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Mechanistic Insight into Long Noncoding RNAs and the Placenta

1. Introduction

More than 75% of the human genome is actively transcribed into non-coding RNAs (ncRNA), which is a stark contrast to the 1–2% of the genome that is protein coding. These ncRNAs are comprised of both small RNAs, including but not limited to micro RNA (miRNA), piwi-interacting RNA (piRNA), small interfering RNA (siRNA), small nucleolar RNA (snoRNA), and transfer RNA (tRNA). A large number of ncRNAs are >200 nucleotides in length and are termed long non-coding RNAs (lncRNA). These are generally poorly conserved between species, for example, only 14% of mouse lncRNAs have a human orthologue. Since the introduction of next generation sequencing there has been a steady increase in the number of lncRNAs identified. Currently it is estimated that there are more lncRNAs than protein coding genes in the genome.

ncRNAs have increasingly appreciated roles in all stages of development, with each type of ncRNA having distinct functions and mechanisms of action. miRNAs act by binding complimentary RNA sequences where they recruit proteins that can destabilise RNA or impair translation leading to a reduction in target protein levels. lncRNAs have a diverse range of molecular functions. They act as scaffolds, signals, and antisense decoys, and engage in transcriptional interference. It is not uncommon for a single lncRNA to have multiple functions. Scaffold lncRNAs bind proteins and other RNAs to form larger functional complexes, such as the telomerase RNA complex required for telomere repeat synthesis or the polycomb repressor complex involved in histone modifications. lncRNAs can act as signals of particular developmental stages, transcriptional regulation or specific locations. The transcription of some lncRNAs can indicate the silencing of co-located protein coding genes, or act as markers of upstream transcriptional events. Decoy lncRNAs can act by binding a target protein, preventing the protein from performing its normal function or by binding and sequestering small regulatory RNAs including miRNAs. Although the number of identified lncRNAs continues to grow, the function and biological significance of the majority of lncRNAs remain unknown. lncRNAs play an important role in regulating gene expression in utero, and likely strongly influence postnatal development and future health.

2. The Placenta

The placenta is one of the products of conception and, thus, is genetically identical to the foetus. Correct placental development and function is critical for both maternal and foetal health. The placenta is central to the cross talk between mother and foetus. It provides many functions beyond the transfer of oxygen, nutrients and water to the foetus and elimination of wastes from it. These include secretion of hormones into the maternal circulation that orchestrate maternal adaptation to pregnancy and transfer of maternal antibodies to the foetus to provide passive immunity to pathogens the newborn is likely to encounter. Defects in placental differentiation and function have been associated with pregnancy complications.

There are some published reports on placental lncRNAs in pregnancy complications assessed after delivery but there is a paucity of literature on the role of lncRNAs in normal placental development.

3.1. Miscarriage

Miscarriage is defined as pregnancy loss that occurs before 20 weeks of gestation. Miscarriage during the first trimester affects up to 15% of clinically recognised pregnancies and up to 50% of recurrent pregnancy losses have no identifiable cause. Up to 50% of first trimester miscarriage is associated with aneuploidy and chromosome translocations while other factors include maternal age, obesity, thrombophilia, smoking, alcohol use, endocrine and immune parameters. To date there have only been two studies identifying a link between altered lncRNA expression and miscarriage. The first study used microarray analysis to compare the expression of lncRNAs by embryonic sac/chorionic villi in miscarriage with those in gestation matched pregnancies with elective induced abortion and identified a large number of differentially expressed lncRNAs. A number of the regulatory pathways represented by these lncRNAs are related to infection and inflammation (although the majority of miscarriages show no sign of infection), metabolism, signalling, and transcription regulation. In a recent study, also using the same microarray approach, 1449 differentially expressed lncRNAs were identified from chorionic villi tissue from recurrent miscarriages (women who had suffered three or more miscarriages before 12 weeks of gestation) compared to normal pregnancy. Some of the pathways represented by these differentially expressed lncRNAs included immunity, steroid hormone biosynthesis and transforming growth factor beta (TGF-β) signalling pathway.

