Comparison of the transcriptome of day 3 human embryo with that of the trophectoderm
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE33025 | GEO | 2012/07/09
SECONDARY ACCESSION(S): PRJNA148011
REPOSITORIES: GEO
Similar Datasets
Project description:In humans, the embryonic genome activation (EGA) program is functional by day 3 after fertilization. The 6-8 cell stage embryo (day 3 post-fertilization) starts the process of “compaction” that leads to the generation of the tightly organized cell mass of the morula and is followed by differentiation of the morula into a blastocyst. The transition from day 3 embryos to day 5 blastocysts is likely to be controlled by many and specific changes in the expression of different genes. We used mRNA amplification technique and compared the transcriptomes of day 3 human embryos and trophectoderm (TE) cells from day 5 human blastocysts to identify transcripts that are differentially expressed during the embryo-to-TE transition and involved in the TE specification. These six embryo samples were compared to our five human trophectoderm samples that are available in GEO under the following accession numbers: GSM706168 GSM706169 GSM706170 GSM706171 GSM706172
2012-07-08 | E-GEOD-33025 | biostudies-arrayexpress
Project description:Early embryo development is a dynamic process involving important molecular and structural changes leading to the embryonic genome activation (EGA) and first cell lineage differentiation. Our aim was to elucidate proteomic changes in bovine embryos developed in vivo. Eleven Holstein females were used as embryo donors and pools of embryos at the 4-6 cell, 8-12 cell, morula, compact morula and blastocyst stages were analyzed by nanoliquid chromatography coupled with tandem MS (nanoLC-MS/MS). A total of 2757 proteins were identified, of which 1950 were quantitatively analyzed. Principal component analysis of data showed a separation of embryo pools according to their developmental stage. Differentially abundant proteins (DAPs) between stages were clustered into 626 upregulated and 400 downregulated proteins with most significant changes at the time of EGA and blastocyst formation. The main pathways and processes overrepresented among upregulated proteins were RNA metabolism, protein translation and ribosome biogenesis whereas Golgi vesicle transport and protein processing in endoplasmic reticulum were overrepresented among downregulated proteins. This is the first comprehensive study of proteome dynamics in non-rodent mammalian embryos developed in vivo. These data provide a number of functional protein candidates and will be useful to evaluate the impact of in vitro conditions on embryo quality.
2022-05-20 | PXD030994 | Pride
Project description:Mammalian preimplantation development involves highly conserved genetic programs across species. However, temporal differences in gene network activation and membership differences in gene modules are also observed. In this study, we focus on understanding the activation of crucial gene networks in trophoectoderm (TE) and inner cell mass across species using human, monkey, and mouse models. By single cell RNA sequencing analysis in cynomolgus monkey early embryos, we find relatively late major embryonic genome activation occurring at early morula stages. Gene network preservation analysis reveals that genetic programs in monkey embryos more closely resemble human embryos compared to mouse, supporting the notion that preimplantation development in primate species are divergent from rodent species. For example, primate blastocysts show differential expression of ICM and TE genes such as X and Y, whereas mouse show differences in A and B expression. Interestingly, the overall conservation of TE gene networks is higher than ICM across three species, suggesting a more conserved developmental program in TE lineage differentiation. Additionally, TE-specific gene networks are exclusively activated at the blastocyst stage with low or no expression in morula or earlier embryos. In contrast, a majority of ICM-specific genes are strongly activated during the first major wave of EGA, which are further fine-tuned during late morula and blastocyst stages. Taken together, our study provides new insight into mammalian preimplantation development and sequential activation of lineage-specific genetic programs of TE versus ICM.
