Daphnane diterpenoids for cancer therapy by suppressing ATR-mediated DNA damage response pathway
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ABSTRACT:
PROVIDER: PRJNA1289710 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:In this study, 26 structurally diverse daphnane diterpenoids (1-26) including six undescribed ones (1-6) were isolated from the whole plants of Daphne odora. Compounds 1 and 2 were the most active with IC50 values of 3.57 ± 0.32 and 4.35 ± 0.14 μM, respectively. Mechanistic study indicated that 1 and 2 could significantly induce cell cycle arrest at the G2/M phase and cause cell apoptosis. Further examination by transcriptome sequencing analysis revealed that 1 and 2 significantly suppressed ATR-mediated DNA damage response and cell cycle checkpoint.
2025-07-15 | GSE302236 | GEO
Project description:Embryonic stem cells (ESCs) which are susceptible to DNA damage depend on a robust and highly efficient DNA damage response (DDR) mechanism for their survival. However, the implications of physical force-mediated DNA damage on ESC fate remains unclear. Here we assessed the importance of DNA damage in ESC differentiation by culturing mouse ESCs (mESCs) on substrates of varying stiffness, which has been shown to induce stem cell differentiation. We show that stiffness-dependent mESC spreading induces DNA damage through nuclear compression that leads to loss of pluripotency, expression of Lamin A/C and germline markers. DNA damage and induction of Lamin A/C are observed in the presence of differentiating agents, as well as during mESC differentiation on cell derived matrices, identifying DNA damage as an early event in differentiation. Differentiation was also associated with reduction of DNA damage and activation of the DDR factor – ATR. While ATR is typically known to play roles in DDR pathway, its role during stiffness-mediated nuclear compression and mESC differentiation is unknown. Nuclear enrichment of activated ATR on stiff substrates and reduction of Lamin A/C expression due to ATR inhibition suggests that mESC differentiation is driven by nuclear compression-mediated DNA damage and involves ATR-dependent modulation of Lamin A/C.
2025-09-01 | GSE262150 | GEO
Project description:Mitochondria are the central metabolic hub of the cell and their function is vital for cellular activities. Mitochondrial autophagy, or mitophagy, is a quality control mechanism to surveille the fitness and functionality of mitochondria and is therefore essential for life. Both mitochondrial dysfunction and malfunctional DNA damage response (DDR) are a major etiology for tissue impairment and aging. ATR has been shown mainly as a nuclear factor to conduct DNA damage response under DNA replication stress. Paradoxically, the human Seckel syndrome caused by ATR mutations is characterized by premature aging and neuropathies, suggesting a role of ATR in non-replicating tissues. Here we report a previously unknown yet direct role of ATR at mitochondria. We find that HSP90 chaperones ATR and PINK1 to mitochondria, where ATR interacts with and thereby stabilizes PINK1 docking at the mitochondrial translocase TOM/TIM complex as well as with the electron transport chain (ETC). ATR mutant cells are refractory to mitophagy initiation, which can be reverted by an ectopic expression of full length, but not ATR-interaction mutant, PINK1. ATR deletion alters mitochondrial dynamics and OXPHOS functions producing aberrantly high reactive oxygen species (ROS) that attack cytosolic macromolecules prior to damaging nuclear DNA. Intriguingly, pharmacological intervention of mitochondrial metabolism to prevent ROS overproduction can mute ATR-mediated nuclear DDR. This study demonstrates that ATR is an integrated component of the mitochondrial membrane to ensure mitochondrial fitness as a primary physiological function, which, together with its essential DDR function, safeguards the cell fate under physiological and genotoxic conditions.
2025-02-26 | GSE244464 | GEO
Project description:High-risk human papillomaviruses (HPVs) constitutively activate the ataxia telangiectasia and Rad3-related (ATR) DNA damage response pathway for their replication. Although ATR has many reported functions, knowledge of how it regulates viral replication is limited. Most studies regarding ATR function focus on its roles in cell survival and initiation of DNA damage response. In this study, we examined whether the transcriptional regulatory properties directed by ATR are critical for HPV pathogenesis, and if so which downstream targets are important. Using RNA-seq approaches, we observed that ATR knockdown increases expression of many inflammatory genes. This mechanism is dependent on the p62/GATA4 signaling pathway.
