Characterization of microRNAs in spent culture medium associated with human embryo quality and development
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ABSTRACT:
PROVIDER: PRJNA705673 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13815400.fastq.gz | Fastqsanger.gz | |||
| SRR13815401.fastq.gz | Fastqsanger.gz | |||
| SRR13815402.fastq.gz | Fastqsanger.gz | |||
| SRR13815403.fastq.gz | Fastqsanger.gz | |||
| SRR13815404.fastq.gz | Fastqsanger.gz |
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Project description:Purpose: Given implantation failure limited the improvement of the in vitro fertilization (IVF) success rate, it was urgent to identify potential biomarkers for embryo quality and predicting the outcomes of IVF-ET. Methods: The expression profiles of 16 spent culture media (SCM) collected from embryos at the cleavage on Day 3 (D3 cleavage) and blastocyst stages on Day 5 (D5 blastocyst) during IVF cycles were determined with RNA-sequencing. Differentially expressed miRNAs (DEmiRNAs) were identified with p-value < 0.05 and |log2FC|> 1. Then, the miRNA-mRNA interaction networks were constructed by using Cytoscape software. Finally, the GO and KEGG pathway analysis of target genes of DEmiRNAs were conducted. Results: Compared with pregnant groups, 29 DEmiRNA were detected in non-pregnant groups at D3 cleavage, and 26 DEmiRNA were detected in non-pregnant group at D5 blastocyst. Among them, a total of six known miRNAs, including hsa-miR-199a-3p>hsa-miR-199b-3p, hsa-miR-199a-5p, hsa-miR-379-5p, hsa-miR-432-5p, hsa-miR-99a-5p and hsa-miR-483-5p, were identified. The results of GO and KEGG pathway analysis indicated that these target genes of DEmiRNAs were associated with various biological processes. Conclusion: In conclusion, we identified three miRNAs, including hsa-miR-199a-5p, hsa-miR-483-5p and hsa-miR-432-5p, may serve as biomarkers for embryo quality during IVF cycles.
2023-10-31 | GSE167961 | GEO
Project description:BackgroundGiven implantation failure limits the improvement of in vitro fertilization (IVF) success rates, there is an urgency to identify potential biomarkers for embryo quality and predict the outcomes of IVF-embryo transfer (IVF-ET).MethodsUsing RNA-sequencing, we identified the expression profiles of 16 spent culture medium (SCM) collected from embryos at the cleavage on day 3 (D3 cleavage) and blastocyst stages on day 5 (D5 blastocyst) during IVF cycles. Differentially expressed miRNAs (DEmiRNAs) were then identified, and microRNA (miRNA)-messenger RNA (mRNA) interaction networks were constructed. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) confirmation and validation in the Gene Expression Omnibus (GEO) database were performed.ResultsCompared with the pregnant group, 29 DEmiRNAs were detected in the non-pregnant group at D3 cleavage, and 26 were detected in the non-pregnant group at D5 blastocyst. Among them, a total of six known miRNAs, including hsa-miR-199a-3p>hsa-miR-199b-3p, hsa-miR-199a-5p, hsa-miR-379-5p, hsa-miR-432-5p, hsa-miR-99a-5p, and hsa-miR-483-5p, were identified. The results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these target genes of DEmiRNAs were associated with various biological processes (BPs). The results of validation in qRT-PCR and the GEO database suggested the reliability of our RNA-sequencing results.ConclusionsIn conclusion, we identified three miRNAs, including hsa-miR-199a-5p, hsa-miR-483-5p, and hsa-miR-432-5p, which may serve as biomarkers for embryo quality during IVF cycles.
| S-EPMC8667117 | biostudies-literature
Project description:BackgroundMetabolites in spent embryo culture medium correlate with the embryo's viability. However, there is no widely accepted method using metabolite dada to predict successful implantation. We sought to combine metabolomic profiling of spent embryo culture medium and clinical variables to create an implantation prediction model as an adjunct to morphological screening of day 3 embryos.MethodsThis investigation was a prospective, nested case-control study. Forty-two day 3 embryos from 34 patients were transferred, and the spent embryo culture medium was collected. Twenty-two embryos implanted successfully, and the others failed. Metabolites in the medium relevant to implantation were detected and measured by Liquid Chromatography-Mass Spectrometry. Clinical signatures relevant to embryo implantation were subjected to univariate analysis to select candidates for a prediction model. Multivariate logistical regression of the clinical and metabolomic candidates was used to construct a prediction model for embryo implantation potential.ResultsThe levels of 13 metabolites were significantly different between the successful and failed groups, among which five were most relevant and interpretable selected by Least Absolute Shrinkage and Selection Operator regression analysis. None of the clinical variables significantly affected day 3 embryo implantation. The most relevant and interpretable set of metabolites was used to construct a prediction model for day 3 embryo implantation potential with an accuracy of 0.88.ConclusionsDay 3 embryos'implantation potential could be noninvasively predicted by the spent embryo culture medium's metabolites measured by LC-MS. This approach may become a useful adjunct to morphological evaluation of day 3 embryos.
| S-EPMC10249307 | biostudies-literature
Project description:Follow-up study of 9 year old IVF children who underwent embryo culture in G3 (Vitrolife) or K-SICM (Cook) medium. Genome-wide DNA methylation profiling of 9 year old IVF children (saliva samples) who had undergone embryo culture in G3 medium (Vitrolife) or K-SICM medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome.
