RESUMEN

Tuberculosis(TB) of the Central nervous system (CNS) is a rare and highly destructive disease. The emergence of drug resistance has increased treatment difficulty, leaving the Bacillus Calmette-Guérin (BCG) vaccine as the only licensed preventative immunization available. This study focused on identifying the epitopes of PknD (Rv0931c) and Rv0986 from Mycobacterium tuberculosis(Mtb) strain H37Rv using an in silico method. The goal was to develop a therapeutic mRNA vaccine for preventing CNS TB. The vaccine was designed to be non-allergenic, non-toxic, and highly antigenic. Codon optimization was performed to ensure effective translation in the human host. Additionally, the secondary and tertiary structures of the vaccine were predicted, and molecular docking with TLR-4 was carried out. A molecular dynamics simulation confirmed the stability of the complex. The results indicate that the vaccine structure shows effectiveness. Overall, the constructed vaccine exhibits ideal physicochemical properties, immune response, and stability, laying a theoretical foundation for future laboratory experiments.

Asunto(s)

Simulación por Computador , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Mycobacterium tuberculosis , Tuberculosis del Sistema Nervioso Central , Humanos , Mycobacterium tuberculosis/inmunología , Tuberculosis del Sistema Nervioso Central/prevención & control , Tuberculosis del Sistema Nervioso Central/inmunología , Vacunas contra la Tuberculosis/inmunología , Epítopos/inmunología , Epítopos/química , Vacunas de ARNm , Vacunas Sintéticas/inmunología

RESUMEN

During pregnancy the immune system needs to maintain immune tolerance of the foetus while also responding to infection, which can cause premature activation of the inflammatory pathways leading to the onset of labour and preterm birth. The vaginal microbiome is an important modifier of preterm birth risk, with Lactobacillus dominance during pregnancy associated with term delivery while high microbial diversity is associated with an increased risk of preterm birth. Glycans on glycoproteins along the lower female reproductive tract are fundamental to microbiota-host interactions and the mediation of inflammatory responses. However, the specific glycan epitopes involved in these processes are not well understood. To address this, we conducted glycomic analyses of cervicovaginal fluid (CVF) from 36 pregnant women at high risk of preterm birth and 4 non-pregnant women. Our analysis of N- and O-glycans revealed a rich CVF glycome. While O-glycans were shown to be the main carriers of ABO blood group epitopes, the main features of N-glycans were the presence of abundant paucimannose and high mannose glycans, and a remarkable diversity of complex bi-, tri-, and tetra-antennary glycans decorated with fucose and sialic acid. We identified immuno-regulatory epitopes, such as Lewis antigens, and found that fucosylation was negatively correlated to pro-inflammatory factors, such as IL-1ß, MMP-8, C3a and C5a, while glycans with only sialylated antennae were mainly positively correlated to those. Similarly, paucimannose glycans showed a positive correlation to pro-inflammatory factors. We revealed a high abundance of glycans which have previously been identified as hallmarks of cancer and viral glycosylation, such as Man8 and Man9 high mannose glycans. Although each pregnant woman had a unique glycomic profile, longitudinal studies showed that the main glycosylation features were consistent throughout pregnancy in women who delivered at term, whereas women who experienced extreme preterm birth exhibited sharp changes in the CVF glycome shortly before delivery. These findings shed light on the processes underlying the role of glycosylation in maintaining a healthy vaginal microbiome and associated host immune responses. In addition, these discoveries facilitate our understanding of the lower female reproductive tract which has broad implications for women's health.

Asunto(s)

Epítopos , Glicómica , Polisacáridos , Nacimiento Prematuro , Vagina , Humanos , Femenino , Nacimiento Prematuro/inmunología , Nacimiento Prematuro/metabolismo , Embarazo , Glicosilación , Vagina/inmunología , Vagina/metabolismo , Vagina/microbiología , Adulto , Epítopos/inmunología , Polisacáridos/metabolismo , Polisacáridos/inmunología , Cuello del Útero/inmunología , Cuello del Útero/metabolismo , Líquidos Corporales/inmunología , Líquidos Corporales/metabolismo , Microbiota/inmunología

RESUMEN

Trypanosoma evansi is a unicellular protozoan responsible for causing a disease known as "surra," which is found in different regions of the world and primarily affects horses and camels. Few information is known about virulence factors released from the parasite within the animals. The organism can secrete extracellular vesicles (EVs), which transport a variety of molecules, including proteins. Before being considered exclusively as a means for eliminating unwanted substances, extracellular vesicles (EVs) have emerged as key players in intercellular communication, facilitating interactions between cells, host cells, and parasites, and even between parasites themselves. Thus, they may be used as potential biomarkers. This study aimed to assess the induction of EVs production by Ca+2, conduct a proteomic analysis of the EVs released by T. evansi, and identify epitopes that could serve as biomarkers. The findings indicated that Ca+2 is not an effective promoter of vesiculation in T. evansi. Furthermore, the proteomic analysis has identified multiple proteins that have been investigated as biomarkers or vaccine antigens, previously. A total of 442 proteins were identified, with 7 of them specifically recognizing 9 epitopes that are unique to T. evansi. At least one of these epitopes of TevSTIB805.9.11580 have been previously identified, which increases the possibility of further investigating its potential as a biomarker.

