Search Results (1,964)

Organoid and organ-on-chip technologies are rapidly evolving platforms for viral research that integrate stem cell biology, tissue engineering, and microfluidics to recapitulate key structural, mechanical, biochemical, and cellular features of human and animal physiology. By incorporating multicellular organoids into perfused microfluidic systems, these models can provide complex, dynamic, and physiologically relevant micro-environments for investigating virus–host interactions that are difficult to capture in conventional two-dimensional cultures and static organoids. Controlled flow, shear stress, extracellular matrix organization, tissue–tissue interfaces, and multicellular signaling enable mechanistic investigation of viral infectivity, dissemination, tissue injury and immune activation. Integration of real-time imaging and biosensors further permits longitudinal monitoring of viral replication, host responses, and tissue integrity, expanding the potential of these platforms for antiviral drug discovery. Recent organoid-on-chip studies using brain, skin, vaginal, respiratory, and intestinal models have demonstrated how tissue architecture, mechanical forces, glycocalyx dynamics, and immune–stromal interactions influence viral tropism and pathogenesis. In this review, we provide a mechanistic and translational overview of organoid and organ-on-chip technologies for studying viral infections, with particular emphasis on models of herpes simplex virus (HSV)-mediated disease. We further examine advances in immune integration, multi-organ systems, biosensing, and computational approaches that are expanding the complexity and predictive potential of these models. Importantly, patient-derived organoids and organ-on-chip platforms can capture interindividual differences in viral susceptibility, host responses, and therapeutic efficacy, providing pharmaceutical research with more precise, patient-relevant data to support drug prioritization and precision antiviral medicine. Finally, we discuss key barriers to broader adoption, including organoid maturation, biological and technical variability, reproducibility, scalability, biosafety, cost, standardization, and regulatory validation. Collectively, these advances position organoid and organ-on-chip technologies as powerful human-relevant models that bridge reductionist in vitro systems and human disease, while continued optimization, standardization, and validation will be essential to realize their full potential for mechanistically informed antiviral discovery, therapeutic development, and precision medicine. Full article

Background: Global antibiotic consumption continues to rise across pediatric and adult populations, while the genotoxic consequences of host eukaryotic exposure remain less systematically characterized than the parallel problem of antimicrobial resistance. Several lines of evidence, from molecular cytogenetics, redox biology, and systems toxicology, now permit a more mechanistically resolved synthesis of antibiotic-induced genome stress than was previously possible, although a substantial fraction of this evidence is preclinical and warrants cautious clinical extrapolation. Scope: This narrative review evaluates the molecular mechanisms, cytogenetic biomarkers, and translational implications of antibiotic-induced genotoxicity, with a primary focus on six clinically prominent classes (fluoroquinolones, nitroimidazoles, aminoglycosides, macrolides, β-lactams, and tetracyclines) and a brief extension to glycopeptides and glycylcyclines. We organize the evidence around three convergent mechanistic axes rather than around individual drugs. Key findings: Accumulating evidence supports three intersecting off-target axes: (i) eukaryotic topoisomerase II interference, principally documented for fluoroquinolones; (ii) mitochondrial dysfunction, reflecting the evolutionary kinship between the mitoribosome and bacterial ribosomes; and (iii) inflammation-coupled redox stress, often amplified by microbiome perturbation. These pathways converge on a common spectrum of DNA lesions—including double-strand breaks, oxidatively modified bases, replication-fork stalling, and chromosomal mis-segregation) detected by complementary assays (CBMN-Cyt, comet, γH2AX, and oxidative and mitochondrial biomarkers). Pediatric, pregnant, geriatric, and oncology populations may represent biologically distinct susceptibility strata, although direct human evidence for several of these inferences remains limited. Limitations: Causal inference is constrained by infection as a confounder, frequent use of supratherapeutic in vitro concentrations, reliance on immortalized cell lines that may not recapitulate primary-cell repair capacity, inter-laboratory variability across cytogenetic assays, and a marked scarcity of pediatric and pregnancy biomonitoring data. Most existing positive signals derive from preclinical models; clinically validated long-term outcomes, particularly carcinogenic endpoints, remain inconsistently demonstrated for most antibiotic classes outside metronidazole. Conclusions: Antibiotic-induced genotoxicity appears to be a measurable and mechanistically tractable dimension of drug safety, though its clinical magnitude in real-world exposure scenarios requires further investigation. Integrating multi-omics, microphysiological systems, single-cell genotoxicology, and AI-assisted prediction may improve risk resolution, particularly in vulnerable populations. We argue that antimicrobial stewardship discussions should consider host genome integrity alongside resistance, while remaining mindful that the mechanistic case currently outpaces clinical-endpoint validation. Full article

