Molecular mechanisms involved in initiation of the DNA damage response

The impact of a mixed neutron-gamma beam on the activation of DNA damage response (DDR) proteins and non-coding RNAs (ncRNAs) is poorly understood. Ionizing radiation is characterized by its biological effectiveness and is related to linear energy transfer (LET). Neutron-gamma mixed beam used in boron neutron capture therapy (BNCT) can induce another type of DNA damage such as clustered DNA or multiple damaged sites, as indicated for high LET particles, such as alpha particles, carbon ions, and protons. We speculate that after exposure to a mixed radiation field, the repair capacity might reduce, leading to unrepaired complex DNA damage for a long period and may promote genome instability and cell death. This review will focus on the poorly studied impact of neutron-gamma mixed beams with an emphasis on DNA damage and molecular mechanisms of repair. In case of BNCT, it is not clear which repair pathway is involved, and recent experimental work will be presented. Further understanding of BNCT-induced DDR mechanisms may lead to improved therapeutic efficiency against different tumors.

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High Fidelity Deep Sequencing Reveals No Effect of ATM, ATR, and DNA-PK Cellular DNA Damage Response Pathways on Adenovirus Mutation Rate

Viruses ◽

10.3390/v11100938 ◽

2019 ◽

Vol 11 (10) ◽

pp. 938 ◽

Cited By ~ 1

Author(s):

Risso-Ballester ◽

Sanjuán

Keyword(s):

Dna Damage ◽

Protein Kinase ◽

Dna Damage Response ◽

Deep Sequencing ◽

Molecular Mechanisms ◽

Spontaneous Mutation ◽

High Fidelity ◽

Dna Viruses ◽

Damage Response ◽

Cellular Dna

Most DNA viruses exhibit relatively low rates of spontaneous mutation. However, the molecular mechanisms underlying DNA virus genetic stability remain unclear. In principle, mutation rates should not depend solely on polymerase fidelity, but also on factors such as DNA damage and repair efficiency. Most eukaryotic DNA viruses interact with the cellular DNA damage response (DDR), but the role of DDR pathways in preventing mutations in the virus has not been tested empirically. To address this goal, we serially transferred human adenovirus type 5 in cells in which the telangiectasia-mutated PI3K-related protein kinase (ATM), the ATM/Rad3-related (ATR) kinase, and the DNA-dependent protein kinase (DNA-PK) were chemically inactivated, as well as in control cells displaying normal DDR pathway functioning. High-fidelity deep sequencing of these viral populations revealed mutation frequencies in the order of one-millionth, with no detectable effect of the inactivation of DDR mediators ATM, ATR, and DNA-PK on adenovirus sequence variability. This suggests that these DDR pathways do not play a major role in determining adenovirus genetic diversity.

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The nucleosome: orchestrating DNA damage signaling and repair within chromatin

Biochemistry and Cell Biology ◽

10.1139/bcb-2016-0017 ◽

2016 ◽

Vol 94 (5) ◽

pp. 381-395 ◽

Cited By ~ 15

Author(s):

Poonam Agarwal ◽

Kyle M. Miller

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Histone Modifications ◽

Chromatin Structure ◽

Molecular Mechanisms ◽

Current View ◽

Target Specificity ◽

Dna Damage Signaling ◽

Damage Response ◽

Transcription And Replication

DNA damage occurs within the chromatin environment, which ultimately participates in regulating DNA damage response (DDR) pathways and repair of the lesion. DNA damage activates a cascade of signaling events that extensively modulates chromatin structure and organization to coordinate DDR factor recruitment to the break and repair, whilst also promoting the maintenance of normal chromatin functions within the damaged region. For example, DDR pathways must avoid conflicts between other DNA-based processes that function within the context of chromatin, including transcription and replication. The molecular mechanisms governing the recognition, target specificity, and recruitment of DDR factors and enzymes to the fundamental repeating unit of chromatin, i.e., the nucleosome, are poorly understood. Here we present our current view of how chromatin recognition by DDR factors is achieved at the level of the nucleosome. Emerging evidence suggests that the nucleosome surface, including the nucleosome acidic patch, promotes the binding and activity of several DNA damage factors on chromatin. Thus, in addition to interactions with damaged DNA and histone modifications, nucleosome recognition by DDR factors plays a key role in orchestrating the requisite chromatin response to maintain both genome and epigenome integrity.

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Dissecting the Molecular Mechanisms of Aneuploidy in Acute Myeloid Leukemia By Next Generation Sequencing

Blood ◽

10.1182/blood.v124.21.1028.1028 ◽

2014 ◽

Vol 124 (21) ◽

pp. 1028-1028

Author(s):

Giorgia Simonetti ◽

Antonella Padella ◽

Anna Ferrari ◽

Viviana Guadagnuolo ◽

Elisa Zago ◽

...

