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Journal of Assisted Reproduction and Genetics

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01-04-2021 | Intrauterine Growth Restriction | Reproductive Physiology and Disease

Deregulation of imprinted genes expression and epigenetic regulators in placental tissue from intrauterine growth restriction

Authors: Carla Caniçais, Sara Vasconcelos, Carla Ramalho, C. Joana Marques, Sofia Dória

Published in: Journal of Assisted Reproduction and Genetics | Issue 4/2021

Abstract

Purpose

Intrauterine growth restriction (IUGR) is a fetal growth complication that can be caused by ineffective nutrient transfer from the mother to the fetus via the placenta. Abnormal placental development and function have been correlated with abnormal expression of imprinted genes, which are regulated by epigenetic modifications at imprinting control regions (ICRs). In this study, we analyzed the expression of imprinted genes known to be involved in fetal growth and epigenetic regulators involved in DNA methylation, as well as DNA methylation at the KvDMR1 imprinting control region and global levels of DNA hydroxymethylation, in IUGR cases.

Methods

Expression levels of imprinted genes and epigenetic regulators were analyzed in term placental samples from 21 IUGR cases and 9 non-IUGR (control) samples, by RT-qPCR. Additionally, KvDMR1 methylation was analyzed by bisulfite sequencing and combined bisulfite restriction analysis (COBRA) techniques. Moreover, global DNA methylation and hydroxymethylation levels were also measured.

Results

We observed increased expression of PHLDA2, CDKN1C, and PEG10 imprinted genes and of DNMT1, DNMT3A, DNMT3B, and TET3 epigenetic regulators in IUGR placentas. No differences in methylation levels at the KvDMR1 were observed between the IUGR and control groups; similarly, no differences in global DNA methylation and hydromethylation were detected.

Conclusion

Our study shows that deregulation of epigenetic mechanisms, namely increased expression of imprinted genes and epigenetic regulators, might be associated with IUGR etiology. Therefore, this study adds knowledge to the molecular mechanisms underlying IUGR, which may contribute to novel prediction tools and future therapeutic options for the management of IUGR pregnancies.

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Rhon-Calderon EA, Vrooman LA, Riesche L, Bartolomei MS. The effects of assisted reproductive technologies on genomic imprinting in the placenta. Placenta. 2019;84:37–43. https://doi.org/10.1016/j.placenta.2019.02.013.CrossRefPubMed

Gude NM, Roberts CT, Kalionis B, King RG. Growth and function of the normal human placenta. Thromb Res. 2004;114:397–407. https://doi.org/10.1016/j.thromres.2004.06.038.CrossRefPubMed

Maccani MA, Marsit CJ. Epigenetics in the placenta. Am J Reprod Immunol (New York, NY : 1989). 2009;62:78–89. https://doi.org/10.1111/j.1600-0897.2009.00716.x.CrossRef

Calkins KL, Devaskar SU. Intrauterine growth restriction. Fanaroff Martin's Neonatal-Perinatal Med. 2015;2-Volume Set:227–35. https://doi.org/10.1016/B978-1-4557-5617-9.00016-6.CrossRef

Bressan FF, De Bem THC, Perecin F, Lopes FLL, Ambrosio CE, Meirelles FVV, et al. Unearthing the roles of imprinted genes in the placenta. Placenta. 2009;30:823–34. https://doi.org/10.1016/j.placenta.2009.07.007.CrossRefPubMed

Monk D. Genomic imprinting in the human placenta. Am J Obstet Gynecol. 2015;213(4, Supplement):S152–S62. https://doi.org/10.1016/j.ajog.2015.06.032.CrossRefPubMed

Pilvar D, Reiman M, Pilvar A, Laan M. Parent-of-origin-specific allelic expression in the human placenta is limited to established imprinted loci and it is stably maintained across pregnancy. Clin Epigenetics. 2019;11(1):94. https://doi.org/10.1186/s13148-019-0692-3.CrossRefPubMedPubMedCentral

Moore T. Genomic imprinting in mammalian development: a parental tug-of-war. Trends Genet. 1991;7:45–9. https://doi.org/10.1016/0168-9525(91)90230-N.CrossRefPubMed

Cassidy FC, Charalambous M. Genomic imprinting, growth and maternal–fetal interactions. J Exp Biol. 2018;221(Suppl 1):jeb164517. https://doi.org/10.1242/jeb.164517.CrossRefPubMed

10.

