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DNA Damage and Repair in Biology and Medicine

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

Deadline for manuscript submissions: closed (15 November 2022) | Viewed by 19107

Special Issue Editors


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Guest Editor
Department of Biochemistry and Molecular Biology, Faculty of Medicine and Odontology-INCLIVA, Service of Clinical Analysis, Dr. Peset University Hospital -FISABIO, University of Valencia, Avda. Blasco Ibañez 15, 36010 Valencia, Spain
Interests: oxidative stress-induced DNA damage and repair and its repair mechanisms in cardiometabolic and cancer diseases
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Endocrinology and Nutrition Department, University Hospital Dr Peset-FISABIO, 46017 Valencia, Spain
Interests: oxidative stress; metabolism; obesity; mitochondria; inflammation; functional foods
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Despite its strategic location and apparent protection, the integrity of the genetic material is the result of a continuous and delicate balance between the mechanisms that induce its injury and those in charge of its repair, whose effectiveness is vital for the normal functioning of the cells and the perpetuity in the transmission of the genetic message in a faithful way. The modalities and mechanisms of DNA damage are very varied, including different forms of structural modification and functional alteration. Together with exogenous factors such as those induced by chemical agents and ionizing radiation, cells must cope with a rate of genetic damage of 103 to 106 impacts per cell and day to which normal aerobic metabolism contributes, with the production of reactive species of oxygen (ROS) (3-5% of breathed oxygen) and the consequent alteration of the redox balance which may have profound effects on the regulation of cell signaling pathways. In DNA molecule structure, many of these lesions can stop replication and alter or inhibit gene transcription. Other lesions, if not repaired before replication takes place, may induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells after it undergoes mitosis. Genomic instability is an essential step in the development of age associated comorbidities, such as cardiometabolic disorders, tissue failure and tumor processes. Higher animals, microorganisms, and plants are susceptible to this potential hazard. Fortunately, evolution has allowed the development of a plethora of diverse, specific and efficient DNA repair systems, under the control of multiple molecules and transcriptional factors. The TP53 protein, also known as the guardian of the genome, together with other onco and tumor suppressor proteins are representative examples.
It is vitally important to know in detail both the mechanisms that lead to genetic instability and those that prevent and repair it. In this sense, the Special Issue "DNA damage and repair in biology in medicine" tries to bring together contributions by research groups that bring new light on their molecular mechanisms and future perspectives on their translational applications.

Prof. Dr. Guillermo T. Sáez
Dr. Celia Banuls
Guest Editors

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Published Papers (8 papers)

