Search Results (2,160)

Background and Objectives: Glioblastoma (GBM) is among the most aggressive and lethal primary brain tumors, characterized by high heterogeneity, invasive growth, and resistance to conventional therapies. The 2021 WHO classification highlights the importance of molecular diagnostics, integrating genetic, transcriptomic, and epigenetic alterations alongside histological and immunohistochemical criteria. Materials and methods: Key molecular regulators, including ATRX, OLIG2, MGMT, and IDH2, play critical roles in chromatin remodeling, transcriptional reprogramming, DNA repair, and metabolic adaptation. However, their specific expression patterns and functional roles in GBM remain incompletely understood. This study utilizes publicly available data from The Cancer Genome Atlas (TCGA) to assess the transcriptional profiles of ATRX, OLIG2, MGMT, and IDH2 in GBM, aiming to identify potential biomarkers and therapeutic targets. Results: The expression analysis revealed that ATRX is downregulated at the gene level but overexpressed at the protein level, while OLIG2 is consistently overexpressed at both levels. MGMT showed no statistically significant changes in either gene or protein expression, whereas IDH2 was not significantly altered at the gene level but was downregulated at the protein level (p < 0.05). These discrepancies suggest potential post-transcriptional regulatory mechanisms influencing GBM molecular profiles. Notably, OLIG2 and MGMT expression correlated significantly with patient survival (p < 0.05), whereas ATRX and IDH2 did not reach statistical significance. Conclusions: Understanding these molecular relationships provides valuable insights into potential therapeutic strategies, paving the way for precision oncology approaches and combination therapies targeting multiple pathways simultaneously. Full article

The Solanaceae family, which includes key crops such as tomato, pepper, eggplant, wolfberry, and groundcherry, is distinguished by its diversity of fruit types. However, the conservation of gene expression regulatory networks across different species remains poorly understood. This study utilizes comparative transcriptomics to analyze 293 transcriptome samples from 22 Solanaceae species, focusing on the expression profiles of reproductive organ (flower and fruit)-specific genes. Our results reveal evolutionary conservation in the expression patterns of these genes, particularly within regulatory pathways essential for plant reproduction. A detailed comparative analysis of gene expression patterns between tomato and pepper reveals common regulatory networks governing fruit development. Furthermore, through co-expression network analysis, we identified functional partners of YABBY in flower/fruit development and found that YABBY genes coordinate fruit development through spatiotemporal dynamic expression, shaping its regulatory role. These findings provide valuable insights that can guide future research on fruit development genes in Solanaceae species. Full article

Gynaephora qinghaiensis is a major pest in the alpine meadow regions of China. While the females are unable to fly, the males can fly and cause widespread damage. The aim of this study was to use transcriptome analysis to identify and verify genes expressed at different developmental stages of Gynaephora qinghaiensis, with particular emphasis on genes associated with wing development. High-throughput sequencing was performed on an Illumina HiSeqTM2000 platform to assess transcriptomic differences in the wings of male and female pupa and male and female adults of Gynaephora qinghaiensis, and the expression levels of the differentially expressed genes (DEGs) were verified by real-time fluorescence quantitative PCR (RT-qPCR). A total of 60,536 unigenes were identified from the transcriptome data, and 25,162 unigenes were obtained from a comparison with four major databases. Further analysis identified 18 DEGs associated with wing development in Gynaephora qinghaiensis. RT-qPCR verification of the expression levels showed consistency with the RNA sequencing results. Spatio-temporal expression profiling of the 18 genes indicated different levels of expression in the thoraces of male and female pupa, as well as between the wing buds of adult females and the wings of adult males. GO annotation analysis showed that the DEGs were associated with similar categories with no significant enrichment and were involved in cellular processes, cellular anatomical entities, and binding. KEGG analysis indicated that the DEGs were associated with endocytosis and metabolic pathways. The results of this study expand the information on genes associated with Gynaephora qinghaiensis wing development and provide support for further investigations of wing development at the molecular level. Full article

