Search Results (479)

Endogenous gene tagging using CRISPR has changed the understanding of the role played by different proteins due to the ability to track and study proteins in their natural state. With CRISPR-based gene tagging, it is possible to insert fluorescent, luminescent, epitope, affinity, and proximity labels into the target protein at its endogenous genomic location without affecting its physiological expression and dynamics. Here, we discuss the DNA-repair mechanisms employed in endogenous gene tagging, including homology-dependent repair, NHEJ-based integration, and alternative approaches that can be used with challenging cell types. Key aspects of efficient CRISPR tagging experiments are also described. Additionally, we review recent advances in the increasing array of protein tag technologies, including fluorescent proteins, split-reporter technologies, NanoLuc/HiBiT, peptide epitopes, and proximity biotinylation enzymes. Lastly, we review the scalability of endogenous tagging approaches using multiplex editing, atlas-scale proteome tagging, iPSC-based disease modeling, and drug discovery platforms for assessing target engagement, protein degradation, phenotype screening, and mechanism of action of compounds. Although difficult in primary and pluripotent cells, new methods based on avoiding double-strand breaks, such as prime editing, PASTE, and CRISPR associated transposases, will drive the future expansion of endogenous tagging approaches. Such developments firmly set up CRISPR gene tagging as a fundamental technology in quantitative cell biology and translational pharmacology. Full article

Ischemic stroke triggers a severe redox disequilibrium that critically shapes cell survival within the penumbra. Although oxidative DNA damage arises from excessive ROS production, the capacity to repair such lesions is tightly constrained by cellular metabolic status. Growing evidence indicates that astrocytes, key metabolic regulators of the neurovascular unit, modulate neuronal susceptibility to genomic injury through redox buffering, NAD⁺ maintenance, and metabolic support. In the metabolically impaired yet structurally preserved penumbra, astrocytic control of glutathione turnover, mitochondrial function, and lactate shuttling may determine whether oxidative DNA lesions are efficiently repaired or progress toward energetic collapse. Poly(ADP-ribose) polymerase 1 activation following DNA strand breaks couples genomic stress to NAD⁺ depletion and bioenergetic failure, forming a critical interface between redox biology and metabolism. This framework posits that astrocytes preserve genomic integrity not by directly altering DNA repair pathways but by sustaining the energetic capacity required for an effective DNA damage response. Elucidating this astrocyte-centered redox–metabolic axis may reveal therapeutic strategies to stabilize penumbral tissue and improve stroke outcomes. Full article

The Chinese bahaba (Bahaba taipingensis), an endangered marine fish, is highly vulnerable to infectious spleen and kidney necrosis virus (ISKNV). In this work, we developed a gill filament-derived cell line, designated BTG, to investigate how these cells respond to ISKNV over time, specifically from 3 to 24 h post-infection (hpi). BTG cells grew steadily, displayed a diploid chromosome number of 2n = 48, demonstrated high transfection efficiency, and were highly susceptible to viral infection. Characteristic cytopathic effects (CPEs) became noticeable as early as 6 hpi at 27 °C. RNA-seq profiling showed that the number of differentially expressed genes (DEGs) steadily increased with time. Standard enrichment analysis at individual time points (3, 6, 12, and 24 hpi) highlighted pathways mainly involved in DNA replication, cell cycle control, ribosome assembly, transcription and translation, mismatch repair, and cell adhesion. Temporal clustering analysis, however, revealed hidden patterns in immune gene expression. Genes that were consistently downregulated were enriched in immune-related pathways, including ECM–receptor interaction, cytokine–receptor signaling, PI3K–AKT, and Wnt signaling, indicating prolonged suppression of host defense mechanisms. In contrast, clusters of genes transiently upregulated during the first 6 h post-infection were associated with antiviral and innate immune pathways, such as NF-κB, JNK, IRF3, IRF7, caspases, JAK, MHC I, and lysosome-related functions, suggesting a rapid but short-lived antiviral response. Genes that were continuously upregulated were primarily involved in nucleic acid replication and protein synthesis, reflecting a gradual host cell reprogramming to support viral replication. Taken together, these findings reveal a temporal shift in BTG cells from an initial burst of immune activity to immune suppression, accompanied by enhanced viral replication. The BTG cell line thus represents a valuable in vitro model for dissecting ISKNV–host interactions and offers new perspectives on the molecular strategies employed by megalocytiviruses in B. taipingensis. Full article

