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Orellana-Guerrero D, Uribe-Salazar JM, El-Sheikh Ali H, Scoggin KE, Ball B, Daels P, Finno CJ, Dini P. Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation. Int J Mol Sci 2023; 24:ijms24087084. [PMID: 37108254 PMCID: PMC10139181 DOI: 10.3390/ijms24087084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The placenta is a temporary organ that is essential for the survival of the fetus, with a lifelong effect on the health of both the offspring and the dam. The functions of the placenta are controlled by its dynamic gene expression during gestation. In this study, we aimed to investigate the equine placental DNA methylome as one of the fundamental mechanisms that controls the gene expression dynamic. Chorioallantois samples from four (4M), six (6M), and ten (10M) months of gestation were used to map the methylation pattern of the placenta. Globally, methylation levels increased toward the end of gestation. We identified 921 differentially methylated regions (DMRs) between 4M and 6M, 1225 DMRs between 4M and 10M, and 1026 DMRs between 6M and 10M. A total of 817 genes carried DMRs comparing 4M and 6M, 978 comparing 4M and 10M, and 804 comparing 6M and 10M. We compared the transcriptomes between the samples and found 1381 differentially expressed genes (DEGs) when comparing 4M and 6M, 1428 DEGs between 4M and 10M, and 741 DEGs between 6M and 10M. Finally, we overlapped the DEGs and genes carrying DMRs (DMRs-DEGs). Genes exhibiting (a) higher expression, low methylation and (b) low expression, high methylation at different time points were identified. The majority of these DMRs-DEGs were located in introns (48.4%), promoters (25.8%), and exons (17.7%) and were involved in changes in the extracellular matrix; regulation of epithelial cell migration; vascularization; and regulation of minerals, glucose, and metabolites, among other factors. Overall, this is the first report highlighting the dynamics in the equine placenta methylome during normal pregnancy. The findings presented serve as a foundation for future studies on the impact of abnormal methylation on the outcomes of equine pregnancies.
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Affiliation(s)
- Daniela Orellana-Guerrero
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | | | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
- College of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Barry Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Peter Daels
- Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
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Lokeswara AW, Hiksas R, Irwinda R, Wibowo N. Preeclampsia: From Cellular Wellness to Inappropriate Cell Death, and the Roles of Nutrition. Front Cell Dev Biol 2021; 9:726513. [PMID: 34805141 PMCID: PMC8602860 DOI: 10.3389/fcell.2021.726513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 10/07/2021] [Indexed: 12/27/2022] Open
Abstract
Preeclampsia is one of the most common obstetrical complications worldwide. The pathomechanism of this disease begins with abnormal placentation in early pregnancy, which is associated with inappropriate decidualization, vasculogenesis, angiogenesis, and spiral artery remodeling, leading to endothelial dysfunction. In these processes, appropriate cellular deaths have been proposed to play a pivotal role, including apoptosis and autophagy. The proper functioning of these physiological cell deaths for placentation depends on the wellbeing of the trophoblasts, affected by the structural and functional integrity of each cellular component including the cell membrane, mitochondria, endoplasmic reticulum, genetics, and epigenetics. This cellular wellness, which includes optimal cellular integrity and function, is heavily influenced by nutritional adequacy. In contrast, nutritional deficiencies may result in the alteration of plasma membrane, mitochondrial dysfunction, endoplasmic reticulum stress, and changes in gene expression, DNA methylation, and miRNA expression, as well as weakened defense against environmental contaminants, hence inducing a series of inappropriate cellular deaths such as abnormal apoptosis and necrosis, and autophagy dysfunction and resulting in abnormal trophoblast invasion. Despite their inherent connection, the currently available studies examined the functions of each organelle, the cellular death mechanisms and the nutrition involved, both physiologically in the placenta and in preeclampsia, separately. Therefore, this review aims to comprehensively discuss the relationship between each organelle in maintaining the physiological cell death mechanisms and the nutrition involved, and the interconnection between the disruptions in the cellular organelles and inappropriate cell death mechanisms, resulting in poor trophoblast invasion and differentiation, as seen in preeclampsia.
