Maternal serum progesterone concentration and early conceptus development of bovine embryos produced in vivo or in vitro

miRNAs in Follicular and Oviductal Fluids Support Global DNA Demethylation in Early-Stage Embryos

Global methylation levels differ in in vitro- and in vivo-developed embryos. Follicular fluid (FF) contains extracellular vesicles (EVs) containing miRNAs that affect embryonic development. Here, we examined our hypothesis that components in FF affect global DNA methylation and embryonic development. Oocytes and FF were collected from bovine ovaries. Treatment of zygotes with a low concentration of FF induced global DNA demethylation, improved embryonic development, and reduced DNMT1/3A levels. We show that embryos take up EVs containing labeled miRNA secreted from granulosa cells and the treatment of zygotes with EVs derived from FF reduces global DNA methylation in embryos. Furthermore, the methylation levels of in vitro-developed blastocysts were higher than those of in their vivo counterparts. Based on small RNA-sequencing and in silico analysis, we predicted miR-29b, -199a-3p, and -148a to target DNMTs and to induce DNA demethylation, thereby improving embryonic development. Moreover, among FF from 30 cows, FF with a high content of these miRNAs demethylated more DNA in the embryos than FF with a lower miRNA content. Thus, miRNAs in FF play a role in early embryonic development.

Review: Overview of the transcriptomic landscape in bovine blastocysts and elongated conceptuses driving developmental competence

In cattle, pregnancy loss due to early embryonic mortality is a major concern that significantly impacts reproductive efficiency. Given the economic importance of cattle in livestock productivity, much research has been carried out to comprehend the regulatory mechanisms underlying this early embryo loss. Thus, understanding the molecular principles behind the reciprocal communication between the maternal uterus and the developing conceptus is paramount. Measurement of mRNA expression through a variety of techniques is widely used to unravel the complex and dynamic interaction between these two players. Development of high-throughput technologies, such as microarrays and RNA sequencing, have allowed global quantification of the full range of expressed mRNA, or transcriptome, of a biological sample. Therefore, numerous investigators have applied one or the other method to study the bovine embryo transcriptome at different developmental checkpoints and under different conditions. The goal of this article was to review studies involving the use of high-throughput techniques to study the transcriptome of the bovine embryo from the blastocyst (∼day 7) to the elongating conceptus stage (∼days 13-16) in terms of developmental capacity and the impact of procedures for in vitro embryo production. Furthermore, the differentially expressed genes reported by each study and enriched pathways were compared to determine common terms. The studies described here highlight differences in the transcriptome (i) between blastocysts with divergent ability to sustain a pregnancy, (ii) between age-matched elongated conceptuses with divergent developmental fates, and (iii) between blastocysts and elongated conceptuses produced in vitro or in vivo. Comparison between these works, supported by other studies involving transcriptomic data integration presented at the end of this review, highlights the involvement of pathways related to energy metabolism in embryonic competence, which may be altered because of the procedures involved in the in vitro production of embryos.

Review: Implantation and placentation in ruminants

Ruminants have a unique placenta in comparison to other mammalian species. Initially, they possess a non-invasive epitheliochorial type of placenta during conceptus elongation. As the conceptus trophectoderm begins to attach to the luminal epithelium (LE) of the endometrium, binucleate cells (BNCs) develop within the trophoblast of the chorion. The BNCs migrate and fuse with the uterine LE to form multinucleate syncytial plaques in sheep and hybrid trinucleate cells in cattle. This area of the ruminant placenta is semi-invasive synepitheliochorial. The BNCs form the foundation of the placental cotyledons and express unique placenta-specific genes including pregnancy-associated glycoproteins and chorionic somatomammotropin hormone 2 or placental lactogen. Attachment and interdigitation of cotyledons into endometrial caruncles form placentomes that are subsequently vascularized to provide essential nutrients for growth of the fetus. This chapter review will discuss historical and current aspects of conceptus implantation and placenta development in ruminant ungulates with a focus on cattle and sheep. Single-cell analysis promises to provide a much more detailed understanding of the different cell populations and insights into pathways mediating trophoblast and placenta. This fundamental is required to understand pregnancy loss and develop strategies to improve pregnancy outcomes in ruminants.

