Search Results (699)

Synovial sarcoma (SySa) is a malignant soft tissue tumor that is characterized by an SS18::SSX fusion protein, which integrates into BAF chromatin remodeling complexes and alters global gene transcription. Despite its uniform genetic driver, SySa displays striking histomorphological and phenotypic heterogeneity, including spindle cell, glandular and poorly differentiated patterns. Prognosis is variable, with around 50% of patients developing metastases. Limited response to chemotherapy highlights the need for a better understanding of the underlying molecular mechanisms to guide alternative therapeutic strategies. Given the pivotal function of BAF complexes in SySa and their recently described impact on cellular differentiation processes, this study aims to investigate the role of SS18::SSX and specific BAF subunits in SySa differentiation. Nanostring analysis revealed that silencing of SS18::SSX and the GBAF subunit BRD9 modulates the cellular differentiation pathways. SS18::SSX and BRD9 were found to regulate epithelial–mesenchymal-transition (EMT)-associated factors of Snail and Slug on different levels, with SS18::SSX repressing E-Cadherin expression. Published single-cell RNA sequencing data were analyzed to validate our finding that BRD9 contributes to SySa EMT regulation. Our study provides novel insights into the multilayered regulation of key EMT players by SS18::SSX and BRD9 in SySa, thereby defining tumor phenotype and (potentially) prognosis. Full article

Myopathy encompasses a group of diseases characterized by abnormalities in both muscle function and structure. However, the underlying regulatory mechanisms of newly formed myofiber development remain poorly defined. No promising therapeutic approach has been developed, but numerous medication options are available to alleviate symptoms. Our previous studies demonstrated that adenosine kinase (ADK) is critical in regulating adenosine metabolism, pathological angiogenesis, pathological vascular remodeling, and vascular inflammatory diseases. Adenosine dynamically distributes between extracellular and intracellular, and adenosine concentration regulates ADK expression. However, the mechanism by which adenosine triggers an ADK-dependent intracellular signaling pathway to regulate skeletal muscle regeneration is not well defined. This study aimed to evaluate whether the adenosine-induced intracellular signaling pathway is involved in regulating myopathy, and how it regulates the development of newly formed myofibers. In this study, an intramuscular injection of cardiotoxin was used to induce a skeletal muscle injury model; satellite cells and C2C12 cells were employed. Whether adenosine regulates satellite cell activity, new myofiber formation and differentiation, as well as fusion of myofibers, were determined by H&E staining, BrdU incorporation assay, and spheroid sprouting assay. Interaction between ADK and PFKFB3 was evaluated by IF staining, PPI network analysis, molecular docking simulation, and CO-immunoprecipitation assay. The results demonstrated that adenosine dynamically distributes between extracellular and intracellular through concentrative nucleoside transports or equilibrative nucleoside transporters, and it rapidly induces an ADK-dependent intracellular signaling pathway, which interacts with PFKFB3-mediated glycolytic metabolism to promote satellite cell activity, new myofiber formation, differentiation, and fusion, and eventually enhances skeletal muscle regeneration after injury stress. The remarkable endogenous regeneration capacity of skeletal muscle, which is regulated by adenosine-triggered intracellular signaling, presents a promising therapeutic strategy for treating muscle trauma and muscular dystrophies. Full article

