Search Results (1,434)

Background: Thymic epithelial tumors (TETs) are rare mediastinal malignancies whose prognosis is largely determined by histology. Current predictive models rely on clinical variables and subjective imaging interpretation, with unsatisfied performance. Non-invasive pre-treatment risk stratification could guide surgical planning and perioperative management in patients with TETs. The role of fluorine-18 (¹⁸F) fluorodeoxyglucose (FDG) positron emission tomography/computed tomography (CT) in identifying aggressive disease is increasingly recognized. In this bicentric study, we aimed to evaluate a machine learning-based radiomics model using PET and CT images to differentiate between low-risk and high-risk TETs. Methods: Seventy-five patients who underwent PET/CT to evaluate the suspected anterior mediastinal mass and histopathologically diagnosed with TETs were included. On PET/CT images, the tumor was manually segmented by two experienced clinicians. First-order, shape, and texture features were extracted using the PyRadiomics library, resulting in 200 radiomics features (186 intensity/texture features and 14 shape features). In addition, rPET (i.e., tumor SUVmax/Liver SUVmax) parameter was included, yielding a grand total of 201 features. The feature set was reduced to 20 variables using ANOVA, with both selection and model evaluation performed via stratified 5-fold cross-validation. Results: The proposed approach achieved an average balanced accuracy of 0.58 ± 0.07 and an average AUC of 0.71 ± 0.04. Average sensitivity and specificity were 0.48 and 0.68, respectively. The model obtained an average Gmean of 0.57, indicating balanced and stable classification performance. Conclusions: Our ML models trained on PET/CT radiomic features showed moderate discriminatory performance for TET risk stratification. Full article

Clonal hematopoiesis of indeterminate potential (CHIP) and the gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) are both linked to NLRP3-mediated cardiovascular inflammation, but their interaction has not previously been explored. This work proposes the CHIDT axis (clonal hematopoiesis–dysbiosis–TMAO), a feed-forward mechanism in which TET2 loss-of-function CHIP- and TMAO-generating Gram-negative gut dysbiosis mutually enhance cardiovascular risk. The model proceeds in three nodes. CHIP-associated intestinal immune dysregulation promotes luminal expansion of Gammaproteobacteria, which produce both trimethylamine via CntA/CntB-mediated L-carnitine oxidation and ADP-heptose as an obligate LPS biosynthetic intermediate. TMAO amplifies NLRP3 inflammasome activation through the SIRT3 → SOD2 → mtROS pathway. The evidence base of the CHIDT model is strongest for TET2-CHIP; the proposed extension to DNMT3A-CHIP rests on indirect, associative data and requires dedicated experimental confirmation before it can be considered established. TXNIP cascade, with predicted disproportionate potency in macrophages epigenetically primed by TET2 haploinsufficiency. High concentrations of TMAO have also been shown to suppress TET2 expression in endothelial cells through CYTB promoter hypermethylation, inducing NLRP3–GSDMD-dependent pyroptosis, although it remains unclear whether physiological TMAO levels can trigger this effect. Concurrently, ADP-heptose activates the ALPK1–TIFA–NF-κB pathway in bone marrow progenitors, favoring the expansion of mutant hematopoietic stem and progenitor cells. The model identifies three potential therapeutic strategies: NLRP3 inhibition, microbial TMA lyase inhibition, and microbiome-targeted reduction in Gram-negative bacteria. None has been tested in CHIP carriers stratified by plasma TMAO. Further studies in preclinical models and human cohorts integrating CHIP genotyping and TMAO quantification are needed to validate the CHIDT axis as a target for precision cardiovascular prevention. Full article

