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Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands

Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands
Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands
CD8+ and CD4+ T cells provide cell-mediated cross-protection against multiple influenza strains by recognising epitopes bound as peptides to human leukocyte antigen (HLA) class I and -II molecules respectively. Two challenges in identifying the immunodominant epitopes needed to generate a universal T cell influenza vaccine are: A lack of cell models susceptible to influenza infection which present population-prevalent HLA allotypes, and an absence of a reliable in-vitro method of identifying class II HLA peptides. Here we present a mass spectrometry-based proteomics strategy for identifying viral peptides derived from the A/H3N2/X31 and A/H3N2/Wisconsin/67/2005 strains of influenza. We compared the HLA-I and -II immunopeptidomes presented by ex-vivo influenza challenged human lung tissues. We then compared these with directly infected immortalised macrophage-like cell line (THP1) and primary dendritic cells fed apoptotic influenza-infected respiratory epithelial cells. In each of the three experimental conditions we identified novel influenza class I and II HLA peptides with motifs specific for the host allotype. Ex-vivo infected lung tissues yielded few class-II HLA peptides despite significant numbers of alveolar macrophages, including directly infected ones, present within the tissues. THP1 cells presented HLA-I viral peptides derived predominantly from internal proteins. Primary dendritic cells presented predominantly viral envelope-derived HLA class II peptides following phagocytosis of apoptotic infected cells. The most frequent viral source protein for HLA-I and -II was matrix 1 protein (M1). This work confirms that internal influenza proteins, particularly M1, are a rich source of CD4+ and CD8+ T cell epitopes. Moreover, we demonstrate the utility of two ex-vivo fully human infection models which enable direct HLA-I and -II immunopeptide identification without significant viral tropism limitations. Application of this epitope discovery strategy in a clinical setting will provide more certainty in rational vaccine design against influenza and other emergent viruses.
1553-7366
Nicholas, Benjamin
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Bailey, Alistair
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Staples, Karl J.
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Wilkinson, Thomas
8c55ebbb-e547-445c-95a1-c8bed02dd652
Elliott, Timothy
16670fa8-c2f9-477a-91df-7c9e5b453e0e
Skipp, Paul
1ba7dcf6-9fe7-4b5c-a9d0-e32ed7f42aa5
Nicholas, Benjamin
785c44fb-6536-4189-803b-4545425e9385
Bailey, Alistair
541e2cd9-ac72-4058-9293-def64fc2c284
Staples, Karl J.
e0e9d80f-0aed-435f-bd75-0c8818491fee
Wilkinson, Thomas
8c55ebbb-e547-445c-95a1-c8bed02dd652
Elliott, Timothy
16670fa8-c2f9-477a-91df-7c9e5b453e0e
Skipp, Paul
1ba7dcf6-9fe7-4b5c-a9d0-e32ed7f42aa5

Nicholas, Benjamin, Bailey, Alistair, Staples, Karl J., Wilkinson, Thomas, Elliott, Timothy and Skipp, Paul (2022) Immunopeptidomic analysis of influenza A virus infected human tissues identifies internal proteins as a rich source of HLA ligands. PLoS Pathogens, 18 (1), [e1009894]. (doi:10.1371/journal.ppat.1009894).

Record type: Article

Abstract

CD8+ and CD4+ T cells provide cell-mediated cross-protection against multiple influenza strains by recognising epitopes bound as peptides to human leukocyte antigen (HLA) class I and -II molecules respectively. Two challenges in identifying the immunodominant epitopes needed to generate a universal T cell influenza vaccine are: A lack of cell models susceptible to influenza infection which present population-prevalent HLA allotypes, and an absence of a reliable in-vitro method of identifying class II HLA peptides. Here we present a mass spectrometry-based proteomics strategy for identifying viral peptides derived from the A/H3N2/X31 and A/H3N2/Wisconsin/67/2005 strains of influenza. We compared the HLA-I and -II immunopeptidomes presented by ex-vivo influenza challenged human lung tissues. We then compared these with directly infected immortalised macrophage-like cell line (THP1) and primary dendritic cells fed apoptotic influenza-infected respiratory epithelial cells. In each of the three experimental conditions we identified novel influenza class I and II HLA peptides with motifs specific for the host allotype. Ex-vivo infected lung tissues yielded few class-II HLA peptides despite significant numbers of alveolar macrophages, including directly infected ones, present within the tissues. THP1 cells presented HLA-I viral peptides derived predominantly from internal proteins. Primary dendritic cells presented predominantly viral envelope-derived HLA class II peptides following phagocytosis of apoptotic infected cells. The most frequent viral source protein for HLA-I and -II was matrix 1 protein (M1). This work confirms that internal influenza proteins, particularly M1, are a rich source of CD4+ and CD8+ T cell epitopes. Moreover, we demonstrate the utility of two ex-vivo fully human infection models which enable direct HLA-I and -II immunopeptide identification without significant viral tropism limitations. Application of this epitope discovery strategy in a clinical setting will provide more certainty in rational vaccine design against influenza and other emergent viruses.

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2021.08.17.456620v1.full - Author's Original
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Accepted/In Press date: 2 January 2022
e-pub ahead of print date: 20 January 2022
Published date: January 2022

Identifiers

Local EPrints ID: 454229
URI: http://eprints.soton.ac.uk/id/eprint/454229
ISSN: 1553-7366
PURE UUID: 1127b4a7-af01-43fb-835a-3b4ec0e4f243
ORCID for Benjamin Nicholas: ORCID iD orcid.org/0000-0003-1467-9643
ORCID for Alistair Bailey: ORCID iD orcid.org/0000-0003-0023-8679
ORCID for Karl J. Staples: ORCID iD orcid.org/0000-0003-3844-6457
ORCID for Timothy Elliott: ORCID iD orcid.org/0000-0003-1097-0222
ORCID for Paul Skipp: ORCID iD orcid.org/0000-0002-2995-2959

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Date deposited: 03 Feb 2022 17:42
Last modified: 28 Apr 2022 02:09

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Contributors

Author: Benjamin Nicholas ORCID iD
Author: Alistair Bailey ORCID iD
Author: Karl J. Staples ORCID iD
Author: Timothy Elliott ORCID iD
Author: Paul Skipp ORCID iD

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