Comprehensive transcriptomic analysis reveals stress physiology behind differential gene expression in vitrified–warmed and fresh mouse blastocysts
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ABSTRACT:
PROVIDER: PRJNA1118697 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29245415_1.fastq.gz | Fastqsanger.gz | |||
| SRR29245415_2.fastq.gz | Fastqsanger.gz | |||
| SRR29245416_1.fastq.gz | Fastqsanger.gz | |||
| SRR29245416_2.fastq.gz | Fastqsanger.gz | |||
| SRR29245417_1.fastq.gz | Fastqsanger.gz |
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Project description:Blastocyst vitrification has improved embryo transfer methods, leading to higher implantation success rates and better pregnancy outcomes in subsequent frozen embryo transfer cycles. In this study, we used mouse blastocysts as a model to simulate the transcriptional changes caused by vitrifying human blastocysts and to further investigate their effects. Utilizing a human vitrification protocol, we implanted both vitrified and fresh embryos into mice and observed a higher implantation success rate for the vitrified embryos. Transcriptomic analysis revealed that vitrified-warmed blastocysts exhibited differential gene expression primarily associated with thermogenesis, chemical carcinogenesis-reactive oxygen species, oxidative phosphorylation, immune response, and MAPK-related signaling pathways. To validate the next-generation sequencing results, we performed reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), which confirmed increased expression of genes such as Cdk6 and Nfat2, and decreased expression of genes such as Dkk3 and Mapk10. Among these pathways, immune responses and MAPK-related signaling pathways indicate that embryos need to communicate with the external environment, likely through microRNAs. We used gene-microRNA interaction predictions to anticipate potential embryonic microRNA expressions and conducted an analysis of embryonic microRNA expression. Twelve microRNAs exhibited expression patterns consistent with the predicted results, potentially affecting uterine epithelial cell adhesion, trophectoderm development, invasive capacity, or immune responses. Our findings suggest that vitrification induces transcriptomic changes in mouse blastocysts, and even small changes in gene expression can increase implantation success.
2024-08-07 | GSE268758 | GEO
Project description:Vitrification is commonly used in the cryopreservation of mammalian blastocysts to overcome the temporal and spatial limitations of embryo transfer. Previous studies have shown that the implantation ability of vitrified blastocysts is impaired and that microRNAs (miRNAs) regulate the critical gene for embryo implantation. However, little information is available about the effect of vitrification on the miRNA transcriptome in blastocysts, which partially explains the impaired implantation ability of vitrified blastocysts. In the present study, the miRNA transcriptomes in fresh and vitrified mouse blastocysts were analyzed by microRNA Taqman assay based method, and the results were validated using quantitative real-time PCR (qRT-PCR). Then, the differentially expressed miRNAs were assessed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Overall, 760 known mouse miRNAs were detected in the vitrified and fresh mouse blastocysts. Of these, the expression levels of five miRNAs differed significantly: in the vitrified blastocysts, four miRNAs (mmu-miR-199a-5p, mmu-miR-329-3p, mmu-miR-136-5p and mmu-miR-16-1-3p) were upregulated, and one (mmu-miR-212-3p) was downregulated. The expression levels of all miRNAs measured by the microRNA Taqman assay based method and qRT-PCR were consistent. The four upregulated miRNAs were predicted to regulate 877 candidate target genes, and the downregulated miRNA was predicted to regulate 231 genes. The biological analysis further showed that the differentially expressed miRNAs mainly regulated the implantation of embryos. In conclusion, the results of our study showed that vitrification significantly altered the miRNA transcriptome in mouse blastocysts, which may decrease the implantation potential of vitrified blastocysts.
2016-12-31 | GSE62581 | GEO
Project description:The aim of this study was to analyze transcriptome profiles with RNA sequencing (RNA-seq) in metaphase II horse oocytes after vitrification before and after in vitro maturation (IVM). To do so, transcriptome profile of three groups were compared: (1) oocytes vitrified immature, warmed, and in vitro matured (VGV), (2) in vitro matured and vitrified (VMAT), and (3) fresh oocytes (CONTROL).
2023-05-03 | GSE225950 | GEO
Project description:Changes in gene expression induced by the Cryotop vitrification procedure in bovine blastocysts using Agilent EmbryoGENE microarray slides. Bovine in vitro-produced embryos at the blastocyst stage (144 to 156 hours post insemination) were vitrified using the Cryotop system and compared with non-vitrified (control) embryos. After vitrification, the embryos were warmed and cultured for an additional 4 hours. Embryos that re-expanded or developed to the expanded blastocyst stage were used for microarray analysis.