3.2. Preeclampsia

Preeclampsia (PE) is a pregnancy complication diagnosed by new onset hypertension after 20 weeks of gestation with either proteinuria and/or other maternal organ dysfunction and/or foetal growth restriction. It is characterised by systemic maternal oxidative stress and endothelial dysfunction. PE occurs in 3–5% of pregnancies worldwide and is a major cause of maternal and perinatal mortality. Microarray analysis (33,045 total probes for lncRNAs) comparing placentas from PE and control pregnancies showed 738 (259 up and 479 down) lncRNAs were differentially expressed. LOC391533, LOC284100 and CEACAMP8 are three lncRNAs found to be more highly expressed in placenta from PE and have been validated by quantitative polymerase chain reaction (qPCR) comparing placentas from 40 PE and 40 control pregnancies. A co-expression analysis of lncRNA and mRNA differential expression identified significant enrichment for pathways involving lipid metabolism and type 2 immune response, consistent with the concept that PE has a disrupted metabolic and immune state compared to uncomplicated pregnancies.

During normal placentation, extravillous cytotrophoblast cells colonise and migrate within the spiral arteries in a retrograde direction transforming their structure to form large compliant vessels lacking their smooth muscle layer. This invasion and remodelling is required for successful pregnancy, whereas in PE this arterial transformation fails or is impaired. A comparison of placentas from 25 control and 25 PE pregnancies found a 2.8-fold increase in the expression of the lncRNA SPRY4-IT1 (708 bp). SPRY4-IT1 has been linked to the formation of endothelial cell-like tubular networks (as discussed below), an important angiogenic process, and may implicate this lncRNA in spiral artery remodelling, in particular in placentas from PE pregnancies where it has higher expression compared to in uncomplicated pregnancies.

A lncRNA microarray comparison of placentas from six early onset PE (EOPE) pregnancies and six preterm deliveries as gestational age matched controls found 15,646 lncRNAs were up regulated and 13,178 were down regulated in EOPE. As the function of the majority of lncRNAs remains largely unknown, standard gene ontology (GO) pathway analysis cannot be performed. In an attempt to assign a function to the differentially expressed lncRNAs, the neighbouring protein coding genes were interrogated by GO which revealed that pathways relating to cell migration and motility were significantly enriched. The lncRNA RP11-465L10.10 was found to be downregulated in placentas from cases of EOPE, along with its target gene MMP9. Studies of MMP9 have linked its expression to PE and trophoblast invasion in women. It is important to note that approximately 80% of the lncRNA probes on the microarray were identified as being differentially expressed, which has implications for interpretation of the analysis. Since preterm birth is itself a pregnancy complication, using placentas from preterm pregnancies may not constitute an ideal control so these results should be viewed with caution.

Altered MALAT1 expression has been found in the placenta of two different pregnancy complications, PE and placenta increta/percreta. Placentas from PE pregnancies show significantly lower expression of MALAT1 compared to control placentas, while placentas from women with placenta increta/percreta show significantly higher expression of MALAT1. MALAT1 expression increases invasion and migration in trophoblast cell lines, as discussed below. The loss of expression of MALAT1 in PE placentas may lead to a reduction in the invasive properties of trophoblast cells resulting in PE pathogenesis. Conversely, the overexpression of MALAT1 observed in placenta increta/percreta may lead to an overly invasive trophoblast phenotype. It should be noted that altered MALAT1 expression has only been shown after trophoblast invasion has occurred; as such, further evidence is required to determine if altered MALAT1 is a cause or merely a marker of altered trophoblast invasion in these pregnancy complications.

