Transcriptional profiling of the age-related response to genotoxic stress points to differential DNA damage response with age

Cells have developed response systems to constantly monitor environmental changes and accordingly adjust growth, differentiation, and cellular stress programs. The evolutionarily conserved, nutrient-responsive, mechanistic target of rapamycin signaling (mTOR) pathway coordinates basic anabolic and catabolic cellular processes such as gene transcription, protein translation, autophagy, and metabolism, and is directly implicated in cellular and organismal aging as well as age-related diseases. mTOR mediates these processes in response to a broad range of inputs such as oxygen, amino acids, hormones, and energy levels, as well as stresses, including DNA damage. Here, we briefly summarize data relating to the interplays of the mTOR pathway with DNA damage response pathways in fission yeast, a favorite model in cell biology, and how these interactions shape cell decisions, growth, and cell-cycle progression. We, especially, comment on the roles of caffeine-mediated DNA-damage override. Understanding the biology of nutrient response, DNA damage and related pharmacological treatments can lead to the design of interventions towards improved cellular and organismal fitness, health, and survival.

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MORC2 regulates DNA damage response through a PARP1-dependent pathway

Nucleic Acids Research ◽

10.1093/nar/gkz545 ◽

2019 ◽

Vol 47 (16) ◽

pp. 8502-8520 ◽

Cited By ~ 4

Author(s):

Lin Zhang ◽

Da-Qiang Li

Keyword(s):

Dna Damage ◽

Zinc Finger ◽

Chromatin Remodeling ◽

Dna Damage Response ◽

Mammalian Cells ◽

Cellular Response ◽

Genotoxic Stress ◽

Underlying Mechanism ◽

Dna Lesions ◽

Damage Response

Abstract Microrchidia family CW-type zinc finger 2 (MORC2) is a newly identified chromatin remodeling enzyme with an emerging role in DNA damage response (DDR), but the underlying mechanism remains largely unknown. Here, we show that poly(ADP-ribose) polymerase 1 (PARP1), a key chromatin-associated enzyme responsible for the synthesis of poly(ADP-ribose) (PAR) polymers in mammalian cells, interacts with and PARylates MORC2 at two residues within its conserved CW-type zinc finger domain. Following DNA damage, PARP1 recruits MORC2 to DNA damage sites and catalyzes MORC2 PARylation, which stimulates its ATPase and chromatin remodeling activities. Mutation of PARylation residues in MORC2 results in reduced cell survival after DNA damage. MORC2, in turn, stabilizes PARP1 through enhancing acetyltransferase NAT10-mediated acetylation of PARP1 at lysine 949, which blocks its ubiquitination at the same residue and subsequent degradation by E3 ubiquitin ligase CHFR. Consequently, depletion of MORC2 or expression of an acetylation-defective PARP1 mutant impairs DNA damage-induced PAR production and PAR-dependent recruitment of DNA repair proteins to DNA lesions, leading to enhanced sensitivity to genotoxic stress. Collectively, these findings uncover a previously unrecognized mechanistic link between MORC2 and PARP1 in the regulation of cellular response to DNA damage.

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Sensitivity of tumor cells deficient in the fanconi anemia pathway to inhibition of ataxia telangiectasia mutated (ATM)

Journal of Clinical Oncology ◽

10.1200/jco.2007.25.18_suppl.10509 ◽

2007 ◽

Vol 25 (18_suppl) ◽

pp. 10509-10509

Author(s):

R. D. Kennedy ◽

P. Stuckert ◽

E. Archila ◽

M. De LaVega ◽

C. Chen ◽

...

Keyword(s):

