A monoallelic immunopeptidome atlas of 10 prevalent canine DLA-88 alleles

A comprehensive atlas of naturally processed MHC class I (MHC-I)-bound peptides from 10 prevalent dog leukocyte antigen (DLA-88) alleles has been established. This research offers substantial expansion to the existing canine DLA-88 immunopeptidome landscape, which previously lacked comprehensive monoallelic ligand datasets for these common alleles. Utilizing liquid chromatography-tandem mass spectrometry, the study identified 32,702 peptides ranging in length from 7 to 15 amino acids across these 10 alleles.

The 10 DLA-88 alleles displayed typical peptide length distributions and allele-specific binding motifs, which correlated with variations in binding-groove pseudo-sequences derived from human MHC-I peptide-contact residues. The study found that ligand sharing between DLA-88 alleles was linked to binding site distance. By incorporating the newly characterized DLA-88 ligand datasets, the number of published canine DLA-I alleles with ligand-characterized reference alleles was increased by over fourfold, enhancing understanding of the alleles' peptide-binding features.

The research also revealed highly conserved antigen-processing signatures in dogs, akin to those reported in humans. As a proof-of-concept application, 54 DLA-88-bound peptides identified in the immunopeptidome analysis were selected as potential candidates for canine cancer immunotherapy. Their peptide-binding features were evaluated based on the normal tissue expression profiles of their source proteins.

This DLA-88 immunopeptidome atlas provides valuable insights into allele-dependent differences in antigen presentation and offers a valuable resource for developing accurate DLA-88-binding peptide prediction tools, as well as supporting peptide-based immunological studies in dogs.