Cancer cells, like yeast, use fermentation despite the presence of oxygen, a phenomenon called aerobic glycolysis. The advantage is that it maintains many C-C bonds of glucose, allowing highly proliferating cells to produce the biomolecules that are necessary for cytokinesis. However, aerobic glycolysis is less energy-efficient than respiration, and it must operate at high frequency and produces large amounts of lactate, which modifies and stimulates DNA repair enzymes via lysine lactylation. This makes cancer cells resistant to radiotherapy, which requires a combination with chemotherapy using drugs that inhibit DNA repair. However, this converts healthy cells to cancer cells, indicating that research is still required regarding the relationship between glycolysis and cancer. Using yeast as a model, we discovered that the glycolytic enzymes TPI and GAPDH (Tpi1p and Tdh1-3p in yeast) interact with the DNA damage-dependent Checkpoint Rad9p (53BP1/BRCA1/MDC1 in humans). We propose that Tpi1p and Tdh1-3p override Rad9p, allowing cells with damaged DNA to proliferate. We isolated tpi and gapdh mutant strains that are deficient in DNA repair. While the tpi mutant strain has lower enzymatic activity, the gapdh mutant strains have normal enzymatic activity, confirming previous reports that GAPDH moonlights in the DNA damage response. Full article

The disinfection process in wastewater treatment is key to the discharge and/or reuse of high-quality effluent. However, disinfection using ultraviolet (UV) light may be inefficient because bacteria possess mechanisms for repairing damaged DNA. This study aimed to assess the photoreactivation and dark repair of total coliform (TC) in wastewater effluent after UV-C disinfection treatment. Four UV-C doses (28.8, 53.1, 57.6, and 106.2 mJ/cm²) and two post-irradiation conditions (light vs. darkness) were applied. Reactivation was monitored after 2, 4, 6 and 24 h (25 °C). Similar TC inactivation efficiencies were observed for the three lowest UV-C doses, whereas the 106.2 mJ/cm² dose achieved the greatest reduction (1.1 Log of TC), decreasing TC concentrations from 3.1 × 10⁵ ± 3.5 × 10⁵ to 1.2 × 10⁵ ± 1.4 × 10⁵ MPN/100 mL. Reactivation assays revealed substantial bacterial recovery after UV treatment, with 24 h survival rates up to 2.3 × 10³ under light and 9.2 × 10² in darkness. Photoreactivation and dark repair assays revealed substantial variability in bacterial recovery after UV treatment depending on UV-C dose, post-irradiation condition and incubation time. In general, bacterial recovery was still detected even at the 106.2 mJ/cm² dose, particularly after 24 h of incubation (178–604%). These findings suggest that effective organic matter removal before UV-C disinfection is critical to improve UV transmittance, reduce shielding effects, and limit subsequent bacterial recovery. Full article

