Nucleic Acid Damage Research Articles

Nightshift work can induce oxidative DNA damage: a pilot study

BackgroundRegular sleep is very important for human health; however, the short-term and long-term effects of nightshift with sleep deprivation and disturbance on human metabolism, such as oxidative stress, have not been effectively evaluated based on a realistic cohort. We conducted the first long-term follow-up cohort study to evaluate the effect of nightshift work on DNA damage.MethodsWe recruited 16 healthy volunteers (aged 33 ± 5 years) working night shifts at the Department of Laboratory Medicine at a local hospital. Their matched serum and urine samples were collected at four time points: before, during (twice), and after the nightshift period. The levels of 8-oxo-7,8-dihydroguanosine (8-oxoG) and 8-oxo-7,8-dihydro-2’-deoxyguanosine (8-oxodG), two important nucleic-acid damage markers, were accurately determined based on a robust self-established LC‒MS/MS method. The Mann–Whitney U or Kruskal–Wallis test was used for comparisons, and Pearson’s or Spearman’s correlation analysis was used to calculate the correlation coefficients.ResultsThe levels of serum 8-oxodG, estimated glomerular filtration rate-corrected serum 8-oxodG, and the serum-to-urine 8-oxodG ratio significantly increased during the nightshift period. These levels were significantly higher than pre-nightshift work level even after 1 month of discontinuation, but no such significant change was found for 8-oxoG. Moreover, 8-oxoG and 8-oxodG levels were significantly positively associated with many routine biomarkers, such as total bilirubin and urea levels, and significantly negatively associated with serum lipids, such as total cholesterol levels.ConclusionThe results of our cohort study suggested that working night shifts may increase oxidative DNA damage even after a month of discontinuing nightshift work. Further studies with large-scale cohorts, different nightshift modes, and longer follow-up times are needed to clarify the short- and long-term effects of night shifts on DNA damage and find effective solutions to combat the negative effects.

Factors Impacting Rhizobium-legume Symbiotic Nitrogen Fixation with the Physiological and Genetic Responses to Overcome the Adverse Conditions: A Review

Symbiotic N2 fixation is essential for the plant’s growth because it can fix reactive nitrogen compounds in soil. However, all steps of this process can be hampered by several biotic and abiotic environmental factors. This study mainly focused on discussing the impacts of 12 major factors on this process by reviewing the significant numbers of research works. According to the information from these works, we found some significant physiological and genetic impacts caused by these factors like plasmid deletion, genomic mismanagement, abnormal molecular signals, toxicity, deficiency of minerals, deformation of rhizobial cells, protein denaturation, nucleic acid damage, acetylene reduction and nod factors limitation. Furthermore, expression of heat or acid shock proteins, internal buffering, genes spanning, extracellular immobilization, periplasmic allocation, change of lipopolysaccharides composition, intracellular accumulation of inorganic and organic solutes (Osmolyte) and activation of hydrogenase expression are shown by both micro and macro symbionts as a natural response to adapt to these stress conditions. Though the stress-tolerant strains like HR-3, HR-6, HR-10, HR-12, acta, actP, exoR, lpiA, actR, actS and phrR can be used to sense the external environment and make signals to change gene transcription during the adverse condition, the application of genetic engineering should be expanded more to promote the commercial inoculation by the production of novel stress-tolerant strains or modified genes of rhizobia and legumes.

Activation of the NLRP1 inflammasome in human keratinocytes by the dsDNA mimetic poly(dA:dT).

The accrual of cytosolic DNA leads to transcription of type I IFNs, proteolytic maturation of the IL-1 family of cytokines, and pyroptotic cell death. Caspase-1 cleaves pro-IL1β to generate mature bioactive cytokine and gasdermin D which facilitates IL-1 release and pyroptotic cell death. Absent in melanoma-2 (AIM2) is a sensor of dsDNA leading to caspase-1 activation, although in human monocytes, cGAS-STING acting upstream of NLRP3 mediates the dsDNA-activated inflammasome response. In healthy human keratinocytes, AIM2 is not expressed yet caspase-1 is activated by the synthetic dsDNA mimetic poly(dA:dT). Here, we show that this response is not mediated by either AIM2 or the cGAS-STING-NLRP3 pathway and is instead dependent on NLRP1. Poly(dA:dT) is unique in its ability to activate NLRP1, as conventional linear dsDNAs fail to elicit NLRP1 activation. DsRNA was recently shown to activate NLRP1 and prior work has shown that poly(dA:dT) is transcribed into an RNA intermediate that stimulates the RNA sensor RIG-I. However, poly(dA:dT)-dependent RNA intermediates are insufficient to activate NLRP1. Instead, poly(dA:dT) results in oxidative nucleic acid damage and cellular stress, events which activate MAP3 kinases including ZAKα that converge on p38 to activate NLRP1. Collectively, this work defines a new activator of NLRP1, broadening our understanding of sensors that recognize poly(dA:dT) and advances the understanding of the immunostimulatory potential of this potent adjuvant.

