Comparison of Genome-Wide and Gene-Specific DNA Methylation Profiling in First-Trimester Chorionic Villi From Pregnancies Conceived With Infertility Treatments

Abstract

Background:

Assisted reproductive technologies are associated with altered methylation in term placenta. However, it is unclear whether methylation patterns are the result of fertility treatments or intrauterine environment. Thus, we set out to determine whether there are differences in the first-trimester placenta that may be altered by the underlying fertility treatments. Genome-wide DNA methylation analyses from chorionic villus sampling (CVS) from matched singleton pregnancies conceived using in vitro fertilization (IVF), non-IVF fertility treatment (NIFT), or those conceived spontaneously were performed using Illumina Infinium HumanMethylation450 BeadChip from 15 matched CVS samples. Nanofluidic quantitative polymerase chain reaction (qPCR) of differently methylated genes was performed in a confirmatory cohort of 23 IVF conceptions and 24 NIFT conceptions.

Results:

Global methylation was similar among the IVF, NIFT, and spontaneous conceptions. However, differential methylation from IVF and NIFT pregnancies was present at 34 CpG sites, which was significantly different. Of those, 14 corresponded to known genes, with methylation changes detected at multiple loci in 3 genes, anaphase-promoting complex subunit 2 (ANAPC2), C-X-C motif chemokine ligand 14 (CXCL14), and regulating synaptic membrane exocytosis 1 (RIMS1). Nanofluidic qPCR of differentially methylated genes identified pre T-cell antigen receptor alpha (PTCRA) to be significantly downregulated in IVF versus NIFT conceptions.

Conclusion:

Although global methylation patterns are similar, there are differences in methylation of specific genes in IVF compared to NIFT conceptions, leading to altered gene expression. PTCRA was differentially methylated and downregulated in IVF conceptions, warranting further investigation. It remains to be determined whether these changes affect placentation and whether it is due to the more profound underlying infertility requiring IVF, yet these data provide unique insight into the first-trimester placental epigenome.

Keywords

epigenetics IVF NIFT placenta PTCRA

Get full access to this article

View all access options for this article.

References

Katari

Turan

Bibikova

. DNA methylation and gene expression differences in children conceived in vitro or in vivo. Hum Mol Genet. 2009;18(20):3769–3778.

Gosden

Trasler

Lucifero

Faddy

. Rare congenital disorders, imprinted genes, and assisted reproductive technology. Lancet. 2003;361(9373):1975–1977.

Sunderam

Chang

Flowers

., Assisted reproductive technology surveillance—United States, 2006. MMWR Surveill Summ. 2009;58(5):1–25.

Hansen

Kurinczuk

Bower

Webb

. The risk of major birth defects after intracytoplasmic sperm injection and in vitro fertilization. N Engl J Med. 2002;346(10):725–730.

Klemetti

Gissler

Sevón

Koivurova

Ritvanen

Hemminki

. Children born after assisted fertilization have an increased rate of major congenital anomalies. Fertil Steril. 2005;84(5):1300–1307.

Schieve

Meikle

Ferre

Peterson

Jeng

Wilcox

. Low and very low birth weight in infants conceived with use of assisted reproductive technology. N Engl J Med. 2002;346(10):731–737.

Strömberg

Dahlquist

Ericson

Finnström

Köster

Stjernqvist

. Neurological sequelae in children born after in-vitro fertilisation: a population-based study. Lancet. 2002;359(9305):461–465.

Manipalviratn

DeCherney

Segars

. Imprinting disorders and assisted reproductive technology. Fertil Steril. 2009;91(2):305–315.

Vermeiden

Bernardus

. Are imprinting disorders more prevalent after human in vitro fertilization or intracytoplasmic sperm injection? Fertil Steril. 2013;99(3):642–651.

10.

Feinberg

. Genome-scale approaches to the epigenetics of common human disease. Virchows Arch. 2010;456(1):13–21.

11.

Feinberg

Irizarry

Fradin

. Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med. 2010;2(49):49ra67.

12.

Monk

Salpekar

. Expression of imprinted genes in human preimplantation development. Mol Cell Endocrinol. 2001;183(suppl 1):S35–S40.

13.

Jirtle

Sander

Barrett

. Genomic imprinting and environmental disease susceptibility. Environ Health Perspect. 2000;108(3):271–278.

14.

