Search Results (1,489)

H9N2 avian influenza virus (AIV) continues to mutate, leading to immunosuppression and secondary infections in poultry. Traditional inactivated vaccines mainly induce humoral immunity and have limited cross-protection efficacy against various subtypes of virus strains. In this study, we targeted the HA2 and M1 proteins of H9N2 as antigens and used immunoinformatics methods to design a broad-spectrum multi-epitope vaccine (MEV) that can simultaneously activate humoral and cellular immunity. Firstly, through systematic evolutionary analysis and sequence comparison, highly conserved amino acid sequence regions were selected from HA2 and M1 proteins. B-cell epitopes were predicted in the HA2 conserved sequence, and cytotoxic T lymphocyte (CTL) and helper T lymphocyte (HTL) epitopes were predicted in the M1 conserved sequence. Three candidate vaccines containing different epitope combinations were constructed. After secondary structure and physicochemical property comparisons, HM1 was determined as the optimal scheme. HM1 contains three B cell epitopes, two CTL epitopes, and three HTL epitopes, and was connected to chicken β-defensin at the N-terminus as a molecular adjuvant; a dendritic cell-targeting peptide was added at the C-terminus. The HM1 tertiary structure optimized by GalaxyRefine met the standards of a reliable model. The molecular docking results indicated that HM1 can form stable binding with chicken TLR2, TLR4, MHC I, and MHC II molecules, with binding free energies of −7.1 kcal/mol and −6.1 kcal/mol, respectively, and can form multiple hydrogen bonds and salt bridges. Normal mode analyses revealed that the HM1–TLR complex exhibits favorable dynamic properties at the computational level. The immune simulation prediction results showed that after vaccination with HM1, specific antibodies can be induced, B cells, helper T cells, and cytotoxic T cells can be activated, and IFN-γ and IL-2 can be secreted. In summary, the HM1 designed based on the conserved regions of HA2 and M1 proteins has good physicochemical stability and immunogenicity, providing a theoretical basis for the development of broad-spectrum and highly effective H9N2 vaccines. Full article

In recent years, nanopore technology has enhanced analyte detection, enabled higher resolution and achieved single-molecule sensing capability. Aptamer-conjugated nanopore sensing technology combines the high specificity of aptamers with the single-molecule resolution of nanopores. By anchoring aptamers to biological, solid-state or hybrid nanopores, target binding events produce distinct electrical signatures that allow sensitive and label-free detection. This approach enables real-time monitoring of small molecules, proteins, and even pathogens, with promising applications in diagnostics, drug screening, environmental monitoring, etc. Hybrid biological/solid state devices produce robust signals and are suitable for PoC applications. The aptamers “magic bullets” have also been exploited to develop single-molecule antigen detection using nanopores, which offers a promising alternative for accurate virus testing to contain their transmission. Chemical conjugation of aptamers to nanopore interfaces improves selectivity for peptides/amino acids and expands robustness for practical samples. Aptamer-based nanopipettes offer high analytical precision by enabling label-free, real-time detection of target molecules in ultra-small sample volumes. This review maps aptamer–nanopore integration across biological, solid-state, and hybrid platforms. It also explores various types of aptamers integrated into nanopore platforms that cater to precise, single-molecule recognition, paving the way for highly sensitive, portable diagnostics and next-generation therapeutic monitoring tools. Full article

