Examination of newborn DNA methylation among women with polycystic ovary syndrome/hirsutism

Figures & data

Table 1. Upstate KIDS study maternal characteristics overall and by self-reported PCOS status, n = 849.

		PCOS Status
	Overall(n = 849)	No PCOS(n = 747)	PCOS without hirsutism(n = 69)	PCOS with hirsutism(n = 33)
Age, years, mean (SD)	32.0 (5.6)	32.0 (5.7)	31.4 (4.5)	32.8 (4.6)
Education, ≥ some college	587 (69.1)	520 (69.6)	44 (63.8)	23 (69.7)
Race/ethnicity, non-Hispanic White^^	750 (88.3)	662 (88.6)	59 (85.5)	29 (87.9)
Pre-pregnancy BMI, kg/m^2, mean (SD)	29.8 (7.0)	26.4 (6.8)	29.0 (7.7)	30.6 (7.5)
Smoking during pregnancy	69 (8.1)	63 (8.4)	6 (8.7)	0 (0.0)
Gestational diabetes	69 (8.1)	52 (7.0)	9 (13.0)	8 (24.2)
Gestational hypertension	72 (8.5)	60 (8.0)	10 (14.5)	2 (6.1)
Fertility treatment	334 (39.3)	254 (34.0)	55 (79.7)	25 (75.8)
Nulliparous	425 (50.8)	371 (50.3)	38 (56.7)	16 (50.0)
Newborns	Overall(n = 849)	No PCOS(n = 747)	PCOS without hirsutism(n = 69)	PCOS with hirsutism(n = 33)
Birthweight	3231.5 (688.2)	3225.1 (688.0)	3273.9 (639.1)	3287.8 (799.5)
Gestational age	38.2 (2.4)	38.2 (2.4)	38.3 (1.8)	37.9 (3.0)
Male Sex	452 (53.2)	397 (53.2)	39 (56.5)	16 (48.5)
Singleton	684 (80.6)	601 (80.5)	55 (79.7)	28 (84.9)
C-section	390 (46.1)	347 (46.6)	28 (40.6)	15 (45.5)
Chromosomal Abnormalities	26 (3.06)	24 (3.21)	1 (1.45)	1 (3.03)

^Other race/ethnicity: non-Hispanic Black, 1.6%; Asian, 2.6%; Hispanic, 5.3%; mixed race or other, 2.2%.

Missing data:parity, n = 12; c-section, n = 3.

Abbreviations: PCOS, polycystic ovary syndrome; SD, standard deviation; BMI, body mass index.

Table 2. Top probes sorted by FDR p-value for PCOS with hirsutism vs no PCOS, Upstate KIDS.

CpG Probe	β (SE)	FDR p-value	Location	Nearby gene	Relation to
Minimally adjusted model*
cg02372539	−0.0947 (0.014)	1.55E–05	Chr6: 168703878	DACT2	Open Sea
cg25209153	−0.0798 (0.014)	2.05E–03	Chr3: 42093455		Open Sea
cg08471713	0.0844 (0.015)	4.28E–03	Chr17: 41738893	MEOX1	Open Sea
cg01185179	0.0087 (0.002)	2.13E–02	Chr17: 7893695		Island
cg17728838	0.0107 (0.002)	3.12E–02	Chr11: 46615784	AMBRA1	South Shore
Fully adjusted model^
cg02372539	−0.0807 (0.010)	0.0095	Chr6: 168703878	DACT2	Open Sea
cg08471713	0.0773 (0.014)	0.0164	Chr17: 41738893	MEOX1	Open Sea
cg17897916	0.0501 (0.009)	0.0095	Chr15: 62681461		North Shore

*Minimally adjusted model adjusted for infant sex, plurality, cell type, and batch.

^{^}Fully adjusted model adjusted for infant sex, plurality, cell type, batch, epigenetically derived ancestry, maternal race, maternal educational attainment, maternal age, maternal prepregnancy BMI, parity, and use of assisted reproductive technologies.

Abbreviations: PCOS, polycystic ovary syndrome; SE, standard error; FDR, false discovery rate.

Table 3. Differentially methylated regions (DMR) identified in PCOS with hirsutism vs. no PCOS analysis, Upstate KIDS.

