Single-cell RNA sequencing provides exciting opportunities to unbiasedly study hematopoiesis. However, our understanding of leukemogenesis was limited due to the high individual differences. Integrated analyses of hematopoiesis and leukemogenesis potentially provides new insights. Here we analyzed ~200,000 single-cell transcriptomes of bone marrow mononuclear cells (BMMCs) and its subsets from 23 clinical samples. We constructed a comprehensive cell atlas as hematopoietic reference. We developed counterpart composite index (CCI; available at GitHub: https://github.com/pengfeeei/cci) to search for the healthy counterpart of each leukemia cell subpopulation, by integrating multiple statistics to map leukemia cells onto reference hematopoietic cells. Interestingly, we found leukemia cell subpopulations from each patient had different healthy counterparts. Analysis showed the trajectories of leukemia cell subpopulations were similar to that of their healthy counterparts, indicating that developmental termination of leukemia initiating cells at different phases leads to different leukemia cell subpopulations thus explained the origin of leukemia heterogeneity. CCI further predicts leukemia subtypes, cellular heterogeneity, and cellular stemness of each leukemia patient. Analyses of leukemia patient at diagnosis, refractory, remission and relapse vividly presented dynamics of cell population during leukemia treatment. CCI analyses showed the healthy counterparts of relapsed leukemia cells were closer to the root of hematopoietic tree than that of other leukemia cells, although single-cell transcriptomic genetic variants and haplotype tracing analyses showed the relapsed leukemia cell were derived from an early minor leukemia cell population. In summary, this study developed a unified framework for understanding leukemogenesis with hematopoiesis reference, which provided novel biological and medical implication.

单细胞RNA测序为公正地研究造血功能提供了令人兴奋的机会。但是，由于个体差异较大，我们对白血病发生的理解受到限制。血细胞生成和白血病发生的综合分析可能提供新的见解。在这里，我们分析了来自23个临床样本的骨髓单核细胞（BMMC）及其子集的约200,000个单细胞转录组。我们构建了全面的细胞图谱作为造血学参考。我们开发了对应的综合索引（CCI；可在GitHub：https：//github.com/pengfeeei/cci），通过整合多个统计数据以将白血病细胞映射到参考造血细胞上来搜索每个白血病细胞亚群的健康对应物。有趣的是 我们发现每个患者的白血病细胞亚群都有不同的健康对应物。分析表明，白血病细胞亚群的轨迹与健康人的轨迹相似，这表明白血病起始细胞在不同阶段的发育终止导致不同的白血病细胞亚群，从而解释了白血病异质性的起源。CCI还可以预测每位白血病患者的白血病亚型，细胞异质性和细胞干性。白血病患者在诊断，难治，缓解和复发方面的分析生动地展现了白血病治疗期间细胞群的动态。CCI分析显示，健康的复发性白血病细胞对应物比其他白血病细胞更接近造血树的根部，尽管单细胞转录组遗传变异和单倍型追踪分析显示复发的白血病细胞来自早期的未成年人白血病细胞群。综上所述，本研究建立了一个统一的框架，以造血学参考了解白血病的发生，提供了新的生物学和医学意义。