Isolation of differentially expressed genes in conceptuses and endometrial tissue of sows in early gestation

Genetic Variations and Differential DNA Methylation to Face Contrasted Climates in Small Ruminants: An Analysis on Traditionally-Managed Sheep and Goats

The way in which living organisms mobilize a combination of long-term adaptive mechanisms and short-term phenotypic plasticity to face environmental variations is still largely unknown. In the context of climate change, understanding the genetic and epigenetic bases for adaptation and plasticity is a major stake for preserving genomic resources and the resilience capacity of livestock populations. We characterized both epigenetic and genetic variations by contrasting 22 sheep and 21 goats from both sides of a climate gradient, focusing on free-ranging populations from Morocco. We produced for each individual Whole-Genome Sequence at 12X coverage and MeDIP-Seq data, to identify regions under selection and those differentially methylated. For both species, the analysis of genetic differences (F_ST) along the genome between animals from localities with high vs. low temperature annual variations detected candidate genes under selection in relation to environmental perception (5 genes), immunity (4 genes), reproduction (8 genes) and production (11 genes). Moreover, we found for each species one differentially methylated gene, namely AGPTA4 in goat and SLIT3 in sheep, which were both related, among other functions, to milk production and muscle development. In both sheep and goats, the comparison between genomic regions impacted by genetic and epigenetic variations suggests that climatic variations impacted similar biological pathways but different genes.

Maternal N-Carbamylglutamate Supplementation during Early Pregnancy Enhances Embryonic Survival and Development through Modulation of the Endometrial Proteome in Gilts

BACKGROUND

Early pregnancy loss is a major concern in humans and animals. N-carbamylglutamate (NCG) has been found to enhance embryonic survival during early pregnancy in rats. However, little is known about the key factors in the endometrium involved in the improvement of embryonic implantation and development induced by maternal NCG supplementation.

OBJECTIVES

Our objectives were to investigate whether NCG supplementation during early gestation enhanced embryonic survival and development in gilts and to uncover the related factors using the approach of endometrium proteome analysis with isobaric tags for relative and absolute quantification (iTRAQ).

METHODS

Uteruses and embryos/fetuses were obtained on days 14 and 28 of gestation from gilts fed a basal diet that was or was not supplemented with 0.05% NCG. The iTRAQ-based quantitative proteomics approach was performed to explore the endometrium proteome altered by NCG supplementation.

RESULTS

Maternal NCG supplementation significantly increased the number of total fetuses and live fetuses on day 28 of gestation by 1.32 and 1.29, respectively (P < 0.05), with a significant decrease in embryonic mortality (P < 0.05). iTRAQ results indicated that a total of 59 proteins showed at least 2-fold differences (P < 0.05), including 52 proteins that were present at higher abundance and 7 proteins present at lower abundance in NCG-supplemented gilts. The differentially expressed proteins primarily are involved in cell adhesion, energy metabolism, lipid metabolism, protein metabolism, antioxidative stress, and immune response. On day 14 of gestation, several proteins closely related to embryonic implantation and development, such as integrin-αv, integrin-β3, talin, and endothelial nitric oxide synthase, were upregulated (3.7-, 4.1-, 2.4-, and 5.4-fold increases, respectively) by NCG supplementation.

CONCLUSION

To our knowledge, our results provide the first evidence that altered abundance of the endometrial proteome induced by NCG supplementation is highly associated with the improvement of embryonic survival and development in gilts.

Transcriptome Analysis Revealed the Embryo-Induced Gene Expression Patterns in the Endometrium from Meishan and Yorkshire Pigs

