Search Results (815)

Euonymus bungeanus is a highly valued ornamental tree/shrub species widely utilized in landscaping and afforestation in Northeast Asia, yet molecular studies on this species remain limited due to the lack of validated reference genes for reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR). In this study, 16 candidate reference genes were selected based on classical plant reference genes and our previous transcriptome data. Their expression stability was comprehensively evaluated using 64 samples collected from diverse tissues and plants subjected to various abiotic stress/hormone treatments across multiple time points. Across all samples analyzed, PBG1 (20S proteasome beta subunit G1) exhibited the highest overall expression stability, followed by VAPD (vacuolar ATP synthase subunit D) and EIF4A (eukaryotic translation initiation factor 4A). For tissue-specific analysis, TSR2 (pre-rRNA-processing protein), VAPD, and PBG1 demonstrated the greatest stability. Under specific stress conditions, PBG1 and EIF4A were identified as the most stable genes under low- and high-temperature conditions. PP2A (protein phosphatase 2A) and TUB6 (beta-6 tubulin) were optimal for drought stress, while TSR2, SRP (nuclear speckle splicing regulatory-like protein), and PBG1 exhibited superior stability under salt stress. These findings establish a validated panel of reference genes enabling accurate and reliable gene expression normalization in E. bungeanus, thereby facilitating future functional genomics studies in this economically and ecologically important species. Full article

Peripartum cardiomyopathy (PPCM) is a pregnancy-associated form of systolic heart failure that develops when hemodynamic, metabolic, and hormonal stress of late gestation exceeds maternal cardiac adaptive capacity. While vascular, inflammatory, and genetic contributions have been implicated in PPCM, the integrated molecular programs connecting pregnancy-related stress to cardiomyocyte failure remain poorly defined. To elucidate these mechanisms, we performed a transcriptome-wide RNA seq of left ventricles from females with PPCM and non-failing female normal donor controls. Differential expression analysis identified 2891 genes with altered expressions (1491 upregulated, 1400 downregulated; fold change ≥ 2, FDR < 0.05). Ingenuity pathway analysis (IPA) revealed the activation of protein ubiquitination pathways, EIF2 signaling, mitochondrial dysfunction, and apoptosis pathways. Upstream regulator analysis indicated the suppression of mitochondrial protease CLPP (Z = −4.075) and activation of COPS5 (Z = +5.982) and TEAD1 (Z = +5.00), delineating dual regulatory modules of disease remodeling. Integrated network analysis demonstrated a loss of protein quality control and survival signaling with the activation of stress response and translational repression programs. This signifies a collapse of proteostasis and maladaptive adaptation. Collectively, these data define PPCM as a disorder of failed proteostasis and impaired translational homeostasis. Our analysis provides a systems-level framework connecting PPCM to ventricular dysfunction with potential therapeutic targets in mitochondria, protein quality-control, integrated stress–response, and COP9 signaling pathways. Full article

Background/Objectives: Saikosaponin D (SSD) is a bioactive compound from traditional Chinese herbs with known anti-tumor activities, including apoptosis induction, autophagy modulation, and inhibition of cell migration and invasion. However, the mechanisms underlying its effects on human endometrial cancer Ishikawa cells remain elusive. This study aimed to investigate the anti-tumor effects of SSD on EC Ishikawa cells and elucidate the molecular pathways involved, focusing on DNA damage, cell cycle regulation, autophagy, endoplasmic reticulum (ER) stress, and AMPK signaling. Methods: We performed in vitro experiments using Ishikawa cells and in vivo studies using a female BALB/c nude mouse xenograft model. DNA damage was assessed via comet assay, intracellular Ca²⁺ concentration via Fluo-3 AM staining, autophagy via transmission electron microscopy, and apoptosis via flow cytometry. Autophagy was inhibited using 3-methyladenine, and ER stress was modulated with the PERK inhibitor GSK2656157. Protein expression levels of related genes were analyzed by western blotting. No preregistration number or CONSORT details applied, as this was a pre-clinical study. Results: SSD treatment was associated with DNA damage and G2/M phase cell cycle arrest in Ishikawa cells both in vitro and in vivo. SSD was associated with an increased LC3II/LC3I ratio and activation of the AMPK pathway. It was also associated with ER stress, as evidenced by downregulation of PERK, mTOR, and eIF2α, and upregulation of p-eIF2α. Furthermore, SSD was associated with modulation of the AMPK signaling pathway to inhibit cell migration and invasion. Conclusions: SSD exerts anti-tumor effects on human EC Ishikawa cells in vitro and in vivo through mechanisms involving DNA damage, G2/M arrest, autophagy, ER stress, and AMPK-mediated inhibition of migration and invasion. These findings suggest that SSD may represent a potential therapeutic agent for EC. Full article

