Microarray analysis of equine endometrium at days 8 and 12 of pregnancy

The Equine Embryo Influences Immune-Related Gene Expression in the Oviduct

Although the equine oviduct clearly affects early embryo development and the selective transport of equine embryos through the oviduct indicates a reciprocal interaction, the influence of the embryo on gene expression in the oviduct remains to be determined in the horse. The aim of this study was to examine this by means of RNA sequencing. Four days after ovulation, epithelial cells ipsilateral and contralateral to the ovulation side from five cyclic and five pregnant mares were collected from the oviduct. RNA was extracted, samples were sequenced, and data analysis was performed to determine differentially expressed genes (DEGs) (P value ≤0.05 and absolute fold change ≥2) and to provide functional interpretation. A total of 10 743 transcripts were identified and 253 genes were found to be upregulated and 108 to be downregulated in the pregnant ipsilateral oviduct when compared to the cyclic ipsilateral oviduct. Comparison of the ipsilateral and the contralateral oviduct indicated 164 DEGs in pregnant mares and 77 DEGs in cyclic mares. Enriched functional categories were detected only in the comparison of pregnant and cyclic ipsilateral oviducts and showed that the equine embryo affects the expression of immune response-related genes in the oviduct, with marked upregulation of interferon-associated genes. This research represents the foundation for further assessment of the role of specific genes in the early embryo-maternal dialogue of the horse.

Proteomes of the Female Genital Tract During the Oestrous Cycle

The female genital tract includes several anatomical regions whose luminal fluids successively interact with gametes and embryos and are involved in the fertilisation and development processes. The luminal fluids from the inner cervix, the uterus and the oviduct were collected along the oestrous cycle at oestrus (Day 0 of the cycle) and during the luteal phase (Day 10) from adult cyclic ewes. The proteomes were assessed by GeLC-MS/MS and quantified by spectral counting. A set of 940 proteins were identified including 291 proteins differentially present along the cycle in one or several regions. The global analysis of the fluid proteomes revealed a general pattern of endocrine regulation of the tract, with the cervix and the oviduct showing an increased differential proteins abundance mainly at oestrus while the uterus showed an increased abundance mainly during the luteal phase. The proteins more abundant at oestrus included several families such as the heat shock proteins (HSP), the mucins, the complement cascade proteins and several redox enzymes. Other proteins known for their interaction with gametes such as oviductin (OVGP), osteopontin, HSPA8, and the spermadhesin AWN were also overexpressed at oestrus. The proteins more abundant during the luteal phase were associated with the immune system such as ceruloplasmin, lactoferrin, DMBT1, or PIGR, and also with tissue remodeling such as galectin 3 binding protein, alkaline phosphatase, CD9, or fibulin. Several proteins differentially abundant between estrus and the luteal phase, such as myosin 9 and fibronectin, were also validated by immunohistochemistry. The potential roles in sperm transit and uterine receptivity of the proteins differentially regulated along the cycle in the female genital tract are discussed.

Early pregnancy in the horse revisited - does exception prove the rule?

Early equine pregnancy shares many features with that of more intensively assessed domestic animals species, but there are also characteristic differences. Some of those are poorly understood. Descent of the equine conceptus into the uterine lumen occurs at day 5 to 6 after ovulation but is only possible when the embryo secretes prostaglandin E2. Although maintenance of equine pregnancy probably involves secretion of a conceptus derived anti-luteolytic factor, this agent has not been identified. Rapid growth, conceptus mobility and presence of an acellular capsule at the time of maternal recognition of pregnancy, i.e. between days 12 and 14, are prerequisites to avoid pregnancy loss. Progesterone together with 5α-pregnanes is secreted by the corpus luteum and induces the production of endometrial histotroph which is responsible for conceptus nutrition until placention. A stable contact between the outer trophoblast layer of the allantochorion and the luminal epithelium of the endometrium is not established before days 40 to 42 of pregnancy.

