Search Results (19,859)

Ectopic ACTH-secreting pheochromocytomas are rare and life-threatening endocrine tumors responsible for hypertension, paroxysmal symptoms, and Cushing’s syndrome. The cellular origin of ACTH and the tumor’s molecular characteristics remain poorly understood. Single-cell RNA sequencing was performed on tumor specimens and adjacent adrenal tissues from three patients with ectopic ACTH-secreting pheochromocytomas. Integrated bioinformatic analyses, including differential expression, functional enrichment, cell–cell communication, and pseudotemporal trajectory inference, were conducted. Key findings were supported by immunofluorescence and immunohistochemical staining. Our study integrated single-cell transcriptomic profiling with detailed clinical characterization of three cases of ectopic ACTH-secreting pheochromocytomas. All patients presented classic Cushing’s features and variable catecholamine secretory patterns. Hormone levels improved after surgical resection. Single-cell analysis revealed a complex tumor microenvironment comprising 11 distinct cell populations. Chromaffin cells expressing the ACTH precursor gene POMC were identified within the tumor cell population, suggesting that these cells may represent the source of ectopic ACTH production. This finding was further supported by immunofluorescence and immunohistochemical staining demonstrating ACTH expression in CHGA-positive chromaffin tumor cells and absence of staining for the adrenocortical marker α-inhibin. These tumor cells exhibited metabolic reprogramming characterized by upregulation of oxidative phosphorylation pathways and downregulation of adaptive immune responses. Cell–cell communication analysis suggested interactions between POMC-expressing chromaffin cells and cytotoxic immune cells. Pseudotemporal trajectory analysis further suggested that these chromaffin cells did not transition toward a steroidogenic fate. This study provided a single-cell atlas of ectopic ACTH-secreting pheochromocytomas. Our integrated analysis suggested POMC-expressing chromaffin cells may represent the cellular source of ectopic ACTH production and revealed a transcriptional signature involving metabolic activation and immune modulation that might contribute to tumor progression. These findings offered new insights into the pathophysiology of this rare disease and provided a framework for future investigations into the molecular mechanisms underlying ectopic ACTH production. Full article

Milk-derived exosomes (MDEs) are bioactive nanocarriers rich in microRNAs (miRNAs) that play critical roles in post-transcriptional regulation during neonatal development and immune adaptation. However, the dynamic changes in miRNA expression across lactation stages and their biological functions remain insufficiently explored. We hypothesized that the miRNA cargo of buffalo MDEs exhibits temporal specificity, thereby dynamically matching the immune requirements of the neonatal calves. Therefore, the present study aimed to systematically characterize the miRNA expression profiles of MDEs derived from colostrum, transitional milk, and mature milk. MDEs were isolated, purified using differential ultracentrifugation, and characterized via transmission electron microscopy, Western blotting, and nanoparticle-tracking analysis. A total of 370 miRNAs were identified in the MDEs, with 220 (59.5%) co-expressed across colostrum, transitional milk, and mature milk. Comparative analysis revealed that colostrum MDEs exhibited the greatest miRNA diversity. Expression patterns of miRNAs showed distinct stage-specific clustering as lactation progressed. Compared to mature milk, 100 differentially expressed miRNAs (DE-miRNAs) were identified in colostrum MDEs, including 39 upregulated and 61 downregulated miRNAs. Bioinformatics analyses indicated that predicted target genes were associated with transmembrane transport, immune response, cell development, and apoptosis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified pathways involved in immune regulation, inflammation, and apoptosis. Moreover, macrophages incubated with buffalo colostrum MDEs showed upregulation of proliferation-related genes and downregulation of pro-inflammatory factors, suggesting an anti-inflammatory effect through activation of the phosphoinositide 3-kinase-protein kinase B (PI3K-Akt) signaling pathway. These findings offer new insights into miRNA profiles of buffalo MDEs across the early postpartum transition and provide a preliminary basis for exploring immunomodulatory potential of buffalo MDEs. Full article

