T cell alloreactivity against minor histocompatibility antigens (mHAgs)—polymorphic peptides resulting from donor–recipient (D–R) disparity at sites of genetic polymorphisms—is at the core of the therapeutic effect of allogeneic hematopoietic cell transplantation (allo-HCT). Despite the crucial role of mHAgs in graft-versus-leukemia (GvL) and graft-versus-host disease (GvHD) reactions, it remains challenging to consistently link patient-specific mHAg repertoires to clinical outcomes. Here we devise an analytic framework to systematically identify mHAgs, including their detection on HLA class I ligandomes and functional verification of their immunogenicity. The method relies on the integration of polymorphism detection by whole-exome sequencing of germline DNA from D–R pairs with organ-specific transcriptional- and proteome-level expression. Application of this pipeline to 220 HLA-matched allo-HCT D–R pairs demonstrated that total and organ-specific mHAg load could independently predict the occurrence of acute GvHD and chronic pulmonary GvHD, respectively, and defined promising GvL targets, confirmed in a validation cohort of 58 D–R pairs, for the prevention or treatment of post-transplant disease recurrence.

针对次要组织相容性抗原 (mHAgs) 的 T 细胞同种异体反应性是同种异体造血细胞移植 (allo-HCT) 治疗效果的核心，​​mHAgs 是由供体-受体 (D-R) 基因多态性位点差异产生的多态性肽。尽管 mHAg 在移植物抗白血病 (GvL) 和移植物抗宿主病 (GvHD) 反应中发挥着至关重要的作用，但将患者特异性 mHAg 库与临床结果一致联系起来仍然具有挑战性。在这里，我们设计了一个分析框架来系统地识别 mHAg，包括对 HLA I 类配体的检测以及其免疫原性的功能验证。该方法依赖于通过 D-R 对种系 DNA 的全外显子组测序进行的多态性检测与器官特异性转录和蛋白质组水平表达的整合。该流程应用于 220 个 HLA 匹配的同种异体 HCT D–R 对，证明总 mHAg 载量和器官特异性 mHAg 载量可以分别独立预测急性 GvHD 和慢性肺部 GvHD 的发生，并确定有希望的 GvL 目标，这在验证中得到了证实由 58 个 D-R 对组成的队列，用于预防或治疗移植后疾病复发。