Biology subjects

Bhojak, K.

Publications and source records attributed to Bhojak, K..

2 recordsLinked to original sources

bioRxiv2022

Immunodominant influenza epitope GILGFVFTL engage common and divergent TCRs when presented as a 9-mer or a 15-mer peptide

Antigen-specific T-cells are a powerful modality for treating cancer and other life-threatening viral and bacterial diseases. Technologies to identify and expand antigen-specific T-cells rapidly can shorten the time, and lower the cost of treatment. In this regard, screening short overlapping peptides to identify antigen-specific T-cells in ex vivo T-cell activation assay is becoming routine. Screening assays typically use 15-mer peptides to stimulate patient-derived, or healthy peripheral blood mononuclear cells to activate T-cells and identify expanded TCRs by next generation sequencing. Previous studies comparing the kinetics of T-cell activation using a 9 and a 15-mer peptide versions of a CMV immunodominant epitope demonstrated that 15-mer peptides induced CD8 T-cell activation at a slower kinetics reaching a lower magnitude compared to 9-mer peptides. The fact that 9-mer peptides are an optimal fit for the MHC class-I binding groove could explain this difference, with the 15-mer peptide requiring additional proteolytic processing before binding to the deeper binding groove of class-I MHC. Alternatively, the delay in kinetics and magnitude can result from the activation of a wider diversity of TCRs engaging novel epitopes generated from the 15-mer peptide whose activation profile may be different from the profile of TCRs that normally respond to the 9-mer immunodominant epitope. We sought to address these two possibilities by comparing T-cell engagement to the HLA-2-restricted GILGFVFTL epitope presented as a 9-mer, or a 15-mer peptide and analyzing CDR3 expansion as a measure of T-cell engagement diversity. This approach also addressed an important question as to whether optimal TCRs could be missed using a 15-mer peptide used routinely in screening assays.

immunology↗

bioRxiv2020

Immunodominant T-cell epitopes from the SARS-CoV-2 spike antigen reveal robust pre-existing T-cell immunity in unexposed individuals

The COVID-19 pandemic has revealed a range of disease phenotypes in infected patients with asymptomatic, mild or severe clinical outcomes, but the mechanisms that determine such variable outcomes remain unresolved. In this study, we identified immunodominant CD8 T-cell epitopes in the RBD and the non-RBD domain of the spike antigen using a novel TCR-binding algorithm. A selected pool of 11 predicted epitopes induced robust T-cell activation in unexposed donors demonstrating pre-existing CD4 and CD8 T-cell immunity to SARS-CoV-2 antigen. The T-cell reactivity to the predicted epitopes was higher than the Spike-S1 and S2 peptide pools containing 157 and 158 peptides both in unexposed donors and in convalescent patients suggesting that strong T-cell epitopes are likely to be missed when larger peptide pools are used in assays. A key finding of our study is that pre-existing T-cell immunity to SARS-CoV-2 is contributed by TCRs that recognize common viral antigens such as Influenza and CMV, even though the viral epitopes lack sequence identity to the SARS-CoV-2 epitopes. This finding is in contrast to multiple published studies in which pre-existing T-cell immunity is suggested to arise from shared epitopes between SARS-CoV-2 and other common cold-causing coronaviruses. Whether the presence of pre-existing T-cell immunity provides protection against COVID-19 or contributes to severe disease phenotype remains to be determined in a larger cohort. However, our findings raise the expectation that a significant majority of the global population is likely to have SARS-CoV-2 reactive T-cells because of prior exposure to flu and CMV viruses, in addition to common cold-causing coronaviruses.

immunology↗