2015-08-03 | GSE65953 | GEO
Project description:Changes in gene expression induced by the Cryotop vitrification procedure in bovine blastocysts using Agilent EmbryoGENE microarray slides. Bovine in vitro-produced embryos at the blastocyst stage (144 to 156 hours post insemination) were vitrified using the Cryotop system and compared with non-vitrified (control) embryos. After vitrification, the embryos were warmed and cultured for an additional 4 hours. Embryos that re-expanded or developed to the expanded blastocyst stage were used for microarray analysis. Four pools of vitrified embryos were hybridized against four pools of control embryos in a dye-swap design.
2015-08-03 | E-GEOD-65953 | biostudies-arrayexpress
Project description:The objective of this study was therefore to evaluate the impact of simultaneous vitrification of large numbers of embryos with the OC (20 embryos per device) system on gene expression patterns of in vivo-derived blastocysts when compared to the Superfine Open Pulled Straw (SOPS) system (5-7 embryos per device) through a microarray approach. In vivo-developed embryos were surgically retrieved from 16 sows in 4 replicates. Embryos at the blastocyst stage (n=180) were selected for the experiment and divided into three experimental groups: blastocysts vitrified with the OC system (n=60), blastocysts vitrified with the SOPS system (n=60), and a control group consisting of fresh, nonvitrified blastocysts (n=60). After in vitro culture for 24 h, six pools of 8 viable embryos (n=48 embryos per group) were prepared for transcriptome analysis. Embryos were placed in sterile tubes with 5 µL of PBS, immediately immersed in LN2 and stored at -80 °C until microarray analysis. After microarray analysis, a list of DEGs was generated for comparison of each vitrification system (OC and SOPS) with the control. Then, the two DEG lists were compared to determine the specific genes altered in each vitrification system and the DEGs shared by both systems. In addition, a list of DEGs was obtained by direct comparison of both vitrification systems. Pathway enrichment analysis was performed for each obtained list of DEGs.
2023-03-06 | E-MTAB-12772 | biostudies-arrayexpress
Project description:The aim of this study was to investigate the effects of vitrification on the miRNA transcriptome profile of porcine blastocysts and to compare the effects of the SOPS and Cryotop methods on miRNA profiles. The interactions of the miRNA data with previous gene expression data (Gonzalez-Plaza et al., 2023) from the same samples were also investigated. Embryos at the blastocyst stage (n=180) were selected for the experiment and divided into three experimental groups: blastocysts vitrified with the OC system (n=60), blastocysts vitrified with the SOPS system (n=60), and a control group consisting of fresh, nonvitrified blastocysts (n=60). After in vitro culture for 24 h, five pools of 8 viable embryos (n=40 embryos per group) were prepared for transcriptome analysis. Embryos were placed in sterile tubes with 5 µL of PBS, immediately immersed in LN2 and stored at -80 °C until microarray analysis.
2024-02-28 | E-MTAB-13814 | biostudies-arrayexpress
Project description:Vitrification is a method for long-term biological sample cryopreservation that transforms cells into a glass-like state by cooling without causing intra- and extra-cellular ice formation, which is a major driver of cell cryoinjury. Using an alginate hydrogel encapsulated in vitro follicle growth (eIVFG) system, we have recently demonstrated that compared to freshly-harvested follicles, vitrified follicles have normal follicle and oocyte reproductive outcomes as well as comparable expression levels of several genes that are essential for gonadotropin-dependent folliculogenesis and oogenesis. However, it is unknown whether vitrification preserves the molecular signatures of folliculogenesis at the whole transcriptomic level, which is the primary research focus in this study. Multilayered secondary follicles with a diameter of 130 -160 µm were mechanically isolated from 16-day-old CD-1 female mice and vitrified using the closed vitrification method. After a 2-week storage in liquid nitrogen, vitrified follicles were warmed, and together with freshly-harvested follicles, cultured for 8 days using the eIVFG method. Next, mature antral follicles from day 8 were collected for single-follicle RNA sequencing using the SMART-seq RNA-seq method. Principal component analysis (PCA) and Pearson’s correlation analysis revealed that vitrified follicles have similar transcriptomic profiles to fresh follicles. Using the criterion of fold change >2 or <0.5 and a false discovery rate (FDR) adjusted p-value < 0.05, there were 35 differentially expressed genes out of a total of 11,806 detected genes between vitrified and fresh follicles, among which 17 were up-regulated and 18 were down-regulated in vitrified follicles. To the best of our knowledge, none of those differentially expressed genes identified between vitrified and fresh follicles have been shown to be critical to