Search Results (8,520)

Background: The clinical efficacy of the BCL-2 inhibitor venetoclax in acute myeloid leukemia (AML) is significantly undermined by the frequent emergence of drug resistance, which precipitates disease progression and poor patient outcomes. However, the molecular landscape of this resistance remains insufficiently understood. Methods: To address this, we developed venetoclax-resistant AML cell models and utilized transcriptomic profiling integrated with comprehensive in vitro and in vivo functional assays. Results: Resistant cells demonstrated sustained proliferation even under the suppression of BCL-2, MCL-1, and key intrinsic apoptotic markers, including cleaved PARP and caspase-9, indicating a bypass mechanism independent of classical BCL-2 signaling. Compared to their sensitive counterparts, resistant Kasumi-1 (VENK) and MV4-11 (VENM) cells exhibit aggressive growth phenotypes in vitro and in vivo, characterized by larger, more numerous spheroids and colonies, alongside heightened tumorigenicity in murine models. Transcriptomic profiling and KEGG analysis identified the neuroactive ligand–receptor interaction (NLRI) pathway as a significant signaling node shared between these resistant lines. While multiple NLRI-associated genes were altered, CHRNB4 was consistently and significantly downregulated in both VENK and VENM cells and tumors. Re-expression of CHRNB4 in resistant cells, a primary gain-of-function approach, significantly impaired colony formation, and tumor growth in vivo. Clinically, CHRNB4 downregulation correlates with shortened overall survival and diminished response to venetoclax. Conclusions: Our findings implicate the NLRI pathway in venetoclax resistance and identify CHRNB4 as a robust prognostic indicator and a promising therapeutic target for developing next-generation AML strategies. Full article

The emergence of variant strains of Avian orthoreovirus (ARV) has caused substantial economic losses in the poultry industry worldwide, but the molecular features of goose-origin strains and viral transmission among different avian species remain poorly understood. Here, we describe a goose-origin avian orthoreovirus strain, SD0407, associated with growth retardation and joint swelling. Complete genome analysis identified ten double-stranded RNA segments. Sequence comparison indicated that SD0407 is closely related to previously reported duck-origin reovirus strains. Phylogenetic and recombination analyses showed that most segments clustered with duck-origin strains, indicating close genetic relatedness among waterfowl-origin orthoreoviruses. Sequence and structural analysis of the σC attachment protein revealed ten unique amino acid substitutions, including D250 within the DE-loop region involved in receptor-binding. Molecular docking suggested that σC interacts with the conserved AnxA2-S100A10 heterotetrameric receptor complex, providing a possible structural basis for receptor compatibility across avian species. Although SD0407 replicated efficiently in goose embryo fibroblasts, it did not induce expression of type I, II or III interferons. Transcriptome profiling revealed weak activation of innate immune signaling and downregulation of metabolic and cytoskeletal genes, consistent with effective suppression of antiviral responses. These findings demonstrate that SD0407 combines structural variability with immune evasion to enhance host adaptability and underscore the importance of sustained ARV surveillance in waterfowl populations. Full article

The human microbiome influences health and disease through diverse biochemical and functional outputs (e.g., enzymes, structural proteins, metabolites, and other cellular components) that affect nearly every aspect of human physiology. Metatranscriptomics (MT), an unbiased RNA sequencing approach, is a high-throughput and high-content method that quantifies both gut microbial taxonomy and active biochemical functions. Because microbial community composition and gene expression are dynamic, understanding temporal variation in the gut metatranscriptome across multiple time scales is essential. Here, we report the temporal dynamics of gut microbiome species and functions using a large cohort (n = 6157) with a clinically validated stool MT test. We quantified microbiome stability from hours to years and assessed taxonomic and functional resilience to major luminal perturbations, such as colonoscopy bowel preparation. Longitudinal analyses of samples collected within the same day, and across days, weeks, months, and years, revealed consistently high stability in both composition and gene expression within a single day and, importantly, across an approximate six-month period. Among individuals reporting stable diets and no antibiotic exposure, taxonomic and functional profiles remained stable for up to three years. Following colonoscopy preparation, our preliminary study of the microbiome demonstrated strong resilience, returning to its pre-procedure state within one week. Overall, these findings demonstrate that the gut microbiome is generally stable over a six-month time frame, with longer-term changes occurring gradually. These findings support the robustness of stool-based MT profiling for species-level and pathway-resolved functional analysis in longitudinal research and health applications. Full article

