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Comparative whole-transcriptomic analysis between normal and AKAP-Lbc-depleted human embryonic stem cells

ABSTRACT: Human embryonic stem cells (hESCs) have the unique property of immortality, ability to infinitely self-renew and survive in vitro. In contrast to tumor-deribed cells, their immortality are free from any genomic abberations. Instead, they depend on the AKAP-Lbc/Rho signaling cascade. To understand the downstream way, we performed RNA-seq analyses between normal and AKAP-Lbc-depleted hESCs using the doxycyclin-inducible gene silensing strategy.

ORGANISM(S): Homo sapiens

PROVIDER: GSE67128 | GEO | 2015/08/27

SECONDARY ACCESSION(S): PRJNA279024

REPOSITORIES: GEO

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Comparative whole-transcriptomic analysis between normal and AKAP-Lbc-depleted human embryonic stem cells

Project description:Human embryonic stem cells (hESCs) have the unique property of immortality, ability to infinitely self-renew and survive in vitro. In contrast to tumor-deribed cells, their immortality are free from any genomic abberations. Instead, they depend on the AKAP-Lbc/Rho signaling cascade. To understand the downstream way, we performed RNA-seq analyses between normal and AKAP-Lbc-depleted hESCs using the doxycyclin-inducible gene silensing strategy. We use the genetically modified hESCs in which AKAP-13-targeting shRNA is induced by doxycyclin(dox) treatment. To minimize cell loss during treatment, anti-apoptotic factor Bcl-XL is overexpressed. We collected RNA from dox-treated and untreated cells in biological triplicate. We measured gene expression in these 2 sample groups using RNA-seq (illumina HiSeq) .

2015-08-27 | E-GEOD-67128 | biostudies-arrayexpress

RNA expression in BRCA2-depleted breast cancer cell lines

Project description:Next generation RNA sequencing was performed to analyze changes in gene expression upon BRCA2 depletion. BRCA2 depletion was introduced in two human breast cancer cell lines with doxycyclin inducible short hairpin RNAs.

2018-12-19 | GSE116943 | GEO

Gene expression profiles of PDX models with acquired resistance to endocrine treatments

2014-07-09 | GSE55561 | GEO

Expression data from retinoic acid-induced differentiation of human embryonic stem cells (hESCs)

Project description:Human embryonic stem cells (hESCs) display a unique ability to self-renew in culture while retaining the potential to form the full repertoire of cell types found in the body. A complex molecular network underlies the maintenance of this pluripotent state. We used microarrays to identify genes that are highly expressed in pluripotent hESCs, but are consequently down-regulated upon differentiation in the presence of retinoic acid.

2017-09-27 | GSE104173 | GEO

The functional role of OGDH for maintaining mitochondrial respiration and identity of primed human embryonic stem cells

Project description:Human embryonic stem cells (hESCs) can self-renew infinitely or differentiate into the 3 germ layer lineages in vitro with certain cues, holding great promise to model early human embryo development ex vivo. It is wildly accepted that hESCs take advantage of both glycolysis and mitochondrial respiration to favor the naïve pluripotency, while prefer glycolysis to support the primed pluripotency. Thus, the function of mitochondrial respiration in primed hESCs has been underestimated for a long time, and has not been fully understood yet. Herein, we report that the adenosine triphosphate (ATP) production rate is comparable between mitochondrial respiration and glycolysis, suggesting that mitoATP may serve as one of the major sources of the ATP pool in primed hESCs. To further reveal the function of mitochondrial respiration, we deployed inducible CRISPRi method to inhibit OGDH expression with high efficiency, resulting in the TCA cycle blockade as well as the diminishment of mitochondrial respiration activity and total ATP level. Of note, OGDH deficiency led to the exit of primed pluripotency accompanied by cell death. Furthermore, the treatment with small molecule inhibitors to block electron transport chain (ETC) can phenocopy the loss-of-function of OGDH in hESCs. Therefore, genetic and pharmacological perturbations on mitochondrial respiration can impair the stemness of primed hESCs. Collectively, the current study unveils that OGDH acts as a key regulator to fine-tune the abundance of TCA cycle metabolites to ensure the mitochondrial respiration activity in primed hESCs, and highlights the pivotal roles of mitochondrial respiration in terms of ATP production and the maintenance of primed pluripotency. Our findings may provide insights into the linkage between pluripotent states and energy metabolism in hESCs.

2022-03-03 | MTBLS4223 | MetaboLights

IGF1R controls mechanosignaling in myofibroblasts required for pulmonary alveologenesis.

Project description:Igf1r signaling is required in fibroblasts to drive the formation of new alveoli, and those activities is depend upon its regulation on mechanical property of myofibroblasts via an Akt/Yap mechanism.

2021-02-11 | GSE158451 | GEO

Expression data from FACS sorted cell populations of immortalized stromovascular fraction mouse cells derived from inguinal white adipose tissue, showing either high or low binding to FcsFNDC4

Project description:Soluble FNDC4 (sFNDC4) is a novel hepatokine which promotes glucose tolerance in mice and positively associates with increased glucose tolerance in humans. To identify potential receptors for sFNDC4 we screened a population of immortalized stromovascular mouse cells derived from inguinal white fat for cells, which showed high (high binding cells-HBC) or low binding (low binding cells-LBC) to recombinant FcsFNDC4. We utilised microarray to identify differentially expressed genes between HBC and LBC. After comparing the global gene expression between HBC and LBC we were able to identify several differentially expressed genes encoding for cellular receptors. Experimental validations of these results and further experimental sutdies supported that GPR116 is the receptor for sFNDC4.

2021-02-01 | GSE165329 | GEO

ChIP-Seq for ERK2/MAPK1 and ELK1 in human embryonic stem cells

Project description:The ERK/MAPK signal transduction cascade is one of the key pathways regulating proliferation and differentiation in development and disease. In human embryonic stem cells (hESCs), ERK signaling is required for their self-renewing property. Here we studied the convergence of the ERK signaling cascade at the DNA by mapping genome-wide kinase-chromatin interactions for ERK2 in hESCs. We observe that ERK2 targets genes coding for small RNAs, histones, and genes involved in cellular metabolism and cell cycle. We find that the transcription factor ELK1 is essential in hESCs and that ERK2 co-occupies promoters bound by ELK1. Strikingly, promoters bound by ELK1 without ERK2 are occupied by Polycomb group proteins that repress genes involved in lineage commitment. In summary, we propose a model where extracellular signaling-stimulated proliferation and intrinsic repression of differentiation is integrated to maintain the identity of hESCs.

2013-05-31 | E-MTAB-1565 | biostudies-arrayexpress

Transcriptional profiling by array after knockdown of ERK2 and ELK1 in human embryonic stem cells

2013-05-31 | E-MTAB-1583 | biostudies-arrayexpress

Gene expression profiles of PDX models with acquired resistance to endocrine treatments

Project description:Acquired resistance to endocrine therapy occurs with high frequency in patients with luminal breast cancer (LBC). We report here the establishment of four patient-derived xenograft models of LBC with acquired resistance in vivo to tamoxifen and estrogen deprivation. CEL files represent expresison data generated from 5 replicates (independent mice) of the following tumor models: HBCx22 (parental), HBCx22 TamR (tamoxifen-resistant), HBCx22 OvaR (ovariectomy-resistant), HBCx34 (parental), HBCx34 TamR (tamoxifen-resistant), HBCx34 OvaR (ovariectomy-resistant)

2014-07-09 | E-GEOD-55561 | biostudies-arrayexpress

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