Bovine pluripotent stem cells (PSCs) hold significant potential for diverse applications in agriculture, reproductive biotechnology, and biomedical research. However, challenges persist in establishing stable bovine PSC lines and understanding the mechanisms underlying their pluripotency maintenance. Here, we derived bovine embryonic stem cells (bESCs) from Holstein cattle embryos. These cells exhibited robust differentiation capacity into three germ layers in vitro and in vivo. Transcriptome analysis revealed distinct molecular profiles compared to primed-state bESCs. Notably, bESC proliferation ceased on methanol-treated feeder cells, in contrast to mouse ESCs (mESCs), which proliferated normally. Pathway analysis identified key signaling events critical for bESC survival and proliferation, highlighting species-specific regulatory mechanisms. Furthermore, the derived bESCs demonstrated chimerism capacity in early bovine embryos, underscoring their functional pluripotency. This work provides a foundation for advancing bovine embryology research and stem cell-based biotechnologies in livestock. Full article

The cell wall integrity (CWI) pathway is responsible for transcriptional regulation of cell wall remodeling in response to cell wall stress. How cell wall remodeling mediated by the CWI pathway is effected by inputs from other signaling pathways is not well understood. Here, we demonstrate that the Mck1 kinase cooperates with Slt2, the MAP kinase of the CWI pathway, to promote cell wall thickening in glucose-starved cells. Integrative analyses of the transcriptome, proteome and metabolic profiling indicate that Mck1 is required for the accumulation of UDP-glucose (UDPG), the substrate for β-glucan synthesis, through the activation of two regulons: the Msn2/4-dependent stress response and the Cat8-/Adr1-mediated metabolic reprogram dependent on the SNF1 complex. Analysis of the phosphoproteome suggests that similar to mammalian Gsk-3 kinases, Mck1 is involved in the regulation of cytoskeleton-dependent cellular processes, metabolism, signaling and transcription. Specifically, Mck1 may be implicated in the Snf1-dependent metabolic reprogram through PKA inhibition and SAGA (Spt-Ada-Gcn5 acetyltransferase)-mediated transcription activation, a hypothesis further underscored by the significant overlap between the Mck1- and Gcn5-activated transcriptomes. Phenotypic analysis also supports the roles of Mck1 in actin cytoskeleton-mediated exocytosis to ensure plasma membrane homeostasis and cell wall remodeling in cell wall-stressed cells. Together, these findings not only reveal the novel functions of Mck1 in metabolic reprogramming and polarized growth but also provide valuable omics resources for future studies to uncover the underlying mechanisms of Mck1 and other Gsk-3 kinases in cell growth and stress response. Full article

Aging is a process of gradual functional decline in complex physiological systems and is closely related to the occurrence of various diseases. Berberine, a bioactive alkaloid derived from Coptis chinensis (Huanglian), has emerged as a promising candidate for anti-aging interventions. This study comprehensively investigated the lifespan-extending effects and molecular mechanisms of berberine in C. elegans through integrated approaches including lifespan assays, locomotor activity analysis, oxidative stress challenges, and transcriptomic profiling. Furthermore, genetic models of mutant and transgenic worms were employed to delineate their interactions with the insulin/IGF-1 signaling (IIS) pathway. Our results demonstrate that berberine extended the mean lifespan of wild-type worms by 27%. By activating transcription factors such as DAF-16/FOXO, HSF-1, and SKN-1/NRF2, berberine upregulated antioxidant enzyme expression, reduced lipofuscin accumulation, and improved stress resistance. Transcriptomic analysis revealed significant changes in lipid metabolism-related genes, particularly in pathways involving fatty acid synthesis, degradation, and sphingolipid metabolism. These findings establish that berberine exerts multi-target anti-aging effects through coordinated activation of stress-responsive pathways and metabolic optimization, providing mechanistic insights for developing natural product-based geroprotective strategies. Full article