Asunto(s)

Vesículas Extracelulares , Proteómica , Proteínas Protozoarias , Trypanosoma , Trypanosoma/metabolismo , Trypanosoma/genética , Vesículas Extracelulares/metabolismo , Proteínas Protozoarias/genética , Proteínas Protozoarias/metabolismo , Animales , Calcio/metabolismo , Biomarcadores , Tripanosomiasis/parasitología , Proteoma , Epítopos/inmunología

RESUMEN

The American manatee (Trichechus manatus), experiencing population declines due to various threats, is the focus of conservation efforts that include the capture, rehabilitation, and release of orphaned calves when their mothers are unable to care for them. These efforts are compromised by the use of commercially available milk substitutes that lack essential components found in natural manatee breast milk, particularly immunoglobulin A (IgA). IgA plays a crucial role in nurturing the immune mucosal system and fostering a healthy microbiota. However, research on IgA in non-maternally fed manatees is limited due to the lack of species-specific reagents. To address this gap, our study employs immuno-informatics analysis to compare IgA sequences from manatees with those from other species, aiming to explore epitope similarity and sharing. We compared the protein sequence of manatee IgA with available IgA sequences, assessing similarity at the sequence, 3D structures, and epitope levels. Our findings reveal that human IgA exhibits the highest similarity in terms of sequence and 3D structure. Additionally, epitope analysis shows high conservation, identity, and similarity of predicted epitopes compared to human IgA. Future studies should focus on functional analysis using human IgA polyclonal reagents to detect manatee IgA in breast milk. Our findings highlight the potential of comparative analysis in advancing the understanding of immunology in non-human animals and overcoming challenges associated with the scarcity of species-specific reagents.

Asunto(s)

Epítopos , Inmunoglobulina A , Animales , Humanos , Inmunoglobulina A/inmunología , Epítopos/inmunología , Biología Computacional/métodos , Secuencia de Aminoácidos

RESUMEN

Limited knowledge exists on the quality of polyclonal antibody responses generated following Marburg virus (MARV) infection and its evolution in survivors. In this study, we evaluate MARV proteome-wide antibody repertoire longitudinally in convalescent phase approximately every six months for five years following MARV infection in ten human survivors. Differential kinetics were observed for IgM vs IgG vs IgA epitope diversity, antibody binding, antibody affinity maturation and Fc-receptor interaction to MARV proteins. Durability of MARV-neutralizing antibodies is low in survivors. MARV infection induces a diverse epitope repertoire with predominance against GP, VP40, VP30 and VP24 that persisted up to 5 years post-exposure. However, the IgM and IgA repertoire declines over time. Within MARV-GP, IgG recognize antigenic sites predominantly in the amino-terminus, wing domain and GP2-heptad repeat. Interestingly, MARV infection generates robust durable FcɣRI, FcɣRIIA and FcɣRIIIA IgG-Fc receptor interactions. Immunization with immunodominant MARV epitopes reveals conserved wing region between GP1 and GP2, induces neutralizing antibodies against MARV. These findings demonstrate that MARV infection generates a diverse, long-lasting, non-neutralizing, IgG antibody repertoire that perturbs disease by FcɣR activity. This information, along with discovery of neutralizing immunogen in wing domain, could aid in development of effective therapeutics and vaccines against Marburg virus.

Asunto(s)

Anticuerpos Neutralizantes , Anticuerpos Antivirales , Enfermedad del Virus de Marburg , Marburgvirus , Proteoma , Marburgvirus/inmunología , Humanos , Enfermedad del Virus de Marburg/inmunología , Enfermedad del Virus de Marburg/virología , Anticuerpos Antivirales/inmunología , Anticuerpos Neutralizantes/inmunología , Proteoma/inmunología , Femenino , Vacunas Virales/inmunología , Inmunoglobulina G/inmunología , Masculino , Epítopos/inmunología , Adulto , Inmunoglobulina M/inmunología , Persona de Mediana Edad , Estudios Longitudinales , Inmunoglobulina A/inmunología , Desarrollo de Vacunas , Proteínas del Envoltorio Viral/inmunología

RESUMEN

Introduction: Tularemia, caused by the bacterium Francisella tularensis, poses health risks to humans and can spread through a variety of routes. It has also been classified as a Tier 1 Select agent by the CDC, highlighting its potential as a bioterrorism agent. Moreover, it is difficult to diagnose in a timely fashion, owing to the non-specific nature of tularemia infections. Rapid, sensitive, and accurate detection methods are required to reduce mortality rates. We aimed to develop antibodies directed against the outer membrane protein A of F. tularensis (FopA) for rapid and accurate diagnosis of tularemia. Methods: We used a baculovirus insect cell expression vector system to produce the FopA antigen and generate anti-FopA antibodies through immunization of BALB/c mice. We then employed hybridoma and phage display technologies to screen for antibodies that could recognize unique epitopes on FopA. Result: Two monoclonal antibodies, 6B12 and 3C1, identified through phage display screening specifically bound to recombinant FopA in a dose-dependent manner. The binding affinity of the anti-FopA 6B12 and 3C1 antibodies was observed to have an equilibrium dissociation constant of 1.76 × 10-10 M and 1.32 × 10-9 M, respectively. These antibodies were used to develop a sandwich ELISA system for the diagnosis of tularemia. This assay was found to be highly specific and sensitive, with detection limits ranging from 0.062 ng/mL in PBS to 0.064 ng/mL in skim milk matrices. Discussion: Our findings demonstrate the feasibility of a novel diagnostic approach for detecting F. tularensis based on targeting FopA, as opposed to existing tests that target the bacterial lipopolysaccharide.

