Search Results (399)

Background: Adrenocortical carcinoma (ACC) is a rare, aggressive malignancy where endogenous steroid excess may foster immune evasion. However, whether this hormonal axis directly modulates the antigen presentation machinery remains unclear. Methods: We applied an immunoinformatics approach to the TCGA-ACC cohort (n = 79) to investigate relationships among steroid phenotype, HLA expression, tumor microenvironment (TME), and patient outcome. Key findings were assessed in an independent validation cohort (ENSAT-ACC, n = 44) using C1A/C1B molecular subtypes corresponding to the steroid phenotypes. Results: Stratification by steroid phenotype revealed two distinct immunological profiles. The high steroid production (HSP) phenotype was associated with suppressed HLA expression and a lymphocyte-depleted “cold” TME. In contrast, the low steroid production (LSP) phenotype displayed elevated HLA expression, enriched T-cell infiltration, and upregulation of immune checkpoints (e.g., PDCD1, CTLA4), consistent with an inflamed but exhausted TME. The core signature of HLA downregulation in the HSP-like phenotype (C1A) and the significant survival advantage of the LSP-like phenotype (C1B) were confirmed in the validation cohort, demonstrating biological robustness despite platform and sample size differences. Conclusions: These findings identify the steroid phenotype as a critical regulator of immune escape in ACC. Our results support incorporating this stratification as a biomarker for patient selection, identifying LSP tumors as the subgroup most likely to benefit from immune checkpoint blockade due to their “hot” yet exhausted microenvironment. Full article

Background: Eosinophilic esophagitis (EoE) is a chronic, food antigen-driven disease of the esophagus that causes considerable morbidity. Elimination of allergenic foods from a patient’s diet is a highly effective treatment. However, existing allergen testing modalities are not effective at identifying EoE-causal foods. We sought to determine the extent to which positive results for two functional T-cell assays, the EoE Milk Test and EoE Soy Test, associated with the clinical outcomes of EoE milk allergy and EoE soy allergy, respectively. Methods: Subjects were enrolled into one of two study designs: a prospective observational study or a retrospective case/control study. Additional control samples were obtained from an institutional core. The EoE Milk and Soy Tests were performed on peripheral blood samples, and the association between positive tests and clinical outcomes was determined using Receiver Operating Characteristic curves and other performance measures. Results: The EoE Milk Test maintained reliability regardless of disease activity or recent milk consumption and had 87% sensitivity and 83% specificity for EoE milk allergy in all study subjects (control and EoE). The EoE Soy Test had 90% sensitivity and 93% specificity in all subjects. Conclusions: Our evaluation of the EoE Milk and Soy Tests demonstrates that these functional T-cell assays hold promise as a predictive tool for identifying causal allergens in eosinophilic esophagitis patients. Full article

Developing effective CAR-T cell therapy for solid tumours remains challenging because of biological barriers such as antigen escape and an immunosuppressive microenvironment. The aim of this study is to develop a mathematical model of the spatio-temporal dynamics of tumour processes in order to assess key factors that limit treatment efficacy. We propose a reaction–diffusion model described by a system of partial differential equations for the densities of tumour cells and CAR-T cells, the concentration of immune inhibitors, and the degree of antigen escape. The methods of investigation include stability analysis and numerical solution of the model using a finite-difference scheme. The simulations show that antigen escape produces a resistant tumour core and relapse after an initial regression; increasing the escape rate from $\gamma =0.001$ to $0.1$ increases the final tumour volume at $t=100$ days from approximately 35.3 a.u. to 36.2 a.u. Parameter mapping further indicates that for $\gamma \le 0.01$ tumour control can be achieved at moderate killing rates ($k_{CT}\approx 1{\mathrm{day}}^{-1}$), whereas for $\gamma \ge 0.05$ comparable control requires $k_{CT}\approx 2$–$5{\mathrm{day}}^{-1}$. Repeated CAR-T administration improves durability: the residual normalised tumour volume at $t=100$ days decreases from approximately 4.5 after a single infusion to approximately 0.9 (double) and approximately 0.5 (triple), with a saturating benefit for further intensification. We conclude that the proposed model is a valuable tool for analysing and optimising CAR-T therapy protocols, and that our results highlight the need for combined strategies aimed at overcoming antigen escape. Full article