Adenoviral vectors are widely used for gene therapy and vaccine development. To circumvent pre-existing immunity against commonly used human adenovirus type 5, vectors based on rare human serotype or animal adenoviruses have attracted increasing interest. Previously, we constructed vectors based on fowl adenovirus 4 (FAdV-4) and replaced the knob of FAdV-4 fiber2 with that of FAdV-1 fiber1 to generate FAdV4-CF1K vectors with enhanced transduction efficiency in human cells. In this study, we aimed to modify the packaging system to efficiently produce FAdV-4 vectors carrying transgenes toxic to viral replication. Chicken LMH cells failed to form colonies at low seeding densities. We collected used medium from LMH cell cultures and used it as a supplement to adapt LMH cells, generating the colony-competent subclone LMH-C3532. A lentiviral vector encoding a codon-optimized tetracycline repressor (tetR) was transduced into LMH-C3532 to establish a tetR-integrated cell line, LMH-tetR24. An adenoviral plasmid, pKFAV4-CF1K-CtG, was constructed in which a tetracycline operator (tetO)-bearing CMV promoter controlled GFP expression. The SwaI-flanked GFP in this plasmid was replaced with the HA gene from an H5N1 influenza virus to generate pKFAV4-CF1K-CtHA. Linearized adenoviral plasmids were transfected into LMH-tetR24 cells, and recombinant FAdV4-CF1K-CtG and FAdV4-CF1K-CtHA viruses were successfully rescued, amplified, and purified. When infected with FAdV4-CF1K-CtG at various multiplicities of infection (MOI), the progeny virus yield from LMH-tetR24 cells was 4–10 times higher than that from LMH-C3532 cells. For FAdV4-CF1K-CtHA, the yield difference between the two cell lines was even more pronounced, reaching 3–4 orders of magnitude. Overexpression of HA in LMH-C3532 cells negatively affected FAdV4-CF1K-CtHA replication, resulting in smaller and fewer plaques. In conclusion, by separately integrating tetR into packaging cells and TetO into the adenoviral plasmid, we established a system that can be routinely used to package FAdV-4 vectors. Notably, this system facilitates the propagation of FAdV-4 vectors carrying toxic transgenes. Full article

Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome is an adult-onset inflammatory disorder caused by acquired mutations in UBA1, the gene encoding the primary ubiquitin-activating enzyme. The recognition of VEXAS has transformed the current understanding of autoinflammatory disease by demonstrating that somatic alterations arising within hematopoietic stem cells can precipitate severe, multisystem inflammation in later life. While pathogenic UBA1 variants are essential to disease pathogenesis, many affected individuals also harbor additional somatic mutations associated with clonal hematopoiesis, most commonly involving DNMT3A and TET2. These concurrent mutations may contribute to clonal architecture; however, their independent impact on inflammatory phenotype and hematologic manifestations remains incompletely defined. Emerging evidence suggests that co-occurring clonal hematopoiesis mutations may be independently associated with poorer overall survival, though their causal role remains unestablished. This review examines the evolving genetic framework of VEXAS syndrome, emphasizing UBA1 as the obligate driver mutation while reviewing current evidence regarding non-Met41 UBA1 variants and co-occurring somatic mutations. Full article

Background: Clonal hematopoiesis of indeterminate potential (CHIP) can lead to adverse outcomes and may begin early in life. This study aimed to investigate the association between early-life events and CHIP. Methods: In total, 456,658 participants from U.K. Biobank without baseline hematologic malignancies were enrolled. Exposures included 17 early-life events, including reproductive, childhood adversity, and pre-adulthood development factors. CHIP was derived from whole-exome sequencing for mutations in 74 driver genes. Logistic regressions were used to estimate associations between early-life events and the presence of any CHIP or gene-specific CHIP mutations. Results: Overall, 17,513 (3.8%) individuals with any CHIP were identified, among which the most common subtype was DNMT3A (2.4%), followed by TET2 (0.6%) and ASXL1 (0.4%). Compared with participants without sexual abuse in childhood, those who experienced such abuse were positively associated with CHIP (OR 1.35, 95% CI 1.02–1.80), especially among ASXL1, JAK2, and TP53 mutations. Long-term/recurrent antibiotic use as a child or teenager was positively associated with CHIP (OR 1.11, 95% CI 1.02–1.21), especially among DNMT3A, ASXL1, and EP300 mutations. Sex-specific differences were observed, including sexual abuse associated with ASXL1-CHIP in males and JAK2/TP53-CHIP in females and long-term/recurrent antibiotic use associated with DNMT3A/EP300-CHIP in males and ASXL1-CHIP in females. Furthermore, we identified circulating proteomic biomarkers shared by six pairs of early-life factors and gene-specific CHIP mutations, including B2M for sexual abuse and JAK2-CHIP. Conclusions: Early-life factors, especially sexual abuse and long-term/recurrent antibiotic use, were positively associated with the presence of CHIP, particularly among specific gene mutations, offering potential targets for susceptibility and pathogenesis exploration. Full article

