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DNA Damage Response (DDR) and DNA Repair 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 10870

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Guest Editor
Department Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
Interests: genetics; chromosome structure and segregation; DNA repair; cell division
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Special Issue Information

Dear Colleagues,

A large body of evidence indicates that DNA alterations such as chromosome aberrations and mutations can lead to several diseases, including cancer, and affect some aspects of aging. Each cell in the human body receives tens of thousands of DNA lesions per day that threaten the integrity of the genome. DNA lesions include base oxidation or alkylation, mismatch of nucleotides, crosslinks between intra- or inter- DNA strands, and single or double DNA strand breaks. Cells have evolved several mechanisms to counteract these various types of DNA damage, the importance of which is emphasized by the fact that mutations in genes required for DNA damage response (DDR) and DNA repair can result in genetic disorders, genomic instability, or cancer predisposition. In addition to radiations (i.e., UV light, X-rays) or chemicals, endogenous processes of oxidative stress and inflammation also cause DNA damage. Furthermore, there is accumulating evidence on how diet can have an impact on DNA and, ultimately, on cancer. The deficiency of micronutrients such as minerals and vitamins—which work as cofactors of enzymes involved in DNA metabolism— has been shown to cause single- and double-strand breaks, oxidative lesions, or both. Moreover, micronutrients can influence DNA folding and remodeling, an essential part of accurate double-strand break repair.

Although a significant number of studies concerning all these topics have been published over the past several decades. more investigation is required to reach a deeper understanding of the underlying molecular mechanisms. In this Special Issue, we aim to offer a comprehensive overview of the current understanding of mechanisms at the basis of DNA integrity maintenance and explore how the impairment of these mechanisms can lead to human diseases such as cancer or neurodegenerative diseases. 

This Special Issue invites original studies and review articles covering the following themes:

  1. Mechanisms at the basis of DDR and DNA repair;
  2. Biological consequences of deficiency in DDR and DNA repair;
  3. Maintenance of genome stability;
  4. Relationship between metabolism and DNA damage;
  5. How chromatin structure influences repair processes;
  6. Perspective or preclinical implications of genome instability in genetic disorders, neurodegenerative diseases, and cancer using cells and animal models.

Dr. Fiammetta Verni
Guest Editor

Manuscript Submission Information

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Keywords

  • DDR
  • DNA repair
  • genome stability

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Published Papers (4 papers)

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Research

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15 pages, 3369 KiB  
Article
CellTool: An Open-Source Software Combining Bio-Image Analysis and Mathematical Modeling for the Study of DNA Repair Dynamics
by Georgi Danovski, Teodora Dyankova-Danovska, Rumen Stamatov, Radoslav Aleksandrov, Petar-Bogomil Kanev and Stoyno Stoynov
Int. J. Mol. Sci. 2023, 24(23), 16784; https://doi.org/10.3390/ijms242316784 - 26 Nov 2023
Cited by 4 | Viewed by 1076
Abstract
Elucidating the dynamics of DNA repair proteins is essential to understanding the mechanisms that preserve genomic stability and prevent carcinogenesis. However, the measurement and modeling of protein dynamics at DNA lesions via currently available image analysis tools is cumbersome. Therefore, we developed CellTool—a [...] Read more.
Elucidating the dynamics of DNA repair proteins is essential to understanding the mechanisms that preserve genomic stability and prevent carcinogenesis. However, the measurement and modeling of protein dynamics at DNA lesions via currently available image analysis tools is cumbersome. Therefore, we developed CellTool—a stand-alone open-source software with a graphical user interface for the analysis of time-lapse microscopy images. It combines data management, image processing, mathematical modeling, and graphical presentation of data in a single package. Multiple image filters, segmentation, and particle tracking algorithms, combined with direct visualization of the obtained results, make CellTool an ideal application for the comprehensive analysis of DNA repair protein dynamics. This software enables the fitting of obtained kinetic data to predefined or custom mathematical models. Importantly, CellTool provides a platform for easy implementation of custom image analysis packages written in a variety of programing languages. Using CellTool, we demonstrate that the ALKB homolog 2 (ALKBH2) demethylase is excluded from DNA damage sites despite recruitment of its putative interaction partner proliferating cell nuclear antigen (PCNA). Further, CellTool facilitates the straightforward fluorescence recovery after photobleaching (FRAP) analysis of BRCA1 associated RING domain 1 (BARD1) exchange at complex DNA lesions. In summary, the software presented herein enables the time-efficient analysis of a wide range of time-lapse microscopy experiments through a user-friendly interface. Full article
(This article belongs to the Special Issue DNA Damage Response (DDR) and DNA Repair 2.0)
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12 pages, 303 KiB  
Article
Clinical Impact of Next-Generation Sequencing Multi-Gene Panel Highlighting the Landscape of Germline Alterations in Ovarian Cancer Patients
by Giorgia Gurioli, Gianluca Tedaldi, Alberto Farolfi, Elisabetta Petracci, Claudia Casanova, Giuseppe Comerci, Rita Danesi, Valentina Arcangeli, Mila Ravegnani, Daniele Calistri, Valentina Zampiga, Ilaria Cangini, Eugenio Fonzi, Alessandra Virga, Davide Tassinari, Marta Rosati, Paola Ulivi and Ugo De Giorgi
Int. J. Mol. Sci. 2022, 23(24), 15789; https://doi.org/10.3390/ijms232415789 - 13 Dec 2022
Cited by 3 | Viewed by 1512
Abstract
BRCA1 and BRCA2 are the most frequently mutated genes in ovarian cancer (OC) crucial both for the identification of cancer predisposition and therapeutic choices. However, germline variants in other genes could be involved in OC susceptibility. We characterized OC patients to detect mutations [...] Read more.
BRCA1 and BRCA2 are the most frequently mutated genes in ovarian cancer (OC) crucial both for the identification of cancer predisposition and therapeutic choices. However, germline variants in other genes could be involved in OC susceptibility. We characterized OC patients to detect mutations in genes other than BRCA1/2 that could be associated with a high risk of developing OC and permit patients to enter the most appropriate treatment and surveillance program. Next-generation sequencing analysis with a 94-gene panel was performed on germline DNA of 219 OC patients. We identified 34 pathogenic/likely pathogenic variants in BRCA1/2 and 38 in other 21 genes. The patients with pathogenic/likely pathogenic variants in the non-BRCA1/2 genes mainly developed OC alone compared to the other groups that also developed breast cancer or other tumors (p = 0.001). Clinical correlation analysis showed that the low-risk patients were significantly associated with platinum sensitivity (p < 0.001). Regarding PARP inhibitors (PARPi) response, the patients with pathogenic mutations in the non-BRCA1/2 genes had worse PFS and OS. Moreover, a statistically significantly worse PFS was found for every increase of one thousand platelets before PARPi treatment. To conclude, knowledge about molecular alterations in genes beyond BRCA1/2 in OC could allow for more personalized diagnostic, predictive, prognostic, and therapeutic strategies for OC patients. Full article
(This article belongs to the Special Issue DNA Damage Response (DDR) and DNA Repair 2.0)