Effect of ovarian hormones on the healthy equine uterus: a global gene expression analysis

The physiological changes associated with the varying hormonal environment throughout the oestrous cycle are linked to the different functions the uterus needs to fulfil. The aim of the present study was to generate global gene expression profiles for the equine uterus during oestrus and Day 5 of dioestrus. To achieve this, samples were collected from five horses during oestrus (follicle >35 mm in diameter) and dioestrus (5 days after ovulation) and analysed using high-throughput RNA sequencing techniques (RNA-Seq). Differentially expressed genes between the two cycle stages were further investigated using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. The expression of 1577 genes was found to be significantly upregulated during oestrus, whereas 1864 genes were expressed at significantly higher levels in dioestrus. Most genes upregulated during oestrus were associated with the extracellular matrix, signal interaction and transduction, cell communication or immune function, whereas genes expressed at higher levels in early dioestrus were most commonly associated with metabolic or transport functions, correlating well with the physiological functions of the uterus. These results allow for a more complete understanding of the hormonal influence on gene expression in the equine uterus by functional analysis of up- and downregulated genes in oestrus and dioestrus, respectively. In addition, a valuable baseline is provided for further research, including analyses of changes associated with uterine inflammation.

Novel equine conceptus?endometrial interactions on Day 16 of pregnancy based on RNA sequencing

Maintenance of pregnancy is dependent on the exchange of signals between the conceptus and the endometrium. The objective of this study was to use next-generation sequencing to determine transcriptome blueprints of the conceptus and endometrium 16 days after ovulation in the horse. There were 7760 and 10 182 genes expressed in the conceptus and endometrium, respectively, of which 7029 were present in both. Genes related to developmental processes were enriched among conceptus-specific transcripts, whereas many endometrium-specific genes had known roles in cell communication, cell adhesion and response to stimuli. The integrin signalling pathway was overrepresented in both transcriptomes. In that regard, it was hypothesised that integrins ITGA5B1 and ITGAVB3 interact with conceptus-derived fibrinogen, potentially contributing to cessation of conceptus mobility. That several growth factors and their corresponding receptors (e.g. HDGF, NOV, CYR61, CTGF, HBEGF) were expressed by conceptus and endometrium were attributed to cross-talk. In addition, Cytoscape interaction analysis revealed a plethora of interactions between genes expressed by the conceptus and endometrium, during a period when the former had substantial movement within the uterus. This is the first report of concurrent transcriptome analysis of conceptus and endometrium in the mare, with numerous findings to provide rationale for further investigation.

Hypoxia-induced overexpression of stanniocalcin-1 is associated with the metastasis of early stage clear cell renal cell carcinoma

Background

Although metastasis of clear cell renal cell carcinoma (ccRCC) is predominantly observed in late stage tumors, early stage metastasis of ccRCC can also be found with indefinite molecular mechanism, leading to inappropriate clinical decisions and poor prognosis. Stanniocalcin-1 (STC1) is a glycoprotein hormone involved in calcium/phosphate homeostasis, which regulates various cellular processes in normal development and tumorigenesis. This study aimed to investigate the role and mechanism of regulation of STC1 in the metastasis of early stage ccRCC.

Methods

STC1 mRNA and protein expression was determined in ccRCC surgical specimens, RCC cell lines, and human kidney tubule epithelial cell line HKC by real-time polymerase chain reaction (RT-PCR) and western blotting. Immunohistochemistry staining (IHC) and immunofluorescence were also used to examine the expression and localization of STC1 in ccRCC tissues and cancer cells. Knockdown and overexpression studies were conducted in vitro in RCC cell lines using small interfering RNAs (siRNA) and lentiviral-mediated gene delivery to evaluate the role of STC1 in cell proliferation, anchorage-dependent and independent growth, cell cycle control, and migration and invasion.

