Search Results (2,080)

Background/Objectives: Breast cancer is a heterogeneous disease, and the role of the transcription factor SPDEF remains controversial. We aimed to clarify the prognostic value of SPDEF, explore demographic and molecular correlates of its expression, and investigate potential regulatory mechanisms underlying its dysregulation. Methods: Genomic and clinical data for 1218 breast cancer tumors were obtained from The Cancer Genome Atlas (TCGA). SPDEF mRNA expression was compared across intrinsic subtypes, age, and race, and prognostic significance was evaluated by Kaplan–Meier analysis. Promoter methylation patterns and DNA methyltransferase (DNMT) expression were examined as potential regulatory drivers. Co-expression analysis was performed using gene panels representing luminal differentiation, basal identity, EMT, proliferation, DNA repair, and immune signaling. Results: Low SPDEF expression was significantly associated with worse overall, relapse-free, and metastasis-free survival across all breast cancers. Expression was lowest in Basal tumors, as well as among younger and Black or African American patients. Promoter methylation at six CpG islands correlated with both reduced SPDEF expression and inferior survival, and DNMT1, DNMT3A, and DNMT3B overexpression also aligned with poor prognosis and Basal enrichment. Co-expression analysis revealed that SPDEF downregulation coincided with loss of luminal markers and increased EMT, proliferation, DNA repair, and immune pathways. Conclusions: SPDEF functions as a tumor suppressor in breast cancer, with reduced expression linked to poor outcomes, aggressive molecular features, and epigenetic regulation. These findings highlight SPDEF and DNMT-driven methylation as potential prognostic biomarkers for enhanced risk stratification and targets for novel therapies, particularly in Basal breast cancers. Full article

Endocrine-disrupting chemicals (EDCs) are widespread contaminants that interfere with hormonal signaling and compromise reproductive success in aquatic organisms. Vitellogenin (VTG) is one of the most widely established biomarkers of estrogenic exposure, especially in males and juveniles. However, evidence from multi-omics studies indicates that VTG induction occurs within broader transcriptional and regulatory networks, involving genes such as cyp19a1 (aromatase), cyp1a (cytochrome P4501A), and other stress-responsive genes, underscoring the complexity of endocrine disruption. This review focuses on nuclear receptor isoforms, including estrogen receptor alpha (ERα), estrogen receptor beta (ERβ), and androgen receptor (AR) variants. We examine the diversification of vtg gene repertoires across teleost genomes and epigenetic mechanisms, such as DNA methylation and microRNAs, that modulate sex-dependent sensitivity. In addition, we discuss integrative approaches that combine VTG with transcriptomic, epigenetic, and histological endpoints. Within the Adverse Outcome Pathway (AOP) and weight-of-evidence (WoE) frameworks, these strategies provide mechanistic links between receptor activation and reproductive impairment. Finally, we outline future directions, focusing on the development of sex-specific biomarker panels, the integration of omics-based data with machine learning, and advances in ecogenomics. Embedding molecular responses into ecological and regulatory contexts will help bridge mechanistic insights with environmental relevance and support sustainability goals such as SDG 14 (Life Below Water). Full article

Stereotactic ablative radiotherapy (SABR) has revolutionized the management of patients with oligometastatic and selected primary cancers due to its ability to deliver highly conformal, high-dose radiation in few fractions with minimal toxicity. However, the biological heterogeneity among patients treated with SABR results in variable outcomes, emphasizing the need for predictive and prognostic biomarkers to guide patient selection and post-treatment management. This narrative review discusses the current landscape of biomarker development in the context of SABR across tumor types. Key classes include circulating tumor DNA (ctDNA), extracellular vesicles (EVs), radiomic features, and immunological markers. We highlight the role of each biomarker category in refining therapeutic approaches, their integration into ongoing clinical trials, and future directions for personalized SABR paradigms. Translating these promising biomarker strategies into clinical SABR workflows will require further standardisation, validation, and regulatory alignment. Full article