Backgrounds: Adamantinomatous craniopharyngiomas (ACPs) are benign intracranial tumors that behave aggressively due to their location, infiltration of the surrounding nervous tissue and high capacity for recurrence. In this study, we aimed to construct ACP primary cell models for further investigation of tumorigenic and recurrent mechanisms. Methods: Primary cells were isolated from primary (one case) and recurrent (one case) ACP. Short tandem repeat (STR) analysis was used to clarify the identity of the ACP primary cells we isolated. Whole exome sequencing (WES), immunofluorescence (IF) and immunohistochemistry (IHC) were performed on primary cells and corresponding ACP tissues, to determine the mutational profile and to clarify the tissue origin and phenotypic of primary cells. Transcriptome RNA-seq was performed to obtain the gene expression characteristics of ACP primary cells. Subsequently, a heterotopic ACP xenograft mouse model was established to confirm the tumorigenesis capacity of ACP primary cells. Results: ACP primary cells were successfully cultured. The genetic variants were similar to the original tumor tissue, and they owned expression of cancer-associated fibroblast (CAF) markers (FSP1/S100A4, Vimentin) and nuclear translocation β-catenin. Meanwhile, they had an high level expression of extracellular matrix components (Fibronectin). The tumor formation ability of ACP primary cells was verified. The transcriptional signatures of ACP primary cells were also explored. Conclusions: We successfully isolated and characterized ACP primary cells that acquired multiple CAF features and demonstrated stable propagation through dozens of passages. These PDC models laid the foundation for further research on ACP. Full article

We investigated the dynamic changes in volatile aroma compound profiles (types and concentrations) and associated gene expression patterns in both the peel and pulp tissues of apples during fruit maturation. This study aimed to elucidate the metabolic regulatory mechanisms underlying volatile aroma biosynthesis in Malus domestica “Ningqiu” apples, thereby providing theoretical support for the comprehensive utilization of aroma resources. Our methodological framework integrated headspace solid-phase microextraction gas chromatography–mass spectrometry (HS-SPME-GC-MS), ultra-high-performance liquid chromatography–orbitrap mass spectrometry (UHPLC-OE-MS), and Illumina high-throughput sequencing to generate comprehensive metabolomic and transcriptomic profiles of peel and pulp tissues. Critical differential aroma compound classes were identified, including esters, aldehydes, alcohols, terpenoids, and ketones, with their metabolic pathways systematically mapped through KEGG functional annotation. Our findings revealed substantial transcriptomic and metabolomic divergence across carotenoid, terpenoid, and fatty acid metabolic pathways. Integrative analysis of multi-omics data revealed 26 and 31 putative biologically significant hub genes in peel and pulp tissues, respectively, putatively associated with the observed metabolic signatures. Among these, five core genes—farnesyl diphosphate synthase (FDPS1.X1), alcohol acyltransferases (AAT1 and AAT3), alcohol dehydrogenase (ADH3), and carotenoid cleavage dioxygenase (CCD3)—were recognized as shared regulatory determinants between both tissue types. Furthermore, terpene synthase (TPS7) emerged as a peel-specific regulatory factor, while hydroperoxide lyase (HPL2), alcohol dehydrogenases (ADH2 and ADH4), and alcohol acyltransferase (AAT2) were identified as pulp-exclusive modulators of metabolic differentiation. The experimental findings provide foundational insights into the molecular basis of aroma profile variation in Malus domestica “Ningqiu” and establish a functional genomics framework for precision breeding initiatives targeting fruit quality optimization through transcriptional regulatory network manipulation. Full article

Background/Objectives: Bone metastasis is a frequent and life-threatening event in advanced cancers, affecting up to 70–85% of prostate cancer patients. Understanding the cellular and molecular mechanisms underlying bone metastasis is essential for developing targeted therapies. This study aimed to systematically characterize the heterogeneity and microenvironmental adaptation of prostate cancer bone metastases using single-cell transcriptomics. Methods: We integrated the largest single-cell transcriptome dataset to date, encompassing 124 samples from primary prostate tumors, various bone metastatic sites, and non-malignant tissues (e.g., benign prostatic hyperplasia, normal bone marrow). After quality control, 602,497 high-quality single-cell transcriptomes were analyzed. We employed unsupervised clustering, gene expression profiling, mutation analysis, and metabolic pathway reconstruction to characterize cancer cell subtypes and tumor microenvironmental remodeling. Results: Cancer epithelial cells dominated the tumor microenvironment but exhibited pronounced heterogeneity, posing challenges for conventional clustering methods. By integrating genetic and metabolic features, we revealed key evolutionary trajectories of epithelial cancer cells during metastasis. Notably, we identified a novel epithelial subpopulation, NEndoCs, characterized by unique differentiation patterns and distinct spatial distribution across metastatic niches. We also observed significant metabolic reprogramming and recurrent mutations linked to prostate-to-bone microenvironmental transitions. Conclusions: This study comprehensively elucidates the mutation patterns, metabolic reprogramming, and microenvironment adaptation mechanisms of bone metastasis in prostate cancer, providing key molecular targets and clinical strategies for the precise treatment of bone metastatic prostate cancer. Full article

