Single-cell transcriptional profiles of the atrioventricular canal of 1-month-old zebrafish treated with DMSO or IWR-1-endo
Ontology highlight
ABSTRACT:
ORGANISM(S): Danio rerio
PROVIDER: GSE261604 | GEO | 2024/08/23
REPOSITORIES: GEO
Similar Datasets
Project description:To understand the function of Wnt/β-catenin signaling-activated cardiomyocytes (β-cat ON CMs), we performed RNA-Seq on β-cat ON and OFF CMs at the atrioventricular canal (AVC) in the heart, respectively. Our analyses indicated that β-cat ON CMs upregulate genes related to blood vessel development.
2024-08-23 | GSE223460 | GEO
Project description:To understand how Wnt/β-catenin signaling-activated cardiomyocytes (β-cat ON CMs) promote coronary vessel development, we performed single-cell RNA sequencing of endothelial cells (ECs) sorted from the hearts ablated β-cat ON CMs and those from control hearts, respectively. Our analyses indicated that β-cat ON CMs regulates coronary vessel development by promoting arterialization, a step in the transition of endocardial ECs to coronary ECs.
2024-08-23 | GSE223461 | GEO
Project description:Sivakumar2011_WntSignalingPathway
The secreted protein Wnt activates the
heptahelical receptor Frizzled on nieghboring cells. Activation of
Frizzled causes the recruitment of additional membrane proteins
which in turn result in 1) the activation of the protein
Dishevelled via phosphorylation and 2) the activation of a
heterotrimeric G protein of unknown type. Activation of Dishevelled
results in the down-regulation of the Beta-Catenin destruction
complex which causes ubiquitination of Beta-Catenin and its
ultimate degradation via the proteasome. Inhibition of the
Beta-Catenin destruction complex yields a higher cytosolic
concentration of Beta-Catenin, which enters the nucleus, binds
various transcriptional regulatory molecules including the TCF/LEF
class of proteins, and results in the transcription of TCF/LEF
target genes. Activation of the heterotrimeric G-protein pathway in
turn activates Phospholipase C which in turn catalyzes the
catalysis of PI(4,5)P2 into DAG and IP3.
Reference:
The Wnt
signalling pathway.
You Wnt
some, you lose some: oncogenes in the Wnt signaling
pathway.
Wnt
signaling pathway.
This model is described in the article:
A systems biology approach
to model neural stem cell regulation by notch, shh, wnt, and
EGF signaling pathways.
Sivakumar KC, Dhanesh SB, Shobana S,
James J, Mundayoor S.
OMICS 2011 Oct; 15(10): 729-737
Abstract:
The Notch, Sonic Hedgehog (Shh), Wnt, and EGF pathways have
long been known to influence cell fate specification in the
developing nervous system. Here we attempted to evaluate the
contemporary knowledge about neural stem cell differentiation
promoted by various drug-based regulations through a systems
biology approach. Our model showed the phenomenon of
DAPT-mediated antagonism of Enhancer of split [E(spl)] genes
and enhancement of Shh target genes by a SAG agonist that were
effectively demonstrated computationally and were consistent
with experimental studies. However, in the case of model
simulation of Wnt and EGF pathways, the model network did not
supply any concurrent results with experimental data despite
the fact that drugs were added at the appropriate positions.
This paves insight into the potential of crosstalks between
pathways considered in our study. Therefore, we manually
developed a map of signaling crosstalk, which included the
species connected by representatives from Notch, Shh, Wnt, and
EGF pathways and highlighted the regulation of a single target
gene, Hes-1, based on drug-induced simulations. These
simulations provided results that matched with experimental
studies. Therefore, these signaling crosstalk models complement
as a tool toward the discovery of novel regulatory processes
involved in neural stem cell maintenance, proliferation, and
differentiation during mammalian central nervous system
development. To our knowledge, this is the first report of a
simple crosstalk map that highlights the differential
regulation of neural stem cell differentiation and underscores
the flow of positive and negative regulatory signals modulated
by drugs.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000397.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000397 | BioModels
Project description:Kim2007 - Crosstalk between Wnt and ERK pathways
Experimental studies have shown that both Wnt and the MAPK pathways are involved in the pathogenesis of various kinds of cancers (eg. colorectal cancer). The crosstalk between the two pathways have also been identified. Here, Kim et al., (2007) have integrated the experimental evidences on crosstalk mechanisms between the two pathways into a pathway model, and have identified the existence of a hidden positive feedback loop and suggest that this positive feedback loop might participate in the pathogenesis of colorectal cancer.
This model is described in the article:
A hidden oncogenic positive feedback loop caused by crosstalk between Wnt and ERK pathways.