Haemolysis, elevated liver enzymes, low platelet count (HELLP) syndrome is considered a severe form of preeclampsia. HELLP symptoms usually present later in pregnancy, however first trimester placentas from women with HELLP show a reduction in trophoblast invasion and impaired spiral artery remodelling. LINC-HELLP is a 205-kb lncRNA located within a genomic region linked to familial HELLP syndrome in Dutch women. LINC-HELLP is found within both the nucleus and cytoplasm of first trimester extravillous cytotrophoblast cells. Single and compound mutagenesis studies of LINC-HELLP have demonstrated that this lncRNA plays an important role in trophoblast proliferation and invasion. Compound mutations found within families that have HELLP syndrome such as the HAPLO215Rev + HAPLO378-M1 compound mutation leads to a significant increase in trophoblast proliferation and a significant reduction in invasion. These changes to proliferation are consistent with a cell cycle exit phenotype. It was also observed that mutations in LINC-HELLP can reduce the differentiation of extravillous trophoblast cells. LINC-HELLP has been shown to interact with ribosomal proteins RPS6 and RPL7 in SGPHL-5 cells (an extra villous trophoblast like cell line). While lncRNAs are not usually associated with the ribosome, as they are not translated, this interaction between lncRNAs and the ribosome has been observed for other lncRNAs and may be linked to lncRNA degradation. It is still unclear as to whether this interaction is a specific function of particular lncRNAs or if it is a coincidental interaction due to the RNA binding nature of the ribosome. LINC-HELLP knockdown followed by RNA-Seq shows a massive reduction in gene expression, which may link this lncRNA to transcriptional and/or posttranscriptional regulation via the ribosome and RNA splicing machinery.

3.3. Intrauterine Growth Restriction

Intrauterine growth restriction (IUGR) is defined as impaired foetal growth where the foetus does not achieve its expected growth potential given its race, sex and gestation. IUGR is well known to increase the risk for perinatal morbidity and mortality. Undetected IUGR is a significant antecedent to stillbirth. IUGR is also known to be a significant risk factor for adult onset non-communicable diseases including cardiovascular disease and Type 2 diabetes and as the placenta mediates nutrient transport to the foetus in response to foetal demand and maternal capacity, it is key to foetal programming.

A complimentary DNA (cDNA) subtraction assay comparing placentas from 12 IUGR and 12 control pregnancies revealed overexpression of the lncRNA NEAT1 in IUGR. NEAT1 expression was observed by in situ hybridisation and was localised exclusively within villous trophoblast cells of the placenta. In addition, more cells express NEAT1 in IUGR villous trophoblast cells compared with control placenta. There are two isoforms of the lncRNA NEAT1, NEAT1_1 and NEAT1_2. NEAT1_2 is required for the formation of paraspeckles, while NEAT1_1 has been shown to increase the number of paraspeckles found in a nucleus when overexpressed. NEAT1 functions by retaining hyper-edited mRNAs in the nucleus. Nuclear paraspeckles are sub nuclear regions where transcription and pre-mRNA transcript processing occurs. Interestingly, paraspeckles have been linked to cell growth and differentiation, and the disruption of paraspeckles is often found in disease states, such as acute promyelocytic leukaemia.

4. H19

H19 was one of the first lncRNAs to be discovered, long before the introduction of next generation sequencing; consequently, it is the most highly studied lncRNA. H19 is located within a large imprinted domain on chromosome 11, 130 kb downstream of IGF2. H19 and IGF2 are reciprocally imprinted that is, for H19 only the paternal allele is expressed, while for IGF2, only the maternal allele is expressed. H19 expression can be regulated by PLAGL1, a zinc finger containing transcription factor, in the human placenta. It has been proposed that due to the high level of sequence conservation, the secondary structure of H19 is very important for its function. Two major functions have been described for H19, specifically a modulator for binding small RNAs and proteins, and as a source of the miRNA mir-675, this function of H19 has been recently reviewed.

DNA methylation of gene regulatory regions typically leads to a reduction in gene expression (however, this is not always the case). Additionally, DNA methylation plays a major role in genomic imprinting, leading to parent-of-origin specific allele expression. H19 has variable levels of biallelic expression in the placenta (reports suggest between 9% and 25% expression occurs from the imprinted allele) until 10 weeks of gestation by which time H19 expression is mostly restricted to the maternal allele. DNA methylation of exon 1 of H19 in placenta shows a significant increase across gestation, from the first trimester to term. Interestingly, there is a significant increase in DNA methylation at a single CpG site within exon 1 of H19 in PE placentas compared to term (first trimester placentas show no methylation at this site). The hypermethylation of this single CpG site has been shown to correlate with an increase in proliferation in the human choriocarcinoma JEG-3 cell line. In direct contrast, the methylation of the H19 differentially methylated region (DMR) is lower at three specific CpG sites in placentas from pregnancies complicated by gestational diabetes mellitus.