A powerful strategy to accelerate bioprocess development is to complement parallel bioreactor systems with an automated approach, often achieved using liquid handling stations. The benefit of such high-throughput experiments is determined by the employed monitoring procedures. To gain a molecular understanding of the microbial production strains in miniaturized parallel single-use bioreactors, we extended the at-line monitoring procedures to transcriptome analysis in a parallel approach using RNA-Seq. To perform automated RNA-Seq experiments, we developed a sample preparation workflow consisting of at-line cell disruption by enzymatic cell lysis, total RNA extraction, nucleic acid concentration normalization, and Nanopore cDNA Library preparation. The pH-controlled aerobic batch growth of Saccharomyces cerevisiae was studied with six different carbon sources (glucose, pyruvate, fructose, galactose, sucrose, and mannose) on a 11 mL scale using 24 parallel stirred tank bioreactors integrated into a liquid handling station while performing at-line sample preparation for RNA-Seq on the same deck. With four biological replicates per condition, 24 cDNA libraries were prepared over 11.5 h. Off-line Nanopore sequencing yielded 20.97 M classified reads with a Q-score > 9. Differential gene expression analysis revealed significant differences in transcriptomic profiles when comparing growth with glucose (exponential growth) to growth with pyruvate (stress conditions), allowing identification of 674 downregulated and 709 upregulated genes. Insignificant changes in gene expression patterns were measured when comparing growth with glucose and fructose, yielding only 64 differentially expressed genes. The expected differences in cellular responses identified in this study show a promising approach for transcriptomic profiling of bioreactor cultures, providing valuable insights on a molecular level at-line in a high-throughput fashion. Full article

Short hairpin RNAs (shRNAs) are potent tools for gene silencing, offering therapeutic potential for gene and cell therapy applications. However, their efficacy and safety depend on precise processing by the RNA interference machinery and the generation of minimal by-products. In this protocol, we describe how to systematically analyze the processing of therapeutic small RNAs by DROSHA and DICER1 and their incorporation into functional AGO complexes. Using standard small RNA sequencing and tailored bioinformatic analysis (QuagmiR), we evaluate the different steps of shRNA maturation that influence processing efficiency and specificity. We provide guidelines for troubleshooting common design pitfalls and off-target effects in transcriptome-wide profiling to identify unintended mRNA targeting via the miRNA-like effect. We provide examples of the bioinformatic analysis that can be performed to characterize therapeutic shRNA. Finally, we provide guidelines for troubleshooting shRNA designs that result in suboptimal processing or undesired off-target effects. This protocol underscores the importance of rational shRNA design to enhance specificity and reduce biogenesis by-products that can lead to off-target effects, providing a framework for optimizing the use of small RNAs in gene and cell therapies. Full article

Dandelions possess a wide range of medicinal properties and demonstrate remarkable adaptability and tolerance to salinity and alkalinity. MYB genes in plants are implicated in growth, differentiation, metabolism, and responses to both biotic and abiotic stresses. The function of MYB genes in dandelions, particularly the R2R3-MYB gene family, requires further investigation. In this study, we identified a total of 130 members of the dandelion R2R3-MYB gene family at the genome-wide level, all of which were mapped to eight dandelion chromosomes. MEME analysis revealed that TmR2R3-MYB proteins contain three conserved motifs. Phylogenetic analysis categorized all TmR2R3-MYBs into 29 subfamilies. Transcriptomic studies in different tissues indicated that TmR2R3-MYBs exhibit distinct expression patterns in different tissues, indicating their diverse functions in dandelions. Notably, TmMYB44 from the S22 subfamily displayed the highest expression level in roots. Additionally, six representative TmR2R3-MYBs were selected from the S22 subfamily for expression profiling under salinity and alkalinity treatments. The results demonstrated that the TmR2R3-MYBs from the S22 subfamily are involved in the response to salinity and alkalinity stress. These findings provide a basis for further exploration of the functions of TmR2R3-MYBs in abiotic stress tolerance. Full article

