Transcriptomic analysis of APC knockdown in proliferating primary myoblasts
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE57898 | GEO | 2015/01/01
SECONDARY ACCESSION(S): PRJNA248381
REPOSITORIES: GEO
Similar Datasets
Project description:The tumor suppressor gene adenomatous polyposis coli (APC) is mutated in most colorectal cancers (CRC) resulting in constitutive Wnt activation. To understand the Wnt-activating mechanism of APC mutation, we applied CRISPR/Cas9 technology to engineer various APC-truncated isogenic lines. We find that the β-catenin inhibitory domain (CID) in APC represents the threshold for pathological levels of Wnt activation and tumor transformation. Mechanistically, CID-deleted APC truncation promotes β-catenin deubiquitination through reverse binding of β-TrCP and USP7 to the destruction complex. USP7 depletion in APC-mutated CRC inhibits Wnt activation by restoring β-catenin ubiquitination, drives differentiation and suppresses xenograft tumor growth. Finally, the Wnt-activating role of USP7 is specific to APC mutations, thus can be used as tumor-specific therapeutic target for most CRCs.
2017-11-09 | PXD007947 | Pride
Project description:Loss of APC is the main driving alteration associated with colorectal cancer (CRC) development. We investigate the immediate outcome of this genetic event on the transcriptomic and DNA methylation profiles of Lgr5+ intestinal stem cells (ISCs), considered as the cell-of-origin of CRC. RNA-seq analyses show that the sequential deletion of Apc alleles has a rapid impact on the transcriptional profiles of ISCs. Indeed, Apc loss-of-function dictates an altered cell fate program at transcriptional level, resuting in an impaired commitment of those cells to differentiation. Reduced-representation bisufite sequencing (RRBS) on the genomic DNA (gDNA) also shows that focal alterations occur in the DNA methylations profiles of ISCs at this stage, and functionally contribute to altered cell fate in those cells. This study sheds light on the earliest events in CRC development, proving evidences on the role exerted by DNA methylation changes associated with Apc inactivation in the homeostatic rupture at CRC initation.
2020-03-22 | GSE123004 | GEO
Project description:Loss of APC is the main driving alteration associated with colorectal cancer (CRC) development. We investigate the immediate outcome of this genetic event on the transcriptomic and DNA methylation profiles of Lgr5+ intestinal stem cells (ISCs), considered as the cell-of-origin of CRC. RNA-seq analyses show that the sequential deletion of Apc alleles has a rapid impact on the transcriptional profiles of ISCs. Indeed, Apc loss-of-function dictates an altered cell fate program at transcriptional level, resuting in an impaired commitment of those cells to differentiation. Reduced-representation bisufite sequencing (RRBS) on the genomic DNA (gDNA) also shows that focal alterations occur in the DNA methylations profiles of ISCs at this stage, and functionally contribute to altered cell fate in those cells. This study sheds light on the earliest events in CRC development, proving evidences on the role exerted by DNA methylation changes associated with Apc inactivation in the homeostatic rupture at CRC initation.
2020-03-22 | GSE123005 | GEO
Project description:Almost all colorectal cancers (CRC) present with mutations in the Apc gene, leading to unrestrained Wnt activation and the initiation of tumour development. We previously reported the competitive benefit of Apc-mutant intestinal stem cells (ISCs) within the crypt, however, the mechanism by which they outcompete their wild type (WT) neighbours remained elusive. Here, we studied the effect of Apc-mutants using an in vitro culture system of WT (Lgr5-CreErt2) and Apc-/- (Lgr5-CreErt2;Apcfl/fl) organoids . The expression patterns of WT and Apc-/- organoids revealed significant upregulation in specific secreted Wnt antagonists Notum, Wif1 and Dkk2. Furthermore, we studied the effect of the secreted antagonist by treating WT organoids with either WT or Apc-/- conditioned medium (CM) for 48 hours and observed a significant decrease in stem cell markers and an increase in goblet cell markers. We report that Apc-mutants act as bona fide supercompetitors by secreting Wnt antagonists that result in active differentiation of WT ISCs.
