Unveiling how vitrification affects the porcine blastocyst: clues from a transcriptomic study

Background

Currently, there is a high demand for efficient pig embryo cryopreservation procedures in the porcine industry as well as for genetic diversity preservation and research purposes. To date, vitrification (VIT) is the most efficient method for pig embryo cryopreservation. Despite a high number of embryos survives in vitro after vitrification/warming procedures, the in vivo embryo survival rates after embryo transfer are variable among laboratories. So far, most studies have focused on cryoprotective agents and devices, while the VIT effects on porcine embryonic gene expression remained unclear. The few studies performed were based on vitrified/warmed embryos that were cultured in vitro (IVC) to allow them to re–expand. Thus, the specific alterations of VIT, IVC, and the cumulative effect of both remained unknown. To unveil the VIT-specific embryonic alterations, gene expression in VIT versus (vs.) IVC embryos was analyzed. Additionally, changes derived from both VIT and IVC vs. control embryos (CO) were analyzed to confirm the VIT embryonic alterations. Three groups of in vivo embryos at the blastocyst stage were analyzed by RNA–sequencing: (1) VIT embryos (vitrified/warmed and cultured in vitro), (2) IVC embryos and (3) CO embryos.

Results

RNA–sequencing revealed three clearly different mRNA profiles for VIT, IVC and CO embryos. Comparative analysis of mRNA profiles between VIT and IVC identified 321, differentially expressed genes (DEG) (FDR < 0.006). In VIT vs. CO and IVC vs. CO, 1901 and 1519 DEG were found, respectively, with an overlap of 1045 genes. VIT-specific functional alterations were associated to response to osmotic stress, response to hormones, and developmental growth. While alterations in response to hypoxia and mitophagy were related to the sum of VIT and IVC effects.

Conclusions

Our findings revealed new insights into the VIT procedure-specific alterations of embryonic gene expression by first comparing differences in VIT vs. IVC embryos and second by an integrative transcriptome analysis including in vivo control embryos. The identified VIT alterations might reflect the transcriptional signature of the embryo cryodamage but also the embryo healing process overcoming the VIT impacts. Selected validated genes were pointed as potential biomarkers that may help to improve vitrification.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-021-00672-1.

Immune Sensing of Synthetic, Bacterial, and Protozoan RNA by Toll-like Receptor 8 Requires Coordinated Processing by RNase T2 and RNase 2

Human toll-like receptor 8 (TLR8) activation induces a potent T helper-1 (Th1) cell response critical for defense against intracellular pathogens, including protozoa. The receptor harbors two distinct binding sites, uridine and di- and/or trinucleotides, but the RNases upstream of TLR8 remain poorly characterized. We identified two endolysosomal endoribonucleases, RNase T2 and RNase 2, that act synergistically to release uridine from oligoribonucleotides. RNase T2 cleaves preferentially before, and RNase 2 after, uridines. Live bacteria, P. falciparum-infected red blood cells, purified pathogen RNA, and synthetic oligoribonucleotides all required RNase 2 and T2 processing to activate TLR8. Uridine supplementation restored RNA recognition in RNASE2^-/- or RNASET2^-/- but not RNASE2^-/-RNASET2^-/- cells. Primary immune cells from RNase T2-hypomorphic patients lacked a response to bacterial RNA but responded robustly to small-molecule TLR8 ligands. Our data identify an essential function of RNase T2 and RNase 2 upstream of TLR8 and provide insight into TLR8 activation.

Uterine fluid proteome changes during diapause and resumption of embryo development in roe deer (Capreolus capreolus)

The uterine microenvironment during pre-implantation presents a pro-survival milieu and is essential for embryo elongation in ruminants. The European roe deer (Careolus capreolus) pre-implantation embryo development is characterised by a 4-month period of reduced development, embryonic diapause, after which the embryo rapidly elongates and implants. We investigated the uterine fluid proteome by label-free liquid chromatography tandem mass spectrometry at four defined stages covering the phase of reduced developmental pace (early diapause, mid-diapause and late diapause) and embryo elongation. We hypothesised that embryo development during diapause is halted by the lack of signals that support progression past the blastocyst stage. Three clusters of differentially abundant proteins were identified by a self-organising tree algorithm: (1) gradual reduction over development; (2) stable abundance during diapause, followed by a sharp rise at elongation; and (3) gradual increase over development. Proteins in the different clusters were subjected to gene ontology analysis. ‘Cellular detoxification’ in cluster 1 was represented by alcohol dehydrogenase, glutathione S-transferase and peroxiredoxin-2. ATP-citrate synthase, nucleolin, lamin A/C, and purine phosphorylase as cell proliferation regulators were found in cluster 2 and ‘cortical cytoskeleton’, ‘regulation of substrate adhesion-dependent cell spreading’ and ‘melanosome’ were present in cluster 3. Cell cycle promoters were higher abundant at elongation than during diapause, and polyamines presence indicates their role in diapause regulation. This study provides a comprehensive overview of proteins in the roe deer uterine fluid during diapause and forms a basis for studies aiming at understanding the impact of the lack of cell cycle promoters during diapause.

56 Spatial analysis of transcriptome changes in porcine endometrium on Day 14 of pregnancy

During the conception cycle, the embryo undergoes a series of developmental processes including cell division, cellular reorganization, and oestrogen secretion before attaching to the uterine epithelium. The uterine endometrium is complex and consists of various layers and cell types [i.e. luminal epithelium (LE), glandular epithelium (GE), blood cells (B), and stromal areas (S)]. The objective of this study was to characterise the complex transcriptome changes in porcine endometrium during the time of conceptus attachment with respect to localization in different endometrial cell types. RNA-sequencing (RNA-Seq) was conducted for LE, GE, B, and S samples isolated from endometrial tissue collected on Day 14 of pregnancy and the oestrous cycle, respectively (each group n=4), by laser capture microdissection (PALM LCM microscope, Zeiss, Jena, Germany). Total RNA was isolated (RNA integrity number&gt;6.5) and used for the preparation of 32 RNA-seq libraries (Ovation SoLo RNA-Seq System, NuGEN Technologies, San Carlos, CA, USA). Multiplexed (barcode-tagged) libraries were run on an Illumina HiSEqn 2500 (Illumina, San Diego, CA, USA). The obtained sequence data were analysed with a RNA-Seq data analysis pipeline on a local Galaxy server installation. The resulting read counts were used for statistical analysis in EdgeR to identify differentially expressed genes (DEG). Furthermore, an RNA-seq dataset for complete Day 14 endometrial tissue samples from a previous study was analysed using the same pipeline. A total of 14297 genes were detectable in complete endometria, and 12000, 11903, 11094, and 11933 genes in LE, GE, B, and S, respectively. Differential expression analysis was performed between the pregnant and the cyclic nonpregnant group for each cell type and the complete tissue. The highest number of DEG was found for LE (1410) when compared with GE, B, and S (800, 1216, and 384, respectively). In total, 3262 DEG were obtained for the complete tissue between pregnant and nonpregnant gilts. The DEG were assigned to Gene Ontology (GO) terms to characterise overrepresented functional categories and pathways specific for the individual endometrial compartments. The GO classification revealed that most DEG in LE were involved in cell communication, such as ‘extracellular exosome’, ‘extracellular vesicle’, ‘homeostatic process’, whereas the ‘response to organic substance’ and ‘regulation of cell migration’ categories were enriched in GE. In blood vessels, categories such as ‘membrane-bounded vesicle’, ‘cell junction’, ‘cell development’, ‘cell adhesion’ and ‘blood vessel morphogenesis’ were found as overrepresented, whereas in stromal regions, most DEG were assigned to ‘cell communication’ and ‘secretion’. These results confirmed the hypothesis that conceptus signals induce specific transcriptomic regulations in the endometrial compartments/cell types related to their functions during recognition of pregnancy adding a new level of spatial gene expression regulation to endometrial transcriptome analysis.

