Search Results (340)

The neurofibromin 1 (NF1) splice-site mutation c.61-2A>G (rs1131691100) is a rare, pathogenic, autosomal dominant variant that disrupts NF1 tumor-suppressor function, causing neurofibromatosis type 1 (NF1). Its pathogenic mechanism is poorly understood, and the potential for personalized therapeutic genome editing remains unknown due to the absence of a standard framework for investigating splicing disorders. Here, we performed a comprehensive multi-omics analysis of a de novo c.61-2A>G case from South Korea, integrating short- and long-read whole genome sequencing, whole transcriptome sequencing, and methylation profiling. We confirm that c.61-2A>G abolishes the canonical splice acceptor site, activating a cryptic splice acceptor 16 nucleotides downstream in exon 2. This splicing shift generates a 16-nucleotide deletion, causing a frameshift and premature stop codon that truncates the protein’s N-terminal region. Long-read sequencing further reveals that the mutation creates a novel CpG dinucleotide, which is methylated in the majority of reads. Finally, we assessed therapeutic correction strategies, revealing that CRISPR-Cas9 prime editing is the only viable approach for in vivo correction. This study provides the first comprehensive multi-omics characterization of the NF1 c.61-2A>G mutation and establishes a minimal framework for precision therapeutic development in silico in monogenic splicing disorders. Full article

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article

Background: Honeybees sustain vital ecological roles through foraging behavior, which provides pollination services and is likely regulated by dopamine signaling coupled to brain energy metabolism. However, the genetic and metabolic mechanisms underlying this regulation remain unclear. Methods: We treated honeybee workers with the dopamine receptor agonist bromocriptine and employed an integrative approach, combining liquid chromatography–mass spectrometry (LC–MS) metabolomics with single-nucleus RNA sequencing (snRNA-seq). Results: Metabolomics revealed increased levels of N6-carboxymethyllysine (CML) and a coordinated shift in central carbon metabolites, including higher glucose, pyruvate, and lactate within glycolysis, and ribose-5-phosphate in the pentose phosphate pathway (PPP). Integration with transcriptomics showed heterogeneous responses: glial cells exhibited higher glycolysis pathway scores and upregulated hexokinase expression compared to neurons, whereas major PPP enzymes were upregulated in both glial and neuronal subsets. Conclusions: These findings suggest that dopamine receptor activation is associated with altered whole-brain metabolic profiles and concurrent, cell-type-specific upregulation of glycolytic and PPP enzyme genes, particularly in glia. This study characterizes these neuro-metabolic associations, offering insights into the cellular and metabolic basis of foraging behavior in worker bees. Full article

Ants act as keystone species in terrestrial ecosystems, providing important ecosystem services. The large-scale production and application of GO constitute a predominant contributor to its inevitable environmental dispersion. Most GO toxicity studies have focused on plants, animals, and microorganisms, with limited research on ground-dwelling ants. In the study, we used Camponotus japonicus as a model to investigate the toxic effects of GO on ants by integrating physiological characteristics, gut microbiota and transcriptome profiling. Results showed that GO exposure induced mitochondrial dysfunction, as evidenced by mitochondrial ROS accumulation and elevated mitochondrial membrane permeability. Physiological assessments revealed that GO exposure induced oxidative stress. Specifically, GO treatment significantly suppressed superoxide dismutase (SOD) and catalase (CAT) activities, while enhancing peroxidase (POD) and carboxylesterase (CarE) activities and increasing the levels of malondialdehyde (MDA) and trehalose. Gut microbiota analyses showed that GO remarkably reduced the relative abundance of beneficial bacterial symbionts (e.g., Candidatus Blochmannia) and destabilized the whole community structure. Furthermore, transcriptome profiling revealed 680 differentially expressed genes (DEGs) in the ants after GO exposure, most of which were significantly enriched in pathways associated with oxidative phosphorylation. This study suggests that GO may compromise ant-mediated ecosystem function and provides a reference for understanding the environmental risks of GO. Our findings also offer new insights for protecting the ecosystem services of ants. Full article