Dna Damage ◽

Cell Lines ◽

Dna Damage Response ◽

Fanconi Anemia ◽

Ataxia Telangiectasia ◽

Pancreatic Head ◽

Genotoxic Stress ◽

Ataxia Telangiectasia Mutated ◽

Chromosomal Breakage ◽

Damage Response

10509 Loss of the fanconi anemia (FA) pathway function has been described in a number of sporadic tumor types including breast, ovarian, pancreatic, head and neck and hematological malignancies. Functionally, the FA pathway responds to stalled DNA replication following DNA damage. Given the importance of the FA pathway in the response to DNA damage, we hypothesized that cells deficient in this pathway may become hyper-dependent on alternative DNA damage response pathways in order to respond to endogenous genotoxic stress such as occurs during metabolism. Therefore, targeting these alternative pathways could offer therapeutic strategies in FA pathway deficient tumors. To identify new therapeutic targets we treated FA pathway competent and deficient cells with a DNA damage response siRNA library, that individually knocked out 230 genes. We identified a number of gene targets that were specifically toxic to FA pathway deficient cells, amongst which was the DNA damage response kinase Ataxia Telangiectasia Mutated (ATM). To test the requirement for ATM in FA pathway deficient cells, we interbred Fancg ± Atm± mice. Consistent with the siRNA screen result, Fancg-/- Atm-/- mice were non viable and Fancg± Atm-/- and Fancg-/- Atm ± progeny were less frequent that would have been expected. Several human cell lines with FA gene mutations were observed to have constitutive activation of ATM which was markedly reduced on correction with the appropriate wild-type FA gene. Interestingly, FA pathway deficient cells, including the FANCC mutant and FANCG mutant pancreatic cancer cell lines, were selectively sensitive to monotherapy with the ATM inhibitor KU55933, as measured by dose inhibition and colony count assays. FA pathway deficient cells also demonstrated an increased level of chromosomal breakage, cell cycle arrest and apoptosis following KU55933 treatment when compared to FA pathway corrected cells. We conclude that FA pathway deficient cells have an increased requirement for ATM activation in order to respond to sporadic DNA damage. This offers the possibility that monotherapy with ATM inhibitors could be a therapeutic strategy for tumors that are deficient for the FA pathway. No significant financial relationships to disclose.

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Dynamics of plant histone modifications in response to DNA damage

Biochemical Journal ◽

10.1042/bj20111956 ◽

2012 ◽

Vol 445 (3) ◽

pp. 393-401 ◽

Cited By ~ 14

Author(s):

Georgina E. Drury ◽

Adam A. Dowle ◽

David A. Ashford ◽

Wanda M. Waterworth ◽

Jerry Thomas ◽

...

Keyword(s):

Dna Damage ◽

Histone Acetylation ◽

Dna Damage Response ◽

Genotoxic Stress ◽

Immunoblot Analysis ◽

X Rays ◽

Histone Proteins ◽

Post Translational Modifications ◽

Damage Response ◽

Dna Damage Signalling

DNA damage detection and repair take place in the context of chromatin, and histone proteins play important roles in these events. Post-translational modifications of histone proteins are involved in repair and DNA damage signalling processes in response to genotoxic stresses. In particular, acetylation of histones H3 and H4 plays an important role in the mammalian and yeast DNA damage response and survival under genotoxic stress. However, the role of post-translational modifications to histones during the plant DNA damage response is currently poorly understood. Several different acetylated H3 and H4 N-terminal peptides following X-ray treatment were identified using MS analysis of purified histones, revealing previously unseen patterns of histone acetylation in Arabidopsis. Immunoblot analysis revealed an increase in the relative abundance of the H3 acetylated N-terminus, and a global decrease in hyperacetylation of H4 in response to DNA damage induced by X-rays. Conversely, mutants in the key DNA damage signalling factor ATM (ATAXIA TELANGIECTASIA MUTATED) display increased histone acetylation upon irradiation, linking the DNA damage response with dynamic changes in histone modification in plants.

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Runx2 (Runt-Related Transcription Factor 2) Links the DNA Damage Response to Osteogenic Reprogramming and Apoptosis of Vascular Smooth Muscle Cells

Arteriosclerosis Thrombosis and Vascular Biology ◽

10.1161/atvbaha.120.315206 ◽

2020 ◽

Author(s):

Andrew M. Cobb ◽

Syabira Yusoff ◽

Robert Hayward ◽

Sadia Ahmad ◽

Mengxi Sun ◽

...

Keyword(s):

Dna Damage ◽

Transcription Factor ◽

Smooth Muscle ◽

Vascular Smooth Muscle ◽

Dna Damage Response ◽

Genotoxic Stress ◽

Dna Damage Signaling ◽

Damage Response ◽

Related Transcription Factor ◽

Osteogenic Gene

Objective: The development of ectopic vascular calcification is strongly linked with organismal aging, which is primarily caused by the accumulation of DNA damage over time. As Runx2 (Runt-related transcription factor 2) has been identified as a regulator of vascular smooth muscle cell osteogenic transition, a key component of vascular calcification, we examined the relationship between DNA damage and Runx2 activation. Approach and Results: We found genotoxic stress-stimulated Runx2 accumulation and transactivation of its osteogenic target genes, leading to enhanced calcification. Inhibition of DNA damage signaling attenuated this response. Runx2 localized to sites of DNA damage and participated in DNA repair by regulating phosphorylation events on histone H2AX, with exogenous expression of Runx2 resulting in unrepaired DNA damage and increased apoptosis. Mechanistically, Runx2 was PARylated in response to genotoxic stress, and inhibition of this modification disrupted its localization at DNA lesions and reduced its binding to osteogenic gene promoters. Conclusions: These data identify Runx2 as a novel component of the DNA damage response, coupling DNA damage signaling to both osteogenic gene transcription and apoptosis and providing a mechanism for accelerated mineralization in aging and chronic disease.

