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Zhang G, Mao Y, Zhang Y, Huang H, Pan J. Assisted reproductive technology and imprinting errors: analyzing underlying mechanisms from epigenetic regulation. HUM FERTIL 2023; 26:864-878. [PMID: 37929309 DOI: 10.1080/14647273.2023.2261628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 08/11/2023] [Indexed: 11/07/2023]
Abstract
With the increasing maturity and widespread application of assisted reproductive technology (ART), more attention has been paid to the health outcomes of offspring following ART. It is well established that children born from ART treatment are at an increased risk of imprinting errors and imprinting disorders. The disturbances of genetic imprinting are attributed to the overlap of ART procedures and important epigenetic reprogramming events during the development of gametes and early embryos, but the detailed mechanisms are hitherto obscure. In this review, we summarized the DNA methylation-dependent and independent mechanisms that control the dynamic epigenetic regulation of imprinted genes throughout the life cycle of a mammal, including erasure, establishment, and maintenance. In addition, we systematically described the dysregulation of imprinted genes in embryos conceived through ART and discussed the corresponding underlying mechanisms according to findings in animal models. This work is conducive to evaluating and improving the safety of ART.
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Affiliation(s)
- Gaochen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Yiting Mao
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Yu Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiexue Pan
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Sainty R, Silver MJ, Prentice AM, Monk D. The influence of early environment and micronutrient availability on developmental epigenetic programming: lessons from the placenta. Front Cell Dev Biol 2023; 11:1212199. [PMID: 37484911 PMCID: PMC10358779 DOI: 10.3389/fcell.2023.1212199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/25/2023] Open
Abstract
DNA methylation is the most commonly studied epigenetic mark in humans, as it is well recognised as a stable, heritable mark that can affect genome function and influence gene expression. Somatic DNA methylation patterns that can persist throughout life are established shortly after fertilisation when the majority of epigenetic marks, including DNA methylation, are erased from the pre-implantation embryo. Therefore, the period around conception is potentially critical for influencing DNA methylation, including methylation at imprinted alleles and metastable epialleles (MEs), loci where methylation varies between individuals but is correlated across tissues. Exposures before and during conception can affect pregnancy outcomes and health throughout life. Retrospective studies of the survivors of famines, such as those exposed to the Dutch Hunger Winter of 1944-45, have linked exposures around conception to later disease outcomes, some of which correlate with DNA methylation changes at certain genes. Animal models have shown more directly that DNA methylation can be affected by dietary supplements that act as cofactors in one-carbon metabolism, and in humans, methylation at birth has been associated with peri-conceptional micronutrient supplementation. However, directly showing a role of micronutrients in shaping the epigenome has proven difficult. Recently, the placenta, a tissue with a unique hypomethylated methylome, has been shown to possess great inter-individual variability, which we highlight as a promising target tissue for studying MEs and mixed environmental exposures. The placenta has a critical role shaping the health of the fetus. Placenta-associated pregnancy complications, such as preeclampsia and intrauterine growth restriction, are all associated with aberrant patterns of DNA methylation and expression which are only now being linked to disease risk later in life.
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Affiliation(s)
- Rebecca Sainty
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Matt J. Silver
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, Gambia
| | - David Monk
- Biomedical Research Centre, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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Sundrani DP, Joshi SR. Assisted reproductive technology (ART) and epigenetic modifications in the placenta. HUM FERTIL 2023; 26:665-677. [PMID: 34706609 DOI: 10.1080/14647273.2021.1995901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 04/19/2021] [Indexed: 10/20/2022]
Abstract
Assisted reproductive technology (ART) has become common amongst couples with infertility issues. ART is known to be successful, but epidemiological data indicates that ART is associated with placental disorders. Additionally, reports show increased risks of short- and long-term complications in children born to mothers undergoing ART. However, the mechanisms responsible for these events are obscure. The placenta is considered as a key organ for programming of diseases and ART procedures are suggested to alter the placental function and intrauterine growth trajectories. Epigenetic changes in maternal and foetal tissues are suggested to be the underlying mechanisms for these outcomes. Epigenetic regulation is known to evolve following fertilisation and before implantation and subsequently across gestation. During these critical periods of epigenetic 'programming', DNA methylation and chromatin remodelling influence the placental structure and function by regulating the expression of various genes. ART treatment coinciding with epigenetic 'programming' events during gametogenesis and early embryo development may alter the programming phases leading to long-term consequences. Thus, disruptions in placental development observed in ART pregnancies could be associated with altered epigenetic regulation of vital genes in the placenta. The review summarises available literature on the influence of ART procedures on epigenetic changes in the placenta.
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Affiliation(s)
- Deepali P Sundrani
- Mother and Child Health, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
| | - Sadhana R Joshi
- Mother and Child Health, Interactive Research School for Health Affairs (IRSHA), Bharati Vidyapeeth (Deemed to be University), Pune, India
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Sciorio R, Tramontano L, Rapalini E, Bellaminutti S, Bulletti FM, D'Amato A, Manna C, Palagiano A, Bulletti C, Esteves SC. Risk of genetic and epigenetic alteration in children conceived following ART: Is it time to return to nature whenever possible? Clin Genet 2023; 103:133-145. [PMID: 36109352 DOI: 10.1111/cge.14232] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 01/07/2023]
Abstract
Assisted reproductive technology may influence epigenetic signature as the procedures coincide with the extensive epigenetic modification occurring from fertilization to embryo implantation. However, it is still unclear to what extent ART alters the embryo epigenome. In vivo fertilization occurs in the fallopian tube, where a specific and natural environment enables the embryo's healthy development. During this dynamic period, major waves of epigenetic reprogramming, crucial for the normal fate of the embryo, take place. Over the past decade, concerns relating to the raised incidence of epigenetic anomalies and imprinting following ART have been raised by several authors. Epigenetic reprogramming is particularly susceptible to environmental conditions during the periconceptional period; therefore, unphysiological conditions, including ovarian stimulation, in vitro fertilization, embryo culture, cryopreservation of gametes and embryos, parental lifestyle, and underlying infertility, have the potential to contribute to epigenetic dysregulation independently or collectively. This review critically appraises the evidence relating to the association between ART and genetic and epigenetic modifications that may be transmitted to the offspring.
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Affiliation(s)
- Romualdo Sciorio
- Edinburgh Assisted Conception Programme, EFREC, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Luca Tramontano
- Department of Women, Infants and Adolescents, Division of Obstetrics, Geneva University Hospitals, Geneva, Switzerland
| | - Erika Rapalini
- IVF Department, Versilia Hospital Lido di Camaiore, Lucca, Italy
| | - Serena Bellaminutti
- Department of Gynaecology and Obstetrics, Ospedale Regionale di Lugano, Lugano, Switzerland
- Gynecology and Fertility Unit, Procrea Institute, Lugano, Switzerland
- Gynecology Unit, Centro Medico, Lugano, Switzerland
| | | | - Antonio D'Amato
- Obstetrics and Gynaecology Clinic, University of Bari, Bari, Italy
| | - Claudio Manna
- Biofertility IVF and Infertility Center, Rome, Italy
| | - Antonio Palagiano
- CFA Napoli, Italy, CFA: Centro Fecondazione Assistita Napoli, Naples, Italy
| | - Carlo Bulletti
- Ostetricia e Ginecologia, EXTRA OMNES Medicina e Salute Riproduttiva, Cattolica, Italy
| | - Sandro C Esteves
- Andrology and Human Reproduction Clinic, Campinas, Brazil
- Department of Surgery (Division of Urology), University of Campinas (UNICAMP), Campinas, Brazil
- Faculty of Health, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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DNA Methylation in Offspring Conceived after Assisted Reproductive Techniques: A Systematic Review and Meta-Analysis. J Clin Med 2022; 11:jcm11175056. [PMID: 36078985 PMCID: PMC9457481 DOI: 10.3390/jcm11175056] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background: In the last 40 years, assisted reproductive techniques (ARTs) have emerged as potentially resolving procedures for couple infertility. This study aims to evaluate whether ART is associated with epigenetic dysregulation in the offspring. Methods. To accomplish this, we collected all available data on methylation patterns in offspring conceived after ART and in spontaneously conceived (SC) offspring. Results. We extracted 949 records. Of these, 50 were considered eligible; 12 were included in the quantitative synthesis. Methylation levels of H19 CCCTC-binding factor 3 (CTCF3) were significantly lower in the ART group compared to controls (SMD −0.81 (−1.53; −0.09), I2 = 89%, p = 0.03). In contrast, H19 CCCTC-binding factor 6 (CTCF6), Potassium Voltage-Gated Channel Subfamily Q Member 1 (KCNQ1OT1), Paternally-expressed gene 3 (PEG3), and Small Nuclear Ribonucleoprotein Polypeptide N (SNRPN) were not differently methylated in ART vs. SC offspring. Conclusion: The methylation pattern of the offspring conceived after ART may be different compared to spontaneous conception. Due to the lack of studies and the heterogeneity of the data, further prospective and well-sized population studies are needed to evaluate the impact of ART on the epigenome of the offspring.
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OUP accepted manuscript. Hum Reprod Update 2022; 28:629-655. [DOI: 10.1093/humupd/dmac010] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/04/2022] [Indexed: 11/13/2022] Open
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Barberet J, Binquet C, Guilleman M, Romain G, Bruno C, Martinaud A, Ginod P, Cavalieri M, Amblot C, Choux C, Fauque P. Does underlying infertility in natural conception modify the epigenetic control of imprinted genes and transposable elements in newborns? Reprod Biomed Online 2022; 44:706-715. [DOI: 10.1016/j.rbmo.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/30/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022]
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Ducreux B, Frappier J, Bruno C, Doukani A, Guilleman M, Simon E, Martinaud A, Bourc’his D, Barberet J, Fauque P. Genome-Wide Analysis of DNA Methylation in Buccal Cells of Children Conceived through IVF and ICSI. Genes (Basel) 2021; 12:1912. [PMID: 34946866 PMCID: PMC8701402 DOI: 10.3390/genes12121912] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 11/25/2022] Open
Abstract
Early life periconceptional exposures during assisted reproductive technology (ART) procedures could alter the DNA methylation profiles of ART children, notably in imprinted genes and repetitive elements. At the genome scale, DNA methylation differences have been reported in ART conceptions at birth, but it is still unclear if those differences remain at childhood. Here, we performed an epigenome-wide DNA methylation association study using Illumina InfiniumEPIC BeadChip to assess the effects of the mode of conception on the methylome of buccal cells from 7- to 8-year-old children (48 children conceived after ART or naturally (control, CTL)) and according to the embryo culture medium in which they were conceived. We identified 127 differentially methylated positions (DMPs) and 16 differentially methylated regions (DMRs) (FDR < 0.05) with low delta beta differences between the two groups (ART vs. CTL). DMPs were preferentially located inside promoter proximal regions and CpG islands and were mostly hypermethylated with ART. We highlighted that the use of distinct embryo culture medium was not associated with DNA methylation differences in childhood. Overall, we bring additional evidence that children conceived via ART display limited genome-wide DNA methylation variation compared with those conceived naturally.