Zaitseva

Zaitsev

Alenina

Bader

Krivokharchenko

. Dynamics of DNA-demethylation in early mouse and rat embryos developed in vivo and in vitro. Mol Reprod Dev. 2007;74(10):1255–1261.

15.

Doherty

Mann

Tremblay

Bartolomei

Schultz

. Differential effects of culture on imprinted H19 expression in the preimplantation mouse embryo. Biol Reprod. 2000;62(6):1526–1535.

16.

Khosla

Dean

Brown

Reik

Feil

. Culture of preimplantation mouse embryos affects fetal development and the expression of imprinted genes. Biol Reprod. 2001;64(3):918–926.

17.

El Hajj

Haaf

. Epigenetic disturbances in in vitro cultured gametes and embryos: implications for human assisted reproduction. Fertil Steril. 2013;99(3):632–641.

18.

Al-Khtib

Blachère

Guérin

Lefèvre

. Methylation profile of the promoters of Nanog and Oct4 in ICSI human embryos. Hum Reprod. 2012;27(10):2948–2954.

19.

Khoueiry

Ibala-Romdhane

Al-Khtib

. Abnormal methylation of KCNQ1OT1 and differential methylation of H19 imprinting control regions in human ICSI embryos. Zygote. 2013;21(2):129–138.

20.

Nelissen

Dumoulin

Daunay

Evers

Tost

van Montfoort

. Placentas from pregnancies conceived by IVF/ICSI have a reduced DNA methylation level at the H19 and MEST differentially methylated regions. Hum Reprod. 2013;28(4):1117–1126.

21.

Wang

., Evaluation of DNA methylation status at differentially methylated regions in IVF-conceived newborn twins. Fertil Steril. 2011;95(6):1975–1979.

22.

Rancourt

Harris

Michels

. Methylation levels at imprinting control regions are not altered with ovulation induction or in vitro fertilization in a birth cohort. Hum Reprod. 2012;27(7):2208–2216.

23.

Oliver

Miles

Cutfield

Hofman

Ludgate

Morison

. Defects in imprinting and genome-wide DNA methylation are not common in the in vitro fertilization population. Fertil Steril. 2012;97(1):147–153.e7.

24.

Wong

Hatakeyama

Robinson

. DNA methylation at H19/IGF2 ICR1 in the placenta of pregnancies conceived by in vitro fertilization and intracytoplasmic sperm injection. Fertil Steril. 2011;95(8):2524–2526.e1–e3.

25.

Melamed

Choufani

Wilkins-Haug

Koren

Weksberg

. Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies. Epigenetics. 2015;10(6):474–483.

26.

Buckberry

Bianco-Miotto

Hiendleder

Roberts

. Quantitative allele-specific expression and DNA methylation analysis of H19, IGF2 and IGF2R in the human placenta across gestation reveals H19 imprinting plasticity. PLoS One. 2012;7(12):e51210.

27.

Herzog

Galvez

Roks

. Tissue-specific DNA methylation profiles in newborns. Clin Epigenetics. 2013;5(1):8.

28.

Bird

. Angelman syndrome: review of clinical and molecular aspects. Appl Clin Genet. 2014;7:93–104.

29.

Niu

Wang

Huang

. Activated pregnane X receptor inhibits cervical cancer cell proliferation and tumorigenicity by inducing G2/M cell-cycle arrest. Cancer Lett. 2014;347(1):88–97.

30.

Kuang

Chen

Zhang

. The cytokine gene CXCL14 restricts human trophoblast cell invasion by suppressing gelatinase activity. Endocrinology. 2009;150(12):5596–5605.

31.

Cheong

Chng

Lim

. Alterations to DNA methylation and expression of CXCL14 are associated with suboptimal birth outcomes. J Hum Genet. 2014;59(9):504–511.

32.

Irizarry

Ladd-Acosta

Wen

. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009;41(2):178–186.

33.

Pennacchio

Bickmore

Dean

Nobrega

Bejerano

. Enhancers: five essential questions. Nat Rev Genet. 2013;14(4):288–295.

34.

Lavrov

Chelysheva

Smirnikhina

. Frequent variations in cancer-related genes may play prognostic role in treatment of patients with chronic myeloid leukemia. BMC Genet. 2016;17(suppl 1):14.

35.

Rodriguez

Suarez-Alvarez

Mosén-Ansorena

. Regulation of the transcriptional program by DNA methylation during human alphabeta T-cell development. Nucleic Acids Res. 2015;43(2):760–774.