8-oxo-dGTP curbs tumor development via S phase arrest and AIF-mediated apoptosis

Oxidative stress can attack precursor nucleotides, resulting in nucleic acid damage in cells. It remains unclear how 8-oxo-dGTP and 8-oxoGTP, oxidized forms of dGTP and GTP, respectively, could affect DNA or RNA oxidation levels and tumor development. To address this, we intravenously administered 8-oxo-dGTP and 8-oxoGTP to wild-type and MTH1-knockout mice. 8-oxoGTP administration increased frequency of tumor incidence, which is more prominent in MTH1-knockout mice. However, 8-oxo-dGTP treatment rather reduced tumor development regardless of the mouse genotype. The tumor suppressive effects of 8-oxo-dGTP were further confirmed using xenograft and C57/6J-ApcMin/Nju mouse models. Mechanistically, 8-oxo-dGTP increased the 8-oxo-dG contents in DNA and DNA strand breakage, induced cell cycle arrest in S phase and apoptosis mediated by AIF, eventually leading to reduced tumor incidence. These results suggest distinct roles of 8-oxo-dGTP and 8-oxoGTP in tumor development.

Java Plum (Syzygium cumini (L.) Skeels) Leaf Extract Lowers Serum Urea Levels in Lead-Acetate-Induced Rats

Lead is a hazardous metal to living things. Lead can cause oxidative stress in the body, inhibit enzyme activity, damage nucleic acids, and prevent DNA repair, resulting in cell death. Java plum (Syzygium cumini (L.) Skeels) leaves are rich with antioxidants. The research aimed to evaluate if Java plum leaf extract affected serum urea levels in lead acetate-induced rats. This study is an experimental study using 24 male rats with a randomized post-test only control group design. Rats were divided into three groups: the group that did not get any treatment, namely the negative control (NC); the group that was given lead acetate (40 mg/kg BW) was a positive control (PC); and the group that was given lead acetate (40 mg/kg BW) and Java plum leaf extract (150 mg/kg BW) was the treatment group (T), using an oral probe. The treatment was carried out for four weeks. After four weeks, the rats were killed, and their serum urea levels were examined using the urease-GLDH: enzymatic UV test method. The results showed the mean serum urea levels in the NC, PC, and T groups were 17.87±2.18, 22.79±2.52, and 18.12±2.19 mg/dl, respectively. There were significant differences in all groups (p-value < 0.05) in the one-way Anova. Additionally, the post hoc Tukey HSD test demonstrated a statistically significant difference between the positive control and treatment groups as well as between the negative and positive control groups (p-value < 0.05). The conclusion was that Java plum leaf extract was able to reduce serum urea levels under lead intoxication conditions.

Psidium cattleianum como posible tratamiento del estrés oxidativo causado por infección de SARS-COV-2

The SARS-CoV-2 virus presents a lot of proteins in its structure that facilitate host cell infection, generating an increase in the concentration of angiotensin II and activating multiple signaling pathways that stimulate the NADPH oxidase enzyme complex and enzymes that take part in the inflammatory answer. As a consequence, there is an increase in reactive oxygen species (ROS) that damage different proteins, lipids and nucleic acids. Given this, Psidium cattleianumcan capture free radicals or inhibit theformation of ROS by transferring hydrogen atoms and electrons. For that, this research has the main objective to determine the influence of Psidium cattleianumas a possible treatment of oxidative stress caused by the SARS-COV-2 infection in order to consider the consumption of this berry as a possible alternative as an antioxidant treatment.