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Affiliation(s)
- Bastien Ducreux
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
| | - Jean Frappier
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Céline Bruno
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Abiba Doukani
- Faculté de Médecine, Sorbonne Université, UMS 37 PASS Plateforme P3S, 91, Bd de l’hôpital, F-75634 Paris, France;
| | - Magali Guilleman
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Emmanuel Simon
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Service de Gynécologie-Obstétrique, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Aurélie Martinaud
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Déborah Bourc’his
- Institut Curie, PSL University, CNRS, INSERM, 26 Rue d’Ulm, F-75248 Paris, France;
| | - Julie Barberet
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
| | - Patricia Fauque
- Equipe Génétique des Anomalies du Développement (GAD), Université Bourgogne Franche-Comté, INSERM UMR1231, 2 Rue Angélique Ducoudray, F-21000 Dijon, France; (B.D.); (J.F.); (C.B.); (M.G.); (E.S.); (A.M.); (J.B.)
- Laboratoire de Biologie de la Reproduction—CECOS, CHU Dijon Bourgogne, 14 Rue Gaffarel, F-21000 Dijon, France
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Barberet J, Romain G, Binquet C, Guilleman M, Bruno C, Ginod P, Chapusot C, Choux C, Fauque P. Do frozen embryo transfers modify the epigenetic control of imprinted genes and transposable elements in newborns compared with fresh embryo transfers and natural conceptions? Fertil Steril 2021; 116:1468-1480. [PMID: 34538459 DOI: 10.1016/j.fertnstert.2021.08.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/02/2021] [Accepted: 08/06/2021] [Indexed: 11/28/2022]
Abstract
OBJECTIVE To determine whether the epigenetic control of imprinted genes (IGs) and transposable elements (TEs) differs at birth between fresh or frozen embryo transfers and natural conceptions. DESIGN Prospective study. SETTING University hospital. PATIENT(S) A total of 202 singleton births were divided into three groups: 84 natural pregnancies (controls), 66 in vitro fertilization/intracytoplasmic sperm injection with fresh embryo transfers, and 52 vitro fertilization/intracytoplasmic sperm injection with frozen embryo transfers. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Pyrosequencing was used to assess the DNA methylation profiles of three IGs (H19/IGF2:IG-DMR [two sequences], KCNQ1OT1:TSS-DMR, and SNURF:TSS-DMR) and two TEs (LINE-1 and HERV-FRD) in cord blood and placenta. The quantitative reverse transcriptase polymerase chain reaction was used to study the transcription of three IGs (H19, KCNQ1, and SNRPN) and two TEs (LINE-1 and ORF2). RESULT(S) After adjustment, the placental DNA methylation levels of H19/IGF2 were lower in the fresh embryo transfer group than in the control (H19/IGF2-seq1) and frozen embryo transfer (H19/IGF2-seq2) groups. The DNA methylation rate for LINE-1 was lower in placentas from the fresh embryo transfer group than in placentas from the control and frozen embryo transfer groups and for HERV-FRD compared with controls. In cord blood, DNA methylation levels were not significantly associated with the mode of conception. The relative expression of LINE-1 and ORF2 was decreased in both cord blood and placental tissues from fresh embryo transfer conceptions compared with natural conceptions and frozen embryo transfer conceptions. CONCLUSION(S) Compared with natural conceptions and frozen embryo transfers, fresh embryo transfers were associated with methylation and/or transcription changes in some TEs and IGs, mostly in placental samples, which could indicate altered placental epigenetic regulation resulting from ovarian stimulation protocols.
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Affiliation(s)
- Julie Barberet
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
| | - Gaelle Romain
- Centre Hospitalier Universitaire Dijon-Bourgogne, Centre d'Investigation Clinique, Module Epidémiologie Clinique/Essais Cliniques (CIC-EC), Dijon, France; INSERM, CIC1432, Module Epidémiologie Clinique, Dijon, France
| | - Christine Binquet
- Centre Hospitalier Universitaire Dijon-Bourgogne, Centre d'Investigation Clinique, Module Epidémiologie Clinique/Essais Cliniques (CIC-EC), Dijon, France; INSERM, CIC1432, Module Epidémiologie Clinique, Dijon, France
| | - Magali Guilleman
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
| | - Céline Bruno
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
| | - Perrine Ginod
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Service de Gynécologie-Obstétrique, Dijon, France
| | - Caroline Chapusot
- Centre Hospitalier Universitaire Dijon-Bourgogne, Plateforme de Génétique des Cancers de Bourgogne, Dijon, France
| | - Cécile Choux
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Service de Gynécologie-Obstétrique, Dijon, France
| | - Patricia Fauque
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD), INSERM UMR1231, Dijon, France; Centre Hospitalier Universitaire Dijon-Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France.
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Anvar Z, Chakchouk I, Demond H, Sharif M, Kelsey G, Van den Veyver IB. DNA Methylation Dynamics in the Female Germline and Maternal-Effect Mutations That Disrupt Genomic Imprinting. Genes (Basel) 2021; 12:genes12081214. [PMID: 34440388 PMCID: PMC8394515 DOI: 10.3390/genes12081214] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Genomic imprinting is an epigenetic marking process that results in the monoallelic expression of a subset of genes. Many of these ‘imprinted’ genes in mice and humans are involved in embryonic and extraembryonic growth and development, and some have life-long impacts on metabolism. During mammalian development, the genome undergoes waves of (re)programming of DNA methylation and other epigenetic marks. Disturbances in these events can cause imprinting disorders and compromise development. Multi-locus imprinting disturbance (MLID) is a condition by which imprinting defects touch more than one locus. Although most cases with MLID present with clinical features characteristic of one imprinting disorder. Imprinting defects also occur in ‘molar’ pregnancies-which are characterized by highly compromised embryonic development-and in other forms of reproductive compromise presenting clinically as infertility or early pregnancy loss. Pathogenic variants in some of the genes encoding proteins of the subcortical maternal complex (SCMC), a multi-protein complex in the mammalian oocyte, are responsible for a rare subgroup of moles, biparental complete hydatidiform mole (BiCHM), and other adverse reproductive outcomes which have been associated with altered imprinting status of the oocyte, embryo and/or placenta. The finding that defects in a cytoplasmic protein complex could have severe impacts on genomic methylation at critical times in gamete or early embryo development has wider implications beyond these relatively rare disorders. It signifies a potential for adverse maternal physiology, nutrition, or assisted reproduction to cause epigenetic defects at imprinted or other genes. Here, we review key milestones in DNA methylation patterning in the female germline and the embryo focusing on humans. We provide an overview of recent findings regarding DNA methylation deficits causing BiCHM, MLID, and early embryonic arrest. We also summarize identified SCMC mutations with regard to early embryonic arrest, BiCHM, and MLID.
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Affiliation(s)
- Zahra Anvar
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Imen Chakchouk
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hannah Demond
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
| | - Momal Sharif
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK;
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
| | - Ignatia B. Van den Veyver
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, TX 77030, USA; (Z.A.); (I.C.); (M.S.)
- Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (G.K.); (I.B.V.d.V.); Tel.: +44-1223-496332 (G.K.); +832-824-8125 (I.B.V.d.V.)
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Naillat F, Saadeh H, Nowacka-Woszuk J, Gahurova L, Santos F, Tomizawa SI, Kelsey G. Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes. Clin Epigenetics 2021; 13:132. [PMID: 34183052 PMCID: PMC8240245 DOI: 10.1186/s13148-021-01116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns. RESULTS An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile. CONCLUSIONS Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.
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Affiliation(s)
- Florence Naillat
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Diseases Network Research Unit, Faculty of Biochemistry and Molecular Medicine, Oulu University, Oulu, Finland.