Inflammatory and oxidative stress within the pancreatic islet microenvironment can alter insulin-derived peptides and generate neoepitopes that may reshape autoreactive T cell recognition in type 1 diabetes (T1D). One such modification, C19S, represents a cysteine-to-serine substitution at position 19 of the insulin B-chain and has recently been identified among human leukocyte antigen class II (HLA-II)-associated insulin neoepitopes recognized by autoreactive CD4+ T cells. Although the biological relevance of C19S has been determined, the molecular features that may distinguish C19S-specific T cell receptor (TCR) engagement from native insulin recognition remain incompletely defined. Here, we used comparative protein–protein docking, molecular dynamics (MD) simulations, interface-contact analysis, conformational landscape analysis, and binding-energy calculations to examine TCR engagement of human leukocyte antigen DQ8 (HLA-DQ8) presenting either native insulin peptide or the corresponding C19S insulin peptide. Initial modeling indicated that both peptide-HLA-DQ8 complexes were compatible with TCR-bound ternary complex formation. However, the C19S-containing complex was predicted to exhibit altered peptide-centered dynamics, changes in peptide backbone presentation, and reorganization of both TCR-peptide and TCR-HLA-DQ8 contacts. Comparative molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular mechanics generalized Born surface area (MM/GBSA) analyses further suggested a distinct calculated energetic profile under the applied modeling conditions for the C19S-containing complex, with residue-level decomposition localizing energetic differences to selected interface hotspots. Together, these findings provide a molecular framework for generating hypotheses about how C19S may reshape the HLA-DQ8-presented insulin recognition surface, with implications for future experimental studies of autoreactive CD4+ T cell recognition and antigen-specific tolerogenic strategies in T1D. Full article

Classical Major Histocompatibility Complex Class I (MHC-I) molecules are traditionally viewed as stable peptide-presenting structures expressed on the surface of all nucleated cells. Their expression by professional antigen-presenting dendritic cells (DCs) enables CD8+ T-cell activation, differentiation, and immune surveillance. However, accumulating evidence indicates that cell-surface MHC-I molecules exist in three major conformational states: (1) β2m-associated, peptide-loaded conformers that originate in the endoplasmic reticulum and pass through the Golgi apparatus after binding proteasome-generated cytosolic peptides (hereafter referred to as closed conformers); (2) β2m-free, peptide-empty conformers that arise following β2m dissociation from closed conformers either at the plasma membrane or after internalization and recycling (hereafter referred to as open conformers); and (3) β2m-associated, peptide-empty conformers that represent an intermediate state between closed and open conformers. Here, we propose a conceptual framework, supported by computational predictors of intrinsically disordered regions, in which transitions between closed and open MHC-I conformers are coupled to intracellular regulatory processes, including post-translational modifications of conserved motifs, intracellular trafficking, and signaling. Although direct experimental evidence linking these processes remains limited, we integrate independent observations into a working model that may guide future investigations into MHC-I-mediated cell–cell communication in both immune and non-immune contexts, in health and disease. For clarity, in this article we define “open conformers” as structurally competent, β2m-free, and peptide-deficient MHC-I molecules. Full article

Small ruminant lentivirus (SRLV) infects goats and sheep of all breeds and ages worldwide. There are no current records regarding the three-dimensional structure or antigenic capacity of the nucleocapsid protein p14 of FESC-752 Mexican strain. The antigenic structure of p14 protein of a B1 genotype was predicted. cDNA from FESC-752 was used to overexpress the recombinant SRLV-rp14 protein. Then, its antigenicity was verified in vitro by evaluating plasma samples from goats and sheep naturally infected with SRLV. Antigenicity prediction showed a “horseshoe”-type structure shared by different lentiviruses and five epitopes distributed throughout the p14 surface regions where they coincide suggesting conserved epitopes in the zinc-finger structures of the nucleoproteins of the SRLV, Human Immunodeficiency Virus (HIV-1), and Feline Immunodeficiency virus (FIV) retroviruses. Multi-species molecular docking showed a notable structural convergence where caprine, bovine, murine, and human immunoglobulins target a predictive 23 amino acid epitope (residues 41–64) within the core zinc-finger region. Furthermore, CABS docking simulations predicted that p14-derived peptides preferentially bind within the antigen-presenting cleft of both caprine and bovine major histocompatibility complex class I (MHC-I) molecules. The stability of these immunological complexes is mediated by dense networks of hydrophobic interactions and highly conserved aromatic anchoring residues. Antigenicity analysis revealed that 78.7% of samples from naturally infected goats showed immunoreactivity toward SRLV-rp14 and the predictive evidence that p14 can simultaneously stimulate both humoral and cellular pathways makes it a strategic candidate for the design of next-generation vaccines aimed at controlling lentiviruses in small ruminants. Full article

