Maternal pre-pregnancy obesity, offspring cord blood DNA methylation, and offspring cardiometabolic health in early childhood: an epigenome-wide association study

Figures & data

Table 1. Selected baseline characteristics of study population (n = 360) mother-offspring pairs), Newborn Epigenetics STudy (NEST).

	N	% or Mean	SD
Maternal age
<25 years	101	28.1
25–29 years	88	24.4
≥30 years	171	47.5
Maternal ethnicity
African American	172	47.8
European	159	44.2
Other	29	8.1
Maternal educational attainment
Less than high school	32	8.9
High school graduate	77	21.4
More than high school	251	69.7
Maternal cigarette smoking
Smoked during pregnancy	115	32.2
Did not smoke during pregnancy	242	67.8
Maternal BMI before pregnancy
<25kg/m2	173	48.1
25–29.9 kg/m2	75	20.8
≥30kg/m2	112	31.1
Child sex
Female	187	51.9
Male	173	48.1
Birth weight
<2500g	62	17.2
≥2500g	298	82.8
Breastfeeding status in first 3 months
Never breastfed	69	19.2
Exclusively breastfed	56	15.6
Bottle and breastfed	109	30.3
Child BMI ≥85th percentile (age 4–5)
Not overweight/obese	160	67.2
Overweight/obese	78	32.8
Child BMI ≥95th percentile (age 4–5)
Not obese	194	81.5
Obese	44	18.5
Child Elevated BP (age 4–5)
No	137	85.6
Yes	23	14.4
Gestational age at delivery, months	360	38.3	2.3
Birth weight, grams	359	3108.2	667.5
BMI for age z score (age 4–5)	238	0.34	1.66
SBP percentile	160	57.98	27.65
DBP percentile	160	67.83	22.91

Table 2. Top 20 genes with differentially methylated CpGs in offspring cord blood associated with maternal obesity before and after adjustment for cell proportions, among females (n = 187).

Unadjusted for cell proportion					Adjusted for cell proportion
Annotated Gene^a	# of CpG sites	Chr.	Median Methylation Difference^b	P-value^c (min, max)	Annotated Gene^a	# of CpG sites	Chr.	Median Methylation Difference^b	P-value^c (min, max)
TAPBP	30	chr6	0.76%	3.39e^−26, 2.65e^−02	TAPBP	57	chr6	0.91%	1.09e^−12, 4.24e^−02
HMHB1	7	chr5	2.83%	7.40e^−10, 2.26e^−03	RP11-109A6.3	13	chr10	−0.90%	1.04e^−17, 1.18e^−02
WT1	25	chr11	−1.93%	1.57e^−07, 2.64e^−02	NFE2L3	6	chr7	4.40%	2.00e^−07, 3.69e^−05
PSMB9	11	chr6	−1.41%	1.73e^−06, 1.80e^−02	GLIPR1L2	11	chr12	2.96%	3.30e^−07, 3.48e^−06
DDR1	30	chr6	−1.48%	2.31e^−06, 4.33e^−02	MFSD1	10	chr3	−1.12%	2.26e^−06, 3.00e^−02
PCDHGA4	38	chr5	−1.52%	4.01e^−06, 4.97e^−02	HOXC4	22	chr12	−1.78%	5.71e^−06, 4.30e^−02
PPT2	42	chr6	−0.97%	4.02e^−06, 4.41e^−02	LSP1	14	chr11	0.56%	8.30e^−06, 1.89e^−02
GLIPR1L2	11	chr12	3.20%	4.10e^−06, 7.31e^−06	WT1	16	chr11	−1.89%	2.01e^−05, 3.60e^−02
BRCA1	26	chr17	0.94%	4.72e^−06, 3.80e^−02	DDR1-006	14	chr6	−1.70%	4.49e^−05, 4.52e^−02
FLJ12825	8	chr12	−1.80%	5.37e^−06, 2.01e^−02	CKMT2	9	chr5	−1.54%	5.23e^−05, 3.70e^−02
FBXO27	9	chr19	−2.3%	6.22e^−06, 1.44e^−02	MEST	15	chr7	1.33%	7.55e^−05, 4.51^e−02
LYPD3	8	chr19	−1.57%	6.68e^−06, 1.13e^−02	APOB	12	chr2	−2.09%	7.97e^−05, 2.08e^−03
TMEM187	12	chrX:	−1.65%	9.09e^−06, 4.66e^−03	LINC00336	9	chr6	2.25%	9.39e^−05, 1.12e^−03
CSNK1E	11	chr22	−1.82%	9.17e^−06, 3.17e^−02	C17orf64	9	chr17	−2.06%	1.50e^−04, 1.25e^−03
GRB7	13	chr17	−1.10%	1.04e^−05, 2.06e^−02	PCDHB15	4	chr5	−2.41%	3.47e^−04, 3.11e^−03
BAT1	29	chr6	1.13%	1.06e^−05, 1.70e^−02	PRR5L	5	chr11	3.64%	4.97e^−04, 6.38e^−04
EIF2C2	5	chr8	1.78%	1.07e^−05, 1.33e^−05	HOXB5	3	chr17	1.51	6.07e^−04, 1.18e^−02
MFSD1	10	chr3	−1.05%	1.13e^−05, 3.64e^−02	SEPT8-003	10	chr5	−1.63%	6.64e^−04, 2.36e^−02
GPSM3	10	chr6	1.68%	1.39e^−05, 2.60e^−02	STK10	4	chr5	−1.45%	6.75e^−04, 1.17e^−03
ATF7	1	chr12	7.16%	1.69e^−05	PCDHGB8P-002	7	chr5	−2.88%	4.20e^−04, 2.48e^−02