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Dna Damage Response ◽

Myeloid Leukemia ◽

Molecular Mechanisms ◽

Chromosome Organization ◽

Single Nucleotide ◽

Damage Response ◽

Generation Sequencing ◽

Acute Myeloid

Abstract Acute Myeloid Leukemia (AML) is a heterogeneous malignancy characterized by the expansion of myeloid precursor cells with limited or abnormal differentiation capacity. A relatively common event in AML is represented by chromosome gain or loss. Numerical chromosome abnormalities, which define aneuploidy, have a detrimental effect in primary non-malignant cells, since they dramatically reduce cellular fitness. However, evidence suggests that they have a causative role in tumorigenesis and are well tolerated in transformed cells belonging to the myeloid lineage. Aim of the study is to elucidate the pathogenic mechanisms causing and sustaining aneuploidy in AML in order to find novel potential therapeutic targets. A panel of genetic alterations was analyzed on 886 AML cases at Seràgnoli Institute in Bologna between 2002 and 2013. Among them, 31 samples were subjected to whole exome sequencing (WES, Illumina Hiseq2000). Raw data were processed with WES Pipeline web tool for variants detection. Gene expression profiling (GEP, Affymetrix) was performed on bone marrow cells from 49 AML patients at diagnosis with more than 80% blast cells, including 22 aneuploid cases (carrying monosomy, trisomy or a monosomal karyotype) and 27 cases with normal karyotype. The aneuploid status was confirmed by single nucleotide polymorphism (SNP) array. WES analysis of 13 aneuploid and 12 euploid AML cases revealed a significantly higher median value of genetic variants and mutated genes in aneuploid compared with euploid samples (aneuploid vs. euploid: median of variants, 30 vs. 20 (p=0.02) including nonsynonimous single nucleotide variants, frameshift insertions and deletions, stopgains; median of mutated genes, 25 vs. 17 (p=0.05); details will be presented at the meeting). Noticeably, by gene ontology analysis of mutated genes in the aneuploid cohort we observed a strong enrichment in genes regulating cell cycle, including chromosome organization (p=5.4x10-4) and mitotic sister chromatid cohesion (p=6.98x10-4), and chromatin modification (p=1.3x10-4), with most of the variants being not annotated in the COSMIC database. Euploid samples were enriched for mutations affecting genes involved in cytoskeleton (p=1.6x10-3) and metabolic activities (p=1.9x10-3). A number of genes mutated in the aneuploid cases belong to the APCCdc20 complex and localize on chromosomes generally spared by aneuploidy, supporting the key role of the identified aberrations in the molecular mechanisms leading to numerical chromosome abnormalities. Among several mutations predicted as “drivers” by DOTS-Finder tool (CCDC144NL, DNMT3A, GXYLT1, MESP1, TPRX1,TPTE, ZNF717), we defined some candidates involved in cell cycle regulation and DNA replication. Functional analysis are ongoing. Furthermore, a tumor suppressor function was associated with mutated genes involved in the DNA repair process. In our WES analysis, we identified a subgroup of genes linked to DNA damage response, including TP53, which are preferentially mutated in the aneuploid cohort. Since P53 is a limiting-factor in aneuploidy-induced tumorigenesis, we analyzed the mutational status in a larger cohort of AML patients by Next Generation sequencing (NGS) and Sanger sequencing. Interestingly, we identified TP53 mutations in 15/58 aneuploid vs. 1/36 euploid cases (p=3.8x10-3). Finally, differential expression of genes involved in DNA damage and integrity checkpoints was identified by GEP of aneuploid and euploid AML samples. Previous evidence showed that loss of the spindle checkpoint gene BUB1B induces aneuploidy and predisposes to tumorigenesis. Our data, obtained by integrated NGS and GEP approaches, support a causal link between mutations in a panel of genes involved in cell cycle control/chromosome organization and aneuploidy in AML. Genetic and transcriptional alterations of genes regulating DNA damage response were detected in our AML cohort, suggesting novel molecular mechanisms for the acquisition and/or maintenance of the aneuploid condition and consequently, of leukemogenesis. The results indicate that the identified genomic aberrations likely drive chromosome gain and/or loss in AML by cooperating with alterations affecting different pathways, in order to overcome the unfitness barrier induced by aneuploidy. Supported by: FP7 NGS-PTL project, ELN, AIL, AIRC, PRIN, progetto Regione-Università 2010-12 (L. Bolondi). Disclosures Martinelli: Novartis: Consultancy, Speakers Bureau; BMS: Consultancy, Speakers Bureau; Pfizer: Consultancy; ARIAD: Consultancy.

