Structural Identification of Immunodominant Human Leukocyte Antigen (HLA) Epitopes Targeted by HLA-Specific Antibodies in Kidney Allograft Recipients

Background: Donor-specific antibody (DSA) targeting Human Leukocyte Antigen (HLA) mismatches causes kidney allograft damage and loss. Currently, there are no reliable methods to predict which HLA epitopes will be recognized by alloreactive B cells and antibodies (Abs), thus limiting optimal matching of kidney transplant (KT) donors and recipients. The purpose of this study was to define structural determinants of HLA immunogenicity by identifying HLA epitopes recognized by DSA. Methods: B cells reactive with donor HLA-A*01:01 (A1) were isolated from blood and allograft of a KT recipient, then B cell receptors (BCR) from these allospecific B cells were cloned and expressed as monoclonal antibodies (mAbs, n=50). Coupling BCR-repertoire sequencing of B cells from peripheral blood and allograft with serum immunoglobulin proteomics, clonally-expanded lineages of A1-specific B cells were identified and linked to DSA in circulation. Three mAbs (E07, L02, M07), each representing distinct immunodominant clonal lineages, were complexed with A1 and the HLA epitopes recognized by these mAbs were determined by either X-Ray Crystallography or Cryo-Electron Microscopy. Epitopic overlap with other A1-reactive mAbs (n=47) and polyclonal DSA in the serum of other A1-mismatched KT recipients (n=11) was assessed by cross inhibition studies and A1 single amino acid point mutants. Results: The E07, L02, and M07 epitopes are distinct and collectively encompass most solvent-accessible mismatched residues (15/20, 75.0%) on the membrane-distal face of A1. All other A1-specific mAbs (n=47) recognize HLA epitopes that overlap with those of E07, L02, or M07 and mAbs with shared epitopes exhibit common binding to specific mismatched HLA residues. Other KT recipients (n=11) who received a mismatched A1 allograft produced Abs that recognized the same immunodominant A1 epitopes and targeted the same mismatched residues irrespective of their self HLA alleles. Conclusion: In our cohort of KT recipients, DSA preferentially targeted mismatched residues exposed on the membrane-distal face of HLA, recognizing a limited number of immunodominant epitopes. These results indicate that mismatched residues in HLA are differentially recognized by the immune system suggesting that some HLA residue mismatches may be more likely to elicit DSA responses than others. Funding: Other NIH Support - NIAID U19 AI142737, NIAID T32 AI007051