Search Results (462)

Background: Mitoxantrone (MX) is regularly used to treat several cancers. Despite its long history in the clinic, recent studies continue to unveil novel protein targets. These targets may contribute to the cytotoxic effects of the drug, as well as potential non-canonical antitumor activity. A better understanding of MX’s cellular targets is required to fully comprehend the molecular consequences of treatment and to interpret MX sensitivity in homologous recombination (HR)-deficient cancer. Methods: Here, we evaluated MX activity in HR-deficient UWB1.289 (BRCA1−) ovarian cancer cells and surveyed the binding profile of MX using TMT-labeled quantitative proteomics and chemoproteomics. Results: Mass spectrometry (MS) analysis of cellular extracts from MX-treated BRCA1−UWB1.289 cells revealed unique downregulation of pathways instrumental in maintaining genomic stability, including single-strand annealing. Moreover, the BRCA1− cells exhibited a significant upregulation of proteins involved in ribosome biogenesis and RNA processing. Additional MS analyses following affinity-purification using a biotinylated-mitoxantrone probe corroborated these findings, which showed considerable targeting of proteins involved in genome maintenance and RNA processing. Conclusions: Our results suggest that an interplay of both canonical and non-canonical MX-antitumor activity overwhelms the BRCA1− UWB1.289 cells. Furthermore, this study characterizes the target landscape of MX, providing insights into off-target effects and MX action in HR-deficient cancer. Full article

Cancer cells can sustain survival independently of exogenous growth factors. To investigate their adaptation to serum deprivation, we analyzed transcriptomic responses in two cancer cell lines. Transcriptome analysis revealed upregulation of mRNAs encoding cholesterol biosynthesis enzymes. This was a critical adaptive response, as a pharmacological inhibition of the pathway with statin triggered a robust apoptotic cell death accompanied by generation of a mitochondrial reactive oxygen species. The mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of cell growth, is known to be engaged in controlling lipid biosynthesis. We detected the high polysomal and preribosomal peaks not only in serum-containing medium but also under serum deprivation, indicating a high rate of protein synthesis and ribosomal biogenesis independent of serum. In addition, the inhibition of mTOR kinase activity substantially reduced polysome abundance, with a more pronounced effect in serum-deprived cancer cells. Notably, the mTOR kinase inhibition also prevented the upregulation of the cholesterol synthesis enzyme that established a direct link between mTOR activity, protein synthesis, and cholesterol biosynthesis. Together, our results show that cancer cells adapt to serum withdrawal by activating the cholesterol synthesis pathway through mTOR-dependent regulation of gene expression and protein synthesis, underscoring a critical mechanism of survival under serum withdrawal. Full article

Targeting juvenile hormone esterase (JHE) is an emerging strategy to combat the broadly resistant pest, Plutella xylostella; this study employed transcriptomics to investigate the sublethal effects of the JHE inhibitor OTFP, revealing a non-monotonic dose response characterized by stronger transcriptional changes at lower concentrations, resulting in low mortality, prolonged pupation time, and increased pupal weight. The results from the Differentially Expressed Genes (DEGs) analysis revealed that the core effect of OTFP is the persistent perturbation of the “insect hormone biosynthesis” pathway and altered expression of components of the JH/20E axis; to cope with this stress, the larvae exhibited a dual defense associated with compensatory upregulation of JH-degrading enzyme genes to attempt to restore hormone homeostasis, and the activation of a broad-spectrum detoxification network to clear the compound. More critically, the developmental delay resulting from endocrine disruption KEGG-enriched growth-related pathways (amino-acid and central-carbon metabolism; ribosome biogenesis; aminoacyl-tRNA biosynthesis), consistent with a growth-permissive milieu during prolonged feeding. This study therefore elucidates a novel integrative regulatory network that links endocrine disruption, detoxification, and compensatory growth, revealing a complex physiological trade-off strategy in this pest that sacrifices developmental tempo for survival. Full article

