mC typically acts as a repressive mark whereas 5hmC is an intermediate form during active demethylation, the inability to separate their signals could lead to incorrect interpretation of the data. Is the extra information contained in 5hmC signals worth the additional experimental and computational costs? Here we combine whole-genome bisulfite sequencing (WGBS) and oxidative WGBS (oxWGBS) data in various human tissues to investigate the quantitative relationships between gene expression and the two forms of DNA methylation at promoters, transcript bodies, and immediate downstream regions. We find that 5mC and 5hmC signals correlate with gene expression in the same direction in most samples. Considering both types of signals increases the accuracy of expression levels inferred from methylation data by a median of 18.2% as compared to having only WGBS data, showing that the two forms of methylation provide complementary information about gene expression. Differential analysis between matched tumor and normal pairs is particularly affected by the superposition of 5mC and 5hmC signals in WGBS data, with at least 25%–40% of the differentially methylated regions (DMRs) identified from 5mC signals not detected from WGBS data. Our results also confirm a previous finding that methylation signals at transcript bodies are more indicative of gene expression levels than promoter methylation signals. Overall, our study provides data for evaluating the cost-effectiveness of some experimental and analysis options in the study of DNA methylation in normal and cancer samples.
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Affiliation(s)
- Le Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Yuwei Gao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Qiong Wu
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Alfred S L Cheng
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Department of Biomedical Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,CUHK-BGI Innovation Institute of Trans-omics, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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22
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Rempel LA, Krautkramer MM, Parrish JJ, Miles JR. Impact of seasonality, storage of semen, and sperm head-shape on whole tissue methylation and expression of methylation responsive candidate genes in swine placenta and fetal livers from summer and winter breedings. Mol Reprod Dev 2019; 86:465-475. [PMID: 30767330 DOI: 10.1002/mrd.23125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/14/2019] [Indexed: 12/22/2022]
Abstract
Epigenetics includes the study of external factors that can influence the expression of genes by altering the accessibility of DNA through methylation. To investigate the epigenetic influence of season, sperm head shape, and semen storage on placental and fetal tissues, pregnancies were generated in the summer or winter using boar semen from either least or most sperm head shape change, collected during cool or warm seasons, and stored as cooled-extended or cryopreserved. The lowest (p < 0.05) ratios of 5-methylcytosine to 5-hydroxymethylcytosine activity (5mC:5hmC) in fetal liver were from summer breedings and in placental tissues from winter breedings. The relative expression of placental CDH1 tended ( p < 0.10) to be greater in placenta generated from cryopreserved semen or semen collected during cool periods. The relative expression of placental GNAS was affected ( p < 0.05) by the interaction of breeding and semen collection seasons. Cryopreserved semen increased ( p < 0.05) the placental relative expression of GNAS. Placental MEST and RHOBTB3 tended ( p < 0.10) to have a greater relative expression from pregnancies generated using semen collected during cool periods used during winter breedings. Within fetal liver, the relative expression of GNAS and HGF was greater ( p < 0.05) from winter breedings. Interaction of winter breedings and least sperm head shape change tended ( p < 0.10) to have the greatest fetal liver expression of CDH1. Seasonality of semen collection, breeding, and the effect on sperm head shape change had an influence on the expression of genes with known differentially methylated regions or response to methylation activity from embryonic and extraembryonic tissues.
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Affiliation(s)
- Lea A Rempel
- U.S. Department of Agriculture, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska
| | | | - John J Parrish
- Department of Animal Science, University of Wisconsin, Madison, Wisconsin
| | - Jeremy R Miles
- U.S. Department of Agriculture, ARS, U.S. Meat Animal Research Center, Clay Center, Nebraska
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Schroeder M, Jakovcevski M, Polacheck T, Drori Y, Ben-Dor S, Röh S, Chen A. Sex dependent impact of gestational stress on predisposition to eating disorders and metabolic disease. Mol Metab 2018; 17:1-16. [PMID: 30174229 PMCID: PMC6197785 DOI: 10.1016/j.molmet.2018.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/08/2018] [Accepted: 08/14/2018] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVE Vulnerability to eating disorders (EDs) is broadly assumed to be associated with early life stress. However, a careful examination of the literature shows that susceptibility to EDs may depend on the type, severity and timing of the stressor and the sex of the individual. We aimed at exploring the link between chronic prenatal stress and predisposition to EDs and metabolic disease. METHODS We used a chronic variable stress protocol during gestation to explore the metabolic response of male and female offspring to food restriction (FR), activity-based anorexia (ABA), binge eating (BE) and exposure to high fat (HF) diet. RESULTS Contrary to controls, prenatally stressed (PNS) female offspring showed resistance to ABA and BE and displayed a lower metabolic rate leading to hyperadiposity and obesity on HF diet. Male PNS offspring showed healthy responses to FR and ABA, increased propensity to binge and improved coping with HF compared to controls. We found that long-lasting abnormal responses to metabolic challenge are linked to fetal programming and adult hypothalamic dysregulation in PNS females, resulting from sexually dimorphic adaptations in placental methylation and gene expression. CONCLUSIONS Our results show that maternal stress may have variable and even opposing effects on ED risk, depending on the ED and the sex of the offspring.
