Human Placenta MicroRNA Differences Between First and Third Trimester

MiRNAs are widespread regulators of gene expression, and altered miRNA expression in the placenta may be involved in abnormal placentation and related pregnancy-associated diseases. It is essential to understand miRNA expression changes across gestation before miRNAs can be used as biomarkers or prognostic indicators. Using next-generation sequencing, we characterize the normative human placenta miRNA transcriptome in both the first and third trimester using leftover chorionic villus sampling tissue from prenatal tests (N=113) as well as placentae collected at delivery (N=47). We identified 2503 miRNAs, including 1647 with stable expression across gestation (p>=0.05). There were 775 significantly differentially expressed miRNAs (FDR<0.05), with 402 upregulated in first trimester and 373 upregulated in third trimester. We also examine expression of the placenta-specific miRNA clusters on chromosomes 14 and 19 which are important in pregnancy. We identified predicted targets with high confidence scores or experimental verification, then used these to identify enriched canonical biological pathways. Our study identified canonical pathways consistently targeted across gestation, including pathways regulating senescence, proliferation and growth factor signaling. We also identified differentially impacted pathways, including growth- and immune-mediated pathways. This work provides a rich atlas to direct functional studies investigating the epigenetic differences in first and third trimester placentae. We gratefully acknowledge support from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD091773) and the Ruth L. Kirschstein National Research Service Award (T32DK007770) of the National Institutes of Health.