Oxidatively induced DNA damage: mechanisms, repair and disease

Bifenthrin induces changes in clinical poisoning symptoms, oxidative stress, DNA damage, histological characteristics, and transcriptome in Chinese giant salamander (Andrias davidianus) larvae

Bifenthrin (BF) is a broad-spectrum insecticide that has gained widespread use due to its high effectiveness. However, there is limited research on the potential toxic effects of bifenthrin pollution on amphibians. This study aimed to investigate the 50 % lethal concentration (LC50) and safety concentration of Chinese giant salamanders (CGS) exposed to BF (at 0, 6.25,12.5,25 and 50 μg/L BF) for 96 h. Subsequently, CGS were exposed to BF (at 0, 0.04, and 4 μg/L BF) for one week to investigate its toxic effects. Clinical poisoning symptoms, liver pathology, oxidative stress factors, DNA damage, and transcriptome differences were observed and analyzed. The results indicate that exposure to BF at 4 μg/L significantly decreased the adenosine-triphosphate (ATP), superoxide dismutase (SOD), glutathione (GSH), and catalase (CAT) contents in the brain, liver, and kidney of CGS. Additionally, the study found that the malondialdehyde (MDA), reactive oxygen species (ROS), and 8-hydroxydeoxyguanosine (8-OHdG) contents were increased. The liver tissue exhibited significant inflammatory reactions and structural malformations. RNA-seq analysis of the liver showed that BF caused abnormal antioxidant indices of CGS. This affected molecular function genes such as catalytic activity, ATP-dependent activity, metabolic processes, signaling and immune system processes, behavior, and detoxification, which were significantly upregulated, resulting in the differential genes significantly enriched in the calcium signaling pathway, PPARα signaling pathway and NF-kB signaling pathway. The results suggest that BF induces the abnormal production of free radicals, which overwhelms the body's self-defense system, leading to varying degrees of oxidative stress. This can result in oxidative damage, DNA damage, abnormal lipid metabolism, autoimmune diseases, clinical poisoning symptoms, and tissue inflammation. This work provides a theoretical basis for the rational application of bifenthrin and environmental risk assessment, as well as scientific guidance for the conservation of amphibian populations.

Oxidatively-induced DNA base damage and base excision repair abnormalities in siblings of individuals with bipolar disorder DNA damage and repair in bipolar disorder

Previous evidence suggests elevated levels of oxidatively-induced DNA damage, particularly 8-hydroxy-2'-deoxyguanosine (8-OH-dG), and abnormalities in the repair of 8-OH-dG by the base excision repair (BER) in bipolar disorder (BD). However, the genetic disposition of these abnormalities remains unknown. In this study, we aimed to investigate the levels of oxidatively-induced DNA damage and BER mechanisms in individuals with BD and their siblings, as compared to healthy controls (HCs). 46 individuals with BD, 41 siblings of individuals with BD, and 51 HCs were included in the study. Liquid chromatography-tandem mass spectrometry was employed to evaluate the levels of 8-OH-dG in urine, which were then normalized based on urine creatinine levels. The real-time-polymerase chain reaction was used to measure the expression levels of 8-oxoguanine DNA glycosylase 1 (OGG1), apurinic/apyrimidinic endonuclease 1 (APE1), poly ADP-ribose polymerase 1 (PARP1), and DNA polymerase beta (POLβ). The levels of 8-OH-dG were found to be elevated in both individuals with BD and their siblings when compared to the HCs. The OGG1 and APE1 expressions were downregulated, while POLβ expressions were upregulated in both the patient and sibling groups compared to the HCs. Age, smoking status, and the number of depressive episodes had an impact on APE1 expression levels in the patient group while body mass index, smoking status, and past psychiatric history had an impact on 8-OH-dG levels in siblings. Both individuals with BD and unaffected siblings presented similar abnormalities regarding oxidatively-induced DNA damage and BER, suggesting a link between abnormalities in DNA damage/BER mechanisms and familial susceptibility to BD. Our findings suggest that targeting the oxidatively-induced DNA damage and BER pathway could offer promising therapeutic strategies for reducing the risk of age-related diseases and comorbidities in individuals with a genetic predisposition to BD.

Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase

8-oxoguanine (oxoG) is formed in DNA by the action of reactive oxygen species. As a highly mutagenic and the most common oxidative DNA lesion, it is an important marker of oxidative stress. Human 8-oxoguanine-DNA glycosylase (OGG1) is responsible for its prompt removal in human cells. OGG1 is a bifunctional DNA glycosylase with N-glycosylase and AP lyase activities. Aspects of the detailed mechanism underlying the recognition of 8-oxoguanine among numerous intact bases and its subsequent interaction with the enzyme's active site amino acid residues are still debated. The main objective of our work was to determine the effect (structural and thermodynamic) of introducing an oxoG-clamp in model DNA substrates on the process of 8-oxoG excision by OGG1. Towards that end, we used DNA duplexes modeling OGG1-specific lesions: 8-oxoguanine or an apurinic/apyrimidinic site with either cytidine or the oxoG-clamp in the complementary strand opposite to the lesion. It was revealed that there was neither hydrolysis of the N-glycosidic bond at oxoG nor cleavage of the sugar-phosphate backbone during the reaction between OGG1 and oxoG-clamp-containing duplexes. Possible structural reasons for the absence of OGG1 enzymatic activity were studied via the stopped-flow kinetic approach and molecular dynamics simulations. The base opposite the damage was found to have a critical effect on the formation of the enzyme-substrate complex and the initiation of DNA cleavage. The oxoG-clamp residue prevented the eversion of the oxoG base into the OGG1 active site pocket and impeded the correct convergence of the apurinic/apyrimidinic site of DNA and the attacking nucleophilic group of the enzyme. An obtained three-dimensional model of the OGG1 complex with DNA containing the oxoG-clamp, together with kinetic data, allowed us to clarify the role of the contact of amino acid residues with DNA in the formation of (and rearrangements in) the enzyme-substrate complex.

Mechanistic Aspects of Photodegradation of Deoxynucleosides Induced by Triplet State of Effluent Organic Matter

Excited triplet states of wastewater effluent organic matter (3EfOM*) are known as important photo-oxidants in the degradation of extracellular antibiotic resistance genes (eArGs) in sunlit waters. In this work, we further found that 3EfOM* showed highly selective reactivity toward 2'-deoxyguanosine (dG) sites within eArGs in irradiated EfOM solutions at pH 7.0, while it showed no photosensitizing capacity toward 2'-deoxyadenosine, 2'-deoxythymidine, and 2'-deoxycytidine (the basic structures of eArGs). The 3EfOM* contributed to the photooxidation of dG primarily via one-electron transfer mechanism, with second-order reaction rate constants of (1.58-1.74) × 108 M-1 s-1, forming the oxidation intermediates of dG (dG(-H)•). The formed dG(-H)• could play a significant role in hole hopping and damage throughout eArGs. Using the four deoxynucleosides as probes, the upper limit for the reduction potential of 3EfOM* is estimated to be between 1.47 and 1.94 VNHE. Compared to EfOM, the role of the triplet state of terrestrially natural organic matter (3NOM*) in dG photooxidation was minor (∼15%) mainly due to the rapid reverse reactions of dG(-H)• by the antioxidant moieties of NOM. This study advances our understanding of the difference in the photosensitizing capacity and electron donating capacity between NOM and EfOM and the photodegradation mechanism of eArGs induced by 3EfOM*.