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Affiliation(s)
- Mariana Schroeder
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
| | - Mira Jakovcevski
- Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Tamar Polacheck
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yonat Drori
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shifra Ben-Dor
- Bioinformatics and Biological Computing Unit, Biological Services, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, 80804, Germany
| | - Alon Chen
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel; Department of Stress Neurobiology and Neurogenetics, Max Planck Institute of Psychiatry, Munich, 80804, Germany.
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24
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Konwar C, Price EM, Wang LQ, Wilson SL, Terry J, Robinson WP. DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes: insights into epigenetic variation in spontaneous preterm births. Epigenetics Chromatin 2018; 11:63. [PMID: 30373633 PMCID: PMC6205793 DOI: 10.1186/s13072-018-0234-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/20/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Placental inflammation, often presenting as acute chorioamnionitis (aCA), is commonly associated with preterm birth. Preterm birth can have both immediate and long-term adverse effects on the health of the baby. Developing biomarkers of inflammation in the placenta can help to understand its effects and potentially lead to new approaches for rapid prenatal diagnosis of aCA. We aimed to characterize epigenetic variation associated with aCA in placenta (chorionic villi) and fetal membranes (chorion and amnion) to better understand how aCA may impact processes that lead to preterm birth. This study lays the groundwork for development of novel biomarkers for aCA. METHODS Samples from 44 preterm placentas (chorionic villi) as well as matched chorion and amnion for 16 of these cases were collected for this study. These samples were profiled using the Illumina Infinium HumanMethylation850 BeadChip to measure DNA methylation (DNAm) at 866,895 CpGs across the genome. An additional 78 placental samples were utilized to independently validate the array findings by pyrosequencing. RESULTS Using a false discovery rate of < 0.15 and average group difference in DNAm of > 0.05, 66 differentially methylated (DM) CpG sites were identified between aCA cases and non-aCA cases in chorionic villi. For the majority of these 66 DM CpGs, the DNAm profile of the aCA cases as compared to the non-aCA cases trended in the direction of the blood cell DNAm. Interestingly, neutrophil-specific DNAm signatures, but not those associated with other immune cell types, were capable of separating aCA cases from the non-aCA cases. CONCLUSIONS Our results suggest that aCA-associated placentas showed altered DNAm signatures that were not observed in the absence of aCA. This DNAm profile is consistent with the activation of the innate immune response in the placenta and/or reflect increase in neutrophils as a response to inflammation.