Transcriptome profiling is a cornerstone of functional genomics, enabling the detailed characterization of gene expression in health and disease. Bulk RNA sequencing (bulk RNAseq) remains the most widely used approach in clinical and large-cohort studies due to its cost-effectiveness, robustness, and comprehensive transcriptome coverage. However, bulk RNAseq inherently averages gene expression signals across heterogeneous cell populations, thereby masking cellular diversity and obscuring rare cell types. In contrast, single-cell RNA sequencing (scRNAseq) enables a high-resolution analysis of cellular heterogeneity, allowing the identification of distinct cell types, transitional states, and developmental trajectories. Nevertheless, scRNAseq is associated with higher cost, limited scalability, increased technical noise, sparse expression matrices, and protocol-dependent biases introduced during tissue dissociation or nuclear isolation. In this review, we summarize the conceptual and methodological foundations of integrating bulk RNAseq and scRNAseq data, emphasizing their complementary strengths and limitations. We discuss how scRNAseq-derived cell-type atlases can serve as reference matrices for computational reconstruction (deconvolution) of bulk RNAseq profiles and examine key sources of technical and biological variability. Furthermore, we outline major integration strategies, including reference-based deconvolution, pseudobulk aggregation, and Bayesian joint modeling to provide an overview of widely used analytical tools and essential components of scRNAseq data processing workflows. Full article

The SHAGGY-like kinase (SK) gene family regulates diverse developmental and abiotic stress response processes in plants. Although genome-wide analyses of SKs have been conducted in model plants such as Arabidopsis thaliana and rice, their characterization in the economically important crop Brassica rapa remains limited. In this study, we conducted a systematic genome-wide analysis of SK genes in three Brassica species. A total of 18, 16, and 18 SK members were identified in B. rapa, B. nigra, and B. oleracea, respectively, and phylogenetic analysis classified them into four distinct clades. Expression profiling revealed that BrSKβ-1 and BrSKβ-2 were specifically expressed in fertile floral buds, suggesting their critical roles in pollen development. Furthermore, co-expression analysis indicated that both genes were co-expressed with key regulators involved in pollen development, pollen sperm cell differentiation and pollen tube growth. Loss of BrSKβ-2 via CRISPR/Cas9 resulted in 25–65% pollen abnormality and reduced the germination rate of normal-appearing pollen to only 10%, confirming its essential role in male fertility. Together, these findings provide a comprehensive characterization of the SK gene family in Brassica and position BrSKβ-2 as a promising candidate for gene editing-based male sterility systems in B. rapa and related crops. Full article

Objectives: The objective of the study was to investigate the mRNA expression of critical gene patterns, including IL-6, CCL2, IL-10, MAPK1, MAPK8, MMP9, COL1A1, COL3A1, and TGFB1, and their associations with adverse postoperative outcomes in reconstructive and plastic surgery patients, depending on age. Methods: A total of 95 women participated in this prospective longitudinal cohort study and underwent reconstructive/plastic surgery. The mean age was 35.48 ± 6.61 years (range: 19–57). mRNA expression of IL-6, CCL2, IL-10, MAPK1, MAPK8, MMP9, COL1A1, COL3A1, and TGFB1 genes was evaluated in peripheral blood leukocytes using a PCR-based method with reverse transcription of cDNA. Results: The risk of postoperative complications significantly increased with elevated expression levels of IL-6 and COL3A1 (7.5-fold, p = 0.007), CCL2 (6.2-fold, p = 0.012), and MAPK1 (25.5-fold, p < 0.001). Increased expression of MAPK8, IL-10, and MMP9 was associated with a 13.2-fold higher risk (p < 0.001). The strongest association was observed for COL1A1 overexpression, which increased complication risk by 58.33-fold (p < 0.001). Risk stratification using the Molecular Complication Risk Index (MCRI), incorporating weighted gene contributions, identified an unfavorable molecular profile predominantly among women aged ≥ 40 years. Receiver operating characteristic analysis confirmed the model’s discriminative ability (AUC = 0.78; 95% CI 0.68–0.87), with an optimal cut-off value of MCRI ≥ 8.5 (sensitivity 76%, specificity 71%, p < 0.05). Conclusions: The transcriptional activity of IL-6, CCL2, IL-10, MAPK1, MAPK8, MMP9, COL1A1, COL3A1, and TGFB1 is associated with postoperative wound healing risk. Women aged over 40 years are at the highest risk of complications. Implementation of the MCRI model may enable early identification of high-risk patients, support targeted preventive strategies, and improve personalized surgical planning. Full article