Foodborne illnesses caused by Salmonella Typhimurium remain a major public health concern worldwide. Although ST19 has historically been a dominant lineage within this serotype, ST213 has become increasingly prevalent in Mexico. The biological factors underlying this epidemiological shift remain incompletely understood. In this study, we compared virulence-associated gene repertoires and stress-related phenotypes in representative S. Typhimurium ST19 and ST213 strains with distinct virulotypes (VTs). Comparative genomic analysis identified 119 virulence-associated genes distributed across 26 VTs, with most genes broadly conserved between genotypes. Representative strains were evaluated under simulated gastrointestinal tract (GIT) stress conditions, in post-stress recovery assays, and in a Caenorhabditis elegans infection model. Under the experimental conditions evaluated, the representative ST213 strains SAL109 (VT1), SAL115 (VT1), and SAL016 (VT12) tended to show higher persistence under host-associated stress conditions and greater intestinal colonization capacity in C. elegans than the ST19 strain SAL004 (VT23). However, strains sharing the same VT did not necessarily exhibit similar phenotypes, indicating that virulence-associated gene repertoires alone do not fully explain stress tolerance or host colonization behavior. Overall, these findings highlight phenotypic variability among strains with similar virulence gene content and support the importance of integrating genomic and phenotypic approaches to better understand the biology of emerging S. Typhimurium lineages. Full article

The orthoflavivirus capsid (C) protein is a multifunctional protein that plays essential roles throughout the viral life cycle. Besides viral RNA encapsidation for nucleocapsid assembly, it associates with lipid droplets, interacts with host proteins, and translocates to the nucleus, although its nuclear functions are still poorly understood. How these diverse activities are coordinated remains an open question. Post-translational modifications (PTMs), which are key regulators of protein function, have emerged as critical modulators of the infection cycle in many RNA viruses. However, little is known about the occurrence and functional significance of PTMs in orthoflavivirus C proteins. Here, we review the current evidence on PTMs in orthoflavivirus C proteins and integrate insights from studies of other RNA viruses to propose mechanisms by which PTMs may regulate C protein function. To complement this review, we performed a comparative in silico analysis of predicted PTM sites in the C proteins of dengue, Zika, West Nile, and Japanese encephalitis viruses. By integrating PTM predictions with experimentally validated modification sites, residue conservation, and structural mapping, we identified conserved regulatory hotspots that represent promising targets for future experimental validation. Together, these findings highlight PTMs as an underexplored regulatory mechanism in orthoflavivirus capsid biology and provide a framework for future mechanistic investigations. Full article

RNA-dependent RNA polymerases (RdRPs) are essential enzymes involved in RNA virus replication and eukaryotic RNA silencing. They are generally absent in vertebrates but present in some invertebrate lineages, such as nematodes and certain arthropods. Brevipalpus yothersi is a phytophagous mite of agricultural relevance due to its role as a vector of plant-infecting viruses. We have identified two RdRPs on the genome of this mite species that, unexpectedly, are not of eukaryotic origin. Phylogenetic reconstruction and comparisons of 3D protein structures revealed similarity with viral RdRPs of the Partitiviridae family. Both RdRPs retain conserved catalytic motifs at the protein sequence level, and expression was confirmed by RNAseq and qPCR across mite developmental stages, with a peak during the nymphal stage. K-mer profiles showed similarity with mite endogenous genes, suggesting gene amelioration after the integration, or being derived from a viral donor already adapted to the mite. Our study also identified orthologs in other Brevipalpus species, but not in other Acari relatives, supporting that the horizontal gene transfer event is circumscribed to the Brevipalpus genus. These findings highlight an intriguing case of viral gene domestication in arthropods that might influence their developmental biology and the host–virus interaction. Full article

Squamous cell carcinoma of the anal canal (SCAC) is a rare malignancy whose incidence has been steadily increasing worldwide. Persistent infection with high-risk human papillomavirus (HPV), particularly HPV16 and HPV18 genotypes, is the main etiological factor and plays a central role in tumor development. While combined chemoradiotherapy remains the standard treatment for localized disease and achieves high rates of tumor control, a considerable proportion of patients experience recurrence or present with advanced disease. For the latter, therapeutic options remain limited. Over the last decade, advances in genomic profiling have significantly expanded our understanding of SCAC biology. Recurrent alterations affecting the PI3K/AKT/mTOR pathway, especially PIK3CA mutations, have emerged as the most common molecular events, particularly in HPV-positive tumors. Additional alterations involve receptor tyrosine kinase signaling, chromatin remodeling genes, DNA damage response pathways, and components of the MAPK cascade. Moreover, HPV-positive and HPV-negative tumors display distinct molecular features with important prognostic implications. Immunotherapy has recently become an important component of treatment for advanced SCAC, although reliable predictive biomarkers are still lacking. This review summarizes the current evidence on the molecular landscape of SCAC, discusses emerging prognostic and predictive biomarkers, and highlights potential opportunities for the development of more personalized therapeutic strategies. Full article

