CD8+ T solu epitooppien etsintää Sars-2 rakenneproteiineista . M-proteiinista löytyi 6 epitooppia.

 https://jlb.onlinelibrary.wiley.com/doi/10.1002/JLB.4MA0621-020R

Abstract

The outbreak of coronavirus disease 2019 (COVID-19) has now become a pandemic, and the etiologic agent is the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). T cell mediated immune responses play an important role in virus controlling; however, the understanding of the viral protein immunogenicity and the mechanisms of the induced responses are still limited. So, identification of specific epitopes and exploring their immunogenic properties would provide valuable information. In our study, we utilized the Immune Epitope Database and Analysis Resource and NetMHCpan to predict HLA-A2 restricted CD8⁺ T cell epitopes in structural proteins of SARS-CoV-2, and screened out 23 potential epitopes. Among them, 18 peptides showed strong or moderate binding with HLA-A2 with a T2A2 cell binding model. Next, the mixed peptides induced the increased expression of CD69 and highly expressed levels of IFN-γ and granzyme B in CD8⁺ T cells, indicating effective activation of specific CD8⁺ T cells. In addition, the peptide-activated CD8⁺ T cells showed significantly increased killing to the target cells. Furthermore, tetramer staining revealed that the activated CD8⁺ T cells mainly recognized seven epitopes. All together, we identified specific CD8⁺ T cell epitopes in SARS-CoV-2 structural proteins, which could induce the production of specific immune competent CD8⁺ T cells. Our work contributes to the understanding of specific immune responses and vaccine development for SARS-CoV-2.

 

3.1 Prediction of HLA-A2 restricted CD8⁺ T cell epitopes in structure proteins of SARS-CoV-2

To broadly screen the epitopes of SARS-CoV-2 and understand the mechanisms of antigen epitope recognition and activation associated with CD8⁺ T cells, we predicted the HLA-A2 restricted CD8⁺ T cell epitopes in S, M, N, and E protein of SARS-CoV-2 by using the IEDB and NetMHCpan EL 4.0. Peptides with the predicted binding capability IC50 below 100 nM were selected. Totally, 23 peptides were selected, including 14 in S protein, 3 in E protein, and 6 in M protein (Fig. 1B). The detailed information is shown in Table 2. Next, these potential epitopes were synthesized for further evaluation.

No.	HLA subtypes	Position	Sequence	Molecular weight	References
n-Sp16	HLA-A2	62-70	VTWFHAIHV	1109.3
n-Sp17	HLA-A2	424-432	KLPDDFTGC	995.12
n-Sp18	HLA-A2	515-524	FELLHAPATV	1097.28
n-Sp19	HLA-A2	721-729	SVTTEILPV	958.12
n-Sp20	HLA-A2	786-794	KQIYKTPPI	1087.33
n-Sp21	HLA-A2	817-826	FIEDLLFNKV	1237.46
n-Sp22	HLA-A2	821-829	LLFNKVTLA	1018.26
n-Sp23	HLA-A2	894-902	LQIPFAMQM	1078.35
n-Sp24	HLA-A2	964-972	KQLSSNFGA	951.05
n-Sp25	HLA-A2	976-984	VLNDILSRL	1042.24	Sekine et al.19, 18
n-Sp26	HLA-A2	983-991	RLDKVEAEV	1058.2
n-Sp27	HLA-A2	1048-1056	HLMSFPQSA	1017.17
n-Sp28	HLA-A2	1062-1070	FLHVTYVPA	1046.23
n-Sp29	HLA-A2	1121-1129	FVSGNCDVV	939.05
n-Ep1	HLA-A2	16-24	SVLLFLAFV	1008.27
n-Ep2	HLA-A2	26-34	FLLVTLAIL	1002.31
n-Ep3	HLA-A2	50-58	SLVKPSFYV	1039.24	Sekine et al.19
n-Mp1	HLA-A2	15-23	KLLEQWNLV	1142.36	Sekine et al.19
n-Mp2	HLA-A2	26-35	FLFLTWICLL	1268.62
n-Mp3	HLA-A2	51-60	LIFLWLLWPV	1299.66
n-Mp4	HLA-A2	61-70	TLACFVLAAV	1007.26
-Mp5	HLA-A2	65-73	FVLAAVYRI	1051.3
n-Mp6	HLA-A2	89-97	GLMWLSYFI	1129.38