Pulmonary vascular proliferative lesions are rarely reported and poorly characterized in animals. In this study, we describe 13 cases identified in wild Korean raccoon dogs (Nyctereutes procyonoides), suggesting a higher-than-expected incidence in this species. Gross examination revealed villous projections within the lumina of pulmonary vessels, sometimes accompanied by pneumonia, hemorrhage, or Dirofilaria immitis (heartworm) infection. Most affected animals also presented with thick, dark gray cutaneous crusts associated with scabies infestation. Histopathologically, the lesions consisted of papillary proliferations within thickened vascular lumens. Special stains (Masson’s trichrome and Elastic Verhoeff–Van Gieson) demonstrated a single layer of endothelial cells lining fibromuscular and collagenous thick cores. Immunohistochemistry confirmed endothelial origin and benign proliferative nature, with positive expression of CD31, collagen types I, III, and IV, and proliferating cell nuclear antigen (PCNA). To date, pulmonary vascular proliferative lesions have not been well documented in N. procyonoides, and baseline pathological data, including findings from special stains, are lacking. These findings indicate that pulmonary vascular proliferative lesions may be underrecognized in raccoon dogs and suggest a likely association with chronic vascular injury related to parasitic infections. Further studies are warranted to elucidate the underlying mechanisms and contributing factors. Full article

Background: Memory B cells (B_mem) facilitate the generation of renewed and rapid antigen-specific antibody responses long after the initial antigen exposure, at a time when circulating serum antibodies may have declined. As the generation and/or recruitment of B_mem is at the core of most vaccination strategies, the assessment of antigen-specific B_mem is highly informative for forecasting and profiling the elicited B cell immune response. Methods: The two prevalent techniques used to detect antigen-specific B_mem cells at single-cell resolution are probe-based flow cytometry and B cell ImmunoSpot, while the measurement of B cell-derived antibodies in culture supernatants of stimulated B cells offers a semi-quantitative alternative. To the best of our knowledge, a direct side-by-side comparison of these assay systems has not yet been reported using the same starting PBMC material in a blinded fashion to test all three assays simultaneously. Results: These three assay systems were run in parallel to detect SARS-CoV-2 Wuhan-1 strain Spike-specific IgG⁺ B_mem in peripheral blood mononuclear cell (PBMC) samples obtained from well-defined cohorts comprising pre-COVID-19 era “naïve” individuals (negative controls), individuals shortly after recovery from a PCR-verified SARS-CoV-2 infection (positive controls), and a cohort of donor PBMCs isolated in 2024 (the experimental group). Each assay was able to discern Spike-exposed individuals from naïve , with ImmunoSpot suggesting superior sensitivity and specificity. ImmunoSpot and flow cytometry results were closely correlated. Conclusions: The study demonstrates that all three assays are suited for the detection of specific B_mem in antigen-primed individuals when such B_mem occur in the mid- to high-frequency range, and that they broadly concur. Strengths and weaknesses of the three test systems are discussed. Full article

