Machine Learning Insights into HLA Noncoding Sequence Mismatches and Their Impact on DPB1 Matching in Hematopoietic Cell Transplantation

Purpose: HCT is vital for treating hematological malignancies, relying on HLA matching between unrelated patient-donor pairs to significantly reduce adverse outcomes. Recent studies recognize the potential impact of HLA-DPB1 mismatches on HCT outcomes. Multiple approaches focus on finding better-tolerated HLA-DPB1 mismatches. Additionally, recent studies suggest matching at noncoding HLA sequence may improve HCT outcomes. This study aims to evaluate different approaches for categorizing DPB1 mismatches in patient-donor pairs and explore the potential impact of noncoding mismatches (available in class I HLA genes) on clinical outcomes. Methods: A retrospective study of 5,106 HCT pairs using Cox proportional hazards models, weighted by a machine learning algorithm, evaluates the impact of particular combinations of HLA-DPB1 mismatches in the context of noncoding HLA class I mismatches on outcomes of HCT. HLA-DPB1 mismatch criteria included T-cell epitope permissive/non-permissive mismatches, expression markers, and evolutionary clade mismatches. Results: Two HLA-DPB1 mismatches, using multiple criteria, lead to significant hazards of acute graft versus host disease grades 2-4, in the T cell replete group. When HLA-DPB1 mismatches occurred across evolutionary clades (DP2 allele/low-expression patient vs DP5 allele/high-expression in the donor), the deplete group showed significant hazards for treatment-related mortality (TRM) (HR=1.94, p-value=8.9x10-7) and overall survival (OS) (HR=1.67, p-value=1.3 x10-5) for additive effects of noncoding mismatches with two HLA-DPB1 mismatches. Conclusion: Two HLA-DPB1 mismatches remain to predict worse outcomes. However, noncoding mismatches in HLA class I genes confer elevated hazards of TRM and OS in conjunction with mismatches across evolutionary branches of HLA-DPB1. Therefore, noncoding mismatches may inform donor selection in the presence of HLA-DPB1 mismatches and improve HCT outcomes, emphasizing the utility of comprehensive sequencing of HLA alleles in HCT settings.