Objectives: To systematically analyze the expression profiles of long non-coding RNAs (lncRNAs) in serum-derived exosomes from patients with age-related hearing loss (ARHL), and to further identify key regulatory lncRNAs involved in the pathogenesis and progression of ARHL. Methods: Peripheral blood samples were collected from patients with ARHL and age-matched normal-hearing controls. Serum was separated and exosomes were extracted. The exosomes were identified by nanoparticle tracking analysis (NTA), transmission electron microscopy (TEM), and Western blot. Subsequently, total RNA was extracted from the purified exosomes for lncRNA transcriptome sequencing. Based on the sequencing results, we identified differentially expressed lncRNAs and mRNAs and conducted multi-dimensional functional analysis, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome pathway database (Reactome), and Disease Ontology (DO). Finally, four key mRNAs (THAP2, ZNF225, MED12, and RNF141) and four differentially expressed lncRNAs (DE-lncRNAs), namely MSTRG.150961.7, ENSG00000273015, MSTRG.336598.1, and ENSG00000273493, were experimentally verified by quantitative real-time polymerase chain reaction (RT-qPCR) technology. Results: Exosomes were successfully isolated from serum and confirmed by particle size, morphological examination, and the expression of exosome-labeled proteins. A total of 2874 DE-lncRNAs were identified, among which 988 were downregulated and 1886 were upregulated. Similarly, 2132 DE-mRNAs were detected, among which 882 were downregulated and 1250 were upregulated. GO analysis revealed significant enrichment in biological processes such as “phospholipid binding”, “phosphatidylinositol binding”, “phosphatase binding”, “phosphatidylinositol bisphosphate binding”, “phosphatidylinositol-4,5-bisphosphate binding”, “phosphatidylinositol-3,5-bisphosphate phosphatase activity”. KEGG is significantly enriched in signaling pathways including “Wnt signaling pathway”, “Hippo signaling pathway”, “Cushing syndrome”, and “Nucleocytoplasmic transport”. The functional annotations of Reactome were significantly enriched in biomolecular pathways including “tRNA processing”, “Cellular response to heat stress”, “Extra-nuclear estrogen signaling”, “Metabolism of non-coding RNA”, and “CTNNB1 T41 mutants aren’t phosphorylated”. DO is significantly enriched in diseases or pathological conditions such as “hepatitis”, “bacterial infectious disease”, “cystic fibrosis”, and “vasculitis”. Conclusions:THAP2, ZNF225, MED12, and RNF141 may serve as potential candidate biomarker for ARHL. Additionally, lncRNA MSTRG.150961.7, lncRNA MSTRG.336598.1, and lncRNA ENSG00000273493 may play significant roles in the pathogenesis of this condition. Full article

Ethylene is a multifunctional phytohormone that regulates plant growth, development, and responses to abiotic/biotic stresses. RTE1 (Reversion-To-Ethylene Sensitivity1) acts as a negative regulator of the ethylene responses in Arabidopsis by positively regulating ethylene receptor ETR1. However, the role of RTE genes in sweet potato (Ipomoea batatas), an import food crop worldwide, remains largely unknown, particularly their involvement in abiotic stress adaptation. In this study, we identified 23 RTE genes in sweet potato, distributed across 21 chromosomes and one scaffold BrgTig00017944. The phylogenetic analysis divided them into two groups, the RTE1 group and RTH (RTE1-Homolog) group. Synteny analysis revealed that whole genome duplication (WGD) was the major force of expansion of the IbRTE gene family. Multiple cis-acting elements responsive to hormones and stress were found in the promoter region of IbRTE genes. The transcriptome expression profiling showed that the majority of IbRTEs have tissue-specific and differential expression under drought and salt stresses. Meanwhile, the qRT–PCR results showed that the 14 representatives IbRTEs have differential expression profilings under salt (NaCl) and drought (PEG) treatments. These findings suggest that the IbRTE genes may be involved in sweet potato’s adaptive responses to salt and drought, providing a valuable foundation for further functional studies. Full article

