Search Results (378)

The HGD gene encodes homogentisate 1,2-dioxygenase. A deficiency of this enzyme causes alkaptonuria (AKU; OMIM 203500), a monogenic autosomal recessive metabolic disorder. The global incidence of alkaptonuria is estimated at 1 in 250,000 to 1,000,000 live births. A large number of pathogenic nucleotide variants disrupt pre-mRNA splicing, leading to hereditary diseases. Many potentially splice-disruptive variants, including those in coding regions, remain uncharacterized. This lack of data makes clinical interpretation more difficult and can complicate diagnosis. We systematically analyzed 27 HGD variants predicted to affect splicing. Candidate variants from public databases (ClinVar, HGDdatabase) and our patient cohort were prioritized using in silico splicing predictions and evaluated with a minigene splicing assay in HEK293T cells. Based on the obtained functional analysis data, the variants were reclassified according to ACMG/AMP guidelines. In total, 13 variants changed their classification (9 were upgraded and 4 were downgraded), while 5 variants retained their pathogenicity class after analysis. Ten missense/nonsense variants were not reclassified, as no significant splicing disruption was detected. These findings improve the pathogenicity assessment of HGD variants, support more accurate diagnosis, and lay the foundation for future therapeutic strategies targeting splicing defects in AKU. Full article

Uterine stromal-derived tumors encompass a spectrum of rare neoplasms, ranging from benign endometrial stromal nodules to aggressive high-grade endometrial stromal sarcomas and undifferentiated uterine sarcomas. The classification of these tumors has advanced through molecular and immunohistochemical profiling, but the role of the extracellular matrix (ECM) in their biology is only beginning to be understood. The ECM provides both structural support and dynamic signaling cues, regulating tumor cell proliferation, invasion, angiogenesis, and immune evasion. Altered expression of collagens, proteoglycans, glycosaminoglycans, and matricellular proteins reshapes stromal architecture and contributes to disease progression. Moreover, ECM remodeling enzymes such as matrix metalloproteinases, together with cross-linking factors, create a stiff and pro-tumorigenic microenvironment that facilitates invasion and therapeutic resistance. Furthermore, these matrix alterations intersect with angiogenesis, mechanotransduction pathways, and immune modulation. Studies to date describe the role of ECM molecules in the function of the physiological uterine tissue and data for the uterine stroma-derived tumors is scarce. This review summarizes the existing knowledge in classification, prognosis and diagnosis, and summarizes the ECM-driven mechanisms in tumors described so far, aiming to identify new and prognostic biomarkers and novel therapeutic targets in uterine sarcomas. Full article

Keratin is a fibrous structural protein found in various natural materials such as hair, feathers, and nails. Its high stability and cross-linked structure make it resistant to degradation by common proteases, leading to the accumulation of keratinous waste in various industries. In this study, we developed and validated an effective bioinformatics-driven strategy for mining novel keratinase genes from the Esmatlas (ESM Metagenomic Atlas) macrogenomic database. Two candidate genes, ker820 and ker907, were identified through sequence alignment, structural modeling, and phylogenetic analysis, and were subsequently heterologously expressed in Escherichia coli Rosetta (DE3) with the assistance of a solubility-enhancing chaperone system. Both enzymes belong to the Peptidase S8 family. Enzymatic characterization revealed that GST-tagged ker820 and ker907 exhibited strong keratinolytic activity, with optimal conditions at pH 9.0 and temperatures of 60 °C and 50 °C, respectively. Both enzymes showed significant degradation of feather and cat-hair keratin. Kinetic analysis showed favorable catalytic parameters, including $K_m$ values of 9.81 mg/mL (ker820) and 5.25 mg/mL (ker907), and $V_{max}$ values of 120.99 U/mg (ker820) and 89.52 U/mg (ker907). Stability tests indicated that GST-ker820 retained 70% activity at 60 °C for 120 min, while both enzymes remained stable at 4 °C for up to 10 days. These results demonstrate the high catalytic capacity, thermal stability, and substrate specificity of the enzymes, supporting their classification as active keratinases. This study introduces a promising strategy for efficiently discovering novel functional enzymes using an integrated computational and experimental approach. Beyond keratinases, this methodology could be extended to screen for enzymes with potential applications in environmental remediation. Full article