Background: Endocrine therapy with tamoxifen remains a cornerstone in the treatment of estrogen receptor-positive (ER+) breast cancer; however, the emergence of resistance to its active metabolites, 4-hydroxytamoxifen (4-OHTAM) and Endoxifen, represents a major clinical limitation. Increasing evidence suggests that drug efflux transporters, redox-adaptive signaling, and translational control mechanisms may converge to promote chemoresistance. This study aimed to investigate the coordinated expression patterns of ABCC transporters, the eukaryotic initiation factor 4F (eIF4F) complex, and NRF2 signaling in tamoxifen-metabolite-resistant MCF-7 breast cancer cells. Methods: MCF-7 cell variants resistant to 4-OHTAM (Variant B) or Endoxifen (Variant C) were established through prolonged drug exposure. Cytotoxicity assays assessed cellular viability and chemoresistance. Protein expression and molecular interactions were analyzed using Western blotting and co-immunoprecipitation. Flow cytometry was employed to evaluate transporter-associated fluorescence intensity. In silico molecular docking was performed to estimate the binding affinity of tamoxifen metabolites to ABCC transporters. Results: Endoxifen-resistant cells exhibited the most pronounced chemoresistant phenotype. Analysis of ABCC transporters revealed modest but consistent increases in fluorescence intensity across resistant variants; however, these differences did not reach statistical significance. Dysregulation of the eIF4F complex was observed, with increased eIF4E and reduced eIF4A levels, suggesting altered translational control associated with resistant phenotypes. Increased NRF2 protein expression was detected in resistant variants, consistent with enhanced redox-adaptive capacity. Analysis of ABCC transporters revealed modest but consistent increases in fluorescence intensity across resistant variants; however, these differences did not reach statistical significance. Molecular docking demonstrated strong binding affinity between Endoxifen and ABCC2, supporting a potential role for transporter-mediated efflux. Conclusions: Tamoxifen-metabolite resistance in ER+ breast cancer is associated with coordinated trends in ABCC transporter-associated signals, altered eIF4F complex expression, and sustained NRF2 signaling. These findings suggest the presence of a multifactorial adaptive network that may contribute to endocrine resistance. Targeting components of this network warrants further mechanistic investigation. Full article

The polyamine metabolic pathway, an evolutionarily conserved nexus integrating nutrient sensing, translation control, and cellular proliferation, is fundamentally rewired in cancer. Melanoma, a malignancy of melanocytes notorious for its metastatic propensity and therapy resistance, exhibits a profound dependency on this pathway, extending beyond mere polyamine abundance to the specialized function of their derivative, hypusine. This review synthesizes cutting-edge insights into the deoxyhypusine synthase (DHPS)/eukaryotic initiation factor 5A (eIF5A) hypusination circuit as a critical amplifier of oncogenic signaling in melanoma. We dissect its role as a translational rheostat for pro-tumorigenic proteomes, a driver of phenotypic plasticity underpinning invasion and vasculogenic mimicry, and a modulator of the immunosuppressive tumor microenvironment. Moving beyond the classical inhibitor GC7, we explore the emergence of novel allosteric DHPS inhibitors with compelling preclinical efficacy. Finally, we propose a paradigm shift: targeting the DHPS/eIF5A axis represents a strategy to disrupt the “non-oncogene addiction” of melanoma—its reliance on hyperactive translation and adaptive survival mechanisms—offering a promising avenue alongside targeted therapies and immunotherapies. Full article