Background: Glioblastoma (GBM) remains a lethal malignancy due to temozolomide (TMZ) resistance and limited drug penetration across the blood–brain barrier, largely driven by hyperactive DNA damage repair mechanisms such as poly (ADP-ribose) polymerase (PARP). To address these challenges, we developed folic acid-targeted PLGA–zein hybrid core–shell nanoparticles for the codelivery of the alkylating agent TMZ and the natural PARP inhibitor Ellagic acid (FA-TMZ/EA-PZ-CS NPs), thereby enabling simultaneous enhancement of drug delivery and suppression of chemoresistance pathways. Methods and Results: The dual-drug nanoplatform was fabricated using a double-emulsion solvent evaporation method and functionalized via EDC/NHS-mediated folic acid conjugation to promote receptor-mediated uptake. Physicochemical characterisation confirmed uniform spherical morphology, high colloidal stability, efficient drug encapsulation, and sustained biphasic drug release consistent with a core–shell diffusion mechanism. In LN229 glioblastoma cells, folic acid conjugation significantly enhanced cellular internalisation and cytotoxic efficacy compared to free drugs and non-targeted nanoparticles. Combination index analysis revealed strong synergism between TMZ and ellagic acid, resulting in markedly reduced IC₅₀ values. Mechanistic studies demonstrated apoptosis induction, increased DNA damage, inhibition of cell migration at sub-cytotoxic concentrations, and downregulation of PARP gene expression. Conclusion: Overall, this study establishes a targeted core–shell nanotherapeutic strategy that integrates chemotherapy with DNA repair inhibition to overcome TMZ resistance, offering a mechanistically sound strategy that serves as a foundational framework for future translational research. Full article

Background/Objectives: Determining homologous recombination repair (HRR) status in metastatic castration-resistant prostate cancer (mCRPC) is essential to ensure access to targeted therapies, particularly PARP inhibitors. Yet, variability in testing access and analysis performance exists. This study evaluated feasibility and outcomes of a centralized HRR testing strategy in Spain for prostate cancer patients. Methods: A total of 1412 formalin-fixed paraffin-embedded (FFPE) tumor samples from mCRPC patients from 89 Spanish institutions within a centralized multicenter molecular testing program were analyzed using a standardized 38-gene-based next-generation sequencing (NGS) assay in a central laboratory (HRR OncoKit, Health in Code, Valencia, Spain), which included five clinically relevant HRR genes: BRCA1, BRCA2, CHEK2, ATM, and CDK12. Results: HRR gene pathogenic or likely pathogenic alterations were identified in 18% (CI 95% = 16–20) of the patients, with BRCA2 being the most frequently altered gene (6%), followed by ATM (5%), CDK12 (4%), BRCA1 (2%), and CHEK2 (1%). Eleven percent had variants of uncertain significance. Only 13% of the samples were rejected due to poor DNA quality, low tumor content or sample age exceeding 5 years, and 2% of the samples analyzed failed since the minimum library technical quality score was not achieved. The average turnaround time for results was 18 ± 3 days. Conclusions: Centralized HRR testing in mCRPC patients in Spain was feasible, efficient and reliable, identifying pathogenic alterations in 18% of the cases, similarly to the prevalence described in the literature. This testing approach facilitates precision medicine by improving the detection of actionable HRR alterations. Full article

Background: Ultraviolet-C (UV-C) radiation is a high-energy physical mutagen capable of inducing DNA damage and oxidative stress, thereby generating genomic variability in photosynthetic organisms. However, its genome-wide effects in unicellular eukaryotic microalgae remain poorly characterized. This study developed a UV-C mutagenesis protocol in Chlamydomonas reinhardtii and evaluated its genomic and physiological impacts. Methods: Axenic cultures of Chlamydomonas reinhardtii (137c+) were exposed to UV-C (100–280 nm) for 12, 48, and 96 min. Viable colonies were analyzed by Random Amplification of Polymorphic DNA PCR (RAPD-PCR) to assess genetic variability, while chlorophyll content and the expression of stress-responsive genes were measured via spectrophotometry and Reverse Transcription quantitative Polymerase Chain Reaction (RT-qPCR), respectively. Results: UV-C treatment induced extensive genomic polymorphism with heterogeneous clustering patterns independent of exposure time, consistent with stochastic mutagenesis. Several mutants exhibited reduced chlorophyll content, indicating impaired photosynthetic efficiency. In contrast, one genotype (pop18) maintained wild-type chlorophyll levels despite marked genetic divergence, coupled with upregulation of antioxidant, DNA repair, and stress-response genes. Conclusions: Overall, UV-C irradiation represents an effective approach to generate non-directional genomic variability in Chlamydomonas reinhardtii, with evidence that random mutagenesis can drive functional reorganization of stress-response pathways, supporting its application in microalgal strain improvement. Full article