Review

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23 pages, 970 KiB  
Review
How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants
by Miriam Szurman-Zubrzycka, Paulina Jędrzejek and Iwona Szarejko
Int. J. Mol. Sci. 2023, 24(3), 2404; https://doi.org/10.3390/ijms24032404 - 26 Jan 2023
Cited by 11 | Viewed by 2692
Abstract
DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. [...] Read more.
DNA damage is induced by many factors, some of which naturally occur in the environment. Because of their sessile nature, plants are especially exposed to unfavorable conditions causing DNA damage. In response to this damage, the DDR (DNA damage response) pathway is activated. This pathway is highly conserved between eukaryotes; however, there are some plant-specific DDR elements, such as SOG1—a transcription factor that is a central DDR regulator in plants. In general, DDR signaling activates transcriptional and epigenetic regulators that orchestrate the cell cycle arrest and DNA repair mechanisms upon DNA damage. The cell cycle halts to give the cell time to repair damaged DNA before replication. If the repair is successful, the cell cycle is reactivated. However, if the DNA repair mechanisms fail and DNA lesions accumulate, the cell enters the apoptotic pathway. Thereby the proper maintenance of DDR is crucial for plants to survive. It is particularly important for agronomically important species because exposure to environmental stresses causing DNA damage leads to growth inhibition and yield reduction. Thereby, gaining knowledge regarding the DDR pathway in crops may have a huge agronomic impact—it may be useful in breeding new cultivars more tolerant to such stresses. In this review, we characterize different genotoxic agents and their mode of action, describe DDR activation and signaling and summarize DNA repair mechanisms in plants. Full article
(This article belongs to the Special Issue DNA Damage Response (DDR) and DNA Repair 2.0)
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32 pages, 657 KiB  
Review
DNA Damage Response in Cancer Therapy and Resistance: Challenges and Opportunities
by Dana Jurkovicova, Christiana M. Neophytou, Ana Čipak Gašparović and Ana Cristina Gonçalves
Int. J. Mol. Sci. 2022, 23(23), 14672; https://doi.org/10.3390/ijms232314672 - 24 Nov 2022
Cited by 24 | Viewed by 4852
Abstract
Resistance to chemo- and radiotherapy is a common event among cancer patients and a reason why new cancer therapies and therapeutic strategies need to be in continuous investigation and development. DNA damage response (DDR) comprises several pathways that eliminate DNA damage to maintain [...] Read more.
Resistance to chemo- and radiotherapy is a common event among cancer patients and a reason why new cancer therapies and therapeutic strategies need to be in continuous investigation and development. DNA damage response (DDR) comprises several pathways that eliminate DNA damage to maintain genomic stability and integrity, but different types of cancers are associated with DDR machinery defects. Many improvements have been made in recent years, providing several drugs and therapeutic strategies for cancer patients, including those targeting the DDR pathways. Currently, poly (ADP-ribose) polymerase inhibitors (PARP inhibitors) are the DDR inhibitors (DDRi) approved for several cancers, including breast, ovarian, pancreatic, and prostate cancer. However, PARPi resistance is a growing issue in clinical settings that increases disease relapse and aggravate patients’ prognosis. Additionally, resistance to other DDRi is also being found and investigated. The resistance mechanisms to DDRi include reversion mutations, epigenetic modification, stabilization of the replication fork, and increased drug efflux. This review highlights the DDR pathways in cancer therapy, its role in the resistance to conventional treatments, and its exploitation for anticancer treatment. Biomarkers of treatment response, combination strategies with other anticancer agents, resistance mechanisms, and liabilities of treatment with DDR inhibitors are also discussed. Full article
(This article belongs to the Special Issue DNA Damage Response (DDR) and DNA Repair 2.0)
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