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Mapping of the SARS-CoV-2 Epitope-Specific T-Cell Response Using dCODE Dextramer® Reagents
Background
In this study, the CD8+ T-cell response in COVID-19 patients experiencing mild or severe disease was investigated using dCODE Dextramer® reagents by bulk and single-cell analysis.
Study Description
Patient-derived T cells were initially screened for SARS-CoV-2-specificity using a panel of 38 different dCODE Dextramer® (HiT) reagents, including 4 positive and 4 negative controls. From the initial screening, a panel of 15 dCODE Dextramer® (10x) reagents plus the 8 controls were selected for subsequent single-cell analysis.
Results
Screening of patient samples using dCODE Dextramer® (HiT) enabled identification of samples holding specifically enriched epitope-binding T-cell populations for subsequent single-cell analysis with dCODE Dextramer® (10x), (Table 1). By clustering epitope specificity based on dCODE Dextramer® (10x) binding, researchers found unique recognition of four epitopes by T cells (Fig. 1) with the A*0101 epitope WTAGAAAYY being the most prevalent. In patients with severe COVID-19, single-cell analysis of T cells binding dCODE Dextramer® (10x) reagents revealed hyperactivation, T-cell exhaustion, and lack of long-lived memory T-cell features (Fig. 2).
Fig. 1 The four uniquely recognized epitopes identified using dCODE Dextramer® (10x) reagents are recognized by different T-cell subsets.
Fig. 2 Distribution of cell type frequency for active, mild, and severe COVID-19. SLEC = short-lived effector cells. MPEC = memory precursor effector cell.
|
HLA |
Peptide |
Target |
|
A*0101 |
WTAGAAAYY |
S Protein |
|
A*0101 |
LTDEMIAQY |
S Protein |
|
A*0201 |
TLACFVLAAV |
M Protein |
|
A*0201 |
GMSRIGMEV |
N Protein |
|
A*0201 |
TLACFVLAAV |
M Protein |
|
A*0201 |
LLLDRLNQL |
N Protein |
|
A*0201 |
NLNESLIDL |
S Protein |
|
A*0201 |
ILLNKHIDA |
N Protein |
|
A*0201 |
FIAGLIAIV |
M Protein |
|
A*0301 |
TLKSFTVEK |
S Protein |
|
A*0301 |
QIYKTPPIK |
S Protein |
|
A*1101 |
LSYFIASFR |
M Protein |
|
A*1101 |
MTSCCSCLK |
S Protein |
|
A*1101 |
GYVFASTEK |
S Protein |
|
A*1101 |
TLKSFTVEK |
S Protein |
Table 1 Top 15 immunogenic epitopes selected in the dCODE Dextramer® (HiT) screening for single-cell immuno-profiling of patient-specific CD8+ T cells.
Conclusions
- Relevant SARS-CoV-2 epitopes were identified in the initial screening using a panel of dCODE Dextramer® (HiT)
- Single-cell analysis of T cells binding dCODE Dextramer® (10x) reagents identified the CD8+ T-cell epitope WTAGAAAYY
- In patients with severe COVID-19, single-cell analysis with dCODE Dextramer® (10x) reagents revealed hyperactivation, T-cell exhaustion, and lack of long-lived memory T-cell characteristics
