Ma2005-digital response of p53 to DNA damage-ATM Activation Module
Ontology highlight
ABSTRACT:
SUBMITTER: 
Ahmad Zyoud
PROVIDER: MODEL2005130001 | BioModels | 2020-05-13
REPOSITORIES: BioModels
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| MODEL2005130001?filename=Ma2005.cps | Other | |||
| MODEL2005130001?filename=Ma2005.xml | Xml |
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Publications
A plausible model for the digital response of p53 to DNA damage.
Ma Lan L Wagner John J Rice John Jeremy JJ Hu Wenwei W Levine Arnold J AJ Stolovitzky Gustavo A GA
Proceedings of the National Academy of Sciences of the United States of America 20050926 40
Recent observations show that the single-cell response of p53 to ionizing radiation (IR) is "digital" in that it is the number of oscillations rather than the amplitude of p53 that shows dependence on the radiation dose. We present a model of this phenomenon. In our model, double-strand break (DSB) sites induced by IR interact with a limiting pool of DNA repair proteins, forming DSB-protein complexes at DNA damage foci. The persisting complexes are sensed by ataxia telangiectasia mutated (ATM), ...[more]
Similar Datasets
Project description:Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by ATM
This model is described in the article:
Explaining oscillations and
variability in the p53-Mdm2 system.
Proctor CJ, Gray DA.
BMC Syst Biol 2008; 2: 75
Abstract:
BACKGROUND: In individual living cells p53 has been found to
be expressed in a series of discrete pulses after DNA damage.
Its negative regulator Mdm2 also demonstrates oscillatory
behaviour. Attempts have been made recently to explain this
behaviour by mathematical models but these have not addressed
explicit molecular mechanisms. We describe two stochastic
mechanistic models of the p53/Mdm2 circuit and show that
sustained oscillations result directly from the key biological
features, without assuming complicated mathematical functions
or requiring more than one feedback loop. Each model examines a
different mechanism for providing a negative feedback loop
which results in p53 activation after DNA damage. The first
model (ARF model) looks at the mechanism of p14ARF which
sequesters Mdm2 and leads to stabilisation of p53. The second
model (ATM model) examines the mechanism of ATM activation
which leads to phosphorylation of both p53 and Mdm2 and
increased degradation of Mdm2, which again results in p53
stabilisation. The models can readily be modified as further
information becomes available, and linked to other models of
cellular ageing. RESULTS: The ARF model is robust to changes in
its parameters and predicts undamped oscillations after DNA
damage so long as the signal persists. It also predicts that if
there is a gradual accumulation of DNA damage, such as may
occur in ageing, oscillations break out once a threshold level
of damage is acquired. The ATM model requires an additional
step for p53 synthesis for sustained oscillations to develop.
The ATM model shows much more variability in the oscillatory
behaviour and this variability is observed over a wide range of
parameter values. This may account for the large variability
seen in the experimental data which so far has examined ARF
negative cells. CONCLUSION: The models predict more regular
oscillations if ARF is present and suggest the need for further
experiments in ARF positive cells to test these predictions.
Our work illustrates the importance of systems biology
approaches to understanding the complex role of p53 in both
ageing and cancer.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000188.
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 | BIOMD0000000188 | BioModels
Project description:Proctor2008 - p53/Mdm2 circuit - p53 stabilisation by p14ARF
This model is described in the article:
Explaining oscillations and
variability in the p53-Mdm2 system.
Proctor CJ, Gray DA.
BMC Syst Biol 2008; 2: 75
Abstract:
BACKGROUND: In individual living cells p53 has been found to
be expressed in a series of discrete pulses after DNA damage.