folliculogenesis and oogenesis. Meanwhile, gene ontology (GO) and KEGG pathway analysis over these 35 genes using the functional annotation tool DAVID revealed that no GO terms or signaling pathways were significantly enriched. Furthermore, the expression of several genes essential for the gonadotropin-dependent folliculogenesis and oogenesis were comparable between vitrified and fresh follicles, including granulosa cell-specific genes (Cyp19a1, Amh, Inha, Inhba, Inhbb, and Fshr), theca cell-specific genes (Cyp17a1, Col1a2, and Col3a1), and oocyte-specific genes (Gdf9, Bmp15, Zp1, Zp2, and Zp3). Equally important, Lhcgr, the gene that is primarily expressed in theca cells of preantral follicles and then greatly induced in mural granulosa cells in antral follicles to prepare for the luteinizing hormone (LH) surge and ovulation, also had comparable mRNA expression levels between vitrified and fresh follicles. Taken together, these results demonstrate that vitrification preserves the follicular cell transcriptome and molecular signatures of gonadotropin-dependent folliculogenesis in the eIVFG system. In conclusion, our study re-evaluates individual follicle cryopreservation by using the closed vitrification method in a more in-depth perspective and proves that vitrification preserves the follicular cell transcriptome in the eIVFG system, thus providing a robust model for fertility preservation, conservation of endangered species, and also establishing a high-content ovarian follicle biobank for studying ovarian biology and female reproductive toxicology.
2021-12-29 | GSE184691 | GEO
Project description:Blastocyst vitrification has significantly changed the embryo transfer method.Vitrification of human blastocysts may result in higher implantation success rates and heavier birth weightsin subsequent frozen embryo transfer cycles. This study investigated the effects of vitrification onthe transcriptome profiles and implantationof mouse blastocysts. First, a fold-change cutoff of±2 was used to distinguish differentially expressed genes. Transcriptomic analysis indicatedthat differentially expressed genes of vitrified–warmed blastocysts were mainly related to cell development, proliferation, projection,motility,and calcium-binding protein and MAPK-related signaling pathways.Second, we performed reverse transcriptase-quantitative polymerase chain reaction to verify the gene expression in the next-generation sequencing results, including increased genes such as GPR132, CDK6, FOS, and NFAT2and decreased genes such as DKK3 and MAPK10. Finally, blastocysts may communicate with the maternal uterine via microRNA to regulate gene expression in the embryo and endometrium. Prediction of microRNA candidateswas performed using the results of next-generation sequencing transcriptomicanalysis and validatedthroughmicroRNA assay. A total of 12 validated blastocyte microRNAs may affect uterine epithelial cell adhesion, trophectoderm development, invasive capacity, or immune responses to increase pregnancy success rates. In conclusion, vitrification alters the transcriptome of mouse blastocysts, resulting in small changes in gene expression and an increased implantation success rate.
2025-02-01 | GSE222958 | GEO
Project description:This study aimed to compare the transcriptome of vitrified and slow frozen embryos with the untreated control. Bovine embryos (compact morulae) were vitrified or slow frozen and post-warm embryos were cultured to expanded blastocyst stage. The vitrified- and slow frozen-derived were subjected to microarray analysis and compared with untreated control embryos for differential gene expression. Morula to blastocyst conversion rate was higher (P<0.05) in control (72%) and vitrified (77%) embryos compared to slow frozen (34%) embryos. Total 20 genes were upregulated and 44 genes were downregulated in the vitrified embryos (fold change ≥ +-2, P<0.05). In slow frozen embryos, 102 genes were upregulated and 63 genes were downregulated (fold change ≥ +-1.5, P<0.05) in comparison with untreated embryos. Vitrified embryos exhibited significant changes in gene expression mainly involving embryo implantation (PTGS2, CALB1), lipid peroxidation and ROS generation (HSD3B1, AKR1B1, APOA1) and cell differentiation (KRT19, CLDN23). The slow frozen embryos, however, showed significant changes in the expression of genes related to cell signaling (SPP1), cell structure and differentiation (DCLK2, JAM2 and VIM), and lipid metabolism (PLA2R1 and SMPD3). In silico comparison between vitrified and slow-frozen (reference) embryos revealed similar changes in gene expression as between vitrified and untreated embryos. In conclusion, the vitrified bovine embryos demonstrated better post-warming embryo development than slow-frozen bovine embryos but their gene expression related to lipid metabolism, steroidogenesis, cell differentiation and placentation changed significantly. Slow freezing killed more embryos than vitrification, and the survived embryos did not express significant change in their gene expression.
2017-03-31 | GSE95381 | GEO