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

• Published in: Cell Vol. 184; no. 15; pp. 3962 - 3980.e17
• Main Authors: Weingarten-Gabbay, Shira, Klaeger, Susan, Sarkizova, Siranush, Pearlman, Leah R., Chen, Da-Yuan, Gallagher, Kathleen M.E., Bauer, Matthew R., Taylor, Hannah B., Dunn, W. Augustine, Tarr, Christina, Sidney, John, Rachimi, Suzanna, Conway, Hasahn L., Katsis, Katelin, Wang, Yuntong, Leistritz-Edwards, Del, Durkin, Melissa R., Tomkins-Tinch, Christopher H., Finkel, Yaara, Nachshon, Aharon, Gentili, Matteo, Rivera, Keith D., Carulli, Isabel P., Chea, Vipheaviny A., Chandrashekar, Abishek, Bozkus, Cansu Cimen, Carrington, Mary, Lavin-Parsons, Kendall, Parry, Blair, Lilley, Brendan, Lodenstein, Carl, McKaig, Brenna, Charland, Nicole, Khanna, Hargun, Margolin, Justin, Gonye, Anna, Gushterova, Irena, Lasalle, Tom, Sharma, Nihaarika, Russo, Brian C., Rojas-Lopez, Maricarmen, Sade-Feldman, Moshe, Manakongtreecheep, Kasidet, Tantivit, Jessica, Fisher Thomas, Molly, Bhardwaj, Nina, Barouch, Dan H., Sette, Alessandro, Maus, Marcela V., Rice, Charles M., Clauser, Karl R., Keskin, Derin B., Pregibon, Daniel C., Hacohen, Nir, Carr, Steven A., Abelin, Jennifer G., Saeed, Mohsan, Sabeti, Pardis C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 22.07.2021; The Authors. Published by Elsevier Inc
• Subjects: A549 Cells; Alleles; Amino Acid Sequence; animal models; Animals; Antigen Presentation - immunology; cell-mediated immunity; coronavirus; COVID-19 - immunology; COVID-19 - virology; COVID-19 infection; epitopes; Epitopes, T-Lymphocyte - immunology; Female; HEK293 Cells; Histocompatibility Antigens Class I - immunology; HLA antigens; HLA Class I; Humans; immunogenicity; Kinetics; Male; mass spectrometry; Mice; nucleocapsid; Open Reading Frames - genetics; out-of-frame ORF immunopeptidomics; peptides; Peptides - chemistry; Peptides - immunology; Proteome - immunology; SARS-CoV-2; SARS-CoV-2 - immunology; Severe acute respiratory syndrome coronavirus 2; T Cell response; T-lymphocytes; T-Lymphocytes - immunology; vaccine development; viral infection; HLA Class I; SARS-CoV-2; out-of-frame ORF immunopeptidomics; viral infection; T Cell response; coronavirus; immunogenicity
• ISSN: 0092-8674; 1097-4172; 1097-4172
• DOI: 10.1016/j.cell.2021.05.046

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. [Display omitted] •Time course analysis of HLA-I immunopeptidome in SARS-CoV-2-infected cells•25% of detected HLA-I peptides originated from out-of-frame ORFs in S and N•Some out-of-frame peptides elicited stronger T cell responses than canonical peptides•Early expressed viral proteins dominated HLA-I presentation and immunogenicity Analysis of the HLA-I peptidome of SARS-CoV-2 infection identifies peptides derived from canonical and out-of-frame ORFs in viral S and N protein that are not captured by current vaccines and yield potent T cell responses in a mouse model as well as individuals with COVID-19.