| | - Heba Saadeh
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Computer Science, King Abdullah II School of Information Technology, The University of Jordan, Amman, Jordan
| | - Joanna Nowacka-Woszuk
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Lenka Gahurova
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Early Mammalian Development, Department of Molecular Biology and Genetics, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Fatima Santos
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Shin-Ichi Tomizawa
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,School of Medicine, Yokohama City University, Yokohama, Japan
| | - Gavin Kelsey
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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12
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Barberet J, Binquet C, Guilleman M, Doukani A, Choux C, Bruno C, Bourredjem A, Chapusot C, Bourc'his D, Duffourd Y, Fauque P. Do assisted reproductive technologies and in vitro embryo culture influence the epigenetic control of imprinted genes and transposable elements in children? Hum Reprod 2021; 36:479-492. [PMID: 33319250 DOI: 10.1093/humrep/deaa310] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 09/10/2020] [Indexed: 11/15/2022] Open
Abstract
STUDY QUESTION Do assisted reproductive technologies (ART) and in vitro embryo culture influence the epigenetic control of imprinted genes (IGs) and transposable elements (TEs) in children? SUMMARY ANSWER Significant differences in the DNA methylation of IGs or transposon families were reported between ART and naturally conceived children, but there was no difference between culture media. WHAT IS KNOWN ALREADY There is concern that ART may play a role in increasing the incidence of adverse health outcomes in children, probably through epigenetic mechanisms. It is crucial to assess epigenetic control, especially following non-optimal in vitro culture conditions and to compare epigenetic analyses from ART-conceived and naturally conceived children. STUDY DESIGN, SIZE, DURATION This follow-up study was based on an earlier randomized study comparing in vitro fertilization outcomes following the use of two distinct culture media. We compared the epigenetic profiles of children from the initial randomized study according to the mode of conception [i.e. ART singletons compared with those of a cohort of naturally conceived singleton children (CTL)], the type of embryo culture medium used [global medium (LifeGlobal) and single step medium (Irvine Scientific)] and the mode of in vitro fertilization (i.e. IVF versus ICSI). PARTICIPANTS/MATERIALS, SETTING, METHODS A total of 57 buccal smears were collected from 7- to 8-year-old children. The DNA methylation profiles of four differentially methylated regions (DMRs) of IGs (H19/IGF2: IG-DMR, KCNQ1OT1: TSS-DMR, SNURF: TSS-DMR, and PEG3: TSS-DMR) and two TEs (AluYa5 and LINE-1) were first assessed by pyrosequencing. We further explored IGs and TEs' methylation changes through methylation array (Human MethylationEPIC BeadChip referred as EPIC array, Illumina). MAIN RESULTS AND THE ROLE OF CHANCE Changes in the IGs' DNA methylation levels were found in ART children compared to controls. DNA methylation levels of H19/IGF2 DMR were significantly lower in ART children than in CTL children [52% versus 58%, P = 0.003, false discovery rate (FDR) P = 0.018] while a significantly higher methylation rate was observed for the PEG3 DMR (51% versus 48%, P = 0.007, FDR P = 0.021). However, no differences were found between the culture media. After observing these targeted modifications, analyses were performed at wider scale. Again, no differences were detected according to the culture media, but imprinted-related DMRs overlapping promoter region near the genes major for the development (MEG3, BLCAP, and DLX5) were detected between the ART and CTL children. LIMITATIONS, REASONS FOR CAUTION The sample size could seem relatively small, but the high consistency of our results was ensured by the homogeneity of the cohort from the initial randomized study, the standardized laboratory techniques and the robust statistical analyses accounting for multiple testing. WIDER IMPLICATIONS OF THE FINDINGS Although this study did not report DNA methylation differences depending on the culture medium, it sheds light on epigenetic changes that could be observed in some children conceived by ART as compared to CTL children. The clinical relevance of such differences remains largely unknown, and it is still unclear whether such changes are due to some specific ART procedures and/or to parental infertility. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by funding from the Agence Nationale pour la Recherche ('CARE'-ANR JCJC 2017). The authors have no conflicts of interest. TRIAL REGISTRATION NUMBER Not concerned.
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Affiliation(s)
- J Barberet
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
| | - C Binquet
- CHU Dijon Bourgogne, Centre d'Investigation Clinique, module Epidémiologie Clinique/essais cliniques (CIC-EC), Dijon, France.,INSERM, CIC1432, module épidémiologie clinique, Dijon, France
| | - M Guilleman
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
| | - A Doukani
- Faculté de Médecine Sorbonne Université, Site Pitié-Salpêtrière, Paris, France
| | - C Choux
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France.,CHU Dijon Bourgogne, Service de Gynécologie-Obstétrique, Dijon, France
| | - C Bruno
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
| | - A Bourredjem
- CHU Dijon Bourgogne, Centre d'Investigation Clinique, module Epidémiologie Clinique/essais cliniques (CIC-EC), Dijon, France.,INSERM, CIC1432, module épidémiologie clinique, Dijon, France
| | - C Chapusot
- CHU Dijon Bourgogne, Plateforme de génétique des Cancers de bourgogne, Dijon, France
| | - D Bourc'his
- Institut Curie, PSL University, CNRS, INSERM, Paris, France
| | - Y Duffourd
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France
| | - P Fauque
- Université Bourgogne Franche-Comté-Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction-CECOS, Dijon, France
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13
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Heber MF, Ptak GE. The effects of assisted reproduction technologies on metabolic health and disease†. Biol Reprod 2020; 104:734-744. [PMID: 33330924 PMCID: PMC8023432 DOI: 10.1093/biolre/ioaa224] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/12/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
The increasing prevalence of metabolic diseases places a substantial burden on human health throughout the world. It is believed that predisposition to metabolic disease starts early in life, a period of great susceptibility to epigenetic reprogramming due to environmental insults. Assisted reproductive technologies (ART), i.e., treatments for infertility, may affect embryo development, resulting in multiple adverse health outcomes in postnatal life. The most frequently observed alteration in ART pregnancies is impaired placental nutrient transfer. Moreover, consequent intrauterine growth restriction and low birth weight followed by catch-up growth can all predict future obesity, insulin resistance, and chronic metabolic diseases. In this review, we have focused on evidence of adverse metabolic alterations associated with ART, which can contribute to the development of chronic adult-onset diseases, such as metabolic syndrome, type 2 diabetes, and cardiovascular disease. Due to high phenotypic plasticity, ART pregnancies can produce both offspring with adverse health outcomes, as well as healthy individuals. We further discuss the sex-specific and age-dependent metabolic alterations reflected in ART offspring, and how the degree of interference of a given ART procedure (from mild to more severe manipulation of the egg) affects the occurrence and degree of offspring alterations. Over the last few years, studies have reported signs of cardiometabolic alterations in ART offspring that are detectable at a young age but that do not appear to constitute a high risk of disease and morbidity per se. These abnormal phenotypes could be early indicators of the development of chronic diseases, including metabolic syndrome, in adulthood. The early detection of metabolic alterations could contribute to preventing the onset of disease in adulthood. Such early interventions may counteract the risk factors and improve the long-term health of the individual.
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Affiliation(s)
| | - Grażyna Ewa Ptak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.,Faculty of Biosciences, University of Teramo, Teramo, Italy
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14
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Choux C, Petazzi P, Sanchez-Delgado M, Hernandez Mora JR, Monteagudo A, Sagot P, Monk D, Fauque P. The hypomethylation of imprinted genes in IVF/ICSI placenta samples is associated with concomitant changes in histone modifications. Epigenetics 2020; 15:1386-1395. [PMID: 32573317 DOI: 10.1080/15592294.2020.1783168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
Although more and more children are born by Assisted Reproductive Technologies (ART), ART safety has not fully been demonstrated. Notably, ART could disturb the delicate step of implantation, and trigger placenta-related adverse outcomes with potential long-term effects, through disrupted epigenetic regulation. We have previously demonstrated that placental DNA methylation was significantly lower after IVF/ICSI than following natural conception at two differentially methylated regions (DMRs) associated with imprinted genes (IGs): H19/IGF2 and KCNQ1OT1. As histone modifications are critical for placental physiology, the aim of this study was to profile permissive and repressive histone marks in placenta biopsies to reveal a better understanding of the epigenetic changes in the context of ART. Utilizing chromatin immunoprecipitation (ChIP) coupled with quantitative PCR, permissive (H3K4me3, H3K4me2, and H3K9ac) and repressive (H3K9me3 and H3K9me2) post-translational histone modifications were quantified. The analyses revealed a significantly higher quantity of H3K4me2 precipitation in the IVF/ICSI group than in the natural conception group for H19/IGF2 and KCNQ1OT1 DMRs (P = 0.016 and 0.003, respectively). Conversely, the quantity of both repressive marks at H19/IGF2 and SNURF DMRs was significantly lower in the IVF/ICSI group than in the natural conception group (P = 0.011 and 0.027 for H19/IGF2; and P = 0.010 and 0.035 for SNURF). These novel findings highlight that DNA hypomethylation at imprinted DMRs following ART is linked with increased permissive/decreased repressive histone marks, altogether promoting a more permissive chromatin conformation. This concomitant change in epigenetic state at IGs at birth might be an important developmental event because of ART manipulations.
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Affiliation(s)
- Cécile Choux
- GAD (Génétique des anomalies du développement), Université Bourgogne Franche-Comté - INSERM UMR1231 , Dijon, France.,CHU Dijon Bourgogne, Service de Gynécologie-Obstétrique , Dijon, France
| | - Paolo Petazzi
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute , Barcelona, Spain
| | - Marta Sanchez-Delgado
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute , Barcelona, Spain
| | - José R Hernandez Mora
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute , Barcelona, Spain
| | - Ana Monteagudo
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute , Barcelona, Spain
| | - Paul Sagot
- CHU Dijon Bourgogne, Service de Gynécologie-Obstétrique , Dijon, France
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Bellvitge Biomedical Research Institute , Barcelona, Spain.,Biomedical Research Centre, University of East Anglia, Norwich Research Park , Norwich Norfolk, UK
| | - Patricia Fauque
- GAD (Génétique des anomalies du développement), Université Bourgogne Franche-Comté - INSERM UMR1231 , Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction , Dijon, France
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15
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Assisted reproductive technologies are associated with limited epigenetic variation at birth that largely resolves by adulthood. Nat Commun 2019; 10:3922. [PMID: 31477727 PMCID: PMC6718382 DOI: 10.1038/s41467-019-11929-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/30/2019] [Indexed: 12/22/2022] Open
Abstract
More than 7 million individuals have been conceived by Assisted Reproductive Technologies (ART) and there is clear evidence that ART is associated with a range of adverse early life outcomes, including rare imprinting disorders. The periconception period and early embryogenesis are associated with widespread epigenetic remodeling, which can be influenced by ART, with effects on the developmental trajectory in utero, and potentially on health throughout life. Here we profile genome-wide DNA methylation in blood collected in the newborn period and in adulthood (age 22–35 years) from a unique longitudinal cohort of ART-conceived individuals, previously shown to have no differences in health outcomes in early adulthood compared with non-ART-conceived individuals. We show evidence for specific ART-associated variation in methylation around birth, most of which occurred independently of embryo culturing. Importantly, ART-associated epigenetic variation at birth largely resolves by adulthood with no direct evidence that it impacts on development and health. Use of Assisted Reproductive Technologies (ART) is increasing globally but their impact on long term health remains unclear. Here the authors show that ART-conceived individuals show variation in epigenetic profile at birth that largely resolves by adulthood, with no evidence of an impact on long term outcomes.
