Integrative analysis of the acquisition of pluripotency in PGCs
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE67616 | GEO | 2015/04/08
SECONDARY ACCESSION(S): PRJNA280494
REPOSITORIES: GEO
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Project description:To elucidate the molecular mechanisms by which PGCs become pluripotent cells, we performed whole transcriptome analysis during the conversion of PGCs into EGCs. There are 3 groups of gene expression profiles, time course analysis of PGCs to EGCs, forced expression of germ cell genes in ESCs, and chemical treatment of PGCs at day2 of the culture
2015-04-08 | E-GEOD-67616 | biostudies-arrayexpress
Project description:Naive pluripotent embryonic stem cells (ESCs) and embryonic germ cells (EGCs) are derived from the preimplantation epiblast and primordial germ cells (PGCs), respectively. We investigated whether differences exist between ESCs and EGCs, in view of their distinct developmental origins. PGCs are programmed to undergo global DNA demethylation; however, we find that EGCs and ESCs exhibit equivalent global DNA methylation levels. Importantly, inhibition of Erk and Gsk3b by 2i conditions leads to pronounced reduction in DNA methylation in both cell types. This is driven by Prdm14 and is associated with downregulation of Dnmt3a and Dnmt3b. However, genomic imprints are maintained in 2i, and we report derivation of EGCs with intact genomic imprints. Collectively, our findings establish that culture in 2i instills a naive pluripotent state with a distinctive epigenetic configuration that parallels molecular features observed in both the preimplantation epiblast and nascent PGCs.
2013-02-17 | GSE43398 | GEO
Project description:Naive pluripotent embryonic stem cells (ESCs) and embryonic germ cells (EGCs) are derived from the preimplantation epiblast and primordial germ cells (PGCs), respectively. We investigated whether differences exist between ESCs and EGCs, in view of their distinct developmental origins. PGCs are programmed to undergo global DNA demethylation; however, we find that EGCs and ESCs exhibit equivalent global DNA methylation levels. Importantly, inhibition of Erk and Gsk3b by 2i conditions leads to pronounced reduction in DNA methylation in both cell types. This is driven by Prdm14 and is associated with downregulation of Dnmt3a and Dnmt3b. However, genomic imprints are maintained in 2i, and we report derivation of EGCs with intact genomic imprints. Collectively, our findings establish that culture in 2i instills a naive pluripotent state with a distinctive epigenetic configuration that parallels molecular features observed in both the preimplantation epiblast and nascent PGCs. EGC lines were derived from E8.5 mouse embryos using three different protocols: FCS+LIF on MEFs (FCS, n = 4)), FCS+LIF on MEFs for 48 hours followed by 2i+LIF (2is, n = 4), and direct derivation into 2i+LIF (2i, n = 4). ESC lines were derived in either FCS+LIF on MEFs or in 2i+LIF conditions and once established the cell lines were also switched between the two culture environments (n = 5 for each culture condition). All cell lines were derived from genetically identical embryos.
2013-02-17 | E-GEOD-43398 | biostudies-arrayexpress
Project description:Primordial germ cells (PGCs) are fate restricted to differentiate into gametes in vivo. However when removed from their embryonic niche PGCs undergo reversion to generate pluripotent embryonic germ cells (EGCs) in vitro. One of the major differences between EGCs and embryonic stem cells (ESCs) involves variable methylation at imprinting control centers (ICCs), a phenomenon that is poorly understood. In the current study we show that reverting PGCs to EGCs involves ICC methylation erasure, which remain stably hypomethylated at Snrpn, Igf2r and Kcnqot1. In contrast, the H19/Igf2 ICC undergoes almost complete de novo remethylation. Using the same approach for PGCs differentiated in vitro from ESCs we show that the Snrpn ICC is erased however the hypomethylated state is highly unstable. We also discovered that when the H19/Igf2 ICC is abnormally hypermethylated in ESCs, ICC methylation is not erased with differentiation into PGCs. This highlights the importance of not only launching germline differentiation with correctly methylated ESC lines but also the need to better stabilize the hypomethylated state in the in vitro derivatives following ICC erasure.