Background: Human insulin-like growth factor 1 (hIGF-1) plays a key role in cell proliferation and tissue repair. While plant expression systems offer a cost-effective and scalable alternative for recombinant protein production, the molecular effects of plant-derived hIGF-1 on mammalian cells remain largely unexplored. Methods: In this study, a recombinant fusion protein of hIGF-1 with human Fc (hIGF-1-Fc) was transiently expressed in Nicotiana benthamiana using the geminiviral pBYR2e system and purified by Protein A affinity chromatography. SDS-PAGE and Western blotting confirmed the predicted molecular weight, and LC-MS identified N-glycosylation at the Fc N229 site with plant-type glycans such as GnMXF, GnGnXF, and MMXF. Bioactivity was evaluated using MCF-7 cell proliferation and NIH3T3 wound healing assays. Label-free quantitative proteomics was performed on NIH3T3 fibroblasts to assess molecular changes. Results: hIGF-1 Fc significantly promoted cancer cell migration and fibroblast proliferation. Proteomic profiling revealed an abundance of cytoskeletal proteins such as actin and tubulin and metabolic enzymes related to energy production. Gene ontology and pathway enrichment analyses indicated significant modulation of ribosome biogenesis and carbon metabolism. Conclusions: This study presents the first proteome-level investigation of plant-produced hIGF-1-Fc in mouse fibroblasts and reveals its impact on cytoskeletal organization and metabolic pathways involved in proliferation and wound healing. Full article

SERBP1 (SERPINE1 mRNA-Binding Protein 1), as an RNA-binding protein with multiple biological functions, has become a research hotspot in the field of life sciences in recent years. Its unique molecular structure, such as the presence of RG/RGG repeat sequences and the absence of typical RNA-binding domains, enables it to exert diverse roles in cells. This article systematically reviews the research progress of SERBP1 in various fields including cellular stress response, tumorigenesis and development, reproductive system regulation, nervous system function, and viral infection, elaborates on its mechanism of action in detail (including newly supplemented content on cell cycle regulation, interaction with PARP1, and ribosome biogenesis), and outlines future research directions. It aims to provide a reference for in-depth understanding of the biological functions of SERBP1 and the diagnosis and treatment of related diseases. Full article

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi’s sarcoma (KS) and several lymphoproliferative diseases. As with all herpesviruses, KSHV replicates in a biphasic manner, with the establishment of a latent, persistent infection from which reactivation occurs, resulting in the completion of the temporal lytic replication cycle and production of infectious virions. Herein, we discuss the impact of KSHV lytic replication on the host cell nucleus and nuclear-related pathways. We highlight the dramatic remodelling of the nuclear architecture driven by the formation of viral replication and transcription centres (vRTCs), and the implications for sub-nuclear organelles, and how pathways involved in DNA damage, ribosomal biogenesis and epitranscriptomic regulation are disrupted or modified during KSHV replication. These changes foster an environment favourable for KSHV replication and may provide novel targets and strategies for therapeutic intervention. Full article

Heat stress typically suppresses systemic immunity in fish; however, its effects on the brain—an organ traditionally regarded as immune-privileged—remain unclear. In this study, we performed histopathological examination and RNA-seq analysis on the brains of juvenile largemouth bass (Micropterus salmoides) exposed to control (28 °C) and elevated (36.5 °C) water temperatures for 8 weeks. Histological analysis revealed distinct cytoarchitectural and pathological changes in specific brain regions. RNA-seq analysis identified a total of 1240 differentially expressed genes, with 22 heat shock protein genes notably showing significant up-regulation. The immune system-associated genes emerged as the most prominently affected category. Gene set enrichment analysis (GSEA) based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotations revealed that up-regulated genes were enriched in immunity-related pathways, including the NOD-like receptor (NLR) signaling pathway, Toll-like receptor (TLR) signaling pathway, and cytosolic DNA-sensing pathway. Additionally, the levels of apoptosis and necroptosis were moderately increased. GSEA based on Gene Ontology (GO) terms indicated that down-regulated genes were primarily associated with cell division. Protein–protein interaction (PPI) and clustering analysis identified 41 core genes in the top three clusters, encompassing those related to nuclear chromosome segregation, ribosome biogenesis, and stress response. The inhibition of genes involved in nuclear chromosome segregation may disrupt cellular homeostasis by significantly impairing microtubule dynamics. In contrast, genes associated with ribosome biogenesis and stress response were up-regulated, which could counteract the adverse effects caused by long-term heat stress. We propose that brain-specific immune activation, particularly via the NLR and TLR signaling pathways, acts as a compensatory strategy to counterbalance heat-induced cell death, thereby revealing a novel neuro-immune adaptation axis. Full article