Brassica crops, encompassing globally important vegetables and oilseeds, face severe threats from diverse biotic and abiotic stresses. Plant secondary metabolites constitute the chemical foundation of defence, and metabolomics has emerged as an effective systems biology tool for comprehensively dissecting stress-induced metabolic changes. Recent progress in applying metabolomics to elucidate defence mechanisms in Brassica crops is systematically synthesised here. Major stresses confronting Brassica crop production and the metabolic basis of plant defence are first outlined. Current analytical platforms, including liquid chromatography–mass spectrometry, gas chromatography–mass spectrometry, ion mobility spectrometry, and mass spectrometry imaging, are critically evaluated alongside data processing workflows and multi-omics integration strategies. Key defence-related metabolite classes identified in Brassica crops, notably glucosinolates (GSLs) and their hydrolysis products, phenolic compounds, and lipid-derived signalling molecules, are surveyed with emphasis on their respective functions in biotic and abiotic stress responses. Metabolomics has been instrumental in revealing distinct metabolic reprogramming patterns triggered by diverse stresses, including pathogen infection, insect herbivory, drought, salinity, temperature extremes, and heavy metal stress. Metabolomics-informed crop improvement strategies, including marker-assisted breeding, genetic and metabolic engineering, and precision agronomic practices, are discussed together with current technical bottlenecks and future directions involving artificial intelligence, metabolic modelling, and spatial metabolomics. The compiled knowledge provides a comprehensive reference for leveraging metabolomics to enhance stress resilience and sustainable production of Brassica crops. Full article

Background and Clinical Significance: Skin-limited Langerhans cell histiocytosis (LCH) is a clinically heterogeneous disease, ranging from self-healing forms to fulminant multi-organ failure, the latter being more often described in infants, especially preterm neonates. The optimal therapy for cutaneous LCH remains controversial; the possibilities vary from a watchful waiting approach to systemic chemotherapy. Case Presentation: This case report describes an exceptionally rare and clinically challenging course of skin-limited LCH in a prematurely born infant treated at the Department of Oncology and Hematology, Children’s Hospital Zagreb, Croatia. At presentation, the patient exhibited several features suggestive of aggressive disease biology. However, therapeutic decision-making was complicated by extreme prematurity and young age, both of which significantly increased vulnerability to treatment-related toxicity. Following failure of topical therapy, systemic treatment was initiated according to the LCH-IV trial, primarily due to concerns regarding potential evolution into multisystem LCH. During treatment, the patient developed multiple life-threatening complications, namely severe infections (Staphylococcus aureus endocarditis, Pneumocystis jirovecii pneumonia, and Enterobacter cloacae sepsis), aggravated by secondary hypogammaglobulinemia, neutropenia, and iatrogenic adrenal insufficiency. Conclusions: The varied nature of cutaneous LCH underscores the necessity for a tailored treatment approach. When deciding on the treatment modality, clinicians should weigh the benefits of aggressive therapies, ensuring better disease control, against the potential for severe adverse effects, particularly in young, fragile infants with immature immunity. Full article

The continuous slowdown in the research and development of new antibiotics and antibiotic overuse have turned the problem of antibacterial resistance into a global public health crisis. As a very promising alternative to multi-drug-resistant bacterial infection, phage therapy is receiving renewed attention. However, the inherent biological limitations of natural phages restrict their extensive clinical application. This review examines how synthetic biology can be harnessed to transform phages and to build the next generation of antibacterial therapies. We outline the main advantages of natural phages, including high host specificity, self-amplification, bactericidal activity and the ability to degrade biofilms. We also point out the bottlenecks of clinical applications of bacteriophages, such as narrow host range, rapid removal in the body and potential genetic safety risks. Moreover, we elaborate on the core synthetic biological tools used to overcome the above limitations, including CRISPR-Cas gene editing, receptor-binding protein reprogramming, functional load delivery and immunogenic regulation, and summarize the recent clinical progress and personalized treatment process. The increasing clinical evidence shows that synthetic biology can effectively overcome the inherent defects of natural bacteriophages, confirming the safety and initial efficacy of bacteriophage therapy. Engineered phages provide a practical strategy to meet the antimicrobial resistance challenge. Clinical applications of such phages will mainly depend on progress in production standardization, regulatory framework construction and scientific and reasonable joint treatment program development. Full article