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16
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Mani S, Ghosh J, Coutifaris C, Sapienza C, Mainigi M. Epigenetic changes and assisted reproductive technologies. Epigenetics 2019; 15:12-25. [PMID: 31328632 DOI: 10.1080/15592294.2019.1646572] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Children conceived by Assisted Reproductive Technologies (ART) are at moderately increased risk for a number of undesirable outcomes, including low birth weight. Whether the additional risk is associated with specific procedures used in ART or biological factors that are intrinsic to infertility has been the subject of much debate, as has the mechanism by which ART or infertility might influence this risk. The potential effect of ART clinical and laboratory procedures on the gamete and embryo epigenomes heads the list of mechanistic candidates that might explain the association between ART and undesirable clinical outcomes. The reason for this focus is that the developmental time points at which ART clinical and laboratory procedures are implemented are precisely the time points at which large-scale reorganization of the epigenome takes place during normal development. In this manuscript, we review the many human studies comparing the epigenomes of ART children with children conceived in vivo, as well as assess the potential of individual ART clinical and laboratory procedures to alter the epigenome.
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Affiliation(s)
- Sneha Mani
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Jayashri Ghosh
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA
| | - Monica Mainigi
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, PA, USA
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17
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Genomic imprinting disorders: lessons on how genome, epigenome and environment interact. Nat Rev Genet 2019; 20:235-248. [PMID: 30647469 DOI: 10.1038/s41576-018-0092-0] [Citation(s) in RCA: 211] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Genomic imprinting, the monoallelic and parent-of-origin-dependent expression of a subset of genes, is required for normal development, and its disruption leads to human disease. Imprinting defects can involve isolated or multilocus epigenetic changes that may have no evident genetic cause, or imprinting disruption can be traced back to alterations of cis-acting elements or trans-acting factors that control the establishment, maintenance and erasure of germline epigenetic imprints. Recent insights into the dynamics of the epigenome, including the effect of environmental factors, suggest that the developmental outcomes and heritability of imprinting disorders are influenced by interactions between the genome, the epigenome and the environment in germ cells and early embryos.
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18
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Monteagudo-Sánchez A, Sánchez-Delgado M, Mora JRH, Santamaría NT, Gratacós E, Esteller M, de Heredia ML, Nunes V, Choux C, Fauque P, de Nanclares GP, Anton L, Elovitz MA, Iglesias-Platas I, Monk D. Differences in expression rather than methylation at placenta-specific imprinted loci is associated with intrauterine growth restriction. Clin Epigenetics 2019; 11:35. [PMID: 30808399 PMCID: PMC6390544 DOI: 10.1186/s13148-019-0630-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/08/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Genome-wide studies have begun to link subtle variations in both allelic DNA methylation and parent-of-origin genetic effects with early development. Numerous reports have highlighted that the placenta plays a critical role in coordinating fetal growth, with many key functions regulated by genomic imprinting. With the recent description of wide-spread polymorphic placenta-specific imprinting, the molecular mechanisms leading to this curious polymorphic epigenetic phenomenon is unknown, as is their involvement in pregnancies complications. RESULTS Profiling of 35 ubiquitous and 112 placenta-specific imprinted differentially methylated regions (DMRs) using high-density methylation arrays and pyrosequencing revealed isolated aberrant methylation at ubiquitous DMRs as well as abundant hypomethylation at placenta-specific DMRs. Analysis of the underlying chromatin state revealed that the polymorphic nature is not only evident at the level of allelic methylation, but DMRs can also adopt an unusual epigenetic signature where the underlying histones are biallelically enrichment of H3K4 methylation, a modification normally mutually exclusive with DNA methylation. Quantitative expression analysis in placenta identified two genes, GPR1-AS1 and ZDBF2, that were differentially expressed between IUGRs and control samples after adjusting for clinical factors, revealing coordinated deregulation at the chromosome 2q33 imprinted locus. CONCLUSIONS DNA methylation is less stable at placenta-specific imprinted DMRs compared to ubiquitous DMRs and contributes to privileged state of the placenta epigenome. IUGR-associated expression differences were identified for several imprinted transcripts independent of allelic methylation. Further work is required to determine if these differences are the cause IUGR or reflect unique adaption by the placenta to developmental stresses.
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Affiliation(s)
- Ana Monteagudo-Sánchez
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospotalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Sánchez-Delgado
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospotalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose Ramon Hernandez Mora
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospotalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Nuria Tubío Santamaría
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospotalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.,Leibniz Institute on Aging, Jena, Germany
| | - Eduard Gratacós
- Fetal I+D Fetal Medicine Research Center, BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine, Hospital Clínic and Hospital Sant Joan de Déu, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Miguel López de Heredia
- Human Molecular Genetics group, Genes, disease and Therapy Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospitalet 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Virgina Nunes
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Human Molecular Genetics group, Genes, disease and Therapy Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospitalet 199-203, 08907, L'Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigaciòn Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Cecile Choux
- Université Bourgogne Franche-Comté - INSERM UMR1231, F-21000, Dijon, France
| | - Patricia Fauque
- Université Bourgogne Franche-Comté - INSERM UMR1231, F-21000, Dijon, France
| | - Guiomar Perez de Nanclares
- (Epi) Genetics Laboratory, BioAraba National Health Institute, Hospital Universitario Araba-Txagorritxu, Vitoria-Gasteiz, Alava, Spain
| | - Lauren Anton
- Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Center for Research on Reproduction and Women's Health, University of Pennsylvania, Philadelphia, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Program, Department of Obstetrics and Gynecology, Center for Research on Reproduction and Women's Health, University of Pennsylvania, Philadelphia, USA
| | - Isabel Iglesias-Platas
- GReN (Grup de Reçerca en Neonatologia), BCNatal - Barcelona Center for Maternal-Fetal and Neonatal Medicine, Institut de Reçerca Sant Joan de Déu, Barcelona, Spain
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute - IDIBELL, Av. Gran Via de L'Hospotalet 199-203, 08907 L'Hospitalet de Llobregat, Barcelona, Spain.
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19
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Paauw ND, Lely AT, Joles JA, Franx A, Nikkels PG, Mokry M, van Rijn BB. H3K27 acetylation and gene expression analysis reveals differences in placental chromatin activity in fetal growth restriction. Clin Epigenetics 2018; 10:85. [PMID: 29983832 PMCID: PMC6020235 DOI: 10.1186/s13148-018-0508-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/29/2018] [Indexed: 01/30/2023] Open
Abstract
Background Posttranslational modification of histone tails such as histone 3 lysine 27 acetylation (H3K27ac) is tightly coupled to epigenetic regulation of gene expression. To explore whether this is involved in placenta pathology, we probed genome-wide H3K27ac occupancy by chromatin immunoprecipitation sequencing (ChIP-seq) in healthy placentas and placentas from pathological pregnancies with fetal growth restriction (FGR). Furthermore, we related specific acetylation profiles of FGR placentas to gene expression changes. Results Analysis of H3K27ac occupancy in FGR compared to healthy placentas showed 970 differentially acetylated regions distributed throughout the genome. Principal component analysis and hierarchical clustering revealed complete segregation of the FGR and control group. Next, we identified 569 upregulated genes and 521 downregulated genes in FGR placentas by RNA sequencing. Differential gene transcription largely corresponded to expected direction based on H3K27ac status. Pathway analysis on upregulated transcripts originating from hyperacetylated sites revealed genes related to the HIF-1-alpha transcription factor network and several other genes with known involvement in placental pathology (LEP, FLT1, HK2, ENG, FOS). Downregulated transcripts in the vicinity of hypoacetylated sites were related to the immune system and growth hormone receptor signaling. Additionally, we found enrichment of 141 transcription factor binding motifs within differentially acetylated regions. Of the corresponding transcription factors, four were upregulated, SP1, ARNT2, HEY2, and VDR, and two downregulated, FOSL and NR4A1. Conclusion We demonstrate a key role for genome-wide alterations in H3K27ac in FGR placentas corresponding with changes in transcription profiles of regions relevant to placental function. Future studies on the role of H3K27ac in FGR and placental-fetal development may help to identify novel targets for therapy of this currently incurable disease. Electronic supplementary material The online version of this article (10.1186/s13148-018-0508-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- N D Paauw
- 1Department of Obstetrics, Wilhelmina Children's Hospital Birth Center, University Medical Center Utrecht, Utrecht, the Netherlands.,6Division Woman and Baby, University Medical Center Utrecht, Postbus 85090, 3508 AB Utrecht, the Netherlands
| | - A T Lely
- 1Department of Obstetrics, Wilhelmina Children's Hospital Birth Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - J A Joles
- 2Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, the Netherlands
| | - A Franx
- 1Department of Obstetrics, Wilhelmina Children's Hospital Birth Center, University Medical Center Utrecht, Utrecht, the Netherlands
| | - P G Nikkels
- 3Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - M Mokry
- 4Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - B B van Rijn
- 1Department of Obstetrics, Wilhelmina Children's Hospital Birth Center, University Medical Center Utrecht, Utrecht, the Netherlands.,5Academic Unit of Human Development and Health, University of Southampton, Southampton, UK.,6Division Woman and Baby, University Medical Center Utrecht, Postbus 85090, 3508 AB Utrecht, the Netherlands
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20
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Tang L, Liu Z, Zhang R, Su C, Yang W, Yao Y, Zhao S. Imprinting alterations in sperm may not significantly influence ART outcomes and imprinting patterns in the cord blood of offspring. PLoS One 2017; 12:e0187869. [PMID: 29136648 PMCID: PMC5685618 DOI: 10.1371/journal.pone.0187869] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/29/2017] [Indexed: 12/13/2022] Open
Abstract
An increase in imprinting disorders in children conceived though assisted reproductive technologies (ARTs) has been the subject of several reports. The transmission of imprinting errors from the sperm of infertile fathers is believed to be a possible reason for the increased occurrence of these disorders. However, whether the imprinting alterations in sperm affect ART outcomes and the imprinting of offspring is unclear. In the current study, we analyzed the methylation of H19, SNRPN and KCNQ1OT1 by pyrosequencing sperm samples from 97 infertile patients and 31 proven fertile males as well as cord blood samples from 13 infantswho were conceived by infertile parents through intracytoplasmic sperm injection (ICSI) and 30 healthy newborns who were conceived naturally. After four cases were excluded owing to the lack of a sequencing signal, the infertile patients were subgrouped into normal (69 cases) and abnormal (24 cases) imprinting groups according to the reference range set by the control group. Between the groups, there were no significant differences in ART outcomes. Significantly different levels of methylation were detected in H19, but none of the imprinted genes were determined to be outside of the methylation reference range set by the values derived from the naturally conceived controls. Three CpG loci were found to be significantly hypomethylated in the maternally imprinted gene KCNQ1OT1 in two patients from the abnormal imprinting group, none of which were caused by sperm imprinting errors. In addition, the paternal H19 gene exhibited discrepant methylation patterns between the sperm controls and the cord blood controls. Our data suggest that increased imprinting errors in the sperm of infertile patients do not have an obvious influence on ART outcomes or the imprinting of offspring.
