Search Results (6,260)

Background/Objectives: The combination of hearing loss and visual impairment in a single patient strongly suggests a genetic aetiology. However, after conventional testing, a considerable proportion of deafblindness cases remain without a genetic diagnosis. The aim of this study was to address this diagnostic gap. Methods: We developed an enhanced exome strategy that uses a whole-exome backbone complemented by spike-in capture probes for (i) low-coverage coding segments and clinically validated, non-coding regions (including deep intronic splice-altering sites and untranslated exonic sequences) across 659 genes associated with hearing loss and/or visual impairment, and (ii) mitochondrial DNA. Results: With 66.6 million paired-end reads per sample, this methodology achieved coverage of at least 20 reads per base at 99.3% of target coding and non-coding positions of genes associated with deafness and/or blindness, as well as 98.8% of the whole exome. The enhanced exome approach correctly identified the genetic variants causative of deafness and/or blindness in 10 out of 10 cases with a previously known genetic cause, in 3 out of 10 additional cases that remained undiagnosed after extensive panel sequencing, and in 4 out of 4 cases that had not been genetically studied before. Comparison of the performance of two commercial bioinformatics platforms for enhanced exome interpretation revealed that eVAI consistently prioritised causative variants higher than, or as high as, VarSome Clinical, resulting in a tendency toward shorter interpretation times using the former. Both platforms offered the same diagnostic yield and both failed to correctly call one of the causative variants. Conclusions: In an era where many centres operate exome analysis through virtual panels, enhanced exome sequencing leverages the advantages of whole-exome and custom panel sequencing: it provides panel-like sensitivity for clinically actionable loci, while offering the flexibility to periodically reanalyse data and discover candidate genes. Full article

Saline–alkali land represents an important reserve of arable resources in China, and exploiting its agricultural potential is crucial for ensuring food security. In maize (Zea mays L.), which is moderately sensitive to salt stress, proline serves as a key osmoprotectant, and Δ¹-pyrroline-5-carboxylate synthetase (P5CS), the rate-limiting enzyme in its biosynthesis, plays a vital role in plant stress responses. In this study, the maize ZmP5CS gene family was systematically identified and characterized through comprehensive bioinformatics analyses. Four ZmP5CS homologs were identified, most of which were predicted to localize to chloroplasts. Phylogenetic analysis classified these genes into four major clades. Among them, ZmP5CS4 (GRMZM2G028535) expression was significantly upregulated under salt stress. Association analysis using a natural population of 278 inbred lines revealed that nine SNPs significantly associated with relative P5CS enzyme activity were located within ZmP5CS4. Haplotype analysis further identified a superior haplotype, HapA, carried by 14 inbred lines. Under salt stress, lines carried by HapA exhibited higher P5CS enzyme activity, greater proline accumulation, lower standard evaluation scores, and slightly enhanced salt tolerance compared to lines carried by HapB. Functional validation via transgenic approaches demonstrated that ZmP5CS4 overexpression significantly increased proline content and plant survival under salt stress, whereas knockout of this gene led to heightened salt sensitivity. Collectively, this study elucidates the structure and function of the maize ZmP5CS gene family, establishes the critical role of ZmP5CS4 in the salt stress response, and provides both a theoretical foundation and a candidate gene resource for improving salt tolerance in maize breeding programs. Full article

Background: Collagen type V alpha 2 (COL5A2) is an important regulator of tumor progression and metastasis in various tumors. microRNAs (miRNAs), key post-transcriptional regulators of gene expression, can act as tumor suppressors or oncogenes. Dysregulated miRNA is closely associated with tumor development and progression. This study aimed to investigate COL5A2 expression across different tumors and to investigate its prognostic, immune cell infiltration, and miRNA associations. Methods: We used the TIMER database to assess COL5A2 expression across various tumor types and tumor-infiltrating immune cells. The UALCAN database was used to study the associations between COL5A2 expression and tumor stages, while overall survival results were obtained using the Kaplan–Meier plotter. We identified tumor suppressor miRNAs predicted to regulate COL5A2 expression in different tumors using the miRNet database and evaluated correlations between their expression levels, COL5A2 expression, and patient survival using the StarBase database. Results: COL5A2 was significantly upregulated in 12 tumors, and the upregulated COL5A2 expression was associated with altered immune cell infiltration and worse overall survival in lung and stomach adenocarcinoma. A total of 29 tumor suppressor miRNAs were identified as potential regulators of COL5A2 expression. We found that hsa-miR-101-3p and hsa-miR-29c-3p were downregulated in lung adenocarcinoma and negatively correlated with COL5A2 expression, and their downregulated expression was associated with unfavorable prognosis. Conclusions: COL5A2 and its regulatory miRNAs, hsa-miR-101-3p and hsa-miR-29c-3p, may represent potential diagnostic and prognostic biomarkers and modulators of the tumor immune microenvironment in lung adenocarcinoma. These results warrant further experimental validation and future evaluation in the context of Sustainable Development Goal (SDG) 3-aligned cancer control strategies. Full article