Colorectal cancer (CRC) persists as a significant public health burden due to its high morbidity and mortality rates worldwide, yet the molecular events that govern its initiation and progression remain incompletely understood. We recently conducted microRNA (miRNA) profiling and identified multiple dysregulated miRNAs in CRC compared to adjacent normal tissue. Among those, miR-138-5p emerged as a potential tumor suppressor due to its marked downregulation in CRC tissue; however, the stage-specific expression of this miRNA during CRC progression and underlying molecular mechanisms remains to be unraveled. In this study, we performed differential expression profiling of healthy colon, adenomatous polyp (AP), and CRC tissues based on public datasets, revealing significant downregulation of miR-138-5p in CRC compared to controls, but not during the AP stage, suggesting a role in later stages of malignant progression. Forced expression of miR-138-5p in HCT116 and HT-29 CRC models suppressed clonogenic survival, proliferation, and migration while inducing cell death. Additionally, miR-138-5p significantly inhibited tumor formation under three-dimensional culture settings, reinforcing its tumor-suppressive function in a physiologically relevant context. Transcriptomic profiling of miR-138-5p-overexpressing CRC models revealed widespread changes in the pathways related to zinc ion binding, cilium morphogenesis, smoothened signaling, and nuclear transport. Integrated computational and experimental analyses identified 41 potential gene targets, among which TCF3, UBE2C, EIF4EBP1, LYPLA1, and CD44 were validated as potential miR-138-5p-regulated genes. Collectively, these findings establish miR-138-5p as a stage-specific tumor suppressor in CRC, acting through coordinated regulation of oncogenic networks across multiple pathways. Downregulation of miR-138-5p appears to be a late oncogenic event, conferring proliferative, survival, and invasive advantages to tumor cells. Restoration of miR-138-5p or therapeutic targeting of its downstream effectors may represent promising avenues for CRC therapeutic intervention. Full article

The tomato hind (Cephalopholis sonnerati) is a marine aquaculture fish species with high economic value. Elucidating the mechanisms underlying its growth regulation is crucial for the development of the aquaculture industry. To analyze the biological mechanisms underlying growth differences, individuals with extreme body sizes at 8 months of age from the same batch were selected in this study. A combined experiment of “body size × feeding status” was constructed, and transcriptome sequencing and weighted gene co-expression network analysis (WGCNA) were performed on brain and muscle tissues. The results showed that 2553 differentially expressed genes (DEGs) were identified between individuals with distinct body sizes, which were significantly enriched in growth regulation pathways such as PI3K–Akt, MAPK, and FoxO. Feeding differences affected 4480 genes, which were significantly enriched in signaling pathways including the insulin signaling pathway. WGCNA further identified co-expression modules (brown4, blue, coral1) significantly correlated with growth, as well as hub genes including pik3r1 and eif4ebp2. Comprehensive analysis demonstrated that the growth regulation of C. sonnerati operates as a cascade network. Brain tissues perceive signals through neuroactive ligand–receptor interactions and integrate and transduce these signals via core pathways including Ras–MAPK and PI3K–Akt. Finally, growth processes are executed in muscle tissues by regulating glycogen metabolism, protein synthesis, and other processes, which are precisely regulated by terminal processes such as cellular senescence. Among them, pik3r1 and eif4ebp2, as key molecular switches, play a central role in integrating upstream signals and precisely regulating downstream growth programs. This study preliminarily clarifies the molecular mechanism network of growth differences in C. sonnerati, providing a theoretical basis and candidate genes for the genetic improvement of its growth traits. Full article

