Search Results (8,748)

Breast cancer is a leading cause of cancer-related mortality in women, necessitating new treatment strategies. Curcumin (Cur), a natural polyphenol, and gemcitabine (Gem), a standard chemotherapeutic, were investigated for their combined anticancer effects. We hypothesized that Cur sensitizes breast cancer cells to Gem via reactive oxygen species (ROS)-mediated apoptosis, and that this effect is associated with selective oxidative vulnerability in malignant cells compared to normal breast epithelial cells. MCF-7 (hormone receptor-positive) and MDA-MB-231 (triple-negative) cells were treated with Cur and Gem alone or in combination. Normal breast epithelial MCF-10A cells were included to evaluate therapeutic selectivity. Cell viability (MTT), apoptosis (Annexin V/PI), oxidative stress (TOS/TAS), intracellular ROS generation (DCFH-DA assay), mitochondrial membrane potential (ΔΨm) (JC-1 staining), caspase activation, synergy (Bliss/HSA/Chou-Talalay), VEGF secretion (ELISA), and transcriptomic changes (RNA-Seq) were assessed. Cur and Gem showed dose-dependent cytotoxicity. Combination treatment demonstrated strong synergistic activity, significantly enhancing apoptosis, oxidative stress, and caspase activation. Direct quantification of intracellular ROS revealed marked ROS accumulation in MCF-7 and MDA-MB-231 cells following combination treatment, whereas MCF-10A cells exhibited only modest oxidative changes. JC-1 analysis demonstrated substantial mitochondrial depolarization in breast cancer cells, which was largely reversible by ROS scavenging and minimal in MCF-10A cells. VEGF secretion was markedly suppressed. Transcriptomic analysis revealed profound alterations in apoptosis, cell cycle, and angiogenesis-related pathways, with more pronounced transcriptional reprogramming observed in the triple-negative subtype. Cur synergistically enhances Gem’s efficacy in breast cancer cells through ROS-mediated apoptosis and anti-angiogenic effects, characterized by cancer-selective ROS amplification and mitochondrial membrane depolarization, supporting its potential as a combination therapy, particularly for triple-negative breast cancer. Full article

Background/Objectives: Bacterial biofilms are structured communities of sessile cells embedded in a self-produced extracellular matrix. Within biofilms, bacteria become highly tolerant toenvironmental stressors such as host immune responses and antimicrobial treatments. In response to specific cues, however, biofilm cells can revert to a planktonic free-swimming lifestyle through a process termed biofilm dispersal. When dispersed cells escape the biofilm matrix, they lose biofilm-associated antibiotic tolerance, a major barrier to treating medical biofilms. As such, dispersal-inducing compounds like nitric oxide (NO) are actively investigated as adjuvants to potentiate the biofilm-eradicating activity of existing antibiotics. We recently characterised the transcriptomic responses elicited during spontaneous biofilm dispersal in closed culture-grown Pseudomonas aeruginosa biofilms. Here, we evaluated the transcriptional profiles of P. aeruginosa biofilms treated with the NO donor Spermine-NONOate (SP-NONO) and the nitroxide C-TEMPO, an NO analogue, to determine potential pathways involved in NO-mediated dispersal. Methods: Dispersal activity on P. aeruginosa PAO1 biofilms by SP-NONOate and C-TEMPO was quantified by crystal violet staining. Cellular responses to each compound were profiled by RNA-seq on treated and untreated cells. Results: While both compounds disrupted the transcription of ANR-regulated energy metabolism pathways, only SP-NONO activated canonical NO-regulated responses. Considering that only SP-NONO showed biofilm dispersal activity in this culture system, we investigated shared transcriptional shifts in SP-NONO-treated and spontaneously dispersed biofilms to identify pathways likely involved in central dispersal responses. These mostly included genes involved in the catabolism of branched-chain amino acids (leucine, valine, isoleucine) and lysine, as well as 9 of 14 genes previously defined as transcriptional biomarkers of spontaneous biofilm dispersal. Conclusions: This study suggests that NO disrupts biofilm maturation by prematurely stimulating central pathways of spontaneous biofilm dispersal and highlights this set of biomarkers as robust indicators of dispersal responses. Full article