Kim D, Rath O, Kolch W, Cho KH.
Oncogene 2007 Jul; 26(31): 4571-4579
Abstract:
The Wnt and the extracellular signal regulated-kinase (ERK) pathways are both involved in the pathogenesis of various kinds of cancers. Recently, the existence of crosstalk between Wnt and ERK pathways was reported. Gathering all reported results, we have discovered a positive feedback loop embedded in the crosstalk between the Wnt and ERK pathways. We have developed a plausible model that represents the role of this hidden positive feedback loop in the Wnt/ERK pathway crosstalk based on the integration of experimental reports and employing established basic mathematical models of each pathway. Our analysis shows that the positive feedback loop can generate bistability in both the Wnt and ERK signaling pathways, and this prediction was further validated by experiments. In particular, using the commonly accepted assumption that mutations in signaling proteins contribute to cancerogenesis, we have found two conditions through which mutations could evoke an irreversible response leading to a sustained activation of both pathways. One condition is enhanced production of beta-catenin, the other is a reduction of the velocity of MAP kinase phosphatase(s). This enables that high activities of Wnt and ERK pathways are maintained even without a persistent extracellular signal. Thus, our study adds a novel aspect to the molecular mechanisms of carcinogenesis by showing that mutational changes in individual proteins can cause fundamental functional changes well beyond the pathway they function in by a positive feedback loop embedded in crosstalk. Thus, crosstalk between signaling pathways provides a vehicle through which mutations of individual components can affect properties of the system at a larger scale.
Figure 6 of the reference publication has been reproduced. The model as such reproduces the plots corresponding to the normal conditions. To obtain simulations under 1) beta-cataenin mutation; set V12=0.846 (two-fold of the beta-catenin synthetic rate than the normal system. i.e. 2*0.426), 2) PP2A mutation; set Vmax4=Vmax5=33.75 (three-fourths of the PP2A activity that the normal system. i.e. (3/4)*45). The simulation was performed using Copasi 4.10 (Build 55).
This model is hosted on BioModels Database
and identified
by: BIOMD0000000149
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2024-09-02 | BIOMD0000000149 | BioModels
Project description:The Wnt/β-catenin signaling pathway is a critical regulator of development and stem cell maintenance. Mounting evidence suggests that the context-specific outcome of Wnt signaling is determined by the collaborative action of multiple transcription factors, including members of the highly conserved forkhead box (FOX) protein family. The contribution of FOX transcription factors to Wnt signaling has not been investigated in a systemic manner. Here, by combining β-catenin reporter assays with Wnt pathway-focused qPCR arrays and proximity proteomics of selected FOX family members, we determine that most FOX proteins are involved in the regulation of Wnt pathway activity and the expression of Wnt ligands and target genes. We conclude that FOX proteins are common regulators of the Wnt/β-catenin pathway that may control the outcome of Wnt signaling in a tissue-specific manner.
2023-04-19 | PXD038811 | Pride
Project description:Canonical Wnt/B-catenin signaling is frequently dysregulated in myeloid leukemias and is implicated in leukemogenesis. Nuclear-localized β-catenin is indicative of active Wnt signaling and is frequently observed in acute myeloid leukemia (AML) patients; however, some patients exhibit little or no β-catenin nuclear-localization even where cytosolic B-catenin is abundant. Differential propensity for nuclear-localized β-catenin is also observed in cell lines. To investigate the factors mediating the nuclear-localization of B-catenin we carried out a nuclear/cytoplasmic proteomic analysis of the B-catenin interactome in myeloid leukemia cells. From this we identified hundreds of putative novel B-catenin-interactors. Comparison of interacting factors between Wnt-responsive cells (high nuclear B-catenin, K562/HEL) versus Wnt-unresponsive cells (low nuclear B-catenin, ML1) suggested the established interactor, LEF1, is a key factor mediating the nuclear-localization of B-catenin in myeloid leukemia. The relative levels of nuclear LEF1 and B-catenin were tightly correlated in both cell lines and in primary AML blasts. Furthermore, LEF1 knockdown inhibited B-catenin nuclear-localization and transcriptional activation in Wnt-responsive cells. Conversely, LEF1 overexpression was able to promote both nuclear-localization and B-catenin-dependent transcriptional responses in previously Wnt-unresponsive cells. This study is the first to present a B-catenin interactome in hematopoietic cells and reveals LEF1 as a critical regulator of canonical Wnt signaling in myeloid leukemia.
