Article
Cell Biology
Wei Zhao, Zhongjie Liu, Jiaming Luo, Changqing Ma, Luying Lai, Zhengyuan Xia, Shiyuan Xu
Summary: The study indicates that PARP-1 plays a key role in repairing oxidative DNA damage induced by bupivacaine, with interactions with XPD protein contributing to DNA integrity maintenance.
Article
Environmental Sciences
Sonalin Rath, Surajit Das
Summary: Bacteria thriving in the mangrove ecosystem play a significant role in elemental cycles, but their performance is influenced by climate change and environmental stressors. This study investigates the genotoxic effect of such stressors on mangrove bacteria and their adaptation strategies. The results show cellular injuries and DNA damage in response to stressors, with different bacterial strains exhibiting varying levels of tolerance and adaptive mechanisms.
ENVIRONMENTAL POLLUTION
(2023)
Article
Biochemistry & Molecular Biology
Merle M. Nicolai, Ann-Kathrin Weishaupt, Jessica Baesler, Vanessa Brinkmann, Anna Wellenberg, Nicola Winkelbeiner, Anna Gremme, Michael Aschner, Gerhard Fritz, Tanja Schwerdtle, Julia Bornhorst
Summary: Although manganese is an essential trace element, overexposure can lead to toxicity and neurological dysfunction. This study investigated the mode of action of manganese toxicity on genomic integrity, focusing on DNA damage and repair mechanisms using Caenorhabditis elegans as a model organism. The results suggest that excessive manganese exposure can decrease genomic integrity and activate base excision repair.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Dandan Sun, Shimei Chen, Shenping Li, Ning Wang, Shuchang Zhang, Li Xu, Shaopin Zhu, Huiming Li, Qing Gu, Xun Xu, Fang Wei
Summary: The accumulation of DNA damage induced by oxidative stress is a crucial pathogenic factor of endothelial loss in diabetic vascular complications. It is still unclear whether aberrant glucose metabolism leads to defective DNA repair and accounts for hyperglycemia-induced endothelial oxidative stress injury. Our study showed that Foxo1 knockdown alleviated diabetes-associated retinal DNA damage and vascular dysfunction by promoting DNA repair mediated by the MRN-ATM pathway and restoring glycolysis capacity. Our findings suggest that defective glycolysis-dependent DNA repair could be a novel therapeutic target for diabetic vascular complications.
Review
Geriatrics & Gerontology
S. G. Chowdhury, S. Misra, Parimal Karmakar
Summary: Ageing is a multi-factorial phenomenon, and accumulation of DNA damage or mutations is a dominant theory which contributes largely to the development of ageing and age-related diseases. Obesity is a complex chronic disease that affects multiple organs and tissues, and it has been found to be associated with higher loads of DNA damage. The present review focuses on the involvement of DNA metabolism in the development of obesity and how it accelerates ageing in mammals.
JOURNAL OF NUTRITION HEALTH & AGING
(2023)
Article
Oncology
Zachary Quinn, Benjamin Leiby, Guru Sonpavde, Atish D. Choudhury, Christopher Sweeney, David Einstein, Russell Szmulewitz, Oliver Sartor, Karen Knudsen, Eddy Shih-Hsin Yang, Wm. Kevin Kelly
Summary: The purpose of this study was to evaluate the safety of combining Radium-223 with the PARP inhibitor niraparib for the treatment of metastatic castrate-resistant prostate cancer (mCRPC) in patients without known BRCA mutations. The results showed that the combination of niraparib and Radium-223 was safe in patients.
CLINICAL CANCER RESEARCH
(2023)
Review
Biochemistry & Molecular Biology
Elle E. M. Scheijen, Sven Hendrix, David M. Wilson
Summary: Oxidative stress plays a crucial role in spinal cord injury (SCI), causing damage to proteins, nucleic acids, lipids, cytoskeleton, and organelles. Oxidative DNA damage is likely a major contributor to the pathogenesis of SCI, although the evidence supporting this hypothesis is limited. Improved analysis methods are needed to uncover the role of DNA damage and repair in SCI.