Reik W, Walter J. Genomic imprinting: parental influence on the genome. Nat Rev Genet. 2001;2(1):21–32. https://doi.org/10.1038/35047554.CrossRefPubMed

11.

Santiago M, Antunes C, Guedes M, Sousa N, Marques CJ. TET enzymes and DNA hydroxymethylation in neural development and function—how critical are they? Genomics. 2014;104(5):334–40. https://doi.org/10.1016/j.ygeno.2014.08.018.CrossRefPubMed

12.

Bourque DKK, Avila L, Peñaherrera M, von Dadelszen P, Robinson WPP. Decreased placental methylation at the H19/IGF2 imprinting control region is associated with normotensive intrauterine growth restriction but not preeclampsia. Placenta. 2010;31:197–202. https://doi.org/10.1016/j.placenta.2009.12.003.CrossRefPubMed

13.

Cordeiro A, Neto AP, Carvalho F, Ramalho C, Dória S. Relevance of genomic imprinting in intrauterine human growth expression of CDKN1C, H19, IGF2, KCNQ1 and PHLDA2 imprinted genes. J Assist Reprod Genet. 2014;31:1361–8. https://doi.org/10.1007/s10815-014-0278-0.CrossRefPubMedPubMedCentral

14.

Chiesa N, De Crescenzo A, Mishra K, Perone L, Carella M, Palumbo O, et al. The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases. Hum Mol Genet. 2012;21:10–25. https://doi.org/10.1093/hmg/ddr419.CrossRefPubMed

15.

Jensen AB, Tunster SJ, John RM. The significance of elevated placental PHLDA2 in human growth restricted pregnancies. Placenta. 2014;35:528–32. https://doi.org/10.1016/j.placenta.2014.04.018.CrossRefPubMed

16.

Jin F, Qiao C, Luan N, Shang T. The expression of the imprinted gene pleckstrin homology-like domain family A member 2 in placental tissues of preeclampsia and its effects on the proliferation, migration and invasion of trophoblast cells JEG-3. Clin Exp Pharmacol Physiol. 2015;42(11):1142–51. https://doi.org/10.1111/1440-1681.12468.CrossRefPubMed

17.

Lee MH, Reynisdottir I, Massague J. Cloning of p57KIP2, a cyclin-dependent kinase inhibitor with unique domain structure and tissue distribution. Genes Dev. 1995;9(6):639–49. https://doi.org/10.1101/gad.9.6.639.CrossRefPubMed

18.

Jacob K, Robinson W, Lefebvre L. Beckwith–Wiedemann and Silver–Russell syndromes: opposite developmental imbalances in imprinted regulators of placental function and embryonic growth. Clin Genet. 2013;84(4):326–34. https://doi.org/10.1111/cge.12143.CrossRefPubMed

19.

Frost JM, Moore GE. The importance of imprinting in the human placenta. PLoS Genet. 2010;6(7):e1001015. https://doi.org/10.1371/journal.pgen.1001015.CrossRefPubMedPubMedCentral

20.

Kotzot D, Schmitt S, Bernasconi F, Robinson WP, Lurie IW, Ilyina H, et al. Uniparental disomy 7 in Silver—Russell syndrome and primordial growth retardation. Hum Mol Genet. 1995;4(4):583–7. https://doi.org/10.1093/hmg/4.4.583.CrossRefPubMed

21.

Mayer W, Hemberger M, Frank HG, Grümmer R, Winterhager E, Kaufmann P, et al. Expression of the imprinted genes MEST/Mest in human and murine placenta suggests a role in angiogenesis. Dev Dyn. 2000;217(1):1–10. https://doi.org/10.1002/(sici)1097-0177(200001)217:1<1::Aid-dvdy1>3.0.Co;2-4.CrossRefPubMed

22.

Chen H, Sun M, Liu J, Tong C, Meng T. Silencing of paternally expressed gene 10 inhibits trophoblast proliferation and invasion. PLoS One. 2015;10(12):e0144845. https://doi.org/10.1371/journal.pone.0144845.CrossRefPubMedPubMedCentral

23.

Carraca T, Ferraz T, Machado L, Bessa Monteiro S, Rodrigues T, Montengro N. Restrição de crescimento fetal- Rastreio, diagnóstico e orientação clínica. In: Lidel, editor. Protocolos de medicina materno-fetal. 3ª ed. Lisboa: Lidel; 2008. p. 133–4.

24.

Figueras F, Gratacós E. Update on the diagnosis and classification of fetal growth restriction and proposal of a stage-based management protocol. Fetal Diagn Ther. 2014;36(2):86–98. https://doi.org/10.1159/000357592.CrossRefPubMed

25.

