Single Cell Multi-Omics of Human Preimplantation Embryos Demonstrates Susceptibility to Excess Glucocorticoid Exposure
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Homo sapiens
SUBMITTER: Cheng Zhao
PROVIDER: E-MTAB-10096 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We then utilized parallel single-cell RNA sequencing and bisulfite sequencing to explore the impact of GC exposure on the human embryo. In addition, to further explore the role of epigenetic regulation as a mechanism for the observed transcriptional changes, we examined the effects of GCs on small non-coding RNA using smallseq.
2022-08-02 | E-MTAB-10098 | biostudies-arrayexpress
Project description:We then utilized parallel single-cell RNA sequencing and bisulfite sequencing to explore the impact of GC exposure on the human embryo. In addition, to further explore the role of epigenetic regulation as a mechanism for the observed transcriptional changes, we examined the effects of GCs on small non-coding RNA using smallseq.
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2016-04-06 | E-MTAB-3929 | biostudies-arrayexpress
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2011-12-16 | E-MEXP-3111 | biostudies-arrayexpress
Project description:Mitochondrial DNA (mtDNA) quantitative and qualitative defects have been associated with impaired human embryonic development, but the underlying mechanisms remain unknown. By using human embryos affected by mitochondrial disorders as models of mitochondrial dysfunction, we compared gene expression between 9 mitochondrial embryos (carriers of a pathogenic variant in a mtDNA or a nuclear gene coding for a mitochondrial protein) to 33 controls. Transcriptomic analyses performed by RNA-Sequencing revealed a similar global transcriptional repression in mitochondrial embryos affecting a significant proportion of differentiation factors and nuclear genes encoding mitochondrial proteins. If oxidative phosphorylation was at the top of the most significant deregulated pathways, cell survival and autophagy were found to be significantly decreased in these embryos, questioning their viability. Differentially expressed genes identified in this study represent good predictive biomarkers of mitochondrial dysfunction and should be tested as markers of preimplantation development.
2023-02-27 | E-MTAB-11531 | biostudies-arrayexpress
Project description:40-PE Smart-Seq of RNA isolated from single 2-cell embryos, single morulae, single blastocysts, single E7 embryos epiblast halves and single E7 trophectoderm halves. For all preimplantation stages, embryos were grown ex-vivo from three experimental groups of zygotes: zygotes injected with the mRNA of a recombinant OGA (named BtGH84) (Btgh_injected), zygotes injected with a catalytically dead version of BtGH84 (dBtgh_injected) (control nr.1) and non-injected zygotes (non_injected) (control nr.2). Postimplantation E7 embryos were grown from two experimental group of zygotes: Btgh-injected and dBtgh-injected (control) and transferred at the 2-cell stage to foster mothers. All samples from the same embryonic stage were processed for single embryo (or single-embryo single-tissue) Smart-Seq library preparation at the same time and then sequenced in the same NextSeq500 run. The different embryonic stages were processed on different days and sequenced in different NextSeq500 runs.
2024-03-30 | E-MTAB-12981 | biostudies-arrayexpress
Project description:In total, 240 single blastomeres from nine top-quality day-4 embryos frozen at day 3 of development and four fresh top-quality day-4 embryos that had one-cell biopsy on day 3 for preimplantation genetic diagnosis (PGD) were collected. Blastomeres' DNA was amplified using SurePlex DNA Amplification System (BlueGnome, Cambridge, UK) . Array-CGH was carried out using 24Sure Cytochip microarrays following the standard protocol (BlueGnome, www.cytochip.com). BAC array-CGH on single blastomeres amplified by SurePlex amplification Kit.
2013-04-05 | E-GEOD-39518 | biostudies-arrayexpress
Project description:Early development in humans is characterised by low and variable embryonic viability, reflected in low fecundity and high rates of miscarriage, relative to other mammals. Data from assisted reproduction programmes provides additional evidence that this is largely mediated at the level of embryonic competence and is highly heterogeneous among embryos. Understanding the basis of this heterogeneity has important implications in a number of areas including: the regulation of early human development, disorders of pregnancy, assisted reproduction programmes, the long term health of children which may be programmed in early development, and the molecular basis of pluripotency in human stem cell populations. We have therefore investigated global gene expression profiles using polyAPCR amplification and microarray technology applied to individual human oocytes and 4-cell and blastocyst stage embryos. In order to explore the basis of any variability in detail, each developmental stage is replicated in triplicate. Our data show that although transcript profiles are highly stage-specific, within each stage they are relatively variable.