Mammalian hearing loss is typically permanent due to the inability to replace damaged cochlear hair cells. However, the neonatal mice inner ear demonstrates regenerative capacity, with cochlear floor cells proliferating and differentiating into organoids containing new hair cells and supporting cells, yet the governing molecular mechanisms remain poorly understood. Here, we isolated extracellular vesicles (EVs) from inner ear organoids at proliferation and differentiation stages, characterized their EV miRNA profiles through sequencing, and validated findings using public transcriptomic datasets to elucidate miRNA-mediated regulatory mechanisms during inner ear development. Inner ear organoids were successfully developed from cochlear duct cells, expressing otic progenitor marker SOX2 and hair cell marker Myo7A and demonstrating functional mechano-transduction activity through FM1-43 uptake. Small RNA sequencing identified 35 differentially expressed EV miRNAs between developmental stages. Integrated analysis with public transcriptome datasets revealed 18 genes with significant differential expression, leading to identification of three key regulatory genes—Trp53, Ezh2, and Zbtb4—that exhibited dynamic spatiotemporal expression during inner ear maturation. Pathway analysis demonstrated that these genes are associated with DNA Repair, P53, and Wnt/β-Catenin signaling with remarkable cell-type specificity. Our results demonstrate that EV miRNAs are temporally regulated during organoid development, with predominant downregulation during differentiation. These findings provide crucial insights into developmental mechanisms that could optimize organoid-based models and guide EV miRNA-based therapeutic strategies for hearing restoration. Full article

In Lolium perenne, a novel growth habit mutant, named VIROIZ, was recovered following colchicine treatment, and it was confirmed to maintain the diploid chromosome number (2n = 2x = 14). The mutation affected the stem morphology by inducing prolific axillary shoot formation at nodal zones, resulting in a spreading growth habit that can extend to ~70 cm in width. Inheritance analysis based on single-plant evaluations in crosses with wild-type plants (F₁, n = 285; F₂, n = 380) and in selfed progeny (S₁, n = 255) consistently showed ~40% expression of the spreading phenotype, deviating from classical Mendelian ratios and indicating complex genetic control. Phenotypic selection further distinguished divergent classes: positively selected lines (C1⁺) averaged 3.90 axillary tillers per stem, whereas negatively selected lines (C1⁻) averaged only 0.22. Partial sequencing of 11 candidate genes implicated in shoot architecture, covering 40–90% of full-length DNA, did not provide a conclusive explanation for the altered stem growth. Notably, a single point mutation was observed in CRT3 (an endoplasmic reticulum chaperone that interacts with brassinosteroid signaling) highlighting it as a primary target for future studies. Cytological analysis of meiosis in F₁ hybrids between VIROIZ and wild-type plants revealed irregular chromosome pairing with persistent univalents (2–4 per cell), supporting the presence of structural chromosomal rearrangements that may disrupt gene organization and function in VIROIZ. The non-Mendelian segregation of the spreading phenotype, together with the observed meiotic irregularities, suggests that the mutation affects regulatory genes responsive to hormonal signals controlling axillary meristem initiation. The mutant represents a valuable resource for turf-type L. perenne breeding and for studying hormonal regulation of shoot morphogenesis in Poaceae. Full article

Camptothecin (CPT) is a natural alkaloid with potent antiproliferative activity, mediated by the inhibition of Topoisomerase I (Topo I), an essential enzyme for deoxyribonucleic acid (DNA) replication. However, its clinical application has been limited by low solubility and the instability of the lactone ring under physiological conditions, both of which decrease its efficacy. Semi-synthetic analogs such as irinotecan (CPT-11) and topotecan (TPT) have been developed and approved for the treatment of various types of cancer; however, challenges related to drug resistance and side effects continue to arise. Therefore, nanomedicine and nanoparticle-based delivery systems, including nanoemulsions, liposomes, and antibody–drug conjugates (ADCs), emerge as promising strategies to improve the stability, bioavailability, and effectiveness of CPT, despite significant challenges such as scalability, pharmacokinetic variability, and regulatory requirements. This review discusses recent advances in CPT, its analogs, and these delivery platforms, highlighting its potential to optimize cancer therapy and reduce toxicity while outlining translational challenges such as scalability, pharmacokinetic variability, and regulatory requirements. Full article

