Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response

Michael J. Hogan; Nikita Maheshwari; Bridget E. Begg; Annalisa Nicastri; Emma J. Hedgepeth; Hiromi Muramatsu; Norbert Pardi; Michael A. Miller; Shanelle P. Reilly; Laurent Brossay; Kristen W. Lynch; Nicola Ternette; Laurence C. Eisenlohr

doi:10.1038/s41590-023-01644-5

Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response

Michael J. Hogan^*, Nikita Maheshwari, Bridget E. Begg, Annalisa Nicastri, Emma J. Hedgepeth, Hiromi Muramatsu, Norbert Pardi, Michael A. Miller, Shanelle P. Reilly, Laurent Brossay, Kristen W. Lynch, Nicola Ternette, Laurence C. Eisenlohr^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of ‘cryptic’ viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.

Original language	English
Pages (from-to)	1933-1946
Number of pages	14
Journal	Nature Immunology
Volume	24
Issue number	11
DOIs	https://doi.org/10.1038/s41590-023-01644-5
Publication status	Published - Nov 2023
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.

Funding

We thank F. Tuluc, J. Murray and J. Lora of the Children’s Hospital of Philadelphia Flow Cytometry Core Facility for technical advice and services; L. Spruce, H. Fazelinia and S. Seeholzer (formerly) of the Children’s Hospital of Philadelphia Proteomics Core Facility for technical guidance and services; the NIH Tetramer Core Facility for providing tetramers for this study; J. R. Melamed and D. Weissman for technical advice on LNP generation; R. Serafin for providing related data; J. J. Rim for assistance with manuscript preparation; and D. F. Jenkins for data management support. We gratefully acknowledge the contributors to the Influenza Research Database, BV-BRC and the GISAID database, including the laboratories and authors responsible for obtaining specimens, generating genetic sequences and sharing data via the GISAID Initiative. M.J.H. was supported by the Cancer Research Institute as a Cancer Research Institute Irvington Fellow and by the Roberts Family–Katalin Karikó Fellowship in Vaccine Development from the Aileen K. and Brian L. Roberts Family Foundation via the University of Pennsylvania Institute for Immunology & Immune Health (I3H). N.M. was supported by the Roy and Diana Vagelos Molecular Life Sciences Program and by a College Alumni Society Research Grant from the University of Pennsylvania. N.P. was supported by NIH R01AI146101 and R01AI153064. S.P.R. is supported by research supplement 3R01AI046709-18S1 to promote diversity and L.B. is supported by NIH R01AI046709. K.W.L. and B.E.B. are supported by R01AI125524. L.C.E. and N.T. were supported by NIH R21AI153978. This work was funded in part by contract #75N93021C00015 from NIH NIAID. BioRender.com was used to create panels in Figs. , and . We thank F. Tuluc, J. Murray and J. Lora of the Children’s Hospital of Philadelphia Flow Cytometry Core Facility for technical advice and services; L. Spruce, H. Fazelinia and S. Seeholzer (formerly) of the Children’s Hospital of Philadelphia Proteomics Core Facility for technical guidance and services; the NIH Tetramer Core Facility for providing tetramers for this study; J. R. Melamed and D. Weissman for technical advice on LNP generation; R. Serafin for providing related data; J. J. Rim for assistance with manuscript preparation; and D. F. Jenkins for data management support. We gratefully acknowledge the contributors to the Influenza Research Database, BV-BRC and the GISAID database, including the laboratories and authors responsible for obtaining specimens, generating genetic sequences and sharing data via the GISAID Initiative. M.J.H. was supported by the Cancer Research Institute as a Cancer Research Institute Irvington Fellow and by the Roberts Family–Katalin Karikó Fellowship in Vaccine Development from the Aileen K. and Brian L. Roberts Family Foundation via the University of Pennsylvania Institute for Immunology & Immune Health (I3H). N.M. was supported by the Roy and Diana Vagelos Molecular Life Sciences Program and by a College Alumni Society Research Grant from the University of Pennsylvania. N.P. was supported by NIH R01AI146101 and R01AI153064. S.P.R. is supported by research supplement 3R01AI046709-18S1 to promote diversity and L.B. is supported by NIH R01AI046709. K.W.L. and B.E.B. are supported by R01AI125524. L.C.E. and N.T. were supported by NIH R21AI153978. This work was funded in part by contract #75N93021C00015 from NIH NIAID. BioRender.com was used to create panels in Figs. 1 , 2 and 8.