Breast carcinoma is a major cause of cancer-related mortality among women worldwide. Identifying novel molecular targets remains essential, particularly for aggressive triple-negative breast cancer (TNBC). Leucine-rich alpha-2-glycoprotein 1 (LRG1) has been linked to tumor progression and angiogenesis, but its molecular mechanisms in breast cancer are poorly defined. We evaluated the effects of recombinant human LRG1 (rhLRG1) on cell viability and migration in MDA-MB-231 TNBC cells and performed transcriptomic profiling followed by functional enrichment analyses using GenArise, Cytoscape, and R-based tools. RhLRG1 treatment significantly increased cell viability and migration. Transcriptomic analysis revealed activation of key oncogenic cascades, including the PI3K/AKT, MAPK, and RAS signaling pathways. Hub-gene analysis identified upregulated genes involved in proliferation (NRAS, STAT5B, IGF2), angiogenesis (PGF, ANGPT2), and apoptosis (CASP8, BAD), whereas downregulated genes were associated with apoptotic resistance (BCL2, MCL1) and adhesion (LAMB1, ITGB4). Functional enrichment highlighted LRG1’s role in the bioinformatic analysis of differentially expressed genes that were obtained from microarray assays. LRG1 remodels the tumor microenvironment by promoting proliferation, angiogenesis, and apoptotic sensitivity while repressing resistance-related genes. These findings position LRG1 as a potential diagnostic biomarker and therapeutic target for advanced breast carcinoma. Full article

Circular RNAs (circRNAs) are stable regulatory RNAs whose developmental patterns in human salivary glands remain poorly defined. Publicly available total RNA-seq data from adult and fetal salivary glands (GSE143702—adult, n = 13; fetal, n = 14) were analyzed to profile the circRNA expression and evaluate developmental-stage differences. Reads were aligned with STAR using chimeric detection, circRNAs were parsed and annotated with CIRCexplorer2, and circRNAs supported by ≥2 back-splice junction reads were retained for quantification. Principal component analysis (PCA) of circRNA expression profiles demonstrated significant (PERMANOVA p = 0.001) separation between adult and fetal salivary glands, with a moderate effect size (R² = 0.118). Differential expression analysis identified 18 circRNAs that were significantly (adjusted p < 0.05) upregulated in adult salivary glands, with three additional circRNAs showing evidence suggestive of differential expression (0.05 ≤ adjusted p < 0.10). In fetal salivary glands, 18 circRNAs were significantly upregulated, with eight additional circRNAs showing suggestive evidence. For functional context, stage-associated circRNAs were linked to predicted miRNA interactions using the circAtlas 3.0 database and then to experimentally supported miRNA target genes using the miRTarBase database. These findings provide a stage-resolved overview of salivary gland circRNAs throughout development and aid in the prioritization of candidates for downstream validation. Full article

Cadmium (Cd) contamination is widely recognized as a major risk factor affecting the security and quality of crop production. Watermelon (Citrullus lanatus) is a globally cultivated fruit that is susceptible to Cd stress. 24-Epibrassinolide (EBR), an active brassinosteroid, is essential for plant growth and abiotic stress responses. However, its protective role in watermelon under Cd stress remains unclear. This study elucidates the physiological and molecular processes underlying EBR-mediated alleviation of Cd toxicity in watermelon seedlings. The results showed that exogenous EBR application effectively mitigated Cd-induced growth inhibition through decreased Cd deposition, reduced the accumulation of reactive oxygen species (ROS), lowered membrane lipid peroxidation, and increased antioxidant capacity in watermelon leaves under Cd treatment. Transcriptome (RNA-Seq) analysis revealed that EBR triggered substantial reprogramming of gene expression patterns, identifying 530 differentially expressed genes (DEGs) in Cd + EBR co-treatment compared with Cd treatment alone, including 204 down-regulated genes and 326 up-regulated genes. These DEGs are vital for controlling several physiological processes, including phenylpropane metabolism, phenylpropanoid biosynthesis, endoplasmic reticulum’s protein production, cell wall organization, and others. Further physiological assays confirmed that EBR increased the activities of PAL and 4CL, the core enzymes driving phenylpropanoid biosynthesis, leading to a significant accumulation of total phenols and flavonoids. Together, the above results give concrete proof of the powerful functions of 24-EBR, acting as an enhancer of plant performance under Cd stress by enhancing the antioxidant system and by activating the phenylpropanoid pathway and its derived metabolic networks. Full article

Brain metastases remain a major problem for cancer patients, impacting their treatment and survival. The pathogenesis of brain metastases is largely unknown. Recent reports indicate that the adhesion molecule protocadherin γ C3 (PCDHGC3) is differentially expressed in various cancer cells and endothelial cells of the blood–brain barrier (BBB), suggesting its involvement in the development of brain metastases. Therefore, we generated a PCDHGC3 knockout (KO) in the triple-negative breast cancer cell line HCC1806 and the malignant melanoma cell line A2058. Control and KO cells were compared using cell proliferation, adhesion and invasion assays, gene expression analyses and matrix metalloproteinase (MMP) activity assays. While the PCDHGC3 KO mutation led to increased proliferation in HCC1806 cells, with no difference observed in A2058, it significantly increased adhesion to in vitro BBB models as well as invasion in both HCC1806 and A2058 KO cell lines. Although changes in mRNA expression of genes involved in metastasis, angiogenesis and cell adhesion were found in PCDHGC3 KO breast cancer and melanoma cells, the number of genes with significantly increased mRNA expression was higher in A2058 KO cells than in HCC1806 KO cells. While the mRNA expression of MMP1 and 2 was increased in A2058 KO cells, no significant changes were found in HCC1806 KO cells. However, increased MMP activity in the cell culture medium was detected in HCC1806 KO cells, while A2058 KO cells showed lower MMP-activity compared to control. These findings provide insights into the role of PCDHGC3 in cancer cell extravasation during metastatic process and identify potential therapeutic targets for further investigation. Full article