Visible light-activated photosensitizer inhibits the plasmid-mediated horizontal gene transfer of antibiotic resistance genes

Inhibition of plasmid transfer, including transformation and conjugation, is essential to prevent the spread of plasmid-encoded antimicrobial resistance. Photosensitizers have been successfully used in the treatment of serious infectious diseases, however, the effects of photosensitizers on the plasmid transfer are still elusive. In this study, we determined the transformation and conjugation efficiency of plasmid pUC19 and pRP4, respectively, when exposed to a photosensitizer (Visible Light-activated Rose Bengal, VLRB). The results showed that the activation of VLRB resulted in up to a 580-fold decrease in the transformation frequency of pUC19 and a 10-fold decrease in the conjugation frequency of pRP4 compared with the non-VLRB control. The inhibition of pUC19 transformation by VLRB exhibited a dose-dependent manner and was attributed to the changes in the plasmid conformation. The inhibition of pRP4 conjugation was associated with the generation of extracellular free radicals, induced oxidative stress, suppression of the mating pair formation gene (trbBp) and DNA transfer and replication gene (trfAp), and enhanced expression of the global regulatory genes (korA, korB, and trbA). These findings highlight the potential of visible light-activated photosensitizer for mitigating the dissemination of plasmid-encoded antibiotic resistance genes.

Facet-Specific Photocatalytic Degradation of Extracellular Antibiotic Resistance Genes by Hematite Nanoparticles in Aquatic Environments

The persistence of extracellular antibiotic resistance genes (ARGs) in aquatic environments has attracted increasing attention due to their potential threat to public health and the environment. However, the fate of extracellular ARGs in receiving water remains largely unknown. This study investigated the influence of hematite nanoparticles, a widespread natural mineral, on the photodegradation of extracellular ARGs in river water. Results showed that under exposure to visible light, hematite nanoparticles, at environmental concentrations, resulted in a 3-5 orders of magnitude reduction in extracellular ARGs. This photodegradation of extracellular ARGs is shown to be facet-dependent; the (001) facet of hematite demonstrates a higher removal rate than that of the (100) facet, which is ascribed to its enhanced adsorption capability and higher hydroxyl radical (•OH) production. Density functional theory (DFT) calculations corroborate this finding, indicating elevated iron density, larger adsorption energy, and lower energy barrier of •OH formation on the (001) facet, providing more active sites and •OH generation for extracellular ARG interaction. Gel electrophoresis and atomic force microscopy analyses further confirm that the (001) facet causes more substantial damage to extracellular ARGs than the (100) facet. These findings pave the way for predicting the photodegradation efficiency of hematite nanoparticles with varied facets, thereby shedding light on the inherent self-purification capacity for extracellular ARGs in both natural and engineered aquatic environments.

Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics

Mutations present a dichotomy in their implications for cellular processes. They primarily arise from DNA replication errors or damage repair processes induced by environmental challenges. Cumulative mutations underlie genetic variations and drive evolution, yet also contribute to degenerative diseases such as cancer and aging. The mutator phenotype elucidates the heightened mutation rates observed in malignant tumors. Evolutionary adaptation, analogous to bacterial and eukaryotic systems, manifests through mutator phenotypes during changing environmental conditions, highlighting the delicate balance between advantageous mutations and their potentially detrimental consequences. Leveraging the genetic tractability of Saccharomyces cerevisiae offers unique insights into mutator phenotypes and genome instability akin to human cancers. Innovative reporter assays in yeast model organisms enable the detection of diverse genome alterations, aiding a comprehensive analysis of mutator phenotypes. Despite significant advancements, our understanding of the intricate mechanisms governing spontaneous mutation rates and preserving genetic integrity remains incomplete. This review outlines various cellular pathways affecting mutation rates and explores the role of mutator genes and mutation-derived phenotypes, particularly prevalent in malignant tumor cells. An in-depth comprehension of mutator and antimutator activities in yeast and higher eukaryotes holds promise for effective cancer control strategies.

Synergistic lethality between auranofin-induced oxidative DNA damage and ATR inhibition in cancer cells

AIMS

Studies in the past have shown that inhibition of the ataxia telangiectasia and Rad3-related (ATR) kinase sensitizes cancer cells to genotoxic anticancer treatments, however, clinical use of ATR inhibitors in combination with DNA damaging chemotherapy is limited due to toxicity in healthy tissues. In this study, we investigated the synergistic anticancer effect between ATR inhibition and oxidative DNA damage induced by the thioredoxin reductase inhibitor auranofin.

MAIN METHODS

Cytotoxicity was evaluated by cell viability assays. Western blot, comet assay, immunostaining and flow cytometry were performed to dissect the underlying mechanisms. In vivo efficacy was examined against tumor xenografts.

KEY FINDINGS

Nontoxic doses of auranofin alone increased the levels of reactive oxygen species (ROS) in cancer but not noncancerous cells, resulting in oxidative DNA damage and activation of the ATR DNA damage response pathway selectively in cancer cells. Inhibition of ATR in auranofin-treated cancer cells resulted in unscheduled firing of dormant DNA replication origins, abrogation of the S phase cell cycle checkpoint and extensive DNA breakage, leading to replication catastrophe and potent synergistic lethality. Both the antioxidant NAC and the DNA polymerase inhibitor aphidicolin reduced replication stress and synergistic cytotoxicity, implicating replication stress-driven catastrophic cell death resulted from collision between oxidative DNA damage and dysregulated DNA replication. In vivo, auranofin and VE822 coadministration enabled marked regressions of tumor xenografts, while each drug alone had no effect.

SIGNIFICANCE

As increased generation of ROS is a universal feature of tumors, our findings may open new routes to broaden the therapeutic potential of ATR inhibitors.

Simultaneous removal of antibiotics and antibiotic resistant genes using a CeO2@CNT electrochemical membrane-NaClO system

The simultaneous removal of antibiotic and antibiotic resistance genes (ARGs) are important to inhibit the spread of antibiotic resistance. In this study, a coupled treatment system was developed using a CeO2 modified carbon nanotube electrochemical membrane and NaClO (denoted as CeO2@CNT-NaClO) to treat simulated water samples containing antibiotics and antibiotic-resistant bacteria (ARB). As the mass ratio of CeO2 to CNT was 5:7 and the current density was 2.0 mA/cm2, the CeO2@CNT-NaClO system removed 99% of sulfamethoxazole, 4.6 log sul1 genes, and 4.7 log intI1 genes from the sulfonamide-resistance water samples, and removed 98% of tetracycline, 2.0 log tetA genes, and 2.6 log intI1 genes of the tetracycline-resistance water samples. The outstanding performance of the CeO2@CNT-NaClO system for simultaneously removing antibiotic and ARGs was mainly ascribed to the generation of multiple reactive species, including •OH, •ClO, •O2- and 1O2. Antibiotics can undergo efficient degradation by •OH. However, the reaction between •OH and antibiotics reduces the availability of •OH to permeate into the cells and react with DNA. Nevertheless, the presence of •OH enhancd the effects of •ClO, •O2-, and 1O on ARG degradation. Through the coupled action of •OH, •ClO, •O2-, and 1O2, the cell membranes of ARB experience severe damage, resulting in an increase in intracellular reactive oxygen species (ROS) and a decrease in superoxide dismutase (SOD) activity. Consequently, this coordinated mechanism leads to superior removal of ARGs.

Effect of Diet and Oxidative Stress in the Pathogenesis of Lymphoproliferative Disorders

Lymphomas are a heterogeneous group of pathologies that result from clonal proliferation of lymphocytes. They are classified into Hodgkin lymphoma and non-Hodgkin lymphoma; the latter develops as a result of B, T, or NK cells undergoing malignant transformation. It is believed that diet can modulate cellular redox state and that oxidative stress is implicated in lymphomagenesis by acting on several biological mechanisms; in fact, oxidative stress can generate a state of chronic inflammation through the activation of various transcription factors, thereby increasing the production of proinflammatory cytokines and causing overstimulation of B lymphocytes in the production of antibodies and possible alterations in cellular DNA. The purpose of our work is to investigate the results of in vitro and in vivo studies on the possible interaction between lymphomas, oxidative stress, and diet. A variety of dietary regimens and substances introduced with the diet that may have antioxidant and antiproliferative effects were assessed. The possibility of using nutraceuticals as novel anticancer agents is discussed; although the use of natural substances in lymphoma therapy is an interesting field of study, further studies are needed to define the efficacy of different nutraceuticals before introducing them into clinical practice.

