Prenatal social support in low-risk pregnancy shapes placental epigenome

Tesfaye, Markos; Wu, Jing; Biedrzycki, Richard J.; Grantz, Katherine L.; Joseph, Paule; Tekola-Ayele, Fasil

doi:10.1186/s12916-022-02701-w

Table 2 Comparison of effect sizes of social support-associated methylation sites between male fetus- and female fetus-bearing pregnancies

From: Prenatal social support in low-risk pregnancy shapes placental epigenome

CpG	Gene	Total Sample ^a			Male Fetus ^a			Female Fetus ^a			Sex difference statistics^b
CpG	Gene	Methylation LogFC ±S.E.	P_FDR	Mean methylation Beta (SD)	Methylation LogFC ± S.E	P_FDR	Mean methylation Beta (SD)	Methylation LogFC ± S.E	P_FDR	Mean methylation Beta (SD)	Welch’s t -test	P_FDR
Associations identified in the overall sample
cg14806252	HAUS3	0.22 ± 0.04	0.019	0.008 (0.005)	0.19 ± 0.06	0.655	0.008 (0.005)	0.23 ± 0.06	0.117	0.008 (0.005)	-	-
cg01924481	SBF1	0.02 ± 0.003	0.021	0.865 (0.020)	0.01 ± 0.005	0.959	0.866 (0.019)	0.02 ± 0.005	0.158	0.865 (0.021)	-	-
cg11364468	VGF	0.11 ± 0.02	0.021	0.011 (0.006)	0.21 ± 0.04	0.001	0.011 (0.006)	0.004 ± 0.02	0.999	0.011 (0.006)	4.61	1.24 × 10⁻⁵
cg00549575	EIF3F	0.08 ± 0.02	0.030	0.040 (0.016)	0.13 ± 0.03	0.066	0.040 (0.015)	0.02 ± 0.01	0.965	0.041 (0.016)	-	-
cg19499754	FAM210B	0.11 ± 0.02	0.030	0.029 (0.013)	0.10 ± 0.03	0.577	0.028 (0.013)	0.11 ± 0.03	0.344	0.030 (0.013)	-	-
cg16763895	ILVBL	0.07 ± 0.01	0.041	0.030 (0.010)	0.11 ± 0.03	0.147	0.030 (0.011)	0.005 ± 0.01	0.998	0.031 (0.010)	-	-
cg02672368	ARHGEF7	0.13 ± 0.03	0.049	0.017(0.008)	0.05 ± 0.03	0.961	0.017 (0.008)	0.21 ± 0.04	0.010	0.017 (0.008)	− 3.20	0.003
Associations identified in male fetus pregnancies
cg00985086	MCTP1	0.08 ± 0.02	0.138	0.011 (0.005)	0.19 ± 0.03	0.001	0.011 (0.005)	− 0.01 ± 0.01	0.997	0.012 (0.004)	6.32	1.69 × 10⁻⁸
cg03215315	GSTCD; INTS12	0.07 ± 0.02	0.705	0.012 (0.005)	0.18 ± 0.03	0.009	0.012 (0.005)	− 0.01 ± 0.03	0.998	0.012 (0.005)	4.48	1.61 × 10⁻⁵
cg23797252	KNDC1	0.01 ± 0.003	0.722	0.482 (0.035)	0.02 ± 0.005	0.026	0.480 (0.036)	− 0.01 ± 0.005	0.979	0.484 (0.034)	4.24	3.79 × 10⁻⁵
cg14065446	FIBCD1	0.02 ± 0.01	0.346	0.334 (0.050)	0.04 ± 0.01	0.046	0.336 (0.051)	0.01 ± 0.01	0.991	0.331 (0.048)	2.12	0.035
cg00140191	FKBP5	0.10 ± 0.02	0.138	0.032 (0.011)	0.20 ± 0.04	0.046	0.032 (0.012)	− 0.02 ± 0.02	0.990	0.032 (0.011)	4.92	5.07 × 10⁻⁶
cg16680530	TATDN1; NDUFB9	0.08 ± 0.02	0.622	0.012 (0.006)	0.21 ± 0.04	0.046	0.012 (0.006)	− 0.04 ± 0.02	0.953	0.012 (0.006)	5.59	2.98 × 10⁻⁷
cg24807054	SFRS18	0.07 ± 0.01	0.138	0.037 (0.012)	0.15 ± 0.03	0.049	0.036 (0.013)	0.003 ± 0.01	0.999	0.038 (0.011)	4.65	1.24 × 10⁻⁵