In response to the growing genetic uniformity within wheat populations, developing efficient wheat–alien translocation strategies has become critically important. We observed that several offspring of the common wheat (Triticum aestivum L.)–wild emmer (Triticum turgidum L. var. dicoccoides) chromosome arm substitution line (CASL4AL) exhibited stunted growth, including significantly reduced plant height, spike length, spikelet number, and stem width compared to normal plants. Integrative transcriptomic analyses (RNA-Seq and BSR-Seq) revealed a statistically significant depletion (p < 0.01) of single nucleotide polymorphisms (SNPs) on chromosome 4B in compromised plants. Chromosome association analysis of differentially expressed genes (DEGs, up- or downregulated) revealed that downregulated genes were predominantly located on chromosome 4B. The 1244 downregulated DEGs on Chr4B were employed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and RNA metabolic processes, DNA repair, and transport systems were significantly enriched by GO analysis; however, only the mRNA surveillance pathway was enriched by KEGG enrichment. Molecular marker profiling showed a complete absence of target amplification in the critical 0–155 Mb region of chromosome 4B in all weak plants. Pearson’s correlation coefficients confirmed significant associations (p < 0.01) between 4B-specific amplification and weak phenotypes. These results demonstrate that 4B segmental deletions drive weak phenotypes in CASL4AL progeny, and provide experimental evidence for chromosome deletions induced in wild emmer chromosome substitution lines. This study highlights the potential of wild emmer as a valuable tool for generating chromosomal variations in wheat breeding programs. Full article

O₃ (ozone) is an environmental pollutant that can exacerbate inflammatory damage and contribute to respiratory diseases. However, the molecular mechanisms and potential targets for intervention in ozone-induced lung inflammatory injury are not yet known. To address this, our study exposed mice to 0.6 ppm and 1.0 ppm of O₃ (3 h/d, 14 d), evaluating lung inflammation through histopathological examinations, lung function assessments, and analyses of white blood cells and inflammatory factors in BALF. Furthermore, we employed transcriptomic and non-targeted metabolomic approaches to decipher differentially expressed genes (DEGs) and metabolites in mouse lung tissue from the 1.0 ppm O₃ exposure group. A comprehensive integration analysis of these omics data was conducted using Pearson correlation analysis. Finally, our findings show that ozone exposure indeed elicits pulmonary inflammation. Transcriptomic analysis identified 311 differentially expressed genes, predominantly implicated in circadian rhythm, IL-17 signaling pathway, and PPAR signaling. Meanwhile, metabolomic profiling revealed 41 differentially regulated metabolites, mainly associated with riboflavin metabolism, glutathione metabolism, and ABC transporter pathways. Integrated multi-omics analysis through Pearson correlation identified three key components (Pla2g10, O-phosphoethanolamine, and phosphorylcholine) showing significant enrichment in glycerophospholipid metabolism. Collectively, our findings suggest that glycerophospholipid metabolism may serve as potential therapeutic targets and diagnostic biomarkers for ozone-induced pulmonary inflammatory injury. Full article

Anthocyanins play a pivotal role in determining the color diversity in the flowers and fruits of Cerasus humilis (Bge.) Sok. This study performed a metabolomic analysis of the flowers and fruits of two varieties differing in pigmentation phenotypes (‘Jinou 1’ and ‘Nongda 5’), and the results indicated that the cyanidin, pelargonidin, paeonidin, and delphinidin were the main substances serving as the primary pigments contributing to their striking chromatic divergence between two varieties. Transcriptome profiling revealed that several key structural genes (ChCHS1, ChDFR, ChF3H, and ChF3’H) in the anthocyanin biosynthesis pathway exhibited significantly elevated expression levels in ’Jinou 1’ compared to ’Nongda 5’. Further metabolomic and transcriptomic correlation analyses identified that ChMYB9 and ChMYB12 exhibited strong positive associations with anthocyanin pathway metabolites in both floral and fruit tissues. Notably, ChMYB9 displayed the strongest correlation with the metabolite profiles, suggesting it may serve as a core regulatory component of the anthocyanin biosynthesis. This research provides new insights into the regulatory mechanisms of anthocyanin biosynthesis in C. humilis. Full article