The commercial viability of B. purificata relies on efficient depuration. While P. pulchellum extract dramatically accelerates this process, its physiological and molecular mechanisms remain unknown. To address this, we integrated behavioural, histological, ultrastructural, and transcriptomic (RNA-seq) analyses to characterize the acute stress and subsequent recovery phases of B. purificata exposed to the botanical extract. Extract exposure induced severe neuromuscular hyperextension response, with histological analysis revealing acute interstitial oedema and neuronal chromatolysis. This structural damage caused sustained cephalopodium extension and muscle fibre uncoupling. Transcriptomic profiling linked this neuromuscular dysfunction to conserved calcium-dependent adrenergic signalling modules and profound endogenous neuroendocrine disruption. The extract also induced cellular stress, downregulating the apoptosis inhibitor BIRC7 and eliciting transcriptomic signatures consistent with a DNA damage response. Crucially, during the short-term recovery phase, surviving tissues mounted a robust transcriptomic repair response. The snails systemically suppressed the cell cycle via MCM2-6 downregulation while upregulating GADD45 and RAD54B, suggesting a prioritization of genomic repair alongside partial morphological reorganization. Ultimately, P. pulchellum accelerates depuration via acute phytochemical stress and neuromuscular dysfunction. Importantly, this stress is accompanied by a highly coordinated transcriptomic repair response and partial short-term restoration, providing foundational molecular insights essential for evaluating and optimizing botanical depuration protocols. Full article

The ability to precisely edit genetic characteristics with a CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) immunity complex is a revolutionary advance in science. Originally discovered in bacteria as part of a natural defense mechanism against viruses, CRISPR/Cas provides a precise, efficient, and relatively simple method for editing genes in microbes, plants, animals, and humans. The process relies on the Cas protein, an enzyme that cleaves and unwinds DNA at targeted locations. This process is guided by RNA sequences complementary to the DNA or RNA sequence of interest, allowing for changes to the genome through innate non-homologous end joining (NHEJ) and homology-directed repair (HDR). The potential applications of CRISPR/Cas are immense and, in agriculture, is facilitating crop development with resistance to abiotic, biotic, and agronomic characteristics that improve yield, quality, and food security. Gene editing also facilitates the relatively rapid modification of regulatory and complex pathways that enable studies to advance our understanding of gene function. This review provides an update of the fast-evolving CRISPR/Cas modification of important crops to address emerging global population, as well as environmental and climate challenges. Full article

Gene amplification resulting from double strand breaks (DSBs) is a typical genetic alteration in tumorigenesis and drug-resistant progression. Amplified oncogenes and drug-resistant genes are present on extrachromosomal DNAs (ecDNAs), or chromosomal homogeneously staining regions (HSRs). Considering the role of mismatch repair (MMR) as a sensor of DSBs, we hypothesized that MMR may be involved in gene amplification. We used two MTX-resistant HT-29 colorectal cancer cell lines, which served as models with amplified genes mainly in HSRs or ecDNAs. Expression of MSH2, a key protein in MMR, was increased following the acquisition of MTX-resistant. MMR inhibition was achieved by depleting MSH2. Suppression of MMR led to decreased copy numbers of amplified genes as well as the quantity of ecDNAs and HSR. This was caused by the decreased efficiency of DSBs repair, which resulted from the reduced ability of MMR to recruit DSBs repair proteins. Additionally, it accelerated the formation of micronuclei (MN)/nuclear buds (NBUDs), which functioned to eliminate the amplified genes. Furthermore, the suppression of MMR was capable of inhibiting cell proliferation and enhancing MTX-sensitivity in ecDNA-containing cells. Conversely, suppression of MMR had no effect on gene amplification in HSR-containing cells. Our findings demonstrate that MMR plays a pivotal role in gene amplification through mediating DSBs repair pathways and facilitating the formation of MN/NBUDs in ecDNA-containing cells. MMR is likely to emerge as a prime therapeutic target worthy of in-depth exploration in future clinical investigations. Full article

