Immunopeptidome Divergence between Mismatched HLA Haplotypes and Survival after Haploidentical HCT: A Retrospective Study from the CIBMTR
Authors: Crivello Pietro , He Meilun , Wang Tao , Gadalla Shahinaz M. , Arrieta-Bolanos Esteban , Marsh Steven GE , Lee Stephanie , Bolon Yung-Tsi , Fleischhauer Katharina 
Published: December 2024

Introduction: Hematopoietic cell transplantation (HCT) from haploidentical family donors is widely used in the US and abroad (Cusatis et al, CIBMTR Summary Slides 2023; Passweg et al, Bone Marrow Transplant 2024). Many patients have several potential haploidentical donors available. The role of human leukocyte antigen (HLA) matching in this setting is controversial, despite recent evidence for locus-specific mismatch combinations associated with outcome (Fuchs et al, Blood 2022). Single HLA class I mismatches presenting highly divergent peptide repertoires (immunopeptidomes), as proxied by their peptide binding motif (PBM) groups, are associated with reduced survival after unrelated HCT (Crivello et al JCO 2023; Arrieta-Bolaños et al, JCO 2024). Here we hypothesized that the cumulative number of PBM mismatches at the loci HLA-A, -B, -C, -DRB1 on the unshared haplotype might inform outcome of haploidentical HCT.
Methods: Leveraging recent comprehensive immunopeptidomics data (Racle et al, Immunity 2023; Gfeller et al, Cell Systems 2023), we updated our previous PBM classification to include 2,488 HLA class I as well as 381 HLA-DR allotypes, for a total of 29 PBM groups. The cumulative number (0-4) of PBM mismatches in the graft-versus-host direction (PBM-GvH) at HLA-A, -B, -C, -DRB1 on the unshared haplotype was calculated in a cohort of 3,429 haploidentical donor-recipient pairs collected by the CIBMTR. Patients had received haploidentical HCT under post-transplantion-cyclophosphamide (PTCy)-based graft-versus-host disease (GvHD) prophylaxis between 2014 and 2020, for the treatment of acute leukemia or myelodysplastic neoplasms. A cohort of 1,451 HLA-A, -B, -C, -DRB1 (8/8) matched unrelated PTCy-based HCT was used as reference (i.e., 0 PBM mismatches). Multivariate Cox-proportional hazards models and adjusted Kaplan-Meier curves were used for testing the number of PBM mismatches with overall survival (OS) as the primary endpoint.
Results:PBM groups could be assigned to both alleles at all 4 HLA loci of interest for patient and donor in 2,198/3,429 (64.1%) haploidentical pairs. Of these, 48 (2%), 304 (14%), 702 (32%), 805 (37%) and 339 (15%) had 0, 1, 2, 3 or 4 PBM-GvH mismatches, respectively. In multivariate analysis, OS appeared worse after haploidentical HCT in all 4 PBM-GvH mismatch groups compared to the 8/8 matched unrelated HCT reference. However, this association was most pronounced for haploidentical transplants across a single PBM-GvH mismatch (Hazard ratio [HR] 1.42, 95% Confidence Interval [CI] 1.19-1.69, p=0.0001), and less so for haploidentical HCT across multiple PBM-GvH mismatches (HR 1.18, 95% CI 0.99-1.41, p=0.06 for 4 PBM-GvH mismatches, similar data for 3 or 2 PBM-GvH mismatches). Mortality risks were similarly worse when the single PBM-GvH mismatch was in HLA class I (HR 1.42, 95% CI 1.17-1.72, p=0.0003) or HLA-DRB1 (HR 1.44, 95% CI 1.02-2.02, p=0.04), independently from the number of HLA allele mismatches. The effects on OS were mirrored by a trend for lower leukemia-free survival (HR 1.21, 95% CI 1.03-1.43, p=0.02) and higher relapse (HR 1.29, 95% CI 1.06-1.58, p=0.01) for the single PBM-GvH mismatch group compared to the reference. No significant associations were observed for acute GvHD 3-4 (HR 0.70, 95% CI 0.38-1.27, p=0.24) or transplant-related mortality (HR 1.22, 95% CI 0.79-1.87, p=0.37).
Conclusion:The cumulative immunopeptidome divergence between mismatched HLA on the unshared haplotype, as proxied by the number of PBM-GvH mismatches, informs survival probabilities after haploidentical HCT with PTCy. Single PBM-GvH mismatches are associated with worse survival than multiple PBM-GvH mismatches, possibly due to higher relapse incidence. Mechanistically, this might suggest a higher threshold of allogeneic stimuli (i.e., a higher number of immunogenic mismatches) needed for optimal T-cell mediated graft-versus-leukemia activity in PTCy-based HCT protocols. Prioritization of PBM-GvH mismatched donors for patients with hematological malignancies could potentially improve outcome of haploidentical HCT.