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Affiliation(s)
- Angga Wiratama Lokeswara
- Faculty of Medicine, Dr. Cipto Mangunkusumo Hospital, University of Indonesia, Jakarta, Indonesia
| | - Rabbania Hiksas
- Faculty of Medicine, Dr. Cipto Mangunkusumo Hospital, University of Indonesia, Jakarta, Indonesia
| | - Rima Irwinda
- Maternal Fetal Division, Department of Obstetrics and Gynaecology, Faculty of Medicine, Dr. Cipto Mangunkusumo Hospital, University of Indonesia, Jakarta, Indonesia
| | - Noroyono Wibowo
- Maternal Fetal Division, Department of Obstetrics and Gynaecology, Faculty of Medicine, Dr. Cipto Mangunkusumo Hospital, University of Indonesia, Jakarta, Indonesia
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Menezo Y, Clement P, Clement A, Elder K. Methylation: An Ineluctable Biochemical and Physiological Process Essential to the Transmission of Life. Int J Mol Sci 2020; 21:ijms21239311. [PMID: 33297303 PMCID: PMC7730869 DOI: 10.3390/ijms21239311] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/28/2020] [Accepted: 12/02/2020] [Indexed: 02/07/2023] Open
Abstract
Methylation is a universal biochemical process which covalently adds methyl groups to a variety of molecular targets. It plays a critical role in two major global regulatory mechanisms, epigenetic modifications and imprinting, via methyl tagging on histones and DNA. During reproduction, the two genomes that unite to create a new individual are complementary but not equivalent. Methylation determines the complementary regulatory characteristics of male and female genomes. DNA methylation is executed by methyltransferases that transfer a methyl group from S-adenosylmethionine, the universal methyl donor, to cytosine residues of CG (also designated CpG). Histones are methylated mainly on lysine and arginine residues. The methylation processes regulate the main steps in reproductive physiology: gametogenesis, and early and late embryo development. A focus will be made on the impact of assisted reproductive technology and on the impact of endocrine disruptors (EDCs) via generation of oxidative stress.
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Affiliation(s)
- Yves Menezo
- Laboratoire CLEMENT, Avenue d’Eylau, 75016 Paris, France; (P.C.); (A.C.)
- Correspondence:
| | - Patrice Clement
- Laboratoire CLEMENT, Avenue d’Eylau, 75016 Paris, France; (P.C.); (A.C.)
| | - Arthur Clement
- Laboratoire CLEMENT, Avenue d’Eylau, 75016 Paris, France; (P.C.); (A.C.)
| | - Kay Elder
- Bourn Hall Clinic, Bourn, Cambridge CB232TN, UK;
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Thakali KM, Zhong Y, Cleves M, Andres A, Shankar K. Associations between maternal body mass index and diet composition with placental DNA methylation at term. Placenta 2020; 93:74-82. [PMID: 32250742 DOI: 10.1016/j.placenta.2020.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Maternal obesity and poor quality diets are associated with greater risk of obesity in offspring. Maternal diet and obesity influence placental gene expression and nutrient transport, but the impact of diet and obesity on global epigenetic changes in the placenta are poorly understood. We hypothesized that placental DNA methylation patterns are associated with maternal body mass index (BMI) and/or maternal diet composition. METHODS Using reduced representation bisulfite sequencing (RRBS), we assessed genome scale DNA methylation of ~300,000 CpGs in 150 term placentas from normal weight mothers (n = 72) and overweight/obese mothers (n = 78). Maternal BMI was assessed before week 10 of gestation and maternal diet composition was assessed using 3-day food records at each trimester. RESULTS In multivariable linear regression models, maternal BMI category (normal weight or overweight/obese), BMI (kg/m2), and maternal saturated fat consumption (g/d) were associated (p < 0.0001) with methylation of 185, 103, and 302 CpGs, respectively. Of the 56 CpGs associated with both maternal BMI category and maternal BMI (p < 0.0001), GO analysis showed biological processes related to SREBP signaling, phospholipid transport, granulocyte differentiation, and RNA pol II transcription to be affected. Maternal saturated fat intake was associated with methylation of 302 CpGs (p < 0.0001). These genes were related to chromatin remodeling, IGF receptor, PI3K, and nitric oxide synthase signaling. DISCUSSION These data suggest that placental DNA methylation status is associated with both maternal obesity and maternal saturated fat intake, possibly contributing to maternal obesity-associated changes in placental function.