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Affiliation(s)
- Li Tang
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Zichao Liu
- Key Laboratory of Special Biological Resource Development and Utilization of Universities in Yunnan Province, Department of Life Science and Technology, Kunming University, Kunming, Yunnan Province, China
| | - Ruopeng Zhang
- Department of Reproductive Medicine, the First Affiliated Hospital of Dali University, Dali, Yunnan Province, China
| | - Cunmei Su
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Wenjuan Yang
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Youlin Yao
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Shuhua Zhao
- Department of Reproduction and Genetics, the First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
- Yunnan Population and Family Planning Research Institute, Kunming, China
- * E-mail:
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21
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Martin-Trujillo A, Vidal E, Monteagudo-Sánchez A, Sanchez-Delgado M, Moran S, Hernandez Mora JR, Heyn H, Guitart M, Esteller M, Monk D. Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors. Nat Commun 2017; 8:467. [PMID: 28883545 PMCID: PMC5589900 DOI: 10.1038/s41467-017-00639-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/17/2017] [Indexed: 02/07/2023] Open
Abstract
It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.Altered genomic imprinting is frequently reported in cancer. Here, the authors analyze copy number and methylation in cancer cell lines and primary tumors to show that imprinted methylation profiles represent the accumulation of copy number alteration, rather than epigenetic alterations.
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Affiliation(s)
- Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Sebastian Moran
- Cancer Epigenetics group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Jose Ramon Hernandez Mora
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Holger Heyn
- Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Miriam Guitart
- Genetics Laboratory, UDIAT- Diagnostic Centre, Corporació Sanitària Parc Taulí, 08208, Sabadell, Spain
| | - Manel Esteller
- Cancer Epigenetics group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, 08907, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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22
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Liu Y, Tang Y, Ye D, Ma W, Feng S, Li X, Zhou X, Chen X, Chen S. Impact of Abnormal DNA Methylation of Imprinted Loci on Human Spontaneous Abortion. Reprod Sci 2017; 25:131-139. [PMID: 28443481 DOI: 10.1177/1933719117704906] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Currently, there is a growing concern regarding the safety of assisted reproductive technology (ART) due to increased risk of spontaneous abortion (SA) and imprinting disorders in ART-conceived offspring. Early investigations suggested that aberrant genetic imprinting may be related to pregnancy loss; however, few studies have used human tissue specimens. Here the DNA methylation patterns of 3 imprinted genes, including maternally inherited GRB10 and the paternally inherited IGF2 and PEG3 genes, were evaluated in human chorionic villus samples by pyrosequencing and bisulfite sequencing polymerase chain reaction. The samples were divided into 4 groups: (1) SA of natural conception (NC; n = 84), (2) induced abortion of NC (n = 94), (3) SA after ART (n = 73), and (4) fetal reduction after ART (n = 86). The methylation levels and the percentages of abnormal methylation of the IGF2, GRB10, and PEG3 genes between the ART group and the NC group showed no significant difference. Both IGF2 and GRB10 genes showed higher methylation levels in the SA group compared to the non-SA group. Additionally, determining the single-nucleotide polymorphisms of 4 loci, including IGF2 rs3741205, rs3741206, rs3741211, and GRB10 rs2237457, showed that the TC+CC genotype of IGF2 rs3741211 had a 1.91-fold increased risk of SA after ART. However, there was no association between the mutant genotype of IGF2 rs3741211 and the methylation levels of IGF2 and H19, and ART might not affect the distribution of the abovementioned genotypes. It provides support for the opinion that genetic imprinting defects may be associated with SA, which might not be due to ART treatments.
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Affiliation(s)
- Yudong Liu
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Yan Tang
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China.,2 Center of Reproductive Medicine, Zhongshan City People's Hospital, Zhongshan, People's Republic of China
| | - Desheng Ye
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Weixu Ma
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shuxian Feng
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xuelan Li
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xingyu Zhou
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Xin Chen
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
| | - Shiling Chen
- 1 Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou, People's Republic of China
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23
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Liu Y, Zheng H, Guo P, Feng S, Zhou X, Ye D, Chen X, Chen S. DNA methyltransferase 3A promoter polymorphism is associated with the risk of human spontaneous abortion after assisted reproduction techniques and natural conception. J Assist Reprod Genet 2017; 34:245-252. [PMID: 27817038 PMCID: PMC5306405 DOI: 10.1007/s10815-016-0837-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/25/2016] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The aim of this study was to explore the association of the DNA-methyltransferase (DNMT)-3A and DNMT3B promoter polymorphisms with the risk of human spontaneous abortion after assisted reproduction techniques (ARTs) and natural conception. METHODS We collected tissues from women who underwent abortion procedures: (a) chorionic villus samples (CVS) and muscle samples (MS) from spontaneous abortions conceived by ART and natural cycle (study group), n = 152; and (b) CVS and MS from normal early pregnancy and second trimester (control group), n = 155. The single-nucleotide polymorphism (SNP) -448A > G in the DNMT3A promoter region and -149C/T polymorphism of DNMT3B were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and confirmed by sequencing. RESULTS The allele frequency of -448A among pregnancy loss group and control group was 34.2 % vs. 16.5 %, respectively. Compared with GG carriers, the DNMT3A -448AA homozygotes had an about 16-fold increased risk of spontaneous abortion [odds ratio (OR) = 16.130, 95 % confidence interval (CI), 3.665-70.984], and AG heterozygotes had an OR of 2.027 (95 % CI, 1.247-3.293). However, the distribution of -448A > G in individuals derived from ART pregnancies was not statistically significantly compared with those derived from spontaneous pregnancies (P = 0.661). For DNMT3B, we observed genotype frequencies of 100 % (TT) in the study group and the control group. CONCLUSIONS The DNMT3A -448A > G polymorphism may be a novel functional SNP and contribute to its genetic susceptibility to spontaneous abortion in Chinese women, and ART may not affect the distribution of -448A > G in pregnancy loss and normal pregnancy. The observed TT genotype of DMNT3B suggests that this is the predominant genotype of this population. The findings provide new insights into the etiology of human spontaneous abortion.
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Affiliation(s)
- Yudong Liu
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Haiyan Zheng
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
- Center of Reproductive Medicine, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, People's Republic of China
| | - Pingping Guo
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Shuxian Feng
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Xingyu Zhou
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Desheng Ye
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Xin Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China
| | - Shiling Chen
- Center for Reproductive Medicine, Department of Gynecology and Obstetrics, Nanfang Hospital, Southern Medical University, No. 1838 Guangzhou Northern Road, Guangzhou, 510515, People's Republic of China.
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24
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Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genet 2016; 12:e1006427. [PMID: 27835649 PMCID: PMC5106035 DOI: 10.1371/journal.pgen.1006427] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Thousands of regions in gametes have opposing methylation profiles that are largely resolved during the post-fertilization epigenetic reprogramming. However some specific sequences associated with imprinted loci survive this demethylation process. Here we present the data describing the fate of germline-derived methylation in humans. With the exception of a few known paternally methylated germline differentially methylated regions (DMRs) associated with known imprinted domains, we demonstrate that sperm-derived methylation is reprogrammed by the blastocyst stage of development. In contrast a large number of oocyte-derived methylation differences survive to the blastocyst stage and uniquely persist as transiently methylated DMRs only in the placenta. Furthermore, we demonstrate that this phenomenon is exclusive to primates, since no placenta-specific maternal methylation was observed in mouse. Utilizing single cell RNA-seq datasets from human preimplantation embryos we show that following embryonic genome activation the maternally methylated transient DMRs can orchestrate imprinted expression. However despite showing widespread imprinted expression of genes in placenta, allele-specific transcriptional profiling revealed that not all placenta-specific DMRs coordinate imprinted expression and that this maternal methylation may be absent in a minority of samples, suggestive of polymorphic imprinted methylation. Differences in gamete DNA methylation is subject to genome-wide reprogramming during preimplantation development to establish an embryo with an epigenetic state compatible with totipotency. DNA sequences associated with imprinted differentially methylated regions (DMRs) are largely protected from this process, retaining their parent-of-origin epigenetic marks. By comparing the methylation profiles of human oocytes, sperm, blastocysts and various somatic tissues including placenta, we observe hundreds of CpG island sequences that maintain methylation on their maternal allele in blastocysts and placenta indicative of incomplete reprogramming. In some cases this maternal methylation influence transcription of nearby genes, revealing transient imprinting in embryos after genome-activation and in placenta. Strikingly, these placenta-specific DMRs are polymorphic between placenta samples with a minority of samples being robustly unmethylated on both alleles.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Franck Court
- Laboratoire GReD, CNRS, UMR6293, Clermont-Ferrand, France
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Isabel Iglesias-Platas
- Neonatal service, Hospital Sant Joan de Déu, BCNatal Hospital Sant Joan de Déu i Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Maria Eugenia Poo-Llanillo
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institute of Research and Advanced Studies, (ICREA), Passeig de Lluís Companys, Barcelona, Spain
- Centro Nacional de Analisis Genomico (CRG-CNAG), Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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25
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Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants. Fertil Steril 2016; 106:629-639.e10. [PMID: 27288894 DOI: 10.1016/j.fertnstert.2016.05.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/10/2016] [Accepted: 05/10/2016] [Indexed: 01/26/2023]
Abstract
OBJECTIVE To evaluate the effect of infertility and intracytoplasmic sperm injection (ICSI) on DNA methylation of offspring. DESIGN Microarray analysis of DNA methylation in archived neonatal bloodspots of in vitro fertilization (IVF)/ICSI-conceived children compared with controls born to fertile and infertile parents. SETTING Academic research laboratory. PATIENT(S) Neonatal blood spots of 137 newborns conceived spontaneously, through intrauterine insemination (IUI), or through ICSI using fresh or cryopreserved (frozen) embryo transfer. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) The Illumina Infinium HumanMethylation450k BeadChip assay determined genome-wide DNA methylation. Methylation differences between conception groups were detected using a Bioconductor package, ChAMP, in conjunction with Adjacent Site Clustering (A-clustering). RESULT(S) The methylation profiles of assisted reproductive technology and IUI newborns were dramatically different from those of naturally (in vivo) conceived newborns. Interestingly, the profiles of ICSI-frozen (FET) and IUI infants were strikingly similar, suggesting that cryopreservation may temper some of the epigenetic aberrations induced by IVF or ICSI. The DNA methylation changes associated with IVF/ICSI culture conditions and/or parental infertility were detected at metastable epialleles, suggesting a lasting impact on a child's epigenome. CONCLUSION(S) Both infertility and ICSI alter DNA methylation at specific genomic loci, an effect that is mitigated to some extent by FET. The impact of assisted reproductive technology and/or fertility status on metastable epialleles in humans was uncovered. This study provides an expanded set of loci for future investigations on IVF populations.