Asunto(s)

Anticuerpos Antibacterianos , Anticuerpos Monoclonales , Proteínas de la Membrana Bacteriana Externa , Francisella tularensis , Ratones Endogámicos BALB C , Proteínas Recombinantes , Tularemia , Tularemia/diagnóstico , Animales , Francisella tularensis/inmunología , Francisella tularensis/genética , Proteínas de la Membrana Bacteriana Externa/inmunología , Proteínas de la Membrana Bacteriana Externa/genética , Proteínas Recombinantes/inmunología , Proteínas Recombinantes/genética , Anticuerpos Monoclonales/inmunología , Ratones , Inmunoensayo/métodos , Sensibilidad y Especificidad , Femenino , Técnicas de Visualización de Superficie Celular , Epítopos/inmunología , Ensayo de Inmunoadsorción Enzimática/métodos , Humanos , Antígenos Bacterianos/inmunología , Antígenos Bacterianos/genética , Hibridomas , Baculoviridae/genética

RESUMEN

The epidemic and outbreaks of influenza B Victoria lineage (Bv) during 2019-2022 led to an analysis of genetic, epitopes, charged amino acids and Bv outbreaks. Based on the National Influenza Surveillance Network (NISN), the Bv 72 strains isolated during 2019-2022 were selected by spatio-temporal sampling, then were sequenced. Using the Compare Means, Correlate and Cluster, the outbreak data were analyzed, including the single nucleotide variant (SNV), amino acid (AA), epitope, evolutionary rate (ER), Shannon entropy value (SV), charged amino acid and outbreak. With the emergence of COVID-19, the non-pharmaceutical interventions (NPIs) made Less distant transmission and only Bv outbreak. The 2021-2022 strains in the HA genes were located in the same subset, but were distinct from the 2019-2020 strains (P < 0.001). The codon G → A transition in nucleotide was in the highest ratio but the transversion of C → A and T → A made the most significant contribution to the outbreaks, while the increase in amino acid mutations characterized by polar, acidic and basic signatures played a key role in the Bv epidemic in 2021-2022. Both ER and SV were positively correlated in HA genes (R = 0.690) and NA genes (R = 0.711), respectively, however, the number of mutations in the HA genes was 1.59 times higher than that of the NA gene (2.15/1.36) from the beginning of 2020 to 2022. The positively selective sites 174, 199, 214 and 563 in HA genes and the sites 73 and 384 in NA genes were evolutionarily selected in the 2021-2022 influenza outbreaks. Overall, the prevalent factors related to 2021-2022 influenza outbreaks included epidemic timing, Tv, Ts, Tv/Ts, P137 (B → P), P148 (B → P), P199 (P → A), P212 (P → A), P214 (H → P) and P563 (B → P). The preference of amino acid mutations for charge/pH could influence the epidemic/outbreak trends of infectious diseases. Here was a good model of the evolution of infectious disease pathogens. This study, on account of further exploration of virology, genetics, bioinformatics and outbreak information, might facilitate further understanding of their deep interaction mechanisms in the spread of infectious diseases.

Asunto(s)

Brotes de Enfermedades , Evolución Molecular , Gripe Humana , Mutación , Polimorfismo de Nucleótido Simple , Humanos , Gripe Humana/epidemiología , Gripe Humana/virología , Gripe Humana/genética , Virus de la Influenza B/genética , Aminoácidos/genética , Epítopos/genética , Filogenia , Sustitución de Aminoácidos , Glicoproteínas Hemaglutininas del Virus de la Influenza/genética

RESUMEN

Repeated exposure of animals to Ixodes scapularis ticks can result in acquired tick resistance (ATR). The first manifestation of ATR is erythema at the tick bite site, however, the specific peptide targets and mechanisms associated with this early aspect of ATR are not understood. In this study, we immunized guinea pigs with a lipid nanoparticle containing the mRNA encoding 25 amino acids in the carboxyl terminus of Salp14 (Salp14-C mRNA-LNP), an I. scapularis salivary protein. The animals produced high titers of IgG directed at the carboxyl terminus of Salp14. Guinea pigs immunized with Salp14-C mRNA-LNP and then exposed to I. scapularis, developed erythema at the tick bite site. Transcriptomics of the skin of guinea pigs at the I. scapularis bite sites elucidated selected pathways, including histamine activation, that are associated with the development of erythema. The study demonstrates that an mRNA vaccine encoding a small peptide can induce the initial phase of ATR in guinea pigs.