Peracetic acid disinfection induces antibiotic-resistant E. coli into VBNC state but ineffectively eliminates the transmission potential of ARGs

The occurrence of a viable but nonculturable (VBNC) state in antibiotic-resistant E. coli (AR E. coli) and inefficient degradation of their antibiotic resistance genes (ARGs) may cause potential health risks during disinfection. Peracetic acid (PAA) is an alternative disinfectant for replacing chlorine-based oxidants in wastewater treatment, and the potential of PAA to induce a VBNC state in AR E. coli and to remove the transformation functionality of ARGs were investigated for the first time. Results show that PAA exhibits excellent performance in inactivating AR E. coli (over 7.0-logs) and persistently inhibiting its regeneration. After PAA disinfection, insignificant changes in the ratio of living to dead cells (∼4%) and the level of cell metabolism, indicating that AR E. coli were induced into VBNC states. Unexpectedly, PAA was found to induce AR E. coli into VBNC state by destroying the proteins containing reactive amino acids at thiol, thioether and imidazole groups, rather than the result of membrane damage, oxidative stress, lipid destruction and DNA disruption in the conventional disinfection processes. Moreover, the result of poor reactivity between PAA and plasmid strands and bases confirmed that PAA hardly reduced the abundance of ARGs and damaged the plasmid's integrity. Transformation assays and real environment validation indicated that PAA-treated AR E. coli could release large abundance of naked ARGs with high-efficiency transformation functionality (∼5.4 × 10-4 - ∼8.3 × 10-6) into the environment. This study has significant environmental implications for assessing the transmission of antimicrobial resistance during PAA disinfection.

Urinary 8-hydroxy-2'-deoxyguanosine levels are elevated in patients with IDH1-wildtype glioblastoma and are associated with tumor recurrence in gliomas

2021 World Health Organization (WHO) Central Nervous System (CNS) Tumor Classification includes molecular diagnostic parameters such as isocitrate dehydrogenase (IDH) mutation or 1p19q codeletion status, in addition to the classical histological classification. Several studies have revealed that patients with IDH1 mutation have a longer survival rate compared to wildtype individuals. In glioma cells, increased oxidative stress has been identified. However, till now, the relation between oxidative stress levels and IDH1 mutation status in those patients was not examined. Therefore, the aim of this study was to investigate the urinary levels of oxidatively induced DNA damage products, 8-hydroxy-2'- deoxyguanosine (8-OH-dG), (5'R) and (5'S)-8,5'-cyclo-2'-deoxyadenosines (R-cdA and S-cdA) as reliable oxidative stress markers in patients with IDH1-wildtype (n = 20) and IDH1-mutant (n = 22) glioma. Absolute quantification of 8-OH-dG, R-cdA and S-cdA was achieved by liquid chromatography-tandem mass spectrometry with isotope dilution. The levels of 8-OH-dG were significantly greater in IDH1-wildtype glioma patients than those in IDH1-mutant ones (p = 0.017). No statistically significant difference was observed for R-cdA and S-cdA levels. 8-OH-dG levels were positively correlated with patients' tumor recurrence in all patients (r = 0.382, p = 0.014). The mutation status of glioma is well correlated with oxidative stress. Examination of noninvasively measured oxidative DNA damage products along with IDH1 mutation status in glioma patients, might be particularly important in terms of evaluating and monitoring the effectiveness of treatment.

Nanodrugs alleviate acute kidney injury: Manipulate RONS at kidney

Currently, there are no clinical drugs available to treat acute kidney injury (AKI). Given the high prevalence and high mortality rate of AKI, the development of drugs to effectively treat AKI is a huge unmet medical need and a research hotspot. Although existing evidence fully demonstrates that reactive oxygen and nitrogen species (RONS) burst at the AKI site is a major contributor to AKI progression, the heterogeneity, complexity, and unique physiological structure of the kidney make most antioxidant and anti-inflammatory small molecule drugs ineffective because of the lack of kidney targeting and side effects. Recently, nanodrugs with intrinsic kidney targeting through the control of size, shape, and surface properties have opened exciting prospects for the treatment of AKI. Many antioxidant nanodrugs have emerged to address the limitations of current AKI treatments. In this review, we systematically summarized for the first time about the emerging nanodrugs that exploit the pathological and physiological features of the kidney to overcome the limitations of traditional small-molecule drugs to achieve high AKI efficacy. First, we analyzed the pathological structural characteristics of AKI and the main pathological mechanism of AKI: hypoxia, harmful substance accumulation-induced RONS burst at the renal site despite the multifactorial initiation and heterogeneity of AKI. Subsequently, we introduced the strategies used to improve renal targeting and reviewed advances of nanodrugs for AKI: nano-RONS-sacrificial agents, antioxidant nanozymes, and nanocarriers for antioxidants and anti-inflammatory drugs. These nanodrugs have demonstrated excellent therapeutic effects, such as greatly reducing oxidative stress damage, restoring renal function, and low side effects. Finally, we discussed the challenges and future directions for translating nanodrugs into clinical AKI treatment.

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AKI is a common clinical acute syndrome with high morbidity and mortality but without effective clinical drug available.

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Hypoxia and accumulation of toxic substances are key pathological features of various heterogeneous AKI.

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Excessive RONS is the core of the pathological mechanism of AKI.

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The development of nanodrugs is expected to achieve successful treatment in AKI.

A comparative meta-analysis of peripheral 8-hydroxy-2'-deoxyguanosine (8-OHdG) or 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) levels across mood episodes in bipolar disorder

OBJECTIVE

Oxidative DNA damage has been associated with the pathophysiology of bipolar disorder (BD) as one of the common pathways between increased medical comorbidity and premature aging in BD. Previous evidence shows increased levels of oxidatively induced DNA damage markers, 8-hydroxy-2'-deoxyguanosine (8-OHdG) or its tautomer 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG), in patients with BD in comparison to healthy individuals. With the current research, we aim to analyze data on peripheral (blood or urine) 8-OHdG/8-oxo-dG levels across mood states of BD using a meta-analytical approach.

METHOD

A literature search was conducted using the databases PubMed, Scopus, and Web of Science to identify eligible studies (January 1989 to July 2022). Relevant studies were systematically reviewed; a random-effects meta-analysis and a meta-regression analysis were conducted.

RESULTS

The current meta-analysis included 12 studies consisting of 808 BD patients (390 in euthymia, 156 in mania, 137 in depression, 16 in mixed episode, 109 not specified) and 563 healthy controls. BD patients that were currently depressed had significantly higher levels of 8-OHdG/8-oxo-dG than healthy controls, while euthymic or manic patients did not differ from healthy controls. A meta-regression analysis showed sex distribution (being female) and older age to be significantly related to increased 8-OHdG/8-oxo-dG levels.

CONCLUSION

Our findings suggest that 8-OHdG/8-oxo-dG may be a state-related marker of depression in BD and may be affected by older age and female gender.

Identification of antioxidant peptides after digestion and absorption of isinglass by serum peptidomics and cellular antioxidant activity analysis

Isinglass, a dried product of the swim bladder, has been widely used in traditional Chinese medicine. This study attempts to identify natural antioxidant peptides after digestion and absorption of isinglass in vivo. The antioxidant effects of dietary isinglass were demonstrated by evaluating the activities of SOD, CAT and MDA contents in the mouse liver. Four novel antioxidant-related peptides (RLLWENGNLL, GSKAENPTNPGP, SPVPDLVPGSF and VPDLVPGSF) were screened based on serum peptidomics and amino acid composition. Furthermore, pretreating with four peptides significantly increased the cell viability, and SOD and CAT activities of AML12 cells with H₂O₂-mediated oxidative damage, meanwhile, significantly reduced the ROS level, MDA content and apoptosis rate and attenuated DNA damage. Therefore, it was concluded that pretreatment of the identified peptides had a protective effect on oxidatively damaged cells. This result can aid in the recognition of active peptides from isinglass consumption for potential application in nutraceuticals or functional ingredients in food.

