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Frontiers in Immunology 2019B-cells can neutralize pathogenic molecules by targeting them with extreme specificity using receptors secreted or expressed on their surface (antibodies). This is...
B-cells can neutralize pathogenic molecules by targeting them with extreme specificity using receptors secreted or expressed on their surface (antibodies). This is achieved via molecular interactions between the paratope (i.e., the antibody residues involved in the binding) and the interacting region (epitope) of its target molecule (antigen). Discerning the rules that define this specificity would have profound implications for our understanding of humoral immunogenicity and its applications. The aim of this work is to produce improved, antibody-specific epitope predictions by exploiting features derived from the antigens and their cognate antibodies structures, and combining them using statistical and machine learning algorithms. We have identified several geometric and physicochemical features that are correlated in interacting paratopes and epitopes, used them to develop a Monte Carlo algorithm to generate putative epitopes-paratope pairs, and train a machine-learning model to score them. We show that, by including the structural and physicochemical properties of the paratope, we improve the prediction of the target of a given B-cell receptor. Moreover, we demonstrate a gain in predictive power both in terms of identifying the cognate antigen target for a given antibody and the antibody target for a given antigen, exceeding the results of other available tools.
Topics: Algorithms; Amino Acid Sequence; Animals; Antibodies; Antibody Specificity; Antigen-Antibody Complex; Binding Sites, Antibody; Epitope Mapping; Epitopes, B-Lymphocyte; Humans; Models, Molecular; Monte Carlo Method; Neural Networks, Computer; Protein Domains; Reproducibility of Results
PubMed: 30863406
DOI: 10.3389/fimmu.2019.00298 -
International Archives of Allergy and... 2021The Global Initiative for Asthma Report updated in 2019 stated that potential benefits of allergen immunotherapy (AIT), compared to pharmacological and avoidance... (Review)
Review
The Global Initiative for Asthma Report updated in 2019 stated that potential benefits of allergen immunotherapy (AIT), compared to pharmacological and avoidance options, must be weighed against the risk of adverse effects and the inconvenience and cost of the prolonged course of therapy in asthma. Thus, with the aim of clarifying some aspects with regard to the possible use of AIT in allergic asthma treatment armamentarium, a group of expert allergists from the Spanish Allergy and Clinical Immunology Scientific Society (SEAIC), particularly from the Immunotherapy and Asthma Interest Groups developed a frequently asked questions in clinical practice. This document updates relevant topics on the use of AIT in asthma and could facilitate physician clinical decisions and improve health outcomes for individual patients.
Topics: Age Factors; Allergens; Antibody Specificity; Asthma; Biomarkers; Clinical Decision-Making; Clinical Trials as Topic; Cost-Benefit Analysis; Desensitization, Immunologic; Disease Management; Humans; Immunoglobulin E; Prognosis; Severity of Illness Index; Treatment Outcome
PubMed: 33631755
DOI: 10.1159/000513811 -
Cold Spring Harbor Perspectives in... Jul 2018Influenza remains a major human pathogen despite seasonal vaccination. At long last, there is energy and resources to develop influenza vaccines that provide more... (Review)
Review
Influenza remains a major human pathogen despite seasonal vaccination. At long last, there is energy and resources to develop influenza vaccines that provide more predictable and durable protection. Vaccines based on inducing antibodies to the conserved stem of the viral hemagglutinin (HA) have emerged as leading candidates for broadening population immunity and ultimately limiting antigenic drift. Here, we discuss the knowns and unknowns of HA-specific B-cell and antibody responses. In particular, we focus on how immunodominance sculpts antibody responses and drives antigenic drift. We propose a number of strategies to overcome immunodominance and improve the breadth and efficacy of antibody responses.
Topics: Antibody Specificity; Antigens, Viral; Humans; Immunodominant Epitopes; Influenza Vaccines; Influenza, Human
PubMed: 28663210
DOI: 10.1101/cshperspect.a028852 -
Frontiers in Immunology 2023T-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens....
INTRODUCTION
T-cell receptor (TCR) recognition of foreign peptides presented by the major histocompatibility complex (MHC) initiates the adaptive immune response against pathogens. While a large number of TCR sequences specific to different antigenic peptides are known to date, the structural data describing the conformation and contacting residues for TCR-peptide-MHC complexes is relatively limited. In the present study we aim to extend and analyze the set of available structures by performing highly accurate template-based modeling of these complexes using TCR sequences with known specificity.
