Search Results (3,053)

Background: The Taiwanese loach (Paramisgurnus dabryanus ssp. Taiwan, Dabry de Thiersant, 1872.) is an economically important aquaculture species in East Asia, and its body color directly affects its ornamental and market value. Our research group recently discovered a golden-red mutant, named “Gan Hong No. 1” (MR), within a wild-type (WT) population. During embryogenesis, MR individuals exhibit almost no melanophore deposition, and after hatching, xanthophores and erythrophores appear sequentially, suggesting that the body color variation likely originates from alterations in the gene regulatory network during early development. Objective: To systematically compare the transcriptomes of WT and MR-Taiwanese loach during early development, to identify the key regulatory pathways underlying red body color formation from a temporal perspective, to test whether the classical melanin synthesis pathway is impaired, and to provide a theoretical basis for selective breeding of body color traits. Methods: High-throughput transcriptome sequencing was performed on eight early developmental stages (0, 5, 10, 15, 20, 23, 28 and 43 h post-fertilization) of both loach types. Differential expression analysis, time-series trend analysis, and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment were used to systematically characterize gene expression dynamics. Transcriptomic data validation was performed using real-time PCR. Results: In MR, the core transcription factor mitfa was significantly downregulated, whereas the expression of melanin synthesis genes such as kita and dct showed no significant difference, indicating that the impairment of melanogenesis is caused by mitfa downregulation. Trend analysis and pathway enrichment revealed that in MR embryos, pathways related to oxidative stress, unsaturated fatty acid biosynthesis, C-type lectin receptor signaling, p53 signaling, and apoptosis were significantly activated, while the thyroid hormone synthesis pathway was markedly upregulated. In WT, these pathways showed the opposite trend. qRT-PCR results were consistent with the transcriptome data. Conclusions: This study demonstrates that downregulation of mitfa serves as the initial trigger for red body color variation in the Taiwanese loach. This mutation impedes melanin synthesis and concurrently activates a coordinated regulatory network involving oxidative stress, immune inflammation, and thyroid hormone signaling. Accumulation of unsaturated fatty acids alleviates oxidative damage and supports carotenoid deposition, while immune signals eliminate aberrant melanocytes and promote compensatory generation of red and yellow chromatophores. The upregulated thyroid hormone further fine-tunes pigment cell differentiation. For the first time in a cobitid species, this study elucidates the mitfa-mediated, multi-pathway synergistic molecular mechanism driving the transition from melanin-based to carotenoid/pteridine-based red coloration in fish, thereby providing a theoretical reference for molecular breeding of body color in aquaculture. Full article

Background: Pancreatic ductal adenocarcinoma (PDAC) belongs to the group of killer human cancers. Its ferocity is sustained by an unusual mix of genetic changes—primarily in KRAS and TP53—a hypoxic as well as desmoplastic tumor microenvironment, plus metabolic and redox adaptations that allow tumor life amidst intense stress situations. Content: This paper will discuss the molecular networks of wild-type and mutant p53, wild-type and mutant KRAS, PUMA, TIGAR, PRMT5, NRF2, oxygen tension, reactive oxygen species (ROS), and oxidative stress pathways that contribute to pancreatic cancer. It will describe how these factors help set the tumor’s redox state and control apoptosis and therapeutic resistance. This shall therefore specifically discuss what role oxygen gradients play in pancreatic tissues, as well as retinoic acid, together with redox-targeted therapies that are specific to vulnerabilities within such types of networks. Summary and Outlook: An understanding of the crosstalk of these molecular pathways will be critical in designing rational therapeutic strategies. Genetics, metabolism, and microenvironmental integration may open a path toward combinatorial therapies that would resensitize PDAC to apoptosis and overcome resistance to current treatments. 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

