Quantification of HLA-DM-Dependent Major Histocompatibility Complex of Class II Immunopeptidomes by the Peptide Landscape Antigenic Epitope Alignment Utility

Frontiers in Immunology
Miguel Álvaro-BenitoChristian Freund

Abstract

The major histocompatibility complex of class II (MHCII) immunopeptidome represents the repertoire of antigenic peptides with the potential to activate CD4+ T cells. An understanding of how the relative abundance of specific antigenic epitopes affects the outcome of T cell responses is an important aspect of adaptive immunity and offers a venue to more rationally tailor T cell activation in the context of disease. Recent advances in mass spectrometric instrumentation, computational power, labeling strategies, and software analysis have enabled an increasing number of stratified studies on HLA ligandomes, in the context of both basic and translational research. A key challenge in the case of MHCII immunopeptidomes, often determined for different samples at distinct conditions, is to derive quantitative information on consensus epitopes from antigenic peptides of variable lengths. Here, we present the design and benchmarking of a new algorithm [peptide landscape antigenic epitope alignment utility (PLAtEAU)] allowing the identification and label-free quantification (LFQ) of shared consensus epitopes arising from series of nested peptides. The algorithm simplifies the complexity of the dataset while allowing the identification of ...Continue Reading

References

Jun 29, 1995·Nature·V S SloanD M Zaller
May 13, 1998·Immunology Today·J S Murray
Oct 25, 2000·The Journal of Immunology : Official Journal of the American Association of Immunologists·P Louis-PlenceJ F Eliaou
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
May 22, 2001·The Journal of Immunology : Official Journal of the American Association of Immunologists·A J GodkinA V Hill
Oct 23, 2002·The Journal of Immunology : Official Journal of the American Association of Immunologists·John D LippolisVictor H Engelhard
Oct 25, 2002·Nature·Darrell J IrvineMark M Davis
Sep 4, 2003·Genome Research·Paul D ThomasApurva Narechania
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Jul 9, 2004·The Journal of Immunology : Official Journal of the American Association of Immunologists·Aura MuntasellDolores Jaraquemada
Nov 8, 2005·Molecular & Cellular Proteomics : MCP·Elena MilnerArie Admon
Nov 3, 2007·The Journal of Clinical Investigation·Jan WahlströmJohan Grunewald
Mar 26, 2008·Molecular Therapy : the Journal of the American Society of Gene Therapy·Kristoffer WeberBoris Fehse
Oct 4, 2008·The Journal of Immunology : Official Journal of the American Association of Immunologists·Lars-Egil FallangLudvig M Sollid
Nov 28, 2008·Immunome Research·Cathal O'BrienConleth Feighery
Jul 28, 2010·The Journal of Experimental Medicine·Rachel A GottschalkJames P Allison
May 21, 2011·Proteomics·Chor Teck TanAnthony W Purcell
Jan 10, 2012·Proceedings of the National Academy of Sciences of the United States of America·Rachel A GottschalkJames P Allison
Jan 10, 2013·Annual Review of Immunology·Janice S BlumPeter Cresswell
Jan 28, 2014·Current Opinion in Immunology·Elizabeth D Mellins, Lawrence J Stern
Apr 10, 2014·Proceedings of the National Academy of Sciences of the United States of America·Dmitry BourdetskyArie Admon
Dec 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·Daniel J KowalewskiJuliane Sarah Stickel
Feb 26, 2016·Annual Review of Immunology·Emil R UnanueJacques Neefjes
Apr 10, 2016·Current Opinion in Immunology·Anthony W PurcellDavid C Tscharke
Jun 28, 2016·Nature Methods·Stefka TyanovaJürgen Cox
Jul 28, 2016·Molecular & Cellular Proteomics : MCP·Tina HeyderA Jimmy Ytterberg
Aug 19, 2016·Open Biology·Miguel Alvaro-BenitoChristian Freund

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Citations

Dec 24, 2018·Molecular & Cellular Proteomics : MCP·Padma P NanawareLawrence J Stern
Nov 24, 2018·Cellular & Molecular Immunology·Miguel Álvaro-BenitoChristian Freund
Aug 9, 2020·HLA : Immune Response Genetics·Miguel Álvaro-Benito, Christian Freund
Sep 8, 2019·Journal of Hematology & Oncology·Tao JiangCaicun Zhou
Nov 14, 2018·Immunogenetics·Mollie M Jurewicz, Lawrence J Stern
Jul 12, 2020·Communications Biology·Eliot MorrisonChristian Freund
Dec 5, 2019·Frontiers in Genetics·Anja MöschDmitrij Frishman
Mar 29, 2020·NPJ Vaccines·Friederike EbnerMiguel Álvaro-Benito
Nov 12, 2019·Frontiers in Immunology·Christian Freund, Thomas Höfer
Mar 1, 2019·Molecular & Cellular Proteomics : MCP·Padma P NanawareLawrence J Stern
Feb 14, 2021·NPJ Vaccines·Friederike EbnerMiguel Álvaro-Benito
Apr 17, 2021·Journal for Immunotherapy of Cancer·Ana MarcuMarian Christoph Neidert
Dec 18, 2020·Journal of Proteome Research·Lichao ZhangJoshua E Elias

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Methods Mentioned

BETA
flow cytometry
Flow
transfection
FCS
Assay
CLIP
immunoprecipitation

Software Mentioned

MaxQuant
Slim
Python script
Weblogo3
GraphPad Prism
FCS express
GO
Panther
PLAtEAU
custom

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