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Research

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12 pages, 948 KiB  
Article
Oxidative Stress and DNA Damage Markers in Colorectal Cancer
by Delia Acevedo-León, Lidia Monzó-Beltrán, Laura Pérez-Sánchez, Eva Naranjo-Morillo, Segundo Ángel Gómez-Abril, Nuria Estañ-Capell, Celia Bañuls and Guillermo Sáez
Int. J. Mol. Sci. 2022, 23(19), 11664; https://doi.org/10.3390/ijms231911664 - 01 Oct 2022
Cited by 11 | Viewed by 1723
Abstract
Oxidative stress (OS) and inflammation are known to play an important role in chronic diseases, including cancer, and specifically colorectal cancer (CRC). The main objective of this study was to explore the diagnostic potential of OS markers in patients with CRC, which may [...] Read more.
Oxidative stress (OS) and inflammation are known to play an important role in chronic diseases, including cancer, and specifically colorectal cancer (CRC). The main objective of this study was to explore the diagnostic potential of OS markers in patients with CRC, which may translate into an early diagnosis of the disease. To do this, we compared results with those in a group of healthy controls and assessed whether there were significant differences. In addition, we explored possible correlations with the presence of tumors and tumor stage, with anemia and with inflammatory markers used in clinical practice. The study included 80 patients with CRC and 60 healthy controls. The following OS markers were analyzed: catalase (CAT), reduced glutathione (GSH) and oxidized glutathione (GSSG) in serum; and 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) and F2-isoprotanes in urine (F2-IsoPs). Tumor markers (CEA and CA 19.9), anemia markers (hemoglobin, hematocrit and medium corpuscular volume) and inflammatory markers (leukocytes, neutrophils, N/L index, platelets, fibrinogen, C-reactive protein, CRP and IL-6) were also determined. Comparison of means between patients and controls revealed highly significant differences for all OS markers, with an increase in the prooxidant markers GSSG, GSSG/GSH ratio, 8-oxodG and F2-IsoPs, and a decrease in the antioxidant markers CAT and GSH. Tumor and inflammatory markers (except CRP) correlated positively with GSSG, GSSG/GSH ratio, 8-oxodG and F2-IsoPs, and negatively with CAT and GSH. In view of the results obtained, OS markers may constitute a useful tool for the early diagnosis of CRC patients. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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17 pages, 1687 KiB  
Article
An Integrated Approach Reveals DNA Damage and Proteotoxic Stress as Main Effects of Proton Radiation in S. cerevisiae
by Laura Vanderwaeren, Rüveyda Dok, Karin Voordeckers, Laura Vandemaele, Kevin J. Verstrepen and Sandra Nuyts
Int. J. Mol. Sci. 2022, 23(10), 5493; https://doi.org/10.3390/ijms23105493 - 14 May 2022
Cited by 2 | Viewed by 2066
Abstract
Proton radiotherapy (PRT) has the potential to reduce the normal tissue toxicity associated with conventional photon-based radiotherapy (X-ray therapy, XRT) because the active dose can be more directly targeted to a tumor. Although this dosimetric advantage of PRT is well known, the molecular [...] Read more.
Proton radiotherapy (PRT) has the potential to reduce the normal tissue toxicity associated with conventional photon-based radiotherapy (X-ray therapy, XRT) because the active dose can be more directly targeted to a tumor. Although this dosimetric advantage of PRT is well known, the molecular mechanisms affected by PRT remain largely elusive. Here, we combined the molecular toolbox of the eukaryotic model Saccharomyces cerevisiae with a systems biology approach to investigate the physiological effects of PRT compared to XRT. Our data show that the DNA damage response and protein stress response are the major molecular mechanisms activated after both PRT and XRT. However, RNA-Seq revealed that PRT treatment evoked a stronger activation of genes involved in the response to proteotoxic stress, highlighting the molecular differences between PRT and XRT. Moreover, inhibition of the proteasome resulted in decreased survival in combination with PRT compared to XRT, not only further confirming that protons induced a stronger proteotoxic stress response, but also hinting at the potential of using proteasome inhibitors in combination with proton radiotherapy in clinical settings. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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17 pages, 4036 KiB  
Article
Glucose Increases STAT3 Activation, Promoting Sustained XRCC1 Expression and Increasing DNA Repair
by Griffin M. Wright and Natalie R. Gassman
Int. J. Mol. Sci. 2022, 23(8), 4314; https://doi.org/10.3390/ijms23084314 - 13 Apr 2022
Cited by 1 | Viewed by 1816
Abstract
Dysregulation of DNA repair is a hallmark of cancer, though few cancer-specific mechanisms that drive the overexpression of DNA repair proteins are known. We previously identified STAT3 as a novel transcriptional regulator of X-ray cross-complementing group 1 (XRCC1), an essential scaffold protein in [...] Read more.
Dysregulation of DNA repair is a hallmark of cancer, though few cancer-specific mechanisms that drive the overexpression of DNA repair proteins are known. We previously identified STAT3 as a novel transcriptional regulator of X-ray cross-complementing group 1 (XRCC1), an essential scaffold protein in base excision repair in triple-negative breast cancers. We also identified an inducible response to IL-6 and epidermal growth factor stimulation in the non-tumorigenic embryonic kidney cell line HEK293T. As IL-6 and EGF signaling are growth and inflammatory-inducible responses, we examined if glucose challenge can increase STAT3 activation, promoting adaptive changes in XRCC1 expression in different cell types. Acute high glucose exposure promoted XRCC1 expression through STAT3 activation, increasing the repair of methyl methanesulfonate-induced DNA damage in HEK293T cells and the osteosarcoma cell line U2OS. Sustained exposure to high glucose promoted the overexpression of XRCC1, which can be reversed upon glucose restriction and down-regulation of STAT3 activation. Thus, we have identified a novel link between XRCC1 expression and STAT3 activation following exogenous exposures, which could play a critical role in dictating a cancer cell’s response to DNA-damaging agents. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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15 pages, 4601 KiB  