Introduction: The Catalan chub (Squalius laietanus) is a freshwater cyprinid endemic to Catalonia, from the lower course of the Ebro River to the Tech, Tet, Agly, and Massane rivers in France. Classified as Vulnerable in the IUCN Red List (2024), its populations face significant threats due to anthropogenic pressures and the potential hybridization with the European chub (Squalius cephalus). Objective: This study aimed to characterize the genetic variation of the mitochondrial control region (CR) of S. laietanus across the main Catalan river basins to determine the population genetic structure of this species in the core of its distribution range. Methodology: A 789 bp fragment of the CR was sequenced in 334 chubs from 24 sampling sites collected by electrofishing between 2021 and 2025. The S. laietanus specific matrilineage of all these specimens had been previously detected by sequencing the Cytochrome c oxidase subunit I (COI) but this marker did not detect clear genetic structuring among basins. Results: In contrast to the low diversity within and among locations reported by COI, the CR showed a population structure distinguishing between northern (Muga, Fluvià, Daró, Ter, and Tordera rivers) and southern basins (Besòs, Llobregat, Gaià, Francolí, and Ebro rivers). In the southern rivers, a single haplotype, (H1), was present. This haplotype declined in abundance towards the north, being replaced with H2. In the Muga River, native Catalan chub populations showed the fixed H3 haplotype, suggesting strong isolation, while populations from the Daró River contained a private haplotype (H4). In contrast, the presence of a common and single haplotype in southern basins possibly resulted from genetic drift under strong summer droughts. Conclusions: Overall, these results reveal population structuring in S. laietanus and highlight the importance of considering regional differentiation in conservation and management strategies. Full article

Cronobacter spp. are opportunistic foodborne pathogens that can cause neonatal meningitis, necrotizing enterocolitis, and sepsis. This study conducted a systematic contamination survey and whole-genome epidemiological analysis of 562 low-water-activity food samples in Hunan Province of China. The results showed an overall Cronobacter spp. detection rate of 41.99% (236/562), with spices exhibiting the highest contamination rate (60.06%), and with high-level contamination samples (>110 MPN/g) concentrated in this category. The 236 isolates comprised 6 species, 120 sequence types, and 39 clonal complexes, with C. sakazakii being the most frequently isolated species (64.83%) and high-risk clones ST4, ST1, ST148, and ST64 prevailing. Multiple virulence genes (TraJ, fur, rcsAB, rpoS) and antimicrobial resistance genes (qnrS1, blaTEM-1, blaCTX-M-55, blaLAP-2, aac(3)-IId, aadA2, tet(A), floR, mcr-9.1, sul2) were detected. Core genome multilocus sequence typing (cgMLST) identified two clustering patterns: Cluster C, whose genetic clustering was consistent with transmission associated with potential common upstream raw materials across different brands and provinces, and Cluster G, whose clustering suggested potential persistent colonization in the production environment across multiple batches of the same brand. This study elucidates the contamination characteristics of Cronobacter spp. in low-water-activity foods from Hunan Province and provides a basis for WGS-based active surveillance and supply chain traceability. Full article

This study aimed to investigate the molecular basis of high-level tetracycline resistance to tetracycline antibiotics in Aeromonas hydrophila isolated from fish farming. Comparative genomic analysis of the tetracycline-sensitive strain NJ-35 and the tetracycline-resistant strain AH823 revealed that the tetracycline repressor gene tetR in AH823 had undergone base mutations, resulting in premature translational termination. The tetR gene in NJ-35 was inhibited using a plasmid-based antisense RNA strategy, and the knockdown efficiency was confirmed by RT-qPCR. The resulting tetR antisense RNA-expressing strain, AHtetR-as, exhibited significantly increased resistance to tetracycline antibiotics (minocycline, tetracycline, and doxycycline), but did not affect biofilm formation or hemolysis. Moreover, tetR knockdown in NJ-35 was associated with increased efflux activity and reduced intracellular doxycycline accumulation. Transcriptomic analysis revealed that genes encoding the 30S ribosomal subunit proteins showed a differential expression pattern, with rpsO upregulated and rpsD and rpsP downregulated. These findings suggest that tetR contributes to tetracycline resistance in A. hydrophila and is associated with broad transcriptional changes related to cellular transport and ribosomal function. Full article