Gliomas are notoriously difficult to treat owing to their pronounced heterogeneity and highly variable treatment responses. This reality drives the development of precise diagnostic and prognostic methods. This review explores the modern arsenal of bioinformatic tools aimed at refining diagnosis and stratifying glioma patients by different malignancy grades and types. We perform a comparative analysis of software solutions for processing whole-exome sequencing data, analyzing DNA methylation profiles, and interpreting transcriptomic data, highlighting their key advantages and limited applicability in routine clinical practice. Special emphasis is placed on the contribution of bioinformatics to fundamental oncology, as these tools aid in the discovery of new biomarker genes and potential targets for targeted therapy. The ninth section discusses the role of computational models in predicting immunotherapy efficacy. It demonstrates how integrative data analysis—including tumor mutational burden assessment, characterization of the tumor immune microenvironment, and neoantigen identification—can help identify patients who are most likely to respond to immune checkpoint inhibitors and other immunotherapeutic approaches. The obtained data provide compelling justification for including immunotherapy in standard glioma treatment protocols, provided that candidates are accurately selected based on comprehensive bioinformatic analysis. The tools discussed pave the way for transitioning from an empirical to a personalized approach in glioma patient management. However, we also note that this field remains largely in the preclinical research stage and has not yet revolutionized clinical practice. This review is intended for biological scientists and clinicians who find traditional bioinformatic tools difficult to use. Full article

Background and Clinical Significance: This report presents the case of a 33-year-old female with recurrent miscarriage, investigated for an adrenal cortical adenoma characterized by autonomous secretion of 17-hydroxyprogesterone (17-OHP). The findings challenge the established diagnostic paradigm, which predominantly attributes elevated serum 17-OHP to congenital adrenal hyperplasia (CAH) or non-classical CAH (NCCAH). Case Presentation: The patient was found to have elevated serum 17-OHP and a 2 cm left adrenal mass. Normal testosterone and precursor levels, along with whole-exome sequencing (WES), argued against a diagnosis of non-classical 21-hydroxylase deficiency (NC-21OHD). An ACTH stimulation test elicited a mild-to-moderate rise in 17-OHP, while adrenal venous sampling (AVS) confirmed marked lateralization of 17-OHP hypersecretion to the left side. Postoperative normalization of 17-OHP levels further supported the diagnosis of a 17-OHP-secreting tumor. Histopathological analysis identified tumor regions with non-uniformly high expression of CYP17A1 and CYP21A2. Preliminary transcriptomic profiling revealed that differentially expressed genes (DEGs) were enriched in microRNA-related and PI3K-Akt signaling pathways. Conclusions: This paradigm-shifting case indicates that, in addition to 21OHD, a 17-OHP-hypersecreting adrenal adenoma should be considered in the differential diagnosis of elevated 17-OHP. The integration of multimodal diagnostic techniques, particularly AVS, is valuable for localizing hormonally active tumors. Preliminary mechanistic insights suggest a potential role for epigenetic dysregulation in the pathogenesis of this tumor type. Full article

Background/Objectives: The poultry industry faces severe heat-stress challenges that threaten both economic sustainability and animal welfare. Embryonic thermal manipulation (ETM) has been proposed as a thermal programming strategy to enhance chick heat tolerance, yet its efficacy in layers requires verification, and its effects on growth performance and neurodevelopment remain unclear. Methods: White Leghorn embryos at embryonic days 13 to 18 (ED 13–18) were exposed to 39.5 °C (ETM). Hatch traits and thermotolerance were recorded, and morphometric and histopathological analyses were performed on brain sections. Transcriptome profiling of the whole brains and hypothalami was conducted to identify differentially expressed genes (DEGs). Representative pathway genes responsive to ETM were validated by RT-qPCR. Results: ETM reduced hatchability, increased deformity rate, and decreased hatch weight and daily weight gain. During a 37.5 °C challenge, ETM chicks exhibited delayed panting and lower cloacal temperature. Histopathology revealed impaired neuronal development and myelination. Transcriptomic analysis of ED18 whole brains showed DEGs enriched in neurodevelopment, stimulus response, and homeostasis pathways. RT-qPCR confirmed hypothalamic sensitivity to ETM: up-regulation of heat-shock gene HSP70, antioxidant gene GPX1, the inflammatory marker IL-6, and apoptotic genes CASP3, CASP6, CASP9; elevated neurodevelopmental marker DCX, indicative of a stress-responsive neuronal state; and reduced orexigenic neuropeptide AGRP. Conclusions: ETM improves heat tolerance in layers but compromises hatching performance and brain development, with widespread perturbation of hypothalamic stress responses and neurodevelopmental gene networks. These findings elucidate the mechanisms underlying ETM and provide a reference for enhancing thermotolerance in poultry. Full article