Background: Polyploid and chromosomal copy number gains (CNGs) cells may serve as key mediators of tumor plasticity, therapeutic resistance, and clonal evolution. Despite growing interest, their biological and clinical relevance in colorectal cancer, particularly in the metastatic setting, remains poorly defined. Methods: We performed an integrated morphological, cytogenetic, and genomic analysis of metastatic colon cancer. A tissue microarray comprising 100 tumors was evaluated, of which 47 cases were fully assessable for morphology and fluorescence in situ hybridization (FISH). Polyploid nuclei and chromosomal CNGs were assessed morphologically and cytogenetically. High-resolution targeted sequencing (TruSight Oncology 500) was conducted to characterize genomic alterations. Bioinformatic analyses included Gene Ontology enrichment and Phenolyzer network modeling. Associations with clinicopathological variables and survival outcomes were explored. Results: Polyploid nuclei and/or chromosomal CNGs were identified in approximately 25% of evaluable cases. These alterations were enriched in right-sided CRCs and in older patients, suggesting a link with age-related genomic instability. Polyploid/CNG tumors did not show significant enrichment for canonical CRC driver mutations (RAS, TP53, SMAD4), although trends toward co-occurrence with BRAF mutation and mutual exclusivity with HER2 amplification were observed. Integrative bioinformatic analyses highlighted dysregulation of pathways involved in mitotic control, centrosome organization, and DNA replication stress. Conclusions: In metastatic colon cancer, the presence of genome-wide copy number gain may delineate a tumor subset with distinctive clinicopathological and molecular characteristics. Further studies are warranted to elucidate the biological significance of these features and to explore their potential implications for tumor evolution, treatment response, and clinical stratification. Full article

Background/Objectives: Mitochondrial DNA (mtDNA) is an important resource for understanding human ancestry, population diversity, and the molecular mechanisms of mitochondrial diseases. However, analyzing mtDNA thoroughly often requires advanced bioinformatics skills and command-line knowledge. To address this challenge, we created Mitochondrial Genome Explorer (MitoGEx), a user-friendly computational pipeline optimized for human mtDNA analysis that combines multiple mtDNA analysis modules within a single graphical user interface. Methods: The platform simplifies key analytical steps, such as quality control, sequence alignment, alignment quality assessment, variant detection, haplogroup classification, and phylogenetic reconstruction. Users can choose between Quick and Advanced modes, which offer default settings or customizable options based on their analysis needs. To demonstrate its effectiveness, we analyzed 15 whole-exome sequencing (WES) samples from Songklanagarind Hospital using MitoGEx. Results: The sequencing data were of high quality, with over 92 percent of bases scoring above a Phred score and consistent GC content across all samples. Variant detection using the GATK mitochondrial pipeline and annotation with ANNOVAR and the MitImpact database revealed multiple high-confidence variants. Haplogroup classification with Haplogrep 3 and phylogenetic analysis with IQ-TREE 2 confirmed diverse maternal lineages within the cohort. Conclusions: Taken together, MitoGEx facilitates mitochondrial genome analysis in a reproducible and accessible manner for both research and clinical bioinformatics applications. The analytical results produced by MitoGEx are concordant with those obtained using standalone bioinformatic tools, demonstrating analytical correctness. By integrating all analysis steps into a single automated workflow, MitoGEx reduces execution time and limits human error inherent to manual, multi-step pipelines. Full article

