Umbilical cord blood methylome analysis of IVF neonates that underwent embryo culture in G5 or HTF medium
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE189531 | GEO | 2022/05/26
REPOSITORIES: GEO
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Project description:Umbilical cord blood methylome analysis of IVF neonates that underwent embryo culture in G5 or HTF medium
| PRJNA783335 | ENA
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: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
Project description:Assisted reproductive technology (ART), especially in vitro fertilization (IVF) and embryo transfer have been widely applied in the treatment of human infertility. However, the accumulating evidences indicate that IVF is associated with low pregnancy rate, placental defect and the metabolic diseases in offspring. Here, we identify ectopic histone H3K4me3 in extraembryonic ectoderm (ExE) as an important reason for embryo implantation failure and extra-embryonic development abnormalities of IVF embryos. IVF manipulation notably disrupt extra-embryonic tissue-specific gene expression, 334 epiblast (Epi)-specific genes and 24 Epi-specific transcription factors were abnormally expressed in ExE of IVF embryos at embryonic day 7.5 (E7.5). Combined histone modification analysis reveal that ectopic H3K4me3 modification at the Epi-active promoter resulted in increased expression of these genes in ExE of IVF embryos at E7.5. By konckdown the expression of H3K4me3 recruited regulator Kmt2e, which highly expressed in IVF embryos, can improve the development of IVF embryo and reduce the abnormal gene expression in ExE. Therefore, our research identifies the abnormal H3K4me3 modification occupied in extra-embryonic tissue may be an important reason for implantation failure and abnormal placental development of IVF embryo.
2022-05-26 | GSE168269 | GEO
Project description:Assisted reproductive technology (ART), especially in vitro fertilization (IVF) and embryo transfer have been widely applied in the treatment of human infertility. However, the accumulating evidences indicate that IVF is associated with low pregnancy rate, placental defect and the metabolic diseases in offspring. Here, we identify ectopic histone H3K4me3 in extraembryonic ectoderm (ExE) as an important reason for embryo implantation failure and extra-embryonic development abnormalities of IVF embryos. IVF manipulation notably disrupt extra-embryonic tissue-specific gene expression, 334 epiblast (Epi)-specific genes and 24 Epi-specific transcription factors were abnormally expressed in ExE of IVF embryos at embryonic day 7.5 (E7.5). Combined histone modification analysis reveal that ectopic H3K4me3 modification at the Epi-active promoter resulted in increased expression of these genes in ExE of IVF embryos at E7.5. By konckdown the expression of H3K4me3 recruited regulator Kmt2e, which highly expressed in IVF embryos, can improve the development of IVF embryo and reduce the abnormal gene expression in ExE. Therefore, our research identifies the abnormal H3K4me3 modification occupied in extra-embryonic tissue may be an important reason for implantation failure and abnormal placental development of IVF embryo.
2022-05-26 | GSE168273 | GEO
Project description:Assisted reproductive technology (ART), especially in vitro fertilization (IVF) and embryo transfer have been widely applied in the treatment of human infertility. However, the accumulating evidences indicate that IVF is associated with low pregnancy rate, placental defect and the metabolic diseases in offspring. Here, we identify ectopic histone H3K4me3 in extraembryonic ectoderm (ExE) as an important reason for embryo implantation failure and extra-embryonic development abnormalities of IVF embryos. IVF manipulation notably disrupt extra-embryonic tissue-specific gene expression, 334 epiblast (Epi)-specific genes and 24 Epi-specific transcription factors were abnormally expressed in ExE of IVF embryos at embryonic day 7.5 (E7.5). Combined histone modification analysis reveal that ectopic H3K4me3 modification at the Epi-active promoter resulted in increased expression of these genes in ExE of IVF embryos at E7.5. By konckdown the expression of H3K4me3 recruited regulator Kmt2e, which highly expressed in IVF embryos, can improve the development of IVF embryo and reduce the abnormal gene expression in ExE. Therefore, our research identifies the abnormal H3K4me3 modification occupied in extra-embryonic tissue may be an important reason for implantation failure and abnormal placental development of IVF embryo.