Pidoux G, Gerbaud P, Laurendeau I, Guibourdenche J, Bertin G, Vidaud M, et al. Large variability of trophoblast gene expression within and between human normal term placentae. Placenta. 2004;25(5):469–73. https://doi.org/10.1016/j.placenta.2003.10.016.CrossRefPubMed

26.

Wyatt SM, Kraus FT, Roh CR, Elchalal U, Nelson DM, Sadovsky Y. The correlation between sampling site and gene expression in the term human placenta. Placenta. 2005;26(5):372–9. https://doi.org/10.1016/j.placenta.2004.07.003.CrossRefPubMed

27.

Marques CJ, Joao Pinho M, Carvalho F, Bieche I, Barros A, Sousa M. DNA methylation imprinting marks and DNA methyltransferase expression in human spermatogenic cell stages. Epigenetics. 2011;6(11):1354–61. https://doi.org/10.4161/epi.6.11.17993.CrossRefPubMed

28.

Hellemans J, Mortier G, De Paepe A, Speleman F, Vandesompele J. qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol. 2007;8:R19. https://doi.org/10.1186/gb-2007-8-2-r19.CrossRefPubMedPubMedCentral

29.

Khoueiry R, Ibala-Romdhane S, Al-Khtib M, Blachere T, Lornage J, Guerin JF, et al. Abnormal methylation of KCNQ1OT1 and differential methylation of H19 imprinting control regions in human ICSI embryos. Zygote. 2013;21(2):129–38. https://doi.org/10.1017/s0967199411000694.CrossRefPubMed

30.

Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res. 1997;25(12):2532–4. https://doi.org/10.1093/nar/25.12.2532.CrossRefPubMedPubMedCentral

31.

Marques CJ, Costa P, Vaz B, Carvalho F, Fernandes S, Barros A, et al. Abnormal methylation of imprinted genes in human sperm is associated with oligozoospermia. Mol Hum Reprod. 2008;14(2):67–74. https://doi.org/10.1093/molehr/gam093.CrossRefPubMed

32.

Gong S, Johnson MD, Dopierala J, Gaccioli F, Sovio U, Constância M, et al. Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta. Epigenetics. 2018;13(3):228–39. https://doi.org/10.1080/15592294.2018.1429857.CrossRefPubMedPubMedCentral

33.

Martin E, Smeester L, Bommarito PA, Grace MR, Boggess K, Kuban K, et al. Sexual epigenetic dimorphism in the human placenta: implications for susceptibility during the prenatal period. Epigenomics. 2017;9(3):267–78. https://doi.org/10.2217/epi-2016-0132.CrossRefPubMedPubMedCentral

34.

Bock C, Reither S, Mikeska T, Paulsen M, Walter J, Lengauer T. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics. 2005;21:4067–8. https://doi.org/10.1093/bioinformatics/bti652.CrossRefPubMed

35.

Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods. 2001;25(4):402–8. https://doi.org/10.1006/meth.2001.1262.CrossRefPubMed

36.

Ishida M, Moore GE. The role of imprinted genes in humans. Mol Asp Med. 2013;34:826–40. https://doi.org/10.1016/j.mam.2012.06.009.CrossRef

37.

Piedrahita JA. The role of imprinted genes in fetal growth abnormalities. Birth Defects Res A, Clin Molec Teratol. 2011;91:682–92. https://doi.org/10.1002/bdra.20795.CrossRef

38.

McMinn J, Wei M, Schupf N, Cusmai J, Johnson EB, Smith AC, et al. Unbalanced placental expression of imprinted genes in human intrauterine growth restriction. Placenta. 2006;27:540–9. https://doi.org/10.1016/j.placenta.2005.07.004.CrossRefPubMed

39.

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. https://doi.org/10.3389/fgene.2016.00062.CrossRefPubMedPubMedCentral

40.

Diplas AI, Lambertini L, Lee M-J, Sperling R, Lee YL, Wetmur J, et al. Differential expression of imprinted genes in normal and IUGR human placentas. Epigenetics. 2009;4:235–40.CrossRef

41.

Janssen AB, Tunster SJ, Heazell AEP, John RM. Placental PHLDA2 expression is increased in cases of fetal growth restriction following reduced fetal movements. BMC Med Genet. 2016;17:17. https://doi.org/10.1186/s12881-016-0279-1.CrossRefPubMedPubMedCentral

42.

