The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference

The Journal of Immunology : Official Journal of the American Association of Immunologists
Thomas TrolleBjoern Peters

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.

References

Feb 1, 1994·The Journal of Experimental Medicine·T N SchumacherH L Ploegh
Oct 15, 1998·Proceedings of the National Academy of Sciences of the United States of America·A K NussbaumH Schild
Sep 15, 2005·Journal of Clinical Immunology·Anna K LidehallOlle Korsgren
Nov 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Shih-Chung ChangAlfred L Goldberg
Nov 22, 2005·Trends in Immunology·Scott R BurrowsJames McCluskey
Jun 23, 2006·PLoS Computational Biology·Bjoern PetersAlessandro Sette
Nov 13, 2008·Immunogenetics·Ilka HoofMorten Nielsen
Apr 9, 2010·The Journal of General Virology·Siok-Keen TeyRajiv Khanna
Oct 12, 2011·Journal of Immunological Methods·Guang Lan ZhangVladimir Brusic
May 1, 2012·The Journal of Immunology : Official Journal of the American Association of Immunologists·Daniela S ThommenBarbara C Biedermann
Jan 10, 2013·Annual Review of Immunology·Janice S BlumPeter Cresswell
Feb 9, 2013·Current Protocols in Immunology·John SidneyAlessandro Sette
Apr 13, 2013·Proceedings of the National Academy of Sciences of the United States of America·Daniela WeiskopfAlessandro Sette
Jun 12, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Melissa J RistScott R Burrows
Nov 6, 2013·The Journal of Immunology : Official Journal of the American Association of Immunologists·Sinu PaulAlessandro Sette
Dec 25, 2013·Molecular & Cellular Proteomics : MCP·Miguel MarcillaJuan Pablo Albar
Mar 7, 2014·The Journal of Immunology : Official Journal of the American Association of Immunologists·Chihiro MotozonoMasafumi Takiguchi
Apr 10, 2014·Nature Communications·Diana Paola GranadosClaude Perreault
Aug 29, 2014·Journal of Virology·Jane C YaciukWilliam H Hildebrand
Oct 11, 2014·Nucleic Acids Research·Randi VitaBjoern Peters
Dec 17, 2014·The Journal of Biological Chemistry·Chopie HassanPeter A van Veelen
Feb 27, 2015·Bioinformatics·Thomas TrolleMorten Nielsen
Feb 1, 2014·Molecular & Cellular Proteomics : MCP·Miguel MarcillaJuan Pablo Albar

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Citations

Jan 12, 2017·Seminars in Immunopathology·David SchramaJürgen C Becker
Nov 22, 2016·Nature Communications·Michal Bassani-SternbergAngela M Krackhardt
Apr 14, 2017·Nucleic Acids Research·Massimo AndreattaMorten Nielsen
Jul 12, 2017·Journal of Chemical Information and Modeling·Cory M AyresBrian M Baker
Feb 10, 2018·Immunology and Cell Biology·Anthony R Di CarluccioWeisan Chen
Oct 6, 2017·The Journal of Immunology : Official Journal of the American Association of Immunologists·Vanessa JurtzMorten Nielsen
Oct 16, 2018·Journal of Cellular Biochemistry·Sathish SankarGopalan Sridharan
Oct 21, 2018·The Journal of Immunology : Official Journal of the American Association of Immunologists·Jin XiaoWilliam J Liu
Nov 9, 2018·Expert Review of Proteomics·Eric A Wilson, Karen S Anderson
Nov 16, 2018·The Journal of Immunology : Official Journal of the American Association of Immunologists·David GfellerMichal Bassani-Sternberg
Dec 18, 2018·Nature Biotechnology·Brendan Bulik-SullivanRoman Yelensky
Jan 11, 2019·The Journal of General Virology·Galina BurmakinaDaniel L Rock
Apr 3, 2019·The Journal of Immunology : Official Journal of the American Association of Immunologists·Julie BoucauSylvie Le Gall
May 17, 2019·Nature Protocols·Anthony W PurcellNicola Ternette
Nov 30, 2019·The Journal of Immunology : Official Journal of the American Association of Immunologists·Lizhen MaMax Chun Xia
Feb 12, 2020·Annual Review of Immunology·Bjoern PetersAlessandro Sette
May 29, 2019·The Cancer Journal·Melinda A BiernackiMarie Bleakley
Aug 19, 2020·International Immunology·Iosif M GershteynLeonardo M R Ferreira
Aug 12, 2016·The Journal of Immunology : Official Journal of the American Association of Immunologists·Michal Bassani-Sternberg, David Gfeller
Aug 10, 2018·Frontiers in Immunology·David Gfeller, Michal Bassani-Sternberg
Nov 26, 2019·Immunogenetics·Sheridan MartiniAlessandro Sette
Dec 22, 2017·NPJ Vaccines·Kamal El BissatiRima McLeod
Nov 1, 2018·Oncoimmunology·Zeynep Koşaloğlu-YalçınBjoern Peters
Mar 3, 2020·Frontiers in Immunology·Melinda A Biernacki, Marie Bleakley
May 2, 2018·Proceedings of the National Academy of Sciences of the United States of America·Philippe GuillaumeDavid Gfeller
Sep 27, 2019·Frontiers in Immunology·Timothy P RileyBrian M Baker
Dec 12, 2019·Frontiers in Immunology·Marta A S PerezVincent Zoete
Mar 21, 2019·Frontiers in Immunology·Giovanni BirruetaVéronique Schulten
Dec 5, 2019·Frontiers in Genetics·Anja MöschDmitrij Frishman
Apr 5, 2018·Cancer Immunology Research·Christa I DeVetteWilliam H Hildebrand
Dec 25, 2019·Cancer Immunology Research·Xiaoshan M ShaoRachel Karchin
Sep 22, 2020·Computational and Structural Biotechnology Journal·Milena VujovicPaolo Marcatili
Jan 20, 2021·Advanced Drug Delivery Reviews·Muhammad Saqib SohailMatthew R McKay
Jan 28, 2021·Expert Review of Vaccines·Daniel Fernandez-RuizLynette Beattie

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