Search Results (2,887)

Hypoxia is a defining feature of physiological stress and the core of solid tumors, where aberrant vascularization limits oxygen delivery; cells respond through mechanisms that extend beyond the canonical stabilization of hypoxia-inducible factors (HIFs). Recent studies suggest that hypoxia can promote the formation of specific biomolecular conden-sates, membraneless compartments generated through liquid–liquid phase separation in which regulatory proteins and RNAs become locally enriched at genomic regions, while chromatin mainly serves as an organizational scaffold. Transcription factors, the coacti-vators p300/CBP, Mediator, and BRD4, chromatin-modifying enzymes, and architectural RNAs such as NEAT1 and MALAT1 partition into these compartments, and their con-densation can help reorganize local chromatin structure and enhancer–promoter interac-tions. Because molecular oxygen is a shared co-substrate for the Jumonji-C histone demethylases and the ten-eleven translocation (TET) DNA dioxygenases, hypoxia reshapes histone methylation and DNA methylation in parallel, and readers that bridge these marks, including UHRF1, may participate in condensate-associated chromatin regulation. Hypoxia-driven condensation of ZHX2 rewires enhancer–promoter contacts and higher-order genome architecture, influencing cell identity, stemness, and metastatic potential, and Polycomb condensates represent another candidate epigenetic compartment that may be influenced by hypoxic signaling. These processes may be particularly important in cancer, where chronic hypoxia provides a sustained stimulus for condensate formation and epigenetic remodeling. Together, these findings support a model in which phase separation and epigenetic reprogramming are not separate layers but one integrated response to low oxygen, offering opportunities to target maladaptive condensates in disease. Full article

Eukaryotic genomes are organized into chromatin, a highly compact structure in which DNA is packaged into nucleosomes. Nucleosome formation, where DNA is wrapped around histone proteins, is essential for genome stability. This compaction protects DNA from damage and regulates accessibility of genes. Nucleosomes must be disassembled and reassembled during DNA replication and repair. These processes require precise regulation of histone folding, transfer, and deposition by a diverse network of histone chaperones. Chromatin assembly factor 1 (CAF-1) is a conserved histone chaperone that specifically deposits newly synthesized histones during replication-coupled and repair-coupled nucleosome assembly. The sliding clamp proliferating cell nuclear antigen (PCNA) serves as a regulatory scaffold during these processes by recruiting CAF-1 and many other proteins to sites of DNA replication and repair. Recent structural and biochemical studies have revealed increasingly complex mechanisms underlying PCNA-mediated CAF-1 recruitment, involving multiple protein interaction motifs, DNA-binding domains, and regulatory mechanisms that ensure efficient nucleosome assembly. This review summarizes current advances in understanding the molecular mechanisms by which human and yeast CAF-1 complexes are recruited to sites of DNA synthesis and how CAF-1 function is coordinated with other histone chaperones during replication and repair. These studies have provided important insights into how cells coordinate DNA metabolism with epigenome maintenance to preserve genome integrity. Full article

Proliferating cell nuclear antigen (PCNA) is an essential sliding clamp that coordinates nearly all DNA-templated processes. It does so by recruiting a diverse array of factors to DNA through PCNA-interacting protein (PIP) motifs on PCNA-binding proteins. Chromatin assembly factor 1 (CAF-1) is a histone chaperone that deposits histones onto silent regions of the genome immediately following DNA replication. PCNA recruitment of CAF-1 to the replication fork is essential for nucleosome assembly and epigenetic inheritance. In yeast, CAF-1 recruitment to PCNA is assumed to be facilitated using one PIP motif. Here, we identify a second PIP motif in CAF-1, designated PIP1, located within the N-terminal intrinsically disordered region of the protein. Binding kinetics demonstrate that the PIP1 motif sequence binds PCNA with substantially lower affinity than the previously characterized PIP motif, designated PIP2. Structural and binding data reveal PIP1 as an extended PIP motif, in which C-terminal flanking residues make extensive, atypical contacts with PCNA that significantly increase its affinity. Neither PIP1 nor PIP2 alone is required for CAF-1–mediated gene silencing in vivo, but simultaneous disruption of both abolishes CAF-1 function. Together, these findings suggest CAF-1 engages PCNA multivalently and provide new insight into how PCNA selectively recognizes binding partners during nucleosome assembly. Full article