Urinary microRNAs (miRNAs) are promising noninvasive biomarkers for cancer detection, but their clinical utility is reduced by inconsistent normalization strategies, reducing reproducibility and comparability across studies. In this study, we assessed the stability of miR-20a as an endogenous normalizer for urinary miRNA profiling in clear cell renal cell carcinoma (ccRCC) while standardizing the pre-analytical phase using a urine stabilizing solution. Ninety-nine urine samples were analyzed: 47 from healthy individuals, 30 from ccRCC patients pre-surgery, and 22 post-operative patients. Six candidate miRNAs—miR-20a, miR-15b, miR-16, miR-15a, miR-210-3p, and miR-let-7b—were quantified via RT-qPCR. Stability analysis with RefFinder, integrating multiple algorithms (geNorm, normFinder, BestKeeper, and ΔCt methods), identified miR-20a as the most stable among the six candidates. Raw Ct values of miR-20a were normally distributed (Shapiro–Wilk test, p > 0.05), with no significant intergroup differences (one-way ANOVA, F(2.96) = 2.324, p = 0.103) and minimal intragroup variability (CV% 4.98–6.38). MiR-20a expression remained stable across different tumor staging, grading, and urine storage durations. These findings confirm miR-20a as a robust endogenous normalizer for urinary miRNA analyses and support the feasibility of developing reproducible urinary liquid biopsy workflows for ccRCC, even in settings where immediate sample processing is not feasible. Full article

Obesity is characterized by chronic low-grade inflammation and immunometabolic dysfunction. However, the influence of obesity degree on circulating inflammatory mediators and immune-cell–specific molecular pathways remains poorly defined. We aimed to examine the effects of obesity severity on plasma cytokines and adipokines, and on the expression of inflammatory, antioxidant, and mitochondrial genes in peripheral immune cells, with emphasis on gender differences. In this cross-sectional study, 134 adults aged 55–80 years were stratified into overweight, moderate, or severe obesity groups. Plasma cytokine and adipokine levels were quantified with multiplex immunoassays. Gene expression in peripheral blood mononuclear cells and neutrophils was measured by quantitative PCR. Standard hematological parameters were assessed. Two-way analysis of variance and correlation analyses were performed to evaluate associations between obesity severity, gender, circulating biomarkers, and gene expression. Severity of obesity was associated with distinct alterations in circulating inflammatory profiles in a gender-dependent manner. Women exhibited progressive increases in plasma interleukin (IL)-6 with obesity severity, whereas men with severe obesity demonstrated elevated IL-15 and IL-1rα plasma levels. Hematological responses also differed by gender. In contrast, expression of classical inflammatory genes in immune cells was largely unchanged across obesity categories. Women showed higher expression of antioxidant and mitochondrial genes than men, suggesting gender-specific resilience in redox and mitochondrial pathways. Correlations between circulating inflammatory mediators and immune-cell gene expression were generally weak. Obesity severity and gender modulate systemic inflammatory, while immune-cell transcriptional responses are limited, highlighting the importance of gender-specific immunometabolic characterization in obesity research. Full article

