Quantification of epitope abundance reveals the effect of direct and cross-presentation on influenza CTL responses

Ting Wu, Jing Guan, Andreas Handel, David C. Tscharke, John Sidney, Alessandro Sette, Linda M. Wakim, Xavier Y. X. Sng, Paul G. Thomas, Nathan P. Croft (), Anthony W. Purcell () and Nicole L. La Gruta ()
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Ting Wu: Monash University
Jing Guan: Monash University
Andreas Handel: University of Georgia
David C. Tscharke: The Australian National University
John Sidney: La Jolla Institute for Allergy and Immunology
Alessandro Sette: La Jolla Institute for Allergy and Immunology
Linda M. Wakim: University of Melbourne
Xavier Y. X. Sng: Monash University
Paul G. Thomas: St Jude Children’s Research Hospital
Nathan P. Croft: Monash University
Anthony W. Purcell: Monash University
Nicole L. La Gruta: Monash University

Nature Communications, 2019, vol. 10, issue 1, 1-14

Abstract: Abstract The magnitude of T cell responses to infection is a function of the naïve T cell repertoire combined with the context and duration of antigen presentation. Using mass spectrometry, we identify and quantify 21 class 1 MHC-restricted influenza A virus (IAV)-peptides following either direct or cross-presentation. All these peptides, including seven novel epitopes, elicit T cell responses in infected C57BL/6 mice. Directly presented IAV epitopes maintain their relative abundance across distinct cell types and reveal a broad range of epitope abundances. In contrast, cross-presented epitopes are more uniform in abundance. We observe a clear disparity in the abundance of the two key immunodominant IAV antigens, wherein direct infection drives optimal nucleoprotein (NP)366–374 presentation, while cross-presentation is optimal for acid polymerase (PA)224–233 presentation. The study demonstrates how assessment of epitope abundance in both modes of antigen presentation is necessary to fully understand the immunogenicity and response magnitude to T cell epitopes.

Date: 2019
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DOI: 10.1038/s41467-019-10661-8

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