Article
Chemistry, Multidisciplinary
Changjiang Fan, Xinyue Meng, Wei Yang, Peiyan Wang, Wenguang Chang, Peifeng Li, Jianxun Wang
Summary: A labeling chemistry-based method, APSC-8-oxoGua-seq, is developed for sequencing 8-oxoGua in the microRNA transcriptome. The method uses N-(3-azidopropyl)-spermine-5-carboxamide (APSC) for selective labeling of 8-oxoGua, allowing the conjugation of a cleavable linker via the click reaction for 8-oxoGua pull-down and sequencing. APSC-8-oxoGua-seq enables identification of 8-oxoGua at single-base resolution.
CHEMICAL COMMUNICATIONS
(2023)
Article
Chemistry, Analytical
Qian Zhang, Shuangnan Zhao, Xiaorui Tian, Jian-Ge Qiu, Chun-yang Zhang
Summary: In this study, a CRISPR-Cas-based biosensor was developed for rapid and sensitive measurement of 8-oxoguanine DNA glycosylase. This biosensor demonstrated high sensitivity and rapidity, allowing isothermal assay within 40 minutes. It has potential applications in molecular diagnostics and point-of-care testing.
ANALYTICAL CHEMISTRY
(2022)
Article
Immunology
Ya Dong, Fei Han, Yue Su, Bei Sun, Wei Zhao, Congqing Pan
Summary: Cigarette smoke exposure is the major cause of chronic obstructive pulmonary disease (COPD) and cigarette smoke extract (CSE) induces the increase of reactive oxygen species (ROS), mitochondrial dynamics disorder, and apoptosis. High uric acid (HUA) aggravates the effects of CSE by decreasing the expression of antioxidant enzyme-peroxiredoxin-2 (PRDX2). Overexpression of PRDX2 inhibits the effects of HUA, while knockdown of PRDX2 promotes the effects of HUA on cellular ROS levels, mitochondrial dynamics disorder, and apoptosis in MLE-12 cells.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2023)
Review
Oncology
Sepideh Nikfarjam, Krishna K. Singh
Summary: DNA damage response (DDR) signaling is crucial for maintaining genomic and proteomic homeostasis and dysregulation in DDR pathways is associated with various pathophysiological states, including cancer and cardiovascular diseases (CVDs). This review comprehensively discusses different DDR pathways, the cross talk among DDR mechanisms, the role of DDR in cancer and CVDs, the similarities and differences between DDR in cancer and CVDs, the role of DDR in the pathophysiology of CVDs, interventional strategies for targeting genomic instability in CVDs, and future perspectives.
Review
Biochemistry & Molecular Biology
Ashna Nagpal, Sripriya Raja, Bennett Van Houten
Summary: Recent data has shown that UV-DDB, XPC, and XPA proteins play important roles in the processing of 8-oxoG. UV-DDB stimulates OGG1, MUTYH, and APE1 to increase their turnover at damage sites and associates with these proteins at abasic moieties on DNA damage arrays. It also interacts with OGG1 at sites of 8-oxoG. Additionally, UV-DDB may be the first responder to modify the structure of damage-containing nucleosomes for access by BER enzymes.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Article
Pharmacology & Pharmacy
Sabry M. Attia, Sheikh F. Ahmad, Ahmed Nadeem, Mohamed S. M. Attia, Mushtaq A. Ansari, Mohammed A. Al-Hamamah, Marwa H. Hussein, Alaa A. Alameen, Abdullah F. Alasmari, Saleh A. Bakheet
Summary: Environmental and genetic factors play significant roles in the pathogenesis of autism. This study focused on the susceptibility of BTBR mice, an autism model, to the genotoxic effects of methylmercury and observed DNA repair dysregulation. BTBR mice exposed to methylmercury exhibited increased micronuclei formation, oxidative DNA damage, elevated lipid peroxides, decreased glutathione ratio, and altered expression of DNA repair-related genes. The results suggest that methylmercury exposure exacerbates genotoxic susceptibility and disrupts antioxidant defense and DNA repair in autistic individuals. Regular medical follow-up and strategies to enhance cellular antioxidants and DNA repair efficiency are important for preventing mutagenic changes caused by methylmercury exposure in autism.