cg18350520	KIAA0664	0.01 ± 0.005	0.896	0.894 (0.019)	0.03 ± 0.01	0.049	0.896 (0.014)	− 0.001 ± 0.01	0.999	0.892 (0.023)	2.19	0.033
Associations identified in female fetus pregnancies
cg04879876	ZFP36L2; LOC100129726	0.04 ± 0.04	0.982	0.020 (0.011)	− 0.20 ± 0.06	0.526	0.019 (0.011)	0.28 ± 0.04	7.4 × 10⁻⁷	0.021(0.011)	− 6.66	3.27 × 10⁻¹⁰
cg16661579	C10orf4	0.12 ± 0.04	0.686	0.010 (0.006)	− 0.02 ± 0.05	0.998	0.010 (0.006)	0.33 ± 0.06	0.0004	0.010(0.006)	− 4.48	0.00012
cg04777683	IVNS1ABP	0.16 ± 0.03	0.110	0.017 (0.009)	0.01 ± 0.05	0.999	0.017 (0.008)	0.31 ± 0.06	0.001	0.017(0.009)	− 3.84	0.00062
cg25928819	AK055957	− 0.06 ± 0.02	0.715	0.155 (0.094)	0.01 ± 0.03	0.998	0.147 (0.089)	− 0.14 ± 0.03	0.004	0.163 (0.099)	3.54	0.0012
cg03432641	SPATS2	0.08 ± 0.03	0.596	0.011 (0.006)	0.04 ± 0.04	0.977	0.011 (0.006)	0.14 ± 0.03	0.010	0.011 (0.006)	− 2.00	0.048
cg23065793	LOC100128164; SEC62	0.07 ± 0.02	0.488	0.021 (0.009)	− 0.01 ± 0.02	0.997	0.021 (0.010)	0.16 ± 0.03	0.010	0.021 (0.009)	− 4.71	6.53 × 10⁻⁵
cg25861327	NUSAP1; OIP5	0.24 ± 0.05	0.146	0.007 (0.005)	0.14 ± 0.09	0.946	0.007 (0.005)	0.35 ± 0.07	0.010	0.007 (0.005)	− 2.21	0.032
cg11149743	HOXB7	0.13 ± 0.04	0.496	0.009 (0.011)	0.04 ± 0.05	0.992	0.008 (0.009)	0.22 ± 0.04	0.014	0.010 (0.012)	− 2.81	0.0067
cg10038542	ENTPD4	0.05 ± 0.02	0.637	0.026 (0.012)	0.01 ± 0.03	0.997	0.026 (0.012)	0.13 ± 0.03	0.015	0.026 (0.012)	− 2.82	0.0066
cg24737639	NUP37; C12orf48	0.09 ± 0.03	0.470	0.016 (0.008)	− 0.04 ± 0.02	0.946	0.017 (0.008)	0.24 ± 0.05	0.019	0.016 (0.007)	− 5.20	1.66 × 10⁻⁵
cg19714762	ABHD11	0.25 ± 0.07	0.445	0.008 (0.007)	0.11 ± 0.12	0.984	0.008 (0.007)	0.42 ± 0.09	0.019	0.009 (0.007)	− 2.07	0.042
cg21490179	ENTPD3-AS1	0.01 ± 0.004	0.863	0.056 (0.010)	− 0.01 ± 0.01	0.985	0.055 (0.010)	0.03 ± 0.01	0.019	0.057 (0.011)	− 2.83	0.0066
cg01952989	MAD1L1	0.07 ± 0.05	0.971	0.955 (0.097)	− 0.06 ± 0.08	0.992	0.953 (0.111)	0.26 ± 0.05	0.019	0.958(0.080)	− 3.39	0.0018
cg06459916	KRCC1	0.08 ± 0.02	0.285	0.009 (0.004)	0.03 ± 0.03	0.981	0.009 (0.004)	0.14 ± 0.03	0.019	0.009 (0.004)	− 2.59	0.012
cg26687565	MAML3	0.07 ± 0.02	0.537	0.032 (0.014)	0.004 ± 0.02	0.998	0.031 (0.014)	0.16 ± 0.03	0.019	0.034 (0.015)	− 4.33	0.00018
cg04484842	MYO9A; SENP8	0.03 ± 0.01	0.863	0.018 (0.007)	− 0.01 ± 0.02	0.990	0.018 (0.007)	0.08 ± 0.02	0.019	0.018 (0.006)	− 3.18	0.0025
cg25585364	INSIG2	0.03 ± 0.01	0.823	0.046 (0.018)	− 0.01 ± 0.02	0.997	0.044 (0.016)	0.09 ± 0.02	0.024	0.048 (0.020)	− 3.54	0.0012
cg22548088	MLLT1	0.02 ± 0.01	0.635	0.537 (0.049)	− 0.01 ± 0.01	0.985	0.541 (0.043)	0.04 ± 0.01	0.028	0.533 (0.054)	− 2.24	0.031
cg09062638	C1QB	0.06 ± 0.04	0.950	0.937 (0.079)	− 0.11 ± 0.05	0.906	0.939 (0.079)	0.24 ± 0.05	0.029	0.935 (0.080)	− 4.95	1.24 × 10⁻⁶