Uterine Fibroids (UFs) are the most common benign tumors in women of reproductive age, affecting ~77% of women overall and are clinically manifest in ~25% by age 45. Bromodomain and extra-terminal domain (BET) proteins play key roles in epigenetic transcriptional regulation, influencing many biological processes, such as proliferation, differentiation, and DNA damage response. Although BET dysregulation contributes to various diseases, their specific role in the pathogenesis of UFs remains largely unexplored. The present study aimed to determine the expression pattern of BET proteins in UFs and matched myometrium and further assess the impact of BET inhibitors on UF phenotype and epigenetic changes. Our studies demonstrated that the levels of Bromodomain-containing protein (BRD)2 and detection rate of BRD4 were significantly altered in UFs compared to matched myometrium, suggesting that aberrant BET protein expression may contribute to the pathogenesis of UFs. To investigate the biological effects of BET proteins, two small-molecule inhibitors, JQ1 and I-BET762, were used to assess their impact on UF cell behavior and transcriptomic profiles. Targeted inhibition of BET proteins markedly reduced UF cell viability compared with myometrial cells and induced cell cycle arrest. Unbiased transcriptomic profiling coupled with bioinformatic analysis revealed that BET inhibition altered multiple biological pathways, including G2M checkpoint, E2F targets, mitotic spindle, mTORC1 signaling, TNF-α signaling via NF-κB, and inflammatory response, as well as reprogrammed the UF cell epigenome. Notably, BET inhibition decreased the expression of several genes encoding extracellular matrix (ECM) proteins, a hallmark of UFs. Collectively, these results support that BET proteins play a pivotal role in regulating key signaling pathways and cellular processes in UFs. Targeting BET proteins may therefore represent a promising non-hormonal therapeutic strategy for UF treatment. Full article

Background: Maize (Zea mays L.) is a vital global crop, and yield improvement through dwarfing breeding—inspired by the Green Revolution—holds promise for addressing food security challenges. Despite the identification of over 60 dwarf genes in maize, their genetic diversity remains limited. Brassinosteroids (BRs) are key phytohormones that regulate plant height, and mutations in BR-related genes often result in dwarf phenotypes. Methods: The zmbrd1 mutant was generated via EMS mutagenesis in the B73 background. Phenotypic traits (plant height, root length) and histological features (e.g., mesocotyl cell length) were compared between mutant and wild-type plants. Transcriptome sequencing of leaves and root tips identified differentially expressed genes (DEGs), followed by GO and KEGG enrichment analyses. Key hormone-related genes were validated by means of qRT-PCR. Results: The zmbrd1 mutant exhibited severe dwarfism and reduced root length, primarily due to inhibited longitudinal cell elongation in internodes. Transcriptome analysis revealed 1652 DEGs in leaves and 1450 DEGs in roots. Enriched pathways included BR biosynthesis, plant hormone signal transduction, and glutathione metabolism. In leaves, upregulated genes were linked to hormone signaling and chloroplast function, while downregulated genes involved oxidoreductase activity and stress response. In roots, DEGs were enriched in ethylene signaling, MAPK pathways, and plant–pathogen interaction, suggesting impaired defense responses. qRT-PCR confirmed dysregulation of hormone-related genes: GA biosynthesis genes were downregulated, whereas auxin-related genes were upregulated in leaves but downregulated in roots. Conclusions: The dwarf phenotype of zmbrd1 stems from disrupted BR biosynthesis, leading to hormonal imbalance (particularly in GA and auxin pathways), oxidative stress, and suppressed cell elongation. Our results suggest that ZmBRD1 plays a key role in integrating aboveground and underground growth likely through modulating hormone crosstalk. This study elucidates BR-mediated height regulation and provides genetic resources for maize breeding. Full article

Pradofloxacin is a third-generation dual enzyme targeting bactericidal veterinary fluoroquinolone, recently approved for use in cattle for bovine respiratory disease, which is active against Gram-positive/negative, atypical and anaerobic bacteria. We compared in vitro killing by pradofloxacin to that by ceftiofur, danofloxacin, enrofloxacin, florfenicol, marbofloxacin, tildipirosin, tilmicosin and tulathromycin against bovine isolates of Mannheimia haemolytica and Pasteurella multocida over a range of bacterial densities (10⁶–10⁹ cfu/mL). Drug concentrations used in the kill assays included the minimum inhibitory and mutant prevention drug concentrations and maximum serum and maximum tissue drug concentrations. Regardless of bacteria density tested and drug concentration used, pradofloxacin consistently killed as many or more (but not fewer) bacterial cells than any other drug tested against M. haemolytica strains. At the 10⁸–10⁹ cfu/mL densities, pradofloxacin killed 99–99.9%, 100% and 100% of bacterial cells at the MPC, maximum serum and maximum tissue drug concentrations, respectively, following 24 h of drug exposure. Indeed, pradofloxacin killed 99.9–99.99% of cells following 30–60 min of exposure to the maximum serum concentration. Similar trends were seen with killing of P. multocida strains by pradofloxacin. Against high-density bacterial populations, pradofloxacin was rapidly bactericidal and consistently killed more cells than the other agents tested. This manuscript represents the most comprehensive comparative in vitro kill study completed to date. Full article