Dengue fever, a rapidly spreading mosquito-borne viral disease, poses a major global health issue, particularly in tropical and subtropical regions. The absence of a universally effective vaccine against all four dengue virus serotypes necessitates continued exploration of novel vaccine strategies. This study evaluated a PrM-derived multiple antigenic peptide (MAP) vaccine candidate in BALB/c mice. Molecular docking analyses predicted favourable interactions of the selected PrM-derived B-cell epitope with both human (human BCR Fab region PDB ID: 5IFH) and mouse (mouse BCR PDB ID: 8EMA) B-cell receptors, supporting its antigenic potential. ChemSketch was used to develop the PrM–MAP vaccine construct, which was then commercially synthesized. Mice received single, double, and triple booster doses of the vaccine, while control groups received either PBS or adjuvant alone. Humoral immune responses were measured by ELISA, and safety was evaluated through in vitro cytotoxicity assays on HEK293 cells and the in vivo histopathological examination of major organs. Mice immunized with a single booster dose produced significant levels of PrM-specific antibodies compared to subsequent booster doses, suggesting variability in the humoral response elicited. Optimal coating concentrations in ELISA demonstrated the importance of antigen concentrations in the sensitivity of the assay. The safety evaluation indicated high cell viability, up to 150 µg/mL of PrM–MAP, in HEK293 cells, and an absence of significant histopathological damage in treated animals. The PrM–MAP vaccine construct elicited a detectable humoral immune response while demonstrating a high safety profile in vitro and in vivo. These findings indicate the potential of MAP-based vaccine platforms as promising candidates for further development against the dengue virus. Full article

Tomato yellow leaf curl virus (TYLCV) is a major threat to tomato production, creating a need for sensitive, low-cost detection methods that can be applied to early symptomatic or low-viral-load samples. Recombinant antigen configuration may influence serological assay development, although the specific contribution of multiple-cloning-site (MCS)-derived intermediate sequences remains uncertain. In this study, a recombinant Trx-His-coat protein (CP) fusion antigen was produced using an MCS-free direct-fusion construct that retained the Trx-His tag while removing the MCS-derived intermediate sequence, followed by gradient refolding. No direct comparison with linker-containing, tag-cleaved, or tag-free antigen constructs was performed. The purified antigen was used to immunize rabbits and generate a high-titre polyclonal antibody (pAb). The resulting indirect enzyme-linked immunosorbent assay (ELISA) achieved a theoretical limit of detection of 1.8 ng/mL and an estimated pre-dilution equivalent the limit of detection (LOD) of 72 ng/mL after sample dilution. The assay showed favourable tolerance to crude tomato leaf matrices, with spike-recovery rates of 95.45–100.40%. In a preliminary evaluation using a balanced panel of 32 field-collected samples, ELISA absorbance correlated with droplet digital PCR quantification (R² = 0.9819) and plant disease index values (R² = 0.9774). Liquid chromatography–tandem mass spectrometry (LC-MS/MS) peptide mapping and AlphaFold2-based modelling were used only to provide preliminary computational context for antigen interpretation. The assay showed cross-recognition toward Tobacco curly shoot virus (TbCSV), indicating that it should not be considered strictly TYLCV species-specific. Therefore, this assay may support preliminary serological screening under the tested conditions, whereas molecular confirmation remains necessary when species-level identification is required. Full article

Alpha-enolase (ENO1) is a multifunctional protein frequently overexpressed in solid tumors, where elevated levels are associated with aggressive behavior and poor prognosis. Beyond its canonical glycolytic role, ENO1 participates in immunoregulatory processes through distinct subcellular pools. Intracellular ENO1 shapes tumor-associated metabolic programs, while surface-exposed ENO1 functions as a plasminogen receptor and can engage innate immune signaling pathways. Post-translational modifications—particularly citrullination and phosphorylation—generate structurally altered epitopes that expand ENO1 antigenicity and enable adaptive immune recognition, including coordinated humoral and T-cell responses in cancer patients. These determinants of ENO1 immunogenicity have downstream consequences within the tumor microenvironment: immune-accessible ENO1 modulates myeloid cell recruitment, dendritic cell maturation, and macrophage polarization, while ENO1-dependent metabolic and signaling programs contribute to immune suppression and escape through multiple interconnected axes. Together, these mechanisms position ENO1 at the interface between tumor metabolism and immune regulation. Preclinical evidence demonstrates that ENO1-directed strategies—including antibody-based targeting, DNA vaccination, and vaccines incorporating post-translationally modified ENO1 peptides—can generate productive antitumor immunity and synergize with checkpoint blockade, supporting the rationale for ENO1 as an immunotherapeutic target. This review synthesizes current evidence within an integrated framework linking ENO1 dysregulation to its immunological consequences in cancer and discusses translational implications for ENO1-centered immunotherapy and immunoprevention. Full article

