Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

Shira Weingarten-Gabbay; Susan Klaeger; Siranush Sarkizova; Leah R Pearlman; Da-Yuan Chen; Kathleen M E Gallagher; Matthew R Bauer; Hannah B Taylor; W Augustine Dunn; Christina Tarr; John Sidney; Suzanna Rachimi; Hasahn L Conway; Katelin Katsis; Yuntong Wang; Del Leistritz-Edwards; Melissa R Durkin; Christopher H Tomkins-Tinch; Yaara Finkel; Aharon Nachshon; Matteo Gentili; Keith D Rivera; Isabel P Carulli; Vipheaviny A Chea; Abishek Chandrashekar; Cansu Cimen Bozkus; Mary Carrington; MGH COVID-19 Collection & Processing Team; Nina Bhardwaj; Dan H Barouch; Alessandro Sette; Marcela V Maus; Charles M Rice; Karl R Clauser; Derin B Keskin; Daniel C Pregibon; Nir Hacohen; Steven A Carr; Jennifer G Abelin; Mohsan Saeed; Pardis C Sabeti

doi:10.1016/j.cell.2021.05.046

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs

Cell. 2021 Jul 22;184(15):3962-3980.e17. doi: 10.1016/j.cell.2021.05.046. Epub 2021 Jun 3.

Authors

Shira Weingarten-Gabbay¹, Susan Klaeger², Siranush Sarkizova³, Leah R Pearlman³, Da-Yuan Chen⁴, Kathleen M E Gallagher⁵, Matthew R Bauer⁶, Hannah B Taylor³, W Augustine Dunn⁷, Christina Tarr⁷, John Sidney⁸, Suzanna Rachimi³, Hasahn L Conway⁴, Katelin Katsis⁹, Yuntong Wang⁷, Del Leistritz-Edwards⁷, Melissa R Durkin⁷, Christopher H Tomkins-Tinch¹⁰, Yaara Finkel¹¹, Aharon Nachshon¹¹, Matteo Gentili³, Keith D Rivera³, Isabel P Carulli¹², Vipheaviny A Chea¹², Abishek Chandrashekar¹³, Cansu Cimen Bozkus¹⁴, Mary Carrington¹⁵; MGH COVID-19 Collection & Processing Team¹⁶; Nina Bhardwaj¹⁴, Dan H Barouch¹⁷, Alessandro Sette¹⁸, Marcela V Maus¹⁹, Charles M Rice²⁰, Karl R Clauser³, Derin B Keskin²¹, Daniel C Pregibon⁷, Nir Hacohen²², Steven A Carr³, Jennifer G Abelin³, Mohsan Saeed²³, Pardis C Sabeti²⁴

Collaborators

MGH COVID-19 Collection & Processing Team:
Kendall Lavin-Parsons, Blair Parry, Brendan Lilley, Carl Lodenstein, Brenna McKaig, Nicole Charland, Hargun Khanna, Justin Margolin, Anna Gonye, Irena Gushterova, Tom Lasalle, Nihaarika Sharma, Brian C Russo, Maricarmen Rojas-Lopez, Moshe Sade-Feldman, Kasidet Manakongtreecheep, Jessica Tantivit, Molly Fisher Thomas

Affiliations

¹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: shirawg@broadinstitute.org.
² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address: sklaeger@broadinstitute.org.
³ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁴ Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA.
⁵ Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA.
⁷ Repertoire Immune Medicines, Cambridge, MA 02139, USA.
⁸ Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
⁹ Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA.
¹⁰ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
¹¹ Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
¹² Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA.
¹³ Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA.
¹⁴ Department of Hematology and Medical Oncology, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA.
¹⁵ Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Basic Science Program, Frederick National Laboratory for Cancer Research in the Laboratory of Integrative Cancer Immunology, National Cancer Institute, Bethesda, MD, USA.
¹⁶ Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA.
¹⁷ Harvard Medical School, Boston, MA 02115, USA; Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA.
¹⁸ Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
¹⁹ Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA.
²⁰ Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
²¹ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute, Boston, MA, USA; Health Informatics Lab, Metropolitan College, Boston University, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
²² Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA.
²³ Department of Biochemistry, Boston University School of Medicine, Boston, MA, USA; National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA. Electronic address: msaeed1@bu.edu.
²⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Massachusetts Consortium on Pathogen Readiness, Boston, MA, USA; Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.

Abstract

T cell-mediated immunity plays an important role in controlling SARS-CoV-2 infection, but the repertoire of naturally processed and presented viral epitopes on class I human leukocyte antigen (HLA-I) remains uncharacterized. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two cell lines at different times post infection using mass spectrometry. We found HLA-I peptides derived not only from canonical open reading frames (ORFs) but also from internal out-of-frame ORFs in spike and nucleocapsid not captured by current vaccines. Some peptides from out-of-frame ORFs elicited T cell responses in a humanized mouse model and individuals with COVID-19 that exceeded responses to canonical peptides, including some of the strongest epitopes reported to date. Whole-proteome analysis of infected cells revealed that early expressed viral proteins contribute more to HLA-I presentation and immunogenicity. These biological insights, as well as the discovery of out-of-frame ORF epitopes, will facilitate selection of peptides for immune monitoring and vaccine development.

Keywords: HLA Class I; SARS-CoV-2; T Cell response; coronavirus; immunogenicity; out-of-frame ORF immunopeptidomics; viral infection.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

A549 Cells
Alleles
Amino Acid Sequence
Animals
Antigen Presentation / immunology
COVID-19 / immunology
COVID-19 / virology
Epitopes, T-Lymphocyte / immunology*
Female
HEK293 Cells
Histocompatibility Antigens Class I / immunology*
Humans
Kinetics
Male
Mice
Open Reading Frames / genetics*
Peptides / chemistry
Peptides / immunology*
Proteome / immunology*
SARS-CoV-2 / immunology*
T-Lymphocytes / immunology

Substances

Epitopes, T-Lymphocyte
Histocompatibility Antigens Class I
Peptides
Proteome

Abstract

Publication types

MeSH terms

Substances

Grants and funding