Liquiritigenin reverses skin aging by inhibiting UV-induced mitochondrial uncoupling and excessive energy consumption.

The accumulation of reactive oxygen species (ROS) generated by UV radiation can lead to lipid, protein, nucleic acid, and organelle damage, one of the core mechanisms mediating skin aging. In the photoaging process, how ROS drives the imbalance of the body's complex repair system to induce senescence-like features is not fully understood. We irradiated human epidermal keratinocytes with 12 J/cm2 of UVA to establish an in vitro photoaging model. Then we employed whole-transcriptome sequencing and O2K mitochondrial function assay to reveal the photoprotective mechanisms of liquiritigenin (LQ). We found that skin reduces endogenous ROS by promoting mitochondrial oxidative phosphorylation uncoupling in response to UVA-induced damage. However, this also causes excessive consumption and idling of nutrients, leading to the inhibition of cell proliferation, and ultimately accelerating the skin aging process. Here, we demonstrated that LQ can reduce stress in keratinocytes, increase oxidative phosphorylation and ATP production efficiency, and block the massive loss of skin nutrients and net energy stress. Furthermore, LQ can promote collagen synthesis and keratinocyte proliferation through the PI3K-AKT pathway, thereby reversing photoaging. This work provides a new skin aging mechanism and solution strategy with high clinical translation value.

A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor.

Genome minimization is an effective way for industrial chassis development. In this study, Zymomonas mobilis ZMNP, a plasmid-free mutant strain of Z. mobilis ZM4 with four native plasmids deleted, was constructed using native type I-F CRISPR-Cas system. Cell growth of ZMNP under different temperatures and industrial effluent of xylose mother liquor were examined to investigate the impact of native plasmid removal. Despite ZMNP grew similarly as ZM4 under different temperatures, ZMNP had better xylose mother liquor utilization than ZM4. In addition, genomic, transcriptomic, and proteomic analyses were applied to unravel the molecular changes between ZM4 and ZMNP. Whole-genome resequencing result indicated that an S267P mutation in the C-terminal of OxyR, a peroxide-sensing transcriptional regulator, probably alters the transcription initiation of antioxidant genes for stress responses. Transcriptomic and proteomic studies illustrated that the reason that ZMNP utilized the toxic xylose mother liquor better than ZM4 was probably due to the upregulation of genes in ZMNP involving in stress responses as well as cysteine biosynthesis to accelerate the intracellular ROS detoxification and nucleic acid damage repair. This was further confirmed by lower ROS levels in ZMNP compared to ZM4 in different media supplemented with furfural or ethanol. The upregulation of stress response genes due to the OxyR mutation to accelerate ROS detoxification and DNA/RNA repair not only illustrates the underlying mechanism of the robustness of ZMNP in the toxic xylose mother liquor, but also provides an idea for the rational design of synthetic inhibitor-tolerant microorganisms for economic lignocellulosic biochemical production.

Micronuclei in Circulating Tumor Associated Macrophages Predicts Progression in Advanced Colorectal Cancer.

Micronuclei (MN) are fragments of damaged nucleic acids which budded from a cell's nuclei as a repair mechanism for chromosomal instabilities, which within circulating white blood cells (cWBCs) signifies increased cancer risk, and in tumor cells indicates aggressive subtypes. MN form overtime and with therapy induction, which requires sequential monitoring of rarer cell subpopulations. We evaluated the peripheral blood (7.5 mL) for MN in Circulating Stromal Cells (CStCs) in a prospective pilot study of advanced colorectal cancer patients (n = 25), identifying MN by DAPI+ structures (<3 µm) within the cellular cytoplasm. MN+ was compared to genotoxic induction, progression free survival (PFS) or overall survival (OS) hazard ratios (HR) over three years. MN were identified in 44% (n = 11/25) of CStCs, but were not associated with genotoxic therapies (p = 0.110) nor stage (p = 0.137). However, presence of MN in CStCs was independently prognostic for PFS (HR = 17.2, 95% CI 3.6-80.9, p = 0.001) and OS (HR = 70.3, 95% CI 6.6-752.8, p = 0.002), indicating a non-interventional mechanism in their formation. Additionally, MN formation did not appear associated with chemotherapy induction, but was correlated with tumor response. MN formation in colorectal cancer is an underlying biological mechanism that appears independent of chemotherapeutic genotoxins, changes during treatment, and predicts for poor clinical outcomes.

