Prenatal and birth associations of epigenetic gestational age acceleration in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) cohort

Figures & data

Table 1. Characteristics of participants in the CHAMACOS birth cohort with Illumina 450K DNA methylation profiles from umbilical cord blood samples (N = 372).

	n (%) or Mean ± SD
Pre-pregnancy body mass index (BMI), kg/m^2	26.78 ± 5.10
Underweight (<18.5)	3 (0.81%)
Normal (18.5 to <25)	152 (40.86%)
Overweight (25 to <30)	140 (37.63%)
Obese (≥30)	77 (20.70%)
Pregnancy weight gain, pounds	30.42 ± 12.35
Maternal serum cholesterol, mg/dL	224.84 ± 39.93
Maternal serum triglyceride, mg/dL	251.07 ± 98.99
Total maternal serum lipid, mg/dL	823.75 ± 157.29
Smoking during pregnancy
No	346 (93.01%)
Yes	24 (6.45%)
Missing	2 (0.54%)
Alcohol use during pregnancy
No	279 (75.00%)
Yes	82 (22.04%)
Missing	11 (2.96%)
Maternal age at delivery, years	25.73 ± 5.00
18–24 years	175 (47.04%)
25–29 years	119 (31.99%)
30–34 years	57 (15.32%)
35–45 years	21 (5.65%)
Type of delivery
Vaginal	295 (79.30%)
Caesarean	77 (20.70%)
Preterm delivery
<37 weeks	26 (6.99%)
≥37 weeks	346 (93.01%)
Baseline maternal marital status
Married/Living as married	293 (78.76%)
Single	55 (14.78%)
Separated/Divorced	22 (5.91%)
Missing	2 (0.54%)
Baseline maternal education status
≤6th grade	157 (42.20%)
7–12th grade	138 (37.10%)
≥ High school graduate	77 (20.70%)
Baseline maternal occupation
Did not work	126 (33.87%)
Agricultural field work	102 (27.42%)
Other agricultural work	46 (12.37%)
Other work only	88 (23.66%)
Missing	10 (2.69%)
Maternal adverse childhood experiences (ACEs)
0	101 (27.15%)
1–2	49 (13.17%)
3+	54 (14.52%)
Missing	168 (45.16%)
Maternal parity
0	134 (36.02%)
1	107 (28.76%)
2+	131 (35.22%)
Chronological gestational age, weeks	39.46 ± 1.54
Infant sex
Female	189 (50.81%)
Male	183 (49.19%)
Birth weight, grams	3453.25 ± 487.57

Figure 1. Performance of the DNAm GA Clock Predictions in the CHAMACOS Cohort Using Illumina 450K (N = 372) and EPIC (N = 108) DNAm Arrays. Pearson’s correlation and median absolute error (MAE) between chronological gestational age and DNAm GA calculated using (a) Knight’s clock and the 450K methylation data, (b) Knight’s clock and the EPIC methylation data, (c) Bohlin’s clock and the 450K methylation data, and (d) Bohlin’s clock and the EPIC methylation data.

Figure 2. Comparison of DNAm GA Predictions by the Knight vs. Bohlin Clock Across the Same DNAm Array. Pearson’s correlation between (a) Knight DNAm GA and Bohlin DNAm GA determined from the 450K DNA methylation data (N = 372) and (b) Knight DNAm GA and Bohlin DNAm GA determined from the EPIC DNA methylation data (N = 108).

Figure 3. Comparison of DNAm GA Predictions by the Illumina 450K vs. EPIC DNAm array across the same epigenetic clock (N=108). Pearson’s correlation between (a) Knight’s DNAm GA from the EPIC array and Knight’s DNAm GA from the 450K array (b) Bohlin’s DNAm GA from the EPIC array and Bohlin’s DNAm GA from the 450K array.

Table 2. Adjusted associations between gestational age acceleration estimated by the Knight and Bohlin epigenetic clocks with prenatal and birth characteristics in the CHAMACOS cohort (N = 372)^†,‡.