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26
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Vincent RN, Gooding LD, Louie K, Chan Wong E, Ma S. Altered DNA methylation and expression of PLAGL1 in cord blood from assisted reproductive technology pregnancies compared with natural conceptions. Fertil Steril 2016; 106:739-748.e3. [PMID: 27178226 DOI: 10.1016/j.fertnstert.2016.04.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 11/30/2022]
Abstract
OBJECTIVE To investigate DNA methylation and expression of imprinted genes and an imprinted gene network (IGN) in neonates conceived via assisted reproductive technology (ART). DESIGN Case control. SETTING Research institution. PATIENT(S) Two hundred sixty-four cases of cord blood and/or placental villi from neonates (101 IVF, 81 ICSI, 82 naturally conceived). INTERVENTION(S) Placentas were obtained at birth for biopsy and cord blood extraction. MAIN OUTCOME MEASURE(S) DNA methylation and expression of imprinted genes. RESULT(S) DNA methylation at the PLAGL1 differentially methylated region (DMR) was significantly higher in IVF cord blood (48.0%) compared with controls (46.0%). No differences were found in DNA methylation between conception modes for KvDMR1 and LINE-1 in cord blood and placenta as well as PLAGL1 and PEG10 in placenta villi. PLAGL1 expression was lower in both IVF and ICSI cord blood groups than in controls (relative quantification of 0.65, 0.74, 0.89, respectively). Analyzing the expression of 3 genes in a PLAGL1 regulated IGN revealed different expression between conception modes and a significant correlation to PLAGL1 expression in only one (KCNQ1OT1). CONCLUSION(S) Our results suggest a stability of DNA methylation at imprinted DMRs; however, we show PLAGL1 methylation/expression to be altered after ART. As PLAGL1 expression correlated with only one of the three IGN genes in cord blood, we propose there is a more complex mechanism of regulating the IGN that may involve other genes and epigenetic modifications in this tissue. Further research investigating IGN-implicated genes in various neonatal tissues is warranted to elucidate the full effects ART-induced alterations to PLAGL1 and the IGN may have on fetal growth/development.
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Affiliation(s)
- Rebecca N Vincent
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke D Gooding
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kenny Louie
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Edgar Chan Wong
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sai Ma
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, British Columbia, Canada.
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27
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López-Abad M, Iglesias-Platas I, Monk D. Epigenetic Characterization of CDKN1C in Placenta Samples from Non-syndromic Intrauterine Growth Restriction. Front Genet 2016; 7:62. [PMID: 27200075 PMCID: PMC4844605 DOI: 10.3389/fgene.2016.00062] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023] Open
Abstract
The cyclin-dependent kinase (CDK)-inhibitor 1C (CDKN1C) gene is expressed from the maternal allele and is located within the centromeric imprinted domain at chromosome 11p15. It is a negative regulator of proliferation, with loss-of-function mutations associated with the overgrowth disorder Beckwith–Wiedemann syndrome. Recently, gain-of-function mutations within the PCNA domain have been described in two disorders characterized by growth failure, namely IMAGe (intra-uterine growth restriction, metaphyseal dysplasia, adrenal hypoplasia congenita and genital abnormalities) syndrome and Silver–Russell syndrome (SRS). Over-expression of CDKN1C by maternally inherited microduplications also results in SRS, suggesting that in addition to activating mutations this gene may regulate growth by changes in dosage. To determine if CDKN1C is involved in non-syndromic IUGR we compared the expression and DNA methylation levels in a large cohort of placental biopsies from IUGR and uneventful pregnancies. We observe higher levels of expression of CDKN1C in IUGR placentas compared to those of controls. All placenta biopsies heterozygous for the PAPA repeat sequence in exon 2 showed appropriate monoallelic expression and no mutations in the PCNA domain were observed. The expression profile was independent of both genetic or methylation variation in the minimal CDKN1C promoter interval and of methylation of the cis-acting maternally methylated region associated with the neighboring KCNQ1OT1 non-coding RNA. Chromatin immunoprecipitation revealed binding sites for CTCF within the unmethylated CDKN1C gene body CpG island and putative enhancer regions, associated with the canonical enhancer histone signature, H3K4me1 and H3K27ac, located ∼58 and 360 kb away. Using 3C-PCR we identify constitutive higher-order chromatin loops that occur between one of these putative enhancer regions and CDKN1C in human placenta tissues, which we propose facilitates expression.
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Affiliation(s)
- Miriam López-Abad
- Servicio de Neonatología, Sant Joan de Déu, Centro de Medicina Maternofetal y Neonatal Barcelona, Hospital Sant Joan de Déu y Hospital Clínic, Universitat de Barcelona Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología, Sant Joan de Déu, Centro de Medicina Maternofetal y Neonatal Barcelona, Hospital Sant Joan de Déu y Hospital Clínic, Universitat de Barcelona Barcelona, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge Barcelona, Spain
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28
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Hoeijmakers L, Kempe H, Verschure PJ. Epigenetic imprinting during assisted reproductive technologies: The effect of temporal and cumulative fluctuations in methionine cycling on the DNA methylation state. Mol Reprod Dev 2016; 83:94-107. [PMID: 26660493 DOI: 10.1002/mrd.22605] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/04/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Lianne Hoeijmakers
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam the Netherlands
| | - Hermannus Kempe
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam the Netherlands
| | - Pernette J. Verschure
- Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam the Netherlands
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Ghosh J, Mainigi M, Coutifaris C, Sapienza C. Outlier DNA methylation levels as an indicator of environmental exposure and risk of undesirable birth outcome. Hum Mol Genet 2015; 25:123-9. [PMID: 26566672 DOI: 10.1093/hmg/ddv458] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 11/04/2015] [Indexed: 12/31/2022] Open
Abstract
We have identified a novel molecular phenotype that defines a subgroup of newborns who have highly disrupted epigenomes. We profiled DNA methylation in cord blood of 114 children selected from the lowest and highest quintiles of the birth weight distribution (irrespective of their mode of conception) at 96 CpG sites in genes we have found previously to be related to birth weight or growth and metabolism. We identified those individuals in each group who differed from the mean of the distribution by the greatest magnitude at each site and for the largest number of sites. Such 'outlier' individuals differ substantially from the rest of the group in having highly disrupted methylation levels at many CpG sites. We find that children from the lowest quintile of the birth weight distribution have a significantly greater number of disrupted CpGs than children from the highest quintile of the birth weight distribution. Among children from the lowest quintile of the birth weight distribution, 'outlier' individuals are significantly more common among children conceived in vitro than children conceived in vivo. These observations are novel and potentially important because they associate a molecular phenotype (multiple and large DNA methylation differences) in normal somatic tissues (cord blood) with both a prenatal exposure (conception in vitro) and a clinically important outcome (low birth weight). These observations suggest that some individuals are more susceptible to environmentally mediated epigenetic alterations than others.