Results

STC1 mRNA and protein expression were significantly up-regulated in tumors when compared with non-tumor tissues, with the greatest increase in expression observed in metastatic tissues. Clinicopathological analysis revealed that STC1 mRNA expression was associated with Fuhrman tumor grade (P = 0.008) and overall Tumor Node Metastasis (TNM) staging (P = 0.018). STC1 expression was elevated in T1 stage metastatic tumors when compared with localized tumors, and was positively correlated with average tumor diameter. Silencing of STC1 expression by Caki-1 and A498 resulted in the inhibition of cell proliferation, migration, and invasion, meanwhile down-regulation of STC1 impaired epithelial–mesenchymal transition (EMT) of ccRCC cell lines. Overexpression of STC1 in Caki-2 enhanced cell growth and proliferation but not migration and invasion. Further investigation identified hypoxia and HIF-1α as candidate regulators of STC1 expression.

Conclusions

Our findings demonstrate a role for STC1 in metastasis of early stage ccRCC and suggest that STC1 may be a biomarker of potential value both for the prognosis of this disease and for guiding clinical decisions regarding surgical strategies and adjuvant treatment.

Electronic supplementary material

The online version of this article (doi:10.1186/s12967-015-0421-4) contains supplementary material, which is available to authorized users.

Uterine responses to the preattachment embryo in domestic ungulates: recognition of pregnancy and preparation for implantation

The endometrium is a tissue newly evolved with the development of mammalian species. Its main function is the support of embryonic growth and development and the nutrition of the fetus. The species-specific differences in establishment and maintenance of pregnancy make the study of this tissue in various mammalian organisms particularly interesting. With the application of omics technologies to various mammalian species, many systematic studies of endometrial gene expression changes during the phase of establishment of pregnancy have been performed to obtain a global view of regulatory events associated with this biological process. This review summarizes the results of trancriptome studies of bovine, porcine, and equine endometrium. Furthermore, the results are compared between these species and to humans. Because an increasing number of studies suggest an important role of small regulatory RNAs (i.e., microRNAs), recent findings related to the regulation of endometrial functions and the development of the conceptus are presented.

Equine oviduct explant culture: a basic model to decipher embryo–maternal communication

Equine embryos remain for 6 days in the oviduct and thus there is a need for an in vitro model to study embryo–oviductal interactions in the horse, since this subtle way of communication is very difficult to analyse in vivo. Until now, no equine oviduct explant culture model has been characterised both morphologically and functionally. Therefore, we established a culture system for equine oviduct explants that maintained epithelial morphology during 6 days of culture, as revealed by light microscopy and transmission electron microscopy. We demonstrated the presence of highly differentiated, tall columnar, pseudostratified epithelium with basal nuclei, numerous nucleoli, secretory granules and apical cilia, which is very similar to the in vivo situation. Both epithelium and stromal cells originating from the lamina propria are represented in the explants. Moreover, at least 98% of the cells remained membrane intact and fewer than 2% of the cells were apoptotic after 6 days of culture. Although dark-cell degeneration, which is a hypoxia-related type of cell death, was observed in the centre of the explants, quantitative real-time PCR failed to detect upregulation of the hypoxia-related marker genes HIF1A, VEGFA, uPA, GLUT1 and PAI1. Since the explants remained morphologically and functionally intact and since the system is easy to set up, it appears to be an excellent tool for proteome, transcriptome and miRNome analysis in order to unravel embryo–maternal interactions in the horse.

Low levels of naturally occurring regulatory T lymphocytes in blood of mares with early pregnancy loss

Early pregnancy loss is a major reason for low reproductive efficiency in the horse. In humans and mice, low numbers of regulatory T cells (Treg cells) are linked to miscarriage. The percentage of Treg cells in oestrous mares at the start of the breeding season was evaluated in relation to the outcome of subsequent pregnancy. For identification and quantification of Treg cells, a highly sensitive and specific qPCR assay targeting the Treg-specific demethylated region in the equine forkhead box transcription factor (FOXP3) gene was established. In a total of 108 mares, pregnancy was followed until detection of early pregnancy loss (n = 17), abortion without identification of an infectious or apparent cause (n = 9) or birth of a viable foal (n = 82). Measured Treg-cell levels did not significantly differ between mares that conceived (82%; 1.50 ± 0.04%) or did not get pregnant (18%; 1.45 ± 0.10%). The Treg-cell percentage at oestrus before breeding was significantly different (P < 0.05) between mares that either underwent early pregnancy loss up to Day 40 of pregnancy (1.29 ± 0.07%) and mares that aborted (1.61 ± 0.15%) or gave birth to a live foal (1.52 ± 0.05%). These results suggest that low levels of Treg cells in mares can contribute to pregnancy loss up to Day 40 after ovulation.

