Search Results (428)

Genotoxic stress, which includes DNA damage and the mis-localization of DNA and RNA, is a defining feature of tauopathies, Alzheimer’s disease, and several other neurodegenerative disorders. Recent findings indicate that activation of the innate immune system in response to genotoxic stress can drive harmful neuroinflammation, compromise neuronal integrity, and promote neurodegeneration. Multiple innate immune sensors of genotoxic stress have recently been discovered, but the contributions of many of these emerging nucleic acid–sensing pathways in neurodegenerative disease pathogenesis remain largely unexplored. Z-DNA binding protein 1 (ZBP1) is one such recently discovered genotoxic stress sensor that has been shown to incite various forms of cell death as well as proinflammatory cytokine production in response to left-handed Z conformations of DNA (Z-DNA) and RNA (Z-RNA). Here, we show that ZBP1 deletion provides protection against tau pathology and neuronal loss in the PS19 mouse model of tauopathy. Moreover, we find that this rescue of tauopathy seen with ZBP1 ablation is associated with dampened activation of microglia and astrocytes. These findings identify ZBP1 as a pivotal genotoxic stress sensor that drives tau pathology, gliosis, and neuronal loss in tauopathy. This work further suggests that targeting ZBP1 may offer a therapeutic strategy to treat tau-mediated neurodegenerative disease. Full article

Alzheimer’s disease (AD) and cancer are both age-related conditions, yet numerous large-scale epidemiological studies have consistently documented an inverse association, with individuals diagnosed with cancer exhibiting a reduced risk of AD and vice versa. Although this relationship has been replicated across diverse populations, its biological basis remains poorly understood. To address this gap, the present study applies a framework that integrates locus-level genetic correlation (rg) with genetically regulated gene expression to clarify the molecular factors contributing to the inverse epidemiological patterns observed between the two diseases. We used the largest available genome-wide association studies (GWAS) (Nmax = 448,150) to quantify local genetic correlations between AD and several age-associated cancers, including breast, prostate, lung, colorectal, melanoma, basal cell carcinoma, bladder, and endometrial cancer. Eight genomic regions showed significant negative local rg, at the 19q13.31–19q13.32 locus demonstrating strong negative correlations across multiple cancers, including breast, prostate, lung, melanoma, and endometrial cancer. To evaluate the contribution of genetically regulated gene expression, we conducted transcriptome-wide association studies (TWAS) using precomputed gene expression weights from cancer tissues (The Cancer Genome Atlas-TCGA), disease-agnostic tissues (Genotype-Tissue Expression-GTEx), and brain tissue (dorsolateral prefrontal cortex-DLPFC). For each AD–cancer pair, we prioritized genes that were nominally significant in both traits (p < 0.05) and exhibited inverse TWAS Z scores. This analysis identified 24 genes with opposite effect directions between AD and at least three cancer types. TWAS signals also aligned with local rg findings at the 19q13.31–19q13.32 region, suggesting that regulatory variation near this locus contributes to shared but opposing genetic effects beyond the canonical APOE signal. Across cancer types, genes inversely associated with AD converged on pathways involved in cell cycle regulation, apoptosis, DNA-damage response, and metabolic processes. These results support the hypothesis that biological mechanisms promoting proliferation and survival in cancer may oppose those contributing to neurodegeneration in AD. Full article

