scholarly journals Identification of B-Cell Epitopes with Potential to Serologicaly Discrimnate Dengue from Zika Infections

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1079 ◽  
Author(s):  
Alice F. Versiani ◽  
Raissa Prado Rocha ◽  
Tiago A. O. Mendes ◽  
Glauco C. Pereira ◽  
Jordana Graziella A. Coelho dos Reis ◽  
...  

Dengue is currently one of the most important arbovirus infections worldwide. Early diagnosis is important for disease outcome, particularly for those afflicted with the severe forms of infection. The goal of this work was to identify conserved and polymorphic linear B-cell Dengue virus (DENV) epitopes that could be used for diagnostic purposes. To this end, we aligned the predicted viral proteome of the four DENV serotype and performed in silico B-cell epitope mapping. We developed a script in Perl integrating alignment and prediction information to identify potential serotype-specific epitopes. We excluded epitopes that were similarly present in the yellow fever and zika viruses’ proteomes. A total of 15 polymorphic and nine conserved peptides among DENV serotypes were selected. Peptides were spotted on cellulose membranes and tested against sera from rabbits that were monoinfected with each DENV serotype. Although serotype-specific peptides failed to recognize any sera, three conserved peptides were recognized by all anti-dengue sera and were included on an ELISA test employing a well-characterized human sera bank. Of the three peptides, one was able to efficiently identify sera from all four DENV serotypes and to discriminate them from Zika virus positive sera.

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Lenka Potocnakova ◽  
Mangesh Bhide ◽  
Lucia Borszekova Pulzova

Identification of B-cell epitopes is a fundamental step for development of epitope-based vaccines, therapeutic antibodies, and diagnostic tools. Epitope-based antibodies are currently the most promising class of biopharmaceuticals. In the last decade, in-depth in silico analysis and categorization of the experimentally identified epitopes stimulated development of algorithms for epitope prediction. Recently, various in silico tools are employed in attempts to predict B-cell epitopes based on sequence and/or structural data. The main objective of epitope identification is to replace an antigen in the immunization, antibody production, and serodiagnosis. The accurate identification of B-cell epitopes still presents major challenges for immunologists. Advances in B-cell epitope mapping and computational prediction have yielded molecular insights into the process of biorecognition and formation of antigen-antibody complex, which may help to localize B-cell epitopes more precisely. In this paper, we have comprehensively reviewed state-of-the-art experimental methods for B-cell epitope identification, existing databases for epitopes, and novel in silico resources and prediction tools available online. We have also elaborated new trends in the antibody-based epitope prediction. The aim of this review is to assist researchers in identification of B-cell epitopes.


2018 ◽  
Vol 9 ◽  
Author(s):  
Monique Paiva Campos ◽  
Fabiano Borges Figueiredo ◽  
Fernanda Nazaré Morgado ◽  
Alinne Rangel dos Santos Renzetti ◽  
Sara Maria Marques de Souza ◽  
...  

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1084-1084
Author(s):  
Shannon Meeks ◽  
W. Hunter Baldwin ◽  
Courtney Cox