The expression patterns in Meishan- and Yorkshire-derived endometrium during early (gestational day 15) and mid-gestation (gestational days 26 and 50) were investigated, respectively. Totally, 689 and 1649 annotated genes were identified to be differentially expressed in Meishan and Yorkshire endometrium during the three gestational stages, respectively. Hierarchical clustering analysis identified that, of the annotated differentially expressed genes (DEGs), 73 DEGs were unique to Meishan endometrium, 536 DEGs were unique to Yorkshire endometrium, and 228 DEGs were common in Meishan and Yorkshire endometriums. Subsequently, DEGs in each of the three types of expression patterns were grouped into four distinct categories according to the similarities in their temporal expression patterns. The expression patterns identified from the microarray analysis were validated by quantitative RT-PCR. The functional enrichment analysis revealed that the common DEGs were enriched in pathways of steroid metabolic process and regulation of retinoic acid receptor signaling. These unique DEGs in Meishan endometrium were involved in cell cycle and adherens junction. The DEGs unique to Yorkshire endometrium were associated with regulation of Rho protein signal transduction, maternal placenta development and cell proliferation. This study revealed the different gene expression patterns or pathways related to the endometrium remodeling in Meishan and Yorkshire pigs, respectively. These unique DEGs in either Meishan or Yorkshire endometriums may contribute to the divergence of the endometrium environment in the two pig breeds.

Microarray Analysis of Gene Expression in the Uterine Endometrium during the Implantation Period in Pigs

During embryo implantation in pigs, the uterine endometrium undergoes dramatic morphological and functional changes accompanied with dynamic gene expression. Since the greatest amount of embryonic losses occur during this period, it is essential to understand the expression and function of genes in the uterine endometrium. Although many reports have studied gene expression in the uterine endometrium during the estrous cycle and pregnancy, the pattern of global gene expression in the uterine endometrium in response to the presence of a conceptus (embryo/fetus and associated extraembryonic membranes) has not been completely determined. To better understand the expression of pregnancy-specific genes in the endometrium during the implantation period, we analyzed global gene expression in the endometrium on day (D) 12 and D15 of pregnancy and the estrous cycle using a microarray technique in order to identify differentially expressed endometrial genes between D12 of pregnancy and D12 of the estrous cycle and between D15 of pregnancy and D15 of the estrous cycle. Results showed that the global pattern of gene expression varied with pregnancy status. Among 23,937 genes analyzed, 99 and 213 up-regulated genes and 92 and 231 down-regulated genes were identified as differentially expressed genes (DEGs) in the uterine endometrium on D12 and D15 of pregnancy compared to D12 and D15 of the estrous cycle, respectively. Functional annotation clustering analysis showed that those DEGs included genes involved in immunity, steroidogenesis, cell-to-cell interaction, and tissue remodeling. These findings suggest that the implantation process regulates differential endometrial gene expression to support the establishment of pregnancy in pigs. Further analysis of the genes identified in this study will provide insight into the cellular and molecular bases of the implantation process in pigs.

Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation

Background

Litter size in pigs is a major factor affecting the profitability in the pig industry. The peri-implantation window in pigs is characterized by the coordinated interactions between the maternal uterine endometrium and the rapidly elongating conceptuses and represents a period of time during which a large percentage of the developing conceptuses are lost. However, the gene expression and regulatory networks in the endometrium contributing to the establishment of the maternal: placental interface remain poorly understood.

Results

We characterized the endometrial gene expression profile during the peri-implantation stage of development by comparing two breeds that demonstrate very different reproductive efficiencies. We employed the porcine Affymetrix GeneChip® to assay the transcriptomic profiles of genes expressed in the uterine endometrium obtained from Meishan and Yorkshire gilts (n = 4 for each breed) on day 12 of gestation (M12 and Y12, respectively). Total of 17,076 probesets were identified as "present" in at least two arrays. A mixed model-based statistical analysis predicted a total of 2,656 (q < 0.1) transcripts as differentially expressed between Meishan and Yorkshire pigs. Eighteen differentially expressed transcripts of interest were validated by quantitative real-time PCR. Gene ontology (GO) annotation revealed that the known functions of the differentially expressed genes were involved in a series of important biological processes relevant to early pregnancy establishment in the pig.

Conclusions

The results identified endometrial gene expression profiles of two breeds differing in litter size and identified candidate genes that are related to known physiological pathways related to reproductive prolificacy. These findings provide a deeper understanding of molecular pathways differing between two breeds at the critical peri-implantation stage of pregnancy, which can be utilized to better understand the events contributing to pregnancy establishment in the pig.

