The epithelial-to-mesenchymal transition (EMT) plays a critical role during normal development and in cancer progression. EMT is induced by various signaling pathways, including TGF-β, BMP, Wnt–β-catenin, NOTCH, Shh, and receptor tyrosine kinases. In this study, we performed single-cell RNA sequencing on MCF10A cells undergoing EMT by TGF-β1 stimulation. Our comprehensive analysis revealed that cells progress through EMT at different paces. Using pseudotime clustering reconstruction of gene-expression profiles during EMT, we found sequential and parallel activation of EMT signaling pathways. We also observed various transitional cellular states during EMT. We identified regulatory signaling nodes that drive EMT with the expression of important microRNAs and transcription factors. Using a random circuit perturbation methodology, we demonstrate that the NOTCH signaling pathway acts as a key driver of TGF-β–induced EMT. Furthermore, we demonstrate that the gene signatures of pseudotime clusters corresponding to the intermediate hybrid EMT state are associated with poor patient outcome. Overall, this study provides insight into context-specific drivers of cancer progression and highlights the complexities of the EMT process.

上皮间质转化 (EMT) 在正常发育和癌症进展过程中起着关键作用。EMT 由多种信号通路诱导，包括 TGF-β、BMP、Wnt-β-catenin、NOTCH、Shh 和受体酪氨酸激酶。在这项研究中，我们对通过 TGF-β1 刺激进行 EMT 的 MCF10A 细胞进行了单细胞 RNA 测序。我们的综合分析表明，细胞以不同的速度通过 EMT。在 EMT 期间使用基因表达谱的伪时间聚类重建，我们发现 EMT 信号通路的顺序和并行激活。我们还观察到 EMT 期间的各种过渡细胞状态。我们确定了通过重要 microRNA 和转录因子的表达来驱动 EMT 的调控信号节点。使用随机电路扰动方法，我们证明了 NOTCH 信号通路是 TGF-β 诱导的 EMT 的关键驱动因素。此外，我们证明了对应于中间混合 EMT 状态的伪时间簇的基因特征与较差的患者预后相关。总体而言，这项研究提供了对癌症进展的特定背景驱动因素的洞察，并突出了 EMT 过程的复杂性。