The study conducted a review of Listeria prevalence, virulence, and adaptations associated with leafy vegetables from small-scale farms and their journey to markets. PubMed, Taylor and Francis, Oxford, and Google Scholar databases were utilised to search for English-language journal articles published between January 1992 and 2025. Studies utilised multi-locus sequence typing (MLST), polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP), multiplex PCR, pulsed-field gel electrophoresis (PFGE), and whole genome sequencing WGS, confocal scanning laser microscopy technique for the detection of Listeria species, followed by transcriptomic, phenotypic analyses, strand-specific RNA-sequencing, and membrane lipid profiling. ST₅, ST₁₂₁, and ST₃₂₁ are considered predominant and virulent and have been identified in two ready-to-eat commodities, while ST₁, ST₂, and ST₂₀₄ are considered hypervirulent strains in food processing environments. Immunocompromised groups can experience severe life-threatening infections, even death. Significant economic losses due to shutdowns for sanitary procedures can occur, impacting food security. Full article

12-oxo-phytodienoic acid reductase (OPR) is a core component of the jasmonic acid (JA) biosynthetic pathway and participates in JA synthesis by catalyzing the reduction in the precursor 12-oxo-phytodienoic acid (OPDA), as well as broadly regulating plant development, stress response, and hormone signaling networks. This study analyzed the OPR gene family using 28 soybean genomes. A total of 15 OPR gene family members in soybean were identified, including 14 core genes and one variable gene. Analysis of gene duplication types showed that whole-genome duplication (WGD)/segmental duplication was the main mode of duplication in GmOPRs. The phylogenetic tree constructed from multiple species showed that the OPRs in subgroup VII were functionally important OPR genes and that the OPRs underwent Leguminosae and Cruciferae divergence, and large-scale duplication occurred in Leguminosae. Analysis of natural selection pressures on 28 soybean accessions indicated that the overall evolutionary pressures on GmOPRs were dominated by purifying selection, but there were also potential positive selection signals. Analysis of cis-acting elements revealed a large number of light- and hormone-responsive cis-acting elements in the GmOPRs. Some specific cis-acting elements were only present in a few genes or accessions. The protein interaction network consisted of 12 GmOPR proteins, 4 allene oxide synthase (AOS) proteins, and 6 allene oxide cyclase (AOC) proteins, where AOCs interact with GmOPRs and AOSs. Tissue transcriptome expression profiling showed that GmOPR3, GmOPR7, and GmOPR15 were specifically expressed in roots, whereas GmOPR2, GmOPR10, and GmOPR14 were specifically expressed in leaves, suggesting that these genes play an important role in the growth and development of the tissues. Moreover, GmOPRs usually responded to salt stress, and GmOPR3, GmOPR8, GmOPR9, GmOPR10, and GmOPR11 were significantly up-regulated in roots and leaves under salt stress. This suggests that these genes may be involved in biological processes such as osmoregulation, ion homeostasis, and scavenging of reactive oxygen species, thus helping soybeans to resist salt stress. This study comprehensively analyzed the OPR gene family in soybean based on the 28 soybean accessions and clarified the salt stress response pattern, which provides a new and more effective and reliable way to analyze the soybean gene family. Full article

Fine particulate matter (PM2.5) is a major air pollutant linked to lung cancer progression. In Southeast Asia, seasonal smoke-haze produces biomass-derived PM2.5, yet its acute effects on genetically diverse lung tumours remain unclear. We investigate how Chiang Mai haze-derived PM2.5 impacts oxidative stress and gene expression in three non-small-cell lung cancer (NSCLC) cell lines: A549 (KRAS-mutant), NCI-H1975 (EGFR-mutant), and NCI-H460 (KRAS/PIK3CA-mutant). Cells were exposed to PM2.5 (0–200 µg/mL) and assessed for viability (MTT), reactive oxygen species (ROS; H₂O₂, •OH) and malondialdehyde (MDA) levels, mitochondrial-associated fluorescence, and whole-transcriptome responses. Acute exposure caused dose- and time-dependent viability loss, with A549 and NCI-H1975 more sensitive than NCI-H460. ROS profiling normalized to viable cells revealed genotype-specific oxidative patterns: cumulative increases in A549, sharp reversible spikes in NCI-H1975, and modest changes in NCI-H460. MitoTracker intensity trended downward without significance, with subtle fluorescence changes and particulate uptake. RNA-seq identified robust induction of xenobiotic metabolism (CYP1A1, CYP1B1), oxidative/metabolic stress mediators (GDF15, TIPARP), and tumour-associated genes (FOSB, VGF), alongside repression of tumour suppressors (FAT1, LINC00472). Pathway enrichment analyses highlighted oxidative stress, IL-17, NF-κB, and immune checkpoint signaling. Together, biomass haze-derived PM2.5 from Northern Thailand drives genotype-dependent oxidative stress and transcriptional remodeling in NSCLC cells. Full article