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Affiliation(s)
- Keshari M Thakali
- Arkansas Children's Nutrition Center, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ying Zhong
- Arkansas Children's Nutrition Center, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mario Cleves
- Department of Pediatrics, University of South Florida, Tampa, FL, USA
| | - Aline Andres
- Arkansas Children's Nutrition Center, Little Rock, AR, USA; Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kartik Shankar
- Department of Pediatrics-Section of Nutrition, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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Clément A, Chouteau J, Clément P, Ménézo Y. [Importance of the determination of MTHFR SNPs (Methylene Tetrahydrofolate Reductase Single Nucleotide Polymorphisms) in couple infertility]. ACTA ACUST UNITED AC 2020; 48:422-427. [PMID: 32145452 DOI: 10.1016/j.gofs.2020.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 02/07/2023]
Abstract
OBJECTIVE MTHFR SNPs (Methylene Tetrahydrofolate reductase Single Nucleotide polymorphisms) are biochemical modifications decreasing the capacity to form 5 MTHF 5 methyltetrahydrofolate (5MTHF). Their presence reduces the capacity of the One Carbon cycle, and so the regeneration of Homocysteine (Hcy) and in fine strongly perturbs all the methylation processes. As methylation processes are major regulators in gametogenesis and embryogenesis. We have determined the prevalence of the 2 most important SNPs A1298C and C677T in our population of patients consulting for infertility. METHODS Determination of the MTHFR SNPs A1298C and C677T, by hybridization using the LAMP Human MTHFR mutation KITs. RESULTS Only 15.8% of our patients (861) do not carry any SNP (WT wid type). Close to 20% of the patients are homozygotes for one mutation or the other. A total of 19.7% are composite heterozygous. A total of 43% of our population is considered "at risk", based on observations collected for the repeat miscarriages. CONCLUSIONS Determination of the 2 major MTHFR SNPs is not a "first row" choice, but it must not be neglected and should be carried out in case of repeat ART failures and repeat miscarriages. Some simple therapeutic options can be proposed: they are based on the use of 5MTHF (5MethyleneTetraHydroFolate) the compound downstream the MTHFR.
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Affiliation(s)
- A Clément
- Laboratoire Clément, avenue d'Eylau, 75016 Paris, France.
| | - J Chouteau
- Laboratoire Oriade-Noviale, avenue de la Plaine-Fleurie, 38240 Meylan, France.
| | - P Clément
- Laboratoire Clément, avenue d'Eylau, 75016 Paris, France.
| | - Y Ménézo
- Laboratoire Clément, avenue d'Eylau, 75016 Paris, France; Laboratoire Oriade-Noviale, avenue de la Plaine-Fleurie, 38240 Meylan, France; London Fertility associates, Harley St, London, Royaume-Uni.
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Polymorphisms of methalenetetrahydrofolate reductase in recurrent pregnancy loss: an overview of systematic reviews and meta-analyses. J Assist Reprod Genet 2019; 36:1315-1328. [PMID: 31254142 DOI: 10.1007/s10815-019-01473-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022] Open
Abstract
PURPOSE The aim is to summarize and evaluate current systematic reviews and meta-analyses on MTHFR polymorphisms in recurrent pregnancy loss (RPL). METHODS We searched Pubmed and Embase databases and selected in form of PICOS (participants, interventions, comparisons, outcomes, and study design). Our methodology was registered on PROSPERO (CRD42017042762). Systematic reviews and meta-analyses containing primary studies were extracted for meta-analyses, along with their OR and 95%CI. We assessed the quality of the included studies using AMSTAR and OQAQ criteria. RESULTS Eleven systematic reviews and meta-analyses were identified. C677T was significantly related to RPL overall in Allele (OR, 95%CI 1.43, 1.29-1.60), Recessive (OR, 95%CI 1.66, 1.42-1.95), and Homozygous (OR, 95%CI 2.08, 1.66-2.61). There was no correlation observed between A1298C and RPL, except for in Heterozygous (OR, 95%CI 1.62, 1.17-2.25). CONCLUSIONS We identified a difference in the association between MTHFR C677T polymorphism and RPL, especially in Asian population. No significant correlation was found between A1298C and RPL.