In inflammatory states, eosinophils are exposed to stimuli leading to activation, increased survival, and/or different cell death subroutines, which have differing effects on tissue inflammation. The mechanisms of signal integration are poorly understood. In this manuscript, we investigated cell death types in response to stimuli mimicking the inflammatory microenvironment. Mouse bone marrow-derived eosinophils (BMDeos) were stimulated with cytokines, cell-cell interaction mimics, pathogen-associated molecular patterns (PAMP), and broad cell activation stimuli. Both PMA and crosslinking of CD95 (cCD95) induced cell death of BMDeos. However, cCD95-induced cell death was consistent with apoptosis, while activation with PMA lead to EETosis. Both stimuli lead to caspase 3 activation and increased total level of histone H3 citrullination, indicating that these outcomes are not able to discriminate between the two cell death types. Flow cytometry for annexinV/7AAD pattern at early time points, and morphologic assessment by immunofluorescence (for DNA, eosinophil granule protein and citH3) were the most reliable outcomes for distinguishing the cell death subtypes. While LPS alone did not decrease BMDeos viability, LPS in the presence of caspase inhibition (zVAD) caused delayed cell death, which did not conform to either of the two cell death types. Finally, LPS and LPS/zVAD led to an increased level of surface expression of CD274 (type 1 activation), while both cCD95 and PMA increased the surface expression of CD101 (type 2 activation). In summary, at least three different activation-associated cell death pathways are seen in BMDeos activated with microenvironment-mimicking stimuli. Crosslinking CD95 leads to type 2 activation and apoptotic cell death. PMA also leads to type 2 activation but EETosis-associated cell death. LPS and LPS/zVAD are associated with type 1 activation, and only LPS/zVAD lead to cell death via a subtype different from both apoptosis and EETosis. Full article

Background/Objectives: Systemic lupus erythematosus (SLE) is an autoimmune disease characterized by B-cell hyperactivation and excessive autoantibody production. Z-DNA binding protein 1 (ZBP1), an innate immune sensor involved in nucleic acid recognition and cell death signaling, has been implicated in antiviral and inflammatory responses. However, its role in B-cell dysregulation during SLE remains unclear. Methods: Integrative transcriptomic analyses were performed using public datasets (GSE61635, GSE235658, GSE136035, and GSE163497) to determine the expression pattern and biological functions of ZBP1 in SLE. Bulk RNA-seq and single-cell RNA-seq data were used to evaluate ZBP1 expression across B-cell subsets. Correlations between ZBP1 expression, disease activity, and immunological parameters were assessed. RNA-seq data following ZBP1 knockdown were analyzed to explore its potential downstream pathways and molecular networks. In addition, in vitro ZBP1 knockdown experiments were conducted to examine its effects on B-cell activation, plasma cell differentiation, and antibody production. Results: ZBP1 was significantly upregulated in peripheral blood and B cells from SLE patients and was enriched in pathways related to type I interferon signaling and cytokine-mediated immune responses. Single-cell transcriptomic profiling further revealed elevated ZBP1 expression across multiple B-cell subsets, including naïve B cells, memory B cells, age-associated B cells (ABCs), and plasma cells. Clinically, ZBP1 expression in peripheral B cells was positively correlated with CD86 mean fluorescence intensity (MFI), SLE Disease Activity Index (SLEDAI) scores, and serum IgG levels, suggesting a link between ZBP1 and B-cell activation. RNA-seq analysis following ZBP1 silencing demonstrated that ZBP1 regulates genes involved in the cell cycle, DNA replication, and p53 signaling, indicating its potential role in promoting B-cell proliferation and activation. Functionally, ZBP1 silencing impaired B-cell activation, reduced plasma cell differentiation, and decreased immunoglobulin production in vitro. Conclusions: Our study identifies ZBP1 as a molecule upregulated in SLE B cells and associated with B-cell activation and disease activity. Although direct causality remains to be established, the data indicate that ZBP1 may contribute to SLE pathogenesis by modulating cell cycle-related pathways and promoting aberrant B-cell responses, highlighting its potential as a biomarker and a candidate therapeutic target in SLE. Full article