2022-06-30 | GSE75764 | GEO
Project description:Background: The transcriptional changes around the time of embryonic genome activation in pre-implantation embryos indicate that this process is highly dynamic. In vitro produced porcine blastocysts are known to be less competent than in vivo developed blastocysts. To understand the conditions that compromise developmental competence of in vitro embryos, it is crucial to evaluate the transcriptional profile of porcine embryos during pre-implantation stages. In this study, we investigated the transcriptome dynamics in in vivo developed and in vitro produced 4-cell embryos, morulae and hatched blastocysts. Results: In vivo developed and in vitro produced embryos displayed largely similar transcriptome profiles during development. Enriched canonical pathways from the 4-cell to the morula transition that were shared between in vivo developed and in vitro produced embryos included oxidative phosphorylation and EIF2 signaling. The shared canonical pathways from the morula to the hatched blastocyst transition were 14-3-3-mediated signaling, xenobiotic metabolism general signaling pathway, and NRF2-mediated oxidative stress response. The in vivo developed and in vitro produced hatched blastocysts were compared to identify molecular signaling pathways indicative of lower developmental competence of in vitro produced hatched blastocysts. A higher metabolic rate and expression of the arginine transporter SLC7A1 were found in in vitro produced hatched blastocysts. Conclusions: Our findings suggest that embryos with compromised developmental potential are arrested at an early stage of development, while embryos developing to the hatched blastocyst stage display largely similar transcriptome profiles, irrespective of the embryo source. The hatched blastocysts derived from the in vitro fertilization-pipeline showed an enrichment in molecular signaling pathways associated with lower developmental competence, compared to the in vivo developed embryos.
2021-01-30 | GSE155043 | GEO
Project description:Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations.
2010-09-28 | GSE22864 | GEO
Project description:Following fertilization, the new embryo reprograms parental genomes to begin transcription (embryonic genome activation, EGA). EGA is indispensable for development, but its dynamics, profile or when it initiates in vertebrates are unknown. We here characterize the onset of transcription in mouse one-cell embryos. Precise embryo staging eliminated noise to reveal a cascading program of de novo transcription initiating within six hours of fertilization. This immediate EGA (iEGA) utilized canonical promoters, produced spliced transcripts, was distinctive and predominantly driven by the maternal genome. Expression represented pathways not only associated with embryo development but with cancer. In human one-cell embryos, hundreds of genes were up-regulated, days earlier than thought, with conservation to mouse iEGA. These findings provide a functional basis for epigenetic analysis in early-stage embryos and illuminate networks governing totipotency and other cell-fate transitions.
2021-12-22 | GSE157834 | GEO
Project description:Selection of high-quality embryos is important to achieve successful pregnancy in assisted reproductive technology (ART). Recently, it has been debated whether RNA-sequencing (RNA-seq) should be applied to ART to predict embryo quality. However, the information on which genes can serve as markers for pregnant expectancy is limited. Furthermore, there is no information on which transcriptome of trophectoderm (TE) or inner cell mass (ICM) is more highly correlated with pregnant expectancy. Here we performed RNA-seq analysis for TE and ICM, respectively, in human blastocysts of which the expectation of pregnancy was retrospectively determined by the clinical outcomes of 1,890 cases of frozen-thawed blastocyst transfer. We identified dozens of genes that were correlated with the expected pregnancy rate in ICM and TE, respectively, with a larger number of genes identified in TE. Importantly, downregulated genes in TE of blastocysts classified as having lower expectation of pregnancy included tight junction-related genes, such as CXADR, CLDN10, and ATP1B1, which were implicated in peri-implantation development. Additionally, we showed that aneuploidy estimation by RNA-seq datasets does not correlate with pregnancy expectation. Our study thus provide an expanded list of candidate genes for prediction of pregnancy in human blastocyst embryos.
