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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Analysis of Liver Progenitor Cells Generated from Yap Expression [Set 2]

ABSTRACT: Hippo signaling is highly associated with activity in the stem cell compartment of many epithelial tissues. In this study, we examined if Hippo signaling inhibition (by inducing Yap expression) could convert differentiated cells into a progenitor like phenotype. Rosa26-lsl-YFP mice had recombination induced and cells were FACS sorted using YFP as a marker at either 1 week or 6 weeks after recombination. YFP expression is a surrogate for Yap expression (our protein of interest) and time was varied in vivo. RNA was immediately extracted after sorting and labeled to be hybridized to the array. FACS sorted Yap expressing liver cells were sorted one or six weeks after induction and compared to fetal liver samples as controls The control data from fetal liver samples have been previously published and is available in the GEO database as GSE12117 (GSM305568, GSM305569, GSM305570). The complete dataset representing: Yap Expressiong Liver samples and the fetal liver control Samples from Series GSE12117 (re-processed in this study), is linked below as a supplementary file.

ORGANISM(S): Mus musculus

SUBMITTER: Dean Yimlamai

PROVIDER: E-GEOD-55559 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Analysis of Liver Progenitor Cells Generated from Yap Expression [Set 1]

Project description:Hippo signaling is highly associated with activity in the stem cell compartment of many epithelial tissues. In this study, we examined if Hippo signaling inhibition (by inducing Yap expression) could convert differentiated cells into a progenitor like phenotype. Organoid cells derived from mouse livers under various conditions, wild-type, Yap ON (Plus Dox), and Yap ON then OFF (Minus Dox) was examined. Comparison between freshly isolated hepatocytes; Uninduced_YPF-#.cel against Organoids grown in wild-type conditions (WT), Yap On (in vivo) off (in vitro) - YapOrganoidDoxMinus , and Yap On continuously - YapOrganoidDoxPlus. Organoids grown in culture or YFP+ sorted liver cells after the indicated time of Yap expression were collected. These were amplified using Nugene technology and hybridized to Affymetrix MoGene1.0 st arrays.

2014-06-06 | E-GEOD-55558 | biostudies-arrayexpress

Analysis of Liver Progenitor Cells Generated from Yap Expression [Set 2]

Project description:Hippo signaling is highly associated with activity in the stem cell compartment of many epithelial tissues. In this study, we examined if Hippo signaling inhibition (by inducing Yap expression) could convert differentiated cells into a progenitor like phenotype. Rosa26-lsl-YFP mice had recombination induced and cells were FACS sorted using YFP as a marker at either 1 week or 6 weeks after recombination. YFP expression is a surrogate for Yap expression (our protein of interest) and time was varied in vivo. RNA was immediately extracted after sorting and labeled to be hybridized to the array.

2014-06-06 | GSE55559 | GEO

Gene expression data from livers of Yap+/+ and Yap+/- mice at postnatal day 30

Project description:Liver undergoes both size increase and differentiation during postnatal period, which in mice is approximately first 30 days. The mechanisms of simultaneous postnatal liver cell proliferation and maturation are not clear. In these experiments, role of yes associated protein (Yap), the downstream effector of Hippo Kinase signaling pathway was investigated. Total RNA isolated from livers of Yap+/+ and Yap+/- mice at Postnatal day 30. Pooled livers from 5 mice per genotype were used.

2012-04-04 | E-GEOD-31281 | biostudies-arrayexpress

Pi3kcb links Hippo-YAP and PI3K-AKT signaling pathways to promote cardiomyocyte proliferation and survival [microarray]

Project description:Background—YAP, the nuclear effector of Hippo signaling, regulates cellular growth and survival in multiple organs, including the heart, by interacting with TEAD sequence specific DNA-binding proteins. Recent studies showed that YAP stimulates cardiomyocyte proliferation and survival. However, the direct transcriptional targets through which YAP exerts its effects are poorly defined. Methods and Results—To identify genes directly regulated by YAP in cardiomyocytes, we combined differential gene expression analysis in YAP gain- and loss-of-function with genome-wide identification of YAP bound loci using chromatin immunoprecipitation and high throughput sequencing. This screen identified Pik3cb, encoding p110β, a catalytic subunit of phosphoinositol-3-kinase (PI3K), as a candidate YAP effector that promotes cardiomyocyte proliferation and survival. We validated YAP and TEAD occupancy of a conserved enhancer within the first intron of Pik3cb, and show that this enhancer drives YAP-dependent reporter gene expression. Yap gain- and loss-of-function studies indicated that YAP is necessary and sufficient to activate the PI3K-Akt pathway. Like Yap, Pik3cb gain-of-function stimulated cardiomyocyte proliferation, and Pik3cb knockdown dampened the YAP mitogenic activity. Reciprocally, Yap loss-of-function impaired heart function and reduced cardiomyocyte proliferation and survival, all of which were significantly rescued by AAV-mediated Pik3cb expression. Conclusion—Pik3cb is a crucial direct target of YAP, through which the YAP activates PI3K-AKT pathway and regulates cardiomyocyte proliferation and survival. Two groups were involved in this study:TNTcreYapfl_het group and TNTcreYapfl_KO group. Each group contained three biological replicates. Embryo hearts were collected at E12.5 and dissociated. Cardiomyocytes were collected by FACS. The total RNA of cardiomyocytes were isolated for microarray analysis.