G-quadruplexes (G4s) are four-stranded DNA or RNA structures formed by guanine-rich sequences. They occur in functional regions of the genomic material, including the promoter part of genes, regulatory region, and telomeric threads. G4s play a key role in various biological processes, including transcription, replication, and telomere maintenance. Guanidine-containing derivatives can bind to G-quadruplexes, either by intercalating into the structure or by interacting with the grooves or loops. The binding can stabilize the G-quadruplex, potentially affecting its biological function. In this paper, the ability of guanidinium-containing hordatines to interact with G4 was evaluated. Analogues lacking the guanidinium group or showing the benzofuran system instead of the dihydrobenzofuran core were prepared and tested as well. NMR titration and docking calculations were used to probe the binding of the compounds to G4 of c-MYC oncogene. Spectroscopic analyses were consistent with a significant interaction of benzofurans 3 and 4 at the 5′-end and 3′-end tetrads and with the formation of ligand/G-quadruplex complexes with a 2:1 stoichiometry. The resulting data were supported by docking simulations. Cytotoxic activity was evaluated on a model of U2OS osteosarcoma (ATCC HTB-96) and breast cancer (MDA-MB-231) cell lines, further highlighting the key role of the guanidinium fragment and the benzofuran core in the G-quadruplex stabilization. Full article

Yersinia enterocolitica is a foodborne pathogen capable of biofilm formation and virulence modulation in response to environmental signals. Among these, glucose—present at physiologically relevant concentrations in the human body—may serve as a regulatory cue affecting infection-associated pathways, including those governed by the pYV virulence plasmid. Although the role of glucose has been investigated under host-mimicking conditions, its impact in non-host environments remains poorly understood. This study was designed to evaluate the glucose-dependent physiological responses of two isogenic Y. enterocolitica strains, KT0001 (pYV-negative) and KT0003 (pYV-positive), under non-host conditions (26 °C). Both strains were cultured in TYE medium containing 0–3% glucose. Comparative analyses were conducted under identical in vitro conditions to elucidate plasmid-associated phenotypic differences. Glucose elicited markedly divergent responses. In KT0001, growth remained unaffected; however, biofilm formation declined by 77.7%, accompanied by a 90% reduction in surface hydrophobicity, a 40% decrease in motility, and a 59% drop in intracellular cyclic AMP—suggesting classical carbon catabolite repression. Conversely, KT0003 exhibited 86% growth inhibition but maintained biofilm levels. This was associated with substantial extracellular polymeric substance induction (~20-fold increase in polysaccharides and ~4.7-fold in extracellular DNA) and nearly fivefold elevation in cyclic AMP levels, despite concurrent decreases in motility (64%) and hydrophobicity (40%). These findings indicate that glucose functions as a strain-specific modulator in Y. enterocolitica. In particular, KT0003’s response suggests that the pYV plasmid enables the bacterium to interpret glucose as a host-associated cue, even under non-host conditions, potentially initiating virulence-related adaptations prior to host contact. Full article

Mycobacteria possess carbon monoxide dehydrogenase (CO-DH) to utilize CO as an energy source and to resist host defense mechanisms. The expression of the CO-DH gene is regulated by CutR, a LysR-type transcriptional regulator (LTTR) that exhibits unique characteristics, suggesting that it functions as a dimer rather than the typical tetramer. Size-exclusion chromatography revealed that CutR forms a stable dimer. Electrophoretic mobility shift assays demonstrated that dimeric CutR specifically binds to an inverted repeat sequence (IR1) containing T-n12-A motifs located upstream of the cutB gene, which encodes the medium subunit of CO-DH. Crystal structure determination at 1.8 Å resolution revealed that CutR consists of an N-terminal DNA-binding domain with a winged helix-turn-helix motif and a C-terminal ligand-binding domain comprising two regulatory subdomains (RD1 and RD2), forming a unique two-fold symmetrical homodimer. This dimer is stabilized through four interfaces, including an extensive 12-stranded antiparallel β-sheet formed between RD1 subdomains via intertwining C-terminal β11 strands. This represents the first symmetric dimeric LTTR structure with tightly associated ligand-binding domains. The recognition helices are spaced closer together than they are in typical DNA-bound LTTRs, despite binding longer T-n12-A sequences, suggesting that a conformational change is required to enhance DNA-binding affinity. A putative ligand-binding site was identified between the RD1 and RD2 subdomains, where glycerol binding induced local conformational changes. Comparative genomic analysis revealed conservation of CutR and the IR1 sequence across Mycobacterium species, supporting the dimeric regulatory mechanism and providing new insights into LTTR diversity. Full article

