Human leucocyte antigen (HLA) class II molecules in humans are encoded by three different loci, HLA-DR, -DQ and -DP. These molecules are expressed on professional antigen presenting cells including Dendritic cells, B-cells and macrophages performing a crucial role in immune surveillance by presenting peptide antigen to CD4+ T cells. This interaction is critical for activation of T-cells and subsequent licensing of immune response including generation of antibodies by B-cells.
While the peptide repertoires of numerous HLA-DR, -DQ and -DP allotypes have been examined, there have been few reports on the combined repertoire of these molecules expressed in a single cell. Here we describe the endogenous peptide repertoire of a human B lymphoblastoid cell line C1R expressing the class II haplotype HLA-DR12/DQ7/DP4. HLA molecules were immunoprecipitated using antibodies and their peptide cargo fractionated and analyzed using either a SCIEX TripleTOF 5600+ or ThermoFisher Q-Exactive plus.
We have identified 71350 naturally processed peptides presented collectively by HLA-DR12, HLA-DQ7 or HLA-DP4. The resulting “haplodome” is complemented by the cellular proteome defined by standard LC-MS/MS approaches. This large dataset has shed light on properties of these class II ligands especially the preference for membrane and extracellular source proteins. Our data also highlights the underpinning molecular basis for the co-evolution of these conserved haplotypes of closely linked and co-inherited HLA molecules which together increase sequence coverage of cellular proteins for immune surveillance with minimal overlap between each co-inherited allomorph.The results of this study shed light on selection of HLA class II ligands with implications in understanding determinants of T-cell and B-cell responses in viral, vaccine-induced and auto-immunity.