Apostolidou S, Abu-Amero S, O’Donoghue K, Frost J, Olafsdottir O, Chavele KM, et al. Elevated placental expression of the imprinted PHLDA2 gene is associated with low birth weight. J Mol Med. 2007;85:379–87. https://doi.org/10.1007/s00109-006-0131-8.CrossRefPubMed

43.

Chen XJ, Chen F, Lv PP, Zhang D, Ding GL, Hu XL, et al. Maternal high estradiol exposure alters CDKN1C and IGF2 expression in human placenta. Placenta. 2018;61:72–9. https://doi.org/10.1016/j.placenta.2017.11.009.CrossRefPubMed

44.

Moore GGE, Ishida M, Demetriou C, Al-Olabi L, Leon LJ, Thomas AC, et al. The role and interaction of imprinted genes in human fetal growth. Philos Trans R Soc Lond Ser B Biol Sci. 2015;370:20140074. https://doi.org/10.1098/rstb.2014.0074.CrossRef

45.

Gou C, Liu X, Shi X, Chai H, He ZM, Huang X, et al. Placental expressions of CDKN1C and KCNQ1OT1 in monozygotic twins with selective intrauterine growth restriction. Twin Res Hum Genet. 2017;20(5):389–94. https://doi.org/10.1017/thg.2017.41.CrossRefPubMed

46.

Shi X, He Z, Gao Y, Luo Y, Gou C, Fang Q. Placental expression of PHLDA2 in selective intrauterine growth restriction in monozygotic twins. Placenta. 2014;35(6):428–30. https://doi.org/10.1016/j.placenta.2014.03.006.CrossRefPubMed

47.

Jin F, Qiao C, Luan N, Li H. Lentivirus-mediated PHLDA2 overexpression inhibits trophoblast proliferation, migration and invasion, and induces apoptosis. Int J Mol Med. 2016;42016:949–57.CrossRef

48.

Hannula-Jouppi K, Muurinen M, Lipsanen-Nyman M, Reinius LE, Ezer S, Greco D, et al. Differentially methylated regions in maternal and paternal uniparental disomy for chromosome 7. Epigenetics. 2014;9(3):351–65. https://doi.org/10.4161/epi.27160.CrossRefPubMed

49.

Vasconcelos S, Ramalho C, Marques CJ, Doria S. Altered expression of epigenetic regulators and imprinted genes in human placenta and fetal tissues from second trimester spontaneous pregnancy losses. Epigenetics. 2019;14:1–11. https://doi.org/10.1080/15592294.2019.1634988.CrossRef

50.

Miranda Furtado CL, Salomão KB, Verruma CG, Paulino Leite SB, Lopes Rios ÁF, Bialecka M, et al. Variation in DNA methylation in the KvDMR1 (ICR2) region in first-trimester human pregnancies. Fertil Steril. 2019;111(6):1186–93. https://doi.org/10.1016/j.fertnstert.2019.01.036.CrossRefPubMed

51.

Ishida M, Monk D, Duncan Andrew J, Abu-Amero S, Chong J, Ring Susan M, et al. Maternal inheritance of a promoter variant in the imprinted PHLDA2 gene significantly increases birth weight. Am J Hum Genet. 2012;90(4):715–9. https://doi.org/10.1016/j.ajhg.2012.02.021.CrossRefPubMedPubMedCentral

52.

Li Y, Meng G, Guo QN. Changes in genomic imprinting and gene expression associated with transformation in a model of human osteosarcoma. Exp Mol Pathol. 2008;84(3):234–9. https://doi.org/10.1016/j.yexmp.2008.03.013.CrossRefPubMed

53.

Wang R, Su L, Yu S, Ma X, Jiang C, Yu Y. Inhibition of PHLDA2 transcription by DNA methylation and YY1 in goat placenta. Gene. 2020;739:144512. https://doi.org/10.1016/j.gene.2020.144512.CrossRefPubMed

54.

De Crescenzo A, Sparago A, Cerrato F, Palumbo O, Carella M, Miceli M, et al. Paternal deletion of the 11p15.5 centromeric-imprinting control region is associated with alteration of imprinted gene expression and recurrent severe intrauterine growth restriction. J Med Genet. 2013;50:99–103. https://doi.org/10.1136/jmedgenet-2012-101352.CrossRefPubMed

55.

He Z, Lu H, Luo H, Gao F, Wang T, Gao Y, et al. The promoter methylomes of monochorionic twin placentas reveal intrauterine growth restriction-specific variations in the methylation patterns. Sci Rep. 2016;6:20181. https://doi.org/10.1038/srep20181.CrossRefPubMedPubMedCentral

56.