The TIFY family, known as a novel group of transcription factors unique to the plant, plays a number of roles and has been functionally characterized in numerous plant species. However, TIFY proteins remain unexplored in litchi. Here, we identified 14 TIFY genes in litchi, which were unevenly located on 8 of 15 chromosomes. All of the LcTIFY proteins were predicted to be nuclear-localized and were phylogenetically categorized into four subfamilies (TIFY, PPD, ZML, and JAZ). Duplication analysis detected no tandem duplications but identified one segmental duplication event with LcTIFY genes, suggesting that segmental duplication served as the primary driving force for the expansion of LcTIFY genes. Comparative collinear analysis revealed 12, 5, and 27 collinear gene pairs between litchi and Arabidopsis, rice, and apple, respectively, providing valuable clues for understanding the evolution of the LcTIFY genes. RNA-Seq and qRT-PCR analyses indicated tissue-preferential expression patterns among LcTIFY genes. Notably, LcPPD1 and LcJAZ5 expressions were negatively correlated with anthocyanin accumulation in the ‘Feizixiao’ variety, except that LcJAZ5 displayed a positive correlation under CPPU treatment. In contrast, LcJAZ7 expression showed a positive correlation across all treatments, implicating these genes in the regulation of pericarp pigmentation. Collectively, these findings lay the groundwork for future investigations into the functional roles of TIFY genes in litchi and offer valuable genetic resources for elucidating the mechanisms underlying litchi pigmentation, thereby providing fresh perspectives for subsequent research into the molecular mechanisms of color formation in plants. Full article

Aspergillus flavus infection and accumulation of carcinogenic aflatoxins are detrimental to maize (Zea mays) production and consumption. We investigated lncRNA–RBP interactions during maize–A. flavus crosstalk using transcriptomic profiling, structural analysis, molecular docking simulations, and machine learning approaches. Analysis of 18 RNA-seq datasets identified 2104 lncRNAs in maize, of which 461 were differentially expressed under A. flavus infection. Distinct lncRNAs were preferentially induced under infection (e.g., Zm00001eb303170) or normal germination (e.g., Zm00001eb144150, Zm00001eb406410). RNA secondary structure predictions indicated high structural heterogeneity and thermodynamic stability, consistent with dynamic regulatory potential. Docking simulations with six key RNA binding proteins (RBPs)—including branch point bridging protein (BPB), KH domain protein, and pentatricopeptide repeat (PPR) proteins—demonstrated strong lncRNA–protein binding, with the lncRNA1–BPB complex exhibiting the highest binding affinity. ML algorithms identified the crucial role of tryptophan in determining interactions, while lncRNA17-KH and lncRNA1-BP complexes were found to have the best interaction under normal germination and A. flavus infection, respectively. The lncRNA–miRNA–mRNA regulatory network highlighted lncRNAs functioning as decoys or precursors of stress-responsive miRNAs (e.g., zma-miR156, zma-miR164, zma-miR399). These interactions targeted transcriptional regulators, splicing factors, and metabolic enzymes implicated in stress tolerance, seed germination, and systemic acquired resistance. The maize lncRNAs are active regulatory molecules embedded in complex RBP and miRNA interaction networks that fine-tune gene expression during A. flavus infection. The study provides novel insights into lncRNA-mediated resistance mechanisms and offers potential molecular targets for breeding or gene editing to mitigate aflatoxin contamination. Full article