Plants are continuously exposed to volatile organic compounds (VOCs) emitted by neighbors. Although the mechanisms governing VOC uptake and metabolism remain unclear, cytochrome P450 monooxygenases (CYP450s) are thought to participate in the detoxification and metabolic conversion of absorbed VOCs. Data from previously conducted cDNA microarray transcriptomic profiling in potato exposed to French marigold essential oil (FM-EO) was here used to filter differentially expressed sequences, and identified 54 unique CYP450 transcripts. Among the 10 most highly expressed sequences, two CYP81D1-like (81D1-1 and 81D1-2) and one CYP81D11-like (81D11-1) transcripts were found. RT-qPCR confirmed their strong induction within 8 h of volatile exposure. Comprehensive bioinformatics identified the most highly induced 81D1-1 gene as a CYP450 containing a predicted N-terminal hydrophobic signal or membrane-anchor region, the conserved heme-binding signature motif, and regulatory elements associated with oxidative stress responses. The other 81D11-1 gene, exhibiting a comparable expression level, was annotated only as a heme-binding protein but possessed seven distinct cis-regulatory elements, suggesting high transcriptional plasticity. Machine learning predictions assigned the highest interaction probability to (Z)-β-ocimene, whereas structure-based docking yielded the most favorable mean score for piperitone. This study provides the first characterization of the potato CYP450 superfamily in the context of volatile-mediated plant–plant interactions and identifies two CYP81D members as strong candidates for the oxidative metabolism of absorbed VOCs. The results support a proposed detoxification pathway in which CYP81-mediated oxidation precedes glutathione conjugation and intracellular sequestration of VOCs. These candidate genes provide a valuable foundation for future functional studies and may facilitate the development of sustainable crop protection strategies based on volatile-mediated plant defense. Full article

Synthetic multi-species consortia provide valuable insights into the ecological and structural dynamics of complex microbial biofilms. However, the specialized functional contributions of individual components under severe nutrient limitations remain poorly understood. This study investigated the population dynamics, matrix biogenesis and metabolic potential of a synthetic ‘protolichen biofilm’ model comprising Asterochloris microalgae, Gordonia bacteria, Thelebolus filamentous fungi and Occultifur yeast. The biofilms were cultivated under strict carbohydrate-deficient conditions for 30 days. Population changes, extracellular polymeric substance (EPS) matrix formation, and the concentrations of extracellular DNA (exDNA) and proteins (exProt), as well as potential dehydrogenase activity (via iodonitrotetrazolium reduction), were evaluated across monocultures, binary, ternary and quaternary consortia. Under carbon starvation, the photoautotrophic microalgae dominated the consortium, driving an 11-fold increase in population size in the four-component system and serving as the primary source of exDNA, which increased by up to three orders of magnitude by day 30. The Gordonia sp. exhibited a tenfold expansion by actively localizing to fungal hyphae and microalgal cell walls. This was directly correlated with a sharp increase in metabolic activity. By contrast, Thelebolus sp. initially provided the structural framework via EPS production, but exhibited limited metabolic activity over time. Meanwhile, the Occultifur sp. yeast population was severely suppressed, adopting a sit-and-wait ecological strategy. Spearman correlation analysis revealed that multi-species integration stabilized the community and triggered significant emergent effects in exDNA accumulation and metabolic potential, but only when microalgae were present. These findings demonstrate that microalgae and bacteria primarily drive metabolism and regulation within the protolichen consortia investigated, while fungi and yeast play structural or opportunistic roles. This provides a robust framework for understanding complex symbiotic interactions. Full article

