Decitabine cytotoxicity is promoted by dCMP deaminase DCTD and mitigated by SUMO-dependent E3 ligase TOPORS.

The nucleoside analogue decitabine (or 5-aza-dC) is used to treat several haematological cancers. Upon its triphosphorylation and incorporation into DNA, 5-aza-dC induces covalent DNA methyltransferase 1 DNA-protein crosslinks (DNMT1-DPCs), leading to DNA hypomethylation. However, 5-aza-dC's clinical outcomes vary, and relapse is common. Using genome-scale CRISPR/Cas9 screens, we map factors determining 5-aza-dC sensitivity. Unexpectedly, we find that loss of the dCMP deaminase DCTD causes 5-aza-dC resistance, suggesting that 5-aza-dUMP generation is cytotoxic. Combining results from a subsequent genetic screen in DCTD-deficient cells with the identification of the DNMT1-DPC-proximal proteome, we uncover the ubiquitin and SUMO1 E3 ligase, TOPORS, as a new DPC repair factor. TOPORS is recruited to SUMOylated DNMT1-DPCs and promotes their degradation. Our study suggests that 5-aza-dC-induced DPCs cause cytotoxicity when DPC repair is compromised, while cytotoxicity in wild-type cells arises from perturbed nucleotide metabolism, potentially laying the foundations for future identification of predictive biomarkers for decitabine treatment.

Effect of Nitrogen Dopant Agents in the Performance of Graphene-Based Cathodes for Li-S Batteries.

Lithium-sulphur (Li-S) batteries offer high energy density compared to lithium-ion batteries, emerging as a promising technology for the next generation of energy storage systems. The ongoing challenge is to improve their electrochemical performance, extend their useful life and mitigate some problems that persist in this technology, by the investigation in materials with diverse properties. This work seeks to elucidate the importance and repercussions associated with functionalisation of graphene-based materials through nitrogen incorporation (more than 9 wt.% N), employing different chemical agents such as ethylenediamine and ammonia. Herein, differences in both the textural properties and the chemical environment of nitrogen within the carbonaceous network are identified, resulting in distinct electrochemical behaviours. The electrochemical performance of electrodes prepared from ammonia-functionalised samples surpasses that of ethylenediamine-functionalised samples in terms of both efficiency and rate performance. Conversely, the ethylenediamine-functionalised samples excel in stability, showing exceptional values in capacity retention per cycle. The outcomes exceeded expectations in energy performance, allowing the Li-S cells to be subjected to ultra-high rate cycling while maintaining appropriate capacity values.

RAD54L2 counters TOP2-DNA adducts to promote genome stability.

The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.

Unrepaired base excision repair intermediates in template DNA strands trigger replication fork collapse and PARP inhibitor sensitivity.

DNA single-strand breaks (SSBs) disrupt DNA replication and induce chromosome breakage. However, whether SSBs induce chromosome breakage when present behind replication forks or ahead of replication forks is unclear. To address this question, we exploited an exquisite sensitivity of SSB repair-defective human cells lacking PARP activity or XRCC1 to the thymidine analogue 5-chloro-2'-deoxyuridine (CldU). We show that incubation with CldU in these cells results in chromosome breakage, sister chromatid exchange, and cytotoxicity by a mechanism that depends on the S phase activity of uracil DNA glycosylase (UNG). Importantly, we show that CldU incorporation in one cell cycle is cytotoxic only during the following cell cycle, when it is present in template DNA. In agreement with this, while UNG induces SSBs both in nascent strands behind replication forks and in template strands ahead of replication forks, only the latter trigger fork collapse and chromosome breakage. Finally, we show that BRCA-defective cells are hypersensitive to CldU, either alone and/or in combination with PARP inhibitor, suggesting that CldU may have clinical utility.

Revolutionizing DNA repair research and cancer therapy with CRISPR-Cas screens.