6 Decelerating embryo development? Characterisation of the uterine environment in European roe deer (Capreolus capreolus) during diapause

The early developing embryo faces a continuously changing microenvironment to supports its growth. In the European roe deer, this environment accompanies embryonic diapause, a period of up to 4 months in which fertilization and subsequent implantation are decoupled. Diapause is characterised by a deceleration of embryonic growth. In most ruminants such as cattle and sheep, interferon tau (IFNt) plays a major role in maternal recognition of pregnancy. Uniquely to ruminants, the roe deer embryo does not secrete IFNt. The roe deer was used as a model species to gain insights into the changing uterine environment devoid of IFNt that supports prolonged decelerated embryo development, resumption of developmental velocity, and subsequent implantation. Uterine fluid samples from 188 female does were collected during regular huntings between September and January, and 4 developmental stages-blastocysts at early, mid, and late diapause and elongated embryos (16, 57, 97, and 18 does per developmental stage, respectively)-were defined. The developmental stages were assigned based on morphological characteristics of the embryo and the embryonic genomic DNA content. For the analysis of amino acids (AA), all 188 uterine fluid samples were subjected to targeted liquid chromatography-tandem mass spectrometry. Almost all AA increased over the course of embryo development. Although most AA showed developmental stage-specific concentration peaks, serine, glycine, alanine, glutamate, and glutamine were most abundantly present irrespective of the developmental progression. For the analysis of the protein abundances in the uterine fluid in a selected subset of samples (n=5 per developmental stage), holistic liquid chromatography-tandem mass spectrometry identified and quantified a total of 819 proteins with a false discovery rate of &lt;1%. Comparison between the developmental stages revealed 106 differentially abundant proteins. Most changes in protein abundance that occurred related to embryo elongation. Interestingly, 713 proteins remained stable during embryo development, indicating that these proteins may contribute to prolonged embryo survival during embryonic diapause. The differentially abundant proteins were clustered with DAVID Bioinformatics Resources 6.8 (https://david.ncifcrf.gov/). The most enriched clusters were cell-cell adhesion, biosynthesis of AA and carbon metabolism, microtubule, structural molecule activity, and chaperone binding. The ongoing detailed identification of stably abundant proteins will advance our basic understanding of the embryos’ needs for sustained survival during prolonged decelerated development. In addition, a comparison with the protein abundances around the time of maternal recognition of pregnancy in other species could advance our knowledge on conserved proteins that support embryo development and establishment of pregnancy in mammals. Our findings may contribute to defining optimal in vitro embryo culture conditions in a species-independent manner and potentially identify factors capable of halting embryo development.

Deciphering the oviductal extracellular vesicles content across the estrous cycle: implications for the gametes-oviduct interactions and the environment of the potential embryo

Background

The success of early reproductive events depends on an appropriate communication between gametes/embryos and the oviduct. Extracellular vesicles (EVs) contained in oviductal secretions have been suggested as new players in mediating this crucial cross-talk by transferring their cargo (proteins, mRNA and small ncRNA) from cell to cell. However, little is known about the oviductal EVs (oEVS) composition and their implications in the reproductive success. The aim of the study was to determine the oEVs content at protein, mRNA and small RNA level and to examine whether the oEVs content is under the hormonal influence of the estrous cycle.

Results

We identified the presence of oEVs, exosomes and microvesicles, in the bovine oviductal fluid at different stages of the estrous cycle (postovulatory-stage, early luteal phase, late luteal phase and pre-ovulatory stage) and demonstrated that their composition is under hormonal regulation. RNA-sequencing identified 903 differentially expressed transcripts (FDR < 0.001) in oEVs across the estrous cycle. Moreover, small RNA-Seq identified the presence of different types of ncRNAs (miRNAs, rRNA fragments, tRNA fragments, snRNA, snoRNA, and other ncRNAs), which were partially also under hormonal influence. Major differences were found between post-ovulatory and the rest of the stages analyzed for mRNAs. Interesting miRNAs identified in oEVs and showing differential abundance among stages, miR-34c and miR-449a, have been associated with defective cilia in the oviduct and infertility. Furthermore, functional annotation of the differentially abundant mRNAs identified functions related to exosome/vesicles, cilia expression, embryo development and many transcripts encoding ribosomal proteins. Moreover, the analysis of oEVs protein content also revealed changes across the estrous cycle. Mass spectrometry identified 336 clusters of proteins in oEVs, of which 170 were differentially abundant across the estrous cycle (p-value< 0.05, ratio < 0.5 or ratio > 2). Our data revealed proteins related to early embryo development and gamete-oviduct interactions as well as numerous ribosomal proteins.

Conclusions

Our study provides with the first molecular signature of oEVs across the bovine estrous cycle, revealing marked differences between post- and pre-ovulatory stages. Our findings contribute to a better understanding of the potential role of oEVs as modulators of gamete/embryo-maternal interactions and their implications for the reproductive success.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4982-5) contains supplementary material, which is available to authorized users.

139 SEX-SPECIFIC GENE EXPRESSION IN PORCINE PRE-IMPLANTATION EMBRYOS

X-Chromosome inactivation in female mammals starts during early blastocyst stage with expression of the X-inactive specific transcript (XIST), which coats and silences the inactive X chromosome. However, this compensation is not complete in blastocysts, as a large number of X-linked transcripts are more highly expressed in female embryos than in males. Furthermore, the process of X chromosome inactivation is altered in IVF and cloned porcine embryos, possibly explaining problems of embryo survival with these techniques. The aim of this study was to gain more insights into the transcriptional dynamics of the porcine pre-implantation embryo, with a particular focus on sex-specific differences. RNA sequencing (RNA-Seq) was performed for individual blastocysts at 8, 10, and 12 days after ovulation, and the temporal development of sex-specific transcripts was analysed. German Landrace sows were cycle synchronized and inseminated with sperm of the same Pietrain boar. On Days 8, 10, and 12 post-insemination, sows were slaughtered and embryos were removed from the uterus using 10 mL of PBS (pH 7.4) per horn. Single embryos were shock frozen in liquid nitrogen and stored at –80°C until the extraction of RNA and DNA (AllPrep DNA/RNA Micro Kit, Qiagen, Valencia, CA, USA). Using the isolated DNA, the sex of the embryos was determined and 5 female and male embryos, respectively, were analysed per stage. Illumina TruSeq Stranded mRNA libraries (Illumina Inc., San Diego, CA, USA) were sequenced on a HiSEqn 2500 (Illumina Inc.), and 15 to 25 million 100-bp single-end reads were generated per sample. Reads were filtered and processed using Trimmomatic and mapped to the porcine genome assembly Sscrofa10.2 with TopHat2. Mapped reads were counted by the use of QuasR qCount based on the current National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/) GFF3 annotation file. Statistical analysis of count data was performed with the BioConductor R (https://www.bioconductor.org/) package DESEqn 2. At all 3 stages, we found 7 Y-linked transcripts that were highly expressed in male embryos (EIF2S3, EIF1AY, LOC100624590, LOC100625207, LOC100624329, LOC102162178, LOC100624937). On the other hand, 47 X-linked transcripts showed increased expression in female blastocysts, most of them at all 3 time points. However, a small number of genes (DDX3X, LAMP2, and RPS6KA3) were more highly expressed in females at Days 8 and 10 but more highly expressed in males at Day 12. Three X-linked genes (OFD1, KAL1, and LOC100525092) were more highly expressed in male embryos, although only at a low fold change of 1.2 to 1.4. Furthermore, expression of 8 transcripts located on autosomes was higher in females. In conclusion, our study expands the current knowledge of sex-specific gene expression in 8- to 12-day-old porcine blastocysts, a critical time period during pre-implantation embryo development.

Serum microRNA profiles in cats with hypertrophic cardiomyopathy

The role of microRNAs (miRNAs) in the pathogenesis of heart diseases of humans and rodents, as well as their diagnostic potential, has recently received much attention, but comparable studies for spontaneous disease models in the domestic cat are missing. Hypertrophic cardiomyopathy (HCM) is the most common heart disease in cats. The pathology is largely unknown, but is suspected to be influenced by genetic background. In this study, we examined the miRNA profiles in the serum of cats with stable congestive heart failure caused by HCM (n = 11) and healthy control cats (n = 12) using miRNA arrays. 965 out of 2026 miRNAs could be detected in at least six samples of either of the groups. Eleven mammalian miRNAs were differentially expressed between the groups with a fold change ≥ 1.6. Hierarchical cluster analysis resulted in distinct separation of the two groups. After correction for multiple testing (adjusted p < 0.05), a higher expression of miR-381-3p, miR-486-3p, miR-4751, miR-476c-3p, miR-5700, miR-513a-3p, and miR-320e in the HCM group was confirmed. Additionally, miR-1246 was found to be upregulated 3-fold in the HCM group using quantitative RT-PCR. Software analysis of the significantly regulated miRNAs revealed 49 mRNA targets involved in cardiac hypertrophy. Cats with primary HCM show a distinct miRNA profile that includes miRNAs that have already been shown to be differentially regulated in human patients and rodent models for cardiac disease. Studying HCM as a spontaneous cardiac disease of the cat may help to reveal additional pathophysiologic pathways.