Asunto(s)

Ixodes , Mordeduras de Garrapatas , Animales , Cobayas , Mordeduras de Garrapatas/inmunología , Ixodes/inmunología , Inmunoglobulina G/sangre , Inmunoglobulina G/inmunología , Vacunación/métodos , Proteínas y Péptidos Salivales/inmunología , Proteínas y Péptidos Salivales/genética , Epítopos/inmunología , Femenino , ARN Mensajero/inmunología , ARN Mensajero/genética , Nanopartículas/química , Eritema/inmunología , Eritema/etiología , Vacunas de ARNm , Liposomas

RESUMEN

Rotavirus, a dsRNA virus in the Reoviridae family, shows a segmented genome. The VP1 gene encodes the RNA-dependent RNA polymerase (RdRp). This study aims to develop a multiepitope-based vaccine targeting RdRp using immunoinformatic approaches. In this study, 100 available nucleotide sequences of VP1-Rotavirus belonging to different strains across the world were retrieved from NCBI database. The selected sequences were aligned, and a global consensus sequence was developed by using CLC work bench. The study involved immunoinformatic approaches and molecular docking studies to reveal the promiscuous epitopes that can be eventually used as active vaccine candidates for Rotavirus. In total, 27 highly immunogenic, antigenic, and non-allergenic T-cell and B-cell epitopes were predicted for the Multiepitope vaccine (MEV) against rotavirus. It was also observed that MEV can prove to be effective worldwide due to its high population coverage, demonstrating the consistency of this vaccine. Moreover, there is a high docking interaction and immunological response with a binding score of -50.2 kcal/mol, suggesting the vaccine's efficacy. Toll-like receptors (TLRs) also suggest that the vaccine is physiologically and immunologically effective. Collectively, our data point to an effective MEV against rotavirus that can effectively reduce viral infections and improve the health status worldwide.

Asunto(s)

Simulación del Acoplamiento Molecular , Vacunas contra Rotavirus , Rotavirus , Vacunas de Subunidad , Rotavirus/inmunología , Rotavirus/genética , Vacunas de Subunidad/inmunología , Vacunas de Subunidad/genética , Vacunas contra Rotavirus/inmunología , ARN Polimerasa Dependiente del ARN/inmunología , ARN Polimerasa Dependiente del ARN/genética , ARN Polimerasa Dependiente del ARN/química , Biología Computacional , Epítopos de Linfocito T/inmunología , Epítopos de Linfocito T/genética , Humanos , Epítopos/inmunología , Epítopos/genética , Epítopos de Linfocito B/inmunología , Epítopos de Linfocito B/genética , Infecciones por Rotavirus/prevención & control , Infecciones por Rotavirus/inmunología , Inmunoinformática , Vacunas de Subunidades Proteicas

RESUMEN

The identification of antibody-specific epitopes on virus proteins is crucial for vaccine development and drug design. Nonetheless, traditional wet-lab approaches for the identification of epitopes are both costly and labor-intensive, underscoring the need for the development of efficient and cost-effective computational tools. Here, EpiScan, an attention-based deep learning framework for predicting antibody-specific epitopes, is presented. EpiScan adopts a multi-input and single-output strategy by designing independent blocks for different parts of antibodies, including variable heavy chain (VH), variable light chain (VL), complementary determining regions (CDRs), and framework regions (FRs). The block predictions are weighted and integrated for the prediction of potential epitopes. Using multiple experimental data samples, we show that EpiScan, which only uses antibody sequence information, can accurately map epitopes on specific antigen structures. The antibody-specific epitopes on the receptor binding domain (RBD) of SARS coronavirus 2 (SARS-CoV-2) were located by EpiScan, and the potentially valuable vaccine epitope was identified. EpiScan can expedite the epitope mapping process for high-throughput antibody sequencing data, supporting vaccine design and drug development. Availability: For the convenience of related wet-experimental researchers, the source code and web server of EpiScan are publicly available at https://github.com/gzBiomedical/EpiScan .

Asunto(s)

Mapeo Epitopo , Epítopos , SARS-CoV-2 , Mapeo Epitopo/métodos , SARS-CoV-2/inmunología , Humanos , Epítopos/inmunología , Anticuerpos Antivirales/inmunología , Aprendizaje Profundo , COVID-19/inmunología , Biología Computacional/métodos , Glicoproteína de la Espiga del Coronavirus/inmunología , Programas Informáticos