Abstract The development of anti-factor VIII (fVIII) antibodies is a significant complication in the management of patients with hemophilia A leading to increased morbidity and treatment cost. Physicians typically base treatment decisions on inhibitor titer as measured by the Bethesda assay. Patients with inhibitor titers greater than 10 Bethesda units (BU/ml) are unlikely to respond to fVIII and are treated with bypassing agents. Using a panel of anti-fVIII monoclonal antibodies (MAbs) to different B-Cell epitopes on fVIII, we have shown that epitope specificity, inhibitor kinetics, and time to maximum inhibition are more important than inhibitor titer in predicting response to fVIII. We have previously reported the mapping of B-Cell epitopes using competition ELISA with murine anti-fVIII MAbs. Although successful, these assays required high volumes of patient plasma. The ability to map the epitope spectrum of patient plasma using a clinically feasible assay may fundamentally change how clinicians approach treatment of high titer inhibitor patients. Methods: B-Cell epitopes were mapped using competition ELISA and a slide based microarray. For the microarray, 15 anti-fVIII MAbs were printed on nitrocellulose slides at concentrations up to 1.0 mg/ml. Inhibitor patient or control samples were prepared at various dilutions containing 8μg/ml biotinylated fVIII (B-fVIII). Required plasma volumes ranged from 3.6-47.5μl. Following a 120' incubation at 37°C, test sample was added directly to the slide. After 60' at room temperature, capture of B-fVIII was detected with 0.5μg/ml Cy-5 conjugated streptavidin. Test samples were considered positive for the presence of antibody with a competing epitope when the average fluorescence intensity was reduced to less than 25% of the control value. Competition ELISAs were performed using our previously published method. For each epitope tested, a single biotinylated anti-fVIII MAb was competed against antibodies present in test plasma. Samples were considered positive when a 3 fold or greater increase in antibody titer over controls was observed. Results: To determine if the microarray method could accurately detect anti-fVIII MAbs in plasma we chose five commercially available anti-fVIII MAbs. We created control inhibitor plasmas by adding 10μg/ml of a single MAb to fVIII deficient plasma. Antibodies selected were against 4 fVIII domains, the A1, A2, C1, and C2. Two MAbs were selected to the C2 domain as previous studies indicate overlapping epitopes. Inhibitor titer for the control MAbs ranged from <2 to 23,300 BU/mg IgG. The microarray accurately detected the presence of all control MAbs tested as measured by a signal reduction greater than or equal to 75% of control. The overlapping epitopes in the C2 domain were also resolved in the microarray as signals in the overlapping portions were significantly decreased. We also tested a patient plasma using both the microarray and ELISA against this panel of five MAbs. The assays showed agreement with detection of antibodies that overlapped C1 antibody 2A9. Neither of the C2 epitopes tested were detected by the microarray. ELISA results confirmed that our test sample was negative for competing antibodies against the C2 epitopes tested by microarray, but positive for other portions of the C2 domain. Conclusions: We have shown that the B-Cell epitope mapping microarray is capable of accurately detecting anti-fVIII antibodies in patient plasma. Obtaining equivalent data by ELISA requires 37 times greater plasma volume. Although initial development testing used 5 MAbs scaling up to the full panel of 13 non-overlapping epitopes requires no larger plasma sample. The ability to map the B-cell epitopes across the fVIII protein in a single assay confers a huge advantage in terms of time, resources, and clinical feasibility. Using well-characertized murine MAbs to define B-cell epitopes may allow for functional correlations to be made. The ability to track the evolution of an individual patients' antibody epitope spectrum will allow for personalized treatment plans that could result in significantly better treatment outcomes for patients with severe Hemophilia A. Figure 1. Figure 1. Disclosures No relevant conflicts of interest to declare.


2018 ◽  
Vol 9 ◽  
Author(s):  
Monique Paiva Campos ◽  
Fabiano Borges Figueiredo ◽  
Fernanda Nazaré Morgado ◽  
Alinne Rangel dos Santos Renzetti ◽  
Sara Maria Marques de Souza ◽  
...  

Author(s):  
Zaytsev Sergey ◽  
Motin Vladimir ◽  
Khizhnyakova Mariya ◽  
Feodorova Valentina Anatolievna ◽  
Elena Lyapina ◽  
...  

2017 ◽  
Vol 8 ◽  
Author(s):  
Rodrigo Nunes Rodrigues-da-Silva ◽  
Isabela Ferreira Soares ◽  
Cesar Lopez-Camacho ◽  
João Hermínio Martins da Silva ◽  
Daiana de Souza Perce-da-Silva ◽  
...  

