Immunopeptidome Analysis of HLA-DPB1 Allelic Variants Reveals New Functional Hierarchies

• Published in: The Journal of immunology (1950) 2020-06, Vol.204 (12), p.3273-3282
• Main Authors: van Balen, Peter, Kester, Michel G D, de Klerk, Wendy, Crivello, Pietro, Arrieta-Bolaños, Esteban, de Ru, Arnoud H, Jedema, Inge, Mohammed, Yassene, Heemskerk, Mirjam H M, Fleischhauer, Katharina, van Veelen, Peter A, Falkenburg, J H Frederik
• Format: Article
• Language: English
• Subjects: Alleles; B-Lymphocytes - immunology; Binding Sites - genetics; Binding Sites - immunology; Cell Line; Cell Line, Tumor; Epitopes, T-Lymphocyte - genetics; Epitopes, T-Lymphocyte - immunology; Hematopoietic Stem Cell Transplantation - methods; Histocompatibility Testing - methods; HLA-DP beta-Chains - genetics; HLA-DP beta-Chains - immunology; Humans; K562 Cells; Peptides - genetics; Peptides - immunology; Polymorphism, Genetic - genetics
• ISSN: 0022-1767; 1550-6606
• DOI: 10.4049/jimmunol.2000192

HLA-DP alleles can be classified into functional T cell epitope (TCE) groups. TCE-1 and TCE-2 are clearly defined, but TCE-3 still represents an heterogeneous group. Because polymorphisms in HLA-DP influence the presented peptidome, we investigated whether the composition of peptides binding in HLA-DP may be used to refine the HLA-DP group classification. Peptidomes of human HLA-DP-typed B cell lines were analyzed with mass spectrometry after immunoaffinity chromatography and peptide elution. Gibbs clustering was performed to identify motifs of binding peptides. HLA-DP peptide-binding motifs showed a clear association with the HLA-DP allele-specific sequences of the binding groove. Hierarchical clustering of HLA-DP immunopeptidomes was performed to investigate the similarities and differences in peptidomes of different HLA-DP molecules, and this clustering resulted in the categorization of HLA-DP alleles into 3-DP peptidome clusters (DPC). The peptidomes of HLA-DPB1*09:01, -10:01, and -17:01 (TCE-1 alleles) and HLA-DPB1*04:01, -04:02, and -02:01 (TCE-3 alleles) were separated in two maximal distinct clusters, DPC-1 and DPC-3, respectively, reflecting their previous TCE classification. HLA-DP alleles categorized in DPC-2 shared certain similar peptide-binding motifs with DPC-1 or DPC-3 alleles, but significant differences were observed for other positions. Within DPC-2, divergence between the alleles was observed based on the preference for different peptide residues at position 9. In summary, immunopeptidome analysis was used to unravel functional hierarchies among HLA-DP alleles, providing new molecular insights into HLA-DP classification.