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Affiliation(s)
- Chaini Konwar
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - E. Magda Price
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
- Department of Pediatrics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Li Qing Wang
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Samantha L. Wilson
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
| | - Jefferson Terry
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Pathology, BC Children’s Hospital, Vancouver, BC V6H 3N1 Canada
| | - Wendy P. Robinson
- BC Children’s Hospital Research Institute, 950 W 28th Ave, Vancouver, BC V5Z 4H4 Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1 Canada
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25
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Alahari S, Garcia J, Post M, Caniggia I. The von Hippel Lindau tumour suppressor gene is a novel target of E2F4-mediated transcriptional repression in preeclampsia. Biochim Biophys Acta Mol Basis Dis 2018; 1864:3298-3308. [DOI: 10.1016/j.bbadis.2018.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/20/2018] [Accepted: 07/16/2018] [Indexed: 12/31/2022]
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Hernandez Mora JR, Sanchez-Delgado M, Petazzi P, Moran S, Esteller M, Iglesias-Platas I, Monk D. Profiling of oxBS-450K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci. Epigenetics 2018; 13:182-191. [PMID: 28678681 DOI: 10.1080/15592294.2017.1344803] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
DNA methylation (5-methylcytosine, 5 mC) is involved in many cellular processes and is an epigenetic mechanism primarily associated with transcriptional repression. The recent discovery that 5 mC can be oxidized to 5-hydromethylcytosine (5hmC) by TET proteins has revealed the "sixth base" of DNA and provides additional complexity to what was originally thought to be a stable repressive mark. However, our knowledge of the genome-wide distribution of 5hmC in different tissues is currently limited. Here, we sought to define loci enriched for 5hmC in the placenta genome by combining oxidative bisulphite (oxBS) treatment with high-density Illumina Infinium HumanMethylation450 methylation arrays and to compare our results with those obtained in brain. Despite identifying over 17,000 high-confidence CpG sites with consistent 5hmC enrichment, the distribution of this modification in placenta is relatively sparse when compared to cerebellum and frontal cortex. Supported by validation using allelic T4 β-glucosyltransferase assays we identify 5hmC at numerous imprinted loci, often overlapping regions associated with parent-of-origin allelic 5 mC in both placenta and brain samples. Furthermore, we observe tissue-specific monoallelic enrichment of 5hmC overlapping large clusters of imprinted snoRNAs-miRNAs processed from long noncoding RNAs (lncRNAs) within the DLK1-DIO3 cluster on chromosome 14 and SNRPN-UBE3A domain on chromosome 15. Enrichment is observed solely on the transcribed alleles suggesting 5hmC is positively associated with transcription at these loci. Our study provides an extensive description of the 5hmC/5 mC landscape in placenta with our data available at www.humanimprints.net , which represents the most comprehensive resource for exploring the epigenetic profiles associated with human imprinted genes.
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Affiliation(s)
- Jose Ramon Hernandez Mora
- a Imprinting and Cancer group, Cancer Epigenetics and Biology Program (PEBC) , Institut d'Investigació Biomedica de Bellvitge (IDIBELL) , Avinguda Granvia, L'Hospitalet de Llobregat , Barcelona , Spain
| | - Marta Sanchez-Delgado
- a Imprinting and Cancer group, Cancer Epigenetics and Biology Program (PEBC) , Institut d'Investigació Biomedica de Bellvitge (IDIBELL) , Avinguda Granvia, L'Hospitalet de Llobregat , Barcelona , Spain
| | - Paolo Petazzi
- a Imprinting and Cancer group, Cancer Epigenetics and Biology Program (PEBC) , Institut d'Investigació Biomedica de Bellvitge (IDIBELL) , Avinguda Granvia, L'Hospitalet de Llobregat , Barcelona , Spain
| | - Sebastian Moran
- b Cancer Epigenetics group, Cancer Epigenetics and Biology Program (PEBC) , Institut d'Investigació Biomedica de Bellvitge (IDIBELL) , Avinguda Granvia, L'Hospitalet de Llobregat , Barcelona , Spain
| | - Manel Esteller
- b Cancer Epigenetics group, Cancer Epigenetics and Biology Program (PEBC) , Institut d'Investigació Biomedica de Bellvitge (IDIBELL) , Avinguda Granvia, L'Hospitalet de Llobregat , Barcelona , Spain.,c Department of Physiological Sciences II, School of Medicine , University of Barcelona , Barcelona , Catalonia , Spain.,d Institucio Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona , Catalonia , Spain
| | - Isabel Iglesias-Platas
- e Servicio de Neonatología , Sant Joan de Déu, Centro de Medicina Maternofetal y Neonatal Barcelona (BCN-Natal) , Hospital Sant Joan de Déu y Hospital Clínic , Universitat de Barcelona , Barcelona , Spain
| | - David Monk
- a Imprinting and Cancer group, Cancer Epigenetics and Biology Program (PEBC) , Institut d'Investigació Biomedica de Bellvitge (IDIBELL) , Avinguda Granvia, L'Hospitalet de Llobregat , Barcelona , Spain
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27