Background: Chromobacterium violaceum is an emerging multidrug-resistant (MDR) Gram-negative bacterium associated with severe septicemia, abscess formation, and high mortality, particularly in immunocompromised individuals. Increasing antimicrobial resistance and the absence of approved vaccines underscore the urgent need for alternative preventive strategies. Traditional vaccine approaches are often inadequate against genetically diverse MDR pathogens, prompting the use of computational immunology and reverse vaccinology for vaccine design. Objectives: This study aimed to design and characterize a novel multi-epitope subunit vaccine (MEV) candidate against C. violaceum using a comprehensive pangenome-guided subtractive proteomics and immunoinformatics pipeline to identify conserved antigenic targets capable of eliciting strong immune responses. Methods: Comparative genomic analysis across eight C. violaceum strains identified 3144 core genes. Subtractive proteomics filtering yielded two essential, non-homologous, surface-accessible, and antigenic proteins—penicillin-binding protein 1A (Pbp1A) and organic solvent tolerance protein (LptD)—as vaccine targets. Cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and B-cell epitopes were predicted and integrated into a 272-amino-acid MEV construct adjuvanted with human β-defensin-4A using optimal linkers. The construct was evaluated through structural modeling, molecular docking with TLR4, molecular dynamics simulation, immune simulation, and in silico cloning into the pET-28a(+) vector. Results: The MEV construct exhibited strong antigenicity, non-allergenicity, and non-toxicity, with stable tertiary structure and favorable physicochemical properties. Docking and dynamics simulations demonstrated high binding affinity and stability with TLR4 (ΔG = −16.2 kcal/mol), while immune simulations predicted durable humoral and cellular immune responses with broad population coverage (≈89%). Codon optimization confirmed high expression potential in E. coli K12. Conclusions: The pangenome-guided immunoinformatics approach enabled the identification of conserved antigenic proteins and rational design of a promising multi-epitope vaccine candidate against MDR C. violaceum. The construct exhibits favorable immunogenic and structural features, supporting its potential for experimental validation and future development as a preventive immunotherapeutic against emerging MDR pathogens. Full article

Streptococcus dysgalactiae subsp. equisimilis (SDSE) has historically been recognized as a human pathogen, yet β-hemolytic streptococci consistent with SDSE have been documented in pigs for nearly a century. To investigate the population structure of porcine SDSE and the phylogenetic relationships between swine and human strains, we characterized 41 isolates recovered from diseased pigs in Quebec, Canada (2019–2022). Infected animals spanned all major production stages and frequently presented with invasive disease, including arthritis, endocarditis, and sudden death. Core-genome phylogenetics resolved two heterogeneous porcine clades separated by long internal branches and clearly distinct from dominant human SDSE lineages. Most porcine isolates were emm-negative or contained structurally altered emm regions compared with human strains. Analysis of Lancefield antigen loci identified a predominant group C lineage and a minority group L lineage, recapitulating historical serogroup distributions described since the early-20th century. Phenotypic testing showed susceptibility to β-lactams and florfenicol but high levels of resistance to tetracycline, macrolides and lincosamides. Detected antimicrobial resistance (AMR) genes correlated well with phenotypes, and multidrug resistance was frequent. Hybrid genome assemblies revealed integrative and mobilizable elements carrying AMR determinants. Collectively, our data indicate that porcine SDSE represents a long-standing, genetically structured, host-adapted population with notable AMR potential, underscoring the need for continued swine SDSE genomic surveillance. Full article

Antibodies against low-molecular-weight compounds exhibit cross-reactivities (CRs) with their structural analogs, varying by orders of magnitude for different substances. This variability limits the informativeness of antibody applications as analytical reagents and for other aims when samples contain several members of the same family, their derivatives, or partial degradation products. Therefore, there is a demand to find some criteria for understanding the relationships between the structural characteristics of antigens of a given chemical class and their immunochemical activity. This study presents an experimental and theoretical investigation of the properties of a monoclonal antibody (MAb) against the S-stereoisomer of gatifloxacin, a member of the widely used (fluoro)quinolone (FQ) family of antibiotics, characterized by high structural diversity. The aim was to determine FQs that form complexes with MAb and suggest a methodology to predict their CRs in silico. For this, the interaction of MAb with 26 FQs was studied using the enzyme-linked immunosorbent assay and presented as CR values to the target antigen. The most pronounced CRs were observed for lomefloxacin, sarafloxacin, and ciprofloxacin. Molecular dynamics (MD) simulations were performed to identify differences in analyte interactions at the MAb antigen-binding site, which determines binding affinity. It has been shown that molecular docking fails to discriminate cross-reactive from non-cross-reactive compounds because FQs have similar cores. Therefore, advanced analysis of MD trajectories was carried out. It allowed for clarification of the dynamic features of analyte–antibody interactions responsible for binding. It was shown by the dynamical network analysis that the sum of betweenness centrality between a node corresponding to the quinolone ring and nodes representing MAb amino acids is higher for cross-reactive haptens. The found regularities can be transferred to other analyte–antibody systems as a binary classifier that discriminates cross-reactive and non-cross-reactive compounds. Full article