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) selectively triggers apoptosis in malignant, infected, or stressed cells while sparing normal tissues, making it an attractive therapeutic candidate. However, many tumors exhibit intrinsic or acquired resistance to TRAIL, driven by reduced DR4/DR5 surface expression, elevated decoy receptor levels, dysregulated DISC assembly, overexpression of c-FLIP and anti-apoptotic Bcl-2 family proteins, or activation of survival pathways such as NF-κB, PI3K/Akt, and MAPK. Moreover, TRAIL receptors can initiate non-canonical signaling pathways that promote migration, invasion, and metastasis in specific oncogenic contexts, thereby further limiting therapeutic efficacy. We aimed to integrate mechanistic insights into TRAIL biology with current therapeutic advances, providing a comprehensive framework for understanding resistance and for designing rational TRAIL-based combination strategies. We summarized the structural and signaling features of TRAIL receptors, outlined the major determinants of TRAIL sensitivity, and evaluated predictive biomarkers that may guide patient selection. In addition, we examined next-generation TRAIL agonists and targeted delivery systems developed to enhance receptor clustering, pharmacokinetics, and tumor specificity. Together, these insights highlight the therapeutic promise of mechanistically informed TRAIL combinations. A deeper understanding of resistance pathways and biomarker-guided stratification will be essential for restoring apoptotic competence and improving clinical outcomes. Full article

Human skin is a complex organ whose functions depend on coordinated interactions between the epidermal and stromal layers. Reproducing this architecture in vitro remains challenging, as existing human models reproduce a restricted subset of the structural and functional features inherent to native tissue. Here, we describe a fibrin-based, multicellular human skin equivalent (HSE) composed of primary human keratinocytes, fibroblasts, preadipocytes, and endothelial cells organized into epidermal and stromal compartments. The resulting constructs achieved mature epidermal stratification with appropriate phenotypic markers, developed robust barrier properties, underwent spontaneous endothelial network assembly, and exhibited transcriptional profiles consistent with native skin. Optimized culture conditions supported long-term structural and functional stability through 42 days, maintaining a proliferative basal cell layer and intact epidermal architecture. Non-destructive optical coherence tomography enabled longitudinal monitoring of epidermal growth, providing a practical method for real-time quality assessment. To evaluate their utility for disease modeling, HSEs were challenged with cowpox virus to model infection by a classic dermotropic virus. Infected HSEs reproduced classic epithelial pathologies of human orthopoxvirus infection and exhibited dose-dependent suppression of host interferon signaling pathways, recapitulating known viral immune-evasion mechanisms. Together, these findings establish the vascularized, adipose-integrated HSE as a platform for long-term studies of human skin biology, host–pathogen dynamics, and therapeutic development. Full article

Immune checkpoint inhibitors have transformed the treatment of multiple malignancies by restoring antitumor T-cell activity. Their clinical identity is therefore that of immune-enhancing therapies. However, the biology of the PD-1/PD-L1 axis is more complex than simple immune inhibition. Human inborn errors of PD-1 or PD-L1 signaling indicate that this pathway contributes to immune homeostasis, tolerance, protection against selected infections, and the development of memory B cells and antibody responses. These observations raise an important translational question: Can prolonged pharmacologic blockade of PD-1 or PD-L1 can, in selected clinical contexts, induce or reveal acquired humoral immune dysfunction? This review synthesizes evidence linking PD-1/PD-L1 disruption to altered class-switched memory B-cell biology, antibody responses, vaccine immunogenicity, infection susceptibility, and secondary antibody deficiency. It also incorporates emerging evidence that checkpoint blockade may expand age-associated B cells, a population associated with impaired neutralizing antibody responses after vaccination, and counterbalances evidence that vaccination during ICI therapy may enhance antitumor immunity and survival. Current clinical evidence does not establish the incidence, prevalence, reversibility, dose dependence, or causality of an ICI-induced antibody-deficiency syndrome. Instead, the available data support a hypothesis-generating model of heterogeneous humoral remodeling, ranging from preserved or enhanced vaccine-associated immune activation to qualitative antibody failure and secondary antibody deficiency in susceptible patients. Future studies should incorporate baseline and longitudinal measurements of immunoglobulins, vaccine-specific and neutralizing antibodies, class-switched memory B cells, age-associated B cells, plasmablasts, infection burden, and exposure to immunosuppressive treatment. Full article