Beneficial in vitro effect of N-acetylcysteine and coenzyme Q10 on DNA damage in neurodegenerative Niemann-Pick type C 1 disease: preliminary results

Niemann-Pick type C1 (NP-C1) is a lysosomal storage disease (LSD) caused by mutations in NPC1 gene that lead to defective synthesis of the respective lysosomal transporter protein and cholesterol accumulation in late endosomes/lysosomes (LE/L) compartments, as well as glycosphingolipids GM2 and GM3 in the central nervous system (CNS). Clinical presentation varies according to the age of onset and includes visceral and neurological symptoms, such as hepatosplenomegaly and psychiatric disorders. Studies have been associating the pathophysiology of NP-C1 with oxidative damage to lipids and proteins, as well as evaluating the benefits of adjuvant therapy with antioxidants for this disease. In this work, we evaluated the DNA damage in fibroblasts culture from patients with NP-C1 treated with miglustat, as well as the in vitro effect of the antioxidant compounds N-acetylcysteine (NAC) and Coenzyme Q10 (CoQ10), using the alkaline comet assay. Our preliminary results demonstrate that NP-C1 patients have increased DNA damage compared to healthy individuals and that the treatments with antioxidants can mitigate it. DNA damage may be due to an increase in reactive species since it has been described that NP-C1 patients have increased peripheral markers of damage to other biomolecules. Our study suggests that NP-C1 patients could benefit from the use of adjuvant therapy with NAC and CoQ10, which should be better evaluated in a future clinical trial.

Evidence of redox imbalance and mitochondrial dysfunction in Niemann-Pick type C 1 patients: the in vitro effect of combined therapy with antioxidants and β-cyclodextrin nanoparticles

Niemann-Pick C disease (NPC) is an autosomal recessive genetic disorder resulting from mutation in one of two cholesterol transport genes: NPC1 or NPC2, causing accumulation of unesterified cholesterol, together with glycosphingolipids, within the endosomal/lysosomal compartment of cells. The result is a severe disease in both multiple peripheral organs and the central nervous system, causing neurodegeneration and early death. However, the pathophysiological mechanisms of NPC1 remain poorly understood. Recent studies have shown that the primary lysosomal defect found in fibroblasts from NPC1 patients is accompanied by a deregulation of mitochondrial organization and function. There is currently no cure for NPC1, but recently the potential of β-cyclodextrin (β-CD) for the treatment of the disease was discovered, which resulted in the redistribution of cholesterol from subcellular compartments to the circulation and increased longevity in an animal model of NPC1. Considering the above, the present work evaluated the in vitro therapeutic potential of β-CD to reduce cholesterol in fibroblasts from NPC1 patients. β-CD was used in its free and nanoparticulate form. We also evaluated the β-CD potential to restore mitochondrial functions, as well as the beneficial combined effects of treatment with antioxidants N-Acetylcysteine (NAC) and Coenzyme Q10 (CoQ10). Besides, we evaluated oxidative and nitrative stress parameters in NPC1 patients. We showed that oxidative and nitrative stress could contribute to the pathophysiology of NPC1, as the levels of lipoperoxidation and the nitrite and nitrate levels were increased in these patients when compared to healthy individuals, as well as DNA damage. The nanoparticles containing β-CD reduced the cholesterol accumulated in the NPC1 fibroblasts. This result was potentiated by the concomitant use of the nanoparticles with the antioxidants NAC and CoQ10 compared to those presented by healthy individuals cells ́. In addition, treatments combining β-CD nanoparticles and antioxidants could reduce mitochondrial oxidative stress, demonstrating advantages compared to free β-CD. The results obtained are promising regarding the combined use of β-CD loaded nanoparticles and antioxidants in the treatment of NPC1 disease.

Amazing roles of extrachromosomal DNA in cancer progression

In cancers, extrachromosomal DNA (ecDNA) has gained renewed interest since its first discovery, presenting its roles in tumorigenesis. Because of the unique structure and genetic characteristics, extrachromosomal DNA shed new light on development, early diagnosis, treatment and prognosis of cancers. Occurs in cancer cells, extrachromosomal DNA, one dissociative circular extrachromosomal element, drives the amplification of oncogenes, promotes the transcription and lifts tumor heterogeneity to participate in tumorigenesis. Given its role act as messenger, extrachromosomal DNA is connected with drug resistance, tumor microenvironment, germline and aging. The diversity of space and time gives extrachromosomal DNA a crucial role in cancer progression that has been ignored for decades. Thus, in this review, we will focus on some unique information of extrachromosomal DNA and the regulation of oncogenes as well as its roles and possible mechanisms in tumorigenesis, which are of great significance for us to understand extrachromosomal DNA comprehensively in carcinogenic mechanism.

Activatable Self-Dissociation of Watson-Crick Structures with Fluorescent Nucleotides for Sensing Multiple Human Glycosylases at Single-Cell Level

Nucleobase oxidation and alkylation can destroy Watson-Crick base-pairing to challenge the genomic integrity. Human 8-oxoguanine glycosylase 1 (hOGG1) and alkyladenine glycosylase (hAAG) are evolved to counter these two cytotoxic lesions through base-excision repair, and their deregulations are implicated with multifactorial diseases and cancers. Herein, we demonstrate activatable self-dissociation of Watson-Crick structures with fluorescent nucleotides for sensing multiple human glycosylases at single-cell level. The presence of hOGG1 and hAAG catalyzes 8-oxoG and deoxyinosine removal in functional probe 1 to release two trigger probes (1 and 2). Then, trigger probes hybridize with functional probe 2 to activate the autocatalytic degradation of functional probes 2 (Cycle I) and 3 (Cycle II), replicating abundant trigger probes (1-4) and releasing two fluorophores (2-aminopurine (2-AP) and pyrrolo-dC (P-dC)). New trigger probes (1, 2) and (3, 4), in turn, hybridize with free functional probes 2 and 3, repeating Cycles I and II turnovers. Through multicycle self-dissociation of Watson-Crick structures, 2-AP and P-dC are exponentially accumulated for the simultaneous quantification of hOGG1 and hAAG. This nanodevice exhibits high sensitivity with a detection limit of 2.9 × 10^-3 U/mL for hOOG1 and 1.5 × 10^-3 U/mL for hAAG, and it can measure enzymatic kinetics, identify potential inhibitors, discriminate glycosylases between cancer and normal cell lines, and even quantify glycosylase activities in a single HeLa cell. Moreover, this assay may be rapidly and isothermally performed in one tube with only one tool enzyme in a quencher-free manner, promising a simple and powerful platform for multiple human glycosylase detection.

Photochemical degradation pathways of cell-free antibiotic resistance genes in water under simulated sunlight irradiation: Experimental and quantum chemical studies

The presence of antibiotic resistance genes (ARGs) in the environment poses a threat to human health and therefore their environmental behavior needs to be studied urgently. A systematic study was conducted on the photodegradation pathways of the cell-free tetracycline resistance gene (Tc-ARG) under simulated sunlight irradiation. The results showed that Tc-ARG can undergo direct photodegradation, which significantly reduces its horizontal transfer efficiency. Suwannee River fulvic acid (SRFA) promoted the photodegradation of Tc-ARG and further inhibited its horizontal transfer by generating reactive intermediates. The photodegradation of Tc-ARG was attributed to degradation of the four bases (G, C, A, T) and the deoxyribose group. Quantum chemical calculations showed that the four bases could be oxidized by the hydroxyl radical (HO) through addition and H-abstraction reactions. The main oxidative product 8-oxo-dG was detected. This product was generated through the addition reaction of G-C with HO, subsequent to dissolved oxygen initiated H-abstraction and H₂O catalyzed H-transfer reactions. The predicted maximum photodegradation rates of Tc-ARG in the Yellow River estuary were 0.524, 0.937, and 0.336 h^-1 in fresh water, estuary water, and seawater, respectively. This study furthermore revealed the microscopic photodegradation pathways and obtained essential degradation parameters of Tc-ARG in sunlit surface water.