2020-07-27 | GSE142482 | GEO
Project description:Maintaining genome integrity presents a particular challenge for plants due to their sedentary lifestyle, which disables direct avoidance of unfavorable external conditions. Additionally, plants’ metabolic processes generate reactive molecules as by-products of e.g. photosynthesis, creating internal DNA-damaging conditions. Due to this, plants have developed a unique and strictly regulated web of DNA damage responses (DDR). We initiated analysis of the DDR system in cultivated barley (Hordeum vulgare), a temperate cereal model with a large and repeat rich genome. A series of DNA damaging assays was established to describe barley plants’ phenotypic response to chemically induced DNA double-strand breaks. The efficacy of assays as a tool to be used for assessing potential new DDR barley mutants was demonstrated. DNA damage response network activation in barley was assessed by transcriptome analysis using RNA sequencing for wild type and mutant in the DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (ATR). Considering the barley genome had only recently been sequenced, and it lacks the in-depth gene analysis, a list of potential DNA damage response genes in barley was compiled based on their homology with Arabidopsis genes. The comparison of transcripts in wild-type plants and atr mutants following genotoxic stress
2023-10-19 | GSE235051 | GEO
Project description:Daphnane diterpenoids as potent and tolerable importin-b1 inhibitors to treat castration-resistant prostate cancer
| PRJNA743226 | ENA
Project description:Comprehensive Model Description
Overview
This model simulates the cellular response to DNA damage under conditions of ATM/ATR deficiency—such as in ataxia telangiectasia—and predicts the potential benefits of drug repositioning with Omaveloxolone and spermidine. It integrates several interconnected modules: DNA damage production and repair, ATM/ATR–p53 signaling, NRF2/KEAP1 regulation, spermidine-induced autophagy (with additional positive modulation of ATR signaling), and downstream p53 effectors involved in cell fate decisions.
1. DNA Damage Production and Repair Module
Basal DNA Damage Production:
DNA damage is continuously generated at a constant rate, representing both endogenous processes and low-level environmental stress. This reaction acts as a source term for the DNA_damage species.
Repair Pathways:
Several mechanisms work to reduce DNA damage:
ATM-Mediated Repair: Active ATM facilitates the direct repair of DNA damage.
ATR-Mediated Repair: Active ATR, in cooperation with CHK1, repairs DNA damage.
NRF2-Mediated Repair: Active NRF2 triggers antioxidant responses that reduce DNA damage.
Autophagy-Mediated Repair: The autophagy pathway, induced by spermidine, repairs DNA damage in a saturable manner (modeled using Michaelis–Menten kinetics). This ensures that even a significant pulse of damage is only partially repaired, leaving a nonzero steady-state level.
2. ATM/ATR–p53 Signaling Module
ATM and ATR Activation:
DNA damage, along with a positive input from TOPBP1, converts inactive ATM and ATR to their active forms. Under ATM/ATR-deficient conditions (as in ataxia telangiectasia), the activation is severely reduced, resulting in higher levels of unrepaired DNA damage.
p53 Activation:
Both ATM_active and ATR_active phosphorylate and activate p53. Active p53 then acts as a central integrator of the DNA damage signal.
Regulatory Proteins:
HDAC4:
HDAC4 cycles between inactive and active states. Its active form can attenuate p53 activity.
TOPBP1:
TOPBP1 is activated in a DNA damage–dependent manner and helps promote ATR activation.
CK2:
CK2 is a constitutively active kinase that supports TOPBP1 activation.
3. NRF2/KEAP1 Module and Omaveloxolone
NRF2 Activation:
DNA damage stimulates the conversion of NRF2_inactive to NRF2_active. Active NRF2 enhances antioxidant defenses and promotes DNA repair.
KEAP1-Mediated Degradation:
Under normal conditions, KEAP1 targets NRF2_inactive for degradation, keeping NRF2 activity low.
Modulation by Omaveloxolone:
Omaveloxolone is modeled as a constant (boundary) species. It inhibits KEAP1’s activity, thereby reducing NRF2 degradation. This shifts the balance in favor of increased NRF2_active, which boosts the cell’s antioxidant and repair responses.
4. Spermidine-Induced Autophagy and Positive Modulation of ATR Signaling
Spermidine is modeled as a constant species and has two major effects:
Induction of Autophagy:
Spermidine promotes the conversion of Autophagy_inactive to Autophagy_active. The active autophagy machinery repairs DNA damage using a saturable (Michaelis–Menten) mechanism. This pathway helps clear DNA damage but is limited by its maximum capacity.
Enhancement of ATR Signaling:
Spermidine also positively modulates ATR signaling by enhancing the CK2-mediated activation of TOPBP1. In the model, the effective rate of TOPBP1 activation is increased proportionally to the concentration of spermidine. This is represented by a modulation factor, where the effective rate constant for TOPBP1 activation is multiplied by a term that increases with spermidine concentration. The boosted TOPBP1_active level in turn enhances ATR activation, partially compensating for the loss of ATM/ATR function.
5. Downstream p53 Targets: Cell Fate Decisions
Activated p53 regulates cell fate by inducing the production of several downstream effectors:
p21:
p21 is produced in response to p53 activation and is associated with cell cycle arrest and senescence. Its production is balanced by a degradation reaction.
BAX and PUMA:
Both BAX and PUMA are pro-apoptotic proteins. They are produced in proportion to p53_active and are subsequently degraded. Their relative levels help determine whether the cell will undergo apoptosis.
6. Reaction Kinetics (Qualitative Overview)
Mass-Action and Michaelis–Menten Kinetics:
Most reactions in the model are governed by mass-action kinetics. For example, activation and deactivation reactions (such as ATM activation by DNA damage or p53 activation by ATM/ATR) follow simple proportional relationships.
Saturable Repair Processes:
The autophagy-mediated DNA repair reaction uses Michaelis–Menten kinetics to reflect a saturation effect; when DNA damage is high, the repair rate approaches a maximum value, ensuring that not all damage is cleared immediately.