Background/Objectives: Immunohistochemical (IHC) profiles assessed on core biopsies guide initial therapy in breast cancer; however, paired changes between biopsy and surgical specimens may alter treatment pathways. We aimed to quantify paired biomarker dynamics (ER, PR, HER2, Ki-67) and the proportion of patients undergoing clinically actionable reclassification. Methods: We conducted a single-center retrospective study of 79 patients with paired pre- and post-surgical IHC for ER, PR, HER2 (0/1+/2+/3+ with reflex ISH for 2+), and Ki-67 (20% cut-off). Paired categorical shifts were tested with McNemar’s test; agreement was quantified using Cohen’s κ (95% CI); and multivariable logistic regression examined correlates of neoadjuvant chemotherapy (NACT). Two-sided p < 0.05 denoted statistical significance. Results: Post-surgical reassessment showed measurable conversions: PR-negative increased from 15.19% to 27.85%, while PR-positive decreased 84.81%→72.15%; HER2 3+ contracted 11.39%→6.33% with a parallel rise in 2+ (equivocal) 17.72%→24.05%; Ki-67 < 20% rose 37.97%→56.96%, whereas the >30% category was absent post-surgery. McNemar tests indicated significant paired shifts for PR (p = 0.016) and Ki-67 (p = 0.009); agreement was substantial for ER (κ = 0.70) and lower for PR (κ = 0.49), HER2 (κ = 0.43), and Ki-67 (κ = 0.29). High proliferation (Ki-67 ≥ 20%) independently predicted NACT (OR = 4.36, 95% CI 1.48–12.80). Conclusions: Paired IHC reassessment from biopsy to surgery reveals biomarker conversions that can reclassify therapeutic eligibility (e.g., anti-HER2 candidacy, endocrine strategies). These data support selective confirmation of IHC on resection specimens in routine practice and provide Δ-metrics to inform decision-making; external validation in prospective cohorts is warranted. Full article

Background: Blood transfusion has an essential place in the treatment of several patient groups but entails alloimmunization risk. The provision of phenotype-matched packed red blood cell concentrates (PRBCCs) is recommended for preventing alloimmunization in lifetime transfusion-dependent patients, while antigen-negative PRBCCs are a prerequisite for patients that already have blood group antibodies against clinically significant antigens. A large blood donor corps that is extendedly typed for clinically important red blood cell (RBC) antigens is therefore extremely valuable and can be achieved by high-throughput RBC genotyping. Probability of finding antigen-negative PRBCCs will then increase. Methods: RBC genotyping was performed using EDTA-blood. Following DNA extraction, ID CORE XT, a multiplex PCR- and hybridization-based genotype test utilizing Luminex xMAP technology, was employed. The predicted phenotypes were reported. Results: In this retrospective study, 92,796 RBC antigens were genotyped in 2508 blood donors, analyzing 48 donor samples in one setup, between 2015 and 2021. These results were compared with results available from serologic phenotyping, and discrepancies were investigated. Antigen-negative blood donors, especially those negative for clinically significant high-frequency antigens, combinations of antigen-negatives and positives for low-frequency antigens, were identified, in addition to variants. Conclusions: In the vast majority of discrepancies, repeat serology confirmed the genotype result. Therefore, we conclude that RBC genotyping using ID CORE XT is an effective and accurate method that complements serology. As many donors stop donating blood due to various reasons, we must continue genotyping to maintain and preferably increase the number of extendedly typed blood donors, which are needed for the provision of antigen-negative blood units. Full article