Bovine respiratory disease (BRD) is a multifactorial syndrome and a leading cause of morbidity and economic loss in global cattle production. Next-generation sequencing (NGS) platforms, including Illumina and Oxford Nanopore Technologies (ONT), have enabled high-resolution profiling of the bovine respiratory microbiome and virome, revealing novel viral contributors such as bovine rhinitis A virus (BRAV) and influenza D virus (IDV). Transcriptomic approaches, including RNA sequencing (RNA-Seq) and microRNA (miRNA) profiling, provide insights into host immune responses and identify potential biomarkers for disease prediction. Traditional diagnostic methods—culture, ELISA, and immunohistochemistry—are increasingly complemented by PCR-based and metagenomic techniques, improving sensitivity and specificity. Despite technological progress, gaps remain in virome characterization, miRNA function, and the integration of multi-omics data. Standardized protocols and longitudinal studies are needed to validate microbial signatures and support field-deployable diagnostics. Advances in bioinformatics, particularly network-based integrative pipelines, are becoming essential for harmonizing multi-omics datasets and revealing complex host–pathogen interactions. The objective of this comprehensive review was to synthesize current understanding of the bovine transcriptomic response to BRD as well as the respiratory microbiome and virome, emphasizing how advanced sequencing technologies have transformed microbial profiling and molecular diagnostics in BRD. Full article

Macrolides are crucial for the management and treatment of bovine respiratory disease (BRD). However, antimicrobial resistance (AMR) threatens the efficacy of these and other antimicrobials. We developed real-time recombinase polymerase amplification (RPA) assays targeting three clinically relevant macrolide antimicrobial resistance genes (ARGs)—msrE-mphE and erm42—in ≤30 min using extracted DNA. A set of 199 deep nasopharyngeal swabs (DNPS) collected from feedlot calves near the time of arrival were selected based on bacterial culture (BC) results for Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni and antimicrobial susceptibility testing (AST) for tulathromycin, tilmicosin, tildipirosin, or gamithromycin. Samples were also tested for the same targets using RPA and polymerase chain reaction (PCR). In samples that were culture-positive for one or more macrolide-resistant BRD-associated bacteria (n = 101), msrE-mphE and/or erm42 were detected in 95% of cases using RPA. The remaining 98 samples were either culture-negative, or the recovered bacteria were macrolide-susceptible: 43% of these were RPA-positive for at least one macrolide ARG. Together with BC-AST and PCR, Bayesian latent class modelling estimated the clinical sensitivity of RPA for macrolide ARGs to be 95% and specificity to be 58%, with moderate agreement between RPA and BC-AST (κ = 0.52) or PCR (κ = 0.55). The estimated sensitivity of the RPA multiplex assay for the targeted macrolide ARGs was very good, although estimated specificity was limited. However, Sanger sequencing confirmed RPA detection of msrE-mphE in BC-AST/PCR-negative samples (n = 23), reflecting the presence of this locus in non-target bacteria, as well as potential ARG variants among BRD bacteria. These findings support the potential of RPA for rapid ARG detection from extracted DNA. Continued assay optimization and evaluation for detection of respiratory bacteria and ARGs will further enhance its diagnostic utility. Full article

