A bioinformatics transcriptome meta-analysis highlights the importance of trophoblast differentiation in the pathology of hydatidiform moles
Introduction
The placenta is a transitory structure that appeared in the Devonian period in some fishes and evolved into a complex organ in mammals, particularly, in humans. The evolution of this transitory organ allowed the embryo to be independent of the constraints of the living environment and required the development of four main mechanisms, (1) the differentiation of cytotrophoblast (CTB) into syncytiotrophoblast (STB) and extravillous trophoblast (EVT); (2) the controlled invasion of the uterine wall by EVT cells; (3) the implementation of a uterine hypoxic environment during the first trimester of gestation; and (4) the emergence of parental imprinting.
The differentiation of the CTB to generate the EVT is a form of epithelio-mesenchymal transition (EMT) [1,2] that was studied by comparing gene expression profiles of villous trophoblast and EVT cells of normal placentas [3]. Apps et al. [3] observed more than 3000 transcripts that are differentially expressed between villous trophoblast and EVT cells and that are related to different functions such as adhesion, cell migration, and immuno-modulation. Similarly, Da Silva-Arnold [1] used a PCR array comprising probes for genes involved in EMT and found that out of the 84 genes potentially associated with EMT, 54 showed significant changes between the CTB and the EVT. Twenty-four of these genes were down-regulated in the EVT as compared to the CTB and 30 genes were up-regulated.
Gene expression analysis of the invasion of the uterus by the EVT were mostly done in vitro cultured trophoblast cells (primary cells or cell lines), which raises some concerns about gene expression changes during cell culture [4]. Despite these concerns, it was observed that there are 991 genes that show differential expression between the CTB and the EVT, of which 370 are specific for the EVT [5].
It is well-documented that the proliferation of the EVT cells in the first trimester of gestation is dependent on low O2 environment (about 2%) and its differentiation into invasive phenotype is dependent on high O2 environment (5% or more) [6,7]. Highet et al. [8] observed 88 genes that are differentially expressed between normal first trimester trophoblastic cell line, HTR8/SVneo, cultured in 1% or 5% of O2. Of these 88 genes, 57 (65%) have binding sites to the hypoxia induced factor 1 alpha (HIF-1α) protein.
Imprinted genes that are paternally expressed are known for their roles in the growth of the placenta and extraembryonic tissues and those that are maternally expressed are known for their roles in the development of embryonic tissues [9].
Hydatidiform mole is an aberrant human pregnancy characterized by abnormal trophoblastic proliferation and may manifest in the form of complete HM (CHM) or partial HM (PHM). CHM do not have fetal vessels, therefore under severe hypoxia (less than 2%), and are characterized by excessive proliferation of the trophoblast while PHM, which have some functional fetal vessels, and therefore higher O2 concentration, are characterized by mild trophoblastic proliferation.
CHM are mostly androgenetic and contain only the paternal genome [10] which leads to a maximum imbalance of imprints. Little data is known about gene networks involved in the pathology of CHM [10]. In this study, we used a text mining approach to search PubMed for all genes that were studied in HM and looked at their expression in transcriptomes of normal human placenta of different trophoblastic cellular types (CTB, STB, EVT and endothelial cells) related to (1) differentiation, (2) migration/invasion, and (3) hypoxia. This approach showed that genes analyzed in past studies in HM are regulated during normal placenta development and mostly during the differentiation of CTB to STB and EVT. We next attempted to construct a functional network of these genes and recapitulated their regulations.
Section snippets
Study design
Because there are no publicly available transcriptome data on HM, we performed text mining to search for all genes that are studied in hydatidiform moles and then looked at their expression in three different transcriptome datasets of normal human placenta that studied the three biological mechanisms associated with HM, trophoblast differentiation, trophoblast invasion, and hypoxic environment.