Oxidative Stress and Intervertebral Disc Degeneration: Pathophysiology, Signaling Pathway, and Therapy.

Intervertebral disc degeneration (IDD), characterized as decreased proteoglycan content, ossification of endplate, and decreased intervertebral height, is one of the major reasons of low back pain, which seriously affects the quality of life and also brings heavy economic burden. However, the mechanisms leading to IDD and its therapeutic targets have not been fully elucidated. Oxidative stress refers to the imbalance between oxidation and antioxidant systems, between too many products of reactive oxygen species (ROS) and the insufficient scavenging function. Excessive ROS can damage cell lipids, nucleic acids and proteins, which has been proved to be related to the development of a variety of diseases. In recent years, an increasing number of studies have reported that oxidative stress is involved in the pathological process of IDD. Excessive ROS can accelerate the IDD process via inducing the pathological activities, such as inflammation, apoptosis, and senescence. In this review, we focused on pathophysiology and molecular mechanisms of oxidative stress-induced IDD. Moreover, the present review also summarized the possible ideas for the future therapy strategies of oxidative stress-related IDD.

Association of Oxidative Stress–Induced Nucleic Acid Damage With Psychiatric Disorders in Adults

Nucleic acid damage from oxidative stress (NA-OXS) may be a molecular mechanism driving the severely increased morbidity and mortality from somatic causes in adults with psychiatric disorders. To systematically retrieve and analyze data on NA-OXS across the psychiatric disorder diagnostic spectrum. The PubMed, Embase, and PsycINFO databases were searched from inception to November 16, 2021. A hand search of reference lists of relevant articles was also performed. Key study inclusion criteria in this meta-analysis were as follows: adult human study population, measurement of any marker of DNA or RNA damage from oxidative stress, and either a (1) cross-sectional design comparing patients with psychiatric disorders (any diagnosis) with a control group or (2) prospective intervention. Two authors screened the studies, and 2 senior authors read the relevant articles in full and assessed them for eligibility. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines were followed. Two authors performed data extraction independently, and a senior coauthor was consulted in cases of disagreement. Data were synthesized with random-effects and multilevel meta-analyses. The predefined hypothesis was that individuals with psychiatric disorders have increased NA-OXS levels. The main outcome was the standardized mean differences (SMDs) among patients and controls in nucleic acid oxidation markers compared across diagnostic groups. Analyses were divided into combinations of biological matrices and nucleic acids. Eighty-two studies fulfilled the inclusion criteria, comprising 205 patient vs control group comparisons and a total of 10 151 patient and 10 532 control observations. Overall, the data showed that patients with psychiatric disorders had higher NA-OXS levels vs controls across matrices and molecules. Pooled effect sizes ranged from moderate for urinary DNA markers (SMD = 0.44 [95% CI, 0.20-0.68]; P < .001) to very large for blood cell DNA markers (SMD = 1.12 [95% CI, 0.69-1.55; P < .001). Higher NA-OXS levels were observed among patients with dementias followed by psychotic and bipolar disorders. Sensitivity analyses excluding low-quality studies did not materially alter the results. Intervention studies were few and too heterogenous for meaningful meta-analysis. The results of this meta-analysis suggest that there is an association with increased NA-OXS levels in individuals across the psychiatric disorder diagnostic spectrum. NA-OXS may play a role in the somatic morbidity and mortality observed among individuals with psychiatric disorders.

Overexpression of mcr-1 disrupts cell envelope synthesis and causes the dysregulation of carbon metabolism, redox balance and nucleic acids