Background: Periostin can be considered a stimulator of Wnt. Elucidating the relationship between Wnt10a and Periostin in dental pulp stem cells is considered necessary for a deeper understanding of the mechanisms of dental pulp regeneration. Methods: Regenerated dental pulp from ectopic root grafts was double-stained with BrdU and Wnt10a, and the positivity rates were analyzed. Furthermore, the expression levels of Wnt10a, LRP5/6, DKK1, and Periostin within the regenerated tissue were analyzed by PCR. The expression levels of Wnt10a, LRP5/6, DKK1, and Periostin in cells stimulated with Periostin were analyzed by PCR. Wnt10a protein expression was analyzed by Western blotting and ELISA. Similar evaluations were performed with co-stimulation by Periostin and DKK1(Sample size:4). In each experiment, cells not stimulated with periostin served as the control group. Statistical analysis involved confirming the normal distribution of data using QQ plots, followed by one-way analysis of variance and post hoc Turkey’s test. Results: Migrating dental pulp stem cells expressed Wnt10a, and migration was additionally inhibited by its antagonist DKK1. Furthermore, Periostin stimulation increased Wnt10a secretion and suppressed DKK1. Conclusions: Periostin significantly increased Wnt10a expression and DPSC migration, while DKK1 inhibited these effects. Full article

Cancer progression is primarily driven by disruptions in critical biological pathways, including ErbB signaling, p53-mediated apoptosis, and GSK3 signaling. However, experimental and clinical studies typically identify only limited disease-associated genes, challenging traditional pathway analysis methods that require larger gene sets. To overcome this limitation, reliably expanded gene sets are required to align with cancer-related pathways. Although various propagation methods are available, the key challenge is to select techniques that can effectively propagate signals from limited seed gene sets through protein interaction networks, thereby generating robust, expanded sets capable of revealing pathway disruptions in cancer. In this study, the number of seed genes was systematically varied to evaluate the alignment of pathways obtained from different propagation methods with known pathways using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. Among the evaluated propagation methods, normalized Laplacian diffusion (NLD) demonstrated the strongest alignment with reference pathways, with an average area under the ROC curve (AUC) of 95.11% and an area under precision–recall (AUPR) of 71.20%. Focusing specifically on well-established cancer pathways, we summarized the enriched pathways and discussed their biological relevance with limited gene input. Results from multiple runs were aggregated to identify genes consistently prioritized but absent from core pathway annotations, representing potential pathway extensions. Notable examples include RAC2 (ErbB pathway), FOXO3 and ESR1 (GSK3 signaling), and XIAP and BRD4 (p53 pathway), which were significantly associated with patient survival. Literature validation confirmed their biological relevance, underscoring their potential as prognostic markers and therapeutic targets. In summary, NLD-based diffusion proves effective for pathway discovery from limited input, extending beyond annotated members to reveal clinically relevant genes with therapeutic and biomarker potential. Full article

Background/Objectives: BrdU (5′-bromo-2′-deoxyuridine), a synthetic thymidine (T) analog, is widely used to study cell proliferation and DNA synthesis. To precisely identify where and when DNA replication starts and terminates, it is essential to determine the BrdU incorporation rate and sites at a single-nucleotide resolution. Although several deep learning-based methods have been developed for detecting BrdU using Oxford nanopore sequencing data, there is a lack of accessible, easy-to-follow tutorials to guide researchers in preparing training data and implementing deep learning approaches as the nanopore sequencing technologies continue to evolve. Methods: Due to the lack of ground truth BrdU-positive data generated on the latest R10 flow cells, we prepared model training data from legacy R9 flow cells, consistent with existing tools. We processed publicly available synthetic and real nanopore DNA sequencing datasets, with and without BrdU incorporation, using a combination of open-source and custom software tools. Subsequently, we trained bidirectional gated recurrent unit (BiGRU)-based recurrent neural networks (RNNs) for BrdU detection using the TensorFlow library on the Google Colab platform. Results: We trained BiGRU-based RNNs for BrdU detection with a high specificity (>94%) but a moderate sensitivity due to limited BrdU-positive data. We detail the setup, training, testing, and fine-tuning of the model using both synthetic and real DNA sequencing data. Conclusions: Though the models were trained with data generated on legacy flow cells, we believe that this detailed protocol, covering both data preparation and model development, can be readily extended to R10 flow cells and basecallers for other base modifications. This work will facilitate the broader adoption of deep learning neural networks in biological research, particularly RNNs, which are well suited for modeling sequential and time-series data. Full article