Funders	Funder number
BV-BRC
College Alumni Society
University of Pennsylvania Institute for Immunology & Immune Health
National Institutes of Health	75N93021C00015, R21AI153978, R01AI046709, R01AI153064, R01AI146101
National Institute of Allergy and Infectious Diseases
Institute of Cancer Research
University of Pennsylvania	R01AI125524

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@article{dcbcd7400b674a3f8bddada1f7555859,

title = "Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response",

abstract = "The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of {\textquoteleft}cryptic{\textquoteright} viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.",

author = "Hogan, {Michael J.} and Nikita Maheshwari and Begg, {Bridget E.} and Annalisa Nicastri and Hedgepeth, {Emma J.} and Hiromi Muramatsu and Norbert Pardi and Miller, {Michael A.} and Reilly, {Shanelle P.} and Laurent Brossay and Lynch, {Kristen W.} and Nicola Ternette and Eisenlohr, {Laurence C.}",

note = "Publisher Copyright: {\textcopyright} 2023, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2023",

month = nov,

doi = "10.1038/s41590-023-01644-5",

language = "English",

volume = "24",

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journal = "Nature Immunology",

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T1 - Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response

AU - Hogan, Michael J.

AU - Maheshwari, Nikita

AU - Begg, Bridget E.

AU - Nicastri, Annalisa

AU - Hedgepeth, Emma J.

AU - Muramatsu, Hiromi

AU - Pardi, Norbert

AU - Miller, Michael A.

AU - Reilly, Shanelle P.

AU - Brossay, Laurent

AU - Lynch, Kristen W.

AU - Ternette, Nicola

AU - Eisenlohr, Laurence C.

PY - 2023/11

Y1 - 2023/11

N2 - The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of ‘cryptic’ viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.

AB - The extent to which unconventional forms of antigen presentation drive T cell immunity is unknown. By convention, CD8 T cells recognize viral peptides, or epitopes, in association with classical major histocompatibility complex (MHC) class I, or MHC-Ia, but immune surveillance can, in some cases, be directed against peptides presented by nonclassical MHC-Ib, in particular the MHC-E proteins (Qa-1 in mice and HLA-E in humans); however, the overall importance of nonclassical responses in antiviral immunity remains unclear. Similarly uncertain is the importance of ‘cryptic’ viral epitopes, defined as those undetectable by conventional mapping techniques. Here we used an immunopeptidomic approach to search for unconventional epitopes that drive T cell responses in mice infected with influenza virus A/Puerto Rico/8/1934. We identified a nine amino acid epitope, termed M-SL9, that drives a co-immunodominant, cytolytic CD8 T cell response that is unconventional in two major ways: first, it is presented by Qa-1, and second, it has a cryptic origin, mapping to an unannotated alternative reading frame product of the influenza matrix gene segment. Presentation and immunogenicity of M-SL9 are dependent on the second AUG codon of the positive sense matrix RNA segment, suggesting translation initiation by leaky ribosomal scanning. During influenza virus A/Puerto Rico/8/1934 infection, M-SL9-specific T cells exhibit a low level of egress from the lungs and strong differentiation into tissue-resident memory cells. Importantly, we show that M-SL9/Qa-1-specific T cells can be strongly induced by messenger RNA vaccination and that they can mediate antigen-specific cytolysis in vivo. Our results demonstrate that noncanonical translation products can account for an important fraction of the T cell repertoire and add to a growing body of evidence that MHC-E-restricted T cells could have substantial therapeutic value.

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Cryptic MHC-E epitope from influenza elicits a potent cytolytic T cell response

Abstract

Bibliographical note

Funding

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