A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation.
A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation.
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DOI：
10.1016/j.stem.2020.04.020
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发表时间：
2020-05
期刊：
影响因子：
23.9
通讯作者：
G. Yeo;Lin Lin-Lin;C. Y. Qi;Minsun Cha;D. Gifford;R. Sherwood
中科院分区：
文献类型：
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作者：
G. Yeo;Lin Lin-Lin;C. Y. Qi;Minsun Cha;D. Gifford;R. Sherwood
干细胞分化方案的经验优化非常耗时、劳动密集型，并且通常不会全面询问所有相关的信号传导途径。在这里，我们描述了条形码单细胞 RNA 测序 (barRNA-seq)，它通过用 RNA“条形码”标记单个细胞，根据它们接受的治疗来识别它们，从而能够系统地探索细胞扰动。我们应用 barRNA-seq 同时操纵多达七个发育途径，并研究对胚胎干细胞 (ESC) 胚层规范和中胚层规范的影响，揭示信号通路激活对基因表达的组合影响。我们进一步开发了一个数据驱动的框架，用于识别驱动细胞走向特定命运的组合信号扰动，包括现有 scRNA-seq 原肠胚形成图集中注释的几个信号扰动，并使用这种方法引导 ESC 分化为脊索样群体。我们预计 barRNA-seq 将在研究和理解协同信号通路如何驱动细胞命运获取方面具有广泛的用途。
Empirical optimization of stem cell differentiation protocols is time consuming, is laborintensive, and typically does not comprehensively interrogate all relevant signaling pathways. Here we describe barcodelet single-cell RNA sequencing (barRNA-seq), which enables systematic exploration of cellular perturbations by tagging individual cells with RNA "barcodelets" to identify them on the basis of the treatments they receive. We apply barRNA-seq to simultaneously manipulate up to seven developmental pathways and study effects on embryonic stem cell (ESC) germ layer specification and mesodermal specification, uncovering combinatorial effects of signaling pathway activation on gene expression. We further develop a data-driven framework for identifying combinatorial signaling perturbations that drive cells toward specific fates, including several annotated in an existing scRNA-seq gastrulation atlas, and use this approach to guide ESC differentiation into a notochord-like population. We expect that barRNA-seq will have broad utility for investigating and understanding how cooperative signaling pathways drive cell fate acquisition.