Aromatic coconut is a special variety of coconut. Its unique “pandan-like” aroma has won it great popularity among consumers, endowing it with considerable market potential. In our previous study, 2-acetyl-1-pyrroline (2AP), which serves as the main source of the “pandan-like” aroma in aromatic coconut, was found to exhibit significant variation among distinct aromatic coconut individuals. Now, the regulatory mechanism of 2AP has been clarified in fragrant rice, and the ProDH gene is the key gene for 2AP regulation. To further understand the regulation mechanism of 2AP content in aromatic coconut, we cloned and identified the CnProDH gene, the key gene of 2AP regulation in aromatic coconut. The results showed that the CnProDH gene had the typical ProDH structural domain, and its full-length sequence is 23,667 bp, containing 5 exons and a coding sequence (CDS) of 1599 bp. The CnProDH gene encodes a protein that possesses a β₈α₈ barrel structure, consisting of 532 amino acids (aa), with a molecular mass of 58,076.63 kDa and an isoelectric point of 7.11. To further understand the regulatory mechanism of CnProDH in aromatic coconut, we also constructed a yeast one-hybrid (Y1H) library for aromatic coconut. Through the Y1H experiment, combined with the prediction and analysis of cis-acting elements in the promoter of the CnProDH gene, three possible regulatory factors, including CnYABBY2, CnSAP8, and CnBRD3, were identified. These findings provide a molecular basis for clarifying and solving the problem of variations in 2AP content across different aromatic coconuts. Full article

Chromodomain helicase DNA-binding protein 8 (CHD8), a frequently mutated gene in autism spectrum disorder (ASD), is an ATP-dependent chromatin remodeler with emerging roles in hematopoiesis. While CHD8 is known to maintain hematopoietic stem and progenitor cells (HSPCs) in the bone marrow, its function during developmental hematopoiesis remains undefined. Here, using a zebrafish model, we demonstrate that chd8 loss severely depletes the HSPC pool in the caudal hematopoietic tissue through a p53-dependent apoptotic mechanism. Furthermore, chd8^−/− embryos exhibit a p53-independent expansion of myelopoiesis. chd8 deficiency upregulates brd4, which promotes systemic inflammatory cytokine expression. Inhibiting brd4 alleviates cytokine expression, suppresses excessive myelopoiesis, and restores HSPC development. Our findings reveal a dual regulatory mechanism in which chd8 governs HSPC development by repressing p53-mediated apoptosis and constraining brd4-driven immune cell differentiation. Full article

Bovine respiratory disease is a significant health concern in dairy calves, impacting short-term growth and potentially long-term productivity. While previous studies have linked early-life lung consolidation, often subclinical and diagnosed by lung ultrasonography, to reduced preweaning average daily gain, its extended effects on production and reproductive parameters remain less studied, particularly in specific geographical contexts. This study presents a follow-up analysis on a cohort of dairy calves originally monitored weekly from birth to weaning for lung consolidation via TUS in an Iranian dairy herd. Two years post-weaning, comprehensive production and reproduction data were collected and analyzed for these same animals. Our objective was to investigate the long-term associations between early-life lung consolidation and subsequent outcomes, including mature equivalent milk yield, corrected milk yield, culling risk before and during lactation, age at first breeding, age at first calving, and reproduction parameters such as services per conception and conception rate (the percentage of cows or heifers that become pregnant after a single insemination or breeding attempt). Data analysis, employing descriptive statistics, survival analysis, and non-parametric tests, revealed that while early-life lung consolidation (defined by ≥1 cm or ≥3 cm depth, and number of episodes) did not show significant associations with culling probability or mature equivalent milk yield, interesting numerical trends were observed. The study highlights the complexities of establishing clear long-term links, suggesting that while subclinical BRD can have immediate growth impacts, its chronic effects on later production and reproduction may be subtle and require larger cohorts or more targeted analysis to achieve statistical significance. The findings reinforce the need for cautious interpretation of p-values in the context of multiple comparisons and underscore the challenges in quantifying long-term economic consequences of early-life respiratory health. Full article