Members of the genus Streptomyces are prominent inhabitants of the plant rhizosphere and endosphere and are increasingly recognized for their roles in plant growth promotion and disease suppression. In this study, we isolated genetically distinct Streptomyces from the tomato (Solanum lycopersicum L.) rhizosphere, designated as TOM isolates, and assembled them into a defined 12-member TOM consortium. Application of the TOM consortium significantly promoted root and shoot growth in tomato. RNA-seq analysis revealed coordinated local and systemic transcriptional responses characterized by a predominance of down-regulated genes in both roots and leaves. In roots, differential gene expression reflected selective attenuation of defense- and cell wall-related processes, alongside increased expression of genes associated with phytoalexin biosynthesis, phosphate starvation responses, and hormonal regulation. In leaves, transcriptional reprogramming was dominated by reduced stress-related responses together with activation of metabolic and growth-associated functions. The TOM consortium also reduced disease severity caused by Fusarium oxysporum f. sp. radicis-lycopersici by approximately 60% compared to infected controls. To further characterize functional traits of individual consortium members, isolates were evaluated in vitro for antifungal activity and five strains displaying inhibition were selected for hybrid whole-genome sequencing. Genome analyses revealed diverse taxonomic affiliations and a rich repertoire of biosynthetic gene clusters, including clusters associated with known antimicrobial metabolites as well as numerous low-similarity clusters indicative of substantial unexplored biosynthetic potential. Collectively, this study provides new insights into plant interactions with beneficial Streptomyces, while revealing molecular signatures involved in Streptomyces-mediated plant growth promotion and pathogen suppression. Full article

Zinc finger proteins (ZFPs) are a diverse group of plant transcription factors essential for regulating development, signaling, and stress responses. In this study, we performed a genome-wide identification and integrative analysis of 140 C3H-type zinc finger transcription factor genes in the soybean genome, exhibiting an uneven distribution across all 20 chromosomes. These C3H-ZFPs contained one (37), two (58), three (19), four (7), five (17), or six (2) C3H domains and were classified into 14 subsets based on their domain architecture. All C3H genes encoding proteins harbored the conserved C3H-ZFP domain and displayed various physicochemical characteristics. Phylogenetic analysis grouped them into 10 clades, closely related to other species like Arabidopsis, rice and alfalfa. Promoter analysis revealed cis-elements associated with stress response (~39.1%), light response (~37.3%), phytohormones (~18.5%), and development (~4.97%). Duplication analysis revealed 78 pairs of segmental and eight tandem duplication events, with purifying selection indicated by Ka/Ks (nonsynonymous/synonymous) ratios, indicating that these C3H-ZFP duplicates were largely maintained under purifying selection. A total of 388 miRNAs from 196 gene families were predicted to target 140 C3H-ZFP genes, with most enriched miRNAs targeting C3H-ZFP genes, including the miR156, miR395, and miR396 families. Transcription factor binding sites for MYB, AP2, MIKC_MADS, BBR-BPC, ERF, C2H2, and Dof were found upstream of most C3H-ZFP genes. RNA-Seq and qRT-PCR analyses showed tissue-specific expression and stress-responsive expression patterns, with several C3H-ZFP genes, especially GmC3H1, GmC3H63, GmC3H124, and GmC3H127, being significantly upregulated under abiotic stress conditions. Together, these results provide a comprehensive overview of soybean C3H-ZFP genes and identify promising candidates for future functional studies on development and abiotic stress adaptation. Full article

Background: The principal glial cells of the retina, Müller glia, play a central role in retinal regeneration in teleost fish and have recently attracted attention as potential sources of neuronal regeneration in mammals. Objectives: In this study, we examined whether SV40-immortalized rat Müller glia could be directed toward neuronal differentiation using a non-genetic approach with defined culture conditions. Methods: Comprehensive transcriptomic profiling by RNA sequencing indicated that changes in culture medium alone could induce transcriptional reprogramming toward a neuronal lineage. Results: Specifically, expression of Müller glia-related genes decreased, while a subset of photoreceptor-related transcription factors and specific genes showed altered expression, suggesting early-stage induction toward a photoreceptor-like fate. This finding suggests that even immortalized cells may exhibit activation of neuronal genes through non-genetic culture interventions. Gene set enrichment analysis further revealed upregulation of pathways related to the synaptic vesicle cycle, metabolic activation, oxidative stress defense, and lysosomal function, consistent with initiation of neuronal differentiation. Conversely, pathways associated with cell cycle regulation and stemness signaling were downregulated, reflecting a transition from a proliferative to a differentiation-prone state. Collectively, these results provide preliminary molecular markers for early neuronal induction and potential targets for chemical screening. Conclusions: Importantly, this strategy enables neuronal-like differentiation of Müller glia without genetic manipulation, offering a safe and cost-effective platform. Overall, our findings may support the development of in vitro models for retinal neuroregeneration and facilitate research toward regenerative therapies for retinal disorders. Full article