Implications of N7-hydrogen and C8-keto on the base pairing, mutagenic potential and repair of 8-oxo-2'-deoxy-adenosine: Investigation by nucleotide analogues

Oxidative lesions, such as 8-oxo-dG and 8-oxo-dA, are continuously generated from exposure to reactive oxygen species. While 8-oxo-dG has been extensively studied, 8-oxo-dA has not received as much attention until recently. Herein, we report the synthesis of duplex DNAs incorporating dA, 8-oxo-dA, 7-deaza-dA, 8-Br-dA, and 8-Br-7-deaza-dA, which have different substitutions at 7- and 8-position, for the investigation into the implications of N7-hydrogen and C8-keto on the base pairing preference, mutagenic potential and repair of 8-oxo-dA. Base pairing study suggested that the polar N7-hydrogen and C8-keto of 8-oxo-dA, rather than the syn-preference, might be essential for 8-oxo-dA to form a stable base pair with dG. Insertion and extension studies using KF-exo^- and human DNA polymerase β indicated that the efficient dGTP insertion opposite 8-oxo-dA and extension past 8-oxo-dA:dG are contingent upon not only the stable base pair with dG, but also the flexibility of the active site in polymerase. The N7-hydrogen in 8-oxo-dA or C7-hydrogen in 7-deaza-dA and 8-Br-7-deaza-dA was suggested to be important for the recognition by hOGG1, although the excision efficiencies of 7-deaza-dA and 8-Br-7-deaza-dA were much lower than 8-oxo-dA. This study provides an insight into the structure-function relationship of 8-oxo-dA by nucleotide analogues.

Simultaneous removal of antibiotic resistant bacteria and antibiotic resistance genes by molybdenum carbide assisted electrochemical disinfection

Considering conventional disinfection methods are not effective in simultaneously removing ARB and ARGs, a novel electrochemical disinfection (ED) process assisted by molybdenum carbide (Mo₂C) electrodes was developed in this study. The established ED process was proved to effectively inactivate multi-resistant ARB (i.e. Escherichia coli K-12 LE392 with resistance to kanamycin, ampicillin, and tetracycline) and to degrade ARGs (including tetA and bla_TEM in the form of both intracellular (iARGs) and extracellular ARGs (eARGs)). Specifically, within 15 min treatment by the Mo₂C-assisted ED under 2.0 V, a 5-log ARB removal was realized, without any ARB regrowth observed, indicating a permanent inactivation of ARB by the process. Moreover, degradation of the iARGs (0.4-log reduction of the bla_TEM and 3.1-log reduction of the tetA) and the eARGs (4.2-log reduction of the bla_TEM and 1.1-log reduction of the tetA) were achieved within 60 min, further underpinning the viability of the Mo₂C-based ED. While e^-, H₂O₂, and •O₂^- played leading roles in the entire process of ED, H⁺ and •OH contributed to bacterial inactivation in the early and late stages of ED, respectively. The reactive species induced by electrolysis posed pressure to the ARB strains, which enhanced oxidative stress response, triggered higher reactive oxygen species generation, induced membrane damage and changed cellular structure. Collectively, the Mo₂C-assisted ED demonstrated in the present study represents an attractive alternative to the traditional disinfection methods in combating the spread of antibiotic resistance.

Causal Association between Chronic Kidney Disease and Risk of 19 Site-Specific Cancers: A Mendelian Randomization Study

BACKGROUND

Results of previous observational studies examining the risk of cancer among patients with chronic kidney disease (CKD) are conflicting. We here explore the causal relationship between estimated glomerular filtration rate (eGFR) and albuminuria, two principal measurements of CKD, and 19 site-specific cancers using Mendelian randomization (MR) analysis.

METHODS

Single-nucleotide polymorphisms reported to be strongly correlated with eGFR and albuminuria in recent large genome-wide association studies were used as instrumental variables to investigate the causal relationship with cancer using summary-level statistics from several cancer-specific consortia, as well as data of 347,408 participants in the UK Biobank and 260,405 participants in the FinnGen.

RESULTS

Our data showed that impaired kidney function was associated with higher odds of leukemia [OR = 1.23; 95% confidence interval (CI), 1.06-1.43; P = 0.007], cervical cancer (OR = 1.22; 95% CI, 1.04-1.43; P = 0.017), and female renal cell carcinoma (OR = 1.4; 95% CI, 1.12-1.77; P = 0.004), per 10% decrease in eGFR. The ORs were 1.21 (95% CI, 1.07-1.36; P = 0.002) for colorectal cancer and 0.76 (95% CI, 0.62-0.92; P = 0.006) for non-Hodgkin lymphoma, per doubling odds of albuminuria. In multivariable MR, effect sizes of eGFR-cervical cancer remained strong after adjusting for confounders.

CONCLUSIONS

The current study indicates that progression of CKD contributes to carcinogenesis of renal cell carcinoma, leukemia, cervical, and colorectal cancer.

IMPACT

The potential association of kidney function and albuminuria with certain cancers warrants further investigation in order to provide appropriate recommendations regarding cancer screening among patients with CKD.

Oxidative Stress and Deregulated DNA Damage Response Network in Lung Cancer Patients

The deregulated DNA damage response (DDR) network is associated with the onset and progression of cancer. Herein, we searched for DDR defects in peripheral blood mononuclear cells (PBMCs) from lung cancer patients, and we evaluated factors leading to the augmented formation of DNA damage and/or its delayed/decreased removal. In PBMCs from 20 lung cancer patients at diagnosis and 20 healthy controls (HC), we analyzed oxidative stress and DDR-related parameters, including critical DNA repair mechanisms and apoptosis rates. Cancer patients showed higher levels of endogenous DNA damage than HC (p < 0.001), indicating accumulation of DNA damage in the absence of known exogenous genotoxic insults. Higher levels of oxidative stress and apurinic/apyrimidinic sites were observed in patients rather than HC (all p < 0.001), suggesting that increased endogenous DNA damage may emerge, at least in part, from these intracellular factors. Lower nucleotide excision repair and double-strand break repair capacities were found in patients rather than HC (all p < 0.001), suggesting that the accumulation of DNA damage can also be mediated by defective DNA repair mechanisms. Interestingly, reduced apoptosis rates were obtained in cancer patients compared with HC (p < 0.001). Consequently, the expression of critical DDR-associated genes was found deregulated in cancer patients. Together, oxidative stress and DDR-related aberrations contribute to the accumulation of endogenous DNA damage in PBMCs from lung cancer patients and can potentially be exploited as novel therapeutic targets and non-invasive biomarkers.

Exploring the Structural Diversity of DNA Bottlebrush Polymers Using an Oligonucleotide Macromonomer Approach

Herein, we demonstrate that macromonomers consisting of organics-soluble, chemically protected oligonucleotides (protDNA) and poly(ethylene glycol) (PEG) chains can be converted into bottlebrush polymers of distinct architectures via ring-opening metathesis polymerization (ROMP). Using a custom norbornene-containing phosphoramidite, two types of macromonomers were obtained: a linear norbornene-protDNA-PEG structure and a Y-shaped structure where the polymerizable norbornene group is situated at the junction where protDNA and PEG meet. With this strategy, the PEG chains can be placed either near the backbone of the bottlebrush or on its periphery, and in principle anywhere between these two extremes by adjusting the norbornene location, which makes this strategy attractive for constructing architecturally sophisticated oligonucleotide-containing copolymers.

Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond

Damaged or mismatched DNA bases are normally thought to be able to flip out of the helical stack, providing enzymes with access to the faulty genetic information otherwise hidden inside the helix. Thymine glycol (Tg) is one of the most common products of nucleic acid damage. However, the static and dynamic structures of DNA duplexes affected by 5R-Tg epimers are still not clearly understood, including the ability of these to undergo spontaneous base flipping. Structural effects of the 5R-Tg epimers on the duplex DNA are herein studied using molecular dynamics together with reliable DFT based calculations. In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA, and a barrier of 4.9 kcal mol^–1 is obtained by meta-eABF for cis-5R,6S-Tg base flipping out of the duplex DNA, comparable to the 5.4 kcal mol^–1 obtained for the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were identified, of which the most stable disrupts the Watson–Crick hydrogen-bonded G5/C20 base pair, leading to conformational distortion of the duplex. Interestingly, the relative barrier height of the 5R-Tg flipping is only 1.0 kcal mol^–1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified to be essential for 5R-Tg flipping. The study clearly demonstrates the occurrence of partial trans-5R,6R-Tg epimer flipping in solution.