Transcriptome changes in the porcine endometrium during the preattachment phase

The porcine conceptus undergoes rapid differentiation and expansion of its trophoblastic membranes between Days 11 and 12 of gestation. Concomitant with trophoblast elongation, production of conceptus estrogen, the porcine embryonic pregnancy recognition signal, increases. Conceptus attachment to the uterine surface epithelium starts after Day 13, initiating epitheliochorial placentation. To analyze the transcriptome changes in the endometrium in the course of maternal recognition of pregnancy, deep sequencing of endometrial RNA samples of Day 12 pregnant animals (n = 4) and corresponding nonpregnant controls (n = 4) was performed using RNA sequencing (RNA-Seq). Between 30 000 000 and 35 000 000 sequence reads per sample were produced and mapped to the porcine genome (Sscrofa10.2). Analysis of read counts revealed 2593 differentially expressed genes (DEGs). Expression of selected genes was validated by the use of quantitative real-time RT-PCR. Bioinformatics analysis identified several functional terms specifically overrepresented for up-regulated or down-regulated genes. Comparison of the RNA-Seq data from Days 12 and 14 of pregnancy was performed at the level of all expressed genes, the level of the DEG, and the level of functional categories. This revealed specific gene expression patterns reflecting the different functions of the endometrium during these stages (i.e., recognition of pregnancy and preparation for conceptus attachment). Genes related to mitosis, immune response, epithelial cell differentiation and development, proteolysis, and prostaglandin signaling and metabolism are discussed in detail. This study identified comprehensive transcriptome changes in porcine endometrium associated with establishment of pregnancy and could be a resource for targeted studies of genes and pathways potentially involved in regulation of this process.

Differential expression and regulation of Cryab in mouse uterus during preimplantation period

The aim of this study was to examine the expression and regulation of the crystallin, alpha B (Cryab) gene in mouse uterus during the peri-implantation period by in situ hybridization and real-time PCR. There was no detectable Cryab mRNA signal on days 1-4 of pregnancy. On day 5 of pregnancy when embryo implanted, a high level of Cryab mRNA signal was found in the subluminal stroma surrounding the implanting blastocyst. On days 6-8, Cryab mRNA was strongly expressed in the primary decidua. By real-time PCR, a high level of Cryab expression was detected on days 7 and 8 of pregnancy, although Cryab expression was seen from days 1 to 8. Under in vivo and in vitro artificial decidualization, Cryab expression was significantly elevated. Compared with the progesterone-primed delayed implantation uterus, a high level of Cryab mRNA expression was observed in estrogen-activated implantation uterus. In the uterine stromal cells, cAMP, estrogen, and progesterone could induce the expression of Cryab gene. In the ovariectomized mouse uterus, estrogen could also induce the expression of Cryab while progesterone inhibited its expression. Our data suggest that Cryab may play an important role during mouse embryo implantation and decidualization and that estrogen and progesterone can regulate the expression of Cryab gene.