Aside from the altered H19 expression observed in placentas from complicated pregnancies, H19 is down-regulated when a hydatiform mole transitions to choriocarcinoma. The expression of H19 may inhibit malignant transformation of trophoblast cells into cancer cells, as is supported by the fact that overexpression of H19 in trophoblast cells leads to reductions in proliferation, migration and invasion. Trophoblast cells, when cultured in the presence of 5-aza-2′-deoxycytidine (a DNA methylation inhibitor), show marked demethylation of a specific CpG site within exon 1 of H19 (the same CpG site, discussed above, that is hypermethylated in PE placentas), followed by an increase in expression of H19. This indicates that the regulation of this one particular site may be important for the expression of H19. It should be noted that 5-aza-2′-deoxycytidine acts globally upon the genome, therefore the increased H19 expression may be a result of reduced DNA methylation elsewhere in the genome.

H19 expression is restricted to intermediate and villous cytotrophoblasts, and is not found within syncytiotrophoblasts in the human placenta. This expression pattern is consistent with the idea that H19 helps regulate the invasive properties of intermediate trophoblasts. DNA methylation analysis of the promotor region of H19 in placentas from EOPE and PE have demonstrated that the H19 promoter is hypermethylated in EOPE placentas compared to controls, while the promoter region in PE placentas is not. H19 expression is also significantly lower in EOPE placentas, which is consistent with hypermethylation of the promoter. While not statistically significant, DNA methylation of H19 showed an increase in PE placentas while H19 expression in PE placentas was lower than control placentas. It is possible that the level of H19 expression and DNA methylation is linked to the severity and stage of onset of PE observed.

Altered H19 and IGF2 expression have been linked to foetal growth restriction and small for gestational age (SGA) in humans. A partial loss of imprinting (LOI), together with biallelic expression of H19, were detected in placentas from SGA and PE pregnancies. Similarly, LOI of H19 and biallelic expression were also linked to foetal growth restriction (FGR) while the maternally inherited single nucleotide polymorphism rs2071094 in H19 has also been shown to associate with increased birth weight. This LOI may result in an increase in expression of H19 and mir-675 (a growth suppressor) resulting in SGA and FGR pregnancies. Both a significant increase in H19 and decrease in IGF2 expression have been observed in placentas from pregnancies with assisted conception by intracytoplasmic sperm injection (ICSI) and in vitro fertilization (IVF). This association indirectly provides evidence that there may be a loss of imprinting at the H19/IGF2 locus in placentas from assisted reproductive technology (ART) pregnancies which a meta-analysis has recently shown are more likely to be affected by a wide range of pregnancy complications. Currently there are conflicting reports as to the effect of altered H19/IGF2 expression on birth weight, with four studies finding an association, while three different studies did not observe this association with placentas from ART pregnancies. Increased 5-hydroxymethlycytosine (5hmC) methylation within the H19 gene body is positively associated with birth weight, but there is no such association between 5hmC methylation and H19 gene expression.

Together evidence indicates that H19 plays an important role in placental development. Changes to the DNA methylation status of either the promoter or the gene body of H19 have been linked with the development of pregnancy complications, PE, EOPE, and IUGR, as well as playing an important role in regulating foetal growth. This indicates the expression of H19 is tightly controlled and deviations from the optimal level of expression have detrimental effects on placental function.