OUP accepted manuscript

HPLC-PDA, LC-MS/MS methods were developed for simultaneous determination of a group of oxidative stress biomarkers (OSBs); 2dA, 2dC, 2dU, 3NLT, 5HMU and 8OHdG in 10 simulated artificial body fluids. O-phosphoric acid and methanol composed mobile phases A and B for gradient elution in HPLC-PDA using ODS-2 column. Linearity obtained for 1.0×10-6-1.0×10-4M range. LODs were 1.73×10-6, 1.19×10-6, 2.59×10-6, 1.40×10-6, 2.21×10-6 and 4.07×10-6M for 2dU, 8OHdG, 2dA, 2dC, 5HMU and 3NLT, respectively. LOQs were 5.29×10-6, 4.02×10-6, 6.82×10-6, 4.02×10-6, 6.82×10-6 and 9.92×10-6M. About 10 mM aqueous ammonium acetate solution and methanol containing 0.1% (v/v) formic acid composed mobile phases A and B for gradient elution in LC-MS/MS. Linearity obtained for 1.0×10-8-1.0×10-6M range. LODs were 2.88×10-10, 1.01×10-8, 3.38×10-9, 1.36×10-7, 1.81×10-7 and 1.40×10-8M for 2dU, 8OHdG, 2dA, 2dC, 5HMU and 3NLT, respectively. LOQs were 9.37×10-10, 3.22×10-8, 1.91×10-8, 4.53×10-7, 5.90×10-7 and 2.18×10-8M. Both methods were validated using ICH Q2(R1) guideline. Specificity, linearity, range, accuracy, precision, reproducibility, LOD, LOQ and recovery were achieved. Chemometric analysis was performed on raw PDA and MS data to check their significance for discrimination of OSBs. Sets of single and triple quadrupole fragmentations were evaluated for principle component analysis. Chosen number of PCs successfully distinguished OSBs of interest.

Changes of DNA Damage Effect of T-2 or Deoxynivalenol Toxins during Three Weeks Exposure in Common Carp (Cyprinus carpio L.) Revealed by LORD-Q PCR

The present study aimed to adapt a Long-run Real-time DNA Damage Quantification (LORD-Q) qPCR-based method for the analysis of the mitochondrial genome of Common carp (Cyprinus carpio L.) and detect the DNA damaging effect of T-2 (4.11 mg kg⁻¹) and deoxynivalenol (5.96 mg kg⁻¹) mycotoxins in a 3-week feeding period. One-year-old Common carp were treated in groups (control, T-2 and DON). The mycotoxins were sprayed over the complete pelleted feed, and samples were taken weekly. Following the adaptation of LORD-Q PCR method for the Common carp species, the number of lesions were calculated to determine the amount of DNA damage. In the first and second weeks, the T-2 and the DON treated groups differed significantly from each other; however these differences disappeared in the third week. There was a significant difference in the DNA lesion values between weeks 1 and 3 in the deoxynivalenol-contaminated groups. While in the T-2 treated groups, the DNA lesion values were significantly reduced on weeks 2 and 3 compared to week 1. The results suggested that the trichothecene mycotoxins have a relevant DNA damaging effect.

Oxidative stress in leukemia and antioxidant treatment

Oxidative stress is caused by the imbalance between the generation of free radicals/reactive oxygen species (ROS) and the antioxidant defense systems, which can activate various transcription factors and affect their transcriptional pathways. Oxidative stress plays an important role in the occurrence and development of leukemia and is closely related to the treatment and prognosis of leukemia. The standard chemotherapy strategies for the pre-treatment of leukemia have many drawbacks. Hence, the usage of antioxidants and oxidants in the treatment of leukemia is being explored and has been preliminarily applied. This article reviews the research progress of oxidative stress and leukemia. In addition, the application of antioxidants treatment in leukemia has been summarized.

Binding Force and Site-Determined Desorption and Fragmentation of Antibiotic Resistance Genes from Metallic Nanomaterials

Interfacial interactions between antibiotic resistance genes (ARGs) and metallic nanomaterials (NMs) lead to adsorption and fragmentation of ARGs, which can provide new avenues for selecting NMs to control ARGs. This study compared the adsorptive interactions of ARGs (tetM-carrying plasmids) with two metallic NMs (ca. 20 nm), i.e., titanium dioxide (nTiO₂) and zero-valent iron (nZVI). nZVI had a higher adsorption rate (0.06 min^-1) and capacity (4.29 mg/g) for ARGs than nTiO₂ (0.05 min^-1 and 2.15 mg/g, respectively). No desorption of ARGs from either NMs was observed in the adsorptive background solution, isopropanol or urea solutions, but nZVI- and nTiO₂-adsorbed ARGs were effectively desorbed in NaOH and NaH₂PO₄ solutions, respectively. Molecular dynamics simulation revealed that nTiO₂ mainly bound with ARGs through electrostatic attraction, while nZVI bound with PO₄^3- of the ARG phosphate backbones through Fe-O-P coordination. The ARGs desorbed from nTiO₂ remained intact, while the desorbed ARGs from nZVI were splintered into small fragments irrelevant to DNA base composition or sequence location. The ARG removal by nZVI remained effective in the presence of PO₄^3-, natural organic matter, or protein at environmentally relevant concentrations and in surface water samples. These findings indicate that nZVI can be a promising nanomaterial to treat ARG pollution.

DNA glycosylases for 8-oxoguanine repair in Staphylococcus aureus

GO system is part of base excision DNA repair and is required for the correct repair of 8-oxoguanine (8-oxoG), one of the most abundant oxidative lesions. Due to the ability of 8-oxoG to mispair with A, this base is highly mutagenic, and its repair requires two enzymes: Fpg that removes 8-oxoG from 8-oxoG:C pairs, and MutY that excises the normal A from 8-oxoG:A mispairs. Here we characterize the properties of putative GO system DNA glycosylases from Staphylococcus aureus, an important human opportunistic pathogen that causes hospital infections and presents a serious health concern due to quick spread of antibiotic-resistant strains. In addition to Fpg and MutY from the reference NCTC 8325 strain (SauFpg1 and SauMutY), we have also studied an Fpg homolog from a multidrug-resistant C0673 isolate (SauFpg2), which is different from SauFpg1 in its sequence. Both SauFpg enzymes showed the highest activity at pH 7.0-9.0 and NaCl concentrations 25-75 mM (SauFpg1) or 50-100 mM (SauFpg2), whereas SauMutY was active at a broad pH range and had a salt optimum at ∼75 mM NaCl. Both SauFpg1 and SauFpg2 bound and cleaved duplexes containing 8-oxoG, 5-hydroxyuracil, 5,6-dihydrouracil or apurinic/apyrimidinic site paired with C, T, or G, but not with A. For SauFpg1 and SauFpg2, 8-oxoG was the best substrate tested, and 5,6-dihydrouracil was the worst one. SauMutY efficiently excised adenine from duplex substrates containing A:8-oxoG or A:G pairs. SauFpg enzymes were readily trapped on DNA by NaBH₄ treatment, indicating formation of a Schiff base reaction intermediate. Surprisingly, SauMutY was also trapped significantly better than its E. coli homolog. All three S. aureus GO glycosylases drastically reduced spontaneous mutagenesis when expressed in an fpg mutY E. coli double mutant. Overall, we conclude that S. aureus possesses an active GO system, which could possibly be targeted for sensitization of this pathogen to oxidative stress.

The Two Faces of the Guanyl Radical: Molecular Context and Behavior

The guanyl radical or neutral guanine radical G(-H)^• results from the loss of a hydrogen atom (H^•) or an electron/proton (e^–/H⁺) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC^•+ pair. The role of the two G(-H)^• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.