Accurate variant classification is crucial for newborn screening (NBS) to prevent missed diagnoses or unnecessary interventions. The IDUA gene variant denoted as c.250G>A (p.Gly84Ser) has been identified in individuals with positive NBS for Mucopolysaccharidosis Type I (MPS I). This variant has conflicting pathogenicity reports including one publication classifying this variant as associated with a severe MPS I phenotype; therefore, we aim to clarify the clinical significance of this variant by presenting a case series describing three individuals, each homozygous for c.250G>A (p.Gly84Ser), identified in Michigan and California. All patients in this case series had low alpha-iduronidase (IDUA) enzyme activity with normal or mildly elevated glycosaminoglycans (GAGs) in blood or urine not falling into the range or pattern seen for affected individuals. None of these patients have developed clinical features of MPS I during follow-up ranging up to 3.5 years of age. Review of functional and population data supports a pseudodeficiency effect, resulting in no need for treatment. Based on our experience with three patients all homozygous for c.250G>A (p.Gly84Ser), despite causing low in vitro IDUA activity, homozygosity for the IDUA gene variant denoted as c.250G>A (p.Gly84Ser), does not cause symptoms of MPS I and may represent a pseudodeficiency allele. Caution should be exercised in newborns with this variant to help reduce unnecessary interventions and alleviate the psychosocial and economic consequences of false-positive NBS results, particularly for the South Asian population. Full article

Background: Women with gestational diabetes mellitus (GDM) are vulnerable to oxidative stress, yet limited data exist on the antioxidant potential of their breast milk. This study aimed to evaluate the antioxidant capacity and basic composition of colostrum in women with GDM compared to healthy controls, focusing on total antioxidant capacity (TAC) and enzymatic antioxidants: superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx). Methods: The study included 77 lactating mothers: 56 with gestational diabetes (15 managed with diet/exercise—GDM G1; 41 required insulin—GDM G2) and 21 healthy controls. Colostrum samples were collected on days 3–5 postpartum and analyzed for macronutrients and antioxidant enzymes. To enable comparisons across study groups and to explore associations with maternal characteristics, a range of statistical methods was applied. A taxonomic (classification) analysis was then performed using the predictors that best fit the data: study group membership, maternal hypothyroidism history (from the medical interview), and gestational weight gain. Results: TAC was significantly lower in the GDM G2 group compared to GDM G1 and controls (p = 0.001), with no differences in enzymatic antioxidants. The control group had the highest energy (p = 0.048) and dry matter content (p = 0.015), while protein, fat, and carbohydrate levels did not differ significantly. After dividing the study group into four clusters, based on maternal health factors, including GDM status and thyroid function, TAC levels differed significantly between clusters, with the highest values observed in Cluster 3 (healthy controls without thyroid dysfunction) and the lowest in Cluster 2 (GDM and hypothyroidism). Analysis of colostrum composition revealed significant differences in energy content (p = 0.047) and dry matter concentration (p = 0.011), while no significant differences were found in other macronutrients. Conclusions: Our findings suggest that maternal metabolic and endocrine conditions, such as GDM and thyroid dysfunction, may differentially influence the nutritional and functional properties of colostrum—particularly its antioxidant potential. Full article

Gastric cancer (GC) often presents a poor prognosis due to its asymptomatic phenotype at early stages. Upper endoscopy, which is the current gold standard to diagnose GC, is invasive with limited sensitivity for detecting gastric preneoplasia. Non-invasive biomarkers, such as blood circulating proteins, offer a promising alternative for the early detection of gastric lesions. In this prospective study, we identified plasma protein biomarkers for gastric preneoplasia and cancer using mass spectrometry-based proteomics in an exploratory cohort (n = 39). Fifteen promising protein candidates emerged to distinguish patient categories and were further confirmed by enzyme-linked immunosorbent assays (ELISA) in plasma samples from a validation cohort of 138 participants. Our predictive models demonstrated high classification performance with a minimal set of biomarkers. A four-protein panel (ARG1, CA2, F13A1, S100A12) achieved 94.1–98.2% AUROC (95% CI) for distinguishing cancer from non-cancer cases, while a five-protein panel (ARG1, CA2, HPT, MAN2A1, LBP) reached 97.3–99.5% AUROC (95% CI) for distinguishing cancer or preneoplasia from healthy or non-atrophic gastritis cases on the full cohort. Leveraging simple blood sampling, this strategy holds promise to detect high-risk gastric lesions, even at asymptomatic stages. Such an approach could significantly improve early detection and clinical management of GC, offering direct benefit for patients. Full article