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Hof1 plays a checkpoint-related role in MMS-induced DNA damage response in Candida albicans

Molecular Biology of the Cell ◽

10.1091/mbc.e19-06-0316 ◽

2020 ◽

Vol 31 (5) ◽

pp. 348-359 ◽

Cited By ~ 3

Author(s):

Jinrong Feng ◽

Amjad Islam ◽

Bjorn Bean ◽

Jia Feng ◽

Samantha Sparapani ◽

...

Keyword(s):

Dna Damage ◽

Candida Albicans ◽

Mutant Strain ◽

Dna Damage Response ◽

Genotoxic Stress ◽

Dependent Manner ◽

Damage Response

Fifty-six strains from the GRACE collection were found to be sensitive to MMS upon repression. Deletion of the HOF1 gene renders sensitivity to genotoxic stress. Hof1 is genetically linked to the Rad53 pathway and is down-regulated in a Rad53-dependent manner. The importance of Hof1 in MMS response is reduced in a Rad23 or Rad4 mutant strain.

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Association of a DNA damage response deficiency (DDRD) assay with prognosis in resected esophageal and gastric adenocarcinoma.

Journal of Clinical Oncology ◽

10.1200/jco.2017.35.15_suppl.4026 ◽

2017 ◽

Vol 35 (15_suppl) ◽

pp. 4026-4026

Author(s):

Richard C. Turkington ◽

Laura A Knight ◽

Rosalie V. Douglas ◽

Jaine K. Blayney ◽

Leanne Stevenson ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Proportional Hazards ◽

Transcriptional Profiling ◽

Cox Proportional Hazards ◽

Distant Relapse ◽

Damage Response ◽

Formalin Fixed Paraffin Embedded ◽

Pre Treatment ◽

Neo Adjuvant Chemotherapy

4026 Background: Current strategies to guide the selection of neo-adjuvant or adjuvant therapy in esophageal and gastric adenocarcinomas (EAC/GAC) are inadequate. We assessed a clinically validated 44 gene DNA Damage Response Deficiency (DDRD) assay to predict prognosis following neo-adjuvant DNA damaging chemotherapy (CT) in EAC and adjuvant CT or chemo-radiotherapy (CRT) in GAC. Methods: Transcriptional profiling of 273 formalin fixed paraffin embedded pre-treatment endoscopic EAC biopsies was performed using the Almac Diagnostics Xcel array. All EAC patients were treated with cisplatin-based neo-adjuvant chemotherapy followed by surgical resection between 2003 and 2014 at four UK centers in the OCCAMS consortium. Further validation was performed using a publically available dataset of 270 resected gastric cancers treated with adjuvant platinum-based CT, CRT or surgery alone at the Samsung Medical Centre, Seoul, Korea. The association between the DDRD score and prognosis was assessed by Kaplan-Meier analysis and Cox Proportional Hazards regression. Results: A total of 66 EAC samples (24%) were characterized as DDRD positive with the remaining 207 samples (76%) being DDRD negative. DDRD assay positivity was associated with improved DFS (HR 0.58; 95% CI 0.36-0.93; p = 0.024) and OS (HR 0.56; 95% CI 0.34-0.92; p = 0.023) following multivariate analysis. DDRD positive patients had a higher pathological response rate (p = 0.033) and a higher rate of loco-regional versus distant relapse (30% vs 20%; p = 0.013). For GAC, 132 samples (49%) were characterized as DDRD positive with the remaining 138 (51%) being DDRD negative. DDRD positivity was associated with improved DFS (HR 0.48; 95% CI 0.25-0.96; p = 0.037) following D2 gastrectomy and adjuvant CT or CRT. DDRD status was not associated with DFS in the surgery alone cohort (HR 0.87; 95% CI 0.55-1.38; p = 0.562). Conclusions: The DDRD assay is strongly predictive of benefit from DNA damaging neo-adjuvant CT and esophagectomy in EAC and gastrectomy and CT/CRT in GAC and can be applied to routine diagnostic material.

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A Role for NIPA in DNA Damage Response.