Rapid dissemination of plasmid-borne polymyxin resistance mcr-1 genes threatens the efficacy of polymyxins. Acquisition of mcr-1 imposes a fitness cost on bacteria; identifying the molecular mechanisms underpinning this fitness cost will help in the development of adjunctive antimicrobial therapies that target polymyxin-resistant Gram-negative pathogens. Phenotypic assays and transcriptomics were acquired to investigate the impact of mcr-1 expression on membrane characteristics and transcriptomic responses in Escherichia coli TOP10 carrying the empty vector pBAD (TOP10+pBAD) and harbouring pBAD-mcr-1 (TOP10+pBAD-mcr-1). The overexpression of mcr-1 increased outer membrane permeability and caused membrane depolarisation, reflective of the transcriptomic results that showed downregulation of multiple genes involved in lipopolysaccharide core and O-antigen biosynthesis. Overexpression of mcr-1 also caused considerable gene expression changes in pathways involving carbohydrate metabolism (phosphotransferase system, pentose phosphate pathway, and pantothenate and coenzyme A biosynthesis), ABC transporters and intracellular responses to stress, especially those associated with oxidative and nucleic acid damage. Expression of mcr-1 also triggered the production of reactive oxygen species. These findings indicate that overexpression of mcr-1 results in persistent transcriptomic changes that primarily involve disruption to cell envelope synthesis via the reduction of LPS modifications, as well as dysregulation of carbon metabolism, redox balance and nucleic acids. These consequences of expression dysregulation may act as the main factors that impose a fitness cost with mcr-1 expression.

Abstract 3762: Applications of innovative whole-genome bisulfite sequencing (WGBS) for cancer biomarker discovery in plasma liquid biopsy

Abstract Circulating cell-free DNA (cfDNA) has been reported to contain valuable genetic and epigenetic information for the diagnosis and prognosis of cancer. Studies have shown that the blood from cancer patients contained more tumor-derived cfDNA compared to the healthy controls. DNA methylation, the most well-studied epigenetic marker, has been validated as one of the key drivers in the development of many diseases including cancer. cfDNA methylation thus holds great potential to become a biomarker that will enable early detection of cancer. However, cfDNA is also a challenging input for library preparation as cfDNA is mostly highly fragmented, and the amount of cfDNA from blood plasma is comparatively low. Therefore, multiple library preparation protocols were evaluated for profiling DNA methylation patterns at single nucleotide resolution from ultra-low amount of blood plasma cfDNA. These methods included two bisulfite conversion-based protocols and an enzymatic based protocol. The bisulfite conversion reaction was optimized allowing a milder treatment for less nucleic acid damage. One of the bisulfite conversion based protocols also contained a further optimized adapter ligation step, allowing a simpler procedure. Circulating cfDNA were extracted from blood plasma of a healthy control, a non-small cell lung cancer patient, and an adenocarcinoma lung cancer patient. 5-ng cfDNA was used as input and the libraries were successfully prepared using all three methods. Each library was sequenced to 300 - 600 million read pairs at a read length of 150 bp, enabling a mean coverage of about 10X per detected CpG, and over 90% of the CpG sites in human genome were detected. Unique alignment rate among all libraries were about or above 80%. The comprehensive coverage of the CpG sites across the entire human genome illustrated that the optimized bisulfite conversion reaction was compatible with fragmented cfDNA, proving the satisfactory efficacy in this simple and classic method for DNA methylation profiling of such a challenging sample type. This opens the door to apply the streamlined and simple Whole-Genome Bisulfite Sequencing (WGBS) protocol for cfDNA methylation profiling, which in turn shall facilitate further understanding in cfDNA epigenetic variations and advance the development of a cancer biomarker from the non-invasive, liquid biopsies. Citation Format: Caila Ruiz, Hanjun Kim, Zhenguo Zhang, Jeffrey Bhasin, Mingda Jin, Yi Xu, Xiaojing Yang. Applications of innovative whole-genome bisulfite sequencing (WGBS) for cancer biomarker discovery in plasma liquid biopsy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3762.

Time-dependent biodistribution profiles and reaction of polyethylene glycol-coated iron oxide nanoclusters in the spleen after intravenous injection in the mice