Actions of FGF2, LIF, and IGF1 on bovine embryo survival and conceptus elongation following slow-rate freezing

Culture environment during in vitro embryo production can affect embryo phenotype and pregnancy outcomes, making culture modifications a logical approach for improving embryo competence. Previously, the addition of the growth factors FGF2, LIF, and IGF1, termed FLI, to the culture medium improved bovine embryo development, and re-expansion following cryopreservation. The objective of this study was to investigate the survival of cryopreserved FLI treated embryos at day 15 of pregnancy and evaluate conceptus transcriptomes. Embryos were produced using in vitro fertilization of abattoir-derived oocytes, cultured to the blastocyst stage in the presence or absence of FLI (+/- FLI), and cryopreserved by slow-rate freezing. Thawed embryos were transferred into non-lactating recipient beef cows and eight days later conceptuses were recovered and analyzed. For a subset of conceptuses whole transcriptome analysis was performed by using the NovaSeq 6000. There was no detectable difference in conceptus recovery or average conceptus length between the two groups. There were 32 differentially expressed transcripts, 23 up-regulated and nine down-regulated in the +FLI group compared to -FLI. Genes were involved in interferon signaling, prostaglandin synthesis, and placental development. This study reveals that embryos cultured with or without FLI and cryopreserved by slow-rate freezing have similar developmental competence up to day 15 of development. Nevertheless, differences in gene expression exhibit an effect of FLI on conceptus signaling during elongation.

Form of dietary selenium affects mRNA encoding cholesterol biosynthesis and immune response elements in the early luteal phase bovine corpus luteum

Widespread regions of the southeast United States have soils, and hence forages, deficient in selenium (Se), necessitating Se supplementation to grazing cattle for optimal immune function, growth, and fertility. We have reported that supplementation with an isomolar 1:1 mix (MIX) of inorganic (ISe) and organic (OSe) forms of Se increases early luteal phase (LP) progesterone (P4) above that in cows on ISe alone. Increased early LP P4 advances embryonic development. Our objective was to determine the effect of form of Se on the transcriptome of the early LP corpus luteum (CL) with the goal of elucidating form of Se-regulated processes affecting luteal steroidogenesis and function. Non-lactating, 3-yr-old Angus-cross cows underwent 45-d Se-depletion, then repletion periods, and then at least 90 d of supplementation (TRT) with 35 ppm Se/d as either ISe (n = 5) or MIX (n = 5). CL were then recovered on day 7 of the estrous cycle, total RNA isolated, and the effect of TRT on the luteal transcriptome evaluated using bovine gene 1.0 ST arrays (Affymetrix, Inc., Santa Clara, CA). The abundance of transcripts in each CL was subjected to one-way ANOVA using Partek Genomic Suite software to determine TRT effects. Microarray analysis indicated a total of 887 transcripts that were differentially expressed and functionally annotated, with 423 and 464 up- and down-regulated (P < 0.05) in MIX vs. ISe CL, respectively. Bioinformatic analysis (Ingenuity Pathway Analysis) revealed the top TRT-affected canonical pathways to include seven specific to cholesterol biosynthesis and two to inflammatory responses. Results from the microarray analysis were corroborated by targeted real-time PCR. MIX CL had increased (P < 0.05) abundance of transcripts regulating cholesterol biosynthesis including DHCR7, DHCR24, and CYP51A1 (fold changes of 1.65, 1.48, and 1.40, respectively), suggesting MIX-induced increases in P4 to be due, in part, to increased availability of substrate to luteal cells. In addition, MIX CL had increased (P < 0.05) abundance of immune-response transcripts including C1QC, FAS, ILR8B, and IL1R1 (fold changes of 2.30, 1.74, 1.66, and 1.63, respectively). SREBF1 mRNA was also increased (1.32-fold, P < 0.05) in the MIX CL, which increases cholesterol synthesis and stimulates IL1B, linking effects of form of supplemental Se (TRT) on cholesterol biosynthesis and immune function in the CL.

Lineage Differentiation Markers as a Proxy for Embryo Viability in Farm Ungulates