Deep sequencing of the porcine endometrial transcriptome on day 14 of pregnancy

In pigs, conceptus attachment to the uterine surface epithelium starts around Day 14 of pregnancy preceded by a pronounced vascularization at the implantation zones, initiating the epitheliochorial placentation. To characterize the complex transcriptome changes in the endometrium in the course of initial conceptus attachment, deep sequencing of endometrial RNA samples of pregnant animals (n = 4) and corresponding cyclic controls (n = 4) was performed using Illumina RNA-Seq. The obtained sequence reads were mapped to the porcine genome, and relative expression values were calculated for the analysis of differential gene expression. Statistical analysis revealed 1933 differentially expressed genes (false discovery rate 1%), 1229 with higher and 704 with lower mRNA concentration, in the samples from pregnant animals. Expression of selected genes was validated by the use of quantitative real-time RT-PCR. The RNA-Seq data were compared to results of a microarray study of bovine endometrium on Day 18 of pregnancy and additional related data sets. Bioinformatics analysis revealed for the genes with higher mRNA concentration in pregnant samples strong overrepresentation, particularly for immune-related functional terms but also for apoptosis and cell adhesion. Overrepresented terms for the genes with lower mRNA concentration in pregnant samples were related to extracellular region, ion transport, cell adhesion, and lipid and steroid metabolic process. In conclusion, RNA-Seq analysis revealed comprehensive transcriptome differences in porcine endometrium between Day 14 of pregnancy and corresponding cyclic endometrium and highlighted new processes and pathways probably involved in regulation of noninvasive implantation in the pig.

Identification of new biomarker candidates for glucocorticoid induced insulin resistance using literature mining

BACKGROUND

Glucocorticoids are potent anti-inflammatory agents used for the treatment of diseases such as rheumatoid arthritis, asthma, inflammatory bowel disease and psoriasis. Unfortunately, usage is limited because of metabolic side-effects, e.g. insulin resistance, glucose intolerance and diabetes. To gain more insight into the mechanisms behind glucocorticoid induced insulin resistance, it is important to understand which genes play a role in the development of insulin resistance and which genes are affected by glucocorticoids.Medline abstracts contain many studies about insulin resistance and the molecular effects of glucocorticoids and thus are a good resource to study these effects.

RESULTS

We developed CoPubGene a method to automatically identify gene-disease associations in Medline abstracts. We used this method to create a literature network of genes related to insulin resistance and to evaluate the importance of the genes in this network for glucocorticoid induced metabolic side effects and anti-inflammatory processes.With this approach we found several genes that already are considered markers of GC induced IR, such as phosphoenolpyruvate carboxykinase (PCK) and glucose-6-phosphatase, catalytic subunit (G6PC). In addition, we found genes involved in steroid synthesis that have not yet been recognized as mediators of GC induced IR.

CONCLUSIONS

With this approach we are able to construct a robust informative literature network of insulin resistance related genes that gave new insights to better understand the mechanisms behind GC induced IR. The method has been set up in a generic way so it can be applied to a wide variety of disease networks.

Domestic animal models for biomedical research

Experimental animals in biomedical research provide insights into disease mechanisms and models for determining the efficacy and safety of new therapies and for discovery of corresponding biomarkers. Although mouse and rat models are most widely used, observations in these species cannot always be faithfully extrapolated to human patients. Thus, a number of domestic species are additionally used in specific disease areas. This review summarizes the most important applications of domestic animal models and emphasizes the new possibilities genetic tailoring of disease models, specifically in pigs, provides.

Effect of cytokines and ovarian steroids on equine endometrial function: an in vitro study

Regulation of immune–endocrine interactions in the equine endometrium is not fully understood. The aims of the present study were to: (1) investigate the presence of tumour necrosis factor alpha (TNF), interferon gamma (IFNG), Fas ligand (FASLG) and their receptors in the mare endometrium throughout the oestrous cycle; and (2) assess endometrial secretory function (prostaglandins), angiogenic activity and cell viability in response to TNF, oestradiol (E2), progesterone (P4) and oxytocin (OXT). Transcription of TNF and FASLG mRNA increased during the early and late luteal phase (LP), whereas IFNG mRNA increased in late LP. Transcription of the mRNA of both TNF receptors was highest in the mid-LP. All cytokines and receptors were expressed in surface and glandular epithelium, as well as in the stroma. Expression of TNF and its receptor TNFRSF1A increased during the follicular phase (FP) and mid-LP. IFNG was expressed in the mid-LP, whereas its receptor IFNR1 was expressed in the in mid- and late LP. The highest expression of FASLG and FAS occurred during the late LP. OXT increased the secretion of prostaglandin (PG) E2 and PGF2α in the FP and mid-LP. In the mid-LP, E2 and P4+E2 stimulated PGF2α secretion, whereas TNF and P4 increased cell viability. All treatments, with the exception of P4, increased nitric oxide and angiogenic activity in both phases. The coordinated action of cytokines and ovarian hormones may regulate secretory, angiogenic and proliferative functions in the equine endometrium.