Autocrine and paracrine mechanisms of prostaglandin E₂ action on trophoblast/conceptus cells through the prostaglandin E₂ receptor (PTGER2) during implantation

The conceptus and endometrium secrete large amounts of prostaglandin E₂ (PGE₂) into the porcine uterine lumen during the periimplantation period. We hypothesized that PGE₂ acts on conceptus/trophoblast cells through auto- and paracrine mechanisms. Real-time RT-PCR analysis revealed that PGE₂ receptor (PTGER)2 mRNA was 14-fold greater in conceptuses/trophoblasts on days 14-25 (implantation and early placentation period) vs preimplantation day 10-13 conceptuses (P < .05). Similarly, expression of PTGER2 protein increased during implantation. Conceptus expression of PTGER4 mRNA and protein did not differ on days 10-19. PGE₂ stimulated PTGER2 mRNA expression in day 15 trophoblast cells through PTGER2 receptor signaling. PGE₂ elevated aromatase expression and estradiol-17β secretion by trophoblast cells. Moreover, PGE₂ and the PTGER2 agonist, butaprost, increased the adhesive capacity of both human HTR-8/SVneo trophoblast and primary porcine trophoblast cells to extracellular matrix. This PGE₂-induced alteration in trophoblast cell adhesion to extracellular matrix was abolished by incubation of these cells with AH6809 (PTGER2 antagonist), ITGAVB3-directed tetrapeptide arg-gly-asp-ser or integrin ITGAVB3 antibody. PGE₂ stimulated adhesion of porcine trophoblast cells via the estrogen receptor and MEK/MAPK signaling pathway. PGE₂ induced phosphorylation of MAPK1/MAPK3 through PTGER2 and up-regulated expression of cell adhesion proteins such as focal adhesion kinase and intercellular adhesion molecule-1. Our study indicates that elevated PGE₂ in the periimplantation uterine lumen stimulates conceptus PTGER2 expression, which in turn promotes trophoblast adhesion via integrins, and synthesis and secretion of the porcine embryonic signal estradiol-17β. Moreover, the mechanism through which PGE₂ increases trophoblast adhesion is not species specific because it is PTGER2- and integrin-dependent in both porcine and human trophoblast cells.

Transcriptomic analysis of the porcine endometrium during early pregnancy and the estrous cycle

The goal of this study was to describe the alterations in the transcriptome of the endometrium in pigs during the beginning of implantation (days 15-16 of pregnancy) compared to cyclic pigs during the onset of luteolysis (days 15-16 of the estrous cycle). The global expression of genes in porcine gravid and non-gravid endometria was investigated using the Porcine (V2) Two-color gene expression microarray, 4 × 44 (Agilent, USA). Analysis of the microarray data showed that, of 589 accurately annotated genes, the expression of 266 genes was up-regulated and expression of 323 was down-regulated in the endometrium harvested during early pregnancy compared with the endometrium during the estrous cycle. In pregnant pigs, genes with the most significantly altered expression were involved in the following biological processes: the metabolic process, cellular process, cell communication, immune system process, developmental process, cell adhesion, antigen processing and presentation, antigen processing and presentation of peptide or polysaccharide antigen via major histocompatibility complex (MHC) class II, immune response, and the polysaccharide metabolic process. In the pregnant endometrium, cell adhesion molecules and steroid hormone biosynthesis pathways were the most significantly enriched biological pathways. Analysis of the interaction network among selected genes showed that androgen receptor (AR) encoding genes interact with genes involved in important processes occurring during early pregnancy. The bioinformatic analysis revealed information about the meaning of differentially expressed genes. The data provided new insight into the dynamic changes of the endometrial gene expression profile during days 15-16 of pregnancy.

Differential gene expression in the endometrium on gestation day 12 provides insight into sow prolificacy

BACKGROUND

Erhualian pigs, one of Chinese Taihu pig breeds, are known to have the largest recorded litter size in the world. A lower prenatal death rate is the major contributing factor to the prolificacy of Taihu pigs. Cross-breeding experiments have demonstrated that Taihu sows exhibit a strong maternal effect and that their large litter sizes are mainly caused by maternal genes. The growth and development of porcine embryos on gestation day (GD) 12 are dependent on histotroph secreted by endometrium. Embryonic loss of Taihu pigs on GD12 is lower than that of Western pigs. Here, endometrial samples were collected from pregnant Erhualian sows (parity 3) and Landrace × Large White (LL) sows (parity 3) on GD12. Digital gene expression profiling (DGE) was used to measure the gene expression in the endometrium of the two breeds.