Anthralin has a long history as a topical treatment for psoriasis, where it reduces keratinocyte hyper-proliferation and effectively clears plaques. While it lowers inflammatory markers in psoriatic skin, it paradoxically induces inflammation in healthy skin through reactive oxygen species (ROS) and related pathways. However, its precise mechanism of action remains incompletely understood. Interestingly, the once undesirable pro-inflammatory effect in healthy skin may now represent a valuable adjuvant property for transcutaneous immunization (TCI). In particular, combining anthralin with the TLR7 agonist imiquimod (IMQ) elicits strong cytotoxic T-cell responses in pre-clinical studies. When paired with antigenic peptides that can penetrate the skin, this immunization approach is especially promising in the context of cancer therapy, given the central role of cytotoxic T-cells in tumor rejection. However, current evidence is largely derived from mouse models, but its efficacy and safety in humans remain to be established. This review therefore examines whether anthralin can be repurposed as a cutaneous adjuvant for transcutaneous immunization, and which mechanistic and translational constraints must be overcome before human application. Full article

Biomarker, the short form of “biological marker”, appeared in the scientific literature in the 1940s. Since then, many different definitions have been suggested, but a generally applicable explanation of the term biomarker in science is extremely challenging. The word biomarker is found in 1.3 million articles in the scientific database PubMed^® that currently comprises more than 39 million citations for biomedical literature. Biomarkers are closely associated with human health and disease. The present article attempts to approach and evaluate the multifaceted term “biomarker” from a clinical perspective by searching the PubMed database. The search term biomarker was combined with other search terms related to medicine, physiology, biochemistry, and chemistry. Currently generally accepted clinical biomarkers, such as the high-molecular-mass N-terminal prohormone of brain natriuretic peptide (NT-proBNP, 60%), prostate-specific antigen (PSA, 67%), and troponin (37%), serve as a kind of positive control. The combination of the search term biomarker with selected low-molecular substances of clinically non-validated and hence rather experimental character yielded surprisingly high fractions of 41% for 8-iso-prostaglandin F_2α, 39% for symmetric dimethylarginine (SDMA), and 28% for asymmetric dimethylarginine (ADMA). The results of our survey are presented and discussed in detail for a wide spectrum of diseases. We focused on mechanisms that are assumed to underlie the biological activity and specificity of biomarkers. We also considered potential roles of the analytical chemistry of biomarkers including the emerging metabolomics and proteomics. Reliable analytical methods have been used for the quantification of the isomeric low-molecular-mass ADMA and SDMA in human biological samples. ADMA, but not SDMA, is considered an endogenous inhibitor of the endothelium-derived nitric oxide (NO) synthesis, one of the most potent endogenous vasodilators. Paradoxically, the utility of ADMA and SDMA as biomarkers in the renal and cardiovascular systems seems to contradict their main biological activity. This prominent pair is representative of many biomarkers and reveals that the supposed biomarker utility is likely to be predicated on not yet considered biological activity. The majority of human diseases are heterogenic, affect many organs and seem to include different and overlapping biochemical pathways. In recent years, especially proteomic studies provided a series of new potential candidate biomarkers. However, such biomarkers must still be validated in the clinic before they can be introduced into clinical practice. This is perhaps the most critical phase in the discovery of disease biomarkers. Our analysis reveals that the area of biomarker research is highly challenging. With minor exceptions, there is no specific biomarker for a single disease. In addition to clinical examinations, a combination of several biomarkers seems to be needed for reliable diagnosis and therapy. Analytical chemistry, especially proteomics, delivers a huge amount of data, which may complicate and even hinder progress in this area. Specific quantitative analysis of candidate biomarkers observed by proteomics (and metabolomics) is highly recommended to proceed with the same biological samples from studies in which the biomarkers were discovered. Full article

