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

S Weingarten-Gabbay, S Klaeger, S Sarkizova… - Cell, 2021 - cell.com
S Weingarten-Gabbay, S Klaeger, S Sarkizova, LR Pearlman, DY Chen, KME Gallagher
Cell, 2021cell.com
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 …
Summary
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.
cell.com