Its negative regulator Mdm2 also demonstrates oscillatory
behaviour. Attempts have been made recently to explain this
behaviour by mathematical models but these have not addressed
explicit molecular mechanisms. We describe two stochastic
mechanistic models of the p53/Mdm2 circuit and show that
sustained oscillations result directly from the key biological
features, without assuming complicated mathematical functions
or requiring more than one feedback loop. Each model examines a
different mechanism for providing a negative feedback loop
which results in p53 activation after DNA damage. The first
model (ARF model) looks at the mechanism of p14ARF which
sequesters Mdm2 and leads to stabilisation of p53. The second
model (ATM model) examines the mechanism of ATM activation
which leads to phosphorylation of both p53 and Mdm2 and
increased degradation of Mdm2, which again results in p53
stabilisation. The models can readily be modified as further
information becomes available, and linked to other models of
cellular ageing. RESULTS: The ARF model is robust to changes in
its parameters and predicts undamped oscillations after DNA
damage so long as the signal persists. It also predicts that if
there is a gradual accumulation of DNA damage, such as may
occur in ageing, oscillations break out once a threshold level
of damage is acquired. The ATM model requires an additional
step for p53 synthesis for sustained oscillations to develop.
The ATM model shows much more variability in the oscillatory
behaviour and this variability is observed over a wide range of
parameter values. This may account for the large variability
seen in the experimental data which so far has examined ARF
negative cells. CONCLUSION: The models predict more regular
oscillations if ARF is present and suggest the need for further
experiments in ARF positive cells to test these predictions.
Our work illustrates the importance of systems biology
approaches to understanding the complex role of p53 in both
ageing and cancer.
This model is hosted on
BioModels Database
and identified by:
BIOMD0000000188.
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 | BIOMD0000000189 | BioModels
Project description:Its a mathematial model studying steady state and oscialltions in p53-MDM2 network triggered by IR induced DNA Damage.
2024-09-02 | BIOMD0000001006 | BioModels
Project description:Integrated-systems model of oxidative stress connecting NRF2 and p53 signaling pathways. Additional crosstalk linking oxidative stress to p53 inhibition, p53 to NRF2 through p21, and NRF2 to MDM2 was incorporated in this model. The NRF2 pathway was encoded as first- and second-order rate equations for KEAP1 oxidation and NRF2 stabilization; NRF2-mediated transcription of antioxidant enzymes was modeled as a Hill function. The p53 pathway was reconstructed from a delay differential equation model of p53 signaling in response to DNA damage. To adapt the p53 DNA-damage model to respond to oxidative stress, we used a first-order oxidation reaction of ATM/CHEK2 by intracellular H2O2.
The integrated base model of NRF2–p53 oxidative-stress signaling contains 42 reactions and 22 ordinary differential equations (ODEs).
2021-10-29 | MODEL2110270001 | BioModels
Project description:The p53 transcription factor is a regulator of key cellular processes including DNA repair, cell cycle arrest, and apoptosis. In this theoretical study, we investigate how the complex circuitry of the p53 network allows for stochastic yet unambiguous cell fate decision-making. The proposed Markov chain model consists of the regulatory core and two subordinated bistable modules responsible for cell cycle arrest and apoptosis. The regulatory core is controlled by two negative feedback loops (regulated by Mdm2 and Wip1) responsible for oscillations, and two antagonistic positive feedback loops (regulated by phosphatases Wip1 and PTEN) responsible for bistability. By means of bifurcation analysis of the deterministic approximation we capture the recurrent solutions (i.e., steady states and limit cycles) that delineate temporal responses of the stochastic system. Direct switching from the limit-cycle oscillations to the "apoptotic" steady state is enabled by the existence of a subcritical Neimark-Sacker bifurcation in which the limit cycle loses its stability by merging with an unstable invariant torus. Our analysis provides an explanation why cancer cell lines known to have vastly diverse expression levels of Wip1 and PTEN exhibit a broad spectrum of responses to DNA damage: from a fast transition to a high level of p53 killer (a p53 phosphoform which promotes commitment to apoptosis) in cells characterized by high PTEN and low Wip1 levels to long-lasting p53 level oscillations in cells having PTEN promoter methylated (as in, e.g., MCF-7 cell line).
