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5. PEPSeek-mediated identification of novel epitopes from viral and bacterial pathogens and the impact on host cell immunopeptidomes

Author

Cormican, John A., Medfai, Lobna, Wawrzyniuk, Magdalena, Pasen, Martin, Afrache, Hassnae, Fourny, Constance, Khan, Sahil, Gneiße, Pascal, Soh, Wai Tuck, Timelli, Arianna, Nolfi, Emanuele, Pannekoek, Yvonne, Cope, Andrew, Urlaub, Henning, Sijts, Alice J.A. M., Mishto, Michele, and Liepe, Juliane

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 monocytogenesor 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. trachomatisinfection cycle could impact on the antigenic landscape of the host human cell system, likely reflecting metabolic changes occurred in the infected cells.

Published
2025
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8. Forum 1974, Vol. 15, Iss. 03

Author

Frost, Lesley ; Metz, Jerred ; Taylor, Charles ; Duffy, James A. ; Thornburg, Thomas R. ; Lazar, Jose ; Cormican, John D. ; Dawson, Leven ; Sattler, Joel ; Moore, J. T. ; Wright, Barry D. ; Brown, Estelle T. ; Nurmi, Earl ; Wall, Sandy A. ; Guillory, Daniel L. ; Stone, Lloyd ; Pinsker, Sanford ; Tyler, Robert L. ; Suderman, Elmer F. ; Wheatcroft, John ; Stewart, Michael, Rippy, Merrill, 1917- ; Rippy, Frances Mayhew, Frost, Lesley ; Metz, Jerred ; Taylor, Charles ; Duffy, James A. ; Thornburg, Thomas R. ; Lazar, Jose ; Cormican, John D. ; Dawson, Leven ; Sattler, Joel ; Moore, J. T. ; Wright, Barry D. ; Brown, Estelle T. ; Nurmi, Earl ; Wall, Sandy A. ; Guillory, Daniel L. ; Stone, Lloyd ; Pinsker, Sanford ; Tyler, Robert L. ; Suderman, Elmer F. ; Wheatcroft, John ; Stewart, Michael, and Rippy, Merrill, 1917- ; Rippy, Frances Mayhew

Abstract

Certain Intensities; Touch; jazz; When I Was a Boy; Robinson Crusoe; The Walk; Samuel Johnson's Struggle with His Personality as Revealed in His Prayers; Prayer Wheel; Impromptu Rain Dance for a Moonday Morning; Hegel's Concept of Individual Freedom; The Tortoise; Romanticism as Manifested in Ballet; Prairie Cycle; Delectable Mountains; Hart Crane, Marianne Moore, and the Brooklyn Bridge; You Turn Off Here on a Side Road; Images in Late Afternoon; Two Birds with One Stone: A Plan of Rescue for the Premodern and the Post-Modern Worlds; We Must Try Words; The Great Television Conspiracy; Frere Jacques, This archival material has been provided for educational purposes. Ball State University Libraries recognizes that some historic items may include offensive content. Our statement regarding objectionable content is available at: https://dmr.bsu.edu/digital/about

Published
1974

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