RESULTS

A total of 13,612 genes were differentially expressed between the two breeds (P < 0.001, FDR < 0.001). Gene Ontology (GO) analysis showed that the differential genes involved in reproduction and growth. Pathway analysis revealed that the differentially expressed genes significantly enriched in 24 KEGG pathways. Quantitative real-time RT-PCR confirmed the differential expression of eight genes. Analyses of the differentially expressed genes suggested possible reasons for the difference in embryonic survival ratio between the two breeds. Specifically, these findings point to a higher ratio of PGE2:PGF2α in the endometrium of Erhualian pigs, which facilitates the establishment and maintenance of pregnancy. We also suggest that the differences in the uterine environment lead to higher uterine capacity in Erhualian pigs.

CONCLUSIONS

The DGE expression profiles of Erhualian and LL endometrium demonstrated differential expression of genes. Our results will increase understanding of the molecular mechanisms of the low rate of embryonic loss in Chinese Taihu pigs, facilitate the identification of major genes that affect litter size, and be valuable for porcine transcriptomic studies.

Effect of conceptus on expression of prostaglandin F2α receptor in the porcine endometrium

Increased synthesis of prostaglandin F(2α) (PGF(2α)) in the endometrium and conceptus during the implantation period results in elevated concentration of PGF(2α) in the uterine lumen in pregnant gilts. PGF(2α) exerts its effects through PGF(2α) receptor (PTGFR), a G-protein-coupled receptor. However, besides studies concerning the function of PTGFR in endometrial abnormalities, the role of PTGFR in the endometrium during early pregnancy has not been elucidated. Therefore, the aim of this study was: (1) to evaluate the profile of PTGFR gene and protein expression in the porcine endometrium during early pregnancy and the estrous cycle; (2) to determine if the effect of conceptus on PTGFR expression is dependent on type of endometrial cells-luminal epithelial (LE) or stromal (ST) cells; and (3) to elucidate if the putative effect of conceptus on endometrial PTGFR expression is mediated by estrogen receptor. We evaluated the expression pattern of PTGFR gene and protein in the endometrium during day 9, 11, 12, 15, and 18 of the estrous cycle and pregnancy (N = 4-6 per group). The expression of PTGFR mRNA was greater on day 18 of pregnancy and the estrous cycle (vs. days 9-15 of the estrous cycle and pregnancy, P < 0.05). Expression of PTGFR protein was approximately 10-fold upregulated in the endometrium on day 15 of pregnancy when compared with day 15 of the estrous cycle (P < 0.01). Endometrial expression of PTGFR protein increased from day 12 to 18 of pregnancy (P < 0.05). PTGFR mRNA was expressed in LE and ST cells. In a subsequent experiment, we used a coculture model in which LE cells were cultured on collagen-coated inserts placed in wells plated with ST cells. Day 11 or 15 conceptus-exposed medium (CEM) elevated expression of PTGFR mRNA (2- and 1.5-fold, respectively, P < 0.05) in LE cells cocultured with ST cells. CEM did not have an effect on PTGFR mRNA expression in ST cells. The 11-day CEM-induced increase of PTGFR mRNA was abolished by incubation of LE cells in the presence of the estrogen receptor antagonist (ICI-182,780; P < 0.01). Summarizing, the conceptus upregulated expression of PTGFR in the endometrium during the implantation period. Moreover, this study indicates that expression of PTGFR gene was elevated in LE cells of endometrium by embryonic signal of estradiol. Our results suggest para- and autocrine effects of PGF(2α) through its receptor PTGFR in the porcine endometrium, especially in luminal epithelium which is in direct contact with the conceptus during the implantation period.

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.

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

Background

The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.

Results

One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (p ≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including WNT10B and DKK2 in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- BAX and BMPR1B were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (p ≤ 0.1 or p ≤ 0.05).

Conclusions

Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of BAX and BMPR1B gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.