Background: Progesterone signaling has been implicated in diffuse glioma biology, but the factors contributing to variability in progesterone receptor (PGR) activity remain incompletely understood. We investigated whether PROGINS-related PGR variants detected in tumor-derived DNA were associated with PGR expression and selected biological features of diffuse gliomas. Methods: This retrospective translational study included 66 patients with histopathologically confirmed diffuse gliomas. Three PROGINS-associated PGR variants—the Alu insertion, V660L (rs1042838), and H770H (rs1042839)—were analyzed using DNA extracted from fresh-frozen tumor tissue. Relative PGR gene expression, tissue PGR protein concentrations, Ki-67 labeling index, and p53 immunoreactivity were evaluated together with IDH status, ATRX expression, and 1p/19q co-deletion. Separate multivariable regression models assessed variant-specific associations and prespecified variant × sex and variant × tumor grade interactions. Multiple testing within the reported multivariable models was addressed using the Benjamini–Hochberg false discovery rate procedure. Results: Relative PGR gene expression was lower in high-grade than in low-grade gliomas (p = 0.039), whereas tissue PGR protein concentrations did not differ significantly according to grade. In multivariable analyses, V660L L-allele carriage was associated with higher PGR expression and lower Ki-67 labeling indices, H770H G-allele carriage was associated with lower PGR expression and higher p53 immunoreactivity, and Alu insertion carrier status was associated with lower PGR expression. Significant variant × sex interactions were identified for several outcomes, and an H770H × tumor grade interaction was observed for PGR expression. All nominally significant associations reported in the multivariable models remained significant after false discovery rate correction. Conclusions: PROGINS-related PGR variants detected in tumor-derived DNA are associated with selected biological features of diffuse gliomas, with several associations differing according to biological sex and, for selected outcomes, tumor grade. These findings support a context-dependent relationship between PGR variant status and glioma phenotype but do not establish functional causality or clinical biomarker utility. Independent functional and longitudinal studies are required to determine the biological and potential clinical relevance of these associations. Full article

Exosomes are nanoscale, double-membrane extracellular vesicles of endocytic origin that are released by diverse cell types under both physiological and pathological conditions. They have emerged as critical mediators of intercellular communication and immune regulation during homeostasis and infection. Accumulating evidence indicates that pathogen-infected mammalian cells actively secrete exosomes enriched with host- and pathogen-derived components, including proteins, lipids, DNA, and regulatory RNAs such as microRNA (miRNA) and circular RNA (circRNA). In the context of infection, exosomes exhibit dual and often opposing functions, contributing to both host defense and disease progression. Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis and a leading cause of mortality from infectious diseases worldwide, has been shown to modulate exosome biogenesis and alter cargo composition in exosomes when secreted by macrophages. These exosomes carry mycobacterial antigens and immunomodulatory molecules that can influence host immune responses, thereby shaping disease outcomes. This review summarizes current insights into the biogenesis and functional roles of exosomes during Mtb infection, highlighting their contributions to host–pathogen interactions, immune modulation, and disease pathogenesis. We further discuss the potential of exosomes as biomarkers and therapeutic targets in tuberculosis, emphasizing their dual roles in mediating protective and detrimental effects. Full article

