Mass spectrometric identification of immunogenic SARS-CoV-2 epitopes and cognate TCRs

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections elicit both humoral and cellular immune responses. For the prevention and treatment of COVID-19, the disease caused by SARS-CoV-2, it has become increasingly apparent that T cell responses are equally if not more important than humoral responses in mediating recovery and immune protection. One major challenge in developing T cell–based therapies for infectious and malignant diseases has been the identification of immunogenic epitopes that can elicit a meaningful T cell response. Traditionally, this has been achieved using sophisticated in silico methods to predict putative epitopes deduced from binding affinities. Our studies find that, in contrast to current convention, “immunodominant” SARS-CoV-2 peptides defined by such in silico methods often fail to elicit T cell responses recognizing naturally presented SARS-CoV-2 epitopes. We postulated that immunogenic epitopes for SARS-CoV-2 are best defined empirically by directly analyzing peptides eluted from the naturally processed peptide–major histocompatibility complex (MHC) and then validating immunogenicity by determining whether such peptides can elicit T cells recognizing SARS-CoV-2 antigen-expressing cells. Using a tandem mass spectrometry approach, we identified epitopes derived from not only structural but also nonstructural genes in regions highly conserved among SARS-CoV-2 strains, including recently recognized variants. Finally, there are no reported T cell receptor–engineered T cell technology that can redirect T cell specificity to recognize and kill SARS-CoV-2 target cells. We report here several SARS-CoV-2 epitopes defined by mass spectrometric analysis of MHC-eluted peptides, provide empiric evidence for their immunogenicity, and demonstrate engineered TCR-redirected killing.

Integrated Immunopeptidomics and Proteomics Study Reveals Imbalanced Innate and Adaptive Immune Responses to SARS-Cov-2 Infection

“…TGSNVFQTR from spike glycoprotein (638-646) was predicted binding to A*68:01 allele and it locates within the SD1 domain. ITFGGPSDSTGSNQNGER from nucelocapsid protein (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32) was also identified in this study and has been predicted to bind to the same allele. Additionally, two class II peptides from nucleocapisd protein SPDDQIGYYRRATRRIR and FSKQLQQSMSSADSTQA were identified, which has not been reported before.…”

“…The approach has been used in other viral infections, revealing new antigens including those peptide sequences that activated T-cell responses against West Nile virus 14 , HIV 15,16 and measles 17 . It was reported that epitopes of SARS-CoV-2 derived not only from structural but also non-structural genes in regions highly conserved among SARS-CoV-2 strains including recently recognized variants 18 . This included epitopes from membrane glycoprotein (MGP) and non-structure protein-13 (NSP13).…”

Patients Recovering from Severe COVID-19 Develop a Polyfunctional Antigen-Specific CD4+ T Cell Response

“…The identification of the most immunogenic epitopes is key to the study and understanding of cellular immune response to gain insights into virus-induced infection mechanisms. An immunogenic peptide is one that is presented by a self-major histocompatibility complex (MHC) and is able to elicit a T cell response [ 43 ]. Thus, the identification of such epitopes is also of importance in the context of future therapies.…”

Vaccine Delivery by Precipitation (VDBP) Lessons from Poison Ivy for Protein Antigens in General and Specifically for SARS Co-V2

“…In 2021, Pan et al reported identification of 4 epitopes on the SARS Co-V2 non-structural protein helicase (NSP13) and one on the membrane glycoprotein (MGP) that could be eluted from naturally processed major histocompatability complex and then demonstrated to induce the production of cytotoxic T-cells specific for the same epitopes [30]. The authors report that these 5 epitopes are coded by a highly conserved region of the SARS Co-V2 genome unchanged between the original pandemic strain and all variants available for study through mid-June 2021.…”