A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation
A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation
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DOI：
10.1182/blood-2016-05-716480
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发表时间：
2016-08-25
期刊：
影响因子：
20.3
通讯作者：
Gottgens, Berthold
中科院分区：
文献类型：
--
作者：
Nestorowa, Sonia;Hamey, Fiona K.;Gottgens, Berthold
维持血液系统需要造血干细胞和祖细胞（HSPC）平衡的细胞命运决定。由于细胞命运选择是在单个细胞水平上进行的，因此新的单细胞分析技术为绘制HSPC分化的动态分子变化提供了令人兴奋的可能性。在这里，我们使用单细胞RNA测序来分析超过1600个单个HSPC，并且深度测序已经能够检测每个细胞平均6558个蛋白质编码基因。索引分选与宽分选门相结合，使我们能够回顾性地将细胞分配到12种通常分选的HSPC表型，同时还捕获通常被常规门控排除的中间细胞。我们进一步表明，独立生成的单细胞数据集可以投影到单细胞分辨率表达图上，以直接比较来自多个组的数据，并建立和完善新的假设。分化轨迹的重建揭示了与早期淋巴细胞、红细胞和粒细胞-巨噬细胞分化相关的动态表达变化。后两种轨迹的特点是共同上调细胞周期和氧化磷酸化转录程序。通过使用外部加标对照，我们估计了每个细胞的绝对信使RNA（mRNA）水平，首次表明尽管总mRNA普遍减少，但一部分基因在未成熟干细胞中显示出更高的表达水平，这与干细胞状态的积极维持一致。最后，我们报告了一个直观的Web界面的开发，作为一种新的社区资源，可以以单细胞分辨率可视化HSPC中任何选择基因的基因表达。
Maintenance of the blood system requires balanced cell fate decisions by hematopoietic stem and progenitor cells (HSPCs). Because cell fate choices are executed at the individual cell level, new single-cell profiling technologies offer exciting possibilities for mapping the dynamic molecular changes underlying HSPC differentiation. Here, we have used single-cell RNA sequencing to profile more than 1600 single HSPCs, and deep sequencing has enabled detection of an average of 6558 protein-coding genes per cell. Index sorting, in combination with broad sorting gates, allowed us to retrospectively assign cells to 12 commonly sorted HSPC phenotypes while also capturing intermediate cells typically excluded by conventional gating. We further show that independently generated single-cell data sets can be projected onto the single-cell resolution expression map to directly compare data from multiple groups and to build and refine new hypotheses. Reconstruction of differentiation trajectories reveals dynamic expression changes associated with early lymphoid, erythroid, and granulocyte-macrophage differentiation. The latter two trajectories were characterized by common upregulation of cell cycle and oxidative phosphorylation transcriptional programs. By using external spike-in controls, we estimate absolute messenger RNA (mRNA) levels per cell, showing for the first time that despite a general reduction in total mRNA, a subset of genes shows higher expression levels in immature stem cells consistent with active maintenance of the stem-cell state. Finally, we report the development of an intuitiveWeb interface as a new community resource to permit visualization of gene expression in HSPCs at single-cell resolution for any gene of choice.