METHODS
Identification of CDR3 sequences and their further clustering, based on available spatial structures, V- and J-genes of corresponding T-cell receptors, and epitopes, was performed using the VDJdb database. Modeling of the selected CDR3 loops was conducted using a stepwise introduction of single amino acid substitutions to the template PDB structures, followed by optimization of the TCR-peptide-MHC contacting interface using the Rosetta package applications. Statistical analysis and recursive feature elimination procedures were carried out on computed energy values and properties of contacting amino acid residues between CDR3 loops and peptides, using R.
RESULTS
Using the set of 29 complex templates (including a template with SARS-CoV-2 antigen) and 732 specificity records, we built a database of 1585 model structures carrying substitutions in either TCRα or TCRβ chains with some models representing the result of different mutation pathways for the same final structure. This database allowed us to analyze features of amino acid contacts in TCR - peptide interfaces that govern antigen recognition preferences and interpret these interactions in terms of physicochemical properties of interacting residues.
CONCLUSION
Our results provide a methodology for creating high-quality TCR-peptide-MHC models for antigens of interest that can be utilized to predict TCR specificity.
Topics: Humans; COVID-19; SARS-CoV-2; Antibody Specificity; T-Cell Antigen Receptor Specificity; Amino Acids; Complement System Proteins
PubMed: 37649481
DOI: 10.3389/fimmu.2023.1224969 -
BMC Bioinformatics Mar 2024Nanobodies, also known as VHH or single-domain antibodies, are unique antibody fragments derived solely from heavy chains. They offer advantages of small molecules and...
BACKGROUND
Nanobodies, also known as VHH or single-domain antibodies, are unique antibody fragments derived solely from heavy chains. They offer advantages of small molecules and conventional antibodies, making them promising therapeutics. The paratope is the specific region on an antibody that binds to an antigen. Paratope prediction involves the identification and characterization of the antigen-binding site on an antibody. This process is crucial for understanding the specificity and affinity of antibody-antigen interactions. Various computational methods and experimental approaches have been developed to predict and analyze paratopes, contributing to advancements in antibody engineering, drug development, and immunotherapy. However, existing predictive models trained on traditional antibodies may not be suitable for nanobodies. Additionally, the limited availability of nanobody datasets poses challenges in constructing accurate models.
METHODS
To address these challenges, we have developed a novel nanobody prediction model, named NanoBERTa-ASP (Antibody Specificity Prediction), which is specifically designed for predicting nanobody-antigen binding sites. The model adopts a training strategy more suitable for nanobodies, based on an advanced natural language processing (NLP) model called BERT (Bidirectional Encoder Representations from Transformers). To be more specific, the model utilizes a masked language modeling approach named RoBERTa (Robustly Optimized BERT Pretraining Approach) to learn the contextual information of the nanobody sequence and predict its binding site.
RESULTS
NanoBERTa-ASP achieved exceptional performance in predicting nanobody binding sites, outperforming existing methods, indicating its proficiency in capturing sequence information specific to nanobodies and accurately identifying their binding sites. Furthermore, NanoBERTa-ASP provides insights into the interaction mechanisms between nanobodies and antigens, contributing to a better understanding of nanobodies and facilitating the design and development of nanobodies with therapeutic potential.
CONCLUSION
NanoBERTa-ASP represents a significant advancement in nanobody paratope prediction. Its superior performance highlights the potential of deep learning approaches in nanobody research. By leveraging the increasing volume of nanobody data, NanoBERTa-ASP can further refine its predictions, enhance its performance, and contribute to the development of novel nanobody-based therapeutics. Github repository: https://github.com/WangLabforComputationalBiology/NanoBERTa-ASP.
Topics: Binding Sites, Antibody; Single-Domain Antibodies; Antibodies; Binding Sites; Antibody Specificity
PubMed: 38515052
DOI: 10.1186/s12859-024-05750-5 -
Frontiers in Immunology 2021Monoclonal antibodies (mAbs) have been a valuable tool to elucidate several biological processes, such as stem cell differentiation and cancer, and contributed to...