Comparative proteomic and regulatory network analyses of the elongating pig conceptus

Embryo loss during peri-implantation can approach 20% in swine following artificial insemination or natural mating and coincides with rapid conceptus elongation. The objective of the present study was to establish a comprehensive profile of the abundant proteins of the pig conceptus at the time prior to implantation and identify stage-specific changes during elongation. The abundant proteins of a homogenous population of gestational day-11 ovoid (0.7-1 cm) and gestational day-12 filamentous (15-20 cm) porcine concepti were compared by extracting proteins from three independent conceptus pools and separating the proteins by 2-DE. Proteins in 305 spots were analyzed by MALDI-TOF or additionally by LC-MS/MS and 275 were positively identified representing 174 distinct proteins. The proteins could be classified into the following functional categories: cell proliferation/differentiation, cytoskeleton, metabolism, and stress response. Based on spot density, 35 proteins associated with cell proliferation, differentiation, apoptosis, and embryo/maternal signaling, were found to be differentially expressed between ovoid and filamentous concepti. A comparison of the protein expression profile with transcriptomic data from pig concepti of the same developmental stages identified similarities and dissimilarities between protein and mRNA expression profiles. This proteomic study helps to elucidate the biological mechanisms underlying the early embryonic development of the pig.

Identification of differentially expressed genes in the uterine endometrium on day 12 of the estrous cycle and pregnancy in pigs

Maternal recognition of pregnancy in pigs occurs approximately on Day (D) 12 of pregnancy and is critical for embryo implantation. The presence of the conceptus in the uterine lumen during this period changes uterine endometrial function to prepare for attachment of the conceptus to the endometrial epithelial cells and maintain luteal function in the ovary. Although much is known about endometrial gene expression, the genes expressed in the uterine endometria and the cellular and molecular mechanisms of those gene products during the period of implantation and maternal recognition of pregnancy in pigs are still not completely defined. To better understand the interactions between the maternal uterus and conceptus during the implantation process, we searched genes differentially expressed in the endometria on D12 of pregnancy compared to those on D12 of the estrous cycle. A new reverse transcription-polymerase chain reaction (RT-PCR)-based method that involves annealing control primers (ACPs) was employed. Using 120 ACPs, we sequenced 12 differentially expressed genes (DEGs) and identified those genes using the Basic Local Alignment Search Tool (BLAST). Northern blot hybridization analysis confirmed the differential expression of those DEGs in the uterine endometrium. In situ hybridization analysis determined the cell-type specific expression of the DEGs in the uterine endometrium. Further analysis of the DEGs found in this study will provide insights into the cellular and molecular basis of maternal and fetal interactions during the period of maternal recognition of pregnancy in the pig. Mol. Reprod. Dev. 76: 75-84, 2009. (c) 2008 Wiley-Liss, Inc.

Transcriptional profiling using a novel cDNA array identifies differential gene expression during porcine embryo elongation

A novel porcine cDNA array, containing 1,015 PCR products selected for embryonic expression, was used for transcriptional profiling of conceptuses at four stages of peri-implantation development. Total conceptus RNA from small spherical, large spherical, tubular, and filamentous stages was amplified, converted to cDNA, and hybridized to membranes. Initially, normalized signal intensities obtained using cDNA from total RNA or from amplified RNA were compared. Uniform distribution of P-values associated with t-tests conducted for each gene indicated no evidence that amplification introduced bias. Analysis of data obtained by using amplified targets and the novel array identified genes differentially expressed across stages. Such genes were identified by testing for significant stage effects in gene-specific mixed models. A total of nine genes were declared differentially expressed. Six of the nine genes had P-values less than 0.001, and a false discovery rate of approximately 17% was associated with this significance threshold. Two out of six genes were significant when using the Bonferroni method to control the probability of one or more false positives. The other three genes had P-values between 0.001 and 0.01 and exhibited differences greater than twofold between stages. All four genes selected for confirmation (steroidogenic acute regulatory protein, interleukin 1 beta, transforming growth factor beta 3, and thymosin beta 10) were shown to be differentially expressed by using quantitative real time RT-PCR. Our study shows that RNA amplification is useful for transcriptional profiling with limiting porcine embryonic RNA, and that this novel targeted array can detect differential gene expression during trophoblastic elongation. Finally, our results contribute to an increased understanding of the temporal patterns of expression of known genes controlling conceptus development, as well as identify novel genes also differentially regulated during implantation.