The classification of mucopolysaccharidoses (MPSs) includes the classical types (I; II; III with subtypes A, B, C, and D; IV with subtypes A and B; VI; VII; IX; X), associated with impaired lysosomal degradation of mucopolysaccharides, also known as glycosaminoglycans (GAGs), as a result of deficiency in the specific enzymes responsible for GAG degradation (MPS IIIE has so far been identified only in animal models) and MPS-plus syndrome (MPSPS), which is characterized by an accumulation of undegraded GAGs, arising from impaired endosomal trafficking and inefficient delivery of these compounds to lysosomes (due to the VPS33A protein deficiency with normal GAG-degrading enzyme activities assessed in vitro). The aim of this comprehensive review is to provide physicians with a clinical, biochemical, and molecular overview of MPS manifestation. A brief summary of available and emerging therapies is also presented. Full article

Physiologically based pharmacokinetic (PBPK) models allow to simulate the behaviour of compounds in diverse physiological populations. However, the categorization of individuals into distinct populations raises questions regarding the classification criteria. In previous research, simulations of the pharmacokinetics of the mycotoxin aflatoxin B1 (AFB1), were performed in the black South African population, using PBPK modeling. This study investigates the prevalence of clinical CYP450 phenotypes (CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A4/5) across Sub-Saharan Africa (SSA), to determine the feasibility of defining SSA as a single population. SSA was subdivided into Central, East, South and West Africa. The phenotype data were assigned to the different regions and a fifth SSA group was composed of all regions’ weighted means. Available data from literature only covered 7.30% of Central, 56.9% of East, 38.9% of South and 62.9% of West Africa, clearly indicating critical data gaps. A pairwise proportion test was performed between the regions on enzyme phenotype data. When achieving statistical significance (p < 0.05), a Cohen’s d-test was performed to determine the degree of the difference. Next, per region populations were built using SimCYP starting from the available SSA based SouthAfrican_Population FW_Custom population, supplemented with the phenotype data from literature. Simulations were performed using CYP probe substrates in all populations, and derived PK parameters (C_max, T_max, AUC_ss and CL) were plotted in bar charts. Significant differences between the African regions regarding CYP450 phenotype frequencies were shown for CYP2B6, CYP2C19 and CYP2D6. Limited regional data challenge the representation of SSA populations in these models. The scarce availability of in vivo data for SSA regions restricted the ability to fully validate the developed PBPK populations. However, observed literature data from specific SSA regions provided partial validation, indicating that SSA populations should ideally be modelled at a regional level rather than as a single entity. The findings, emerging from the initial AFB1-focused PBPK work, underscore the need for more extensive and region-specific data to enhance model accuracy and predictive value across SSA. Full article

Genetic variants in nutrition-related genes exhibit variable functional consequences; however, systematic characterization across different nutritional domains remains limited. This highlights the need for detailed exploration of variant distribution and functional effects across nutritional gene categories. Therefore, the main objective of this computational study is to delve deeper into the distribution and functional impact of missense variants in nutrition-related genes. We analyzed Genetic polymoRphism variants using Personalized Medicine (GRPM) dataset, focusing on ten groups of nutrition-related genes. Missense variants were characterized using ProtVar for functional/structural impact, Pharos for functional classification, network analysis for pathway identification, and Gene Ontology enrichment for biological process annotation. The analysis of 63,581 Single Nucleotide Polymorphisms (SNP) revealed 27,683 missense variants across 1589 genes. Food intolerance (0.23) and food allergy (0.15) groups showed the highest missense/SNP ratio, while obesity-related genes showed the lowest (0.04). Enzymes predominated in xenobiotic and vitamin metabolism groups, while G-protein-coupled receptors were enriched in eating behavior genes. The vitamin metabolism group had the highest proportion of pathogenic variants. Network analysis identified apolipoproteins as central hubs in metabolic groups and inflammatory proteins in allergy-related groups. These findings offer insights into personalized nutrition approaches and underscore the utility of computational variant analysis in elucidating gene-diet interactions. Full article