The eukaryotic translation initiation factor 4E (eIF4E) family plays a dual role in plants, regulating cap-dependent protein synthesis and mediating susceptibility to viruses in the family Potyviridae. In cowpea (Vigna unguiculata (L.) Walp.), an economically important legume cultivated worldwide, the structural determinants of these isoforms remain largely unexplored. This study characterizes the genomic organization, evolutionary history, and conformational dynamics of eIF4E, eIF(iso)4E, and nCBP in cowpea using a multi-omics approach. Genome mining identified three paralogous genes located on chromosomes 4, 6, and 7, showing high synteny with Phaseolus vulgaris. Phylogenetic analysis confirmed nCBP as the ancestral Class I lineage, distinct from the Class II eIF4E and eIF(iso)4E clades. Theoretical models for the isoforms were generated and subsequently validated by molecular dynamics simulations, revealing that while all isoforms preserve the canonical tertiary architecture and an electropositive cap-binding pocket, eIF(iso)4E exhibits superior structural compactness and hydrogen-bond stability. These biophysical features highlight their role as a stable anchor for viral VPg proteins. By elucidating the atomic-level landscape of these factors, we provide a robust structural framework to guide allele mining and genome-editing strategies aiming to engineer virus-resistant cowpea cultivars without compromising agronomic performance. Full article

Plant viruses from the Potyviridae family have a significant impact on crop productivity worldwide. We conducted a bioinformatic analysis of the VPg sequences from several members of the Potyviridae family. All analyzed primary structures of VPg contain an invariant arginine, which, according to the model we proposed earlier, is located in the functionally important α1–α2 hairpin of the viral protein and forms a recognition contact during the formation of its complex with the eIF4E host cell. Among the amino acid mutations observed in the sequences of VPg PVY, we separately considered those associated with adaptation to the host plant. Several strain-specific mutations were identified, the functional roles of which are currently unclear. For each of the Potyviridae species considered, a consensus VPg sequence was determined. 3D-models of the corresponding proteins were constructed by de novo molecular modelling using the consensus amino acid sequences. Cross-comparative analysis of the theoretical models and the experimental VPg PVY structure obtained by NMR showed that all these proteins share a high degree of structural homology and contain the conserved arginine within the α1–α2 hairpin. However, the spatial position of this arginine may vary across models, which apparently reflects species-specific differences in the VPg recognition module. Full article

Hepatitis C Virus (HCV) is a plus-strand RNA virus that replicates its genome via a minus-strand intermediate, which in turn is the template for the synthesis of progeny plus-strand genomes. In order to characterize sequence elements in the HCV 5′-untranslated region (5′UTR) that are possibly involved in the regulation of minus-strand RNA synthesis starting at the genome’s 3′end, we used a replicon system in which a possible function of these sequences is uncoupled from other functions like translation regulation. For the specific detection by RT-qPCR of minus strands newly synthesized in the cells from the transfected replicon RNAs, we carefully eliminated the contaminating DNA and transfected RNA and avoided self-priming caused by hairpin formation. We found that the absence of any HCV sequences at the 5′end does not allow genome replication. Stem-loop I-II sequences only allow extremely low-level replication, whereas the presence of stem-loops I-III or the complete 5′UTR allows efficient replication. The mutation of sequences required for the binding of translation initiation factor 3 (eIF3) and the ribosomal 40S subunit in the 5′UTR of the plus strand severely impairs minus-strand synthesis. This suggests that eIF3 and the 40S subunit are involved in plus-strand 5′-3′-end communication and the regulation of minus-strand synthesis. Full article