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Affiliation(s)
- Jayashri Ghosh
- Fels Institute for Cancer Research and Molecular Biology
| | - Monica Mainigi
- Department of Obstetrics & Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA 19119, USA
| | - Christos Coutifaris
- Department of Obstetrics & Gynecology, University of Pennsylvania School of Medicine, Philadelphia, PA 19119, USA
| | - Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology, Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140, USA and
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Sanchez-Delgado M, Martin-Trujillo A, Tayama C, Vidal E, Esteller M, Iglesias-Platas I, Deo N, Barney O, Maclean K, Hata K, Nakabayashi K, Fisher R, Monk D. Absence of Maternal Methylation in Biparental Hydatidiform Moles from Women with NLRP7 Maternal-Effect Mutations Reveals Widespread Placenta-Specific Imprinting. PLoS Genet 2015; 11:e1005644. [PMID: 26544189 PMCID: PMC4636177 DOI: 10.1371/journal.pgen.1005644] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 10/12/2015] [Indexed: 11/18/2022] Open
Abstract
Familial recurrent hydatidiform mole (RHM) is a maternal-effect autosomal recessive disorder usually associated with mutations of the NLRP7 gene. It is characterized by HM with excessive trophoblastic proliferation, which mimics the appearance of androgenetic molar conceptuses despite their diploid biparental constitution. It has been proposed that the phenotypes of both types of mole are associated with aberrant genomic imprinting. However no systematic analyses for imprinting defects have been reported. Here, we present the genome-wide methylation profiles of both spontaneous androgenetic and biparental NLRP7 defective molar tissues. We observe total paternalization of all ubiquitous and placenta-specific differentially methylated regions (DMRs) in four androgenetic moles; namely gain of methylation at paternally methylated loci and absence of methylation at maternally methylated regions. The methylation defects observed in five RHM biopsies from NLRP7 defective patients are restricted to lack-of-methylation at maternal DMRs. Surprisingly RHMs from two sisters with the same missense mutations, as well as consecutive RHMs from one affected female show subtle allelic methylation differences, suggesting inter-RHM variation. These epigenotypes are consistent with NLRP7 being a maternal-effect gene and involved in imprint acquisition in the oocyte. In addition, bioinformatic screening of the resulting methylation datasets identified over sixty loci with methylation profiles consistent with imprinting in the placenta, of which we confirm 22 as novel maternally methylated loci. These observations strongly suggest that the molar phenotypes are due to defective placenta-specific imprinting and over-expression of paternally expressed transcripts, highlighting that maternal-effect mutations of NLRP7 are associated with the most severe form of multi-locus imprinting defects in humans.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alejandro Martin-Trujillo
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Enrique Vidal
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona, Spain
| | - Nandita Deo
- Whipps Cross University Hospital, Barts Health NHS Trust, Leytonstone, London, United Kingdom
| | - Olivia Barney
- Leicester Royal Infirmary, Leicester, United Kingdom
| | | | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Rosemary Fisher
- Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, United Kingdom
- Trophoblastic Tumour Screening and Treatment Centre, Department of Oncology, Imperial College London, London, United Kingdom
| | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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Monk D. Genomic imprinting in the human placenta. Am J Obstet Gynecol 2015; 213:S152-62. [PMID: 26428495 DOI: 10.1016/j.ajog.2015.06.032] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 05/28/2015] [Accepted: 06/15/2015] [Indexed: 12/22/2022]
Abstract
With the launch of the National Institute of Child Health and Human Development/National Institutes of Health Human Placenta Project, the anticipation is that this often-overlooked organ will be the subject of much intense research. Compared with somatic tissues, the cells of the placenta have a unique epigenetic profile that dictates its transcription patterns, which when disturbed may be associated with adverse pregnancy outcomes. One major class of genes that is dependent on strict epigenetic regulation in the placenta is subject to genomic imprinting, the parent-of-origin-dependent monoallelic gene expression. This review discusses the differences in allelic expression and epigenetic profiles of imprinted genes that are identified between different species, which reflect the continuous evolutionary adaption of this form of epigenetic regulation. These observations divulge that placenta-specific imprinted gene that is reliant on repressive histone signatures in mice are unlikely to be imprinted in humans, whereas intense methylation profiling in humans has uncovered numerous maternally methylated regions that are restricted to the placenta that are not conserved in mice. Imprinting has been proposed to be a mechanism that regulates parental resource allocation and ultimately can influence fetal growth, with the placenta being the key in this process. Furthermore, I discuss the developmental dynamics of both classic and transient placenta-specific imprinting and examine the evidence for an involvement of these genes in intrauterine growth restriction and placenta-associated complications. Finally, I focus on examples of genes that are regulated aberrantly in complicated pregnancies, emphasizing their application as pregnancy-related disease biomarkers to aid the diagnosis of at-risk pregnancies early in gestation.
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Affiliation(s)
- David Monk
- Imprinting and Cancer Group, Cancer Epigenetic and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain.
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Januar V, Desoye G, Novakovic B, Cvitic S, Saffery R. Epigenetic regulation of human placental function and pregnancy outcome: considerations for causal inference. Am J Obstet Gynecol 2015; 213:S182-96. [PMID: 26428498 DOI: 10.1016/j.ajog.2015.07.011] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 07/03/2015] [Accepted: 07/13/2015] [Indexed: 12/14/2022]
Abstract
Epigenetic mechanisms, often defined as regulating gene activity independently of underlying DNA sequence, are crucial for healthy development. The sum total of epigenetic marks within a cell or tissue (the epigenome) is sensitive to environmental influence, and disruption of the epigenome in utero has been associated with adverse pregnancy outcomes. Not surprisingly, given its multifaceted functions and important role in regulating pregnancy outcome, the placenta shows unique epigenetic features. Interestingly however, many of these are only otherwise seen in human malignancy (the pseudomalignant placental epigenome). Epigenetic variation in the placenta is now emerging as a candidate mediator of environmental influence on placental functioning and a key regulator of pregnancy outcome. However, replication of findings is generally lacking, most likely due to small sample sizes and a lack of standardization of analytical approaches. Defining DNA methylation "signatures" in the placenta associated with maternal and fetal outcomes offers tremendous potential to improve pregnancy outcomes, but care must be taken in interpretation of findings. Future placental epigenetic research would do well to address the issues present in epigenetic epidemiology more generally, including careful consideration of sample size, potentially confounding factors, issues of tissue heterogeneity, reverse causation, and the role of genetics in modulating epigenetic profile. The importance of animal or in vitro models in establishing a functional role of epigenetic variation identified in human beings, which is key to establishing causation, should not be underestimated.
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Affiliation(s)
- Vania Januar
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Boris Novakovic
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia
| | - Silvija Cvitic
- Department of Obstetrics and Gynecology, Medical University of Graz, Graz, Austria
| | - Richard Saffery
- Cancer and Disease Epigenetics, Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Australia; Department of Pediatrics, University of Melbourne, Parkville, Australia.
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The placenta: phenotypic and epigenetic modifications induced by Assisted Reproductive Technologies throughout pregnancy. Clin Epigenetics 2015; 7:87. [PMID: 26300992 PMCID: PMC4546204 DOI: 10.1186/s13148-015-0120-2] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/02/2015] [Indexed: 02/07/2023] Open
Abstract
Today, there is growing interest in the potential epigenetic risk related to assisted reproductive technologies (ART). Much evidence in the literature supports the hypothesis that adverse pregnancy outcomes linked to ART are associated with abnormal trophoblastic invasion. The aim of this review is to investigate the relationship between epigenetic dysregulation caused by ART and subsequent placental response. The dialogue between the endometrium and the embryo is a crucial step to achieve successful trophoblastic invasion, thus ensuring a non-complicated pregnancy and healthy offspring. However, as described in this review, ART could impair both actors involved in this dialogue. First, ART may induce epigenetic defects in the conceptus by modifying the embryo environment. Second, as a result of hormone treatments, ART may impair endometrial receptivity. In some cases, it results in embryonic growth arrest but, when the development of the embryo continues, the placenta could bring adaptive responses throughout pregnancy. Amongst the different mechanisms, epigenetics, especially thanks to a finely tuned network of imprinted genes stimulated by foetal signals, may modify nutrient transfer, placental growth and vascularization. If these coping mechanisms are overwhelmed, improper maternal-foetal exchanges occur, potentially leading to adverse pregnancy outcomes such as abortion, preeclampsia or intra-uterine growth restriction. But in most cases, successful placental adaptation enables normal progress of the pregnancy. Nevertheless, the risks induced by these modifications during pregnancy are not fully understood. Metabolic diseases later in life could be exacerbated through the memory of epigenetic adaptation mechanisms established during pregnancy. Thus, more research is still needed to better understand abnormal interactions between the embryo and the milieu in artificial conditions. As trophectoderm cells are in direct contact with the environment, they deserve to be studied in more detail. The ultimate goal of these studies will be to render ART protocols safer. Optimization of the environment will be the key to improving the dialogue between the endometrium and embryo, so as to ensure that placentation after ART is similar to that following natural conception.
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Song S, Ghosh J, Mainigi M, Turan N, Weinerman R, Truongcao M, Coutifaris C, Sapienza C. DNA methylation differences between in vitro- and in vivo-conceived children are associated with ART procedures rather than infertility. Clin Epigenetics 2015; 7:41. [PMID: 25901188 PMCID: PMC4404660 DOI: 10.1186/s13148-015-0071-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/10/2015] [Indexed: 12/29/2022] Open
Abstract
Background We, and others, have demonstrated previously that there are differences in DNA methylation and transcript levels of a number of genes in cord blood and placenta between children conceived using assisted reproductive technologies (ART) and children conceived in vivo. The source of these differences (the effect of ART versus the underlying infertility) has never been determined in humans. In this study, we have attempted to resolve this issue by comparing placental DNA methylation levels at 37 CpG sites in 16 previously identified candidate genes in independent populations of children conceived in vivo (‘fertile control’ group) with ART children conceived from two groups: either autologous oocytes with infertility in one or both parents (‘infertile ART’ group) or donor oocytes (obtained from young fertile donors) without male infertility (‘donor oocyte ART’ group). Results Of the 37 CpG sites analyzed, significant differences between the three groups were found in 11 CpGs (29.73 %), using ANOVA. Tukey’s post hoc test on the significant results indicated that seven (63.63 %) of these differences were significant between the donor oocyte ART and fertile control groups. In addition, 20 of the 37 CpGs analyzed had been identified as differentially methylated between ART and fertile control groups in an independent population in a prior study. Of these 20 CpG sites, 9 also showed significant differences in the present population. An additional 9 CpGs were found to be significantly different between the two groups. Of these 18 candidate CpGs, 12 CpGs (in seven candidate genes) also showed significant differences in placental DNA methylation levels between the donor oocyte ART and fertile control groups. Conclusions These data suggest strongly that the DNA methylation differences observed between ART and in vivo conceptions are associated with some aspect of ART protocols, not simply the underlying infertility. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0071-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sisi Song
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 N Broad Street, Philadelphia, PA 19140 USA
| | - Jayashri Ghosh
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 N Broad Street, Philadelphia, PA 19140 USA
| | - Monica Mainigi
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, 3701 Market Street, 8th Floor, Philadelphia, PA 19119 USA
| | - Nahid Turan
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 N Broad Street, Philadelphia, PA 19140 USA
| | - Rachel Weinerman
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, 3701 Market Street, 8th Floor, Philadelphia, PA 19119 USA
| | - May Truongcao
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 N Broad Street, Philadelphia, PA 19140 USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, 3701 Market Street, 8th Floor, Philadelphia, PA 19119 USA
| | - Carmen Sapienza
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, 3307 N Broad Street, Philadelphia, PA 19140 USA ; Department of Pathology and Laboratory Medicine, Temple University School of Medicine, Philadelphia, PA 19140 USA
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Distinct promoter methylation and isoform-specific expression of RASFF1A in placental biopsies from complicated pregnancies. Placenta 2015; 36:397-402. [DOI: 10.1016/j.placenta.2015.01.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/20/2014] [Accepted: 01/21/2015] [Indexed: 01/13/2023]
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Abstract
This review provides an overview of the unique features of DNA methylation in the human placenta. We discuss the importance of understanding placental development, structure, and function in the interpretation of DNA methylation data. Examples are given of how DNA methylation is important in regulating placental-specific gene expression, including monoallelic expression and X-chromosome inactivation in the placenta. We also discuss studies of global DNA methylation changes in the context of placental pathology and environmental exposures.