Nitrogen limitation restricts plant growth, development, and yield in crops and forage species. Although TCP transcription factors are implicated in diverse abiotic-stress responses, the functions of most TCP genes in oat remain unclear. Here, we cloned and characterized the AsTCP38 gene, which is 1215 bp long and encodes a 405-amino-acid protein. The predicted protein contains a conserved TCP domain and shares its highest sequence similarity with Arabidopsis thaliana (A. thaliana) AtTCP15. The AsTCP38 protein localized to the nucleus, and promoter analysis identified cis-elements associated with light, hormone, and stress responses. We generated AsTCP38-overexpressing A. thaliana and wheat plants and screened an oat leaf yeast cDNA library for candidate interacting proteins. In these heterologous overexpression lines, AsTCP38 overexpression was associated with greater abscisic acid (ABA) sensitivity and improved seedling growth under low-nitrogen conditions. Changes in antioxidant-enzyme activities, nitrogen-metabolism-related enzyme activities, and endogenous hormone contents were also observed. Together, these findings suggest that AsTCP38 may participate in low-nitrogen responses and provide a basis for further functional studies in oat. Direct regulatory targets and the contribution of AsTCP38 to low-nitrogen adaptation in oat remain to be established. Full article

Background: Congenital pulmonary airway malformation (CPAM) is a rare developmental disorder characterized by cystic lung lesions, yet its extracellular matrix (ECM) composition remains poorly understood. This study employed decellularization and data-independent acquisition (DIA) proteomics to compare ECM profiles between cystic (CPAM) and histologically normal non-diseased (ND) regions from the lungs of four patients. Results: The decellularized scaffolds retained their native architecture with minimal residual DNA (<50 ng/mg). Proteomic analysis revealed 431 differentially expressed proteins (DEPs), with 171 upregulated and 260 downregulated in CPAM. Key findings revealed CPAM-specific enrichment of collagens (COL4A6, COL4A2, COL10A1, COL21A1 and PIIINP), glycoproteins (SPP1, FRAS1, FREM1, FREM2, LTBP1 and FBLN7), ECM regulators (TENM2, ROR2 and OMD), and ECM-affiliated proteins (ANXA7), alongside downregulation of glycoproteins (VASN and ABI3BP), proteoglycans (PODN and MXRA7), ECM regulators (SCARA5, PAPPA, SAA4, CPXM1, CTSC, THY1, SERPINA6/A1/D1, BSG, LYVE1, ITIH4 and CD44), and ECM-affiliated proteins (LGALSL). Pathway analysis highlighted the dysregulation of TGF-β, PI3K–AKT, and mTOR signaling in CPAM and aberrant ECM–cell interactions in pathogenesis. We also evaluated their functional properties and investigated the impact of ECM-based hydrogels on recellularization. Conclusions: These findings provide a comprehensive proteomic atlas of CPAM ECM alterations, offering insights into disease mechanisms and potential therapeutic targets. Full article

Efficient regulation of recombinant enzyme expression is an important consideration for the development of microbial biocatalysts. Heat-inducible promoters regulated by the alternative sigma factor σ³² provide an inducer-free strategy for controlling gene expression in Escherichia coli. In this study, four σ³²-dependent promoters (PdnaK, PgrpE, PibpA, and PclpB) were comparatively characterized using the PET-degrading enzyme FAST-PETase fused to superfolder green fluorescent protein as a model recombinant protein. Promoter performance was evaluated based on basal leakage, induction kinetics, and expression strength following heat induction. Among the promoters examined, PdnaK exhibited the strongest heat-inducible expression and was dissected to examine the autonomous and combinatorial behavior of its promoter-derived elements. Molecular docking analysis further supported the experimental observations by showing qualitative agreement between predicted σ³²–DNA interactions and promoter performance. Together, these findings provide a comparative characterization of σ³²-dependent promoters and identify promoter architectures that may facilitate the development of heat-inducible recombinant enzyme expression systems in E. coli. Full article

