BACKGROUND Overcoming therapeutic resistance is one of the major hurdles in cancer care. One mechanism contributing to therapeutic resistance is a process in which epithelial cells switch to a mesenchymal state (epithelial-to-mesenchymal transition or EMT). The precise mechanisms driving EMT-mediated therapeutic resistance have, however, not been elucidated. RESULTS Here, we study ten cell line pairs, for which parental cell lines were made resistant to either a targeted or chemotherapy-based treatment. First, we show by miRNA-200 overexpression that treatment resistance is driven by EMT. Next, we demonstrate that DNA methylation changes occur within each cell line pair and show that exposure to 5-azacytidine or knock down of DNA methyltransferases (DNMTs), both of which globally demethylate cells, result in EMT reversal and increased therapeutic sensitivity. This suggests DNA methylation to causally underlie EMT and treatment resistance. We also observe significant overlap in methylation profiles between resistant lines, suggesting a common epigenetic mechanism to cause resistance to therapy. In line with this hypothesis, cross-resistance to other targeted and chemotherapies is observed, while importantly, this is lost upon demethylation of the cells. Finally, we clinically validate that DNA methylation changes drive EMT-mediated resistance to sorafenib in patients with advanced hepatocellular carcinoma (HCC). Specifically, we develop a capture-based protocol to interrogate DNA methylation in low amounts of circulating tumor DNA (ctDNA). By interrogating the methylation status in liquid biopsies, longitudinally collected during sorafenib treatment, we assess whether DNA methylation changes also drive EMT and therapy resistance in a clinical setting. Particularly, by monitoring methylation changes in EMT genes, we are able to predict tumor response and acquired resistance to sorafenib. CONCLUSIONS We propose methylation changes underlying EMT to constitute a common resistance mechanism to cancer therapies. This process can be reversed pharmacologically and monitored non-invasively in ctDNA to predict resistance to treatment.

中文翻译：

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DNA甲基化驱动的EMT是抵抗癌症中各种治疗剂的常见机制。

背景技术克服治疗抗性是癌症护理中的主要障碍之一。促成治疗抗性的一种机制是上皮细胞转换为间充质状态（上皮到间充质转变或EMT）的过程。然而，尚未阐明驱动EMT介导的治疗抗性的确切机制。结果在这里，我们研究了十对细胞系，使它们的亲本细胞系对靶向治疗或基于化学疗法的治疗产生抗性。首先，我们通过miRNA-200过表达来表明治疗耐药性是由EMT驱动的。接下来，我们证明DNA甲基化变化发生在每个细胞系对中，并表明暴露于5-氮胞苷或击倒DNA甲基转移酶（DNMT），这两种物质均会使细胞甲基化，导致EMT逆转并提高治疗敏感性。这表明DNA甲基化是EMT和治疗抗性的因果关系。我们还观察到耐药系之间的甲基化分布存在显着重叠，表明引起治疗耐药的常见表观遗传机制。与该假设一致，观察到了与其他靶向和化学疗法的交叉耐药性，而重要的是，当细胞脱甲基时，这种耐药性就消失了。最后，我们在临床上验证了DNA甲基化变化可驱动EMT介导的晚期肝细胞癌（HCC）患者对索拉非尼的耐药性。具体来说，我们开发了一种基于捕获的协议，可在少量循环肿瘤DNA（ctDNA）中询问DNA甲基化。通过询问液体活检中的甲基化状态，在索拉非尼治疗期间纵向收集，我们评估在临床环境中DNA甲基化变化是否还驱动EMT和治疗耐药性。特别地，通过监测EMT基因的甲基化变化，我们能够预测肿瘤反应和获得​​的索拉非尼耐药性。结论我们提出了EMT的甲基化变化，以构成对癌症治疗的共同耐药机制。该过程可以通过药理学逆转，并在ctDNA中进行非侵入性监测，以预测对治疗的耐药性。结论我们提出了EMT的甲基化变化，以构成对癌症治疗的共同耐药机制。该过程可以通过药理学逆转，并在ctDNA中进行非侵入性监测，以预测对治疗的耐药性。结论我们提出了EMT的甲基化变化，以构成对癌症治疗的共同耐药机制。该过程可以通过药理学逆转，并在ctDNA中进行非侵入性监测，以预测对治疗的耐药性。