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Goyco Ortiz LE, Servy EJ, Menezo YJR. A successful treatment with 5 methyltetrahydrofolate of a 677 TT MTHFR woman suffering premature ovarian insufficiency post a NHL (non-Hodgkin's lymphoma) and RPL (repeat pregnancy losses). J Assist Reprod Genet 2019; 36:65-67. [PMID: 30406447 PMCID: PMC6338595 DOI: 10.1007/s10815-018-1332-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/03/2018] [Indexed: 10/27/2022] Open
Affiliation(s)
- Luz E. Goyco Ortiz
- Servy Institute of Reproductive Endocrinology, 812 Chafee Avenue, Augusta, GA 30904 USA
| | - Edouard J. Servy
- Servy Institute of Reproductive Endocrinology, 812 Chafee Avenue, Augusta, GA 30904 USA
| | - Yves J. R. Menezo
- Servy Institute of Reproductive Endocrinology, 812 Chafee Avenue, Augusta, GA 30904 USA
- Laboratoire Clement, Avenue d ‘Eylau, Paris, France
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Clément A, Menezo Y, Cohen M, Cornet D, Clément P. WITHDRAWN: 5-Methyltetrahydrofolate reduces blood homocysteine level significantly in C677T methyltetrahydrofolate reductase single-nucleotide polymorphism carriers consulting for infertility. Reprod Biomed Online 2018. [DOI: 10.1016/j.rbmo.2018.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ozek MA, Karaagaoglu E, Orgul G, Gumruk F, Yurdakök M, Beksac MS. Comparison of different types of twin pregnancies in terms of obstetric and perinatal outcomes: association of vanished twins with methylenetetrahydrofolate reductase (MTHFR) polymorphism(s). J Assist Reprod Genet 2018; 35:2149-2154. [PMID: 30362058 DOI: 10.1007/s10815-018-1346-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/16/2018] [Indexed: 11/29/2022] Open
Abstract
PURPOSE Vanished twin (VT) has been associated with poor perinatal outcomes. Our research aimed to investigate the outcomes of pregnancies with vanished twin and its possible association with methylenetetrahydrofolate reductase (MTHFR) polymorphisms. METHODS This study consisted of 30 of 38 VT pregnancies (group 1, VT group), 109 singletons (group 2), 70 spontaneous twins (group 3), and 101 in vitro fertilization (IVF)/intracytoplasmic sperm injection (ICSI) twins (group 4). RESULTS Most patients in group 1 (28/30) were tested for MTHFR genes (C677T or A1298C polymorphisms). Eight of the 38 pregnancies with VT (21.1%) resulted in miscarriage. The prevalence of "2 or more pregnancy losses" in the "obstetric history" in group 1 was higher (23.3%) than those in the other groups (p = 0.007, χ2 = 17.8). The allelic frequencies of MTHFR 677 and MTHFR 1298 in group 1 were 0.268 and 0.429, respectively (higher than those in healthy population). The median birthweights in groups 1, 2, 3, and 4 were 2940, 3200, 2300, and 2095 g, respectively. The prevalence of respiratory distress syndrome was significantly higher in the IVF/ICSI twin pregnancy group (p < 0.001, χ2 = 21.2). Early pregnancy loss and the presence of "2 or more miscarriages" in the obstetric history of pregnancies with VT were more frequent. CONCLUSION The coincidence of VT and MTHFR polymorphisms might play an incidental or factual role in this connection.
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Affiliation(s)
- Murat Aykut Ozek
- Division of Perinatal Medicine, Department of Obstetrics and Gynecology, Hacettepe University Medical Faculty, Ankara, Turkey. .,Gazi University School of Medicine, 06500, Besevler-Ankara, Turkey.
| | - Ergun Karaagaoglu
- Department of Biostatistics, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Gokcen Orgul
- Division of Perinatal Medicine, Department of Obstetrics and Gynecology, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Fatma Gumruk
- Division of Hematology Department of Pediatrics, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Murat Yurdakök
- Division of Neonatology, Department of Pediatrics, Hacettepe University Medical Faculty, Ankara, Turkey
| | - M Sinan Beksac
- Division of Perinatal Medicine, Department of Obstetrics and Gynecology, Hacettepe University Medical Faculty, Ankara, Turkey
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Servy EJ, Jacquesson-Fournols L, Cohen M, Menezo YJR. MTHFR isoform carriers. 5-MTHF (5-methyl tetrahydrofolate) vs folic acid: a key to pregnancy outcome: a case series. J Assist Reprod Genet 2018; 35:1431-1435. [PMID: 29882091 DOI: 10.1007/s10815-018-1225-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