118 DEEP SEQUENCING OF THE PORCINE ENDOMETRIAL TRANSCRIPTOME ON DAYS 12 AND 14 OF PREGNANCY

Establishment of pregnancy in mammals requires prolongation of luteal life span for sustained progesterone (P4) production. P4 stimulates secretory functions of the endometrium required for conceptus growth and development and is essential for endometrial receptivity. The porcine conceptus undergoes rapid differentiation and expansion of its trophoblastic membranes between Day 11 and Day 12 of gestation. With trophoblast elongation production of estrogen, the porcine embryonic pregnancy recognition signal, by the conceptus increases. A complex interplay of estrogen signaling and prostaglandin (PG) metabolism in the endometrium finally results in prevention of luteolysis. 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 maternal recognition of pregnancy and initial placentation, deep sequencing of endometrial RNA samples of pregnant animals (n = 4) and corresponding non-pregnant controls (n = 4) was performed on Day 12 and Day 14 after ovulation using Illumina RNA-Seq (Illumina Inc., San Diego, CA, USA). Between 21 and 36 million 76-bp single-end reads were produced per sample. Reads were mapped with TopHat to the porcine genome assembly Sscrofa10.2 and relative expression values were calculated based on the National Center for Biotechnology Information’s gene annotation for the analysis of differential gene expression. Statistical analysis revealed more than 3500 differentially expressed genes (DEG) for Day 12 and almost 2500 DEG for Day 14 of pregnancy (DESeq, FDR 1%). Differential expression of selected genes was validated by the use of quantitative real-time PCR (RT-PCR). Comparison of the RNA-Seq data from Day 12 and Day 14 of pregnancy based on a comparison of the DEGs and of overrepresented functional categories revealed distinct differences in gene regulation, reflecting the different functions of the endometrium during these stages; that is, recognition of pregnancy on Day 12 and preparation for conceptus implantation on Day 14. The data from Day 14 was also compared to the published microarray data set from Day 14 of pregnancy (Østrup et al. 2010 Biol. Reprod.) and other sets of DEG by the use of gene set enrichment analysis (GSEA). Overall, a very good agreement with the results of the previous microarray study was found. Furthermore, a significant overlap with genes upregulated in bovine endometrium on Day 18 of pregnancy was found for the genes upregulated in porcine endometrium on Day 14. More than half of these genes were known interferon-regulated genes. In conclusion, RNA-Seq revealed distinct transcriptome changes on Day 12 and Day 14 of pregnancy in porcine endometrium associated with MRP and initiation of implantation.

87 IS HOXA10 EXPRESSION REGULATED THROUGH PROMOTER DNA METHYLATION IN THE PIG?

In utero and early postnatal exposure to exogenous oestrogens may alter the epigenome, possibly influencing health later in life. The reproductive organs are the main target of oestrogens. Uterine HOXA10 expression and promoter DNA methylation have been shown to be sensitive to endocrine disruptors in rodents. In the endometrium of pigs, in vitro exposure to estradiol-17β resulted in an increase of HOXA10 mRNA and protein expression, and a regulation for HOXA10 has also been shown during early pregnancy. However, it is unclear whether modification in promoter DNA methylation was involved herein. In the present study, we investigated the effect of oral estradiol-17β supplementation to pregnant pigs from Day 0 until delivery (0, 0.05, 10, and 1000 µg kg–1 per day; n = 8–12/group) on HOXA10 expression and promoter DNA methylation in the uterus of prepubertal and the endometrium of postpubertal porcine offspring. In addition, endometrial samples from 2 physiological situations were analyzed, namely the oestrous cycle at Day 0, 3, 6, 12, and 18 (n = 6/day), and early pregnancy at Day 10, 12, and 14 (n = 4/day). Furthermore, different reproductive and nonreproductive tissues from pre- and postpubertal untreated animals were investigated (n = 2/tissue). Gene expression was measured using RT-qPCR. The DNA was first bisulfite converted, amplified by using methylation-sensitive high-resolution melting qPCR, followed by pyrosequencing. Statistical analyses were conducted using one-way ANOVA. In utero estradiol-17β exposure did neither alter HOXA10 expression compared to the control group nor HOXA10 promoter DNA methylation in pre- and postpubertal porcine offspring, respectively. Because the prepubertal group displayed higher HOXA10 mRNA expression than did postpubertal animals, while DNA methylation was lower in the younger animals, a potential role of DNA methylation may be assumed. During the oestrous cycle, HOXA10 expression was significantly regulated (P < 0.001); it was highest at oestrous (Day 0), decreased 2.5-fold by Day 3, and increased again 1.5-fold by Day 6. In early pregnant sows, endometrial HOXA10 transcripts were significantly higher at Day 14 (P = 0.031) compared with nonpregnant controls. In both settings promoter DNA methylation did not change. Regarding HOXA10 expression between different tissues, the DNA methylation at one CpG site was significantly correlated with mRNA expression in prepubertal animals (R2 = 0.582) but not in the adult (R2 = 0.004). We conclude that HOXA10 expression is regulated through other mechanisms than is promoter DNA methylation in adult sows. Still, in prepubertal pigs promoter DNA methylation may influence HOXA10 expression. In utero estradiol-17β exposure did not affect HOXA10 expression and promoter DNA methylation.

243 IMPACT OF MATERNAL LOW-DOSE ESTRADIOL-17β EXPOSURE DURING PREGNANCY ON THE REPRODUCTIVE ORGANS OF MALE PIG PROGENY

In male developing piglets, low endogenous oestrogenic hormone levels prevail. Sensitive tissues expressing high levels of oestrogen receptors, such as the epididymis, might thus be of specific relevance for early disturbances by estrogenic endocrine disruptors. We have previously shown that distinct concentrations of the natural oestrogen oestradiol-17β (E2) orally applied during the whole period of pregnancy in sows lead to a distinct shift in body composition. Therefore, we aimed at investigating whether prenatal E2 exposure had the potential to program male reproductive organs toward altered semen quality. The E2 treatment groups (n = 4 sows/group) were designed to represent doses of pharmacological relevance (PR; 1000 µg kg–1 of body weight per day), oral no-effect level (10 µg kg–1 of body weight per day), and acceptable daily intake level (0.05 µg kg–1 of body weight per day). Total RNA was extracted from the epididymis of 8-week-old piglet twins (n = 2 per sow). The RNA of littermates was pooled and subjected to microarray analysis (MA) using Agilent Porcine Genome Arrays (Agilent Technologies Inc., Santa Clara, CA, USA). Ejaculates of adult male pigs from the control group and the pharmacological group (n = 4) were collected and analysed for quantitative and qualitative parameters by using computer-assisted sperm analysis and flow cytometry. In total, 105 transcripts exhibited a significant difference of more than 1.5-fold for at least one of the treatment groups compared with the control group (P < 0.05; FDR 5%). Several transcripts revealed gradually decreasing amounts subject to the dose of E2 exposure. Eight transcripts showed significant differences in all 3 treatment groups compared with the control group. Thirty-two transcripts had reduced abundance in the PR group and the oral no-effect level group, whereas 20 transcripts were downregulated in the PR group only. Semen parameters of adult males did not differ regarding volume and semen concentration, morphology, and membrane integrity. Computer-assisted sperm analysis evaluations did not show differences in motility and other kinematic parameters. Eight weeks after E2 exposure, male prepubertal piglets exhibited significant differences in epididymal messenger RNA transcript abundance subject to an in utero E2 treatment. This points toward possible epigenetic programming of the epididymis. Although the differential transcript abundance indicates a perturbation, normal semen quality was found after adolescence. Either these transcriptional changes are of minor functional importance or flexible mechanisms account for the developmental adaptations. Considering that identical transcripts were regulated in offspring exposed to both pharmacological and very low doses, further investigations of set points obviating long-term adverse consequences are needed.

119 QUANTITATIVE PROTEOME ANALYSIS OF ENDOMETRIUM FROM PREGNANT AND NONPREGNANT PIGS

In mammals, an efficient exchange of molecular signals between the embryo and the maternal environment plays a crucial role for the implantation and development of early embryos as well as for recognition and maintenance of pregnancy. So far, only a few molecular signals involved in this process have been identified. To address the underlying biochemical processes in pigs at the protein level, we performed a quantitative proteome study with endometrial tissue samples from non-pregnant and pregnant (Day 14) sows. Endometrium samples (lamina epithelialis, lamina propria and tela submucosa; n = 4 per group) were taken from sites of embryonic attachment and from comparable locations in nonpregnant animals. Proteome data were generated by iTRAQ labelling and nano-LC-MS/MS measurements of tryptic endometrium peptides on a high-resolution Orbitrap XL mass spectrometer. To further address and visualize protein isoforms, LC-MS/MS experiments were complemented by 2D gel-based analyses. To enhance the accuracy of protein quantification, the 2D fluorescence difference gel electrophoresis (2D-DIGE) technique was used, including internal pooled standards for inter-gel matching and normalization. The statistical and bioinformatics analysis of 2D-DIGE and iTRAQ data revealed 14 proteins being significantly altered in abundance (fold-change values >1.5, maximum fold-change 13; P < 0.05) between the endometrium proteomes of pregnant and non-pregnant animals. Several of the affected proteins are already known to play an important role in embryo-maternal communication in other species; for example, signal transducer and activator of transcription 1 (STAT1), a protein mediating the cellular response of cells to interferons (IFN) or aldose reductase (AKR1B1), for which a key role in the synthesis of endometrial prostaglandin F is supposed. Several other proteins showing alterations in abundance between pregnant and nonpregnant endometrial tissues were not described previously and represent new and interesting targets for further functional studies addressing their role during early pregnancy.