Background: Adolescents and young adults (AYA) with papillary thyroid carcinoma (PTC) often present with more extensive cervical lymph node metastasis (LNM) than older adults (AD). We aimed to identify age-associated molecular and immune features that might explain this phenotype and to explore potential translational implications for managing aggressive AYA PTC. Methods: We analyzed clinical and transcriptomic data from 501 PTC cases in The Cancer Genome Atlas (TCGA), stratified as AYA (<30 years, n = 64) and AD (≥30 years, n = 437). An institutional RNA-seq cohort (n = 13; 7 AYA, 6 AD) was used to screen for differentially expressed genes (DEGs). DEGs were defined by p ≤ 0.05 and |log2 fold change| ≥ 1. Intersection with invasion- and dissemination-related gene sets yielded a final age-related DEG list. Functional enrichment (GO/KEGG via DAVID), PPI network analysis (STRING, Cytoscape/cytoHubba), and immune deconvolution (CIBERSORT LM22) were performed. Protein-level validation was carried out by immunohistochemistry (IHC) in an independent cohort (n = 56; 28 AYA, 28 AD). Statistical comparisons used chi-square/Fisher’s exact tests for categorical variables, t-tests or nonparametric tests for continuous variables, and EdgeR with FDR correction for transcriptomic analyses. Results: In TCGA, LNM was more frequent in AYA than in AD (62.1% vs. 47.8%, p = 0.031). From intersected analyses, we identified 239 core DEGs distinguishing highly invasive, age-related tumors. Key upregulated genes in AYA included CXCR4, OPCML and S100A2; downregulated genes included ATP1A3, CHL1, HLA-DRA and IL-1β. Enriched pathways involved extracellular matrix organization, cell adhesion, calcium signaling and canonical oncogenic cascades (PI3K-Akt, MAPK, Wnt, Ras). Immune deconvolution showed reduced naïve B cells, M1 and M2 macrophages and resting mast cells and an increased proportion of M0 macrophages in AYA tumors. IHC validated differential protein expression for seven markers. Collectively, the data indicate an immune-suppressed, immune-excluded microenvironment in AYA PTC. Conclusions: AYA PTC exhibits distinct molecular and immune features that may underlie its propensity for lymphatic dissemination. These findings support evaluation of translational strategies, such as CXCR4 inhibition, restoration of antigen presentation, and macrophage reprogramming, to convert “cold” tumors into immune-permissive lesions. Validation in larger, prospective, multicenter cohorts is required. Full article

Since the beginning of the 21st century, major epidemics and pandemics such as SARS, H1N1pdm09, Ebola, and COVID-19 have repeatedly challenged global systems of disease diagnostics and control. These crises exposed the weaknesses of traditional diagnostic models, including long turnaround times, uneven resource distribution, and supply chain bottlenecks. As a result, there is an urgent need for more advanced diagnostic technologies and integrated diagnostics strategies. Our review summarizes key lessons learned from four recent major outbreaks and highlights advances in diagnostic technologies. Among these, molecular techniques such as loop-mediated isothermal amplification (LAMP), transcription-mediated amplification (TMA), recombinase polymerase amplification (RPA), and droplet digital polymerase chain reaction (ddPCR) have demonstrated significant advantages and are increasingly becoming core components of the detection framework. Antigen testing plays a critical role in rapid screening, particularly in settings such as schools, workplaces, and communities. Serological assays provide unique value for retrospective outbreak analysis and assessing population immunity. Next-generation sequencing (NGS) has become a powerful tool for identifying novel pathogens and monitoring viral mutations. Furthermore, point-of-care testing (POCT), enhanced by miniaturization, biosensing, and artificial intelligence (AI), has extended diagnostic capacity to the front lines of epidemic control. In summary, the future of epidemic and pandemic response will not depend on a single technology, but rather on a multi-layered and complementary system. By combining laboratory diagnostics, distributed screening, and real-time monitoring, this system will form a global diagnostic network capable of rapid response, ensuring preparedness for the next global health crisis. Full article