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Ponnaluri VKC, Ehrlich KC, Zhang G, Lacey M, Johnston D, Pradhan S, Ehrlich M. Association of 5-hydroxymethylation and 5-methylation of DNA cytosine with tissue-specific gene expression. Epigenetics 2017; 12:123-138. [PMID: 27911668 PMCID: PMC5330441 DOI: 10.1080/15592294.2016.1265713] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/10/2016] [Accepted: 11/21/2016] [Indexed: 12/15/2022] Open
Abstract
Differentially methylated or hydroxymethylated regions (DMRs) in mammalian DNA are often associated with tissue-specific gene expression but the functional relationships are still being unraveled. To elucidate these relationships, we studied 16 human genes containing myogenic DMRs by analyzing profiles of their epigenetics and transcription and quantitatively assaying 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) at specific sites in these genes in skeletal muscle (SkM), myoblasts, heart, brain, and diverse other samples. Although most human promoters have little or no methylation regardless of expression, more than half of the genes that we chose to study-owing to their myogenic DMRs-overlapped tissue-specific alternative or cryptic promoters displaying corresponding tissue-specific differences in histone modifications. The 5mC levels in myoblast DMRs were significantly associated with 5hmC levels in SkM at the same site. Hypermethylated myogenic DMRs within CDH15, a muscle- and cerebellum-specific cell adhesion gene, and PITX3, a homeobox gene, were used for transfection in reporter gene constructs. These intragenic DMRs had bidirectional tissue-specific promoter activity that was silenced by in vivo-like methylation. The CDH15 DMR, which was previously associated with an imprinted maternal germline DMR in mice, had especially strong promoter activity in myogenic host cells. These findings are consistent with the controversial hypothesis that intragenic DNA methylation can facilitate transcription and is not just a passive consequence of it. Our results support varied roles for tissue-specific 5mC- or 5hmC-enrichment in suppressing inappropriate gene expression from cryptic or alternative promoters and in increasing the plasticity of gene expression required for development and rapid responses to tissue stress or damage.
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Affiliation(s)
| | - Kenneth C. Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA, USA
| | | | - Michelle Lacey
- Department of Mathematics, Tulane Health Sciences Center and Tulane University, New Orleans, LA, USA
| | - Douglas Johnston
- Department of Microbiology, Immunology and Parasitology, LSU Health Sciences Center, New Orleans, LA, USA
| | | | - Melanie Ehrlich
- Center for Bioinformatics and Genomics, Tulane University Health Sciences Center, New Orleans, LA, USA
- Hayward Genetics Center and Tulane Cancer Center, Tulane University Health Sciences Center, New Orleans, LA, USA
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28
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Otero M, Peng H, El Hachem K, Culley KL, Wondimu EB, Quinn J, Asahara H, Tsuchimochi K, Hashimoto K, Goldring MB. ELF3 modulates type II collagen gene (COL2A1) transcription in chondrocytes by inhibiting SOX9-CBP/p300-driven histone acetyltransferase activity. Connect Tissue Res 2017; 58:15-26. [PMID: 27310669 PMCID: PMC5326708 DOI: 10.1080/03008207.2016.1200566] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AIM We showed previously that E74-like factor 3 (ELF3) protein levels are increased in osteoarthritic (OA) cartilage, that ELF3 accounts for inflammatory cytokine-driven MMP13 gene expression, and that, upon induction by interleukin-1β, ELF3 binds to the COL2A1 promoter and suppresses its activity in chondrocytes. Here, we aimed to further investigate the mechanism/s by which ELF3 represses COL2A1 transcription in chondrocytes. METHODS AND RESULTS We report that ELF3 inhibits Sox9-driven COL2A1 promoter activity by interfering with the activator functions of CBP/300 and Sox9. Co-transfection of the pGL2B-COL2A1 (-577/+3428 bp) reporter construct with Sox9 and with Sox5 and/or Sox6 increased COL2A1 promoter activity, and ELF3 overexpression significantly reduced the promoter transactivation. Co-transfection of ELF3 with the pLuc 4x48 enhancer construct, containing the 89-bp COL2A1 promoter and lacking the previously defined ELF3 binding sites, decreased both basal and Sox9-driven promoter activity. Co-transfection of ELF3 with a Gal4 reporter construct also inhibited Gal4-Sox9-driven transactivation, suggesting that ELF3 directly interacts with Sox9. Using truncated Sox9 fragments, we found that ELF3 interacts directly with the HMG domain of Sox9. Importantly, overexpression of ELF3 significantly decreased Sox9/CBP-dependent HAT activity. Finally, we show evidence that increased ELF3 mRNA expression in OA chondrocytes correlates with hypermethylation of the proximal promoter, suggesting that ELF3 transcription is subjected to epigenetic control in OA disease. CONCLUSION Our results highlight the contribution of ELF3 to transcriptional regulation of COL2A1 and its potential role in OA disease, and uncover epigenetic mechanisms at play in the regulation of ELF3 and its downstream targets in articular chondrocytes.