PURPOSE To evaluate the possibility of correcting metabolic defects in gametes and embryos due to methylene tetra hydrofolate reductase (MTHFR) isoforms C677T and A1298C, by supplementation with 5-methyl THF instead of synthetic folic acid. In these couples, high doses of folic acid lead to UMFA (un-metabolized folic acid) syndrome. METHODS Thirty couples with fertility problems lasting for at least 4 years, such as recurrent fetal loss, premature ovarian insufficiency, or abnormal sperm parameters, with two thirds of them having failed assisted reproductive technology (ART) attempts were included in this program. For all couples, at least one of the partners was a carrier of one of the two main MTHFR isoforms. Most of the women had been previously treated unsuccessfully with high doses of folic acid (5 mg/day), according to what is currently proposed in the literature. The couples carrying one of the isoforms were treated for 4 months with 5-MTHF, at a dose of 600 micrograms per day, before attempting conception or starting another attempt at ART. The duration of treatment corresponding to an entire cycle of spermatogenesis is approximately 74 days. RESULTS In this first series of 33 couples, one couple was not followed-up, and two are still currently under treatment. No adverse effects were observed. Thirteen of the couples conceived spontaneously, the rest needing ART treatment in order to achieve pregnancy. Only three couples have, so far, not succeeded. CONCLUSION The conventional use of large doses of folic acid (5 mg/day) has become obsolete. Regular doses of folic acid (100-200 μg) can be tolerated in the general population but should be abandoned in the presence of MTHFR mutations, as the biochemical/genetic background of the patient precludes a correct supply of 5-MTHF, the active compound. A physiological dose of 5-MTHF (800 μg) bypasses the MTHFR block and is suggested to be an effective treatment for these couples. Moreover, it avoids potential adverse effects of the UMFA syndrome, which is suspected of causing immune dysfunction and other adverse pathological effects such as cancer (especially colorectal and prostate).
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Affiliation(s)
- Edouard J Servy
- Servy Institute of Reproductive Endocrinology, 812 Chafee Avenue, Augusta, GA, 30904, USA
| | | | | | - Yves J R Menezo
- Laboratoire Clement, Avenue d'Eylau, 75016, Paris, France.
- London Fertility Associates, Harley St, London, UK.
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Rahat B, Thakur S, Hamid A, Bagga R, Kaur J. Association of aberrant methylation at promoter regions of tumor suppressor genes with placental pathologies. Epigenomics 2016; 8:767-87. [PMID: 27337502 DOI: 10.2217/epi.16.7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aim: The resemblance between invasive behavior of cancer cells and placental trophoblasts and the role of aberrant epigenetic regulation in cancer development is well known. Methods: We analyzed the role of promoter region CpG-methylation and H3K9/27me3 of tumor suppressor genes in normal and pathological pregnancies and utilized their CpG-methylation data to search for fetal DNA epigenetic marker in maternal blood. Results: CpG and H3K9/27-methylation associated decreased expression of RASSF1A and APC and increased expression of P16, RB1 and PRKCDBP was observed with advancing normal gestation. Gestational trophoblastic diseases and preeclampsia revealed gene-specific epigenetic deregulation of candidate tumor suppressor genes. Furthermore, APC and PRKCDBP showed the potential to act as fetal DNA epigenetic markers, similar to RASSF1A. Conclusion: Deregulation of methylation of tumor suppressor genes contributes to the development of preeclampsia and gestational trophoblastic diseases. APC and PRKCDBP may act as fetal DNA epigenetic markers for prenatal diagnosis.
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Affiliation(s)
- Beenish Rahat
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Shilpa Thakur
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Abid Hamid
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India
| | - Rashmi Bagga
- Department of Obstetrics & Gynecology, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
| | - Jyotdeep Kaur
- Department of Biochemistry, Postgraduate Institute of Medical Education & Research, Chandigarh 160012, India
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Tan K, Zhang Z, Miao K, Yu Y, Sui L, Tian J, An L. Dynamic integrated analysis of DNA methylation and gene expression profiles in in vivo and in vitro fertilized mouse post-implantation extraembryonic and placental tissues. Mol Hum Reprod 2016; 22:485-98. [PMID: 27090932 DOI: 10.1093/molehr/gaw028] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 03/30/2016] [Indexed: 01/02/2023] Open
Abstract
STUDY HYPOTHESIS How does in vitro fertilization (IVF) alter promoter DNA methylation patterns and its subsequent effects on gene expression profiles during placentation in mice? STUDY FINDING IVF-induced alterations in promoter DNA methylation might have functional consequences in a number of biological processes and functions during IVF placentation, including actin cytoskeleton organization, hematopoiesis, vasculogenesis, energy metabolism and nutrient transport. WHAT IS KNOWN ALREADY During post-implantation embryonic development, both embryonic and extraembryonic tissues undergo de novo DNA methylation, thereby establishing a global DNA methylation pattern, and influencing gene expression profiles. Embryonic and placental tissues of IVF conceptuses can have aberrant morphology and functions, resulting in adverse pregnancy outcomes such as pregnancy loss, low birthweight, and long-term health effects. To date, the IVF-induced global profiling of DNA methylation alterations, and their