Epigenetic changes and assisted reproductive technologies

Figures & data

Table 1. Studies using genome-wide approaches to investigate epigenetic differences due to ART.

Study	Number of samples	Technical Approach	Genes/regions	Tissue	Outcome	Reference
Katari et al., 2009	10 IVF and 13 naturally conceived	Illumina GoldenGate array	1536 CpG sites in 736 genes	Cord blood, Placenta	Lower mean methylation of IVF at CpG sites in placenta Higher mean methylation of IVF at CpG sites in cord blood	^[10]
Camprubi et al., 2013	73 ART and 121 naturally conceived	Illumina GoldenGate methylation array, Bisulfite PCR, Pyrosequencing	25 imprinted DMRs	Cord blood, Placenta	No significant differences in methylation between the two groups	^[73]
Castillo-Fernandez et al., 2017	47 IVF and 60 naturally conceived twins	MeDIP-seq	9,592,803 bins(cord blood), 9,285,089 bins (CBMC)	Cord blood, CBMC	Significant methylation differences in TNP1, C9orf3 and H19/IGF2 regions	^[91]
Melamed et al., 2015	10 ART and 8 naturally conceived	Illumina Infinium Human Methylation27K array	27,578 CpGs	Cord blood	733 (2.7%) CpGs significantly different between the two groups. Hypomethylation of 63.2% of the significantly differentially methylated sites in ART	^[86]
Hajj et al., 2017	34 IVF, 89 ICSI and 53 naturally conceived	Illumina Infinium Human Methylation450K BeadChip assay, Pyrosequencing	428,227 CpGs, ATG4C, BAZ2B, SNORD114-9	Cord blood	Significant methylation differences in 4730 (0.11%) CpGs between the groups. Hypermethylation of ATG4C in ICSI and IVF. Significant methylation difference in SNORD114-9 CpG between ICSI and controls.	^[88]
Estill et al., 2016	94 ART (IUI/ICSI) and 43 naturally conceived	Illumina Infinium Human Methylation450K BeadChip assay	394,454 probes	Fetal blood spots	Significant difference in methylation profiles of the groups.	^[87]
Litzky et al., 2017	18 IVF, 79 subfertile and 158 naturally conceived	Illumina Infinium Human Methylation450K BeadChip assay	42 genes (1730 CpGs)	Placenta	No significant relationship between CpG methylation and fertility status.	^[89]
Choufani et al., 2018	44 ART and 44 naturally conceived	Illumina Infinium Human Methylation450K BeadChip assay, Pyrosequencing	414,320 probes, LINE-1	Placenta	No statistically significant methylation differences between the two groups.	^[90]
Xu et al., 2017	5 IVF, 5 NIFT and 5 naturally conceived	Illumina Infinium Human Methylation450K BeadChip assay	485,148 probes	CVS (first trimester)	No significant differences in overall methylation between the groups.	^[95]

MS-PCR: Methylation specific PCR; MSED-qPCR: Methylation sensitive enzymatic digestion associated with real-time PCR; SeQMA: Sequence – based quantitative methylation analysis; COBRA: combined bisulfite PCR restriction analysis; SNuPe: single nucleotide primer extension; IP RP HPLC: ion pair reverse phase high performance liquid chromatography; MS-SNuPe: Methylation sensitive single nucleotide primer extension; COH: Controlled ovarian hyperstimulation; MSQ-PCR: Methylation sensitive quantitative polymerase chain reaction; MeDIP: Methylated DNA immunoprecipitation; CBMC: Cord blood mononuclear cells; LUMA: Luminometric methylation assay; Bio-COBRA: Combined bisulfite restriction analysis coupled with Agilent 2200 TapeStation platform; NIFT: non-IVF fertility treatments

Table 2. Genes epigenetically perturbed by ART identified by studies using whole genome approaches.

