| Reference | ||
|---|---|---|
| Reference Type | Dual | IEDB_Reference:1029624 |
| Title | The length distribution of class I restricted T cell epitopes is determined by both peptide supply and MHC allele specific binding preference | |
| Submission Title | The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference. | |
| Authors | Thomas Trolle (1); Curtis P McMurtrey (2); John Sidney (3); Wilfried Bardet (2); Sean C Osborn (2); Thomas Kaever (3); Alessandro Sette (3); William H Hildebrand (2); Morten Nielsen (1,4); Bjoern Peters (3) | |
| Submission Authors | Thomas Trolle; Curtis P McMurtrey; John Sidney; Wilfried Bardet; Sean C Osborn; Thomas Kaever; Alessandro Sette; William H Hildebrand; Morten Nielsen; Bjoern Peters | |
| Affiliations | 1) Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, Kongens Lyngby, Denmark. 2) Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. 3) Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California, USA. 4) Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina. | |
| Submission Affiliations | Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark; Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, B 1650 HMP Buenos Aires, Argentina; and bpeters@lji.org. | |
| Journal | J Immunol | |
| Submitter | Thomas Trolle | IEDB_Submission:1000685 |
| Year | 2015 | |
| Submission Date | 2016 | |
| 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 and sometimes 9-10 amino acids, despite multiple examples of dominant epitopes of other lengths. Here, we examined if epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that while 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. The HLA ligands included in the final filtered datasets described in the manuscript are here submitted to the IEDB. | |
| Submission 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. | |
| Curation Last Updated | 2023-08-18 22:21:55 | |
| Related Information | |
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| Epitopes | |
| Bcell Assays | 0 |
| Tcell Assays | 0 |
| MHC Ligand Assays | |