Background/Objectives: The NHX gene family plays a critical role in regulating ion homeostasis and enhancing plant tolerance to abiotic stresses. This study aimed to comprehensively analyze the structural, phylogenetic, and functional characteristics of the NHX gene family in the genome of Spinacia oleracea L. Methods: Through bioinformatic approaches, a total of 44 NHX genes were identified, and their chromosomal distribution, exon-intron organization, and conserved motifs were thoroughly characterized. Protein-protein interaction network analysis revealed that SoNHX14, SoNHX20, and SoNHX33 act as central regulators, playing key roles in cellular stress response mechanisms. Furthermore, the majority of SoNHX proteins were predicted to localize primarily to the plasma membrane, endoplasmic reticulum, and vacuole. Promoter analyses indicated a widespread presence of cis-acting elements responsive to stresses such as low temperature, drought, and wounding, as well as elements responsive to plant hormones, suggesting a complex and multilayered regulatory mechanism. Results: miRNA target predictions demonstrated that NHX genes are extensively regulated at the post-transcriptional level, predominantly by stress-associated miRNA families. Conclusions: These findings support a central role for the NHX gene family in abiotic stress adaptation in S. oleracea and provide a valuable foundation for future genetic interventions aimed at improving stress tolerance. Full article

Background: Advanced liver fibrosis (LF) is a major determinant of prognosis across chronic liver diseases. Current biomarkers are often etiology-specific and lack cross-cohort robustness. Shared molecular drivers across etiologies remain incompletely defined, and effective anti-fibrotic therapies are limited. Methods: We developed a multi-algorithm consensus machine-learning framework to derive a robust LF progression signature. In the training non-alcoholic fatty liver disease (NAFLD) cohort GSE213621 (n = 368), samples were formulated as a binary classification task (mild fibrosis, F0–F2; advanced fibrosis, F3–F4). Candidate genes were screened in parallel using Boruta, Least Absolute Shrinkage and Selection Operator (LASSO), random forest, and eXtreme Gradient Boosting (XGBoost). Genes selected by at least two algorithms were defined as a high-consensus pool, and genes consistently selected by all four algorithms were prioritized to construct a core signature. Model performance was evaluated by stratified cross-validation in the training cohort and externally validated in four independent cohorts of different etiologies (GSE49541, GSE84044, GSE130970, and GSE276114). Cellular sources of signature genes were characterized using single-cell RNA sequencing (scRNA-seq) datasets GSE136103 (human) and GSE172492 (mouse). For therapeutic discovery, the high-consensus expression profile was queried against the Connectivity Map (CMap) to prioritize compounds predicted to reverse the fibrotic transcriptional program. Withaferin A (WFA) was selected for experimental validation in a carbon tetrachloride (CCl₄)-induced mouse LF model and in the transforming growth factor-β1 (TGF-β1)-stimulated human hepatic stellate cell line LX-2. Bulk liver RNA-seq profiling was performed to interrogate WFA-associated molecular changes in vivo. Results: We identified a six-gene signature (CLEC4M, COL25A1, ITGBL1, NALCN, PAPPA, and PEG3) that discriminated advanced from mild fibrosis, achieving a mean AUC of 0.890 in internal cross-validation and an average AUC of 0.864 across external validation cohorts. scRNA-seq analysis revealed cell-type-specific expression with prominent enrichment in fibroblast populations. In vivo, WFA markedly attenuated CCl₄-induced fibrosis (p < 0.05) and reversed 1314 fibrosis-associated differentially expressed genes (adjusted p < 0.05), which were enriched in fatty acid metabolism and PPAR signaling, as well as extracellular matrix (ECM)–receptor interaction and focal adhesion (adjusted p < 0.05). In vitro, WFA suppressed TGF-β1-induced LX-2 activation, reducing α-SMA and Fibronectin expression (p < 0.05). Conclusions: We report a six-gene signature that robustly predicts advanced LF across etiologies, define its cellular context using single-cell atlases, and validate the anti-fibrotic activity of WFA in both in vivo and in vitro models. Bulk liver RNA-seq and cellular evidence further suggest that WFA-associated effects are linked to lipid metabolic programs, ECM remodeling, and attenuation of hepatic stellate cell activation. Full article