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Affiliation(s)
- Miguel Otero
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Haibing Peng
- Beth Israel Deaconess Medical Center, New England Baptist Bone and Joint Institute, Boston, MA, USA
| | - Karim El Hachem
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Kirsty L. Culley
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Elisabeth B. Wondimu
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA,Weill Cornell Graduate Program of Medical Sciences, New York, NY, USA
| | - Justin Quinn
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Hiroshi Asahara
- Department of Molecular and Experimental Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Kaneyuki Tsuchimochi
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
| | - Ko Hashimoto
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA,Department of Orthopaedics, Tohoku University Hospital, Sendai, Japan
| | - Mary B. Goldring
- HSS Research Institute, Hospital for Special Surgery, and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA,Weill Cornell Graduate Program of Medical Sciences, New York, NY, USA,To whom correspondence should be addressed: Mary B. Goldring, Ph.D., Hospital for Special Surgery, HSS Research Institute, Room 601, 515 East 71st Street, New York, NY 10021, USA; Tel. 212-774-7564; Fax. 617-249-2373;
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29
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Kramer A, Challen GA. The epigenetic basis of hematopoietic stem cell aging. Semin Hematol 2016; 54:19-24. [PMID: 28088983 DOI: 10.1053/j.seminhematol.2016.10.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 10/19/2016] [Accepted: 10/19/2016] [Indexed: 12/12/2022]
Abstract
Highly proliferative tissues such as the gut, skin, and bone marrow lose millions of cells each day to normal attrition and challenge from different biological adversities. To achieve a lifespan beyond the longevity of individual cell types, tissue-specific stem cells sustain these tissues throughout the life of a human. For example, the lifespan of erythrocytes is about 100 days and adults make about two million new erythrocytes every second. A small pool of hematopoietic stem cells (HSCs) in the bone marrow is responsible for the lifetime maintenance of these populations. However, there are changes that occur within the HSC pool during aging. Biologically, these changes manifest as blunted immune responses, decreased bone marrow cellularity, and increased risk of myeloid diseases. Understanding the molecular mechanisms underlying dysfunction of aging HSCs is an important focus of biomedical research. With advances in modern health care, the average age of the general population is ever increasing. If molecular or pharmacological interventions could be discovered that rejuvenate aging HSCs, it could reduce the burden of age related immune system compromise as well as open up new opportunities for treatment of hematological disorders with regenerative therapy.
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Affiliation(s)
- Ashley Kramer
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO
| | - Grant A Challen
- Section of Stem Cell Biology, Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO; Developmental, Regenerative and Stem Cell Biology Program, Division of Biology and Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, MO.
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30
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Sheinkopf SJ, Righi G, Marsit CJ, Lester BM. Methylation of the Glucocorticoid Receptor (NR3C1) in Placenta Is Associated with Infant Cry Acoustics. Front Behav Neurosci 2016; 10:100. [PMID: 27313516 PMCID: PMC4889592 DOI: 10.3389/fnbeh.2016.00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
Epigenetic mechanisms regulating expression of the glucocorticoid receptor gene (NR3C1) promoter may influence behavioral and biological aspects of stress response in human infants. Acoustic features of infant crying are an indicator of neurobehavioral and neurological status not yet investigated in relation to epigenetic mechanisms. We examined NR3C1 methylation in placental tissue from a series of 120 healthy newborn infants in relation to a detailed set of acoustic features extracted from newborn infant cries. We identified significant associations of NR3C1 methylation with energy variation in infants' cries as well as with the presence of very high fundamental frequency in cry utterances. The presence of high fundamental frequency in cry (above 1 kHz) has been linked to poor vocal tract control, poor regulation of stress response, and may be an indicator or poor neurobehavioral integrity. Thus, these results add to evidence linking epigenetic alteration of the NR3C1 gene in the placenta to neurodevelopmental features in infants.
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Affiliation(s)
- Stephen J Sheinkopf
- The Brown Center for the Study of Children at Risk, Women and Infants HospitalProvidence, RI, USA; Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA; Department of Pediatrics, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA
| | - Giulia Righi
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University Providence, RI, USA
| | - Carmen J Marsit
- Section of Biostatistics and Epidemiology, Department of Pharmacology and Toxicology and of Community and Family Medicine, Geisel School of Medicine at Dartmouth Hanover, NH, USA
| | - Barry M Lester
- The Brown Center for the Study of Children at Risk, Women and Infants HospitalProvidence, RI, USA; Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA; Department of Pediatrics, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA
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