Katari et al., 2009			Melamed et al., 2015	Estill et al., 2016	Hajj et al., 2017	Castillo-Fernandez et al., 2017
ACBD4	HIST1H2AD	PTK2	ABL2	CYP2E1	ACTRT3	AC006449.1	ORMDL3
ACVR1B	HNRPA0	PYY	ADAMDEC1	DUSP22	ATG4C	AC007557.1	PCGF2
APOE	HSPA1L	RAET1L	C9orf762	SDK1	BAZ2B	ACSBG2	PDZD8
ARNT	IDH1	RANBP1	CHIA	SFT2D3	C17orf98	ADAMTS2	PIP4K2B
BCAN	IGF2AS	RPE65	CPA2	SPATC1L	C21orf128	AGPAT4	POLD3
BMI1	IL6	RPL7A	GNAS	SPRN	EIF4E2	ANKS1B	PRCP
BMP1	IRX3	RPS15	HIST2H2AB	WDR33	ELL2P1	AP1M2	PSMA8
CARHSP1	KLF7	RPS18	HOP		EMR4P	APAF1	PSMB3
CEBPA	KRT5	SEPHS1	IL5		GNAS	APOPT1	PTPRB
CHEK2	LAMC1	SERPINF1	IL9		GUSBP6	ARHGAP26	RAB30
CLDN6	LBX2	SHC1	KCNMB3		HERC3	ARID1B	REEP2
COL3A1	LEFTY2	SHC2	KIAA0355		HM13	ATG4D	RFX2
COL6A3	LRRC47	SHC3	MGMT		KBTBD4	BAG5	RP11-73M18.2
COPG2	LYPLA2	SLC22A2	MPP7		L3MBTL	C11orf82	RUNX3
CPA4	MAPK14	SNAI2	MPZ		LINC00189	C16orf95	S1PR5
CXCL12	MCM5	SOX1	NEUROD6		MIR1296	C9orf3	SEMA5A
CYP26C1	MDH1	SOX14	NRIP2		MIR215	CCDC69	SGPP2
DES	MEOX1	STAT3	NTNG2		MIRLET7C	CDKN2D	SLC36A3
DGCR8	MEST	TAT	OR2S2		MTHFD2P1	CERS6	SS18
DLG7	MGC3101	TBX20	PDE6C		NAP1L5	CHODL	STOX2
DLX1	MUC3B	TDGF1	POLR1C		PEG10	CHST12	TBC1D9
DLX2	MYH11	TJP1	PRCP		SGCE	CISD3	TNP1
DPF3	MYL2	TJP3	PRSS22		SNORD11	CTB	TPK1
DPPA4	NASP	TNNI1	PTH		SNORD114-9	CWC25	WDR63
EFEMP2	NNAT	TRIM8	RASSF5		STX19	DEC1	XYLT1
EGF	NODAL	TTR	RNF185			DEPTOR	ZPBP2
EGFR	ONECUT1	UBE2I	RUNX3			GM2A
ESRRB	ORC1L	USF1	SERPINA6			GPATCH8
FGF5	OTX2	UTF1	SERPINB5			GSDMB
FGFR2	PABPC4	WNT5A	SLC2A9			IKZF3
FOXD3	PAX4	ZFP42	SRMS			KCNE3
FUBP1	PDPK1		TESSP1			KDM3B
FURIN	PEG10		UGT2B4			KEAP1
GNAS	PEG3					KLC1
GPR176	PIK3CA					KRI1
GPR19	PMAIP1					LIPT2
GRB10	PRDX3					MCOLN3
GTL2	PRKCI					MLLT1
GYLTL1B	PSMB6					MLLT6
H1FNT	PSMC3					NCOA7

Figure 1. In vitro fertilization involved multiple exposures and manipulations to the gamete and embryo including superovulation, the surgical retrieval of oocytes, in vitro fertilization by sperm or injection of a single sperm into the oocyte (Intracytoplasmic sperm injection), the culture of fertilized embryos for 3–5 days, and the transfer of fresh embryos and/or embryo cryopreservation.

Katari S, Turan N, Bibikova M, et al. DNA methylation and gene expression differences in children conceived in vitro or in vivo. Hum Mol Genet. 2009;18(20):3769–3778.

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Camprubí C, Iglesias-Platas I, Martin-Trujillo A, et al. Stability of genomic imprinting and gestational-age dynamic methylation in complicated pregnancies conceived following assisted reproductive technologies. Biol Reprod. 2013;89(3):50.

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Castillo-Fernandez JE, Loke YJ, Bass-Stringer S, et al. DNA methylation changes at infertility genes in newborn twins conceived by in vitro fertilisation. Genome Med. 2017;9(1):28.

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Melamed N, Choufani S, Wilkins-Haug LE, et al. Comparison of genome-wide and gene-specific DNA methylation between ART and naturally conceived pregnancies. Epigenetics. 2015;10(6):474–483.

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El Hajj N, Haertle L, Dittrich M, et al. DNA methylation signatures in cord blood of ICSI children. Hum Reprod. 2017;32(8):1761–1769.

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Estill MS, Bolnick JM, Waterland RA, et al. Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants. Fertil Steril. 2016;106(3):629–639.e610.

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Litzky JF, Deyssenroth MA, Everson TM, et al. Placental imprinting variation associated with assisted reproductive technologies and subfertility. Epigenetics. 2017;12(8):653–661.

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Choufani S, Turinsky AL, Melamed N, et al. Impact of assisted reproduction, infertility, sex, and paternal factors on the placental DNA methylome. Hum Mol Genet. 2018;28(3):372–385.

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Xu N, Barlow GM, Cui J, et al. Comparison of genome-wide and gene-specific DNA methylation profiling in first-trimester chorionic villi from pregnancies conceived with infertility treatments. Reprod Sci. 2017;24(7):996–1004.

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