Exploration of global gene expression changes during the estrous cycle in equine endometrium

The equine endometrium exhibits characteristic morphological and functional changes during the estrous cycle controlled by the interplay of progesterone and estradiol. A microarray analysis of endometrial tissue samples derived from five time points of the estrous cycle (Day [D] 0, D3, D8, D12, and D16) was performed to study the dynamics of equine endometrial gene expression. Statistical analysis revealed 4996 genes differentially expressed during the estrous cycle. Clustering of similar expression profiles was performed to find groups of coregulated genes. This revealed eight major profiles: highest mRNA concentrations on D0, from D0 to D3, on D3, from D3 to D8, on D8, from D8 to D12, from D12 to D16, and on D16. Bioinformatics analysis revealed distinct molecular functions and biological processes for the individual expression profiles characterizing the different phases of the estrous cycle (e.g., extracellular matrix and inflammatory response during the estrus phase, cell division and cell cycle during early luteal phase, and endoplasmic reticulum, protein transport, and lipid metabolism in the luteal phase). A comparison to dynamic gene expression changes in bovine endometrium identified common and species-specific gene regulations in cyclic endometrium. Analysis of expression changes during the estrous cycle for genes previously found to be differentially expressed on D12 of pregnancy provided new evidence for possible regulation of these genes. This study provides new insights regarding global changes of equine endometrial gene expression as molecular reflections of physiological changes in the cyclic equine endometrium with regard to the crucial role of this tissue for successful reproduction.

Transcriptional profiling to address molecular determinants of endometrial receptivity--lessons from studies in livestock species

The development of a fertilized oocyte into a differentiated multi-cellular organism is a major challenge with regard to the orchestration of the expression of the mammalian genome. Highly complex networks of genes are temporally and spatially regulated during cellular differentiation to generate specific cell types. Embryonic development is critically influenced by external impacts in the female reproductive tract. A most critical phase of pregnancy in mammals is the pre- and peri-implantation period, during which the uterine environment plays a crucial role in supporting the development of the conceptus. The analytical description of the transcriptome, proteome and metabolome of the embryo-maternal interface is a prerequisite for the understanding of the complex regulatory processes taking place during this time. This review lines out potentials and limitations of different approaches to unravel the determinants of endometrial receptivity in cattle, the pig and the horse. Suitable in vivo and in vitro models, which have been used to elucidate factors participating in the embryo-maternal dialog are discussed. Taken together, transcriptome analyses and specified selective candidate gene driven approaches contribute to the understanding of endometrial function. The endometrium as sensor and driver of fertility may indicate the qualitative and quantitative nature of signaling molecules sent by the early embryo and in turn, accordingly impact on embryonic development.

Transcriptome analyses of bovine, porcine and equine endometrium during the pre-implantation phase

Different reproductive strategies evolved in various mammalian groups to achieve recognition, establishment and maintenance of pregnancy. The complexity of these processes is reflected by a high incidence of embryonic loss during this critical period in many mammalian species. Besides studies in mice and humans a number of transcriptome studies of endometrial tissue samples and also of early embryos have been performed during the pre-implantation phase in cattle, swine and horse to identify genes associated with embryo-maternal interaction. Results of these studies are reviewed and compared between species. The comparison of data sets from different species indicated a general role of interferons for the establishment of pregnancy. In addition to many species-specific changes in gene expression, which may reflect different pregnancy recognition signals and mechanisms of embryo implantation, a number of transcriptome changes were found to be similar across species. These genes may have conserved roles during the establishment of pregnancy in mammals and reflect basic principles of mammalian reproduction. The relevance and strategies, but also the challenges of cross-species comparisons of gene expression data are discussed.

