Meta-analysis examining fetal sex-specific placental DNA methylation intensities and estimated cell composition post IVF

Infertility impacts up to 17.5% of reproductive-aged couples worldwide. To aid in conception, many couples turn to ART, such as IVF. IVF can introduce both physical and environmental stressors that may alter DNA methylation regulation, an important and dynamic process during early fetal development. This meta-analysis aims to assess the differences in the placental DNA methylome between spontaneous and IVF pregnancies. Potential datasets were identified by searching the NCBI Gene Expression Omnibus (GEO) using keywords related to IVF in human participant studies published before November 2023. In our combined fetal sex population (N = 575) from three eligible GEO datasets, 127 autosomal cytosine guanine dinucleotides (CpGs) were significant (False Discovery Rate (FDR) <0.05) between IVF (n = 96) and spontaneous (n = 479) placentae, with 47 CpGs considered differentially methylated (FDR < 0.05 and |Δβ| > 0.05). Stratification by fetal sex revealed no significant autosomal CpGs in fetal female placentae (N = 281); however, in the fetal male placentae (N = 294), we identified nine autosomal CpGs that reached statistical significance between IVF (n = 56) and spontaneous (n = 238) placentae, with three CpGs considered differentially methylated. Fetal male placentae had lower proportions of trophoblasts (P < 0.0001) and stromal cells (P = 0.007) and higher proportions of syncytiotrophoblasts (P = 0.0001) compared to fetal female placentae, regardless of conception type. IVF placentae had higher proportions of stromal cells (P = 0.01) and lower proportions of syncytiotrophoblasts (P = 0.01) compared to spontaneous placentae, regardless of sex. Controlling for cell-type proportions in linear models reduced test statistic inflation and identified new significant CpGs that may previously have been masked by cell-type heterogeneity. The results of this meta-analysis are critical to further understand the impact of IVF on tissue epigenetics, which may help with understanding the connections between IVF and negative pregnancy outcomes. Additionally, our study suggests that sex-specific differences in placental DNA methylation and cell composition should be considered as factors for future placental DNA methylation analyses.