Dry direct seeding (DDS) is a water-saving and high-efficiency rice cultivation system. However, drought stress during DDS severely constrains seedling establishment. This study used the conventional rice variety Zhonghua 11 (ZH11) and the drought-tolerant hybrid Hanyou 73 to investigate the effects of exogenous silicon (Si) on seed germination and seedling growth under drought stress, and to explore the underlying mechanisms of Si-enhanced drought tolerance. Drought stress was imposed using PEG-6000 simulation and pot experiments with different soil relative water contents (60%, 45%, 25%, and 10%). Si treatment significantly alleviated simulated drought inhibition of seed germination, increasing germination percentage and index, improving seedling growth in both varieties. Under simulated DDS conditions, Si significantly improved plant height, biomass, and root development, while maintaining higher net photosynthetic rate, stomatal conductance, intercellular CO₂ concentration, transpiration rate, and chlorophyll content. Meanwhile, Si reduced oxidative damage by promoting proline accumulation, enhancing peroxidase (POD) and catalase (CAT) activities in both leaves and roots, reducing malondialdehyde (MDA) accumulation, and upregulating the expression of key drought-responsive genes (SNAC1, DREB1A, SKIPa, P5CS2). Furthermore, Si upregulated the expression of genes involved in abscisic acid (ABA) (ABA1, ABA2, MHZ5, ABI3) and jasmonic acid (JA) (AOS2, AOS3, JAR1, JAR2, MYC2, COI1a) biosynthesis and signaling. Compared with the wild-type, the ABA signaling mutant abi3 and the JA signaling mutant myc2 exhibited significantly attenuated improvement of plant growth by Si treatment. Collectively, Si enhances antioxidant capacity and osmotic adjustment, maintains photosynthetic function, and is associated with the activation of ABA and JA signaling pathways, which together alleviate the inhibition of rice seedling establishment under DDS-associated drought stress. Our findings provide a theoretical basis for the application of Si fertilizer in DDS rice production. Full article

Background/Objectives: Non–small cell lung cancer (NSCLC) is a leading cause of cancer-related mortality, driven by invasive behavior and frequent resistance to systemic therapies. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) benefit patients with EGFR-mutant NSCLC, but their efficacy is often limited by tumor-intrinsic and environmental resistance mechanisms. Benzo[a]pyrene (BaP), a ubiquitous polycyclic aromatic hydrocarbon from tobacco smoke, combustion, and dietary sources, is a known carcinogen; however, its role in modulating therapeutic responses is poorly understood. Studies, including ours, implicate the platelet-activating factor-receptor (PAFR) pathway in mediating environmental pollutant and therapy-induced effects on tumor growth and microvesicle particle (MVP) release. We hypothesized that PAFR activation mediates BaP-induced NSCLC progression and influences EGFR-TKI responses. Methods: We assessed the effects of BaP, PAFR agonist CPAF, EGFR-TKIs, and their combinations on cell viability, proliferation, migration, anchorage-independent growth, and MVP secretion. Results: BaP did not alter cell survival but significantly increased migration, growth, colony formation, and MVP release, similar to CPAF, and these effects were blocked by a PAFR antagonist or acid sphingomyelinase inhibitor. Notably, BaP did not significantly reduce EGFR-TKI efficacy at tested concentrations. Conclusions: These results show that environmental carcinogens modulate NSCLC behavior through PAFR signaling without compromising EGFR-TKI responsiveness, highlighting PAFR as a potential therapeutic target. Full article