RESUMEN

High-risk human papilloma virus (HR-HPV) persistent infection is closely associated with the development of cervical cancer and squamous intraepithelial lesion (SIL).The α-9 HPVs, which is predominantly composed of HR-HPV types, account for 75% of HR-HPV infection in Sichuan. The oncoproteins E6 and E7 of HPV play a crucial role in tumor initiation and progression. Notably, HPV-35 is the only HR-HPV type within the α-9 genus that is not included in the nine-valent HPV prophylactic vaccine. Cervical cell samples obtained from Sichuan were collected for HPV detection and genotyping. Among the 406 HPV-positive samples, 31 HPV-35 were detected, 24 HPV-35 E6 and 26 E7 were successfully amplified and sequenced, five nucleotide mutations in E6 and three in E7 were detected, T232C, T434G of E6 (W78R, I145R) and C67T, G84T of E7 (H23Y, L28F) were non-synonymy mutation. PAML 4.8 server was used to detect positive selection sites of HPV-35 E6, E7, and E6 is W78R. Phyre2 were used to predict and analyze protein structures, W78R made influences on protein structure. IEDB were used to screen epitopes vaccine target for HPV-35 affection therapy, and 5 HPV-35 E6 and 3 HPV-35 E7 most potential epitopes were obtained, the most potential peptides for therapy vaccine design were 79-91YRYSVYGETLEKQ, 45-60FACYDLCIVREGQPY, 124-135RFHNIGGRWTGR of E6; 3-19GEITTLQDYVLDLEPEA, 38-47TIDGPAGQAK, 70-88VQSTHIDIRKLEDLLMGTF of E7 and W78R mainly decreased the epitopes affinity.Conclusions Amino acid substitution in the positive selection sites of HPV-35 E6 and E7 genes have been found to influence protein structure and to decrease the overall affinity of antigen epitopes. This observation aligns with the evolutionary significance of positive selection site, which may confer advantages to the virus by making infected cells more challenging for the immune system to detect, thereby enhancing HPV's adaptability to the host environment. The polymorphism analysis of HPV-35 E6, E7 contributes to the enrichment of α-9 HPV data in Sichuan China, which is instrumental in improving the effectiveness of clinical detection. Furthermore, these findings provide a relevant theoretical foundation for the prevention and treatment of HPV-related diseases.

Asunto(s)

Proteínas Oncogénicas Virales , Infecciones por Papillomavirus , Vacunas contra Papillomavirus , Humanos , Proteínas Oncogénicas Virales/genética , Proteínas Oncogénicas Virales/inmunología , Femenino , China , Infecciones por Papillomavirus/virología , Infecciones por Papillomavirus/prevención & control , Vacunas contra Papillomavirus/inmunología , Vacunas contra Papillomavirus/genética , Polimorfismo Genético , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/inmunología , Genotipo , Adulto , Neoplasias del Cuello Uterino/virología , Neoplasias del Cuello Uterino/prevención & control , Epítopos/inmunología , Epítopos/genética , Alphapapillomavirus/genética , Alphapapillomavirus/inmunología , Alphapapillomavirus/clasificación , Persona de Mediana Edad , Mutación , Virus del Papiloma Humano

RESUMEN

Electron microscopy paired with immunogold labeling is the most precise tool for protein localization. However, these methods are either cumbersome, resulting in small sample numbers and restricted quantification, or limited to identifying protein epitopes external to the membrane. Here, we introduce SUB-immunogold-SEM, a scanning electron microscopy technique that detects intracellular protein epitopes proximal to the membrane. We identify four critical sample preparation factors contributing to the method's sensitivity. We validate its efficacy through precise localization and high-powered quantification of cytoskeletal and transmembrane protein distribution. We evaluate the capabilities of SUB-immunogold-SEM on cells with highly differentiated apical surfaces: (i) auditory hair cells, revealing the presence of nanoscale MYO15A-L rings at the tip of stereocilia; and (ii) respiratory multiciliate cells, mapping the distribution of the SARS-CoV-2 receptor ACE2 along the motile cilia. SUB-immunogold-SEM extends the application of SEM-based nanoscale protein localization to the detection of intracellular epitopes on the exposed surfaces of any cell.

Asunto(s)

Cilios , Epítopos , Inmunohistoquímica , Microscopía Electrónica de Rastreo , Epítopos/inmunología , Epítopos/metabolismo , Animales , Microscopía Electrónica de Rastreo/métodos , Humanos , Inmunohistoquímica/métodos , Cilios/metabolismo , Cilios/ultraestructura , Células Ciliadas Auditivas/metabolismo , Células Ciliadas Auditivas/ultraestructura , Enzima Convertidora de Angiotensina 2/metabolismo , SARS-CoV-2/inmunología , SARS-CoV-2/metabolismo , Miosinas/metabolismo , Estereocilios/metabolismo , Estereocilios/ultraestructura , COVID-19/virología , COVID-19/inmunología

RESUMEN

BACKGROUND: Cross-reactivity between nonspecific lipid transfer proteins could cause anaphylaxis, further influencing food avoidance and nutrient deficiencies. The one affecting olive pollen (Ole e 7) and peach (Pru p 3) may underlie a variety of pollen-food syndromes, though a deep molecular analysis is necessary. METHODS: Three Ole e 7-monosensitised patients (MON_OLE), three Pru p 3-monosensitised patients (MON_PRU) and three bisensitised patients (BI) were selected. For epitope mapping, both digested proteins were incubated with patient sera, and the captured IgE-bound peptides were characterised by LC-MS. RESULTS: The analysis revealed two Ole e 7 epitopes and the three Pru p 3 epitopes previously described. Interestingly, the "KSALALVGNKV" Ole e 7 peptide was recognised by MON_OLE, BI and MON_PRU patients. Conversely, all patients recognised the "ISASTNCATVK" Pru p 3 peptide. Although complete sequence alignment between both proteins revealed 32.6% identity, local alignment considering seven residue fragments showed 50 and 57% identity when comparing "ISASTNCATVK" with Ole e 7 and "KSALALVGNKV" with Pru p 3. CONCLUSIONS: This study mapped sIgE-Ole e 7-binding epitopes, paving the way for more precise diagnostic tools. Assuming non-significant sequence similarity, structural homology and shared key residues may underlie the potential cross-reactivity between Ole e 7 and Pru p 3 nsLTPs.