Antisense oligonucleotides (ASOs) are short, synthetic DNA fragments that offer a powerful means of modulating gene expression. By leveraging endogenous regulatory pathways, ASOs enable precise control over gene activity at multiple levels, including genomic DNA, transcription, RNA processing, and translation. Their applications span basic research and translational science, ranging from the generation of epigenetically modified organisms as potential GMO alternatives to the development of therapies for rare or treatment-resistant diseases. This review highlights the molecular mechanisms of ASO action, design and modification strategies, and delivery approaches across diverse cell types. Future directions include elucidating detailed molecular pathways, optimizing experimental conditions, and enhancing the persistence of therapeutic effects. Overall, ASOs represent a versatile and innovative tool in functional genomics, with broad implications for molecular biology, biotechnology, and medicine. Full article

Lung cancer is among the most aggressive malignancies, with the highest incidence and mortality rates worldwide. Standard treatments include surgery, radiotherapy, and chemotherapy; however, chemoresistance often develops, reducing therapeutic efficacy. Combination therapy offers a promising strategy to enhance drug effectiveness and overcome resistance. In lung cancer, the increased energy demands within cells result in a marked rise in the expression of PFKFB3, a regulatory protein involved in the glucose metabolic pathway. The small-molecule inhibitor KAN0438757, recognized as a novel PFKFB3 inhibitor, is significant in targeted therapy due to its essential role in the DNA damage response mechanism in cancer cells. Curcumin, the primary bioactive compound found in the rhizomes of Curcuma longa, has demonstrated a variety of biological functions and anticancer properties. This study aimed to evaluate the anticancer effects of KAN0438757 in combination with curcumin in lung cancer cells. Evaluation of cell viability and IC₅₀ values (KAN0438757: A549, 41.13 µM; H1299, 53.74 µM; Curcumin: A549, 44.37 µM; H1299, 66.25 µM) using the WST-1 and RTCA assays revealed pronounced inhibition of proliferation in the combination groups, accompanied by decreased cell migration (fold change, untreated cell; 1, CUR-20 µM; 0.681, KAN-20 µM; 0.530, and COMB; 0.0039 for 48 h). The comet assay revealed severe DNA damage (Tail DNA, fold change, untreated cell; 1, CUR-20 µM; 1.2, KAN-20 µM; 3, and COMB; 4.6) in the A549 cells, while MMP analysis (color change from red to green) and apoptotic staining confirmed cell death morphologically (color change from green to orange). Moreover, Western blot analysis demonstrated that the combination markedly enhanced apoptosis in the A549 cells. Full article

DNA methylation is an epigenetic modification that plays a crucial role in the regulation of gene expression, genome defense, and numerous biological processes. DNA methyltransferase (MTase) is the pivotal enzyme catalyzing the DNA methylation reaction. To explore the regulation mechanism of DNA methylation in rubber trees (Hevea brasiliensis), we identified 13 genome-wide MTase genes containing conserved structural domains of DNA methyltransferase based on the rubber tree reference genome. Through phylogenetic analysis, these genes were classified into four subfamilies: MET1, CMT, DRM, and DNMT2. A significant expansion of DNA methyltransferase genes was found in rubber trees, especially in the DRM subfamily. Notably, among the four members of the MET1 subfamily, only HbMET1-1 contains the complete UBA and RFD domains, suggesting its critical role in the function of MET1 in plants, while the other members may have developed different functions during evolution. Gene expression pattern analysis revealed that most DNA methyltransferases were specifically expressed at low levels in latex. However, following tapping from unharvested rubber trees, the expression levels of HbMTase genes are altered, and these alterations exhibit variability. Among them, HbMET1-1 and HbDRM2-1 exhibited a response to tapping stress, with their expression levels rapidly increasing after stress application and subsequently decreasing gradually. The expression levels of HbCMT3-1 and HbCMT3-2 continued to increase as the rubber tapping process progressed, which was consistent with the observed changes in HbMTase enzyme activity. These findings suggest that tapping, as a form of mechanical stress, affects the expression of particular genes. Through subcellular localization analysis, we found that HbDNMT2 is the only DNA methyltransferase located in the cytoplasm its expression level gradually decreases during the rubber tapping process. It is hypothesized that this gene activates a multitude of genes involved in the rubber biosynthesis pathway and participates actively in rubber biosynthesis. In conclusion, the comprehensive analysis of the structural characterization, conserved domains analysis, cis-regulatory elements, subcellular localization, expression profiling, and HbMTase enzyme activity detection provides critical insights into the functional characteristics of DNA methyltransferases in rubber trees and initially reveals the DNA methylation response in rubber tree tapping. Full article

