DNA methylation differences in human placenta from female and male bearing pregnancies

Qianhui Wan⁰, Melanie Smith¹, Konstantinos Bogias¹, Tanja Jankovic-Karasoulos⁰, Dale McAninch², Dylan McCullough⁰, Shalem Leemaqz⁰, Jimmy Breen², Claire Roberts⁰
(0) Flinders Health and Medical Research Institute (FHMRI), Flinders University, Adelaide, South Australia
(1) the University of Adelaide
(2) South Australian Health & Medical Research Institute (SAHMRI), Adelaide, South Australia

Find me on Wed Nov 25th, 1:30-2:50pm AEDT in Remo, table 108

Abstract
Sex differences in fetal growth and development are well known. Males are generally larger than females at birth and sex-specific pregnancy outcomes are associated with maternal diet and health status, though the underlying mechanisms of sex differences are not fully understood. DNA methylation differences between female and male placentas could be one of the reasons that explain the sex-specific disease risks. In this study, we profiled placental DNA methylation across early to mid-gestation according to fetal sex using Illumina Infinium® MethylationEPIC BeadChips (EPIC arrays) on 131 human placenta samples (63 female and 68 male) from 6-23 weeks’ gestation. ENmix was used to correct the dye bias and background of array data, failed probes and samples were identified and removed by quality control methods using minfi, and BMIQ method implemented in ChAMP was used for data normalisation. Differential methylation analysis was performed using DMRcate for female and male placenta samples with DMRs identified between 6-10 and 11-23 weeks’ gestation groups. Weighted linear regression models were used to deal with heteroskedasticity such that samples with more variances were weighted less in the models to reduce the effects of non-constant variations. Batch effects were considered and adjusted in the models for identifying DMRs. When comparing 6-10 and 11-23 weeks’ gestation groups for female and male placentas, the majority of DMRs were identified on autosomes except for 3 DMRs on the X chromosome (overlapped SMARCA1, ACE2 and FIRRE). 99 DMRs increased in methylation and 4 DMRs with decreased methylation in 11-23 compared to 6-10 weeks’ gestation groups were found in both female and male placentas, which was in line with previous reports that global DNA methylation increased across gestational weeks. Between 11-23 versus 6-10 weeks’ gestation groups, we also found increased DNA methylation of 348 and 4 DMRs and decreased DNA methylation of 3 and 2 DMRs were identified only in female and male placentas, respectively. Upon functional enrichment of 313 genes that overlapped 348 DMRs with increased methylation using methylGSA, we identified genes regulating transmembrane transport. Overall, our study is the first to show DNA methylation differences associated with fetal sex in human placenta during early to mid-gestation with a large sample size, which could provide novel insights to understand sex differences in neonatal and early programming of adult disease. In future, different omics data from these placenta samples will be integrated to investigate sex-specific features in placental development.