83 EFFECTS OF HUMAN INTERFERON-α ON GENE EXPRESSION IN THE BOVINE ENDOMETRIUM IN COMPARISON TO DAYS 15 AND 18 OF PREGNANCY

Interferon-τ (IFNT), a Type-I interferon (IFN), is the pregnancy recognition signal produced by the ruminant conceptus (Godkin et al. 1984; Hansen et al. 1985; Helmer et al. 1987; Spencer et al. 2007). In addition to these specific functions of IFNT in ruminants, many studies suggest that IFNs play a general role in establishment of pregnancy and conceptus attachment/implantation in most mammalian species (Bazer et al. 2009; Bazer et al. 2010; Johnson et al. 2009; Roberts et al. 2008). To characterise the effects of prototype Type-I IFNs on bovine endometrium, in experiment one, Simmental heifers were treated from Day 14 to Day 16 of the oestrous cycle with a rod-shaped intrauterine device releasing human interferon-α (IFNA) or placebo lipid extrudates or PBS only as controls (n = 4 each). Lipid formulation and concentration of human IFNA were adjusted to release 8–9 × 107 IU of IFNA over a period of 2 days in in vitro release experiments. On Day 16, endometrial biopsy samples were collected after flushing the uterus. In experiment 2, endometrial tissue samples were obtained on Day 12, 15 and 18 post-mating from nonpregnant or pregnant heifers. All samples from both experiments were analysed with an Affymetrix Bovine Genome Array (Santa Clara, CA). In experiment one, IFNA treatment resulted in differential gene expression in the bovine endometrium. Significant differences were found between the IFNA group and both control groups, whereas no differences were observed between the placebo and the PBS control group. In experiment 2, differentially expressed genes were found between pregnant and nonpregnant endometria on Day 15 and 18, but not on Day 12, with many of them known IFN-stimulated genes. The comparison of the data sets from both experiments showed very similar gene expression changes for most of the typical IFN-stimulated genes. In addition, several genes were identified which were differentially expressed after IFNA treatment but not different at Day 15 or 18 of pregnancy compared with nonpregnant animals. Conversely, some genes were found as differentially expressed during pregnancy but not after IFNA treatment. Differential expression of selected genes was verified by quantitative real-time PCR and 4 genes, namely jumonji C domain containing histone demethylase 1 homologue D (JHDM1D), indoleamine 2,3-dioxygenase 1 (IDO1), fatty acid binding protein 3, muscle and heart (mammary-derived growth inhibitor) (FABP3) and dickkopf homologue 1 (DKK1), were selected for localization of mRNA expression in endometrial tissue sections. The findings of this study suggest that there may be differential effects of bovine IFNT compared with human IFNA and that some pregnancy-specific changes in the endometrium are elicited by conceptus-derived factors other than IFNT. This study was supported by the German Ministry for Education and Research (BMBF, FUGATO-plus, COMPENDIUM) and the German Research Foundation (DFG FOR478). The authors are part of the European Union COST action GEMINI.

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

Establishment and maintenance of pregnancy in equids is only partially understood. To provide new insights into early events of this process, we performed a systematic analysis of transcriptome changes in the endometrium at Days 8 and 12 of pregnancy. Endometrial biopsy samples from pregnant and nonpregnant stages were taken from the same mares. Composition of the collected biopsy samples was analyzed using quantitative stereological techniques to determine proportions of surface and glandular epithelium and blood vessels. Microarray analysis did not reveal detectable changes in gene expression at Day 8, whereas at Day 12 of pregnancy 374 differentially expressed genes were identified, 332 with higher and 42 with lower transcript levels in pregnant endometrium. Expression of selected genes was validated by quantitative real-time RT-PCR. Gene set enrichment analysis, functional annotation clustering, and cocitation analysis were performed to characterize the genes differentially expressed in Day 12 pregnant endometrium. Many known estrogen-induced genes and genes involved in regulation of estrogen signaling were found, but also genes known to be regulated by progesterone and prostaglandin E2. Additionally, differential expression of a number of genes related to angiogenesis and vascular remodeling suggests an important role of this process. Furthermore, genes that probably have conserved functions across species, such as CRYAB, ERRFI1, FGF9, IGFBP2, NR2F2, STC1, and TNFSF10, were identified. This study revealed the potential target genes and pathways of conceptus-derived estrogens, progesterone, and prostaglandin E2 in the equine endometrium probably involved in the early events of establishment and maintenance of pregnancy in the mare.

Creating new knowledge for ruminant reproduction from rapidly expanding and evolving scientific databases

Declining fertility is a major problem for the dairy industry. Recent developments of Omics-technologies facilitate a comprehensive analysis of molecular patters in gametes, embryos and tissues of the reproductive tract which may help to identify the reasons for impaired fertility. Large Omics-datasets require appropriate bioinformatics analysis in the context of rapidly expanding and evolving scientific databases. This overview summarizes the current status of ruminant genome projects, describes currently existing resources for ruminant genomics, transcriptomics and proteomics as well as databases and tools for the interpretation and exploitation of transcriptomics and proteomics datasets. Gene set enrichment analysis (GSEA) and transcription factor binding site (TFBS) analyses are strategies for the identification of regulatory genes. In general, the comprehensive analysis of molecular traits by Omics-technologies can enhance the interpretation of genome-wide association studies, providing insights into the biological pathways linking genotype and phenotype, and their modulation by endogenous and environmental factors.

102 EVIDENCE FOR PRE-IMPLANTATION ORIGIN OF PLACENTAL FAILURE IN BOVINE CLONE PREGNANCIES

Placental abnormalities account for a high proportion of pregnancy loss after transfer of cloned (SCNT) bovine embryos. The high rate of pregnancy failure has been linked to the finding of abnormal placental formation and function. Because bovine SCNT embryos were shown to exhibit altered trophoblast differentiation (Arnold DR et al. 2006 Reproduction 132, 279–290), we hypothesized that placental abnormalities in bovine clone pregnancies may originate from disturbed embryo-maternal communication in the pre-implantation period. To test this hypothesis, we evaluated the response of the endometrium to SCNT v. IVF embryos. The SCNT embryos were produced from fibroblast cultures derived from 4 different fetuses to exclude specific effects of a particular donor cell culture. After SCNT or IVF, embryos were cultured under identical conditions. Two SCNT or IVF blastocysts (grade 1) were transferred per recipient heifer (Day 8 of estrous cycle). Ten days later the recipients were slaughtered, the uteri were recovered, and pregnancy was verified by the presence of at least one normally developed embryo. Endometrium samples of 9 SCNT and 10 IVF pregnancies were used for transcriptome profiling with a custom cDNA microarray (BOE array; Bauersachs S et al. 2007 J. Dairy Sci. 90, 4420–4423). In total, 58 transcripts were found to be differently abundant between endometrium samples from SCNT v. IVF pregnancies (SAM, FDR 5.24%). Interestingly, for some of them an important role in implantation and/or placentation has already been shown. NR2F2, encoding the orphan nuclear receptor superfamily member NR2F2 (COUP-TFII), was downregulated in endometrium from SCNT pregnancies (1.5-fold; P < 0.01). Uterine-specific Nr2f2 mutant mice are infertile due to implantation failure (Kurihara I et al. 2007 PLoS Genetics 3, e102). Another interesting candidate is GJA1, encoding connexin 43 (Cx43), with 1.8-fold (P < 0.001) downregulated transcript levels in SCNT pregnancies. A striking increase of stromal Cx43 has been observed in the ovine intercaruncular and caruncular endometrium during intensification of the feto-maternal contact (Gabriel et al. 2005 Placenta 25, 287–296), suggesting that reduced GJA1 mRNA expression in bovine clone pregnancies may negatively affect placentation. In view of the well-orchestrated spectrum of transcriptome changes in endometrium during the peri-attachment period (Bauersachs S et al. 2006 Reproduction 132, 319–331), these findings suggest that placental failure in bovine clone pregnancies may originate from abnormal embryo-maternal communication already in the pre- or peri-implantation period. This study was supported by the Deutsche Forschungsgemeinschaft (FOR 478).