Article
Biochemistry & Molecular Biology
Alessio Cardinale, Serena Saladini, Leonardo Lupacchini, Irene Ruspantini, Chiara De Dominicis, Marco Papale, Francesca Silvagno, Enrico Garaci, Cristiana Mollinari, Daniela Merlo
Summary: The study reveals that DNA-PK complex may play a role in cellular response to oxidative stress independently from its function in DNA repair. It acts as an anti-apoptotic factor in proliferating PC12 cells under oxidative stress conditions, but inhibition of DNA-PK activity in differentiated PC12 cells leads to accumulation of DNA damage.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Chemistry, Analytical
Chenyu Cui, Ting-Hsuan Chen
Summary: In this study, a novel strategy for detecting hOGG1 activity based on CRISPR/Cas12a trans-cleavage triggered by cleavage ligation of a dumbbell DNA probe (DBP) designed with an 8-oxoG modification was developed. The method showed high sensitivity and selectivity, and demonstrated good compatibility for detecting hOGG1 activity in cell lysates, suggesting its potential application in disease diagnosis and scientific research.
Article
Biochemistry & Molecular Biology
Artem Artemov, Svetlana Zhenilo, Daria Kaplun, Alexey Starshin, Alexey Sokolov, Alexander M. Mazur, Justyna Szpotan, Maciej Gawronski, Martyna Modrzejewska, Daniel Gackowski, Egor B. Prokhortchouk
Summary: DNA methylation plays a significant role in cancer progression and can be affected by various environmental conditions, such as hypoxia. In renal cancer cells, inactivation of the VHL gene under normoxic conditions induces global genome hypermethylation, which can be reversed by exogenous expression of wild-type VHL. The hypermethylation in VHL mutants is caused by transcriptional changes in MDH and L2HGDH genes leading to accumulation of 2-hydroxyglutarate, inhibiting DNA demethylation by TET enzymes.
Review
Chemistry, Multidisciplinary
Maciej Staszak, Katarzyna Staszak, Karolina Wieszczycka, Anna Bajek, Krzysztof Roszkowski, Bartosz Tylkowski
Summary: The paper provides a comprehensive overview of the use of artificial intelligence systems, particularly neural networks, in drug design to identify chemical structures with medical relevance. Successful training of neural networks requires a large set of training data related to the chemical structure-biological activity relationship, which can be obtained from experimental measurements or appropriate quantum models. Recent advancements in computing power have led to rapid development in neural network systems and a growing interest in deep learning techniques, allowing for a new level of abstraction in network modeling.
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE
(2022)
Article
Public, Environmental & Occupational Health
Oliwia Kowalczyk, Krzysztof Roszkowski, Wojciech Pawliszak, Agnieszka Rypel, Szymon Roszkowski, Jolanta Kowalska, Bartosz Tylkowski, Anna Bajek
Summary: The study found that strategies used for coping with patients' death, stress reduction, empathy, communication with patients and/or their relatives, or breaking bad news skills may be influenced by gender and the length of time employed in a cancer-related work environment.
JOURNAL OF RELIGION & HEALTH
(2022)
Article
Immunology
Nazli Ecem Dal-Bekar, Agnieszka Siomek-Gorecka, Daniel Gackowski, Aydan Koken-Avsar, Handan Yarkan-Tugsal, Merih Birlik, Huray Islekel
Summary: This study provides the first absolute quantification of epigenetic DNA modification products in systemic sclerosis (SSc). The results demonstrate a global hypomethylation pattern in SSc, and also suggest a relationship between lung, gastrointestinal, and vascular involvement with epigenetic changes.
CLINICAL IMMUNOLOGY
(2022)
Article
Cell Biology
Aleksandra Skalska-Bugala, Marta Starczak, Lukasz Szukalski, Maciej Gawronski, Agnieszka Siomek-Gorecka, Justyna Szpotan, Anna Labejszo, Ewelina Zarakowska, Anna Szpila, Anna Jachalska, Adriana Szukalska, Marcin Kruszewski, Anna Sadowska, Aleksandra Wasilow, Patrycja Baginska, Jaroslaw Czyz, Ryszard Olinski, Rafal Rozalski, Daniel Gackowski
Summary: This study found that the levels of DNA methylation products in urine and blood can be useful in supporting the diagnostic process of patients with MDS and AML. Additionally, certain parameters were found to predict the risk of MDS progressing into AML.