The modified DNA base 2,6 aminopurine (2-aminoadenine, (d)Z base) was originally found in phages to counteract host-encoded restriction systems. However, only a limited number of restriction endonucleases (REases) have been tested on dZ-modified DNA. Here, we report the activity results of 147 REases on dZ-modified PCR DNA. Among the enzymes tested, 53% are resistant or partially resistant, and 47% are sensitive when their restriction sites contain one to six modified bases. Sites with four to six dZ substitutions are most likely to resist Type II restriction. Our results support the notion that dZ-modified phage genomes evolved to combat host-encoded restriction systems. dZ-modified DNA can also reduce phage T5 exonuclease degradation, but has no effect on RecBCD digestion. When two genes for dZ biosynthesis and one gene for dATP hydrolysis from Salmonella phage PMBT28 (purZ (adenylosuccinate synthetase), datZ (dATP triphosphohydrolase), and mazZ ((d)GTP-specific diphosphohydrolase) were cloned into an E. coli plasmid, the level of dZ incorporation reached 19–20% of adenosine positions. dZ levels further increased to 29–44% with co-expression of a DNA polymerase gene from the same phage. High levels of dZ incorporation in recombinant plasmid are possible by co-expression of purZ, mazZ, datZ and phage DNA helicase, dpoZ (DNA polymerase) and ssb (single-stranded DNA binding protein SSB). This work expands our understanding of the dZ modification of DNA and opens new avenues for engineering restriction systems and therapeutic applications. Full article

This study investigated the chemical composition, antioxidant activity, and genotoxic potential of essential oils (EOs) obtained by hydrodistillation from aerial parts of four wild-growing Lamiaceae species in eastern Morocco: Spanish ziziphora (Ziziphora hispanica L.), felty germander (Teucrium polium L.), French lavender (Lavandula dentata L.), and topped lavender (Lavandula stoechas L.). Gas chromatography–mass spectrometry (GC-MS) analysis revealed eucalyptol (40.08%), thujopsene (11.25%), β-myrcene (15.82%), and fenchone (30.69%) as the major constituents in Z. hispanica, T. polium, L. dentata, and L. stoechas, respectively. Antioxidant capacity was evaluated using three complementary assays: 2,2-diphenyl-1-picrylhydrazyl radical scavenging, ferric reducing antioxidant power, and β-carotene bleaching. L. stoechas and L. dentata exhibited the strongest antioxidant activities, with IC₅₀ values ranging from 0.284 to 1.71 mg/mL across assays. Genotoxicity was assessed in rat leukocytes using the alkaline Comet assay at EO concentrations of 2.5, 5, and 10 µg/mL. All tested EOs induced statistically significant DNA damage compared to the negative control, though the extent varied by species and concentration; notably, L. stoechas at 2.5 µg/mL showed the lowest genotoxic impact. These findings highlight the dual potential of these EOs as natural antioxidants while underscoring the need for dose-dependent safety evaluation prior to therapeutic or industrial application. Given that DNA damage was detectable even at 2.5 µg/mL, a conservative practical recommendation is to keep EO levels below 2.5 µg/mL-equivalent in preliminary applications, pending further in vivo toxicology to establish NOAEL-based exposure limits. Full article

In the search for solutions to the global health threat posed by antimicrobial resistance, the development of new compounds is crucial. In this context, the in vitro testing of known indolizinoquinolinedione analogs 1–7 revealed that N,N-syn regioisomers are more active than N,N-anti regioisomers. In particular, compound 2 (ethyl 5,12-dihydro-5,12-dioxoindolizino[2,3-g]quinoline-6-carboxylate) exhibited the most significant activity against Bacillus subtilis, B. cereus, Staphylococcus aureus, and methicillin-resistant S. aureus (MRSA) bacteria. The reported increased bioactivity of metal complexes and their ability to overcome drug resistance through metal coordination have induced the study of new metal complexes of compound 2. FT-IR spectroscopy combined with DFT-simulated spectra confirmed the C=O chelation in all Zn, Cu, and Mn complexes 8–10. ESI-MS isotopic cluster analysis and UV-Vis-derived Job’s plot provided significant evidence for 1:1 chelation. Finally, ¹H NMR data were correlated to the DFT-calculated charge distribution. Complexes 8–10 displayed similar activity against B. subtilis, although this was lower than that for 2, and there were comparable effects with 2 and vancomycin antibiotic against S. aureus. FTsZ protein as a potential target of B. subtilis and DNA gyrase of S. aureus and MRSA were studied by docking calculations, revealing a good correlation with the in vitro results. Full article