Transcriptome studies of bovine endometrium reveal molecular profiles characteristic for specific stages of estrous cycle and early pregnancy

The endometrium undergoes marked functional changes during estrous cycle and pregnancy. As the adjacent environment of the conceptus, it represents the maternal interface for embryo-maternal communication, which is essential to maintain pregnancy. Transcriptome studies provide the unique opportunity to assess molecular profiles changing in response to endocrine or metabolic stimuli or to embryonic pregnancy recognition signals. Here we review the current state of transcriptome profiling techniques and the results of a series of transciptome studies comparing bovine endometrium samples during the estrous cycle or endometrium samples from pregnant vs. non-pregnant animals. These studies revealed specific mRNA profiles which are characteristic for the functional status of the endometrium. Transcriptome studies of endometrial samples recovered during the pre-attachment period identified many interferon-stimulated genes, genes that are possibly involved in embryo-maternal immune modulation ( C1S, C1R, C4, SERPING1, UTMP, CD81, IFITM1, BST2), as well as genes affecting cell adhesion ( AGRN, CD81, LGALS3BP, LGALS9, GPLD1, MFGE8, and TGM2) and remodeling of the endometrium ( CLDN4, MEP1B, LGMN, MMP19, TIMP2, TGM2, MET, and EPSTI1). The results of these transcriptome studies were compared to those of similar microarray analyses in human, mouse and Rhesus monkey to identify similarities in endometrial biology between mammalian species and species-specific differences. Future studies will cover dynamic transcriptome changes between different stages of early pregnancy, the relationship between metabolic problems in dairy cows and the functionality of reproductive tissues as well as endometrium transcriptome profiles in recipients of somatic cell nuclear transfer embryos.

175 TRANSCRIPTOME ANALYSIS OF BOVINE DAY 150 FETAL LIVER AND COTYLEDON REVEALS GENES INVOLVED IN FETAL GROWTH

Major problems in breeding of modern dairy cows include increasing rates of stillbirth and dystocia, associated with elevated costs for veterinary intervention (caesarean section) and loss of production animals (cows and calves). Rates of stillbirth as high as 12% have been reported, primarily caused by fetal overgrowth and increased birth weight. In order to discover molecular markers for selection against stillbirth, we developed a model for the inheritance of fetal growth traits. A Fleckvieh bull segregating for paternal stillbirth was used for insemination of 36 cows that were slaughtered at Day 150 of pregnancy in order to recover and phenotype the fetuses. The mode of inheritance indicated involvement of imprinting. Mapping results suggested an imprinted region on chromosome 9 as candidate for the stillbirth QTL. Due to the complexity of the trait, we opted for a holistic approach that is not restricted to the QTL candidate region but allows identification of genes and networks that influence fetal growth. Transcriptome profiles of liver and cotyledon samples from the fetuses with the highest (n = 10) and the lowest total weight n = 10) were analyzed using Affymetrix Bovine GeneChips (Affymetrix, Inc., Santa Clara, CA, USA). Analysis with the program SAM showed 41 up- and 4 down-regulated genes in liver samples of the heavy-weight group. Most of these genes are involved in immune response. Interestingly, many of these genes are reported to be regulated by vitamin D. Furthermore, vitamin D is closely connected to the IGF1 system and thus the most important fetal growth regulation circuit. Seasonal effects on vitamin D levels could mostly be excluded by the experimental design and did not correlate with growth traits. Most likely, the mRNA levels of our candidate genes were influenced by alterations in the IGF1/vitamin D circuit and did not cause the observed weight differences. The imprinted candidate genes showed no correlation with fetal weight. Gene set enrichment analysis indicated enhanced metabolic activity in the liver of heavy-weight fetuses. Genes from the QTL region showed a clear enrichment in correlation with fetal weight, confirming their involvement in fetal growth. The gene with the best correlation, GHITM (growth hormone inducible transmembrane protein), could give an explanation for the enhanced metabolic activity, as it is reported to function as a metabolic regulator. Simultaneous analysis of the data sets for liver and placenta in a linear model (R-package LIMMA; Smyth 2004 Stat. Applic. Genet. Mol. Biol. 3, art. 3) yielded essentially the same differentially expressed genes for liver and a higher number of differentially expressed genes for placenta (89 up- and 114 down-regulated), with little overlap between the two tissues. This work was supported by Grant BMBF FUGATO-Fertilink.

181 MESSENGER RNA PROFILING OF BOVINE ENDOMETRIUM DURING THE ESTROUS CYCLE USING A CUSTOM-MADE cDNA ARRAY

The endometrium provides the optimal conditions for the transport of sperm to the oviduct, to the site of fertilization, and later on for the reception of the embryo. This is reflected by specific morphological and functional changes during the estrous cycle, which are mainly regulated by the hormones progesterone, estradiol, and oxytocin. To study these changes on the level of messenger RNA, a microarray analysis of endometrial tissue samples was performed. Tissue samples were collected from 20 cyclic heifers (Deutsches Fleckvieh, between 17 and 31 months of age) after slaughter at Days 0, 3.5, 12, and 18 of the estrous cycle. The Day 18 group split into two subgroups, one with high and one with low progesterone levels in peripheral blood. Altogether there were 4 heifers in each experimental group. RNA was extracted from these tissue samples and analyzed with a custom-made bovine oviduct and endometrium (BOE) cDNA array (Bauersachs et al. 2007 J. Dairy Sci. 90, in press). The cDNAs present on the array were derived from several previously conducted differential gene expression studies of bovine endometrium between different stages of the estrous cycle, during early pregnancy, and from studies of bovine oviduct epithelial cells. In all of these studies, cDNAs of differentially expressed genes were identified using a combination of subtracted cDNA libraries and cDNA array hybridization. Redundant cDNA clones were removed, resulting in 1440 cDNA fragments on the array, representing 950 different genes. Twenty radioactively (33P) labeled cDNA samples (n = 4 for each cycle stage) were hybridized with the BOE array. After normalization of raw data (using BioConductor open source software) and significance analysis (SAM, FDR 1%), 272 mRNAs were identified that showed alterations of their concentration during the estrous cycle. Expression data from cDNAs with significant changes during the estrous cycle were used for cluster analyses with MultiExperiment Viewer 4.0 (Saeed et al. 2003 Biotechniques 34, 374–378). The main clusters represented genes upregulated either during the estrus or during the diestrus phase. Quantitatively enriched Gene Ontology (GO) categories were identified to find relevant functional groups and prominent biological processes. At estrus, e.g., GO categories extracellular matrix, cytoskeleton organization, and growth factor activity indicate changes in the composition of the endometrium during the estrous cycle. At diestrus, only a few overrepresented GO categories were found, mostly related to immune response and metabolism. The genes of known function were further analyzed in the context of interaction and regulatory networks. One of a number of central factors was TGF-β, which controls the expression of 12 genes upregulated at estrus and 8 at diestrus. In conclusion, the present study extended the results of our previously conducted analysis of bovine endometrium between the estrus and diestrus stages (Bauersachs et al. 2005 J. Mol. Endocrinol. 32, 449–466), revealed distinct temporal expression profiles, and identified additional genes differentially expressed during the estrous cycle. This work was supported by Grant BMBF FUGATO-Fertilink.

Technical Note: Bovine Oviduct and Endometrium Array Version 1: A Tailored Tool for Studying Bovine Endometrium Biology and Pathophysiology

Fertility problems are the main reason for slaughter of high-performance milk cows, because elongated calving intervals result in financial losses for the farmer and retard genetic progress. Genetic improvement of fertility would be of great benefit, but functional traits for effective selection are missing. Recent advances in functional genomics tools like DNA microarrays could be the key to identify gene expression patterns in the endometrium that correlate with maternal fertility. Therefore, a first version of a bovine oviduct and endometrium cDNA array was established that contains a set of 1,440 cDNA clones and long oligonucleotides representing 950 different genes. The major part of these genes has been identified in a series of differential gene expression studies in endometrium (different stages of the estrous cycle, d 18 pregnant vs. nonpregnant) and in oviduct epithelial cells (different stages of the estrous cycle) using a combination of subtracted cDNA libraries and cDNA array hybridization. Furthermore, cDNA clones of genes, which showed no changes in their mRNA levels in the analyzed tissues, were added as controls. Reproducibility of the array hybridization, a comparison with the Affymetrix bovine genome array, and confirmation of differential gene expression with reverse transcription-quantitative PCR is shown. Potential future applications include systematic studies of interactions between metabolic status and functionality of the endometrium to identify genes that could be used for differential diagnosis of fertility problems. Further, endometrium transcriptome profiles may serve as novel traits to improve fertility by genetic selection.

