Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage
Background Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" the...
Published in: | BMC Bioinformatics |
---|---|
Main Authors: | , , , , , |
Format: | Text |
Language: | unknown |
Published: |
DigitalCommons@URI
2014
|
Subjects: | |
Online Access: | https://digitalcommons.uri.edu/immunology_facpubs/11 https://doi.org/10.1186/1471-2105-15-S4-S1 https://digitalcommons.uri.edu/context/immunology_facpubs/article/1008/viewcontent/DeGroot_Integrated_2014.pdf |
id |
ftunivrhodeislan:oai:digitalcommons.uri.edu:immunology_facpubs-1008 |
---|---|
record_format |
openpolar |
spelling |
ftunivrhodeislan:oai:digitalcommons.uri.edu:immunology_facpubs-1008 2024-09-15T17:56:49+00:00 Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage He, Lu DeGroot, Anne S. Gutierrez, Andres H. Martin, William D. Moise, Lenny Bailey-Kellogg, Chris 2014-01-01T08:00:00Z application/pdf https://digitalcommons.uri.edu/immunology_facpubs/11 https://doi.org/10.1186/1471-2105-15-S4-S1 https://digitalcommons.uri.edu/context/immunology_facpubs/article/1008/viewcontent/DeGroot_Integrated_2014.pdf unknown DigitalCommons@URI https://digitalcommons.uri.edu/immunology_facpubs/11 doi:10.1186/1471-2105-15-S4-S1 https://digitalcommons.uri.edu/context/immunology_facpubs/article/1008/viewcontent/DeGroot_Integrated_2014.pdf http://creativecommons.org/licenses/by/3.0/ Institute for Immunology and Informatics Faculty Publications text 2014 ftunivrhodeislan https://doi.org/10.1186/1471-2105-15-S4-S1 2024-08-21T00:09:33Z Background Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" themselves, avoiding immune recognition by reducing the MHC and/or TCR binding of their constituent peptides. Computer-driven T cell epitope mapping tools have been used to evaluate the degree to which particular viruses have used this means of avoiding immune response, but most such analyses focus on MHC-facing 'agretopes'. Here we set out a new means of evaluating the TCR faces of viral peptides in addition to their agretopes, integrating evaluations of both sides of the ternary complex in a single analysis. Methods This paper develops what we call the Janus Immunogenicity Score (JIS), bringing together a well-established method for predicting MHC binding, with a novel assessment of the potential for TCR binding based on similarity with self. Intuitively, both good MHC binding and poor self-similarity are required for high immunogenicity (i.e., a robust T effector response). Results Focusing on the class II antigen-processing pathway, we show that the JIS of T effector epitopes and null or regulatory epitopes deposited in a large database of epitopes (Immune Epitope Database) are significantly different. We then show that different types of viruses display significantly different patterns of scores over their constituent peptides, with viruses causing chronic infection (Epstein-Barr and cytomegalovirus) strongly shifted to lower scores relative to those causing acute infection (Ebola and Marburg). Similarly we find distinct patterns among influenza proteins in H1N1 (a strain against which human populations rapidly developed immunity) and H5N1 and H7N9 (highly pathogenic avian flu strains, with significantly greater case mortality rates). Conclusion The Janus Immunogenicity Score, which integrates MHC binding and TCR ... Text Avian flu University of Rhode Island: DigitalCommons@URI BMC Bioinformatics 15 S4 |
institution |
Open Polar |
collection |
University of Rhode Island: DigitalCommons@URI |
op_collection_id |
ftunivrhodeislan |
language |
unknown |
description |
Background Immune recognition of foreign proteins by T cells hinges on the formation of a ternary complex sandwiching a constituent peptide of the protein between a major histocompatibility complex (MHC) molecule and a T cell receptor (TCR). Viruses have evolved means of "camouflaging" themselves, avoiding immune recognition by reducing the MHC and/or TCR binding of their constituent peptides. Computer-driven T cell epitope mapping tools have been used to evaluate the degree to which particular viruses have used this means of avoiding immune response, but most such analyses focus on MHC-facing 'agretopes'. Here we set out a new means of evaluating the TCR faces of viral peptides in addition to their agretopes, integrating evaluations of both sides of the ternary complex in a single analysis. Methods This paper develops what we call the Janus Immunogenicity Score (JIS), bringing together a well-established method for predicting MHC binding, with a novel assessment of the potential for TCR binding based on similarity with self. Intuitively, both good MHC binding and poor self-similarity are required for high immunogenicity (i.e., a robust T effector response). Results Focusing on the class II antigen-processing pathway, we show that the JIS of T effector epitopes and null or regulatory epitopes deposited in a large database of epitopes (Immune Epitope Database) are significantly different. We then show that different types of viruses display significantly different patterns of scores over their constituent peptides, with viruses causing chronic infection (Epstein-Barr and cytomegalovirus) strongly shifted to lower scores relative to those causing acute infection (Ebola and Marburg). Similarly we find distinct patterns among influenza proteins in H1N1 (a strain against which human populations rapidly developed immunity) and H5N1 and H7N9 (highly pathogenic avian flu strains, with significantly greater case mortality rates). Conclusion The Janus Immunogenicity Score, which integrates MHC binding and TCR ... |
format |
Text |
author |
He, Lu DeGroot, Anne S. Gutierrez, Andres H. Martin, William D. Moise, Lenny Bailey-Kellogg, Chris |
spellingShingle |
He, Lu DeGroot, Anne S. Gutierrez, Andres H. Martin, William D. Moise, Lenny Bailey-Kellogg, Chris Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage |
author_facet |
He, Lu DeGroot, Anne S. Gutierrez, Andres H. Martin, William D. Moise, Lenny Bailey-Kellogg, Chris |
author_sort |
He, Lu |
title |
Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage |
title_short |
Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage |
title_full |
Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage |
title_fullStr |
Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage |
title_full_unstemmed |
Integrated Assessment of Predicted MHC binding and Cross-conservation with Self Reveals Patterns of Viral Camouflage |
title_sort |
integrated assessment of predicted mhc binding and cross-conservation with self reveals patterns of viral camouflage |
publisher |
DigitalCommons@URI |
publishDate |
2014 |
url |
https://digitalcommons.uri.edu/immunology_facpubs/11 https://doi.org/10.1186/1471-2105-15-S4-S1 https://digitalcommons.uri.edu/context/immunology_facpubs/article/1008/viewcontent/DeGroot_Integrated_2014.pdf |
genre |
Avian flu |
genre_facet |
Avian flu |
op_source |
Institute for Immunology and Informatics Faculty Publications |
op_relation |
https://digitalcommons.uri.edu/immunology_facpubs/11 doi:10.1186/1471-2105-15-S4-S1 https://digitalcommons.uri.edu/context/immunology_facpubs/article/1008/viewcontent/DeGroot_Integrated_2014.pdf |
op_rights |
http://creativecommons.org/licenses/by/3.0/ |
op_doi |
https://doi.org/10.1186/1471-2105-15-S4-S1 |
container_title |
BMC Bioinformatics |
container_volume |
15 |
container_issue |
S4 |
_version_ |
1810433005761593344 |