Polyethylene glycol (PEG) is widely used polymer in the field of pharmaceutics, particularly in which related to drug delivery systems (DDS). Surface coating of the nanoparticles (NPs) with PEG (i.e. pegylation) adds novel characteristics that make their use in vivo more effective with lower cytotoxicity. The biodistribution profiles, reaction, and fate of PEG-coated NPs in vivo still unclear and need more detailed studies. Here in this study, we prepared PEG-coated iron oxide nanoclusters (PEG-coated IONCs) to investigate their biodistribution profiles and reactions in spleen after intravenous injection time-dependently. Using Prussian blue staining method as specific histochemical reaction for iron detection in the tissues, the PEG-coated IONCs were observed in a higher ratio in spleen red pulp after 1 day of injection but decreased time-dependently after 10 days and 20 days. Interestingly, PEG-coated IONCs moved from red pulp into the white pulp specially after 20 days of injection. After long time exposure (20 days), higher amount of PEG-coated IONCs was observed in the center of spleen white pulp follicle. Using histological staining, the reaction of PEG-coated IONCs with splenocytes or immune cells induced cellular abnormalities such as, nucleic acid damages, induction of megakaryocytes number, and sever vacuolation in the white pulp area specially after 20 days of injection. Histochemically, the localization of PEG-coated IONCs in the splenic parenchyma induced the level of the collagen fibers particularly after 1 day and 10 days of injection. Interestingly, cellular abnormalities in the splenic red pulp as well as collagen levels decreased after 20 days of injection due to the clearance of PEG-coated IONCs from this area. This data indicated that cytotoxicity produced by the reaction of PEG-coated IONCs in the spleen are reversible specially after 20 days of in the intravenous injection. Understanding the detailed mechanism of the fate and reaction of the coated nanomaterials after intravenous injection is important to design effective and safe DDS based NPs.

Oxidative nucleic acid damage as a biomarker for preeclampsia

Recent studies have reported that nucleic acid oxidation is elevated in preeclampsia. Furthermore, it is known that products of nucleic acid oxidation are eventually removed through the urine. The aim of this study was to check whether urine can be used as a non-invasive specimen to analyse nucleic acid oxidation in preeclampsia. We carried out a case-control study by enrolling preeclamptic pregnant (n = 31) and normotensive pregnant (n = 31) women. Urine samples from the study participants were collected and the levels of oxidised guanine species (a common product of nucleic acid oxidation) were determined by ELISA method. The urinary levels of oxidised guanine species were significantly higher in the preeclamptic pregnant group compared to the normotensive pregnant group (p = 0.001). The results were also analysed after stratifying the preeclamptic group in terms of severity and gestational age of onset. A significant difference was observed in both mild (p = 0.005) and severe preeclampsia (p = 0.01). However, a significant difference was observed only in the late onset (p = 0.001) and not in the early onset preeclampsia (p = 0.56). The results of this study show that oxidised guanine level is elevated in the urine of preeclamptic pregnant women. IMPACT STATEMENT What is already known on this subject? Nucleic acid oxidation is elevated in preeclampsia. However, the utility of urine (a non-invasive specimen) to analyse nucleic acid oxidation is not known. What do the results of this study add? This study shows that the levels of oxidised guanine (a marker of nucleic acid oxidation) are elevated in the urine of preeclamptic women. What are the implications of these findings for clinical practice and/or further research? Urinary levels of oxidised guanine may be developed as a non-invasive biomarker for preeclampsia.

A Nuclear‐Targeted AIE Photosensitizer for Enzyme Inhibition and Photosensitization in Cancer Cell Ablation

AbstractThe nucleus is considered the ideal target for anti‐tumor therapy because DNA and some enzymes in the nucleus are the main causes of cell canceration and malignant proliferation. However, nuclear target drugs with good biosafety and high efficiency in cancer treatment are rare. Herein, a nuclear‐targeted material MeTPAE with aggregation‐induced emission (AIE) characteristics was developed based on a triphenylamine structure skeleton. MeTPAE can not only interact with histone deacetylases (HDACs) to inhibit cell proliferation but also damage telomere and nucleic acids precisely through photodynamic treatment (PDT). The cocktail strategy of MeTPAE caused obvious cell cycle arrest and showed excellent PDT anti‐tumor activity, which offered new opportunities for the effective treatment of malignant tumors.

A Nuclear-Targeted AIE Photosensitizer for Enzyme Inhibition and Photosensitization in Cancer Cell Ablation.

The nucleus is considered the ideal target for anti-tumor therapy because DNA and some enzymes in the nucleus are the main causes of cell canceration and malignant proliferation. However, nuclear target drugs with good biosafety and high efficiency in cancer treatment are rare. Herein, a nuclear-targeted material MeTPAE with aggregation-induced emission (AIE) characteristics was developed based on a triphenylamine structure skeleton. MeTPAE can not only interact with histone deacetylases (HDACs) to inhibit cell proliferation but also damage telomere and nucleic acids precisely through photodynamic treatment (PDT). The cocktail strategy of MeTPAE caused obvious cell cycle arrest and showed excellent PDT anti-tumor activity, which offered new opportunities for the effective treatment of malignant tumors.