Chr	Positions	# of CpG probes*	Nearby Gene(s)	Function^†	β (SE)	Bonferroni p-value
2	202506468- 202507561	4	TMEM237	Required for ciliogenesis; enhanced expression in retina	0.363 (0.07)	0.027
3	196295364- 196296266	3	WDR53/FBXO45	Unknown function (WDR53); Tissue enriched (testis)/Role in neurodevelopment; low tissue specificity (FBXO45)	−0.523 (0.10)	0.011
4	140222502–140223687	6	NAA15	Vascular and neuronal growth and development; associated with neurodevelopmental delays; low tissue specificity	0.421 (0.07)	0.001
6	30181425–30181742	3	TRIM26	Associated with neural tube defects; low tissue specificity	0.542 (0.10)	0.012
6	32937355 – 32940489	11	BRD2	Possible role in spermatogenesis or folliculogenesis; low tissue specificity	0.372 (0.06)	<0.001
12	113573421–113573809	4	RASAL1	Involved in cellular proliferation and differentiation; enhanced expression in the parathyroid	0.436 (0.08)	0.01
16	29826926–29827345	3	PAGR1/C16orf53	Important for cell survival; enhanced expression in the ovary	0.496 (0.10)	0.040
20	61050885- 61051795	5	GATA5	Cardiovascular development; enhanced expression in intestine, testis, urinary bladder	0.346 (0.10)	0.02

*Defined as genomic regions covering a set of nominal EWAS p-value CpG probes with at most 1000bp between consecutive probes that were consistently positively or negatively correlated with the exposure.

^†Look up in the Human Protein Atlas (proteinatlas.org).

Abbreviations: PCOS, polycystic ovary syndrome; SE, standard error.

Table 4. EAGeR maternal characteristics overall and by testosterone quartiles, n = 351.

		Testosterone (min-max)
	Overall	Quartile 1 (5.27–15.31 ng/dL)	Quartile 2 (15.34–20.37 ng/dL)	Quartile 3 (20.4–26.31 ng/dL)	Quartile 4 (26.35–73.99 ng/dL)	p-value*
Testosterone ng/dL, median (IQR)	20.4 (11.6)	12.7 (2.7)	18.0 (2.2)	22.6 (3.1)	30.9 (9.2)
Age, years, mean (SD)	28.3 (4.4)	29.3 (4.6)	29.0 (4.4)	27.7 (4.2)	27.4 (4.2)	0.0083
Education, > high school	317 (90.3)	81 (90.0)	80 (94.1)	75 (89.3)	81 (88.0)	0.8810
Pre-pregnancy BMI, kg/m^2, mean (SD)	25.1 (5.4)	24.4 (5.7)	24.1 (4.8)	25.7 (5.1)	26.1 (5.7)	0.0359
Smoker, never	326 (92.9)	86 (95.6)	78 (91.8)	78 (92.9)	84 (91.3)	0.0797
Parous, 1–2 prior live births	212 (60.4)	62 (68.9)	53 (62.3)	54 (64.3)	43 (46.7)	0.0144
Age at menarche, years, mean (SD)	12.8 (1.4)	12.8 (1.5)	12.9 (1.5)	12.6 (1.3)	12.8 (1.4)	0.4662
Number of periods 6 months prior to baseline, mean (SD)	4.3 (1.6)	4.3 (1.6)	4.5 (1.5)	4.3 (1.7)	4.3 (1.4)	0.8775
Menstrual regularity 12 months prior to baseline, yes	288 (84.0)	75 (84.3)	70 (83.3)	71 (88.7)	72 (80.0)	0.1471

All values n (%) unless otherwise stated.

* ANOVA p-values presented for continuous characteristics and chi-square or Fisher’s exact p-values for categorical characteristics. Missing data: BMI, n = 3; age at menarche, n = 12; number of periods, n = 13; menstrual regularity, n = 8. Abbreviations: EAGeR, Effects of Aspirin in Gestation and Reproduction; SD, standard deviation; BMI, body mass index.

Table 5. Top probes sorted by FDR p-value for testosterone analysis, EAGeR*.

CpG Probe	β (SE)	FDR p-value	Location	Annotation	Relation to Island
Testosterone (log), ng/dL
cg24233293	−0.0032 (0.001)	0.1602	Chr10:130303915		Open Sea
cg04152675	0.0009 (0.0002)	0.1602	Chr2:202085364	CASP10	Open Sea
cg00280270	0.0004 (0.0001)	0.1884	Chr22:21320131	AIFM3	South Shore
cg22628339	−0.0012 (0.0003)	0.4031	Chr7:134296773		Open Sea

*Adjusted for infant sex, maternal age, cell type, batch, maternal pre-pregnancy BMI and parity.

Abbreviations: EAGeR, Effects of Aspirin in Gestation and Reproduction; SE, standard error; FDR, false discovery rate.

Data availability statement

Data that support the findings of this study are available on request from the corresponding author [EY]. Data are not on a public database due to New York State restrictions (i.e.,

releasing information that could compromise participant privacy/consent).