Background: Dysregulated G protein-coupled receptor (GPCR) signaling is increasingly implicated as an important driver for oncogenesis. Uveal melanoma (UM) represents a highly metastatic intraocular malignancy primarily driven by activating mutations in G protein family members Gαq/11. Although Tebentafusp, the first FDA-approved bi-specific T-cell engager for UM, improves survival, its activity is restricted to specific human leukocyte antigen (HLA) alleles, highlighting the need to identify broadly expressed targetable proteins for immunotherapeutic strategies. Here we aimed to define surfaceome and phospho-signaling signatures associated with oncogenic Gαq-signaling. Methods: Heterologous and UM in vitro systems were used to interrogate Gαq-driven changes. HEK293T cells were transfected with wild-type Gαq or the oncogenic Gαq (R183Q) mutant, with surface marker profiles quantified by flow cytometry. Complementary immunophenotyping was performed in the Gαq-mutant UM cell line MP46 and Gα11-mutant line MP41. Kinase phosphorylation was assessed in control and Gαq mutant conditions followed by effect size estimation (Hedges’ g), Welch’s t-test, principal component analysis, and Spearman correlation-based network analysis of surface and phosphoprotein readouts. Results: Hyperactive Gαq in HEK293T cells induced graded remodeling of surface protein profiles, including reduced CD56 (NCAM) and CD49c (ITGA3) expression. Similarly, in UM models, MP46 versus MP41 had limited expression of CD56 and CD49c. Moreover, phospho kinase profiling and network analysis identified altered surface-phosphoprotein relationships, including a CD56-p70 S6 kinase association. Conclusions: These data provide new insights into Gαq-driven modulators of UM phenotype of relevance for studies of tumor–microenvironment interaction and metastasis. Full article

The Lysobacter capsici XL1 β-lytic protease (Blp) is a bacteriolytic enzyme that hydrolyzes peptide bonds in the interpeptide bridge of the peptidoglycan of Gram-positive bacteria, including antibiotic-resistant strains of pathogenic bacteria. The Blp has been extensively characterized. The only unexplored aspect is the mechanism by which this enzyme recognizes target cells. In this work, we demonstrated for the first time that the Blp structure contained a C-terminal subdomain that can be responsible for this interaction. Molecular modeling suggested a hydrophobic nature of the interaction between the Blp and peptidoglycan. Model mutant forms of the Blp, which have fewer hydrophobic areas in the C-terminal subdomain, also had fewer sites for potential interaction with the ligand. Wet lab experiments showed that these mutant Blp forms exhibited poorer binding to peptidoglycan and living Staphylococcus aureus 209P cells, resulting in decreased bacteriolytic and proteolytic activity. Amino acid residues N136 and Y160 in the C-terminal subdomain were identified and can be important for the interaction of the enzyme with target cells. Further research into the mechanism of target cell recognition by bacterial bacteriolytic proteases will enable the use of this knowledge to expand the specificity of action of these enzymes, including as antimicrobial agents for medical applications. Full article

Background/Objectives: Staphylococcus haemolyticus is a common skin commensal that has emerged as a multidrug-resistant nosocomial pathogen, with sequence type 42 frequently implicated in clinical settings. The genetic basis of fusidic acid (FA) resistance mediated by mutations in elongation factor-G (fusA/EF-G) has not been systematically characterized in S. haemolyticus. Methods: Five representative FA-susceptible S. haemolyticus isolates were selected. In vitro FA resistance was induced by incubating each isolate on Mueller–Hinton agar containing 4 µg/mL FA at 37 °C for 48 h. Resistant colonies were recovered and fusA was sequenced by Sanger sequencing to identify mutations. Growth doubling times of EF-G mutant isolates were measured and compared with those of the parental susceptible strains. Potential fitness-compensatory changes in fusA were assessed by serial passage of selected mutants for ten successive passages and re-sequencing of fusA. Results: A total of 28 FA-resistant colonies were recovered. Sequencing identified mutations at seven nucleotide loci corresponding to ten distinct amino acid substitutions in EF-G: Q115L, L430S, E433G, G452C, H457Y, H457N, H457L, H457Q, R464L, and A655G. The mean doubling time of EF-G mutant isolates was significantly longer than that of the wild-type parental strains (mutants: 55.75 ± 7.78 min, n = 28; wild type: 40.78 ± 4.13 min, n = 5; Welch’s two-sample t test: t = −6.34, df ≈ 10.0, two-tailed p < 0.0001). Following ten serial passages, we did not detect compensatory mutations in fusA that restored the ancestral growth rate. Conclusions: FA resistance in S. haemolyticus can be rapidly induced in vitro through mutations in EF-G/fusA. Compared with previously reported EF-G mutations in other staphylococci, we identified two novel substitution sites (L430S, E433G) and previously unreported substitutions at established resistance positions (H457N, H457L, A655G). Mutations in EF-G (encoded by fusA) were associated with a measurable in vitro fitness cost; following ten serial passages, compensatory mutation was not detected in fusA. These findings support systematic surveillance of EF-G/fusA mutations in clinical S. haemolyticus isolates. Further studies should address their prevalence, stability, transmissibility, and clinical impact, particularly where FA use is increasing and patient populations are vulnerable. Full article