2024-09-02 | BIOMD0000000943 | BioModels
Project description:The DNA damage response network modulates a wide array of signaling pathways, including DNA repair, cell cycle checkpoints, apoptotic pathways and numerous stress signals. The ATM protein kinase, functionally missing in patients with the human genetic disorder ataxia-telangiectasia (A-T), is a master regulator of this network when the inducing DNA lesions are double strand breaks. The ATM gene is also frequently mutated in sporadic cancers of lymphoid origin. Here, we applied a functional genomics approach that combines gene expression profiling and computational promoter analysis to obtain global dissection of the transcriptional response to ionizing radiation (IR) in murine lymphoid tissue. Cluster analysis revealed six major expression patterns in the data. Prominent among them was a gene cluster that contained dozens of genes whose response to irradiation was Atm-dependent. Computational analysis identified significant enrichment of the binding site signatures of the transcription factors NF-kB and p53 among promoters of these genes, pointing to the major role of these two transcription factors in mediating the Atm-dependent transcriptional response in the irradiated lymphoid tissue. Examination of the response showed that pro- and anti-apoptotic signals were simultaneously induced, with the pro-apoptotic pathway mediated by p53, and the pro-survival pathway by NF-kB. These findings further elucidate the molecular network induced by IR and have implications for cancer management as they suggest that a combined treatment that restores the p53-mediated apoptotic arm while blocking the NF-kB-mediated pro-survival arm could be most successful in increasing the radiosensitivity of lymphoid tumors.
2007-12-04 | E-GEOD-2118 | biostudies-arrayexpress
Project description:DNA damage response (DDR) is a complex process, essential for cell survival. Especially deleterious type of DNA damage are DNA double-strand breaks (DSB), which can lead to genomic instability and malignant transformation if not repaired correctly. The central player in DSB detection and repair is the ATM kinase which orchestrates the action of several downstream factors. Despite substantial knowledge of DNA repair processes, still several aspects of DNA damage detection and signaling are not fully understood. Recent studies have suggested that long non-coding RNAs (lncRNAs) are involved in DDR. Here, we aimed to identify lncRNAs induced upon DNA damage in an ATM-dependent manner. 7 mRNAs and 10 lncRNAs were significantly induced 1h after ionizing radiation (IR) in healthy donors, whereas none in AT patients. 447 mRNAs and 149 lncRNAs were induced 8h after IR in the control group, while only 100 mRNAs and 3 lncRNAs in AT patients. Among IR-induced mRNAs, we found several genes with well-known functions in DDR. Gene Set Enrichment Analysis and Gene Ontology revealed delayed induction of key DDR pathways in AT patients compared to controls. The induction and dynamics of selected 9 lncRNAs were confirmed by RT-qPCR at several time-points after IR on a larger cohort. Moreover, inhibition of ATM with a specific inhibitor (KU-60019) proved that those lncRNAs are dependent on ATM. Some of the detected lncRNAs are localized next to protein-coding genes involved in DDR. We observed that induction of lncRNAs after IR preceded changes in expression of adjacent genes. This indicates that IR-induced lncRNAs may regulate the transcription of nearby genes. Subcellular fractionation into chromatin, nuclear, and cytoplasmic fractions revealed that the majority of studied lncRNAs are localized in chromatin, which further suggests their role in regulation of gene expression. In summary, our study revealed several lncRNAs induced by IR in an ATM-dependent manner. Their co-localization and co-expression with genes involved in DDR suggest that those lncRNAs may be important players in cellular response to DNA damage.
2024-02-16 | GSE243468 | GEO
Project description:The tightly controlled BMP-Smad1 pathway is essential for embryonic development and postnatal tissue homeostasis. Dysfunction of BMP-Smad1 signaling also leads to tumor development such as juvenile polyposis and Cowden syndromes and various tumors in mouse models, with unknown pathological mechanisms. Here we establish a link between the BMP-Smad pathway and the prominent tumor suppressor Atm-p53 pathway. We identify activated nuclear Smad1 as an Atm substrate under genotoxic stress. Atm-mediated Smad1 S239 phosphorylation disrupts Smad1 interaction with protein phosphatase PPM1A and enhances Smad1 activation and up-regulation, which not only turns on target genes including Cdk1nc but also interacts with p53 and inhibits Mdm2-mediated p53 ubiquitination, leading to p53 stabilization. Functionally, Smad1 acts like a tumor suppressor in DNA damage response, cell transformation and tumorigenesis in a p53-dependent manner. Sequencing of the gastric cancer samples revealed that Smad1 is frequently mutated, with S239 as mutational hotspot. This study thus establishes the BMP-Smad1 pathway as an integral part of DNA damage response, which can suppresses tumorigenesis via p53. Transformed MEFs (Smad1f/f, Smad1f/f Cre) treated with 50ng/ml BMP2, 1 ug/ml doxorubincin, or both for different periods of time. The mRNA levels of all genes were compared using microarray analysis.
