Screening for immunodominant epitopes of SARS-CoV-2 based on CD8+ T cell responses from individuals with HLA-A homozygous alleles

Rui He; Lingxin Meng; Yuting Sun; Jingsong Wang; Shufeng Wang; Yueping Liu; Lei Fei; Zhongfang Wang; Qinggao Zhang; Yuzhang Wu; Yongwen Chen; Bo Diao

doi:10.1016/j.molimm.2025.01.010

Screening for immunodominant epitopes of SARS-CoV-2 based on CD8⁺ T cell responses from individuals with HLA-A homozygous alleles

Mol Immunol. 2025 Jan 25:178:52-63. doi: 10.1016/j.molimm.2025.01.010. Online ahead of print.

Authors

Rui He¹, Lingxin Meng², Yuting Sun², Jingsong Wang², Shufeng Wang², Yueping Liu³, Lei Fei², Zhongfang Wang⁴, Qinggao Zhang⁵, Yuzhang Wu², Yongwen Chen⁶, Bo Diao⁷

Affiliations

¹ School of Medicine, Chongqing University, Chongqing 400030, PR China; Institute of Immunology, PLA, The Army Medical University, Chongqing 400038, PR China.
² Institute of Immunology, PLA, The Army Medical University, Chongqing 400038, PR China.
³ Institute of Immunology, PLA, The Army Medical University, Chongqing 400038, PR China; Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei 430015, PR China.
⁴ State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, Guangdong 511436, PR China.
⁵ Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, PR China.
⁶ Institute of Immunology, PLA, The Army Medical University, Chongqing 400038, PR China; Chronic Disease Research Center, Medical College, Dalian University, Dalian, Liaoning 116622, PR China. Electronic address: chenyongwen@tmmu.edu.cn.
⁷ Department of Medical Laboratory Center, General Hospital of Central Theater Command, Wuhan, Hubei 430015, PR China. Electronic address: dpitao@163.com.

PMID: 39864283
DOI: 10.1016/j.molimm.2025.01.010

Abstract

Purpose: SARS-CoV-2-specific CD8⁺ cytotoxic T lymphocytes (CTLs) are crucial in viral clearance, disease progression, and reinfection control. However, numerous SARS-CoV-2 immunodominant CTL epitopes theoretically are still unidentified due to the genetic polymorphism of human leukocyte antigen class I (HLA-I) molecules.

Methods: The CTL epitopes of SARS-CoV-2 were predicted by the epitope affinity and immunogenicity prediction platforms: the NetMHCpan and the PromPPD. Individuals with HLA-A homozygous alleles were screened from 252 COVID-19 vaccinees, including the Ad5-nCoV vaccine (CanSino, n = 183) and the CoronaVac inactivated vaccine (Sinovac, n = 69) using MiSeqDx™ generation sequencing, and their PBMCs were further stimulated by the predicted peptides to screen the immunodominant epitopes according to the secretion of IFN-γ from CD8⁺ T cells. Peptide-MHC tetramers were constructed and used to detect the frequency of antigen specific CTLs in vivo.

Results: Individuals with HLA-A homozygous alleles including HLA-A*01 (n = 1), -A*02 (n = 9), - A*03 and -A*11 (n = 12), and -A*24 (n = 7) supertypes were selected. Twelve immunodominant CTL epitopes for these HLA-A allotypes were finally screened based on the frequency of IFN-γ⁺CD8⁺ T cells in homozygous individuals. The SARS-CoV-2 specific CTLs from Omicron variant infected patients were successfully evaluated by these novel peptide-HLA tetramers.

Conclusion: A set of immunodominant CTL epitopes of SARS-CoV-2 was identified, and the antigen-specific CD8⁺ T cells in viral infected patients or COVID-19 vaccinees could be rapidly detected by a mixture of the peptide-MHC tetramers.

Keywords: COVID-19 vaccinees; CTL epitope; PromPPD; SARS-CoV-2; Tetramer.