Modulatory Effects:
Spermidine increases the effective rate of TOPBP1 activation (and hence ATR activation) via a modulation term that is proportional to its concentration. Omaveloxolone reduces the degradation rate of NRF2 by inhibiting KEAP1.
Biological Implications and Model Utility
ATM/ATR Deficiency:
In ataxia telangiectasia, ATM/ATR functions are diminished, leading to increased DNA damage. The model simulates this scenario and examines how alternative pathways (NRF2-mediated repair, autophagy, and enhanced ATR signaling via spermidine) help mitigate the damage.
Drug Repositioning Predictions:
The model can be used to predict the outcomes of repositioning drugs:
Omaveloxolone is expected to stabilize NRF2, enhancing antioxidant defenses and reducing DNA damage.
Spermidine acts dually by promoting autophagy (with a saturable repair capacity) and by boosting ATR signaling via TOPBP1 activation.
Cell Fate Outcomes:
The downstream p53 targets (p21, BAX, and PUMA) serve as markers for cell cycle arrest/senescence and apoptosis. By simulating the dynamics of these proteins, the model can predict whether a cell is likely to survive, arrest its cycle, or undergo apoptosis based on the integrated response to DNA damage and drug interventions.
Conclusion
This detailed and comprehensive model integrates multiple layers of the cellular response to DNA damage in ATM/ATR-deficient conditions. It includes upstream damage sensing, multiple repair pathways (including direct kinase-mediated repair, antioxidant responses via NRF2, and autophagy-mediated repair), and downstream effectors that determine cell fate. Omaveloxolone and spermidine are modeled to specifically modulate the NRF2/KEAP1 pathway and ATR signaling (via TOPBP1 activation), respectively. This framework provides a robust platform for exploring drug repositioning strategies and predicting cellular outcomes in diseases such as ataxia telangiectasia.
2025-11-25 | MODEL2503190002 | BioModels
Project description:Microcephaly and medulloblastoma result from mutations that compromise genomic stability. We report that Atr, which is mutated in the microcephalic disorder Seckel syndrome, is required to maintain chromosomal integrity during postnatal cerebellar neurogenesis. Atr deletion in cerebellar granule neuron progenitors (CGNPs) induced proliferation-associated DNA damage, p53 activation, apoptosis, and cerebellar hypoplasia. Co-deletions of either Bax and Bak or p53 prevented apoptosis in Atr-deleted CGNPs, but failed to fully rescue cerebellar growth. Atr-deficient CGNPs showed impaired cell cycle checkpoint function and continued to proliferate, accumulating chromosomal abnormalities. RNA-Seq demonstrated that the transcriptional response to Atr-deficient proliferation was p53-driven. Acute Atr inhibition in vivo by nanoparticle-formulated VE-822 reproduced the disruptions seen with Atr deletion. Our data show that p53-driven apoptosis and senescence, and non-apoptotic cell death redundantly limit growth in Atr-deficient progenitors. These overlapping mechanisms that suppress growth in Atr-disrupted CGNPs may be exploited for treatment of CGNP-derived medulloblastoma using Atr inhibition.
2016-09-01 | GSE85393 | GEO
Project description:Microcephaly and medulloblastoma result from mutations that compromise genomic stability. We report that Atr, which is mutated in the microcephalic disorder Seckel syndrome, is required to maintain chromosomal integrity during postnatal cerebellar neurogenesis. Atr deletion in cerebellar granule neuron progenitors (CGNPs) induced proliferation-associated DNA damage, p53 activation, apoptosis, and cerebellar hypoplasia. Co-deletions of either Bax and Bak or p53 prevented apoptosis in Atr-deleted CGNPs, but failed to fully rescue cerebellar growth. Atr-deficient CGNPs showed impaired cell cycle checkpoint function and continued to proliferate, accumulating chromosomal abnormalities. RNA-Seq demonstrated that the transcriptional response to Atr-deficient proliferation was p53-driven. Acute Atr inhibition in vivo by nanoparticle-formulated VE-822 reproduced the disruptions seen with Atr deletion. Our data show that p53-driven apoptosis and senescence, and non-apoptotic cell death redundantly limit growth in Atr-deficient progenitors. These overlapping mechanisms that suppress growth in Atr-disrupted CGNPs may be exploited for treatment of CGNP-derived medulloblastoma using Atr inhibition.
2016-09-01 | GSE83720 | GEO
Project description:The DNA-damaging agent gemcitabine (GEM) is a first-line treatment for pancreatic cancer but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs including kinase inhibitors but the experimental evidence for such rational is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 140 clinical kinase inhibitors and observed strong synergy for the ATR inhibitor Elimusertib in most cell lines. Dose-dependent phosphoproteome profiling of four ATR inhibitors following DNA damage induction by GEM revealed a strong block of the DNA damage response pathway including phosphorylated pS468 of CHEK1 as the underlying mechanism of drug synergy. The current work provides a strong rationale for why the combination of GEM and ATR inhibition may be useful for the treatment of PDAC patients and constitutes a rich phenotypic and molecular resource for further investigating effective drug combinations.
2024-03-18 | MSV000094340 | MassIVE