All organisms possess molecular mechanisms that govern DNA repair and associated DNA damage response (DDR) processes. Owing to their relevance to human disease, most notably cancer, these mechanisms have been studied extensively, yet new DNA repair and/or DDR factors and functional interactions between them are still being uncovered. The emergence of CRISPR technologies and CRISPR-based genetic screens has enabled genome-scale analyses of gene-gene and gene-drug interactions, thereby providing new insights into cellular processes in distinct DDR-deficiency genetic backgrounds and conditions. In this Review, we discuss the mechanistic basis of CRISPR-Cas genetic screening approaches and describe how they have contributed to our understanding of DNA repair and DDR pathways. We discuss how DNA repair pathways are regulated, and identify and characterize crosstalk between them. We also highlight the impacts of CRISPR-based studies in identifying novel strategies for cancer therapy, and in understanding, overcoming and even exploiting cancer-drug resistance, for example in the contexts of PARP inhibition, homologous recombination deficiencies and/or replication stress. Lastly, we present the DDR CRISPR screen (DDRcs) portal , in which we have collected and reanalysed data from CRISPR screen studies and provide a tool for systematically exploring them.

Effect of the Heating Rate to Prevent the Generation of Iron Oxides during the Hydrothermal Synthesis of LiFePO4.

Lithium-ion batteries (LIBs) have gained much interest in recent years because of the increasing energy demand and the relentless progression of climate change. About 30% of the manufacturing cost for LIBs is spent on cathode materials, and its level of development is lower than the negative electrode, separator diaphragm and electrolyte, therefore becoming the "controlling step". Numerous cathodic materials have been employed, LiFePO4 being the most relevant one mainly because of its excellent performance, as well as its rated capacity (170 mA·h·g-1) and practical operating voltage (3.5 V vs. Li+/Li). Nevertheless, producing micro and nanoparticles with high purity levels, avoiding the formation of iron oxides, and reducing the operating cost are still some of the aspects still to be improved. In this work, we have applied two heating rates (slow and fast) to the same hydrothermal synthesis process with the main objective of obtaining, without any reducing agents, the purest possible LiFePO4 in the shortest time and with the lowest proportion of magnetite impurities. The reagents initially used were: FeSO4, H3PO4, and LiOH, and a crucial phenomenon has been observed in the temperature range between 130 and 150 °C, being verified with various techniques such as XRD and SEM.

Simple and Sustainable Preparation of Cathodes for Li-S Batteries: Regeneration of Granular Activated Carbon from the Odor Control System of a Wastewater Treatment Plant.

To obtain a wide variety of green materials, numerous investigations have been undertaken on industrial waste that can act as sustainable resources. The use of hazardous wastes derived from wastewater treatment plants (WWTPs), especially the activated carbon used in odor control systems, is a highly abundant, scalable, and cost-effective strategy. The reuse of waste materials is a key aspect, especially for the sustainable development of emerging energy storage systems, such as lithium-sulfur (Li-S) batteries. Herein, granular active carbons from two WWTP treatment lines were regenerated in air at low temperature and utilized as the sulfur host with micro-/mesoporous framework. The resulting regenerated carbon and sulfur composites were employed as cathodes for Li-S cells. The SL-ACt3@S composite electrode with 60 wt% loaded sulfur exhibited a remarkable initial capacity of 1100 mAh g-1 at C/10 rate and higher than 800 mAh g-1 at C/2. Even at a rate of 1C, it maintained a high capacity of almost 700 mAh g-1 with a capacity retention of 85.4 % after 350 cycles, demonstrating a very low capacity fading of only 0.042 % per cycle. It is essential to note that the coulombic efficiency was always higher than 96 % during all the cycles. In this proposal, the only used source material was expired carbon from WWTP that was obtained with a simple and effective regeneration process. This "trash into treasure" strategy leads to a new way for using hazardous waste material as high-performance and environmentally safe electrodes for advanced Li-S batteries.

A Genetic Map of the Response to DNA Damage in Human Cells.