^aAnnotated genes shown according to FDR-corrected p-value in ascending order

^bMedian Methylation difference across all significant CpG sites annotated to denoted gene

^cMinimum and maximum p-value for significant CpG sites annotated to denoted gene

Table 3. Top 20 genes with differentially methylated CpGs in offspring cord blood associated with maternal obesity before and after adjustment for cell proportions, among males (n = 173).

Unadjusted for cell proportion					Adjusted for cell proportion
Annotated Gene^a	# of CpG sites	Chr.	Median Methylation Difference^b	P-value^c (min, max)	Annotated Gene	# of CpG sites	Chr.	Median Methylation Difference	P-value (min, max)
GFI1	9	chr1	3.74%	3.48e^−10, 1.04e-°^3	CYP26C1	10	chr10	1.73%	1.15e^−08, 9.35e^−03
HOXA3	15	chr7	1.37%	2.15e^−9, 3.84e^−02	GFI1	10	chr1	2.42%	1.15e^−08, 2.92e^−02
WDFY4	17	chr10	−1.94%	2.43e^−08, 3.55e^−02	STMN1	16	chr1	−1.49%	1.15e^−08, 2.95e^−02
AGPAT1	13	chr6	−1.09%	2.67e^−08, 4.38e^−06	CPT1B	14	chr22	1.76%	3.29e^−05, 4.40e^−03
RNF5	2	chr6	−0.70%	2.67e^−08, 2.67e^−08	HOXA5	33	chr7	1.14%	3.29e^−05, 4.26e^−02
RNF5P1	22	chr6	−1.02%	6.54e^−08, 1.90e^−04	ZNF135	10	chr19	1.47%	2.07e^−04, 5.94e^−03
STMN1	15	chr1	−1.50%	1.41e^−07, 3.90e^−02	MOV10L1	8	chr22	1.33%	7.80e^−04, 9.00e^−04
GABBR1	18	chr6	1.59%	1.61e^−07, 3.18e^−03	PIGZ	3	chr3	2.84%	1.15e^−03, 3.12e^−03
CYP26C1	9	chr10	1.64%	3.15e^−06, 3.84e^−02	HOXA	8	chr7	1.21%	2.53e^−03, 7.84e^−03
FOXK2	6	chr17	3.10%	7.97e^−06, 1.56e^−05	C17orf98	8	chr17	−2.28%	3.12e^−03, 4.41e^−02
TLR5	5	chr1	2.18%	9.32e^−06, 4.97e^−03	TAPBP	17	chr6	1.22%	4.01e^−03, 3.90e^−02
CUX2	8	chr12	−2.28%	1.57e^−05, 4.07e^−05	TLR5	5	chr1	1.35%	4.20e^−03, 3.73e^−02
CMYA5	12	chr5	3.2%	2.15e^−05, 4.79e^−04	CMYA5	12	chr5	2.78%	5.23e^−03, 2.97e^−02
C1orf210	8	chr1	1.52%	2.44e^−05, 2.09e^−02	POU2AF	3	chr11	1.50%	5.23e^−03, 3.72e^−02
PIGZ	3	chr3	3.05%	7.96e^−05, 2.55e^−04	KIAA0101	9	chr15	−0.87%	5.41e^−03, 7.07e^−03
CSNK1E	10	chr22	−1.52%	9.77e^−05, 1.52e^−03	PTPN3	2	chr9	0.65%	5.41e^−03, 5.76e^−03
PCDHB3	1	chr5	−6.60%	1.15e^−04	BRSK2	2	chr11	5.4%	6.25e^−03, 8.78e^−03
CPT1B	14	chr22	1.65%	1.62e^−4, 1.41e^−02	RNU6	5	chr1	2.35%	7.26e^−03, 2.32e^−02
KIAA0101	9	chr15	−1.25%	1.75e^−04, 2.70e^−04	TMEM72	4	chr10	3.47%	7.31e^−03, 1.10e^−02
BRD2	12	chr6	1.23%	1.78e^−04, 3.39e^−02	AGPAT1	21	chr6	−0.78	7.82e^−03, 4.78e^−02