The study of protein enzymatic activities has always been a significant area of scientific and industrial research. The key steps typically undertaken in the characterization of a certain enzyme family include establishing the mechanism of catalysis, measuring kinetic parameters, determining structural organization and the architecture of the catalytic center, and subsequent classification. In this review, we tried to touch upon only a few points from the classical description of enzymes of the dUTPase family and added some additional functional properties of a number of representatives of this family. The existence of such extra functions raises questions about the reasons for this function duality. Based on the information known in the literature and our previous research, in this review, we conclude that the enzymatic activity of dUTPases supplements other functions independent of the hydrolysis reaction occurring in the catalytic center. In this context, it seems that dUTP acts not just as a substrate but as a signaling molecule, whose binding induces the realization of a special, non-enzymatic role of dUTPases. Full article

Bladder cancer (BCa) is one of the most diagnosed cancers worldwide. It is classified as non-muscle-invasive (NMIB), confined to the mucosa, and muscle-invasive (MIB), extended to deeper layers or formed metastases. The poor outcomes associated with MIBC indicate the urgent need for candidate biomarkers to improve treatment strategies. Molecular characterisation of both NMIBC and MIBC, and especially the classification of tumours into molecular subtypes, could provide the development of novel therapeutics in high-risk muscle-invasive bladder cancer. A few studies have focused on pathways implicated in MIBC, including growth factors, DNA–RNA modifying enzymes and the differential roles played by the NOTCH receptors. NOTCH1 has been revealed as a tumour suppressor; in contrast, NOTCH2 and NOTCH3 have demonstrated an oncogenic role in BCa. Recent reports have found that NOTCH2 and NOTCH3 are associated with poor prognosis. Moreover, inhibiting these NOTCH receptors effectively restrained BCa growth and metastasis, suggesting the potential value of targeting NOTCH as a promising therapeutic strategy for bladder cancer. Given the crucial role of the NOTCH pathway, we will discuss the different predictive value of the four NOTCH receptors and the potential of NOTCH-combined therapy in BCa. Full article

Enzymes are highly selective and efficient biological catalysts that play a critical role in modern industrial biocatalysis. Their ability to operate under mild conditions and reduce environmental impact makes them ideal alternatives to conventional chemical catalysts. This review provides a comprehensive overview of advances in enzyme-based catalysis, focusing on enzyme classification, engineering strategies, and industrial applications. The six major enzyme classes—hydrolases, oxidoreductases, transferases, lyases, isomerases, and ligases—are discussed in the context of their catalytic roles across sectors such as pharmaceuticals, food processing, textiles, biofuels, and environmental remediation. Recent developments in protein engineering, including directed evolution, rational design, and computational modeling, have significantly enhanced enzyme performance, stability, and substrate specificity. Emerging tools such as machine learning and synthetic biology are accelerating the discovery and optimization of novel enzymes. Progress in enzyme immobilization techniques and reactor design has further improved process scalability, reusability, and operational robustness. Enzyme sourcing has expanded from traditional microbial and plant origins to extremophiles, metagenomic libraries, and recombinant systems. These advances support the integration of enzymes into green chemistry and circular economy frameworks. Despite challenges such as enzyme deactivation and cost barriers, innovative solutions continue to emerge. Enzymes are increasingly enabling cleaner, safer, and more efficient production pathways across industries, supporting the global shift toward sustainable and circular manufacturing. Full article