The response to DNA damage is critical for cellular homeostasis, tumor suppression, immunity, and gametogenesis. In order to provide an unbiased and global view of the DNA damage response in human cells, we undertook 31 CRISPR-Cas9 screens against 27 genotoxic agents in the retinal pigment epithelium-1 (RPE1) cell line. These screens identified 890 genes whose loss causes either sensitivity or resistance to DNA-damaging agents. Mining this dataset, we discovered that ERCC6L2 (which is mutated in a bone-marrow failure syndrome) codes for a canonical non-homologous end-joining pathway factor, that the RNA polymerase II component ELOF1 modulates the response to transcription-blocking agents, and that the cytotoxicity of the G-quadruplex ligand pyridostatin involves trapping topoisomerase II on DNA. This map of the DNA damage response provides a rich resource to study this fundamental cellular system and has implications for the development and use of genotoxic agents in cancer therapy.

Pistachio Shell-Derived Carbon Activated with Phosphoric Acid: A More Efficient Procedure to Improve the Performance of Li-S Batteries.

A sustainable and low-cost lithium-sulfur (Li-S) battery was produced by reusing abundant waste from biomass as a raw material. Pistachio shell was the by-product from the agri-food industry chosen to obtain activated carbon with excellent textural properties, which acts as a conductive matrix for sulfur. Pistachio shell-derived carbon activated with phosphoric acid exhibits a high surface area (1345 m2·g-1) and pore volume (0.67 cm3·g-1), together with an interconnected system of micropores and mesopores that is capable of accommodating significant amounts of S and enhancing the charge carrier mobility of the electrochemical reaction. Moreover, preparation of the S composite was carried out by simple wet grinding of the components, eliminating the usual stage of S melting. The cell performance was very satisfactory, both in long-term cycling measurements and in rate capability tests. After the initial cycles required for cell stabilization, it maintained good capacity retention for the 300 cycles measured (the capacity loss was barely 0.85 mAh·g-1 per cycle). In the rate capability test, the capacity released was around 650 mAh·g-1 at 1C, a higher value than that supplied by other activated carbons from nut wastes.

MIL-88A Metal-Organic Framework as a Stable Sulfur-host Cathode for Long-cycle Li-S Batteries.

Lithium-sulfur (Li-S) batteries have received enormous interest as a promising energy storage system to compete against limited, non-renewable, energy sources due to their high energy density, sustainability, and low cost. Among the main challenges of this technology, researchers are concentrating on reducing the well-known "shuttle effect" that generates the loss and corrosion of the active material during cycling. To tackle this issue, metal-organic frameworks (MOF) are considered excellent sulfur host materials to be part of the cathode in Li-S batteries, showing efficient confinement of undesirable polysulfides. In this study, MIL-88A, based on iron fumarate, was synthesised by a simple and fast ultrasonic-assisted probe method. Techniques such as X-ray diffraction (XRD), Raman spectroscopy, Thermogravimetric Analysis (TGA), Scanning Electron Microscopy (SEM), and N2 adsorption/desorption isotherms were used to characterise structural, morphological, and textural properties. The synthesis process led to MIL-88A particles with a central prismatic portion and pyramidal terminal portions, which exhibited a dual micro-mesoporous MOF system. The composite MIL-88A@S was prepared, by a typical melt-diffusion method at 155°C, as a cathodic material for Li-S cells. MIL-88A@S electrodes were tested under several rates, exhibiting stable specific capacity values above 400 mAh g-1 at 0.1 C (1C = 1675 mA g-1). This polyhedral and porous MIL-88A was found to be an effective cathode material for long cycling in Li-S cells, retaining a reversible capacity above 300 mAh g-1 at 0.5 C for more than 1000 cycles, and exhibiting excellent coulombic efficiency.

Endogenous topoisomerase II-mediated DNA breaks drive thymic cancer predisposition linked to ATM deficiency.

The ATM kinase is a master regulator of the DNA damage response to double-strand breaks (DSBs) and a well-established tumour suppressor whose loss is the cause of the neurodegenerative and cancer-prone syndrome Ataxia-Telangiectasia (A-T). A-T patients and Atm-/- mouse models are particularly predisposed to develop lymphoid cancers derived from deficient repair of RAG-induced DSBs during V(D)J recombination. Here, we unexpectedly find that specifically disturbing the repair of DSBs produced by DNA topoisomerase II (TOP2) by genetically removing the highly specialised repair enzyme TDP2 increases the incidence of thymic tumours in Atm-/- mice. Furthermore, we find that TOP2 strongly colocalizes with RAG, both genome-wide and at V(D)J recombination sites, resulting in an increased endogenous chromosomal fragility of these regions. Thus, our findings demonstrate a strong causal relationship between endogenous TOP2-induced DSBs and cancer development, confirming these lesions as major drivers of ATM-deficient lymphoid malignancies, and potentially other conditions and cancer types.