2015-06-01 | GSE69354 | GEO
Project description:Gene-expression profile of human embryonic germ cells (EGCs), primordial germ cells (PGCs), embryonal carcinoma cells (ECCs), pluripotent embryonic stem cells (ESCs) and induced pluripotent stem cells (IPSCs)
2018-06-28 | E-MTAB-6851 | biostudies-arrayexpress
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Project description:To study the mechanisms of pluripotency induction, we compared gene expression in pluripotent embryonic germ cells (EGCs) and unipotent primordial germ cells (PGCs). We found 11 genes ≥1.5-fold overexpressed in EGCs. None of the genes identified were Yamanaka's genes, but instead related to glycolytic metabolism. The prospect of pluripotency induction by cell metabolism manipulation was investigated by hypoxic culturing. We demonstrate that hypoxia alone induces reprogramming in PGCs, giving rise to hypoxia-induced EGC-like cells (hiEGL), which differentiate into cells of the three germ layers in vitro, and contribute to the ICM in vivo, demonstrating pluripotency. The mechanism of hypoxia induction involves HIF1? stabilization and Oct4 deregulation. However, hiEGL cannot be passaged long term. Self-renewal capacity is not achieved by hypoxia likely due to lack of upregulation of c-Myc and Klf4. Gene expression analysis of hypoxia signalling suggests that hiEGLs have not reached the stabilization phase of cell reprogramming. The data suggests that the properties of stemness, pluripotency and selfrenewal, are differentially regulated in primordial germ cell reprogramming induced by hypoxia. 8.5 dpc Oct4-GFP PGCs cultured in hypoxia conditions for 6 days were isolated by FACS. To eliminate the possibility of differences due solely to anaerobic respiration, TGC-10 EGC line was exposed to the hypoxia-mimetic agent Cl2Co at 150 microM for four hours prior to RNA isolation. RNA samples to be analyzed by microarrays were prepared using Qiagen RNeasy columns with on-column DNA digestion. 300 ng of total RNA per sample was used as input into a linear amplification protocol (Tetu-Bio), which involved synthesis of T7-linked double-stranded cDNA and 12 hours of in vitro transcription incorporating biotin-labelled nucleotides. Purified and labeled cRNA was then hybridized for 18h onto MouseRef-8 v2 expression BeadChips (Illumina) following the manufacturer's instructions. After washing, chips were stained with streptavidin-Cy3 (GE Healthcare) and scanned using the iScan reader (Illumina) and accompanying software. Samples were exclusively hybridized as biological replicates. The bead intensities were mapped to gene information using BeadStudio 3.2 (Illumina). Background correction was performed using the Affymetrix Robust Multi-array Analysis (RMA) background correction model. Variance stabilization was performed using the log2 scaling and gene expression normalization was calculated with the method implemented in the lumi package of RBioconductor. Data post-processing and graphics were performed with in-house developed functions in Matlab. Hierarchical clustering of genes and samples was performed with one minus correlation metric and the unweighted average distance (UPGMA) (also known as group average) linkage method. 14 samples were analyzed EG: pluripotent Embryonic Germ Cells (EGCs), 2 replicates hiEGL1: hypoxia-induced EGC-like cells (hiEGL), 2 replicates hiEGL2: hypoxia-induced EGC-like cells (hiEGL), 2 replicates ESCm: Embryonic Stem Cells (ESCs) male, 2 replicates ESCf: Embryonic Stem Cells (ESCs) female, 2 replicates EpiT9: Epiblast Stem Cells T9, 1 replicate EpiE3: Epiblast Stem Cells E3, 1 replicate PGC11.5: unipotent Primordial Germ Cells (PGCs) from dpc 11.5 , 2 replicates
2014-09-18 | E-GEOD-61472 | biostudies-arrayexpress
Project description:Totipotent cells with bidirectional chimeric ability attracts more attention from developmental biology and regenerative medicine. Human extended pluripotent stem cells can be obtained and maintained by converting conventional embryonic stem cells using the combo of chemicals, however, the transition and culture system is based on feeder and the mechanism during the acquisition of extended pluripotency is largely unknown. Here we first showed an adapted Matrigel-based feeder-free conversion and maintenance system to generate extended pluripotent stem cells from human embryonic stem cells. We demonstrated the extended pluripotency by molecular markers, chimeric ability and transcriptome. Our data provided an epigenetic and metabolic insight into the maintenance and transition of extended pluripotency.
2020-10-02 | GSE137208 | GEO
Project description:Transcriptomes of mouse E12.5 primordial germ cells (PGCs), primordial germ cell-like cells (PGCLCs) isolated from 6-day culture embryoid bodies, and the precursor pluripotent stem cells [embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs)] and epiblast-like cells (EpiLCs) Total RNA was isolated from FACS-enriched, SSEA1+/CD61+ double-positive PGCs and PGCLCs. RNA was also isolated from ESC, iPSC, and EpiLC cultured without enrichment. Transcriptomes were determined using Affymetrix microarray.
2016-08-22 | E-GEOD-80983 | biostudies-arrayexpress
Project description:The growth factors and signaling pathways that are essential for the inducing proliferation of chicken PGCs is unclear. We investigated the effect of basic fibroblast growth factor (bFGF) on the survival and proliferation of PGCs under feeder-free conditions. We used microarrays to examine the genes regulated by bFGF treatment in chicken PGCs. Cultured PGCs were collected before and after withdrawal of bFGF for 24 h, and 24 h after bFGF replacement. The RNA was extracted and hybridized on Affymetrix microarrays. Three replicates each.
2011-02-01 | E-GEOD-22592 | biostudies-arrayexpress