Special Issue: Immunopeptidomics

Coordinating Editors: Pierre Thibault and Claude Perreault (guest)

Special Issue: Immunopeptidomics

Fifty years have passed since the study of Benacerraf and McDevitt describing the exquisite regulation of the immune response by the major histocompatibility complex (MHC). The landmark discovery that T cell activation requires co-recognition of peptide antigens and self-MHC molecules revealed not only a unique receptor-ligand interaction but also a delicate balance between autoimmune response and effective protection against infection. These seminal studies laid the foundation to our current understanding of how immune cells distinguish between self and nonself.

T cells display a remarkable selectivity and discriminate self and nonself from an astonishing number of antigen peptides presented by MHC molecules, a property that is largely defined during their development in the thymus. Furthermore, the MHC locus is the most polymorphic region of the human genome and this structural diversity enables MHC molecules to present a wide distribution of peptide antigens originating from the degradation of endogenous (MHC Class I) or exogenous (MHC Class II) proteins. The biogenesis of peptide antigens is an intricate process shaped not only by environmental stimuli but also by specific proteolytic enzymes located in distinct organelles. The antigen repertoire, collectively referred to as the immunopeptidome, cannot be inferred from transcript or protein abundance, and mainly relies on mass spectrometry analyses of peptides eluted from MHC complex. However, mass spectrometry alone is not sufficient to unveil the full repertoire of antigens concealed by MHC molecules. Indeed, structural variants arising from genomic polymorphisms or non canonical regions of the genome are absent from the reference proteomes and their discovery requires more elaborated databases that leverage proteogenomic search strategies. Recent technological advances in MHC isolation methods, mass spectrometry sensitivity and novel database search approaches have fueled immunopeptidomic discoveries and open up new perspectives for cancer immunotherapy. It is in this context that we assembled experts and opinion leaders in immunopeptidomics to contribute to this special issue and share their findings and views of this blossoming field of research.

Artistic rendition of antigen presentation by the major histocompatibility complex class I molecules’. Credit: Luciana Giono.




  • Pierre Thibault, Claude Perreault
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  • Hannah B. Taylor, Susan Klaeger, Karl R. Clauser, Siranush Sarkizova, Shira Weingarten-Gabbay, Daniel B. Graham, Steven A. Carr, Jennifer G. Abelin
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  • Liran Komov, Dganit Melamed Kadosh, Eilon Barnea, Arie Admon
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  • Arie Admon
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  • Greta Forlani, Justine Michaux, HuiSong Pak, Florian Huber, Elodie Lauret Marie Joseph, Elise Ramia, Brian J. Stevenson, Michael Linnebacher, Roberto S. Accolla, Michal Bassani-Sternberg
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  • HuiSong Pak, Justine Michaux, Florian Huber, Chloe Chong, Brian J. Stevenson, Markus Müller, George Coukos, Michal Bassani-Sternberg
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  • Rachel Marty Pyke, Dattatreya Mellacheruvu, Steven Dea, Charles W. Abbott, Simo V. Zhang, Nick A. Phillips, Jason Harris, Gabor Bartha, Sejal Desai, Rena McClory, John West, Michael P. Snyder, Richard Chen, Sean Michael Boyle
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  • Niclas Olsson, Wei Jiang, Lital N. Adler, Elizabeth D. Mellins, Joshua E. Elias
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  • Yue A. Qi, Tapan K. Maity, Constance M. Cultraro, Vikram Misra, Xu Zhang, Catherine Ade, Shaojian Gao, David Milewski, Khoa D. Nguyen, Mohammad H. Ebrahimabadi, Ken-ichi Hanada, Javed Khan, Cenk Sahinalp, James C. Yang, Udayan Guha
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  • Youra Kim, Prathyusha Konda, J. Patrick Murphy, Joao A. Paulo, Steven P. Gygi, Shashi Gujar
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  • Laura C. Demmers, Wei Wu, Albert J.R. Heck
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  • Keira E. Mahoney, Jeffrey Shabanowitz, Donald F. Hunt
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  • Susan Klaeger, Annie Apffel, Karl R. Clauser, Siranush Sarkizova, Giacomo Oliveira, Suzanna Rachimi, Phuong M. Le, Anna Tarren, Vipheaviny Chea, Jennifer G. Abelin, David A. Braun, Patrick A. Ott, Hasmik Keshishian, Nir Hacohen, Derin B. Keskin, Catherine J. Wu, Steven A. Carr
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  • Samuel B. Pollock, Christopher M. Rose, Martine Darwish, Romain Bouziat, Lélia Delamarre, Craig Blanchette, Jennie R. Lill
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  • Katherine E. Scull, Kirti Pandey, Sri H. Ramarathinam, Anthony W. Purcell
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  • Brian Reardon, Zeynep Koşaloğlu-Yalçın, Sinu Paul, Bjoern Peters, Alessandro Sette
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  • Kevin A. Kovalchik, Qing Ma, Laura Wessling, Frederic Saab, Jérôme D. Duquette, Peter Kubiniok, David J. Hamelin, Pouya Faridi, Chen Li, Anthony W. Purcell, Anne Jang, Eustache Paramithiotis, Marco Tognetti, Lukas Reiter, Roland Bruderer, Joël Lanoix, Éric Bonneil, Mathieu Courcelles, Pierre Thibault, Etienne Caron, Isabelle Sirois
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  • Robert Parker, Arun Tailor, Xu Peng, Annalisa Nicastri, Johannes Zerweck, Ulf Reimer, Holger Wenschuh, Karsten Schnatbaum, Nicola Ternette
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  • Jenna Cleyle, Marie-Pierre Hardy, Robin Minati, Mathieu Courcelles, Chantal Durette, Joel Lanoix, Jean-Philippe Laverdure, Krystel Vincent, Claude Perreault, Pierre Thibault
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  • Annika Nelde, Hans-Georg Rammensee, Juliane S. Walz
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  • Jens Fritsche, Daniel J. Kowalewski, Linus Backert, Frederik Gwinner, Sonja Dorner, Martin Priemer, Chih-Chiang Tsou, Franziska Hoffgaard, Michael Römer, Heiko Schuster, Oliver Schoor, Toni Weinschenk
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  • Jonathan W. Yewdell
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  • Michele Mishto
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