Impact of the functional ERAP2 rs2248374 polymorphism on the HLA class I immunopeptidome in primary human epidermal keratinocytes

Endoplasmic reticulum aminopeptidase 2 (ERAP2) trims endogenous peptides before loading onto Human leukocyte antigen (HLA) class I molecules. A common polymorphism in ERAP2 (rs2248374) causes nonsense-mediated decay of ERAP2 mRNA, resulting in loss of protein expression. This polymorphism is associated with several HLA class I-associated inflammatory diseases including psoriasis. This study aimed to determine whether this specific polymorphism is sufficient to drive measurable differences in HLA-C expression and HLA class I immunopeptidome in primary human epidermal keratinocytes (HEKs). HEKs from 34 healthy donors were genotyped for ERAP2 (rs2248374) and HLA-C (rs4406273). HLA-C expression was assessed by flow cytometry. The immunopeptidome was isolated by immunoaffinity purification and analysed by liquid chromatography-mass spectrometry. HLA-C expression and global immunopeptidome features, including peptide yield, length distribution, and amino acid composition, were comparable across ERAP2 genotypes. However, ERAP2 genotype was associated with differences in peptide repertoire with the presence of genotype-specific peptides, an effect that became more pronounced in HLA-C*06:02-positive donors and even more among predicted HLA-C*06:02 majority-voted binder peptides. Within this HLA-C*06:02-stratified context, distinct sequence and chemical composition at the P1 anchor position also emerged. This suggests that the impact of ERAP2 is strongly context-dependent and partially masked in heterogeneous HLA settings.