Background: Many inhibitors have been discovered to target hypoxia-induced carbonic anhydrase IX (CAIX) due to its critical role in lung cancers. This study discovers a novel compound, 3-(E-3,4-dihydroxycinnamaoyloxyl)-2-hydroxypropyl-9Z,12Z-octadeca-9,12-dienoate, which is produced by the seagrass Cymodocea serrulata and has binding sites at CAIX that are distinct from those of current inhibitors. Methods: Compound and reference drug treatment for cell lines; Cell viability: MTT; Staining: Ao/PI/DAPI; MMP shifts and cell cycle: FACS; Gene and protein expression of CAIX, BAX, BAD: qPCR and Western blotting. Results: The compound binds to the CAIX protein, raises extracellular pH, and kills A549 cells [IC₅₀: 11.61 µM], producing results that are lower than those of the reference drug doxorubicin [13.7 µM]. The substance depolarised the electrical potential of the mitochondrial membrane, caused S-phase arrest, and fragmented DNA. Additionally, it downregulated CAIX by 0.9 times while increasing apoptotic mRNA, BAX and BAD by 5.2 and 3.08 times, respectively, as demonstrated by qPCR. Between 0 and 24 h, the untreated hypoxic cells had a ΔpHe of 0.15, but the compound-treated cells had a ΔpHe of 0.6 indicative of intracellular acidosis. MD simulations verify the stability of the CAIX–C1 complex for more than 100 ns, and in silico studies show a strong binding affinity of the molecule to CAIX [−7.55 kcal/mol]. Conclusions: This implies that the amount of extracellular alkalosis was increased by the combination of treatment and hypoxia induction. As a result, when the cells were deprived of O₂, the compound provided less defense against ROS. The compound binds to the glutamine and alanine amino acids at positions 242 and 392, respectively, at the central Zn atom of CAIX, which sets it apart from conventional sulphonamide CAIX inhibitors. This naturally occurring compound may be a potent CAIX inhibitor with newer binding sites, which could help treat hypoxic lung cancers. Full article

Radiotherapy, a cornerstone of cancer treatment, is critically limited by tumor radioresistance and off-target toxicity. Lanthanide-based nanomaterials (Ln-NPs) have recently emerged as a versatile and promising class of theranostic radiosensitizers to overcome these hurdles. This review comprehensively outlines the state-of-the-art in Ln-NP-enabled radiotherapy, beginning with their fundamental physicochemical properties and synthesis and then delving into the multi-level mechanisms of radiosensitization, including high-Z element-mediated physical dose amplification, catalytic generation of reactive oxygen species (ROS), and disruption of DNA damage repair pathways. The unique capacity of certain Ln-NPs to serve as MRI contrast agents is highlighted as the foundation for image-guided, dose-painting radiotherapy. We critically summarize the preclinical and clinical progress of representative systems, benchmarking them against other high-Z nanomaterials. Finally, this work discusses the ongoing challenges, such as biocompatibility, targeted delivery, and regulatory hurdles, and envisages future directions, including combinatorial strategies with immunotherapy and the development of personalized nanotheranostic paradigms. Through this synthesis, this review aims to provide a clear roadmap for the continued development and clinical integration of lanthanide nanotheranostics in oncology. Full article

The role of alternative nucleic acid structures (ANS) in biology is an area of increasing interest. These non-canonical structures include the Z-DNA and Z-RNA duplexes (ZNA), the three-stranded triplex, the four-stranded G-quadruplex (GQ), and i-motifs. Previously, the biological relevance of ANS was dismissed. Their formation in vitro often required non-physiological conditions, and there was no genetic evidence for their function. Further, structural studies confirmed that sequence-specific transcription factors (TFs) bound B-DNA. In contrast, ANS are formed dynamically by a subset of repeat sequences, called flipons. The flip requires energy, but not strand cleavage. Flipons are enriched in promoters where they modulate transcription. Here, computational modeling based on AlphaFold V3 (AF3), under optimized conditions, reveals that known B-DNA-binding TFs also dock to ANS, such as ZNA and GQ. The binding of HLH and bZIP homodimers to Z-DNA is promoted by methylarginine modifications. Heterodimers only bind preformed Z-DNA. The interactions of TFs with ANS likely enhance genome scanning to identify cognate B-DNA-binding sites in active genes. Docking of TF homodimers to Z-DNA potentially facilitates the assembly of heterodimers that dissociate and are stabilized by binding to a cognate B-DNA motif. The process enables rapid discovery of the optimal heterodimer combinations required to regulate a nearby promoter. Full article