The cultivated chrysanthemum is the most important ornamental species in the genus Chrysanthemum. However, because it is predominantly hexaploid and additionally exhibits self-incompatibility, it harbors numerous functionally redundant genes and displays extremely high heterozygosity. As a result, its genomic architecture is highly complex, making it challenging to interpret data obtained from omics analyses such as RNA-seq. To provide a genetically tractable model, we previously developed Gojo-0, a self-compatible, pure line of the diploid wild species C. seticuspe. In this study, we established Gojo-1, an improved self-compatible pure line derived from Gojo-0 and its sibling lines, exhibiting enhanced viability and culture performance. Leveraging these traits, we performed CRISPR–Cas9 editing of the AGAMOUS orthologs and successfully isolated mutants with altered floral organ morphology, demonstrating the line’s suitability for functional genomics. Comparative genome analysis showed that, aside from chromosome 1, the Gojo-1 genome is highly similar to that of Gojo-0, whose complete sequence has been determined. Taken together, these features indicate that Gojo-1 will serve as a valuable resource for future omics-based studies and a broad range of additional research applications. Full article

Goat reproductive performance is a key determinant of the productivity and economic value of goat farming, especially in meat and milk production. In a previous study, to investigate the genetic basis of prolificacy, we divided goats into groups according to their consistent reproductive performance (producing either single kids or twins) over five consecutive kidding cycles, and performed whole-genome resequencing and RNA-seq analysis on their ovarian tissues. Through integrated analysis, we identified three candidate genes—IGF2BP1 (insulin-like growth factor 2 mRNA-binding protein 1), CDC25A (cell division cycle 25A), and RXFP2 (relaxin family peptide receptor 2)—as potential key regulators of reproductive capacity. Using goat ovarian granulosa cells, we systematically assessed the impact of each gene through gain- and loss-of-function experiments. Overexpression of IGF2BP1 promoted cell proliferation and suppressed apoptosis, underscoring its role in maintaining cellular viability. Conversely, its knockdown significantly impeded growth and induced cell death. Similarly, CDC25A enhanced granulosa cell proliferation, whereas its knockdown led to marked growth impairment and increased apoptosis. Proliferation was also enhanced by RXFP2 overexpression but impaired upon its knockdown, suggesting that RXFP2 is functionally important for follicular development. Collectively, these findings establish IGF2BP1, CDC25A, and RXFP2 as fundamental regulators of granulosa cell dynamics and ovarian follicular development, providing crucial functional insights and promising targets for genetic selection to enhance reproductive efficiency in goats. Full article

Pharmacological activation of brain Retinoid X Receptors (RXRs) enhances cognition and facilitates amyloid-beta (Aβ) clearance in Alzheimer’s disease (AD) mouse models, partly by upregulating apolipoprotein E (Apoe), a major AD genetic risk factor. However, the specific cellular contributions to these effects are unclear. Here, we used single-cell transcriptomic profiling to investigate cell subpopulation-specific responses to bexarotene, an RXR agonist, in APP/PS1 mice. Our analysis revealed that bexarotene activated cholesterol biosynthesis and lipid metabolism transcriptional programs in homeostatic astrocytes and oligodendrocytes. Astrocytes also upregulated neurodevelopmental genes, while oligodendrocytes and endothelial cells showed enhanced protein folding and cellular growth pathways. Bexarotene further modulated immune responses, promoting Aβ-responsive signatures in disease-associated microglia and reactive astrocytes while dampening pro-inflammatory responses in homeostatic microglia and endothelial cells. Furthermore, Apoe expression was significantly elevated across multiple cell types, especially in microglia and oligodendrocytes. Cell–cell communication analysis highlighted increased astrocyte-centered signaling, with APOE-driven pathways emerging as a prominent mediator. These findings clarify the molecular complexity of RXR-mediated regulation, revealing the cellular origins of bexarotene’s known effects as well as novel, cell-type-specific responses. This study provides mechanistic insights into RXR-targeted interventions and supports APOE-associated pathways as promising therapeutic targets in AD. Full article

