Comparison of HLA-A and HLA-B ligandomes

Abstract

Aim Advances in mass spectrometry and HLA protein availability have allowed for very a detailed look at the self-peptides naturally presented by HLA. To date, there is considerable variation among studies such that a comparison of the ligands presented by HLA-A and HLA-B has been difficult. Here we set out to characterize the self-ligandome of 5 HLA-A and 3 HLA-B molecules representing various peptide binding supertypes with highly controlled methods - varying only the HLA molecule. Methods HeLa cells were separately transfected with 5 different HLA-A (A1, A2, A3, A11, A24) and 3 HLA-B (B7, B27, B51) as soluble class I gene constructs. HLA-complexes were affinity purified and the eluted ligands were characterized by two-dimensional LCMS. Sequences were identified from the fragment spectra using PEAKS v7.0 at a 1% FDR. Results We find that nonamers are the preferred length for all alleles, however there is wide diversity in the ligand length distributions between allomorphs. For example, HLA-B51 shows a high tolerance for 8-mers while HLA-A11 equally prefers 11mers and nonamers. However there is no overall length bias when comparing HLA-A to HLA-B. For both HLA-A and HLA-B, one or two ligands are typically sampled per protein. However, proteins like GAPDH, alpha-enolase 1, carbamoyl-phosphate synthase 1, and dynenin provide on average approximately 20 ligands per allomorph. For all allomorphs there is an uneven sampling of proteins in the genome with biases shown towards particular proteins. Especially noteworthy is that proteins involved in translation, particularly ribosomal RNA binding proteins, are extensively represented by HLA-A and HLA-B. For both HLA-A and HLA-B there is also a significant enrichment of proteins localized to the lumen of the nucleus including histones, proteins involved in RNA splicing, and factors for biogenesis of ribosomes in the nucleolus. Conclusion The ligands sampled by HLA-A and HLA-B vary in length between the allomorphs in a manner that is highly diverse and independent of locus. Overall, there is little to no difference in the source proteins sampled by HLA-A and HLA-B with all allomorphs showing a ligand sampling bias in RNA binding proteins and nuclear proteins. W. Hildebrand: Scientific/Medical Advisor; Company/Organization; Pure Protein LLC. 5. Employee; Company/Organization; Pure Protein LLC.