Combinatorial peptide library scans of multiple HLA A*0201 restricted CTL reveal high levels of degeneracy at MHCI anchor positions (100.12)

Abstract

Abstract CD8+ cytotoxic T lymphocytes (CTLs) hold the key to the successful prevention and eradication of infectious and neoplastic disease. T-cells recognize ‘foreign’ peptide fragments often referred to as epitopes, in the context of ‘self’ major histocompatibility complex class I (MHCI) molecules. Epitope identification is essential to define targets for the effective control of disease. Peptides bind to MHCI molecules by anchoring at position 2 and the C-terminus of the peptide ligand. Techniques such as pool sequencing have been hugely instrumental in revealing HLA allele-specific peptide binding motifs. However, this approach only reveals the most dominant MHC anchor residues. The preferred binding motif identified by pool sequencing for the most common MHCI, HLA A*0201, is L/M at position 2 and V/I/L/A at the C-terminus. Here, we use an extremely sensitive combinatorial library screening approach to show that in the context of HLA A*0201, degeneracy at anchor residue positions is much higher than previously appreciated. We also examined the recognition of peptides with substitutions of all 20 amino acids at both anchor positions in three different clonal systems which confirm these observations. Indeed, in one clonal system, 9-mer peptides containing A, C, F, I, K, L, M, Q, S, T, V in position 2 and A, C, F, I, L, M, T, V at position 9 were recognized efficiently. These observations have implications for T-cell epitope prediction and future vaccine design.