Article
Multidisciplinary Sciences
Marta Starczak, Maciej Gawronski, Aleksandra Wasilow, Pawel Mijewski, Ryszard Olinski, Daniel Gackowski
Summary: This study investigated the level of DNA modifications in different stages of fruit flies and in an in vitro model, using a two-dimensional ultra-performance liquid chromatography with tandem mass spectrometry. The results showed that each stage had a specific pattern of DNA modifications, and the levels of these compounds changed throughout the fruit fly life cycle. The study also found that breeding temperature and supplementation of a certain substance affected the level of DNA modifications.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Aleksandra Skalska-Bugala, Agnieszka Siomek-Gorecka, Zbigniew Banaszkiewicz, Ryszard Olinski, Rafal Rozalski
Summary: The study used 2D-UPLC-MS/MS to compare DNA methylation marks and 8-oxodG in urine samples from colorectal cancer and pre-cancerous condition patients. The results showed that the level of 5-fCyt was significantly lower in the urine of colorectal cancer and polyp patients compared to the control group, while the level of 5-hmCyt was significantly higher only in the colorectal cancer group.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Anna Kalinka, Marta Starczak, Daniel Gackowski, Edyta Stepien, Magdalena Achrem
Summary: 5-Hydroxymethylcytosine (5hmC) is found in the genomic DNA of rye species, and its quantity and chromosomal distribution suggest that it may play a role in regulating the rye genome.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Review
Plant Sciences
Dolores Rita Agius, Aliki Kapazoglou, Evangelia Avramidou, Miroslav Baranek, Elena Carneros, Elena Caro, Stefano Castiglione, Angela Cicatelli, Aleksandra Radanovic, Jean-Paul Ebejer, Daniel Gackowski, Francesco Guarino, Andrea Gulyas, Norbert Hidvegi, Hans Hoenicka, Vera Inacio, Frank Johannes, Erna Karalija, Michal Lieberman-Lazarovich, Federico Martinelli, Stephane Maury, Velimir Mladenov, Leonor Morais-Cecilio, Ales Pecinka, Eleni Tani, Pilar S. Testillano, Dimitar Todorov, Luis Valledor, Valya Vassileva
Summary: Epigenetic modifications, particularly DNA methylation, play a crucial role in preserving genome integrity and regulating gene expression, impacting growth, development, and stress response in plants. Detecting DNA methylation marks is essential for understanding these processes and enhancing crop productivity and stress resistance. This review provides an overview of different methods for detecting plant DNA methylation and compares their efficacy between model and crop plants. It also highlights the strengths and limitations of each method and emphasizes the importance of considering technical and biological factors. Overall, this review will assist scientists in selecting an appropriate DNA methylation profiling method.
FRONTIERS IN PLANT SCIENCE
(2023)
Review
Chemistry, Analytical
Rafal Rozalski, Fabian Lesniewski, Patrycja Baginska, Daniel Gackowski
Summary: This review article focuses on the recent developments and advances in the quantification of deoxynucleosides in clinical applications using liquid chromatography coupled with mass spectrometry. It discusses the use of stable isotopes as internal standards, the increasing automation in sample preparation and analysis, as well as the potential sources and importance of contamination in this type of analysis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Article
Cell Biology
Jolanta Guz, Ewelina Zarakowska, Pawel Mijewski, Aleksandra Wasilow, Justyna Szpotan, Marek Foksinski, Bartosz Brzoszczyk, Daniel Gackowski, Piotr Jarzemski, Ryszard Olinski
Summary: The study found that the level of vitamin C in prostate tissues is exceptionally high, and the DNA epigenetic patterns are similar to other soft tissues but with unique characteristics. The findings suggest that prostatic vitamin C and DNA modifications may play an important role in maintaining prostate health.
CELLULAR PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Nanoscience & Nanotechnology
Kinga Malinowska, Bozena Bukowska, Ireneusz Piwonski, Marek Foksinski, Aneta Kisielewska, Ewelina Zarakowska, Daniel Gackowski, Paulina Sicinska
Summary: This study investigated the genotoxic potential of non-functionalized polystyrene nanoparticles (PS-NPs) of different diameters on human peripheral blood mononuclear cells (PBMCs). The results showed that PS-NPs decreased the metabolic activity of PBMCs, increased DNA strand break formation, oxidized purines and pyrimidines, and increased 8-oxodG levels. The extent of genotoxic changes in PBMCs depended on the size of the particles and their zeta-potential value.
