Effects of in vitro production on the transcriptomic profile of the embryonic disc and extra-embryonic membranes of day 15 elongated bovine embryo.
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ABSTRACT:
ORGANISM(S): Bos taurus
PROVIDER: GSE278243 | GEO | 2025/09/24
REPOSITORIES: GEO
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Project description:In vitro produced (IVP) bovine embryos are used to enhance herd genetics and support advanced reproductive technologies, however, less than 40% survive the first month of gestation after transfer to the surrogate. While the biochemical consequences of in vitro culture on the embryo before transfer have been well documented, less is known after transfer when the embryo interacts with the endometrium and pregnancy failure occurs. To investigate this, we utilized a Day 16 trophectoderm-endometrial mono-culture and co-culture system, integrating transcriptomic and proteomic analyses, to compare crosstalk between the IVP or in vivo derived (IVD) bovine conceptus and endometrium. We found that the IVP conceptus transcriptome (differentially expressed genes; DEG), diverged from the IVD conceptus but only after co-culture with endometrium (377 DEG; FDR < 0.05). Further, of the IVP conceptus DEG, 81 genes (21%) were associated with abnormal embryonic or fetal development. Significant biological processes associated with abundant endometrial DEG induced by IVP conceptuses were related to GTPase activity and the inflammatory response (FDR < 0.01), the latter of which may be associated with increased MHC class II expression, which was specific to IVP conceptuses. Proteomic analysis of the culture media identified 1,031 and 604 differentially abundant proteins (FDR < 0.05) associated with the IVD and IVP conceptus-endometrial co-cultures, respectively, compared to endometrium alone, indicating the proteomic environment surrounding the IVP conceptus may be suboptimal. Collectively, compared to the IVD conceptus, it appears the endometrium drives and responds to divergence of IVP conceptus biochemistry, likely contributing to pregnancy failure.
2025-07-31 | GSE295732 | GEO
Project description:This study compared the gene expression of extraembryonic membranes (EEM) from in vitro produced (IVP) and in vivo (AI) derived embryos. Samples of EEM from AI and IVP pregnancies were collected on days 18 and 32. A piece of the conceptus (day 18) or chorioallantois (day 32) were used for DNA and RNA isolation and subsequent determination of the sex by amplification of a Y-linked region of the DNA. The male and female ratios were analyzed by Chi-square of SAS. A subset of three female and three male EEM samples from each group (AI and IVP, days 18 and 32) were used for transcriptome analysis. Differentially expressed genes (DEGs) between groups, sex, and days were determined using edgeR-robust. A false discovery rate (FDR) <0.05 was used for statistical significance, and Toppgene platform was used for biological processes analysis. Sex ratio was similar on day 18 for AI and IVP groups. On day 32, the IVP group had a greater number of females than males (75 vs 25%, P=0.004). On day 18 female embryos, out of 71 DEGs identified, 50 were upregulated in IVP, and 21 in AI. The trophectoderm marker, TKDP2, was upregulated in the AI group, whereas IGF2, which is involved in placenta development, and APOA2, APOB, and APOE, which are important for lipid metabolism, were upregulated in the IVP group. Male embryos on day 18 had 22 DEGs, being 15 upregulated in AI and 7 in IVP. Female embryos on day 32 had 74 DEGs, with 21 upregulated in AI and 53 in IVP embryos. Some of the genes with increased expression in the IVP group were PTGIS, APOB, and APOH, which are related to lipid synthesis and metabolism. Male embryos on day 32 presented 899 DEGs, 564 upregulated in AI and 335 in IVP. Embryos from IVP had increased expression of genes related to embryo development, morphogenesis, neurogenesis, and developmental growth. In addition, male IVP embryos had decreased expression of genes related to lipid and carbohydrate metabolism. Interestingly, PLAC8B, BRB, pregnancy-associated glycoproteins (PAG) 7, 9, 10, and 19, were also downregulated in IVP male EEM. When comparing IVP males and females, there were 6753 DEGs, with 3091 being upregulated in females, and 3662 in male conceptuses on day 18. Some of the genes upregulated in females were related to placental function such as TKDP4, PLAC8A and PAGs 6, 8, 10, 12, 17, 18 and 19. On males, IFNT-related genes were upregulated (IFNT, IFNT2 IFNT3 and IFN-T). On day d32, there were 6772 DEGs, with 3252 genes with increased expression in female, and 3520 in male placentas. Among the genes increased in female placentas are genes involved in placentation: PAGs 17, 19, 9 and PLAC8B. On the other hand, PAG1 was detected as highly expressed in male placentas. In conclusion, IVP-derived male embryos were more susceptible to alterations in gene expression and these effects extend to the peri-implantation period including genes associated with placental development and markers of placental function.
