Leukemic relapse remains a major barrier to successful allogeneic hematopoietic stem cell transplantation (allo-HSCT) for aggressive hematologic malignancies. The basis for relapse of advanced lymphoid malignancies remains incompletely understood and may involve escape from the graft-versus-leukemia (GvL) effect. We hypothesized that for patients with chronic lymphocytic leukemia (CLL) treated with allo-HSCT, leukemic cell–intrinsic features influence transplant outcomes by directing the evolutionary trajectories of CLL cells. Integrated genetic, transcriptomic, and epigenetic analyses of CLL cells from 10 patients revealed that the clinical kinetics of post-HSCT relapse are shaped by distinct molecular dynamics. Early relapses after allo-HSCT exhibited notable genetic stability; single CLL cell transcriptional analysis demonstrated a cellular heterogeneity that was static over time. In contrast, CLL cells relapsing late after allo-HSCT displayed notable genetic evolution and evidence of neoantigen depletion, consistent with marked single-cell transcriptional shifts that were unique to each patient. We observed a greater rate of epigenetic change for late relapses not seen in early relapses or relapses after chemotherapy alone, suggesting that the selection pressures of the GvL bottleneck are unlike those imposed by chemotherapy. No selective advantage for human leukocyte antigen (HLA) loss was observed, even when present in pretransplant subpopulations. Gain of stem cell modules was a common signature associated with leukemia relapse regardless of posttransplant relapse kinetics. These data elucidate the biological pathways that underlie GvL resistance and posttransplant relapse.

白血病复发仍然是成功进行侵袭性血液系统恶性肿瘤的同种异体造血干细胞移植 (allo-HSCT) 的主要障碍。晚期淋巴恶性肿瘤复发的基础仍不完全清楚，可能涉及逃避移植物抗白血病 (GvL) 效应。我们假设对于接受 allo-HSCT 治疗的慢性淋巴细胞白血病 (CLL) 患者，白血病细胞固有特征通过指导 CLL 细胞的进化轨迹来影响移植结果。对来自 10 名患者的 CLL 细胞的综合遗传、转录组和表观遗传分析表明，HSCT 后复发的临床动力学是由不同的分子动力学决定的。allo-HSCT 后的早期复发表现出显着的遗传稳定性；单个 CLL 细胞转录分析表明细胞异质性随着时间的推移是静态的。相比之下，allo-HSCT 后晚期复发的 CLL 细胞显示出显着的遗传进化和新抗原耗竭的证据，这与每个患者所特有的显着单细胞转录转变一致。我们观察到晚期复发的表观遗传变化率更高，这在早期复发或单独化疗后的复发中未见，这表明 GvL 瓶颈的选择压力与化疗施加的压力不同。即使存在于移植前亚群中，也没有观察到人类白细胞抗原 (HLA) 丢失的选择性优势。无论移植后复发动力学如何，干细胞模块的获得是与白血病复发相关的常见特征。