Background: This study investigated the phenotypic and genotypic antibiotic resistance profiles of 50 Lactic Acid Bacteria (LAB) strains—25 Lactiplantibacillus plantarum and 25 Lacticaseibacillus paracasei—isolated from traditional Sardinian fermented foods of animal origin. Methods: The sensitivity of the isolates to antibiotics such as β-lactams, tetracyclines, aminoglycosides, macrolides, phenicols, and glycopeptides was initially assessed using disc diffusion and minimum inhibitory concentration (MIC) tests. Subsequently, PCR analyses were performed on both genomic DNA and plasmid DNA to detect blaZ, tet(W), strA, aac(6′)-Ie–aph(2″)-Ia, and vanX genes associated with resistance to ampicillin, tetracycline, streptomycin, gentamicin, and vancomycin. Results: The analysis revealed that L. plantarum strains frequently carried the tet(W) gene on the chromosome and strA on plasmids, while vanX was detected in most strains as a chromosomal determinant. By contrast, L. paracasei strains exhibited a predominantly plasmid-mediated distribution of resistance genes. For example, strA, aac(6′)-Ie–aph(2″)-Ia and blaZ were often found on plasmids, whereas vanX remained chromosomally encoded. Phenotypic assays confirmed high intrinsic resistance to vancomycin in both species, with L. plantarum showing a higher overall frequency and diversity of resistant phenotypes compared to L. paracasei. Conclusions: The co-occurrence of multiple resistance determinants, including plasmid-encoded ones, in most strains suggests that even autochthonous isolates from artisanal products may represent potential reservoirs for transmissible resistance genes. Full article

High-yielding dairy cows suffer from a high metabolic load and oxidative stress, which lead to systemic inflammation and metabolic disorders, increasing the susceptibility of these cows to various production diseases. Dihydromyricetin (DMY) has demonstrated potent antioxidant and anti-inflammatory physiological functions; however, research into its application in ruminants remains limited. This study investigated whether DMY supplementation is associated with the maintenance of metabolic homeostasis through the regulation of gut microbiota and metabolite profiles. A total of 14 mid-lactation Holstein dairy cows were randomly divided into two groups (n = 7 per group) and supplemented with DMY at 0 or 0.05% in their basal diet for 60 consecutive days. The effects of DMY on the blood biochemical indicators and the antioxidant capacity of the dairy cows were then determined. Alterations to the gut microbiome and the fecal and plasma metabolome were analyzed through 16S rDNA sequencing and untargeted metabolomics. The results showed that DMY significantly improved the activity of serum glutathione peroxidase (GSH-Px) and presented a trend of increasing the total antioxidant capacity (T-AOC). The abundance of multiple fiber-degrading and beneficial commensal bacteria in the gut, including Fibrobacter_succinogenes, Ruminococcus_albus, and Turicibacter, was significantly elevated by the DMY intervention, accompanied by the upregulation of 8,11,14-eicosatrienoic acid, myricetin, dihydro-3-coumaric acid, PGE1, L-leucine, nicotinuric acid, pantothenic acid, and pyruvate in the feces and plasma. Moreover, DMY supplementation notably reduced the abundance of potential pathogenic microbes, such as Chloroflexi, Deltaproteobacteria, RFP12, and Succinivibrio, and downregulated the levels of 12-hydroxydodecanoic acid, 12,13-DHOME (12,13-dihydroxy-9Z-octadecenoic acid), 16-hydroxyhexadecanoic acid, niacin, and glycerol 3-phosphate. These differential metabolites were principally enriched in the mTOR signaling pathway; pantothenate, nicotinate, and thiamine metabolism; glutathione metabolism; and glycolysis/gluconeogenesis. In summary, dietary supplementation with DMY increased the abundance of intestinal fiber-degrading bacteria and multiple metabolites with known anti-inflammatory and antioxidant properties in the feces and plasma, and was associated with alterations in metabolic pathways involving B-vitamins, amino acids, and glutathione. This suggests a potential role for DMY in supporting metabolic homeostasis in dairy cows. Full article