Text mining
Most of the biological discoveries are communicated by means of scientific publications with
Hydatidiform mole-linked genes and placental differentiation
Searching the PubMed database on January 8th, 2016 with the MESH term « hydatidiform mole » revealed 7696 relations with 162 identifiers from RefSeq database [17]. Multi-testing mathematical correction [18] was applied on raw data from text mining in order to remove redundancy and control for false discovery rate and take into account the cumulative error of multi-testing (Fig. 1A). The text mining raw p-values and q-values were graphically represented as quantile-quantile-plot (Q-Q plot) in
Discussion
In this study, we used text mining and identified 72 genes associated with the pathology of HM that were analyzed in transcriptomes of normal human placenta samples that looked at three main placental features, trophoblast differentiation (CTB versus STB), migration and invasion (CTB versus EVT), and hypoxic environment that mimics first trimester placenta environment (2%). We found that the expression of these 72 genes in normal placentas has a discriminating tissue distribution that is
Declaration of conflicting interest
The authors declared no potential conflicts of interest with respect to the research, authorship, and publication of this article.
References (41)
- et al.
Differentiation of first trimester cytotrophoblast to extravillous trophoblast involves an epithelial-mesenchymal transition
Placenta
(2015) - et al.
Genome-wide expression profile of first trimester villous and extravillous human trophoblast cells
Placenta
(2011) - et al.
Trophoblast cell lines: a response to the Workshop Report by King et al
Placenta
(2001) - et al.
Hypoxia induced HIF-1/HIF-2 activity alters trophoblast transcriptional regulation and promotes invasion
European journal of cell biology
(2015) - et al.
Imprinted genes in the placenta–a review
Placenta
(2005) - et al.
Differential expression profiling of genes in a complete hydatidiform mole using cDNA microarray analysis
Gynecol. Oncol.
(2006) - et al.
Hypoxia stimulates urokinase receptor expression through a heme protein-dependent pathway
Blood
(1998) - et al.
Use of Matrigel in culture affects cell phenotype and gene expression in the first trimester trophoblast cell line HTR8/SVneo
Placenta
(2012) - et al.
Genomic imprinting in mammalian development: a parental tug-of-war, Trends in genetics
TIG (Trends Genet.)
(1991) - et al.
Differential gene expression identified in complete hydatidiform mole by combining suppression subtractive hybridization and cDNA microarray
Placenta
(2006)
Epithelial-mesenchymal transition during extravillous trophoblast differentiation
Cell Adhes. Migrat.
Identification of novel trophoblast invasion-related genes: heme oxygenase-1 controls motility via peroxisome proliferator-activated receptor gamma
Endocrinology
Oxygen, the Janus gas; its effects on human placental development and function
J. Anat.
Regulation of human placental development by oxygen tension
Science (Washington, D.C.)
The hydatidiform mole
Cell Adhes. Migrat.
Database resources of the national center for Biotechnology information
Nucleic Acids Res.
The gene Ontology annotation (Goa) database: sharing knowledge in Uniprot with gene Ontology
Nucleic Acids Res.
Semantic biomedical resource discovery: a Natural Language Processing framework
BMC Med Inform Decis Mak
Linking genes to literature: text mining, information extraction, and retrieval applications for biology
Genome Biol.
Inflammation as a keystone of bone marrow stroma alterations in primary myelofibrosis
Mediators Inflamm
Cited by (3)
Immune cells in normal pregnancy and gestational trophoblastic diseases
2020, PlacentaCitation Excerpt :Gestational trophoblastic diseases (GTD) are rare pregnancy-related diseases having an overall favorable survival rate [1–4]. GTD develop from abnormal proliferation of trophoblastic tissue and exhibit alterations of molecular pathways involved in placental development and immune processes [1–7]. Measuring β-human chorionic gonadotropin (β-hCG) is crucial for early diagnosis and monitoring treatment of GTD [1–4].
Current approaches and developments in transcript profiling of the human placenta
2020, Human Reproduction UpdateDysregulation of placental functions and immune pathways in complete hydatidiform moles
2019, International Journal of Molecular Sciences