Assemblysomes are ribosome-nascent chain condensates that regulate co-translational processes through liquid–liquid phase separation, yet the sequence determinants underlying their formation remain incompletely understood. Previous studies identified the DNA helicase Sgs1 as an assemblysome-associated protein; however, whether its N-terminal region possesses intrinsic phase separation propensity has not been experimentally examined. Here, we investigated the first 135 amino acids of Sgs1 using a light-inducible optoDroplet assay. A mCherry–Cry2–Sgs1_1–135 fusion construct was compared with the established positive control FUS–mCherry–Cry2 and the negative control mCherry–Cry2 in live HEK293T cells. Following blue-light activation, Sgs1_1–135 reproducibly formed reversible condensates, indicating intrinsic phase separation propensity. Quantitative image analysis revealed light-dependent increases in condensate number, average condensate area, and integrated condensate fluorescence intensity. Compared with FUS, Sgs1_1–135 formed slightly fewer and smaller condensates but displayed reproducible light-dependent condensate formation. These findings indicate that the Sgs1 N-terminal region exhibits intrinsic phase separation propensity in a validated optogenetic assay. Although this proof-of-principle study does not establish the molecular mechanism of assemblysome formation, the results are consistent with the hypothesis that the Sgs1 N-terminus may contribute to the multivalent interactions underlying assemblysome organization. Full article

N-acetylcysteine (NAC) is a synthetic derivative of L-cysteine, known since the mid-20th century as a mucolytic agent and, in recent decades, has attracted attention for its antioxidant and antibiofilm properties. Bacterial biofilms are structured communities of microorganisms enclosed in an extracellular polymeric matrix, which accounts for their markedly increased resistance to antibiotics (up to 1000-fold higher than in planktonic forms) and to the host immune response. According to the literature, up to 65% of infectious agents are associated with biofilm formation, making them a challenging therapeutic target. This review systematizes current data on the molecular mechanisms of the antibiofilm action of NAC, including disruption of matrix proteins and polysaccharides, degradation of extracellular DNA, suppression of the quorum sensing system, and disturbance of bacterial redox homeostasis. Particular attention is given to synergistic combinations of NAC with antibiotics of five major classes; effective concentrations are provided, and the types of interaction are characterized. The results of clinical studies from the last decade are reviewed, demonstrating the potential of NAC as an adjuvant in urinary tract infections, chronic rhinosinusitis, diabetic osteomyelitis, and cystic fibrosis. The main limitations (pH dependence, instability, low oral bioavailability) are critically evaluated, and approaches to overcoming them using nanoparticles, hydrogels, and combinations with propolis or chitosan are proposed. The review is intended for researchers in antimicrobial chemotherapy and developers of new drug delivery systems. Full article

Background/Objectives: Hepatocellular carcinoma (HCC) is the most prevalent primary liver tumor and is often diagnosed at advanced stages with very poor therapeutic response, leading to high mortality. Thus, new therapeutic strategies and biomarkers are urgently needed. We previously showed that the combination of loratadine, raloxifene, and sorafenib exerts synergistic cytotoxicity on HCC cells. Here, we explored potential molecular mechanisms underlying the anticancer effects of this combination using multiomics analyses. Methods: We performed proteomic analyses based on mass spectrometry, transcriptomic analyses using the Clariom D Plus human microarray (Affymetrix), and metabolomic analyses based on nuclear magnetic resonance to investigate the profile changes induced by the drug combination in HuH7 cells. Bioinformatic analyses were applied to associate the omics changes with biological functions, molecular interactions, and clinical relevance in terms of patient survival. Results: We identified several molecules whose expression changed in response to treatment across the three omics profiles analyzed. Some of them were found to be involved in hallmarks of cancer, including sustained proliferation, evasion of growth suppressors, and resistance to cell death. Integrated multi-omics analyses revealed that the drug combination suppresses critical oncogenic drivers (C7orf50, NUP188, and HS2ST1) and that the mitotic cell cycle process, DNA synthesis and cholesterol biosynthesis are the primary pathways affected. Protein–protein interaction analysis revealed five key hubs (KIF2C, PCNA, TRIP13, NDC80, and RPA3), whose expression in HCC is associated with poor clinical prognosis. Conclusions: The combined treatment rewired molecular networks involved in HCC progression. These findings identify clinically relevant molecular targets associated with poor prognosis and provide mechanistic insights into the synergistic anticancer activity of this drug combination. Full article