Background: Tartary buckwheat (Fagopyrum tataricum) serves as an excellent model for studying plant water adaptation mechanisms due to its exceptional drought tolerance. While aquaporins (AQPs) mediate the transmembrane transport of water and solutes in plants, their fine-tuned regulatory networks underlying stress resilience in Tartary buckwheat remain largely elusive. Methods: Here, we combined bioinformatics and transcriptomics to systematically identify 30 highly conserved FtAQP genes at the genome-wide level. Results: Cross-validated by qRT-PCR, our analysis revealed their distinct expression patterns across different organs. Based on our transcriptomic data, we hypothesize that FtAQP family members potentially participate in a coordinated whole-plant water management network through differential spatiotemporal expression. Specifically, the robust transcription of FtAQP8, FtAQP12, and FtAQP28 in roots is associated with the initial water uptake process. As water undergoes long-distance transport, the synergistic upregulation of FtAQP13, FtAQP17, FtAQP20, and FtAQP29 in the stem suggests a potential role in facilitating critical lateral water flow. Furthermore, during reproductive development, FtAQP27 exhibits extreme tissue specificity in floral organs, implying its possible involvement in maintaining local osmotic homeostasis. Furthermore, the promoter regions of FtAQPs are highly enriched with cis-acting elements responsive to light, abscisic acid (ABA), and cold stress, suggesting they are intimately regulated by a coupling of endogenous phytohormones and environmental cues. Conclusions: Ultimately, this study provides valuable insights into the potential molecular basis of multidimensional water regulation in Tartary buckwheat, and identifies candidate genetic targets for improving water use efficiency in dryland agriculture through the precise manipulation of aquaporins. Collectively, while these observational findings provide valuable predictive models, future in vivo experimental validations are required to confirm their exact biological functions. Full article

The accumulated ammonia within the recirculating aquaculture systems threaten fish health, while little is known about the influences during early fish ontogeny. Using larval and juvenile yellow catfish (Pelteobagrus fulvidraco) as a model, a comprehensive experiment exposing fish to varying total ammonia nitrogen concentrations (0, 10, 20 mg/L for larvae; 0, 25, 125 mg/L for juveniles) was conducted to evaluate the effects on gill transcriptome and microbiota along with the serotonergic regulation. First, the serotonin (5-HT) signal, which controls oxygen chemoreception and ventilation, was mainly detected in the surface of the body of the larvae, and then shifted to gill filaments of juveniles, showing a transition from cutaneous to branchial respiration. Both larval and juvenile yellow catfish exhibited reduced survival, damaged gill structure, and elevated 5-HT expression after ammonia exposure, as well as upregulated tph1b, slc6a4b, scgn and lama5 expression with the increased ammonia concentration, indicating the effects on respiratory function via serotonergic regulation. Further transcriptome analysis was conducted in juveniles to identify the differentially expressed genes (DEGs) and thus, to illustrate more detailed responses after ammonia exposure; KEGG enrichment analysis of DEGs indicated the coping strategy shifted from metabolic buffering to metabolic elimination via glutamine synthesis with the increased ammonia level. The qRT-PCR experiment also identified the increased expression of genes involved in the urea cycle—such as ass1, asl and glula—with the increased ammonia level. Considering the potential contributary role of microbiome to gill health, 16S sequencing was conducted on the gill in the control and the 125 mg/L ammonia-exposed group. Ammonia exposure at 125 mg/L induced significant variation in Simpson index and a marked decline in β diversity. Notably, the abundance of opportunistic pathogens such as Pseudomonadota increased, while the abundance of Deinococcota and Deinococcus—which were renowned for exceptional stress resistance capacity—decreased after ammonia exposure. Thus ammonia exposure disrupts the transcriptomic and microecological balance within gill mucosa, which may elevate the risk of pathogenic infection. Overall, our study provided the first evidence of serotonergic regulation on early fish respiration during ammonia exposure, and also offered new theoretical insights into the involvement of microorganisms in ammonia toxicity. Full article