Central chondrosarcoma is the second most common primary malignant bone tumour, and grade progression markedly worsens prognosis. The contributions of lipid metabolic reprogramming and epigenetic co-dysregulation to grade progression remain poorly characterised. We integrated a bulk RNA-seq discovery cohort of 53 graded central chondrosarcomas (GSE299759) with a single-cell analysis of eight chondrosarcomas (GSE184118). Because the atypical cartilaginous tumour (ACT) and dedifferentiated groups each comprised only three samples, the Grade 3 versus Grade 2 contrast was pre-specified as the primary comparison. Curated panels of 44 lipid metabolism genes and 50 epigenetic regulators were assessed by differential expression and a correlation-based connectivity ranking, evaluated by permutation testing. In the primary Grade 3 versus Grade 2 comparison, SQLE, ACACA, and FASN were upregulated (FDR < 0.05), indicating a grade-associated increase in de novo lipogenesis. In the exploratory Grade 3 versus ACT comparison, additional lipid genes (HMGCR, LDLRAP1) and the epigenetic regulators EHMT2 and SIRT2 showed altered expression, although the small ACT group limits these estimates. A connectivity ranking highlighted FASN, KMT2C, TET2, SETD5, and KDM5B; permutation testing confirmed this co-expression structure was non-random (p < 0.0001). Single-cell analysis showed FASN, SETD5, and KDM5B are expressed predominantly in malignant cells, whereas KMT2C and TET2 are not, indicating cell-type heterogeneity. De novo lipogenesis upregulation is the most consistent lipid alteration in high-grade central chondrosarcoma, nominating SQLE, ACACA, and FASN as candidates for experimental investigation. Full article

Enterococci are among the most frequently isolated environmental bacteria that cause mastitis in cows. This study aimed to determine the prevalence of virulence genes, as well as phenotypic and genotypic antibiotic resistance, among eighty enterococcal isolates from cases of bovine mastitis in Polish herds. The presence of virulence and antibiotic resistance genes was determined by PCR. E. faecalis isolates were found to carry more virulence genes than E. faecium isolates, including the efaA_fs (100%), ace (98.1%), gelE (86.5%), asa1 (63.5%), esp (57.7%) and cylA (17.3%) genes. The efaA_fm gene was the only virulence gene detected in E. faecium isolates. This study revealed that E. faecalis showed a higher virulence gene burden. The ermB gene was present in 90.9% of the Enterococcus spp. that were phenotypically resistant to erythromycin. Almost all tetracycline-resistant Enterococcus isolates carried the tet(M) gene (94.3%), either alone or in combination with the tet(L) and tet(O) genes. Three isolates harboured vanC genes and were susceptible to vancomycin (MIC = 4 μg/mL). The results confirm the high level of antimicrobial resistance of enterococci isolated from cows with mastitis and indicate the genes that may be responsible for this resistance. Full article

Background/Objectives. Pulmonary arterial hypertension (PAH) is a rare but severe disease which leads to right ventricular (RV) maladaptation, failure and death. Currently approved drugs have limited impact on disease progression. A multitarget strategy consisting of adenosine A₂B receptor activation and phosphodiesterase-4 (PDE4) inhibition, combined with human mesenchymal stromal cells (hMSCs) therapy, was tested in experimental PAH. The main objective was to determine whether the combination improved pulmonary hemodynamics, vascular remodeling, and RV function, given the limited disease-modifying effects of currently approved vasodilators. Methods. Vascular reactivity was assessed in isolated rat pulmonary artery rings exposed to the dual-target compound (LASSBio-1860) alone or in the presence of either ZM-241385 or MRS-1706. PAH was induced in male Wistar rats with monocrotaline (MCT, 60 mg·kg⁻¹) and confirmed by a decrease in pulmonary artery acceleration time to ejection time ratio (PAAT/TET). Animals were randomized to receive vehicle, hMSC (single i.v. dose, 1 × 10⁵ cells), LASSBio-1860 (62 mg·kg⁻¹·day⁻¹, p.o., 14 days), or their combination. Outcomes included PAAT/TET and RV cardiac output (RV-CO) by echocardiography, RV systolic pressure (RVSP) by direct puncture, Fulton index and RV wall thickness, lung histology (perivascular cell counts and wall thickness), and RV protein expression (TGF-β, CaMKII) by Western blot. Results. LASSBio-1860 produced endothelium-independent vasorelaxation of rat pulmonary arteries, consistent with A₂B agonism and PDE4 inhibition. In MCT-induced PAH, combination of LASSBio-1860 and hMSCs resulted in recovery of PAAT/TET and RV-CO, decrease in RVSP, RV hypertrophy, vascular inflammation and remodeling by downregulation of ventricular TGF-β and CaMKII. Conclusions. Combination of LASSBio-1860 with hMSC improved RV function, attenuated pulmonary hypertension, RV and vascular remodeling, and reduced inflammatory/proliferative signaling in MCT induced-PAH, supporting a promising multitarget therapeutic strategy for PAH. Full article