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Exploring the Roles of HERC2 and the NEDD4L HECT E3 Ubiquitin Ligase Subfamily in p53 Signaling and the DNA Damage Response

Frontiers in Oncology ◽

10.3389/fonc.2021.659049 ◽

2021 ◽

Vol 11 ◽

Author(s):

Nicholas A. Mathieu ◽

Rafael H. Levin ◽

Donald E. Spratt

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Ubiquitin Ligase ◽

Posttranslational Modifications ◽

Molecular Mechanisms ◽

P53 Signaling ◽

Expression Of Genes ◽

Genetic Abnormalities ◽

Damage Response ◽

Precise Expression

Cellular homeostasis is governed by the precise expression of genes that control the translation, localization, and termination of proteins. Oftentimes, environmental and biological factors can introduce mutations into the genetic framework of cells during their growth and division, and these genetic abnormalities can result in malignant transformations caused by protein malfunction. For example, p53 is a prominent tumor suppressor protein that is capable of undergoing more than 300 posttranslational modifications (PTMs) and is involved with controlling apoptotic signaling, transcription, and the DNA damage response (DDR). In this review, we focus on the molecular mechanisms and interactions that occur between p53, the HECT E3 ubiquitin ligases WWP1, SMURF1, HECW1 and HERC2, and other oncogenic proteins in the cell to explore how irregular HECT-p53 interactions can induce tumorigenesis.

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Molecular mechanisms of Mn induced neurotoxicity: RONS generation, genotoxicity, and DNA-damage response

Molecular Nutrition & Food Research ◽

10.1002/mnfr.201200758 ◽

2013 ◽

Vol 57 (7) ◽

pp. 1255-1269 ◽

Cited By ~ 20

Author(s):

Julia Bornhorst ◽

Sören Meyer ◽

Till Weber ◽

Carolina Böker ◽

Talke Marschall ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Molecular Mechanisms ◽

Damage Response

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Replication fork dynamics and the DNA damage response

Biochemical Journal ◽

10.1042/bj20112100 ◽

2012 ◽

Vol 443 (1) ◽

pp. 13-26 ◽

Cited By ~ 77

Author(s):

Rebecca M. Jones ◽

Eva Petermann

Keyword(s):

Dna Damage ◽

Dna Replication ◽

Dna Damage Response ◽

Replication Fork ◽

Molecular Mechanisms ◽

S Phase ◽

Replication Initiation ◽

Developmental Defects ◽

Replication Fork Progression ◽

Damage Response

Prevention and repair of DNA damage is essential for maintenance of genomic stability and cell survival. DNA replication during S-phase can be a source of DNA damage if endogenous or exogenous stresses impair the progression of replication forks. It has become increasingly clear that DNA-damage-response pathways do not only respond to the presence of damaged DNA, but also modulate DNA replication dynamics to prevent DNA damage formation during S-phase. Such observations may help explain the developmental defects or cancer predisposition caused by mutations in DNA-damage-response genes. The present review focuses on molecular mechanisms by which DNA-damage-response pathways control and promote replication dynamics in vertebrate cells. In particular, DNA damage pathways contribute to proper replication by regulating replication initiation, stabilizing transiently stalled forks, promoting replication restart and facilitating fork movement on difficult-to-replicate templates. If replication fork progression fails to be rescued, this may lead to DNA damage and genomic instability via nuclease processing of aberrant fork structures or incomplete sister chromatid separation during mitosis.

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The Role of E3, E4 Ubiquitin Ligase (UBE4B) in Human Pathologies

Cancers ◽

10.3390/cancers12010062 ◽

2019 ◽

Vol 12 (1) ◽

pp. 62 ◽

Cited By ~ 1

Author(s):

Nikolaos Antoniou ◽

Nefeli Lagopati ◽

Dimitrios Ilias Balourdas ◽

Michail Nikolaou ◽

Alexandros Papalampros ◽

...

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Ubiquitin Ligase ◽

Molecular Mechanisms ◽

Ubiquitin Ligases ◽

Cellular Functions ◽

P53 Expression ◽

Damage Response ◽

Mechanisms Of Carcinogenesis

The genome is exposed daily to many deleterious factors. Ubiquitination is a mechanism that regulates several crucial cellular functions, allowing cells to react upon various stimuli in order to preserve their homeostasis. Ubiquitin ligases act as specific regulators and actively participate among others in the DNA damage response (DDR) network. UBE4B is a newly identified member of E3 ubiquitin ligases that appears to be overexpressed in several human neoplasms. The aim of this review is to provide insights into the role of UBE4B ubiquitin ligase in DDR and its association with p53 expression, shedding light particularly on the molecular mechanisms of carcinogenesis.