Background/Objectives: DNA methylation is a key epigenetic modification involved in regulating many cellular processes, including gene expression and the maintenance of genome stability. Ultraviolet (UV) radiation induces DNA damage in the form of pyrimidine-pyrimidone (6-4) photoproducts [(6-4)PPs] and cyclobutane pyrimidine dimers (CPDs), which can lead to mutations if not efficiently repaired. While cytosine methylation has been implicated in influencing UV-induced DNA damage formation, the effect of DNA methylation modulators such as S-adenosyl-L-methionine (SAM) and RG108 on UV damage formation and repair remains unclear. Methods: Here, using immunoslot blot assays, we investigated the effects of SAM and RG108 on UV-induced DNA damage formation and repair in human lymphoblastoid cells. Results: We found that SAM, but not RG108, rapidly suppresses the formation of both (6-4)PP and CPD, with detectable effects within minutes of exposure. Although SAM pretreatment was associated with modestly accelerated early (6-4)PP repair, this effect was accompanied by substantially lower initial damage levels. When cells were treated with SAM or RG108 immediately after UV irradiation to ensure equivalent initial damage burden, no significant differences in repair were observed for either lesion type, demonstrating that the accelerated early (6-4)PP repair reflects reduced lesion burden rather than increased intrinsic nucleotide excision repair (NER). Global 5-methylcytosine (5mC) levels remained stable following SAM or RG108 treatment and during UV damage repair, suggesting that these effects occur independently of global alterations in DNA methylation. Conclusions: Together, our findings reveal that SAM modulates UV damage susceptibility at the level of lesion formation without altering repair, highlighting a previously unrecognized role for DNA methylation modulators in regulating genome stability. Full article

The widespread occurrence of macrolide antibiotics (MLs) in aquatic environments poses potential ecological risks; however, the interactive effects of MLs, especially combined MLs on microalgae and their removal mechanisms, remain poorly understood. This study investigated the removal efficiency, physiological–biochemical responses, and molecular mechanisms of Chlorella pyrenoidosa under single and combined exposure to erythromycin (ERY) and roxithromycin (ROX) over 14 days. The results demonstrated that antibiotic removal efficiency was concentration-dependent and higher in low-concentration treatment. The removal rates of ERY (0.15 mg/L) and ROX (0.02 mg/L) reached 100% and 66.86%, respectively. Notably, in the combined low-concentration group, the presence of ROX promoted the degradation of ERY, with the removal being 11.06–14.77% higher than in single treatment. Conversely, in high-concentration combined treatments (1.63 mg/L ERY + 0.5 mg/L ROX), the removal of ERY was inhibited and the removal of ROX was comparable with the corresponding single treatment. High-concentration treatment groups and combined-treatment groups significantly inhibited microalgae growth and total chlorophyll content, modified the chlorophyll composition, and induced severe oxidative stress. Correlation analysis revealed that antibiotic removal was positively correlated with cell density, chlorophyll content, CAT, CYP450, and GST activities while negatively correlated with SOD, ROS, and MDA. Transcriptomic analysis revealed significant disruption of xenobiotic metabolism pathways, photosynthesis-related processes, and DNA replication/mismatch repair pathways. Key genes involved in stress signaling (e.g., MKK3, MPK3), detoxification (e.g., CYP97, GSTP), and photosynthesis (e.g., HemL) were differentially regulated, providing molecular evidence for the observed physiological responses and removal behaviors. These findings provide valuable insights for the ecological risk assessment of antibiotic mixtures and the development of microalgae-based wastewater treatment technologies. Full article