Monoclonal antibodies (mAbs) have been a valuable tool to elucidate several biological processes, such as stem cell differentiation and cancer, and contributed to virtually all areas of biomedical sciences. Yet, it remains a challenge to obtain mAbs specific to poorly expressed epitopes, or to epitopes that are actually involved in important biological phenomena, such as cell differentiation and metastasis. Drug-induced subtractive immunization, and recently the multiple tolerization subtractive immunization (MTSI) technique, reported by our group, have the potential to level up the field, as they direct the host´s immune response towards these epitopes. However, due to cyclophosphamide (CY) treatment, high mice mortality can be observed, and only a few data are available on how these techniques affect the immune system of mice. Tolerogen and immunogen cells, RWPE-1 and PC-3 cells, respectively, were individually seeded at 2 × 10 cells/cm, and then adjusted to 2 × 10 cells per mouse before immunization, which was conducted in a subtractive approach (MTSI) with CY. Immunosuppression of mice was recorded total white blood counting, as well the reactivity of circulating polyclonal antibodies (pAbs). General parameters, including weight, physical appearance, and behavior on mice subjected to three different concentrations of CY were recorded. mAbs were obtained using classical hybridoma techniques, using the spleen of immunized mice. After purification, antibodies were characterized by Western blotting, and Indirect immunofluorescence. In conclusion, all CY dosage were efficient in creating an immunosuppression state, but only the 100 mg/kg body weight was feasible, as the others resulted in extensive mice mortality. pAbs obtained in the peripheral blood of mice showed more reactivity towards tumor cells. MAbs 2-7A50 and 2-5C11 recognized antigens from tumor cells, but not from their non-tumor counterparts, as shown in western blotting and immunofluorescence assays. MTSI technique was successful in generating mAbs that recognize tumor-specific antigens.
Topics: Animals; Antibodies, Monoclonal; Antibody Specificity; Cell Line; Cyclophosphamide; Epitopes; Humans; Immunosuppression Therapy; Immunosuppressive Agents; Leukocyte Count; Male; Mice, Inbred BALB C; Mice
PubMed: 34950138
DOI: 10.3389/fimmu.2021.760817 -
EBioMedicine Jul 2021Approximately 40% of human pregnancies are unintended, indicating a need for more acceptable effective contraception methods. New antibody production systems make it...
BACKGROUND
Approximately 40% of human pregnancies are unintended, indicating a need for more acceptable effective contraception methods. New antibody production systems make it possible to manufacture reagent-grade human monoclonal antibodies (mAbs) for clinical use. We used the Nicotiana platform to produce a human antisperm mAb and tested its efficacy for on-demand topical contraception.
METHODS
Heavy and light chain variable region DNA sequences of a human IgM antisperm antibody derived from an infertile woman were inserted with human IgG constant region sequences into an agrobacterium and transfected into Nicotiana benthamiana. The product, an IgG mAb ["Human Contraception Antibody" (HCA)], was purified on Protein A columns, and QC was performed using the LabChip GXII Touch protein characterization system and SEC-HPLC. HCA was tested for antigen specificity by immunofluorescence and western blot assays, antisperm activity by sperm agglutination and complement dependent sperm immobilization assays, and safety in a human vaginal tissue (EpiVaginal™) model.
FINDINGS
HCA was obtained at concentrations ranging from 0.4 to 4 mg/ml and consisted of > 90% IgG monomers. The mAb specifically reacted with a glycan epitope on CD52g, a glycoprotein produced in the male reproductive tract and found in abundance on sperm. HCA potently agglutinated sperm under a variety of relevant physiological conditions at concentrations ≥ 6.25 µg/ml, and mediated complement-dependent sperm immobilization at concentrations ≥ 1 µg/ml. HCA and its immune complexes did not induce inflammation in EpiVaginal™ tissue.
INTERPRETATION
HCA, an IgG1 mAb with potent sperm agglutination and immobilization activity and a good safety profile, is a promising candidate for female contraception.
FUNDING
This research was supported by grants R01 HD095630 and P50HD096957 from the National Institutes of Health.
Topics: Antibodies, Monoclonal; Antibody Specificity; CD52 Antigen; Contraception, Immunologic; Female; Humans; Male; Spermatozoa; Vaccines, Contraceptive
PubMed: 34256345
DOI: 10.1016/j.ebiom.2021.103478 -
Arthritis & Rheumatology (Hoboken, N.J.) Dec 2014The serologic hallmark of primary Sjögren's syndrome (SS) is the presence of IgG antibodies specific for Ro (SSA) and La (SSB). The molecular characteristics of...