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The Prognostic Significance Of DUSP3 In DLBCL

Blood ◽

10.1182/blood.v122.21.3025.3025 ◽

2013 ◽

Vol 122 (21) ◽

pp. 3025-3025

Author(s):

Rachel R. Fang ◽

Yulian Xu ◽

Chen-feng Qi ◽

Herbert Morse ◽

Jeff Xiwu Zhou

Keyword(s):

Dna Damage ◽

Dna Damage Response ◽

Animal Studies ◽

Molecular Mechanisms ◽

Conflicts Of Interest ◽

Prognostic Significance ◽

B Cell Lymphoma ◽

Control Group ◽

Damage Response ◽

Low Levels

Abstract DUSP3 (also called VHR) is a member of the dual-specificity protein phosphatase family which can dephosphorylate target proteins at phosphoserine/threonine and phosphotyrosine residuals. There are evidences that DUSP3 is highly expressed in cervical and prostate cancers, and may exert its function in inhibiting apoptosis. By analyzing publicly available data on diffuse large B-cell lymphoma (DLBCL), we found that the expression levels of DUSP3 mRNA were inversely associated with overall survival (OS) in DLBCL. Patients with low levels of DUSP3 mRNA had significant longer OS than did those with high levels of DUSP3 (P=0.0002) (Figure 1). The association between the levels of DUSP3 mRNA and clinical outcome was confirmed using an independent DLBCL cohort. To decipher the role of DUSP3 in DLBCL, we used lentiviral system to stably express shRNA against DUSP3 in the DLBCL cell line, OCI-Ly01. Reduced expression of DUSP3 was associated with significantly decreased proliferation of cells as compared to the control group (P<0.001) (Figure 2). Because the standard chemotherapy for DLBCL depends largely on induction of DNA damage, we were interested in examining possible effects of DUSP3 on the DNA damage response. We found that the levels of phosphorylated H2A.X, a marker for DNA damage response, were significantly increased in cells with reduced levels of DUSP3 (P<0.01) (Figure 3). This may suggest that low levels of DUSP3 in tumor tissues render cells more vulnerable to therapy-induced DNA damage, leading to increasing efficacy of chemotherapy. More molecular and animal studies are underway to determine if DUSP3 can serve as a prognostic biomarker for DLBCL and to identify the underlying molecular mechanisms. Disclosures: No relevant conflicts of interest to declare.

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Accelerated carcinogenesis following liver regeneration is associated with chronic inflammation-induced double-strand DNA breaks

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0908867107 ◽

2010 ◽

Vol 107 (5) ◽

pp. 2207-2212 ◽

Cited By ~ 76

Author(s):

Hila Barash ◽

Eitan R. Gross ◽

Yifat Edrei ◽

Ezra Ella ◽

Ariel Israel ◽

...

Keyword(s):

Cell Cycle ◽

Dna Damage ◽

Liver Regeneration ◽

Chronic Inflammation ◽

Dna Damage Response ◽

Molecular Mechanisms ◽

Survival Rates ◽

Dna Breaks ◽

Double Strand Dna Breaks ◽

Damage Response

Hepatocellular carcinoma (HCC) is the third leading cause of cancer mortality worldwide and is considered to be the outcome of chronic liver inflammation. Currently, the main treatment for HCC is surgical resection. However, survival rates are suboptimal partially because of tumor recurrence in the remaining liver. Our aim was to understand the molecular mechanisms linking liver regeneration under chronic inflammation to hepatic tumorigenesis. Mdr2-KO mice, a model of inflammation-associated cancer, underwent partial hepatectomy (PHx), which led to enhanced hepatocarcinogenesis. Moreover, liver regeneration in these mice was severely attenuated. We demonstrate the activation of the DNA damage-response machinery and increased genomic instability during early liver inflammatory stages resulting in hepatocyte apoptosis, cell-cycle arrest, and senescence and suggest their involvement in tumor growth acceleration subsequent to PHx. We propose that under the regenerative proliferative stress induced by liver resection, the genomic unstable hepatocytes generated during chronic inflammation escape senescence and apoptosis and reenter the cell cycle, triggering the enhanced tumorigenesis. Thus, we clarify the immediate and long-term contributions of the DNA damage response to HCC development and recurrence.

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