	N	Knight Clock 450K DNAm Array GAA Residuals			Bohlin Clock 450K DNAm Array GAA Residuals
		β (95% CI)	P-Value^†	BH Adjusted P-Value^‡	β (95% CI)	P-Value^†	BH Adjusted P-Value^‡
Pre-pregnancy BMI, kg/m^2	369	−0.09 (−0.30, 0.12)	0.40	0.70	−0.02 (−0.15, 0.11)	0.75	0.96
Ref = Underweight/Normal (<25)
Overweight (25 to <30)		1.44 (−0.91, 3.78)	0.23	0.59	0.26 (−1.14, 1.67)	0.71	0.96
Obese (30 or higher)		−2.77 (−5.65, 0.11)	0.06	0.56	−1.20 (−2.92, 0.53)	0.17	0.68
Pregnancy weight gain, pounds	368	0.03 (−0.06, 0.12)	0.48	0.79	−2.24x10^−3 (−0.05, 0.05)	0.93	0.96
Maternal serum cholesterol, mg/dL	306	−2.49x10^−3 (−0.03, 0.03)	0.86	0.99	−8.37x10^−3 (−0.03, 8.82 × 10^−3)	0.34	0.90
Maternal serum triglyceride, mg/dL	306	−0.01 (−0.2, 1.96 × 10^−3)	0.11	0.59	−0.01 (−0.01, −8.95x10^−4)	0.03	0.28
Total maternal serum lipid, mg/dL	306	−4.02x10^−3 (−0.01, 3.04 × 10^−3)	0.26	0.61	−4.31x10^−3 (−8.82x10^−3, −1.12x10^−4)	0.04	0.28
Smoking during pregnancy (Ref = No)
Yes	369	−0.01 (−4.34, 4.32)	0.99	0.99	−0.87 (−3.45, 1.71)	0.51	0.95
Alcohol use during pregnancy (Ref = No)
Yes	360	−1.57 (−4.17, 1.03)	0.23	0.59	−1.28 (−2.81, 0.26)	0.10	0.56
Maternal age at delivery, years	369	−0.04 (−0.25, 0.17)	0.68	0.86	−0.01 (−0.13, 0.12)	0.90	0.96
Ref = 18–24 years
25–29 years		−1.53 (−3.93, 0.87)	0.21	0.59	−0.41 (−1.84, 1.02)	0.58	0.96
30–34 years		−0.05 (−3.14, 3.04)	0.97	0.99	−4.37x10^−3 (−1.85, 1.84)	0.99	0.99
35–45 years		−0.03 (−4.68, 4.62)	0.99	0.99	0.41 (−2.36, 3.18)	0.77	0.96
Type of delivery (Ref = Caesarean)
Vaginal	369	−0.78 (−3.36, 1.80)	0.55	0.85	−0.27 (−1.81, 1.26)	0.73	0.96
Preterm delivery (Ref = ≥37 weeks)
<37 weeks	369	−3.17 (−7.23, 0.88)	0.12	0.59	−4.03 (−6.41, −1.65)	9.64x10^−4	0.03
Baseline maternal marital status (Ref = Married/Living as married)	369
Single		2.13 (−0.88, 5.13)	0.16	0.59	1.24 (−0.55, 3.03)	0.17	0.68
Separated/Divorced		2.14 (−2.29, 6.56)	0.34	0.65	0.49 (−2.14, 3.13)	0.71	0.96
Baseline maternal education status (Ref = ≤ 6th grade)	369
7–12th grade		1.12 (−1.23, 3.47)	0.35	0.65	0.79 (−0.60, 2.19)	0.26	0.81
≥ High school graduate		−0.54 (−3.41, 2.32)	0.71	0.86	−0.72 (−2.43, 0.98)	0.40	0.90
Baseline maternal occupation (Ref = Did not work)	361
Field work		0.58 (−2.17, 3.32)	0.68	0.86	0.67 (−0.95, 2.29)	0.42	0.90
Other agricultural work		−0.20 (−3.69, 3.29)	0.91	0.99	0.24 (−1.82, 2.30)	0.82	0.96
Other work only		1.47 (−1.47, 4.41)	0.33	0.65	0.74 (−1.00, 2.47)	0.40	0.90
Maternal ACEs (Ref = 0)	203
1–2		−1.04 (−4.72, 2.65)	0.58	0.85	−0.17 (−2.25, 1.91)	0.87	0.96
3+		−2.31 (−5.92, 1.30)	0.21	0.59	−0.77 (−2.80, 1.27)	0.46	0.92
Maternal parity (Ref = 0)	369
1		−0.67 (−3.32, 1.98)	0.62	0.86	−0.42 (−2.00, 1.15)	0.60	0.96
2+		−4.07 (−6.96, −1.19)	0.01	0.14	−2.43 (−4.15, −0.72)	0.01	0.14
Infant sex (Ref = Female)
Male	369	−3.15 (−5.22, −1.07)	3.10x10^−3	0.09	0.14 (−1.10, 1.37)	0.82	0.96
Birth weight, grams	369	1.58x10^−3 (−6.06x10^−4, 3.76 × 10^−3)	0.16	0.59	8.29x10^−4 (−4.70x10^−4, 2.13 × 10^−3)	0.21	0.74

^† Adjusted for maternal age at delivery, smoking during pregnancy, maternal education, marital status, and infant sex

^‡ Adjusted for multiple comparisons using the Benjamini-Hochberg method

GAA, gestational age acceleration; BH, Benjamini-Hochberg; CI, confidence interval; BMI, body mass index; ACE, adverse childhood experience

Figure 4. Adjusted Associations between Gestational Age Acceleration and Prenatal and Birth Characteristics in the CHAMACOS Cohort (N = 372)^†. Estimates (β) and 95% CIs for characteristics significantly associated with gestational age acceleration after adjusting for maternal age at delivery, maternal smoking during pregnancy, maternal education, marital status, and infant sex across the two clocks. ^†Units for maternal serum triglyceride and maternal serum lipid levels converted from standard mg/dL to d/L for greater comparability of effect sizes in plot.

Figure 5. Correlations Coefficients Between Estimated Cell-Type Proportions and Gestational Age Acceleration Estimated by the Knight and Bohlin Clocks (N = 372). Pearson’s correlations between cell-type proportions estimated from DNA methylation profiles and gestational age acceleration calculated by the Bohlin and Knight models using the 450K array (blank/white cell = non-significant correlation p > 0.05).