Embryonic losses constitute a major burden for reproductive efficiency of farm animals. Pregnancy losses in ungulate species, which include cattle, pigs, sheep and goats, majorly occur during the second week of gestation, when the embryo experiences a series of cell differentiation, proliferation, and migration processes encompassed under the term conceptus elongation. Conceptus elongation takes place following blastocyst hatching and involves a massive proliferation of the extraembryonic membranes trophoblast and hypoblast, and the formation of flat embryonic disc derived from the epiblast, which ultimately gastrulates generating the three germ layers. This process occurs prior to implantation and it is exclusive from ungulates, as embryos from other mammalian species such as rodents or humans implant right after hatching. The critical differences in embryo development between ungulates and mice, the most studied mammalian model, have precluded the identification of the genes governing lineage differentiation in livestock species. Furthermore, conceptus elongation has not been recapitulated in vitro, hindering the study of these cellular events. Luckily, recent advances on transcriptomics, genome modification and post-hatching in vitro culture are shedding light into this largely unknown developmental window, uncovering possible molecular markers to determine embryo quality. In this review, we summarize the events occurring during ungulate pre-implantation development, highlighting recent findings which reveal that several dogmas in Developmental Biology established by knock-out murine models do not hold true for other mammals, including humans and farm animals. The developmental failures associated to in vitro produced embryos in farm animals are also discussed together with Developmental Biology tools to assess embryo quality, including molecular markers to assess proper lineage commitment and a post-hatching in vitro culture system able to directly determine developmental potential circumventing the need of experimental animals.

Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos

Pregnancy rates for in vitro produced (IVP) embryos are usually lower than for embryos produced in vivo after ovarian superovulation (MOET). This is potentially due to alterations in their trophectoderm (TE), the outermost layer in physical contact with the maternal endometrium. The main objective was to apply a multi-omics data integration approach to identify both temporally differentially expressed and differentially methylated genes (DEG and DMG), between IVP and MOET embryos, that could impact TE function. To start, four and five published transcriptomic and epigenomic datasets, respectively, were processed for data integration. Second, DEG from day 7 to days 13 and 16 and DMG from day 7 to day 17 were determined in the TE from IVP vs. MOET embryos. Third, genes that were both DE and DM were subjected to hierarchical clustering and functional enrichment analysis. Finally, findings were validated through a machine learning approach with two additional datasets from day 15 embryos. There were 1535 DEG and 6360 DMG, with 490 overlapped genes, whose expression profiles at days 13 and 16 resulted in three main clusters. Cluster 1 (188) and Cluster 2 (191) genes were down-regulated at day 13 or day 16, respectively, while Cluster 3 genes (111) were up-regulated at both days, in IVP embryos compared to MOET embryos. The top enriched terms were the KEGG pathway "focal adhesion" in Cluster 1 (FDR = 0.003), and the cellular component: "extracellular exosome" in Cluster 2 (FDR<0.0001), also enriched in Cluster 1 (FDR = 0.04). According to the machine learning approach, genes in Cluster 1 showed a similar expression pattern between IVP and less developed (short) MOET conceptuses; and between MOET and DKK1-treated (advanced) IVP conceptuses. In conclusion, these results suggest that early conceptuses derived from IVP embryos exhibit epigenomic and transcriptomic changes that later affect its elongation and focal adhesion, impairing post-transfer survival.

Benefits and Risks of Preventing Twin Pregnancies

Clinical problems associated with twin pregnancies have been well established, and twin births are now considered undesirable or even disastrous for the dairy cattle industry and the individual cow. The high incidence of early fetal loss, abortion during the mid-lactation period, dystocia, stillbirth, and placenta retention should be considered a preventable consequence of management, as these disorders greatly compromise the welfare and productive lifespan of a cow carrying or delivering twins. The use of sexed semen generates herd replacements and additional heifers, so a proposed strategy for twin pregnancy prevention is the transfer of a single in vitro-produced female beef cow embryo to cows not suitable for producing replacements. Another proposed strategy is drainage at insemination of co-dominant follicles to prevent twin pregnancies in cows with genetic merit. As a result, embryo survival should improve, economic losses associated with twin pregnancies will be prevented, beef output from the herd will be increased, and the health and welfare of the cow will certainly benefit. In this review, the clinical prospects of preventing or avoiding twin pregnancies using both procedures are discussed.

Comparison of gene expression and mitochondria number between bovine blastocysts obtained <i>in vitro</i> and <i>in vivo</i>

Embryo transfer uses embryos developed in vivo or in vitro for cattle production, however there is a difference in the quality of the embryos obtained by the two methods. This study addresses the differences in gene expression between blastocysts developed in vitro and in vivo. In vivo blastocysts were flushed from the uteri of super-ovulated cows and blastocysts developed in vitro were derived from in vitro matured and fertilized embryos. The same batch of frozen bull sperm was used for insemination and in vitro fertilization. Blastocysts were then subjected to RNA sequencing. Differentially expressed genes upregulated in in vitro blastocysts were annotated to focal adhesion, extracellular matrix (ECM)-receptor interaction, and PI3K-Akt signaling and the genes that were upregulated in in vivo blastocysts were annotated to oxidation-reduction processes, mitochondrion organization, and mitochondrial translation. Although the total cell number of the two types of blastocysts was similar, the mitochondrial quantity (determined by mitochondrial DNA copy numbers and expression levels of TOMM20), and ATP content in the blastocysts were lower in in vivo blastocysts compared with those developed in vitro. In conclusion, RNAseq revealed differential molecular backgrounds between in vitro and in vivo developed blastocysts and mitochondrial number and function are responsible for these differences.