Background/Objectives: Cancer cells are subjected to various stress conditions and have stress adaptability strategies to survive. Various types of stresses lead to the aggregation of cytoplasmic RNA granules known as stress granules (SGs), seen in normal and tumor cells, and aid in cell survival by avoiding cell apoptosis. G3BP stress granule assembly factor 2 (G3BP2) encodes a multifunctional protein with known roles as a critical component of SGs and is also associated with chemoresistance in cancer, but its known roles in non-small cell cancer (NSCLC) are limited. Methods: We evaluated the expression of G3BP2 via qPCR and immunohistochemistry on a retrospective cohort of NSCLC isolated at surgery in St James’s Hospital, Dublin, Ireland. Expression levels were correlated with clinicopathological parameters. Survival analyses, including Kaplan–Meier analyses, were used to determine the prognostic value. Additional correlations with other available NSCLC datasets were explored. Results: In contrast to other studies, we did not observe upregulated expression of G3BP2. Furthermore, Kaplan–Meier analyses did not identify any prognostic value associated with G3BP2 expression in patient tissues in contrast to other published data. Bioinformatic analyses on these other datasets found strong correlations between G3BP2 and core stress granule genes in NSCLC. Additional analyses also identified correlations between G3BP2 expression and immune cell infiltration, immune cell exhaustion, and DNA Damage Response pathways. An examination of the available datasets did not find any overall prognostic value for altered DNA methylation and survival. However, two individual CpG residues were identified for which higher methylation was associated with worse overall survival. Finally, the effects of a G3BP2 inhibitor on cellular proliferation were assessed. Conclusions: In our analysis, G3BP2 was not associated with survival benefit. However, clear associations were observed between altered expression of this gene and a number of important pathways linked to cancer pathogenesis, and further studies are warranted to assess this gene (and/or) stress granules in cancer. Full article

(1) Background: Swine hepatitis E (SHE) is an emerging zoonotic disease caused by the swine hepatitis E virus (SHEV). The open reading frame 3 (ORF3) protein is a recognized virulence factor of SHEV. Jaundice, the typical clinical sign of SHE, primarily results from disruptions in bile production, secretion, and excretion. However, the mechanism by which SHEV ORF3 influences bile metabolism remains unclear. (2) Methods: Building on our previous work involving adenovirus-mediated overexpression of genotype IV SHEV ORF3 in HepG2 cells and subsequent high-throughput lncRNA/transcriptome sequencing, this study performed KEGG enrichment analysis on differentially expressed lncRNAs. Candidate lncRNAs were validated via qRT-PCR. Cis-regulated target genes were predicted by integrating differentially expressed mRNA data. Furthermore, AlphaFold 3.0 was employed to analyze the molecular binding sites between lncRNA UBC (MSTRG.6881.4) and its target, UBC protein. (3) Results: We identified three lncRNAs associated with the bile secretion pathway (ko 04976) in HepG2 cells expressing genotype IV SHEV ORF3, which were further confirmed by qRT-PCR: lncRNA UBC (MSTRG.6881.4), lncRNA UBC (MSTRG.6881.9), and lncRNA UBC (MSTRG.6881.12). Bioinformatics prediction suggested six lncRNA-mRNA regulatory networks involved these lncRNAs and two downregulated UBC mRNA transcripts (ENST00000540700 and ENST00000536769). Molecular docking indicated that nucleotides 395U and 41C of lncRNA UBC (MSTRG.6881.4) could potentially bind to residues 82Lys, 88Thr, and 90Thr of the UBC protein, with predicted binding energies ranging from −4.73 to −0.75 kcal/mol. (4) Conclusions: The successful identification of bile secretion-related lncRNAs, coupled with the prediction of their regulatory networks and molecular interaction sites, has advanced our understanding of SHEV ORF3 function and the pathogenesis of SHEV infection. Full article