Association between early oxidative DNA damage and iron status in women with gestational diabetes mellitus

This study aims to assess the relationship between oxidative DNA damage and iron status in women with gestational diabetes mellitus (GDM) compared to those with normal glucose tolerance in the first and the second trimesters of pregnancy. Maternal serum and urine samples were collected in the 11th-14th weeks and the 24th-28th weeks of gestation. In addition to oral glucose tolerance test in the second trimester, fasting blood glucose, HbA1c, ferritin and hemoglobin levels were measured in blood samples. Urinary levels of oxidative DNA damage products 8-hydroxy-2'-deoxyguanosine (8-OH-dG) and 8,5'-cyclo-2'-deoxyadenosines (S-cdA, R-cdA) were determined using liquid chromatography-tandem mass spectrometry with isotope-dilution. In the first trimester, urinary 8-OH-dG levels were found higher in the GDM group (n = 33) than in the control group (n = 84) (p = 0.006). R-cdA and S-cdA levels were not significantly different between the two groups (p = 0.794 and p = 0.792 respectively). When the cases were stratified according to their first trimester ferritin levels, women with ≥50th centile (≥130 ng/mL) demonstrated higher levels of 8-OH-dG and R-cdA than those under <50th centile (p = 0.034, p = 0.009). In the GDM group, there was a positive correlation between the second trimester 8-OH-dG and ferritin and 1st-hour glucose levels (p = 0.014, p = 0.020). This is the first study where oxidative DNA damage is evaluated in both early and late periods of pregnancy. Our findings reveal an association between GDM and iron status and oxidative DNA damage.

Synthetic Approaches for Copolymers Containing Nucleic Acids and Analogues: Challenges and Opportunities

A deep integration of nucleic acids with other classes of materials have become the basis of many useful technologies. Among these biohybrids, nucleic acid-containing copolymers has seen rapid development in both chemistry and application. This review focuses on the various synthetic approaches to access nucleic acid-polymer biohybrids spanning post-polymerization conjugation, nucleic acids in polymerization, solid-phase synthesis, and nucleoside/nucleobase-functionalized polymers. We highlight the challenges associated with working with nucleic acids with each approach and the ingenuity of the solutions, with the hope of lowering the entry barrier and inpsiring further investigations in this exciting area.

Telomere maintenance in interplay with DNA repair in pathogenesis and treatment of colorectal cancer

Colorectal cancer (CRC) continues to be one of the leading malignancies and causes of tumour-related deaths worldwide. Both impaired DNA repair mechanisms and disrupted telomere length homeostasis represent key culprits in CRC initiation, progression and prognosis. Mechanistically, altered DNA repair results in the accumulation of mutations in the genome and, ultimately, in genomic instability. DNA repair also determines the response to chemotherapeutics in CRC treatment, suggesting its utilisation in the prediction of therapy response and individual approach to patients. Telomere attrition resulting in replicative senescence, simultaneously by-passing cell cycle checkpoints, is a hallmark of malignant transformation of the cell. Telomerase is almost ubiquitous in advanced solid cancers, including CRC, and its expression is fundamental to cell immortalisation. Therefore, there is a persistent effort to develop therapeutics, which are telomerase-specific and gentle to non-malignant tissues. However, in practice, we are still at the level of clinical trials. The current state of knowledge and the route, which the research takes, gives us a positive perspective that the problem of molecular models of telomerase activation and telomere length stabilisation will finally be solved. We summarise the current literature herein, by pointing out the crosstalk between proteins involved in DNA repair and telomere length homeostasis in relation to CRC.

Surface modified multifaceted nanocarriers for oral non-conventional cancer therapy; synthesis and evaluation

Inflammatory cells orchestrate tumor niche for the proliferating neoplastic cells, leading to neoangiogenesis, lymphangiogenesis, tumor growth and metastasis. Emergence of severe side effects, multiple drug resistance and associated high cost has rendered conventional chemotherapy less effectual. The aim was to develop a multipurpose, less toxic, more potent and cheaper, oral non-conventional anticancer therapeutic. Cyclooxygenase associated with tumor niche inflammation and proliferative neoplastic cells were targeted synergistically, through anti-inflammatory and anti-proliferative effects of model drug, diclofenac sodium and fluorescent silver nanoparticles (AgNPs), respectively. Drug entrapped AgNPs were surface modified with PVA (for controlling particle size, preferred cellular uptake, evading opsonization and improved dispersion). XRD, FTIR, DSC, TGA, LIBS, particle size and surface plasmon resonance analysis confirmed the efficient drug encapsulation and PVA coating with 62% loading efficiency. In-vitro, the formulation exhibited 1st order release kinetics with sustained and maximal release at slightly acidic conditions (pH 4.5) enabling the potential for passive tumor targeting. Also, nanoparticles showed efficient protein denaturation inhibition potential, hemo-compatibility (<0.8%) and potent anti-cancer activity (P < 0.05) against breast cancer cell line (MCF-7). In-vivo, developed nanoparticles improved pharmacokinetics (2.8 fold increased AUC, 6.9 h t_1/2, C_max = 1.6 ± 0.03 μg/ml, K_el = 0.1) and pharmacodynamics manifested by potent anti-inflammatory, analgesic and anti-pyretic effects (P < 0.05) at 20 fold lower doses. LD₅₀ determination revealed a wide therapeutic window. The study showed promise of synthesized nanomaterials as cheaper, less toxic, hemo-compatible, oral and more potent anti-inflammatory and non-conventional fluorescent anti-cancer agents, vanquishing tumor niche inflammation and repressing proliferation of malignant cells.

New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps

Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.

The effect of computed tomography on oxidative stress level and some antioxidant parameters

BACKGROUND

X-rays are defined as ionizing radiation and hydrolyze the water, causing free radical formation. Oxidative stress is the damage that occurs in cells due to the lack of antioxidants, which detoxifies them, with the increased production of free radicals that occur during normal cellular metabolism.

PURPOSE

To examine the acute effects of computed tomography (CT), i.e. ionizing radiation, on oxidative stress and antioxidant defense mechanisms.

MATERIAL AND METHODS

The study included a total of 53 patients that were selected among the patients that underwent non-contrast full-body CT. Malondialdehyde (MDA) and reduced glutathione (GSH) levels and superoxide dismutase (SOD) and catalase (CAT) activities were investigated in blood samples taken from patients.

RESULTS

The post-scan levels of MDA increased significantly while the post-scan levels of GSH, SOD, and CAT decreased significantly compared to their pre-scan levels.

CONCLUSION

CT, which is a widely used X-ray imaging technique and has numerous known side effects, was found to increase the levels of MDA, which is an indicator of oxidative stress, and to decrease the levels of some antioxidants including GSH, SOD, and CAT.

Fight to the bitter end: DNA repair and aging

DNA carries the genetic information that directs complex biological processes; thus, maintaining a stable genome is critical for individual growth and development and for human health. DNA repair is a fundamental and conserved mechanism responsible for mending damaged DNA and restoring genomic stability, while its deficiency is closely related to multiple human disorders. In recent years, remarkable progress has been made in the field of DNA repair and aging. Here, we will extensively discuss the relationship among DNA damage, DNA repair, aging and aging-associated diseases based on the latest research. In addition, the possible role of DNA repair in several potential rejuvenation strategies will be discussed. Finally, we will also review the emerging methods that may facilitate future research on DNA repair.

DNAzyme and rGO based fluorescence assay for Fpg activity analysis, drug screening, and bacterial imaging

Due to the significant role of formamidopyrimidine DNA glycosylase (Fpg) in physiological processes and DNA oxidative damage-related diseases, it is essential to establish sensitive methods for monitoring the Fpg activity in vitro and in vivo so as to illustrate its concrete role in these events. In this work, a sensitive, simple and reliable fluorescence assay was developed by taking the advantages of DNAzyme assisted cascade signal amplification and ultra-high fluorescence quenching efficiency of reduced graphene oxide (rGO). This detection system consisted of DNAzyme, rGO and fluorescence probe allows the activity of Fpg to be detected in a linear range from 0 to 80 U/mL with a detection limit of 0.66 U/mL. With the help of this method, 11 natural compounds were screened, and 7 compounds were identified as activators of Fpg. More importantly, the developed assay was used to monitor the activity of Fpg through fluorescence imaging in living Escherichia coli for the first time. The imaging results visually demonstrated the dynamic activation effect of natural compound Ginsenoside Re on the Fpg of Escherichia coli. In summary, these results indicated that this DNAzyme and rGO based fluorescence assay provides a potent strategy for Fpg quantitative assay in vitro and real-time monitoring in living bacteria, which holds great potential for applying on biological study and Fpg-targeted drug screening.