Non-small-cell lung cancer (NSCLC) constitutes approximately all lung cancers (LCs), and metastasis remains a major challenge in its treatment, thus necessitating the detection of novel molecular players involved in this process. In this study, we performed a comprehensive analysis of microarray and RNA-seq cohorts extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) and associated them with metastasis-related genes involved in brain metastasis (BM) in NSCLC. We thus identified differentially expressed metastatic genes (DEMGs) and constructed a protein–protein interaction network (PPIN) using these DEMGs. These DEMGs were further analyzed for associations with patient age, gender, and tumor stage, and the significant impact of specific genes on overall survival (OS) was assessed to determine the prognostic significance of the identified targets. We finally constructed a three-node microRNA (miRNA) feed-forward loop (FFL) involving miR-23b-3p, CD44, and five transcription factors (TFs) [EOMES, FOS, FOSL1, GLIS3, TP63] specific to NSCLC metastasis. Further mutational analysis of these FFL elements revealed that all were altered in the patient samples analyzed. Thus, our study identified potential genomic drivers that may play crucial roles in NSCLC BM. Overall, it provides valuable insights for the discovery of novel therapeutic targets in the management of NSCLC metastasis. However, further in vitro and in vivo experimentations are needed to justify the prognostic role of NSCLC biomarkers in BM pathogenesis. Full article

Jasmonate ZIM-domain (JAZ) proteins, as core negative regulatory factors of the jasmonic acid (JA) signaling pathway, play a key role in the growth and development of plants and the response to biotic and abiotic stress. In this study, 11 flax JAZ members were identified, all of which contain a ZIM domain and a Jas domain. LuJAZs comprise 3–16 exons, encoding 187–808 amino acids (aa) with molecular weights ranging from 20.24 to 88.76 kDa and isoelectric points (PI) of 5.68–9.77. They are all hydrophilic proteins located in the nucleus. These 11 LuJAZ genes are divided into five subfamilies and are unevenly distributed on chromosomes. Transcriptome and qRT-PCR analyses revealed that six LuJAZ genes, including LUSG00004384, LUSG00030782, LUSG00016742, LUSG00004390, LUSG00010997, and LUSG00029783, are significantly induced by JA. The protein–protein interaction (PPI) prediction and analysis of differential expression genes (DEGs) suggest that the MYC2 gene (LUSG00028070) may play a role in the JA-induced response. This study provides a theoretical basis for further exploring the function of the JAZ family in flax. Full article

Podocyte injury is a characteristic feature of focal segmental glomerulosclerosis (FSGS) that leads to the development of nephrosis as its loss causes proteinuria and progressive glomerulosclerosis. The physiological function of podocytes is critically dependent on proper intracellular calcium levels; an excess or shortage of calcium influx in these cells may result in foot process effacement, apoptosis, and nephron degeneration. A key protein responsible for the regulation of calcium flux is the canonical transient receptor potential 6 (TRPC6) expressed in podocytes. Several mutations in the TRPC6 gene have been associated with FSGS. Here we present a systematically optimized inducible FSGS model system in human induced pluripotent stem cells (hiPSCs). We generated and phenotypically characterized three transgenic hiPSC lines with regulatable overexpression of TRPC6 wild-type and FSGS-associated gain-of-function (GoF, P112Q) and loss-of-function (LoF, G757D) mutations. Moreover, these cell lines were differentiated into induced podocytes (ipodocytes). We assessed the impact of TRPC6 GoF and LoF mutants on calcium influx in combination with TRPC6 agonists and antagonists. Our data showed relative calcium responses consistent with the GoF and LoF phenotypes. Transgenic iPSC-based models, like the one presented here, are instrumental to studying disease mechanisms in vitro and investigating the outcomes of, and possible therapeutic interventions for, this complex disease. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extensive desmoplastic microenvironment; however, reproducible stromal-associated biomarkers linked to disease progression remain limited. This study therefore aimed to identify and validate a biologically relevant stromal/extracellular matrix (ECM)-associated candidate biomarker for PDAC. Methods: Three GEO bulk transcriptomic PDAC cohorts (GSE15471, GSE16515, and GSE62452) were integrated for differential expression, functional enrichment, protein–protein interaction, and hub-gene analyses. Candidates identified as a promising biomarker were further evaluated using the following: public proteomic and survival resources; head-to-head receiver operating characteristic (ROC) comparisons against COL1A1, COL3A1, and COL5A1; a progression cohort (GSE43288); and single-nucleus RNA sequencing data (GSE202051). Results: Among 206 shared differentially expressed genes, COL5A2 was the only consensus hub retained across multiple network-ranking methods. COL5A2 protein expression was found to be elevated in tumor tissue and associated with worse overall and disease-free survival. In ROC analyses, COL5A2 exhibited stable tumor-versus-non-tumor discrimination across GSE15471, GSE16515, and GSE62452 (AUC = 0.932, 0.760, and 0.782, respectively) and significantly outperformed COL3A1 in two cohorts. In GSE43288, COL5A2 expression increased along the normal–pancreatic intraepithelial neoplasia–PDAC axis and remained positively associated with ECM and cancer-associated fibroblast (CAF) signature scores after adjustment for disease group. Reanalysis of GSE202051 restricted to the original 18 untreated PDAC specimens revealed that COL5A2 expression was concentrated in fibroblast-lineage compartments, with CAFs accounting for the largest overall contribution and myCAFs demonstrating the strongest per-specimen expression enrichment. Conclusions: COL5A2 is a reproducible stromal/ECM-associated candidate biomarker linked to PDAC progression, with predominant expression in fibroblast/CAF compartments. Full article