Insights into the formation of N doped 3D-graphene quantum dots. Spectroscopic and computational approach.

In this work, we utilize a top-down approach to synthesize nitrogen doped graphene quantum dots from a 3D-graphene precursor via an eco-friendly hydrothermal method. The nanoparticles obtained showed a 2-3 nm diameter and well dispersion behavior in aqueous media. The reaction mechanism of insertion of nitrogen from polyvinylpolypyrrolidone onto the 3D-graphene structure, via an esterification reaction, was studied by the density functional theory, in addition, the kinetic and thermodynamic magnitudes of the reaction was analyzed with the help of Eyring's transition state theory and statistical thermodynamics. After analysis by ss-NMR and XPS spectroscopies, the functional groups involved in this process were characterized, and N was found mainly as amide/amine groups. Fluorescence emission, which exhibited a red shift (552 nm) and an emission maximum at 512 nm when excited at 480 nm, demonstrated a low stoke shift (Δλ = 32 nm), explained by the proposed structural model.

A Comparative Study of Particle Size Distribution of Graphene Nanosheets Synthesized by an Ultrasound-Assisted Method.

Graphene-based materials are highly interesting in virtue of their excellent chemical, physical and mechanical properties that make them extremely useful as privileged materials in different industrial applications. Sonochemical methods allow the production of low-defect graphene materials, which are preferred for certain uses. Graphene nanosheets (GNS) have been prepared by exfoliation of a commercial micrographite (MG) using an ultrasound probe. Both materials were characterized by common techniques such as X-ray diffraction (XRD), Transmission Electronic Microscopy (TEM), Raman spectroscopy and X-ray photoelectron spectroscopy (XPS). All of them revealed the formation of exfoliated graphene nanosheets with similar surface characteristics to the pristine graphite but with a decreased crystallite size and number of layers. An exhaustive study of the particle size distribution was carried out by different analytical techniques such as dynamic light scattering (DLS), nanoparticle tracking analysis (NTA) and asymmetric flow field flow fractionation (AF4). The results provided by these techniques have been compared. NTA and AF4 gave higher resolution than DLS. AF4 has shown to be a precise analytical technique for the separation of GNS of different sizes.

GSE4 peptide suppresses oxidative and telomere deficiencies in ataxia telangiectasia patient cells.

Ataxia telangiectasia (AT) is a genetic disease caused by mutations in the ATM gene but the mechanisms underlying AT are not completely understood. Key functions of the ATM protein are to sense and regulate cellular redox status and to transduce DNA double-strand break signals to downstream effectors. ATM-deficient cells show increased ROS accumulation, activation of p38 protein kinase, and increased levels of DNA damage. GSE24.2 peptide and a short derivative GSE4 peptide corresponding to an internal domain of Dyskerin have proved to induce telomerase activity, decrease oxidative stress, and protect from DNA damage in dyskeratosis congenita (DC) cells. We have found that expression of GSE24.2 and GSE4 in human AT fibroblast is able to decrease DNA damage, detected by γ-H2A.X and 53BP1 foci. However, GSE24.2/GSE4 expression does not improve double-strand break signaling and repair caused by the lack of ATM activity. In contrast, they cause a decrease in 8-oxoguanine and OGG1-derived lesions, particularly at telomeres and mitochondrial DNA, as well as in reactive oxygen species, in parallel with increased expression of SOD1. These cells also showed lower levels of IL6 and decreased p38 phosphorylation, decreased senescence and increased ability to divide for longer times. Additionally, these cells are more resistant to treatment with H202 and the radiomimetic-drug bleomycin. Finally, we found shorter telomere length (TL) in AT cells, lower levels of TERT expression, and telomerase activity that were also partially reverted by GSE4. These observations suggest that GSE4 may be considered as a new therapy for the treatment of AT that counteracts the cellular effects of high ROS levels generated in AT cells and in addition increases telomerase activity contributing to increased cell proliferation.

