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

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.

Hallmarks of immune response in COVID-19: Exploring dysregulation and exhaustion

“…Moreover, it should be considered that additional SARS-CoV-2 antigens, different from the “classic” Spike, Nucleoprotein and Membrane may be of importance to track SARS-CoV-2-specific memory durability. This is further supported by the recent identification of antibodies against non-structural/accessory proteins in COVID-19 patients, as well as of HLA-I peptides derived from both canonical open reading frames (ORFs) and internal out-of-frame ORFs of S and N proteins [ 230 , 217 ]. These data open the way to further investigation and strategic approach in monitoring SARS-CoV-2 specific immune response.…”

“…SARS-CoV-2 infection induces a wide spectrum of clinical manifestations ranging from no symptoms to pauci-, mild- or severe symptoms culminating in ARDS and multi-organ failure up to death. Many authors reported that the entity of SARS-CoV-2-specific immune response, both humoral and cell-mediated is lower in the asymptomatic patients than in the symptomatic ones [ 48 , 49 , 217 ],Seattler et al, Long et al). However, T cells from asymptomatic individuals produced higher levels of IFN-γ and IL-2, while those from symptomatic subjects secreted more proinflammatory cytokines TNF-α, IL-1β and IL-6 [ 218 ].…”

Clusters of SARS-CoV-2 Lineage B.1.1.7 Infection after Vaccination with Adenovirus-Vectored and Inactivated Vaccines

“…In addition, we observed higher antibody levels in vaccinated, PCR-positive, symptomatic individuals than in vaccinated, asymptomatic, PCR-positive individuals, indicating that the neutralizing antibody levels may not reliably predict protection against mild COVID-19. In fact, other components of the immunological response are probably essential for SARS-CoV-2 restriction, such as T-cellmediated immunity, which plays a crucial role in controlling SARS-CoV-2 infection [39].…”

T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations

“…Thus, clinical implications of significant alterations in HLA-peptide binding affinity should be further experimentally assessed. The second limitation involves officially unannotated SARS-CoV-2 proteins which could contain T cell epitopes: proteomics analysis carried out by Weingarten-Gabbay with co-authors resulted in detection of highly affine HLA-I peptides from out-of-frame ORFs (25). While some of these ORFs were included in our analysis (e.g., ORF9b), the other entries like S.iORF1/2 were not considered.…”