Dissolved organic matter dominating the photodegradation of free DNA bases in aquatic environments

Free DNA bases are widely present in the environments, and can be utilized by bacteria for their nucleic acids synthesis or as nutrition sources. In sunlit natural waters, these free bases probably undergo photodegradation which would change the bioavailable bases contents. Though the photodegradation of DNA has been investigated, the photodegradation behaviors of free bases may be quite different from those of DNA-confined bases in consideration of their different chemical environments. Herein, the photodegradation of four free bases (guanine, adenine, thymine and cytosine) was investigated. Results show that direct photodegradation of free bases in phosphate buffer caused by UV was slow. However, the photodegradation of these free bases were greatly enhanced in dissolved organic matter (DOM) solution. In the presence of 10-50 mg/L DOM, the photodegradation rates of free bases were increased by 1.85-14.6 times compared to the controls without DOM. DOM could result in indirect photodegradation by producing hydroxyl radical (•OH) and singlet oxygen (¹O₂) under irradiation, and this indirect photodegradation enhanced and dominated the free bases photodegradation. The •OH was involved in all four bases photodegradation, while the ¹O₂ only participated in guanine photodegradation. In phosphate buffer, the fastest photodegradation bases were pyrimidine, however, guanine became the fastest photodegradation base in DOM solution due to the selective oxidation of guanine by ¹O₂. In summary, DOM may be a determinant for free bases photodegradation in natural waters and thereby deeply influence free bases fates in aquatic environments.

XPD/ERCC2 mutations interfere in cellular responses to oxidative stress

Nucleotide excision repair (NER) is a conserved, flexible mechanism responsible for the removal of bulky, helix-distorting DNA lesions, like ultraviolet damage or cisplatin adducts, but its role in the repair of lesions generated by oxidative stress is still not clear. The helicase XPD/ERCC2, one of the two helicases of the transcription complex IIH, together with XPB, participates both in NER and in RNA pol II-driven transcription. In this work, we investigated the responses of distinct XPD-mutated cell lines to the oxidative stress generated by photoactivated methylene blue (MB) and KBrO3 treatments. The studied cells are derived from patients with XPD mutations but expressing different clinical phenotypes, including xeroderma pigmentosum (XP), XP and Cockayne syndrome (XP-D/CS) and trichothiodystrophy (TTD). We show by different approaches that all XPD-mutated cell lines tested were sensitive to oxidative stress, with those from TTD patients being the most sensitive. Host cell reactivation (HCR) assays showed that XP-D/CS and TTD cells have severely impaired repair capacity of oxidised lesions in plasmid DNA, and alkaline comet assays demonstrated the induction of significantly higher amounts of DNA strand breaks after treatment with photoactivated MB in these cells compared to wild-type cells. All XPD-mutated cells presented strong S/G2 arrest and persistent γ-H2AX staining after photoactivated MB treatment. Taken together, these results indicate that XPD participates in the repair of lesions induced by the redox process, and that XPD mutations lead to differences in the response to oxidatively induced damage.

Detection of Hydroxyl Radicals Using Cerium Oxide/Graphene Oxide Composite on Prussian Blue

A composite sensor consisting of two separate inorganic layers of Prussian blue (PB) and a composite of cerium oxide nanoparticles (CeNPs) and graphene oxide (GO), is tested with •OH radicals. The signals from the interaction between the composite layers and •OH radicals are characterized using cyclic voltammetry (CV). The degradation of PB in the presence of H₂O₂ and •OH radicals is observed and its impact on the sensor efficiency is investigated. The results show that the composite sensor differentiates between the solutions with and without •OH radicals by the increase of electrochemical redox current in the presence of •OH radicals. The redox response shows a linear relation with the concentration of •OH radicals where the limit of detection, LOD, is found at 60 µM (100 µM without the PB layer). When additional composite layers are applied on the composite sensor to prevent the degradation of PB layer, the PB layer is still observed to be degraded. Furthermore, the sensor conductivity is found to decrease with the additional layers of composite. Although the CeNP/GO/PB composite sensor demonstrates high sensitivity with •OH radicals at low concentrations, it can only be used once due to the degradation of PB.

Challenge-comet assay, a functional and genomic biomarker for precision risk assessment and disease prevention among exposed workers

Advancements in genomic technologies have ushered application of innovative changes into biomedical sciences and clinical medicine. Consequently, these changes have created enormous opportunities to implement precision population/occupational disease prevention and target-specific disease intervention (or personalized medicine). To capture the opportunities, however, it is necessary is to develop novel, especially genomic-based, biomarkers which can provide precise and individualized health risk assessment. In this review, development of the Challenge-comet assay is used as an example to demonstrate how assays need to be validated for its sensitivity, specificity, and functional and quantitative features, and how assays can be used to provide individualized health risk assessment for precision prevention and intervention. Other examples of genomic-based novel biomarkers will also be discussed. Furthermore, no biomarkers can be used alone therefore their integrated usage with other biomarkers and with personal data bases will be discussed.

Alterations in levels of 8-Oxo-2'-deoxyguanosine and 8-Oxoguanine DNA glycosylase 1 during a current episode and after remission in unipolar and bipolar depression

INTRODUCTION

Previous studies showed significant increases in DNA base damage markers and significant alterations in base excision repair enzymes in patients with unipolar and bipolar depression. We aimed to investigate changes in urine 8-Oxo-2'-deoxyguanosine (8-oxo-dG) and gene expression levels of 8-Oxoguanine DNA glycosylase 1 (OGG1) during a current depressive episode and after remission in bipolar and unipolar disorders.

METHODS

Twenty-four acutely depressed bipolar (BD), 33 unipolar depression (UD) patients and 61 healthy controls were included in the study. Clinical evaluations, blood and urine sampling were completed at baseline and at remission after eight weeks. The urine 8-oxo-dG levels were assessed by liquid chromatography tandem mass spectrometry and adjusted for urine creatinine levels. The gene expression levels of OGG1 were determined from cDNA extracted from blood samples, using real time-polymerase chain reaction.

RESULTS

At baseline, patients presented significantly higher levels of 8-oxo-dG (p = 0.008), and lower gene expression of OGG1 (p = 0.024) compared to controls. Levels of either 8-oxo-dG or OGG1 expression did not differ between BD and UD. In patients who remitted by the 8th week (n = 30), 8-oxo-dG decreased significantly (p = 0.001), and gene expression levels of OGG1 increased by 2.95 times compared to baseline levels (p = 0.001). All comparisons were adjusted for age, sex, smoking status and body mass index.

CONCLUSION

Our results suggest that patients with bipolar and unipolar mood disorders present increased 8-oxo-dG and decreased gene expression levels of OGG1 in current depressive episodes, and that these changes might be reversed by the resolution of depressive symptoms. The causal relationship between DNA damage and repair requires further exploration.

Redox basis of exercise physiology

Redox reactions control fundamental processes of human biology. Therefore, it is safe to assume that the responses and adaptations to exercise are, at least in part, mediated by redox reactions. In this review, we are trying to show that redox reactions are the basis of exercise physiology by outlining the redox signaling pathways that regulate four characteristic acute exercise-induced responses (muscle contractile function, glucose uptake, blood flow and bioenergetics) and four chronic exercise-induced adaptations (mitochondrial biogenesis, muscle hypertrophy, angiogenesis and redox homeostasis). Based on our analysis, we argue that redox regulation should be acknowledged as central to exercise physiology.