5. lncRNAs Are Important for Trophoblast Cell Function

HTR8/SVneo is a cell line derived from first trimester extravillous cytotrophoblast cells and is often used for in vitro cell culture experiments. siRNA knockdown of the lncRNA SPRY4-IT1 in these cells leads to an increase in their migratory phenotype, as well as a reduction in the number of dead cells. HTR8/SVneo cells can be cultured on Matrigel to stimulate endothelial-like capillary networks and are a useful cell culture model for studying spiral artery remodelling. siRNA knockdown of SPRY4-IT1 in HTR8/SVneo trophoblast cells leads to a reduced ability of the cells to form tube like networks reminiscent of endothelial tubes, while overexpression of SPRY4-IT1 leads to an increase in their capacity to form these networks. The mechanism of action of SPRY4-IT1 in endothelial cell tube-like network remodelling remains unknown, but the expression of VEGF, ANG1 and ANG2 remain unchanged, indicating it is not via a classical angiogenic pathway. Conversely, when SPRY14-IT1 is overexpressed (expression plasmid) in HTR8/SVneo cells they show a large reduction in migration. A similar but not significant trend was observed in proliferation assays. Knockdown of SPRY14-IT1 leads to reduced mRNA and protein expression of E-cadherin and β-catenin mRNA, and an increase in vimentin. SPRY14-IT1 was shown to bind the cytoplasmic RNA binding protein HuR in HTR8/SVneo cells and the complex formed was then demonstrated to directly bind β-catenin mRNA. The interaction of HuR and β-catenin mRNA has been shown to destabilize β-catenin mRNA in other cell types. WNT3 and WNT5B are two downstream targets of β-catenin that are also downregulated as a result of SPRY14-IT1 knockdown. Tight regulation of Wnt/β-catenin signalling is important for maintaining an epithelial phenotype and cell–cell junctions, and loss of this pathway leads to epithelial-mesenchymal transition (EMT). Extravillous cytotrophoblast cells undergo EMT which is the critical first step for their invasion of the maternal decidua, remodelling of the spiral arterioles and successful pregnancy.

As mentioned above, MALAT1 shows altered expression in two pregnancy complications. The function of MALAT1 was investigated in JEG-3 choriocarcinoma cells and following the knockdown of MALAT1 expression there was reduced proliferation, migration and invasion and increased cell death. Additionally, lower MALAT1 expression resulted in cell cycle arrest in the G0/G1 phase. The downregulation of MALAT1 in HeLa cells also leads to a cell cycle arrest phenotype, but these cells arrested at the G2/M phase. MALAT1 has been shown to act as a molecular sponge (a mechanism by which lncRNAs bind miRNAs preventing them from binding their targets) for miRNAs belonging to the miR-200 family in clear cell kidney carcinoma. The miR-200 family targets ZEB2, a transcription factor known for its role in promoting EMT; a reduction in MALAT1 expression can lead to an increase in free miRNAs that can target ZEB2. This reduction in ZEB2 could be responsible for a loss of EMT-like properties observed in JEG-3 cells when MALAT1 expression is lost.

MIR503HG and LINC00629 are two long intergenic non-coding RNAs (lincRNA) found on the X chromosome between HPRT1 and PLAC1. Expression of MIR503HG is similar to that of PLAC1 with expression found in placenta. Unlike PLAC1, MIRG503HG expression is also found in human umbilical vein epithelial cells (HUVECS). By contrast, LINC00629 is expressed not only in the placenta but also in other tissues such as the ovary, cervix, testis and heart. MIR503HG is localised to the nucleus of JEG-3 cells, while LINC00629 is found evenly throughout the cell. Overexpression of either of these lincRNAs in JEG-3 cells has been shown to reduce both migration (30% lower) and invasion (40% lower). By contrast, it has been reported that silencing of endogenous MIR503HG in HUVEC cells leads to a reduction in cell migration. This evidence surrounding MIR503HG function suggests that it may be cell context specific.

MEG3 is an imprinted, maternally expressed, lncRNA that has been shown by qPCR to be down-regulated in placentas from preeclamptic pregnancies when compared to normotensive pregnancies. Using the HTR8/SVneo and JEG-3 cells, overexpression of MEG3 resulted in a reduction in apoptosis and an increase in migration (Figure 2). A recent study has also shown that MEG3’s role in apoptosis and migration may be critical factor in regulating vascular smooth muscle cells during spiral artery remodelling. Another lncRNA identified as altered in preeclampsia is RPAIN, which by qPCR was shown to be overexpressed in placentas from preeclamptic pregnancies when compared to uncomplicated controls. Overexpression of RPAIN in HTR8/SVneo cells resulted in inhibition of proliferation and invasion. The authors went on to show that C1q, a protein that is important for trophoblast invasion and spiral artery remodelling, was also inhibited when RPAIN was overexpressed.