172 DOES ESTRADIOL-17β CAUSE CYCLE-DEPENDENT MODULATIONS OF UTERINE MILK PROTEIN IN BOVINE ENDOMETRIUM?

Uterine secretion from the endometrial glandular epithelium provides optimal conditions for early embryonic development. The uterine milk protein (UTMP), a member of the serine proteinase inhibitor superfamily, has been demonstrated to be a major progesterone-induced glycoprotein secreted by the endometrium during pregnancy. Previous transcriptomic analysis revealed that UTMP was highly abundant at estrus in the bovine endometrium (Bauersachs et al. 2005 J. Mol. Endocrinol. 34, 889–908). Here we describe a detailed characterization of UTMP mRNA expression at several time points during the bovine estrous cycle and the pre-implantation period. Simmental heifers were monitored with respect to serum progesterone (P4) and estradiol-17β (E2), and slaughtered at estrus or 3.5, 12, 15, or 18 days after estrus, or at Day 15 or 18 of pregnancy (n = 4 per group). The uterus was divided into corpus and caudal, middle and cranial parts of the ipsilateral uterine horn for sampling of intercaruncular endometrium. In addition, effects of steroid hormones were investigated by stimulating an endometrial cell culture obtained from Day 8 animals (n = 4) with physiological doses of P4 or E2. In all cases, UTMP mRNA was quantified by real-time RT-PCR. Pronounced changes of UTMP mRNA abundance were detected during the estrous cycle. Expression was highest at estrus, followed by a remarkable decrease at Day 3.5. There was no difference between pregnant and non-pregnant animals at Day 15. Cycling animals displaying a high P4 and low E2 content (P4 &gt; 2 ng mL-1 and E2 &lt; 1 pg mL-1) revealed a lower expression of UTMP at Day 18 compared to the pregnant heifers, whereas animals at Day 18 progressing toward estrus (P4 &lt; 1.5 ng mL-1 and E2 &gt; 3 pg mL-1) exceeded the mRNA expression of the pregnant group. Following stimulation with estradiol-17β, the in vitro UTMP transcripts increased significantly. These results indicate that two different interfering stimulatory events might take place. While estradiol-17β appeared to increase UTMP mRNA expression at estrus, a second factor, most probably embryo-derived or embryo-induced, is assumed to be responsible for the UTMP rise during early pregnancy. The distinct gradient from the cranial uterine horn to the corpus at estrus was less pronounced at Day 3.5 and absent at Days 12, 15, and 18, pointing toward functional implications regarding the passing gametes, particularly sperm. An antibody raised against bovine UTMP will further validate the observed mRNA regulations on the protein level. In conclusion, bovine UTMP seems to play a decisive role for precise cyclic regulation of the bovine uterine milieu and during early embryo-maternal communication. This work was supported by the DFG FOR 478.

Region-specific expression of nitric oxide synthases in the bovine oviduct during the oestrous cycle and in vitro

Nitric oxide synthases (NOS) account for the endogenous production of nitric oxide (NO), a small and permeable bioreactive molecule. NO is known to act as a paracrine mediator during various processes associated with female reproduction. In the present study, the mRNA expression of the endothelial (eNOS) and inducible (iNOS) NO synthases were examined in bovine oviduct epithelial cells (BOEC) during the oestrous cycle. In addition, eNOS and iNOS mRNA and protein were localised by in situ hybridisation and immunocytochemistry respectively. Furthermore, the effects of exogenously applied oestradiol-17beta and progesterone on NOS mRNA regulation were studied in a suspension culture of BOEC. The eNOS mRNA abundance was low around ovulation (day 0) and increased significantly until pro-oestrus (day 18) in the ampulla. Immunoreactive protein of eNOS was detected predominantly in endothelial cells as well as in secretory oviduct epithelial cells at pro-oestrus. The iNOS mRNA concentration was significantly reduced in the isthmus at pro-oestrus (day 18) and oestrus (day 0) compared with persistently high levels in the ampulla. By in situ hybridisation, specific iNOS transcripts were additionally demonstrated in the oviduct epithelium. Immunoreactive iNOS protein was localised in secretory epithelial cells as well as in the lamina muscularis. The in vitro stimulation showed that both NOS were stimulated by progesterone, but not by oestradiol-17beta. The region-specific modulated expression of eNOS and iNOS provides evidence for an involvement of endogenously produced NO in the regulation of oviductal functions.

2 IDENTIFICATION OF GENES INDUCED BY THE CONCEPTUS IN THE BOVINE ENDOMETRIUM DURING THE PRE-IMPLANTATION PERIOD

Early embryonic development, implantation, and maintenance of a pregnancy are critically dependent on an intact embryo-maternal communication. So far, only few signals involved in this dialogue have been identified. In ruminants, interferon tau (IFN�) plays a key role in the process of maternal recognition of pregnancy by exhibiting antiluteolytic activity. Even though many experimental findings indicate a pivotal role of IFN� in the context of embryo-maternal communication in ruminants, a number of other systems may be involved. To identify genes induced in the bovine endometrium by the signaling of the embryo, a combination of subtracted cDNA libraries and cDNA array hybridization was applied. Monozygotic twin pairs (n = 5) were used as the biological model. Pregnancy was created in one twin by transferring two in vitro-produced embryos on Day 7 of the estrous cycle; the other twin received a sham embryo transfer. Pregnant and nonpregnant twins were slaughtered at Day 18; endometrial tissue samples were recovered and processed for transcriptome analysis as described (Bauersachs et al. 2005 J. Mol. Endocrinol. 34, 889-908). Screening of 4608 clones of two subtracted libraries revealed 90 different up-regulated genes and mRNAs, of which almost 50% are known to be stimulated by type I interferons. Among these interferon-stimulated genes, the ISG15 system is assumed to be of particular interest, and several components were studied in more detail using in situ hybridization. The pattern of mRNA expression suggests that modification of endometrial proteins through ISG15ylation plays a fundamental role during the pre-implantation period. A classification of the identified genes based on Gene Ontologies revealed the prevalence of genes involved in regulation of gene expression, cell communication, cell growth, cell differentiation, cell proliferation, and cell adhesion, and also the prevalence of genes with immune-related functions. These results underline the intense response of the endometrium to the presence of a conceptus, culminating in the preparation of the maternal environment for embryonic implantation. Further, for eleven selected genes the expression in the endometrium was quantified by the use of real-time RT-PCR. Overall, the results of quantitative RT-PCR and array hybridization correlated very well. To our knowledge this study provides the first holistic gene expression analysis of the bovine endometrium during the pre-implantation period. The results underline the importance of IFN� as an embryo-derived pregnancy recognition signal and depict the molecular mechanisms at the mRNA level underlying the intense embryo-maternal dialog taking place at Day 18 of gestation.

Gene expression profiling of bovine endometrium during the oestrous cycle: detection of molecular pathways involved in functional changes

The endometrium plays a central role among the reproductive tissues in the context of early embryo-maternal communication and pregnancy. It undergoes typical changes during the sexual/oestrous cycle, which are regulated by the ovarian hormones progesterone and oestrogen. To identify the underlying molecular mechanisms we have performed the first holistic screen of transcriptome changes in bovine intercaruncular endometrium at two stages of the cycle--end of day 0 (late oestrus, low progesterone) and day 12 (dioestrus, high progesterone). A combination of subtracted cDNA libraries and cDNA array hybridisation revealed 133 genes showing at least a 2-fold change of their mRNA abundance, 65 with higher levels at oestrus and 68 at dioestrus. Interestingly, genes were identified which showed differential expression between different uterine sections as well. The most prominent example was the UTMP (uterine milk protein) mRNA, which was markedly upregulated in the cranial part of the ipsilateral uterine horn at oestrus. A Gene Ontology classification of the genes with known function characterised the oestrus time by elevated expression of genes, for example related to cell adhesion, cell motility and extracellular matrix and the dioestrus time by higher expression of mRNAs encoding for a variety of enzymes and transport proteins, in particular ion channels. Searching in pathway databases and literature data-mining revealed physiological processes and signalling cascades, e.g. the transforming growth factor-beta signalling pathway and retinoic acid signalling, which are potentially involved in the regulation of changes of the endometrium during the oestrous cycle.

Functional genomics: tools for improving farm animal health and welfare

The first genome sequence assemblies of farm animal species are now accessible through public domain databases, and further sequencing projects are in rapid progress. In addition, large collections of expressed sequences have been obtained, which will aid in constructing annotated transcript maps for many economically important species. Thus, the breeding of farm animals is entering the post-genome era. Functional genomics, defined as applying global experimental approaches to assess gene function, by using the information and reagents provided by structural genomics (i.e. mapping and sequencing), has become the focus of interest. Combining a holistic view of phenotypes at the molecular level with genetic marker data seems a particularly promising approach for improving health and welfare traits in farm animals. These traits are often difficult to define. They suffer from low heritabilities and a corresponding lack of genetic gain in conventional selection and breeding programmes. At the same time, genomic information from micro-organisms and parasites offers the potential for new vaccines and therapeutics. This review describes major functional genomics tools, lists genomic resources available for farm animals and discusses the prospects and challenges of functional genomics in improving the health and welfare of farm animals.

