Prenatal maternal stress is associated with site-specific and age acceleration changes in maternal and newborn DNA methylation

Figures & data

Table 1. Descriptive statistics of newborns and mothers included in the study.

Variable	General maternity population (N = 90)	Sexual violence population (N = 65)	Total (N = 155)§	General maternity population (N = 90)	Sexual violence population (N = 65)	Total (N = 155)§
		Newborns			Mothers
Sex
Female	43 (47.8%)	33 (5.8%)	76 (49.0%)	90 (1.0%)	65 (1.0%)	155 (100.0%)
Male	47 (52.2%)	32 (49.2%)	79 (51.0%)	0 (.0%)	0 (.0%)	0 (0.0%)
Maternal age (years)
Mean (SD)	26.2 (5.92)	17.5 (3.97)***	22.6 (6.75)	26.3 (5.95)	17.3 (3.99)***	22.6 (6.83)
Maternal BMI
Mean (SD)	28.1 (4.09)	25.9 (2.80)***	27.2 (3.76)	28.1 (4.08)	25.8 (2.78)***	27.2 (3.76)
Delivery mode
Vaginal	73 (81.1%)	46 (7.8%)	119 (76.8%)	73 (81.1%)	48 (73.8%)	121 (78.1%)
Caesarean section	17 (18.9%)	19 (29.2%)	36 (23.2%)	17 (18.9%)	17 (26.2%)	34 (21.9%)
Alcohol in pregnancy
No	75 (83.3%)	55 (84.6%)	130 (83.9%)	75 (83.3%)	56 (86.2%)	131 (84.5%)
Yes	15 (16.7%)	7 (1.8%)	22 (14.2%)	15 (16.7%)	7 (1.8%)	22 (14.2%)
Parity
Multigravida	63 (7.0%)	8 (12.3%)***	71 (45.8%)	63 (7.0%)	8 (12.3%)***	71 (45.8%)
Primigravida	24 (26.7%)	54 (83.1%)	78 (50.3%)	24 (26.7%)	55 (84.6%)	79 (51.0%)
Gestational age† (weeks)
Mean (SD)	40.1 (1.00)	39.6 (1.44)*	39.9 (1.23)	40.1 (1.00)	39.5 (1.43)**	39.9 (1.23)
Birthweight (grams) Mean (SD)	3220 (449)	2900 (553)	3080 (519)	3220 (448)	2870 (536)	3080 (516)
General trauma
Mean (SD)	2.42 (1.90)	2.22 (1.46)	2.34 (1.73)	2.46 (1.88)	2.22 (1.45)	2.35 (1.71)
Sexual trauma
Mean (SD)	.911 (1.63)	1.69 (1.60)**	1.24 (1.66)	.956 (1.63)	1.72 (1.60)**	1.28 (1.66)
War trauma
Mean (SD)	1.04 (.886)	.969 (.968)	1.01 (0.919)	1.04 (.886)	.954 (.959)	1.01 (0.915)
Chronic stress
Mean (SD)	4.57 (3.58)	8.40 (3.10)***	6.17 (3.87)	4.63 (3.60)	8.43 (2.87)***	6.23 (3.80)

Note: Differences between populations were tested with Fischer’s exact tests for categorical variables and ANOVA for continuous variables. The small differences in descriptive statistics between newborns and mothers were due to some dyads being represented by only a newborn or only a mother.

*p < 0.05, **p < 0.01, ***p < 0.001.

§Four participants were excluded from the EWAS analyses to improve protection against batch effects.

†Gestational age was measured using DNA methylation gestational age clock.

SD: standard deviation.

BMI: Body mass index.

Figure 1. Manhattan plots of eight epigenome-wide association tests of maternal stress measures among mothers (a–d) and newborns (e–h). Dashed lines indicate the Bonferroni level of significance (p = 7.07 × 10⁻⁸ for mothers and 7.23 × 10⁻⁸ for newborns). A total of 706,981 probes for mothers and 691,867 for newborns were included in analyses. N = 145.