Background/Objectives: Long-read metagenomic sequencing can assign antimicrobial resistance genes (ARGs) to speciated bacterial reads. This study evaluated whether metagenomic data from respiratory bacteria derived from feedlot calves sampled in the early feeding period were associated with subsequent bovine respiratory disease (BRD) treatment and phenotypic antimicrobial resistance (AMR) at treatment. Methods: Deep nasopharyngeal swabs (DNPSs) obtained at arrival processing (1 day on feed; DOF), 13 DOF, and the time of BRD treatment were cultured and subjected to antimicrobial susceptibility testing (AST) and long-read metagenomic sequencing. Analyses focused on macrolide (mphE-msrE, EstT) and tetracycline (tet(H)) ARGs within reads assigned to Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Bibersteinia trehalosi. Generalized estimating equations assessed associations between metagenomic results from 1 and 13 DOF and subsequent BRD treatment risk and AST outcomes at treatment, at both the individual animal (calf) and pen levels. Results: Calf-level detection of H. somni at 13 DOF was associated with a greater BRD treatment risk between 14 and 45 DOF. An increased pen prevalence of either M. haemolytica or P. multocida at 13 DOF was associated with a greater BRD treatment risk from 14 to 45 DOF. At 13 DOF, detections of mphE-msrE, EstT, or tet(H) in target bacteria were associated with corresponding phenotypic AMR at BRD treatment. Similarly, a higher pen-level prevalence of mphE-msrE or EstT at 13 DOF was also associated with increased macrolide resistance at BRD treatment. Conclusions: The results from long-read metagenomic sequencing of DNPSs collected at 13 DOF were associated with both BRD risk and AMR at treatment. These findings align with prior culture-based results and support the potential utility of pen-level metagenomic testing for AMR surveillance and informing antimicrobial selection in feedlots. Full article

Background: Bone metastasis of breast cancer (BC) is a key reason for poor prognosis. Recently, natural ingredients derived from plants have been found to exert a broad anti-tumor effect and are considered to be promising candidates for adjuvant therapy. Astragalin (AS) was found to inhibit the progression of several types of tumors; however, the role of AS in regulating the bone metastasis of BC is still unclear. Methods: The effects of AS on the progression of bone metastasis of BC were detected in vivo through safranin O and fast green staining, in vivo living imaging and microCT. The BrdU assay and Annexin V-PI analysis were used to detect the effects of AS on the growth of BC cells. Furthermore, TRAP staining was performed to examine the formation of osteoclasts regulated by AS. A transcriptome was performed to explore the downstream effects of AS on regulating the growth of BC cells, and the mechanism was further confirmed by Western blot and real-time PCR. Results: Administration of AS could effectively attenuate the bone destruction and the progression of bone metastasis of BC. The growth of BC cells can be inhibited by AS by inducing ER stress-mediated upregulation of Ddit3. In addition, AS can also prevent osteoclastogenesis through inhibiting the activation of the AKT pathway. Conclusions: Our studies suggest that AS could be an ideal adjuvant therapy for attenuating the progression of bone metastasis of BC, since it can directly restrict the growth of tumor, as well as attenuate osteolysis. Full article