Porcine diarrheagenic Escherichia coli strains exhibit heterogeneous virulence profiles involving multiple factors, complicating broad-spectrum serological diagnosis. Here, we designed a multiepitope fusion antigen, MEAET, containing predicted B-cell epitopes from six major virulence factors, K88/F4, F18, LT, Stx2e, HlyA, and Tir, and developed an indirect ELISA for broad antibody detection. Structural modeling predicted a well-folded conformation with multiple discontinuous B-cell epitopes, and molecular docking suggested favorable interactions between the C-terminal dendritic cell-targeting peptide and the porcine immune receptor SLA1. Immunization of piglets with purified recombinant MEAET generated hyperimmune serum with a titer exceeding 1:102,400, which specifically recognized all six individual antigens by Western blot. The optimized ELISA demonstrated satisfactory repeatability (intra-assay CV ≤ 4.26%) and reproducibility (inter-assay CV ≤ 5.57%), showed no detectable cross-reactivity with antibodies against other tested porcine pathogens, and exhibited good analytical sensitivity, with positive sera detectable at dilutions up to 1:3200. The optimized ELISA showed good repeatability and reproducibility, with intra-assay and inter-assay coefficients of variation of ≤4.26% and ≤5.57%, respectively, no detectable cross-reactivity with the tested heterologous controls, and good analytical sensitivity, with positive sera remaining detectable at dilutions up to 1:3200. The S/P ratio cut-off was 0.203. In field sera, positivity rates were 74.5% (35/47) in diarrheic pigs and 34.0% (36/106) in asymptomatic pigs. These primary results indicate that the MEAET-based indirect ELISA represents a promising tool for serological detection of antibodies against multiple virulence factors of diarrheagenic E. coli in pigs and for field surveillance in swine herds. Full article

A single vaccine cannot prevent or treat all cancers; however, recurrent tumor-specific epitopes may facilitate the development of pre-manufactured, HLA-matched mRNA vaccines tailored for specific molecular subgroups. We define the shared tumor-specific epitope as a recurring peptide derived from a viral oncoprotein, a driver mutation, a frameshift, an altered protein C-terminus, or a fusion junction, and we employ a rigorous cancer-cell-only criterion: a target must be recurrent within a defined subgroup, absent from essential normal tissues at the peptide–HLA level, naturally presented on tumor cells, and sufficiently clonal to minimize immune escape. Under this criterion, we present fifteen sequence-anchored reference designs alongside one conceptual placeholder across thirteen candidates divided into four superclasses: viral oncoproteins (such as HPV16/18 E6 and E7 as attenuated antigenic reference designs; Merkel cell polyomavirus serving as a design-specific placeholder), recurrent driver neoepitopes (including KRAS G12/G13, IDH1 R132H, and H3 K27M), hematologic neoantigens (such as NPM1 Type A C-terminus; and a single CALR exon 9 construct encoding the shared novel C-terminus of types 1 and 2 mutations), and fusion junctions (notably EWS-FLI1 and BCR-ABL). Each open reading frame is anchored to a canonical accession with its documented event; representative ORFs are provided as reference designs, with the intended residue-level verification records. These sequence designs are intended as reference constructs and are not suitable as clinical-grade or manufacturing-ready products; they require independent residue-level validation and comprehensive safety assessments prior to laboratory or clinical application. The historical record of non-personalized vaccination—including HPV and hepatitis B prophylaxis, intravesical BCG, and unsuccessful tumor-associated antigen trials—frames both the potential and limitations of such approaches. The practical product is not a universal vaccine but rather a governed library aligned with specific genotype, viral etiology, HLA context, and clinical setting. Currently, none of these designs have established proof-of-benefit-tier evidence. Full article