2023-12-15 | GSE192417 | GEO
Project description:Production of embryos in vitro has enormous potential for research and commercial applications. Unfortunately, in vitro production of porcine embryos is extremely inefficient. Despite the characterization of distinct phenotypes, little is known about the molecular mechanisms and altered physiological processes that account for poor IVP development. The objective of the current study was to compare global gene expression patterns from IVO and IVP embryos using small amplified RNA (SAR)-SAGE. Whole-cell RNA from pools of Day 6 in vivo-(IVO) and in vitro-produced (IVP) blastocysts was used to construct SAR-SAGE libraries. Sequence analysis of the IVO and IVP libraries yielded a total of 98,771 and 98,408 tags, respectively. A total of 20,029 and 23,453 unique putative transcripts were detected in the IVO and IVP libraries, respectively. Statistical analyses of SAGE tag frequencies between the IVO and IVP libraries indicated that 938 and 193 tags were differentially expressed at a P < 0.05 and P < 0.001 level of significance, respectively. Tentative annotation of the differentially expressed SAGE tags was determined using BLAST sequence alignment with the TIGR porcine specific gene index (SSGI) and cross-species alignment using RepeatMasker to determine homologous human orthologs. Annotated tags were categorized into functional groupings according to gene ontology annotations. Real-time PCR was used to confirm differential expression for several transcripts from IVO and IVP blastocysts. These results demonstrate compromised gene expression from IVP blastocysts compared with IVO blastocysts for a number of biological processes including cellular metabolism, organization and response to stress; thereby providing potential target pathways for improvement of IVP methods. Keywords: Comparative (in vivo- vs. in vitro-produced porcine embryos)
2006-08-23 | GSE5571 | GEO
Project description:Production of embryos in vitro has enormous potential for research and commercial applications. Unfortunately, in vitro production of porcine embryos is extremely inefficient. Despite the characterization of distinct phenotypes, little is known about the molecular mechanisms and altered physiological processes that account for poor IVP development. The objective of the current study was to compare global gene expression patterns from IVO and IVP embryos using small amplified RNA (SAR)-SAGE. Whole-cell RNA from pools of Day 6 in vivo-(IVO) and in vitro-produced (IVP) blastocysts was used to construct SAR-SAGE libraries. Sequence analysis of the IVO and IVP libraries yielded a total of 98,771 and 98,408 tags, respectively. A total of 20,029 and 23,453 unique putative transcripts were detected in the IVO and IVP libraries, respectively. Statistical analyses of SAGE tag frequencies between the IVO and IVP libraries indicated that 938 and 193 tags were differentially expressed at a P < 0.05 and P < 0.001 level of significance, respectively. Tentative annotation of the differentially expressed SAGE tags was determined using BLAST sequence alignment with the TIGR porcine specific gene index (SSGI) and cross-species alignment using RepeatMasker to determine homologous human orthologs. Annotated tags were categorized into functional groupings according to gene ontology annotations. Real-time PCR was used to confirm differential expression for several transcripts from IVO and IVP blastocysts. These results demonstrate compromised gene expression from IVP blastocysts compared with IVO blastocysts for a number of biological processes including cellular metabolism, organization and response to stress; thereby providing potential target pathways for improvement of IVP methods. Keywords: Comparative (in vivo- vs. in vitro-produced porcine embryos) Whole-cell RNA from pools of Day 6 in vivo- and in vitro-produced blastocysts was used to construct small amplified RNA (SAR)-SAGE libraries.
2006-08-23 | E-GEOD-5571 | biostudies-arrayexpress
Project description:In cattle, the in vitro production (IVP) of embryos is becoming more relevant than embryos produced in vivo, i.e., after ovarian stimulation and embryo transfer (MOET). However, the effects of IVP on the developmental programming of specific organs in the postnatal calves are yet unknown. The objective of this study was to compare the hepatic and muscular transcriptomic modifications between IVP and MOET male calves of three months of age (n=4 per group). Tissue samples from liver and semitendinosus muscle were obtained at 3 months of age, and the extracted RNA was sequenced through RNAseq to determine differentially expressed genes (DEG; FDR<0.05). KEGG pathways enrichment analysis showed that DEG up-regulated in the liver and the muscle of the IVP calves were involved in oxidative phosphorylation and the tricarboxylic acid cycle. In contrast, ribosome and translation were up-regulated in the liver but down-regulated in the muscle of the IVP calves compared to the MOET calves (FDR<0.05). In conclusion, our findings indicated an altered hepatic and muscular energy regulation in phenotypically normal IVP calves compared to MOET calves.