BOARD INVITED REVIEW: Post-transfer consequences of in vitro-produced embryos in cattle

In vitro embryo production (IVP) in cattle has gained worldwide interest in recent years, but the efficiency of using IVP embryos for calf production is far from optimal. This review will examine the pregnancy retention rates of IVP embryos and explore causes for pregnancy failures. Based on work completed over the past 25 yr, only 27% of cattle receiving IVP embryos will produce a live calf. Approximately 60% of these pregnancies fail during the first 6 wk of gestation. When compared with embryos generated by superovulation, pregnancy rates are 10% to 40% lower for cattle carrying IVP embryos, exemplifying that IVP embryos are consistently less competent than in vivo-generated embryos. Several abnormalities have been observed in the morphology of IVP conceptuses. After transfer, IVP embryos are less likely to undergo conceptus elongation, have reduced embryonic disk diameter, and have compromised yolk sac development. Marginal binucleate cell development, cotyledon development, and placental vascularization have also been documented, and these abnormalities are associated with altered fetal growth trajectories. Additionally, in vitro culture conditions increase the risk of large offspring syndrome. Further work is needed to decipher how the embryo culture environment alters post-transfer embryo development and survival. The risk of these neonatal disorders has been reduced by the use of serum-free synthetic oviductal fluid media formations and culture in low oxygen tension. However, alterations are still evident in IVP oocyte and embryo transcript abundances, timing of embryonic cleavage events and blastulation, incidence of aneuploidy, and embryonic methylation status. The inclusion of oviductal and uterine-derived embryokines in culture media is being examined as one way to improve the competency of IVP embryos. To conclude, the evidence presented herein clearly shows that bovine IVP systems still must be refined to make it an economical technology in cattle production systems. However, the current shortcomings do not negate its current value for certain embryo production needs and for investigating early embryonic development in cattle.

Role of progesterone in embryo development in cattle

Progesterone (P4) from the corpus luteum is critical for the establishment and maintenance of pregnancy and plays a major role in regulating endometrial secretions essential for stimulating and mediating changes in conceptus growth and differentiation throughout early pregnancy in ruminants. Numerous studies have demonstrated an association between elevated systemic P4 and acceleration in conceptus elongation. A combination of in vivo and in vitro experiments found that the effects of P4 on conceptus elongation are indirect and mediated through P4-induced effects in the endometrium. Despite effects on elongation, data on the effects of post-insemination supplementation with P4 on pregnancy rates are conflicting. This review highlights the effects of P4 on conceptus development and examines strategies that have been undertaken to manipulate P4 concentrations to increase fertility.

Characterization and comparative analyses of transcriptomes for in vivo and in vitro produced peri-implantation conceptuses and endometria from sheep

An increasing number of reports indicate that in vitro fertilization (IVF) is highly associated with long‑term side effects on embryonic and postnatal development, and can sometimes result in embryonic implant failure. While high‑throughput gene expression analysis has been used to explore the mechanisms underlying IVF-induced side effects on embryonic development, little is known about the effects of IVF on conceptus–endometrial interactions during the peri-implantation period. Using sheep as a model, we performed a comparative transcriptome analysis between in vivo (IVO; in vivo fertilized followed by further development in the uterus) and in vitro produced (IVP; IVF with further culture in the incubator) conceptuses, and the caruncular and intercaruncular areas of the ovine endometrium. We identified several genes that were differentially expressed between the IVO and IVP groups on day 17, when adhesion between the trophoblast and the uterine luminal epithelium begins in sheep. By performing Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, we found that, in the conceptus, differentially expressed genes (DEGs) were associated mainly with functions relating to cell binding and the cell cycle. In the endometrial caruncular area, DEGs were involved in cell adhesion/migration and apoptosis, and in the intercaruncular area, they were significantly enriched in pathways of signal transduction and transport. Thus, these DEGs are potential candidates for further exploring the mechanism underlying IVF/IVP-induced embryonic implant failure that occurs due to a loss of interaction between the conceptus and endometrium during the peri-implantation period.