Comparative bioinformatic analysis of human and swine MHC sequences: implications for xenotransplantation

Introduction Xenotransplantation using genetically engineered pig organs has advanced toward clinical evaluation, but immune-mediated rejection remains a major barrier to durable graft survival. Deletion of dominant carbohydrate xenoantigens has reduced hyperacute antibody-mediated injury, increasing the relative importance of residual protein antigens, including swine leukocyte antigens (SLA). Because SLA and human leukocyte antigen (HLA) molecules share major histocompatibility complex functions and structural features, defining their molecular relationships may help prioritize mechanisms of human humoral and cellular xenoreactivity. Methods We compared HLA and SLA using protein sequence alignment, an HLA-trained classifier combining five models, analysis of positions contributing to potential HLA antibody-recognition sites (eplets), and structural modeling. The sequence dataset included 452 SLA proteins; classifier analysis included 260 class I and 152 class II β-chain proteins. Results Sequence identity supported corresponding DRB1 and DQB1 relationships between species, while class I relationships differed across loci. Class I SLA classifier predictions favored HLA-B, and 97 of 99 SLA-DRB1 proteins showed their strongest classifier relationship to HLA-DRB1. Individual SLA assignments varied across models. Among covered residues, mismatch was greater at HLA eplet-associated positions than elsewhere: 41.0% versus 21.8% in class I and 27.7% versus 16.3% in class II. This pattern depended on sequence coverage, particularly in class II, where counting gaps as mismatches reversed the comparison. Structural overlays showed conserved MHC-domain folds with local substitutions at HLA eplet-associated positions. Discussion Together, the sequence, classifier, eplet-position, and structural comparisons identify molecular relationships and candidate sites for investigating HLA/SLA cross-reactivity. These findings provide a basis for antibody-binding, peptide-presentation, and cellular studies to refine xenotransplant compatibility assessment.