2022-06-30 | GSE196974 | GEO
Project description:Exposure of bovine conceptuses to colony stimulating factor 2 (CSF2) from Day 5 to 7 of development can increase the percent of transferred conceptuses that develop to term. The purpose of this experiment was to understand the mechanism by which CSF2 increases embryonic and fetal survival. Conceptuses were produced in vitro in the presence or absence of 10 ng/ml CSF2 from Day 5 to 7 after insemination, transferred into cows, and flushed from the uterus at Day 15 of pregnancy. There was a tendency (P=0.07) for the proportion of cows with a recovered conceptus to be greater for those receiving a CSF2 treated conceptus (35% for control vs. 66% for CSF2). Antiviral activity in uterine flushings, a measure of the amount of interferon-{tau} (IFNT2) secreted by the conceptus, tended to be greater for cows receiving CSF2-treated conceptuses than for cows receiving control conceptuses. This difference approached significance when only cows with detectable antiviral activity were considered (P=0.07). In addition, CSF2 increased mRNA for IFNT2 (P=0.06) and keratin 18 (P<0.05) in extraembryonic membranes. Among a subset of filamentous conceptuses that were analyzed by microarray hybridization, there was no effect of CSF2 on gene expression in the embryonic disc or extraembryonic membranes. Results suggest that the increase in calving rate caused by CSF2 treatment involves, in part, more extensive development of extraembryonic membranes and capacity of the conceptus to secrete IFNT2 at Day 15 of pregnancy. Experimental conditions: CSF2 treated vs. CSF2 nontreated bovine in vitro produced preimplantation embryos were tranfered to a receptor cow and recovered at Day 15 of embryo development. The embryonic disc (ED) and the trophectoderm (Tr) were used for the expression analysis separately. Biological replicates: CSF2 treated vs. nontreated bovine preimplantation embryos were used in a dye switch two-color microarray experimental design.
2011-12-15 | E-GEOD-26842 | biostudies-arrayexpress
Project description:Pregnancy loss is a significant problem when embryos produced in vitro are transferred to a synchronized uterus. Currently, mechanisms that underly losses of in vitro produced embryos during implantation are largely unknown. We investigated this problem using cattle (Bos taurus) as a biomedical model of conceptus attachment by analyzing transcriptome data of paired extraembryonic membrane and endometrial samples collected on gestation days 18 and 25, which spans the attachment window in cattle.
2023-05-17 | GSE232489 | GEO
Project description:More than 1.2 million in vitro produced (IVP) bovine embryos are transferred annually worldwide, significantly outnumbering those from traditional superovulation, but there are limited reports on the birth and postnatal development of such calves. The conditions imposed during in vitro embryo culture may cause modifications of the embryo genome, including the transcriptome, potentially affecting postnatal organ function. This study compared the liver and muscle transcriptome in 4-month-old male and female dairy calves conceived by artificial insemination (AI) or IVP (n = 4 per sex per treatment). Biopsy tissue samples were collected and processed for RNA sequencing. Analysis of the RNAseq data revealed a distinct separation between the liver transcriptomes of female and male calves, regardless of method of production. Moreover, within the cohort of female calves, a strong separation between female calves derived from IVP vs AI was observed. Analysis of differentially expressed genes (DEGs) indicated downregulation of oxidative phosphorylation pathways and upregulation of pathways strongly enriching immune system processes, specifically Th17 cell differentiation and antigen processing and presentation. For the muscle transcriptome, the separation between male and female calves was less apparent compared with liver transcriptome, but there was still a clear separation between female calves derived from IVP vs AI, with downregulated genes enriching the p53 signalling pathway and upregulated genes enriching muscle structure development pathways. These results suggest that female embryos derived from IVP vs AI have developmental differences that manifest as differential transcriptomic profiles postnatally. In conclusion, these findings demonstrate that the IVP process induces significant alterations in the liver and muscle transcriptome of female postnatal calves. Further exploration is necessary to understand the potential implications for lifetime growth, health and production characteristics.
2025-09-24 | GSE289870 | GEO
Project description:Bovine IVP blastocysts (day 8) were produced with and without thyroid hormones and gene expression profiles were compared.
2014-09-01 | GSE58901 | GEO
Project description:The key lncRNAs that regulate embryo development were screened through analyzing expression pattern of lncRNA in porcine in vivo fertilization (IVV) embryos. By knocking down lncRNA expression in in vitro fertilization (IVF) embryos, we investigated its function and mechanism of regulating embryonic development. The RNAseq was curry out to explore the genes influenced by lncT(LOC102165808).
2022-08-30 | GSE207258 | GEO