Piyasena C, Reynolds RM, Khulan B, Seckl JR, Menon G, Drake AJ. Placental 5-methylcytosine and 5-hydroxymethylcytosine patterns associate with size at birth. Epigenetics. 2015;10:692–7. https://doi.org/10.1080/15592294.2015.1062963.CrossRefPubMedPubMedCentral

57.

Zhang Y, Zheng D, Fang Q, Zhong M. Aberrant hydroxymethylation of ANGPTL4 is associated with selective intrauterine growth restriction in monochorionic twin pregnancies. Epigenetics. 2020;15:1–13. https://doi.org/10.1080/15592294.2020.1737355.CrossRef

58.

Logan PC, Mitchell MD, Lobie PE. DNA methyltransferases and TETs in the regulation of differentiation and invasiveness of extra-villous trophoblasts. Front Genet. 2013;4:265. https://doi.org/10.3389/fgene.2013.00265.CrossRefPubMedPubMedCentral

59.

Putiri EL, Tiedemann RL, Thompson JJ, Liu C, Ho T, Choi J-H, et al. Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells. Genome Biol. 2014;15(6):R81. https://doi.org/10.1186/gb-2014-15-6-r81.CrossRefPubMedPubMedCentral

60.

Rakoczy J, Padmanabhan N, Krzak AM, Kieckbusch J, Cindrova-Davies T, Watson ED. Dynamic expression of TET1, TET2, and TET3 dioxygenases in mouse and human placentas throughout gestation. Placenta. 2017;59:46–56. https://doi.org/10.1016/j.placenta.2017.09.008.CrossRefPubMed

61.

Hernandez Mora JR, Sanchez-Delgado M, Petazzi P, Moran S, Esteller M, Iglesias-Platas I, et al. Profiling of oxBS-450 K 5-hydroxymethylcytosine in human placenta and brain reveals enrichment at imprinted loci. Epigenetics. 2018;13(2):182–91. https://doi.org/10.1080/15592294.2017.1344803.CrossRefPubMedPubMedCentral

62.

Li W, Liu M. Distribution of 5-hydroxymethylcytosine in different human tissues. J Nucleic Acids. 2011;2011:870726–5. https://doi.org/10.4061/2011/870726.CrossRefPubMedPubMedCentral

63.

Nestor CE, Ottaviano R, Reddington J, Sproul D, Reinhardt D, Dunican D, et al. Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes. Genome Res. 2012;22(3):467–77. https://doi.org/10.1101/gr.126417.111.CrossRefPubMedPubMedCentral

64.

Green BB, Houseman EA, Johnson KC, Guerin DJ, Armstrong DA, Christensen BC, et al. Hydroxymethylation is uniquely distributed within term placenta, and is associated with gene expression. FASEB J. 2016;30(8):2874–84. https://doi.org/10.1096/fj.201600310R.CrossRefPubMedPubMedCentral

65.

Chabrun F, Huetz N, Dieu X, Rousseau G, Bouzillé G, Chao de la Barca JM, et al. Data-mining approach on transcriptomics and methylomics placental analysis highlights genes in fetal growth restriction. Front Genet. 2019. https://doi.org/10.3389/fgene.2019.01292.

66.

O'Callaghan JL, Clifton VL, Prentis P, Ewing A, Miller YD, Pelzer ES. Modulation of Placental Gene Expression in Small-for-Gestational-Age Infants. Genes (Basel). 2020;11(1):80. https://doi.org/10.3390/genes11010080.

Title: Deregulation of imprinted genes expression and epigenetic regulators in placental tissue from intrauterine growth restriction
Authors: Carla Caniçais
Sara Vasconcelos
Carla Ramalho
C. Joana Marques
Sofia Dória
Publication date: 01-04-2021
Publisher: Springer US
Keywords: Intrauterine Growth Restriction
Epigenetics
Published in: Journal of Assisted Reproduction and Genetics / Issue 4/2021
Print ISSN: 1058-0468
Electronic ISSN: 1573-7330
DOI: https://doi.org/10.1007/s10815-020-02047-3

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Deregulation of imprinted genes expression and epigenetic regulators in placental tissue from intrauterine growth restriction

Abstract

Purpose

Methods

Results

Conclusion

Keynote webinar | Spotlight on medication adherence

Springer Medicine

Abstract

Purpose

Methods

Results

Conclusion

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