Lumpy Skin Disease Virus (LSDV), a member of the poxvirus family, represents a significant threat to global cattle industries. This review presents an analysis of LSDV-encoded proteins and their interactions with host systems, elucidating the molecular mechanisms governing viral life cycle progression and immune evasion strategies. We provide detailed characterization of the complex architecture of LSDV virions, including Intracellular Mature Virus (IMV), Extracellular Enveloped Virus (EEV), lateral bodies, and the core components, while summarizing the crucial functions of viral proteins throughout various stages of infection—entry, replication, transcription, translation, assembly, and egress. Particular attention is given to the immunomodulatory strategies employed by LSDV to subvert both innate and adaptive immune responses. These mechanisms encompass molecular mimicry of cytokines and chemokines, interference with antigen presentation pathways, inhibition of key immune signaling cascades, and modulation of apoptosis and autophagy processes. Through comparative analysis with homologs from related poxviruses, especially vaccinia virus, we highlight both evolutionarily conserved functions and potential unique adaptations in LSDV proteins. This review further identifies critical knowledge gaps in current understanding and proposes promising research directions. We emphasize that integrating multi-omics approaches with structural biology will be essential for advancing our understanding of LSDV pathogenesis and for developing novel preventive and therapeutic strategies against this important animal pathogen. Full article

Background: Pancreatic ductal adenocarcinoma (PDAC) exhibits marked resistance to immunotherapy. Beyond its characteristically low tumor mutational burden, post-translational modifications (PTMs) remodel the immunopeptidome and promote immune escape through reversible, enzyme-driven programs. Subject Matter: We synthesize evidence that aberrant glycosylation, O-GlcNAcylation, phosphorylation, and citrullination constitute core determinants of antigen visibility operating within spatially discrete tumor niches and a desmoplastic stroma. In hypoxic regions, HIF-linked hexosamine metabolism and OGT activity stabilize immune checkpoints and attenuate antigen processing; at tumor margins, sialylated mucins engage inhibitory Siglec receptors on innate and adaptive lymphocytes; within the stroma, PAD4-dependent NET formation enforces T cell exclusion. We also delineate technical barriers to discovering PTM antigens labile chemistry, low stoichiometry, and method-embedded biases and outline practical solutions: ETD/EThcD/AI-ETD fragmentation, PTM-aware database searching and machine-learning models, and autologous validation in patient-derived organoid–T cell co-cultures. Finally, we highlight therapeutic strategies that either immunize against PTM neoepitopes or inhibit PTM machinery (e.g., PAD4, OGT, ST6GAL1), with stromal remodeling as an enabling adjunct. Conclusions: PTM biology, spatial omics, and patient sample models can uncover targetable niches and speed up PDAC vaccination, TCR, and enzyme-directed treatment development. Full article

Cancer immunotherapy has redefined oncology’s goals, aiming for durable systemic immunity rather than mere cytoreduction. However, many solid tumors remain refractory due to immunosuppressive microenvironments and antigenic heterogeneity. Local tumor ablation techniques—including radiofrequency ablation (RFA), microwave ablation (MWA), cryoablation, irreversible electroporation (IRE), and high-intensity focused ultrasound (HIFU)—are being re-evaluated beyond their historic cytoreductive role. This comprehensive review synthesizes the paradigm of tumor ablation as an in situ vaccination strategy, a concept that leverages the tumor itself as a source of antigens and the ablation process to generate endogenous adjuvants. We detail the mechanistic underpinnings, highlighting how ablation induces immunogenic cell death (ICD), releasing damage-associated molecular patterns (DAMPs) such as calreticulin, ATP, HMGB1, and cytosolic DNA. These signals activate innate immunity via pathways like cGAS-STING, promote dendritic cell maturation, and facilitate epitope spreading. We critically examine the determinants of efficacy, including the critical impact of ablation modality on the “DAMP signature,” the necessity of complete ablation, and the pivotal role of the host’s immune contexture. Furthermore, we explore the induction of tertiary lymphoid structures (TLS) as a key anatomical site for sustained immune priming. Translational strategies are extensively discussed, focusing on optimizing procedural techniques, rationally combining ablation with immune checkpoint inhibitors (ICIs) and innate immune agonists, and developing a robust biomarker framework. By adopting the core principles of vaccinology—meticulous attention to antigen, adjuvant, route, and schedule—ablation can be engineered into a reproducible platform for systemic immunotherapy. This review concludes by addressing current limitations and outlining a roadmap for clinical translation, positioning interventional oncology as a central discipline in the future of immuno-oncology. Full article