Immunogenicity of 2019-nCoV peptides to 1G4 CD8+ TCR molecule
While our de novo candidates are appealing shortlisted targets for experimental validation, it does not provide information about target T cell receptors (TCRs). We therefore set out to interrogate the possibility of cross reactivity with one well-studied TCR.
T cell cross-reactivity has been instrumental for the T cell immunity against both tumor antigens and external pathogens. In that regard, a number of T cells have been extensively characterized including 1G4 CD8+ TCR, which is known to recognize the ‘SLLMWITQC’ peptide presented by HLA-A*02:01. We therefore set out to leverage the data from a recently published study 7 and exploit the possibility of cross reactivity of this TCR to any 2019-nCoV peptide.
Here, we scanned all 9-mers from the 2019-nCoV proteome (9613 peptides) with Binding, Activating and Killing Position Weight Matrices (PWM, see the method section) and associated each peptide with the geometric mean of these three assays as a measure of immunogenicity (Data Table 4 4). The distributions of binding, activation and killing scores along with their multiplicative score and geometric mean are illustrated in Figure 4. Based on geometric mean, we observed 20 2019-nCoV peptides with a score > 0.8 and 516 peptides > 0.7. The 9-mer peptides with geometric mean > 0.7 and positive HLA-A*02:01 binding prediction by NetMHCpan 4.0 are listed in Table 4.
Figure 4.  Distribution of 1G4 TCR positional weight matrix scores for 2019-nCoV peptides.
The positional weight matrices were obtained from 7 and 9613 9-mers generated from 10 2019-nCoV ORFs were computed for their TCR recognition potential.
Table 4.  2019-nCoV 9-mer peptides with geometric mean ≥ 0.7 by 1G4 TCR positional weight matrix and predicted positive to bind HLA-A*02:01 by NetMHCpan 4.0 (Rank = NetMHCpan rank).
Peptide  Binding score  Activation score  Killing score  geoMean  Rank  Binder
RIMTWLDMV  0.866377428  0.853995  0.776303  0.831249  0.3481  SB
ALNTLVKQL  0.802453741  0.75073  0.785957  0.779413  0.6159  WB
LLLDRLNQL  0.809895414  0.7752  0.741096  0.774888  0.0423  SB
MIAQYTSAL  0.766262499  0.789511  0.749477  0.768242  0.9238  WB
VLSTFISAA  0.799672451  0.756117  0.687278  0.746239  0.536  WB
NVLAWLYAA  0.761297552  0.686117  0.739944  0.728423  1.4457  WB
RLANECAQV  0.783161706  0.719705  0.680504  0.726572  0.2049  SB
KLLKSIAAT  0.748896679  0.708996  0.697463  0.718118  1.0923  WB
QLSLPVLQV  0.70128376  0.715259  0.708405  0.708293  0.4768  SB
VQMAPISAM  0.729320768  0.698514  0.689612  0.705612  1.4677  WB
LLLTILTSL  0.7131709  0.715194  0.680064  0.702623  0.2712  SB
SVLLFLAFV  0.736972762  0.690855  0.679534  0.70202  1.1449  WB
LMWLIINLV  0.727847374  0.681119  0.694007  0.700717  1.304  WB We further analysed the MHC binding propensities and gathered peptides not only predicted positive by NetMHCpan but also to have leucine (L) and valine (V) in anchor positions 2 (P2) and 9 (P9) respectively. Previous studies have shown that for MHC-I HLA-A02:01 specific peptides, 9-mer peptides with leucine at P2 and valine at P9 are preferably presented on the surface of HLA-A02:01 8. Looking at the LV peptide, we identified 44 2019-nCoV peptides of which 2 peptides had immunogenicity score > 0.7 and 12 peptides > 0.6 ( Table 5). Thus, here we provide the list of peptides that are potential targets for 1G4 TCR recognition for subjects with HLA-A02:01 haplotype.
Table 5.  2019-nCoV 9-mer peptides having leucine-valine in anchor positions.
Peptides have geometric mean ≥ 0.6 and ≤ 0.7 (for those ≥ 0.7, refer to Table 4) by 1G4 TCR positional weight matrix and predicted positive for HLA-A*02:01 binding by NetMHCpan 4.0 (Rank = NetMHCpan rank).
Peptide  Binding score  Activation score  Killing score  geoMean  Rank  Binder
TLMNVLTLV  0.723687  0.658986  0.652178  0.677534  0.0444  SB
QLEMELTPV  0.711291  0.651003  0.608605  0.655625  1.6769  WB
MLAKALRKV  0.668756  0.610664  0.65968  0.645854  0.3524  SB
GLFKDCSKV  0.675952  0.632375  0.594753  0.633494  0.2677  SB
ALSKGVHFV  0.652549  0.604952  0.586236  0.613954  0.0425  SB
YLNTLTLAV  0.624147  0.610826  0.575445  0.603119  0.0453  SB