^aAnnotated genes shown according to FDR-corrected p-value in ascending order

^bMedian Methylation difference across all significant CpG sites annotated to denoted gene

^cMinimum and maximum p-value for significant CpG sites annotated to denoted gene

Table 4. Associations^a of TAPBP DNA methylation sites^b with child BMI z-score and elevated blood pressure at 4–5 years of age, among 238 female and male offspring in NEST cohort.

	Females			Males
TAPBP gene^c, d	BMI z-score β (95% CI)	Systolic Blood Pressure Percentile β (95% CI)	Diastolic Blood Pressure Percentile β (95% CI)	BMI z-score β (95% CI)	Systolic Blood Pressure Percentile β (95% CI)	Diastolic Blood Pressure Percentile β (95% CI)
cg23922433	1.58 (0.73, 0.14)	4.23 (−22.46, 30.92)	10.51 (13.64, 34.66)	–	–	–
cg16632096	0.28 (−1.08, 1.63)	−10.24 (−35.84, 15.37)	−11.44 (−34.65, 11.77)	–	–	–
cg17621507	−1.18 (−2.22, −0.16)	−2.77 (−25.12, 19.59)	2.67 (−17.64, 22.97)	–	–	–
cg03780271	0.21 (−1.22, 1.63)	2.64 (−22.29, 27.56)	4.29 (−18.34, 26.91)	−0.32 (−1.19, 0.55)	−5.78 (−30.15, 15.59)	−23.70 (−41.17, −6.23)
cg12589538	−0.09 (−1.21, 1.03)	0.70 (−20.09, 21.50)	5.63 (−13.22, 24.48)	0.04 (−0.81, 0.89)	3.55 (−20.11, 27.22)	−8.59 (−26.19, 9.00)
cg11796996	−0.08 (−2.51, 0.87)	−2.10 (−33.46, 29.25)	3.65 (−.24.82, 32.12)	−0.59 (−1.69, 0.51)	11.01 (−20.65, 42.68)	−14.60 (−38.11, 8.92)
cg02863594	0.59 (−0.95, 2.12)	−23.56 (−50.58, 3.46)	6.15 (−18.82, 31.11)	−0.58 (−1.71, 0.56)	22.31 (−8.27, 52.90)	−5.05 (−28.18, 18.08)
cg01253676	−0.03 (−1.38, 1.31)	−9.21 (−33.86, 15.43)	0.51 (−23.95, 22.97)	−0.21 (−1.22, 0.80)	9.22 (−18.95, 37.40)	0.41 (−20.70, 21.53)
cg20998791	0.25 (−0.84, 1.35)	−10.25 (−29.39, 8.89)	−1.06 (−18.56, 16.45)	−0.13 (−1.02, 0.77)	9.41 (−14.18, 33.00)	−4.68 (−22.25, 12.99)
cg18353226	0.28 (−0.80, 1.35)	−6.19 (−25.22, 12.84)	−0.92 (−18.25, 16.41)	0.12 (−0.68, 0.92)	7.84 (−14.20, 29.88)	−3.01 (−19.52, 13.50)
cg14419102	0.32 (−0.57, 1.22)	−12.56 (−28.44, 3.31)	−0.07 (−14.58, 14.71)	0.28 (−0.39, 0.95)	5.60 (−12.82, 24.01)	−3.38 (−17.16, 10.39)
cg06375761	0.26 (−0.46, 0.97)	−9.30 (−22.28, 3.68)	−2.58 (−14.51, 9.34)	0.12 (−0.41, 0.64)	7.60 (−6.55, 21.75)	−2.47 (−13.11, 8.17)
cg26083458	0.05 (−0.85, 0.95)	−7.73 (−24.27, 8.81)	2.66 (−12.44, 17.75)	0.26 (−0.41, 0.93)	6.29 (−11.56, 24.13)	−3.56 (−16.92, 9.80)
cg13638257	−0.30 (−1.49, 0.89)	−0.84 (−21.85, 20.16)	5.82 (−13.21, 24.86)	−0.08 (−0.92, 0.77)	15.05 (−7.33, 37.44)	0.59 (−16.32, 17.51)
cg05700142	0.21 (−0.47, 0.89)	−5.47 (−18.17, 7.23)	3.65 (−7.91, 15.21)	0.05 (−0.44, 0.53)	9.61 (−3.29, 22.51)	−0.77 (−10.54, 9.00)