Therapeutic cancer vaccines have emerged as a promising approach in cancer immunotherapy, aiming to stimulate the immune system to recognize and eliminate malignant cells. Despite this potential, clinical efficacy has remained variable across multiple vaccine platforms. This review synthesizes completed clinical trials evaluating major therapeutic cancer vaccine modalities, including peptide-based, nucleic acid--based, dendritic cell, whole cell, and viral and bacterial vector--based vaccines, with a focus on safety, immunogenicity, and clinical outcomes for diverse tumor types. Overall, these vaccines demonstrate a favorable safety profile; however, clinical efficacy as monotherapy has been limited. Clinical outcomes vary by platform and tumor type and are influenced by factors such as antigen selection, tumor heterogeneity and immunosuppressive tumor microenvironment (TME). Recent advances in antigen design, vaccine technologies, and combination strategies are redefining the role of therapeutic cancer vaccines in oncology. Future progress will depend on optimizing their integration with standard treatment modalities, particularly immune checkpoint inhibitors. Full article

Rhodococcus equi (R. equi) primarily induces fatal pulmonary and extrapulmonary pyogenic granulomatous infections in foals, imposing substantial economic burdens on the equine industry. The emergence and spread of multidrug-resistant (MDR) R. equi have led to a therapeutic impasse in clinical settings. Although vaccination is a proven strategy against MDR pathogens, no commercial vaccine is currently available for R. equi. In this study, we employed a bioinformatics approach to systematically identify and prioritize antigenic epitopes derived from R. equi for multi-epitope vaccine design. Using ABCPred, NetMHCpan EL, and IEDB servers, 27 MHC-I and 9 MHC-II epitopes were selected from five previously validated R. equi vaccine candidates: ABC transporter, PBD2, NlpC/P60, Esterase, and M23. These epitopes were coupled with distinct peptide linkers to construct six multi-epitope vaccine constructs, designated V1–V6. The physicochemical properties, antigenicity, immunogenicity, and toxicity of the six vaccine constructs were analyzed, and the V3 and V4 constructs were ultimately selected. Using the HDOCK and Gromacs tools, the intermolecular interactions, binding affinity, and thermal stability of the V3 and V4 constructs with the equine MHC molecules EQCA-I and EQCA-II were evaluated. The results confirm that V3 and V4 exhibit strong binding affinity to EQCA-I and EQCA-II, with stable conformations following binding, indicating theoretical potential to induce humoral and cellular immunity in foals. Recombinant plasmids for V3 and V4 were constructed, and the V3 and V4 proteins were successfully prepared, confirming the feasibility of prokaryotic expression for these vaccine constructs. Immunization assays in SPF BALB/c mice showed that the multi-epitope vaccines elicited robust antigen-specific IgG antibody responses, reflecting preliminary humoral immunogenicity. However, these murine data have translational limitations, as they cannot fully represent equine immune responses. The findings establish a crucial theoretical foundation for the advancement of vaccines targeting R. equi while offering a reference for the design of vaccines against other drug-resistant microbial pathogens. Full article

Penile squamous cell carcinoma (PSCC) is a rare malignancy with limited therapeutic options in advanced and recurrent diseases. Advanced PSCC is typically managed with multimodal therapy, including neoadjuvant chemotherapy or chemoradiation followed by surgery; however, durable responses remain uncommon, and outcomes after recurrence are poor. Cancer vaccines represent a promising immunotherapeutic strategy, as these treatments induce tumor-specific immunity and heightened immune surveillance against penile cancer cells. While therapeutic cancer vaccines have not yet demonstrated consistent clinical efficacy as monotherapy in PSCC, their integration with complementary immune-modulating approaches, particularly immune checkpoint blockade, represents a rational strategy to enhance antitumor immunity. This review summarizes the rationale for vaccine development in PSCC, with emphasis on HPV-derived antigens, neoantigens, and emerging tumor-associated targets. We examine major vaccine platforms, including viral-vector, peptide-based, nucleic acid, and dendritic cell-based approaches. We also discuss how spatial transcriptomics, single-cell RNA sequencing, artificial intelligence-assisted antigen prediction, and nanotechnology-enhanced delivery systems may support future personalized vaccine development. Overall, therapeutic vaccines remain investigational in PSCC but may become relevant within biomarker-driven, combination-based immunotherapy strategies. Full article