Cargando…
Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases
T-cell recognition of antigen epitopes is a crucial step for the induction of adaptive immune responses, and the identification of such T-cell epitopes is, therefore, important for understanding diverse immune responses and controlling T-cell immunity. A number of bioinformatic tools exist that pred...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10221809/ https://www.ncbi.nlm.nih.gov/pubmed/37243272 http://dx.doi.org/10.3390/v15051186 |
_version_ | 1785049545114124288 |
---|---|
author | Nakamura, Yukio Moi, Meng Ling Shiina, Takashi Shin-I, Tadasu Suzuki, Ryuji |
author_facet | Nakamura, Yukio Moi, Meng Ling Shiina, Takashi Shin-I, Tadasu Suzuki, Ryuji |
author_sort | Nakamura, Yukio |
collection | PubMed |
description | T-cell recognition of antigen epitopes is a crucial step for the induction of adaptive immune responses, and the identification of such T-cell epitopes is, therefore, important for understanding diverse immune responses and controlling T-cell immunity. A number of bioinformatic tools exist that predict T-cell epitopes; however, many of these methods highly rely on evaluating conventional peptide presentation by major histocompatibility complex (MHC) molecules, but they ignore epitope sequences recognized by T-cell receptor (TCR). Immunogenic determinant idiotopes are present on the variable regions of immunoglobulin molecules expressed on and secreted by B-cells. In idiotope-driven T-cell/B-cell collaboration, B-cells present the idiotopes on MHC molecules for recognition by idiotope-specific T-cells. According to the idiotype network theory formulated by Niels Jerne, such idiotopes found on anti-idiotypic antibodies exhibit molecular mimicry of antigens. Here, by combining these concepts and defining the patterns of TCR-recognized epitope motifs (TREMs), we developed a T-cell epitope prediction method that identifies T-cell epitopes derived from antigen proteins by analyzing B-cell receptor (BCR) sequences. This method allowed us to identify T-cell epitopes that contain the same TREM patterns between BCR and viral antigen sequences in two different infectious diseases caused by dengue virus and SARS-CoV-2 infection. The identified epitopes were among the T-cell epitopes detected in previous studies, and T-cell stimulatory immunogenicity was confirmed. Thus, our data support this method as a powerful tool for the discovery of T-cell epitopes from BCR sequences. |
format | Online Article Text |
id | pubmed-10221809 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-102218092023-05-28 Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases Nakamura, Yukio Moi, Meng Ling Shiina, Takashi Shin-I, Tadasu Suzuki, Ryuji Viruses Article T-cell recognition of antigen epitopes is a crucial step for the induction of adaptive immune responses, and the identification of such T-cell epitopes is, therefore, important for understanding diverse immune responses and controlling T-cell immunity. A number of bioinformatic tools exist that predict T-cell epitopes; however, many of these methods highly rely on evaluating conventional peptide presentation by major histocompatibility complex (MHC) molecules, but they ignore epitope sequences recognized by T-cell receptor (TCR). Immunogenic determinant idiotopes are present on the variable regions of immunoglobulin molecules expressed on and secreted by B-cells. In idiotope-driven T-cell/B-cell collaboration, B-cells present the idiotopes on MHC molecules for recognition by idiotope-specific T-cells. According to the idiotype network theory formulated by Niels Jerne, such idiotopes found on anti-idiotypic antibodies exhibit molecular mimicry of antigens. Here, by combining these concepts and defining the patterns of TCR-recognized epitope motifs (TREMs), we developed a T-cell epitope prediction method that identifies T-cell epitopes derived from antigen proteins by analyzing B-cell receptor (BCR) sequences. This method allowed us to identify T-cell epitopes that contain the same TREM patterns between BCR and viral antigen sequences in two different infectious diseases caused by dengue virus and SARS-CoV-2 infection. The identified epitopes were among the T-cell epitopes detected in previous studies, and T-cell stimulatory immunogenicity was confirmed. Thus, our data support this method as a powerful tool for the discovery of T-cell epitopes from BCR sequences. MDPI 2023-05-17 /pmc/articles/PMC10221809/ /pubmed/37243272 http://dx.doi.org/10.3390/v15051186 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Nakamura, Yukio Moi, Meng Ling Shiina, Takashi Shin-I, Tadasu Suzuki, Ryuji Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases |
title | Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases |
title_full | Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases |
title_fullStr | Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases |
title_full_unstemmed | Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases |
title_short | Idiotope-Driven T-Cell/B-Cell Collaboration-Based T-Cell Epitope Prediction Using B-Cell Receptor Repertoire Sequences in Infectious Diseases |
title_sort | idiotope-driven t-cell/b-cell collaboration-based t-cell epitope prediction using b-cell receptor repertoire sequences in infectious diseases |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10221809/ https://www.ncbi.nlm.nih.gov/pubmed/37243272 http://dx.doi.org/10.3390/v15051186 |
work_keys_str_mv | AT nakamurayukio idiotopedriventcellbcellcollaborationbasedtcellepitopepredictionusingbcellreceptorrepertoiresequencesininfectiousdiseases AT moimengling idiotopedriventcellbcellcollaborationbasedtcellepitopepredictionusingbcellreceptorrepertoiresequencesininfectiousdiseases AT shiinatakashi idiotopedriventcellbcellcollaborationbasedtcellepitopepredictionusingbcellreceptorrepertoiresequencesininfectiousdiseases AT shinitadasu idiotopedriventcellbcellcollaborationbasedtcellepitopepredictionusingbcellreceptorrepertoiresequencesininfectiousdiseases AT suzukiryuji idiotopedriventcellbcellcollaborationbasedtcellepitopepredictionusingbcellreceptorrepertoiresequencesininfectiousdiseases |