The increasing demand for different value-added products from natural seaweeds requires a sustainable cultivation method for the regular supply of biomass and to safeguard the natural ecosystem from overexploitation. This study evaluated laboratory acclimatization of the green seaweed Acrosiphonia orientalis (DGR: 2.71 ± 0.21%; GPP: 12.55 ± 0.1 mg O₂ L⁻¹ day⁻¹), followed by a comparative evaluation of its physicochemical and biochemical characteristics, metabolite profile, and antiproliferative activity compared with naturally harvested seaweed. Metabolite profiling identified 47 compounds exhibiting differential accumulation patterns, with the natural specimens enriched in omega-3 polyunsaturated fatty acids, including docosahexaenoic acid, and the laboratory-acclimatized specimens exhibited elevated arachidonic acid levels. Amino acid profiling revealed higher concentrations of essential and non-essential amino acids in the natural specimens, with prominent levels of phenylalanine and aspartic acid, while the lab-acclimatized specimens were enriched in isoleucine, methionine, proline, and cysteine. The lab-acclimatized specimens exhibited significantly enhanced water absorption (WSC: 6 ± 0.25 mL/g DW; WHC: 2.68 ± 0.11 g/g DW) and higher total sugar (47.11 ± 0.52% Glc eq. DW) and phenolic contents (51.28 ± 0.54 mg GAE g⁻¹ extract), while the natural specimens had a superior oil-holding capacity (OHC: 1.8 ± 0.12 g/g DW); higher total flavonoid (123.62 ± 2.97 mg Q g⁻¹ extract), protein (5.11 ± 0.36 µg BSA eq/mg DW), and chlorophyll contents (8.82 ± 0.58 mg/L); and higher antioxidant activities (ABTS-EC₅₀: 67.33 ± 0.97 μg/mL extract). The mineral analysis revealed distinct elemental profiles, with enrichment of sodium, magnesium, and calcium in the lab-acclimatized specimens and a more favorable Na/K ratio (0.14 vs. 0.78) in the natural specimens. Of note, extracts from both seaweeds exhibited significant dose-dependent antiproliferative activity against HeLa cervical cancer cells (Wild EC₅₀: 118.63 ± 14.14 µg/mL extract; lab EC₅₀: 153.35 ± 10.18 µg/mL extract), suppressed colony formation in soft agar assays, induced nuclear condensation (based on Hoechst staining), and modulated the expression of key oncogenes (upregulating NDRG1, TP53, and CASP3 and downregulating BCL2, MYC, and CCND1). Collectively, this study provides an approach to acclimatize A. orientalis that may be utilized for developing a cultivation method. Moreover, this green seaweed has a great potential to be used for nutraceutical and functional food applications. Full article

Corolla movement is a typical plant movement behavior that enables plants to optimize pollination and adapt to environmental changes. Nevertheless, its molecular mechanism remains poorly understood. In the present study, we conduct a comprehensive transcriptome analysis of Mirabilis jalapa (Nyctaginaceae) corolla at five stages (AG-EG) to elucidate the regulatory networks underlying movement. The results showed that the differentially expressed genes (DEGs) were mainly associated with cellular processes, catalytic activity, MAPK signaling, plant hormone signal transduction, and photosynthesis-related pathways, highlighting their involvement in corolla dynamics. Transcriptome profiling further demonstrated that auxin, ethylene, and abscisic acid signaling pathways were key hormonal regulators of corolla movement. Moreover, Ca²⁺ transport genes (CNGCs and CMLs) and respiratory burst oxidase homologs (RBOHs) were significantly enriched, indicating that Ca²⁺–ROS signaling oscillations also play an important role in driving differential cell expansion and turgor changes. Transcription factor analysis also revealed the upregulation of WRKY2, WRKY22, and WRKY33, suggesting that WRKYs act as the critical transcriptional regulators linking ROS–Ca²⁺ signals with downstream gene expression. The reliability of RNA-Seq data was confirmed by RT-qPCR, which showed high consistency with transcriptome profiles. These findings suggested that corolla movement in M. jalapa is carried through the integration of hormonal pathways, Ca²⁺–ROS signaling, and WRKY-mediated transcriptional regulation. This research provided novel insights into the molecular basis of plant movement and established a foundation for further study on floral dynamics and adaptive strategies in angiosperms. Full article