36.

Brandeis

Frank

Keshet

. Sp1 elements protect a CpG island from de novo methylation. Nature. 1994;371(6496):435–438.

37.

Macleod

Charlton

Mullins

Bird

. Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 1994;8(19):2282–2292.

38.

Smale

. Pioneer factors in embryonic stem cells and differentiation. Curr Opin Genet Dev. 2010;20(5):519–526.

39.

Brameld

Dickinson

O’Leary

. First trimester predictors of adverse pregnancy outcomes. Aust N Z J Obstet Gynaecol. 2008;48(6):529–535.

40.

Jelliffe-Pawlowski

Shaw

Currier

. Association of early-preterm birth with abnormal levels of routinely collected first- and second-trimester biomarkers. Am J Obstet Gynecol. 2013;208(6):492.e1–e11.

41.

Feng

Lin

. High maternal serum estradiol environment in the first trimester is associated with the increased risk of small-for-gestational-age birth. J Clin Endocrinol Metab. 2014;99(6):2217–2224.

42.

Smith

McNay

Fleming

. First-trimester growth and the risk of low birth weight. N Engl J Med. 1998;339(25):1817–1822.

43.

Chu

Handley

Bunce

Surti

Hogge

Peters

. Structural and regulatory characterization of the placental epigenome at its maternal interface. PLoS One. 2011;6(2):e14723.

44.

Banister

Koestler

Maccani

Padbury

Houseman

Marsit

. Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas. Epigenetics. 2011;6(7):920–927.

45.

Anton

Brown

Bartolomei

Elovitz

. Differential methylation of genes associated with cell adhesion in preeclamptic placentas. PLoS One. 2014;9(6):e100148.

46.

Song

Ghosh

Mainigi

. DNA methylation differences between in vitro- and in vivo-conceived children are associated with ART procedures rather than infertility. Clin Epigenetics. 2015;7(1):41.

47.

El Hajj

Schneider

Lehnen

Haaf

. Epigenetics and life-long consequences of an adverse nutritional and diabetic intrauterine environment. Reproduction. 2014;148(6):R111–R120.

48.

Founds

Conley

Lyons-Weiler

Jeyabalan

Hogge

Conrad

. Altered global gene expression in first trimester placentas of women destined to develop preeclampsia. Placenta. 2009;30(1):15–24.

49.

Conway

Liem

Patel

Fan

Williams

III Pisarska

. The effect of infertility and assisted reproduction on first-trimester placental and fetal development. Fertil Steril. 2011;95(5):1801–1804.

50.

Jackson

Hong

Wang

Alexander

Gregory

Pisarska

. Pregnancy outcomes in very advanced maternal age pregnancies: the impact of assisted reproductive technology. Fertil Steril. 2015;103(1):76–80.

51.

Chandra

Copen

Stephen

. Infertility service use in the United States: data from the National Survey of Family Growth, 1982-2010. Natl Health Stat Report. 2014;(73):1–21.

52.

Huang

Adusumalli

Patel

Liem

Williams

III Pisarska

. Prevalence of chromosomal mosaicism in pregnancies from couples with infertility. Fertil Steril. 2009;91(6):2355–2360.

53.

Conway

Patel

Liem

. The risk of cytogenetic abnormalities in the late first trimester of pregnancies conceived through assisted reproduction. Fertil Steril. 2011;95(2):503–506.

54.

Clifton

VL.

Review: Sex and the human placenta: mediating differential strategies of fetal growth and survival. Placenta. 2010;31(suppl):S33–S39.

55.

Morris

Butcher

Feber

. ChAMP: 450k Chip Analysis Methylation Pipeline. Bioinformatics. 2014;30(3):428–430.

56.

Benjamini

Hochberg

. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B (Methodol). 1995;57(1):289–300.

57.

Kalisky

Quake

. Single-cell genomics. Nat Methods. 2011;8(4):311–314.

Supplementary Material

Please find the following supplemental material available below.

For Open Access articles published under a Creative Commons License, all supplemental material carries the same license as the article it is associated with.

For non-Open Access articles published, all supplemental material carries a non-exclusive license, and permission requests for re-use of supplemental material or any part of supplemental material shall be sent directly to the copyright owner as specified in the copyright notice associated with the article.

0.00 MB

0.01 MB