The human placenta is a temporary organ structured to optimize exchange between the maternal and fetal circulatory systems. Its fetal component consists of highly branched chorionic villi, which are anchored to the maternal uterine wall and project into the intervillous space. The outer surface of these villi is lined by a multinucleated, continuous layer called the syncytiotrophoblast, which is supported by an underlying layer of proliferative cytotrophoblast cells and the invasive extravillous trophoblast (EVT). This cellular bilayer forms a selective barrier that directly bathes in maternal blood, allowing for the efficient transfer of oxygen and nutrients while structurally preventing the direct mixing of maternal and fetal blood cells. Human placental studies have been stymied by ethical and accessibility constraints. Stem cell biology has now revolutionized the capacity to model human placental development, in particular with the derivation of human trophoblast stem cells (hTSCs) and organoids. Authentic, self-renewing human trophoblast stem cells (hTSCs) were first derived not from pluripotent stem cells but from primary tissue—first-trimester villous cytotrophoblasts and blastocysts. Derivation from human pluripotent stem cells (PSCs) followed only subsequently, along two principal routes: conversion of naive PSCs, which retain extraembryonic competence, and induction from primed PSCs, as well as by direct reprogramming of somatic cells to induced hTSCs. An important advance underlying these improvements is the mapping of a global reprogramming roadmap. Multi-omic and lineage-tracing experiments have mapped the stepwise transcriptional and epigenetic conversions of fibroblasts to hTSCs, including sequential chromatin reconfiguration, trophoblast gene network activation, and repression of somatic signatures. These results identify major regulatory bottlenecks and intermediate states, improving reprogramming fidelity. The derivation of stem-cell-based trophoblast organoids now enables complex modeling of placental architecture, function, and disease susceptibility in vitro. These organoids accurately recapitulate placental barrier functions and immunological features, allowing for examinations of maternal–fetal health, pregnancy disorders, and placental infection response to viruses like cytomegalovirus and SARS-CoV-2. Looking ahead, the integration of reprogramming and organoid technologies will propel patient-specific and tailor-made models for personalized diagnostics, drug screening, and mechanism studies. As we unravel the molecular ballet of trophoblast induction, such discoveries have the potential to bridge basic translational gaps in reproductive biology and maternal–fetal medicine. Full article

Pseudomonas savastanoi pv. phaseolicola, the causal agent of halo blight of bean, is a useful model for studying bacterial adaptation to plant infection. Although its toxins, effectors, population dynamics, and epidemiology have been investigated for decades, these aspects have often been treated separately. This narrative synthesis reinterprets the available literature within a stage-based infection framework encompassing host-surface colonization, establishment of a compatible apoplastic habitat, evasion of host immune responses, multiplication, and spread to another compatible host. Particular attention was given to studies published after the last major review on this pathovar, whereas older studies were retained when they represented primary reports, classical experimental evidence, or information that has not been superseded. The review shows that successful infection is best understood as involving opportunistic entry, rapid transition from an epiphytic to a pathogenic lifestyle, effector-dependent immune suppression, phaseolotoxin-mediated manipulation of host primary metabolism, the exploitation or establishment of hydrated apoplastic conditions, and environmentally driven dissemination. It also distinguishes experimentally supported mechanisms from unresolved or hypothesis-generating areas, including stomatal reopening, micronutrient acquisition, population-level division of labor, alternative hosts, and symptomless reservoirs. The major synthesis emerging from this review is that the infection biology of P. savastanoi pv. phaseolicola cannot be reduced to individual virulence factors because disease development depends on how these factors are coordinated with host-derived resources, immune constraints, and environmental opportunities. Full article

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system characterized by immune-mediated demyelination and neurodegeneration. Although the exact cause of MS remains unclear, accumulating epidemiological and immunological evidence strongly implicates Epstein–Barr virus (EBV) infection as a major environmental factor associated with disease development. Nearly all individuals with MS are EBV seropositive, and longitudinal studies have demonstrated that EBV infection precedes MS onset, supporting a causal relationship. EBV establishes lifelong latency in B cells and can profoundly influence host immune responses, providing several potential mechanisms through which it may contribute to autoimmunity. In this review, we summarize current knowledge of EBV biology and discuss epidemiological findings linking EBV infection with MS risk. We then examine alterations in EBV-specific immune responses observed in MS, including dysregulated humoral and cellular immunity. Particular attention is given to molecular mimicry involving the Epstein–Barr nuclear antigen 1 (EBNA1) and central nervous system proteins, which may promote cross-reactive autoimmune responses. Finally, we discuss evidence for the presence and potential role of EBV-infected immune cells within the MS brain and highlight key unanswered questions that remain critical for understanding EBV-driven neuroinflammation. Full article