lncRNAs are important for a number of critical trophoblast cell functions, from proliferation, invasion and migration, to cell cycle progression. In particular, the altered expression of any of the lncRNAs described above can lead to changes in these functions, and potentially lead to pregnancy complications. So far only a small number of lncRNAs have been studied with respect to their importance in trophoblast cell function, yet a majority influence proliferation and migration, two key processes in trophoblast cell function (Figure 2). It is possible that the strong phenotypes observed upon altering the expression of single lncRNAs are due to their being involved in multiple pathways. Additionally, this emphasizes how complicated molecular control of trophoblast function is, and how delicate the system is, where altered expression of a single lncRNA can have significant downstream effects. Due to knowledge of lncRNA expression and function being in its infancy, it is likely that there are many more unidentified lncRNAs required for trophoblast function, potentially opening up a large future array of therapeutic targets.

6. Links between lncRNAs and the Placental Immune/Inflammatory Functions

The placenta is formed from the extraembryonic tissue derived from the conceptus and as such is a unique combination of both the maternal and paternal genomes. Hence, the placenta and the foetus are foreign to the maternal immune system. The development and maintenance of immune tolerance of foetal/placental antigens is a complicated and dynamic process that changes over the course of pregnancy, making it a unique immune state. It includes dramatic changes in the immune profiles in both the maternal circulation and decidua (uterine mucosa in pregnancy) particularly uterine natural killer cells, T regulatory cells and M2 macrophages. Since immune tolerance involves changes to both adaptive and innate immunity, pregnant women are at greater risk of infection, especially viral illness. During pregnancy there are several viral pneumonias that have the potential to become more severe than in non-pregnant women, these include but are not limited to influenza, coronavirus, and varicella. Transmission of viral pathogens from the mother to the conceptus can lead to complications in the developing foetus.

lncRHOFX1 is a newly-discovered 4.8-kb lncRNA located on the X chromosome and is one of the most abundantly expressed lncRNAs in the trophectoderm and primitive endoderm. In addition, lncRHOFX1 is expressed highly within syncytio- and extravillous cytotrophoblast (EVTs) cells obtained by differentiating human embryonic stem cells (hESCs) in an in vitro culture model. lncRHOFX1 is also expressed by JEG-3 cells and primary isolated EVTs. lncRHOFX1 localises to nuclear paraspeckles but it is not known if these speckles are also positive for NEAT1.

Knockdown of lncRHOFX1 in hESC-derived placental cells leads to the increased expression of a number of different immune response genes (Table 2). Trophoblast cells with lncRHOFX1 knockdown that are subsequently exposed to Sendai virus show reduced expression of viral mRNA compared to control trophoblast cells. This indicates that lncRHOFX1 expression suppresses antiviral activity. It is proposed that lncRHOFX1 acts in trans to supress the cellular viral immune response. In hESCs, overexpression of lncRHOFX1 leads to a switch from cell growth to cell differentiation, while no change to antiviral genes is observed. This is another example of cell context influencing the function of lncRNAs.

Further understanding of the molecular regulation of immune tolerance in pregnancy would facilitate better prevention and treatment of pregnancy complications in which it is implicated, as well as new insights into greater prevalence and severity of viral infections in pregnant women.

7. Conclusions

In recent years, the number of lncRNAs identified in the human placenta has increased dramatically, and as more RNA sequencing data becomes available, this number is likely to increase. lncRNAs are involved in many different cellular and gene regulatory networks, a discovery that has changed the fundamental understanding of how these networks function and interact with one another. Currently, the specific mechanisms of action for most lncRNAs remain largely unknown, partially due to a lack of conservation across evolution that has limited the suitability of using animal models. This is compounded by the cell type-specific function that a number of lncRNAs exhibit (such as MALAT1 and MIR503HG). Therefore, it is likely that each lncRNA will need to be independently investigated in all cell types in which they are expressed.

Here we have discussed the current literature surrounding lncRNA expression and function in the placenta, trophoblast cells, and how altered expression of several lncRNAs is linked to a number of pregnancy complications. Increasing our understanding of lncRNA function in normal placental development will be critical to unravelling the complex pathogenesis of pregnancy complications and may lead to new diagnostic or therapeutic options.