Citrus genomes as storehouses of genetic information of immense commercial utility remain untapped for the improvement of fruit quality traits and other production-related stresses. With the rapid expansion of transcriptomic datasets, integrative meta-analysis has further aided in uncovering interspecies molecular mechanisms associated with fruit quality development. In this study, we performed a cross-project RNA-Seq meta-analysis, integrating multiple publicly available BioProjects encompassing diverse citrus species, viz., Citrus sinensis, C. reticulata, C. maxima, C. clementina, C. japonica, and C. papeda, known to dominate the morphogenetic evolution of the citrus industry. High-throughput RNA-Seq data were processed using various bioinformatics tools. A total of 15 interspecies comparisons identified 676 unique DEGs, enriched in pathways related to secondary juice yield and processing quality traits. We also established that domestication aided in metabolism, oxidative stress responses, phenylpropanoid and flavonoid biosynthesis, and hormone-mediated signaling. Multivariate analyses (PCA and heatmap visualization) highlighted distinct yet overlapping expression patterns across these citrus species. By combining differential expression, co-expression network analysis and QTL-GWAS integration, we identified 19 high-confidence candidate genes responsible for transcriptomic variation associated with measurable fruit quality traits. Genes such as LOC102612823 and LOC102607495, which co-localized with seed number QTLs on chromosome 1, represented strong candidates regulating reproductive development and seed formation, the traits that directly influence fruit texture and market acceptability. Genes linked to juice content QTLs, including LOC102611137 and LOC102612553 on chromosome 5, suggested their roles in metabolic regulations behind juice accumulation. These loci provided definitive breeding clues for enhancing the reshaping of citrus fruit transcriptomes while retaining key ancestral regulatory components. Full article

Feline calicivirus (FCV) is a major pathogen that threatens feline health worldwide. Its global prevalence, extensive genetic variability, and limited cross-protection among strains present significant challenges for vaccine development. In this study, an infectious clone of the FCV-GDJM202201 strain was constructed using the eukaryotic expression plasmid pcDNA3.1 under the control of the cytomegalovirus (CMV) promoter. The rescued virus, rGDJM-A4822T, exhibited growth kinetics comparable to those of the parental strain in vitro. Subsequently, two recombinant viruses, rGDJM-VP1_JL and rGDJM-VP1_SH, were generated by replacing the VP1 gene in the GDJM202201 backbone with those from heterologous FCV strains. Notably, these recombinant viruses exhibited reduced viral titers compared to rGDJM-A4822T. Finally, neutralization assays revealed differential neutralizing antibody titers among the recombinant FCVs, with rGDJM-A4822T inducing higher neutralizing antibody titers and cross-neutralizing activity. Collectively, this study establishes an FCV infectious clone that can be used to rescue recombinant viruses carrying heterologous VP1 proteins and to evaluate neutralizing antibody responses. Full article

The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly of G. chilensis using Nanopore long-reads and Illumina short-reads, integrated with structural and functional annotations from RNA-seq data of the intestine and head kidney. The resulting genome assembly was 439.89 Mb in size, with an N50 of 7.96 Mb, containing 35,029 coding genes. Comparative genomics with G. blacodes revealed high similarity in genome size and completeness. Additionally, 14,681 lncRNAs were annotated, with 641 lncRNAs and 7323 coding genes differentially expressed in a tissue-specific expression pattern. These findings provide a high-quality genomic resource that enhances the understanding of lncRNA regulation and genome structure in the Genypterus genus. This study establishes a foundation for future research on commercial traits, conservation, and the evolution of the Ophidiiformes order. Full article