2021-03-25 | GSE144325 | GEO
Project description:Although the role of the Wnt pathway in colon carcinogenesis has been described previously, it has been recently demonstrated that Wnt signaling originates from highly dynamic nano-assemblies at the plasma membrane. However, little is known regarding the role of oncogenic APC in reshaping Wnt nanodomains. This is noteworthy, because oncogenic APC does not act autonomously and requires activation of Wnt effectors upstream of APC to drive aberrant Wnt signaling. Here, we demonstrate the role of oncogenic APC in increasing plasma membrane free cholesterol and rigidity, thereby modulating Wnt signaling hubs. This results in an overactivation of Wnt signaling in the colon. Finally, using the Drosophila sterol auxotroph model, we demonstrate the unique ability of exogenous free cholesterol to disrupt plasma membrane homeostasis and drive Wnt signaling in a wildtype APC background. Collectively, these findings provide a mechanistic link between oncogenic APC, loss of plasma membrane homeostasis and CRC development.
2023-06-21 | GSE234522 | GEO
Project description:Wnt signaling plays a pivotal role in colorectal cancer. Intrinsic activation of Wnt by mutational events, such as mutations in the tumor suppressor gene APC, represents the most frequent initiating event in this disease background. Long truncated versions of APC retain partial functionality, which leads to a sub-maximal, “just right” activation state of Wnt signaling supposed to be beneficial for disease initiation. In order to study the transcriptomic alterations of an over-stimulated Wnt signaling pathway, conditional shRNA-mediated silencing of APC was performed in chromosomal instable HT-29 CRC cells which express a 1555 amino acid variant of APC protein able to bind and partially inactivate β-catenin. To achieve this, cells were stably transduced with lentiviral particles encoding for a doxycyline-inducible shRNA directed against APC, or, as a control, a non-silencing shRNA (pTRIPZ inducible shRNA vectors, RHS4740-EG324, Horizon Dharmacon, CO, USA). 72 hours after APC silencing, total RNA was isolated and quality controlled for subsequent RNA-Seq Analysis (DKFZ Heidelberg, Genomic and Proteomic Core Facility) on a HiSeq 2000 instrument (Illumina). Overall, we observed bona-fide Wnt target genes, such as NKD1, AXIN2, PTK7, ASCL2, and SMOC2, and additional putative direct or indirect targets of Wnt signaling up-regulated upon shRNA-mediated APC silencing.
2020-06-25 | GSE131575 | GEO
Project description:Nearly all colorectal cancers have dysregulated Wnt signalling, predominantly through the mutation of the Apc (Adenomatous Polyposis Coli) gene. Therefore it is of vital importance to elucidate the key Wnt target genes in intestinal cells in vivo. We have used a novel inducible cre-lox based murine system (designated ApcFlox) to investigate the consequences of perturbation of Wnt signalling following inactivation of Apc in vivo within 100% of the intestinal epithelium. We have employed microarray analysis at 3 time points within our ApcFlox system (Day 3 prior to the onset of phenotype, day 4 the establishment of the phenotype and day 5 gross phenotype of altered proliferation, differentiation and migration) and from adenomas arising in the ApcMin/+ background allowing us characterise Wnt/beta-catenin target genes based on their expression profiles during different stages of intestinal tumourigenesis. Furthermore, we have employed microarray analysis using livers from our ApcFlox system and have demonstrated that there is very little overlap in the Wnt target genes induced by Apc loss in the liver and the intestine. More importantly, we have been able to determine a novel set of putative Wnt/beta-catenin target genes which are upregulated at both early and late stages of tumourigenesis in the intestine and may represent novel therapeutic targets in colon cancer. Samples were collected from Genetcially modified mice of the genotypes indicated on the sample records. Where appropriate, gene recombination was induced using IP administration of beta-napthoflavone. Cohorts of samples were used to compare the affects of APC loss in the small intestine at three time points (and compared to matched control samples in which the gene was not recombined). Furthermore, these samples were compared to colonic polyps (and normal colon) taken from the Apcmin Mouse.