Alzheimer’s disease (AD) continues to be one of the greatest challenges in public health due to its multifactorial and heterogeneous nature, involving multiple physiological axes that encompass a large number of genetic, metabolic, vascular, and inflammatory interactions. In current clinical practice, medical specialties, mainly neurology and psychiatry, still rely on targeted gene panels for genetic evaluation. Although these panels remain effective for certain predefined hypotheses, their restricted and predefined nature limits the detection of the broader spectrum of genetic variation that may contribute to the complex biological interactions underlying neurodegeneration. Whole-exome sequencing (WES) is, from our clinic-based perspective, one of the most comprehensive genomic approaches currently available, since it allows the analysis of the ~19,500 protein-coding regions, and depending on the library approximately 5500 additional clinically relevant genomic loci, including splice sites, untranslated regions, long non-coding RNAs (lncRNAs), pseudogenes, regulatory elements and mitochondrial DNA (mtDNA). It enables the identification of pathogenic variants and variants of uncertain significance (VUS) under the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) classification frameworks. It also expands biological interpretation to variants conventionally classified as benign, which, when interpreted collectively, may contribute to pathway-level contextualization within the hypothesis-generating theoretical framework proposed in this review without implying pathogenicity, causal inference, or immediate clinical actionability. Additionally, WES enables the identification of secondary and incidental findings that may provide clinically relevant information beyond the primary phenotype, thereby supporting preventive surveillance and clinical risk management. This review analyzes the use of WES as a strategic platform for personalized decision-making in contemporary practice given the multifactorial and heterogeneous complexity of AD. It also addresses the complexities and limitations of the ACMG/AMP recommendations for filtering and classification of variants, the lack of standardization between reports and platforms, and the need for physician training, which constitute a great challenge for the translation of data to therapeutic decision-making. While the clinical utility of whole-exome sequencing (WES) in genetic diagnosis and precision medicine is well established, this review additionally proposes a hypothesis-generating theoretical framework whereby variants conventionally classified as benign or of uncertain significance may contribute to pathway-level biological contextualization in Alzheimer’s disease. Full article

Neural crest cells give rise to the craniofacial skeleton and multiple pigment cell lineages, yet how duplicated developmental regulators partition their ancestral functions after teleost-specific whole-genome duplication remains unclear. Here, we employed CRISPR/Cas9 to generate alx4a and alx4b single and double mutants in Nile tilapia (Oreochromis niloticus). By integrating phenotype, skeleton, transcriptome, quantitative PCR, and AlphaFold-based structural modeling analyses, we revealed their functional divergence. Loss of alx4a caused a regionally restricted reduction in iridophore-derived reflectance and abnormal cranial morphology, whereas alx4b single mutants showed no obvious phenotype under the conditions examined. By contrast, double mutants exhibited an almost complete loss of iridophore-derived structural coloration and substantially more severe cranial defects, accompanied by reduced calcein labeling in the opercular region, consistent with altered cranial mineralization. Skin transcriptomic and quantitative PCR analyses revealed marked downregulation of pnp4a and tfec, which are associated with iridophore differentiation and coloration, whereas no significant expression differences were detected for the iridophore survival-related genes ltk and mpv17. AlphaFold2-assisted HDOCK protein–DNA modeling yielded more favorable docking metrics for Alx4a than for Alx4b with the pnp4a promoter, supporting a potential Alx4a–pnp4a promoter interaction that requires experimental validation. In contrast, no significant genotype-dependent differences were detected in the measured abundance of melanophores, xanthophores, or erythrophores, and no obvious difference in gross dorsal-fin spine formation was observed under the conditions examined. Together, these findings reveal unequal functional contributions of alx4a and alx4b, with alx4a acting as the dominant paralog in iridophore-associated structural coloration and both paralogs contributing unequally to cranial development, and support pnp4a as a candidate downstream gene associated with Alx4a activity. Full article