Proteomic analysis of sputum in patients with active pulmonary tuberculosis

The protein composition of sputum most faithfully reflects the state of the lungs. The aim of this study was to determine whether relative qualitative and quantitative differences in protein expression of sputum could be related to active pulmonary tuberculosis. Sputum samples were collected from 65 patients with active pulmonary tuberculosis and 38 healthy controls. Comprehensive proteomic approaches were used to profile the proteome changes of host sputum in response to Mycobacterium tuberculosis infection using two-dimensional electrophoresis in combination with matrix-assisted laser desorption ionization time-of-flight/time-of-flight mass spectrometry. Mascot software was used to identify proteins from protein databases. Enzyme-linked immunosorbent assay was used to confirm the proteomic results. A total of 62 differentially expressed proteins were identified, among which, 15 proteins were up-regulated and 47 proteins were down-regulated in the tuberculosis sputum compared with the controls. Bacterial protein UqhC was the most increased protein, whereas serum albumin was the most decreased protein in the tuberculosis sputum compared with the controls. The enzyme-linked immunosorbent assay analysis was consistent with proteomic data. Bioinformatics analysis suggested that multiple host cell pathways were involved in the tuberculosis infection processes, including acute phase response, signal transduction, cytoskeleton structure, immune response and so on. In all, for the first time, our results revealed that a number of proteins were differentially expressed during active pulmonary tuberculosis infection. These data will provide valuable clues for further investigation of tuberculosis pathogenesis and biomarkers for detection of active pulmonary tuberculosis infection.

Exploring the application of high-throughput genomics technologies in the field of maternal-embryo communication

Deciphering the complex molecular dialogue between the maternal tract and embryo is crucial to increasing our understanding of pregnancy failure, infertility problems and in the modulation of embryo development, which has consequences through adulthood. High-throughput genomic technologies have been applied to look for a holistic view of the molecular interactions occurring during this dialogue. Among these technologies, microarrays have been widely used, being one of the most popular tools in maternal-embryo communication. Today, next generation sequencing technologies are dwarfing the capabilities of microarrays. The application of these new technologies has broadened to almost all areas of genomics research, because of their massive sequencing capacity. We review the current status of high-throughput genomic technologies and their application to maternal-embryo communication research. We also survey next generation technologies and their huge potential in many research areas. Given the diversity of unanswered questions in the field of maternal-embryo communication and the wide range of possibilities that these technologies offer, here we discuss future perspectives on the use of these technologies to enhance maternal-embryo research.

ERBB receptor feedback inhibitor 1: identification and regulation by estrogen in chickens

The ERBB receptor feedback inhibitor 1 (ERRFI1) is a scaffolding adaptor protein, that plays a pivotal role in the epidermal growth factor receptor (EGFR) cell signaling cascade as a negative regulator affecting many important physiological processes. It was recently reported that ERRFI1 is a critical regulator of the response of the endometrium to estrogen regulation of tissue homeostasis in mice. But, very little is known about ERRF11 and hormonal regulation of the ERRFI1 gene in chickens. Therefore, in the present study, ERRFI1 gene was cloned and its differential expression profile analyzed at different embryonic stages, in various adult organs, and in oviducts from estrogen-treated chickens. Chicken ERRFI1 has an open-reading frame of 2848 nucleotides that encode for a protein of 465 amino acids that has considerable homology to mammalian ERRFI1 proteins (>62% identity). Importantly, ERRFI1 mRNA is abundantly distributed in various organs from chickens. We then determined that DES (diethylstilbestrol, a synthetic nonsteroidal estrogen) induced ERRFI1 mRNA and protein predominantly in luminal and glandular epithelial cells of the oviduct. Further, we determined whether microRNAs, specifically miR-200b, miR-429 and miR-1639, influence ERRFI1 expression via its 3'UTR and found that it does not directly target the 3'UTR of ERRFI1 mRNA. Therefore, it is unlikely that post-transcriptional regulation influences ERRFI1 expression in the chicken oviduct. In conclusion, our results indicate that ERRFI1 is a novel estrogen-stimulated gene expressed in epithelial cells of the chicken oviduct that likely plays an important role in oviduct growth and differentiation during early development of the chicken.