Background: Cytochrome P450 3A4 (CYP3A4) is a key membrane-anchored drug-metabolizing enzyme. Its expression and purification in heterologous systems are severely hindered by low yield and detergent-induced structural inactivation. Although extracellular vesicles (EVs) provide an ideal natural lipid bilayer environment to stabilize membrane proteins, targeted loading remains challenging. The ESCRT and ALIX-binding region (EABR) of CEP55 can efficiently recruit core components of the endosomal sorting complex (ESCRT) to mediate membrane fission. Objectives: This study used the EABR motif to drive the targeted vesicular secretion of CYP3A4, thereby establishing a novel membrane protein engineering platform. Methods and Results: EABR was fused with fluorescent protein, confirming its specific mediation of vesicular secretion. Recombinant plasmids of EABR/CYP3A4 and its reverse mutant (R-EABR) were transfected into HEK293T cells. Western blot and midazolam-based metabolic assays showed that forward EABR significantly enhanced CYP3A4 expression and EV secretion, while R-EABR lost exocytosis function. EVs isolated by ultracentrifugation verified EABR’s role in recruiting ESCRT and improving CYP3A4 activity. Conclusions: Forward CEP55-EABR specifically and efficiently drives vesicular encapsulation of CYP3A4, enhancing its expression and secretion. This ESCRT-mediated strategy avoids destructive purification, provides a stable lipid-rich bioreactor for CYP3A4, and has great translational potential in high-throughput in vitro drug metabolism and screening platforms. Full article

TP53 is the most frequently altered tumor-suppressor gene in human cancer, yet efforts to therapeutically target p53 have yielded limited and inconsistent clinical success. We argue that this gap reflects not a lack of druggable biology, but an oversimplified conceptual framework that treats p53 as a binary wild-type versus mutant entity. Here, we synthesize emerging evidence supporting a model in which p53 operates across a spectrum of functional states defined by mutation class, allelic burden, isoform composition, aggregation propensity, post-translational regulation, and cellular context. These states shape distinct biological outputs, including transcriptional activity, dominant-negative and gain-of-function effects, immune modulation, and checkpoint dependency, which collectively determine therapeutic vulnerability. We review current strategies targeting the p53 pathway, including mutant p53 reactivation, targeted degradation, anti-aggregation approaches, immune-directed therapies, restoration of wild-type pathway activity, gene replacement, and synthetic lethal targeting of DNA damage response dependencies. Clinical and preclinical evidence highlights key limitations of each approach, including stoichiometric constraints, mutation specificity, context-dependent efficacy, and adaptive resistance. Notably, emerging evidence from preclinical and correlative clinical studies suggests that therapeutic outcomes may be more closely associated with p53 functional state than with TP53 mutation status alone. We further emphasize the emerging roles of p53 isoforms and the tumor immune microenvironment as critical modifiers of p53 activity and determinants of treatment response. Collectively, these insights support a paradigm shift toward mechanism-matched, biomarker-stratified strategies that align therapeutic modality with the operative p53 network. Future progress will depend on integrating multi-parameter diagnostics with rational combination therapies to fully exploit p53 as a central vulnerability in cancer. Full article