Soybean is a critical oil and protein crop for both food and forage production; however, its growth and development are severely impacted by drought stress. Nevertheless, the molecular regulatory mechanisms underlying drought tolerance in soybean remain poorly understood. In this study, two soybean varieties, Jindou 21 (JD21, drought-tolerant) and Suinong 26 (SN26, drought-sensitive), were used as experimental materials and subjected to 15% PEG6000 to simulate drought stress. Roots and leaves were sampled at 0 h, 6 h, and 12 h after treatment to determine physiological indicators and conduct RNA-seq analysis. The results showed that JD21 exhibited a lower malondialdehyde (MDA) content but higher soluble sugar and proline contents than SN26. A total of 2603 and 3128 osmotic-stress-responsive genes were identified in the roots and leaves of SN26 and JD21, respectively. Additionally, 256 genes in the roots and 215 genes in the leaves showed consistent differential expression between the two varieties across the three treatment time points. KEGG enrichment analysis revealed that the differentially expressed genes were significantly enriched in pathways related to glutathione metabolism, arginine and proline metabolism, glycolysis/gluconeogenesis, and starch and sucrose metabolism. Within these pathways, the functions of GmGST, GmAMD1, GmADH1, GmENO, GmsacA, and GmSUS3 were validated through transgenic hairy root assays, demonstrating that these genes play positive regulatory roles in osmotic stress response. This study provides valuable data for elucidating plant PEG-induced osmotic-stress-response mechanisms and offers theoretical support for drought-resistant soybean breeding. Full article

Background/Objectives: HPV status is a key prognostic determinant in head and neck squamous cell carcinoma (HNSCC), yet the immunological mechanisms underlying the survival advantage of HPV-positive (HPV⁺) over HPV-negative (HPV⁻) disease remain poorly defined. This study aimed to characterize the tumor-infiltrating natural killer (NK) cell landscape in HPV-stratified HNSCC and identify novel therapeutic targets. Methods: We performed an NK-cell-centric re-analysis of published scRNA-seq data from 28 HNSCC patients (10 HPV⁺, 18 HPV⁻; GEO: GSE139324, GSE164690), encompassing NK subset identification, pseudotime trajectory inference, and cell–cell interaction analysis. Key findings were validated by immunohistochemistry (IHC) in an independent cohort of 10 FFPE tissue sections, and prognostic associations were assessed using TCGA-HNSC data. Results: Four transcriptionally distinct NK cell subsets were identified: adaptive, cell-killing, CD56^bright, and virus-responsive. A cytotoxic CX3CR1⁺KLRB1^dim NK subset was specifically enriched in HPV⁺ tumors and independently associated with favorable survival. Conversely, HPV⁻ tumors upregulated CLEC2C and CLEC2D ligands on tumor cell surfaces, engaging the inhibitory receptor KLRB1 on NK cells; this CLEC2–KLRB1 axis correlated with suppressed NK activity and poorer prognosis, and was confirmed at the protein level by IHC. Conclusions: NK cell function in HNSCC is dichotomously regulated by HPV status. The CX3CR1⁺KLRB1^dim subset represents a candidate prognostic biomarker in HPV⁺ disease, and the CLEC2–KLRB1 axis is a targetable immune evasion mechanism in HPV⁻ HNSCC. These insights support the development of HPV-stratified immunotherapies; however, clinical translation requires validation in large, prospectively designed, subsite-matched cohorts to disentangle HPV-specific effects from anatomical site-dependent immune contextures. Full article

