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Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [RNA-seq]

ABSTRACT: Human embryonic stem cells were converted into GATA3-expressing extraembryonic cells (GATA3+ ExE cells) when they were exposed to chemical inhibitors for ACTIVIN/NODAL (A83-01, 1uM) and FGF signaling (PD03714, 100nM). We refer here to this inhibitor-induced differentiation method as an 'AP' protocol. To understand the transcriptome dynamics during AP-induced differentiation, we performed timecourse profiling of genome-wide gene expression by RNA sequencing.

ORGANISM(S): Homo sapiens

PROVIDER: GSE175977 | GEO | 2022/06/21

REPOSITORIES: GEO

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Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [scRNA-seq]

Project description:Human embryonic stem cells were converted into GATA3-expressing extraembryonic cells (GATA3+ ExE cells) when they were exposed to chemical inhibitors for ACTIVIN/NODAL (A83-01, 1uM) and FGF signaling (PD173074, 100nM). We refer here to this inhibitor-induced differentiation method as an 'AP' protocol. To understand the transcriptional properties of the AP-induced GATA3+ ExE cells, we obtained the gene expression profile from the single cells treated with AP for 2, 3 and 4 days.

2022-06-21 | GSE196365 | GEO

Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model.

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-06-21 | GSE175980 | GEO

Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model.

Project description:Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model.

| PRJNA734488 | ENA

Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [scRNA-seq]

Project description:Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [scRNA-seq]

| PRJNA804526 | ENA

Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [RNA-seq]

Project description:Delamination of trophoblast-like syncytia from the amniotic ectodermal analogue in human primed embryonic stem cell-based differentiation model [RNA-seq]

| PRJNA734491 | ENA

AP-2β activates enhancers that define mammary hormone sensing cell identity [RNA-seq]

Project description:The Activating Protein 2β transcription factor (TFAP2B; AP-2β) is a marker for both lobular and molecular apocrine/HER2-E breast cancers, despite these tumours having very different prognoses. We show that simultaneous expression of both AP-2β and the estrogen receptor (ESR1, ER) marks well differentiated, low proliferation cells that are characteristic of luminal A lobular tumours, but loss of ER expression occurs when the tumour cells progress to molecular apocrine tumours. To discover potential explanations for this behaviour we performed chromatin immunoprecipitation sequencing (ChIP-seq) for AP-2β, AR, GATA3, FOXA1 and H3K27 acetylation in ER-negative MDA-MB-453 breast cancer cells. We find that all four transcription factors frequently bind to the same enhancers and that these enhancers are more likely to be active when AP-2β is present. Molecular apocrine genes are significantly more likely to have enhancers bound to all four transcription factors flanked by H3K27 acetylation. When AP-2β binds separately from the other factors, it binds close to the transcription start site, where it shows very high enrichment for H3K27 acetylation. AP-2 family proteins activate transcription by recruiting CITED proteins and p300/CBP. Since AR, FOXA1 and GATA3 are themselves able to recruit histone acetyl-transferases, we infer that AP-2β regulates the activity of those histone acetyl-transferases. We propose that this broad fundamental role in transcription explains the contradictory functions, both oncogenic and tumour suppressing, that have been assigned to AP-2 family members in previous studies on cancer.

2023-12-31 | GSE207472 | GEO

AP-2β activates enhancers that define mammary hormone sensing cell identity [ChIP-Seq]

2023-12-31 | GSE207230 | GEO

Temporal effects of BMP4 on mouse embryonic and extraembryonic development

Project description:The developing placenta, originated in the mouse through the extra-embryonic ectoderm (ExE), is essential for mammalian embryonic development. Yet, unbiased characterization of ExE differentiation dynamics and interaction with the embryo proper remains incomplete. Here, we develop a temporal single-cell model of mouse gastrulation that maps continuous and parallel differentiation in embryonic and extraembryonic lineages. This is matched with a 3-way perturbation approach to target signaling from the embryo proper, the ExE alone, or both. We show that ExE specification involves early spatial and transcriptional bifurcation of uncommitted ectoplacental cone cells (EPCs) and chorion progenitors. Early BMP4 signaling from chorion progenitors is required for proper differentiation of uncommitted EPCs and later for their specification towards trophoblast giant cells. We also find bi-phasic regulation by BMP4 in the embryo. The early ExE-originating BMP4 signal is necessary for proper endo-mesoderm bifurcation, allantois, and primordial germ cells (PGCs) specification. However, commencing at E7.5, embryonic-derived BMP4 source restricts PGC pool size by favoring differentiation of their extraembryonic mesoderm precursors towards an allantois fate. ExE and embryonic tissues are therefore entangled in time, space, and signaling axes, highlighting the importance of their integrated understanding and modeling in vivo and in vitro.

2024-05-21 | GSE267870 | GEO

The¬¬¬ androgen receptor interacts with GATA3 to transcriptionally regulate a luminal epithelial cell phenotype in breast cancer

Project description:Background: The androgen receptor (AR) is a tumor suppressor in estrogen receptor (ER) positive breast cancer, a role sustained in some ER negative breast cancers. Key factors dictating AR genomic activity in a breast context are largely unknown. Herein, we employed an unbiased chromatin immunoprecipitation-based proteomic technique to identify endogenous AR interacting co-regulatory proteins in ER positive and negative models of breast cancer to gain new insight into mechanisms of AR signaling in this disease. Results: The DNA-binding factor GATA3 is identified and validated as a novel AR interacting protein in breast cancer cells irrespective of ER status. AR activation by the natural ligand 5α-dihydrotestosterone (DHT) increases nuclear AR-GATA3 interactions, resulting in AR-dependent enrichment of GATA3 chromatin binding at a sub-set of genomic loci. Silencing GATA3 reduces but does not prevent AR DNA binding and transactivation of genes associated with AR/GATA3 co-occupied loci, indicating a co-regulatory role for GATA3 in AR signaling. DHT-induced AR/GATA3 binding coincides with upregulation of luminal differentiation genes, including EHF and KDM4B, established master regulators of a breast epithelial cell lineage. These findings are validated in a patient-derived xenograft model of breast cancer. Interaction between AR and GATA3 is also associated with AR-mediated growth inhibition in ER positive and ER negative breast cancer.

2024-01-30 | PXD047997 | Pride

Identification of differentially expressed genes due to LBH589 treatment in aromatase inhibitor-resistant tumors

Project description:In order to validate the utility of a novel pathway algorithm (BD-Func), we test if an LBH589 signature based data from 3 cell lines (GSE36509) in an independent experiment in vivo. Xenograft tumor treatment (see Kubo et al. 2012; PMID 23160924), microarray gene expression profiling, functional analysis using BD-Func. Mouse xenograft (from MCF-7aro cell line) was treated with exemestane (EXE) or EXE + LBH589.

2014-03-10 | E-GEOD-47346 | biostudies-arrayexpress

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