Enhancer RNAs (eRNAs) are abundant in most human cells and tissues, and quantifying eRNAs has become a robust approach for biomarker discovery. While eRNAs play crucial roles in regulating biological processes and cancer progression, their functions in lung adenocarcinoma (LUAD) remain poorly understood. Here, we developed a LUAD prognostic model based on eRNA expression data from The Cancer Genome Atlas (TCGA). Through rigorous validation, a 7-eRNA signature was identified, which robustly stratified LUAD patients into high-risk and low-risk groups in both training and testing sets. Functional analyses revealed distinct enrichment of pathways related to amino acid biosynthesis, ribosome biogenesis, and proteasome activity in high-risk patients. Somatic mutation profiling highlighted TP53 and TTN as frequently mutated genes, while drug sensitivity prediction identified four potential therapeutic agents (including AZD4547 and Nutlin-3a) for high-risk individuals. Collectively, this study constructed a 7-eRNA prognostic model for LUAD, providing a powerful tool for clinical risk assessment and uncovering eRNA-mediated regulatory mechanisms. Full article

Background: Meningiomas are common intracranial tumors in adults. Most are benign WHO grade I (GI) tumors, while approximately 20% are diagnosed as more aggressive WHO grade II (GII) and grade III (GIII) meningiomas. The study aimed to identify genes with tumor grade-related expression and to assess their functional relevance. Methods: RNA sequencing (RNA-seq) was performed to analyze transcriptomes of benign meningothelial (n = 19) and fibrous (n = 11), atypical (n = 18) and anaplastic (n = 12) meningiomas. The data were analyzed for differential genes expression and Gene Set Enrichment Analysis (GSEA). A deposited scRNA-seq dataset was used to define meningioma cellular composition and cell type-specific gene expression enabling deconvolution of RNA-seq data. Results: Unsupervised analysis revealed three tumor clusters corresponding to the histological subtypes of meningothelial (GI), fibrous (GI) and atypical/anaplastic (GII/GIII) meningiomas. Differential analysis identified 5518 protein-coding genes with grade-related changes in expression. GSEA showed that high-grade meningiomas were enriched for processes of cell proliferation, ribosome biogenesis, and metabolism, whereas benign tumors were enriched for cell morphogenesis, transmembrane ion transport, and immune regulation. PGK1 was the most significantly grade-related gene and increased expression of phosphoglycerate kinase 1 in GII and GIII tumors was confirmed by immunohistochemistry. Deconvolution of RNA-seq data revealed grade-related changes in the tumor microenvironment, notably a progressive decrease in border-associated macrophages from WHO GI to GIII tumors. Conclusions: In our study, we characterized key genes and processes dysregulated in high-grade meningiomas, including less understood mechanisms such as metabolic reprogramming, disrupted ion transport, altered immune regulation, and differences in the tumor microenvironment between benign and aggressive tumors. Full article