Article
BRCA2 C-Terminal RAD51-Binding Domain Confers Resistance to DNA-Damaging Agents
by Zida Zhu, Taisuke Kitano, Masami Morimatsu, Arisa Tanaka, Ryo Morioka, Xianghui Lin, Koichi Orino and Yasunaga Yoshikawa
Int. J. Mol. Sci. 2022, 23(7), 4060; https://doi.org/10.3390/ijms23074060 - 06 Apr 2022
Viewed by 2210
Abstract
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In [...] Read more.
Breast cancer type 2 susceptibility (BRCA2) protein is crucial for initiating DNA damage repair after chemotherapy with DNA interstrand crosslinking agents or X-ray irradiation, which induces DNA double-strand breaks. BRCA2 contains a C-terminal RAD51-binding domain (CTRBD) that interacts with RAD51 oligomer-containing nucleofilaments. In this study, we investigated CTRBD expression in cells exposed to X-ray irradiation and mitomycin C treatment. Surprisingly, BRCA2 CTRBD expression in HeLa cells increased their resistance to X-ray irradiation and mitomycin C. Under endogenous BRCA2 depletion using shRNA, the sensitivities of the BRCA2-depleted cells with and without the CTRBD did not significantly differ. Thus, the resistance to X-ray irradiation conferred by an exogenous CTRBD required endogenous BRCA2 expression. BRCA2 CTRBD-expressing cells demonstrated effective RAD51 foci formation and increased homologous recombination efficiency, but not nonhomologous end-joining efficiency. To the best of our knowledge, our study is the first to report the ability of the BRCA2 functional domain to confer resistance to X-ray irradiation and mitomycin C treatment by increased homologous recombination efficiency. Thus, this peptide may be useful for protecting cells against X-ray irradiation or chemotherapeutic agents. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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15 pages, 2311 KiB  
Article
Nucleotide Excision Repair Pathway Activity Is Inhibited by Airborne Particulate Matter (PM10) through XPA Deregulation in Lung Epithelial Cells
by Ericka Marel Quezada-Maldonado, Yolanda I. Chirino, María Eugenia Gonsebatt, Rocío Morales-Bárcenas, Yesennia Sánchez-Pérez and Claudia M. García-Cuellar
Int. J. Mol. Sci. 2022, 23(4), 2224; https://doi.org/10.3390/ijms23042224 - 17 Feb 2022
Cited by 1 | Viewed by 1799
Abstract
Airborne particulate matter with a diameter size of ≤10 µm (PM10) is a carcinogen that contains polycyclic aromatic hydrocarbons (PAH), which form PAH–DNA adducts. However, the way in which these adducts are managed by DNA repair pathways in cells exposed to [...] Read more.
Airborne particulate matter with a diameter size of ≤10 µm (PM10) is a carcinogen that contains polycyclic aromatic hydrocarbons (PAH), which form PAH–DNA adducts. However, the way in which these adducts are managed by DNA repair pathways in cells exposed to PM10 has been partially described. We evaluated the effect of PM10 on nucleotide excision repair (NER) activity and on the levels of different proteins of this pathway that eliminate bulky DNA adducts. Our results showed that human lung epithelial cells (A549) exposed to 10 µg/cm2 of PM10 exhibited PAH–DNA adducts as well as an increase in RAD23 and XPD protein levels (first responders in NER). In addition, PM10 increased the levels of H4K20me2, a recruitment signal for XPA. However, we observed a decrease in total and phosphorylated XPA (Ser196) and an increase in phosphatase WIP1, aside from the absence of XPA–RPA complex, which participates in DNA-damage removal. Additionally, an NER activity assay demonstrated inhibition of the NER functionality in cells exposed to PM10, indicating that XPA alterations led to deficiencies in DNA repair. These results demonstrate that PM10 exposure induces an accumulation of DNA damage that is associated with NER inhibition, highlighting the role of PM10 as an important contributor to lung cancer. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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13 pages, 830 KiB  
Article
Monte Carlo Simulation of Double-Strand Break Induction and Conversion after Ultrasoft X-rays Irradiation
by Ya-Yun Hsiao, Fang-Hsin Chen, Chun-Chieh Chan and Ching-Chih Tsai
Int. J. Mol. Sci. 2021, 22(21), 11713; https://doi.org/10.3390/ijms222111713 - 28 Oct 2021
Cited by 4 | Viewed by 1662
Abstract
This paper estimates the yields of DNA double-strand breaks (DSBs) induced by ultrasoft X-rays and uses the DSB yields and the repair outcomes to evaluate the relative biological effectiveness (RBE) of ultrasoft X-rays. We simulated the yields of DSB induction and [...] Read more.
This paper estimates the yields of DNA double-strand breaks (DSBs) induced by ultrasoft X-rays and uses the DSB yields and the repair outcomes to evaluate the relative biological effectiveness (RBE) of ultrasoft X-rays. We simulated the yields of DSB induction and predicted them in the presence and absence of oxygen, using a Monte Carlo damage simulation (MCDS) software, to calculate the RBE. Monte Carlo excision repair (MCER) simulations were also performed to calculate the repair outcomes (correct repairs, mutations, and DSB conversions). Compared to 60Co γ-rays, the RBE values for ultrasoft X-rays (titanium K-shell, aluminum K-shell, copper L-shell, and carbon K-shell) for DSB induction were respectively 1.3, 1.9, 2.3, and 2.6 under aerobic conditions and 1.3, 2.1, 2.5, and 2.9 under a hypoxic condition (2% O2). The RBE values for enzymatic DSBs were 1.6, 2.1, 2.3, and 2.4, respectively, indicating that the enzymatic DSB yields are comparable to the yields of DSB induction. The synergistic effects of DSB induction and enzymatic DSB formation further facilitate cell killing and the advantage in cancer treatment. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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Review