Background and Objectives: Immunohistochemistry (IHC) is a keystone in gastric cancer (GC) management, allowing treatment customization, including for advanced or metastatic diseases. This review aims to evaluate the critical role of IHC markers, analyzing their efficiency in molecular subclassification and prediction of response to gastric cancer-targeted therapies, while also describing state-of-the-art IHC techniques and perspectives. Results: The major challenges for the GC management were structured in two main sections, as follows: (i) the current paradigm of gastric neoplasia diagnosis, which includes subsections related to the methodological and morphological foundations, the epidemiological dynamics, and risk factors, as well as differential diagnosis of poorly differentiated tumors; and (ii) the progress in 3,3′-diaminobenzidine (DAB) application and advanced reagents in gastric cancer immunohistochemistry. Discussion: Considering the role of IHC and DAB, the following topics were successively addressed in seven sections: GC key biomarkers, such as human epidermal growth factor receptor 2 (HER2), programmed death-ligand 1 (PD-L1), and DNA replication mismatch repair (MMR) system, allow direct correlation between tissue morphology and protein expression; intestinal and gastrointestinal differentiation markers; emerging and aggressive histological subtypes; epithelial–mesenchymal transition, E-cadherin, and the process of tumor budding; implementation of innovative procedures in gastric cancer immunohistochemistry; and automation, quality control, and sustainability in the pathology laboratory. Perspectives: The main directions were focused on the integration of artificial intelligence (AI) algorithms for digital quantification of the IHC signal and also on the expansion of panels to new targets, such as Claudin 18.2 (CLDN 18.2), which redefines treatment approaches in advanced stages. Conclusions: Although faced with technical and biological limitations, immunohistochemistry remains indispensable in modern gastric oncology. The evolution towards digital pathology and the refinement of scoring criteria will transform IHC from a complementary test into a visual tool that is essential for personalizing oncological treatment. Full article

Background/Objectives: Exposure of cells to ionizing radiation induces isolated DNA lesions, including single-strand breaks, apurinic/apyrimidinic sites, and oxidized bases, as well as clustered damages of different complexity. The latter types of damage are difficult to repair, and the failure to process them accurately and efficiently is related to the induction of mutagenesis, genomic instability, cancer, and aging. Since various types of clustered lesions may occur simultaneously after radiation exposure, leading to a complex architecture of DNA damage, the study of the concomitant formation and the removal kinetics of clustered DNA damage is important to determine the mutagenic and, consequently, the carcinogenic potential of ionizing radiation. Methods: With the aim of capturing real-time coexisting lesion types and assessing the repair kinetics of clustered damages, the simultaneous determination of double-strand breaks, apurinic/apyrimidinic site clusters, and oxypurine clusters induced by γ-irradiation of Saccharomyces cerevisiae yeast cells was performed immediately after exposure and at time intervals during incubation in Liquid Holding Recovery conditions. Results: Ionizing radiation induced lethal and mutagenic events, leading to a dose-dependent linear increase in double-strand breaks, apurinic/apyrimidinic site clusters, and oxypurine clusters. The kinetic study showed that double-strand break frequencies declined during Liquid Holding Recovery, although a transient increase was detected at early time points. At 160 Gy, apurinic/apyrimidinic site clusters repair was evident, whereas at 400 Gy the frequency of damage increased before returning to the initial value at 24 h. In contrast, oxypurine clusters showed no net increase in repaired lesions over 24 h. Conclusions: The complex nature and topological characteristics of ionizing radiation-induced clustered DNA damage may influence lesion processing. Also, ionizing radiation may disrupt redox cellular homeostasis, leading to DNA damage and delayed effects. Full article