Xyloglucan endotransglucosylases/hydrolases (XTHs) are key enzymes involved in cell wall remodeling that play roles in plant responses to environmental stress. Despite their importance, a comprehensive investigation of the XTH gene family in cassava (Manihot esculenta Crantz), a crucial drought-tolerant crop in tropical and subtropical regions, has not yet been conducted. In the present study, we identified 37 XTH genes (MeXTH1-37) within the cassava genome, and most of them contain two conserved structures (Glyco_hydro_16 and XET_C domain). Phylogenetic analysis grouped 37 MeXTH genes into three distinct clades, a classification further supported by exon–intron organizations and the conserved protein motif architectures. Duplication events, particularly segmental duplication, were identified as the main driving force for MeXTH gene expansion in cassava. Comparative synteny analysis revealed orthologous relationships between MeXTH genes and XTH-related genes in seven other plant species, including soybean, poplar, tomato, Arabidopsis, maize, wheat, and rice. Global expression analysis revealed that MeXTH genes display different expression patterns in various cassava tissues, shedding light on their potential biological functions. Furthermore, quantitative real-time PCR (qRT-PCR) analysis of 12 representative MeXTH genes under salt and osmotic stress, as well as salicylic acid (SA) and methyl jasmonate (MeJA) treatments, demonstrated their differential responses to these stimuli. These results provide novel insights into the role of the MeXTH gene family in enhancing cassava’s tolerance to abiotic stress. Full article

Graph Neural Networks (GNNs) have become a cornerstone for graph classification, yet their vulnerability to backdoor attacks remains a significant security concern. While clean-label attacks provide a stealthier approach by preserving original labels, they tend to be less effective in graph settings compared to traditional dirty-label methods. This performance gap arises from the inherent dominance of rich, benign structural patterns in target-class graphs, which overshadow the injected backdoor trigger during the GNNs’ learning process. We demonstrate that prior strategies, such as adversarial perturbations used in other domains to suppress benign features, fail in graph settings due to the amplification effects of the GNNs’ message-passing mechanism. To address this issue, we propose two strategies aimed at enabling the model to better learn backdoor features. First, we introduce a long-distance trigger injection method, placing trigger nodes at topologically distant locations. This enhances the global propagation of the backdoor signal while interfering with the aggregation of native substructures. Second, we propose a vulnerability-aware sample selection method, which identifies graphs that contribute more to the success of the backdoor attack based on low model confidence or frequent forgetting events. We conduct extensive experiments on benchmark datasets such as NCI1, NCI109, Mutagenicity, and ENZYMES, demonstrating that our approach significantly improves attack success rates (ASRs) while maintaining a low clean accuracy drop (CAD) compared to existing methods. This work offers valuable insights into manipulating the competition between benign and backdoor features in graph-structured data. Full article

Water pollution continues to pose a critical global challenge, largely due to the unregulated discharge of industrial, agricultural, and municipal effluents. Among emerging solutions, enzymatic bioremediation stands out as a sustainable and environmentally friendly approach, offering high specificity and efficiency under mild conditions. Nonetheless, the practical application of free enzymes is hindered by their inherent instability, poor reusability, and susceptibility to denaturation. To address these limitations, the immobilization of enzymes onto solid supports, particularly clay minerals, has garnered increasing attention. This review presents a detailed analysis of clay minerals as promising carriers for enzyme immobilization in wastewater treatment. It explores their classification, structural characteristics, and physicochemical properties, highlighting key advantages such as a large surface area, cation exchange capacity, and thermal stability. Functionalization techniques, including acid/base activation, intercalation, grafting, and pillaring, are discussed in terms of improving enzyme compatibility and catalytic performance. Various immobilization methods such as physical adsorption, covalent bonding, entrapment, crosslinking, and intercalation are critically evaluated with regard to enhancing enzyme activity, stability, and recyclability. Recent case studies demonstrate the effective removal of pollutants such as dyes, pharmaceuticals, and heavy metals using enzyme–clay composites. Despite these advances, challenges such as enzyme leaching, mass transfer resistance, and variability in clay composition persist. This review concludes by outlining future prospects, including the development of hybrid and magnetic clay-based systems and their integration into advanced water treatment technologies. Overall, enzyme immobilization on clay minerals represents a promising and scalable approach for the next generation of wastewater bioremediation strategies. Full article