Background: Cholangiocarcinoma (CCA) is a highly heterogeneous malignancy in which numerous biomarker candidates have been reported, yet few progress to clinical use. Beyond biological complexity, this low translational yield reflects the lack of systematic criteria for prioritizing biomarkers during the discovery stage. In particular, tumor-derived signals identified in tissue often fail to persist in clinically accessible biofluids, as cross-compartment signal behavior is rarely evaluated explicitly. Methods: We developed an extracellular vesicle (EV)-guided, multi-compartment proof-of-concept framework to assess biomarker robustness and translatability early in discovery. EV proteomes from three biologically distinct CCA cell lines and a normal cholangiocyte were analyzed using multivariate and machine-learning-assisted approaches to identify conserved EV-associated features. These were integrated with public transcriptomic, epigenetic, copy-number, promoter usage, and miRNA regulatory data. Tissue relevance was assessed using TCGA/GTEx RNA-seq datasets, and exploratory signal behavior was examined in pooled serum- and urine-derived EVs from CCA patients and controls. Results: EV proteomics revealed marked molecular heterogeneity across CCA models but identified a small subset of conserved EV-associated proteins. SERPINF2 was used as a representative example, showing consistently reduced EV-associated abundance across all CCA models with coordinated regulation across multiple molecular layers. SERPINF2 expression was independent of patient sex and tumor stage and clearly distinguished tumor from normal bile duct tissue. Exploratory biofluid analyses demonstrated compartment-dependent signal behavior, with SERPINF2 depletion detectable in urine-derived EVs but not in serum-derived EVs. Conclusions: Rather than validating a single biomarker, this study presents an EV-guided, multi-compartment framework for prioritizing biomarker candidates at the discovery stage. By explicitly accounting for tumor heterogeneity and compartment-specific signal preservation, this proof-of-concept approach provides a practical decision-support strategy for identifying biomarkers with greater translational potential in heterogeneous cancers such as CCA. Full article

Bovine mastitis threatens the dairy industry with limited effective therapies. The selenoprotein family offers potential anti-inflammatory interventions, yet the role of Selenoprotein F (SELENOF) remains unclear. This study investigated SELENOF in mitochondrial damage and pyroptosis using clinical mammary biopsies and a Staphylococcus aureus-induced Mammary alveolar cell-type T (MAC-T) cell model. Histology, TEM, immunofluorescence, Western blot, qPCR, RNA-seq, and mitochondrial staining (MitoTracker Red and JC-1) were employed. Mastitic mammary tissue exhibited severe architectural disruption, including focal necrosis with coalescing vacuoles of variable size, extensive epithelial denudation, and interstitial thickening with dense inflammatory infiltrates. At the ultrastructural level, mitochondrial swelling, cristae loss, and plasma membrane rupture were evident. Additionally, these tissue specimens exhibited marked upregulation of inflammatory mediator transcripts, notably IL-1β, IL-6, and TNF-α, alongside heightened abundance of pyroptosis-associated proteins including NOD-like receptor family pyrin domain containing 3 (NLRP3), cleaved caspase-1, and GSDMD-N (Gasdermin D N-terminal domain). RNA-seq identified SELENOF as significantly downregulated. The MAC-T model recapitulated the mitochondrial dysfunction, inflammatory response, and pyroptosis observed in mastitic tissue. SELENOF overexpression restored mitochondrial membrane potential, dampened the output of inflammatory signaling molecules, and suppressed NLRP3-mediated pyroptosis via attenuation of caspase-1/GSDMD-N pathway activation. These findings establish SELENOF as a novel target that mitigates bovine mastitis by preserving mitochondrial homeostasis and suppressing NLRP3-mediated pyroptosis. Full article

Background: The reproductive cycle of Octopus mimus is regulated by environmental and hormonal factors, with photoperiod playing a key role in spawning induction and reproductive maturation. Understanding its underlying molecular mechanisms is essential for developing strategies to enhance controlled reproduction in aquaculture. Methods: We analyzed the expression of genes involved in the photoperiod-activated spawning induction cascade in the optic lobe and its downstream effects on the oviducal gland by performing transcriptomic analyses on females exposed to continuous light (24:0), which inhibits reproductive development, and a natural photoperiod, which induces spawning. The mRNA sequencing (RNA-Seq), quality control, gene annotation, and differential expression analyses were conducted using edgeR. Results: Spawning was completely inhibited under constant light, while 80% of control females spawned. Expression profiling revealed 89 downregulated and 34 upregulated genes in the optic lobe, and 178 downregulated and 237 upregulated genes in the oviducal gland (FDR < 0.05, |log2FC| ≥ 2), including key orthologs such as FMRFamide and myomodulin. Conclusions: These results show that the optic lobe integrates photoperiodic cues that modulate reproductive activation via a neuroendocrine cascade and coordinates spawning regulation through the oviducal gland, providing insights for improving reproductive control in aquaculture systems. Full article