2022-05-26 | GSE168272 | GEO
Project description:Telomere dysfunctional CMP/GMP have deregulated pathways that are associated with DNA damage signaling We compared differentially expressed genes in the G4/G5 CMP relative to the G0 control to identify pathways that may affect CMP differentiation. Bone marrow CMP and GMP cells were sorted from two paired pools of G0 TERTER/+ or G4/G5 TERTER/ER mice (5,000-20,000 cells per sample) using the Influx Cell Sorter. Every paired pool includes CMP or GMP sorted from 4 age and gender matched G0 or G4/G5 mice. RNA from the respective sorted cells was extracted using Trizol (Ambion) and profiled on 2100 Bioanalyzer (Agilent). Gene expression profiling was performed at the Sequencing and Non-coding RNA Program at MD Anderson Cancer Center. Briefly, the GeneChip® 3 IVT Express Kit (Affymetrix) was used to generate biotin-labeled cRNA, which were purified and fragmented, before target hybridization on the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix) according to the manufacturer's instructions. Affymetrix raw data (CEL files) were normalized using Affymetrix Microarray Suite (MAS) version 5.0 using a TGT=100. Paired pools used in the study were: CMP pool 1: G0-1 and G4/5-1 CMP pool 2: G0-2 and G4/G5-2 GMP pool 1: G0-1 and G4/G5-1 GMP pool 2: G0-2 and G4/G5-2
2015-04-09 | E-GEOD-62278 | 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:The regulation of necrotic death and its relevance in anti-cancer therapy are largely unknown. Here we have investigated the pro-apoptotic and pro-necrotic activities of two ubiquitin-proteasome system inhibitors (UPSIs): bortezomib and G5. The present study points out that the glioblastoma cell lines U87MG and T98G are useful models to study the susceptibility to apoptosis and necrosis in response to UPSIs. U87MG cells are resistant to apoptosis induced by bortezomib and G5 but susceptible to necrosis induced by G5. On the opposite T98G cells are susceptible to apoptosis induced by both inhibitors but show some resistance to G5-induced necrosis. By comparing the transcriptional profiles of the two cell lines, we have found that the resistance to G5-induced necrosis could arise from differences in glutathione synthesis/utilization and in the microenvironment. In particular collagen IV, which is highly expressed in T98G cells, and fibronectin, whose adhesive function is counteracted by tenascin-C in U87MG cells, can restrain the necrotic response to G5. Collectively, our results provide an initial characterization of the molecular signals governing cell death by necrosis in glioblastoma cell lines. Keywords: cell line comparison
2009-10-13 | GSE14889 | GEO
Project description:Implantation is crucial for placental development which directly impacts fetal growth and pregnancy success with possible consequences on post-natal health. We postulated that early perturbations of the conceptus-maternal environment communication may alter the endometrium physiology that could account for the final reproductive outcome. Using cattle as an animal model, we compared gene expression profiles of the endometrial caruncular and intercaruncular areas during the critical period of implantation in three types of pregnancies: artificial insemination (AI), in vitro fertilization with embryo transfer (IVF-ET) or somatic cell nuclear transfer (SCNT). Less than 35% of the differentially expressed genes were found to be common between AI, IVF-ET, and SCNT conditions. Compared to AI, numerous biological functions and several canonical pathways and genes were found to be significantly affected in IVF-ET or SCNT, with a major impact on metabolism and immune function in SCNT. Our data show that the endometrium can fine-tune its physiology and could be considered as a biological sensor in response to pregnancy manipulations. Determining the limits of the endometrial plasticity should bring new insights on the contribution of the maternal compartment to the pregnancy outlet. Keywords: Fluorescence Microarray - Dye switch loop design
2009-11-01 | GSE14050 | GEO