functional consequences on aberrant gene expression profiles in IVF placentas have not been systematically studied. STUDY DESIGN, SAMPLES/MATERIALS, METHODS Institute for Cancer Research mice (6 week-old females and 8-9 week-old males) were used to generate in vivo fertilization (IVO) and IVF blastocysts. After either IVO and development (IVO group as control) or in vitro fertilization and culture (IVF group), blastocysts were collected and transferred to pseudo-pregnant recipient mice. Extraembryonic (ectoplacental cone and extraembryonic ectoderm) and placental tissues from both groups were sampled at embryonic day (E) 7.5 (IVO, n = 822; IVF, n = 795) and E10.5 (IVO, n = 324; IVF, n = 278), respectively. The collected extraembryonic (E7.5) and placental tissues (E10.5) were then used for high-throughput RNA sequencing (RNA-seq) and methylated DNA immunoprecipitation sequencing (MeDIP-seq). The main dysfunctions indicated by bioinformatic analyses were further validated using molecular detection, and morphometric and phenotypic analyses. MAIN RESULTS AND THE ROLE OF CHANCE Dynamic functional profiling of high-throughput data, together with molecular detection, and morphometric and phenotypic analyses, showed that differentially expressed genes dysregulated by DNA methylation were functionally involved in: (i) actin cytoskeleton disorganization in IVF extraembryonic tissues, which may impair allantois or chorion formation, and chorioallantoic fusion; (ii) disturbed hematopoiesis and vasculogenesis, which may lead to abnormal placenta labyrinth formation and thereby impairing nutrition transport in IVF placentas; (iii) dysregulated energy and amino acid metabolism, which may cause placental dysfunctions, leading to delayed embryonic development or even lethality; (iv) disrupted genetic information processing, which can further influence gene transcriptional and translational processes. LIMITATIONS, REASONS FOR CAUTION Findings in mouse placental tissues may not be fully representative of human placentas. Further studies are necessary to confirm these findings and determine their clinical significance. WIDER IMPLICATIONS OF THE FINDINGS Our study is the first to provide the genome-wide analysis of gene expression dysregulation caused by DNA methylation during IVF placentation. Systematic understanding of the molecular mechanisms implicated in IVF placentation can be useful for the improvement of existing assisted conception systems to prevent these IVF-associated safety concerns. STUDY FUNDING AND COMPETING INTERESTS This work was supported by grants from the National Natural Science Foundation of China (No. 31472092), and the National High-Tech R&D Program (Nos. 2011|AA100303, 2013AA102506). There was no conflict of interest.
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Affiliation(s)
- Kun Tan
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Zhenni Zhang
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Kai Miao
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Yong Yu
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Linlin Sui
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Jianhui Tian
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
| | - Lei An
- National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction of the Ministry of Agriculture; College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing 100193, P. R. China
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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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Novakovic B, Saffery R. The ever growing complexity of placental epigenetics – Role in adverse pregnancy outcomes and fetal programming. Placenta 2012; 33:959-70. [DOI: 10.1016/j.placenta.2012.10.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/02/2012] [Accepted: 10/06/2012] [Indexed: 02/01/2023]
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Abstract
A striking feature of mammalian genomes is the paucity of the CG dinucleotide. There are approximately 20,000 regions termed CpG islands where CGs cluster. This represents 5% of all CGs and 1% of the genome. CpG islands are typically unmethylated and are often promoters for housekeeping genes. The remaining 95% of CG dinucleotides are disposed throughout 99% of the genome and are typically methylated and found in half of all promoters. CG methylation facilitates binding of the C/EBP family of transcription factors, proteins critical for differentiation of many tissues. This allows these proteins to localize in the methylated CG poor regions of the genome where they may produce advantageous changes in gene expression at nearby or more distant regions of the genome. In this review, our growing understanding of the consequences of CG methylation will be surveyed.
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Affiliation(s)
- Charles Vinson
- Laboratory of Metabolism, NCI, NIH, Building 37, Room 3128, Bethesda, MD 20892, USA
| | - Raghunath Chatterjee
- Laboratory of Metabolism, NCI, NIH, Building 37, Room 3128, Bethesda, MD 20892, USA
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