Discordance between the predicted vs. the actually recognized CD8+ T cell epitopes of HCMV pp65 antigen and aleatory epitope dominance

• Published in: bioRxiv
• Main Authors: Lehmann, Alexander, Zhang, Ting, Reche, Pedro A, Lehmann, Paul V
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 07.11.2020; Cold Spring Harbor Laboratory
• Edition: 1.1
• Subjects: Alleles; Antigens; CD8 antigen; Cell-mediated immunity; Cytotoxicity; Discordance; Dominance; Enzyme-linked immunosorbent assay; Epitope mapping; Histocompatibility antigen HLA; Immunology; Lymphocytes; Lymphocytes T; Peptide mapping; Peptides; Pp65 protein; Predictions; epitope prediction; ImmunoSpot; Elispot; high throughput; brute force epitope mapping
• ISSN: 2692-8205; 2692-8205
• DOI: 10.1101/2020.11.06.371633

Abstract CD8+ T cell immune monitoring aims at measuring the numbers and functions of antigen-specific CD8+ T cell populations engaged during immune responses, providing insights into the magnitude and quality of cell-mediated immunity operational in a test subject. The selection of peptides for ex vivo CD8+ T cell detection is critical, however, because for each restricting HLA class I molecule present in a human individual there is a multitude of potential epitopes within complex antigens, and HLA diversity between the test subjects predisposes CD8+ T cell responses to individualized epitope recognition profiles. We report here on a brute force CD8+ T cell epitope mapping approach for the human cytomegalovirus (HCMV) pp65 antigen on ten HLA-A*02:01-matched HCMV infected human subjects. In this approach, in each test subject, every possible CD8+ T cell epitope was systematically tested; that is 553 individual peptides that walk the sequence of the HCMV pp65 protein in steps of single amino acids. Highly individualized CD8+ T cell response profiles with aleatory epitope recognition patterns were observed. We compared the actually detected epitope utilization in each individual with epitope prediction ranking for the shared HLA-A*02:01 allele, and for additional HLA class I alleles expressed by each individual. No correlation was found between epitopes’ ranking on the prediction scale and their actual immune dominance. The data suggest that accurate CD8+ T cell immune monitoring might depend on the agnostic reliance on mega peptide pools, or brute force mapping, rather than individualized epitope predictions. Competing Interest Statement All authors, except PAR, are employees of Cellular Technology Limited (CTL), a company that specializes on immune monitoring via ELISPOT testing, producing high-throughput-suitable readers, test kits, and offering GLP-compliant contract research. PAR declares no financial, commercial or other relationships that might be perceived by the academic community as representing a potential conflict of interest.