Objective: CDCA8 is frequently overexpressed in malignant tumors and linked to poor prognosis. This study evaluated the prognostic significance of CDCA8 expression in glioma patients using the CGGA and TCGA datasets. Methods: Clinical and expression data of glioma patients from CGGA and TCGA were analyzed. CDCA8 expression was compared across subgroups based on tumor grade (GBM vs. LGG) and IDH mutation status, and meta-analyses were performed to assess inter-database differences. Results: This study included 1125 glioma patients from CGGA and TCGA. CDCA8 expression was higher in TCGA GBM (p < 0.001) but comparable between databases in LGG (p = 0.501). CGGA showed lower CDCA8 in IDH-mutant gliomas (p < 0.001), with no difference in IDH-wildtype cases (p = 0.154). CGGA patients had longer overall survival in all above subgroups. Meta-analysis found no significant prognostic association of CDCA8 in GBM, IDH-wildtype and IDH-mutant gliomas. In LGG, high CDCA8 was significantly linked to reduced adverse events (p < 0.001, OR = 0.22, 95% CI [0.11–0.43]). Conclusion: CDCA8 has grade-dependent prognostic roles in gliomas. Its overexpression correlates with poor prognosis in GBM but favorable outcomes in LGG. Inter-database variations support CDCA8 as a promising prognostic biomarker for LGG, and reflect the influences of regional, therapeutic and genetic factors. Full article

Background and Objectives: Migraine is a chronic, throbbing type of headache that affects large populations worldwide. This condition is associated with neuroinflammation. Materials and Methods: In this study, polymorphism analyses were performed by KASP PCR. Serum interleukin-6 (IL-6) and 8-hydroxy-2′-deoxyguanosine (8-OHdG) levels were measured using kits based on the enzyme-linked immunosorbent assay (ELISA) principle. Results: In the APE1 Asp148Glu (rs1130409) gene polymorphism analysis, the frequency of the mutant G (Glu) allele was 93.1% and 48.0% in the control and migraine populations, respectively, while the frequency of the wild-type T (Asp) allele was 6.9% and 52.0% (p < 0.001). The frequency of the T/T (Asp/Asp) genotype was high in the migraine group (p < 0.001), while the frequency of the G/G (Glu/Glu) genotype was higher in the control group at 86.2%, compared to the migraine group (p < 0.001). The total frequency of the T/G+ G/G (Asp/Glu+Glu/Glu) composite genotype was determined to be 65.9% in the control group and 34.1% in the migraine group (p < 0.001). There was no statistical difference in allele and genotype frequency between the control and migraine groups for the XRCC1 Arg399Gln (rs25487) gene polymorphism. Serum 8-OHdG and IL-6 levels were comparable between the groups, with no statistically significant differences observed. Conclusions: Future studies with larger and more homogeneous populations are needed to further elucidate the potential interactions between inflammatory processes and DNA damage in migraine. Consideration of attack duration and environmental exposures may improve interpretation of biomarker variability. Expanding the analysis to additional DNA repair gene polymorphisms may also contribute to a better understanding of the molecular background of migraine and the evaluation of potential biomarkers. Full article

