A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding
Open Access
- 4 July 2022
- journal article
- research article
- Published by eLife Sciences Publications, Ltd in eLife
Abstract
T cells play a critical role in the adaptive immune response, recognizing peptide antigens presented on the cell surface by Major Histocompatibility Complex (MHC) proteins. While assessing peptides for MHC binding is an important component of probing these interactions, traditional assays for testing peptides of interest for MHC binding are limited in throughput. Here we present a yeast display-based platform for assessing the binding of tens of thousands of user-defined peptides in a high throughput manner. We apply this approach to assess a tiled library covering the SARS-CoV-2 proteome and four dengue virus serotypes for binding to human class II MHCs, including HLA-DR401, -DR402, and -DR404. While the peptide datasets show broad agreement with previously described MHC-binding motifs, they additionally reveal experimentally validated computational false positives and false negatives. We therefore present this approach as able to complement current experimental datasets and computational predictions. Further, our yeast display approach underlines design considerations for epitope identification experiments and serves as a framework for examining relationships between viral conservation and MHC binding, which can be used to identify potentially high-interest peptide binders from viral proteins. These results demonstrate the utility of our approach to determine peptide-MHC binding interactions in a manner that can supplement and potentially enhance current algorithm-based approaches.Keywords
Funding Information
- David and Lucile Packard Foundation
- Schmidt Futures
- National Science Foundation
- National Institutes of Health (U19-AI110495)
This publication has 62 references indexed in Scilit:
- T-cell epitope vaccine design by immunoinformaticsOpen Biology, 2013
- Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletionNucleic Acids Research, 2012
- PANDAseq: paired-end assembler for illumina sequencesBMC Bioinformatics, 2012
- Divergent Motifs but Overlapping Binding Repertoires of Six HLA-DQ Molecules Frequently Expressed in the Worldwide Human PopulationThe Journal of Immunology, 2010
- High-throughput engineering and analysis of peptide binding to class II MHCProceedings of the National Academy of Sciences of the United States of America, 2010
- Overview of the immune responseJournal of Allergy and Clinical Immunology, 2010
- Functional recombinant MHC class II molecules and high-throughput peptide-binding assaysImmunome Research, 2009
- Weak Proinsulin Peptide–Major Histocompatibility Complexes Are Targeted in Autoimmune Diabetes in MiceDiabetes, 2008
- Peptide length significantly influences in vitro affinity for MHC class II moleculesImmunome Research, 2008
- The Kinetic Stability of MHC Class II:Peptide Complexes Is a Key Parameter that Dictates ImmunodominanceImmunity, 2005