Asunto(s)

Antígenos de Plantas , Reacciones Cruzadas , Hipersensibilidad a los Alimentos , Inmunoglobulina E , Olea , Proteínas de Plantas , Polen , Prunus persica , Humanos , Antígenos de Plantas/inmunología , Hipersensibilidad a los Alimentos/inmunología , Polen/inmunología , Inmunoglobulina E/inmunología , Inmunoglobulina E/sangre , Olea/inmunología , Proteínas de Plantas/inmunología , Femenino , Masculino , Prunus persica/inmunología , Mapeo Epitopo , Adulto , Rinitis Alérgica Estacional/inmunología , Secuencia de Aminoácidos , Epítopos/inmunología , Alérgenos/inmunología , Persona de Mediana Edad , Proteínas Portadoras/inmunología

RESUMEN

Helicobacter pylori (H. pylori) is an infectious bacterium that colonizes the stomach of approximately half of the global population. It has been classified as a Group I carcinogen by the World Health Organization due to its strong association with an increased incidence of gastric cancer and exacerbation of stomach diseases. The primary treatment for H. pylori infection currently involves triple or quadruple therapy, primarily consisting of antibiotics and proton pump inhibitors. However, the increasing prevalence of antibiotic resistance poses significant challenges to this approach, underscoring the urgent need for an effective vaccine. In this study, a novel multi-epitope H. pylori vaccine was designed using immunoinformatics. The vaccine contains epitopes derived from nine essential proteins. Software tools and online servers were utilized to predict, evaluate, and analyze the physiochemical properties, secondary and tertiary structures, and immunogenicity of the candidate vaccine. These comprehensive assessments ultimately led to the formulation of an optimal design scheme for the vaccine. Through constructing a novel multi-epitope vaccine based on immunoinformatics, this study offers promising prospects and great potential for the prevention of H. pylori infection. This study also provides a reference strategy to develop multi-epitope vaccines for other pathogens.

Asunto(s)

Vacunas Bacterianas , Biología Computacional , Infecciones por Helicobacter , Helicobacter pylori , Helicobacter pylori/inmunología , Vacunas Bacterianas/inmunología , Biología Computacional/métodos , Infecciones por Helicobacter/inmunología , Infecciones por Helicobacter/prevención & control , Humanos , Antígenos Bacterianos/inmunología , Epítopos/inmunología , Desarrollo de Vacunas , Inmunoinformática

RESUMEN

COVID-19 has caused millions of deaths and many times more infections worldwide, emphasizing the unpreparedness of the global health system in the face of new infections and the key role for vaccines and therapeutics, including virus-neutralizing antibodies, in prevention and containment of the disease. Continuous evolution of the SARS-CoV-2 coronavirus has been causing its new variants to evade the action of the immune system, which highlighted the importance of detailed knowledge of the epitopes of already selected potent virus-neutralizing antibodies. A single-chain antibody ("nanobody") targeting the SARS-CoV-2 receptor-binding domain (RBD), clone P2C5, had exhibited robust virus-neutralizing activity against all SARS-CoV-2 variants and, being a major component of the anti-COVID-19 formulation "GamCoviMab", had successfully passed Phase I of clinical trials. However, after the emergence of the Delta and XBB variants, a decrease in the neutralizing activity of this nanobody was observed. Here we report on the successful crystal structure determination of the RBD:P2C5 complex at 3.1 Å, which revealed the intricate protein-protein interface, sterically occluding full ACE2 receptor binding by the P2C5-neutralized RBD. Moreover, the structure revealed the developed RBD:P2C5 interface centered around residues Leu452 and Phe490, thereby explaining the evasion of the Delta or Omicron XBB, but not Omicron B.1.1.529 variant, as a result of the single L452R or F490S mutations, respectively, from the action of P2C5. The structure obtained is expected to foster nanobody engineering in order to rescue neutralization activity and will facilitate epitope mapping for other neutralizing nanobodies by competition assays.