"An End to a Means": How DNA-End Structure Shapes the Double-Strand Break Repair Process.

Endogenously-arising DNA double-strand breaks (DSBs) rarely harbor canonical 5'-phosphate, 3'-hydroxyl moieties at the ends, which are, regardless of the pathway used, ultimately required for their repair. Cells are therefore endowed with a wide variety of enzymes that can deal with these chemical and structural variations and guarantee the formation of ligatable termini. An important distinction is whether the ends are directly "unblocked" by specific enzymatic activities without affecting the integrity of the DNA molecule and its sequence, or whether they are "processed" by unspecific nucleases that remove nucleotides from the termini. DNA end structure and configuration, therefore, shape the repair process, its requirements, and, importantly, its final outcome. Thus, the molecular mechanisms that coordinate and integrate the cellular response to blocked DSBs, although still largely unexplored, can be particularly relevant for maintaining genome integrity and avoiding malignant transformation and cancer.

Almond Shell as a Microporous Carbon Source for Sustainable Cathodes in Lithium⁻Sulfur Batteries.

A microporous carbon derived from biomass (almond shells) and activated with phosphoric acid was analysed as a cathodic matrix in Li⁻S batteries. By studying the parameters of the carbonization process of this biomass residue, certain conditions were determined to obtain a high surface area of carbon (967 m² g-1) and high porosity (0.49 cm³ g-1). This carbon was capable of accommodating up to 60% by weight of sulfur, infiltrated by the disulphide method. The C⁻S composite released an initial specific capacity of 915 mAh g-1 in the Li⁻S cell at a current density of 100 mA g-1 with a high retention capacity of 760 mAh g-1 after 100 cycles and a coulombic efficiency close to 100%. The good performance of the composite was also observed under higher current rates (up to 1000 mA g-1). The overall electrochemical behaviour of this microporous carbon acting as a sulfur host reinforces the possibility of using biomass residues as sustainable sources of materials for energy storage.

A Lithium-Ion Battery using a 3 D-Array Nanostructured Graphene-Sulfur Cathode and a Silicon Oxide-Based Anode.

An efficient lithium-ion battery was assembled by using an enhanced sulfur-based cathode and a silicon oxide-based anode and proposed as an innovative energy-storage system. The sulfur-carbon composite, which exploits graphene carbon with a 3 D array (3DG-S), was synthesized by a reduction step through a microwave-assisted solvothermal technique and was fully characterized in terms of structure and morphology, thereby revealing suitable features for lithium-cell application. Electrochemical tests of the 3DG-S electrode in a lithium half-cell indicated a capacity ranging from 1200 to 1000 mAh g-1 at currents of C/10 and 1 C, respectively. Remarkably, the Li-alloyed anode, namely, Liy SiOx -C prepared by the sol-gel method and lithiated by surface treatment, showed suitable performance in a lithium half-cell by using an electrolyte designed for lithium-sulfur batteries. The Liy SiOx -C/3DG-S battery was found to exhibit very promising properties with a capacity of approximately 460 mAh gS-1 delivered at an average voltage of approximately 1.5 V over 200 cycles, suggesting that the characterized materials would be suitable candidates for low-cost and high-energy-storage applications.

ATM specifically mediates repair of double-strand breaks with blocked DNA ends.

Ataxia telangiectasia is caused by mutations in ATM and represents a paradigm for cancer predisposition and neurodegenerative syndromes linked to deficiencies in the DNA-damage response. The role of ATM as a key regulator of signalling following DNA double-strand breaks (DSBs) has been dissected in extraordinary detail, but the impact of this process on DSB repair still remains controversial. Here we develop novel genetic and molecular tools to modify the structure of DSB ends and demonstrate that ATM is indeed required for efficient and accurate DSB repair, preventing cell death and genome instability, but exclusively when the ends are irreversibly blocked. We therefore identify the nature of ATM involvement in DSB repair, presenting blocked DNA ends as a possible pathogenic trigger of ataxia telangiectasia and related disorders.