The filarioid nematode Dirofilaria immitis is the causative agent of heartworm disease, a major parasitic infection of canids, felids and occasionally humans. Current prevention relies on macrocyclic lactone-based chemoprophylaxis, but the emergence of drug resistance highlights the need for new intervention strategies. Here, we applied a machine learning (ML)-based framework to predict and prioritise essential genes in D. immitis in silico, using genomic, transcriptomic and functional datasets from the model organisms Caenorhabditis elegans and Drosophila melanogaster. With a curated set of 26 predictive features, we trained and evaluated multiple ML models and, using a defined threshold, we predicted 406 ‘high-priority’ essential genes. These genes showed strong transcriptional activity across developmental stages and were inferred to be enriched in pathways related to ribosome biogenesis, translation, RNA processing and signalling, underscoring their potential as anthelmintic targets. Transcriptomic analyses suggested that these genes are associated with key reproductive and neural tissues, while chromosomal mapping revealed a relatively even genomic distribution, in contrast to patterns observed in C. elegans and Dr. melanogaster. In addition, initial evidence suggested structural variation in the X chromosome compared with a recently published D. immitis assembly, indicating the importance of integrating long-read sequencing with high-throughput chromosome conformation capture (Hi-C) mapping. Overall, this study reinforces the potential of ML-guided approaches for essential gene discovery in parasitic nematodes and provides a foundation for downstream validation and therapeutic target development. Full article

Grain amaranths are recalcitrant to conventional in vitro plant regeneration by organogenesis de novo or through somatic embryogenesis. Consequently, floral organogenesis by these methods, representing the culminating developmental point in angiosperms, is rarely achieved. In the present study, the manipulation of in vitro flowering was explored as part of a strategy designed to overcome grain amaranth’s regeneration recalcitrance. It led to an efficient and reproducible in vitro protocol in which half-longitudinally dissected zygotic embryos generated fully developed Amaranthus hypochondriacus (Ah) plants. The use of high-irradiance illumination with LED lamps with a 3:1 red–blue irradiance ratio was a critical factor, leading to a 70% rate of early flowering events under flowering-inhibiting long-day photoperiod conditions. Contrariwise, no flowering was induced under LED white lights. All in vitro flowering Ah plants yielded viable seeds. To understand the basic molecular mechanisms of the phenomenon observed, gene expression patterns and principal component analysis of key flowering-related genes were analyzed after cultivation in vitro for 4, 8, and 12 weeks under both lighting regimes. These coded for photoreceptors, photomorphogenetic regulators, embryogenic modulators, and flowering activators/repressors. The results highlighted the upregulation of key flowering-regulatory genes, including CONSTANS, FLOWERING LOCUS T, and LEAFY, together with the downregulation of the floral repressor TERMINAL FLOWER1. Ribosome biogenesis- and seed-development-related genes were also differentially expressed, supporting a key role in this process for protein synthesis and embryogenesis. A model is proposed to explain how this light-regulated molecular framework enables in vitro flowering and seed production in Ah plants kept under long-day photoperiods. Full article

In the chicken industry, sex determination significantly affects production efficiency and raises ethical concerns in poultry farming. As a key economic species, maximizing the advantages of each sex is vital in modern intensive breeding. Therefore, understanding the mechanisms of sex determination and regulation is critical to advancing the poultry industry. Transcriptome analysis of 3.5-day-old White Leghorn chicken embryonic genital ridges (n = 30, 15 males and 15 females) was performed using sex-pooled samples (five embryos/replicate, three replicates/sex). Sequencing generated 39.6 GB of high-quality reads for inter-sex comparative analysis, revealing 283 significantly differentially expressed genes (DEGs). The DEGs were primarily enriched in pathways such as ribosome biogenesis, glycan biosynthesis and metabolism, and TGF-β signaling, which are potential candidate pathways for the differentiation of chicken embryonic gonads. Key DEGs (including SMAD2Z, FREM1, NR2F1, SEMA6A, NFIB, RNF165, SMAD7B, SMAD2W, SPIN1W, and HINTW) were validated by RT-qPCR, confirming the transcriptome sequencing results. Among the DEGs, we predict binding sites for NR2F1 and NFIB within the DMRT1 gene promoter and suggest that these factors may serve as potential upstream activators for the expression of DMRT1, and they may initiate high DMRT1 expression in the subsequent stages of male embryos and regulate testicular development. In conclusion, this study investigated DEGs in the gonads of male and female chicken embryos after 3.5 days of incubation and found that NR2F1 and NFIB may serve as potential upstream activators for the expression of DMRT1, which is involved in the early determination of chicken sex. Full article