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Li Cen Lim ◽  
Yee Ying Lim ◽  
Yee Siew Choong

Abstract B-cell epitope will be recognized and attached to the surface of receptors in B-lymphocytes to trigger immune response, thus are the vital elements in the field of epitope-based vaccine design, antibody production and therapeutic development. However, the experimental approaches in mapping epitopes are time consuming and costly. Computational prediction could offer an unbiased preliminary selection to reduce the number of epitopes for experimental validation. The deposited B-cell epitopes in the databases are those with experimentally determined positive/negative peptides and some are ambiguous resulted from different experimental methods. Prior to the development of B-cell epitope prediction module, the available dataset need to be handled with care. In this work, we first pre-processed the B-cell epitope dataset prior to B-cell epitopes prediction based on pattern recognition using support vector machine (SVM). By using only the absolute epitopes and non-epitopes, the datasets were classified into five categories of pathogen and worked on the 6-mers peptide sequences. The pre-processing of the datasets have improved the B-cell epitope prediction performance up to 99.1 % accuracy and showed significant improvement in cross validation results. It could be useful when incorporated with physicochemical propensity ranking in the future for the development of B-cell epitope prediction module.


2018 ◽  
Vol 49 (4) ◽  
pp. 1600-1614 ◽  
Author(s):  
Shudong He ◽  
Jinlong Zhao ◽  
Walid Elfalleh ◽  
Mohamed Jemaà ◽  
Hanju  Sun ◽  
...  

Background/Aims: The incidence of lectin allergic disease is increasing in recent decades, and definitive treatment is still lacking. Identification of B and T-cell epitopes of allergen will be useful in understanding the allergen antibody responses as well as aiding in the development of new diagnostics and therapy regimens for lectin poisoning. In the current study, we mainly addressed these questions. Methods: Three-dimensional structure of the lectin from black turtle bean (Phaseolus vulgaris L.) was modeled using the structural template of Phytohemagglutinin from P. vulgaris (PHA-E, PDB ID: 3wcs.1.A) with high identity. The B and T-cell epitopes were screened and identified by immunoinformatics and subsequently validated by ELISA, lymphocyte proliferation and cytokine profile analyses. Results: Seven potential B-cell epitopes (B1 to B7) were identified by sequence and structure based methods, while three T-cell epitopes (T1 to T3) were identified by the predictions of binding score and inhibitory concentration. The epitope peptides were synthesized. Significant IgE binding capability was found in B-cell epitopes (B2, B5, B6 and B7) and T2 (a cryptic B-cell epitope). T1 and T2 induced significant lymphoproliferation, and the release of IL-4 and IL-5 cytokine confirmed the validity of T-cell epitope prediction. Abundant hydrophobic amino acids were found in B-cell epitope and T-cell epitope regions by amino acid analysis. Positively charged amino acids, such as His residue, might be more favored for B-cell epitope. Conclusion: The present approach can be applied for the identification of epitopes in novel allergen proteins and thus for designing diagnostics and therapies in lectin allergy.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kanokporn Polyiam ◽  
Waranyoo Phoolcharoen ◽  
Namphueng Butkhot ◽  
Chanya Srisaowakarn ◽  
Arunee Thitithanyanont ◽  
...  

AbstractSARS-CoV-2 continues to infect an ever-expanding number of people, resulting in an increase in the number of deaths globally. With the emergence of new variants, there is a corresponding decrease in the currently available vaccine efficacy, highlighting the need for greater insights into the viral epitope profile for both vaccine design and assessment. In this study, three immunodominant linear B cell epitopes in the SARS-CoV-2 spike receptor-binding domain (RBD) were identified by immunoinformatics prediction, and confirmed by ELISA with sera from Macaca fascicularis vaccinated with a SARS-CoV-2 RBD subunit vaccine. Further immunoinformatics analyses of these three epitopes gave rise to a method of linear B cell epitope prediction and selection. B cell epitopes in the spike (S), membrane (M), and envelope (E) proteins were subsequently predicted and confirmed using convalescent sera from COVID-19 infected patients. Immunodominant epitopes were identified in three regions of the S2 domain, one region at the S1/S2 cleavage site and one region at the C-terminus of the M protein. Epitope mapping revealed that most of the amino acid changes found in variants of concern are located within B cell epitopes in the NTD, RBD, and S1/S2 cleavage site. This work provides insights into B cell epitopes of SARS-CoV-2 as well as immunoinformatics methods for B cell epitope prediction, which will improve and enhance SARS-CoV-2 vaccine development against emergent variants.


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