Background: Renal allograft rejection remains a major challenge in transplantation. Current diagnostic approaches, including biopsies, are invasive and may fail to detect subclinical immune activation, potentially contributing to progressive graft dysfunction. Reliable, non-invasive biomarkers capable of monitoring immune activation and distinguishing rejection phenotypes are therefore needed. Methods: In this retrospective study, we evaluated serum neopterin as a biomarker of immune activation and graft status over 12 months following transplantation. Associations between neopterin levels and immune parameters, including natural killer (NK)-to-CD3⁺CD16/CD56⁺ T cell ratios, cytokines (IFN-γ and IL-10), and CD4⁺CD25⁺FoxP3⁺ T cell frequencies, were assessed. A total of 211 first renal allograft recipients were followed longitudinally, including patients with acute rejection (AR) and matched stable graft (SG) recipients. Serum neopterin was quantified by enzyme immunoassay, and immunophenotyping, mRNA expression, and cytokine profiling were performed on peripheral blood samples. Results: Serum neopterin levels were significantly elevated in AR compared to SG recipients, with a threshold of 57 nmol/L distinguishing AR with 81% sensitivity and 80% specificity. While IFN-γ demonstrated higher diagnostic performance in cross-sectional analysis, neopterin showed a more sustained elevation over time, remaining increased in AR recipients even at later post-transplant time points. Neopterin correlated positively with IFN-γ, but not IL-10, and inversely with CD4⁺CD25⁺FoxP3⁺ T cell frequency. NK cells were enriched during rejection, whereas CD3⁺CD16/CD56⁺ T cells were more prominent in graft stability. The NK-to-CD3⁺CD16/CD56⁺ T cell ratio was highest during acute cellular rejection. Conclusions: Neopterin reflects Th1-associated immune activation in renal allograft recipients and provides a temporally stable, non-invasive marker of immune status. Although it does not outperform IFN-γ levels at the time of rejection, its stability and sustained elevation suggest a complementary role in longitudinal monitoring. Integration of neopterin with immune parameters, including cytokine profiles and cellular subsets, may enhance the assessment of graft immunological status and support clinical decision-making. Full article

Tyrosinase promotes excessive deposition of melanin, which may lead to severe skin diseases. Passiflora edulis f. edulis seeds have been reported to be rich in diverse bioactive constituents exhibiting potential tyrosinase inhibitory activity. However, the principal bioactive constituents responsible for tyrosinase inhibitory activity and its underlying mechanisms remain largely unclear. Therefore, this study aimed to: (1) optimize SC-CO₂ extraction of Passiflora edulis f. edulis seed oil (PFSO) for maximum yield and bioactive preservation; (2) comprehensively characterize its physicochemical and phytochemical profile; (3) elucidate the tyrosinase inhibition mechanism through kinetic, spectroscopic, and computational approaches; and (4) validate its safety, antioxidant, and anti-pigmentation efficacy in a zebrafish model. PFSO exhibited a yield of 24.96%, with a high content of unsaturated fatty acids (88.03%, mainly linoleic acid at 74.40%). The oil inhibited tyrosinase via a reversible mixed-type mechanism (IC₅₀ = 1.12 mg/mL). Fluorescence spectroscopy and molecular docking revealed that linoleic acid binds to LYS180 and β-sitosterol binds to TYR78, mainly driven by hydrogen bonding and hydrophobic interaction, which changed the microenvironment of tryptophan residues and indicated static quenching. Further validation experiments revealed that the major constituent, linoleic acid, exhibited only weak inhibitory activity against tyrosinase (IC₅₀ = 29.44 mg/mL), whereas the key component β-sitosterol markedly suppressed tyrosinase activity (IC₅₀ = 46.43 μg/mL). In vitro assays demonstrated PFSO’s significant efficacy in reducing the melanin content and tyrosinase activity in α-MSH-stimulated B16F10 murine melanoma cells. In vivo experiments in zebrafish that received dietary supplementation with PFSO confirmed that PFSO (≤5 mg/mL) reduced ROS production, suppressed melanin deposition, inhibited tyrosinase activity, and downregulated the expression of melanogenesis-related genes (TYR, TYRP1, TYRP2, MITF). This study provides, for the first time, a comprehensive elucidation of PFSO’s potential as a natural tyrosinase inhibitor, integrating extraction optimization, multicomponent characterization, multimodal inhibition analysis, and in vivo validation. Full article