CoPub update: CoPub 5.0 a text mining system to answer biological questions

In this article, we present CoPub 5.0, a publicly available text mining system, which uses Medline abstracts to calculate robust statistics for keyword co-occurrences. CoPub was initially developed for the analysis of microarray data, but we broadened the scope by implementing new technology and new thesauri. In CoPub 5.0, we integrated existing CoPub technology with new features, and provided a new advanced interface, which can be used to answer a variety of biological questions. CoPub 5.0 allows searching for keywords of interest and its relations to curated thesauri and provides highlighting and sorting mechanisms, using its statistics, to retrieve the most important abstracts in which the terms co-occur. It also provides a way to search for indirect relations between genes, drugs, pathways and diseases, following an ABC principle, in which A and C have no direct connection but are connected via shared B intermediates. With CoPub 5.0, it is possible to create, annotate and analyze networks using the layout and highlight options of Cytoscape web, allowing for literature based systems biology. Finally, operations of the CoPub 5.0 Web service enable to implement the CoPub technology in bioinformatics workflows. CoPub 5.0 can be accessed through the CoPub portal http://www.copub.org.

Maternal recognition of pregnancy in the horse: a mystery still to be solved

Maternal recognition of pregnancy in the horse is the sum of events leading to maintenance of pregnancy; in a narrow sense, maternal recognition of pregnancy refers to the physiological process by which the lifespan of the corpus luteum is prolonged. The horse is one of the few domestic species in which the conceptus-derived pregnancy recognition signal has not been identified. The presence of the conceptus reduces pulsatile prostaglandin F2α secretion by the endometrium during early gestation in the mare, partly attributed to the reduced expression of cyclooxygenase-2. Cyclooxygenase-2 has therefore been suggested as one of the regulators of endometrial prostaglandin F2α release modified by the antiluteolytic factor secreted by the conceptus. In addition, altered oxytocin responsiveness has been implicated in the adjustment of prostaglandin release in pregnant mares. While conceptus mobility has proven to be essential for establishment of pregnancy, conceptus-derived oestrogens and prostaglandins, principally prostaglandin E2, have not been confirmed as the critical antiluteolytic factor. Various ways to induce prolonged luteal function in the non-pregnant mare will be highlighted in the current review, specifically, how they may pertain to the process of maternal recognition of pregnancy. Furthermore, recently published microarray experiments comparing the transcriptome of pregnant and non-pregnant endometria and different stages of conceptus development will be reviewed. Findings include the prevention of conceptus adhesion, the provision of nutrients to the conceptus and the avoidance of immunological rejection, among others.

Production of calcium maintenance factor Stanniocalcin-1 (STC1) by the equine endometrium during the early pregnant period

A factor responsible for progression to pregnancy establishment in the mare has not been definitively characterized. To identify factors possibly involved in the establishment of equine pregnancy, the endometrium was collected from day 13 (day 0=day of ovulation) cyclic and day 13, 19 and 25 pregnant animals. From initial subtractive hybridization studies, a calcium regulating factor, Stanniocalcin-1 (STC1) mRNA, was found as a candidate molecule expressed uniquely in the pregnant endometrium. Endometrial expression of STC1 mRNA was noted on day 19 and was markedly increased in the day 25 gravid endometrium. STC1 protein was found in the extracts of day 25 gravid endometrium and immunochemically localized in the uterine glands. In addition, STC1 protein was detected in uterine flushing media collected from day 25 pregnant mares. High concentrations of estradiol-17 β (E(2)) were detected in day 25 conceptuses. E(2) levels were much higher in the gravid endometrium than in other regions, whereas progesterone levels did not differ among the samples from different endometrial regions. Expression of STC1 mRNA, however, was not significantly upregulated in cultured endometrial explants treated with various concentrations of E(2) (0.01-100 ng/ml) with or without 10 ng/ml progesterone. These results indicate that an increase in STC1 expression appears to coincide with capsule disappearance in the conceptus, and suggest that STC1 from the uterine glands likely plays a role in conceptus development during the pregnancy establishment period in the mare.