Asunto(s)

Anticuerpos Neutralizantes , SARS-CoV-2 , Anticuerpos de Dominio Único , Glicoproteína de la Espiga del Coronavirus , SARS-CoV-2/inmunología , SARS-CoV-2/efectos de los fármacos , Anticuerpos de Dominio Único/inmunología , Anticuerpos de Dominio Único/química , Anticuerpos de Dominio Único/farmacología , Anticuerpos Neutralizantes/inmunología , Anticuerpos Neutralizantes/química , Humanos , Glicoproteína de la Espiga del Coronavirus/inmunología , Glicoproteína de la Espiga del Coronavirus/química , Glicoproteína de la Espiga del Coronavirus/genética , Glicoproteína de la Espiga del Coronavirus/metabolismo , Anticuerpos Antivirales/inmunología , COVID-19/inmunología , COVID-19/virología , Dominios Proteicos , Unión Proteica , Epítopos/inmunología , Epítopos/química , Modelos Moleculares , Evasión Inmune , Enzima Convertidora de Angiotensina 2/metabolismo , Enzima Convertidora de Angiotensina 2/química , Enzima Convertidora de Angiotensina 2/inmunología , Sitios de Unión

RESUMEN

BACKGROUND/AIM: Wilms' tumors are pediatric renal tumors that generally have a good prognosis and outcomes. Viral illnesses have been linked to development of neoplasms and should be considered as a factor that could modulate overall survival. MATERIALS AND METHODS: We considered recently developed adaptive immune receptor, genomics and bioinformatics approaches to assess the potential impact of cytomegalovirus (CMV) infections in Wilms' tumor. RESULTS: T-cell receptor (TCR) complementarity determining region-3 (CDR3) amino acid sequences from Wilms' tumor specimens represented by the Therapeutically Applicable Research to Generate Effective Treatments dataset were compared with known anti-CMV TCR CDR3s, indicating that cases representing the anti-CMV TCR CDR3s had worse outcomes. Then, a chemical complementarity scoring approach for the Wilms' tumor, TCR CDR3s and a series of CMV antigens further indicated that cases representing a higher chemical complementarity to the CMV antigens had worse outcomes. CONCLUSION: Overall, we present a potentially novel method to assess CMV infections and identify patients who could benefit from therapies that address such infections.

Asunto(s)

Regiones Determinantes de Complementariedad , Citomegalovirus , Neoplasias Renales , Receptores de Antígenos de Linfocitos T , Tumor de Wilms , Humanos , Tumor de Wilms/inmunología , Tumor de Wilms/genética , Regiones Determinantes de Complementariedad/genética , Regiones Determinantes de Complementariedad/inmunología , Receptores de Antígenos de Linfocitos T/inmunología , Receptores de Antígenos de Linfocitos T/genética , Receptores de Antígenos de Linfocitos T/metabolismo , Neoplasias Renales/inmunología , Neoplasias Renales/genética , Citomegalovirus/inmunología , Infecciones por Citomegalovirus/inmunología , Infecciones por Citomegalovirus/virología , Pronóstico , Epítopos/inmunología

RESUMEN

Understanding binding epitopes involved in protein-protein interactions and accurately determining their structure are long-standing goals with broad applicability in industry and biomedicine. Although various experimental methods for binding epitope determination exist, these approaches are typically low throughput and cost-intensive. Computational methods have potential to accelerate epitope predictions; however, recently developed artificial intelligence (AI)-based methods frequently fail to predict epitopes of synthetic binding domains with few natural homologues. Here we have developed an integrated method employing generalized-correlation-based dynamic network analysis on multiple molecular dynamics (MD) trajectories, initiated from AlphaFold2Multimer structures, to unravel the structure and binding epitope of the therapeutic PD-L1:Affibody complex. Both AlphaFold2 and conventional molecular dynamics trajectory analysis were ineffective in distinguishing between two proposed binding models, parallel and perpendicular. However, our integrated approach, utilizing dynamic network analysis, demonstrated that the perpendicular mode was significantly more stable. These predictions were validated using a suite of experimental epitope mapping protocols, including cross-linking mass spectrometry and next-generation sequencing-based deep mutational scanning. Conversely, AlphaFold3 failed to predict a structure bound in the perpendicular pose, highlighting the necessity for exploratory research in the search for binding epitopes and challenging the notion that AI-generated protein structures can be accepted without scrutiny. Our research underscores the potential of employing dynamic network analysis to enhance AI-based structure predictions for more accurate identification of protein-protein interaction interfaces.

Asunto(s)

Antígeno B7-H1 , Epítopos , Simulación de Dinámica Molecular , Antígeno B7-H1/química , Antígeno B7-H1/inmunología , Epítopos/química , Epítopos/inmunología , Inteligencia Artificial , Humanos , Unión Proteica

RESUMEN

Continued evolution of SARS-CoV-2 generates variants to challenge antibody immunity established by infection and vaccination. A connection between population immunity and genesis of virus variants has long been suggested but its molecular basis remains poorly understood. Here, we identify a class of SARS-CoV-2 neutralizing public antibodies defined by their shared usage of VL6-57 light chains. Although heavy chains of diverse genotypes are utilized, convergent HCDR3 rearrangements have been observed among these public antibodies to cooperate with germline VL6-57 LCDRs to target a convergent epitope defined by RBD residues S371-S373-S375. Antibody repertoire analysis identifies that this class of VL6-57 antibodies is present in SARS-CoV-2-naive individuals and is clonally expanded in most COVID-19 patients. We confirm that Omicron-specific substitutions at S371, S373 and S375 mediate escape of antibodies of the VL6-57 class. These findings support that this class of public antibodies constitutes a potential immune pressure promoting the introduction of S371L/F-S373P-S375F in Omicron variants. The results provide further molecular evidence to support that antigenic evolution of SARS-CoV-2 is driven by antibody mediated population immunity.