Foot-and-mouth disease virus (FMDV) is a highly contagious picornavirus that affects cloven-hoofed animals and carries significant economic implications for the global livestock industry. FMDV features two Leader (L) protein isoforms, Lab and Lb, differing at their amino termini by 28 amino acids (La region). Currently, the activity of La protein sequences has not been investigated. To address this issue, the comparison study of biological and functional roles of Lab and Lb was performed as the La region alone did not independently perform protein function. We found that Lab and Lb significantly regulated FMDV replication and pathogenicity, and their coexistence afforded optimal FMDV properties. Subsequently, we observed that both L isoforms cleaved eukaryotic translation initiation factor 4G (eIF4G) I, suppressed type I and type III interferon (IFN) expression, and exhibited marked cytotoxicity, indicating that they were all key components in FMDV’s antagonism of host antiviral defenses. Finally, the subcellular distribution of Lab and Lb was detected. Despite dual localization in cytoplasmic and nuclear compartments, both isoforms displayed different spatial distribution patterns, and Lb induced more pronounced morphological changes to host cells than Lab. Furthermore, bioinformatics predicted that the La region might contain a non-classical secretory signal peptide, potentially facilitating Lab distribution to the cell membrane or extracellular space. Collectively, the primary encoding role of La region was to control the intracellular distribution of L protein, as opposed to regulating its functional activity. This study may help to deepen our understanding of why FMDV encoded two isoforms of L protein. Full article

Addressing principal challenges in common bean (Phaseolus vulgaris L.) breeding requires a holistic approach. A combined strategy was implemented to assess seven genotypes (landraces and commercial varieties) for yield potential, stability and resistance to bean common mosaic virus (BCMV) under Mediterranean low-input conditions. Pure-line selection and prognostic breeding together with SSR and CAPS-SCAR marker-assisted selection (MAS) formed the core methodology. Significant variation was detected across 24 morpho-agronomic descriptors, while SSR revealed 48.57% polymorphic loci and private alleles in specific landraces. High genetic coefficients of variation and high heritability were recorded for yield-related traits. Phenotypical evaluation showed diverse responses to BCMV, with mild symptoms predominating (52.14%). Entries G1 (45%) and G5 (35%) exhibited the highest frequency of the symptomless resistant phenotype. Molecular screening at I and bc-3/eIF4E loci confirmed G5’s robust dominant I gene profile, while G1 included individuals carrying both the dominant I gene and recessive bc-3, offering a valuable source for pyramiding resistance. Additionally, G1 (LI = 2.35; 100%) performed strongly in productivity, whereas G2 (SI = 3.1; 100%) and G7 (SI = 2.8; 89.7%) exhibited exceptional stability. Overall, the mixed-model approach highlighted the complementary characteristics of the tested genotypes and identified G1, G2, G5 and G7 as promising candidates for future breeding programs targeting high yield, low-input adaptability and resistance to BCMV. Full article

Background: Identifying patients most likely to benefit from immune checkpoint inhibitors (ICIs) remains a significant challenge in advanced melanoma. We evaluated the association between tumor somatic mutations and clinical outcomes, focusing on relapse-free survival (RFS) and overall survival (OS) in locoregionally advanced melanoma patients treated with neoadjuvant ipilimumab. Methods: Tumor specimens and matched peripheral blood samples from 22 patients underwent whole-exome sequencing (WES) to identify non-synonymous somatic mutations. Tumor mutational burden (TMB) was quantified, and specific mutations were analyzed for associations with survival outcomes. Results: The analysis revealed a mutational landscape dominated by single-nucleotide missense mutations with a median TMB of 11.4 mutations/MB. BRAF and NRAS mutations were detected in 73% of patients and exhibited mutual exclusivity and concurrence patterns (p < 0.05). Positional clustering identified NRAS and SLC35B4 as key contributors to melanoma (FDR p-value < 0.05). Log-rank analysis indicated that mutations in ODZ1, USP34, CEP192, EML5, KIAA1797, ATAD5, and ANKHD1–EIF4EBP were associated with shorter survival outcomes (RFS or OS). The associations remained significant in both univariate and multivariable Cox regression models adjusted for TMB. These genes can be broadly grouped into functional categories relevant to tumor progression and immune modulation. In applying multiple testing correction, none maintained statistical significance, indicating that these findings should be interpreted as exploratory and require validation in independent cohorts. Conclusions: This study identified tumor genomic alterations associated with clinical outcomes in melanoma patients treated with neoadjuvant ipilimumab, suggesting their potential role in anti-tumor immunity. These findings warrant further investigation in larger cohorts and across other ICIs in melanoma and other malignancies. Full article