Escherichia coli displays strong adaptability for growth and reproduction at low temperatures, with ribosome biogenesis being a critical process for its growth in cold environments. The cold-shock proteins (CSPs) encompass a protein family that can assist bacterial growth at low temperatures by acting as molecular chaperones. In this study, we investigated whether CSP CspA, CspE, and CspI affect ribosomal RNA (rRNA) transcription. Deletion of the single genes encoding these proteins had only a very marginal effect on cellular growth at low temperatures, and rRNA synthesis was hardly affected. Double and triple deletion of the genes encoding these proteins resulted in a much stronger phenotype providing evidence that CspA, CspE, and CspI play an essential role in maintaining 16S rRNA synthesis and enabling optimal cellular growth at low temperatures. These findings suggest the existence of efficient backup mechanisms able to compensate for the absence of a single CSP. Full article

To date, more than 170 chemical modifications have been identified in RNA. m⁶A (N⁶-methyladenine) RNA methylation is the most abundant form of mRNA modification in eukaryotes, playing an important role in RNA post-transcriptional processes. To investigate the function of m⁶A methylation modification in the development and lactation of dairy goat mammary glands, mammary gland tissue samples were collected in the early (20 days postpartum), peak (90 days postpartum), and late period (210 days postpartum) of three dairy goats. MeRIP-seq and RNA-seq were used to explore m⁶A methylation modification events. We identified 1638 differential peaks in the MeRIP-seq data across 1539 differentially methylated genes, which were enriched in ribosome biogenesis in eukaryotes, Toll-like receptor signaling pathway, TNF signaling pathway, MAPK, and other pathways related to mammary gland development and lactation. A conjoint analysis revealed that 179 common differential expressed genes were obtained, of which 150 were negatively regulated by their m⁶A modifications, while 5 common differentially expressed genes—PPARG, HSPA2, CDK5, ACTB and NOTCH3, were screened out in the two groups. In conclusion, m⁶A modification involves the pathways related to mammary gland development and lactation by modifying gene expression. This studyprovides new insights into m⁶A epigenetic regulation, mammary epithelial gene networks, and actionable molecular targets for high-value dairy product production and the breeding of new varieties. Full article

As a major source of high-quality protein in China, duck meat such as the renowned Beijing Duck plays a critical role in the poultry industry. Sansui duck, a prized native breed, is valued for its tender meat and rich flavor, yet molecular mechanisms underlying its meat quality remain poorly studied. This study employed metabolomics and proteomics techniques to conduct a comprehensive comparative analysis of the breast and thigh muscles from 90-day-old (90X, 90T) and 468-day-old (468X, 468T) Sansui ducks. The meat quality traits indicated that the shear force and redness (a*) were significantly higher in the 468T and 468X groups compared to the 90X and 90T groups (p < 0.05). Similarly, the shear force values of the 90T and 468T groups were significantly higher than those of the 90X and 468X groups (p < 0.05). Quantitative proteomics analysis revealed differentially expressed proteins (DEPs) significantly enriched in oxidative phosphorylation and ribosomal biogenesis pathways. Non-targeted metabolomics identified differentially expressed metabolites (DEMs) concentrated in amino acid and lipid metabolism pathways. Correlation analysis indicated that in the comparison between 90X and 468X, 18 DEPs and 10 DEMs were closely associated with fleshiness, whereas in the comparison between 468X and 468T, 23 DEPs and 19 DEMs were closely associated with fleshiness. Integrating proteomics and metabolomics data analysis, proteins such as A0A8B9TTI1, R0JRM6, and A0A8B9SQI5, along with metabolites including L-lysine, L-pyrrolidone, and γ-aminobutyric acid from lysine degradation, butanoate metabolism, and 2-oxocarboxylic acid metabolism pathways, can be proposed as key factors influencing meat quality through pathways including lysine degradation, butanoate metabolism, and 2-oxocarboxylic acid metabolism in older ducks. In contrast, the protein R0JXJ3 and metabolites choline and L-glutamine may determine meat quality differences between anatomical sites through the ABC transporter pathway. These findings provide molecular insights and potential biomarkers for genetic breeding and meat quality improvement in Sansui ducks. Full article