2015-02-20 | E-GEOD-57718 | biostudies-arrayexpress

The effect of YAP/TAZ knockdown on the intestinal epithelium

Project description:The Hippo pathway plays a crucial in organ size control during development and tissue homeostasis in adult life. To examine a role for Hippo signaling in the intestinal epithelium, we analyzed gene expression patterns in the mouse intestinal epithelilum transfected with siRNAs or expression plasmids for shRNAs targeting the Hippo pathway effectors, YAP and TAZ. We performed two independent series of experiments (siGFP (n=3) vs siYAP/siTAZ (n=3), and shLacZ (n=1) vs shYAP/shTAZ (n=1)). Control siRNA (siGFP), YAP/TAZ siRNAs, or expression plasmids for control shRNA (shLacZ) or YAP/TAZ shRNAs were introduced into the mouse intestinal epithelium by the newly-developed in vivo transfection method. Four days after transfection, intestinal epithelial cells were isolated from the tissues and total RNA was extracted.

2014-07-18 | E-GEOD-45155 | biostudies-arrayexpress

Global microRNA expression analysis in HaCaT human keratinocytes transfected with siRNA for YAP or negative control

Project description:Global downregulation of microRNAs (miRNAs) is commonly observed in human cancers and can have a causative role in tumorigenesis. The mechanisms responsible for this phenomenon remain poorly understood. Here we show that YAP, the downstream target of the tumor-suppressive Hippo signaling pathway regulates miRNA biogenesis in a cell density-dependent manner. At low cell density, nuclear YAP binds and sequesters p72 (DDX17), a regulatory component of the miRNA processing machinery. At high cell density, Hippo-mediated cytoplasmic retention of YAP facilitates p72 association with Microprocessor and binding to a specific sequence motif in pri-miRNAs. Inactivation of the Hippo pathway or expression of constitutively active YAP causes widespread miRNA suppression in cells and tumors and a corresponding post-transcriptional induction of MYC expression. Thus, the Hippo pathway links contact-inhibition regulation to miRNA biogenesis and may be responsible for the widespread miRNA repression observed in cancer. Two conditions (siCtrl and siYAP) were analyzed in duplicate.

2014-03-03 | E-GEOD-52188 | biostudies-arrayexpress

YAP regulates cell mechanics by controlling focal adhesion assembly

Project description:Hippo effectors YAP/TAZ act as on-off mechanosensing switches by sensing modifications in extracellular matrix (ECM) composition and mechanics. The regulation of their activity has been described so far through a hierarchical model in which elements of Hippo pathway are under the control of Focal Adhesions (FAs). Here we unveiled the molecular mechanism by which cell spreading and RhoA GTPase control FA formation through YAP to stabilize the anchorage of actin cytoskeleton to cell membrane. This mechanism required YAP co-transcriptional function and involved the activation of genes encoding for integrins and FA docking proteins. Tuning YAP transcriptional activity led to the modification of cell mechanics, force development, adhesion strength, determined cell shaping, migration and differentiation. These results provide new insights into the mechanism of YAP mechanosensing activity and qualify Hippo effector as the key determinant of cell mechanics in response to ECM cues.

2017-05-17 | E-MTAB-5217 | biostudies-arrayexpress

Identification of Yap-interacting proteins in Xenopus egg extracts by co-immunoprecipitation coupled to LC/MS/MS

Project description:Yap (Yes-associated protein 1) is a downstream effector of the Hippo signaling pathway and known as a transcriptional co-activator. We previously identified Yap1 as a novel factor implicated in the control of the temporal DNA replication program in Xenopus retinal stem cells. However, whether Yap is directly involved in DNA replication dynamics and whether it could regulate DNA replication during early embryonic divisions in the absence of transcription remained to be investigated. We now found that in Yap depleted Xenopus laevis egg extracts the activation of replication origins was increased. In order to understand by which mechanism Yap could regulate the initiation of DNA replication in the absence of transcription we searched for new interacting factors. We immunoprecipitated Yap from Xenopus laevis egg extracts using anti-Yap, compared to control antibodies, and analyzed co-immunoprecipitating proteins by nanoLC/MS/MS.

2022-08-09 | PXD029345 | Pride

Single-cell sequencing of yolk sac and fetal liver hematopoietic progenitors

Project description:Erythro-myeloid progenitors (EMP) and their progeny were labeled with YFP in mouse embryos using genetic fate mapping (constitutive Csf1r-iCre;Rosa26-eYFP or inducible Csf1r-MeriCreMer;Rosa26-eYFP injected at embryonic day E8.5 with 4-hydroxytamoxifen). EMP-derived progenitors (Lin- Kit+ YFP+) were sorted by FACS for single-cell transcriptomic analysis using the MARS-Seq approach. The purpose was to uncover heterogeneity and differentiation trajectories of EMP by comparing their transcriptional status at different developmental timepoints (E9.5, E10.5 and E12.5) and across niches (yolk sac and fetal liver).

2021-02-05 | GSE166223 | GEO

Regulation of gene expression by the Hippo effectors, Taz and Yap, in muscle stem cells

Project description:The Hippo pathway downstream effectors, Yap and Taz, play key roles in cell proliferation and tissue growth, regulating gene expression especially via interaction with Tead transcription factors. To investigate their role in skeletal muscle stem cells, we analysed gene expression changes driven by Taz and compared these to Yap mediated changes to the transcriptome by measurement of gene expression on Affymetrix microarrays. To interrogate overlapping and unique transcriptional changes driven by these Hippo effectors, satellite cell-derived myoblasts were transduced with constitutively active TAZ S89A or YAP S127A retrovirus for 24h or 48h, with empty retrovirus as control. Triplicate microarray analyses of empty vector controls, hYAP1 S127A and TAZ S89A transgenic primary myoblasts were conducted.

2017-06-20 | E-MTAB-5395 | biostudies-arrayexpress

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