Structural insights into the interactions and epigenetic functions of human nucleic acid repair protein ALKBH6

Human AlkB homolog 6, ALKBH6, plays key roles in nucleic acid damage repair and tumor therapy. However, no precise structural and functional information are available for this protein. In this study, we determined atomic resolution crystal structures of human holo-ALKBH6 and its complex with ligands. AlkB members bind nucleic acids by NRLs (nucleotide recognition lids, also called Flips), which can recognize DNA/RNA and flip methylated lesions. We found that ALKBH6 has unusual Flip1 and Flip2 domains, distinct from other AlkB family members both in sequence and conformation. Moreover, we show that its unique Flip3 domain has multiple unreported functions, such as discriminating against double-stranded nucleic acids, blocking the active center, binding other proteins, and in suppressing tumor growth. Structural analyses and substrate screening reveal how ALKBH6 discriminates between different types of nucleic acids and may also function as a nucleic acid demethylase. Structure-based interacting partner screening not only uncovered an unidentified interaction of transcription repressor ZMYND11 and ALKBH6 in tumor suppression but also revealed cross talk between histone modification and nucleic acid modification in epigenetic regulation. Taken together, these results shed light on the molecular mechanism underlying ALKBH6-associated nucleic acid damage repair and tumor therapy.

Investigation of nucleic acid damage induced by a novel ruthenium anti-cancer drug using multiple analytical techniques: Sequence specificity and damage kinetics.

Cis-diacetonitrilo-bis(bipyridine) ruthenium(II) chloride is a recently introduced cis-platin analogue that has anti-cancer properties with lower side effects. However, the sequence dependence of its DNA damaging mechanism is unclear. Here, we present a simple, sensitive, multiplexed mix-and-read assay for ascertaining the molecular mechanism of DNA damage induced by the studied ruthenium complex (Ru-complex). The damage kinetics and sequence specificity for the Ru-complex induced DNA damage are examined by studying the induced damage in various oligonucleotide sequences by EvaGreen-DNA intercalator probe. High-through-put measurements were established using a 96-well microplate platform that allows multiple sequences to be measured simultaneously. The results show that the extent of damage increases with an increasing number of guanines, with considerable amount of damage at GA, GT and GC sites, in particular. Furthermore, the interaction of Ru-complex with DNA was confirmed using thermal analysis and MALDI-TOF-MS. Results indicate that the activated Ru-complex preferentially binds via both mono- and di-adduct formation at G and GG sites, respectively. Moreover, the developed method was successfully applied for the determination of the potency of the studied Ru-complex to induce DNA damage in K-Ras and N-Ras family of genes, one of the most common oncogenic events in cancer.

The Oxidative Potential of Fine Particulate Matter and Biological Perturbations in Human Plasma and Saliva Metabolome.

Particulate oxidative potential may comprise a key health-relevant parameter of particulate matter (PM) toxicity. To identify biological perturbations associated with particulate oxidative potential and examine the underlying molecular mechanisms, we recruited 54 participants from two dormitories near and far from a congested highway in Atlanta, GA. Fine particulate matter oxidative potential ("FPMOP") levels at the dormitories were measured using dithiothreitol assay. Plasma and saliva samples were collected from participants four times for longitudinal high-resolution metabolic profiling. We conducted metabolome-wide association studies to identify metabolic signals with FPMOP. Leukotriene metabolism and galactose metabolism were top pathways associated with ≥5 FPMOP-related indicators in plasma, while vitamin E metabolism and leukotriene metabolism were found associated with most FPMOP indicators in saliva. We observed different patterns of perturbed pathways significantly associated with water-soluble and -insoluble FPMOPs, respectively. We confirmed five metabolites directly associated with FPMOP, including hypoxanthine, histidine, pyruvate, lactate/glyceraldehyde, and azelaic acid, which were implications of perturbations in acute inflammation, nucleic acid damage and repair, and energy perturbation. The unique metabolic signals were specific to FPMOP, but not PM mass, providing initial indication that FPMOP might constitute a more sensitive, health-relevant measure for elucidating etiologies related to PM2.5 exposures.