231 TEMPORAL AND SPATIAL GENE EXPRESSION ANALYSIS OF THE BOVINE OVIDUCT EPITHELIUM

The fallopian tube plays a central role in reproduction, providing the appropriate environmental conditions for oocyte maturation as well as for sperm capacitation. Furthermore, fertilization and the first cleavage stages of embryonic development take place in the oviduct. At the molecular level, only fragmentary data are available regarding the physiological changes in the oviduct epithelium during the estrous cycle. Therefore, we performed a systematic study of gene expression changes in bovine ipsilateral oviduct epithelial cells derived from either the ampulla or the isthmus part of the oviduct at four different time points of the estrous cycle. A cDNA array consisting of approximately 400 candidate genes, primarily identified in different studies in the context of gene expression regulation in the oviduct, was designed and hybridized with 33P-labeled cDNA probes prepared from 28 different tissue samples. These tissue samples were collected from cyclic Simmental heifers at Day 0 (n = 3), Day 3.5 (n = 3), Day 12 (n = 4) and Day 18 (n = 4) of the estrous cycle. Ipsilateral epithelial cells were separately collected from ampulla and isthmus. After array evaluation (AIDA Image Analyzer, version 3.41, Raytest, Straubenhardt, Germany), the raw data were normalized to internal reference cDNAs on the arrays. Statistical analysis was done using ANOVA and the Tukey post-hoc test (GeneSpring® version 6.1, Silicon Genetics, Redwood City, CA, USA). For selected genes, differential expression was verified by real-time RT-PCR. A simplified Gene Ontology was built for the genes present on the array and a pathway analysis was performed to elucidate gene networks involved in the regulation of oviduct epithelial cell function. The expression patterns of two functional groups of genes are presented here: genes that are related to immune functions and genes of the secretory pathway or encoding secreted proteins. Messenger-RNA levels of immune-related genes were higher in epithelial cells of the ampulla compared to the isthmus part of the oviduct. This implies that certain immune functions may be differentially regulated in ampulla and isthmus. Furthermore, mRNAs of genes of the secretory pathway showed highest levels mainly in the ampulla around time of estrus, which may be explained with the increase of the secretory activity in the epithelium of the ampulla beginning at pre-estrus. In general, this study shows the importance of a separate analysis of the oviduct compartments and the influence of the estrous cycle on the expression level of a variety of genes. In the context of fertilization and early embryo-maternal communication, these results could provide an insight into the physiological changes during the estrous cycle, which are the bases for these processes. This work was supported by the Deutsche Forschungsgemeinschaft (Research Unit “Mechanisms of Embryo-Maternal Communication”; FOR 478/1).

211 TEMPORAL AND SPATIAL EXPRESSION PROFILE OF THE UTERINE MILK PROTEIN — A MEMBER OF THE SERINE PROTEASE INHIBITOR SUPERFAMILY — IN THE BOVINE ENDOMETRIUM

A combination of subtracted cDNA libraries and cDNA array hybridization was applied to identify differentially expressed genes in the bovine intercaruncular endometrium at estrus and diestrus. Six cyclic Simmental heifers were cycle-synchronized and slaughtered the morning after standing heat occurred (n = 3) or 12 days after estrus (n = 3), respectively. The uterus was divided into seven sections: corpus, plus the caudal, middle, and cranial parts of both uterine horns. Samples were collected from the epithelial layer of the lamina propria of the intercaruncular endometrium. Two subtracted libraries were prepared and analyzed by array hybridization with probes produced from the 42 tissue samples. More than 130 differentially expressed genes were identified. Among these genes, the mRNA for the uterine milk protein (UTMP) showed a much higher expression level at estrus versus diestrus. Furthermore, the expression level differed markedly between the uterus sections. Statistical significance was tested using ANOVA and Student Newman Keuls post-hoc test (GeneSpring® version 6.1, Silicon Genetics, Redwood City, CA, USA). There was a pronounced expression gradient from both cranial uterine horns (highest) to the corpus (lowest) at estrus. UTMP mRNA level was highest in the ipsilateral cranial horn. A more accurate quantification was done by quantitative real-time RT-PCR using the same RNA samples as for array hybridization and, in addition, samples from further time points of the estrous cycle and early pregnancy. The results obtained by array hybridization were clearly confirmed. UTMPs, also known as uterine serpins (US), were previously shown to be the major products secreted by the uteri of cattle, sheep, and pigs during pregnancy. The US are glycoproteins belonging to the serpin (serine proteinase inhibitor) superfamily of proteins. However, no inhibitory activity to any serine proteinase has been found. The ovine uterine serpin (OvUS) has been shown to inhibit a wide variety of immune responses, including mixed lymphocyte reaction, T cell-dependent antibody production, and NK (natural killer)-like activity, indicating a major role in protecting the conceptus from maternal immune reactions. The four members of the US family form a clade distinct from other serpins, which have probably adopted important biological functions in the reproductive biology of Artiodactyla. Therefore, the identified expression gradient of the UTMP mRNA at estrus may be of particular importance, e.g. for sperm selection, and deserves further investigation at the protein level and in functional studies. This work was supported by the Deutsche Forschungsgemeinschaft (Research Unit “Mechanisms of Embryo-Maternal Communication”; FOR 478/1).

106 GENOMIC IMPRINTING OF IGF2R IN TISSUES OF BOVINE FETUSES GENERATED BY ARTIFICIAL INSEMINATION OR IN VITRO FERTILIZATION

The insulin-like growth factor 2 receptor gene (IGF2R) is involved in fetal growth regulation. A study in sheep associated fetal overgrowth after in vitro embryo culture with abnormal DNA methylation and expression of IGF2R (Young et al. 2001 Nat. Genet. 27, 153–154). This suggested that abnormal IGF2R imprinting is a major cause of fetal overgrowth. To test this hypothesis in bovine fetuses, we developed a microsatellite marker for IGF2R from cDNA sequence data and screened 45 Day-80 fetuses generated in vivo, by artificial insemination (AI), or in vitro, by in vitro fertilization (IVF) procedures, for parent-of-origin-specific gene expression. A total of 17 fetuses were heterozygous, but available parental DNA samples showed that only 12 (8 AI, 4 IVF) allowed unambiguous discrimination of parental alleles. Parent-of-origin-specific allelic expression patterns indicated that bovine IGF2R was expressed predominantly from the maternal allele and thus imprinted in fetal heart, kidney, liver, lung, muscle, and cotyledon tissue. However, the relative amount of expression from the paternal allele was tissue-specific and ranged from 6.4 ± 0.8% in skeletal muscle up to 27.4 ± 0.9% in cotyledon (SPSS or 11.5, ANOVA, P < 0.001). Tissues that originated from the same germ layer showed similar allelic expression ratios whereas significantly different expression ratios (P < 0.05) were observed between tissues originating from different germ layers. Contrary to expectations from sheep data, there was no evidence for gross abnormalities in IGF2R imprinting in tissues from overgrown (n = 2) or normal sized (n = 2) IVF fetuses. However, relative paternal expression levels in several tissues showed significant relationships (P < 0.05–0.001) with growth parameters and pointed to subtle changes in paternal IGF2R expression in overgrown IVF fetuses. We thank W. Scholz and M. Weppert for excellent technical assistance.

Monitoring gene expression changes in bovine oviduct epithelial cells during the oestrous cycle

The oviduct epithelium undergoes marked morphological and functional changes during the oestrous cycle. To study these changes at the level of the transcriptome we did a systematic gene expression analysis of bovine oviduct epithelial cells at oestrus and dioestrus using a combination of subtracted cDNA libraries and cDNA array hybridisation. A total of 3072 cDNA clones of two subtracted libraries were analysed by array hybridisation with cDNA probes derived from six cyclic heifers, three of them slaughtered at oestrus and three at dioestrus. Sequencing of cDNAs showing significant differences in their expression levels revealed 77 different cDNAs. Thirty-seven were expressed at a higher level at oestrus, for the other 40 genes expression levels were higher at dioestrus. The identified genes represented a variety of functional classes. During oestrus especially genes involved in the regulation of protein secretion and protein modification, and mRNAs of secreted proteins, were up-regulated, whereas during dioestrus particularly transcripts of genes involved in transcription regulation showed a slight up-regulation. The concentrations of seven selected transcripts were quantified by real-time RT-PCR to validate the cDNA array hybridisation data. For all seven transcripts, RT-PCR results were in excellent correlation (r>0.92) with the results obtained by array hybridisation. Our study is the first to analyse changes in gene expression profiles of bovine oviduct epithelial cells during different stages of the oestrous cycle, providing a starting point for the clarification of the key transcriptome changes in these cells.

