Concurrent stem- and lineage-affiliated chromatin programs precede hematopoietic lineage restriction

The emerging notion of hematopoietic stem- and progenitor cells (HSPCs) as a low-primed cloud without sharply demarcated gene expression programs raises the question on how cellular fate options emerge, and at which stem-like stage lineage priming is initiated. Here we investigated single-cell chromatin accessibility of Lineage-, cKit+, Sca1+ (LSK) HSPCs spanning the early differentiation landscape. Application of a signal-processing algorithm to detect transition points corresponding to massive alterations in accessibility of 521 transcription factor-motifs revealed a population of LSK FMS-like tyrosine kinase 3(Flt3)intCD9high cells that concurrently display stem-like and lineage-affiliated chromatin signatures pointing to simultaneous gain of both Lympho-Myeloid and Megakaryocyte-Erythroid programs. Molecularly and functionally, these cells position between stem cells and committed progenitors, display multi-lineage capacity in vitro and in vivo, but lack self-renewal activity. This integrative molecular analysis resolves the heterogeneity of cells along hematopoietic differentiation trajectories, and permits investigation of chromatin-mediated transition between multipotency and lineage restriction.

造血干祖细胞（hematopoietic stem- and progenitor cells, HSPCs）作为一类处于低致敏状态的细胞群，并无清晰界定的基因表达程序，这一新兴概念引出了关键科学问题：细胞命运选择是如何产生的，以及谱系致敏起始于哪个干细胞样阶段。本研究针对覆盖早期分化谱系的谱系阴性（Lineage⁻）、cKit阳性（cKit⁺）、Sca1阳性（Sca1⁺）的造血干祖细胞（LSK HSPCs）开展了单细胞染色质可及性分析。通过应用信号处理算法检测对应521个转录因子基序可及性发生大规模改变的转换节点，研究发现了一群LSK来源的、中间表达FMS样酪氨酸激酶3（FMS-like tyrosine kinase 3, Flt3）且高表达CD9的细胞群体；这类细胞同时展现出干细胞样特征与谱系相关的染色质特征，提示其同时获得了淋巴-髓系与巨核细胞-红细胞系的分化程序。从分子与功能层面而言，这类细胞定位于干细胞与定向祖细胞之间，在体外与体内均表现出多系分化能力，但缺乏自我更新活性。本整合性分子分析解析了造血分化轨迹中细胞的异质性，同时为研究多能性与谱系限制性之间的染色质介导转换提供了可行途径。