Background/Objectives: Recurrent or metastatic adenoid cystic carcinoma (R/M ACC) has no standard systemic therapy. VEGFR-targeting tyrosine kinase inhibitors (TKIs) are commonly used first-line, though no international standard exists; cisplatin-based chemotherapy is an alternative. We retrospectively reviewed the cyclophosphamide–epirubicin–cisplatin (CEP) regimen to determine whether prior TKI exposure compromises subsequent chemotherapy efficacy. Methods: We studied 31 patients given CEP for progressive R/M ACC (2018–2023). Tumor response was assessed by RECIST 1.1. Molecular subtype was determined by c-MYC/p63 immunohistochemistry (ACC-I, c-MYC-positive/p63-negative; ACC-II, p63-positive/c-MYC-low or negative). Multivariable models used Firth’s penalized likelihood Cox regression. Next-generation sequencing (NGS) was available in 21 of 31 patients. Results: Thirty-one patients were enrolled (median age 48; 17 [54.8%] with prior TKI). At median follow-up of 22.6 months, the objective response rate (ORR) was 19.4%, disease control rate 71.0%, median progression-free survival (PFS) 5.3 months, and median overall survival (OS) 10.3 months. Prior TKI did not lower efficacy: ORR 17.6% vs. 21.4%, PFS hazard ratio 0.76 (p = 0.519). All six partial responses occurred in ACC-I tumors (35.3% vs. 0% in ACC-II, p = 0.021). In the NGS subset (5 PIK3CA-mutant), PIK3CA mutation (OS HR 6.19, p = 0.024) and bone metastasis (OS HR 5.84, p = 0.027) remained associated with shorter OS after adjustment. No treatment-related deaths occurred. Conclusions: CEP is active in R/M ACC, and prior TKI exposure did not appear to reduce efficacy. Higher response rates in ACC-I tumors and the apparent PIK3CA-related survival deficit are exploratory observations that need prospective testing before they can guide treatment. Full article

Background: Given the challenges in early detection and diagnosis, understanding the molecular underpinnings of endometrioid ovarian cancer (EOC) is crucial for improving patient outcomes. This multi-level study provides a new perspective on EOC, focusing on the expression of ARID1a (BAF250a) and RIF1. Methods: This study evaluates patient cohorts with EOC through semi-quantitative immunohistochemical staining of BAF250a (protein encoded by ARID1a) and RIF1 proteins alongside mutations that influence the gene expression of ARID1a and RIF1. Besides survival analyses, platinum- and taxane-based treatment responsiveness with regard to ARID1a and RIF1 expression has been analyzed using an online available database. Results: Histological and immunohistochemical analysis of clinical samples revealed a significant reciprocal alteration in protein expression, characterized by a marked reduction in the tumor suppressor BAF250a (p < 0.0001) and a concomitant elevation of RIF1 (p < 0.0001) in EOC compared to controls. Tumors harboring mutations in BRCA1 exhibited significantly (p = 2.82 × 10⁻⁴) lower ARID1a expression levels compared with corresponding wild-type tumors, whereas LAMB3-mutant tumors showed a significant (p = 5.16 × 10⁻³) upregulation of RIF1 mRNA expression. Conclusions: In conclusion, our study offers a new perspective, emphasizing that EOC is a distinct clinical and molecular entity. We demonstrated the expression patterns of ARID1a/BAF250a and RIF1 in EOC, establishing their potential relevance in the context of tumor biology and malignant transformation. Full article

Cysteine biosynthesis is increasingly recognized as a critical determinant of bacterial virulence, highlighting this pathway as a promising reservoir of novel antimicrobial targets. In Pseudomonas aeruginosa, however, the molecular basis of cysteine production has only recently begun to emerge. Here, we identify PA3816 as the major P. aeruginosa serine acetyltransferase (PaCysE), the enzyme responsible for generating the activated serine intermediate that feeds O-acetylserine sulfhydrylase-mediated cysteine synthesis. Through a combination of biochemical and genetic approaches, we demonstrate that PaCysE efficiently catalyzes L-serine acetylation in vitro, and in turn, deletion mutants exhibit cysteine auxotrophy, underscoring its essential contribution to O-acetylserine production. Notably, PaCysE is less sensitive to feedback inhibition by cysteine and does not appear to form the canonical cysteine synthase complex, suggesting a regulatory architecture that diverges from well-characterized orthologs. Loss of PaCysE function has broad physiological consequences, including enhanced biofilm formation, reduced pyocyanin production, and attenuated infectivity in an animal model, linking cysteine biosynthesis directly to pathogen fitness. Finally, we identify a thiazole derivative that inhibits PaCysE activity (IC₅₀ ≈ 30 µM) and suppresses bacterial growth in a cysteine-dependent manner, providing a proof-of-concept for therapeutically targeting this pathway. Full article