Abstract
The placenta is a crucial organ that functions as an interface between the mother and fetus. At this boundary, the interaction between numerous signalling molecules and maternal immune cells is essential to modulate the response to fetal alloantigens. A successful pregnancy requires the placenta to undergo numerous complex processes, including extensive trophoblast differentiation to invade into the maternal layers of the uterus and remodel the maternal spiral arteries. Pre-eclampsia (PE) is a dangerous pregnancy condition that typically presents around 20 weeks of gestation and is associated with abnormal placental development, characterised by shallow invasion of placental trophoblast cells and poor remodelling of maternal spiral arteries. PE occurs in approximately 5% of pregnancies worldwide; however, despite extensive research, the intricate mechanisms involved in the placental processes underlying PE remain incompletely understood.
Emerging evidence suggests that transposable elements (TEs) may play a crucial role in healthy placental function and dysfunction. TEs are repetitive DNA elements that once had, and few of which still have, the ability to mobilise within the genome, and greatly contribute to regulating gene expression. Over the course of mammalian evolution, it is believed that the co-option of TEs has been selected for, leading to the establishment of TE genes that are typically silenced in somatic tissues. Recent studies have shown that the activation of normally silenced TEs is associated with somatic diseases, such as cancer. In the placenta, however, active TE genes are essential for successful placentation. Interestingly, some placental TE genes are also expressed in cancer, and share similar functions to those observed in the placenta, which provided further insight into their functional roles. Thus, it was hypothesised that aberrant expression of TE genes may lead to the placental dysfunction that is associated with PE.
Previous members of the Macaulay lab identified candidate TE genes as highly expressed within both normal placenta tissue and melanoma samples, in comparison to somatic tissues. The first aim of this project sought to investigate the expression and epigenetic regulation of these candidate TE genes within PE placental cohorts to provide further understanding of how these genes are expressed in comparison to healthy placental control samples. Three TE genes (GALNT6, P3H4, and LINC00698) exhibited significant upregulated expression in PE and LINC00346 revealed significantly lower DNA methylation at the promoter region.
The second aim of this project involved analysing four publicly available RNA seq datasets to discover new differentially expressed TE genes in PE. This work was done by utilising RepExpress, a new bioinformatic pipeline recently designed by members of the Macaulay lab. RepExpress identified 34 significantly upregulated TEs and 17 significantly downregulated TEs in PE, 11 of which overlapped with exons in the genome (TE genes). Many of these TE genes have been previously associated with PE. Due to the substantial regulatory activity associated with TEs, a selection of 10 significant TEs were investigated further for putative regulatory elements. This analysis revealed four TEs that overlapped with either a promoter or enhancer region. Another objective within Aim Two of this project revealed significant differences in TE gene expression among isolated placental cells from publicly available single-cell RNA-seq data.
Placental cell heterogeneity within tissue sampling poses a caveat in placental research. The complex issue of differing cell populations changing throughout gestation, coupled with expression variations, makes interpretation difficult and hard to consistently validate biomarkers. Placental research would benefit from using isolated placental cell types for future experiments, thus providing a deeper understanding of the gene expression contributing to placental pathologies. This is crucial for validating potential biomarkers and creating effective strategies to potentially detect, treat or even prevent pregnancy conditions such as PE.