230TRANSCRIPTOMICS ANALYSIS OF CHANGES IN GENE EXPRESSION IN BOVINE OVIDUCT EPITHELIAL CELLS DURING THE ESTROUS CYCLE

The oviduct epithelium undergoes marked morphological and functional changes during the estrous cycle. It has been shown that a dramatic change in the frequencies of ciliated and non-ciliated cells occurs during the estrous cycle. At estrus the epithelium consists of secretory and ciliated cells and at diestrus mainly of ciliated cells. The oviduct provides the microenvironment for sperm capacitation, fertilization, and early cleavage-stage embryonic development. At the molecular level, only a few genes or proteins are known that change during the estrous cycle and which may be important for fertility, so as the bovine oviduct-specific glycoprotein, the major secretory protein in the oviduct. Therefore, we studied systematically the changes in gene expression in bovine ipsilateral oviduct epithelial cells at estrus and diestrus. To identify differentially expressed genes, a combination of subtracted cDNA libraries and cDNA array hybridization was used. Two subtracted libraries were produced to enrich cDNAs of upregulated genes at estrus and at diestrus. A total of 1536 cDNA clones of each library were analyzed with radioactively (33-P) labeled probes generated from the oviduct epithelial cells of six Simmental heifers, three of them slaughtered at Day 0 (estrus) and three at Day 12 after standing heat (diestrus). After normalization of the raw data and statistical analysis, all cDNAs showing significant differences in their expression levels at estrus compared to diestrus were sequenced. Sequencing revealed 84 different cDNAs;; 42 of them matched bovine genes or their human/mouse homologs with known functions, and 42 matched genes without a known function. Half of the genes (n=42) were expressed at a higher level at estrus;; for the other (n=42) expression levels were higher at diestrus. The regulated genes or their products represented a variety of functional classes, such as genes of the secretory pathway, genes involved in transcription regulation, cell-surface proteins, cell–cell interaction proteins, secreted proteins, members of signal transduction pathways, immune-related proteins, and some enzymes. The identification of genes differentially regulated in ipsilateral oviduct epithelial cells at estrus v. diestrus is the first step of a systematic analysis of differential gene expression during the estrous cycle. Further studies will follow, focusing on different compartments of the bovine oviduct and additional times of the estrous cycle.

Embryo-maternal communication in bovine - strategies for deciphering a complex cross-talk

Early embryonic development, implantation and maintenance of a pregnancy are critically dependent on an intact embryo-maternal communication. So far, only few signals involved in this dialogue have been identified. In bovine and other ruminants, interferon tau is the predominant embryonic pregnancy recognition signal, exhibiting antiluteolytic activity. However, this is just one aspect of the complex process of embryo-maternal signalling, and a number of other systems are more likely to be involved. To gain a more comprehensive understanding of these important mechanisms, integrated projects involving specialists in embryology, reproductive biotechnology and functional genome research are necessary to perform a systematic analysis of interactions between pre-implantation stage embryos and oviduct or uterine epithelial cells, respectively. State-of-the-art transcriptomic and proteomic technologies will identify reciprocal signals between embryos and their maternal environment and the respective downstream reaction cascades. For in vivo studies, the use of monozygotic twins as recipient animals provides elegant model systems, thus eliminating genetic variability as a cause of differential gene expression. In addition, suitable systems for the co-culture of oviduct epithelial or endometrium cells with the respective embryonic stages need to be established for functional validation of candidate genes potentially involved in the dialogue between embryos and their maternal environment. The knowledge of these mechanisms should help to increase the pregnancy rate following embryo transfer and to avoid embryonic losses. Candidate genes involved in embryo-maternal communication will also be used to define new quality criteria for the selection of embryos for transfer to recipients. Another application is the supplementation of embryotrophic factors or components of embryo-maternal signalling in optimized formulations, such as bioartificial matrices. As a long-term goal, signalling mechanisms identified in bovine will also be functionally evaluated in other species, including the human.

Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs

With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences and physical clones, which contains the complete and noninterrupted protein coding regions of all human genes will provide the indispensable tools for the systematic and comprehensive analysis of protein function to eventually understand the molecular basis of man. Here we report the sequencing and analysis of 500 novel human cDNAs containing the complete protein coding frame. Assignment to functional categories was possible for 52% (259) of the encoded proteins, the remaining fraction having no similarities with known proteins. By aligning the cDNA sequences with the sequences of the finished chromosomes 21 and 22 we identified a number of genes that either had been completely missed in the analysis of the genomic sequences or had been wrongly predicted. Three of these genes appear to be present in several copies. We conclude that full-length cDNA sequencing continues to be crucial also for the accurate identification of genes. The set of 500 novel cDNAs, and another 1000 full-coding cDNAs of known transcripts we have identified, adds up to cDNA representations covering 2%--5 % of all human genes. We thus substantially contribute to the generation of a gene catalog, consisting of both full-coding cDNA sequences and clones, which should be made freely available and will become an invaluable tool for detailed functional studies.

Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs

With the complete human genomic sequence being unraveled, the focus will shift to gene identification and to the functional analysis of gene products. The generation of a set of cDNAs, both sequences and physical clones, which contains the complete and noninterrupted protein coding regions of all human genes will provide the indispensable tools for the systematic and comprehensive analysis of protein function to eventually understand the molecular basis of man. Here we report the sequencing and analysis of 500 novel human cDNAs containing the complete protein coding frame. Assignment to functional categories was possible for 52% (259) of the encoded proteins, the remaining fraction having no similarities with known proteins. By aligning the cDNA sequences with the sequences of the finished chromosomes 21 and 22 we identified a number of genes that either had been completely missed in the analysis of the genomic sequences or had been wrongly predicted. Three of these genes appear to be present in several copies. We conclude that full-length cDNA sequencing continues to be crucial also for the accurate identification of genes. The set of 500 novel cDNAs, and another 1000 full-coding cDNAs of known transcripts we have identified, adds up to cDNA representations covering 2%--5 % of all human genes. We thus substantially contribute to the generation of a gene catalog, consisting of both full-coding cDNA sequences and clones, which should be made freely available and will become an invaluable tool for detailed functional studies.

A hybrid outer membrane protein antigen for vaccination against Pseudomonas aeruginosa

Recently a hybrid protein containing parts of the outer membrane proteins OprF (aa 190-342) and OprI (aa 21-83) from Pseudomonas aeruginosa fused to the glutathione-S-transferase was shown to protect mice against a 975-fold 50% lethal dose of P. aeruginosa. To omit the use of the GST-protein, the hybrid protein OprF-OprI was expressed in E. coli using distinct modifications which have not to be eliminated after its expression. Using different signal peptides, the yield of the hybrid protein OprF-OprI in E. coli could be increased to 30% of the total cell protein, however, only a very small amount of the hybrid preprotein was processed and could be isolated from the periplasm of the host. A construct containing an N-terminal extension of 11 amino acids from the original OprF gene gave rise to a significantly higher expression in the cytoplasm. Purification was facilitated by the addition of a five histidine tag at the C-terminus. An even higher expression was obtained by a construct in which a six histidine tag was attached to the N-terminus of the hybrid protein. The N-terminal extended OprF-OprI as well as the N-terminal his-tagged OprF-OprI hybrid antigens were purified by immobilized-metal affinity chromatography under native and denaturing conditions and can now be tested for protectivity against P. aeruginosa in animal model systems.

Effects of different levels of dietary selenium and vitamin E on the humoral immunity of rats

The aim of the present study was to investigate whether the level of selenium and selenium/vitamin E supply influences the humoral immunity of rats. In order to detect the effect of Se supply and age, 36 weaned Sprague-Dawley rats divided into two equal groups were killed after 22 or 45 experimental days by decapitation (Exp. I). In Exp. II 9 groups of 10 rats each were exposed to each combination of deficient, normal or excessive selenium with a vitamin E supply and killed after 44 days. The basic (deficiency) diet which was the same in both experiments contained 0.04mg Se and 8mg vitamin E per kg dry matter. The supplementation per kg diet was 0 or 0.2mg Se and 30mg vitamin E in Exp. I and 0, 0.2 or 1mg Se and 0, 30 or 200mg vitamin E in Exp. II. The concentration of selenium in serum, liver and spleen samples and the activity of glutathione peroxidase, which were determined to define the selenium status of the animals, corresponded well to the required supply situation. The immunoglobulins of type IgA, IgM and IgG with the subtypes IgG1, IgG2a, IgG2b and IgG2c were measured by immunoelectrophoresis. In both experiments selenium deficiency decreased the values of the IgG groups only nominally, IgA was not changed. IgM was significantly reduced, especially with prolonged selenium deficiency and simultaneous vitamin E deficiency. An excessive selenium supply compensated to a great extent for the effects of vitamin E deficiency on IgG and IgA.