2019-01-11 | PXD009305 | Pride
Project description:Breast cancer is one of the most common types of cancer in women. One key signaling pathway known to regulate tumor growth, metabolic adaptation, and cellular stress response in breast cancer is Wnt signaling. Breast cancer patients, specifically triple negative breast cancer (TNBC), with upregulated Wnt signaling often have a poor clinical prognosis. However, the effects of Wnt/β-catenin signaling on the nucleolus and the resultant impact on cancer development and progression remain unclear. A notable reduction was observed in the number of nucleoli per nucleus in response to Wnt/β-catenin signaling inhibition in multiple TNBC cell lines. Our comparative proteomic analysis revealed several changes in the composition of the nucleolar proteome of TNBC cells upon inhibition of Wnt signaling. Overall, we demonstrate that Wnt/β-catenin signaling will affects nucleolar functionality and thus influences breast cancer progression. Understanding the role of Wnt signaling in the nucleolus and breast cancer is a critical step towards developing novel therapeutic options for the treatment of breast cancer.
2021-03-05 | PXD021181 | Pride
Project description:Multiple human autism risk genes are predicted to converge on the β‐catenin (β‐cat)/Wnt pathway. However, direct tests to link β‐cat up‐ or down‐regulation with autism are largely lacking, and the associated pathophysiological changes are poorly defined. Here we identify excessive β‐cat as a risk factor that causes expression changes in several genes relevant to human autism. Our studies utilize mouse lines with β‐cat dysregulation in forebrain excitatory neurons, identified as cell types with convergent expression of autism‐linked genes in both human and mouse brains. We show that mice expressing excessive β‐cat display behavioral and molecular changes, including decreased social interest, increased repetitive behaviors, reduced parvalbumin and altered expression levels of additional genes identified as potential risk factors for human autism. These behavioral and molecular phenotypes are averted by reducing β‐cat in neurons predisposed by gene mutations to express elevated β‐cat. Using next-generation sequencing of the prefrontal cortex, we identify dysregulated genes that are shared between mouse lines with excessive β‐cat and autism‐like behaviors, but not mouse lines with reduced β‐cat and normal social behavior. Our findings provide critical new insights into β‐cat, Wnt pathway dysregulation in the brain causing behavioral phenotypes relevant to the disease and the molecular etiology which includes several human autism risk genes.
2020-03-17 | GSE147034 | GEO
Project description:The WNT/β-catenin signaling pathway is evolutionarily conserved and controls normal embryonic development, adult tissue homeostasis, and regeneration. Aberrant activation or suppression of WNT signaling contributes to cancer initiation and progression, developmental disorders, neurodegeneration, and bone disease. Despite great need and more than 40 years of research, targeted therapies for the WNT pathway have yet to be fully realized. Kinases are exceptionally druggable and occupy key nodes within the WNT signaling network, but several pathway-relevant kinases remain understudied and ‘dark’. Here we studied the function of the CSNK1g subfamily of human kinases. miniTurbo-based proximity biotinylation and mass spectrometry analysis of CSNK1γ1, CSNK1γ2, and CSNK1γ3 revealed numerous established components of the β-catenin-dependent and independent WNT signaling pathways, as well as novel interactors. In gain-of-function experiments using a panel of transcriptional reporters, CSNK1γ3 but not CSNK1γ1 or CSNK1γ2 activated β-catenin-dependent WNT signaling, with minimal effect on other signaling pathways. Within the family, CSNK1γ3 expression uniquely induced LRP6 phosphorylation. Conversely, siRNA-mediated silencing of CSNK1γ3 alone had no impact on WNT signaling, though co-silencing of all three family members decreased WNT pathway activity. We characterized two moderately selective and potent small molecule inhibitors of the CSNK1γ family. These inhibitors and a CSNK1γ3 kinase dead mutant suppressed but did not eliminate WNT-driven LRP6 phosphorylation and β-catenin stabilization. Our data suggest that while CSNK1γ3 expression uniquely drives pathway activity, potential functional redundancy within the family necessitates loss of all three family members to suppress the WNT signaling pathway.
2022-06-09 | PXD032138 | Pride
Project description:To investigate mechanisms by which activated β-catenin signaling promotes liver tumor formation and to identify potential therapeutics for these cancers, we generated transgenic zebrafish expressing hepatocyte-specific activated β-catenin (Tg(fabp10a:pt-β-cat) zebrafish. As adults, these animals show increased liver size, decreased survival, and histologic abnormalities similar to human HCC. To further characterize our model, we used microarray analysis to compare gene expression in Tg(fabp10a:pt-β-cat) zebrafish livers to that of non-transgenic control sibling livers. This experiment includes 2 biological replicates. Each replicate represents one Tg(fabp10a:pt-beta-catenin) zebrafish compared to non-transgenic control sibling.
2015-04-30 | E-GEOD-68124 | biostudies-arrayexpress