Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells
Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells
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DOI：
10.1073/pnas.1621412114
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发表时间：
2017-02-28
影响因子：
11.1
通讯作者：
Hood, Leroy
中科院分区：
文献类型：
--
作者：
Bargaje, Rhishikesh;Trachanaa, Kalliopi;Hood, Leroy
引导诱导多能干细胞（iPSC）向特定细胞类型分化对于患者特异性疾病建模和药物测试至关重要。这项工作需要有能力预测和控制多能祖细胞何时以及如何致力于所需的细胞命运。细胞命运承诺代表了一个关键的状态转换或“临界点”，在这个临界点上，复杂的系统会发生突然的质的转变。为了表征iPSC向心肌细胞分化过程中的这种转变，我们以单细胞分辨率分析了96个发育基因的基因表达模式。我们确定了一个分叉事件早期的轨迹时，一个原始的条纹样细胞群体分离成中胚层和内胚层谱系。在这个分支点之前，我们可以检测到一个即将到来的关键转变的标志：细胞异质性的增加和基因表达的协调。在临界点的基因表达谱的相关性分析表明，转录因子驱动的状态过渡到每个替代细胞的命运和他们的关系与特定的表型读数。后者有助于我们促进小分子筛选的分化效率。为此，我们建立了一个分析的细胞群体结构的临界点后，系统的变化的协议，偏向中胚层或内胚层细胞系的分化。我们能够在细胞表现出分化表型之前许多天预测心肌细胞的比例。因此，对经历临界状态转变的细胞群体的分析提供了预测细胞命运结果的工具，并且可以用于优化分化方案以获得所需的细胞群体。
Steering the differentiation of induced pluripotent stem cells (iPSCs) toward specific cell types is crucial for patient-specific disease modeling and drug testing. This effort requires the capacity to predict and control when and how multipotent progenitor cells commit to the desired cell fate. Cell fate commitment represents a critical state transition or "tipping point" at which complex systems undergo a sudden qualitative shift. To characterize such transitions during iPSC to cardiomyocyte differentiation, we analyzed the gene expression patterns of 96 developmental genes at single-cell resolution. We identified a bifurcation event early in the trajectory when a primitive streak-like cell population segregated into the mesodermal and endodermal lineages. Before this branching point, we could detect the signature of an imminent critical transition: increase in cell heterogeneity and coordination of gene expression. Correlation analysis of gene expression profiles at the tipping point indicates transcription factors that drive the state transition toward each alternative cell fate and their relationships with specific phenotypic readouts. The latter helps us to facilitate small molecule screening for differentiation efficiency. To this end, we set up an analysis of cell population structure at the tipping point after systematic variation of the protocol to bias the differentiation toward mesodermal or endodermal cell lineage. We were able to predict the proportion of cardiomyocytes many days before cells manifest the differentiated phenotype. The analysis of cell populations undergoing a critical state transition thus affords a tool to forecast cell fate outcomes and can be used to optimize differentiation protocols to obtain desired cell populations.