2022-09-30 | GSE205171 | GEO
Project description:We collected over 8000 mouse embryos of each developmental stage (zygote, 2-cell, 4-cell, 8-cell, morula, blastocyst) and performed tandem mass tag (TMT)-based quantitative mass spectrometry and identified nearly 5000 proteins for each stage. In-depth analysis indicates that protein expression profiles of zygote, morula and blastocyst show apparent difference from 2- to 8-cell embryos due to the maternal-totipotent-differentiation transition. We further identified novel factors and proved that they play important roles in determining pre-implantation embryo development
2015-12-10 | MSV000079417 | MassIVE
Project description:Aneuploidy has been well documented in blastocyst embryos, but prior studies have been limited in scale and/or lack mechanistic data. We previously reported preclinical validation of microarray 24-chromosome preimplantation genetic screening (PGS) in a 24-hour protocol. The method diagnoses chromosome copy number, structural chromosome aberrations, parental source of aneuploidy, and distinguishes certain meiotic from mitotic errors. In this study our objective was to examine aneuploidy in human blastocysts and determine correspondence of karyotypes between trophectoderm (TE) and inner cell mass (ICM). We disaggregated 51 blastocysts from seventeen couples into ICM and one or two TE fractions. The average maternal age was 31. Next, we ran 24-chromosome microarray molecular karyotyping on all of the samples, and then performed a retrospective analysis of the data. The average per-chromosome confidence was 99.95%. Approximately 80% of blastocysts were euploid. The majority of aneuploid embryos were simple aneuploid, i.e., one or two whole-chromosome imbalances. Structural chromosome aberrations, which are common in cleavage stage embryos, occurred in only three blastocysts (5.8%). All TE biopsies derived from the same embryos were concordant. Forty-nine of fifty-one (96.1%) inner cell mass (ICM) samples were concordant with TE biopsies derived from the same embryos. Discordance between TE and ICM occurred only in the two embryos with structural chromosome aberration. We conclude that trophectoderm karyotype is an excellent predictor of inner cell mass karyotype. Discordance between TE and ICM occurred only in embryos with structural chromosome aberrations. We thawed all fractions at 22°C, and then added Arcturus PicoPure Lysis Buffer (Molecular Devices, Sunnyvale, CA) to each of the biopsies. The tubes were incubated at 56°C for one hour, and then heat inactivated at 95°C for 10 minutes. DNA from the lysed biospsies was amplified using a commercial kit (GE Healthcare, Waukesha, WI) for multiple displacement amplification (MDA). MDA reactions were incubated at 30°C for 2.5 hours and then heat-inactivated at 65°C for five minutes. The amplified samples were genotyped using Illumina (San Diego, CA, USA) Infinium II genotyping microarrays (CytoSNP-12 chips) using a modified 24-hour protocol, as described previously*. Previously, we developed a genotyping microarray molecular karyotyping technology that uses parental genetic data to increase accuracy and determine mechanism and source of aneuploidy*. The algorithm uses parental genotypes and the observed distribution of unprocessed single cell microarray channel intensities to diagnose whole-chromosome imbalances and structural chromosome aberrations*. Because parental genotypes are available, the algorithm readily identifies parental source of whole-chromosome imbalances and structural chromosome aberrations. Additionally, the algorithm uses parental information, high confidence disomic single cell measurements on children, and recombination probabilities (genome.ucsc.edu) to determine the phase of the parental chromosomes. The phased data is then used to determine whether certain trisomies and uniparental disomies were mitotic or meiotic in origin*. *Johnson DS, Gemelos G, Baner J, Ryan A, Cinnioglu C, Banjevic M, Ross R, Alper M, Barrett B, Frederick J, Potter D, Behr B, Rabinowitz M. (2010). Preclinical validation of a microarray method for full molecular karyotyping of blastomeres in a 24-hour protocol. Human Reproduction January 24 [Epub ahead of print].
2010-09-28 | E-GEOD-22864 | biostudies-arrayexpress
Project description:Background: In vitro culture of preimplantation mouse embryos is associated with changes in gene expression. It is however not known if the method of fertilization affects the global pattern of gene expression. Method: We compared gene expression and development of mouse blastocysts produced by intra-cytoplasmic sperm injection and cultured in Whitten’s medium (ICSIWM) or KSOM medium with amino acids (ICSIKSOMaa) with control blastocysts flushed out of the uterus on post coital day 3.5 (In vivo). Global pattern of gene expression was assessed using the Affymetrix 430 2.0 chip. In addition we compared gene expression in embryos generated in IVF or ICSI using WM. Results: Blastocysts resulting from ICSI fertilization have a reduction in the number of trophoblastic and inner cell mass cells compared to in vivo generated embryos. Approximately 1000 genes are different between ICSI blastocyst and in vivo blastocysts; proliferation, apoptosis and morphogenetic pathways are the most common pathways altered after in vitro culture. Unexpectedly, only 41 genes were statistically different between embryo cultured in suboptimal conditions (WM) or optimal conditions (KSOMaa). Conclusion: The method of fertilization plays a more important role in shaping the transcriptome of the developing mouse embryo than the culture media used.
2010-11-10 | GSE23009 | GEO