2013-12-13 | E-MEXP-3870 | biostudies-arrayexpress
Project description:Study question: Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media? Summary answer: A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these were quantifiable. What is known already: There are no data in the literature on what non-declared proteins are present in un-conditioned (fresh media in which no embryos have been cultured) commercial embryo media. Study design, size, duration: The following eight commercial embryo culture media were included in this study: G-1 PLUS and G-2 PLUS G5 Series from Vitrolife, Sydney IVF Cleavage Medium and Sydney IVF Blastocyst Medium from Cook Medical and EmbryoAssist, BlastAssist, Sequential Cleav and Sequential Blast from ORIGIO. Two batches were analysed for each of the Sydney IVF media and one batch from each of the other media. All embryo culture media are supplemented by the manufacturers with purified human serum albumin (HSA 5 mg/ml). The purified HSA (HSA-solution from Vitrolife) and the recombinant human albumin supplement (G-MM from Vitrolife) were also analysed. Participants/materials, setting, methods: For protein quantification, media samples were in-solution digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For in-depth protein identification, media were albumin depleted, dialyzed and concentrated before sodium dodecyl sulphate polyacrylamide gel electrophoresis. The gel was cut into 14 slices followed by in-gel trypsin digestion, and analysis by LC-MS/MS. Proteins were further investigated using gene ontology (GO) terms analysis. Main results and the role of chance: Using advanced mass spectrometry and high confidence criteria for accepting proteins (p< 0.01), a total of 110 proteins other than HSA were identified. The average serum albumin content was found to be 94% (92% - 97%) of total protein. Other individual proteins accounted for up to 4.7% of the total protein. Analysis of purified HSA strongly suggests that these non-declared proteins are introduced to the media when the albumin is added. GO analysis showed that many of these proteins have roles in defence pathways, for example 18 were associated with the innate immune response and 17 with inflammatory responses. Eight proteins have been reported previously as secreted embryo proteins. Limitations, reasons for caution: For six of the commercial embryo culture media only one batch was analyzed. However, this does not affect the overall conclusions. Wider implications of the findings: The results showed that the HSA added to IVF media contained many other proteins and that the amount varies from batch to batch. These variations in protein profiles are problematic when attempting to identify proteins derived from the embryos. Therefore, when studying the embryo secretome and analysing conditioned media with the aim of finding potential biomarkers that can distinguish normal and abnormal embryo development, it is important that the medium used in the experimental and control groups is from the same batch. Furthermore, the proteins present in un-conditioned media could potentially influence embryonic development, gestation age, birthweight and perhaps have subsequent effects on health of the offspring.
2014-09-01 | PXD001174 | Pride
Project description:Study question: Is gene expression in human preimplantation embryos affected by medium used for culturing embryos during an IVF treatment? Summary answer: Six days of in vitro culture of human preimplantation embryos resulted in a medium-dependent expression level of genes involved in apoptosis, protein degradation, metabolism and cell cycle regulation. What is known already: Several human studies have shown an effect of culture medium on embryo development, pregnancy outcome and birthweight. However, the underlying mechanisms in human embryos are still unknown. In animal blastocysts, it has been demonstrated that culture of preimplantation embryos affects gene expression. In humans, it has been found that culture medium affects gene expression of cryopreserved embryos that, after thawing, were cultured in two different media for 2 more days. Study design, size, duration: In a multicenter trial, women were randomly assigned to two culture media groups (G5 and HTF). Data on embryonic development were collected for all embryos. In one center, embryos originating from 2PN zygotes that were not selected for transfer or cryopreservation on day 2 or 3, were further cultured until day 6 and collected for this study, if couples consented. Participants/materials, setting, methods: Ten blastocysts from each study group, matched for fertilization method, maternal age and blastocyst quality, were selected and their mRNA was isolated and amplified. Embryos were individually examined for genome-wide gene expression using Agilent microarrays and PathVisio was used to identify the pathways that showed a culture medium-dependent activity. Main results and the role of chance: Expression of 951 genes differed significantly (P < 0.01) between the two study groups. Eighteen pathways, involved in apoptosis, metabolism, protein processing and cell cycle regulation, showed a significant overrepresentation of differentially expressed genes (DEGs). The DNA replication, G1 to S cell cycle control and oxidative phosphorylation pathways were upregulated in the G5 group compared with the HTF group. This is in agreement with the higher number of cells seen in G5 embryos on day 2 and 3. Limitations, reasons for caution: Despite careful matching of the embryos, it cannot be ruled out that differences observed between the study groups are affected by factors not investigated. Extrapolation of these results to embryos used for transfer demands caution as in the present study embryos that were not selected for either embryo transfer or cryopreservation have been used for the culture experiment until day 6. Wider implications of the findings: This study shows that gene expression in human preimplantation embryos is affected by the culture medium used during an IVF treatment. Furthermore, it provides insight into the biological mechanisms that are affected. The increased cell cycle regulation is reflected by a higher number of blastomeres. Whether these results are also connected to long-term effects remains unknown. However, it is not unlikely that early adaptations of the preimplantation embryo to its environment persist during fetal and post-natal development. Note: this study has been conducted using the Agilent-028004 SurePrint G3 Human GE 4x180K Microarray. This array contains the same reporters as the Agilent-028004 SurePrint G3 Human GE 8x60K Microarray. As such we have linked this entry to the A-GEOD-14550 array design, belonging to the latter.
2015-07-08 | E-MTAB-3405 | biostudies-arrayexpress