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Affiliation(s)
- Wendy P Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
| | - E Magda Price
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada Child & Family Research Institute, Vancouver, British Columbia V5Z 4H4, Canada
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Melamed N, Choufani S, Wilkins-Haug LE, Koren G, Weksberg R. Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies. Epigenetics 2015; 10:474-83. [PMID: 25580569 DOI: 10.4161/15592294.2014.988041] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Data linking assisted reproductive technologies (ART) with aberrant DNA methylation is limited and inconclusive. In addition, most studies to date have analyzed only a small number of CpG sites and focused on methylation changes in placentas, while data on cord blood are scarce. Our aim was to compare DNA methylation in cord blood samples from ART (N = 10) and control pregnancies (N = 8) using a genome-wide approach with the Illumina® Infinium Human Methylation27 array, which interrogates 27,578 CpG sites. A total of 733 (2.7%) of the CpG sites were significantly differentially methylated between the 2 groups (P < 0.05), with an overall relative hypomethylation in the ART group (P < 0.001). Differences in DNA methylation were more pronounced for CpG sites in certain types of genomic locations and were related to baseline methylation levels and distance from CpG islands and transcription start sites. ART was associated with significantly higher variation in DNA methylation, suggesting that differences in DNA methylation between cases and controls may result from stochastic (or random) genome-wide changes in DNA methylation in ART pregnancies. We identified 24 candidate genes with 2 or more CpG sites that were significantly different between the IVF and control groups. The current study provides support for the hypothesis that ART or associated subfertility may be associated with genome-wide changes in DNA methylation, and these changes appear to be, at least in part, due to epigenetic instability in ART pregnancies. Further studies are required in order to determine the extent to which such ART-related epigenetic instability may have phenotypic consequences.
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Affiliation(s)
- Nir Melamed
- a Department of Obstetrics and Gynecology; Mount Sinai Hospital ; Toronto , ON Canada
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Iglesias-Platas I, Martin-Trujillo A, Petazzi P, Guillaumet-Adkins A, Esteller M, Monk D. Altered expression of the imprinted transcription factor PLAGL1 deregulates a network of genes in the human IUGR placenta. Hum Mol Genet 2014; 23:6275-85. [PMID: 24993786 DOI: 10.1093/hmg/ddu347] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Genomic imprinting is the epigenetic process that results in monoallelic expression of genes depending on parental origin. These genes are known to be critical for placental development and fetal growth in mammals. Aberrant epigenetic profiles at imprinted loci, such as DNA methylation defects, are surprisingly rare in pregnancies with compromised fetal growth, while variations in transcriptional output from the expressed alleles of imprinted genes are more commonly reported in pregnancies complicated with intrauterine growth restriction (IUGR). To determine if PLAGL1 and HYMAI, two imprinted transcripts deregulated in Transient Neonatal Diabetes Mellitus, are involved in non-syndromic IUGR we compared the expression and DNA methylation levels in a large cohort of placental biopsies from IUGR and uneventful pregnancies. This revealed that despite appropriate maternal methylation at the shared PLAGL1/HYMAI promoter, there was a loss of correlation between PLAGL1 and HYMAI expression in IUGR. This incongruity was due to higher HYMAI expression in IUGR gestations, coupled with PLAGL1 down-regulation in placentas from IUGR girls, but not boys. The PLAGL1 protein is a zinc-finger transcription factor that has been shown to be a master coordinator of a genetic growth network in mice. We observe PLAGL1 binding to the H19/IGF2 shared enhancers in placentae, with significant correlations between PLAGL1 levels with H19 and IGF2 expression levels. In addition, PLAGL1 binding and expression also correlate with expression levels of metabolic regulator genes SLC2A4, TCF4 and PPARγ1. Our results strongly suggest that fetal growth can be influenced by altered expression of the PLAGL1 gene network in human placenta.
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Affiliation(s)
- Isabel Iglesias-Platas
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona 08950, Spain,
| | | | - Paolo Petazzi
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut D'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08907, Spain
| | - Amy Guillaumet-Adkins
- Servicio de Neonatología, Hospital Sant Joan de Déu, Fundació Sant Joan de Déu, Barcelona 08950, Spain, Imprinting and Cancer Group
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetic and Biology Program, Institut D'Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona 08907, Spain, Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona 08097, Spain and Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain
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Court F, Camprubi C, Garcia CV, Guillaumet-Adkins A, Sparago A, Seruggia D, Sandoval J, Esteller M, Martin-Trujillo A, Riccio A, Montoliu L, Monk D. The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus. Epigenetics Chromatin 2014; 7:5. [PMID: 24667089 PMCID: PMC3986935 DOI: 10.1186/1756-8935-7-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/05/2014] [Indexed: 12/16/2022] Open
Abstract
Background Genomic imprinting is the epigenetic marking of genes that results in parent-of-origin monoallelic expression. Most imprinted domains are associated with differentially DNA methylated regions (DMRs) that originate in the gametes, and are maintained in somatic tissues after fertilization. This allelic methylation profile is associated with a plethora of histone tail modifications that orchestrates higher order chromatin interactions. The mouse chromosome 15 imprinted cluster contains multiple brain-specific maternally expressed transcripts including Ago2, Chrac1, Trappc9 and Kcnk9 and a paternally expressed gene, Peg13. The promoter of Peg13 is methylated on the maternal allele and is the sole DMR within the locus. To determine the extent of imprinting within the human orthologous region on chromosome 8q24, a region associated with autosomal recessive intellectual disability, Birk-Barel mental retardation and dysmorphism syndrome, we have undertaken a systematic analysis of allelic expression and DNA methylation of genes mapping within an approximately 2 Mb region around TRAPPC9. Results Utilizing allele-specific RT-PCR, bisulphite sequencing, chromatin immunoprecipitation and chromosome conformation capture (3C) we show the reciprocal expression of the novel, paternally expressed, PEG13 non-coding RNA and maternally expressed KCNK9 genes in brain, and the biallelic expression of flanking transcripts in a range of tissues. We identify a tandem-repeat region overlapping the PEG13 transcript that is methylated on the maternal allele, which binds CTCF-cohesin in chromatin immunoprecipitation experiments and possesses enhancer-blocker activity. Using 3C, we identify mutually exclusive approximately 58 and 500 kb chromatin loops in adult frontal cortex between a novel brain-specific enhancer, marked by H3K4me1 and H3K27ac, with the KCNK9 and PEG13 promoters which we propose regulates brain-specific expression. Conclusions We have characterised the molecular mechanism responsible for reciprocal allelic expression of the PEG13 and KCNK9 transcripts. Therefore, our observations may have important implications for identifying the cause of intellectual disabilities associated with the 8q24 locus.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - David Monk
- Imprinting and Cancer Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08907, Spain.
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Romanelli V, Nakabayashi K, Vizoso M, Moran S, Iglesias-Platas I, Sugahara N, Simón C, Hata K, Esteller M, Court F, Monk D. Variable maternal methylation overlapping the nc886/vtRNA2-1 locus is locked between hypermethylated repeats and is frequently altered in cancer. Epigenetics 2014; 9:783-90. [PMID: 24589629 PMCID: PMC4063837 DOI: 10.4161/epi.28323] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Cancer is as much an epigenetic disease as a genetic one; however, the interplay between these two processes is unclear. Recently, it has been shown that a large proportion of DNA methylation variability can be explained by allele-specific methylation (ASM), either at classical imprinted loci or those regulated by underlying genetic variants. During a recent screen for imprinted differentially methylated regions, we identified the genomic interval overlapping the non-coding nc886 RNA (previously known as vtRNA2-1) as an atypical ASM that shows variable levels of methylation, predominantly on the maternal allele in many tissues. Here we show that the nc886 interval is the first example of a polymorphic imprinted DMR in humans. Further analysis of the region suggests that the interval subjected to ASM is approximately 2 kb in size and somatically acquired. An in depth analysis of this region in primary cancer samples with matching normal adjacent tissue from the Cancer Genome Atlas revealed that aberrant methylation in bladder, breast, colon and lung tumors occurred in approximately 27% of cases. Hypermethylation occurred more frequently than hypomethylation. Using additional normal-tumor paired samples we show that on rare occasions the aberrant methylation profile is due to loss-of-heterozygosity. This work therefore suggests that the nc886 locus is subject to variable allelic methylation that undergoes cancer-associated epigenetic changes in solid tumors.
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Affiliation(s)
- Valeria Romanelli
- Imprinting and Cancer Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo, Japan
| | - Miguel Vizoso
- Cancer Epigenetics Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - Sebastián Moran
- Cancer Epigenetics Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - Isabel Iglesias-Platas
- Servicio de Neonatología; Hospital Sant Joan de Déu; Fundació Sant Joan de Déu; Barcelona, Spain
| | - Naoko Sugahara
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo, Japan
| | - Carlos Simón
- Fundación IVI; Instituto Universitario IVI; Universidad de Valencia; INCLIVA; Valencia, Spain
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology and Department of Molecular Endocrinology; National Research Institute for Child Health and Development; Tokyo, Japan
| | - Manel Esteller
- Cancer Epigenetics Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain; Department of Physiological Sciences II; School of Medicine; University of Barcelona; Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA); Barcelona, Spain
| | - Franck Court
- Imprinting and Cancer Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
| | - David Monk
- Imprinting and Cancer Group; Cancer Epigenetic and Biology Program; Institut d'Investigació Biomedica de Bellvitge; Hospital Duran i Reynals; Barcelona, Spain
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