Acute heat stress frequently causes mass mortality in farmed red swamp crayfish (Procambarus clarkii), yet the mechanisms underlying immune collapse remain poorly understood. We established an acute heat stress model (37 °C, 6 h) and performed an integrative analysis combining hemocyte profiling, redox and immune assays, RNA-seq, and qRT-PCR. Heat stress significantly increased mortality and disrupted the hemocyte system, with a ~25% reduction in total hemocyte count and a selective decline in granular cells. This was associated with severe redox imbalance, evidenced by ROS/H₂O₂ accumulation, suppressed SOD and CAT activities, and lipid peroxidation damage. Transcriptomic analysis revealed 1446 differentially expressed genes, indicating concurrent activation of ER stress and autophagy alongside suppression of energy metabolism. Key gene validation confirmed upregulation of pro-apoptotic factors (CASP3, P53) and ER stress markers (GRP78, XBP1), consistent with hemocyte depletion. These findings provide multi-level evidence that acute heat stress triggers a redox crisis (“oxidative burst–defense suppression”), which in turn activates ER stress and apoptosis, leading to selective loss of granular cells and systemic immune compromise. This study establishes a mechanistic framework for understanding heat-induced mortality in crustaceans and offers a theoretical basis for developing targeted interventions to enhance thermal resilience in crayfish aquaculture. Full article

Alveolar macrophages (AMs) play essential roles in maintaining homeostasis and immunity in the lung. The transcription factor PU.1, encoded by SPI1, is a core regulator in multiple immune cell lineages. However, its binding property and regulatory role in AMs remain unclear. The pig serves as an important livestock species and a valuable biomedical model. Using porcine AMs (PAMs) as a model, we combined gene knockdown experiments with multiomic profiling to elucidate the regulatory role of PU.1 in AMs. By integrating the RNA-seq data before and after SPI1 knockdown, we demonstrate that disruption of PU.1 impairs the expression of numerous immune-related genes, including many crucial for innate immune responses. We further employed CUT&Tag to characterize the genome-wide occupancy of PU.1 and the active histone modification H3K27ac, and found that PU.1 primarily binds active cis-regulatory elements (CREs), including a large proportion of enhancers derived from transposable elements. Moreover, integrative analysis identifies a set of CREs and their associated genes, which are putative direct targets of PU.1. Overall, this study provides novel insights into the regulatory role of PU.1 in AMs and extends our knowledge about this core regulator in the mammalian immune system. Full article

Background: PYR/PYL/RCAR proteins are core abscisic acid (ABA) receptors that play essential roles in ABA signal transduction, plant growth and development, and abiotic stress responses. However, the PYL gene family in watermelon (Citrullus lanatus) has not been systematically characterized, limiting our understanding of ABA-mediated stress adaptation in this economically important crop. Methods: A genome-wide analysis was performed to identify ClPYL genes in watermelon using a hidden Markov model search. Phylogenetic relationships were reconstructed using the maximum likelihood method. Segmental duplication events were analyzed using synteny analysis. Conserved motifs, gene structures, and promoter cis-acting elements were characterized using MEME and PlantCARE. Expression profiles under drought, salt, and cold stresses were examined by quantitative real-time PCR (qRT-PCR) with three biological replicates. Results: In this study, 15 ClPYL genes were identified in watermelon through genome-wide analysis. Phylogenetic reconstruction classified these genes into four subfamilies, with subfamily II being exclusively present in cucurbits—a lineage-specific feature not observed in Arabidopsis. Synteny analysis revealed eight segmental duplication events involving members of subfamilies I, III, and IV, while subfamily II members were not associated with these duplications. Members within the same subfamily share similar exon-intron structures and conserved motifs. Promoter analysis revealed that ClPYL genes are enriched with various cis-acting elements associated with hormone signaling and abiotic stress responses. Expression profiling demonstrated that ClPYL genes exhibit diverse and dynamic expression patterns under drought, high-salinity, and cold stresses. Notably, genes such as ClPYL5 under drought, ClPYL02 under salt, and ClPYL15 under cold stress displayed persistent stress-responsive expression. Conclusions: These findings reveal the evolutionary conservation and diversification of the PYL family in watermelon and provide a set of candidate genes for functional studies aimed at dissecting ABA-mediated stress adaptation. This work establishes a genomic framework for developing stress-resilient watermelon varieties through molecular breeding. Full article