2015-01-31 | E-GEOD-65461 | biostudies-arrayexpress
Project description:APC is a classical tumor suppressor in humans, and truncating mutations are early somatic events in most cases of sporadic colon cancer. APC directly enhances the activity of glycogen synthase kinase 3 (GSK-3) and therefore loss of full length APC reduces GSK-3 activity, leading to stabilization of b-catenin protein and activation of downstream Wnt/b-catenin signaling. GSK-3 also phosphorylates multiple core mRNA splicing factors and loss of Gsk3a/b in mouse ES cells and human lymphocytes alters mRNA splicing at a genome wide level. We therefore predict that loss of APC should similarly alter splicing by reducing GSK-3 activity. Here we use RNA-seq to assess differential gene expression and altered splicing in apc-mcr mutant zebrafish embryos at 48hpf. We find robust activation of known Wnt/b-catenin target genes, as expected. Surprisingly, we also find markedly increased expression of multiple genes related to inflammation and cytokine signaling. We also identify 340 mRNA splicing variations in apc mutant zebrafish. Many of these local splice variants (LSVs) occur in mRNAs the regulate cell adhesion, migration, and morphogenesis.
2023-06-19 | GSE234986 | GEO
Project description:Lee2003 - Roles of APC and Axin in Wnt
Pathway (without regulatory loop)
This model is described in the article:
The roles of APC and Axin
derived from experimental and theoretical analysis of the Wnt
pathway.
Lee E, Salic A, Krüger R,
Heinrich R, Kirschner MW.
PLoS Biol. 2003 Oct; 1(1): E10
Abstract:
Wnt signaling plays an important role in both oncogenesis
and development. Activation of the Wnt pathway results in
stabilization of the transcriptional coactivator beta-catenin.
Recent studies have demonstrated that axin, which coordinates
beta-catenin degradation, is itself degraded. Although the key
molecules required for transducing a Wnt signal have been
identified, a quantitative understanding of this pathway has
been lacking. We have developed a mathematical model for the
canonical Wnt pathway that describes the interactions among the
core components: Wnt, Frizzled, Dishevelled, GSK3beta, APC,
axin, beta-catenin, and TCF. Using a system of differential
equations, the model incorporates the kinetics of
protein-protein interactions, protein synthesis/degradation,
and phosphorylation/dephosphorylation. We initially defined a
reference state of kinetic, thermodynamic, and flux data from
experiments using Xenopus extracts. Predictions based on the
analysis of the reference state were used iteratively to
develop a more refined model from which we analyzed the effects
of prolonged and transient Wnt stimulation on beta-catenin and
axin turnover. We predict several unusual features of the Wnt
pathway, some of which we tested experimentally. An insight
from our model, which we confirmed experimentally, is that the
two scaffold proteins axin and APC promote the formation of
degradation complexes in very different ways. We can also
explain the importance of axin degradation in amplifying and
sharpening the Wnt signal, and we show that the dependence of
axin degradation on APC is an essential part of an
unappreciated regulatory loop that prevents the accumulation of
beta-catenin at decreased APC concentrations. By applying
control analysis to our mathematical model, we demonstrate the
modular design, sensitivity, and robustness of the Wnt pathway
and derive an explicit expression for tumor suppression and
oncogenicity.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000658.
To cite BioModels Database, please use:
Chelliah V et al. BioModels: ten-year
anniversary. Nucl. Acids Res. 2015, 43(Database
issue):D542-8.
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 | BIOMD0000000658 | BioModels
Project description:The APC (Adenomatous Polyposis Coli) gene encodes a large multidomain protein that plays an integral role in the Wnt/beta-catenin signaling pathway. The loss-of-function mutation in APC is considered the earliest genetic alteration in the course of adenoma-carcinoma sequence of colorectal cancer progression, and the resulting constitutive activation of Wnt/beta-catenin signaling is required for the maintenance of advanced colorectal cancer. In order to identify genes affected by loss of Apc function, we performed transcription profiling of mouse small intestinal tissues comparing polyps with normal mucosa of Apc+/Delta716 mice. We isolated total RNA from intestinal polyps and normal intestinal mucosa from 3 individual Apc+/Delta716 mice. Total RNA samples were then employed to perform microarray analysis (Agilent Whole Mouse Genome Microarray Ver. 2.0, 4x44K).
2020-11-01 | E-MTAB-9187 | biostudies-arrayexpress