Objectives: This study utilized IPEC-J2, a neonatal pig jejunum-derived cell line, to assess how iron deficiency (ID) and excess (IE) alter enterocyte metabolism and the transcription of inflammatory markers. Methods: Cells were treated with deferiprone (DFP) or ferric ammonium citrate (FAC) to induce ID or IE, respectively. The study evaluated: (1) transcriptional changes in iron-regulatory genes over 96 h under ID or IE; (2) the interaction between iron imbalance and lipopolysaccharide (LPS) exposure on mRNA expression of inflammation markers and iron transporters; and (3) cellular metabolic responses to ID, IE, and iron repletion using untargeted metabolomics. Results: ID triggered dynamic transcriptional changes in iron regulatory genes and suppressed cellular proliferation via impaired DNA replication. IE resulted in a persistent reduction in TFRC expression. LPS increased CYBRD1 (p < 0.001) and IL8 (p = 0.004) and tended to elevate TLR4 and TNF expression (p ≤ 0.07), while iron deficiency upregulated IL8 expression (p < 0.001). ID disrupted the TCA cycle, reduced glucuronic acid synthesis, and elevated glycolysis for energy production, whereas IE increased cholesterol biosynthesis and decreased alpha-tocopherol levels. Repletion of iron partially reversed ID-induced metabolic changes. Conclusions: ID impaired enterocyte proliferation and profoundly disrupted cellular metabolism, whereas IE enhanced cholesterol synthesis and depleted alpha-tocopherol levels. Restoration of cellular metabolism following iron repletion was observed, highlighting the resilience of enterocytes. Full article

Mismatch repair (MMR) system alterations can trigger transient hypermutation, promoting adaptive mutations under stress, such as antibiotic exposure. While most organisms use MutS and MutL protein families for MMR, many archaea and actinobacteria, including the major human pathogen Mycobacterium tuberculosis, lack these components and instead rely on NucS, a structurally distinct enzyme driving a non-canonical MMR pathway. Given the role of MMR in mutation control, understanding how nucS expression is regulated could be essential for uncovering the molecular basis of antibiotic resistance development in mycobacteria. In this study, we characterized the nucS promoter and transcription start site in Mycobacterium smegmatis. We found that nucS expression declines during the stationary phase in both M. smegmatis and M. tuberculosis, paralleling replication activity and canonical MMR downregulation. Our data suggest that the alternative sigma factor σ^B may negatively regulate nucS expression during this phase. Additionally, we identified candidate compounds that may modulate nucS expression, underscoring its responsiveness to environmental cues. These findings enhance our understanding of mycobacterial stress responses and lay the groundwork for exploring antibiotic resistance mechanisms. Strikingly, our work reveals a case of double convergent evolution: both canonical (MutS/MutL) and non-canonical (NucS) pathways have independently evolved not only the same DNA repair function, but also similar regulatory frameworks for genome integrity preservation under stress conditions. Full article

Glucosinolates (GSLs) are nitrogen- and sulfur-containing secondary metabolites central to the defense, development, and environmental responsiveness of Brassicaceae species. While the enzymatic steps and transcriptional networks underlying GSL biosynthesis have been extensively characterized, mounting evidence reveals that chromatin-based processes add a critical, yet underexplored, layer of regulatory complexity. Recent studies highlight the roles of DNA methylation, histone modifications, and non-coding RNAs in modulating the spatial and temporal expression of GSL biosynthetic genes and their transcriptional regulators in response to developmental cues and environmental signals. This review provides a comprehensive overview of GSL classification, biosynthetic pathway architecture, transcriptional regulation, and metabolite transport, with a focus on emerging epigenetic mechanisms that shape pathway plasticity. We also discuss how these insights may be leveraged in precision breeding and epigenome engineering, including the use of CRISPR/dCas9-based chromatin editing and epigenomic selection, to optimize GSL content, composition, and stress resilience in cruciferous crops. Integrating transcriptional and epigenetic regulation thus offers a novel framework for the dynamic control of specialized metabolism in plants. Full article