Soft tissue sarcomas are rare malignant mesenchymal tumors for which accurate diagnosis, prognostic stratification, and therapeutic decision-making remain challenging. Although histopathology and immunohistochemistry are essential diagnostic tools, they frequently fail to capture the molecular complexity underlying tumor aggressiveness and treatment resistance. In this study, we evaluated the utility of RNA-based next-generation sequencing for the molecular characterization of STS and for elucidating transcriptomic mechanisms associated with aggressive tumor behavior. An observational cohort of 24 patients with histologically confirmed soft tissue sarcomas was analyzed, using adipose and skeletal muscle tissue as controls. RNA was extracted from tumor samples, libraries were prepared with a targeted pan-cancer panel, and sequencing was performed on the Illumina platform, followed by bioinformatic analysis using DRAGEN pipelines and DESeq2. RNA-NGS identified a predominance of single-nucleotide polymorphisms and significant differential gene expression, with overexpression of proliferation-related genes (TOP2A, MKI67, BUB1B), extracellular matrix and microenvironment-associated genes (COL11A1, SPP1), and developmental regulators (HOXD13, MELK). Subgroup analysis revealed a distinct transcriptomic profile in leiomyosarcoma, while gene fusion analysis detected clinically relevant alterations. These findings demonstrate that RNA-NGS provides biologically and clinically meaningful insights into the molecular landscape of soft tissue sarcomas and supports its integration into precision medicine-oriented diagnostic workflows. Full article

Gibberellin 2-oxidase (GA2ox) is instrumental in gibberellin (GA) catabolism and the modulation of plant growth. In this investigation, nine LcGA2ox genes (LcGA2ox1-LcGA2ox9) were identified within the litchi (Litchi chinensis Sonn.) genome. Bioinformatics analyses revealed that the proteins encoded by these genes uniformly possess 2OG-Fe (II)_Oxy and DIOX_N domains, exhibiting a range of physicochemical properties and subcellular localizations. Phylogenetic analysis categorized these genes into three subgroups, C₁₉-GA2ox-I, C₁₉-GA2ox-II, and C₂₀-GA2ox-I, with each subgroup characterized by specific motif compositions and gene structures. These gene promoters harbor cis-regulatory elements implicated in light signaling, hormonal pathways, abiotic stress responses, and developmental processes. The LcGA2ox gene family contributes to the maintenance of GA metabolic homeostasis through interactions with GA synthases, receptors, and repressors. This gene family demonstrates distinct tissue-specific and spatiotemporal expression patterns: LcGA2ox1/6/7 are predominantly expressed in flowers, LcGA2ox8 in fruits, and LcGA2ox9 in buds. Notably, LcGA2ox6/7 are key regulators of male and female flower development in litchi, exhibiting a negative correlation with the female flower genes AGL1 and SPT. The overexpression studies conducted in Arabidopsis have demonstrated that LcGA2ox6 acts as an inhibitor of both vegetative and reproductive development. This study characterizes the LcGA2ox family, establishing a theoretical basis for understanding GA regulation in litchi reproductive development and genetic improvement. Full article

Vaccines worldwide reduce severe coronavirus disease 2019 (COVID-19) consequences; however, viral evolution escapes immunity, raising global concerns about vaccine protection and requiring monitoring. Bioinformatics is crucial for studying vaccine escape, speeding up variant detection, mapping antibody evasion epitopes and ensuring updated vaccines and public health responses. This study combines bibliometric analysis of the Scopus literature (n = 416) on SARS-CoV-2 immune evasion using bioinformatics tools with descriptive analysis of the top ten most highly cited original articles. Our results showed the United States (USA) as the dominant contributor, leading in publication output, citation impact and collaboration networks. The key themes identified were immune evasion, spike protein mutations, and viral evolution, highlighting the structural, functional and immune evasion mechanisms of spike mutations. Leading authors and journals reveal a globally connected research community that is making advances in our understanding of SARS-CoV-2 vaccine evasion, and supporting the development of future treatments and vaccines. The top ten articles showed molecular docking, dynamics simulations, and protein modeling as crucial to studying vaccine escape. In conclusion, global research led mainly by the USA and supported by active contributions has used bioinformatics to elucidate SARS-CoV-2 immune evasion, guiding variant future vaccine and treatment development, variant monitoring, and preparedness for emerging variants. Full article