2012-12-31 | E-GEOD-36843 | biostudies-arrayexpress
Project description:This a model from the article:
Stress-specific response of the p53-Mdm2 feedback loop
Alexander Hunziker, Mogens H Jensen and Sandeep Krishna
BMC Systems Biology 2010, Jul 12;4(1):94
20624280,
Abstract:
ABSTRACT: BACKGROUND: The p53 signalling pathway has hundreds of inputs and outputs. It can trigger cellular senescence, cell-cycle arrest and apoptosis in response to diverse stress conditions, including DNA damage, hypoxia and nutrient deprivation. Signals from all these inputs are channeled through a single node, the transcription factor p53. Yet, the pathway is flexible enough to produce different downstream gene expression patterns in response to different stresses. RESULTS: We construct a mathematical model of the negative feedback loop involving p53 and its inhibitor, Mdm2, at the core of this pathway, and use it to examine the effect of different stresses that trigger p53. In response to DNA damage, hypoxia, etc., the model exhibits a wide variety of specific output behaviour -- steady states with low or high levels of p53 and Mdm2, as well as spiky oscillations with low or high average p53 levels. CONCLUSIONS: We show that even a simple negative feedback loop is capable of exhibiting the kind of flexible stress-specific response observed in the p53 system. Further, our model provides a framework for predicting the differences in p53 response to different stresses and single nucleotide polymorphisms.
The parameters of the model corresponds to the resting state, with delta = 11hr-1, gamma = 0.2hr-1, kt = 0.03nM-1hr-1 and kf = 5000nM-1hr-1.
To simulate different stress conditions as in figure 2A (also look at the curation figure of this model) of the reference publication, the above parameter should be changed. The parameter values corresponding to different stress conditions are shown in the following table.
Stress Condition/Parameter
delta
gamma
kt
kf
Nutlin
11hr-1
0.2hr-1
0.03nM-1hr-1
500nM-1hr-1
Oncogene
2hr-1
0.2hr-1
0.03nM-1hr-1
5000nM-1hr-1
DNA damage
2hr-1
0.5hr-1
0.03nM-1hr-1
2500nM-1hr-1
Hypoxia
2hr-1
0.2hr-1
0.01nM-1hr-1
5000nM-1hr-1
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2011 The BioModels.net Team.For more information see the terms of use.To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2024-09-02 | BIOMD0000000252 | BioModels
Project description:The tightly controlled BMP-Smad1 pathway is essential for embryonic development and postnatal tissue homeostasis. Dysfunction of BMP-Smad1 signaling also leads to tumor development such as juvenile polyposis and Cowden syndromes and various tumors in mouse models, with unknown pathological mechanisms. Here we establish a link between the BMP-Smad pathway and the prominent tumor suppressor Atm-p53 pathway. We identify activated nuclear Smad1 as an Atm substrate under genotoxic stress. Atm-mediated Smad1 S239 phosphorylation disrupts Smad1 interaction with protein phosphatase PPM1A and enhances Smad1 activation and up-regulation, which not only turns on target genes including Cdk1nc but also interacts with p53 and inhibits Mdm2-mediated p53 ubiquitination, leading to p53 stabilization. Functionally, Smad1 acts like a tumor suppressor in DNA damage response, cell transformation and tumorigenesis in a p53-dependent manner. Sequencing of the gastric cancer samples revealed that Smad1 is frequently mutated, with S239 as mutational hotspot. This study thus establishes the BMP-Smad1 pathway as an integral part of DNA damage response, which can suppresses tumorigenesis via p53.
2012-12-31 | GSE36843 | GEO