OBJECTIVE
The serologic hallmark of primary Sjögren's syndrome (SS) is the presence of IgG antibodies specific for Ro (SSA) and La (SSB). The molecular characteristics of gland-derived B cells at the site of primary SS inflammation have been described previously; however, parallels between glandular antibody-secreting cells (ASCs) and serologic antibody specificities have not been evaluated. We used recombinant monoclonal antibody (mAb) technology to study the specificities of salivary gland (SG)-derived ASCs, evaluate their molecular characteristics, and identify IgG antibody specificity.
METHODS
Human antibodies were generated from glandular IgG ASCs. Heavy chain and light chain use and immunoglobulin subclass were analyzed by sequencing. Enzyme-linked immunosorbent assay, indirect immunofluorescence, enzyme immunoassay, and (35) S-labeled protein immunoprecipitation analysis were used to determine antibody specificity.
RESULTS
Evaluation of single ASCs in SG biopsy specimens from a patient with primary SS and a patient with SS and overlapping systemic lupus erythematosus revealed significant concordance between serum autoantibody and glandular ASC specificities. Gland-derived ASC heavy chains and light chains were extensively somatically hypermutated, which is indicative of antigen-driven responses. Specifically, we produced the first fully human mAb derived from SGs.
CONCLUSION
In patients with SS, the SGs are a site for the production of antibodies that extend beyond the canonical Ro and/or La SS specificities. Glandular antibody production strongly reflected the serologic humoral response in the 2 patients whom we studied.
Topics: Adult; Antibodies, Antinuclear; Antibody Specificity; Antibody-Producing Cells; Autoantibodies; B-Lymphocytes; Female; Humans; Lip; Middle Aged; Ribonucleoproteins; Salivary Glands, Minor; Sjogren's Syndrome
PubMed: 25199908
DOI: 10.1002/art.38872 -
Scientific Reports Jul 2020Zika virus (ZIKV) is an emerging flavivirus transmitted to humans by Aedes mosquitos. ZIKV can be transmitted from mother to fetus during pregnancy and can cause...
Zika virus (ZIKV) is an emerging flavivirus transmitted to humans by Aedes mosquitos. ZIKV can be transmitted from mother to fetus during pregnancy and can cause microcephaly and other birth defects. Effective vaccines for Zika are yet to be approved. Detection of the ZIKV is based on serological testing that often shows cross-reactivity with the Dengue virus (DENV) and other flaviviruses. We aimed to assemble a highly specific anti-Zika antibody panel to be utilized in the development of a highly specific and cost-effective ZIKV rapid quantification assay for viral load monitoring at point-of-care settings. To this end, we tested the affinity and specificity of twenty one commercially available monoclonal and polyclonal antibodies against ZIKV and DENV envelope proteins utilizing nine ZIKV and twelve DENV strains. We finalized and tested a panel of five antibodies for the specific detection and differentiation of ZIKV and DENV infected samples.
Topics: Animals; Antibodies, Viral; Antibody Specificity; Chlorocebus aethiops; Cross Reactions; Dengue Virus; Limit of Detection; Mice; Rabbits; Reproducibility of Results; Sensitivity and Specificity; Vero Cells; Viral Envelope Proteins; Zika Virus
PubMed: 32681135
DOI: 10.1038/s41598-020-68635-6 -
Nature Communications Oct 2018There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the...
There is a need for standardized validation methods for antibody specificity and selectivity. Recently, five alternative validation pillars were proposed to explore the specificity of research antibodies using methods with no need for prior knowledge about the protein target. Here, we show that these principles can be used in a streamlined manner for enhanced validation of research antibodies in Western blot applications. More than 6,000 antibodies were validated with at least one of these strategies involving orthogonal methods, genetic knockdown, recombinant expression, independent antibodies, and capture mass spectrometry analysis. The results show a path forward for efforts to validate antibodies in an application-specific manner suitable for both providers and users.
Topics: Animals; Antibodies; Antibody Specificity; Blotting, Western; High-Throughput Screening Assays; Humans; Reference Standards; Reproducibility of Results; Validation Studies as Topic
PubMed: 30297845
DOI: 10.1038/s41467-018-06642-y