2022-09-01 | GSE196432 | GEO
Project description:Follow-up study of IVF neonates who underwent embryo culture in G5 (Vitrolife) or HTF (Lonza) medium. Genome-wide DNA methylation profiling of IVF neonates (umbilical cord blood samples) who had undergone embryo culture in G5 medium (Vitrolife) or HTF medium (Lonza). The EPIC array was used to profile the methylome at approximately 850,000 CpG sites across the human genome.
2022-05-26 | GSE189531 | GEO
Project description:The metabolomic profile of an embryo culture medium can aid in the advanced prediction of embryonic developmental potential and genetic integrity. But it is not known if this technology can be used to determine the in vitro potential of inner cell mass (ICM) in adherence and proliferation. Here, we investigated the developmental potential of mouse 2-cell embryos carrying cisplatin-induced DNA lesions (IDL), beyond blastocyst stage using ICM outgrowth assay. The genetic integrity of ICM cells was determined by comet assay. The metabolic signatures of spent medium were recorded 84 hours post injection of hCG (hpi-hCG), and after 96 hours of extended in vitro culture (Ex 96) by NMR spectroscopy. We observed that blastocysts that lack the ability to adhere in vitro had an increased requirement of pyruvate (p < 0.01), lactate (p < 0.01), and were accompanied by a significant reduction of pyruvate-alanine ratio in the culture medium. We propose that the aforementioned metabolites from 84 hpi-hCG spent medium be further explored using appropriate experimental models, to prove their potential as biomarkers in the prediction of implantation ability of in vitro derived human embryos in clinical settings.
| S-EPMC6242932 | biostudies-literature
Project description:We reported transcriptional characterization of BMDCs stimulated by filter-sterilized spent medium of Parabacteroides goldsteinii ASF519 (ASF519 SSM) alone or in comination with zymosan. We identified that ASF519 SSM-induced differentially expressed genes have a wide association with the regulation of immune functions, cell communication, apoptosis. We observed that ASF519 SSM induced transcriptomic changes towards immune tolerance, such as a dramatic induction of tolerogenic Il10, lipocalin-2(Lcn2) and indoleamine 2, 3-dioxygenases (Ido1/2), and a reduction of the co-stimulatory molecule Cd40 and inflammatory cytokines, including Il12b, Il23a, and Il1f9 (or Il-36 gamma).
2021-04-07 | GSE171658 | GEO
Project description:ObjectivesTo compare successful beta-thalassemia (β-thalassemia) detection rates obtained using spent culture medium and spent culture medium containing blastocoelic fluid (BF).MethodThis study involved data from 10 couples who underwent preimplantation genetic testing (PGT) for β-thalassemia. A total of 26 samples of spent culture medium containing BF (group A) and 33 samples without BF (group B) were collected and analyzed. The DNA concentration and β-thalassemia detection rates were evaluated.ResultsThe HBB mutation analysis results of 34 samples were concordant with the biopsy results (34/59, 57.6%). In group A, the HBB mutation analysis results of 19 of 26 samples (73.1%) were concordant with the biopsy results. The concordance rate in group A was higher than that in group B (15/33, 45.5%; P < 0.05). The haplotyping results of 38 samples were concordant with the biopsy results (38/59, 64.4%). The concordance rate in group B was 17/33 (51.5%), which was significantly lower than that in group A (21/26, 80.8%) (P < 0.05). In group A, the mean DNA concentration of samples with <10% fragmentation was 107.3 ± 70.1 ng/μL, which was lower than that of samples with ≥10% fragmentation (194.6 ± 28.0 ng/μL) (P < 0.05). However, the detection rates of <10% and ≥10% fragmentation were not significantly different (P > 0.05).ConclusionThe β-thalassemia detection rate with non-invasive PGT using the spent culture medium containing BF was higher than that using the spent culture medium alone. Fragmentation is associated with DNA concentration in the spent culture medium containing BF.
| S-EPMC8810495 | biostudies-literature
Project description:Bovine embryos are typically cultured at reduced oxygen tension to lower the impact of oxidative stress on embryo development. However, oocyte in vitro maturation (IVM) is performed at atmospheric oxygen tension since low oxygen during maturation has a negative impact on oocyte developmental competence. Lycopene, a carotenoid, acts as a powerful antioxidant and may protect the oocyte against oxidative stress during maturation at atmospheric oxygen conditions. Here, we assessed the effect of adding 0.2 μM lycopene (antioxidant), 5 μM menadione (pro-oxidant), and their combination on reactive oxygen species (ROS) generation in mature oocytes and subsequent blastocyst development, quality, and transcriptome in a bovine in vitro model. ROS fluorescent intensity in mature oocytes was significantly lower in the lycopene group, and resulting embryos showed a significantly higher blastocyst rate on day 8 and lower apoptotic cell ratio than all other groups. Transcriptomic analysis disclosed a total of 296 differentially expressed genes (Benjamin-Hochberg adjusted P < 0.05 and ≥ 1 log2 fold change) between lycopene and control groups with pathways associated with cellular function, metabolism, DNA repair, and anti-apoptosis upregulated in lycopene. Lycopene supplementation in serum-free maturation medium neutralizes excess ROS during maturation, enhances blastocyst development and quality, and modulates the transcriptomic landscape.
2022-01-06 | GSE192908 | GEO
Project description:Lycopene supplementation in serum-free maturation medium improves bovine in vitro embryo development, quality, and modulates embryonic transcriptomic profile
| PRJNA793780 | ENA