Infertility and treatments used have minimal effects on first-trimester placental DNA methylation and gene expression

Abstract

To determine if DNA methylation alterations exist in first trimester human placenta between conceptions utilizing fertility treatments and those that do not, and if so, if they are the result of underlying infertility or fertility treatments. We also assessed if significant alterations led to changes in gene expression. We compared DNA methylation of first trimester placenta from singleton pregnancies that resulted in live births from unassisted, non-IVF fertility treatment (NIFT), and IVF conceptions using the Infinium MethylationEPIC BeadChip array. Significant CpG sites were compared to corresponding RNA-seq analysis in similar cohorts to determine if methylation alterations lead to differences in gene expression. 138 singleton pregnancies undergoing chorionic villus sampling resulting in a live birth were recruited for methylation analysis (56 unassisted, 38 NIFT, 44 IVF conceptions). RNA-seq data consisted of 141 subjects (74 unassisted, 33 NIFT, and 34 IVF) of which 116 overlap with the methylation cohort. IVF conceived pregnancy, or pregnancy conceived via non-IVF fertility treatment such as ovulation induction and/or intrauterine insemination. Significant methylation changes at CpG sites after adjustment for multiple comparisons. Secondary outcome is gene expression changes of significant CpG sites. Of the 741,145 probes analyzed in placenta, few were significant at Bonferroni<0.05: 185 CpG sites (0.025%) significant in pregnancies conceived with fertility treatment (NIFT+IVF) vs unassisted conceptions; 28 in NIFT vs unassisted; 195 in IVF vs unassisted; and only 13 (0.0018%) significant in IVF vs NIFT conceptions. Of all significant CpG sites combined, 10% (35 total) were located in genes with suggestive gene expression changes (RNA-seq P<0.05), but none were significant after adjustment for multiple comparisons (RNA-seq FDR<0.05). None of the 13 differentially methylated probes in IVF vs NIFT placenta were located in genes with suggestive IVF vs NIFT gene expression differences. Underlying infertility is the most significant contributor to the minimal differences in first trimester placental methylation, and not the specific fertility treatment utilized, such as IVF.