Blood ◽

10.1182/blood.v104.11.1265.1265 ◽

2004 ◽

Vol 104 (11) ◽

pp. 1265-1265

Author(s):

Christine von Klitzing ◽

Florian Bassermann ◽

Stephan W. Morris ◽

Christian Peschel ◽

Justus Duyster

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Dna Damage Response ◽

Phosphorylation Site ◽

Genotoxic Stress ◽

S Phase ◽

Damage Response ◽

A Cell ◽

Cycle Dependent

Abstract The nuclear interaction partner of ALK (NIPA) is a nuclear protein identified by our group in a screen for NPM-ALK interaction partners. We recently reported that NIPA is an F-box protein that assembles with SKP1, Cul1 and Roc1 to establish a novel SCF-type E3 ubiquitin ligase. The formation of the SCFNIPA complex is regulated by cell cycle-dependent phosphorylation of NIPA that restricts SCFNIPA assembly from G1- to late S-phase, thus allowing its substrates to be active from late S-phase throughout mitosis. Proteins involved in cell cycle regulation frequently play a role in DNA damage checkpoints. We therefore sought to determine whether NIPA has a function in the cellular response to genotoxic stress. For this reason we treated NIH/3T3 cells with various DNA-damaging agents. Surprisingly, we observed phosphorylation of NIPA in response to some of these agents, including UV radiation. This phosphorylation was cell cycle phase independent and thus independent of the physiological cell cycle dependent phosphorylation of NIPA. The relevant phosphorylation site is identical to the respective site in the course of cell cycle-dependent phosphorylation of NIPA. Thus, phosphorylation of NIPA upon genotoxic stress would inactivate the SCFNIPA complex in a cell cycle independent manner. Interestingly, this phosphorylation site lies within a consensus site of the Chk1/Chk2 checkpoint kinases. These kinases are central to DNA damage checkpoint signaling. Chk1 is activated by ATR in response to blocked replication forks as they occur after treatment with UV. We performed experiments using the ATM/ATR inhibitor caffeine and the Chk1 inhibitor SB218078 to investigate a potential role of Chk1 in NIPA phosphorylation. Indeed, we found both inhibitors to prevent UV-induced phosphorylation of NIPA. Current experiments applying Chk1 knock-out cells will unravel the role of Chk1 in NIPA phosphorylation. Additional experiments were performed to investigate a function for NIPA in DNA-damage induced apoptosis. In this regard, we observed overexpression of NIPA WT to induce apoptosis in response to UV, whereas no proapoptotic effect was seen with the phosphorylation deficient NIPA mutant. Therefore, the phosphorylated form of NIPA may be involved in apoptotic signaling pathways. In summary, we present data suggesting a cell cycle independent function for NIPA. This activity is involved in DNA damage response and may be involved in regulating apoptosis upon genotoxic stress.

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G Protein-Coupled Receptor Systems as Crucial Regulators of DNA Damage Response Processes

International Journal of Molecular Sciences ◽

10.3390/ijms19102919 ◽

2018 ◽

Vol 19 (10) ◽

pp. 2919 ◽

Cited By ~ 11

Author(s):

Hanne Leysen ◽

Jaana van Gastel ◽

Jhana Hendrickx ◽

Paula Santos-Otte ◽

Bronwen Martin ◽

...

Keyword(s):

Dna Damage ◽

G Protein ◽

Dna Damage Response ◽

Dna Damage And Repair ◽

Signaling Systems ◽

Age Related ◽

Complex Biological Process ◽

Damage Response ◽

G Protein Coupled

G protein-coupled receptors (GPCRs) and their associated proteins represent one of the most diverse cellular signaling systems involved in both physiological and pathophysiological processes. Aging represents perhaps the most complex biological process in humans and involves a progressive degradation of systemic integrity and physiological resilience. This is in part mediated by age-related aberrations in energy metabolism, mitochondrial function, protein folding and sorting, inflammatory activity and genomic stability. Indeed, an increased rate of unrepaired DNA damage is considered to be one of the ‘hallmarks’ of aging. Over the last two decades our appreciation of the complexity of GPCR signaling systems has expanded their functional signaling repertoire. One such example of this is the incipient role of GPCRs and GPCR-interacting proteins in DNA damage and repair mechanisms. Emerging data now suggest that GPCRs could function as stress sensors for intracellular damage, e.g., oxidative stress. Given this role of GPCRs in the DNA damage response process, coupled to the effective history of drug targeting of these receptors, this suggests that one important future activity of GPCR therapeutics is the rational control of DNA damage repair systems.

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