cg01654446	0.06 (−0.68, 0.81)	−2.96 (−17.24, 11.32)	3.64 (−9.31, 16.60)	−0.28 (−0.74, 0.17)	4.56 (−8.46, 17.57)	4.15 (−5.56, 13.86)
cg18930100	−0.24 (−1.44, 0.97)	−3.94 (−26.46, 18.58)	3.09 (−17.37, 23.55)	−0.58 (−1.47, 0.31)	24.21 (−1.16, 49.57)	7.93 (−11.37, 27.22)
cg06230948	−0.13 (−0.60, 0.34)	9.54 (1.16, 17.93)	0.38 (−7.47, 8.23)	0.17 (−0.13, 0.47)	8.11 (0.29, 15.95)	3.87 (−2.07, 9.81)
cg08814531	−0.43 (−2.07, 1.21)	3.80 (−26.09, 33.69)	20.99 (−5.77, 47.75)	−0.01 (−1.11, 1.09)	4.76 (−23.05, 32.57)	0.15 (−20.65, 20.95)
cg03591496	−1.26 (−2.61, 0.28)	8.55 (−18.60, 35.70)	14.88 (−9.63, 39.38)	−0.28 (−1.28, 0.73)	18.04 (−6.87, 42.96)	7.18 (−11.61, 25.98)
cg20973878	0.92 (−0.72, 2.56)	−13.86 (−43.11, 15.40)	−20.93 (−47.25, 5.38)	–	–	–
cg27020289	−0.78 (−2.26, 0.70)	16.46 (−12.31, 45.23)	1.23 (−25.11, 27.57)	–	–	–
cg00274587	−0.29 (−1.60, 1.03)	−3.05 (−24.47, 18.37)	−5.59 (−25.02, 13.84)	–	–	–
cg00558147	0.09 (−1.49, 1.68)	6.69 (−19.27, 32.65)	9.95 (−13.56, 33.47)	–	–	–
cg00792719	0.92 (−0.59, 2.43)	11.61 (−16.31, 39.53)	−16.99 (−42.17, 8.20)	–	–	–
cg07500019	0.00 (−1.76, 1.76)	1.67 (−30.75, 34.09)	−8.62 (−38.01, 20.77)	–	–	–
cg07955457	−0.12 (−1.48, 1.25)	23.49 (0.03, 46.96)	18.71 (−2.72, 40.15)	–	–	–
cg27385940	−0.69 (−3.58, 2.20)	−1.88 (−13.38, 9.62)	−3.68 (−14.10, 6.74)	–	–	–

^a Adjusted for maternal age at delivery, race/ethnicity, maternal pre-pregnancy obesity, and smoking status during pregnancy.

^bAll CpG sites listed are located in Chromosome 6.

^cCpG sites listed were all associated with maternal pre-pregnancy BMI after accounting for multiple testing (q < 0.05). Associations between TAPBP gene CpGs and offspring BMI z-score and elevated blood pressure were not statistically significant after applying the Bonferroni test for multiple testing (female offspring p < 0.002 for 28 tests; male offspring p < 0.003 for 17 tests).

^dCpGs were all located in the gene body of the TAPBP gene

Bold represents associations with p < 0.05.

Figure 1. Manhattan plot for the associations between maternal pre-pregnancy obesity and offspring cord blood DNA methylation among females (n = 187) after adjustment for estimated cell proportions. A total of 876 CpGs had an FDR-adjusted P-value <0.05 (solid horizontal blue line).

Figure 2. Manhattan plot for the associations between maternal pre-pregnancy obesity and offspring cord blood DNA methylation among males (n = 173) after adjustment for estimated cell proportions. A total of 293 CpGs had an FDR-adjusted P-value <0.05 (solid horizontal blue line).