Antibiotic resistance genes (ARGs) are increasingly recognized as a concern in drinking water, yet the factors influencing their persistence from raw to finished water in drinking water treatment plants remain poorly understood. This study investigated the occurrence, removal, and potential factors associated with the persistence of ARGs (sul1, sul2, and tetG) in a full-scale rapid sand filtration drinking water treatment system with intermediate and post-chlorination. ARGs were detected in raw water at a median total concentration of 10⁶ copies/L and remained detectable in finished water at 10⁴ copies/L. Relative ARG abundance increased after treatment despite substantial absolute reductions (2.1–3.6 log). Intermediate chlorination achieved the greatest ARG log reduction value (0.53–2.4 log), likely due to higher chlorine dose and lower pH favoring HOCl formation. By contrast, post-chlorination at higher pH provided limited additional removal, possibly due to predominance of less reactive OCl⁻ and survival of chlorine-tolerant bacteria. Multivariate analyses showed a shift from particle-bound ARGs in raw water to dissolved organic matter (DOM) and fine-particle-associated fractions along the treatment train. These findings suggest that reducing fine particles and DOM, together with optimized disinfection, may help lower ARG-associated risk in finished water. Full article

Acinetobacter is one of the most relevant pathogenic and nosocomial bacteria in human medicine. However, in veterinary medicine, particularly in Spain, there are very few studies on the impact and frequency of infections due to this genus. The main objective of this study was to characterise Acinetobacter isolates recovered at the Complutense Veterinary Teaching Hospital of the Complutense University of Madrid (HCV-UCM), with special emphasis on detecting antimicrobial resistance. A total of 23 isolates obtained from different animal species and samples over a 25-year period were included in the study, based on their identification as Acinetobacter by VITEK-2. Identification was made by using MALDI-TOF, VITEK-2, whole-genome sequencing (WGS) and a chromogenic medium. WGS confirmed that 13 of the 23 isolates belonged to Acinetobacter spp. Antimicrobial susceptibility was interpreted according to CLSI guidelines using the Kirby–Bauer disk diffusion and broth microdilution method. The proportion of clinical isolates identified as Acinetobacter spp. at the HCV-UCM was 0.3%. Of these, 15.4% (2/13 isolates) were classified as multidrug-resistant. Two isolates with the highest MIC for tigecycline carried the tet(X) gene, and two isolates harboured mutations in both gyrA and parC QRDR regions. The results of this study suggest that, in this hospital, antimicrobial resistance among Acinetobacter isolates may not yet be widespread. Full article

We report a female in her late 80s with high-risk pleomorphic mantle cell lymphoma (MCL) harboring germline ATM mutation and 17p deletion who achieved complete metabolic response with zanubrutinib plus rituximab. Serial peripheral blood next-generation sequencing (NGS) during remission revealed emergence of a molecularly distinct pre-leukemic clone characterized by DNMT3A, TET2, and a TP53 point mutation (p.Tyr220Cys)—distinct from the original 17p deletion. Approximately 20 months after MCL diagnosis, she developed acute myeloid leukemia (AML) with FLT3-TKD and NPM1 mutations, confirming transformation of the pre-leukemic clone. Longitudinal VAF tracking demonstrated complete eradication of MCL-associated mutations (ID3, BIRC3) while the myeloid clone expanded. This case provides direct molecular evidence that AML arose from clonal evolution of a pre-existing hematopoietic clone rather than direct MCL transformation, with implications for understanding second malignancies in BTK inhibitor-treated patients. Full article

DNA methylation, the covalent addition of methyl groups to cytosine (5mC) or adenine (6mA) in DNA, is a fundamental mechanism of epigenetic inheritance conserved from bacteria to humans. Fungi provide a uniquely informative window into the evolutionary logic of methylation systems. Spanning more than 1 billion years of diversification, the kingdom encompasses species that have lost cytosine methylation entirely, lineages that use 5mC to silence transposons and drive the irreversible genome-defense process known as repeat-induced point mutation (RIP), and early-diverging lineages, in which 6mA has emerged as a prominent chromatin mark. The methyltransferases underlying these strategies (DIM-2, RID, DNMT1-RFD, DNMT5, and the MT-A70 complex) and the recently characterized demethylases Dmt1 and CcTet are structurally and mechanistically distinct from their mammalian counterparts. Here we review the mechanisms, targets, and biological functions of fungal DNA methyltransferases and demethylases, incorporating cryo-EM structural insights into DIM-2 and DNMT5 catalysis, analyses of DNMT gene loss as a continuous evolutionary process, the antiviral role of DIM-2 in vegetative hyphae, and the emerging model of 6mA as a heritable regulatory mark in early-diverging lineages. By integrating these advances, this review offers the updated and comprehensive account of DNA methylation across fungi. Full article