cg08130668	C2orf73	0.08 ± 0.04	0.888	0.014 (0.008)	− 0.08 ± 0.06	0.970	0.014 (0.008)	0.25 ± 0.05	0.029	0.014 (0.008)	− 4.23	0.00018
cg19715081	CDK5RAP3	0.15 ± 0.04	0.503	0.010 (0.006)	− 0.01 ± 0.06	0.999	0.010 (0.007)	0.29 ± 0.06	0.034	0.009 (0.005)	− 3.54	0.0012
cg22830707	HOXC13	− 0.02 ± 0.01	0.537	0.172 (0.030)	− 0.01 ± 0.01	0.980	0.173 (0.032)	− 0.03 ± 0.01	0.034	0.171 (0.027)	1.41	0.158
cg11078433	SLC25A13	0.01 ± 0.004	0.833	0.040 (0.008)	− 0.01 ± 0.01	0.984	0.038 (0.007)	0.03 ± 0.01	0.036	0.040 (0.008)	− 2.83	0.0066
cg05064665	PNMT	0.10 ± 0.04	0.867	0.050 (0.027)	0.01 ± 0.05	0.999	0.047 (0.023)	0.27 ± 0.06	0.036	0.053 (0.030)	− 3.33	0.0020
cg04680746	NACAD	0.19 ± 0.05	0.470	0.008 (0.005)	0.07 ± 0.08	0.990	0.008 (0.005)	0.30 ± 0.07	0.036	0.008 (0.005)	− 2.16	0.034
cg13190531	POLR3B	0.16 ± 0.06	0.787	0.003 (0.003)	− 0.02 ± 0.09	0.998	0.003 (0.003)	0.39 ± 0.09	0.036	0.004 (0.003)	− 3.22	0.0025
cg24776326	IRX4	− 0.02 ± 0.01	0.914	0.597 (0.060)	0.01 ± 0.01	0.977	0.602 (0.055)	− 0.05 ± 0.01	0.036	0.593 (0.065)	4.24	0.00018
cg07576517	SDCCAG8; CEP170	0.07 ± 0.02	0.738	0.031 (0.011)	− 0.02 ± 0.04	0.995	0.030 (0.010)	0.16 ± 0.04	0.036	0.033 (0.011)	− 3.18	0.0025
cg23808931	TMEM183A; TMEM183B	0.06 ± 0.03	0.820	0.019 (0.014)	− 0.02 ± 0.03	0.990	0.020 (0.014)	0.20 ± 0.05	0.036	0.018 (0.014)	− 3.77	0.00074
cg02376269	UBR1	0.06 ± 0.02	0.852	0.036 (0.014)	− 0.01 ± 0.04	0.997	0.034 (0.013)	0.15 ± 0.03	0.036	0.038(0.015)	− 3.20	0.0025
cg10835423	RAP1A	0.09 ± 0.03	0.635	0.012 (0.006)	− 0.01 ± 0.04	0.998	0.012 (0.006)	0.19 ± 0.04	0.036	0.012 (0.007)	− 3.53	0.0012
cg03734035	NDUFB8	0.11 ± 0.04	0.759	0.011 (0.006)	− 0.03 ± 0.06	0.996	0.011 (0.006)	0.26 ± 0.06	0.042	0.011 (0.007)	− 3.42	0.0017
cg07147063	TMEM208; LRRC29	0.03 ± 0.02	0.980	0.022 (0.010)	− 0.04 ± 0.04	0.990	0.021 (0.009)	0.10 ± 0.02	0.042	0.022 (0.010)	− 3.13	0.0030
cg23890800	FBRSL1	0.07 ± 0.04	0.947	0.011 (0.007)	− 0.08 ± 0.06	0.972	0.011 (0.007)	0.24 ± 0.05	0.045	0.011 (0.007)	− 4.10	0.00026

^aAdjusted for maternal age, race/ethnicity, pre-pregnancy BMI, education, job status, gestational age, parity, perceived stress, methylation principal components, genotype principal components, and surrogate variable. Total sample additionally adjusted for fetal sex
^bAll the test statistics are for sex-specific effects except those for cg04879876 and cg09062638 representing opposite effect directions
CpG cytosine-(phosphate)-guanine site, FDR false discovery rate, LogFC logarithm of fold change, S.E standard error, SD standard deviation

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ISSN: 1741-7015

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