Table 2. Bonferroni-corrected differentially methylated positions in EWAS in mothers and newborns.

Maternal stress measure	Probe	Unstandardized beta coefficient	p	Gene(s)
Mothers
General trauma
	cg11408019	0.003	1.10e − 10	NA
	cg14519777	0.006	6.87e − 08	CTA−339C12.1;CUX1
	cg14282695	0.009	1.48e − 08	SAMD4A
	cg16543391	−0.001	6.25e − 08	EML2;MIR330
Sexual trauma
	cg21219607	−0.002	5.50e − 08	PARP15
	cg06308131	−0.004	9.71e − 10	MUC4
	cg04358942	−0.001	2.86e − 08	RP11-64D24.2
	cg23527517	−0.008	1.23e − 08	OTOP3
	cg14859642	0.007	6.99e − 08	NA
	cg00489624	−0.003	1.10e − 08	DLGAP4
	cg24308336	−0.007	3.79e − 08	ARHGAP40
	cg16765764	−0.002	9.46e − 09	DHX35
	cg10897169	−0.003	6.81e − 08	BCAS4
War trauma
	cg13740840	−0.002	5.99e − 08	KIF15;MIR564;TMEM42
	cg26486174	0.013	1.61e − 08	NA
Newborns
General trauma
	cg24590750	0.000	4.25e − 08	TBPL1
	cg10783680	0.000	6.23e − 08	EXOC7
Sexual trauma
	cg10338475	0.006	4.74e − 11	CTC−436P18.1;SMIM15
	cg11386818	0.002	3.97e − 09	SYNCRIP
	cg02176407	0.003	5.69e − 08	POU3F2
	cg20807701	0.003	2.80e − 11	DNAJB9;PNPLA8;THAP5
	cg09631059	−0.005	8.48e − 09	RP11-1391J7.1;TSPAN4
	cg06873316	0.001	4.03e − 08	NELL1
War trauma
	cg08985979	0.006	2.10e − 08	AC108142.1
	cg21172322	0.018	5.88e − 10	BCAT1;RP11-662I13.3
	cg00741900	0.007	2.98e − 08	DIO3;DIO3OS;MIR1247

Figure 2. Epigenetic age acceleration and maternal stress measures in mothers and newborns. Colors correspond to the unstandardized beta coefficient of a regression of epigenetic age acceleration measures on maternal stress measures. N = 149 for mothers and N = 145 for newborns.

NOTE: IEAA: Intrinsic Epigenetic Age Acceleration.

EEAA: Extrinsic Epigenetic Age Acceleration.

*p < 0.05.

**p < 0.01.

Figure 3. Maternal stress and epigenetic age acceleration in mothers (a–d) and newborns (e–f). Darker colour corresponds to greater biological ageing. Sample sizes were N = 149 for mothers and N = 145 for newborns.

Figure 4. eFORGE analysis for enrichment of DNase I hypersensitive sites in newborns. Analyses were performed with the top 125 differentially methylated, hyper-methylated, and hypo-methylated CpG sites for the three maternal stress measures with Bonferroni-corrected significant sites in the EWAS. The top 125 DMPs were compared to the EPIC array distribution of probes to test whether the top 125 DMPs were significantly associated with DNase I hypersensitive locations in genome.

NOTE: * q < 0.05.

** q < 0.01.

Figure 5. War trauma was associated with DNA methylation and birthweight in newborns. (a) War trauma was negatively associated with birthweight. (b) DNA methylation at cg08985979 was negatively associated with birthweight. (c) War trauma was positively associated with DNA methylation at cg08985979 in an EWAS. (d) Model linking war trauma with DNA methylation and birthweight.

Data availability statement

DNA methylation data are available at gene expression omnibus under record GSE224365. R scripts are available at github.com/edward-quinn/congo_ewas.