Mandibular prognathism (Class III malocclusion) is a craniofacial anomaly characterized by an anteriorly positioned mandible, a concave facial profile and impaired mastication, and appears unusually frequently in Dolang sheep (Ovis aries). We combined clinical phenotyping and three-dimensional (3D) genome profiling to investigate this trait in a Dolang sheep flock. We examined 959 animals using standardized criteria, estimated a local prevalence of 10.3%, and assembled a 200 affected/200 unaffected case–control cohort for genomic analyses. As an exploratory pilot study of 3D genome architecture, we generated in situ Hi-C datasets from mandibular bone of two affected and two control sheep. At 40 kb resolution, global topologically associating domain (TAD) organization and boundary strength were broadly conserved between groups, but sliding-window analyses identified a small number of 1 Mb hotspots where affected animals showed increased TAD-boundary density and strengthened insulation. These UNDER-enriched windows lay near genes with plausible roles in craniofacial development, including ROBO2, COL27A1, VRK2 and a cytokine cluster (IL22/IL26/IFNG with MDM1). Together, our data indicate that mandibular prognathism in Dolang sheep is associated with localized remodeling of chromatin insulation at a restricted set of gene-proximal loci and highlight candidate regions and mechanisms for integration with whole-genome sequencing, association and transcriptomic data. Full article

Non-animal methods for identification and characterization of skin sensitizers are continuously evolving, advancing towards more effective, accurate, and informational assays. The GARDskin assay is a scientifically and regulatory recognized assay for the assessment of skin sensitizers. It currently relies on targeted gene expression measurement to derive hazard classifications. With the progression of next generation sequencing technologies, whole transcriptome analysis provides an interesting alternative to the currently implemented targeted gene expression approach. RNA-seq was evaluated for its use in the GARDskin assay as a gene expression quantification method. Based on 24 paired samples acquired on both RNA-seq and the NanoString nCounter platform (the currently standard GARDskin acquisition method), gene expression profiles were found to be highly similar. Comparisons of treatment effects yielded a Spearman’s correlation coefficient of 0.95 and a Lin’s concordance correlation coefficient of 0.87. RNA-seq data was also used to classify the sensitizing hazard of 24 treatments using the standard GARDskin analysis pipeline. The classifications corresponded completely with references, rendering correct classifications for all treatments. In conclusion, it was found that the RNA-seq data strongly resembled NanoString nCounter data, and that it could be used to derive reliable hazard classifications in the GARDskin assay. Full article

(1) Background: After HBV infection, viral transcripts and host RNA form a multi-layered interwoven regulatory network. However, a comprehensive map encompassing mRNA, miRNA, lncRNA, and circRNA is still lacking. This absence complicates the systematic explanation of the molecular mechanisms driving immune escape and metabolic reprogramming during the persistent infection stage. (2) Methods: In this study, we established a mouse model of chronic HBV infection and analyzed the differential expression of mRNA, miRNA, lncRNA, and circRNA through whole transcriptome sequencing (WTS). We constructed a competing endogenous RNA (ceRNA) network to systematically evaluate the overall impact of HBV on the host’s immune-metabolic pathways. (3) Results: RNA sequencing results indicated that HBV infection significantly up-regulated 194 mRNAs, 18 miRNAs, 184 lncRNAs, and 28 circRNAs, while down-regulating 42, 16, 122, and 31 corresponding transcripts, respectively. The differentially expressed genes were primarily enriched in pathways related to metabolism, immunity/inflammation, and signal transduction-ligand receptor interactions. Furthermore, the competitive endogenous RNA networks of lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA constructed on this basis further identified miR-185-3p as a key core node. (4) Conclusions: In this study, based on whole transcriptome data, the gene expression profiles of rcccDNA/Ad-infected Alb-Cre transgenic mice (chronic HBV infection model) and normal Alb-Cre mice were systematically compared, and the core regulatory factor miR-185-3p of key differentially expressed genes was screened. The microRNA is expected to provide a new target for the precise treatment of chronic hepatitis B by targeted intervention of viral replication and high liver inflammation. Full article