The interaction between Angiostrongylus vasorum and the vascular endothelium of the host plays a key role in the pathogenesis of canine angiostrongylosis. The adult stage of A. vasorum resides in right ventricles and pulmonary arteries of dogs and foxes and maintains close contact with the endothelium, whose activation may contribute to the hemostatic and hemorrhagic disorders observed in infected animals. However, the molecular mechanisms underlying this endothelial dysfunction remain poorly understood. To investigate this interaction, an in vitro model of vascular endothelial cells was stimulated with the adult A. vasorum homogenate. Quantitative proteomic analysis, combined with bioinformatic tools, identified 691 and 6011 protein groups in the cell supernatants and the cell lysates, respectively. Of these, 213 proteins in the cell supernatants (193 up-regulated and 20 down-regulated) and 564 in the cell lysates (358 up-regulated and 206 down-regulated) showed differential expression compared to control cells. Up-regulated proteins included TFPI, CD59, VWF, ANGPT2, MMRN1, and FLT1, which are involved in endothelial activation, angio-genesis, and coagulation regulation. Conversely, C3, SERPINE1, SERPINB2, PLAU, PLAUR, and ICAM1 were down-regulated, suggesting modulation of fibrinolysis, inflammation, and cell adhesion pathways. These findings indicate that adult A. vasorum homogenate induces a multifactorial endothelial activation characterized by dysregulation of coagulation, complement, and vascular remodelling pathways. Future studies focusing on the temporal and molecular characterization of endothelial responses to excretory/secretory antigens in both definitive and accidental hosts will further clarify the mechanisms of vascular pathology and parasite tolerance. Full article

BASIC PENTACYSTEINE (BPC) transcription factors are plant-specific and play crucial roles in regulating plant development and responses to abiotic stresses. However, the genomic characteristics of the BPC gene family in Brassica juncea and its regulatory mechanisms in response to light and salicylic acid remain poorly understood. In this study, we identified 25 BjuBPC genes in the B. juncea genome using bioinformatic approaches. All BjuBPC proteins were predicted to localize exclusively to the nucleus, with their distribution scattered across 14 chromosomes of B. juncea. Phylogenetic analysis classified these BjuBPC genes into three subfamilies (A, B, and C). The 25 BjuBPC genes showed strong collinearity with BPC orthologs from Arabidopsis thaliana, Brassica rapa, and Brassica nigra, and members of the same subfamily shared highly conserved exon–intron architectures and motif compositions, and a highly conserved canonical GAGA DNA-binding domain. Expression profiling across tissues revealed both tissue-specific and constitutive expression patterns among BjuBPC members. Subsequent expression analyses under four light qualities and exogenous salicylic acid treatment demonstrated that BjuBPC1, BjuBPC9, and BjuBPC24 were specifically responsive to both light and salicylic acid signals, with markedly strong induction by blue light. These findings provide valuable insights for future functional characterization of BjuBPC genes and enhance our understanding of their biological roles in B. juncea. Full article

Accumulating studies have identified the pivotal role of long non-coding RNAs (lncRNAs) in participating in host–virus interactions during virus infections. However, the regulatory roles of lncRNAs in influenza A virus (IAV) infection are still not fully elucidated. In this study, using high-throughput sequencing, we comprehensively compared the expression profiles of lncRNAs and mRNAs in mouse lungs infected either with the nonpathogenic parental (SDL124) H7N9 virus or its moderately pathogenic mouse-adapted (S8) variant. A total of 7636 significantly differentially expressed (SDE) lncRNAs were obtained in the S8-infected group compared to the mock group. As for the SDL124 group, 1042 SDE lncRNAs were identified. Subsequently, the mRNAs co-expressed with SDE lncRNAs were subjected to functional annotation and pathway enrichment analysis. The results indicated that the target mRNAs regulated by the S8 virus were mainly enriched in various immunological processes and exhibited a strong correlation with inflammatory-related signaling pathways. Moreover, 12 lncRNAs and 10 mRNAs co-expressed with SDE lncRNAs were selected and successfully verified by RT-qPCR. Among these lncRNAs, NONMMUG032982.2 and NONMMUG032328.2 exhibited strong antiviral activity against IAV. Additionally, these two lncRNAs were chosen for further in-depth bioinformatics analysis, including transcription factor prediction, coding capacity assessment, genomic location, construction of secondary structure, and prediction of potential interacting proteins. Taken together, these findings provide a cluster of lncRNAs probably associated with the virulence of IAV in mice and shed light on the anti-IAV effects of two functional lncRNAs, establishing a molecular foundation for further exploring the regulatory mechanisms of lncRNAs in IAV infection. Full article