1. PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes.
- Author
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Cormican JA, Medfai L, Wawrzyniuk M, Pasen M, Afrache H, Fourny C, Khan S, Gneiße P, Soh WT, Timelli A, Nolfi E, Pannekoek Y, Cope A, Urlaub H, Sijts AJAM, Mishto M, and Liepe J
- Abstract
Here, we develop PEPSeek, a web-server based software to allow higher performance in the identification of pathogen-derived epitope candidates detected via mass spectrometry in MHC class I immunopeptidomes. We apply it to human and mouse cell lines infected with either SARS-CoV-2, Listeria monocytogenes or Chlamydia trachomatis, thereby identifying a large number of novel antigens and epitopes that we prove to be recognized by CD8
+ T cells. In infected cells, we identified antigenic peptide features that suggested how processing and presentation of pathogenic antigens differ between pathogens. The quantitative tools of PEPSeek also helped to define how C. trachomatis infection cycle could impact on the antigenic landscape of the host human cell system, likely reflecting metabolic changes occurred in the infected cells., Competing Interests: DECLARATION OF INTERESTS The Authors have no competing interests to declare., (Copyright © 2025 The Authors. Published by Elsevier Inc. All rights reserved.)- Published
- 2025
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