Asunto(s)

Anticuerpos Neutralizantes , Anticuerpos Antivirales , COVID-19 , Epítopos , SARS-CoV-2 , Glicoproteína de la Espiga del Coronavirus , SARS-CoV-2/inmunología , SARS-CoV-2/genética , Humanos , Glicoproteína de la Espiga del Coronavirus/inmunología , Glicoproteína de la Espiga del Coronavirus/genética , COVID-19/inmunología , COVID-19/virología , Anticuerpos Antivirales/inmunología , Anticuerpos Neutralizantes/inmunología , Epítopos/inmunología , Epítopos/genética , Cadenas Ligeras de Inmunoglobulina/genética , Cadenas Ligeras de Inmunoglobulina/inmunología

RESUMEN

HIV-1 envelope glycoproteins (Envs) of most primary HIV-1 strains exist in closed conformation and infrequently sample open states, limiting access to internal epitopes. Thus, immunogen design aims to mimic the closed Env conformation as preferred target for eliciting broadly neutralizing antibodies (bnAbs). Here we identify incompletely closed Env conformations of 6 out of 13 transmitted/founder (T/F) strains that are sensitive to antibodies that recognize internal epitopes typically exposed on open Envs. A 3.6 Å cryo-electron microscopy structure of unliganded, incompletely closed T/F Envs (1059-SOSIP) reveals protomer motion that increased sampling of states with incompletely closed trimer apex. We reconstruct de novo the post-transmission evolutionary pathway of a second T/F. Evolved viruses exhibit increased Env resistance to cold, soluble CD4 and 19b, all of which correlate with closing of the adapted Env trimer. Lastly, we show that the ultra-broad N6 bnAb efficiently recognizes different Env conformations and exhibits improved antiviral breadth against VRC01-resistant Envs isolated during the first-in-humans antibody-mediated-prevention trial.

Asunto(s)

Anticuerpos Neutralizantes , Microscopía por Crioelectrón , Anticuerpos Anti-VIH , VIH-1 , Conformación Proteica , Productos del Gen env del Virus de la Inmunodeficiencia Humana , VIH-1/inmunología , Humanos , Productos del Gen env del Virus de la Inmunodeficiencia Humana/inmunología , Productos del Gen env del Virus de la Inmunodeficiencia Humana/química , Productos del Gen env del Virus de la Inmunodeficiencia Humana/metabolismo , Anticuerpos Anti-VIH/inmunología , Anticuerpos Neutralizantes/inmunología , Infecciones por VIH/inmunología , Infecciones por VIH/virología , Epítopos/inmunología , Epítopos/química , Anticuerpos ampliamente neutralizantes/inmunología , Anticuerpos ampliamente neutralizantes/química , Células HEK293 , Antígenos CD4/metabolismo , Antígenos CD4/inmunología , Antígenos CD4/química , Modelos Moleculares

RESUMEN

The central immunological role of HLA class I (HLA-I) in presenting peptide Ags to cellular components of the immune system has been the focus of intense study for >60 y. A confounding factor in the study of HLA-I has been the extreme polymorphism of these molecules. The mAb W6/32 has been a fundamental reagent bypassing the issue of polymorphism by recognizing an epitope that is conserved across diverse HLA-I allotypes. However, despite the widespread use of W6/32, the epitope of this Ab has not been definitively mapped. In this study, we present the crystal structure of the Fab fragment of W6/32 in complex with peptide-HLA-B*27:05. W6/32 bound to HLA-B*27:05 beneath the Ag-binding groove, recognizing a discontinuous epitope comprised of the α1, α2, and α3 domains of HLA-I and ß2-microglobulin. The epitope comprises a region of low polymorphism reflecting the pan-HLA-I nature of the binding. Notably, the W6/32 epitope neither overlaps the HLA-I binding sites of either T cell Ag receptors or killer cell Ig-like receptors. However, it does coincide with the binding sites for leukocyte Ig-like receptors and CD8 coreceptors. Consistent with this, the use of W6/32 to block the interaction of NK cells with HLA-I only weakly impaired inhibition mediated by KIR3DL1, but impacted HLA-LILR recognition.

Asunto(s)

Anticuerpos Monoclonales , Humanos , Anticuerpos Monoclonales/inmunología , Anticuerpos Monoclonales/química , Cristalografía por Rayos X , Antígenos HLA-B/inmunología , Antígenos HLA-B/química , Antígenos HLA-B/genética , Unión Proteica , Epítopos/inmunología , Fragmentos Fab de Inmunoglobulinas/inmunología , Fragmentos Fab de Inmunoglobulinas/química , Antígenos de Histocompatibilidad Clase I/inmunología , Antígenos de Histocompatibilidad Clase I/química , Antígeno HLA-B27