{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Trolle T"],"funding":["NIAID NIH HHS","PHS HHS"],"pagination":["1480-7"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC4744552"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["196(4)"],"pubmed_abstract":["HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes."],"journal":["Journal of immunology (Baltimore, Md. : 1950)"],"pubmed_title":["The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference."],"pmcid":["PMC4744552"],"funding_grant_id":["HHSN272201200010C"],"pubmed_authors":["McMurtrey CP","Sette A","Peters B","Bardet W","Kaever T","Osborn SC","Hildebrand WH","Sidney J","Nielsen M","Trolle T"],"additional_accession":[]},"is_claimable":false,"name":"The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference.","description":"HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes.","dates":{"release":"2016-01-01T00:00:00Z","publication":"2016 Feb","modification":"2025-04-21T19:23:28.763Z","creation":"2019-03-27T02:08:37Z"},"accession":"S-EPMC4744552","cross_references":{"pubmed":["26783342"],"doi":["10.4049/jimmunol.1501721"]}}