Background/Objectives: Programmed death ligand 1 (PD-L1) is often overexpressed in triple-negative breast cancer (TNBC), where it helps the tumor evade the immune system and promotes tumor growth. Interleukin-24 (IL-24) is recognized for its anti-tumor activity, although its role in immune regulation remains unclear. In this study, we examined the role of IL-24 in regulating PD-L1 and its anti-cancer activity in TNBC cells. Methods: The study used TNBC cell lines treated with IL-24, delivered via a non-replicating adenovirus vector expressing the IL-24 gene. Assays included MTT for cell viability, Annexin V for apoptosis, Western blot for protein analysis, and qRT-PCR for mRNA analysis. Results: We found that the highly aggressive MDA-MB-231 cells had significantly higher PD-L1 levels. We discovered that treatment with IL-24 reduced cell growth, induced apoptosis, and significantly decreased PD-L1 protein levels in MDA-MB-231 cells. Mechanistically, we identified PKR, also known as eukaryotic translation initiation factor 2 alpha kinase 2, as a key mediator of IL-24–induced PD-L1 suppression. Additionally, doxorubicin, a primary chemotherapy drug used to treat triple-negative breast cancer, decreases PD-L1 expression and increases the sensitivity when combined with IL-24. Conclusions: In this study, we show that IL-24 decreases PD-L1 expression in MDA-MB-231 cells through PKR activation, enhances the anti-tumor effects of Doxorubicin, and may enable lower doses that reduce toxicity and further decrease PD-L1 levels. These findings suggest that IL-24 could serve as a valuable target for therapeutic intervention and suggest that it can improve doxorubicin’s effectiveness against aggressive breast cancer. Full article

Background: Oral Submucous Fibrosis (OSMF) is a significant global oral health problem, particularly prevalent in India, with a high risk of progression to Oral Squamous Cell Carcinoma (OSCC). This study investigates the molecular mechanisms involved in the transformation of OSMF to OSCC using transcriptomic profiling. Methods: High-throughput RNA sequencing was performed on fresh de novo OSCC samples (n = 8) and OSMF derived OSCC using Illumina-compatible NEXTflex Rapid Directional RNA Sequencing. Normalization and differential gene expression analysis were conducted, and genes exhibiting an absolute log2 fold change of ≥2 with a co-variate-adjusted p-value ≤ 0.05 were identified as significant. Results: Upregulated genes were associated with cytokine and immune responses (ABRA, TTTY14, EIF1AY), cellular proliferation and apoptosis (LINC00314, RPS4Y1, SERPINA5, TRIM63, FABP7), and energy metabolism, indicating metabolic adaptations during malignant progression. Pathway analysis showed increased expression of TNNT1, TNNI1, MYL4, and ACTN3, implicating muscle development and embryonic pathways in OSMF transformation. Conversely, genes related to epithelial differentiation and keratinization (FLG, FLG2, HRNR, TCHH, KRT73), immune regulation and tumor suppression (HLA-G, UNC5D), and metabolic signaling were downregulated, reflecting loss of tissue integrity and immune control. Conclusions: OSMF-derived OSCC exhibits a distinct transcriptomic landscape compared with de novo OSCC, characterized by altered epithelial differentiation, immune modulation, and activation of developmental pathways. The observed gene dysregulation findings establish that OSCC developing in the background of OSMF is molecularly distinct from de novo OSCC, underscoring the biological impact of the pre-existing fibrotic milieu on tumor transcriptional architecture. Full article