The SNF2-related chromatin remodeler Srcap is the principal ATPase responsible for the deposition of the histone variant H2A.Z at promoters and regulatory chromatin regions. Although this activity is known to modulate transcription, its contribution to DNA replication remains unexplored. Here we show that Srcap is required for efficient replication fork progression and origin firing in mammalian cells. Using RNA interference in human PC3 cells, we found that Srcap depletion leads to a ~25% reduction in fork elongation rate, decreased replication fork density, accumulation of the replication-stress marker γH2AX, and reduced chromatin-bound H2A.Z. High-resolution expansion microscopy further revealed diminished intensity and increased spacing of replication foci, consistent with reduced origin activation. Transcriptomic analysis of published data identified broad downregulation of replication-associated genes. These data uncover a dual mechanism by which Srcap sustains replication efficiency—through both H2A.Z-dependent chromatin organization and transcriptional maintenance of the replication machinery. Our findings establish Srcap as an important coordinator of replication dynamics, with implications for genome stability. Full article

CRISPR/Cas12a systems coupled with lateral flow tests (LFTs) are a promising route to rapid, instrument-free nucleic acid diagnostics due to conversion target recognition into a simple visual readout via cleavage of dual-labeled single-stranded DNA reporters. However, the conventional CRISPR/Cas12a–LFT system is constructed in a format where the intact reporter should block nanoparticle conjugate migration and can produce false-positive signals and shows strong dependence on component stoichiometry and kinetics. Here, we present the first combined experimental and theoretical analysis quantifying these limitations and defining practical solutions. The experimental evaluation included 480 variants of LFT configuration with reporters differing in the concentration of interacting components and the kinetic conditions of the interactions. The most influential factor leading to 100% false-positive results was insufficient interaction time between the components; pre-incubation of the conjugate with the reporter for 5 min eliminated these artifacts. Theoretical analysis of the LFT kinetics based on a mathematical model confirmed kinetic constraints at interaction times below a few minutes, which affect the detectable signal. Reporter concentration and conjugate architecture represented the second major factors: lowering reporter concentration to 20 nM and using smaller gold nanoparticles with multivalent fluorescent reporters markedly improved sensitivity. The difference in sensitivity between various LFT configurations exceeded 50-fold. The combination of identified strategies eliminated false-positive reactions and enabled the detection of up to 20 pM of DNA target (the hisZ gene of Erwinia amylovora, a bacterial phytopathogen). The strategies reported here are general and readily transferable to other DNA targets and CRISPR/Cas12a amplification-free diagnostics. Full article

African swine fever virus (ASFV) causes a highly fatal disease in domestic pigs, resulting in substantial economic losses to the global swine industry. Vaccine development continues to be hindered by limited characterization of viral proteins and their functional redundancies. In this study, we employ combined experimental and computational approaches to characterize the ASFV I73R protein (pI73R), which contains a Z-DNA binding domain and plays a critical role in ASFV virulence and pathogenesis. We demonstrate that pI73R shares significant structural similarity with transcription factors of the forkhead box (FOX) protein family. Overexpression of pI73R results in downregulation of Crooked neck-like protein 1 (CRNKL1), a core spliceosome component, suggesting a potential mechanism by which pI73R modulates host protein synthesis. Using high-resolution mass spectrometry, we map the pI73R interactome and identify the host protein Guanine nucleotide-binding protein subunit beta-1 (GNB1) as a novel direct interactor of pI73R which may facilitate its nuclear transport. Furthermore, we show that pI73R exhibits consistent oligomerization and expression across different ASFV genotypes, highlighting its functional importance. Taken together, these results provide new insights into pI73R function, ASFV–host dynamics, and offer promising directions for antiviral strategy development. Full article