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19 pages, 1547 KiB  
Review
Roles of Mitochondrial DNA Damage in Kidney Diseases: A New Biomarker
by Jun Feng, Zhaowei Chen, Wei Liang, Zhongping Wei and Guohua Ding
Int. J. Mol. Sci. 2022, 23(23), 15166; https://doi.org/10.3390/ijms232315166 - 02 Dec 2022
Cited by 11 | Viewed by 2459
Abstract
The kidney is a mitochondria-rich organ, and kidney diseases are recognized as mitochondria-related pathologies. Intact mitochondrial DNA (mtDNA) maintains normal mitochondrial function. Mitochondrial dysfunction caused by mtDNA damage, including impaired mtDNA replication, mtDNA mutation, mtDNA leakage, and mtDNA methylation, is involved in the [...] Read more.
The kidney is a mitochondria-rich organ, and kidney diseases are recognized as mitochondria-related pathologies. Intact mitochondrial DNA (mtDNA) maintains normal mitochondrial function. Mitochondrial dysfunction caused by mtDNA damage, including impaired mtDNA replication, mtDNA mutation, mtDNA leakage, and mtDNA methylation, is involved in the progression of kidney diseases. Herein, we review the roles of mtDNA damage in different setting of kidney diseases, including acute kidney injury (AKI) and chronic kidney disease (CKD). In a variety of kidney diseases, mtDNA damage is closely associated with loss of kidney function. The level of mtDNA in peripheral serum and urine also reflects the status of kidney injury. Alleviating mtDNA damage can promote the recovery of mitochondrial function by exogenous drug treatment and thus reduce kidney injury. In short, we conclude that mtDNA damage may serve as a novel biomarker for assessing kidney injury in different causes of renal dysfunction, which provides a new theoretical basis for mtDNA-targeted intervention as a therapeutic option for kidney diseases. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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26 pages, 3501 KiB  
Review
Saccharomyces cerevisiae as a Model System for Eukaryotic Cell Biology, from Cell Cycle Control to DNA Damage Response
by Laura Vanderwaeren, Rüveyda Dok, Karin Voordeckers, Sandra Nuyts and Kevin J. Verstrepen
Int. J. Mol. Sci. 2022, 23(19), 11665; https://doi.org/10.3390/ijms231911665 - 01 Oct 2022
Cited by 9 | Viewed by 3679
Abstract
The yeast Saccharomyces cerevisiae has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for [...] Read more.
The yeast Saccharomyces cerevisiae has been used for bread making and beer brewing for thousands of years. In addition, its ease of manipulation, well-annotated genome, expansive molecular toolbox, and its strong conservation of basic eukaryotic biology also make it a prime model for eukaryotic cell biology and genetics. In this review, we discuss the characteristics that made yeast such an extensively used model organism and specifically focus on the DNA damage response pathway as a prime example of how research in S. cerevisiae helped elucidate a highly conserved biological process. In addition, we also highlight differences in the DNA damage response of S. cerevisiae and humans and discuss the challenges of using S. cerevisiae as a model system. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Biology and Medicine)
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